Query psy11423
Match_columns 655
No_of_seqs 254 out of 1828
Neff 6.4
Searched_HMMs 46136
Date Fri Aug 16 18:03:19 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy11423.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/11423hhsearch_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 1E-193 2E-198 1593.5 67.4 633 10-647 3-667 (667)
2 PRK07956 ligA NAD-dependent DN 100.0 3E-179 6E-184 1523.7 73.3 634 11-648 2-664 (665)
3 PRK14350 ligA NAD-dependent DN 100.0 9E-177 2E-181 1496.4 72.2 621 13-649 4-668 (669)
4 TIGR00575 dnlj DNA ligase, NAD 100.0 1E-176 3E-181 1500.6 70.5 617 21-642 1-652 (652)
5 PRK14351 ligA NAD-dependent DN 100.0 1E-175 3E-180 1493.1 73.6 633 7-652 25-688 (689)
6 PRK08097 ligB NAD-dependent DN 100.0 2E-153 4E-158 1276.4 61.9 533 8-593 24-558 (562)
7 smart00532 LIGANc Ligase N fam 100.0 7E-138 2E-142 1131.7 51.8 440 15-459 2-441 (441)
8 cd00114 LIGANc NAD+ dependent 100.0 5.8E-95 1.3E-99 762.5 35.0 306 17-327 2-307 (307)
9 PF01653 DNA_ligase_aden: NAD- 100.0 2.5E-94 5.4E-99 760.7 31.9 313 13-328 2-315 (315)
10 PF03120 DNA_ligase_OB: NAD-de 100.0 1.5E-31 3.2E-36 227.1 10.2 82 330-411 1-82 (82)
11 PF12826 HHH_2: Helix-hairpin- 99.6 4.5E-16 9.8E-21 127.6 6.6 64 521-584 1-64 (64)
12 cd07894 Adenylation_RNA_ligase 99.2 3.7E-10 8E-15 121.5 15.1 144 119-303 49-194 (342)
13 PRK06063 DNA polymerase III su 98.8 5.4E-09 1.2E-13 111.6 5.1 49 600-648 257-307 (313)
14 cd07896 Adenylation_kDNA_ligas 98.8 5E-08 1.1E-12 95.3 11.2 139 119-307 17-162 (174)
15 PF14520 HHH_5: Helix-hairpin- 98.7 8.3E-09 1.8E-13 83.4 4.0 56 456-512 4-59 (60)
16 PRK09125 DNA ligase; Provision 98.7 1.2E-06 2.6E-11 92.4 19.9 198 119-375 44-248 (282)
17 cd07898 Adenylation_DNA_ligase 98.6 1.2E-06 2.7E-11 87.6 16.2 166 117-319 20-195 (201)
18 PRK06195 DNA polymerase III su 98.5 9.1E-08 2E-12 102.1 5.0 49 600-648 246-308 (309)
19 PF03119 DNA_ligase_ZBD: NAD-d 98.4 1E-07 2.2E-12 65.2 2.1 28 417-445 1-28 (28)
20 cd07901 Adenylation_DNA_ligase 98.4 3.3E-06 7.1E-11 85.0 13.8 156 118-307 25-193 (207)
21 PF14520 HHH_5: Helix-hairpin- 98.4 6.9E-07 1.5E-11 72.2 6.6 55 522-576 4-59 (60)
22 PF01068 DNA_ligase_A_M: ATP d 98.4 5.3E-06 1.1E-10 82.5 13.9 158 118-307 19-190 (202)
23 PRK03180 ligB ATP-dependent DN 98.4 1.7E-05 3.8E-10 90.1 19.6 216 119-376 205-435 (508)
24 TIGR02779 NHEJ_ligase_lig DNA 98.4 2.1E-05 4.5E-10 83.7 18.6 209 118-376 12-234 (298)
25 cd07906 Adenylation_DNA_ligase 98.3 6.1E-06 1.3E-10 81.9 13.2 163 118-319 16-184 (190)
26 TIGR01448 recD_rel helicase, p 98.3 5.9E-07 1.3E-11 106.1 6.9 125 520-646 81-215 (720)
27 PRK07636 ligB ATP-dependent DN 98.3 8.2E-05 1.8E-09 78.3 21.8 205 118-377 18-228 (275)
28 cd07900 Adenylation_DNA_ligase 98.3 2.5E-05 5.5E-10 79.5 15.9 159 118-307 31-204 (219)
29 TIGR00574 dnl1 DNA ligase I, A 98.2 7.4E-05 1.6E-09 85.3 19.3 218 119-378 188-433 (514)
30 cd06846 Adenylation_DNA_ligase 98.2 1.8E-05 4E-10 77.8 12.6 150 118-319 19-177 (182)
31 COG5275 BRCT domain type II [G 98.2 1.5E-06 3.3E-11 85.7 4.6 50 600-649 182-232 (276)
32 PRK08224 ligC ATP-dependent DN 98.2 7E-05 1.5E-09 81.4 17.8 215 119-377 25-250 (350)
33 cd07903 Adenylation_DNA_ligase 98.2 0.00012 2.6E-09 74.5 18.0 168 117-319 32-216 (225)
34 cd07897 Adenylation_DNA_ligase 98.1 4.2E-05 9.1E-10 77.1 14.4 157 118-307 24-191 (207)
35 COG1793 CDC9 ATP-dependent DNA 98.1 0.00019 4E-09 80.4 20.6 215 119-376 134-366 (444)
36 PRK00116 ruvA Holliday junctio 98.1 1.2E-05 2.6E-10 80.2 8.5 69 526-594 76-163 (192)
37 COG1796 POL4 DNA polymerase IV 98.0 2.1E-06 4.6E-11 90.0 2.6 59 458-516 94-153 (326)
38 cd07905 Adenylation_DNA_ligase 98.0 6.1E-05 1.3E-09 75.1 12.9 159 118-307 16-181 (194)
39 KOG2841|consensus 98.0 4.3E-06 9.4E-11 83.9 4.2 60 520-579 191-251 (254)
40 PHA00454 ATP-dependent DNA lig 98.0 0.0016 3.5E-08 69.9 23.6 240 85-376 5-269 (315)
41 PRK14670 uvrC excinuclease ABC 98.0 8.5E-06 1.8E-10 93.3 6.1 51 527-577 518-568 (574)
42 PRK09247 ATP-dependent DNA lig 98.0 0.00044 9.6E-09 79.4 20.1 219 118-378 225-466 (539)
43 cd08039 Adenylation_DNA_ligase 98.0 0.0002 4.4E-09 73.7 15.2 170 117-307 21-215 (235)
44 PHA02587 30 DNA ligase; Provis 97.9 0.00075 1.6E-08 76.6 21.1 235 119-378 153-412 (488)
45 PRK12766 50S ribosomal protein 97.9 1.4E-05 2.9E-10 80.9 6.2 51 527-577 7-58 (232)
46 cd07902 Adenylation_DNA_ligase 97.9 0.00018 3.9E-09 72.8 14.1 157 119-307 35-200 (213)
47 PRK09633 ligD ATP-dependent DN 97.9 0.0005 1.1E-08 79.7 18.7 217 118-377 16-254 (610)
48 PRK01109 ATP-dependent DNA lig 97.9 0.00035 7.6E-09 81.1 17.5 216 119-377 249-492 (590)
49 PRK09632 ATP-dependent DNA lig 97.8 0.00089 1.9E-08 79.1 19.9 208 118-377 477-695 (764)
50 PRK08609 hypothetical protein; 97.8 7.3E-06 1.6E-10 94.4 2.6 59 458-516 89-148 (570)
51 PRK14667 uvrC excinuclease ABC 97.8 2.2E-05 4.8E-10 89.9 6.2 49 527-576 518-566 (567)
52 PRK00558 uvrC excinuclease ABC 97.7 7.3E-05 1.6E-09 86.6 7.1 51 527-577 547-597 (598)
53 PF12826 HHH_2: Helix-hairpin- 97.6 9.2E-05 2E-09 60.8 5.0 57 459-517 5-61 (64)
54 PRK14669 uvrC excinuclease ABC 97.6 0.00012 2.6E-09 84.8 6.9 50 527-578 556-605 (624)
55 COG1948 MUS81 ERCC4-type nucle 97.6 0.00015 3.2E-09 74.7 6.7 54 525-578 184-237 (254)
56 cd07895 Adenylation_mRNA_cappi 97.5 0.0012 2.6E-08 66.8 12.6 156 118-324 41-214 (215)
57 PRK05972 ligD ATP-dependent DN 97.5 0.0013 2.7E-08 78.7 14.4 179 119-343 250-435 (860)
58 PLN03113 DNA ligase 1; Provisi 97.5 0.0033 7.1E-08 74.4 17.6 221 118-377 391-638 (744)
59 PRK14973 DNA topoisomerase I; 97.5 0.00052 1.1E-08 83.0 11.3 127 448-576 789-931 (936)
60 TIGR01448 recD_rel helicase, p 97.5 0.00042 9.1E-09 82.2 10.0 121 449-576 78-202 (720)
61 PRK14666 uvrC excinuclease ABC 97.4 0.00023 4.9E-09 82.6 6.9 50 527-576 641-690 (694)
62 PRK14672 uvrC excinuclease ABC 97.4 0.0002 4.3E-09 82.8 6.3 50 527-576 612-661 (691)
63 PRK14671 uvrC excinuclease ABC 97.4 0.00024 5.3E-09 82.5 6.8 49 526-576 572-620 (621)
64 COG0322 UvrC Nuclease subunit 97.3 0.00029 6.2E-09 80.9 6.1 48 527-575 534-581 (581)
65 PRK13482 DNA integrity scannin 97.3 0.00046 1E-08 74.2 6.5 51 527-577 291-341 (352)
66 PRK00116 ruvA Holliday junctio 97.2 0.00084 1.8E-08 67.1 7.5 57 458-514 74-131 (192)
67 PRK12766 50S ribosomal protein 97.2 0.00056 1.2E-08 69.4 5.6 54 458-512 4-57 (232)
68 PF00633 HHH: Helix-hairpin-he 97.2 0.00061 1.3E-08 47.5 4.1 30 545-574 1-30 (30)
69 PRK14668 uvrC excinuclease ABC 97.1 0.00074 1.6E-08 77.9 6.2 49 527-575 529-577 (577)
70 PLN03122 Poly [ADP-ribose] pol 97.1 0.00053 1.1E-08 81.4 4.9 50 600-649 214-267 (815)
71 PF12738 PTCB-BRCT: twin BRCT 97.0 0.00064 1.4E-08 55.1 3.8 41 600-640 22-62 (63)
72 TIGR01209 RNA ligase, Pab1020 97.0 0.011 2.4E-07 64.3 14.3 168 84-304 60-228 (374)
73 PRK14605 ruvA Holliday junctio 96.9 0.003 6.5E-08 63.2 8.4 90 490-594 54-162 (194)
74 PRK13901 ruvA Holliday junctio 96.8 0.0041 8.8E-08 62.2 8.3 72 490-576 53-128 (196)
75 PRK00254 ski2-like helicase; P 96.8 0.0026 5.7E-08 75.6 8.2 54 525-578 647-701 (720)
76 PRK08609 hypothetical protein; 96.8 0.0027 5.9E-08 73.4 7.7 84 491-574 48-142 (570)
77 PRK14973 DNA topoisomerase I; 96.8 0.013 2.8E-07 71.3 13.5 149 415-575 635-796 (936)
78 PRK14606 ruvA Holliday junctio 96.8 0.0049 1.1E-07 61.4 8.1 90 490-594 54-157 (188)
79 TIGR00084 ruvA Holliday juncti 96.7 0.003 6.5E-08 63.0 6.3 69 490-573 53-125 (191)
80 PRK14601 ruvA Holliday junctio 96.7 0.0061 1.3E-07 60.4 8.3 90 490-594 54-156 (183)
81 PRK13766 Hef nuclease; Provisi 96.7 0.0025 5.4E-08 76.3 6.3 54 526-579 718-771 (773)
82 PRK14604 ruvA Holliday junctio 96.6 0.0081 1.8E-07 60.2 8.2 73 490-577 54-130 (195)
83 TIGR00084 ruvA Holliday juncti 96.5 0.002 4.3E-08 64.3 3.7 52 458-512 73-128 (191)
84 PRK14600 ruvA Holliday junctio 96.5 0.0084 1.8E-07 59.6 7.5 70 490-575 54-127 (186)
85 PF03118 RNA_pol_A_CTD: Bacter 96.4 0.0048 1E-07 51.0 4.8 51 461-512 15-65 (66)
86 TIGR00596 rad1 DNA repair prot 96.4 0.005 1.1E-07 73.7 6.3 51 526-578 760-811 (814)
87 COG1423 ATP-dependent DNA liga 96.4 0.083 1.8E-06 56.5 14.5 168 83-306 68-238 (382)
88 PRK14602 ruvA Holliday junctio 96.3 0.0075 1.6E-07 60.8 6.5 73 490-577 55-131 (203)
89 TIGR01259 comE comEA protein. 96.3 0.0031 6.6E-08 58.3 3.4 24 552-575 95-118 (120)
90 TIGR00426 competence protein C 96.3 0.0063 1.4E-07 50.4 4.9 43 528-575 22-67 (69)
91 TIGR00575 dnlj DNA ligase, NAD 96.2 0.0072 1.6E-07 70.9 6.4 83 458-548 467-555 (652)
92 PRK14603 ruvA Holliday junctio 96.1 0.01 2.2E-07 59.6 6.1 73 490-577 53-129 (197)
93 PRK05601 DNA polymerase III su 96.1 0.0043 9.4E-08 67.4 3.8 48 600-647 319-368 (377)
94 PF14229 DUF4332: Domain of un 96.0 0.019 4.2E-07 53.2 6.8 83 463-559 1-90 (122)
95 PRK07758 hypothetical protein; 95.9 0.016 3.4E-07 51.0 5.6 51 462-513 39-89 (95)
96 TIGR02307 RNA_lig_RNL2 RNA lig 95.8 0.045 9.7E-07 58.8 9.7 128 117-279 24-165 (325)
97 PRK07956 ligA NAD-dependent DN 95.8 0.014 3.1E-07 68.7 6.1 82 458-547 480-567 (665)
98 PRK00254 ski2-like helicase; P 95.7 0.013 2.8E-07 69.8 5.6 53 459-512 647-699 (720)
99 PRK14351 ligA NAD-dependent DN 95.6 0.017 3.6E-07 68.2 6.2 92 458-559 497-594 (689)
100 PRK14605 ruvA Holliday junctio 95.6 0.034 7.4E-07 55.7 7.3 51 459-512 75-129 (194)
101 COG0632 RuvA Holliday junction 95.6 0.024 5.2E-07 56.9 6.1 73 490-577 54-130 (201)
102 PF00533 BRCT: BRCA1 C Terminu 95.4 0.025 5.5E-07 46.7 4.9 47 600-646 30-78 (78)
103 TIGR01259 comE comEA protein. 95.4 0.024 5.2E-07 52.4 5.0 61 481-543 58-118 (120)
104 PRK02362 ski2-like helicase; P 95.4 0.015 3.3E-07 69.4 4.6 53 458-513 653-705 (737)
105 PRK02515 psbU photosystem II c 94.9 0.031 6.6E-07 52.1 4.2 41 528-576 66-108 (132)
106 PRK08097 ligB NAD-dependent DN 94.9 0.025 5.5E-07 65.0 4.5 92 458-559 460-554 (562)
107 PHA02142 putative RNA ligase 94.8 0.48 1E-05 51.8 13.6 147 117-302 168-343 (366)
108 TIGR02236 recomb_radA DNA repa 94.6 0.17 3.8E-06 53.9 9.6 50 527-576 3-53 (310)
109 PRK04301 radA DNA repair and r 94.5 0.063 1.4E-06 57.6 5.9 55 458-513 7-61 (317)
110 cd00027 BRCT Breast Cancer Sup 94.5 0.089 1.9E-06 41.6 5.5 47 600-646 24-71 (72)
111 TIGR03252 uncharacterized HhH- 94.5 0.18 4E-06 49.6 8.6 81 471-576 41-136 (177)
112 PRK01172 ski2-like helicase; P 94.4 0.052 1.1E-06 64.2 5.6 62 450-512 602-666 (674)
113 COG1796 POL4 DNA polymerase IV 94.3 0.11 2.3E-06 55.4 7.0 93 480-575 44-148 (326)
114 PRK14670 uvrC excinuclease ABC 94.2 0.065 1.4E-06 62.0 5.7 57 454-513 512-568 (574)
115 PRK13913 3-methyladenine DNA g 94.2 0.18 3.9E-06 51.5 8.2 81 469-574 51-140 (218)
116 PRK14604 ruvA Holliday junctio 94.0 0.048 1E-06 54.7 3.6 53 458-513 74-130 (195)
117 PRK14602 ruvA Holliday junctio 94.0 0.053 1.1E-06 54.7 3.9 52 459-513 76-131 (203)
118 PRK14666 uvrC excinuclease ABC 94.0 0.069 1.5E-06 62.6 5.3 54 458-513 638-691 (694)
119 PF09414 RNA_ligase: RNA ligas 93.9 0.044 9.5E-07 53.9 3.1 155 119-304 2-174 (186)
120 PRK14606 ruvA Holliday junctio 93.9 0.052 1.1E-06 54.1 3.6 52 459-513 75-130 (188)
121 PRK02515 psbU photosystem II c 93.9 0.11 2.3E-06 48.5 5.3 57 481-543 51-107 (132)
122 PRK14603 ruvA Holliday junctio 93.9 0.053 1.1E-06 54.5 3.6 53 458-513 73-129 (197)
123 PRK13901 ruvA Holliday junctio 93.8 0.056 1.2E-06 54.1 3.7 52 459-513 74-129 (196)
124 TIGR02236 recomb_radA DNA repa 93.8 0.11 2.3E-06 55.6 6.0 51 461-512 3-53 (310)
125 PRK00024 hypothetical protein; 93.8 0.13 2.8E-06 52.7 6.4 55 521-575 31-86 (224)
126 PRK14600 ruvA Holliday junctio 93.8 0.053 1.1E-06 54.0 3.4 51 459-513 75-129 (186)
127 TIGR01954 nusA_Cterm_rpt trans 93.8 0.2 4.4E-06 38.4 6.0 47 465-512 1-47 (50)
128 cd00141 NT_POLXc Nucleotidyltr 93.7 0.15 3.3E-06 54.7 7.0 62 491-552 45-115 (307)
129 cd00141 NT_POLXc Nucleotidyltr 93.7 0.049 1.1E-06 58.4 3.2 48 458-516 86-133 (307)
130 PRK14601 ruvA Holliday junctio 93.7 0.062 1.3E-06 53.4 3.6 52 459-513 75-130 (183)
131 TIGR00426 competence protein C 93.6 0.13 2.8E-06 42.6 4.8 58 483-542 8-66 (69)
132 PRK04301 radA DNA repair and r 93.4 0.37 8.1E-06 51.7 9.3 50 527-576 10-60 (317)
133 COG1623 Predicted nucleic-acid 93.3 0.099 2.1E-06 54.7 4.5 50 527-576 297-346 (349)
134 PF00633 HHH: Helix-hairpin-he 93.3 0.1 2.2E-06 36.4 3.2 27 483-509 3-29 (30)
135 TIGR00608 radc DNA repair prot 93.3 0.19 4E-06 51.4 6.4 55 521-575 21-80 (218)
136 COG2003 RadC DNA repair protei 93.1 0.31 6.7E-06 49.7 7.6 57 518-574 28-85 (224)
137 PF12836 HHH_3: Helix-hairpin- 92.7 0.065 1.4E-06 44.0 1.8 30 484-513 7-36 (65)
138 PRK14350 ligA NAD-dependent DN 92.4 0.2 4.3E-06 59.2 5.9 81 491-577 436-525 (669)
139 PF14490 HHH_4: Helix-hairpin- 92.4 0.02 4.3E-07 50.5 -1.7 69 577-646 5-80 (94)
140 PRK14672 uvrC excinuclease ABC 92.3 0.19 4.1E-06 58.8 5.6 60 459-520 610-669 (691)
141 COG1555 ComEA DNA uptake prote 92.3 0.2 4.3E-06 48.2 4.8 23 553-575 125-147 (149)
142 COG0272 Lig NAD-dependent DNA 92.2 0.14 3.1E-06 59.4 4.3 88 452-547 474-567 (667)
143 TIGR00194 uvrC excinuclease AB 92.1 0.13 2.7E-06 59.8 3.8 30 527-556 545-574 (574)
144 COG0177 Nth Predicted EndoIII- 92.0 0.54 1.2E-05 47.7 7.7 76 467-544 48-131 (211)
145 smart00483 POLXc DNA polymeras 91.7 0.3 6.5E-06 53.0 6.0 63 491-553 48-120 (334)
146 COG0632 RuvA Holliday junction 91.7 0.15 3.2E-06 51.3 3.3 18 493-510 75-92 (201)
147 smart00483 POLXc DNA polymeras 91.7 0.55 1.2E-05 51.0 8.0 57 517-573 42-107 (334)
148 KOG0967|consensus 91.6 2.4 5.2E-05 49.0 12.9 180 86-303 344-532 (714)
149 PRK14667 uvrC excinuclease ABC 91.4 0.3 6.5E-06 56.6 5.8 51 458-511 515-565 (567)
150 PRK01172 ski2-like helicase; P 91.3 0.74 1.6E-05 54.6 9.1 55 521-575 610-665 (674)
151 PRK10702 endonuclease III; Pro 91.2 0.72 1.6E-05 46.9 7.7 43 468-512 49-94 (211)
152 PF10391 DNA_pol_lambd_f: Fing 91.1 0.19 4.1E-06 39.7 2.7 26 460-486 5-30 (52)
153 cd00080 HhH2_motif Helix-hairp 91.1 0.21 4.5E-06 42.3 3.1 26 527-552 26-51 (75)
154 PRK00558 uvrC excinuclease ABC 90.4 0.34 7.3E-06 56.7 5.1 52 459-512 545-596 (598)
155 COG1555 ComEA DNA uptake prote 90.2 0.43 9.3E-06 45.9 4.8 56 485-542 91-146 (149)
156 smart00292 BRCT breast cancer 90.0 0.57 1.2E-05 37.8 4.8 48 600-647 28-78 (80)
157 PRK14668 uvrC excinuclease ABC 89.7 0.4 8.6E-06 55.8 4.9 50 459-510 527-576 (577)
158 PRK09482 flap endonuclease-lik 89.0 0.49 1.1E-05 49.5 4.5 26 527-552 186-211 (256)
159 COG1645 Uncharacterized Zn-fin 88.8 0.25 5.4E-06 46.2 2.0 23 414-438 27-49 (131)
160 TIGR02238 recomb_DMC1 meiotic 88.1 0.85 1.8E-05 49.1 5.8 53 461-514 5-57 (313)
161 TIGR01954 nusA_Cterm_rpt trans 88.0 1.6 3.4E-05 33.4 5.7 43 532-574 2-45 (50)
162 PTZ00035 Rad51 protein; Provis 87.5 0.94 2E-05 49.3 5.7 54 460-514 26-79 (337)
163 cd00008 53EXOc 5'-3' exonuclea 87.3 0.7 1.5E-05 47.8 4.4 26 527-552 187-212 (240)
164 smart00475 53EXOc 5'-3' exonuc 87.3 0.62 1.3E-05 48.8 4.0 26 527-552 190-215 (259)
165 PF01367 5_3_exonuc: 5'-3' exo 87.0 0.042 9.1E-07 49.3 -4.2 25 527-551 22-46 (101)
166 PRK00420 hypothetical protein; 86.5 0.45 9.8E-06 43.5 2.1 24 414-438 22-45 (112)
167 PRK05182 DNA-directed RNA poly 86.5 1.1 2.4E-05 48.2 5.5 51 462-513 253-303 (310)
168 PRK13482 DNA integrity scannin 86.5 1.2 2.6E-05 48.4 5.7 54 461-516 291-344 (352)
169 PLN03187 meiotic recombination 86.4 1.2 2.6E-05 48.6 5.8 54 459-513 33-86 (344)
170 smart00478 ENDO3c endonuclease 86.0 3 6.6E-05 39.4 7.7 41 469-511 13-56 (149)
171 PF12836 HHH_3: Helix-hairpin- 85.6 0.64 1.4E-05 38.1 2.4 28 549-576 8-35 (65)
172 TIGR01084 mutY A/G-specific ad 85.1 2.9 6.4E-05 44.2 7.8 78 470-551 48-134 (275)
173 cd00056 ENDO3c endonuclease II 84.9 2.3 5.1E-05 40.5 6.4 80 469-575 21-103 (158)
174 COG2231 Uncharacterized protei 84.8 4.2 9.2E-05 41.0 8.2 115 468-585 50-181 (215)
175 TIGR02027 rpoA DNA-directed RN 84.8 1.5 3.2E-05 47.0 5.3 53 460-513 237-289 (297)
176 smart00278 HhH1 Helix-hairpin- 84.3 0.78 1.7E-05 30.7 2.0 18 492-509 2-19 (26)
177 PRK14669 uvrC excinuclease ABC 84.2 1.1 2.4E-05 52.5 4.6 56 458-517 553-608 (624)
178 PRK14976 5'-3' exonuclease; Pr 84.0 0.86 1.9E-05 48.3 3.2 25 527-551 195-219 (281)
179 KOG2534|consensus 84.0 2 4.2E-05 45.9 5.7 70 490-560 55-134 (353)
180 TIGR02776 NHEJ_ligase_prk DNA 83.9 15 0.00033 42.6 13.5 178 151-376 3-192 (552)
181 TIGR01083 nth endonuclease III 83.9 4.6 9.9E-05 40.2 8.2 41 470-512 48-91 (191)
182 PF01331 mRNA_cap_enzyme: mRNA 83.7 3.9 8.4E-05 40.5 7.5 141 119-306 17-180 (192)
183 PRK02362 ski2-like helicase; P 83.6 3 6.5E-05 50.1 7.9 54 521-576 650-704 (737)
184 PRK13766 Hef nuclease; Provisi 83.5 1.6 3.6E-05 52.4 5.7 50 461-512 719-768 (773)
185 COG1948 MUS81 ERCC4-type nucle 83.5 1.6 3.5E-05 45.4 4.8 51 460-512 185-235 (254)
186 PF01396 zf-C4_Topoisom: Topoi 82.9 1.2 2.6E-05 32.9 2.7 28 416-444 2-31 (39)
187 PRK00423 tfb transcription ini 82.4 2 4.3E-05 46.2 5.2 148 415-571 11-202 (310)
188 COG5241 RAD10 Nucleotide excis 82.0 0.82 1.8E-05 45.0 1.9 52 527-578 171-222 (224)
189 COG0322 UvrC Nuclease subunit 81.9 1.6 3.5E-05 50.7 4.6 119 372-510 462-580 (581)
190 PRK07758 hypothetical protein; 81.9 3.7 8.1E-05 36.4 5.7 47 529-575 40-87 (95)
191 smart00278 HhH1 Helix-hairpin- 81.8 1.2 2.5E-05 29.8 2.0 20 556-575 2-21 (26)
192 TIGR03491 RecB family nuclease 81.6 2.6 5.7E-05 47.7 6.1 64 443-513 199-262 (457)
193 PF14229 DUF4332: Domain of un 80.9 1.6 3.4E-05 40.5 3.3 49 443-494 41-89 (122)
194 PF06677 Auto_anti-p27: Sjogre 80.8 1.3 2.7E-05 33.3 2.1 24 414-438 16-39 (41)
195 PRK10736 hypothetical protein; 80.7 4.5 9.7E-05 44.7 7.3 67 522-593 7-73 (374)
196 PRK14671 uvrC excinuclease ABC 80.7 1.8 3.8E-05 51.0 4.4 49 459-511 571-619 (621)
197 smart00279 HhH2 Helix-hairpin- 80.2 1.4 3E-05 32.0 2.1 17 527-543 20-36 (36)
198 PF09151 DUF1936: Domain of un 80.0 1.9 4.2E-05 30.1 2.6 26 417-444 3-33 (36)
199 PRK13910 DNA glycosylase MutY; 79.9 3.8 8.3E-05 43.6 6.3 75 480-556 23-106 (289)
200 PF09297 zf-NADH-PPase: NADH p 79.1 1.5 3.3E-05 30.8 2.0 23 416-438 4-26 (32)
201 smart00611 SEC63 Domain of unk 78.1 4.9 0.00011 42.7 6.5 63 449-513 144-206 (312)
202 PRK09202 nusA transcription el 77.9 8.1 0.00018 44.0 8.4 102 460-562 359-466 (470)
203 TIGR02239 recomb_RAD51 DNA rep 77.2 4.1 9E-05 43.9 5.6 51 462-513 6-56 (316)
204 PRK10308 3-methyl-adenine DNA 77.0 11 0.00023 40.2 8.5 69 480-549 156-234 (283)
205 PLN03186 DNA repair protein RA 76.9 4.4 9.6E-05 44.2 5.8 55 459-514 30-84 (342)
206 COG0122 AlkA 3-methyladenine D 76.4 12 0.00025 39.9 8.7 82 467-574 124-217 (285)
207 PF14803 Nudix_N_2: Nudix N-te 76.1 2.5 5.3E-05 30.5 2.3 23 416-438 1-27 (34)
208 PF01927 Mut7-C: Mut7-C RNAse 75.6 3 6.4E-05 39.9 3.6 55 371-428 50-104 (147)
209 PF11731 Cdd1: Pathogenicity l 75.4 2.9 6.2E-05 37.0 3.1 31 459-490 14-44 (93)
210 PF13248 zf-ribbon_3: zinc-rib 75.1 1.5 3.2E-05 29.5 0.9 21 414-438 1-21 (26)
211 PF03118 RNA_pol_A_CTD: Bacter 74.5 5.6 0.00012 32.9 4.5 49 524-575 15-64 (66)
212 cd01703 PolY_Pol_iota DNA Poly 73.5 4.5 9.7E-05 44.8 4.8 50 458-510 173-237 (379)
213 CHL00013 rpoA RNA polymerase a 73.2 4.6 0.0001 43.8 4.7 49 464-513 269-317 (327)
214 KOG0966|consensus 72.8 1.2E+02 0.0026 36.7 16.0 198 117-348 249-466 (881)
215 PRK07220 DNA topoisomerase I; 72.3 5.7 0.00012 47.8 5.6 47 459-506 688-734 (740)
216 cd08689 C2_fungal_Pkc1p C2 dom 71.5 5.2 0.00011 36.4 3.9 59 287-353 21-79 (109)
217 COG0258 Exo 5'-3' exonuclease 71.3 4.4 9.6E-05 43.4 4.0 26 527-552 202-227 (310)
218 PRK03352 DNA polymerase IV; Va 70.9 4.8 0.0001 43.6 4.3 50 458-510 178-227 (346)
219 PLN03123 poly [ADP-ribose] pol 70.9 4.2 9.1E-05 50.1 4.2 49 600-648 418-469 (981)
220 TIGR00593 pola DNA polymerase 70.9 3.3 7.2E-05 50.7 3.3 25 527-551 189-213 (887)
221 KOG1921|consensus 69.9 3.9 8.5E-05 42.2 3.0 35 534-572 141-176 (286)
222 PF11731 Cdd1: Pathogenicity l 69.9 8.3 0.00018 34.2 4.7 31 527-557 16-47 (93)
223 PRK03980 flap endonuclease-1; 69.8 4 8.7E-05 43.6 3.3 25 527-551 193-217 (292)
224 KOG2841|consensus 69.3 5.4 0.00012 41.0 3.9 58 450-513 192-249 (254)
225 COG1623 Predicted nucleic-acid 69.1 7.4 0.00016 41.2 4.9 99 435-544 241-346 (349)
226 cd01701 PolY_Rev1 DNA polymera 68.7 5.8 0.00013 44.2 4.4 50 459-511 224-275 (404)
227 cd01702 PolY_Pol_eta DNA Polym 68.1 5.8 0.00013 43.5 4.2 50 459-510 184-235 (359)
228 COG2231 Uncharacterized protei 67.5 5 0.00011 40.5 3.2 39 537-575 96-135 (215)
229 COG1096 Predicted RNA-binding 67.4 14 0.00031 36.7 6.2 75 362-451 103-179 (188)
230 KOG0442|consensus 67.2 5.9 0.00013 47.4 4.2 51 526-577 824-874 (892)
231 PF14716 HHH_8: Helix-hairpin- 67.1 8.9 0.00019 31.6 4.1 20 556-575 48-67 (68)
232 PF09862 DUF2089: Protein of u 66.9 4.1 8.8E-05 37.4 2.2 24 418-449 1-24 (113)
233 cd00128 XPG Xeroderma pigmento 66.7 5 0.00011 43.0 3.3 25 527-551 227-251 (316)
234 PRK01216 DNA polymerase IV; Va 66.6 7.4 0.00016 42.6 4.6 48 459-509 180-227 (351)
235 TIGR03674 fen_arch flap struct 65.9 5.3 0.00011 43.5 3.3 26 527-552 240-265 (338)
236 PRK05755 DNA polymerase I; Pro 65.5 4.8 0.0001 49.4 3.2 24 527-550 191-214 (880)
237 TIGR00588 ogg 8-oxoguanine DNA 65.2 15 0.00032 39.6 6.5 21 554-574 219-239 (310)
238 COG4277 Predicted DNA-binding 64.6 7.3 0.00016 41.5 3.8 63 529-595 304-368 (404)
239 PF10391 DNA_pol_lambd_f: Fing 64.3 7.6 0.00017 30.6 3.0 26 526-551 5-31 (52)
240 TIGR00596 rad1 DNA repair prot 64.2 7.3 0.00016 47.3 4.3 19 493-511 759-777 (814)
241 KOG3084|consensus 63.8 3.5 7.6E-05 44.0 1.3 29 415-445 150-178 (345)
242 PRK03858 DNA polymerase IV; Va 63.3 8 0.00017 42.7 4.2 49 458-509 174-222 (396)
243 PTZ00217 flap endonuclease-1; 62.5 6.6 0.00014 43.7 3.3 25 527-551 239-263 (393)
244 smart00661 RPOL9 RNA polymeras 62.5 5.2 0.00011 30.8 1.8 23 416-438 1-25 (52)
245 COG2251 Predicted nuclease (Re 62.5 10 0.00022 42.5 4.7 64 443-513 217-280 (474)
246 PRK03348 DNA polymerase IV; Pr 62.1 9.1 0.0002 43.4 4.4 49 459-510 182-230 (454)
247 PRK10880 adenine DNA glycosyla 62.1 15 0.00032 40.3 5.9 72 471-545 53-132 (350)
248 PTZ00035 Rad51 protein; Provis 61.9 16 0.00034 39.9 6.0 54 523-576 23-77 (337)
249 PF04994 TfoX_C: TfoX C-termin 61.4 4.8 0.0001 34.6 1.6 31 457-488 3-33 (81)
250 KOG2534|consensus 61.4 15 0.00032 39.5 5.4 56 518-573 51-115 (353)
251 PRK00398 rpoP DNA-directed RNA 61.3 5.4 0.00012 30.3 1.7 22 417-438 5-26 (46)
252 COG3877 Uncharacterized protei 60.7 7.1 0.00015 35.2 2.5 29 413-449 4-32 (122)
253 PF09889 DUF2116: Uncharacteri 60.4 3.5 7.7E-05 33.4 0.5 29 415-450 3-31 (59)
254 COG1997 RPL43A Ribosomal prote 59.8 7.6 0.00016 33.9 2.5 24 415-438 35-58 (89)
255 PF14952 zf-tcix: Putative tre 59.4 5.4 0.00012 30.3 1.3 26 416-447 12-37 (44)
256 PRK11088 rrmA 23S rRNA methylt 57.7 4.4 9.5E-05 42.4 0.8 36 417-456 4-39 (272)
257 smart00611 SEC63 Domain of unk 57.7 16 0.00035 38.7 5.2 52 526-577 154-206 (312)
258 cd01700 PolY_Pol_V_umuC umuC s 57.5 13 0.00028 40.3 4.4 48 459-510 178-225 (344)
259 PF13240 zinc_ribbon_2: zinc-r 57.5 4.4 9.5E-05 26.5 0.5 18 417-438 1-18 (23)
260 COG3743 Uncharacterized conser 57.2 8.6 0.00019 36.1 2.5 41 457-498 67-107 (133)
261 PF08271 TF_Zn_Ribbon: TFIIB z 56.7 10 0.00022 28.4 2.4 22 417-438 2-24 (43)
262 PLN03187 meiotic recombination 56.6 22 0.00048 38.9 6.0 51 524-574 32-83 (344)
263 PRK10880 adenine DNA glycosyla 55.5 13 0.00029 40.7 4.1 23 552-574 106-128 (350)
264 PF07754 DUF1610: Domain of un 55.4 8.6 0.00019 25.6 1.6 21 418-438 1-21 (24)
265 TIGR02238 recomb_DMC1 meiotic 55.3 21 0.00046 38.5 5.6 48 529-576 7-55 (313)
266 TIGR00608 radc DNA repair prot 55.3 15 0.00032 37.7 4.1 69 445-516 17-85 (218)
267 cd00729 rubredoxin_SM Rubredox 54.7 6.8 0.00015 28.1 1.1 11 414-424 17-27 (34)
268 PF02371 Transposase_20: Trans 54.4 6.9 0.00015 33.8 1.4 21 528-548 7-27 (87)
269 PRK14133 DNA polymerase IV; Pr 54.0 16 0.00035 39.6 4.5 49 459-511 175-223 (347)
270 PRK00241 nudC NADH pyrophospha 53.7 8.6 0.00019 40.2 2.2 24 415-438 99-122 (256)
271 PRK14976 5'-3' exonuclease; Pr 53.7 34 0.00074 36.3 6.7 45 460-513 194-238 (281)
272 PRK13844 recombination protein 53.3 11 0.00025 37.9 2.9 24 491-514 15-38 (200)
273 PRK10445 endonuclease VIII; Pr 52.8 9.1 0.0002 40.2 2.2 22 417-438 237-260 (263)
274 PF06044 DRP: Dam-replacing fa 52.3 6.5 0.00014 40.6 1.0 28 416-447 32-63 (254)
275 COG1779 C4-type Zn-finger prot 52.1 10 0.00022 38.1 2.2 31 457-487 86-116 (201)
276 PF04606 Ogr_Delta: Ogr/Delta- 52.1 15 0.00032 28.2 2.8 31 417-449 1-39 (47)
277 PLN03186 DNA repair protein RA 52.1 38 0.00082 37.1 6.9 53 523-575 28-81 (342)
278 PRK00076 recR recombination pr 51.6 13 0.00028 37.5 3.0 22 491-512 11-32 (196)
279 TIGR00615 recR recombination p 51.6 13 0.00028 37.4 2.9 22 491-512 11-32 (195)
280 COG0258 Exo 5'-3' exonuclease 51.4 22 0.00048 38.1 4.9 48 458-515 199-247 (310)
281 PRK02406 DNA polymerase IV; Va 51.3 18 0.0004 39.1 4.4 48 458-509 169-216 (343)
282 KOG2906|consensus 50.9 12 0.00025 33.4 2.2 26 416-445 2-29 (105)
283 PRK11827 hypothetical protein; 50.2 12 0.00027 30.5 2.1 22 417-438 10-31 (60)
284 TIGR02239 recomb_RAD51 DNA rep 49.9 28 0.00062 37.5 5.5 48 528-575 6-54 (316)
285 PRK09482 flap endonuclease-lik 49.9 20 0.00043 37.6 4.2 49 456-513 181-229 (256)
286 TIGR00686 phnA alkylphosphonat 49.0 14 0.0003 33.6 2.4 21 417-438 4-24 (109)
287 PRK01103 formamidopyrimidine/5 48.9 9.5 0.0002 40.3 1.6 22 417-438 247-270 (274)
288 PRK03103 DNA polymerase IV; Re 48.5 22 0.00047 39.5 4.5 50 459-512 183-232 (409)
289 cd00424 PolY Y-family of DNA p 48.2 24 0.00052 38.2 4.7 49 459-511 175-224 (343)
290 KOG1921|consensus 48.0 63 0.0014 33.7 7.2 73 469-542 99-178 (286)
291 COG2888 Predicted Zn-ribbon RN 48.0 7.1 0.00015 31.6 0.4 25 414-438 8-32 (61)
292 KOG2875|consensus 47.4 41 0.0009 35.6 5.9 39 535-573 191-236 (323)
293 PRK01810 DNA polymerase IV; Va 47.3 22 0.00048 39.4 4.3 50 459-512 181-230 (407)
294 cd03468 PolY_like DNA Polymera 47.3 25 0.00054 37.6 4.6 50 456-509 169-218 (335)
295 cd00080 HhH2_motif Helix-hairp 47.1 24 0.00051 29.8 3.5 29 457-487 22-50 (75)
296 smart00279 HhH2 Helix-hairpin- 47.0 15 0.00032 26.8 1.9 16 461-476 20-35 (36)
297 PF02643 DUF192: Uncharacteriz 46.7 55 0.0012 29.5 6.0 89 299-388 4-107 (108)
298 PRK03760 hypothetical protein; 46.6 25 0.00054 32.4 3.8 54 335-389 61-116 (117)
299 PRK02794 DNA polymerase IV; Pr 46.6 21 0.00045 39.9 4.0 49 459-511 211-259 (419)
300 PF04919 DUF655: Protein of un 45.8 42 0.00091 33.3 5.4 55 488-542 113-168 (181)
301 PTZ00205 DNA polymerase kappa; 45.2 23 0.00049 41.3 4.0 47 459-509 311-357 (571)
302 COG1656 Uncharacterized conser 45.0 12 0.00025 36.6 1.4 53 371-428 56-110 (165)
303 COG1491 Predicted RNA-binding 45.0 67 0.0015 32.0 6.6 23 490-512 129-151 (202)
304 PRK07945 hypothetical protein; 44.4 35 0.00076 37.1 5.2 49 492-541 50-98 (335)
305 COG2093 DNA-directed RNA polym 44.3 23 0.00051 29.0 2.8 15 417-431 20-35 (64)
306 PF13549 ATP-grasp_5: ATP-gras 44.2 48 0.001 34.0 5.9 48 247-305 10-57 (222)
307 PRK10220 hypothetical protein; 44.2 19 0.00041 32.8 2.5 21 417-438 5-25 (111)
308 cd00008 53EXOc 5'-3' exonuclea 43.9 34 0.00075 35.3 4.8 43 460-512 186-229 (240)
309 PF11798 IMS_HHH: IMS family H 43.6 17 0.00037 25.6 1.8 19 459-477 13-31 (32)
310 PRK14182 bifunctional 5,10-met 43.4 78 0.0017 33.7 7.4 67 564-652 6-86 (282)
311 COG1592 Rubrerythrin [Energy p 43.3 12 0.00026 36.7 1.2 12 413-424 147-158 (166)
312 PRK01229 N-glycosylase/DNA lya 43.2 80 0.0017 32.1 7.2 20 554-573 117-137 (208)
313 COG0353 RecR Recombinational D 43.1 20 0.00044 36.0 2.8 15 493-507 14-28 (198)
314 PRK00432 30S ribosomal protein 43.0 16 0.00035 28.6 1.7 22 416-438 21-42 (50)
315 PRK03352 DNA polymerase IV; Va 42.9 41 0.0009 36.4 5.5 71 502-574 147-227 (346)
316 PRK01229 N-glycosylase/DNA lya 42.9 29 0.00063 35.3 4.0 59 487-545 68-141 (208)
317 cd00166 SAM Sterile alpha moti 42.8 56 0.0012 25.3 4.9 44 467-513 17-61 (63)
318 KOG1968|consensus 42.8 13 0.00028 45.4 1.7 42 599-640 198-240 (871)
319 PRK12495 hypothetical protein; 41.7 13 0.00029 37.8 1.3 23 414-438 41-63 (226)
320 PRK14906 DNA-directed RNA poly 41.4 31 0.00067 44.1 4.6 52 461-513 1317-1368(1460)
321 PRK14890 putative Zn-ribbon RN 41.2 9.8 0.00021 30.8 0.2 24 415-438 7-30 (59)
322 COG5216 Uncharacterized conser 40.8 27 0.0006 28.2 2.7 27 409-438 18-49 (67)
323 PRK14810 formamidopyrimidine-D 40.7 18 0.0004 38.1 2.3 22 417-438 246-269 (272)
324 PRK03609 umuC DNA polymerase V 40.5 36 0.00078 38.1 4.7 48 458-509 180-227 (422)
325 PRK07945 hypothetical protein; 40.4 44 0.00096 36.3 5.2 64 527-593 53-126 (335)
326 TIGR00577 fpg formamidopyrimid 39.9 19 0.00042 37.9 2.3 22 417-438 247-270 (272)
327 PRK13945 formamidopyrimidine-D 39.9 20 0.00042 38.1 2.3 22 417-438 256-279 (282)
328 PF02371 Transposase_20: Trans 39.7 30 0.00066 29.8 3.1 40 555-594 2-42 (87)
329 PF02150 RNA_POL_M_15KD: RNA p 39.6 10 0.00022 27.4 0.1 26 416-445 2-28 (35)
330 PTZ00446 vacuolar sorting prot 39.5 60 0.0013 32.6 5.5 52 7-58 125-176 (191)
331 PRK14811 formamidopyrimidine-D 39.3 19 0.00042 37.9 2.2 22 417-438 237-260 (269)
332 TIGR02306 RNA_lig_DRB0094 RNA 39.2 49 0.0011 36.2 5.2 67 118-186 159-235 (341)
333 KOG2875|consensus 39.0 37 0.0008 36.0 4.0 92 443-544 131-240 (323)
334 smart00475 53EXOc 5'-3' exonuc 39.0 37 0.0008 35.6 4.2 27 459-487 188-214 (259)
335 PRK14193 bifunctional 5,10-met 38.8 98 0.0021 33.1 7.3 67 564-652 8-88 (284)
336 PF13005 zf-IS66: zinc-finger 38.7 17 0.00038 27.4 1.3 14 415-428 2-15 (47)
337 PF00763 THF_DHG_CYH: Tetrahyd 38.3 54 0.0012 30.0 4.7 65 564-650 5-83 (117)
338 PF09851 SHOCT: Short C-termin 38.1 60 0.0013 22.7 3.8 27 24-53 4-30 (31)
339 PRK14171 bifunctional 5,10-met 38.1 1.2E+02 0.0026 32.5 7.8 67 564-652 7-88 (288)
340 cd01702 PolY_Pol_eta DNA Polym 38.0 49 0.0011 36.3 5.2 76 498-575 147-236 (359)
341 COG2835 Uncharacterized conser 37.9 25 0.00055 28.6 2.1 22 417-438 10-31 (60)
342 PF13719 zinc_ribbon_5: zinc-r 37.8 16 0.00036 26.5 1.0 23 416-438 3-30 (37)
343 PRK00024 hypothetical protein; 37.0 53 0.0011 33.7 4.9 37 480-516 55-91 (224)
344 PF09511 RNA_lig_T4_1: RNA lig 36.9 25 0.00055 35.7 2.5 61 82-147 13-74 (221)
345 PF11672 DUF3268: Protein of u 36.7 24 0.00053 31.8 2.0 15 415-429 2-16 (102)
346 PHA00626 hypothetical protein 36.5 28 0.00062 27.9 2.1 36 417-464 2-42 (59)
347 PRK14166 bifunctional 5,10-met 36.4 1.1E+02 0.0023 32.7 7.2 66 564-651 6-85 (282)
348 PF10772 DUF2597: Protein of u 36.3 1.3E+02 0.0028 28.4 6.7 44 163-223 31-74 (134)
349 PF14354 Lar_restr_allev: Rest 36.2 31 0.00068 27.4 2.5 25 417-445 5-37 (61)
350 PF02889 Sec63: Sec63 Brl doma 35.9 48 0.001 35.1 4.6 54 457-511 148-201 (314)
351 COG0353 RecR Recombinational D 35.7 26 0.00057 35.2 2.3 26 518-543 6-32 (198)
352 PF07282 OrfB_Zn_ribbon: Putat 35.4 25 0.00055 28.7 1.8 24 415-438 28-51 (69)
353 PF07191 zinc-ribbons_6: zinc- 35.3 28 0.0006 29.3 2.0 27 412-438 27-55 (70)
354 PF13453 zf-TFIIB: Transcripti 35.1 34 0.00073 25.3 2.3 22 417-438 1-24 (41)
355 PRK14189 bifunctional 5,10-met 35.1 1.3E+02 0.0029 32.1 7.6 67 564-652 8-88 (285)
356 PRK14185 bifunctional 5,10-met 35.0 1E+02 0.0023 33.0 6.8 66 564-651 6-86 (293)
357 cd03586 PolY_Pol_IV_kappa DNA 35.0 49 0.0011 35.4 4.5 48 459-510 173-220 (334)
358 PRK14188 bifunctional 5,10-met 34.9 1.4E+02 0.0031 32.0 7.9 67 564-652 7-88 (296)
359 PRK09678 DNA-binding transcrip 34.9 34 0.00074 28.9 2.5 41 417-459 3-53 (72)
360 PF08792 A2L_zn_ribbon: A2L zi 34.6 35 0.00077 24.4 2.2 24 415-438 3-26 (33)
361 PF03564 DUF1759: Protein of u 34.5 1.4E+02 0.003 27.8 6.9 73 520-594 43-116 (145)
362 PF00536 SAM_1: SAM domain (St 34.4 29 0.00062 27.7 2.0 44 468-514 19-63 (64)
363 PRK14194 bifunctional 5,10-met 34.1 1.3E+02 0.0028 32.4 7.4 67 564-652 9-89 (301)
364 PTZ00111 DNA replication licen 33.7 29 0.00063 42.6 2.7 44 381-424 226-292 (915)
365 PLN02616 tetrahydrofolate dehy 33.7 1.3E+02 0.0028 33.3 7.4 67 564-652 78-159 (364)
366 PF04014 Antitoxin-MazE: Antid 33.4 48 0.001 25.1 2.9 22 371-392 13-34 (47)
367 PF01071 GARS_A: Phosphoribosy 33.3 79 0.0017 31.8 5.3 44 253-306 7-50 (194)
368 PRK14175 bifunctional 5,10-met 33.0 1.3E+02 0.0027 32.3 7.0 67 564-652 8-88 (286)
369 TIGR03037 anthran_nbaC 3-hydro 32.6 62 0.0013 31.6 4.3 67 378-456 73-147 (159)
370 PRK14168 bifunctional 5,10-met 32.4 1.4E+02 0.0031 32.1 7.3 67 564-652 8-89 (297)
371 smart00834 CxxC_CXXC_SSSS Puta 32.0 27 0.00059 25.3 1.4 14 414-427 25-38 (41)
372 TIGR02098 MJ0042_CXXC MJ0042 f 32.0 27 0.00059 25.1 1.3 22 417-438 4-30 (38)
373 COG4068 Uncharacterized protei 31.8 16 0.00034 29.5 0.1 25 414-445 7-31 (64)
374 COG1439 Predicted nucleic acid 31.8 23 0.0005 35.0 1.2 12 416-427 154-165 (177)
375 PF11948 DUF3465: Protein of u 31.7 89 0.0019 29.5 4.9 65 283-388 30-95 (131)
376 PF12482 DUF3701: Phage integr 31.7 55 0.0012 29.3 3.4 45 466-511 22-70 (96)
377 PF07647 SAM_2: SAM domain (St 31.7 64 0.0014 25.8 3.6 48 464-514 17-65 (66)
378 PRK14184 bifunctional 5,10-met 31.7 1.5E+02 0.0033 31.7 7.3 66 564-651 6-86 (286)
379 COG0266 Nei Formamidopyrimidin 31.5 30 0.00066 36.6 2.1 23 416-438 246-270 (273)
380 PRK14172 bifunctional 5,10-met 31.2 1.6E+02 0.0035 31.3 7.4 67 564-651 7-87 (278)
381 COG1571 Predicted DNA-binding 31.1 20 0.00044 40.0 0.8 73 377-457 314-387 (421)
382 PF08394 Arc_trans_TRASH: Arch 31.1 46 0.00099 24.6 2.3 31 418-451 1-37 (37)
383 PF14579 HHH_6: Helix-hairpin- 31.1 58 0.0012 28.3 3.5 29 459-487 29-60 (90)
384 cd00350 rubredoxin_like Rubred 31.0 26 0.00055 24.8 1.0 11 414-424 16-26 (33)
385 PRK14186 bifunctional 5,10-met 31.0 1.6E+02 0.0035 31.7 7.4 67 564-652 7-88 (297)
386 PRK08402 replication factor A; 30.8 26 0.00056 38.5 1.5 24 414-438 212-235 (355)
387 PRK14169 bifunctional 5,10-met 30.8 1.7E+02 0.0036 31.3 7.5 66 564-651 6-85 (282)
388 PF14490 HHH_4: Helix-hairpin- 30.7 41 0.00088 29.5 2.5 53 520-576 12-67 (94)
389 PRK00076 recR recombination pr 30.4 44 0.00096 33.7 2.9 23 554-576 10-32 (196)
390 PF14716 HHH_8: Helix-hairpin- 30.2 49 0.0011 27.2 2.7 20 492-511 48-67 (68)
391 PF04423 Rad50_zn_hook: Rad50 30.1 19 0.00042 28.2 0.3 10 417-426 22-31 (54)
392 PRK09521 exosome complex RNA-b 30.0 1.7E+02 0.0036 29.0 7.0 63 377-452 117-181 (189)
393 COG1194 MutY A/G-specific DNA 29.8 98 0.0021 33.9 5.6 73 480-554 64-145 (342)
394 PF11858 DUF3378: Domain of un 29.7 90 0.002 26.9 4.4 44 97-141 8-51 (81)
395 PF14690 zf-ISL3: zinc-finger 29.7 45 0.00097 25.0 2.2 14 415-428 2-15 (47)
396 PF09723 Zn-ribbon_8: Zinc rib 29.5 37 0.0008 25.4 1.7 14 414-427 25-39 (42)
397 COG2104 ThiS Sulfur transfer p 29.5 1E+02 0.0022 25.7 4.5 25 371-396 21-45 (68)
398 PRK00366 ispG 4-hydroxy-3-meth 29.4 33 0.00072 37.6 2.0 14 380-393 232-245 (360)
399 PF03811 Zn_Tnp_IS1: InsA N-te 29.1 49 0.0011 24.1 2.2 24 415-438 5-34 (36)
400 PF07820 TraC: TraC-like prote 29.1 1.8E+02 0.0039 25.8 6.1 46 10-55 3-58 (92)
401 PRK12496 hypothetical protein; 28.9 23 0.0005 34.6 0.6 15 181-195 19-33 (164)
402 PLN02897 tetrahydrofolate dehy 28.9 1.8E+02 0.0039 32.0 7.5 67 564-652 61-142 (345)
403 TIGR01057 topA_arch DNA topois 28.8 36 0.00078 40.2 2.4 27 416-443 590-618 (618)
404 TIGR00615 recR recombination p 28.8 49 0.0011 33.3 3.0 22 554-575 10-31 (195)
405 PRK14167 bifunctional 5,10-met 28.8 1.8E+02 0.0039 31.3 7.4 67 564-652 7-87 (297)
406 PF00122 E1-E2_ATPase: E1-E2 A 28.5 33 0.00071 34.5 1.7 28 374-402 47-74 (230)
407 smart00746 TRASH metallochaper 28.4 51 0.0011 21.7 2.2 27 418-447 1-35 (39)
408 PF08605 Rad9_Rad53_bind: Fung 28.4 20 0.00044 33.8 0.2 27 371-402 52-78 (131)
409 COG4469 CoiA Competence protei 28.4 28 0.00061 37.6 1.2 16 415-430 25-40 (342)
410 COG0821 gcpE 1-hydroxy-2-methy 28.3 24 0.00051 38.3 0.6 14 380-393 225-238 (361)
411 cd01703 PolY_Pol_iota DNA Poly 28.1 1E+02 0.0022 34.2 5.6 33 521-553 167-203 (379)
412 TIGR01206 lysW lysine biosynth 28.0 43 0.00093 26.7 1.9 11 417-427 4-14 (54)
413 PRK14190 bifunctional 5,10-met 28.0 1.8E+02 0.0039 31.0 7.2 67 564-652 8-88 (284)
414 COG2816 NPY1 NTP pyrophosphohy 27.9 36 0.00078 36.1 1.9 23 416-438 112-134 (279)
415 PF14579 HHH_6: Helix-hairpin- 27.6 1.4E+02 0.0031 25.8 5.4 47 493-541 29-75 (90)
416 cd04482 RPA2_OBF_like RPA2_OBF 27.3 82 0.0018 27.5 3.8 12 377-388 46-57 (91)
417 PRK10308 3-methyl-adenine DNA 26.9 64 0.0014 34.3 3.6 21 554-574 206-226 (283)
418 COG1885 Uncharacterized protei 26.6 31 0.00067 31.1 0.9 11 416-426 50-60 (115)
419 PRK13844 recombination protein 26.6 56 0.0012 33.1 2.9 23 554-576 14-36 (200)
420 PF07191 zinc-ribbons_6: zinc- 26.6 56 0.0012 27.5 2.4 20 417-438 3-22 (70)
421 PRK14170 bifunctional 5,10-met 26.4 1.9E+02 0.0042 30.8 7.1 67 564-652 7-87 (284)
422 KOG2093|consensus 26.4 48 0.0011 40.1 2.8 55 456-513 548-602 (1016)
423 COG1241 MCM2 Predicted ATPase 26.3 76 0.0016 38.0 4.4 53 362-428 85-142 (682)
424 COG0389 DinP Nucleotidyltransf 26.3 63 0.0014 35.4 3.6 48 458-509 177-224 (354)
425 PF02889 Sec63: Sec63 Brl doma 26.1 87 0.0019 33.1 4.5 52 526-577 151-203 (314)
426 PF13717 zinc_ribbon_4: zinc-r 26.0 38 0.00082 24.6 1.2 22 417-438 4-30 (36)
427 COG1321 TroR Mn-dependent tran 25.8 1.5E+02 0.0033 28.6 5.7 76 470-577 45-122 (154)
428 PRK14180 bifunctional 5,10-met 25.7 2.2E+02 0.0048 30.3 7.4 67 564-652 6-87 (282)
429 PRK05179 rpsM 30S ribosomal pr 25.3 99 0.0021 28.8 4.1 37 523-559 16-55 (122)
430 PF10571 UPF0547: Uncharacteri 25.1 35 0.00077 23.0 0.8 9 417-425 2-10 (26)
431 PRK14174 bifunctional 5,10-met 24.9 2.3E+02 0.005 30.4 7.4 67 564-652 6-87 (295)
432 PF00416 Ribosomal_S13: Riboso 24.9 99 0.0021 27.9 4.0 24 521-544 12-36 (107)
433 PF09237 GAGA: GAGA factor; I 24.5 26 0.00057 27.7 0.1 30 413-456 22-51 (54)
434 COG0551 TopA Zn-finger domain 24.5 63 0.0014 30.4 2.7 29 416-445 18-48 (140)
435 PRK04053 rps13p 30S ribosomal 24.4 73 0.0016 30.8 3.1 24 521-544 22-46 (149)
436 COG1430 Uncharacterized conser 24.4 3.4E+02 0.0074 25.5 7.5 93 298-391 17-123 (126)
437 COG0777 AccD Acetyl-CoA carbox 24.1 61 0.0013 34.3 2.7 172 414-618 27-223 (294)
438 PF14066 DUF4256: Protein of u 23.9 66 0.0014 31.3 2.7 32 623-654 93-124 (173)
439 PRK03348 DNA polymerase IV; Pr 23.8 1.4E+02 0.0031 33.9 5.9 53 520-574 174-230 (454)
440 PF01780 Ribosomal_L37ae: Ribo 23.8 41 0.0009 29.7 1.2 24 415-438 35-58 (90)
441 TIGR02609 doc_partner putative 23.7 80 0.0017 26.5 2.9 23 371-393 16-38 (74)
442 COG1326 Uncharacterized archae 23.7 39 0.00084 33.9 1.1 22 417-438 8-35 (201)
443 PRK09612 rpl2p 50S ribosomal p 23.5 76 0.0016 33.0 3.3 93 330-450 39-132 (238)
444 PF11372 DUF3173: Domain of un 23.5 66 0.0014 26.2 2.2 23 488-511 4-26 (59)
445 PF14164 YqzH: YqzH-like prote 23.5 2.3E+02 0.005 23.5 5.3 40 21-60 6-46 (64)
446 PRK03858 DNA polymerase IV; Va 23.5 1.3E+02 0.0028 33.1 5.4 34 527-560 177-211 (396)
447 cd01701 PolY_Rev1 DNA polymera 23.4 1.2E+02 0.0027 33.7 5.2 14 493-506 224-237 (404)
448 PRK00564 hypA hydrogenase nick 23.3 54 0.0012 30.1 2.0 80 328-431 20-104 (117)
449 PF04551 GcpE: GcpE protein; 23.3 39 0.00085 37.0 1.2 38 248-285 161-198 (359)
450 PRK14183 bifunctional 5,10-met 22.9 2.6E+02 0.0057 29.8 7.2 66 564-651 6-86 (281)
451 PF05191 ADK_lid: Adenylate ki 22.9 53 0.0012 23.9 1.5 18 412-429 18-35 (36)
452 PRK07726 DNA topoisomerase III 22.8 50 0.0011 39.3 2.1 27 416-444 611-639 (658)
453 PRK14724 DNA topoisomerase III 22.7 1E+02 0.0022 38.6 4.7 52 417-480 757-816 (987)
454 TIGR03595 Obg_CgtA_exten Obg f 22.6 73 0.0016 26.5 2.4 15 374-388 49-63 (69)
455 PRK12278 50S ribosomal protein 22.6 75 0.0016 32.7 3.0 40 457-497 158-197 (221)
456 PRK14176 bifunctional 5,10-met 22.4 3E+02 0.0066 29.4 7.6 67 564-652 13-94 (287)
457 PF12760 Zn_Tnp_IS1595: Transp 22.3 59 0.0013 24.6 1.7 22 417-438 20-42 (46)
458 PRK14714 DNA polymerase II lar 22.3 3.7E+02 0.0081 34.5 9.2 174 248-443 475-698 (1337)
459 PRK14177 bifunctional 5,10-met 22.2 3.1E+02 0.0067 29.3 7.6 68 564-652 8-89 (284)
460 PF00730 HhH-GPD: HhH-GPD supe 22.1 85 0.0018 27.6 3.0 39 537-575 19-62 (108)
461 TIGR00373 conserved hypothetic 22.0 41 0.00089 32.6 0.9 13 417-429 130-142 (158)
462 PHA02325 hypothetical protein 22.0 78 0.0017 26.1 2.3 22 415-438 3-24 (72)
463 PF08443 RimK: RimK-like ATP-g 21.9 1.6E+02 0.0034 28.9 5.1 34 250-284 5-38 (190)
464 PRK10792 bifunctional 5,10-met 21.8 2.5E+02 0.0053 30.1 6.8 68 564-652 8-89 (285)
465 PF04919 DUF655: Protein of un 21.7 95 0.0021 30.9 3.4 49 525-577 117-171 (181)
466 PRK00419 DNA primase small sub 21.6 42 0.00091 37.2 1.0 77 483-562 213-295 (376)
467 PRK07194 fliG flagellar motor 21.6 5E+02 0.011 28.2 9.3 26 563-588 139-164 (334)
468 TIGR00100 hypA hydrogenase nic 21.4 59 0.0013 29.8 1.8 77 330-428 22-99 (115)
469 PF04216 FdhE: Protein involve 21.4 54 0.0012 34.8 1.8 24 415-438 172-202 (290)
470 TIGR00593 pola DNA polymerase 21.3 1.3E+02 0.0029 37.2 5.2 46 460-513 188-233 (887)
471 COG2824 PhnA Uncharacterized Z 21.1 69 0.0015 29.1 2.1 21 417-438 5-25 (112)
472 TIGR01384 TFS_arch transcripti 20.9 61 0.0013 28.8 1.8 26 417-448 2-27 (104)
473 PRK06266 transcription initiat 20.8 47 0.001 32.9 1.1 12 417-428 138-149 (178)
474 PF04475 DUF555: Protein of un 20.8 45 0.00097 29.9 0.8 11 416-426 48-58 (102)
475 KOG2041|consensus 20.7 1.5E+02 0.0033 35.4 5.2 52 103-156 104-155 (1189)
476 TIGR01562 FdhE formate dehydro 20.6 62 0.0013 34.9 2.0 10 415-424 184-193 (305)
477 TIGR03252 uncharacterized HhH- 20.6 97 0.0021 30.8 3.2 23 491-513 115-137 (177)
478 COG0099 RpsM Ribosomal protein 20.5 1.1E+02 0.0024 28.4 3.3 39 522-560 15-56 (121)
479 COG2336 MazE Growth regulator 20.4 1.1E+02 0.0023 26.7 3.0 22 371-392 18-39 (82)
480 PRK14187 bifunctional 5,10-met 20.4 3.6E+02 0.0079 29.0 7.7 67 564-652 7-88 (294)
481 PHA00439 exonuclease 20.3 73 0.0016 34.0 2.5 15 527-542 192-206 (286)
482 TIGR02605 CxxC_CxxC_SSSS putat 20.3 64 0.0014 24.8 1.6 10 414-423 25-34 (52)
483 PRK03922 hypothetical protein; 20.2 46 0.001 30.3 0.8 11 416-426 50-60 (113)
484 PRK01216 DNA polymerase IV; Va 20.2 1.7E+02 0.0038 32.0 5.5 52 520-573 172-227 (351)
485 PRK14191 bifunctional 5,10-met 20.2 3.2E+02 0.007 29.2 7.3 67 564-652 6-87 (285)
486 COG1998 RPS31 Ribosomal protei 20.1 61 0.0013 25.4 1.3 24 415-438 19-42 (51)
No 1
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=100.00 E-value=1.1e-193 Score=1593.49 Aligned_cols=633 Identities=45% Similarity=0.733 Sum_probs=613.8
Q ss_pred ChhhHHHHHHHHHHHHHHHHHHhhcCCCCCCChHHHHHHHHHHHHHHHhCCCCCCCCCCccccCcccCCCCcceeccccc
Q psy11423 10 NFSKLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVGGENSKYVHHTFKM 89 (655)
Q Consensus 10 ~~~~~~~~~~~L~~~l~~~~~~Yy~~~~p~isD~~YD~L~~~L~~le~~~p~~~~~~spt~~Vg~~~~~~~~kv~H~~pM 89 (655)
++.++++++++|+++|++|+++||++|+|.|||++||+|+++|++||.+||++.++|||||+||+.+..+|.+|+|.+||
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 cCCCCCCChHHHHHHHHHHHHhhccCCCceEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcccCCccc
Q psy11423 90 MSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVL 169 (655)
Q Consensus 90 lSL~k~~~~~el~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l 169 (655)
|||+|+||++||.+|++|+.+.++. +..|+|||||||+||+|+|+||+|++|+|||||.+|||||+|+++|++||++|
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 ccCCCCceEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCCCCCH
Q psy11423 170 NIKYPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSH 249 (655)
Q Consensus 170 ~~~~~p~~~evRGEv~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~~~~~ 249 (655)
++ +|..+||||||||++++|+++|+++++.|+++|+||||+|||+|||+||++++.|+|.||+|+|+...+...+.||
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 6999999999999999999999999999999999999999999999999999999999999999875532336899
Q ss_pred HHHHHHHHhCCCCCCCCceeeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCcce
Q psy11423 250 SELLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKE 329 (655)
Q Consensus 250 ~e~l~~L~~~GF~~~~~~~~~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~ 329 (655)
+|.|++|++|||+|+++...|.|.+||.+||++|.+.|++|||+|||+|||+||+++|+.||+|+|+||||||||||+++
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 eeEEEEEEEEeecCcceeeeEEEEEEEEECCEEEEEeeCCCHHHHHhcCCCCCCEEEEEecCcccceeecccccCCCCCC
Q psy11423 330 ALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDS 409 (655)
Q Consensus 330 ~~T~v~~I~~qvGRTG~itPvA~lePV~l~G~tVsratLhN~~~i~~~~i~iGd~V~v~raGdVIP~I~~vv~~~r~~~~ 409 (655)
+.|+|++|+|||||||+|||||+|+||.|+|+||+||||||.++|+++||+|||+|.|+|||||||+|++|+.+.|++++
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 ccccCCCCCCCCCCcceeecCceeEEecCCCcCCHHHHHhhccccccccccccCCCCHHHHHHHHHcCCCCChHHHhcCC
Q psy11423 410 KIFKIPNICPICNSKIIYIESNLIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKIN 489 (655)
Q Consensus 410 ~~~~~P~~CP~C~~~l~~~~~~~~~~C~n~~~~C~~q~~~~i~~F~sk~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~ 489 (655)
.+|.+|++||+|||+|++.++++.+||+|++. ||+|.+++|+||+||+||||+|||+|+|++|+++++|++++|||+|+
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 99999999999999999999999999999767 99999999999999999999999999999999999999999999999
Q ss_pred hhhhccccCCcHHHHHHHHHHHHHhcccchhHHHHHhCCCCccHHHHHHHHHhCCCHHHHHhcCHHHHhcCCCCCHHHHH
Q psy11423 490 FKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVK 569 (655)
Q Consensus 490 ~~~L~~l~GfG~Ksa~nll~~I~~sk~~~l~r~L~algIpgIG~~~Ak~L~~~fgsl~~l~~as~eeL~~i~GIG~~~A~ 569 (655)
.++|..|+|||+|+++||+++|++||+.+|+|||+||||||||+++|+.|+++|+|+++|..|+.++|..++|||+++|.
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 HHHHHhcChhHHHHHHHHHHcCcccccCC--------------------------------CCCCCeEecccccCccEEE
Q psy11423 570 AFIKFINQPLHRLLISQLRDVGIYWLNNP--------------------------------NTKGGKVVNFISKNTNYLV 617 (655)
Q Consensus 570 ~I~~~f~~~~n~~li~~L~~~Gi~~~~~~--------------------------------~~~G~~v~~sVsk~t~ylv 617 (655)
+|.+||++++|++++++|.+.|+.+.... .++||+|++||||||||||
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 99999999999999999999998653310 1889999999999999999
Q ss_pred ecCCCCchHHHHHHcCCeeeCHHHHHHHHh
Q psy11423 618 KGQKPGKKLEKAIKLNIKILDEKNFVKIVK 647 (655)
Q Consensus 618 ~g~~~g~K~~kA~~lgi~ii~e~~f~~~l~ 647 (655)
+|+++|||++||++|||+||+|++|++++.
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=3e-179 Score=1523.72 Aligned_cols=634 Identities=45% Similarity=0.734 Sum_probs=605.9
Q ss_pred hhhHHHHHHHHHHHHHHHHHHhhcCCCCCCChHHHHHHHHHHHHHHHhCCCCCCCCCCccccCcccCCCCcceecccccc
Q psy11423 11 FSKLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVGGENSKYVHHTFKMM 90 (655)
Q Consensus 11 ~~~~~~~~~~L~~~l~~~~~~Yy~~~~p~isD~~YD~L~~~L~~le~~~p~~~~~~spt~~Vg~~~~~~~~kv~H~~pMl 90 (655)
+..++++|++|+++|++||++||+.|+|+|||++||+|+++|++||++||++..++|||++||+.+..+|.||+|++|||
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 45567889999999999999999999999999999999999999999999999999999999999988999999999999
Q ss_pred CCCCCCChHHHHHHHHHHHHhhccCCCceEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcccCCcccc
Q psy11423 91 SLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLN 170 (655)
Q Consensus 91 SL~k~~~~~el~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~ 170 (655)
||+|+|+.+||.+|++++.+.++. .+..|+|||||||+||+|+|+||+|++|+|||||.+|||||+|+++|++||++|+
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 999999999999999999877652 2457999999999999999999999999999999999999999999999999996
Q ss_pred cCCCCceEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEeccccc-CCCCCCCH
Q psy11423 171 IKYPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELR-GMNMPSSH 249 (655)
Q Consensus 171 ~~~~p~~~evRGEv~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~-~~~~~~~~ 249 (655)
. ..|..+|||||+||++++|+++|+++.+.|+++|+||||+|||+|||+||.+++.|+|+||+|+|...+ +.. +.+|
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 212 4799
Q ss_pred HHHHHHHHhCCCCCCCCceeeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCcce
Q psy11423 250 SELLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKE 329 (655)
Q Consensus 250 ~e~l~~L~~~GF~~~~~~~~~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~ 329 (655)
++.|++|++|||+|+++...+.+++++++|+++|.+.|+.+||+|||+|||+||+.+|+.||+|+|+||||||||||+++
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 eeEEEEEEEEeecCcceeeeEEEEEEEEECCEEEEEeeCCCHHHHHhcCCCCCCEEEEEecCcccceeecccccCCCCCC
Q psy11423 330 ALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDS 409 (655)
Q Consensus 330 ~~T~v~~I~~qvGRTG~itPvA~lePV~l~G~tVsratLhN~~~i~~~~i~iGd~V~v~raGdVIP~I~~vv~~~r~~~~ 409 (655)
++|+|++|+|||||||+|||||+|+||.|+|+||+||||||+++|+++||++||+|.|+|||||||+|++|+.+.|+++.
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 99999999999999999999999999999999999999999999999999999999999999999999999999999888
Q ss_pred ccccCCCCCCCCCCcceeecCceeEEecCCCcCCHHHHHhhccccccccccccCCCCHHHHHHHHHcCCCCChHHHhcCC
Q psy11423 410 KIFKIPNICPICNSKIIYIESNLIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKIN 489 (655)
Q Consensus 410 ~~~~~P~~CP~C~~~l~~~~~~~~~~C~n~~~~C~~q~~~~i~~F~sk~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~ 489 (655)
.+|.+|++||+||++|++.++++.+||+|..+ ||+|++++|.||+||+||||+||||++|++||++|+|++++|||+|+
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 89999999999999999988899999999756 99999999999999999999999999999999999999999999999
Q ss_pred hhhhccccCCcHHHHHHHHHHHHHhcccchhHHHHHhCCCCccHHHHHHHHHhCCCHHHHHhcCHHHHhcCCCCCHHHHH
Q psy11423 490 FKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVK 569 (655)
Q Consensus 490 ~~~L~~l~GfG~Ksa~nll~~I~~sk~~~l~r~L~algIpgIG~~~Ak~L~~~fgsl~~l~~as~eeL~~i~GIG~~~A~ 569 (655)
.++|..|+|||+|+++||+++|+.+|+.+|+|||+||||||||+++|++|+++|+|+++|..|+.++|.+++|||+++|+
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 HHHHHhcChhHHHHHHHHHHcCcccccC------C----------------------CCCCCeEecccccCccEEEecCC
Q psy11423 570 AFIKFINQPLHRLLISQLRDVGIYWLNN------P----------------------NTKGGKVVNFISKNTNYLVKGQK 621 (655)
Q Consensus 570 ~I~~~f~~~~n~~li~~L~~~Gi~~~~~------~----------------------~~~G~~v~~sVsk~t~ylv~g~~ 621 (655)
+|++||+++.|+++++.|.+.|+.+... . ..+|++|++|||++|||||||+.
T Consensus 558 sI~~ff~~~~~~~~i~~L~~~gv~~~~~~~~~~~~g~~~v~TG~l~~~~R~e~~~~i~~~G~~v~~sVs~kt~~lv~G~~ 637 (665)
T PRK07956 558 SIVEFFAVEENRELIDELLEAGVNMEYKGEEVDLAGKTVVLTGTLEQLSRDEAKEKLEALGAKVSGSVSKKTDLVVAGEA 637 (665)
T ss_pred HHHHHHhhhhHHHHHHHHHHcCCCccccccCCCccccEEEEeCCCCCCCHHHHHHHHHHcCCEEeCcccCCCCEEEECCC
Confidence 9999999999999999999988864310 0 18999999999999999999999
Q ss_pred CCchHHHHHHcCCeeeCHHHHHHHHhc
Q psy11423 622 PGKKLEKAIKLNIKILDEKNFVKIVKG 648 (655)
Q Consensus 622 ~g~K~~kA~~lgi~ii~e~~f~~~l~~ 648 (655)
+|+|++||+++||+||+|++|.+||++
T Consensus 638 ~gsK~~kA~~lgI~ii~E~~f~~~l~~ 664 (665)
T PRK07956 638 AGSKLAKAQELGIEVLDEEEFLRLLGE 664 (665)
T ss_pred CChHHHHHHHcCCeEEcHHHHHHHHhc
Confidence 999999999999999999999999864
No 3
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=100.00 E-value=9.5e-177 Score=1496.37 Aligned_cols=621 Identities=31% Similarity=0.501 Sum_probs=584.9
Q ss_pred hHHHHHHHHHHHHHHHHHHhhcCCCCCCChHHHHHHHHHHHHHHHhCCCCCCCCCCccccCcccCCCCcceeccccccCC
Q psy11423 13 KLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVGGENSKYVHHTFKMMSL 92 (655)
Q Consensus 13 ~~~~~~~~L~~~l~~~~~~Yy~~~~p~isD~~YD~L~~~L~~le~~~p~~~~~~spt~~Vg~~~~~~~~kv~H~~pMlSL 92 (655)
+++++|++|+++|++||++||++++|+|||++||+|+++|++||++||++.+++|||++||+.+...|.||+|++|||||
T Consensus 4 ~~~~~i~~L~~~i~~~~~~YY~~~~p~IsD~~YD~L~~eL~~lE~~~p~~~~~~Spt~~Vg~~~~~~f~kv~H~~pMlSL 83 (669)
T PRK14350 4 DIQDEILDLKKLIRKWDKEYYVDSSPSVEDFTYDKALLRLQELESKYPEYKTLDSPTLKFGSDLLNDFKEVEHSFPILSL 83 (669)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHhCcccCCCCCCCccCCccccccCCceecCCccccc
Confidence 44678999999999999999999999999999999999999999999999999999999999988899999999999999
Q ss_pred CCCCChHHHHHHHHHHHHhhcc-CCCceEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcccCCccccc
Q psy11423 93 DNGFSDEDVIIFNKRITNELKL-TKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNI 171 (655)
Q Consensus 93 ~k~~~~~el~~~~~~~~~~l~~-~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~ 171 (655)
+|+|+.+||.+|++|+...+.. ..+..|+|||||||+||+|+|+||+|++|+|||||.+|||||+|+++|++||++|+.
T Consensus 84 ~k~~~~~el~~~~~r~~~~~~~~~~~~~~~~epKiDGlaisL~YenG~L~~a~TRGDG~~GEDVT~n~~~I~~IP~~l~~ 163 (669)
T PRK14350 84 DKVYDLKLLKLWIEKMDLENSNLGFDFGISVEPKIDGCSIVLYYKDGILEKALTRGDGRFGNDVTENVRTIRNVPLFIDE 163 (669)
T ss_pred cccCCHHHHHHHHHHHHHhhccCCCCceEEEEEecccEEEEEEEECCEEEEEEecCCCCcchhHhhhhhhhcccchhcCC
Confidence 9999999999999999732210 113579999999999999999999999999999999999999999999999999963
Q ss_pred CCCCceEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCCCCCHHH
Q psy11423 172 KYPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSE 251 (655)
Q Consensus 172 ~~~p~~~evRGEv~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~~~~~~e 251 (655)
|..+|||||+||++++|+++|+++ .++|+||||+|||+|||+||.+++.|+|+||+|+|...+. . ..+|++
T Consensus 164 ---~~~levRGEv~m~~~~F~~lN~~~----~~~faNpRNaaAGsLr~~d~~~~a~r~L~f~~y~~~~~~~-~-~~t~~e 234 (669)
T PRK14350 164 ---KVELVLRGEIYITKENFLKINKTL----EKPYTNARNLASGILRRIDSREVANFPLDIFVYDILYSSL-E-LKTNHD 234 (669)
T ss_pred ---CceEEEEEEEEeeHHHHHHHHHhh----hccCCChhHHHHHHHHccCchhhhcCceEEEEEEcccCCC-C-CCCHHH
Confidence 678999999999999999999876 3689999999999999999999999999999999964332 1 369999
Q ss_pred HHHHHHhCCCCCCCCceeeCC---HHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCcc
Q psy11423 252 LLNWYQKIGLSICGEYSVLSG---VNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSK 328 (655)
Q Consensus 252 ~l~~L~~~GF~~~~~~~~~~~---~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~ 328 (655)
.|++|++|||+++++...+++ .+++++|+++|.+.|+.+||+|||+|||+|++.+|+.||+|+|+||||||||||++
T Consensus 235 ~l~~L~~~GF~v~~~~~~~~~~~~~~e~~~~~~~~~~~R~~l~y~iDGiViKvn~~~~q~~lG~ts~~PrWaiA~Kf~~~ 314 (669)
T PRK14350 235 AFDKLKKFGFKVNPFCRFFDGKNSIEEILNYVKDIEKKRNSFEYEIDGVVLKVSDFALREILGYTSHHPKWSMAYKFESL 314 (669)
T ss_pred HHHHHHHCCCCCCcceEEEcCCCcHHHHHHHHHHHHHHHhcCCCCCCcEEEEecCHHHHHhcCCcCCCCCceEEEcCCCc
Confidence 999999999999998888876 99999999999999999999999999999999999999999999999999999999
Q ss_pred eeeEEEEEEEEeecCcceeeeEEEEEEEEECCEEEEEeeCCCHHHHHhcCCCCCCEEEEEecCcccceeecccccCCCCC
Q psy11423 329 EALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPND 408 (655)
Q Consensus 329 ~~~T~v~~I~~qvGRTG~itPvA~lePV~l~G~tVsratLhN~~~i~~~~i~iGd~V~v~raGdVIP~I~~vv~~~r~~~ 408 (655)
+++|+|++|+|||||||+|||||+|+||+|+|+||+||||||+++|+++||++||+|.|+|||||||+|++|+.+.|++.
T Consensus 315 ~~~T~l~~I~~qVGRTG~iTPVA~l~PV~l~G~tVsrATLhN~~~I~~~di~iGD~V~V~raGdVIP~I~~v~~~~r~~~ 394 (669)
T PRK14350 315 SGFSKVNDIVVQVGRSGKITPVANIEKVFVAGAFITNASLHNQDYIDSIGLNVGDVVKISRRGDVIPAVELVIEKLSVGF 394 (669)
T ss_pred eeEEEEEEEEEecCCceeeeEEEEEEeEEECCEEEEEeccCCHHHHHHcCCCCCCEEEEEecCCCCCceeeecccccCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999988764
Q ss_pred CccccCCCCCCCCCCcceeecCceeEEecCCCcCCHHHHHhhccccccccccccCCCCHHHHHHHHHcCCCCChHHHhcC
Q psy11423 409 SKIFKIPNICPICNSKIIYIESNLIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKI 488 (655)
Q Consensus 409 ~~~~~~P~~CP~C~~~l~~~~~~~~~~C~n~~~~C~~q~~~~i~~F~sk~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L 488 (655)
|.+|++||+||++|++ +++.+||+|+ . ||+|++++|.||+||+||||+|||+++|++|+++|+|++++|||+|
T Consensus 395 ---~~~P~~CP~C~s~l~~--~~~~~~C~n~-~-C~aq~~~~i~hf~sr~aldI~GlG~~~i~~L~~~G~i~~~~Dly~L 467 (669)
T PRK14350 395 ---FKIPDNCPSCKTALIK--EGAHLFCVNN-H-CPSVIVERIKYFCSKKCMNIVGLSDKTIEFLFEKKFISSEIDLYTF 467 (669)
T ss_pred ---CCCCCCCCCCCCEeee--CCEEEEECCC-C-CHHHHHhhhheeccCCcccccCcCHHHHHHHHHcCCcCCHHHHhhC
Confidence 8899999999999986 4699999996 6 9999999999999999999999999999999999999999999999
Q ss_pred ChhhhccccCCcHHHHHHHHHHHHHhcccchhHHHHHhCCCCccHHHHHHHH-HhCCCHHHHHh------cCHHHHhcCC
Q psy11423 489 NFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELA-NYFKNLECMFK------ATEEQLLNIP 561 (655)
Q Consensus 489 ~~~~L~~l~GfG~Ksa~nll~~I~~sk~~~l~r~L~algIpgIG~~~Ak~L~-~~fgsl~~l~~------as~eeL~~i~ 561 (655)
+.++|++++|||+|+++||+++|+.||+.+|+|||+|||||+||+.+|+.|+ ++|++++++.+ ++.++|.+|+
T Consensus 468 ~~~~l~~l~g~geksa~nl~~~Ie~sk~~~l~r~l~ALGI~~vG~~~ak~La~~~f~~~~~l~~~~~~~~~~~e~l~~i~ 547 (669)
T PRK14350 468 NFDRLINLKGFKDKRINNLKRSIEASKKRPFSKLLLSMGIKDLGENTILLLINNNLNSFDKISTLCQDREFALSKLLKIK 547 (669)
T ss_pred CHHHHhhccCccHHHHHHHHHHHHHHhCCCHHHHHHHcCCCchhHHHHHHHHHHhhCCHHHHHhhhhccCCCHHHHhhCC
Confidence 9999999999999999999999999999999999999999999999999999 89999999986 5889999999
Q ss_pred CCCHHHHHHHHHHhcChhHHHHHHHHHHcCccccc------C-C--------------------------CCCCCeEecc
Q psy11423 562 KIGSTTVKAFIKFINQPLHRLLISQLRDVGIYWLN------N-P--------------------------NTKGGKVVNF 608 (655)
Q Consensus 562 GIG~~~A~~I~~~f~~~~n~~li~~L~~~Gi~~~~------~-~--------------------------~~~G~~v~~s 608 (655)
|||+++|++|++||+++.|+++++.|.+.|+.+.. . . +++||+|++|
T Consensus 548 giG~~~a~si~~ff~~~~~~~~i~~l~~~gv~~~~~~~~~~~~~~~l~gktfV~TG~l~~~~R~e~~~lie~~Ggkv~ss 627 (669)
T PRK14350 548 GIGEKIALNIIEAFNDKIILDKFNFFKNLGFKMEEDSINIDVENSFLFGKKFCITGSFNGYSRSVLIDKLTKKGAIFNTC 627 (669)
T ss_pred CccHHHHHHHHHHHcCHHHHHHHHHHHHcCCCcccccccccccCCccCCcEEEEecccCCCCHHHHHHHHHHcCCEEecc
Confidence 99999999999999999999999999988875320 0 0 1899999999
Q ss_pred cccCccEEEecCCCCchHHHHHHcCCeeeCHHHHHHHHhcc
Q psy11423 609 ISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKNFVKIVKGF 649 (655)
Q Consensus 609 Vsk~t~ylv~g~~~g~K~~kA~~lgi~ii~e~~f~~~l~~~ 649 (655)
||++|||||+|+++|+|++||++|||+||+|++|.+||+.+
T Consensus 628 VSkktd~LV~G~~aGsKl~KA~~LGI~Ii~e~~f~~~l~~~ 668 (669)
T PRK14350 628 VTKYLDFLLVGEKAGLKLKKANNLGIKIMSLFDIKSYVDLD 668 (669)
T ss_pred ccCCCcEEEECCCCCchHHHHHHcCCEEecHHHHHHHhcCC
Confidence 99999999999999999999999999999999999999743
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=1.4e-176 Score=1500.59 Aligned_cols=617 Identities=45% Similarity=0.744 Sum_probs=591.6
Q ss_pred HHHHHHHHHHHhhcCCCCCCChHHHHHHHHHHHHHHHhCCCCCCCCCCccccCcccCCCCcceeccccccCCCCCCChHH
Q psy11423 21 LKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVGGENSKYVHHTFKMMSLDNGFSDED 100 (655)
Q Consensus 21 L~~~l~~~~~~Yy~~~~p~isD~~YD~L~~~L~~le~~~p~~~~~~spt~~Vg~~~~~~~~kv~H~~pMlSL~k~~~~~e 100 (655)
|+++|++||++||++|+|+|||++||+|+++|++||++||++.+++|||++||+.+.++|.||+|++|||||+|+|+.+|
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 67899999999999999999999999999999999999999999999999999999899999999999999999999999
Q ss_pred HHHHHHHHHHhhccCCCceEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcccCCcccccCCCCceEEE
Q psy11423 101 VIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEV 180 (655)
Q Consensus 101 l~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~p~~~ev 180 (655)
|.+|++++.+.++ .+..|+|||||||+||+|+|+||+|++|+|||||.+|||||+|+++|++||++|++.+.|..+||
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 9999999987765 13579999999999999999999999999999999999999999999999999974335889999
Q ss_pred EEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCCCCCHHHHHHHHHhCC
Q psy11423 181 RCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNWYQKIG 260 (655)
Q Consensus 181 RGEv~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~~~~~~e~l~~L~~~G 260 (655)
|||+||++++|+++|+++.+.|+++|+||||+|||+|||+||++++.|+|+||+|+|...++.. +.+|++.|++|++||
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 9999999999999999999999999999999999999999999999999999999996433222 379999999999999
Q ss_pred CCCCCCceeeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCcceeeEEEEEEEEe
Q psy11423 261 LSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQ 340 (655)
Q Consensus 261 F~~~~~~~~~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~~~T~v~~I~~q 340 (655)
|+|+++...+++++++++|+++|.+.|+.+||+|||+|||+||+.+|+.||+|+|+||||||||||+++++|+|++|+||
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 ecCcceeeeEEEEEEEEECCEEEEEeeCCCHHHHHhcCCCCCCEEEEEecCcccceeecccccCCCCCCccccCCCCCCC
Q psy11423 341 IGRTGIITPVALLKPVLIDGITITRATLHNESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPI 420 (655)
Q Consensus 341 vGRTG~itPvA~lePV~l~G~tVsratLhN~~~i~~~~i~iGd~V~v~raGdVIP~I~~vv~~~r~~~~~~~~~P~~CP~ 420 (655)
|||||+|||||+|+||.|+|+||+||||||+++|+++||++||+|.|+|||||||+|++|+.+.|+++.++|.+|++||+
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 99999999999999999999999999999999999999999999999999999999999999999988889999999999
Q ss_pred CCCcceeecCceeEEecCCCcCCHHHHHhhccccccccccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCc
Q psy11423 421 CNSKIIYIESNLIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVS 500 (655)
Q Consensus 421 C~~~l~~~~~~~~~~C~n~~~~C~~q~~~~i~~F~sk~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG 500 (655)
||++|++.++++.+||+|+ . ||+|++++|.||+||+||||+|||+++|++||++|+|++++|||+|+.++|..|+|||
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 9999999888999999995 6 9999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHhcccchhHHHHHhCCCCccHHHHHHHHHhCCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHhcChhH
Q psy11423 501 NKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQPLH 580 (655)
Q Consensus 501 ~Ksa~nll~~I~~sk~~~l~r~L~algIpgIG~~~Ak~L~~~fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f~~~~n 580 (655)
+|+++||+++|+.+|..+|+|||.+|||||||+++|++|+++|+|+++|..|+.++|.+++|||+++|++|++||+++.|
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 HHHHHHHHHcCcccc---c----C--C--------------------------CCCCCeEecccccCccEEEecCCCCch
Q psy11423 581 RLLISQLRDVGIYWL---N----N--P--------------------------NTKGGKVVNFISKNTNYLVKGQKPGKK 625 (655)
Q Consensus 581 ~~li~~L~~~Gi~~~---~----~--~--------------------------~~~G~~v~~sVsk~t~ylv~g~~~g~K 625 (655)
+++|+.|.+.|+.+. . . . .++||+|.+|||++|||||+|+.+|+|
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 999999999888642 0 1 0 189999999999999999999999999
Q ss_pred HHHHHHcCCeeeCHHHH
Q psy11423 626 LEKAIKLNIKILDEKNF 642 (655)
Q Consensus 626 ~~kA~~lgi~ii~e~~f 642 (655)
++||+++||+||+|++|
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=1.3e-175 Score=1493.13 Aligned_cols=633 Identities=34% Similarity=0.590 Sum_probs=601.9
Q ss_pred cCCChhhHHHHHHHHHHHHHHHHHHhhcCCCCCCChHHHHHHHHHHHHHHHhCCCCCCCCCCccccCcccCCCCcceecc
Q psy11423 7 KKINFSKLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVGGENSKYVHHT 86 (655)
Q Consensus 7 ~~~~~~~~~~~~~~L~~~l~~~~~~Yy~~~~p~isD~~YD~L~~~L~~le~~~p~~~~~~spt~~Vg~~~~~~~~kv~H~ 86 (655)
...+.+..+++|++|+++|++||++||++++|+|||++||+|+++|++||++| ++.+++|||++||+.+..+|.||+|+
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 45566777789999999999999999999999999999999999999999999 89999999999999999999999999
Q ss_pred ccccCCCCCCChHHHHHHHHHHHHhhccCCCceEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcccCC
Q psy11423 87 FKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIP 166 (655)
Q Consensus 87 ~pMlSL~k~~~~~el~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP 166 (655)
+|||||+|+|+.+|+.+|++|+.+.++ ...|+||||+||+||+|+|+||+|++|+|||||.+|||||+|+++|++||
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 cccccCCCCceEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCCC
Q psy11423 167 LVLNIKYPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMP 246 (655)
Q Consensus 167 ~~l~~~~~p~~~evRGEv~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~~ 246 (655)
++|+. .+|..+|||||+||++++|+++|+++.+.|+++|+||||+|||+|||+||++++.|+|+||+|+|...++ . +
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 2688999999999999999999999999999999999999999999999999999999999999965432 2 4
Q ss_pred CCHHHHHHHHHhCCCCCCCCceeeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCC
Q psy11423 247 SSHSELLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFL 326 (655)
Q Consensus 247 ~~~~e~l~~L~~~GF~~~~~~~~~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~ 326 (655)
.+|++.|++|++|||+++++...|++++++++|+++|.+.|+.+||+|||+|||+||+.+|+.||+|+|+||||||||||
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 cceeeEEEEEEEEeecCcceeeeEEEEEEEEECCEEEEEeeCCCHHHHHhcCCCCCCEEEEEecCcccceeecccccCCC
Q psy11423 327 SKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRP 406 (655)
Q Consensus 327 ~~~~~T~v~~I~~qvGRTG~itPvA~lePV~l~G~tVsratLhN~~~i~~~~i~iGd~V~v~raGdVIP~I~~vv~~~r~ 406 (655)
+++++|+|++|+|||||||+|||||+|+||.|+|+||+||||||+++|+++||++||+|.|+|||||||+|++|+.+.|+
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 99999999999999999999999999999999999999999999999999999999999999999999999999997654
Q ss_pred CCCccccCCCCCCCCCCcceeecCceeEEecCCCcCCHHHHHhhccccccccccccCCCCHHHHHHHHHcCCCCChHHHh
Q psy11423 407 NDSKIFKIPNICPICNSKIIYIESNLIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLY 486 (655)
Q Consensus 407 ~~~~~~~~P~~CP~C~~~l~~~~~~~~~~C~n~~~~C~~q~~~~i~~F~sk~~l~I~GLG~k~i~~L~~~g~I~~i~DL~ 486 (655)
+. |.+|++||+||++|++ +++.++|+|... ||+|++++|.||+||++|||+|||+++|++|+++|+|++++|||
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 8899999999999986 467889999756 99999999999999999999999999999999999999999999
Q ss_pred cCChhhhccccCCcHHHHHHHHHHHHHhcccchhHHHHHhCCCCccHHHHHHHHHhCCCHHHHHhcCHHHHhcCCCCCHH
Q psy11423 487 KINFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGST 566 (655)
Q Consensus 487 ~L~~~~L~~l~GfG~Ksa~nll~~I~~sk~~~l~r~L~algIpgIG~~~Ak~L~~~fgsl~~l~~as~eeL~~i~GIG~~ 566 (655)
+|+.++|..|+|||+|+++||+++|++||+.+|+|||+||||||||+++|++|+++|+++++|..|+.++|.+++|||++
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 HHHHHHHHhcChhHHHHHHHHHHcCcccccC------C------------------------CCCCCeEecccccCccEE
Q psy11423 567 TVKAFIKFINQPLHRLLISQLRDVGIYWLNN------P------------------------NTKGGKVVNFISKNTNYL 616 (655)
Q Consensus 567 ~A~~I~~~f~~~~n~~li~~L~~~Gi~~~~~------~------------------------~~~G~~v~~sVsk~t~yl 616 (655)
+|++|++||++++|+++++.|.+.|+.+... . .++||+|.+|||++||||
T Consensus 572 ~A~sI~~ff~~~~n~~~i~~L~~~Gv~~~~~~~~~~~~l~g~~~v~TG~l~~~~R~~~~~~i~~~Gg~v~~sVs~kt~~L 651 (689)
T PRK14351 572 VAEEIREFFDSERNRAVIDDLLDHGVDPQPAESEGGDALDGLTFVFTGSLSGYTRSEAQELVEAHGGNATGSVSGNTDYL 651 (689)
T ss_pred HHHHHHHHHhhhHHHHHHHHHHhcccccccccccCCCCCCCcEEEEccCCCCCCHHHHHHHHHHcCCEEcCCcCCCccEE
Confidence 9999999999999999999999988864210 0 189999999999999999
Q ss_pred EecCCCC-chHHHHHHcCCeeeCHHHHHHHHhcccCC
Q psy11423 617 VKGQKPG-KKLEKAIKLNIKILDEKNFVKIVKGFSTE 652 (655)
Q Consensus 617 v~g~~~g-~K~~kA~~lgi~ii~e~~f~~~l~~~~~~ 652 (655)
|+|+.+| ||++||+++||+||+|++|.+||++.+..
T Consensus 652 v~G~~~g~sKl~kA~~lgi~ii~E~~f~~ll~~~~~~ 688 (689)
T PRK14351 652 VVGENPGQSKRDDAEANDVPTLDEEEFEELLAERGVA 688 (689)
T ss_pred EEcCCCChhHHHHHHHCCCeEecHHHHHHHHHhcCCC
Confidence 9999999 99999999999999999999999876654
No 6
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=100.00 E-value=2.1e-153 Score=1276.39 Aligned_cols=533 Identities=21% Similarity=0.317 Sum_probs=502.8
Q ss_pred CCChhhHHHHHHHHHHHHHHHHHHhhcCCCCCCChHHHHHHHHHHHHHHHhCCCCCCCCCCccccCcccCCCCcceeccc
Q psy11423 8 KINFSKLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVGGENSKYVHHTF 87 (655)
Q Consensus 8 ~~~~~~~~~~~~~L~~~l~~~~~~Yy~~~~p~isD~~YD~L~~~L~~le~~~p~~~~~~spt~~Vg~~~~~~~~kv~H~~ 87 (655)
..+...++++|++|+++|++||++||+.++|+|||++||+|+++|++||++||++.+++|||++||+ ||+|++
T Consensus 24 ~~~~~~~~~~i~~L~~~l~~~~~~YY~~~~p~IsD~eYD~L~~eL~~LE~~~p~~~~~~spt~~vg~-------kv~H~~ 96 (562)
T PRK08097 24 DWSPARAQEEIAALQQQLAQWDDAYWRQGKSEVDDEVYDQLRARLTQWQRCFGGPEPRDVPLPPLNG-------KVLHPV 96 (562)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHhCcCcCCCCCCCCCCCC-------ceECCC
Confidence 3466778889999999999999999999999999999999999999999999999999999999986 899999
Q ss_pred cccCCCCCCChHHHHHHHHHHHHhhccCCCceEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcccCCc
Q psy11423 88 KMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPL 167 (655)
Q Consensus 88 pMlSL~k~~~~~el~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~ 167 (655)
|||||+|+||.+||.+|++++. .|+|||||||+||+|+|+||+|++|+|||||.+|||||+|+++|++||+
T Consensus 97 PMlSL~k~~s~eel~~w~~~~~---------~~~vepKiDGlsisL~Ye~G~Lv~a~TRGDG~~GEDVT~nv~~I~~IP~ 167 (562)
T PRK08097 97 AHTGVKKLADKQALARWMAGRS---------DLWVQPKVDGVAVTLVYRDGKLVQAISRGNGLKGEDWTAKARLIPAIPQ 167 (562)
T ss_pred CcccccccCCHHHHHHHHhhcc---------ceEEEEecccEEEEEEEECCEEEEEEecCCCccchhHHhhHhhhcccch
Confidence 9999999999999999998852 5999999999999999999999999999999999999999999999999
Q ss_pred ccccCCCCceEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCCCC
Q psy11423 168 VLNIKYPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPS 247 (655)
Q Consensus 168 ~l~~~~~p~~~evRGEv~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~~~ 247 (655)
+|+. .|..+|||||+||++++|++.+ .| |+||||+|||+|||+||+++ .|+|+||+|++.. + +.
T Consensus 168 ~l~~--~~~~levRGEv~m~~~~F~~~~-----~g---~aNPRN~AAGsLr~~d~~~~-~r~L~~f~y~~~~--~---~~ 231 (562)
T PRK08097 168 QLPG--ALANLVLQGELFLRREGHIQQQ-----MG---GINARAKVAGLMMRKDPSPT-LNQIGVFVWAWPD--G---PA 231 (562)
T ss_pred hhcC--CCCeEEEEEEEEEeHHHHHHHh-----cC---cCCchHHHhHHHhhcCcHhh-hccceEEEEECCC--C---CC
Confidence 9974 4778999999999999998632 22 89999999999999999999 8999999999842 2 47
Q ss_pred CHHHHHHHHHhCCCCCCC-CceeeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCC
Q psy11423 248 SHSELLNWYQKIGLSICG-EYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFL 326 (655)
Q Consensus 248 ~~~e~l~~L~~~GF~~~~-~~~~~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~ 326 (655)
+|++.|++|++|||++++ +...+.+.+++.+|+++|. |..+||+|||+|||+||+.+|+ |+|+|+||||||||||
T Consensus 232 t~~e~l~~L~~~GF~v~~~~~~~~~~~~~i~~~~~~~~--r~~l~y~iDGiViKvn~~~~~~--~~ts~~PrWAiAyKf~ 307 (562)
T PRK08097 232 SMPERLAQLATAGFPLTQRYTHPVKNAEEVARWRERWY--RAPLPFVTDGVVVRQAKEPPGR--YWQPGQGEWAVAWKYP 307 (562)
T ss_pred CHHHHHHHHHHCCCCcCccceEeeCCHHHHHHHHHHHh--hccCCCCCCcEEEEecCHHHHh--hccCCCCCceEEEcCC
Confidence 999999999999999996 7778999999999999886 9999999999999999999998 7899999999999999
Q ss_pred cceeeEEEEEEEEeecCcceeeeEEEEEEEEECCEEEEEeeCCCHHHHHhcCCCCCCEEEEEecCcccceeecccccCCC
Q psy11423 327 SKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRP 406 (655)
Q Consensus 327 ~~~~~T~v~~I~~qvGRTG~itPvA~lePV~l~G~tVsratLhN~~~i~~~~i~iGd~V~v~raGdVIP~I~~vv~~~r~ 406 (655)
+++++|+|++|+|||||||++||||+|+||+|+|+||+||||||+++|+++||++||+|.|+|||||||+|++|+. |+
T Consensus 308 ~~~~~T~l~~I~~qVGRTG~iTPVA~lePV~l~GttVsrATLhN~~~i~~~~I~iGD~V~V~raGdVIP~I~~vv~--~~ 385 (562)
T PRK08097 308 PVQQVAEVRAVQFAVGRTGKITVVLELEPVMLDDKRVSRVNIGSVRRWQQWDIAPGDQVLVSLAGQGIPRLDKVVW--RG 385 (562)
T ss_pred CcEEEEEEEEEEEecCCCceeeEEEEEEEEEeCCEEEEEeecCCHHHHHHcCCCCCCEEEEEecCCCCcceeeeec--cc
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999999998 55
Q ss_pred CCCccccCCCCCCCCCCcceeecCceeEEecC-CCcCCHHHHHhhccccccccccccCCCCHHHHHHHHHcCCCCChHHH
Q psy11423 407 NDSKIFKIPNICPICNSKIIYIESNLIARCSG-SWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDL 485 (655)
Q Consensus 407 ~~~~~~~~P~~CP~C~~~l~~~~~~~~~~C~n-~~~~C~~q~~~~i~~F~sk~~l~I~GLG~k~i~~L~~~g~I~~i~DL 485 (655)
+.+.++.+|+. ++++.+||+| ... ||+|++++|.|||||+||||+|||+++|++|+++|+|++++||
T Consensus 386 ~~~~~~~~P~~-----------~~~~~~~C~n~~~~-Cpaq~~~~i~hf~Sr~amdI~GlGe~~i~~L~~~G~i~~~~Di 453 (562)
T PRK08097 386 AERTKPTPPDA-----------DRFHSLSCFRASPG-CQEQFLARLVWLSGKQGLGLDGIGEGTWRALHQTGLFEHLFSW 453 (562)
T ss_pred ccCCCCcCCCC-----------CCceEEEeCCCCCC-CHHHHHHHhHhhhcccccCCCCcCHHHHHHHHHcCCcCCHHHH
Confidence 55556777764 2457899998 556 9999999999999999999999999999999999999999999
Q ss_pred hcCChhhhccccCCcHHHHHHHHHHHHHhcccchhHHHHHhCCCCccHHHHHHHHHhCCCHHHHHhcCHHHHhcCCCCCH
Q psy11423 486 YKINFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGS 565 (655)
Q Consensus 486 ~~L~~~~L~~l~GfG~Ksa~nll~~I~~sk~~~l~r~L~algIpgIG~~~Ak~L~~~fgsl~~l~~as~eeL~~i~GIG~ 565 (655)
|+|+.++|++++|||+|+++||+++|++||+.+|+|||+|||||+||+.+|+. +|+++++|.+++.++|.+|+|||+
T Consensus 454 y~L~~~~l~~l~gfgeks~~nll~aIe~sk~~~l~r~l~aLGI~~vG~~~ak~---~~~~i~~l~~a~~e~l~~i~gIG~ 530 (562)
T PRK08097 454 LALTPEQLANTPGIGKARAEQLWHQFNLARQQPFSRWLKALGIPLPQAALNAL---DDRSWQQLLSRSEQQWQQLPGIGE 530 (562)
T ss_pred hcCCHHHHhcCcCccHHHHHHHHHHHHHHcCCCHHHHHHHcCCccHHHHHHHH---hcCCHHHHHcCCHHHHhcCCCchH
Confidence 99999999999999999999999999999999999999999999999988876 899999999999999999999999
Q ss_pred HHHHHHHHHhcChhHHHHHHHHHHcCcc
Q psy11423 566 TTVKAFIKFINQPLHRLLISQLRDVGIY 593 (655)
Q Consensus 566 ~~A~~I~~~f~~~~n~~li~~L~~~Gi~ 593 (655)
++|++|++||++++|+++++.|.+.|++
T Consensus 531 ~~a~si~~~f~~~~~~~~i~~L~~~gv~ 558 (562)
T PRK08097 531 GRARQLIAFLQHPEVKALADWLAAQGIT 558 (562)
T ss_pred HHHHHHHHHHcCHHHHHHHHHHHHcCCC
Confidence 9999999999999999999999998875
No 7
>smart00532 LIGANc Ligase N family.
Probab=100.00 E-value=7.5e-138 Score=1131.69 Aligned_cols=440 Identities=47% Similarity=0.758 Sum_probs=420.3
Q ss_pred HHHHHHHHHHHHHHHHHhhcCCCCCCChHHHHHHHHHHHHHHHhCCCCCCCCCCccccCcccCCCCcceeccccccCCCC
Q psy11423 15 SFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVGGENSKYVHHTFKMMSLDN 94 (655)
Q Consensus 15 ~~~~~~L~~~l~~~~~~Yy~~~~p~isD~~YD~L~~~L~~le~~~p~~~~~~spt~~Vg~~~~~~~~kv~H~~pMlSL~k 94 (655)
+++|++|+++|++||++||+.++|+|||++||+|+++|++||++||++..++|||++||+.+.++|.||+|++|||||+|
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 46799999999999999999999999999999999999999999999999999999999999899999999999999999
Q ss_pred CCChHHHHHHHHHHHHhhccCCCceEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcccCCcccccCCC
Q psy11423 95 GFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYP 174 (655)
Q Consensus 95 ~~~~~el~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~ 174 (655)
+|+.+||.+|++++.+.++ .+..|+||||+||+||+|+|+||+|++|+|||||.+|||||+|+++|++||++|+. +.
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 9999999999999987665 24689999999999999999999999999999999999999999999999999974 25
Q ss_pred CceEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCCCCCHHHHHH
Q psy11423 175 PELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLN 254 (655)
Q Consensus 175 p~~~evRGEv~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~~~~~~e~l~ 254 (655)
|..+|||||+||++++|+++|+++.+.|+++|+||||+|||+|||+||++++.|+|+||+|++...++.....+|++.|+
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 psy11423 255 WYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEALTKI 334 (655)
Q Consensus 255 ~L~~~GF~~~~~~~~~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~~~T~v 334 (655)
+|++|||+|+++...+.+++++++|+++|.+.|..+||+|||+|||+||+.+|+.||+|+|+||||||||||+++++|+|
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 EEEEEeecCcceeeeEEEEEEEEECCEEEEEeeCCCHHHHHhcCCCCCCEEEEEecCcccceeecccccCCCCCCccccC
Q psy11423 335 KAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKI 414 (655)
Q Consensus 335 ~~I~~qvGRTG~itPvA~lePV~l~G~tVsratLhN~~~i~~~~i~iGd~V~v~raGdVIP~I~~vv~~~r~~~~~~~~~ 414 (655)
++|+|||||||+|||||+|+||.|+|+||+||||||+++|+++||++||+|.|+|||||||+|++|+.+.|++++.+|.+
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 99999999999999999999999999999999999999999999999999999999999999999999999888889999
Q ss_pred CCCCCCCCCcceeecCceeEEecCCCcCCHHHHHhhccccccccc
Q psy11423 415 PNICPICNSKIIYIESNLIARCSGSWIECIAQRKAGLQHFSSRKA 459 (655)
Q Consensus 415 P~~CP~C~~~l~~~~~~~~~~C~n~~~~C~~q~~~~i~~F~sk~~ 459 (655)
|++||+||++|++.++++.+||+|. . ||+|++++|.||+||+|
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=5.8e-95 Score=762.49 Aligned_cols=306 Identities=47% Similarity=0.768 Sum_probs=292.6
Q ss_pred HHHHHHHHHHHHHHHhhcCCCCCCChHHHHHHHHHHHHHHHhCCCCCCCCCCccccCcccCCCCcceeccccccCCCCCC
Q psy11423 17 RVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVGGENSKYVHHTFKMMSLDNGF 96 (655)
Q Consensus 17 ~~~~L~~~l~~~~~~Yy~~~~p~isD~~YD~L~~~L~~le~~~p~~~~~~spt~~Vg~~~~~~~~kv~H~~pMlSL~k~~ 96 (655)
+|++|+++|++||++||++|+|+|||++||+|+++|++||++||++.+++|||++||+.+.+.|.||+|++|||||+|+|
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 68999999999999999999999999999999999999999999999999999999999988999999999999999999
Q ss_pred ChHHHHHHHHHHHHhhccCCCceEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcccCCcccccCCCCc
Q psy11423 97 SDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPE 176 (655)
Q Consensus 97 ~~~el~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~p~ 176 (655)
+.+||.+|++++.+.++ .+..|+|||||||+||+|+|+||+|++|+|||||.+|||||+|+++|++||++|+. .|.
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 eEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCCCCCHHHHHHHH
Q psy11423 177 LLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNWY 256 (655)
Q Consensus 177 ~~evRGEv~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~~~~~~e~l~~L 256 (655)
.+||||||||++++|+++|+++.+.|+++|+||||+|||+|||+||.+++.|+|+||+|+|+..++.. +.+|++.|++|
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 99999999999999999999999999999999999999999999999999999999999997543322 47999999999
Q ss_pred HhCCCCCCCCceeeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCc
Q psy11423 257 QKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLS 327 (655)
Q Consensus 257 ~~~GF~~~~~~~~~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~ 327 (655)
++|||+|+++...|.+++++++|+++|.+.|..+||+|||+|||+|++.+|+.||.|+|+||||||||||+
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=2.5e-94 Score=760.75 Aligned_cols=313 Identities=44% Similarity=0.689 Sum_probs=270.6
Q ss_pred hHHHHHHHHHHHHHHHHHHhhcCCCCCCChHHHHHHHHHHHHHHHhCCCCCCCCCCccccCcc-cCCCCcceeccccccC
Q psy11423 13 KLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLV-GGENSKYVHHTFKMMS 91 (655)
Q Consensus 13 ~~~~~~~~L~~~l~~~~~~Yy~~~~p~isD~~YD~L~~~L~~le~~~p~~~~~~spt~~Vg~~-~~~~~~kv~H~~pMlS 91 (655)
++++++++|+++|++||++||+.|+|+|||++||+|+++|++||++||++.+++|||++||+. +.+.|.+|+|++||||
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 357899999999999999999999999999999999999999999999999999999999954 4566999999999999
Q ss_pred CCCCCChHHHHHHHHHHHHhhccCCCceEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcccCCccccc
Q psy11423 92 LDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNI 171 (655)
Q Consensus 92 L~k~~~~~el~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~ 171 (655)
|+|+|+.+||.+|++++.+.++.. ...|+|||||||+||+|+|+||+|++|+|||||.+|||||+|+++|.+||++|+.
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 999999999999999999888742 2269999999999999999999999999999999999999999999999999985
Q ss_pred CCCCceEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCCCCCHHH
Q psy11423 172 KYPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSE 251 (655)
Q Consensus 172 ~~~p~~~evRGEv~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~~~~~~e 251 (655)
. |+.+||||||||++++|+++|+++.+.|+++|+||||+|||+|||+||++++.|+|+||+|+|..+++...+.+|++
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 79999999999999999999999999999999999999999999999999999999999999997654223589999
Q ss_pred HHHHHHhCCCCCCCCceeeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCcc
Q psy11423 252 LLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSK 328 (655)
Q Consensus 252 ~l~~L~~~GF~~~~~~~~~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~ 328 (655)
.|++|++|||+|+++...+.+.++|++++++|.+.|..+||+|||+|||+||+.+|+.||+|+|+||||||||||++
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=1.5e-31 Score=227.09 Aligned_cols=82 Identities=51% Similarity=0.764 Sum_probs=70.7
Q ss_pred eeEEEEEEEEeecCcceeeeEEEEEEEEECCEEEEEeeCCCHHHHHhcCCCCCCEEEEEecCcccceeecccccCCCCCC
Q psy11423 330 ALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDS 409 (655)
Q Consensus 330 ~~T~v~~I~~qvGRTG~itPvA~lePV~l~G~tVsratLhN~~~i~~~~i~iGd~V~v~raGdVIP~I~~vv~~~r~~~~ 409 (655)
++|+|++|+|||||||++||||+|+||.|+|++|+||||||+++|+++||++||+|.|+|||||||+|++|++++|++++
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 47999999999999999999999999999999999999999999999999999999999999999999999999999887
Q ss_pred cc
Q psy11423 410 KI 411 (655)
Q Consensus 410 ~~ 411 (655)
+|
T Consensus 81 ~p 82 (82)
T PF03120_consen 81 QP 82 (82)
T ss_dssp BB
T ss_pred CC
Confidence 54
No 11
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=99.63 E-value=4.5e-16 Score=127.57 Aligned_cols=64 Identities=45% Similarity=0.719 Sum_probs=55.4
Q ss_pred HHHHHhCCCCccHHHHHHHHHhCCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHhcChhHHHHH
Q psy11423 521 RFIYALGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQPLHRLLI 584 (655)
Q Consensus 521 r~L~algIpgIG~~~Ak~L~~~fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f~~~~n~~li 584 (655)
|||+||||||||+++|+.|+++|+|+++|.+|+.++|.+++|||+++|++|++||+++.|+++|
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 7999999999999999999999999999999999999999999999999999999999999875
No 12
>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=3.7e-10 Score=121.47 Aligned_cols=144 Identities=22% Similarity=0.195 Sum_probs=109.3
Q ss_pred eEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcccCCcccccCCCCceEEEEEEEEeehhhHHHHHHHH
Q psy11423 119 EYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNKYR 198 (655)
Q Consensus 119 ~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~p~~~evRGEv~~~~~~F~~~n~~~ 198 (655)
.|+||+|+||.++.+.|.+|+ +.|.||| |..++++|++++.+ +|..+.. ..| .+.+.||++++...|..
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 5776642 234 49999999998755421
Q ss_pred HHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCCCCCHHHHHHHHHhCCCCCCCCc--eeeCCHHHH
Q psy11423 199 YHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNWYQKIGLSICGEY--SVLSGVNKL 276 (655)
Q Consensus 199 ~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~~~~~~e~l~~L~~~GF~~~~~~--~~~~~~~ev 276 (655)
. . .|. .+++.||+|++...++. ...++.+..++|.++||+.++.. ..+.+.+++
T Consensus 118 ----~---~-------------~~~---~~~v~F~vFDI~~~~~~-~~lp~~eR~~lLe~lg~~~v~~~~~~~~~d~~~l 173 (342)
T cd07894 118 ----G---S-------------YPE---VEDVGFFVFDIRKKNTG-RPLPVEERRELLEKYGLPTVRLFGEFTADEIEEL 173 (342)
T ss_pred ----c---c-------------Ccc---ccccEEEEEeeEEcCCC-CCCCHHHHHHHHHhcCCCCcceEEEEecCCHHHH
Confidence 0 0 111 26899999999864322 23678999999999999877642 234567788
Q ss_pred HHHHHHHHHhhcCCCCccceEEEEECC
Q psy11423 277 IEFYKKINIKRFNLPYEIDGVVYKINC 303 (655)
Q Consensus 277 ~~~~~~~~~~r~~l~y~iDGiVikv~~ 303 (655)
.++++.+.+.- --|||+|--+
T Consensus 174 ~~~l~~~~~~G------~EGVVlK~~~ 194 (342)
T cd07894 174 KEIIRELDKEG------REGVVLKDPD 194 (342)
T ss_pred HHHHHHHHHCC------CceEEEeccc
Confidence 88887764322 5799998765
No 13
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=98.77 E-value=5.4e-09 Score=111.64 Aligned_cols=49 Identities=20% Similarity=0.332 Sum_probs=47.1
Q ss_pred CCCCeEecccccCccEEEecCCCC--chHHHHHHcCCeeeCHHHHHHHHhc
Q psy11423 600 TKGGKVVNFISKNTNYLVKGQKPG--KKLEKAIKLNIKILDEKNFVKIVKG 648 (655)
Q Consensus 600 ~~G~~v~~sVsk~t~ylv~g~~~g--~K~~kA~~lgi~ii~e~~f~~~l~~ 648 (655)
++|++|.+|||++|||||||+++| ||++||+++||+||+|++|++||..
T Consensus 257 ~~G~~v~~sVs~~t~~lv~g~~~~~ssK~~kA~~~gi~ii~e~~f~~ll~~ 307 (313)
T PRK06063 257 HAGLAYSDSVDRDTSLVVCNDPAPEQGKGYHARQLGVPVLDEAAFLELLRA 307 (313)
T ss_pred HcCCEecCccccCccEEEECCCCCcccHHHHHHHcCCccccHHHHHHHHHh
Confidence 899999999999999999999988 9999999999999999999999953
No 14
>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=98.76 E-value=5e-08 Score=95.34 Aligned_cols=139 Identities=16% Similarity=0.239 Sum_probs=94.6
Q ss_pred eEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcccCCcccccCCCCceEEEEEEEEeehhhHHHHHHHH
Q psy11423 119 EYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNKYR 198 (655)
Q Consensus 119 ~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~p~~~evRGEv~~~~~~F~~~n~~~ 198 (655)
.|++|+|+||+.+.+ +|. ++.||+ |+++|....... .+|. +.+.||+++....|+.+
T Consensus 17 ~~~~e~K~DG~R~~~---~~~--~~~SR~----g~~~t~~~~~~~---------~l~~-~ilDGElv~~~~~f~~l---- 73 (174)
T cd07896 17 GYLVSEKLDGVRAYW---DGK--QLLSRS----GKPIAAPAWFTA---------GLPP-FPLDGELWIGRGQFEQT---- 73 (174)
T ss_pred HeeechhhceEEEEE---ecc--EEEecC----CcCCCCCHHHHh---------hCCC-CccCceEEcCCCCHHHH----
Confidence 689999999999854 454 889996 999997522111 1343 78999999987777665
Q ss_pred HHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCCCCCHHHHHHHHHhC-------CCCCCCCceeeC
Q psy11423 199 YHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNWYQKI-------GLSICGEYSVLS 271 (655)
Q Consensus 199 ~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~~~~~~e~l~~L~~~-------GF~~~~~~~~~~ 271 (655)
+|.++++++......++.|++|++... ..+..+..+.|.++ .|.+++ ...+.
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 344444444333446799999999872 24555655555332 233333 23567
Q ss_pred CHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhh
Q psy11423 272 GVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQ 307 (655)
Q Consensus 272 ~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~ 307 (655)
+.+++.++++...+. ..+|+|+|-.|..++
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 579999999887774
No 15
>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=8.3e-09 Score=83.45 Aligned_cols=56 Identities=29% Similarity=0.361 Sum_probs=52.2
Q ss_pred cccccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHH
Q psy11423 456 SRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQ 512 (655)
Q Consensus 456 sk~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~ 512 (655)
.+..++|+|+|++++.+|++.| +.|+.||+.++.++|..++|||+++|++|+++++
T Consensus 4 ~~~L~~I~Gig~~~a~~L~~~G-~~t~~~l~~a~~~~L~~i~Gig~~~a~~i~~~~~ 59 (60)
T PF14520_consen 4 FDDLLSIPGIGPKRAEKLYEAG-IKTLEDLANADPEELAEIPGIGEKTAEKIIEAAR 59 (60)
T ss_dssp HHHHHTSTTCHHHHHHHHHHTT-CSSHHHHHTSHHHHHHTSTTSSHHHHHHHHHHHH
T ss_pred HHhhccCCCCCHHHHHHHHhcC-CCcHHHHHcCCHHHHhcCCCCCHHHHHHHHHHHh
Confidence 3467899999999999999998 6999999999999999999999999999999875
No 16
>PRK09125 DNA ligase; Provisional
Probab=98.70 E-value=1.2e-06 Score=92.39 Aligned_cols=198 Identities=17% Similarity=0.179 Sum_probs=124.5
Q ss_pred eEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcccCCcccccCCCCceEEEEEEEEeehhhHHHHHHHH
Q psy11423 119 EYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNKYR 198 (655)
Q Consensus 119 ~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~p~~~evRGEv~~~~~~F~~~n~~~ 198 (655)
.|++|+|+||+-+. .+| +++.|| .|+|+|+-- .+.. .+| .+.+-||+++...+|+.+....
T Consensus 44 ~~~~E~K~DG~R~~---~~~--v~l~SR----~g~~it~p~--------~~~~-~~~-~~vLDGElv~~~~~F~~l~~r~ 104 (282)
T PRK09125 44 GYLVSEKLDGVRAY---WDG--KQLLTR----QGNPIAAPA--------WFTA-GFP-PFPLDGELWAGRGQFEAISSIV 104 (282)
T ss_pred hEEEEeeeeeEeEE---ECC--eEEEcC----CCCcCCCch--------hHHh-cCC-CccEeEEEEeCCCCHHHHHHHH
Confidence 69999999999994 366 589999 788998721 1111 134 5789999999989998775532
Q ss_pred HHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCCCCCHHHHHHHHHhCCCCC-CCC-----ceeeCC
Q psy11423 199 YHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNWYQKIGLSI-CGE-----YSVLSG 272 (655)
Q Consensus 199 ~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~~~~~~e~l~~L~~~GF~~-~~~-----~~~~~~ 272 (655)
+++++......++.|++|++...+ .+..+..+.|+++==+. .+. ...+.+
T Consensus 105 -------------------~~k~~~~~~~~~v~~~vFDll~~~-----gpl~eRr~~L~~li~~~~~~~i~~~~~~~~~~ 160 (282)
T PRK09125 105 -------------------RDKTPDDAAWRKVRFMVFDLPDAP-----GDFEERLAVLKKLLAKLPSPYIKIIEQIRVRS 160 (282)
T ss_pred -------------------ccCCcchhhhcccEEEEEEcCCCC-----CCHHHHHHHHHHHHhhCCCCcEEEEeEEEcCC
Confidence 222222122347999999997643 25566666666541111 111 223568
Q ss_pred HHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCcceeeEEEEEEEEeecC-cceeeeEE
Q psy11423 273 VNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQIGR-TGIITPVA 351 (655)
Q Consensus 273 ~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~~~T~v~~I~~qvGR-TG~itPvA 351 (655)
.+++.++++.+.+ -...|+|+|--|..+. -| ++..| +=+| +....+..|.++.|..|| +|.+.-..
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 8899998887653 2368999997776654 24 45567 4444 335578899999998874 45443221
Q ss_pred EEEEEEECCEEEEEeeCCCHHHHH
Q psy11423 352 LLKPVLIDGITITRATLHNESEIY 375 (655)
Q Consensus 352 ~lePV~l~G~tVsratLhN~~~i~ 375 (655)
.- .-+|.+++=+|....+.-+
T Consensus 228 v~---~~~g~~~~VgsG~t~~~r~ 248 (282)
T PRK09125 228 VE---TPDGREFKIGSGFSDAERE 248 (282)
T ss_pred EE---eCCCCEEEeCCCCCHHHhc
Confidence 11 1256555445666666544
No 17
>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=98.61 E-value=1.2e-06 Score=87.60 Aligned_cols=166 Identities=16% Similarity=0.155 Sum_probs=105.9
Q ss_pred CceEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcccCCcccccCCCCceEEEEEEEEeehh----hHH
Q psy11423 117 NIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKK----DFI 192 (655)
Q Consensus 117 ~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~p~~~evRGEv~~~~~----~F~ 192 (655)
...|++|+|+||.-+.+.+..|. +++.|| -|.|+|+....+... +. ..|..+.+-||++.-.. .|.
T Consensus 20 ~~~~~~E~K~DG~R~~~~~~~~~-v~l~SR----~g~~~t~~~p~i~~~---~~--~~~~~~vLDGElv~~~~~~~~~f~ 89 (201)
T cd07898 20 PAAAWVEDKYDGIRAQVHKDGGR-VEIFSR----SLEDITDQFPELAAA---AK--ALPHEFILDGEILAWDDNRGLPFS 89 (201)
T ss_pred CCeEEEEEeeceEEEEEEEeCCE-EEEEcC----CChhchhhhhhHHHH---HH--hCCCCEEEEEEEEEEeCCCCCcHH
Confidence 35799999999999998776554 699999 467898755433221 11 13567899999986432 365
Q ss_pred HHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCC-CCCHHHHHHHHHhCCCCCCCCc----
Q psy11423 193 KLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLSICGEY---- 267 (655)
Q Consensus 193 ~~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~GF~~~~~~---- 267 (655)
.+..... . |+.. .. .....++.|++|++....+.++ ..+..+..+.|+++.-+.+...
T Consensus 90 ~~~~~~~---~------~~~~------~~--~~~~~~~~~~vFDil~~~g~~l~~~p~~eR~~~L~~~~~~~~~~i~~~~ 152 (201)
T cd07898 90 ELFKRLG---R------KFRD------KF--LDEDVPVVLMAFDLLYLNGESLLDRPLRERRQLLEELFVEIPGRIRIAP 152 (201)
T ss_pred HHHHHhc---c------cccc------hh--hhccCcEEEEEEeEEeECCcchhhCCHHHHHHHHHHhhcCCCCcEEEee
Confidence 5433210 0 0000 00 1123469999999986544332 2578899999999865543332
Q ss_pred -eeeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCc
Q psy11423 268 -SVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRF 319 (655)
Q Consensus 268 -~~~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~Prw 319 (655)
..+++.+++.++++.+.+ -..+|+|+|--+..+. .| .++..|
T Consensus 153 ~~~~~~~~~~~~~~~~~~~------~g~EGim~K~~~s~Y~--~g--~Rs~~w 195 (201)
T cd07898 153 ALPVESAEELEAAFARARA------RGNEGLMLKDPDSPYE--PG--RRGLAW 195 (201)
T ss_pred eEEcCCHHHHHHHHHHHHH------cCCceEEEeCCCCCcC--CC--CcCCCc
Confidence 235688888888776654 3369999999876553 12 235667
No 18
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=98.51 E-value=9.1e-08 Score=102.14 Aligned_cols=49 Identities=43% Similarity=0.636 Sum_probs=45.7
Q ss_pred CCCCeEecccccCccEEEecC---------CCCchHHHHHHc-----CCeeeCHHHHHHHHhc
Q psy11423 600 TKGGKVVNFISKNTNYLVKGQ---------KPGKKLEKAIKL-----NIKILDEKNFVKIVKG 648 (655)
Q Consensus 600 ~~G~~v~~sVsk~t~ylv~g~---------~~g~K~~kA~~l-----gi~ii~e~~f~~~l~~ 648 (655)
.+||+|.+|||++|||||+|+ .+|+|++||++| ||+||+|++|.+||..
T Consensus 246 ~~Gg~v~~sVs~~t~~lV~G~~~~~~~~~~~~~~K~~kA~~l~~~g~~i~ii~E~~f~~l~~~ 308 (309)
T PRK06195 246 RLGGTVGSSVTKKTTYLVTNTKDIEDLNREEMSNKLKKAIDLKKKGQNIKFLNEEEFLQKCKE 308 (309)
T ss_pred HhCCEecCCcccCceEEEECCCcchhhcccCcChHHHHHHHHHhCCCCcEEecHHHHHHHHhh
Confidence 899999999999999999995 457999999999 9999999999999863
No 19
>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=98.43 E-value=1e-07 Score=65.19 Aligned_cols=28 Identities=36% Similarity=0.816 Sum_probs=19.2
Q ss_pred CCCCCCCcceeecCceeEEecCCCcCCHH
Q psy11423 417 ICPICNSKIIYIESNLIARCSGSWIECIA 445 (655)
Q Consensus 417 ~CP~C~~~l~~~~~~~~~~C~n~~~~C~~ 445 (655)
+||+||++|++.++++.+||+|++. |||
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 6999999999999999999999767 997
No 20
>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=98.43 E-value=3.3e-06 Score=85.02 Aligned_cols=156 Identities=20% Similarity=0.130 Sum_probs=103.6
Q ss_pred ceEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcccCCcccccCCCC-ceEEEEEEEEeehh-----hH
Q psy11423 118 IEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPP-ELLEVRCEVLIYKK-----DF 191 (655)
Q Consensus 118 ~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~p-~~~evRGEv~~~~~-----~F 191 (655)
..|++|+|+||.-+.+.+.+| =+++.||+ |.|+|+.+..+...-..+ .+ ..+.+-||+++... +|
T Consensus 25 ~~~~~E~K~DG~R~~~~~~~~-~v~~~SR~----~~~~t~~~pel~~~~~~~----~~~~~~iLDGElv~~~~~g~~~~F 95 (207)
T cd07901 25 GEAAVEYKYDGIRVQIHKDGD-EVRIFSRR----LEDITNALPEVVEAVREL----VKAEDAILDGEAVAYDPDGRPLPF 95 (207)
T ss_pred CcEEEEEeEcceeEEEEEeCC-EEEEEeCC----CccccchhhHHHHHHHhc----CCCCCEEEeCEEEEECCCCCccCH
Confidence 479999999999999877655 47999996 899999876654321112 12 46899999998762 57
Q ss_pred HHHHHHHHHcCCCCCCChhhhHHhHhhhcCc--ccccccceEEEEEecccccCCCC-CCCHHHHHHHHHhCCCCCCC--C
Q psy11423 192 IKLNKYRYHLGLKKFTNPRNAAAGILRQLNP--KINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLSICG--E 266 (655)
Q Consensus 192 ~~~n~~~~~~g~~~f~NpRN~aaG~lr~~d~--~~~~~r~L~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~GF~~~~--~ 266 (655)
+.+-... ++... ......++.|++|++....+.++ .....+..+.|.++.-+... .
T Consensus 96 ~~l~~r~-------------------~~~~~~~~~~~~~~~~~~vFDil~~~g~~l~~~pl~eR~~~L~~~~~~~~~i~~ 156 (207)
T cd07901 96 QETLRRF-------------------RRKYDVEEAAEEIPLTLFLFDILYLDGEDLLDLPLSERRKILEEIVPETEAILL 156 (207)
T ss_pred HHHHHHh-------------------ccccchhhhhccCcEEEEEEEEEEECCcchhcCCHHHHHHHHHHhcCcCCcEEE
Confidence 6543321 11110 01123579999999986554332 24788888899887654311 0
Q ss_pred --ceeeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhh
Q psy11423 267 --YSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQ 307 (655)
Q Consensus 267 --~~~~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~ 307 (655)
...+.+.+++.++++.+.+. ...|+|+|--+..+.
T Consensus 157 ~~~~~~~~~~~~~~~~~~~~~~------g~EGiv~K~~~s~Y~ 193 (207)
T cd07901 157 APRIVTDDPEEAEEFFEEALEA------GHEGVMVKSLDSPYQ 193 (207)
T ss_pred EEEEecCCHHHHHHHHHHHHHc------CCceEEEeCCCCCcC
Confidence 12356788999988877543 368999998775543
No 21
>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=98.41 E-value=6.9e-07 Score=72.21 Aligned_cols=55 Identities=33% Similarity=0.421 Sum_probs=50.5
Q ss_pred HHHHhCCCCccHHHHHHHHHh-CCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHhc
Q psy11423 522 FIYALGIRHVGETTAKELANY-FKNLECMFKATEEQLLNIPKIGSTTVKAFIKFIN 576 (655)
Q Consensus 522 ~L~algIpgIG~~~Ak~L~~~-fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f~ 576 (655)
|...+.|||||++++++|.+. |.+++.|..++.++|.+++|||+++|++|++.++
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 444568999999999999999 9999999999999999999999999999998764
No 22
>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=98.38 E-value=5.3e-06 Score=82.49 Aligned_cols=158 Identities=17% Similarity=0.192 Sum_probs=101.4
Q ss_pred ceEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcc-cCCcccccCCCCceEEEEEEEEe------ehhh
Q psy11423 118 IEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIH-KIPLVLNIKYPPELLEVRCEVLI------YKKD 190 (655)
Q Consensus 118 ~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~-~iP~~l~~~~~p~~~evRGEv~~------~~~~ 190 (655)
..|++|+|+||+-+.+.+.+|. +++.|| .|.++|+....+. .+...+.. -+..+.+-||+++ +...
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 6889998544331 12222211 1236999999999 3344
Q ss_pred HHHHHHHHHHcCCCCCCChhhhHHhHhhhcCccc-ccccceEEEEEecccccCCCC-CCCHHHHHHHHHhCCCCCCCC--
Q psy11423 191 FIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKI-NKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLSICGE-- 266 (655)
Q Consensus 191 F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~-~~~r~L~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~GF~~~~~-- 266 (655)
|. ..++.+++.+... ....++.|++|++...++..+ ..+..+..+.|.++--.....
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 114579999999986544221 247888888888765111121
Q ss_pred ---ceeeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhh
Q psy11423 267 ---YSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQ 307 (655)
Q Consensus 267 ---~~~~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~ 307 (655)
...+.+.+++.++++.+.+.. -.|+|+|--+..+.
T Consensus 153 ~~~~~~~~~~~~~~~~~~~~~~~g------~EG~v~K~~~~~Y~ 190 (202)
T PF01068_consen 153 IVESYVVNSKEELEELFEEAIDQG------FEGLVLKDPDSPYE 190 (202)
T ss_dssp EEEEEEESSHHHHHHHHHHHHHTT------SSEEEEEETTSSC-
T ss_pred EeeeecCCCHHHHHHHHHHHHHcC------CceEEEECCCCccC
Confidence 234678999999988775433 58999998665443
No 23
>PRK03180 ligB ATP-dependent DNA ligase; Reviewed
Probab=98.38 E-value=1.7e-05 Score=90.10 Aligned_cols=216 Identities=17% Similarity=0.108 Sum_probs=137.3
Q ss_pred eEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcccCCcccccCCCCceEEEEEEEEeehh-----hHHH
Q psy11423 119 EYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKK-----DFIK 193 (655)
Q Consensus 119 ~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~p~~~evRGEv~~~~~-----~F~~ 193 (655)
.|++|+|+||.-+.+...+|. ++..||+ |+|+|+....+......++ ...+.+-||++.-.. .|+.
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 7999995 8999988765543222221 246889999998653 5654
Q ss_pred HHHHHHHcCCCCCCChhhhHHhHhhhcCc--ccccccceEEEEEecccccCCCC-CCCHHHHHHHHHhCCCCC-CCCcee
Q psy11423 194 LNKYRYHLGLKKFTNPRNAAAGILRQLNP--KINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLSI-CGEYSV 269 (655)
Q Consensus 194 ~n~~~~~~g~~~f~NpRN~aaG~lr~~d~--~~~~~r~L~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~GF~~-~~~~~~ 269 (655)
+-.. ++++.+ ......++.|++|++...++.++ ..+..+..+.|.++--+. ......
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 4221 111111 01123579999999987655443 257788888888763211 111234
Q ss_pred eCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCcceeeEEEEEEEEeec-Ccceee
Q psy11423 270 LSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQIG-RTGIIT 348 (655)
Q Consensus 270 ~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~~~T~v~~I~~qvG-RTG~it 348 (655)
+.+.+++.++++...+. ..-|+|+|--+..++ .|. +...| +-+|- .......|.+..|.-| |+|.++
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 67889999988876432 468999998775553 232 23445 45663 5677888999888888 566654
Q ss_pred e--EEEEEEEEECCE--EEEEe-eCCCHHHHHh
Q psy11423 349 P--VALLKPVLIDGI--TITRA-TLHNESEIYR 376 (655)
Q Consensus 349 P--vA~lePV~l~G~--tVsra-tLhN~~~i~~ 376 (655)
. +|..+|- +|. +|.++ |.++-+++++
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 2433331 244 45555 6677755554
No 24
>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=98.36 E-value=2.1e-05 Score=83.72 Aligned_cols=209 Identities=19% Similarity=0.189 Sum_probs=131.9
Q ss_pred ceEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcccCCcccccCCCCceEEEEEEEEee----hhhHHH
Q psy11423 118 IEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIY----KKDFIK 193 (655)
Q Consensus 118 ~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~p~~~evRGEv~~~----~~~F~~ 193 (655)
..|++|+|+||.-+.+...+| -++..|| .|+|+|+....+...-..++ ...+.+-||+++- ..+|+.
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 5799999 79999987654433322221 2368999999983 456766
Q ss_pred HHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCC-CCCHHHHHHHHHhCCCCCCCC-c-e--
Q psy11423 194 LNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLSICGE-Y-S-- 268 (655)
Q Consensus 194 ~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~GF~~~~~-~-~-- 268 (655)
+-.. ++... ..++.|++|++...++.++ .....+..+.|+++-=+.... . .
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 1579999999987655433 246778888887762111111 1 1
Q ss_pred eeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCcceeeEEEEEEEEeecCcceee
Q psy11423 269 VLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQIGRTGIIT 348 (655)
Q Consensus 269 ~~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~~~T~v~~I~~qvGRTG~it 348 (655)
...+.+++.++++...+. ...|||+|--|..++. | +++.| +-+| +....+..|.+.....||.|.+.
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 235677888887766532 3689999998866542 3 36778 4555 33456778888888877665544
Q ss_pred eE--EEEEEEEECCE--EEEEe-eCCCHHHHHh
Q psy11423 349 PV--ALLKPVLIDGI--TITRA-TLHNESEIYR 376 (655)
Q Consensus 349 Pv--A~lePV~l~G~--tVsra-tLhN~~~i~~ 376 (655)
.. +..++ |. .|-++ |..+.+..++
T Consensus 206 slll~~~~~----~~l~~vg~vgsG~s~~~~~~ 234 (298)
T TIGR02779 206 ALLLGVYEG----GGLRYVGRVGTGFSEAELAT 234 (298)
T ss_pred eEEEEEECC----CeEEEEeEecCCCCHHHHHH
Confidence 33 22222 32 34454 6777776665
No 25
>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=98.35 E-value=6.1e-06 Score=81.89 Aligned_cols=163 Identities=17% Similarity=0.192 Sum_probs=101.9
Q ss_pred ceEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcccCCcccccCCCCceEEEEEEEEeeh----hhHHH
Q psy11423 118 IEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYK----KDFIK 193 (655)
Q Consensus 118 ~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~p~~~evRGEv~~~~----~~F~~ 193 (655)
..|++|+|+||.-+.+.+.+| -+++.|| .|+++|+....|...=..+ .+..+.+-||+++-. ..|..
T Consensus 16 ~~~~~e~K~DG~R~~i~~~~~-~v~~~SR----~g~~~t~~~p~l~~~~~~~----~~~~~iLDGElv~~~~~~~~~F~~ 86 (190)
T cd07906 16 EDWLYEIKWDGYRALARVDGG-RVRLYSR----NGLDWTARFPELAEALAAL----PVRDAVLDGEIVVLDEGGRPDFQA 86 (190)
T ss_pred CCeEEEEeEceEEEEEEEECC-EEEEEcC----CCCcchhhhHHHHHHHHhc----CCCCEEEEeEEEEECCCCCCCHHH
Confidence 369999999999999988666 5799999 6888887554433211111 134688999999843 35654
Q ss_pred HHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCC-CCCHHHHHHHHHhCCCCCCCCceeeCC
Q psy11423 194 LNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLSICGEYSVLSG 272 (655)
Q Consensus 194 ~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~GF~~~~~~~~~~~ 272 (655)
+-. ..++.+ .......+.|++|++...++..+ ..+..+..+.|.++.-+..+...++..
T Consensus 87 l~~-------------------~~~~~~-~~~~~~~~~~~vFDil~~~~~~~~~~p~~eR~~~L~~~~~~~~~~i~~~~~ 146 (190)
T cd07906 87 LQN-------------------RLRLRR-RLARTVPVVYYAFDLLYLDGEDLRGLPLLERKELLEELLPAGSPRLRVSEH 146 (190)
T ss_pred HHH-------------------hhcccc-hhcccCceEEEEEeeeeeCCcchhhCCHHHHHHHHHHHhccCCCcEEECce
Confidence 321 111111 12234579999999976544332 257889999999987665343333332
Q ss_pred H-HHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCc
Q psy11423 273 V-NKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRF 319 (655)
Q Consensus 273 ~-~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~Prw 319 (655)
. .+..++++++.+ -..+|+|+|--+..+. .|. +++.|
T Consensus 147 ~~~~~~~~~~~~~~------~g~EGiv~K~~~s~Y~--~g~--rs~~w 184 (190)
T cd07906 147 FEGGGAALFAAACE------LGLEGIVAKRADSPYR--SGR--RSRDW 184 (190)
T ss_pred EcCCHHHHHHHHHH------cCCcEEEEecCCCCcC--CCC--CCCcc
Confidence 2 222455554432 2469999999886554 233 34667
No 26
>TIGR01448 recD_rel helicase, putative, RecD/TraA family. This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD.
Probab=98.34 E-value=5.9e-07 Score=106.05 Aligned_cols=125 Identities=20% Similarity=0.334 Sum_probs=103.6
Q ss_pred hHHHHHhCCCCccHHHHHHHHHhCCC--HHHHHhcCHHHHhcCCCCCHHHHHHHHHHhc-ChhHHHHHHHHHHcCccccc
Q psy11423 520 SRFIYALGIRHVGETTAKELANYFKN--LECMFKATEEQLLNIPKIGSTTVKAFIKFIN-QPLHRLLISQLRDVGIYWLN 596 (655)
Q Consensus 520 ~r~L~algIpgIG~~~Ak~L~~~fgs--l~~l~~as~eeL~~i~GIG~~~A~~I~~~f~-~~~n~~li~~L~~~Gi~~~~ 596 (655)
.+||..-.|||||+++|++|.++||. ++.|.+ +++.|..|+|||++.++.|.+-+. ....++++.+|...|++...
T Consensus 81 ~~yL~s~~~~GIG~~~A~~iv~~fg~~~~~~i~~-~~~~L~~v~gi~~~~~~~i~~~~~~~~~~~~~~~~L~~~gi~~~~ 159 (720)
T TIGR01448 81 VAYLSSRSIKGVGKKLAQRIVKTFGEAAFDVLDD-DPEKLLEVPGISKANLEKFVSQWSQQGDERRLLAGLQGLGIGIKL 159 (720)
T ss_pred HHHHhcCCCCCcCHHHHHHHHHHhCHhHHHHHHh-CHHHHhcCCCCCHHHHHHHHHHHHHhHHHHHHHHHHHHcCCCHHH
Confidence 47777667999999999999999993 444544 588999999999999999998554 45578899999999997544
Q ss_pred CC---CCCCCeEecccccCccEEEecCCCC---chHHH-HHHcCCeeeCHHHHHHHH
Q psy11423 597 NP---NTKGGKVVNFISKNTNYLVKGQKPG---KKLEK-AIKLNIKILDEKNFVKIV 646 (655)
Q Consensus 597 ~~---~~~G~~v~~sVsk~t~ylv~g~~~g---~K~~k-A~~lgi~ii~e~~f~~~l 646 (655)
.. ..+|......|..|| |.++.+..| .++|+ |+++|++..++..+...+
T Consensus 160 a~ki~~~yg~~~~~~i~~nP-Y~L~~~i~gigF~~aD~iA~~~g~~~~d~~Ri~a~i 215 (720)
T TIGR01448 160 AQRIYKFYQADTLDRVEKDP-YLLAEDVKGIGFLTADQLAQALGIALNDPRRITAGL 215 (720)
T ss_pred HHHHHHHHhHHHHHHHHhCc-hhhhhhcCCCCHHHHHHHHHHcCCCCCCHHHHHHHH
Confidence 33 478999999999999 999876554 89999 999999999999877654
No 27
>PRK07636 ligB ATP-dependent DNA ligase; Reviewed
Probab=98.32 E-value=8.2e-05 Score=78.31 Aligned_cols=205 Identities=18% Similarity=0.213 Sum_probs=128.4
Q ss_pred ceEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcccCCcccccCCCCceEEEEEEEEeeh----hhHHH
Q psy11423 118 IEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYK----KDFIK 193 (655)
Q Consensus 118 ~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~p~~~evRGEv~~~~----~~F~~ 193 (655)
..|++|+|+||.-+.+.-.+| -+++.|| .|.|+|+....+-.. ..|..+.+-||++... .+|+.
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 479999999999997754455 4799999 688999876544321 1345689999999843 46766
Q ss_pred HHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCC-CCCHHHHHHHHHhCCCCCCCCceeeCC
Q psy11423 194 LNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLSICGEYSVLSG 272 (655)
Q Consensus 194 ~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~GF~~~~~~~~~~~ 272 (655)
+-... ++..+ ....++.|++|++...++.++ ..+..+..+.|+++.-+. +....+..
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 53210 11111 124579999999987655433 247889999999886543 33333332
Q ss_pred -HHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCcceeeEEEEEEEEeecCcceeeeEE
Q psy11423 273 -VNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQIGRTGIITPVA 351 (655)
Q Consensus 273 -~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~~~T~v~~I~~qvGRTG~itPvA 351 (655)
.++..++++...+ -...|||+|--|..++ ...++..| +-.| ..+..+..|.+. ..|..|.+ ++
T Consensus 144 ~~~~~~~~~~~~~~------~g~EGiV~K~~ds~Y~----~g~Rs~~W-lKiK-~~~~~e~vV~G~--~~~~~g~l--lg 207 (275)
T PRK07636 144 IEGHGTAYFELVEE------RELEGIVIKKANSPYE----INKRSDNW-LKVI-NYQYTDVLITGY--RKEEFGLL--LS 207 (275)
T ss_pred ccccHHHHHHHHHH------cCCcEEEEeCCCCCCC----CCCCCCCe-EEEe-cCCeEEEEEEEE--ecCCCcEE--EE
Confidence 2355566655532 2356999999887664 12345678 6666 345566777666 34445533 44
Q ss_pred EEEEEEECCEEEEEeeCCCHHHHHhc
Q psy11423 352 LLKPVLIDGITITRATLHNESEIYRK 377 (655)
Q Consensus 352 ~lePV~l~G~tVsratLhN~~~i~~~ 377 (655)
.. +|..|-++.-...+..+++
T Consensus 208 ~~-----~g~~~G~vgt~~~~~~~~l 228 (275)
T PRK07636 208 YL-----DGRSAGIMEFMPYDARKKF 228 (275)
T ss_pred ec-----CCeEEEEECCCCHHHHHHH
Confidence 32 5667777643555555544
No 28
>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=98.27 E-value=2.5e-05 Score=79.45 Aligned_cols=159 Identities=17% Similarity=0.172 Sum_probs=103.7
Q ss_pred ceEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcccC-CcccccCCCCceEEEEEEEEeehh------h
Q psy11423 118 IEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKI-PLVLNIKYPPELLEVRCEVLIYKK------D 190 (655)
Q Consensus 118 ~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~i-P~~l~~~~~p~~~evRGEv~~~~~------~ 190 (655)
..|++|+|+||.-+.+.+.+|.-++..|| .|+|+|+....+... ...+.. -+..+.+-||+++-.. .
T Consensus 31 ~~~~~E~K~DG~R~~~h~~~~~~v~l~SR----~g~~~t~~~pel~~~~~~~~~~--~~~~~iLDGElv~~~~~~g~~~~ 104 (219)
T cd07900 31 KEFTCEYKYDGERAQIHLLEDGKVKIFSR----NLENNTEKYPDIVAVLPKSLKP--SVKSFILDSEIVAYDRETGKILP 104 (219)
T ss_pred CeEEEEEeecceEEEEEEcCCCeEEEECC----CCccccchhhHHHHHHHHHhcc--cCccEEEeeEEEEEEcCCCCCcC
Confidence 47999999999999999976334799999 589999887655432 222210 1456899999987543 4
Q ss_pred HHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCC-CCCHHHHHHHHHhCCCCCCCCc--
Q psy11423 191 FIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLSICGEY-- 267 (655)
Q Consensus 191 F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~GF~~~~~~-- 267 (655)
|+.+-.. .+...+......++.|++|++...++..+ ..+..+..+.|.++-=+.+...
T Consensus 105 F~~l~~r-------------------~~~~~~~~~~~~~~~~~vFDiL~l~g~~l~~~pl~eRr~~L~~~~~~~~~~~~~ 165 (219)
T cd07900 105 FQVLSTR-------------------KRKDVDANDIKVQVCVFAFDLLYLNGESLLKKPLRERRELLHSLFKEVPGRFQF 165 (219)
T ss_pred hHHHhhh-------------------cccccccccCcccEEEEEEEEEEECCchhhcCCHHHHHHHHHHhcCCCCCeEEE
Confidence 5443211 01111111234679999999987655443 2477788888887632222111
Q ss_pred ---eeeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECC--hhhh
Q psy11423 268 ---SVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINC--LSTQ 307 (655)
Q Consensus 268 ---~~~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~--~~~~ 307 (655)
..+.+.+++.++++.+.+. ..-|||+|--+ ..++
T Consensus 166 ~~~~~~~~~~~~~~~~~~~~~~------g~EGiv~K~~~~~s~Y~ 204 (219)
T cd07900 166 ATSKDSEDTEEIQEFLEEAVKN------NCEGLMVKTLDSDATYE 204 (219)
T ss_pred EEEEecCCHHHHHHHHHHHHHc------CCceEEEecCCCCCccC
Confidence 2356788999988877543 46899999877 5553
No 29
>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=98.19 E-value=7.4e-05 Score=85.32 Aligned_cols=218 Identities=18% Similarity=0.175 Sum_probs=134.5
Q ss_pred eEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhc-cc-CCcccccCCCCceEEEEEEEEeehh------h
Q psy11423 119 EYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHII-HK-IPLVLNIKYPPELLEVRCEVLIYKK------D 190 (655)
Q Consensus 119 ~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i-~~-iP~~l~~~~~p~~~evRGEv~~~~~------~ 190 (655)
.|++|+|+||.-+.+.+.+|. ++..|| .|+|+|+....+ .. +...++. .....+-||++.-.. .
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 799999999999999875554 799999 688999766443 21 1111210 125789999997643 4
Q ss_pred HHHHHHHHHHcCCCCCCChhhhHHhHhhhcC-cccccccceEEEEEecccccCCCC-CCCHHHHHHHHHhCCCCCCCCc-
Q psy11423 191 FIKLNKYRYHLGLKKFTNPRNAAAGILRQLN-PKINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLSICGEY- 267 (655)
Q Consensus 191 F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~d-~~~~~~r~L~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~GF~~~~~~- 267 (655)
|+.+-... ++.+ .......++.||+|++...++.++ ..+..+..+.|.++-=+.+...
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 55432210 1101 011134579999999987555332 2578888888988643333222
Q ss_pred ----eeeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCC-------cceeeEEEEE
Q psy11423 268 ----SVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFL-------SKEALTKIKA 336 (655)
Q Consensus 268 ----~~~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~-------~~~~~T~v~~ 336 (655)
..+.+.+++.++++...+. ...|+|+|--+..++ .| .+++.| +|+- .......|.+
T Consensus 321 ~~~~~~~~~~e~~~~~~~~~~~~------g~EGlv~K~~ds~Y~--~G--~Rs~~W---lK~K~~y~~~~~~~~D~vvig 387 (514)
T TIGR00574 321 IAEMKITSNVEELEKFLNEAISE------GCEGLMLKDLKSIYE--PG--KRGWLW---LKFKPEYLEGMGDTLDLVVIG 387 (514)
T ss_pred EEEEEecCCHHHHHHHHHHHHHc------CCceEEEecCCCccc--CC--CCCCcc---eeCchhhcccccCceeEEEEe
Confidence 2346888999988766543 368999998776554 23 345667 4554 3566778888
Q ss_pred EEEeecC-cceeeeEE--EEEEEEECCE--EEEEe-eCCCHHHHHhcC
Q psy11423 337 INIQIGR-TGIITPVA--LLKPVLIDGI--TITRA-TLHNESEIYRKN 378 (655)
Q Consensus 337 I~~qvGR-TG~itPvA--~lePV~l~G~--tVsra-tLhN~~~i~~~~ 378 (655)
..+.-|| .|.++... ..++- .|. +|.++ |.+..+.++++.
T Consensus 388 ~~~g~gk~~g~~~~~l~g~~d~~--~~~~~~v~kvgsG~sd~~l~~l~ 433 (514)
T TIGR00574 388 AYYGKGKRTGMYGSFLLACYDPE--SEEFKTITKVGTGFTDADLQELG 433 (514)
T ss_pred eEecCCccCCceeEEEEEEEcCC--CCeEEEEEEECCCCCHHHHHHHH
Confidence 8888774 45444332 22220 021 45444 777777777653
No 30
>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=98.19 E-value=1.8e-05 Score=77.76 Aligned_cols=150 Identities=17% Similarity=0.152 Sum_probs=96.7
Q ss_pred ceEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcccCCcccccCCCCceEEEEEEEEeehhhHHHHHHH
Q psy11423 118 IEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNKY 197 (655)
Q Consensus 118 ~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~p~~~evRGEv~~~~~~F~~~n~~ 197 (655)
..|++|+|.||.-+.+.+.+|. +.+.|| .|+++|.-...+.. ..+. ..+....+-||+++....+
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 5799999999999999887665 789999 67788875433321 0111 1244689999999865433
Q ss_pred HHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCC-CCCHHHHHHHHHhCCCCCCC--Cce-----e
Q psy11423 198 RYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLSICG--EYS-----V 269 (655)
Q Consensus 198 ~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~GF~~~~--~~~-----~ 269 (655)
....+.|++|++...++.++ ..+..+.++.|+++-=.... ... .
T Consensus 84 ----------------------------~~~~~~~~~FDil~~~~~~~~~~p~~eR~~~L~~~v~~~~~~~~~~i~~~~~ 135 (182)
T cd06846 84 ----------------------------ANPKPTYYAFDVVPLSGVGLRDLPYSDRFAYLKSLLKEFEGLDPVKLVPLEN 135 (182)
T ss_pred ----------------------------ccceeEEEEEEEEEECCCccccCCHHHHHHHHHHHhhhhccCCceeEEEeec
Confidence 12369999999987554332 24778888888775422210 011 1
Q ss_pred eC-CHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCc
Q psy11423 270 LS-GVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRF 319 (655)
Q Consensus 270 ~~-~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~Prw 319 (655)
+. ..+++.+++++. .....||+|+|--+..+. |...+.+.|
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 12 222366666544 346789999999887664 445566666
No 31
>COG5275 BRCT domain type II [General function prediction only]
Probab=98.18 E-value=1.5e-06 Score=85.71 Aligned_cols=50 Identities=38% Similarity=0.618 Sum_probs=47.9
Q ss_pred CCCCeEecccccCccEEEecCCCC-chHHHHHHcCCeeeCHHHHHHHHhcc
Q psy11423 600 TKGGKVVNFISKNTNYLVKGQKPG-KKLEKAIKLNIKILDEKNFVKIVKGF 649 (655)
Q Consensus 600 ~~G~~v~~sVsk~t~ylv~g~~~g-~K~~kA~~lgi~ii~e~~f~~~l~~~ 649 (655)
.|||+|..+.|.+|+|||.|+++| +|++|+++|+|+.|+|++|..||..-
T Consensus 182 ~yGgrvT~~pSskTtflvlGdnaGP~K~ekiKqlkIkaidEegf~~LI~~~ 232 (276)
T COG5275 182 VYGGRVTAVPSSKTTFLVLGDNAGPSKMEKIKQLKIKAIDEEGFDSLIKDT 232 (276)
T ss_pred HhCCeeecccccceeEEEecCCCChHHHHHHHHhCCccccHHHHHHHHhcC
Confidence 899999999999999999999999 99999999999999999999999643
No 32
>PRK08224 ligC ATP-dependent DNA ligase; Reviewed
Probab=98.18 E-value=7e-05 Score=81.37 Aligned_cols=215 Identities=14% Similarity=0.129 Sum_probs=131.3
Q ss_pred eEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcccCCcccccCCCCceEEEEEEEEeeh---hhHHHHH
Q psy11423 119 EYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYK---KDFIKLN 195 (655)
Q Consensus 119 ~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~p~~~evRGEv~~~~---~~F~~~n 195 (655)
.|.+|+|+||.-+.+.+.+|. ++..|| .|.|+|+....|...-..+ .|..+.+-||++.-. .+|+.+.
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 699999999999988776555 799999 7999998776654322222 255789999999865 3788774
Q ss_pred HHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCC-CCCHHHHHHHHHhCCCCCCCCcee---eC
Q psy11423 196 KYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLSICGEYSV---LS 271 (655)
Q Consensus 196 ~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~GF~~~~~~~~---~~ 271 (655)
.... . ++.+ .+++ ....++.|++|++...++.++ .....+..+.|+++ |...+..++ +.
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 0100 1111 123479999999987655443 24677888888877 333222222 33
Q ss_pred CHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCcceeeEEEEEEEEeecCcceeeeE-
Q psy11423 272 GVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQIGRTGIITPV- 350 (655)
Q Consensus 272 ~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~~~T~v~~I~~qvGRTG~itPv- 350 (655)
+.++..++++... .-...|||+|--|..++ -|..+ | +-+| +....+..|.+..+.-|+ |.+.-.
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-FKVK-HERTADCVVAGYRYHKSG-PVVGSLL 223 (350)
T ss_pred CHHHHHHHHHHHH------hCCCcEEEEeCCCCCcC--CCCcC----E-EEEc-cCCcEEEEEEEEEcCCCC-CccccEE
Confidence 4567777776553 23468999999887664 23322 7 4555 345567778887776655 332221
Q ss_pred -EEEEEEEECCE--EEEEeeCCCHHHHHhc
Q psy11423 351 -ALLKPVLIDGI--TITRATLHNESEIYRK 377 (655)
Q Consensus 351 -A~lePV~l~G~--tVsratLhN~~~i~~~ 377 (655)
+..++ +|. .|-+++..+.+..+++
T Consensus 224 lg~~d~---~g~l~~vG~v~Gf~~~~~~~L 250 (350)
T PRK08224 224 LGLYDD---DGQLHHVGVTSAFPMARRREL 250 (350)
T ss_pred EEEECC---CCcEEEEEEECCCCHHHHHHH
Confidence 21121 242 4556666666666543
No 33
>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=98.15 E-value=0.00012 Score=74.51 Aligned_cols=168 Identities=18% Similarity=0.148 Sum_probs=104.4
Q ss_pred CceEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcccCC---ccccc--CCCCceEEEEEEEEeehh--
Q psy11423 117 NIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIP---LVLNI--KYPPELLEVRCEVLIYKK-- 189 (655)
Q Consensus 117 ~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP---~~l~~--~~~p~~~evRGEv~~~~~-- 189 (655)
...|++|+|+||.-+.+.+.+|. +++.|| .|.|+|+....+...- ..|.. ...+..+.+-||+++-..
T Consensus 32 ~~~~~~E~K~DG~R~~i~~~~~~-v~l~SR----~g~~~t~~~p~~~~~~~~~~~l~~~~~~~~~~~iLDGElv~~~~~~ 106 (225)
T cd07903 32 GKPFYIETKLDGERIQLHKDGNE-FKYFSR----NGNDYTYLYGASLTPGSLTPYIHLAFNPKVKSCILDGEMVVWDKET 106 (225)
T ss_pred CCeEEEEEeeCceEEEEEecCCE-EEEEeC----CCccccccccccccccccchhhhhhccccCcEEEeceEEEEEEcCc
Confidence 35799999999999999887664 799999 6889997654332210 01100 012457899999997432
Q ss_pred ----hHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCC-CCCHHHHHHHHHhCCCCCC
Q psy11423 190 ----DFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLSIC 264 (655)
Q Consensus 190 ----~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~GF~~~ 264 (655)
.|..+ ++.++ ++. .......+.|++|++...++.++ .....+..+.|.++--+..
T Consensus 107 ~~~~~f~~l---------------~~~~~--~~~---~~~~~~~~~~~vFDiL~~~g~~l~~~pl~eR~~~L~~~~~~~~ 166 (225)
T cd07903 107 KRFLPFGTL---------------KDVAK--LRE---VEDSDLQPCFVVFDILYLNGKSLTNLPLHERKKLLEKIITPIP 166 (225)
T ss_pred CeeccchHH---------------HHHHh--hcc---cccCCccEEEEEEEEEEECCeecccCcHHHHHHHHHHhcCCCC
Confidence 34332 11111 110 01123568999999986554332 2477888888888743322
Q ss_pred CCc-----eeeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCc
Q psy11423 265 GEY-----SVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRF 319 (655)
Q Consensus 265 ~~~-----~~~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~Prw 319 (655)
... ..+.+.+++.++++.+.+. ...|+|+|--+..+.. | .++..|
T Consensus 167 ~~i~~~~~~~~~~~~~~~~~~~~~~~~------g~EGlv~K~~~s~Y~~--g--~Rs~~w 216 (225)
T cd07903 167 GRLEVVKRTEASTKEEIEEALNEAIDN------REEGIVVKDLDSKYKP--G--KRGGGW 216 (225)
T ss_pred CeEEEEEEEeCCCHHHHHHHHHHHHHc------CCceEEEecCCCCCcc--C--CcCCCc
Confidence 211 2345778999988877643 3799999998866542 2 245667
No 34
>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=98.15 E-value=4.2e-05 Score=77.11 Aligned_cols=157 Identities=17% Similarity=0.104 Sum_probs=101.1
Q ss_pred ceEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcccCCcccccCCCCceEEEEEEEEeehh----hHHH
Q psy11423 118 IEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKK----DFIK 193 (655)
Q Consensus 118 ~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~p~~~evRGEv~~~~~----~F~~ 193 (655)
-.|++|+|+||.-+.+.. +|.=++..|| .|+|+|+....+...-. ..|..+.+-||+++-.. +|+.
T Consensus 24 ~~~~~E~K~DG~R~~~~~-~~~~v~l~SR----~g~~~t~~~p~l~~~~~-----~l~~~~iLDGElv~~~~~~~~~F~~ 93 (207)
T cd07897 24 SDWQAEWKWDGIRGQLIR-RGGEVFLWSR----GEELITGSFPELLAAAE-----ALPDGTVLDGELLVWRDGRPLPFND 93 (207)
T ss_pred ccEEEEEeEceEEEEEEE-cCCEEEEEeC----CCCcccccchHHHHHHH-----hCCCCeEEEeEEEEecCCCccCHHH
Confidence 369999999999998765 4445799999 56789876654432211 13557899999998654 7876
Q ss_pred HHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCCC-CCHHHHHHHHHhCCCCCC-CC-----
Q psy11423 194 LNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMP-SSHSELLNWYQKIGLSIC-GE----- 266 (655)
Q Consensus 194 ~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~~-~~~~e~l~~L~~~GF~~~-~~----- 266 (655)
+..... . ++ +... .....++.|++|++....+.++. ....+..+.|.++--+.. ..
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 643211 0 01 0011 11235799999999876553321 357778888877622221 11
Q ss_pred ceeeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhh
Q psy11423 267 YSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQ 307 (655)
Q Consensus 267 ~~~~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~ 307 (655)
...+.+.+++.++++...+. ...|||+|--+..++
T Consensus 157 ~~~~~~~~~~~~~~~~~~~~------g~EGiv~K~~~s~Y~ 191 (207)
T cd07897 157 LIAFADWEELAALRAQSRER------GAEGLMLKRRDSPYL 191 (207)
T ss_pred eEecCCHHHHHHHHHHHHHc------CCeEEEEeCCCCCcC
Confidence 22356788999988866532 358999999886654
No 35
>COG1793 CDC9 ATP-dependent DNA ligase [DNA replication, recombination, and repair]
Probab=98.14 E-value=0.00019 Score=80.42 Aligned_cols=215 Identities=19% Similarity=0.211 Sum_probs=138.4
Q ss_pred eEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhh-hcccCCcccccCCCCceEEEEEEEEee----hhhHHH
Q psy11423 119 EYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIH-IIHKIPLVLNIKYPPELLEVRCEVLIY----KKDFIK 193 (655)
Q Consensus 119 ~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~-~i~~iP~~l~~~~~p~~~evRGEv~~~----~~~F~~ 193 (655)
.|.+|+|+||.-+.+...+|. ++.+|| .|+|||+... .+..+=..++ +....+-||+++- ..+|+.
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 699999999999999998885 799999 7999998876 3333322232 3468999999995 568887
Q ss_pred HHHHHHHcCCCCCCChhhhHHhHhhhcCc--ccccccceEEEEEecccccCCCCC-CCHHHHHHHHHhC--C---CCCCC
Q psy11423 194 LNKYRYHLGLKKFTNPRNAAAGILRQLNP--KINKNKILHFFAHGVGELRGMNMP-SSHSELLNWYQKI--G---LSICG 265 (655)
Q Consensus 194 ~n~~~~~~g~~~f~NpRN~aaG~lr~~d~--~~~~~r~L~f~~y~~~~~~~~~~~-~~~~e~l~~L~~~--G---F~~~~ 265 (655)
+.... +++.+ ......++.||+|++...++.++. ....+..+.|.++ + |...+
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 111334799999999987766543 2455666666553 1 33333
Q ss_pred CceeeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCcceeeEEEEEEEEeecCcc
Q psy11423 266 EYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQIGRTG 345 (655)
Q Consensus 266 ~~~~~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~~~T~v~~I~~qvGRTG 345 (655)
... +.+.++...+++... ...+.|||+|--|..++. ..+.-.| +-+| +.++..-.|.+..++-|+-+
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 333 377888888876543 346899999965555541 1122233 3444 33778899999999998765
Q ss_pred eeeeEEEEEEEEECCE-----EEEEeeCCCHHHHHh
Q psy11423 346 IITPVALLKPVLIDGI-----TITRATLHNESEIYR 376 (655)
Q Consensus 346 ~itPvA~lePV~l~G~-----tVsratLhN~~~i~~ 376 (655)
..=+-+-.+.-++. .++=.|...-++.++
T Consensus 333 --~~~slll~~~~~~~~~~~~v~kVgtGf~~~~l~~ 366 (444)
T COG1793 333 --LYGSLLLGVYDGDGGGLLYVGKVGTGFSDAELEE 366 (444)
T ss_pred --ccceEEEEEEcCCCceEEEEecccCCCCHHHHHH
Confidence 44455556666664 333345555444433
No 36
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=98.07 E-value=1.2e-05 Score=80.19 Aligned_cols=69 Identities=17% Similarity=0.256 Sum_probs=57.4
Q ss_pred hCCCCccHHHHHHHHHhCCC---HHHHHhcCHHHHhcCCCCCHHHHHHHHHHhcChh----------------HHHHHHH
Q psy11423 526 LGIRHVGETTAKELANYFKN---LECMFKATEEQLLNIPKIGSTTVKAFIKFINQPL----------------HRLLISQ 586 (655)
Q Consensus 526 lgIpgIG~~~Ak~L~~~fgs---l~~l~~as~eeL~~i~GIG~~~A~~I~~~f~~~~----------------n~~li~~ 586 (655)
+.|||||+++|++|+++|+. .+++.+++.++|.++||||+++|+.|+..|+... ..+++..
T Consensus 76 ~~i~GIGpk~A~~il~~fg~~~l~~~i~~~d~~~L~~v~Gig~k~A~~I~~~l~~~~~~~~~~~~~~~~~~~~~~ev~~a 155 (192)
T PRK00116 76 ISVSGVGPKLALAILSGLSPEELVQAIANGDVKALTKVPGIGKKTAERIVLELKDKLAAAASAAAAAAAASSALEEAVSA 155 (192)
T ss_pred hcCCCCCHHHHHHHHHhCCHHHHHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHHHHhhcccccccccccccchHHHHHHH
Confidence 47999999999999999997 6778888999999999999999999998776432 3456666
Q ss_pred HHHcCccc
Q psy11423 587 LRDVGIYW 594 (655)
Q Consensus 587 L~~~Gi~~ 594 (655)
|...|++.
T Consensus 156 L~~LG~~~ 163 (192)
T PRK00116 156 LVALGYKP 163 (192)
T ss_pred HHHcCCCH
Confidence 77777653
No 37
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=98.04 E-value=2.1e-06 Score=90.00 Aligned_cols=59 Identities=20% Similarity=0.205 Sum_probs=54.8
Q ss_pred cccccCCCCHHHHHHHHHcCCCCChHHHhc-CChhhhccccCCcHHHHHHHHHHHHHhcc
Q psy11423 458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYK-INFKNLLRLDRVSNKLANNILLAIQKSKL 516 (655)
Q Consensus 458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~-L~~~~L~~l~GfG~Ksa~nll~~I~~sk~ 516 (655)
..|.++|+|||++..||+++.|++.++|-. +....+..|+|||+|++++|++++.....
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 378999999999999999999999999998 78899999999999999999999987544
No 38
>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=98.04 E-value=6.1e-05 Score=75.12 Aligned_cols=159 Identities=15% Similarity=0.105 Sum_probs=98.9
Q ss_pred ceEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcccCCcccccCCCCceEEEEEEEEee---hhhHHHH
Q psy11423 118 IEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIY---KKDFIKL 194 (655)
Q Consensus 118 ~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~p~~~evRGEv~~~---~~~F~~~ 194 (655)
..|++|+|+||.-+.+.+.+|. ++..|| .|+|+|+....+...-..+ .|..+.+-||+++- ..+|+.+
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 7889998654433211111 35578999999984 3467665
Q ss_pred HHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCCC-CCHHHHHHHHHhCCCCCCCCc---eee
Q psy11423 195 NKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMP-SSHSELLNWYQKIGLSICGEY---SVL 270 (655)
Q Consensus 195 n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~~-~~~~e~l~~L~~~GF~~~~~~---~~~ 270 (655)
-... +.+.. + . +......++.|++|++...++.++. ....+..+.|.++-=+..+.. ..+
T Consensus 87 ~~r~---~~~~~---~------~----~~~~~~~~~~~~vFDiL~l~g~~l~~~pl~eRr~~L~~~~~~~~~~i~~~~~~ 150 (194)
T cd07905 87 QQRI---HPAAS---R------V----RRLAEETPASFVAFDLLALGGRDLRGRPLRERRAALEALLAGWGPPLHLSPAT 150 (194)
T ss_pred HHHh---ccccc---c------h----hhhhccCCEEEEEEeeeeeCCcccccCCHHHHHHHHHHHhcccCCCeEECCcc
Confidence 3321 11000 0 0 1112356799999999875544322 467777777776521111111 223
Q ss_pred CCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhh
Q psy11423 271 SGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQ 307 (655)
Q Consensus 271 ~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~ 307 (655)
.+.+++.++++...+ -..-|||+|--+..++
T Consensus 151 ~~~~~~~~~~~~~~~------~g~EGiv~K~~~s~Y~ 181 (194)
T cd07905 151 TDRAEAREWLEEFEG------AGLEGVVAKRLDGPYR 181 (194)
T ss_pred CCHHHHHHHHHHHHH------CCCceEEEeCCCCCcC
Confidence 566778887776543 2357999998776553
No 39
>KOG2841|consensus
Probab=98.02 E-value=4.3e-06 Score=83.86 Aligned_cols=60 Identities=32% Similarity=0.450 Sum_probs=54.9
Q ss_pred hHHHHHh-CCCCccHHHHHHHHHhCCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHhcChh
Q psy11423 520 SRFIYAL-GIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQPL 579 (655)
Q Consensus 520 ~r~L~al-gIpgIG~~~Ak~L~~~fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f~~~~ 579 (655)
.+++..| .||||++.-|..|+.+|||+..|.+||.++|.+++|+|+..|++|++||+.|.
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 3455555 79999999999999999999999999999999999999999999999999764
No 40
>PHA00454 ATP-dependent DNA ligase
Probab=97.99 E-value=0.0016 Score=69.91 Aligned_cols=240 Identities=19% Similarity=0.143 Sum_probs=134.0
Q ss_pred ccccccCCCCCCChHHHHHHHHHHHHhhccCCCceEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhc--
Q psy11423 85 HTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHII-- 162 (655)
Q Consensus 85 H~~pMlSL~k~~~~~el~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i-- 162 (655)
|+.||+-.+ ||+..+.+=.+++ | .|++|+|+||.-+.+...+|.=+++.||. |.+++.-+...
T Consensus 5 ~~~~~~~~~--~~~~~i~~~~~~~----g-----~~~~E~K~DG~R~~~~~~~~~~v~l~SR~----g~~~p~l~~~~~~ 69 (315)
T PHA00454 5 KTNPFRAVD--FNESAIEKALEKA----G-----YLIADVKYDGVRGNIVVDNTADHGWLSRE----GKTIPALEHLNGF 69 (315)
T ss_pred cCCcccccc--CCHHHHHHHHHhC----C-----cEEEEEccceEEEEEEEcCCCeEEEEeCC----CCcccchhhhhhh
Confidence 566664333 4554444333332 2 69999999999999887666447999994 34554422111
Q ss_pred -ccCCccccc--CCCCceEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcC--cccccccceEEEEEec
Q psy11423 163 -HKIPLVLNI--KYPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLN--PKINKNKILHFFAHGV 237 (655)
Q Consensus 163 -~~iP~~l~~--~~~p~~~evRGEv~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~d--~~~~~~r~L~f~~y~~ 237 (655)
..++..+.. ...|..+.+-||++....+|+.+. |.|+++. +......++.|++|++
T Consensus 70 ~~~~~~~~~~~~~~l~~~~vLDGElv~~~~~f~~~~-------------------~~l~~k~~~~~~~~~~~v~~~vFDl 130 (315)
T PHA00454 70 DRRWAKLLNDDRCIFPDGFMLDGELMVKGVDFNTGS-------------------GLLRRKWKVLFELHLKKLHVVVYDV 130 (315)
T ss_pred hhhhhhhhhhhhhcCCCCeEEEEEEEecCCCHHHHH-------------------HHhccCccchhhhccCceEEEEEEe
Confidence 011222211 013457899999999766676543 3333332 1222346899999999
Q ss_pred ccccCC----CC----CCCHHHHHHHHHhC----C---CCCCCCceeeCCHHHHHHHHHHHHHhhcCCCCccceEEEEEC
Q psy11423 238 GELRGM----NM----PSSHSELLNWYQKI----G---LSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKIN 302 (655)
Q Consensus 238 ~~~~~~----~~----~~~~~e~l~~L~~~----G---F~~~~~~~~~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~ 302 (655)
...++. ++ .....+.-+.|.++ + +..++ ...+.+.+++.++++...+ -...|||+|--
T Consensus 131 l~l~~~~~g~~l~~l~~~pl~~Rr~~L~~l~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~------~g~EGiv~K~~ 203 (315)
T PHA00454 131 TPLDVLESGEDYDVMSLLMYEHVRAMVPLLMEYFPEIDWFLSE-SYEVYDMESLQELYEKKRA------EGHEGLVVKDP 203 (315)
T ss_pred eEeccccCCccccccccccHHHHHHHHHHHHhhCCCcceEeec-eEEcCCHHHHHHHHHHHHh------CCCceEEEeCC
Confidence 865421 11 12344444445433 1 22222 2245678899998876642 34689999988
Q ss_pred ChhhhhhhCCCCCCCCceEeecCCcceeeEEEEEEEEeecC-c--ceeeeEEEEEEEEECCEEEEEeeCCCHHHHHh
Q psy11423 303 CLSTQKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQIGR-T--GIITPVALLKPVLIDGITITRATLHNESEIYR 376 (655)
Q Consensus 303 ~~~~~~~lG~ts~~PrwaiA~Kf~~~~~~T~v~~I~~qvGR-T--G~itPvA~lePV~l~G~tVsratLhN~~~i~~ 376 (655)
+..++ -|.. ..|- -+| +....+..|.+..+-.|+ . |.+. +-+--. =+|. ...+|..+.+..++
T Consensus 204 ds~Y~--~Grr---~~~~-K~K-~~~~~d~vIvG~~~g~g~~~~~g~~~--~~~~~~-~~g~-l~~gtGfs~~~~~~ 269 (315)
T PHA00454 204 SLIYR--RGKK---SGWW-KMK-PECEADGTIVGVVWGTPGLANEGKVI--GFRVLL-EDGR-VVNATGISRALMEE 269 (315)
T ss_pred CCCCC--CCCc---cCcE-EEc-ccCceeEEEEEEEECCCCccCCceEE--EEEEEe-CCCc-EEEccCCCHHHHHH
Confidence 76654 2332 2362 444 334678888888887742 3 3332 211101 1343 33477777766654
No 41
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=97.98 E-value=8.5e-06 Score=93.31 Aligned_cols=51 Identities=22% Similarity=0.335 Sum_probs=49.8
Q ss_pred CCCCccHHHHHHHHHhCCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHhcC
Q psy11423 527 GIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQ 577 (655)
Q Consensus 527 gIpgIG~~~Ak~L~~~fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f~~ 577 (655)
+|||||+++.++|+++|||+++|..||.+||.+++||++++|+.|+++|+.
T Consensus 518 ~I~GiG~kr~~~LL~~Fgs~~~I~~As~eeL~~v~gi~~~~A~~I~~~l~~ 568 (574)
T PRK14670 518 KIKGIGEKKAKKILKSLGTYKDILLLNEDEIAEKMKINIKMAKKIKKFAEK 568 (574)
T ss_pred cCCCCCHHHHHHHHHHhCCHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHHH
Confidence 899999999999999999999999999999999999999999999999964
No 42
>PRK09247 ATP-dependent DNA ligase; Validated
Probab=97.97 E-value=0.00044 Score=79.36 Aligned_cols=219 Identities=16% Similarity=0.140 Sum_probs=137.9
Q ss_pred ceEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcccCCcccccCCCCceEEEEEEEEeeh------hhH
Q psy11423 118 IEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYK------KDF 191 (655)
Q Consensus 118 ~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~p~~~evRGEv~~~~------~~F 191 (655)
..|++|+|.||.-+.+...+|. ++..|| -|+|+|+....|...-.. .|..+.+-||++.-. ..|
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 578999877665443222 355689999998754 466
Q ss_pred HHHHHHHHHcCCCCCCChhhhHHhHhhhcCc--ccccccceEEEEEecccccCCCC-CCCHHHHHHHHHhCCCCC-----
Q psy11423 192 IKLNKYRYHLGLKKFTNPRNAAAGILRQLNP--KINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLSI----- 263 (655)
Q Consensus 192 ~~~n~~~~~~g~~~f~NpRN~aaG~lr~~d~--~~~~~r~L~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~GF~~----- 263 (655)
+.+... ++++.. ......++.|++|++....+.++ .....+..+.|+++ |..
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 655432 111111 11123579999999987655443 24677888888765 221
Q ss_pred ---CCCceeeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCcceeeEEEEEEEEe
Q psy11423 264 ---CGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQ 340 (655)
Q Consensus 264 ---~~~~~~~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~~~T~v~~I~~q 340 (655)
++ ...+.+.+++.++++...+ -...|+|+|--+..++ .|.. ...| +=+|-........|.+..|-
T Consensus 355 i~~~~-~~~~~~~~e~~~~~~~a~~------~g~EGlm~K~~~s~Y~--~Grr--~~~W-lK~K~~~~t~DlVvig~~~G 422 (539)
T PRK09247 355 LDLSP-LVPFSDWDELAALRAAARE------RGVEGLMLKRRDSPYL--VGRK--KGPW-WKWKRDPLTIDAVLMYAQRG 422 (539)
T ss_pred EEecC-ceecCCHHHHHHHHHHHHH------CCCceEEEecCCCCcC--CCCC--cchh-hcccCCCCcEEEEEEEeecC
Confidence 12 2335678899998876543 3479999998775543 2322 2223 23443334667777777776
Q ss_pred ecC-cceeee--EEEEEEEEECC--EEEEEe-eCCCHHHHHhcC
Q psy11423 341 IGR-TGIITP--VALLKPVLIDG--ITITRA-TLHNESEIYRKN 378 (655)
Q Consensus 341 vGR-TG~itP--vA~lePV~l~G--~tVsra-tLhN~~~i~~~~ 378 (655)
.|| +|.++. +|..+|=.=.+ ++|-++ |.++.++++++.
T Consensus 423 ~Gkr~g~~~~~lla~~~~~~~~~~~~~v~kvgsGftd~~l~~l~ 466 (539)
T PRK09247 423 HGRRASLYTDYTFGVWDGPEGGRQLVPFAKAYSGLTDEEIKQLD 466 (539)
T ss_pred CCCcCCccccEEEEEEcCCCCceeEEEEEEECCCCCHHHHHHHH
Confidence 665 465654 56655421001 256666 889988887763
No 43
>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=97.95 E-value=0.0002 Score=73.67 Aligned_cols=170 Identities=16% Similarity=0.140 Sum_probs=103.1
Q ss_pred CceEEEEEecceeEEEEEEe---CCEEeEEEecCCCCccchhhhhhhhcccC-Ccccc----cCCCCceEEEEEEEEeeh
Q psy11423 117 NIEYIAELKFDGIAVNLRYE---YGYLKQASTRGDGNIGENITTNIHIIHKI-PLVLN----IKYPPELLEVRCEVLIYK 188 (655)
Q Consensus 117 ~~~~~~e~KiDGlsi~l~Y~---~G~l~~a~TRGdG~~GeDvT~n~~~i~~i-P~~l~----~~~~p~~~evRGEv~~~~ 188 (655)
...|++|+|.||.-+.+.+. +|.-++..|| -|+|+|+....+..+ ...+. ....+..+.+-||+++-.
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 34699999999999999875 2445899999 789999865443211 11110 000135799999996532
Q ss_pred ------hhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCC-CCCHHHHHHHHHhCCC
Q psy11423 189 ------KDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGL 261 (655)
Q Consensus 189 ------~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~GF 261 (655)
..|+.+.... ..++..... ..++......++.|++|++....+.++ ..+..+..+.|.++--
T Consensus 97 ~~~g~~~~F~~L~~~~---------~~~~~~~~~--~~~~~~~~~~~v~~~vFDlL~lnG~~l~~~pl~eRr~~L~~l~~ 165 (235)
T cd08039 97 DRQGKIDPFHKIRKHV---------ERSGSFIGT--DNDSPPHEYEHLMIVFFDVLLLDDESLLSKPYSERRDLLESLVH 165 (235)
T ss_pred CCCCccCCHHHHHhhc---------ccccchhcc--ccccccccccceEEEEEEEEEECChhhhcCCHHHHHHHHHHhcc
Confidence 3787763210 111111000 111122234679999999987554433 2578888888988743
Q ss_pred CCCCCce-----ee-----CCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhh
Q psy11423 262 SICGEYS-----VL-----SGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQ 307 (655)
Q Consensus 262 ~~~~~~~-----~~-----~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~ 307 (655)
+++.... .+ .+.+++.++++...+. ..-|||+|--+..+.
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 3332211 11 2677888888765432 357999999886654
No 44
>PHA02587 30 DNA ligase; Provisional
Probab=97.95 E-value=0.00075 Score=76.58 Aligned_cols=235 Identities=14% Similarity=0.110 Sum_probs=130.8
Q ss_pred eEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcc----cCCcccccCCCCceEEEEEEEEeehhh----
Q psy11423 119 EYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIH----KIPLVLNIKYPPELLEVRCEVLIYKKD---- 190 (655)
Q Consensus 119 ~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~----~iP~~l~~~~~p~~~evRGEv~~~~~~---- 190 (655)
.|++|+|.||.-+.+...+|. ++..|| .|+|+|. ...|. .+...+.. .|..+.+-||++.-..+
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 699999999999999887665 799999 5778764 22221 11122211 24578999999976321
Q ss_pred HHHHHHHHHHcCCCCCC---ChhhhHHhHhh---hcCcccccccceEEEEEecccc----cCCCCCCCHHHHHHHHHhC-
Q psy11423 191 FIKLNKYRYHLGLKKFT---NPRNAAAGILR---QLNPKINKNKILHFFAHGVGEL----RGMNMPSSHSELLNWYQKI- 259 (655)
Q Consensus 191 F~~~n~~~~~~g~~~f~---NpRN~aaG~lr---~~d~~~~~~r~L~f~~y~~~~~----~~~~~~~~~~e~l~~L~~~- 259 (655)
|- ++--..+.+.+.|. -.|..-.|..+ +.........++.|++|++... .+........+..+.|.++
T Consensus 225 ~~-~~f~~~~~~~~~f~q~l~~R~~~~~i~~~~l~~~~~~~~~~pv~~~vFDiL~ld~y~~~~~~~~pl~eRr~~L~~l~ 303 (488)
T PHA02587 225 NG-LSFLFDDSKAKEFVGVVADRATGNGIVNKSLKGTISKEEAQEIVFQVWDIVPLEVYYGKEKSDMPYDDRFSKLAQMF 303 (488)
T ss_pred cc-chhhcccccccchhhhhhhhhhccchhhhhhccccchhhccceEEEEEEeechhhccCCccccCCHHHHHHHHHHHH
Confidence 00 00000000000000 01221122211 1111123456799999999731 1111125677777777665
Q ss_pred ---CCCCCCC--ceeeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCcceeeEEE
Q psy11423 260 ---GLSICGE--YSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEALTKI 334 (655)
Q Consensus 260 ---GF~~~~~--~~~~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~~~T~v 334 (655)
+.+.... ...+.+.+++.+++++..+ -...|+|+|--+..++ -| +...| +=+| +.......|
T Consensus 304 ~~~~~~~i~l~~~~~~~~~ee~~~~~~~a~~------~G~EGimlK~~ds~Y~--~G---Rs~~W-lKiK-~~~~~dlvV 370 (488)
T PHA02587 304 EDCGYDRVELIENQVVNNLEEAKEIYKRYVD------QGLEGIILKNTDGLWE--DG---RSKDQ-IKFK-EVIDIDLEI 370 (488)
T ss_pred hhcCCCcEEEEeeEEcCCHHHHHHHHHHHHh------CCCCeEEEECCCCCCC--CC---CCCCc-EEec-CCCceEEEE
Confidence 2111111 1236788999998876643 2468999998776654 24 22235 5566 345578889
Q ss_pred EEEEEeecCcceeeeEEEEEEEEECCEEEEE-eeCCCHHHHHhcC
Q psy11423 335 KAINIQIGRTGIITPVALLKPVLIDGITITR-ATLHNESEIYRKN 378 (655)
Q Consensus 335 ~~I~~qvGRTG~itPvA~lePV~l~G~tVsr-atLhN~~~i~~~~ 378 (655)
.++.++-+|.|.+.-...- .-+|.++-+ .|.+.-+.+++++
T Consensus 371 vG~~~~~k~~~~~gs~ll~---~~~g~~~~~vgsGftd~~~~~l~ 412 (488)
T PHA02587 371 VGVYEHKKDPNKVGGFTLE---SACGKITVNTGSGLTDTTHRKKD 412 (488)
T ss_pred EeEEeCCCCCCceeEEEEE---ecCCcEEEEECCCCChHHhhhhc
Confidence 9999987777665432211 114544434 4788888877653
No 45
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=97.94 E-value=1.4e-05 Score=80.88 Aligned_cols=51 Identities=22% Similarity=0.302 Sum_probs=49.5
Q ss_pred CCCCccHHHHHHHHHh-CCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHhcC
Q psy11423 527 GIRHVGETTAKELANY-FKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQ 577 (655)
Q Consensus 527 gIpgIG~~~Ak~L~~~-fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f~~ 577 (655)
.|||||++++++|+++ |+|++.|..|+.++|.+++|||.++|+.|+++|+.
T Consensus 7 ~IpGIG~krakkLl~~GF~Sve~Ik~AS~eEL~~V~GIg~k~AekI~e~l~~ 58 (232)
T PRK12766 7 DISGVGPSKAEALREAGFESVEDVRAADQSELAEVDGIGNALAARIKADVGG 58 (232)
T ss_pred cCCCcCHHHHHHHHHcCCCCHHHHHhCCHHHHHHccCCCHHHHHHHHHHhcc
Confidence 7899999999999999 99999999999999999999999999999999974
No 46
>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=97.92 E-value=0.00018 Score=72.83 Aligned_cols=157 Identities=15% Similarity=0.148 Sum_probs=96.0
Q ss_pred eEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhh-hhhccc-CCcccccCCCCceEEEEEEEEeehhhHHHHHH
Q psy11423 119 EYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTN-IHIIHK-IPLVLNIKYPPELLEVRCEVLIYKKDFIKLNK 196 (655)
Q Consensus 119 ~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n-~~~i~~-iP~~l~~~~~p~~~evRGEv~~~~~~F~~~n~ 196 (655)
.|++|+|+||.-+.+.+.+|. +++.||+ |.|+|.. +..+.. ++..+. ....+.+-||+++-...
T Consensus 35 ~~~~E~K~DG~R~~i~~~~~~-v~l~SR~----g~~~t~~~~~~~~~~~~~~~~---~~~~~iLDGEiv~~d~~------ 100 (213)
T cd07902 35 GMYAEIKYDGERVQVHKQGDN-FKFFSRS----LKPVLPHKVAHFKDYIPKAFP---HGHSMILDSEVLLVDTK------ 100 (213)
T ss_pred ceEEEeccCCEEEEEEEcCCE-EEEEcCC----CcccccchhHHHHHHHHHhcc---cccceeeeeEEEEEECC------
Confidence 599999999999988776554 7999995 8888853 322211 232222 13368999999984321
Q ss_pred HHHHcCCC-CCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCC-CCCHHHHHHHHHhCCCCCCCC-----cee
Q psy11423 197 YRYHLGLK-KFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLSICGE-----YSV 269 (655)
Q Consensus 197 ~~~~~g~~-~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~GF~~~~~-----~~~ 269 (655)
.|.+ .|.. .....+. .....++.|++|++....+.++ .....+..+.|.++--+.+.. ...
T Consensus 101 ----~g~~~~F~~----l~~~~~~----~~~~~~v~~~vFDiL~l~g~~l~~~pl~eR~~~L~~~~~~~~~~~~~~~~~~ 168 (213)
T cd07902 101 ----TGKPLPFGT----LGIHKKS----AFKDANVCLFVFDCLYYNGESLMDKPLRERRKILEDNMVEIPNRIMLSEMKF 168 (213)
T ss_pred ----CCcccccch----hhhhhcc----ccccCceEEEEEEEeeeCCcchhcCcHHHHHHHHHHhccCCCCeEEEEEEEE
Confidence 1111 1211 1000010 0123469999999987555332 246778888888763222221 123
Q ss_pred eCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhh
Q psy11423 270 LSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQ 307 (655)
Q Consensus 270 ~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~ 307 (655)
+.+.+++.++++.+.+. ...|+|+|--+..++
T Consensus 169 ~~~~~~l~~~~~~~~~~------g~EGvV~K~~~s~Y~ 200 (213)
T cd07902 169 VKKADDLSAMIARVIKE------GLEGLVLKDLKSVYE 200 (213)
T ss_pred cCCHHHHHHHHHHHHHC------CCCeEEEeCCCCCcc
Confidence 56888999988877532 368999999886654
No 47
>PRK09633 ligD ATP-dependent DNA ligase; Reviewed
Probab=97.89 E-value=0.0005 Score=79.71 Aligned_cols=217 Identities=16% Similarity=0.176 Sum_probs=128.3
Q ss_pred ceEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcccC----CcccccCCCCceEEEEEEEEee----hh
Q psy11423 118 IEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKI----PLVLNIKYPPELLEVRCEVLIY----KK 189 (655)
Q Consensus 118 ~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~i----P~~l~~~~~p~~~evRGEv~~~----~~ 189 (655)
-.|++|.|+||.-+.+.+.+|. ++..|| -|+|+|+....|... +..++. ...+.+-||++.- ..
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 899999 789999876654332 222211 1147899999984 46
Q ss_pred hHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCCC-CCHHHHHHHHHhC----CCCCC
Q psy11423 190 DFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMP-SSHSELLNWYQKI----GLSIC 264 (655)
Q Consensus 190 ~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~~-~~~~e~l~~L~~~----GF~~~ 264 (655)
+|+.+...... .++.+ +.+ .....++.|++|++....+.++. .+..+..+.|+++ +.+..
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 78776432110 11111 111 12345799999999876654432 4677777777665 21100
Q ss_pred ------CCceeeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCcceeeEEEEEEE
Q psy11423 265 ------GEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEALTKIKAIN 338 (655)
Q Consensus 265 ------~~~~~~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~~~T~v~~I~ 338 (655)
.....+.+.+++.++++...+ ....|||+|--+..++. ..++..| +-+|. ....+..|.+..
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 134456677788888776543 23599999988865531 2244556 34453 345566666654
Q ss_pred EeecCcceeeeEEEEEEEEECCE--EEEEe-eCCCHHHHHhc
Q psy11423 339 IQIGRTGIITPVALLKPVLIDGI--TITRA-TLHNESEIYRK 377 (655)
Q Consensus 339 ~qvGRTG~itPvA~lePV~l~G~--tVsra-tLhN~~~i~~~ 377 (655)
+ | .|.+. ++.. -+|. .|-++ |..+.+..+++
T Consensus 221 ~--~-~g~~l-lgv~----~~g~l~~vGkvgtGft~~~~~~L 254 (610)
T PRK09633 221 P--S-NGYFT-GSVY----KDGQLTEVGSVKHGMEDEERQTL 254 (610)
T ss_pred c--C-CceEE-EEEe----cCCeEEEEEEecCCCCHHHHHHH
Confidence 4 3 34321 2222 2454 34443 56666555443
No 48
>PRK01109 ATP-dependent DNA ligase; Provisional
Probab=97.89 E-value=0.00035 Score=81.07 Aligned_cols=216 Identities=17% Similarity=0.149 Sum_probs=134.6
Q ss_pred eEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcccCC-cccccCCCCceEEEEEEEEeehh------hH
Q psy11423 119 EYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIP-LVLNIKYPPELLEVRCEVLIYKK------DF 191 (655)
Q Consensus 119 ~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP-~~l~~~~~p~~~evRGEv~~~~~------~F 191 (655)
.|++|.|.||.-+.+.+.+|. ++..|| -|+|+|+....|...- ..+. +..+.+-||++.-.. .|
T Consensus 249 ~~~~E~K~DG~R~qih~~~~~-v~l~SR----~~~d~T~~~pel~~~~~~~~~----~~~~ILDGElv~~d~~~g~~~~F 319 (590)
T PRK01109 249 EALVEYKYDGERAQIHKKGDK-VKIFSR----RLENITHQYPDVVEYAKEAIK----AEEAIVEGEIVAVDPETGEMRPF 319 (590)
T ss_pred CeEEEecCCceEEEEEEcCCE-EEEEeC----CchhhccccchHHHHHHHhcC----ccceEEeeeEEEEECCCCcccCh
Confidence 589999999999998876664 799999 4999998876654322 1231 346899999987541 46
Q ss_pred HHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCC-CCCHHHHHHHHHhCCCCCCCCc---
Q psy11423 192 IKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLSICGEY--- 267 (655)
Q Consensus 192 ~~~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~GF~~~~~~--- 267 (655)
+.+-.. . |...... .....++.|++|++...++.++ ..+..+..+.|.++- ...+..
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 654221 0 1100000 1124579999999987665443 247788888888763 222221
Q ss_pred --eeeCCHHHHHHHHHHHHHhhcCCCCccceEEEEEC--ChhhhhhhCCCCCCCCceEeecCC-------cceeeEEEEE
Q psy11423 268 --SVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKIN--CLSTQKKLGFTSRAPRFALAYKFL-------SKEALTKIKA 336 (655)
Q Consensus 268 --~~~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~--~~~~~~~lG~ts~~PrwaiA~Kf~-------~~~~~T~v~~ 336 (655)
....+.+++.++++...+. ..-|||+|-- +..++ -| .+...| +|+- .+.....|.+
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 2356788999988766543 3689999997 65543 13 355677 5554 3456667888
Q ss_pred EEEeecC-cceeeeE--EEEEEEEECCE--EEEEe-eCCCHHHHHhc
Q psy11423 337 INIQIGR-TGIITPV--ALLKPVLIDGI--TITRA-TLHNESEIYRK 377 (655)
Q Consensus 337 I~~qvGR-TG~itPv--A~lePV~l~G~--tVsra-tLhN~~~i~~~ 377 (655)
..|--|| +|.+... |..+| =+|. +|.++ |..+.+.++++
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 7777665 5554432 22222 1232 44454 77887777665
No 49
>PRK09632 ATP-dependent DNA ligase; Reviewed
Probab=97.84 E-value=0.00089 Score=79.14 Aligned_cols=208 Identities=17% Similarity=0.163 Sum_probs=126.9
Q ss_pred ceEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcccCCcccccCCCCceEEEEEEEEee----hhhHHH
Q psy11423 118 IEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIY----KKDFIK 193 (655)
Q Consensus 118 ~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~p~~~evRGEv~~~----~~~F~~ 193 (655)
-.|++|.|+||.-+.+.+.+|. ++..|| .|.|+|+....|..+...+. ...+.+-||+++- ..+|+.
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 79999998766554444442 2368999999983 346765
Q ss_pred HHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCCC-CCHHHHHHHHHhCCCCCCCCceeeCC
Q psy11423 194 LNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMP-SSHSELLNWYQKIGLSICGEYSVLSG 272 (655)
Q Consensus 194 ~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~~-~~~~e~l~~L~~~GF~~~~~~~~~~~ 272 (655)
+... ....++.|++|++...++.++. ....+..+.|+++- ...+...+...
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 0124699999999876665432 46778888887763 21111122111
Q ss_pred -HHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCcceeeEEEEEEEEeecC-cceeeeE
Q psy11423 273 -VNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQIGR-TGIITPV 350 (655)
Q Consensus 273 -~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~~~T~v~~I~~qvGR-TG~itPv 350 (655)
..++.++++...+ -..-|||+|--+..++ -| .++..| +-+| +....+..|.+..+.-|| .|.+.-.
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-IKDK-HWRTQEVVIGGWRPGEGGRSSGIGSL 667 (764)
T ss_pred ecccHHHHHHHHHH------cCCcEEEEeCCCCCCC--CC--CcCCCe-EEEe-cCCceEEEEEEEEcCCCCcCCceeeE
Confidence 1234455554432 2468999999886654 12 224445 3445 234456677777776663 4444333
Q ss_pred --EEEEEEEECC-EEEEEe-eCCCHHHHHhc
Q psy11423 351 --ALLKPVLIDG-ITITRA-TLHNESEIYRK 377 (655)
Q Consensus 351 --A~lePV~l~G-~tVsra-tLhN~~~i~~~ 377 (655)
+..+. +| ..|-++ |..+.+..+++
T Consensus 668 LlGv~d~---~~L~yvGkVGTGftd~~l~~L 695 (764)
T PRK09632 668 LLGIPDP---GGLRYVGRVGTGFTERELASL 695 (764)
T ss_pred EEEEEcC---CeeEEEEEEeCCCCHHHHHHH
Confidence 22222 12 345566 77888777664
No 50
>PRK08609 hypothetical protein; Provisional
Probab=97.84 E-value=7.3e-06 Score=94.44 Aligned_cols=59 Identities=25% Similarity=0.245 Sum_probs=53.5
Q ss_pred cccccCCCCHHHHHHHHHcCCCCChHHHhc-CChhhhccccCCcHHHHHHHHHHHHHhcc
Q psy11423 458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYK-INFKNLLRLDRVSNKLANNILLAIQKSKL 516 (655)
Q Consensus 458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~-L~~~~L~~l~GfG~Ksa~nll~~I~~sk~ 516 (655)
..+.|+|+|||++.+||+...|+|++||.. +..++|..++|||+|++++|+++|+..+.
T Consensus 89 ~l~~i~GiGpk~a~~l~~~lGi~tl~~L~~a~~~~~~~~~~gfg~k~~~~il~~i~~~~~ 148 (570)
T PRK08609 89 PLLKLPGLGGKKIAKLYKELGVVDKESLKEACENGKVQALAGFGKKTEEKILEAVKELGK 148 (570)
T ss_pred HHhcCCCCCHHHHHHHHHHhCCCCHHHHHHHHHhCChhhccCcchhHHHHHHHHHHHHhc
Confidence 357899999999999999888999999998 67889999999999999999999987543
No 51
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=97.83 E-value=2.2e-05 Score=89.90 Aligned_cols=49 Identities=24% Similarity=0.407 Sum_probs=48.0
Q ss_pred CCCCccHHHHHHHHHhCCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHhc
Q psy11423 527 GIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFIN 576 (655)
Q Consensus 527 gIpgIG~~~Ak~L~~~fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f~ 576 (655)
+|||||+++.++|+++|||+++|..||.+||.++ ||++++|+.|+++|+
T Consensus 518 ~I~GiG~kr~~~Ll~~Fgs~~~ik~As~eeL~~v-gi~~~~A~~I~~~l~ 566 (567)
T PRK14667 518 KIKGIGEVKKEIIYRNFKTLYDFLKADDEELKKL-GIPPSVKQEVKKYLS 566 (567)
T ss_pred cCCCCCHHHHHHHHHHhCCHHHHHhCCHHHHHHc-CCCHHHHHHHHHHhc
Confidence 8999999999999999999999999999999999 999999999999985
No 52
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=97.66 E-value=7.3e-05 Score=86.57 Aligned_cols=51 Identities=24% Similarity=0.393 Sum_probs=49.8
Q ss_pred CCCCccHHHHHHHHHhCCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHhcC
Q psy11423 527 GIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQ 577 (655)
Q Consensus 527 gIpgIG~~~Ak~L~~~fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f~~ 577 (655)
+|||||++++++|+++|+|++.+..|+.++|.+++|||+++|++|.+||++
T Consensus 547 ~IpGIG~k~~k~Ll~~FgS~~~i~~As~eeL~~v~Gig~~~A~~I~~~l~~ 597 (598)
T PRK00558 547 DIPGIGPKRRKALLKHFGSLKAIKEASVEELAKVPGISKKLAEAIYEALHK 597 (598)
T ss_pred hCCCcCHHHHHHHHHHcCCHHHHHhCCHHHHhhcCCcCHHHHHHHHHHhcc
Confidence 999999999999999999999999999999999999999999999999975
No 53
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=97.61 E-value=9.2e-05 Score=60.76 Aligned_cols=57 Identities=21% Similarity=0.255 Sum_probs=44.4
Q ss_pred ccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHHHhccc
Q psy11423 459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKLT 517 (655)
Q Consensus 459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~sk~~ 517 (655)
+|+|+|+|+++.+.|.++= .+++.|...+.++|..+||+|++.|++|.+-++..++.
T Consensus 5 aLGI~~VG~~~ak~L~~~f--~sl~~l~~a~~e~L~~i~gIG~~~A~si~~ff~~~~n~ 61 (64)
T PF12826_consen 5 ALGIPGVGEKTAKLLAKHF--GSLEALMNASVEELSAIPGIGPKIAQSIYEFFQDPENR 61 (64)
T ss_dssp HCTSTT--HHHHHHHHHCC--SCHHHHCC--HHHHCTSTT--HHHHHHHHHHHH-HHHH
T ss_pred eCCCCCccHHHHHHHHHHc--CCHHHHHHcCHHHHhccCCcCHHHHHHHHHHHCCHHhh
Confidence 6999999999999998754 58999999999999999999999999999988776543
No 54
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=97.56 E-value=0.00012 Score=84.78 Aligned_cols=50 Identities=32% Similarity=0.426 Sum_probs=48.3
Q ss_pred CCCCccHHHHHHHHHhCCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHhcCh
Q psy11423 527 GIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQP 578 (655)
Q Consensus 527 gIpgIG~~~Ak~L~~~fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f~~~ 578 (655)
+|||||++++++|+++|||+++|..||.++|.++ ||+++|+.|+++|+.+
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 9999999999999864
No 55
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=97.55 E-value=0.00015 Score=74.71 Aligned_cols=54 Identities=24% Similarity=0.449 Sum_probs=51.4
Q ss_pred HhCCCCccHHHHHHHHHhCCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHhcCh
Q psy11423 525 ALGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQP 578 (655)
Q Consensus 525 algIpgIG~~~Ak~L~~~fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f~~~ 578 (655)
-..|||||...|++|+++|+|+..+..|+.++|..+.|||++.|..|+.||..+
T Consensus 184 l~s~pgig~~~a~~ll~~fgS~~~~~tas~~eL~~v~gig~k~A~~I~~~~~t~ 237 (254)
T COG1948 184 LESIPGIGPKLAERLLKKFGSVEDVLTASEEELMKVKGIGEKKAREIYRFLRTE 237 (254)
T ss_pred HHcCCCccHHHHHHHHHHhcCHHHHhhcCHHHHHHhcCccHHHHHHHHHHHhch
Confidence 348999999999999999999999999999999999999999999999999765
No 56
>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=97.50 E-value=0.0012 Score=66.78 Aligned_cols=156 Identities=20% Similarity=0.174 Sum_probs=97.6
Q ss_pred ceEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcccCCcccccCCCCceEEEEEEEEeehhhHHHHHHH
Q psy11423 118 IEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNKY 197 (655)
Q Consensus 118 ~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~p~~~evRGEv~~~~~~F~~~n~~ 197 (655)
..|++|+|.||+-+.+...+..-+.+.||+ |+++|.....+..+.. .. ..+....+-||++.....
T Consensus 41 ~~y~ve~K~DG~R~~l~~~~~~~v~l~sR~----~~~~~~~~~~~~~~~~-~~--~~~~~~ilDGElv~~~~~------- 106 (215)
T cd07895 41 NDYFVCEKSDGVRYLLLITGRGEVYLIDRK----NDVFKVPGLFFPRRKN-LE--PHHQGTLLDGELVIDKVP------- 106 (215)
T ss_pred CCeEEEEeEcCeEEEEEEecCCcEEEEeCC----CCeEEeccccCCCccc-cc--ccccCeeeEEEEEEEcCC-------
Confidence 479999999999998866541457999996 5567665544321101 11 123467899999965321
Q ss_pred HHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCC-CCCHHHHHHHHHhCCCCCCCC----------
Q psy11423 198 RYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLSICGE---------- 266 (655)
Q Consensus 198 ~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~GF~~~~~---------- 266 (655)
+ ..++.|++|++....+.++ .....+.++.|.++-......
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 2368999999987655433 246778888887764332110
Q ss_pred ----ceeeC---CHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeec
Q psy11423 267 ----YSVLS---GVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYK 324 (655)
Q Consensus 267 ----~~~~~---~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~K 324 (655)
..... ..+++.+..+.+ +..++...||+|+|-.+..+.- | +.+.| +=||
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 3467899999999999977642 2 56677 5555
No 57
>PRK05972 ligD ATP-dependent DNA ligase; Reviewed
Probab=97.49 E-value=0.0013 Score=78.70 Aligned_cols=179 Identities=18% Similarity=0.145 Sum_probs=112.2
Q ss_pred eEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcccCCcccccCCCCceEEEEEEEEee----hhhHHHH
Q psy11423 119 EYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIY----KKDFIKL 194 (655)
Q Consensus 119 ~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~p~~~evRGEv~~~----~~~F~~~ 194 (655)
.|++|.|+||.-+.+.+.+|. ++..|| .|+|+|+....|...-..+. .....+-|||++- ..+|+.+
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 68899988765543322221 2357899999983 4577765
Q ss_pred HHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCCC-CCHHHHHHHHHhCCCCC-CCCceeeCC
Q psy11423 195 NKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMP-SSHSELLNWYQKIGLSI-CGEYSVLSG 272 (655)
Q Consensus 195 n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~~-~~~~e~l~~L~~~GF~~-~~~~~~~~~ 272 (655)
.... +.. ...++.|++|++...++.++. ....+..+.|+++-=+. .+..++...
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 123689999999887665432 46788888888763111 122333332
Q ss_pred H-HHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCcceeeEEEEEEEEeecC
Q psy11423 273 V-NKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQIGR 343 (655)
Q Consensus 273 ~-~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~~~T~v~~I~~qvGR 343 (655)
+ .+..++++...+ -...|||+|--|..++- | ++..| +=+|.- ...+..|-+....-|+
T Consensus 377 ~~~~g~~ll~~a~~------~GlEGIVaKr~dS~Y~~--G---Rs~~W-lKiK~~-~~~E~VIgGy~~~~Gk 435 (860)
T PRK05972 377 FDAGGDAVLASACR------LGLEGVIGKRADSPYVS--G---RSEDW-IKLKCR-ARQEFVIGGYTDPKGS 435 (860)
T ss_pred ecchHHHHHHHHHH------cCCceEEEeCCCCCCCC--C---CCCCc-EEEecC-CCceEEEEEEeCCCCc
Confidence 2 234455554432 33689999998877652 3 45556 344432 3345666666665554
No 58
>PLN03113 DNA ligase 1; Provisional
Probab=97.49 E-value=0.0033 Score=74.44 Aligned_cols=221 Identities=16% Similarity=0.152 Sum_probs=130.7
Q ss_pred ceEEEEEecceeEEEEEEe-CCEEeEEEecCCCCccchhhhhhhhcccCCcccccCCCCceEEEEEEEEeeh------hh
Q psy11423 118 IEYIAELKFDGIAVNLRYE-YGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYK------KD 190 (655)
Q Consensus 118 ~~~~~e~KiDGlsi~l~Y~-~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~p~~~evRGEv~~~~------~~ 190 (655)
..|+||.|.||.-+.+.|. +|. ++..|| -|+|+|+....+-..-..+... ....+.+-||++.-. -.
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 4799999999999999985 665 799999 6899998876543321122100 124689999999753 35
Q ss_pred HHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCCC-CCHHHHHHHHHhCCCCC-CCCce
Q psy11423 191 FIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMP-SSHSELLNWYQKIGLSI-CGEYS 268 (655)
Q Consensus 191 F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~~-~~~~e~l~~L~~~GF~~-~~~~~ 268 (655)
|+.+-.. .|..+. + .....++.||+|++....|.++. .+..+..+.|.++ |.. +....
T Consensus 465 Fq~Lq~R-----------~rk~~~--~------~~~~~pv~~~aFDlLylnG~~L~~~PL~eRR~~L~~~-~~~~~~~i~ 524 (744)
T PLN03113 465 FQILSTR-----------ARKNVV--M------SDIKVDVCIFAFDMLYLNGQPLIQEQLKIRREHLYES-FEEDPGFFQ 524 (744)
T ss_pred HHHHHhh-----------hccccc--h------hccccceEEEEEeccccCccChhcCCHHHHHHHHHHH-hccCCCcEE
Confidence 7655331 011000 0 01135799999999876665432 4677888888775 432 22222
Q ss_pred e-----eCCHHHHHHHHHHHHHhhcCCCCccceEEEEEC--ChhhhhhhCCCCCCCCceEeecCCc-----ceeeEEEEE
Q psy11423 269 V-----LSGVNKLIEFYKKINIKRFNLPYEIDGVVYKIN--CLSTQKKLGFTSRAPRFALAYKFLS-----KEALTKIKA 336 (655)
Q Consensus 269 ~-----~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~--~~~~~~~lG~ts~~PrwaiA~Kf~~-----~~~~T~v~~ 336 (655)
+ ..+.+++.+|++...+ ...-|||+|-- +..++ ...+...| +=+|-.. ......|.+
T Consensus 525 ~~~~~~~~~~ee~~~~~~~ai~------~g~EGlmvK~l~~dS~Y~----pGkRs~~W-lKlK~dy~~~~~dtlDlVvIG 593 (744)
T PLN03113 525 FATAITSNDLEEIQKFLDAAVD------ASCEGLIIKTLNKDATYE----PSKRSNNW-LKLKKDYMESIGDSLDLVPIA 593 (744)
T ss_pred EeeeeccCCHHHHHHHHHHHHH------cCCceEEEeccCCCCCcc----CCCCCCCe-EEEechhhccccccccEEEEE
Confidence 2 3568899998876643 34789999972 22222 12344556 2344221 244555566
Q ss_pred EEEeec-CcceeeeE--EEEEEEEECC--EEEEEe-eCCCHHHHHhc
Q psy11423 337 INIQIG-RTGIITPV--ALLKPVLIDG--ITITRA-TLHNESEIYRK 377 (655)
Q Consensus 337 I~~qvG-RTG~itPv--A~lePV~l~G--~tVsra-tLhN~~~i~~~ 377 (655)
-.|--| |+|.++.. |..+|- +| .+|-++ |.+.-++++++
T Consensus 594 a~~G~GkR~g~~g~fLla~yd~~--~~~~~~v~KvgTGfsd~~l~~l 638 (744)
T PLN03113 594 AFHGRGKRTGVYGAFLLACYDSN--KEEFQSICKIGTGFSEAVLEER 638 (744)
T ss_pred EEeCCCCcCCccceEEEEEEcCC--CCEEEEeeEECCCCCHHHHHHH
Confidence 666555 56655543 344442 12 244455 77777776653
No 59
>PRK14973 DNA topoisomerase I; Provisional
Probab=97.49 E-value=0.00052 Score=83.05 Aligned_cols=127 Identities=16% Similarity=0.141 Sum_probs=102.2
Q ss_pred Hhhccccc----cccccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHHHh--cccch--
Q psy11423 448 KAGLQHFS----SRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKS--KLTTF-- 519 (655)
Q Consensus 448 ~~~i~~F~----sk~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~s--k~~~l-- 519 (655)
.+++.-|+ -...|.++|+-+.++++||+.|+ +++.|+-....+.|+.++|+.+-.+.++....... +..+-
T Consensus 789 ~~~~~~~a~~~~~~~~~~~~gv~~~~~~~~~~~G~-~~~~d~~~a~p~~La~~~g~~~~~~~~~~~~~~~~~~~~~~~~~ 867 (936)
T PRK14973 789 AASLLAEAKSLCNISRLKEIGVPAVSLKKYQEAGF-DTPEDFCSVHPAYLALKTGISPETICRHAKLVCEKLGRPVPEKI 867 (936)
T ss_pred HHHHHHHHHHHHHHHhhcccCCCHHHHHHHHHhcC-CCHHHHHhcCHHHHhcCCCCChhhHHHHHHHHHHHhcCCCchhh
Confidence 34555555 34489999999999999999996 99999999999999999999999998886655422 11110
Q ss_pred -------hHHHHHhCCCCccHHHHHHHHH-hCCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHhc
Q psy11423 520 -------SRFIYALGIRHVGETTAKELAN-YFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFIN 576 (655)
Q Consensus 520 -------~r~L~algIpgIG~~~Ak~L~~-~fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f~ 576 (655)
.+. ..+.|+|+|+++..+|.. -+.+.+.|.+++.++|....||+.+.+..++.+..
T Consensus 868 ~~~~~~~~~~-el~~vkg~ge~t~~~l~~ag~~~~e~l~~~d~~~la~~~~i~~k~~~~~~~~~~ 931 (936)
T PRK14973 868 SKAAFERGRA-ELLSVPGLGETTLEKLYLAGVYDGDLLVSADPKKLAKVTGIDEKKLRNLQAYAK 931 (936)
T ss_pred hhhhhcccch-hhhhccCCCHHHHHHHHHcCCCCHHHhccCCHHHHhhhcCCCHHHHHHHHHHHh
Confidence 011 035799999999988776 47789999999999999999999999999988764
No 60
>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=97.46 E-value=0.00042 Score=82.20 Aligned_cols=121 Identities=17% Similarity=0.224 Sum_probs=89.2
Q ss_pred hhccccccccccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHHHhcc-cchhHHHHHhC
Q psy11423 449 AGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKL-TTFSRFIYALG 527 (655)
Q Consensus 449 ~~i~~F~sk~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~sk~-~~l~r~L~alg 527 (655)
..|..|.|- . .|+|+||++++++++.-....+.-|.+ ..+.|..++|+|+|.++.|.++++..+. ..+..||..+|
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 344445442 2 599999999999999877555544433 4678999999999999999999987653 44556777767
Q ss_pred CCCccHHHHHHHHHhCCC--HHHHHhcCHHHHh-cCCCCCHHHHHHHHHHhc
Q psy11423 528 IRHVGETTAKELANYFKN--LECMFKATEEQLL-NIPKIGSTTVKAFIKFIN 576 (655)
Q Consensus 528 IpgIG~~~Ak~L~~~fgs--l~~l~~as~eeL~-~i~GIG~~~A~~I~~~f~ 576 (655)
|+ ...|.+|.++||+ ++.|. .++=.|. .++|||-++|.+|...+.
T Consensus 155 i~---~~~a~ki~~~yg~~~~~~i~-~nPY~L~~~i~gigF~~aD~iA~~~g 202 (720)
T TIGR01448 155 IG---IKLAQRIYKFYQADTLDRVE-KDPYLLAEDVKGIGFLTADQLAQALG 202 (720)
T ss_pred CC---HHHHHHHHHHHhHHHHHHHH-hCchhhhhhcCCCCHHHHHHHHHHcC
Confidence 65 7899999999984 23333 3443455 699999999999987653
No 61
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=97.43 E-value=0.00023 Score=82.65 Aligned_cols=50 Identities=30% Similarity=0.450 Sum_probs=48.7
Q ss_pred CCCCccHHHHHHHHHhCCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHhc
Q psy11423 527 GIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFIN 576 (655)
Q Consensus 527 gIpgIG~~~Ak~L~~~fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f~ 576 (655)
.|||||++++++|+++|||+++|..|+.++|.+++|||+++|+.|+++|+
T Consensus 641 ~IPGIGpkr~k~LL~~FGSle~I~~AS~eELa~V~Gig~k~Ae~I~~~L~ 690 (694)
T PRK14666 641 RVEGIGPATARLLWERFGSLQAMAAAGEEGLAAVPGIGPARAAALHEHLK 690 (694)
T ss_pred hCCCCCHHHHHHHHHHhCCHHHHHhcCHHHHHhcCCcCHHHHHHHHHHHH
Confidence 89999999999999999999999999999999999999999999999985
No 62
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=97.42 E-value=0.0002 Score=82.83 Aligned_cols=50 Identities=20% Similarity=0.291 Sum_probs=47.6
Q ss_pred CCCCccHHHHHHHHHhCCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHhc
Q psy11423 527 GIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFIN 576 (655)
Q Consensus 527 gIpgIG~~~Ak~L~~~fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f~ 576 (655)
.|||||++++++|+++|||+++|..||.++|.+++||+.++|+.|+.--.
T Consensus 612 ~IpGiG~kr~~~LL~~FgS~~~i~~As~eel~~v~gi~~~~A~~i~~~~~ 661 (691)
T PRK14672 612 RLPHVGKVRAHRLLAHFGSFRSLQSATPQDIATAIHIPLTQAHTILHAAT 661 (691)
T ss_pred cCCCCCHHHHHHHHHHhcCHHHHHhCCHHHHHhCCCCCHHHHHHHHHHhh
Confidence 89999999999999999999999999999999999999999999987543
No 63
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=97.40 E-value=0.00024 Score=82.51 Aligned_cols=49 Identities=29% Similarity=0.451 Sum_probs=47.4
Q ss_pred hCCCCccHHHHHHHHHhCCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHhc
Q psy11423 526 LGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFIN 576 (655)
Q Consensus 526 lgIpgIG~~~Ak~L~~~fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f~ 576 (655)
.+|||||+++++.|+++|+|++.|..|+.++|.++ ||+++|++|.+||+
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 49999999999999999999999999999999999 99999999999986
No 64
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]
Probab=97.32 E-value=0.00029 Score=80.90 Aligned_cols=48 Identities=21% Similarity=0.302 Sum_probs=46.5
Q ss_pred CCCCccHHHHHHHHHhCCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHh
Q psy11423 527 GIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFI 575 (655)
Q Consensus 527 gIpgIG~~~Ak~L~~~fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f 575 (655)
+|||||+++.++|+++|||++.|..||.+||.++ ||+.++|+.|+++|
T Consensus 534 ~I~GiG~~r~~~LL~~Fgs~~~i~~As~eel~~v-gi~~~~a~~i~~~~ 581 (581)
T COG0322 534 DIPGIGPKRRKALLKHFGSLKGIKSASVEELAKV-GISKKLAEKIYEAL 581 (581)
T ss_pred cCCCcCHHHHHHHHHHhhCHHHHHhcCHHHHHHc-CCCHHHHHHHHhhC
Confidence 8999999999999999999999999999999999 99999999998864
No 65
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=97.26 E-value=0.00046 Score=74.25 Aligned_cols=51 Identities=20% Similarity=0.304 Sum_probs=48.1
Q ss_pred CCCCccHHHHHHHHHhCCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHhcC
Q psy11423 527 GIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQ 577 (655)
Q Consensus 527 gIpgIG~~~Ak~L~~~fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f~~ 577 (655)
.||++++..|++|.++|||+..+.+|+.++|.+++|||++.|..|.+.+..
T Consensus 291 ~IPrl~k~iAk~Ll~~FGSL~~Il~As~eeL~~VeGIGe~rA~~I~e~l~R 341 (352)
T PRK13482 291 KIPRLPSAVIENLVEHFGSLQGLLAASIEDLDEVEGIGEVRARAIREGLSR 341 (352)
T ss_pred cCCCCCHHHHHHHHHHcCCHHHHHcCCHHHHhhCCCcCHHHHHHHHHHHHH
Confidence 799999999999999999999999999999999999999999998877653
No 66
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=97.23 E-value=0.00084 Score=67.06 Aligned_cols=57 Identities=16% Similarity=0.261 Sum_probs=44.5
Q ss_pred cccccCCCCHHHHHHHHHcCCCCCh-HHHhcCChhhhccccCCcHHHHHHHHHHHHHh
Q psy11423 458 KAMNIIGLGKKMIEKLVNANIVVTA-VDLYKINFKNLLRLDRVSNKLANNILLAIQKS 514 (655)
Q Consensus 458 ~~l~I~GLG~k~i~~L~~~g~I~~i-~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~s 514 (655)
..++|+|+|||++.++++.-....+ ..+..-+.+.|.++||+|+|+|++|+..+...
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 3678999999999999986533322 22334567889999999999999999998753
No 67
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=97.18 E-value=0.00056 Score=69.39 Aligned_cols=54 Identities=24% Similarity=0.316 Sum_probs=50.5
Q ss_pred cccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHH
Q psy11423 458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQ 512 (655)
Q Consensus 458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~ 512 (655)
...+|+|+|++++.+|++.|+ .|+.+|-..+.++|.+++|+|++.|++|++.+.
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 68
>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=97.18 E-value=0.00061 Score=47.47 Aligned_cols=30 Identities=33% Similarity=0.667 Sum_probs=26.3
Q ss_pred CHHHHHhcCHHHHhcCCCCCHHHHHHHHHH
Q psy11423 545 NLECMFKATEEQLLNIPKIGSTTVKAFIKF 574 (655)
Q Consensus 545 sl~~l~~as~eeL~~i~GIG~~~A~~I~~~ 574 (655)
+++.+..++.++|.++||||+++|+.|.+|
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 467788999999999999999999999876
No 69
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=97.08 E-value=0.00074 Score=77.89 Aligned_cols=49 Identities=27% Similarity=0.415 Sum_probs=47.3
Q ss_pred CCCCccHHHHHHHHHhCCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHh
Q psy11423 527 GIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFI 575 (655)
Q Consensus 527 gIpgIG~~~Ak~L~~~fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f 575 (655)
.|||||++++++|+++|||++++..|+.++|.++||+|+++|+.|.+++
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 8999999999999999999999999999999999999999999998764
No 70
>PLN03122 Poly [ADP-ribose] polymerase; Provisional
Probab=97.07 E-value=0.00053 Score=81.36 Aligned_cols=50 Identities=24% Similarity=0.372 Sum_probs=46.0
Q ss_pred CCCCeEecccccCccEEEecCC---CC-chHHHHHHcCCeeeCHHHHHHHHhcc
Q psy11423 600 TKGGKVVNFISKNTNYLVKGQK---PG-KKLEKAIKLNIKILDEKNFVKIVKGF 649 (655)
Q Consensus 600 ~~G~~v~~sVsk~t~ylv~g~~---~g-~K~~kA~~lgi~ii~e~~f~~~l~~~ 649 (655)
.+||+++++|+++|++|++|+. +| +|+++|+++||+|++|++|.+++...
T Consensus 214 ~~GGkvsssVs~~T~lIvt~~ev~k~gsSKlkkAk~lgIpIVsEd~L~d~i~~~ 267 (815)
T PLN03122 214 KHGGKVANSVEGVTCLVVSPAERERGGSSKIAEAMERGIPVVREAWLIDSIEKQ 267 (815)
T ss_pred HcCCEEccccccceEEEEcCccccccCccHHHHHHHcCCcCccHHHHHHHHhcC
Confidence 7899999999999999888876 66 89999999999999999999999754
No 71
>PF12738 PTCB-BRCT: twin BRCT domain; PDB: 3PA6_A 3KTF_C 2WT8_C 3EF1_A 3EF0_A.
Probab=97.05 E-value=0.00064 Score=55.08 Aligned_cols=41 Identities=29% Similarity=0.396 Sum_probs=35.2
Q ss_pred CCCCeEecccccCccEEEecCCCCchHHHHHHcCCeeeCHH
Q psy11423 600 TKGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDEK 640 (655)
Q Consensus 600 ~~G~~v~~sVsk~t~ylv~g~~~g~K~~kA~~lgi~ii~e~ 640 (655)
.+||.+...+++++++|||++..|.|.++|++.||||++.+
T Consensus 22 ~~Gg~~~~~lt~~~THLI~~~~~~~K~~~A~~~gi~vV~~~ 62 (63)
T PF12738_consen 22 ALGGKYSKDLTKKTTHLICSSPEGKKYRKAKEWGIPVVSPD 62 (63)
T ss_dssp CTT-EEESSSSTT-SEEEEES--HHHHHHHHHCTSEEEEHH
T ss_pred HCCCEEeccccCCceEEEEeCCCcHHHHHHHHCCCcEECCC
Confidence 88999999999999999998888899999999999999875
No 72
>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=97.04 E-value=0.011 Score=64.30 Aligned_cols=168 Identities=24% Similarity=0.205 Sum_probs=98.0
Q ss_pred eccccccCCCCCCChHHHHHHHHHHHHhhccCCCceEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcc
Q psy11423 84 HHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIH 163 (655)
Q Consensus 84 ~H~~pMlSL~k~~~~~el~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~ 163 (655)
+|-..++.|+.. +.+.+. ...+++|.|+||-.+.+..-+|++ .|.||| |.+=-==|+.++..-
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 566788888875 222222 235999999999999998889985 899999 332110112333332
Q ss_pred cCCcccccCCCCceEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCC
Q psy11423 164 KIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGM 243 (655)
Q Consensus 164 ~iP~~l~~~~~p~~~evRGEv~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~ 243 (655)
+ ..+-. +.| ++.+-||++=+..- |+ ..+... ...+..||+|++-+.+..
T Consensus 123 ~--~~~~~-d~p-~l~LcGE~iGpenp---------------Y~-----------~hs~~y-~~l~~~FfvFDI~d~~t~ 171 (374)
T TIGR01209 123 D--LEFFD-DNP-DLVLCGEMAGPENP---------------YT-----------PEYYPE-VKEDLGFFLFDIREGKTN 171 (374)
T ss_pred h--HHhhc-cCC-CeEEEEEEcCCCCC---------------Cc-----------ccCccc-cCCCceEEEEEEEECCCC
Confidence 2 23322 133 58899998733111 10 000111 122689999998643222
Q ss_pred CCCCCHHHHHHHHHhCCCCCCCCceeeCCHHHHH-HHHHHHHHhhcCCCCccceEEEEECCh
Q psy11423 244 NMPSSHSELLNWYQKIGLSICGEYSVLSGVNKLI-EFYKKINIKRFNLPYEIDGVVYKINCL 304 (655)
Q Consensus 244 ~~~~~~~e~l~~L~~~GF~~~~~~~~~~~~~ev~-~~~~~~~~~r~~l~y~iDGiVikv~~~ 304 (655)
. +-+..+..+++..+||+.++....+ +.+++. +..+.+.+.-... --|||+|-.+-
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 4688899999999999988754343 334433 3332222211111 47999997653
No 73
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=96.95 E-value=0.003 Score=63.21 Aligned_cols=90 Identities=14% Similarity=0.212 Sum_probs=63.1
Q ss_pred hhhhccccCCcHHHHHHHHHHHHHhcccchhHHHHHhCCCCccHHHHHHHHHhCCCHHHH----HhcCHHHHhcCCCCCH
Q psy11423 490 FKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECM----FKATEEQLLNIPKIGS 565 (655)
Q Consensus 490 ~~~L~~l~GfG~Ksa~nll~~I~~sk~~~l~r~L~algIpgIG~~~Ak~L~~~fgsl~~l----~~as~eeL~~i~GIG~ 565 (655)
.||-..|=||..+....+.. .-++++|||+++|..++..|+ .+.+ ..-+.+.|.++||||+
T Consensus 54 rEd~~~LyGF~~~~Er~lF~--------------~Li~V~GIGpK~Al~ILs~~~-~~~l~~aI~~~D~~~L~~vpGIGk 118 (194)
T PRK14605 54 REDALSLFGFATTEELSLFE--------------TLIDVSGIGPKLGLAMLSAMN-AEALASAIISGNAELLSTIPGIGK 118 (194)
T ss_pred ecCCceeeCCCCHHHHHHHH--------------HHhCCCCCCHHHHHHHHHhCC-HHHHHHHHHhCCHHHHHhCCCCCH
Confidence 46667777998776654442 234899999999999999987 5543 4457889999999999
Q ss_pred HHHHHHHHHhcCh---------------hHHHHHHHHHHcCccc
Q psy11423 566 TTVKAFIKFINQP---------------LHRLLISQLRDVGIYW 594 (655)
Q Consensus 566 ~~A~~I~~~f~~~---------------~n~~li~~L~~~Gi~~ 594 (655)
++|++|+--+.+. ...+++..|...|++.
T Consensus 119 KtAerIilELk~Ki~~~~~~~~~~~~~~~~~e~~~aL~~LGy~~ 162 (194)
T PRK14605 119 KTASRIVLELKDKIAKNWEAGVLSQVTEANSDILATLTALGYSS 162 (194)
T ss_pred HHHHHHHHHHHHHHHhhhhccccccccchHHHHHHHHHHcCCCH
Confidence 9999955322211 2234566666667653
No 74
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=96.84 E-value=0.0041 Score=62.19 Aligned_cols=72 Identities=15% Similarity=0.166 Sum_probs=54.6
Q ss_pred hhhhccccCCcHHHHHHHHHHHHHhcccchhHHHHHhCCCCccHHHHHHHHHhCCCHHHHHhc----CHHHHhcCCCCCH
Q psy11423 490 FKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKA----TEEQLLNIPKIGS 565 (655)
Q Consensus 490 ~~~L~~l~GfG~Ksa~nll~~I~~sk~~~l~r~L~algIpgIG~~~Ak~L~~~fgsl~~l~~a----s~eeL~~i~GIG~ 565 (655)
.||-..|=||..+....+.. .-+++.|||+++|-.++..+. +++|..| +...|.++||||+
T Consensus 53 rED~~~LYGF~t~~Er~lF~--------------~LisVsGIGPK~ALaILs~~~-~~el~~aI~~~D~~~L~~vpGIGk 117 (196)
T PRK13901 53 REDELKLFGFLNSSEREVFE--------------ELIGVDGIGPRAALRVLSGIK-YNEFRDAIDREDIELISKVKGIGN 117 (196)
T ss_pred ecCCceeeCCCCHHHHHHHH--------------HHhCcCCcCHHHHHHHHcCCC-HHHHHHHHHhCCHHHHhhCCCCCH
Confidence 46666777898776654442 224889999999999999874 6655554 7889999999999
Q ss_pred HHHHHHHHHhc
Q psy11423 566 TTVKAFIKFIN 576 (655)
Q Consensus 566 ~~A~~I~~~f~ 576 (655)
|+|++|+--+.
T Consensus 118 KtAeRIIlELk 128 (196)
T PRK13901 118 KMAGKIFLKLR 128 (196)
T ss_pred HHHHHHHHHHH
Confidence 99999875443
No 75
>PRK00254 ski2-like helicase; Provisional
Probab=96.83 E-value=0.0026 Score=75.64 Aligned_cols=54 Identities=24% Similarity=0.456 Sum_probs=50.6
Q ss_pred HhCCCCccHHHHHHHHHh-CCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHhcCh
Q psy11423 525 ALGIRHVGETTAKELANY-FKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQP 578 (655)
Q Consensus 525 algIpgIG~~~Ak~L~~~-fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f~~~ 578 (655)
-..|||+|++++++|.++ |+|+++|..|+.++|.+++|||+++|++|+++++..
T Consensus 647 L~~ipgig~~~~~~l~~~g~~s~~~i~~a~~~el~~~~gi~~~~a~~i~~~~~~~ 701 (720)
T PRK00254 647 LMRLPMIGRKRARALYNAGFRSIEDIVNAKPSELLKVEGIGAKIVEGIFKHLGVE 701 (720)
T ss_pred hhcCCCCCHHHHHHHHHccCCCHHHHHhCCHHHHhcCCCCCHHHHHHHHHHhccc
Confidence 348999999999999999 999999999999999999999999999999998743
No 76
>PRK08609 hypothetical protein; Provisional
Probab=96.79 E-value=0.0027 Score=73.43 Aligned_cols=84 Identities=13% Similarity=0.185 Sum_probs=65.6
Q ss_pred hhhccccCCcHHHHHHHHHHHHHhcccch--------hHHHHHhCCCCccHHHHHHHHHh--CCCHHHHHhcCH-HHHhc
Q psy11423 491 KNLLRLDRVSNKLANNILLAIQKSKLTTF--------SRFIYALGIRHVGETTAKELANY--FKNLECMFKATE-EQLLN 559 (655)
Q Consensus 491 ~~L~~l~GfG~Ksa~nll~~I~~sk~~~l--------~r~L~algIpgIG~~~Ak~L~~~--fgsl~~l~~as~-eeL~~ 559 (655)
++|..+||+|++.|++|-+-++.-+-..+ ..++.-+.|||||++++++|-+. +.|+++|..+.. ..+..
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 37899999999999998887764222111 24555569999999999999875 568999998754 35889
Q ss_pred CCCCCHHHHHHHHHH
Q psy11423 560 IPKIGSTTVKAFIKF 574 (655)
Q Consensus 560 i~GIG~~~A~~I~~~ 574 (655)
++|+|+++.++|..-
T Consensus 128 ~~gfg~k~~~~il~~ 142 (570)
T PRK08609 128 LAGFGKKTEEKILEA 142 (570)
T ss_pred ccCcchhHHHHHHHH
Confidence 999999999998653
No 77
>PRK14973 DNA topoisomerase I; Provisional
Probab=96.77 E-value=0.013 Score=71.26 Aligned_cols=149 Identities=13% Similarity=0.243 Sum_probs=106.4
Q ss_pred CCCCCCCCCcceee--cC--ceeEEecCCCcCCHHHHHhhccccccccccccCCCCHHHHHHHHHcCCCCChHHHhcCCh
Q psy11423 415 PNICPICNSKIIYI--ES--NLIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINF 490 (655)
Q Consensus 415 P~~CP~C~~~l~~~--~~--~~~~~C~n~~~~C~~q~~~~i~~F~sk~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~ 490 (655)
...||.||.+++.. .| +-++-| + . |..... ..+.+-+++|+|+++.++|-.++ +.++.++-..+.
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 46799999964433 22 336667 3 3 743221 33367789999999999999888 588899988888
Q ss_pred hhhccccCCcHHHHHHHHHHHHH-----hcccchhHHHHHhCCCCccHHHHHHHHH----hCCCHHHHHhcCHHHHhcCC
Q psy11423 491 KNLLRLDRVSNKLANNILLAIQK-----SKLTTFSRFIYALGIRHVGETTAKELAN----YFKNLECMFKATEEQLLNIP 561 (655)
Q Consensus 491 ~~L~~l~GfG~Ksa~nll~~I~~-----sk~~~l~r~L~algIpgIG~~~Ak~L~~----~fgsl~~l~~as~eeL~~i~ 561 (655)
+++..--+.+.+.++++...-+. .+...+.+|+...-.|.=|...|+.+.. -..++.+|..|++..|..-
T Consensus 704 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~- 782 (936)
T PRK14973 704 EALAKSLGLSKKEAEKLIREAGDVLELLRRRSELRKFVRKHVPPRRGRSHAKIMKALISSGINDIAALARADPADLKKA- 782 (936)
T ss_pred hHhhhhcCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCccHHHHHHHHHhcCcchHHHHhhCCHHHHHHc-
Confidence 88887666777777777664332 2234577888888888888887764433 4567888999988877764
Q ss_pred CCCHHHHHHHHHHh
Q psy11423 562 KIGSTTVKAFIKFI 575 (655)
Q Consensus 562 GIG~~~A~~I~~~f 575 (655)
|+++.-+.++.++-
T Consensus 783 ~~sE~~~~~~~~~a 796 (936)
T PRK14973 783 GLSEAEAASLLAEA 796 (936)
T ss_pred CCCHHHHHHHHHHH
Confidence 88888887777655
No 78
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=96.76 E-value=0.0049 Score=61.40 Aligned_cols=90 Identities=17% Similarity=0.194 Sum_probs=64.4
Q ss_pred hhhhccccCCcHHHHHHHHHHHHHhcccchhHHHHHhCCCCccHHHHHHHHHhCCCHHHHHhc----CHHHHhcCCCCCH
Q psy11423 490 FKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKA----TEEQLLNIPKIGS 565 (655)
Q Consensus 490 ~~~L~~l~GfG~Ksa~nll~~I~~sk~~~l~r~L~algIpgIG~~~Ak~L~~~fgsl~~l~~a----s~eeL~~i~GIG~ 565 (655)
.||-..|=||..+....+.. .-+++.|||+++|-.++..+. ++++..| +...|.++||||+
T Consensus 54 rEd~~~LyGF~~~~Er~lF~--------------~Li~V~GIGpK~AL~iLs~~~-~~el~~aI~~~D~~~L~~vpGIGk 118 (188)
T PRK14606 54 SQDGITLYGFSNERKKELFL--------------SLTKVSRLGPKTALKIISNED-AETLVTMIASQDVEGLSKLPGISK 118 (188)
T ss_pred ecCCceeeCCCCHHHHHHHH--------------HHhccCCccHHHHHHHHcCCC-HHHHHHHHHhCCHHHHhhCCCCCH
Confidence 56677777898776554432 224789999999999998874 6655554 7889999999999
Q ss_pred HHHHHHHHHhcCh----------hHHHHHHHHHHcCccc
Q psy11423 566 TTVKAFIKFINQP----------LHRLLISQLRDVGIYW 594 (655)
Q Consensus 566 ~~A~~I~~~f~~~----------~n~~li~~L~~~Gi~~ 594 (655)
++|++|+--+.+. ...+.++.|...|.+.
T Consensus 119 KtAerIilELkdK~~~~~~~~~~~~~e~~~AL~~LGy~~ 157 (188)
T PRK14606 119 KTAERIVMELKDEFESAGIKDMRIYHESLEALVSLGYPE 157 (188)
T ss_pred HHHHHHHHHHHHhhccccCCCcccHHHHHHHHHHcCCCH
Confidence 9999988644432 1234566677777653
No 79
>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=96.71 E-value=0.003 Score=63.05 Aligned_cols=69 Identities=16% Similarity=0.178 Sum_probs=51.6
Q ss_pred hhhhccccCCcHHHHHHHHHHHHHhcccchhHHHHHhCCCCccHHHHHHHHHhCCCHHHHHhc----CHHHHhcCCCCCH
Q psy11423 490 FKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKA----TEEQLLNIPKIGS 565 (655)
Q Consensus 490 ~~~L~~l~GfG~Ksa~nll~~I~~sk~~~l~r~L~algIpgIG~~~Ak~L~~~fgsl~~l~~a----s~eeL~~i~GIG~ 565 (655)
.+|-..|=||..+....+. ..-+++||||+++|..|+..+. ++++..| +...|.++||||+
T Consensus 53 red~~~LyGF~~~~Er~lF--------------~~L~~V~GIGpK~Al~iL~~~~-~~el~~aI~~~d~~~L~~ipGiGk 117 (191)
T TIGR00084 53 REDAELLFGFNTLEERELF--------------KELIKVNGVGPKLALAILSNMS-PEEFVYAIETEEVKALVKIPGVGK 117 (191)
T ss_pred ecCCceeeCCCCHHHHHHH--------------HHHhCCCCCCHHHHHHHHhcCC-HHHHHHHHHhCCHHHHHhCCCCCH
Confidence 4566667788877554443 3335899999999999988875 6555544 5688999999999
Q ss_pred HHHHHHHH
Q psy11423 566 TTVKAFIK 573 (655)
Q Consensus 566 ~~A~~I~~ 573 (655)
++|++|.-
T Consensus 118 KtAerIil 125 (191)
T TIGR00084 118 KTAERLLL 125 (191)
T ss_pred HHHHHHHH
Confidence 99999973
No 80
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=96.70 E-value=0.0061 Score=60.42 Aligned_cols=90 Identities=19% Similarity=0.278 Sum_probs=64.4
Q ss_pred hhhhccccCCcHHHHHHHHHHHHHhcccchhHHHHHhCCCCccHHHHHHHHHhCCCHHHHHhc----CHHHHhcCCCCCH
Q psy11423 490 FKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKA----TEEQLLNIPKIGS 565 (655)
Q Consensus 490 ~~~L~~l~GfG~Ksa~nll~~I~~sk~~~l~r~L~algIpgIG~~~Ak~L~~~fgsl~~l~~a----s~eeL~~i~GIG~ 565 (655)
.||-..|=||..+....+.. .-+++.|||+++|-.++..+. .+++..| +...|.++||||+
T Consensus 54 rEd~~~LyGF~~~~Er~lF~--------------~Li~VsGIGpK~Al~ILs~~~-~~el~~aI~~~D~~~L~~vpGIGk 118 (183)
T PRK14601 54 KEDSNKLYGFLDKDEQKMFE--------------MLLKVNGIGANTAMAVCSSLD-VNSFYKALSLGDESVLKKVPGIGP 118 (183)
T ss_pred ecCCceeeCCCCHHHHHHHH--------------HHhccCCccHHHHHHHHcCCC-HHHHHHHHHhCCHHHHhhCCCCCH
Confidence 46677777898775544432 224789999999999998875 6666554 7788999999999
Q ss_pred HHHHHHHHHhcCh---------hHHHHHHHHHHcCccc
Q psy11423 566 TTVKAFIKFINQP---------LHRLLISQLRDVGIYW 594 (655)
Q Consensus 566 ~~A~~I~~~f~~~---------~n~~li~~L~~~Gi~~ 594 (655)
|+|++|+--+.+. ...+.++.|.+.|.+.
T Consensus 119 KtAeRIilELkdK~~~~~~~~~~~~ea~~AL~~LGy~~ 156 (183)
T PRK14601 119 KSAKRIIAELSDAKTKLENVSDDKSEALAALLTLGFKQ 156 (183)
T ss_pred HHHHHHHHHHHHHhhccCCCCccHHHHHHHHHHcCCCH
Confidence 9999987544332 1235666677777653
No 81
>PRK13766 Hef nuclease; Provisional
Probab=96.66 E-value=0.0025 Score=76.34 Aligned_cols=54 Identities=26% Similarity=0.451 Sum_probs=51.1
Q ss_pred hCCCCccHHHHHHHHHhCCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHhcChh
Q psy11423 526 LGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQPL 579 (655)
Q Consensus 526 lgIpgIG~~~Ak~L~~~fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f~~~~ 579 (655)
.+|||||++++++|+++|++++.+..++.++|..++|+|++.|+.|.+||+.+.
T Consensus 718 ~~ipgig~~~a~~Ll~~fgs~~~i~~as~~~L~~i~Gig~~~a~~i~~~~~~~~ 771 (773)
T PRK13766 718 ESLPDVGPVLARNLLEHFGSVEAVMTASEEELMEVEGIGEKTAKRIREVVTSEY 771 (773)
T ss_pred hcCCCCCHHHHHHHHHHcCCHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHhhhh
Confidence 389999999999999999999999999999999999999999999999998653
No 82
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=96.57 E-value=0.0081 Score=60.19 Aligned_cols=73 Identities=19% Similarity=0.228 Sum_probs=54.2
Q ss_pred hhhhccccCCcHHHHHHHHHHHHHhcccchhHHHHHhCCCCccHHHHHHHHHhCCCHHHHHhc----CHHHHhcCCCCCH
Q psy11423 490 FKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKA----TEEQLLNIPKIGS 565 (655)
Q Consensus 490 ~~~L~~l~GfG~Ksa~nll~~I~~sk~~~l~r~L~algIpgIG~~~Ak~L~~~fgsl~~l~~a----s~eeL~~i~GIG~ 565 (655)
.||-..|=||..+....+.. .-+++.|||+++|-.++..+. +++|..| +...|.++||||+
T Consensus 54 rEd~~~LyGF~~~~Er~lF~--------------~Li~V~GIGpK~Al~iLs~~~-~~el~~aI~~~D~~~L~kvpGIGk 118 (195)
T PRK14604 54 REDALTLYGFSTPAQRQLFE--------------LLIGVSGVGPKAALNLLSSGT-PDELQLAIAGGDVARLARVPGIGK 118 (195)
T ss_pred ecCCceeeCCCCHHHHHHHH--------------HHhCcCCcCHHHHHHHHcCCC-HHHHHHHHHhCCHHHHhhCCCCCH
Confidence 46666777888776654432 224789999999999998864 6555544 7788999999999
Q ss_pred HHHHHHHHHhcC
Q psy11423 566 TTVKAFIKFINQ 577 (655)
Q Consensus 566 ~~A~~I~~~f~~ 577 (655)
++|++|+--+++
T Consensus 119 KtAerIilELk~ 130 (195)
T PRK14604 119 KTAERIVLELKG 130 (195)
T ss_pred HHHHHHHHHHHH
Confidence 999998765543
No 83
>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=96.54 E-value=0.002 Score=64.34 Aligned_cols=52 Identities=21% Similarity=0.429 Sum_probs=43.0
Q ss_pred cccccCCCCHHHHHHHHHcCCCCChHHHhc-CCh---hhhccccCCcHHHHHHHHHHHH
Q psy11423 458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYK-INF---KNLLRLDRVSNKLANNILLAIQ 512 (655)
Q Consensus 458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~-L~~---~~L~~l~GfG~Ksa~nll~~I~ 512 (655)
..++|+|+|||++..+.. +-++.+|.. +.. +.|.++||||+|+|++|+-.+.
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 478999999999999955 347888887 444 7799999999999999994443
No 84
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=96.46 E-value=0.0084 Score=59.63 Aligned_cols=70 Identities=20% Similarity=0.248 Sum_probs=47.8
Q ss_pred hhhhccccCCcHHHHHHHHHHHHHhcccchhHHHHHhCCCCccHHHHHHHHHhCCCHHHHHhc----CHHHHhcCCCCCH
Q psy11423 490 FKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKA----TEEQLLNIPKIGS 565 (655)
Q Consensus 490 ~~~L~~l~GfG~Ksa~nll~~I~~sk~~~l~r~L~algIpgIG~~~Ak~L~~~fgsl~~l~~a----s~eeL~~i~GIG~ 565 (655)
.+|-..|=||..+....+.. .-+++.|||+++|-.++..+. ++++..| +...| ++||||+
T Consensus 54 rEd~~~LyGF~~~~Er~lF~--------------~LisV~GIGpK~Al~iLs~~~-~~~l~~aI~~~D~~~L-~vpGIGk 117 (186)
T PRK14600 54 RDNVTQLYGFLNREEQDCLR--------------MLVKVSGVNYKTAMSILSKLT-PEQLFSAIVNEDKAAL-KVNGIGE 117 (186)
T ss_pred ecCCceeeCCCCHHHHHHHH--------------HHhCcCCcCHHHHHHHHccCC-HHHHHHHHHcCCHhhe-ECCCCcH
Confidence 45555666787665544332 224778888888888888774 5555443 66778 8888888
Q ss_pred HHHHHHHHHh
Q psy11423 566 TTVKAFIKFI 575 (655)
Q Consensus 566 ~~A~~I~~~f 575 (655)
++|++|+--+
T Consensus 118 KtAerIilEL 127 (186)
T PRK14600 118 KLINRIITEL 127 (186)
T ss_pred HHHHHHHHHH
Confidence 8888887543
No 85
>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=96.44 E-value=0.0048 Score=51.00 Aligned_cols=51 Identities=24% Similarity=0.297 Sum_probs=43.0
Q ss_pred ccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHH
Q psy11423 461 NIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQ 512 (655)
Q Consensus 461 ~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~ 512 (655)
+-=||...+...|-..| |.++.||..++.++|..++|||+|+.+.|.+.++
T Consensus 15 ~~L~LS~Ra~n~L~~~~-I~tv~dL~~~s~~~L~~i~n~G~ksl~EI~~~L~ 65 (66)
T PF03118_consen 15 EDLGLSVRAYNCLKRAG-IHTVGDLVKYSEEDLLKIKNFGKKSLEEIKEKLK 65 (66)
T ss_dssp GGSTSBHHHHHHHHCTT---BHHHHHCS-HHHHHTSTTSHHHHHHHHHHHHH
T ss_pred HHhCCCHHHHHHHHHhC-CcCHHHHHhCCHHHHHhCCCCCHhHHHHHHHHHc
Confidence 34478899999998877 6999999999999999999999999999988775
No 86
>TIGR00596 rad1 DNA repair protein (rad1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit
Probab=96.37 E-value=0.005 Score=73.69 Aligned_cols=51 Identities=20% Similarity=0.353 Sum_probs=48.2
Q ss_pred hCCCCccHHHHHHHHHhCCCHHHHHhcCHHHHhcCCCCC-HHHHHHHHHHhcCh
Q psy11423 526 LGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIG-STTVKAFIKFINQP 578 (655)
Q Consensus 526 lgIpgIG~~~Ak~L~~~fgsl~~l~~as~eeL~~i~GIG-~~~A~~I~~~f~~~ 578 (655)
+.|||||++.|++|+.+|+|+.+|.+++.++|..+ +| ++.|+.|++||+.+
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 39999999999999999999999999999999996 77 99999999999865
No 87
>COG1423 ATP-dependent DNA ligase, homolog of eukaryotic ligase III [DNA replication, recombination, and repair]
Probab=96.36 E-value=0.083 Score=56.53 Aligned_cols=168 Identities=21% Similarity=0.167 Sum_probs=111.4
Q ss_pred eeccccccCCCCCCChHHHHHHHHHHHHhhccCCCceEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhc
Q psy11423 83 VHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHII 162 (655)
Q Consensus 83 v~H~~pMlSL~k~~~~~el~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i 162 (655)
.+|-..|+-|+.+ +++|. + -..++||.|+||-.+.+.=-+|. +-|+||| |.+====|+.++.+
T Consensus 68 fPkI~R~llL~p~-----ik~~F-------~---~~~v~VEEKmnGYNVRV~k~~g~-vyAiTRg-G~ICPfTT~r~~~l 130 (382)
T COG1423 68 FPKIRRALLLEPT-----IKKHF-------G---RGKVVVEEKMNGYNVRVVKLGGE-VYAITRG-GLICPFTTERLRDL 130 (382)
T ss_pred Cchhheeeccchh-----hHhhc-------C---CCcEEEEEeccCceEEEEEECCE-EEEEecC-ceecCchhHHHHhh
Confidence 3677788888875 44443 2 13799999999999999888887 5899998 66555557777654
Q ss_pred ccCCcccccCCCCceEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccC
Q psy11423 163 HKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRG 242 (655)
Q Consensus 163 ~~iP~~l~~~~~p~~~evRGEv~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~ 242 (655)
+|+.+-. ++| .+.+-||++=+ .||= + . .++- ...++.||.|++..-..
T Consensus 131 --~~~eff~-d~p-~lvlcgEmvG~-------------------enPY--v----~-~~~y--~~e~v~fFvFDire~~t 178 (382)
T COG1423 131 --IDLEFFD-DYP-DLVLCGEMVGP-------------------ENPY--V----P-GPYY--EKEDVGFFVFDIREKNT 178 (382)
T ss_pred --cchhhHh-hCC-CcEEEEEeccC-------------------CCCC--C----C-CCCC--ccCCceEEEEEEEecCC
Confidence 5666654 355 57899998733 2331 1 1 1111 23579999999976322
Q ss_pred CCCCCCHHHHHHHHHhCCCCCCCCceee--CCH-HHHHHHHHHHHHhhcCCCCccceEEEEECChhh
Q psy11423 243 MNMPSSHSELLNWYQKIGLSICGEYSVL--SGV-NKLIEFYKKINIKRFNLPYEIDGVVYKINCLST 306 (655)
Q Consensus 243 ~~~~~~~~e~l~~L~~~GF~~~~~~~~~--~~~-~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~ 306 (655)
. .+-++.+.++.+.+.||+.+..--.. +.. ++|.+.++++.+.. --|||+|-.|-..
T Consensus 179 g-r~Lp~eer~~l~ekYgl~~V~~fg~~~~~e~~eei~eIve~L~keG------REGVV~Kdpdm~~ 238 (382)
T COG1423 179 G-RPLPVEERLELAEKYGLPHVEIFGEFPADEAGEEIYEIVERLNKEG------REGVVMKDPDMRV 238 (382)
T ss_pred C-CCCCHHHHHHHHHHcCCCceEEeeeechhHhHHHHHHHHHHHhhcC------CcceEecCccccc
Confidence 2 25789999999999999877532222 122 45555556554432 3799999887543
No 88
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=96.35 E-value=0.0075 Score=60.82 Aligned_cols=73 Identities=16% Similarity=0.200 Sum_probs=55.9
Q ss_pred hhhhccccCCcHHHHHHHHHHHHHhcccchhHHHHHhCCCCccHHHHHHHHHhCCCHHHHH----hcCHHHHhcCCCCCH
Q psy11423 490 FKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMF----KATEEQLLNIPKIGS 565 (655)
Q Consensus 490 ~~~L~~l~GfG~Ksa~nll~~I~~sk~~~l~r~L~algIpgIG~~~Ak~L~~~fgsl~~l~----~as~eeL~~i~GIG~ 565 (655)
.||-..|=||..+....+.. .-+++.|||+++|-.++..+. .++|. +-+...|.++||||+
T Consensus 55 rEd~~~LyGF~~~~Er~lF~--------------~Li~V~GIGpK~Al~iLs~~~-~~~l~~aI~~~D~~~L~~ipGIGk 119 (203)
T PRK14602 55 REDALELFGFATWDERQTFI--------------VLISISKVGAKTALAILSQFR-PDDLRRLVAEEDVAALTRVSGIGK 119 (203)
T ss_pred ecCcceeeCCCCHHHHHHHH--------------HHhCCCCcCHHHHHHHHhhCC-HHHHHHHHHhCCHHHHhcCCCcCH
Confidence 56777788998776654432 224889999999999999875 55444 448899999999999
Q ss_pred HHHHHHHHHhcC
Q psy11423 566 TTVKAFIKFINQ 577 (655)
Q Consensus 566 ~~A~~I~~~f~~ 577 (655)
|+|++|+--+++
T Consensus 120 KtAerIilELkd 131 (203)
T PRK14602 120 KTAQHIFLELKY 131 (203)
T ss_pred HHHHHHHHHHHH
Confidence 999999865543
No 89
>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=96.35 E-value=0.0031 Score=58.34 Aligned_cols=24 Identities=13% Similarity=0.396 Sum_probs=19.6
Q ss_pred cCHHHHhcCCCCCHHHHHHHHHHh
Q psy11423 552 ATEEQLLNIPKIGSTTVKAFIKFI 575 (655)
Q Consensus 552 as~eeL~~i~GIG~~~A~~I~~~f 575 (655)
++.++|.+++|||+++++.|..|+
T Consensus 95 ~s~eeL~~V~GIg~k~~~~i~~~l 118 (120)
T TIGR01259 95 KSVDDLTKVSGIGEKSLEKLKDYA 118 (120)
T ss_pred CCHHHHHcCCCCCHHHHHHHHhce
Confidence 466888888899998888888775
No 90
>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=96.32 E-value=0.0063 Score=50.44 Aligned_cols=43 Identities=28% Similarity=0.519 Sum_probs=29.3
Q ss_pred CCCccHHHHHHHHHh---CCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHh
Q psy11423 528 IRHVGETTAKELANY---FKNLECMFKATEEQLLNIPKIGSTTVKAFIKFI 575 (655)
Q Consensus 528 IpgIG~~~Ak~L~~~---fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f 575 (655)
+||+|++.|++|.++ ++.+. +.++|.+++|||+++++.|..|+
T Consensus 22 ipgig~~~a~~Il~~R~~~g~~~-----s~~dL~~v~gi~~~~~~~i~~~~ 67 (69)
T TIGR00426 22 MNGVGLKKAEAIVSYREEYGPFK-----TVEDLKQVPGIGNSLVEKNLAVI 67 (69)
T ss_pred CCCCCHHHHHHHHHHHHHcCCcC-----CHHHHHcCCCCCHHHHHHHHhhc
Confidence 555555555555554 44332 67788888888888888888775
No 91
>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=96.21 E-value=0.0072 Score=70.95 Aligned_cols=83 Identities=23% Similarity=0.354 Sum_probs=57.2
Q ss_pred cccccCCCCHHHHHHHHHcCC---CCChHHHhcCChhhhccccCCcHHHHHHHHHHH---HHhcccchhHHHHHhCCCCc
Q psy11423 458 KAMNIIGLGKKMIEKLVNANI---VVTAVDLYKINFKNLLRLDRVSNKLANNILLAI---QKSKLTTFSRFIYALGIRHV 531 (655)
Q Consensus 458 ~~l~I~GLG~k~i~~L~~~g~---I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I---~~sk~~~l~r~L~algIpgI 531 (655)
+.+.++|+|+|++++|++.-- -.....++ ..+.+||+|++.|..|++.+ +.-++.+...+ ..|+||
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 567899999999999987421 11112221 24578999999999998864 33333333332 379999
Q ss_pred cHHHHHHHHHhCCCHHH
Q psy11423 532 GETTAKELANYFKNLEC 548 (655)
Q Consensus 532 G~~~Ak~L~~~fgsl~~ 548 (655)
|+++|+.|.+.|.+...
T Consensus 539 G~~~A~~I~~ff~~~~~ 555 (652)
T TIGR00575 539 GPKVAESIVNFFHDPNN 555 (652)
T ss_pred CHHHHHHHHHHHhhhhH
Confidence 99999999999976443
No 92
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=96.14 E-value=0.01 Score=59.60 Aligned_cols=73 Identities=14% Similarity=0.154 Sum_probs=54.4
Q ss_pred hhhhccccCCcHHHHHHHHHHHHHhcccchhHHHHHhCCCCccHHHHHHHHHhCCCHHHHHh----cCHHHHhcCCCCCH
Q psy11423 490 FKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFK----ATEEQLLNIPKIGS 565 (655)
Q Consensus 490 ~~~L~~l~GfG~Ksa~nll~~I~~sk~~~l~r~L~algIpgIG~~~Ak~L~~~fgsl~~l~~----as~eeL~~i~GIG~ 565 (655)
.||-..|=||..+....+.. .-+++.|||+++|-.++..+. ++.+.. -+...|.++||||+
T Consensus 53 rEd~~~LyGF~~~~Er~lF~--------------~L~~V~GIGpK~AL~iLs~~~-~~~l~~aI~~~D~~~L~kvpGIGk 117 (197)
T PRK14603 53 REDALSLYGFPDEDSLELFE--------------LLLGVSGVGPKLALALLSALP-PALLARALLEGDARLLTSASGVGK 117 (197)
T ss_pred ccCCceeeCcCCHHHHHHHH--------------HHhCcCCcCHHHHHHHHcCCC-HHHHHHHHHhCCHHHHhhCCCCCH
Confidence 45666777888776544432 224789999999999999875 555544 47889999999999
Q ss_pred HHHHHHHHHhcC
Q psy11423 566 TTVKAFIKFINQ 577 (655)
Q Consensus 566 ~~A~~I~~~f~~ 577 (655)
|+|++|+--+.+
T Consensus 118 KtAerIilELkd 129 (197)
T PRK14603 118 KLAERIALELKG 129 (197)
T ss_pred HHHHHHHHHHHH
Confidence 999999865544
No 93
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=96.14 E-value=0.0043 Score=67.39 Aligned_cols=48 Identities=21% Similarity=0.252 Sum_probs=45.0
Q ss_pred CCCCeEecccccCccEEEecCCCC--chHHHHHHcCCeeeCHHHHHHHHh
Q psy11423 600 TKGGKVVNFISKNTNYLVKGQKPG--KKLEKAIKLNIKILDEKNFVKIVK 647 (655)
Q Consensus 600 ~~G~~v~~sVsk~t~ylv~g~~~g--~K~~kA~~lgi~ii~e~~f~~~l~ 647 (655)
.+|..++.+||..|++|||.+... +|+..|+.+|||++++++|+.++.
T Consensus 319 ~agL~y~~~~~r~tslvv~n~~~~~~gk~~~a~~~gipl~~d~~fl~~~~ 368 (377)
T PRK05601 319 RAGLAYSEKLTRQTSVVVCNQTRDLDGKAMHAQRKGIPLLSDVAFLAAVE 368 (377)
T ss_pred HccchhhhccccceeEEEeCCCCCccchhhhhhhcCCCccCHHHHHHHHH
Confidence 788999999999999999998754 999999999999999999999985
No 94
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=95.97 E-value=0.019 Score=53.21 Aligned_cols=83 Identities=22% Similarity=0.182 Sum_probs=61.7
Q ss_pred CCCCHHHHHHHHHcCCCCChHHHhcCChh-----hhccccCCcHHHHHHHHHHHHHhcccchhHHHHHh-CCCCccHHHH
Q psy11423 463 IGLGKKMIEKLVNANIVVTAVDLYKINFK-----NLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYAL-GIRHVGETTA 536 (655)
Q Consensus 463 ~GLG~k~i~~L~~~g~I~~i~DL~~L~~~-----~L~~l~GfG~Ksa~nll~~I~~sk~~~l~r~L~al-gIpgIG~~~A 536 (655)
||+|++...+|-+.| |.|..||+..... .|+.--|+..+...++.. ++.| -|||||+.-|
T Consensus 1 pgi~~~~~~~L~~~G-I~t~~~Ll~~~~~~~~r~~La~~~~i~~~~l~~w~~-------------~AdL~ri~gi~~~~a 66 (122)
T PF14229_consen 1 PGIGPKEAAKLKAAG-IKTTGDLLEAGDTPLGRKALAKKLGISERNLLKWVN-------------QADLMRIPGIGPQYA 66 (122)
T ss_pred CCCCHHHHHHHHHcC-CCcHHHHHHcCCCHHHHHHHHHhcCCCHHHHHHHHh-------------HHHhhhcCCCCHHHH
Confidence 799999999997777 7999999996532 255555566554444332 1222 6899999999
Q ss_pred HHHHH-hCCCHHHHHhcCHHHHhc
Q psy11423 537 KELAN-YFKNLECMFKATEEQLLN 559 (655)
Q Consensus 537 k~L~~-~fgsl~~l~~as~eeL~~ 559 (655)
..|.. .+.|+++|..+++++|.+
T Consensus 67 ~LL~~AGv~Tv~~LA~~~p~~L~~ 90 (122)
T PF14229_consen 67 ELLEHAGVDTVEELAQRNPQNLHQ 90 (122)
T ss_pred HHHHHhCcCcHHHHHhCCHHHHHH
Confidence 98876 588999999999887764
No 95
>PRK07758 hypothetical protein; Provisional
Probab=95.95 E-value=0.016 Score=50.99 Aligned_cols=51 Identities=18% Similarity=0.177 Sum_probs=46.3
Q ss_pred cCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHHH
Q psy11423 462 IIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK 513 (655)
Q Consensus 462 I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~ 513 (655)
.++|+-...+.|..+| |.++.||..+++++|+++.|||+|+.+.|.+.+.+
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 4578888899999998 69999999999999999999999999999988865
No 96
>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=95.84 E-value=0.045 Score=58.78 Aligned_cols=128 Identities=16% Similarity=0.135 Sum_probs=80.3
Q ss_pred CceEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhh---------hhhhhcccCCcccccCC--CCceEEEEEEEE
Q psy11423 117 NIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENIT---------TNIHIIHKIPLVLNIKY--PPELLEVRCEVL 185 (655)
Q Consensus 117 ~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT---------~n~~~i~~iP~~l~~~~--~p~~~evRGEv~ 185 (655)
...|+++.|+||.-.+++|.+|.-++..+| +|..++|-. +....+..+...|.... -...+.|-||++
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 358999999999999999988834677788 566665421 11112222333331110 135799999999
Q ss_pred eehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccC--CCCCCCHHHHHHHHHhCC-CC
Q psy11423 186 IYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRG--MNMPSSHSELLNWYQKIG-LS 262 (655)
Q Consensus 186 ~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~--~~~~~~~~e~l~~L~~~G-F~ 262 (655)
=+ .+.+|.+ .. .+.|++|++..... ..+ -+.-+.++.+...| |+
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 33 2344544 12 47999999955421 112 45556777888886 98
Q ss_pred CCCCceeeCCHHHHHHH
Q psy11423 263 ICGEYSVLSGVNKLIEF 279 (655)
Q Consensus 263 ~~~~~~~~~~~~ev~~~ 279 (655)
.++. ....++++++++
T Consensus 150 ~ap~-L~rGt~~e~l~~ 165 (325)
T TIGR02307 150 YAPL-LGRGTLDELLAF 165 (325)
T ss_pred cchh-hcccCHHHHHhc
Confidence 7763 344678888876
No 97
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=95.76 E-value=0.014 Score=68.66 Aligned_cols=82 Identities=18% Similarity=0.326 Sum_probs=56.4
Q ss_pred cccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhh---ccccCCcHHHHHHHHHHH---HHhcccchhHHHHHhCCCCc
Q psy11423 458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNL---LRLDRVSNKLANNILLAI---QKSKLTTFSRFIYALGIRHV 531 (655)
Q Consensus 458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L---~~l~GfG~Ksa~nll~~I---~~sk~~~l~r~L~algIpgI 531 (655)
+.+.++|+|+|++++|+++- ..--...-+++ +.++|+|++.|..|++.+ +.-++.+...+ ..|+||
T Consensus 480 ~L~~l~gfG~Ksa~~ll~~I-----e~sk~~~l~R~l~algi~~IG~~~ak~L~~~f~sl~~l~~As~eeL---~~i~GI 551 (665)
T PRK07956 480 DLLGLEGFGEKSAQNLLDAI-----EKSKETSLARFLYALGIRHVGEKAAKALARHFGSLEALRAASEEEL---AAVEGV 551 (665)
T ss_pred HHhcCcCcchHHHHHHHHHH-----HHhhcCCHHHhhHhhhccCcCHHHHHHHHHHcCCHHHHHhCCHHHH---hccCCc
Confidence 46689999999999998732 21112222232 367999999999888754 34334444443 378999
Q ss_pred cHHHHHHHHHhCCCHH
Q psy11423 532 GETTAKELANYFKNLE 547 (655)
Q Consensus 532 G~~~Ak~L~~~fgsl~ 547 (655)
|+++|+.|.+.|.+.+
T Consensus 552 G~~~A~sI~~ff~~~~ 567 (665)
T PRK07956 552 GEVVAQSIVEFFAVEE 567 (665)
T ss_pred CHHHHHHHHHHHhhhh
Confidence 9999999999987543
No 98
>PRK00254 ski2-like helicase; Provisional
Probab=95.70 E-value=0.013 Score=69.78 Aligned_cols=53 Identities=21% Similarity=0.343 Sum_probs=49.6
Q ss_pred ccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHH
Q psy11423 459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQ 512 (655)
Q Consensus 459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~ 512 (655)
.+.|||+|++++.+|+++|+ .|+.||..++.++|.+++|+|+|.|++|.+.+.
T Consensus 647 L~~ipgig~~~~~~l~~~g~-~s~~~i~~a~~~el~~~~gi~~~~a~~i~~~~~ 699 (720)
T PRK00254 647 LMRLPMIGRKRARALYNAGF-RSIEDIVNAKPSELLKVEGIGAKIVEGIFKHLG 699 (720)
T ss_pred hhcCCCCCHHHHHHHHHccC-CCHHHHHhCCHHHHhcCCCCCHHHHHHHHHHhc
Confidence 44799999999999999995 999999999999999999999999999999876
No 99
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=95.65 E-value=0.017 Score=68.16 Aligned_cols=92 Identities=17% Similarity=0.224 Sum_probs=58.2
Q ss_pred cccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhh---ccccCCcHHHHHHHHHHH---HHhcccchhHHHHHhCCCCc
Q psy11423 458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNL---LRLDRVSNKLANNILLAI---QKSKLTTFSRFIYALGIRHV 531 (655)
Q Consensus 458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L---~~l~GfG~Ksa~nll~~I---~~sk~~~l~r~L~algIpgI 531 (655)
+...++|+|+|++++|+++---+ -...-+++ +.+||+|++.|.+|++.+ +.-++.+...+ ..|+||
T Consensus 497 ~L~~l~g~g~Ksa~~Ll~~Ie~s-----k~~~l~r~l~ALgIpgIG~~~ak~L~~~F~si~~L~~As~eeL---~~i~GI 568 (689)
T PRK14351 497 DLAELEGWGETSAENLLAELEAS-----REPPLADFLVALGIPEVGPTTARNLAREFGTFEAIMDADEEAL---RAVDDV 568 (689)
T ss_pred HHhcCcCcchhHHHHHHHHHHHH-----ccCCHHHHHHHcCCCCcCHHHHHHHHHHhCCHHHHHhCCHHHH---hccCCc
Confidence 45578999999999988742111 01112222 457899999999998754 33333343333 368999
Q ss_pred cHHHHHHHHHhCCCHHHHHhcCHHHHhc
Q psy11423 532 GETTAKELANYFKNLECMFKATEEQLLN 559 (655)
Q Consensus 532 G~~~Ak~L~~~fgsl~~l~~as~eeL~~ 559 (655)
|+++|+.|.+.|.+.+.... .++|.+
T Consensus 569 G~k~A~sI~~ff~~~~n~~~--i~~L~~ 594 (689)
T PRK14351 569 GPTVAEEIREFFDSERNRAV--IDDLLD 594 (689)
T ss_pred CHHHHHHHHHHHhhhHHHHH--HHHHHh
Confidence 99999999988876554332 344544
No 100
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=95.61 E-value=0.034 Score=55.71 Aligned_cols=51 Identities=25% Similarity=0.375 Sum_probs=40.9
Q ss_pred ccccCCCCHHHHHHHHHcCCCCChHHHhc-C---ChhhhccccCCcHHHHHHHHHHHH
Q psy11423 459 AMNIIGLGKKMIEKLVNANIVVTAVDLYK-I---NFKNLLRLDRVSNKLANNILLAIQ 512 (655)
Q Consensus 459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~-L---~~~~L~~l~GfG~Ksa~nll~~I~ 512 (655)
.+.|+|+|||++..+.... ++.+|.. + +.+.|.++||+|+|+|++|+-.+.
T Consensus 75 Li~V~GIGpK~Al~ILs~~---~~~~l~~aI~~~D~~~L~~vpGIGkKtAerIilELk 129 (194)
T PRK14605 75 LIDVSGIGPKLGLAMLSAM---NAEALASAIISGNAELLSTIPGIGKKTASRIVLELK 129 (194)
T ss_pred HhCCCCCCHHHHHHHHHhC---CHHHHHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHH
Confidence 6789999999999999865 4556544 2 356788999999999999886664
No 101
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=95.57 E-value=0.024 Score=56.95 Aligned_cols=73 Identities=15% Similarity=0.191 Sum_probs=51.2
Q ss_pred hhhhccccCCcHHHHHHHHHHHHHhcccchhHHHHHhCCCCccHHHHHHHHHhCCCHHHHHhc----CHHHHhcCCCCCH
Q psy11423 490 FKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKA----TEEQLLNIPKIGS 565 (655)
Q Consensus 490 ~~~L~~l~GfG~Ksa~nll~~I~~sk~~~l~r~L~algIpgIG~~~Ak~L~~~fgsl~~l~~a----s~eeL~~i~GIG~ 565 (655)
.||-..|=||..+....+.. .-+.+.|||+++|-.++..+. ++.|.+| +...|.++||||+
T Consensus 54 REd~~~LyGF~~~~ER~lF~--------------~LisVnGIGpK~ALaiLs~~~-~~~l~~aI~~~d~~~L~k~PGIGk 118 (201)
T COG0632 54 REDAHLLYGFLTEEERELFR--------------LLISVNGIGPKLALAILSNLD-PEELAQAIANEDVKALSKIPGIGK 118 (201)
T ss_pred hhhHHHHcCCCCHHHHHHHH--------------HHHccCCccHHHHHHHHcCCC-HHHHHHHHHhcChHhhhcCCCCCH
Confidence 34445555787665544432 233678999999988888764 6666554 6788999999999
Q ss_pred HHHHHHHHHhcC
Q psy11423 566 TTVKAFIKFINQ 577 (655)
Q Consensus 566 ~~A~~I~~~f~~ 577 (655)
|+|++|+--+.+
T Consensus 119 KtAerivleLk~ 130 (201)
T COG0632 119 KTAERIVLELKG 130 (201)
T ss_pred HHHHHHHHHHhh
Confidence 999998765543
No 102
>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=95.43 E-value=0.025 Score=46.72 Aligned_cols=47 Identities=30% Similarity=0.367 Sum_probs=42.3
Q ss_pred CCCCeEecccccCccEEEecCC--CCchHHHHHHcCCeeeCHHHHHHHH
Q psy11423 600 TKGGKVVNFISKNTNYLVKGQK--PGKKLEKAIKLNIKILDEKNFVKIV 646 (655)
Q Consensus 600 ~~G~~v~~sVsk~t~ylv~g~~--~g~K~~kA~~lgi~ii~e~~f~~~l 646 (655)
.+||++...+++.++++|++.. ...|...|...|++|++++-+.+.|
T Consensus 30 ~~GG~v~~~~~~~~thvI~~~~~~~~~k~~~~~~~~i~iV~~~Wi~~ci 78 (78)
T PF00533_consen 30 KHGGTVSNSFSKKTTHVIVGNPNKRTKKYKAAIANGIPIVSPDWIEDCI 78 (78)
T ss_dssp HTTEEEESSSSTTSSEEEESSSHCCCHHHHHHHHTTSEEEETHHHHHHH
T ss_pred HcCCEEEeecccCcEEEEeCCCCCccHHHHHHHHCCCeEecHHHHHHhC
Confidence 8899999999999999999988 4588888999999999999887653
No 103
>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=95.39 E-value=0.024 Score=52.45 Aligned_cols=61 Identities=18% Similarity=0.250 Sum_probs=46.1
Q ss_pred ChHHHhcCChhhhccccCCcHHHHHHHHHHHHHhcccchhHHHHHhCCCCccHHHHHHHHHhC
Q psy11423 481 TAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYF 543 (655)
Q Consensus 481 ~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~sk~~~l~r~L~algIpgIG~~~Ak~L~~~f 543 (655)
.+-||-+++.++|..+||+|++.|++|++..+. +.++..+-.-..++|||++++.+|...+
T Consensus 58 ~~iniNtA~~~eL~~lpGIG~~~A~~Ii~~R~~--~g~f~s~eeL~~V~GIg~k~~~~i~~~l 118 (120)
T TIGR01259 58 AAVNINAASLEELQALPGIGPAKAKAIIEYREE--NGAFKSVDDLTKVSGIGEKSLEKLKDYA 118 (120)
T ss_pred CCEeCCcCCHHHHhcCCCCCHHHHHHHHHHHHh--cCCcCCHHHHHcCCCCCHHHHHHHHhce
Confidence 455788888999999999999999999998875 2233333233478999999988886643
No 104
>PRK02362 ski2-like helicase; Provisional
Probab=95.36 E-value=0.015 Score=69.39 Aligned_cols=53 Identities=25% Similarity=0.395 Sum_probs=48.8
Q ss_pred cccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHHH
Q psy11423 458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK 513 (655)
Q Consensus 458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~ 513 (655)
..+.|||+|++++.+|++.| |+|+.||..++.++|..+ ||+|.|++|++++..
T Consensus 653 ~L~~ip~i~~~~a~~l~~~g-i~s~~dl~~~~~~~l~~~--~g~~~~~~i~~~~~~ 705 (737)
T PRK02362 653 DLVGLRGVGRVRARRLYNAG-IESRADLRAADKSVVLAI--LGEKIAENILEQAGR 705 (737)
T ss_pred HHhCCCCCCHHHHHHHHHcC-CCCHHHHHhCCHHHHHHH--HCHHHHHHHHHHhCc
Confidence 46789999999999999966 799999999999999999 999999999999863
No 105
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=94.94 E-value=0.031 Score=52.06 Aligned_cols=41 Identities=15% Similarity=0.268 Sum_probs=22.5
Q ss_pred CCCccHHHHHHHHHh--CCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHhc
Q psy11423 528 IRHVGETTAKELANY--FKNLECMFKATEEQLLNIPKIGSTTVKAFIKFIN 576 (655)
Q Consensus 528 IpgIG~~~Ak~L~~~--fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f~ 576 (655)
+||||++.|++|.++ |. +.|||.+++|||++..+.+..+.+
T Consensus 66 lpGigP~~A~~IV~nGpf~--------sveDL~~V~GIgekqk~~l~k~~~ 108 (132)
T PRK02515 66 FPGMYPTLAGKIVKNAPYD--------SVEDVLNLPGLSERQKELLEANLD 108 (132)
T ss_pred CCCCCHHHHHHHHHCCCCC--------CHHHHHcCCCCCHHHHHHHHHhhc
Confidence 455555555555532 33 345666666777666666555543
No 106
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=94.92 E-value=0.025 Score=65.00 Aligned_cols=92 Identities=17% Similarity=0.115 Sum_probs=54.8
Q ss_pred cccccCCCCHHHHHHHHHcCC---CCChHHHhcCChhhhccccCCcHHHHHHHHHHHHHhcccchhHHHHHhCCCCccHH
Q psy11423 458 KAMNIIGLGKKMIEKLVNANI---VVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGET 534 (655)
Q Consensus 458 ~~l~I~GLG~k~i~~L~~~g~---I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~sk~~~l~r~L~algIpgIG~~ 534 (655)
+.+.++|+|+|.++.|+++=- =..+.-++. =+.++++|++.+..-...|+.-.+.+...+ ..|+|||+.
T Consensus 460 ~l~~l~gfgeks~~nll~aIe~sk~~~l~r~l~-----aLGI~~vG~~~ak~~~~~i~~l~~a~~e~l---~~i~gIG~~ 531 (562)
T PRK08097 460 QLANTPGIGKARAEQLWHQFNLARQQPFSRWLK-----ALGIPLPQAALNALDDRSWQQLLSRSEQQW---QQLPGIGEG 531 (562)
T ss_pred HHhcCcCccHHHHHHHHHHHHHHcCCCHHHHHH-----HcCCccHHHHHHHHhcCCHHHHHcCCHHHH---hcCCCchHH
Confidence 677899999999999987411 011111111 134677888766553333444333333332 278899999
Q ss_pred HHHHHHHhCCCHHHHHhcCHHHHhc
Q psy11423 535 TAKELANYFKNLECMFKATEEQLLN 559 (655)
Q Consensus 535 ~Ak~L~~~fgsl~~l~~as~eeL~~ 559 (655)
+|..|.+.|.+-+.... .++|.+
T Consensus 532 ~a~si~~~f~~~~~~~~--i~~L~~ 554 (562)
T PRK08097 532 RARQLIAFLQHPEVKAL--ADWLAA 554 (562)
T ss_pred HHHHHHHHHcCHHHHHH--HHHHHH
Confidence 99999888876543322 345555
No 107
>PHA02142 putative RNA ligase
Probab=94.81 E-value=0.48 Score=51.79 Aligned_cols=147 Identities=17% Similarity=0.202 Sum_probs=80.8
Q ss_pred CceEEEEEecceeEEEEEEe--CCEEeE--------EEecCCCCccc---hhh-----hh-----hhhcccCCcccccCC
Q psy11423 117 NIEYIAELKFDGIAVNLRYE--YGYLKQ--------ASTRGDGNIGE---NIT-----TN-----IHIIHKIPLVLNIKY 173 (655)
Q Consensus 117 ~~~~~~e~KiDGlsi~l~Y~--~G~l~~--------a~TRGdG~~Ge---DvT-----~n-----~~~i~~iP~~l~~~~ 173 (655)
...|.++.|+||.|+++.|. .+.+-. |.+..+|..|- +.. .| +.. .+||..|..
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 121111 11122222211 111 11 112 236667753
Q ss_pred CCceEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCCCCCHHHHH
Q psy11423 174 PPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELL 253 (655)
Q Consensus 174 ~p~~~evRGEv~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~~~~~~e~l 253 (655)
++..+.|.||+|=+ |. |.+.-- ...-+|++|++-.-+...+ -+..+..
T Consensus 245 ~~~~iaIqGEl~Gp---------------------------~I--Q~N~~~--~~~~~F~vF~v~~i~~~~y-l~~~e~~ 292 (366)
T PHA02142 245 LGMSVAIQGELMGP---------------------------GI--QKNREN--FDKYRIFAFRAWFIDEQRF-ATDEEFQ 292 (366)
T ss_pred hCCcEEEEEEEecc---------------------------cc--cCcccc--CCCCceEEEEEEEecccee-CCHHHHH
Confidence 45679999999931 11 111111 1123789998832222223 5778888
Q ss_pred HHHHhCCCCCCCCc------eeeCCHHHHHHHHHHHHHhhcCCCCccceEEEEEC
Q psy11423 254 NWYQKIGLSICGEY------SVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKIN 302 (655)
Q Consensus 254 ~~L~~~GF~~~~~~------~~~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~ 302 (655)
++++++|++.++.. ...++++|++++-. ...-.+-.--|+|+|--
T Consensus 293 ~~~~~~gl~~VPvL~~~~~~~~~~s~eE~L~~A~----~p~~~~~~~EGiViKp~ 343 (366)
T PHA02142 293 DLCRTLGMEIVPQLGYSYPFQEFTNVKEMLAAAD----IPSINHKIAEGVVYKSV 343 (366)
T ss_pred HHHHHcCCceeeeecccccccccCCHHHHHhhcC----CCcccccccceEEEeec
Confidence 89999999876532 12237888888642 11111122579999763
No 108
>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=94.59 E-value=0.17 Score=53.91 Aligned_cols=50 Identities=24% Similarity=0.349 Sum_probs=46.5
Q ss_pred CCCCccHHHHHHHHHh-CCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHhc
Q psy11423 527 GIRHVGETTAKELANY-FKNLECMFKATEEQLLNIPKIGSTTVKAFIKFIN 576 (655)
Q Consensus 527 gIpgIG~~~Ak~L~~~-fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f~ 576 (655)
.|||||++++++|.+. |.+++.|..++.++|.++.|+++..|+.|++...
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 5899999999999998 9999999999999999999999999999987664
No 109
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=94.47 E-value=0.063 Score=57.63 Aligned_cols=55 Identities=22% Similarity=0.215 Sum_probs=49.9
Q ss_pred cccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHHH
Q psy11423 458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK 513 (655)
Q Consensus 458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~ 513 (655)
....++|+|++++++|.+.|+ .++.||+.++.++|.++.|++++.++.|++....
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 8999999999999999999999999999987754
No 110
>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=94.46 E-value=0.089 Score=41.64 Aligned_cols=47 Identities=38% Similarity=0.538 Sum_probs=41.1
Q ss_pred CCCCeEecccccCccEEEecCCCCc-hHHHHHHcCCeeeCHHHHHHHH
Q psy11423 600 TKGGKVVNFISKNTNYLVKGQKPGK-KLEKAIKLNIKILDEKNFVKIV 646 (655)
Q Consensus 600 ~~G~~v~~sVsk~t~ylv~g~~~g~-K~~kA~~lgi~ii~e~~f~~~l 646 (655)
.+||++..+++..++++|+++.... +...|...|++|++++-+.+.+
T Consensus 24 ~~Gg~v~~~~~~~~thvI~~~~~~~~~~~~~~~~~~~iV~~~Wi~~~~ 71 (72)
T cd00027 24 KLGGKVTSSVSKKTTHVIVGSDAGPKKLLKAIKLGIPIVTPEWLLDCL 71 (72)
T ss_pred HcCCEEeccccCCceEEEECCCCCchHHHHHHHcCCeEecHHHHHHHh
Confidence 7899999999999999999988774 4778999999999999887654
No 111
>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=94.46 E-value=0.18 Score=49.64 Aligned_cols=81 Identities=16% Similarity=0.296 Sum_probs=54.0
Q ss_pred HHHHHcCCCCChHHHhcCChhhhcccc-------CCcHHHHHHHHHHHHHhcccchhHHHHHhCCCCccHHHHHHHHHhC
Q psy11423 471 EKLVNANIVVTAVDLYKINFKNLLRLD-------RVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYF 543 (655)
Q Consensus 471 ~~L~~~g~I~~i~DL~~L~~~~L~~l~-------GfG~Ksa~nll~~I~~sk~~~l~r~L~algIpgIG~~~Ak~L~~~f 543 (655)
..|++..+..++.+|..++.++|..+= ||-..+|.+|.+. |+.|.+.|
T Consensus 41 ~~L~~~~g~~tp~~La~a~~eeL~~lI~~~pal~Gfy~~KAk~Lk~~-------------------------a~~iie~y 95 (177)
T TIGR03252 41 HKIARRMGSLDAEDIAKYDPQAFVALFSERPAVHRFPGSMAKRVQAL-------------------------AQYVVDTY 95 (177)
T ss_pred HHHHHHhCCCCHHHHHcCCHHHHHHHHhcCccccCchHHHHHHHHHH-------------------------HHHHHHHh
Confidence 477654444689999888876665441 6666666666543 33444444
Q ss_pred C-CHHHHHhc----C---HHHHhcCCCCCHHHHHHHHHHhc
Q psy11423 544 K-NLECMFKA----T---EEQLLNIPKIGSTTVKAFIKFIN 576 (655)
Q Consensus 544 g-sl~~l~~a----s---~eeL~~i~GIG~~~A~~I~~~f~ 576 (655)
+ +++.|... + .++|.++||||+++|.-+..+|.
T Consensus 96 ~G~v~~L~~~~~p~t~~lre~Ll~LpGVG~KTAnvVL~~l~ 136 (177)
T TIGR03252 96 DGDATAVWTEGDPDGKELLRRLKALPGFGKQKAKIFLALLG 136 (177)
T ss_pred CCChhhhhcccCCCcHHHHHHHHcCCCCCHHHHHHHHHHHH
Confidence 3 45566541 1 36899999999999999988875
No 112
>PRK01172 ski2-like helicase; Provisional
Probab=94.41 E-value=0.052 Score=64.23 Aligned_cols=62 Identities=18% Similarity=0.180 Sum_probs=53.5
Q ss_pred hccccccc---cccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHH
Q psy11423 450 GLQHFSSR---KAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQ 512 (655)
Q Consensus 450 ~i~~F~sk---~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~ 512 (655)
||.|=+.. ..+.|||+|..++.+|+++| ++|+.||-.++.+++..+.|+|++.+++|+++..
T Consensus 602 rl~~gv~~~~~~L~~ip~~~~~~a~~l~~~g-~~~~~di~~~~~~~~~~i~~~~~~~~~~i~~~~~ 666 (674)
T PRK01172 602 RIKEGIREDLIDLVLIPKVGRVRARRLYDAG-FKTVDDIARSSPERIKKIYGFSDTLANAIVNRAM 666 (674)
T ss_pred HHHcCCCHHHHhhcCCCCCCHHHHHHHHHcC-CCCHHHHHhCCHHHHHHHhccCHHHHHHHHHHHH
Confidence 45554443 35679999999999999999 5999999999999999999999999999999854
No 113
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=94.29 E-value=0.11 Score=55.36 Aligned_cols=93 Identities=16% Similarity=0.165 Sum_probs=63.1
Q ss_pred CChHHHhcCChhhhccccCCcHHHHHHHHHHHHHh---------cccchhHHHHHhCCCCccHHHHHHHHHhC--CCHHH
Q psy11423 480 VTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKS---------KLTTFSRFIYALGIRHVGETTAKELANYF--KNLEC 548 (655)
Q Consensus 480 ~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~s---------k~~~l~r~L~algIpgIG~~~Ak~L~~~f--gsl~~ 548 (655)
.++++++.. +.+..|+|+|+..|++|-+-++.- +..|. -++.-|.+||+|++.-..|.+.+ .+++.
T Consensus 44 e~~~ei~e~--~~~t~l~gIGk~ia~~I~e~l~tG~~~~le~lk~~~P~-gl~~Ll~v~GlGpkKi~~Ly~elgi~~~e~ 120 (326)
T COG1796 44 EDLEEIEER--GRLTELPGIGKGIAEKISEYLDTGEVKKLEALKKEVPE-GLEPLLKVPGLGPKKIVSLYKELGIKDLEE 120 (326)
T ss_pred cchHHHHhh--cccCCCCCccHHHHHHHHHHHHcCccHHHHHHHHhCCc-chHHHhhCCCCCcHHHHHHHHHHCcccHHH
Confidence 344455442 257788999988888877665431 12332 35556688999998877777765 46777
Q ss_pred HHhcCH-HHHhcCCCCCHHHHHHHHHHh
Q psy11423 549 MFKATE-EQLLNIPKIGSTTVKAFIKFI 575 (655)
Q Consensus 549 l~~as~-eeL~~i~GIG~~~A~~I~~~f 575 (655)
|..|-. -.+..++|+|++.+..|..+.
T Consensus 121 l~~a~~~~~~~~l~GfG~kse~~il~~i 148 (326)
T COG1796 121 LQEALENGKIRGLRGFGKKSEAKILENI 148 (326)
T ss_pred HHHHHHhCCccccCCccchhHHHHHHHH
Confidence 776533 357889999998888888743
No 114
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=94.24 E-value=0.065 Score=61.99 Aligned_cols=57 Identities=21% Similarity=0.253 Sum_probs=50.9
Q ss_pred cccccccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHHH
Q psy11423 454 FSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK 513 (655)
Q Consensus 454 F~sk~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~ 513 (655)
+-| ...+|||+||++..+|++.= .|+.+|...+.++|.+++|++++.|++|++.+.+
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 445 46799999999999999874 4899999999999999999999999999998865
No 115
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=94.20 E-value=0.18 Score=51.46 Aligned_cols=81 Identities=23% Similarity=0.322 Sum_probs=49.4
Q ss_pred HHHHHHHcCCC-----CChHHHhcCChhhhccc---cCCcHHHHHHHHHHHHHhcccchhHHHHHhCCCCccHHHHHHHH
Q psy11423 469 MIEKLVNANIV-----VTAVDLYKINFKNLLRL---DRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELA 540 (655)
Q Consensus 469 ~i~~L~~~g~I-----~~i~DL~~L~~~~L~~l---~GfG~Ksa~nll~~I~~sk~~~l~r~L~algIpgIG~~~Ak~L~ 540 (655)
.+..|.+.+.. .++.+|..++.++|.++ -||-..+|..|.+-. +.+.
T Consensus 51 a~~~L~~~~~~~~~~~~t~e~L~~a~~eeL~~~Irp~Gf~~~KA~~Lk~la-------------------------~~i~ 105 (218)
T PRK13913 51 SLENLKNAFILENDDEINLKKIAYIEFSKLAECVRPSGFYNQKAKRLIDLS-------------------------ENIL 105 (218)
T ss_pred HHHHHHHhcccccccCCCHHHHHcCCHHHHHHHHHhcCCHHHHHHHHHHHH-------------------------HHHH
Confidence 33456555432 38999999988887766 477776676665432 2222
Q ss_pred HhCCCHHHHHh-cCHHHHhcCCCCCHHHHHHHHHH
Q psy11423 541 NYFKNLECMFK-ATEEQLLNIPKIGSTTVKAFIKF 574 (655)
Q Consensus 541 ~~fgsl~~l~~-as~eeL~~i~GIG~~~A~~I~~~ 574 (655)
+.|++++.+.. .+.++|.+++|||+++|..|.-|
T Consensus 106 ~~~g~~~~~~~~~~re~Ll~l~GIG~kTAd~iLly 140 (218)
T PRK13913 106 KDFGSFENFKQEVTREWLLDQKGIGKESADAILCY 140 (218)
T ss_pred HHcCCchhccCchHHHHHHcCCCccHHHHHHHHHH
Confidence 33333332221 23467888888888888887764
No 116
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=94.01 E-value=0.048 Score=54.69 Aligned_cols=53 Identities=25% Similarity=0.395 Sum_probs=42.9
Q ss_pred cccccCCCCHHHHHHHHHcCCCCChHHHhc-C---ChhhhccccCCcHHHHHHHHHHHHH
Q psy11423 458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYK-I---NFKNLLRLDRVSNKLANNILLAIQK 513 (655)
Q Consensus 458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~-L---~~~~L~~l~GfG~Ksa~nll~~I~~ 513 (655)
..+.|.|+|||++-.+.... ++.+|.. + +...|..+||+|+|+|++|+-.++.
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 6777776 2 2456889999999999999977753
No 117
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=94.00 E-value=0.053 Score=54.74 Aligned_cols=52 Identities=21% Similarity=0.354 Sum_probs=42.6
Q ss_pred ccccCCCCHHHHHHHHHcCCCCChHHHhc-C---ChhhhccccCCcHHHHHHHHHHHHH
Q psy11423 459 AMNIIGLGKKMIEKLVNANIVVTAVDLYK-I---NFKNLLRLDRVSNKLANNILLAIQK 513 (655)
Q Consensus 459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~-L---~~~~L~~l~GfG~Ksa~nll~~I~~ 513 (655)
.+.|.|+|||++-.+.... ++.+|.. + +...|..+||+|+|+|++|+-.++.
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 6789999999999998864 6777776 2 3466889999999999999977754
No 118
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=93.99 E-value=0.069 Score=62.58 Aligned_cols=54 Identities=9% Similarity=0.056 Sum_probs=49.1
Q ss_pred cccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHHH
Q psy11423 458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK 513 (655)
Q Consensus 458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~ 513 (655)
...+|+|+|++++.+|++.= .|+.+|...+.++|.+++|+|++.|++|++.++.
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 47799999999999999973 4999999999999999999999999999998864
No 119
>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=93.92 E-value=0.044 Score=53.94 Aligned_cols=155 Identities=16% Similarity=0.150 Sum_probs=75.1
Q ss_pred eEEEEEecceeEEEEEEeCCEEeEEEecCC---------CCc-cch-hhhhhhhcccCCcccc---cCCCCceEEEEEEE
Q psy11423 119 EYIAELKFDGIAVNLRYEYGYLKQASTRGD---------GNI-GEN-ITTNIHIIHKIPLVLN---IKYPPELLEVRCEV 184 (655)
Q Consensus 119 ~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGd---------G~~-GeD-vT~n~~~i~~iP~~l~---~~~~p~~~evRGEv 184 (655)
+|+++.|+||-++++.+.++.-++..+|.. |.. +.+ .+..+..+. ....+. ....+..+.|.||+
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 589999999999999886554345555543 111 111 111111111 111111 00136789999999
Q ss_pred EeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCC---CCCCCHHHHHHHHHhCCC
Q psy11423 185 LIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGM---NMPSSHSELLNWYQKIGL 261 (655)
Q Consensus 185 ~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~---~~~~~~~e~l~~L~~~GF 261 (655)
+=.+.. --.|.= + ...+..|++|+|...... .+ .+..+...++..+||
T Consensus 81 ~G~~~~--------------Iq~~~~--------~------~~~~~~F~~Fdi~~~~~~~~~~~-l~~~~~~~~~~~~gl 131 (186)
T PF09414_consen 81 VGAKPS--------------IQKNRY--------Q------LDPPKDFYVFDIYDIDEQGEIRY-LSWDEVREFAEELGL 131 (186)
T ss_dssp ECEECT--------------TCSS------------------ECCCEEEEEEEEEEETCCGEEE--HHHHHHHHHCCCT-
T ss_pred eeeccc--------------cccccc--------c------cCCCceEEEEEEEEcCCCCeeEE-CCHHHHHHHHHHCCC
Confidence 953210 001100 0 012589999999765322 12 356677788889999
Q ss_pred CCCCCceeeCCHHHHHHHHHHHHHh-hcCCCCccceEEEEECCh
Q psy11423 262 SICGEYSVLSGVNKLIEFYKKINIK-RFNLPYEIDGVVYKINCL 304 (655)
Q Consensus 262 ~~~~~~~~~~~~~ev~~~~~~~~~~-r~~l~y~iDGiVikv~~~ 304 (655)
+++|... ...+.+...+-...... .....=.-=|+|+|..+.
T Consensus 132 ~~VPvl~-~g~~~~~~~~~~~~~~~~~~~~~~~~EGiVik~~~~ 174 (186)
T PF09414_consen 132 KTVPVLY-RGTFTELDDLDDLFESGKPSGEGNIREGIVIKPEDE 174 (186)
T ss_dssp EES-ECE-EECHHHHCTS-CCGBBTTS-STT-B--EEEEEETTT
T ss_pred CEeCEEE-EEccchhhhhhHHHhhcccCCCCCccCEEEEEEeEe
Confidence 9887432 22444443321110000 111123346999999875
No 120
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=93.91 E-value=0.052 Score=54.12 Aligned_cols=52 Identities=25% Similarity=0.384 Sum_probs=42.3
Q ss_pred ccccCCCCHHHHHHHHHcCCCCChHHHhc-CC---hhhhccccCCcHHHHHHHHHHHHH
Q psy11423 459 AMNIIGLGKKMIEKLVNANIVVTAVDLYK-IN---FKNLLRLDRVSNKLANNILLAIQK 513 (655)
Q Consensus 459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~-L~---~~~L~~l~GfG~Ksa~nll~~I~~ 513 (655)
.+.|.|+|||++-.+.... ++.+|.. +. ...|..+||+|+|+|++|+-.+..
T Consensus 75 Li~V~GIGpK~AL~iLs~~---~~~el~~aI~~~D~~~L~~vpGIGkKtAerIilELkd 130 (188)
T PRK14606 75 LTKVSRLGPKTALKIISNE---DAETLVTMIASQDVEGLSKLPGISKKTAERIVMELKD 130 (188)
T ss_pred HhccCCccHHHHHHHHcCC---CHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHHHHHH
Confidence 6789999999999998754 6777776 32 456889999999999999977754
No 121
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=93.90 E-value=0.11 Score=48.51 Aligned_cols=57 Identities=14% Similarity=0.205 Sum_probs=44.3
Q ss_pred ChHHHhcCChhhhccccCCcHHHHHHHHHHHHHhcccchhHHHHHhCCCCccHHHHHHHHHhC
Q psy11423 481 TAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYF 543 (655)
Q Consensus 481 ~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~sk~~~l~r~L~algIpgIG~~~Ak~L~~~f 543 (655)
..-||-+.+..+|.++||+|++.|++|++ +-++..+=.-+.+||||++..+.+.+..
T Consensus 51 ~kIdiN~A~~~el~~lpGigP~~A~~IV~------nGpf~sveDL~~V~GIgekqk~~l~k~~ 107 (132)
T PRK02515 51 EKIDLNNSSVRAFRQFPGMYPTLAGKIVK------NAPYDSVEDVLNLPGLSERQKELLEANL 107 (132)
T ss_pred CcccCCccCHHHHHHCCCCCHHHHHHHHH------CCCCCCHHHHHcCCCCCHHHHHHHHHhh
Confidence 44577788888999999999999999993 6677666666789999998766555543
No 122
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=93.88 E-value=0.053 Score=54.48 Aligned_cols=53 Identities=25% Similarity=0.337 Sum_probs=42.6
Q ss_pred cccccCCCCHHHHHHHHHcCCCCChHHHhc-C---ChhhhccccCCcHHHHHHHHHHHHH
Q psy11423 458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYK-I---NFKNLLRLDRVSNKLANNILLAIQK 513 (655)
Q Consensus 458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~-L---~~~~L~~l~GfG~Ksa~nll~~I~~ 513 (655)
..+.|.|+|||++-.+.... ++.+|.. + +...|.++||+|+|+|++|+-.+..
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 6777776 2 3456889999999999999977753
No 123
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=93.84 E-value=0.056 Score=54.15 Aligned_cols=52 Identities=15% Similarity=0.377 Sum_probs=42.1
Q ss_pred ccccCCCCHHHHHHHHHcCCCCChHHHhc-C---ChhhhccccCCcHHHHHHHHHHHHH
Q psy11423 459 AMNIIGLGKKMIEKLVNANIVVTAVDLYK-I---NFKNLLRLDRVSNKLANNILLAIQK 513 (655)
Q Consensus 459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~-L---~~~~L~~l~GfG~Ksa~nll~~I~~ 513 (655)
.+.|.|+|||++-.+.... ++.+|.. . +...|..+||+|+|+|++|+-.+..
T Consensus 74 LisVsGIGPK~ALaILs~~---~~~el~~aI~~~D~~~L~~vpGIGkKtAeRIIlELkd 129 (196)
T PRK13901 74 LIGVDGIGPRAALRVLSGI---KYNEFRDAIDREDIELISKVKGIGNKMAGKIFLKLRG 129 (196)
T ss_pred HhCcCCcCHHHHHHHHcCC---CHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHHHHHH
Confidence 6789999999999998754 6777776 3 2456889999999999999977753
No 124
>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=93.82 E-value=0.11 Score=55.57 Aligned_cols=51 Identities=25% Similarity=0.263 Sum_probs=47.5
Q ss_pred ccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHH
Q psy11423 461 NIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQ 512 (655)
Q Consensus 461 ~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~ 512 (655)
.|+|+|++++++|.+.|+ .++.||..++.++|..+.|++++.++.|++...
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 125
>PRK00024 hypothetical protein; Reviewed
Probab=93.81 E-value=0.13 Score=52.74 Aligned_cols=55 Identities=22% Similarity=0.318 Sum_probs=45.4
Q ss_pred HHHHHhCCCCccH-HHHHHHHHhCCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHh
Q psy11423 521 RFIYALGIRHVGE-TTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFI 575 (655)
Q Consensus 521 r~L~algIpgIG~-~~Ak~L~~~fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f 575 (655)
.+|...|+|+-.. ..|++|+++|+++.++..++.++|.+++|||+..|..|..-+
T Consensus 31 a~lL~~g~~~~~~~~LA~~LL~~fgsL~~l~~as~~eL~~i~GIG~akA~~L~a~~ 86 (224)
T PRK00024 31 AILLRTGTKGKSVLDLARELLQRFGSLRGLLDASLEELQSIKGIGPAKAAQLKAAL 86 (224)
T ss_pred HHHHcCCCCCCCHHHHHHHHHHHcCCHHHHHhCCHHHHhhccCccHHHHHHHHHHH
Confidence 4445568887543 378899999999999999999999999999999998876643
No 126
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=93.80 E-value=0.053 Score=53.98 Aligned_cols=51 Identities=22% Similarity=0.351 Sum_probs=40.6
Q ss_pred ccccCCCCHHHHHHHHHcCCCCChHHHhc-CC---hhhhccccCCcHHHHHHHHHHHHH
Q psy11423 459 AMNIIGLGKKMIEKLVNANIVVTAVDLYK-IN---FKNLLRLDRVSNKLANNILLAIQK 513 (655)
Q Consensus 459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~-L~---~~~L~~l~GfG~Ksa~nll~~I~~ 513 (655)
.+.+.|+|||++-.+.... ++.+|.. +. ...| ++||+|+|+|++|+-.++.
T Consensus 75 LisV~GIGpK~Al~iLs~~---~~~~l~~aI~~~D~~~L-~vpGIGkKtAerIilELk~ 129 (186)
T PRK14600 75 LVKVSGVNYKTAMSILSKL---TPEQLFSAIVNEDKAAL-KVNGIGEKLINRIITELQY 129 (186)
T ss_pred HhCcCCcCHHHHHHHHccC---CHHHHHHHHHcCCHhhe-ECCCCcHHHHHHHHHHHHH
Confidence 6789999999999998754 6777776 32 3457 8999999999999977753
No 127
>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=93.77 E-value=0.2 Score=38.36 Aligned_cols=47 Identities=17% Similarity=0.325 Sum_probs=42.2
Q ss_pred CCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHH
Q psy11423 465 LGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQ 512 (655)
Q Consensus 465 LG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~ 512 (655)
+.+..+.+|+++| +.++.||-.+..++|..++|+++..+++|+....
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 4578899999999 5899999999999999999999999999987654
No 128
>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=93.74 E-value=0.15 Score=54.67 Aligned_cols=62 Identities=26% Similarity=0.365 Sum_probs=42.8
Q ss_pred hhhccccCCcHHHHHHHHHHHHHhcccch--------hHHHHHhCCCCccHHHHHHHHH-hCCCHHHHHhc
Q psy11423 491 KNLLRLDRVSNKLANNILLAIQKSKLTTF--------SRFIYALGIRHVGETTAKELAN-YFKNLECMFKA 552 (655)
Q Consensus 491 ~~L~~l~GfG~Ksa~nll~~I~~sk~~~l--------~r~L~algIpgIG~~~Ak~L~~-~fgsl~~l~~a 552 (655)
.++..+||+|++.+++|.+-++.-+-..+ .-++.-++|||||+++|+++.+ .+.|+++|..+
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 35688899999998888877664222112 2234445899999999998884 35678877765
No 129
>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=93.68 E-value=0.049 Score=58.36 Aligned_cols=48 Identities=29% Similarity=0.319 Sum_probs=40.3
Q ss_pred cccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHHHhcc
Q psy11423 458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKL 516 (655)
Q Consensus 458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~sk~ 516 (655)
..++|+|+||+++.+|| +..|+|++||...- |.|+.++++.+|+..+.
T Consensus 86 ~l~~i~GiGpk~a~~l~-~lGi~sl~dL~~a~----------g~k~~~~i~~gl~~~~~ 133 (307)
T cd00141 86 LLLRVPGVGPKTARKLY-ELGIRTLEDLRKAA----------GAKLEQNILIGLEYYED 133 (307)
T ss_pred HHHcCCCCCHHHHHHHH-HcCCCCHHHHHHHh----------ccccHHHHHHHHHHHHH
Confidence 45789999999999999 56689999999732 88999999999986543
No 130
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=93.67 E-value=0.062 Score=53.35 Aligned_cols=52 Identities=15% Similarity=0.298 Sum_probs=42.4
Q ss_pred ccccCCCCHHHHHHHHHcCCCCChHHHhc-CC---hhhhccccCCcHHHHHHHHHHHHH
Q psy11423 459 AMNIIGLGKKMIEKLVNANIVVTAVDLYK-IN---FKNLLRLDRVSNKLANNILLAIQK 513 (655)
Q Consensus 459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~-L~---~~~L~~l~GfG~Ksa~nll~~I~~ 513 (655)
.+.|.|+|||++-.+.... ++.+|.. +. ...|.++||+|+|+|++|+-.+..
T Consensus 75 Li~VsGIGpK~Al~ILs~~---~~~el~~aI~~~D~~~L~~vpGIGkKtAeRIilELkd 130 (183)
T PRK14601 75 LLKVNGIGANTAMAVCSSL---DVNSFYKALSLGDESVLKKVPGIGPKSAKRIIAELSD 130 (183)
T ss_pred HhccCCccHHHHHHHHcCC---CHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHHHHHH
Confidence 6789999999999998754 7778887 33 456888999999999999977753
No 131
>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=93.56 E-value=0.13 Score=42.55 Aligned_cols=58 Identities=16% Similarity=0.159 Sum_probs=40.0
Q ss_pred HHHhcCChhhhcc-ccCCcHHHHHHHHHHHHHhcccchhHHHHHhCCCCccHHHHHHHHHh
Q psy11423 483 VDLYKINFKNLLR-LDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANY 542 (655)
Q Consensus 483 ~DL~~L~~~~L~~-l~GfG~Ksa~nll~~I~~sk~~~l~r~L~algIpgIG~~~Ak~L~~~ 542 (655)
-||-++..+.|.. ++|+|++.|++|++...... ++..+-.-..++|+|++++++|...
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 4566667778888 88999998888888776432 2222222246888888888887764
No 132
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=93.37 E-value=0.37 Score=51.69 Aligned_cols=50 Identities=24% Similarity=0.372 Sum_probs=46.1
Q ss_pred CCCCccHHHHHHHHHh-CCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHhc
Q psy11423 527 GIRHVGETTAKELANY-FKNLECMFKATEEQLLNIPKIGSTTVKAFIKFIN 576 (655)
Q Consensus 527 gIpgIG~~~Ak~L~~~-fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f~ 576 (655)
.+||||++++++|.+. |.+++.|..++.++|.++.|++++.|+.+++..+
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 6899999999999987 9999999999999999999999999999987654
No 133
>COG1623 Predicted nucleic-acid-binding protein (contains the HHH domain) [General function prediction only]
Probab=93.32 E-value=0.099 Score=54.66 Aligned_cols=50 Identities=20% Similarity=0.300 Sum_probs=46.1
Q ss_pred CCCCccHHHHHHHHHhCCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHhc
Q psy11423 527 GIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFIN 576 (655)
Q Consensus 527 gIpgIG~~~Ak~L~~~fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f~ 576 (655)
.||.+-......|...|++++.|..||.++|.+++|||+..|..|.+-++
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 78888888899999999999999999999999999999999999987653
No 134
>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=93.31 E-value=0.1 Score=36.42 Aligned_cols=27 Identities=30% Similarity=0.386 Sum_probs=20.3
Q ss_pred HHHhcCChhhhccccCCcHHHHHHHHH
Q psy11423 483 VDLYKINFKNLLRLDRVSNKLANNILL 509 (655)
Q Consensus 483 ~DL~~L~~~~L~~l~GfG~Ksa~nll~ 509 (655)
..+...+.++|.++||+|+|+|+.|+.
T Consensus 3 ~g~~pas~eeL~~lpGIG~~tA~~I~~ 29 (30)
T PF00633_consen 3 DGLIPASIEELMKLPGIGPKTANAILS 29 (30)
T ss_dssp HHHHTSSHHHHHTSTT-SHHHHHHHHH
T ss_pred CCcCCCCHHHHHhCCCcCHHHHHHHHh
Confidence 345566788899999999999988764
No 135
>TIGR00608 radc DNA repair protein radc. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=93.25 E-value=0.19 Score=51.38 Aligned_cols=55 Identities=22% Similarity=0.338 Sum_probs=45.4
Q ss_pred HHHHHhCCCCc-c-HHHHHHHHHhC---CCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHh
Q psy11423 521 RFIYALGIRHV-G-ETTAKELANYF---KNLECMFKATEEQLLNIPKIGSTTVKAFIKFI 575 (655)
Q Consensus 521 r~L~algIpgI-G-~~~Ak~L~~~f---gsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f 575 (655)
.+|...|.|+- . ...|+.|+++| +++..+..++.++|.+++|||+..|..|..-+
T Consensus 21 ailL~~g~~~~~~~~~lA~~ll~~f~~~g~l~~l~~a~~~eL~~i~GiG~aka~~l~a~~ 80 (218)
T TIGR00608 21 AIILRTGTPKGLDVLSLSKRLLDVFGRQDSLGHLLSAPPEELSSVPGIGEAKAIQLKAAV 80 (218)
T ss_pred HHHHhCCCCCCCCHHHHHHHHHHHhcccCCHHHHHhCCHHHHHhCcCCcHHHHHHHHHHH
Confidence 44555688875 2 24788999999 99999999999999999999999998887643
No 136
>COG2003 RadC DNA repair proteins [DNA replication, recombination, and repair]
Probab=93.11 E-value=0.31 Score=49.65 Aligned_cols=57 Identities=23% Similarity=0.260 Sum_probs=45.8
Q ss_pred chhHHHHHhCCCCccH-HHHHHHHHhCCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHH
Q psy11423 518 TFSRFIYALGIRHVGE-TTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKF 574 (655)
Q Consensus 518 ~l~r~L~algIpgIG~-~~Ak~L~~~fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~ 574 (655)
.|-.++..-|+||--. ..|+.|+++||++..+..|+.++|+.++|+|...|-++..-
T Consensus 28 ELLailLrtG~~~~~~~~la~~lL~~fg~L~~l~~a~~~el~~v~GiG~aka~~l~a~ 85 (224)
T COG2003 28 ELLAILLRTGTKGESVLDLAKELLQEFGSLAELLKASVEELSSVKGIGLAKAIQIKAA 85 (224)
T ss_pred HHHHHHHhcCCCCCCHHHHHHHHHHHcccHHHHHhCCHHHHhhCCCccHHHHHHHHHH
Confidence 3445555668886543 35689999999999999999999999999999888887664
No 137
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=92.73 E-value=0.065 Score=43.99 Aligned_cols=30 Identities=23% Similarity=0.231 Sum_probs=21.1
Q ss_pred HHhcCChhhhccccCCcHHHHHHHHHHHHH
Q psy11423 484 DLYKINFKNLLRLDRVSNKLANNILLAIQK 513 (655)
Q Consensus 484 DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~ 513 (655)
||-+++.++|..+||+|++.|++|++.-++
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 556677888999999999999888876543
No 138
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=92.44 E-value=0.2 Score=59.16 Aligned_cols=81 Identities=16% Similarity=0.215 Sum_probs=54.2
Q ss_pred hhhccccCCcHHHHHHHHHHHHHhcccchhHHH-----HHhCCCCccHHHHHHHHHhCCCHHHHHhcCHHHHh---cCCC
Q psy11423 491 KNLLRLDRVSNKLANNILLAIQKSKLTTFSRFI-----YALGIRHVGETTAKELANYFKNLECMFKATEEQLL---NIPK 562 (655)
Q Consensus 491 ~~L~~l~GfG~Ksa~nll~~I~~sk~~~l~r~L-----~algIpgIG~~~Ak~L~~~fgsl~~l~~as~eeL~---~i~G 562 (655)
.+-+.++|+|++.++.|++.= .-.....+. .-+.++|+|++.|+.|.+.+ +.=+..+.+.+. .||+
T Consensus 436 r~aldI~GlG~~~i~~L~~~G---~i~~~~Dly~L~~~~l~~l~g~geksa~nl~~~I---e~sk~~~l~r~l~ALGI~~ 509 (669)
T PRK14350 436 KKCMNIVGLSDKTIEFLFEKK---FISSEIDLYTFNFDRLINLKGFKDKRINNLKRSI---EASKKRPFSKLLLSMGIKD 509 (669)
T ss_pred CCcccccCcCHHHHHHHHHcC---CcCCHHHHhhCCHHHHhhccCccHHHHHHHHHHH---HHHhCCCHHHHHHHcCCCc
Confidence 345788999999999988631 111111111 11257999999999888754 333444555443 3899
Q ss_pred CCHHHHHHHH-HHhcC
Q psy11423 563 IGSTTVKAFI-KFINQ 577 (655)
Q Consensus 563 IG~~~A~~I~-~~f~~ 577 (655)
||+..|+.|. .+|.+
T Consensus 510 vG~~~ak~La~~~f~~ 525 (669)
T PRK14350 510 LGENTILLLINNNLNS 525 (669)
T ss_pred hhHHHHHHHHHHhhCC
Confidence 9999999999 78865
No 139
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=92.42 E-value=0.02 Score=50.54 Aligned_cols=69 Identities=22% Similarity=0.282 Sum_probs=45.4
Q ss_pred ChhHHHHHHHHHHcCcccccCC---CCCCCeEecccccCccEEEecCCCC---chHHH-HHHcCCeeeCHHHHHHHH
Q psy11423 577 QPLHRLLISQLRDVGIYWLNNP---NTKGGKVVNFISKNTNYLVKGQKPG---KKLEK-AIKLNIKILDEKNFVKIV 646 (655)
Q Consensus 577 ~~~n~~li~~L~~~Gi~~~~~~---~~~G~~v~~sVsk~t~ylv~g~~~g---~K~~k-A~~lgi~ii~e~~f~~~l 646 (655)
+...++++.+|...|++..... ..+|......|.+|| |.++++..| .++|+ |+++|++..++.-....+
T Consensus 5 ~~~~~~~~~~L~~~gl~~~~a~kl~~~yg~~ai~~l~~nP-Y~L~~~i~gi~F~~aD~iA~~~g~~~~d~~Ri~A~i 80 (94)
T PF14490_consen 5 NRGLRELMAFLQEYGLSPKLAMKLYKKYGDDAIEILKENP-YRLIEDIDGIGFKTADKIALKLGIEPDDPRRIRAAI 80 (94)
T ss_dssp ----HHHHHHHHHTT--HHHHHHHHHHH-TTHHHHHHH-S-TCCCB-SSSSBHHHHHHHHHTTT--TT-HHHHHHHH
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHHHHhHHHHHHHHHCh-HHHHHHccCCCHHHHHHHHHHcCCCCCCHHHHHHHH
Confidence 3445667777888888754333 477888888999999 999997665 89999 999999999999877654
No 140
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=92.34 E-value=0.19 Score=58.83 Aligned_cols=60 Identities=15% Similarity=0.088 Sum_probs=53.5
Q ss_pred ccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHHHhcccchh
Q psy11423 459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKLTTFS 520 (655)
Q Consensus 459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~sk~~~l~ 520 (655)
.-+|+|+|+++..+|++.= .|+.+|...+.++|.+++|++.+.|++|+.+-..+-..|..
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 5699999999999999864 48999999999999999999999999999998777666653
No 141
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=92.30 E-value=0.2 Score=48.18 Aligned_cols=23 Identities=22% Similarity=0.492 Sum_probs=15.8
Q ss_pred CHHHHhcCCCCCHHHHHHHHHHh
Q psy11423 553 TEEQLLNIPKIGSTTVKAFIKFI 575 (655)
Q Consensus 553 s~eeL~~i~GIG~~~A~~I~~~f 575 (655)
+.+||..++|||+++.+.+..++
T Consensus 125 sv~dL~~v~GiG~~~~ekl~~~i 147 (149)
T COG1555 125 SVDDLAKVKGIGPKTLEKLKDYI 147 (149)
T ss_pred cHHHHHhccCCCHHHHHHHHhhc
Confidence 45667777777777777776654
No 142
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=92.21 E-value=0.14 Score=59.41 Aligned_cols=88 Identities=20% Similarity=0.310 Sum_probs=57.1
Q ss_pred cccccccccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhh---ccccCCcHHHHHHHHHHHHH---hcccchhHHHHH
Q psy11423 452 QHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNL---LRLDRVSNKLANNILLAIQK---SKLTTFSRFIYA 525 (655)
Q Consensus 452 ~~F~sk~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L---~~l~GfG~Ksa~nll~~I~~---sk~~~l~r~L~a 525 (655)
-++-..+.+.++++|+|.+++|+++- ..=-+....++ +.++.+|++.|..|...+.. -...++..+
T Consensus 474 y~Lt~~~l~~l~~~~~ks~~nLl~aI-----e~sK~~~l~r~l~aLGIr~VG~~~Ak~La~~f~sl~~l~~a~~e~l--- 545 (667)
T COG0272 474 YTLTEEDLLSLEGFGEKSAENLLNAI-----EKSKKQPLARFLYALGIRHVGETTAKSLARHFGTLEALLAASEEEL--- 545 (667)
T ss_pred HhCCHHHHhhccchhhhHHHHHHHHH-----HHhccCCHHHHHHHcCCchhhHHHHHHHHHHhhhHHHHHhcCHHHH---
Confidence 34445678899999999999998631 11111112222 45678999999888776543 222333222
Q ss_pred hCCCCccHHHHHHHHHhCCCHH
Q psy11423 526 LGIRHVGETTAKELANYFKNLE 547 (655)
Q Consensus 526 lgIpgIG~~~Ak~L~~~fgsl~ 547 (655)
..|||||+..|+.|.+.|....
T Consensus 546 ~~i~giG~~vA~si~~ff~~~~ 567 (667)
T COG0272 546 ASIPGIGEVVARSIIEFFANEE 567 (667)
T ss_pred hhccchhHHHHHHHHHHHcCHH
Confidence 2699999999999999887543
No 143
>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=92.11 E-value=0.13 Score=59.79 Aligned_cols=30 Identities=37% Similarity=0.534 Sum_probs=28.5
Q ss_pred CCCCccHHHHHHHHHhCCCHHHHHhcCHHH
Q psy11423 527 GIRHVGETTAKELANYFKNLECMFKATEEQ 556 (655)
Q Consensus 527 gIpgIG~~~Ak~L~~~fgsl~~l~~as~ee 556 (655)
+|||||+++.++|+++|||+++|..||.++
T Consensus 545 ~I~GIG~kr~~~LL~~Fgs~~~i~~As~ee 574 (574)
T TIGR00194 545 KIPGVGEKRVQKLLKYFGSLKGIKKASVEE 574 (574)
T ss_pred cCCCCCHHHHHHHHHHcCCHHHHHhCCccC
Confidence 999999999999999999999999999764
No 144
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=92.01 E-value=0.54 Score=47.71 Aligned_cols=76 Identities=21% Similarity=0.139 Sum_probs=41.7
Q ss_pred HHHHHHHHHcCCCCChHHHhcCChhhhccc---cCCcHHHHHHHHHHHHHhcc---cchhHHHH-HhCCCCccHHHHHHH
Q psy11423 467 KKMIEKLVNANIVVTAVDLYKINFKNLLRL---DRVSNKLANNILLAIQKSKL---TTFSRFIY-ALGIRHVGETTAKEL 539 (655)
Q Consensus 467 ~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l---~GfG~Ksa~nll~~I~~sk~---~~l~r~L~-algIpgIG~~~Ak~L 539 (655)
.+....|++.- .+++|+..+..++|..+ =||-..+|.||++--+.-.. -....-+. -+.+||||.++|...
T Consensus 48 n~at~~Lf~~~--~t~e~l~~a~~~~l~~~I~~iGlyr~KAk~I~~~~~~l~e~~~g~vP~~~~eL~~LPGVGrKTAnvV 125 (211)
T COG0177 48 NKATPALFKRY--PTPEDLLNADEEELEELIKSIGLYRNKAKNIKELARILLEKFGGEVPDTREELLSLPGVGRKTANVV 125 (211)
T ss_pred HHHHHHHHHHc--CCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHHcCCCCCchHHHHHhCCCcchHHHHHH
Confidence 44556666654 49999999887655433 47888888877654332111 11111111 225566666666544
Q ss_pred HHh-CC
Q psy11423 540 ANY-FK 544 (655)
Q Consensus 540 ~~~-fg 544 (655)
+.. ||
T Consensus 126 L~~a~g 131 (211)
T COG0177 126 LSFAFG 131 (211)
T ss_pred HHhhcC
Confidence 443 44
No 145
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=91.72 E-value=0.3 Score=53.02 Aligned_cols=63 Identities=22% Similarity=0.231 Sum_probs=46.4
Q ss_pred hhhccccCCcHHHHHHHHHHHHHhcc--------cch-hHHHHHhCCCCccHHHHHHHHHh-CCCHHHHHhcC
Q psy11423 491 KNLLRLDRVSNKLANNILLAIQKSKL--------TTF-SRFIYALGIRHVGETTAKELANY-FKNLECMFKAT 553 (655)
Q Consensus 491 ~~L~~l~GfG~Ksa~nll~~I~~sk~--------~~l-~r~L~algIpgIG~~~Ak~L~~~-fgsl~~l~~as 553 (655)
++|.++||+|++.|++|.+=++.-+- .+. .-++.-+.|||||+++|+++.+. +.|+++|..+-
T Consensus 48 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~~~e~l~~~~p~~l~~l~~i~GiGpk~a~~l~~lGi~tl~eL~~a~ 120 (334)
T smart00483 48 KDLKGLPGIGDKIKKKIEEIIETGKSSKVLEILNDEVYKSLKLFTNVFGVGPKTAAKWYRKGIRTLEELKKNK 120 (334)
T ss_pred HHHhcCCCccHHHHHHHHHHHHhCcHHHHHHHhcCcHHHHHHHHHccCCcCHHHHHHHHHhCCCCHHHHHhcc
Confidence 47889999999999999887764221 111 23455559999999999999882 45888887763
No 146
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=91.70 E-value=0.15 Score=51.34 Aligned_cols=18 Identities=33% Similarity=0.447 Sum_probs=9.6
Q ss_pred hccccCCcHHHHHHHHHH
Q psy11423 493 LLRLDRVSNKLANNILLA 510 (655)
Q Consensus 493 L~~l~GfG~Ksa~nll~~ 510 (655)
|.++.|+|+|+|=+|+..
T Consensus 75 LisVnGIGpK~ALaiLs~ 92 (201)
T COG0632 75 LISVNGIGPKLALAILSN 92 (201)
T ss_pred HHccCCccHHHHHHHHcC
Confidence 445555555555555544
No 147
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=91.68 E-value=0.55 Score=50.97 Aligned_cols=57 Identities=11% Similarity=0.170 Sum_probs=41.1
Q ss_pred cchhHHHHHhCCCCccHHHHHHHHHh--CCCHH-HHHhc------CHHHHhcCCCCCHHHHHHHHH
Q psy11423 517 TTFSRFIYALGIRHVGETTAKELANY--FKNLE-CMFKA------TEEQLLNIPKIGSTTVKAFIK 573 (655)
Q Consensus 517 ~~l~r~L~algIpgIG~~~Ak~L~~~--fgsl~-~l~~a------s~eeL~~i~GIG~~~A~~I~~ 573 (655)
.++..+-....|||||++.|++|.+- -|++. .+... ...+|.+|+|||+++|..+++
T Consensus 42 ~~i~~~~~l~~lpgIG~~ia~kI~Eil~tG~~~~~~e~l~~~~p~~l~~l~~i~GiGpk~a~~l~~ 107 (334)
T smart00483 42 FPINSMKDLKGLPGIGDKIKKKIEEIIETGKSSKVLEILNDEVYKSLKLFTNVFGVGPKTAAKWYR 107 (334)
T ss_pred CCCCCHHHHhcCCCccHHHHHHHHHHHHhCcHHHHHHHhcCcHHHHHHHHHccCCcCHHHHHHHHH
Confidence 34444434558999999999988763 36655 22221 246899999999999999988
No 148
>KOG0967|consensus
Probab=91.56 E-value=2.4 Score=49.00 Aligned_cols=180 Identities=17% Similarity=0.230 Sum_probs=109.1
Q ss_pred cccccCCCCCCChHHHHHHHHHHHHhhccCCCceEEEEEecceeEEEEEE-eCCEEeEEEecCCCCccchhhhhhhhccc
Q psy11423 86 TFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRY-EYGYLKQASTRGDGNIGENITTNIHIIHK 164 (655)
Q Consensus 86 ~~pMlSL~k~~~~~el~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y-~~G~l~~a~TRGdG~~GeDvT~n~~~i~~ 164 (655)
..|||. | .-..+.+.++|++ ...|+||+|.||=-..+.+ ++|. +...+| .+|+.|....-|-.
T Consensus 344 lKPMLA--k--pTK~i~evl~rf~-------~~~FTCEyKYDGeRAQIH~~edG~-v~IfSR----N~E~~T~kYPDi~~ 407 (714)
T KOG0967|consen 344 LKPMLA--K--PTKGIQEVLERFQ-------DKAFTCEYKYDGERAQIHKLEDGT-VEIFSR----NSENNTGKYPDIIE 407 (714)
T ss_pred Ccchhc--C--cchhHHHHHHHhh-------CceeEEEeecCceeeeeEEccCCc-EEEEec----ccccccccCccHHH
Confidence 359975 2 2235666777764 4579999999999999986 6776 689999 78999987765433
Q ss_pred -CCcccccCCCCceEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCccc-ccccceEEEEEecccccC
Q psy11423 165 -IPLVLNIKYPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKI-NKNKILHFFAHGVGELRG 242 (655)
Q Consensus 165 -iP~~l~~~~~p~~~evRGEv~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~-~~~r~L~f~~y~~~~~~~ 242 (655)
+++.... --..+.+-||++--..+ |. --.+|. +.-+=++++-.. ...-..+.|+|++....+
T Consensus 408 ~~~~~~kp--~v~sFIlD~EvVA~Dr~----~~-----~IlpFQ-----vLSTRkRk~v~v~dikV~Vcvf~FDily~ng 471 (714)
T KOG0967|consen 408 VISKLKKP--SVKSFILDCEVVAWDRE----KG-----KILPFQ-----VLSTRKRKNVDVNDIKVKVCVFVFDILYLNG 471 (714)
T ss_pred HHHHhhCC--ccceeEEeeeEEEEecc----CC-----ccCchh-----hhhhhhccccchhhceEEEEEEEEeeeeeCC
Confidence 2322221 01468999999854332 10 112333 111112222211 112257888898877654
Q ss_pred CCCC-CCHHHHHHHHHhCCCCCCCCcee-----eCCHHHHHHHHHHHHHhhcCCCCccceEEEEECC
Q psy11423 243 MNMP-SSHSELLNWYQKIGLSICGEYSV-----LSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINC 303 (655)
Q Consensus 243 ~~~~-~~~~e~l~~L~~~GF~~~~~~~~-----~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~ 303 (655)
..+. ..-.+.-+.|.+-+=.++.+.++ +.+++++.+|.++.. +--.-|+-||.=+
T Consensus 472 ~~Li~~pL~eRR~~l~e~f~e~~g~f~fat~~~tn~~~eiq~Fl~~sv------~~~cEGlMvKtLd 532 (714)
T KOG0967|consen 472 ESLIQEPLRERRELLHESFKEIPGEFQFATSLDTNDIDEIQEFLEESV------QNSCEGLMVKTLD 532 (714)
T ss_pred hhhhhhhHHHHHHHHHhhcccCCCceeEeeeeccCCHHHHHHHHHHhh------ccCcceeEEEeec
Confidence 3322 45566677777764444444444 357899999987643 3346799998865
No 149
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=91.42 E-value=0.3 Score=56.60 Aligned_cols=51 Identities=18% Similarity=0.189 Sum_probs=46.3
Q ss_pred cccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHH
Q psy11423 458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAI 511 (655)
Q Consensus 458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I 511 (655)
...+|+|+||++..+|++.= .|+.+|...+.++|.++ |++++.|++|++.+
T Consensus 515 ~Ld~I~GiG~kr~~~Ll~~F--gs~~~ik~As~eeL~~v-gi~~~~A~~I~~~l 565 (567)
T PRK14667 515 ILDKIKGIGEVKKEIIYRNF--KTLYDFLKADDEELKKL-GIPPSVKQEVKKYL 565 (567)
T ss_pred ccccCCCCCHHHHHHHHHHh--CCHHHHHhCCHHHHHHc-CCCHHHHHHHHHHh
Confidence 35689999999999999875 59999999999999999 99999999998865
No 150
>PRK01172 ski2-like helicase; Provisional
Probab=91.26 E-value=0.74 Score=54.58 Aligned_cols=55 Identities=22% Similarity=0.311 Sum_probs=48.8
Q ss_pred HHHHHhCCCCccHHHHHHHHHh-CCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHh
Q psy11423 521 RFIYALGIRHVGETTAKELANY-FKNLECMFKATEEQLLNIPKIGSTTVKAFIKFI 575 (655)
Q Consensus 521 r~L~algIpgIG~~~Ak~L~~~-fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f 575 (655)
..+.-+.|||+|..+|++|.+. +.|+.+|..++.+++.+|.|+|++.|++|++..
T Consensus 610 ~~~~L~~ip~~~~~~a~~l~~~g~~~~~di~~~~~~~~~~i~~~~~~~~~~i~~~~ 665 (674)
T PRK01172 610 DLIDLVLIPKVGRVRARRLYDAGFKTVDDIARSSPERIKKIYGFSDTLANAIVNRA 665 (674)
T ss_pred HHHhhcCCCCCCHHHHHHHHHcCCCCHHHHHhCCHHHHHHHhccCHHHHHHHHHHH
Confidence 4444458999999999999874 899999999999999999999999999998874
No 151
>PRK10702 endonuclease III; Provisional
Probab=91.22 E-value=0.72 Score=46.86 Aligned_cols=43 Identities=16% Similarity=0.192 Sum_probs=30.0
Q ss_pred HHHHHHHHcCCCCChHHHhcCChhhhccc---cCCcHHHHHHHHHHHH
Q psy11423 468 KMIEKLVNANIVVTAVDLYKINFKNLLRL---DRVSNKLANNILLAIQ 512 (655)
Q Consensus 468 k~i~~L~~~g~I~~i~DL~~L~~~~L~~l---~GfG~Ksa~nll~~I~ 512 (655)
+....|+... .++++|..+..++|..+ -||-...|.+|++..+
T Consensus 49 ~~~~~L~~~~--pt~e~l~~a~~~~l~~~i~~~G~y~~kA~~l~~~a~ 94 (211)
T PRK10702 49 KATAKLYPVA--NTPAAMLELGVEGVKTYIKTIGLYNSKAENVIKTCR 94 (211)
T ss_pred HHHHHHHHHc--CCHHHHHCCCHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence 3445666543 58999999998888753 3676778887776554
No 152
>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=91.14 E-value=0.19 Score=39.67 Aligned_cols=26 Identities=35% Similarity=0.360 Sum_probs=20.2
Q ss_pred cccCCCCHHHHHHHHHcCCCCChHHHh
Q psy11423 460 MNIIGLGKKMIEKLVNANIVVTAVDLY 486 (655)
Q Consensus 460 l~I~GLG~k~i~~L~~~g~I~~i~DL~ 486 (655)
++|-|+||++++++++.|+ +|++||-
T Consensus 5 ~~I~GVG~~tA~~w~~~G~-rtl~Dl~ 30 (52)
T PF10391_consen 5 TGIWGVGPKTARKWYAKGI-RTLEDLR 30 (52)
T ss_dssp HTSTT--HHHHHHHHHTT---SHHHHH
T ss_pred hhcccccHHHHHHHHHhCC-CCHHHHh
Confidence 5799999999999999885 9999995
No 153
>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=91.08 E-value=0.21 Score=42.33 Aligned_cols=26 Identities=27% Similarity=0.488 Sum_probs=24.4
Q ss_pred CCCCccHHHHHHHHHhCCCHHHHHhc
Q psy11423 527 GIRHVGETTAKELANYFKNLECMFKA 552 (655)
Q Consensus 527 gIpgIG~~~Ak~L~~~fgsl~~l~~a 552 (655)
||||||+++|.+|+..|++++.+..+
T Consensus 26 gv~giG~k~A~~ll~~~~~~~~~~~~ 51 (75)
T cd00080 26 GVPGIGPKTALKLLKEYGSLENLLEN 51 (75)
T ss_pred CCCcccHHHHHHHHHHhCCHHHHHHH
Confidence 89999999999999999999998875
No 154
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=90.42 E-value=0.34 Score=56.66 Aligned_cols=52 Identities=23% Similarity=0.297 Sum_probs=46.9
Q ss_pred ccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHH
Q psy11423 459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQ 512 (655)
Q Consensus 459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~ 512 (655)
...|+|+|++++.+|++.= .|+.+|+..+.++|.+++|+|++.|++|.+.+.
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 4689999999999999865 589999999999999999999999999988764
No 155
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=90.17 E-value=0.43 Score=45.87 Aligned_cols=56 Identities=18% Similarity=0.245 Sum_probs=34.4
Q ss_pred HhcCChhhhccccCCcHHHHHHHHHHHHHhcccchhHHHHHhCCCCccHHHHHHHHHh
Q psy11423 485 LYKINFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANY 542 (655)
Q Consensus 485 L~~L~~~~L~~l~GfG~Ksa~nll~~I~~sk~~~l~r~L~algIpgIG~~~Ak~L~~~ 542 (655)
|-+.+.++|..|||+|+|+|+.|++.-++.- +|..+=.-..++|||+++-+++...
T Consensus 91 iNtAs~eeL~~lpgIG~~kA~aIi~yRe~~G--~f~sv~dL~~v~GiG~~~~ekl~~~ 146 (149)
T COG1555 91 INTASAEELQALPGIGPKKAQAIIDYREENG--PFKSVDDLAKVKGIGPKTLEKLKDY 146 (149)
T ss_pred ccccCHHHHHHCCCCCHHHHHHHHHHHHHcC--CCCcHHHHHhccCCCHHHHHHHHhh
Confidence 4445567777777788777777777665532 3333333336777777776665543
No 156
>smart00292 BRCT breast cancer carboxy-terminal domain.
Probab=90.03 E-value=0.57 Score=37.80 Aligned_cols=48 Identities=33% Similarity=0.451 Sum_probs=41.0
Q ss_pred CCCCeEeccccc-CccEEEecCCCC--chHHHHHHcCCeeeCHHHHHHHHh
Q psy11423 600 TKGGKVVNFISK-NTNYLVKGQKPG--KKLEKAIKLNIKILDEKNFVKIVK 647 (655)
Q Consensus 600 ~~G~~v~~sVsk-~t~ylv~g~~~g--~K~~kA~~lgi~ii~e~~f~~~l~ 647 (655)
.+||.+...++. +++++|+++... .+...|...+++|++++-+.+.+.
T Consensus 28 ~~Gg~~~~~~~~~~~thvi~~~~~~~~~~~~~~~~~~~~iV~~~Wi~~~~~ 78 (80)
T smart00292 28 ALGGKVTSSLSSKTTTHVIVGSPEGGKLELLLAIALGIPIVTEDWLLDCLK 78 (80)
T ss_pred HcCCEEecccCccceeEEEEcCCCCccHHHHHHHHcCCCCccHHHHHHHHH
Confidence 789999999998 888999988765 335778999999999999988775
No 157
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=89.68 E-value=0.4 Score=55.76 Aligned_cols=50 Identities=16% Similarity=0.196 Sum_probs=45.3
Q ss_pred ccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHH
Q psy11423 459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLA 510 (655)
Q Consensus 459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~ 510 (655)
...|+|+|++++.+|++.= .|+.+++..+.++|..+||+|++.|+.|.+.
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 4489999999999999975 5999999999999999999999999988754
No 158
>PRK09482 flap endonuclease-like protein; Provisional
Probab=88.98 E-value=0.49 Score=49.50 Aligned_cols=26 Identities=35% Similarity=0.709 Sum_probs=24.2
Q ss_pred CCCCccHHHHHHHHHhCCCHHHHHhc
Q psy11423 527 GIRHVGETTAKELANYFKNLECMFKA 552 (655)
Q Consensus 527 gIpgIG~~~Ak~L~~~fgsl~~l~~a 552 (655)
|+||||+++|.+|++.|+|++.|...
T Consensus 186 GVpGIG~KtA~~LL~~~gsle~i~~~ 211 (256)
T PRK09482 186 GVAGIGPKSAAELLNQFRSLENIYES 211 (256)
T ss_pred CCCCcChHHHHHHHHHhCCHHHHHHh
Confidence 89999999999999999999999854
No 159
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=88.82 E-value=0.25 Score=46.18 Aligned_cols=23 Identities=17% Similarity=0.541 Sum_probs=18.9
Q ss_pred CCCCCCCCCCcceeecCceeEEecC
Q psy11423 414 IPNICPICNSKIIYIESNLIARCSG 438 (655)
Q Consensus 414 ~P~~CP~C~~~l~~~~~~~~~~C~n 438 (655)
+-.|||.||.||.+.+| ..||++
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 34699999999998655 669988
No 160
>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=88.14 E-value=0.85 Score=49.12 Aligned_cols=53 Identities=23% Similarity=0.233 Sum_probs=47.9
Q ss_pred ccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHHHh
Q psy11423 461 NIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKS 514 (655)
Q Consensus 461 ~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~s 514 (655)
.=.|||+.++++|-++|+ .|+.|+...+..+|..+.|+++..+++|+++..+.
T Consensus 5 ~~~g~~~~~~~~L~~~g~-~t~~~~~~~~~~~L~~~~gls~~~~~~i~~~~~~~ 57 (313)
T TIGR02238 5 QAHGINAADIKKLKSAGI-CTVNGVIMTTRRALCKIKGLSEAKVDKIKEAASKI 57 (313)
T ss_pred hcCCCCHHHHHHHHHcCC-CcHHHHHhCCHHHHHHhcCCCHHHHHHHHHHHHhh
Confidence 346799999999999995 89999999999999999999999999999987654
No 161
>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=87.97 E-value=1.6 Score=33.37 Aligned_cols=43 Identities=26% Similarity=0.289 Sum_probs=35.7
Q ss_pred cHHHHHHHHH-hCCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHH
Q psy11423 532 GETTAKELAN-YFKNLECMFKATEEQLLNIPKIGSTTVKAFIKF 574 (655)
Q Consensus 532 G~~~Ak~L~~-~fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~ 574 (655)
.+..+.+|.+ .|.+++.+..++.++|..++|+++..+..|+.-
T Consensus 2 ~~~~~~~L~~~G~~s~e~la~~~~~eL~~i~g~~~e~a~~ii~~ 45 (50)
T TIGR01954 2 DEEIAQLLVEEGFTTVEDLAYVPIDELLSIEGFDEETAKELINR 45 (50)
T ss_pred CHHHHHHHHHcCCCCHHHHHccCHHHHhcCCCCCHHHHHHHHHH
Confidence 3456666665 599999999999999999999999988888653
No 162
>PTZ00035 Rad51 protein; Provisional
Probab=87.47 E-value=0.94 Score=49.25 Aligned_cols=54 Identities=24% Similarity=0.239 Sum_probs=48.3
Q ss_pred cccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHHHh
Q psy11423 460 MNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKS 514 (655)
Q Consensus 460 l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~s 514 (655)
+.=+||++..+++|-++|+ .|+.||...+..+|..+.|+++..|++|++...+.
T Consensus 26 l~~~g~~~~~~~kL~~~g~-~t~~~~~~~~~~~L~~~~gis~~~~~~i~~~~~~~ 79 (337)
T PTZ00035 26 LQSAGINAADIKKLKEAGI-CTVESVAYATKKDLCNIKGISEAKVEKIKEAASKL 79 (337)
T ss_pred HhcCCCCHHHHHHHHHcCC-CcHHHHHhCCHHHHHHhhCCCHHHHHHHHHHHHHh
Confidence 4448999999999999985 89999999999999999999999999999877653
No 163
>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=87.33 E-value=0.7 Score=47.79 Aligned_cols=26 Identities=31% Similarity=0.556 Sum_probs=24.2
Q ss_pred CCCCccHHHHHHHHHhCCCHHHHHhc
Q psy11423 527 GIRHVGETTAKELANYFKNLECMFKA 552 (655)
Q Consensus 527 gIpgIG~~~Ak~L~~~fgsl~~l~~a 552 (655)
||||||+++|.+|++.|+|++++...
T Consensus 187 Gv~GiG~ktA~~Ll~~~gsle~i~~~ 212 (240)
T cd00008 187 GVPGIGEKTAAKLLKEYGSLEGILEN 212 (240)
T ss_pred CCCccCHHHHHHHHHHhCCHHHHHHh
Confidence 89999999999999999999999864
No 164
>smart00475 53EXOc 5'-3' exonuclease.
Probab=87.31 E-value=0.62 Score=48.80 Aligned_cols=26 Identities=35% Similarity=0.583 Sum_probs=24.1
Q ss_pred CCCCccHHHHHHHHHhCCCHHHHHhc
Q psy11423 527 GIRHVGETTAKELANYFKNLECMFKA 552 (655)
Q Consensus 527 gIpgIG~~~Ak~L~~~fgsl~~l~~a 552 (655)
|+||||+++|.+|++.|+|++.+...
T Consensus 190 GV~GIG~KtA~~Ll~~ygsle~i~~~ 215 (259)
T smart00475 190 GVPGIGEKTAAKLLKEFGSLENILEN 215 (259)
T ss_pred CCCCCCHHHHHHHHHHhCCHHHHHHH
Confidence 88999999999999999999999764
No 165
>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=87.00 E-value=0.042 Score=49.32 Aligned_cols=25 Identities=28% Similarity=0.507 Sum_probs=21.8
Q ss_pred CCCCccHHHHHHHHHhCCCHHHHHh
Q psy11423 527 GIRHVGETTAKELANYFKNLECMFK 551 (655)
Q Consensus 527 gIpgIG~~~Ak~L~~~fgsl~~l~~ 551 (655)
|+||||+++|.+|+++|||+++|..
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 8999999999999999999998876
No 166
>PRK00420 hypothetical protein; Validated
Probab=86.50 E-value=0.45 Score=43.48 Aligned_cols=24 Identities=17% Similarity=0.534 Sum_probs=18.7
Q ss_pred CCCCCCCCCCcceeecCceeEEecC
Q psy11423 414 IPNICPICNSKIIYIESNLIARCSG 438 (655)
Q Consensus 414 ~P~~CP~C~~~l~~~~~~~~~~C~n 438 (655)
+..+||.||++|.+..+ ...+|++
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 45899999999997433 3678987
No 167
>PRK05182 DNA-directed RNA polymerase subunit alpha; Provisional
Probab=86.49 E-value=1.1 Score=48.18 Aligned_cols=51 Identities=20% Similarity=0.181 Sum_probs=45.6
Q ss_pred cCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHHH
Q psy11423 462 IIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK 513 (655)
Q Consensus 462 I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~ 513 (655)
-=+|.-.+..-|-.+| |.++.||..++.++|.++++||+||.+.|.+.+++
T Consensus 253 ~L~LS~R~~n~Lk~~~-I~ti~dL~~~~~~~l~~~~n~G~ksl~ei~~~L~~ 303 (310)
T PRK05182 253 ELELSVRSYNCLKRAG-INTIGDLVQRTEEELLKTRNLGKKSLEEIKEKLAE 303 (310)
T ss_pred HhccchHHHHHHHHcC-CcCHHHHHhCCHHHHhcCCCCChhhHHHHHHHHHH
Confidence 3477888888888887 79999999999999999999999999999998876
No 168
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=86.47 E-value=1.2 Score=48.44 Aligned_cols=54 Identities=19% Similarity=0.168 Sum_probs=46.5
Q ss_pred ccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHHHhcc
Q psy11423 461 NIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKL 516 (655)
Q Consensus 461 ~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~sk~ 516 (655)
.||++++..++.|+++=. ++..+++.+.++|...+|+|++.|..|.+.+.+.+.
T Consensus 291 ~IPrl~k~iAk~Ll~~FG--SL~~Il~As~eeL~~VeGIGe~rA~~I~e~l~Rl~e 344 (352)
T PRK13482 291 KIPRLPSAVIENLVEHFG--SLQGLLAASIEDLDEVEGIGEVRARAIREGLSRLAE 344 (352)
T ss_pred cCCCCCHHHHHHHHHHcC--CHHHHHcCCHHHHhhCCCcCHHHHHHHHHHHHHHHH
Confidence 489999999999998753 889999999999999999999999998888766543
No 169
>PLN03187 meiotic recombination protein DMC1 homolog; Provisional
Probab=86.37 E-value=1.2 Score=48.57 Aligned_cols=54 Identities=26% Similarity=0.249 Sum_probs=48.0
Q ss_pred ccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHHH
Q psy11423 459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK 513 (655)
Q Consensus 459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~ 513 (655)
.|.=.||++.++++|-++|+ .|+.||...+..+|..+.|+++..+++|++...+
T Consensus 33 ~l~~~g~~~~~~~kL~~~g~-~tv~~~~~~~~~~L~~~~g~s~~~~~ki~~~a~~ 86 (344)
T PLN03187 33 KLISQGINAGDVKKLQDAGI-YTCNGLMMHTKKNLTGIKGLSEAKVDKICEAAEK 86 (344)
T ss_pred HHhhCCCCHHHHHHHHHcCC-CcHHHHHhCCHHHHHHhcCCCHHHHHHHHHHHHH
Confidence 34447899999999999995 8999999999999999999999999999987654
No 170
>smart00478 ENDO3c endonuclease III. includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=86.02 E-value=3 Score=39.35 Aligned_cols=41 Identities=20% Similarity=0.113 Sum_probs=26.0
Q ss_pred HHHHHHHcCCCCChHHHhcCChhhhccc---cCCcHHHHHHHHHHH
Q psy11423 469 MIEKLVNANIVVTAVDLYKINFKNLLRL---DRVSNKLANNILLAI 511 (655)
Q Consensus 469 ~i~~L~~~g~I~~i~DL~~L~~~~L~~l---~GfG~Ksa~nll~~I 511 (655)
.+.+|.+.- .++.+|..++.++|..+ =||....++.|.+..
T Consensus 13 ~~~~l~~~~--~~~~~l~~~~~~eL~~~l~~~g~~~~ka~~i~~~a 56 (149)
T smart00478 13 ATERLFEKF--PTPEDLAAADEEELEELIRPLGFYRRKAKYLIELA 56 (149)
T ss_pred HHHHHHHHC--CCHHHHHCCCHHHHHHHHHHcCChHHHHHHHHHHH
Confidence 334444432 38888888888777332 177777887777543
No 171
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=85.63 E-value=0.64 Score=38.10 Aligned_cols=28 Identities=29% Similarity=0.546 Sum_probs=20.0
Q ss_pred HHhcCHHHHhcCCCCCHHHHHHHHHHhc
Q psy11423 549 MFKATEEQLLNIPKIGSTTVKAFIKFIN 576 (655)
Q Consensus 549 l~~as~eeL~~i~GIG~~~A~~I~~~f~ 576 (655)
|..|+.++|.++||||+..|++|++|-.
T Consensus 8 iN~as~~eL~~lpgi~~~~A~~Iv~~R~ 35 (65)
T PF12836_consen 8 INTASAEELQALPGIGPKQAKAIVEYRE 35 (65)
T ss_dssp TTTS-HHHHHTSTT--HHHHHHHHHHHH
T ss_pred CccCCHHHHHHcCCCCHHHHHHHHHHHH
Confidence 4567888888888888888888888753
No 172
>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=85.12 E-value=2.9 Score=44.20 Aligned_cols=78 Identities=18% Similarity=0.138 Sum_probs=48.2
Q ss_pred HHHHHHcCCCCChHHHhcCChhhhc----cccCCcHHHHHHHHHHHHHhcc---cchhHHHHH-hCCCCccHHHHHHHHH
Q psy11423 470 IEKLVNANIVVTAVDLYKINFKNLL----RLDRVSNKLANNILLAIQKSKL---TTFSRFIYA-LGIRHVGETTAKELAN 541 (655)
Q Consensus 470 i~~L~~~g~I~~i~DL~~L~~~~L~----~l~GfG~Ksa~nll~~I~~sk~---~~l~r~L~a-lgIpgIG~~~Ak~L~~ 541 (655)
..+|++. ..++.+|..++.++|. .+ ||- ..|.+|.+..+.-.. ..+..-... +.+||||+++|..++.
T Consensus 48 ~~rl~~~--fpt~~~La~a~~eeL~~~~~~l-G~y-~RAr~L~~~A~~i~~~~~g~~p~~~~~L~~LpGIG~~TA~~Il~ 123 (275)
T TIGR01084 48 FERFLER--FPTVQALANAPQDEVLKLWEGL-GYY-ARARNLHKAAQEVVEEFGGEFPQDFEDLAALPGVGRYTAGAILS 123 (275)
T ss_pred HHHHHHh--CCCHHHHHCcCHHHHHHHHHHC-CcH-HHHHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCCCHHHHHHHHH
Confidence 3444443 2689999999998884 44 665 457788776653221 112222333 3899999999987775
Q ss_pred -hCCCHHHHHh
Q psy11423 542 -YFKNLECMFK 551 (655)
Q Consensus 542 -~fgsl~~l~~ 551 (655)
.|+-...+.+
T Consensus 124 ~a~~~~~~~vD 134 (275)
T TIGR01084 124 FALNKPYPILD 134 (275)
T ss_pred HHCCCCCCcch
Confidence 4664443333
No 173
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=84.85 E-value=2.3 Score=40.49 Aligned_cols=80 Identities=21% Similarity=0.206 Sum_probs=40.4
Q ss_pred HHHHHHHcCCCCChHHHhcCChhhhccccCCc---HHHHHHHHHHHHHhcccchhHHHHHhCCCCccHHHHHHHHHhCCC
Q psy11423 469 MIEKLVNANIVVTAVDLYKINFKNLLRLDRVS---NKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKN 545 (655)
Q Consensus 469 ~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG---~Ksa~nll~~I~~sk~~~l~r~L~algIpgIG~~~Ak~L~~~fgs 545 (655)
.+.+|.+... -++++|..++.++|..+ +.+ ..+|+.|.+..+ .+.+.+.+
T Consensus 21 ~~~~l~~~~g-pt~~~l~~~~~~~l~~~-~~~~G~~~kA~~i~~~a~-------------------------~~~~~~~~ 73 (158)
T cd00056 21 AYERLFERYG-PTPEALAAADEEELREL-IRSLGYRRKAKYLKELAR-------------------------AIVEGFGG 73 (158)
T ss_pred HHHHHHHHhC-CCHHHHHCCCHHHHHHH-HHhcChHHHHHHHHHHHH-------------------------HHHHHcCC
Confidence 3344444432 57788887777777664 222 345554444332 22222222
Q ss_pred HHHHHhcCHHHHhcCCCCCHHHHHHHHHHh
Q psy11423 546 LECMFKATEEQLLNIPKIGSTTVKAFIKFI 575 (655)
Q Consensus 546 l~~l~~as~eeL~~i~GIG~~~A~~I~~~f 575 (655)
...=.....++|.+++|||+++|+.+.-|.
T Consensus 74 ~~~~~~~~~~~L~~l~GIG~~tA~~~l~~~ 103 (158)
T cd00056 74 LVLDDPDAREELLALPGVGRKTANVVLLFA 103 (158)
T ss_pred ccCCCcccHHHHHcCCCCCHHHHHHHHHHH
Confidence 111001124567777777777777766543
No 174
>COG2231 Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]
Probab=84.82 E-value=4.2 Score=40.99 Aligned_cols=115 Identities=19% Similarity=0.297 Sum_probs=58.6
Q ss_pred HHHHHHHHcCCCCChHHHhcCChhhhccc---cCCcHHHHHHH----------HHHHHHhcccchhHHHHHhCCCCccHH
Q psy11423 468 KMIEKLVNANIVVTAVDLYKINFKNLLRL---DRVSNKLANNI----------LLAIQKSKLTTFSRFIYALGIRHVGET 534 (655)
Q Consensus 468 k~i~~L~~~g~I~~i~DL~~L~~~~L~~l---~GfG~Ksa~nl----------l~~I~~sk~~~l~r~L~algIpgIG~~ 534 (655)
+-++.|-.++. -++..|..++.++|+.+ -||=..+|..| ..+++..+...++.+| |+|.|||+.
T Consensus 50 kAlenLk~~~~-~~l~~I~~~~~~~L~elIrpsGFYnqKa~rLk~l~k~l~~~~~~~~~~~~~~~R~~L--L~iKGIG~E 126 (215)
T COG2231 50 KALENLKNEGI-LNLKKILKLDEEELAELIRPSGFYNQKAKRLKALSKNLAKFFINLESFKSEVLREEL--LSIKGIGKE 126 (215)
T ss_pred HHHHHHHHccc-CCHHHHhcCCHHHHHHHHhccchHHHHHHHHHHHHHHHHHHhhhhhccchHHHHHHH--HccCCcchh
Confidence 33455555553 45777777776666554 56666555555 2222222222222232 367777777
Q ss_pred HHHHHHHh-CCCHHHHHhc-CHHHHhcCCCCCHHHHHHHHHHhcC--hhHHHHHH
Q psy11423 535 TAKELANY-FKNLECMFKA-TEEQLLNIPKIGSTTVKAFIKFINQ--PLHRLLIS 585 (655)
Q Consensus 535 ~Ak~L~~~-fgsl~~l~~a-s~eeL~~i~GIG~~~A~~I~~~f~~--~~n~~li~ 585 (655)
+|..|+-. |.-...+..+ +.--|..+-++-.+.-++|.++|.. +++..+.+
T Consensus 127 TaDsILlYa~~rp~FVvD~Yt~R~l~rlg~i~~k~ydeik~~fe~~l~~~~~lyq 181 (215)
T COG2231 127 TADSILLYALDRPVFVVDKYTRRLLSRLGGIEEKKYDEIKELFEENLPENLRLYQ 181 (215)
T ss_pred hHHHHHHHHhcCcccchhHHHHHHHHHhcccccccHHHHHHHHHhcchhHHHHHH
Confidence 77666543 4333333332 2333555555555556667766652 44444333
No 175
>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=84.78 E-value=1.5 Score=47.00 Aligned_cols=53 Identities=17% Similarity=0.201 Sum_probs=45.6
Q ss_pred cccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHHH
Q psy11423 460 MNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK 513 (655)
Q Consensus 460 l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~ 513 (655)
++-=+|.-.+..-|-.+| |.++.||..++.++|+.+++||+||.+.|.+.+++
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 344467777888888877 69999999999999999999999999999988865
No 176
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=84.28 E-value=0.78 Score=30.65 Aligned_cols=18 Identities=33% Similarity=0.473 Sum_probs=11.2
Q ss_pred hhccccCCcHHHHHHHHH
Q psy11423 492 NLLRLDRVSNKLANNILL 509 (655)
Q Consensus 492 ~L~~l~GfG~Ksa~nll~ 509 (655)
+|..++|+|+|+|++|++
T Consensus 2 ~L~~i~GiG~k~A~~il~ 19 (26)
T smart00278 2 ELLKVPGIGPKTAEKILE 19 (26)
T ss_pred hhhhCCCCCHHHHHHHHH
Confidence 455666666666666664
No 177
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=84.24 E-value=1.1 Score=52.48 Aligned_cols=56 Identities=16% Similarity=0.238 Sum_probs=48.5
Q ss_pred cccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHHHhccc
Q psy11423 458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKLT 517 (655)
Q Consensus 458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~sk~~ 517 (655)
...+|+|+|+++..+|++.= .|+.+|...+.++|.++ +|+|.|++|++.+...-..
T Consensus 553 ~L~~IpGIG~kr~~~LL~~F--gSi~~I~~As~eeL~~v--i~~k~A~~I~~~l~~~~~~ 608 (624)
T PRK14669 553 ELLEIPGVGAKTVQRLLKHF--GSLERVRAATETQLAAV--VGRAAAEAIIAHFTTEEAA 608 (624)
T ss_pred HHhcCCCCCHHHHHHHHHHc--CCHHHHHhCCHHHHHHH--hCHHHHHHHHHHhcCcCCC
Confidence 36699999999999999864 58999999999999998 9999999999988754443
No 178
>PRK14976 5'-3' exonuclease; Provisional
Probab=84.04 E-value=0.86 Score=48.32 Aligned_cols=25 Identities=32% Similarity=0.667 Sum_probs=23.6
Q ss_pred CCCCccHHHHHHHHHhCCCHHHHHh
Q psy11423 527 GIRHVGETTAKELANYFKNLECMFK 551 (655)
Q Consensus 527 gIpgIG~~~Ak~L~~~fgsl~~l~~ 551 (655)
|+||||+++|..|++.|+|++.+..
T Consensus 195 GVpGIG~KtA~~LL~~~gsle~i~~ 219 (281)
T PRK14976 195 GVKGIGPKTAIKLLNKYGNIENIYE 219 (281)
T ss_pred CCCcccHHHHHHHHHHcCCHHHHHH
Confidence 8999999999999999999999875
No 179
>KOG2534|consensus
Probab=84.01 E-value=2 Score=45.90 Aligned_cols=70 Identities=19% Similarity=0.144 Sum_probs=47.5
Q ss_pred hhhhccccCCcHHHHHHHHHHHHHhc--------ccchhHHH-HHhCCCCccHHHHHHHHH-hCCCHHHHHhcCHHHHhc
Q psy11423 490 FKNLLRLDRVSNKLANNILLAIQKSK--------LTTFSRFI-YALGIRHVGETTAKELAN-YFKNLECMFKATEEQLLN 559 (655)
Q Consensus 490 ~~~L~~l~GfG~Ksa~nll~~I~~sk--------~~~l~r~L-~algIpgIG~~~Ak~L~~-~fgsl~~l~~as~eeL~~ 559 (655)
.+++..|||+|+|.|++|.+=++.-. +-+....| +=-.|-|||.++|++--. -|.|++.+. -+.+.|..
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 57788899999999988877665322 11222222 223899999999987654 588998888 44555554
Q ss_pred C
Q psy11423 560 I 560 (655)
Q Consensus 560 i 560 (655)
-
T Consensus 134 q 134 (353)
T KOG2534|consen 134 Q 134 (353)
T ss_pred H
Confidence 3
No 180
>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=83.93 E-value=15 Score=42.64 Aligned_cols=178 Identities=15% Similarity=0.094 Sum_probs=98.1
Q ss_pred ccchhhhhhhhcccCCcccccCCCCceEEEEEEEEe----ehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCccccc
Q psy11423 151 IGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLI----YKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINK 226 (655)
Q Consensus 151 ~GeDvT~n~~~i~~iP~~l~~~~~p~~~evRGEv~~----~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~ 226 (655)
.|+|+|+....|-..-..+. ...+.+-||+++ ...+|+.+... ++. ..
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 68999988876654333332 236899999998 44567765331 010 12
Q ss_pred ccceEEEEEecccccCCCC-CCCHHHHHHHHHhCCCCC-CCCceeeC-CHHHHHHHHHHHHHhhcCCCCccceEEEEECC
Q psy11423 227 NKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLSI-CGEYSVLS-GVNKLIEFYKKINIKRFNLPYEIDGVVYKINC 303 (655)
Q Consensus 227 ~r~L~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~GF~~-~~~~~~~~-~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~ 303 (655)
..++.|++|++...++.++ .....+..+.|+++-=+. .....+.. ..++..++++...+ -...|||+|--+
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 3579999999987665443 246777777777652111 11111111 11222355554432 236899999988
Q ss_pred hhhhhhhCCCCCCCCceEeecCCcceeeEEEEEEEEeecCcceeeeE--EEEEEEEECCEE--EEEe-eCCCHHHHHh
Q psy11423 304 LSTQKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQIGRTGIITPV--ALLKPVLIDGIT--ITRA-TLHNESEIYR 376 (655)
Q Consensus 304 ~~~~~~lG~ts~~PrwaiA~Kf~~~~~~T~v~~I~~qvGRTG~itPv--A~lePV~l~G~t--Vsra-tLhN~~~i~~ 376 (655)
..++ -| ++..| +-+|. ....+..|.+....- |++... +..+ +|.- |-++ |..+.+..++
T Consensus 129 S~Y~--~G---Rs~~W-lKlK~-~~~~e~vI~Gy~~~~---r~~gslLlg~~d----~g~l~~vgkVgsGfsd~~~~~ 192 (552)
T TIGR02776 129 SPYR--SG---RSKDW-LKLKC-RRRQEFVITGYTPPN---RRFGALLVGVYE----GGQLVYAGKVGTGFGADTLKT 192 (552)
T ss_pred CCCC--CC---CCcch-hcccc-cccceEEEEEEecCC---CceeeEEEEEec----CCeEEEEEEEcCCCCHHHHHH
Confidence 6654 23 55667 44553 344566676655443 222222 1111 5553 3455 6677666653
No 181
>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=83.90 E-value=4.6 Score=40.19 Aligned_cols=41 Identities=20% Similarity=0.180 Sum_probs=26.3
Q ss_pred HHHHHHcCCCCChHHHhcCChhhhccc---cCCcHHHHHHHHHHHH
Q psy11423 470 IEKLVNANIVVTAVDLYKINFKNLLRL---DRVSNKLANNILLAIQ 512 (655)
Q Consensus 470 i~~L~~~g~I~~i~DL~~L~~~~L~~l---~GfG~Ksa~nll~~I~ 512 (655)
..+|++. + .++.+|..++.++|..+ -||...+|+.|.+-.+
T Consensus 48 ~~~l~~~-~-pt~~~l~~~~~~~L~~~ir~~G~~~~Ka~~i~~~a~ 91 (191)
T TIGR01083 48 TKKLFEV-Y-PTPQALAQAGLEELEEYIKSIGLYRNKAKNIIALCR 91 (191)
T ss_pred HHHHHHH-C-CCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHH
Confidence 3445553 2 48899999988887432 2776677777765433
No 182
>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=83.68 E-value=3.9 Score=40.55 Aligned_cols=141 Identities=16% Similarity=0.144 Sum_probs=76.9
Q ss_pred eEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhhhcc--cCCccccc--CCCCceEEEEEEEEeehhhHHHH
Q psy11423 119 EYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIH--KIPLVLNI--KYPPELLEVRCEVLIYKKDFIKL 194 (655)
Q Consensus 119 ~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~--~iP~~l~~--~~~p~~~evRGEv~~~~~~F~~~ 194 (655)
.|+|.+|-||+-.-|...++ =+-++.|- .++..+. ..|....+ .......-+-||+++....
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 69999999999998755443 34455653 3344433 24544420 0123468899999987442
Q ss_pred HHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCC-CCCHHHHHHHHHh--------C----C-
Q psy11423 195 NKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQK--------I----G- 260 (655)
Q Consensus 195 n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~-~~~~~e~l~~L~~--------~----G- 260 (655)
. .+.+.|.+|++....|... ..+..+.+..|++ . |
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 3368999999987655432 1345566666542 1 1
Q ss_pred CCC--CCCceeeCCH---HHHHHHHHHHHHhhcCCCCccceEEEEECChhh
Q psy11423 261 LSI--CGEYSVLSGV---NKLIEFYKKINIKRFNLPYEIDGVVYKINCLST 306 (655)
Q Consensus 261 F~~--~~~~~~~~~~---~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~ 306 (655)
... .+......+. ..+.... .......+++++||+|+.-.+..+
T Consensus 132 ~~~~~~pf~i~~K~~~~~~~~~~~~--~~~~~~~l~h~~DGLIFtp~~~pY 180 (192)
T PF01331_consen 132 IKKKKEPFSIRIKDFFPIYQIEKLL--FEEFIPKLPHETDGLIFTPVNTPY 180 (192)
T ss_dssp CTCTTSSSEEEE---EEGGGHHHHC--HHCCCCCTTSTEEEEEEEESSSB-
T ss_pred ccccccceeeeccccHHHHhhHHHH--HHHhhccCCCCCCEEEEecCCCCc
Confidence 010 1111111211 2222211 334567899999999998877543
No 183
>PRK02362 ski2-like helicase; Provisional
Probab=83.61 E-value=3 Score=50.10 Aligned_cols=54 Identities=20% Similarity=0.345 Sum_probs=47.1
Q ss_pred HHHHHhCCCCccHHHHHHHHHh-CCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHhc
Q psy11423 521 RFIYALGIRHVGETTAKELANY-FKNLECMFKATEEQLLNIPKIGSTTVKAFIKFIN 576 (655)
Q Consensus 521 r~L~algIpgIG~~~Ak~L~~~-fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f~ 576 (655)
..+.-+.|||+|+++|++|.+. +.|+++|..++.++|.++ +|+++|++|.+-+.
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 4444558999999999999874 779999999999999999 99999999988765
No 184
>PRK13766 Hef nuclease; Provisional
Probab=83.52 E-value=1.6 Score=52.42 Aligned_cols=50 Identities=12% Similarity=0.216 Sum_probs=38.4
Q ss_pred ccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHH
Q psy11423 461 NIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQ 512 (655)
Q Consensus 461 ~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~ 512 (655)
.|+|+|++++.+|++.= .++.+++.++.++|..++|+|++.++.|.+.++
T Consensus 719 ~ipgig~~~a~~Ll~~f--gs~~~i~~as~~~L~~i~Gig~~~a~~i~~~~~ 768 (773)
T PRK13766 719 SLPDVGPVLARNLLEHF--GSVEAVMTASEEELMEVEGIGEKTAKRIREVVT 768 (773)
T ss_pred cCCCCCHHHHHHHHHHc--CCHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHh
Confidence 67888888888887753 477888888888888888888888887776654
No 185
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=83.45 E-value=1.6 Score=45.43 Aligned_cols=51 Identities=22% Similarity=0.363 Sum_probs=42.8
Q ss_pred cccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHH
Q psy11423 460 MNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQ 512 (655)
Q Consensus 460 l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~ 512 (655)
+.|||+|++.+..|++.= .++.++++++.+.|...+|+|+|.|..|..-+.
T Consensus 185 ~s~pgig~~~a~~ll~~f--gS~~~~~tas~~eL~~v~gig~k~A~~I~~~~~ 235 (254)
T COG1948 185 ESIPGIGPKLAERLLKKF--GSVEDVLTASEEELMKVKGIGEKKAREIYRFLR 235 (254)
T ss_pred HcCCCccHHHHHHHHHHh--cCHHHHhhcCHHHHHHhcCccHHHHHHHHHHHh
Confidence 468899999999998764 488899999989999999999999988776554
No 186
>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=82.87 E-value=1.2 Score=32.92 Aligned_cols=28 Identities=21% Similarity=0.507 Sum_probs=21.8
Q ss_pred CCCCCCCCcceeec--CceeEEecCCCcCCH
Q psy11423 416 NICPICNSKIIYIE--SNLIARCSGSWIECI 444 (655)
Q Consensus 416 ~~CP~C~~~l~~~~--~~~~~~C~n~~~~C~ 444 (655)
..||.||+.|+... .+..+-|+|.+. |.
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 36999999998553 358899999766 84
No 187
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=82.42 E-value=2 Score=46.20 Aligned_cols=148 Identities=20% Similarity=0.338 Sum_probs=73.9
Q ss_pred CCCCCCCCC-cceeecCceeEEecCCCcCCHHHHHhhccc-------cccccccccCCCCHHHHHHHHHcCCCCChH---
Q psy11423 415 PNICPICNS-KIIYIESNLIARCSGSWIECIAQRKAGLQH-------FSSRKAMNIIGLGKKMIEKLVNANIVVTAV--- 483 (655)
Q Consensus 415 P~~CP~C~~-~l~~~~~~~~~~C~n~~~~C~~q~~~~i~~-------F~sk~~l~I~GLG~k~i~~L~~~g~I~~i~--- 483 (655)
+..||.||+ .++.+.....+.|.+ |-..+-+++.. |..-+..+=.-.|..+-..+.+.|+-+.+.
T Consensus 11 ~~~Cp~Cg~~~iv~d~~~Ge~vC~~----CG~Vl~e~~iD~g~EWR~f~~~~~~~~~RvG~~~~~~~~~~gl~T~I~~~~ 86 (310)
T PRK00423 11 KLVCPECGSDKLIYDYERGEIVCAD----CGLVIEENIIDQGPEWRAFDPEQREKRSRVGAPMTYTIHDKGLSTDIDWRN 86 (310)
T ss_pred CCcCcCCCCCCeeEECCCCeEeecc----cCCcccccccccCCCccCCCccccCCccccCCCCCccccCCCCceEeecCC
Confidence 457999999 455555567899988 87767666653 332222232334443333444444422221
Q ss_pred -HHhc--CC---hhhhccccC------CcHHHHHHHHHHHHHhcccchhHHHHHhCCCCccHHHHHHHHHhC--------
Q psy11423 484 -DLYK--IN---FKNLLRLDR------VSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYF-------- 543 (655)
Q Consensus 484 -DL~~--L~---~~~L~~l~G------fG~Ksa~nll~~I~~sk~~~l~r~L~algIpgIG~~~Ak~L~~~f-------- 543 (655)
|-+. +. ...+..|.. ...+...+|..++.. +.++-..|++|..=..+|..|.+.+
T Consensus 87 ~~~~g~~l~~~~~~~~~rl~~~~~~~~~~~~~er~l~~a~~~-----I~~~~~~L~Lp~~v~e~A~~iyk~~~~~~~~rg 161 (310)
T PRK00423 87 KDSYGKSISGKNRAQLYRLRKWQRRIRVSNAAERNLAFALSE-----LDRIASQLGLPRSVREEAAVIYRKAVEKGLIRG 161 (310)
T ss_pred cccccccccHHHHHHHHHHHHHhhhcccCChHhHHHHHHHHH-----HHHHHHHcCCCHHHHHHHHHHHHHHHhcCcccC
Confidence 0010 10 011111111 112333444444432 4677788899865555665555433
Q ss_pred CCHHHHHhc-------------CHHHHhcCCCCCHHHHHHH
Q psy11423 544 KNLECMFKA-------------TEEQLLNIPKIGSTTVKAF 571 (655)
Q Consensus 544 gsl~~l~~a-------------s~eeL~~i~GIG~~~A~~I 571 (655)
.+++.+..| +..|+..+-++..+...+.
T Consensus 162 rs~~~i~AAclYiACR~~~~prtl~eI~~~~~v~~k~i~~~ 202 (310)
T PRK00423 162 RSIEGVVAAALYAACRRCKVPRTLDEIAEVSRVSRKEIGRC 202 (310)
T ss_pred CCHHHHHHHHHHHHHHHcCCCcCHHHHHHHhCCCHHHHHHH
Confidence 245566554 3456666666665544443
No 188
>COG5241 RAD10 Nucleotide excision repair endonuclease NEF1, RAD10 subunit [DNA replication, recombination, and repair]
Probab=82.00 E-value=0.82 Score=44.95 Aligned_cols=52 Identities=17% Similarity=0.242 Sum_probs=49.0
Q ss_pred CCCCccHHHHHHHHHhCCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHhcCh
Q psy11423 527 GIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQP 578 (655)
Q Consensus 527 gIpgIG~~~Ak~L~~~fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f~~~ 578 (655)
-|++|.+.-+.-++..+|++.....|+.+|+..+.|+|+..|+.+++|++.|
T Consensus 171 ~i~~Vnksds~~~L~d~g~L~rf~gaSrdE~e~l~g~g~~ka~~~ieyln~p 222 (224)
T COG5241 171 LIFIVNKSDSEDTLNDIGKLCRFNGASRDEFELLLGFGFEKAAKYIEYLNLP 222 (224)
T ss_pred EEEeeccccHHHHHHHHHHHHHHhccchhHHHHHHccCHHHHHHHHHHhccc
Confidence 5799999999999999999999999999999999999999999999999865
No 189
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]
Probab=81.93 E-value=1.6 Score=50.68 Aligned_cols=119 Identities=17% Similarity=0.199 Sum_probs=73.7
Q ss_pred HHHHhcCCCCCCEEEEEecCcccceeecccccCCCCCCccccCCCCCCCCCCcceeecCceeEEecCCCcCCHHHHHhhc
Q psy11423 372 SEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICNSKIIYIESNLIARCSGSWIECIAQRKAGL 451 (655)
Q Consensus 372 ~~i~~~~i~iGd~V~v~raGdVIP~I~~vv~~~r~~~~~~~~~P~~CP~C~~~l~~~~~~~~~~C~n~~~~C~~q~~~~i 451 (655)
+.++++||.+- .|-|.|.-+ .++.. +...++.+|..-|.=. -|.+.-|+++-|-... + +..+.=
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 22221 1223566665433211 1122334555444442 2 233333
Q ss_pred cccccccccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHH
Q psy11423 452 QHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLA 510 (655)
Q Consensus 452 ~~F~sk~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~ 510 (655)
.++-| ...+|+|+|+++..+|.+.= .++.++...+.++|... |++.+.|++|.+.
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 34444 46789999999999999864 48889999999999999 9999999999864
No 190
>PRK07758 hypothetical protein; Provisional
Probab=81.90 E-value=3.7 Score=36.38 Aligned_cols=47 Identities=15% Similarity=0.296 Sum_probs=36.2
Q ss_pred CCccHHHHHHHHH-hCCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHh
Q psy11423 529 RHVGETTAKELAN-YFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFI 575 (655)
Q Consensus 529 pgIG~~~Ak~L~~-~fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f 575 (655)
|+++....+.|.. .+.++++|...+.+||.++.|+|++..+.|.+-+
T Consensus 40 ~~LSvRA~N~Lk~AGI~TL~dLv~~te~ELl~iknlGkKSL~EIkekL 87 (95)
T PRK07758 40 SLLSAPARRALEHHGIHTVEELSKYSEKEILKLHGMGPASLPKLRKAL 87 (95)
T ss_pred ccccHHHHHHHHHcCCCcHHHHHcCCHHHHHHccCCCHHHHHHHHHHH
Confidence 4444445566654 5789999999999999999999999887776543
No 191
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=81.82 E-value=1.2 Score=29.83 Aligned_cols=20 Identities=30% Similarity=0.602 Sum_probs=16.7
Q ss_pred HHhcCCCCCHHHHHHHHHHh
Q psy11423 556 QLLNIPKIGSTTVKAFIKFI 575 (655)
Q Consensus 556 eL~~i~GIG~~~A~~I~~~f 575 (655)
+|.+++|||+++|+.|.++.
T Consensus 2 ~L~~i~GiG~k~A~~il~~~ 21 (26)
T smart00278 2 ELLKVPGIGPKTAEKILEAX 21 (26)
T ss_pred hhhhCCCCCHHHHHHHHHhc
Confidence 57889999999999988754
No 192
>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=81.64 E-value=2.6 Score=47.68 Aligned_cols=64 Identities=19% Similarity=0.209 Sum_probs=52.0
Q ss_pred CHHHHHhhccccccccccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHHH
Q psy11423 443 CIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK 513 (655)
Q Consensus 443 C~~q~~~~i~~F~sk~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~ 513 (655)
|-+...+. .| ...++|++.++...|.++| |.|+.||-......|..++|++..++.+|..+.+.
T Consensus 199 C~~~~~~~-~~-----lslv~gi~~~~~~~L~~~G-I~ti~~La~~~~~~l~~~~~~~~~~~~~l~~qA~a 262 (457)
T TIGR03491 199 CEAVAKEE-GH-----LSLVPGIGPSRYRLLQELG-IHTLEDLAAADPNDLEDFGEQGLGVAEQLVQQARA 262 (457)
T ss_pred HHHHHHhc-CC-----eeecCCCCHHHHHHHHHcC-CCcHHHHhcCCccccccccccCHHHHHHHHHHHHH
Confidence 86665543 33 4579999999999999999 69999999987667888889999999998776654
No 193
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=80.86 E-value=1.6 Score=40.55 Aligned_cols=49 Identities=24% Similarity=0.224 Sum_probs=40.0
Q ss_pred CHHHHHhhccccccccccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhc
Q psy11423 443 CIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLL 494 (655)
Q Consensus 443 C~~q~~~~i~~F~sk~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~ 494 (655)
|+++.+.++.--+ +.|.|+|+|+..+..|+.+|+ .|+.+|-..+.++|.
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 888888776665544
No 194
>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=80.81 E-value=1.3 Score=33.32 Aligned_cols=24 Identities=17% Similarity=0.513 Sum_probs=18.5
Q ss_pred CCCCCCCCCCcceeecCceeEEecC
Q psy11423 414 IPNICPICNSKIIYIESNLIARCSG 438 (655)
Q Consensus 414 ~P~~CP~C~~~l~~~~~~~~~~C~n 438 (655)
+-++||.||.||.+..++ ..+|++
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 457999999999984443 578976
No 195
>PRK10736 hypothetical protein; Provisional
Probab=80.73 E-value=4.5 Score=44.66 Aligned_cols=67 Identities=6% Similarity=0.059 Sum_probs=49.7
Q ss_pred HHHHhCCCCccHHHHHHHHHhCCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHhcChhHHHHHHHHHHcCcc
Q psy11423 522 FIYALGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIY 593 (655)
Q Consensus 522 ~L~algIpgIG~~~Ak~L~~~fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f~~~~n~~li~~L~~~Gi~ 593 (655)
||.-..+||||.++.++|+++|++.+ .++.++|... |++++.+..+.++ ...+..+.++.+...|+.
T Consensus 7 ~l~L~~~~giG~~~~~~L~~~~~~~~---~~~~~~l~~~-g~~~~~~~~~~~~-~~~~~~~~~~~~~~~~i~ 73 (374)
T PRK10736 7 WLRLMSVSSLYGDKMVRIAHRLLAQS---QIDAVVLQAT-GLTLRQAQQFLQL-PRKSLESTLRWLEQPNHH 73 (374)
T ss_pred HHHHHhCCCCCHHHHHHHHHHhcChh---hCCHHHHHHc-CCCHHHHHHHhcc-CHHHHHHHHHHHHhcCCE
Confidence 44444789999999999999999987 4678888886 9999999888655 333334455666666654
No 196
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=80.66 E-value=1.8 Score=50.96 Aligned_cols=49 Identities=24% Similarity=0.303 Sum_probs=43.5
Q ss_pred ccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHH
Q psy11423 459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAI 511 (655)
Q Consensus 459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I 511 (655)
..+|+|+|+++...|...- .|+.+|...+.++|.++ +|+|.|++|.+.+
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 48899999999999988 9999999998764
No 197
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=80.17 E-value=1.4 Score=32.05 Aligned_cols=17 Identities=35% Similarity=0.622 Sum_probs=11.8
Q ss_pred CCCCccHHHHHHHHHhC
Q psy11423 527 GIRHVGETTAKELANYF 543 (655)
Q Consensus 527 gIpgIG~~~Ak~L~~~f 543 (655)
||||||+++|.+|+++|
T Consensus 20 Gv~giG~ktA~~ll~~~ 36 (36)
T smart00279 20 GVKGIGPKTALKLLREF 36 (36)
T ss_pred CCCcccHHHHHHHHHhC
Confidence 67777777777766654
No 198
>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=80.01 E-value=1.9 Score=30.13 Aligned_cols=26 Identities=27% Similarity=0.694 Sum_probs=14.2
Q ss_pred CCCCCCCccee---ec-C-ceeEEecCCCcCCH
Q psy11423 417 ICPICNSKIIY---IE-S-NLIARCSGSWIECI 444 (655)
Q Consensus 417 ~CP~C~~~l~~---~~-~-~~~~~C~n~~~~C~ 444 (655)
-||.||-.+.. .+ | -..+||.|+ . |.
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 59999986532 11 2 267899996 6 85
No 199
>PRK13910 DNA glycosylase MutY; Provisional
Probab=79.94 E-value=3.8 Score=43.64 Aligned_cols=75 Identities=17% Similarity=0.138 Sum_probs=47.8
Q ss_pred CChHHHhcCChhhhccc-c--CCcHHHHHHHHHHHHHhcc-----cchhHHHHHhCCCCccHHHHHHHHH-hCCCHHHHH
Q psy11423 480 VTAVDLYKINFKNLLRL-D--RVSNKLANNILLAIQKSKL-----TTFSRFIYALGIRHVGETTAKELAN-YFKNLECMF 550 (655)
Q Consensus 480 ~~i~DL~~L~~~~L~~l-~--GfG~Ksa~nll~~I~~sk~-----~~l~r~L~algIpgIG~~~Ak~L~~-~fgsl~~l~ 550 (655)
.++++|-.++.++|+.+ . ||- ..|.||.+..+.-.. .|. .+=.-+.+||||+++|..++. .|+-.....
T Consensus 23 Pt~e~La~a~~~el~~~~~glGyy-~RAr~L~~~A~~i~~~~~g~~P~-~~~~L~~LpGIG~kTA~aIl~~af~~~~~~V 100 (289)
T PRK13910 23 PTLKDLANAPLEEVLLLWRGLGYY-SRAKNLKKSAEICVKEHHSQLPN-DYQSLLKLPGIGAYTANAILCFGFREKSACV 100 (289)
T ss_pred CCHHHHHCCCHHHHHHHHHcCCcH-HHHHHHHHHHHHHHHHhCCCCCh-hHHHHHhCCCCCHHHHHHHHHHHCCCCcCcc
Confidence 58899999998888653 3 554 458888777654321 221 222224899999999988776 477544444
Q ss_pred hcCHHH
Q psy11423 551 KATEEQ 556 (655)
Q Consensus 551 ~as~ee 556 (655)
+.....
T Consensus 101 D~nV~R 106 (289)
T PRK13910 101 DANIKR 106 (289)
T ss_pred cHHHHH
Confidence 444433
No 200
>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=79.12 E-value=1.5 Score=30.80 Aligned_cols=23 Identities=17% Similarity=0.433 Sum_probs=15.5
Q ss_pred CCCCCCCCcceeecCceeEEecC
Q psy11423 416 NICPICNSKIIYIESNLIARCSG 438 (655)
Q Consensus 416 ~~CP~C~~~l~~~~~~~~~~C~n 438 (655)
.+||.||++++..+++-..+|++
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 47999999999988889999955
No 201
>smart00611 SEC63 Domain of unknown function in Sec63p, Brr2p and other proteins.
Probab=78.11 E-value=4.9 Score=42.71 Aligned_cols=63 Identities=13% Similarity=0.180 Sum_probs=51.2
Q ss_pred hhccccccccccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHHH
Q psy11423 449 AGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK 513 (655)
Q Consensus 449 ~~i~~F~sk~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~ 513 (655)
+++-.+.+ ..+.+|++|++.+.+|.+.| +.++.||..++.+++..+-|++++.++.+++.++.
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 44444443 68899999999999998765 68999999999988888888998888888876643
No 202
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=77.88 E-value=8.1 Score=43.99 Aligned_cols=102 Identities=16% Similarity=0.261 Sum_probs=70.7
Q ss_pred cccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHHHhccc-ch---hHH-HHHhCCCCccHH
Q psy11423 460 MNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKLT-TF---SRF-IYALGIRHVGET 534 (655)
Q Consensus 460 l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~sk~~-~l---~r~-L~algIpgIG~~ 534 (655)
+...++.+..+..|++.|+ .++.++.+...++|..++||.+..++.|.+........ .. ... -.-+.++|+...
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 79999999999999999999999999888877532211 00 010 011135666666
Q ss_pred HHHHHHHh-CCCHHHHHhcCHHHHhcCCC
Q psy11423 535 TAKELANY-FKNLECMFKATEEQLLNIPK 562 (655)
Q Consensus 535 ~Ak~L~~~-fgsl~~l~~as~eeL~~i~G 562 (655)
.+..+... +.+.+.+...+.+++..+.+
T Consensus 438 ~~~~~~~~~~~~~edl~~~~~d~~~~~~~ 466 (470)
T PRK09202 438 LAFKLAEKGIKTLEDLAEQAVDELIDIEG 466 (470)
T ss_pred HHHhhhhcCCcchhhhhhccchhhhhccc
Confidence 66555543 55666666666666665543
No 203
>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=77.24 E-value=4.1 Score=43.88 Aligned_cols=51 Identities=27% Similarity=0.257 Sum_probs=46.2
Q ss_pred cCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHHH
Q psy11423 462 IIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK 513 (655)
Q Consensus 462 I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~ 513 (655)
=.||++.++.+|-++|+ .|+.||+..+..+|..+-|+.+..+++++..+.+
T Consensus 6 ~~~~~~~~~~~l~~~g~-~t~~~~~~~~~~~L~~i~~ls~~~~~~~~~~~~~ 56 (316)
T TIGR02239 6 GNGITAADIKKLQEAGL-HTVESVAYAPKKQLLEIKGISEAKADKILAEAAK 56 (316)
T ss_pred cCCCCHHHHHHHHHcCC-CcHHHHHhCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 35699999999999885 8999999999999999999999999999987764
No 204
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=76.95 E-value=11 Score=40.17 Aligned_cols=69 Identities=16% Similarity=0.121 Sum_probs=44.2
Q ss_pred CChHHHhcCChhhhccccCCcHHHHHHHHHHHHHhcc--cch------hHHHHHh-CCCCccHHHHHHHH-HhCCCHHHH
Q psy11423 480 VTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKL--TTF------SRFIYAL-GIRHVGETTAKELA-NYFKNLECM 549 (655)
Q Consensus 480 ~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~sk~--~~l------~r~L~al-gIpgIG~~~Ak~L~-~~fgsl~~l 549 (655)
-++++|..++.++|..+ |++..+++.|.+--+...+ .++ ......| .|||||+.+|.-++ ..++..|.+
T Consensus 156 Ptpe~La~~~~~eL~~~-Gl~~~Ra~~L~~lA~~i~~g~l~l~~~~~~~~~~~~L~~LpGIGpwTA~~vllr~lg~~D~f 234 (283)
T PRK10308 156 PTPERLAAADPQALKAL-GMPLKRAEALIHLANAALEGTLPLTIPGDVEQAMKTLQTFPGIGRWTANYFALRGWQAKDVF 234 (283)
T ss_pred CCHHHHHcCCHHHHHHC-CCCHHHHHHHHHHHHHHHcCCCCccccCCHHHHHHHHhcCCCcCHHHHHHHHHHhCCCCCCC
Confidence 58899998998999888 9998888887765543322 111 1223333 67777777776554 345554444
No 205
>PLN03186 DNA repair protein RAD51 homolog; Provisional
Probab=76.93 E-value=4.4 Score=44.21 Aligned_cols=55 Identities=29% Similarity=0.302 Sum_probs=48.6
Q ss_pred ccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHHHh
Q psy11423 459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKS 514 (655)
Q Consensus 459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~s 514 (655)
.+.-.||++..+.+|-++|+ .|+.|+...+..+|..+.|+.+..+++++..+.+.
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 34447899999999999885 89999999999999999999999999999888543
No 206
>COG0122 AlkA 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=76.42 E-value=12 Score=39.93 Aligned_cols=82 Identities=24% Similarity=0.238 Sum_probs=43.2
Q ss_pred HHHHHHHHHcCC--------CCChHHHhcCChhhhccccCCcHHHHHHHHHHHHHhcccchhHHHHHhCCCCccHHHHHH
Q psy11423 467 KKMIEKLVNANI--------VVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKE 538 (655)
Q Consensus 467 ~k~i~~L~~~g~--------I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~sk~~~l~r~L~algIpgIG~~~Ak~ 538 (655)
.+.+.+|.+... --+++.|..++.++|... |+-..+++-|.. +|+.
T Consensus 124 ~~i~~rl~~~~g~~~~~~~~fptpe~l~~~~~~~l~~~-g~s~~Ka~yi~~-------------------------~A~~ 177 (285)
T COG0122 124 AKIWARLVSLYGNALEIYHSFPTPEQLAAADEEALRRC-GLSGRKAEYIIS-------------------------LARA 177 (285)
T ss_pred HHHHHHHHHHhCCccccccCCCCHHHHHhcCHHHHHHh-CCcHHHHHHHHH-------------------------HHHH
Confidence 344555555433 356777777777777654 444444443332 2333
Q ss_pred HHHhCCCHHHHHhcCH----HHHhcCCCCCHHHHHHHHHH
Q psy11423 539 LANYFKNLECMFKATE----EQLLNIPKIGSTTVKAFIKF 574 (655)
Q Consensus 539 L~~~fgsl~~l~~as~----eeL~~i~GIG~~~A~~I~~~ 574 (655)
+++..-+++.+...+. +.|++++|||+.+|+-+.-|
T Consensus 178 ~~~g~~~~~~l~~~~~e~a~e~L~~i~GIG~WTAe~~llf 217 (285)
T COG0122 178 AAEGELDLSELKPLSDEEAIEELTALKGIGPWTAEMFLLF 217 (285)
T ss_pred HHcCCccHHHhccCCHHHHHHHHHcCCCcCHHHHHHHHHH
Confidence 3333333444444332 45677777777777766554
No 207
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=76.08 E-value=2.5 Score=30.47 Aligned_cols=23 Identities=17% Similarity=0.495 Sum_probs=11.8
Q ss_pred CCCCCCCCcceee----cCceeEEecC
Q psy11423 416 NICPICNSKIIYI----ESNLIARCSG 438 (655)
Q Consensus 416 ~~CP~C~~~l~~~----~~~~~~~C~n 438 (655)
++||.||++|+.. ++...+.|++
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 4799999999853 3456778865
No 208
>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=75.62 E-value=3 Score=39.85 Aligned_cols=55 Identities=16% Similarity=0.330 Sum_probs=37.3
Q ss_pred HHHHHhcCCCCCCEEEEEecCcccceeecccccCCCCCCccccCCCCCCCCCCcceee
Q psy11423 371 ESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICNSKIIYI 428 (655)
Q Consensus 371 ~~~i~~~~i~iGd~V~v~raGdVIP~I~~vv~~~r~~~~~~~~~P~~CP~C~~~l~~~ 428 (655)
-+..++....-+ .+.| +++++..++.+|+..-.... ..-.+.+.||.||++|+..
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 355666666656 5555 99999999999987532211 1222358999999998754
No 209
>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=75.36 E-value=2.9 Score=37.05 Aligned_cols=31 Identities=23% Similarity=0.215 Sum_probs=25.7
Q ss_pred ccccCCCCHHHHHHHHHcCCCCChHHHhcCCh
Q psy11423 459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINF 490 (655)
Q Consensus 459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~ 490 (655)
..+|||+|+++++.|..-| |.+++||-.-..
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 4589999999999999777 689988876543
No 210
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=75.07 E-value=1.5 Score=29.48 Aligned_cols=21 Identities=24% Similarity=0.548 Sum_probs=14.3
Q ss_pred CCCCCCCCCCcceeecCceeEEecC
Q psy11423 414 IPNICPICNSKIIYIESNLIARCSG 438 (655)
Q Consensus 414 ~P~~CP~C~~~l~~~~~~~~~~C~n 438 (655)
++..||.||.++. ....||++
T Consensus 1 m~~~Cp~Cg~~~~----~~~~fC~~ 21 (26)
T PF13248_consen 1 MEMFCPNCGAEID----PDAKFCPN 21 (26)
T ss_pred CcCCCcccCCcCC----cccccChh
Confidence 3568999998654 23557876
No 211
>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=74.52 E-value=5.6 Score=32.86 Aligned_cols=49 Identities=20% Similarity=0.291 Sum_probs=34.4
Q ss_pred HHhCCCCccHHHHHHHHH-hCCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHh
Q psy11423 524 YALGIRHVGETTAKELAN-YFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFI 575 (655)
Q Consensus 524 ~algIpgIG~~~Ak~L~~-~fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f 575 (655)
..|+++ ..+...|.. .+.++..|...+.++|.+++|||++..+.|.+-+
T Consensus 15 ~~L~LS---~Ra~n~L~~~~I~tv~dL~~~s~~~L~~i~n~G~ksl~EI~~~L 64 (66)
T PF03118_consen 15 EDLGLS---VRAYNCLKRAGIHTVGDLVKYSEEDLLKIKNFGKKSLEEIKEKL 64 (66)
T ss_dssp GGSTSB---HHHHHHHHCTT--BHHHHHCS-HHHHHTSTTSHHHHHHHHHHHH
T ss_pred HHhCCC---HHHHHHHHHhCCcCHHHHHhCCHHHHHhCCCCCHhHHHHHHHHH
Confidence 345554 333333433 3568999999999999999999999999998765
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=73.47 E-value=4.5 Score=44.78 Aligned_cols=50 Identities=18% Similarity=0.254 Sum_probs=38.9
Q ss_pred cccccCCCCHHHHHHHHHcCCCCChHHHhcCC---------------hhhhccccCCcHHHHHHHHHH
Q psy11423 458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYKIN---------------FKNLLRLDRVSNKLANNILLA 510 (655)
Q Consensus 458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~---------------~~~L~~l~GfG~Ksa~nll~~ 510 (655)
..-+++|+|+++.++|.+.| |.++.||..+. ...|... ||++..+.|++.
T Consensus 173 pv~~l~GiG~~~~~kL~~~G-I~tigdl~~~~~~~~~~~~~~~~~~s~~~L~~~--fG~~~g~~l~~~ 237 (379)
T cd01703 173 DLRKIPGIGYKTAAKLEAHG-ISSVRDLQEFSNRNRQTVGAAPSLLELLLMVKE--FGEGIGQRIWKL 237 (379)
T ss_pred CccccCCcCHHHHHHHHHcC-CCcHHHHHhCCcccccccccccccccHHHHHHH--HCHHHHHHHHHH
Confidence 35578999999999999877 79999999877 5555553 887767666654
No 213
>CHL00013 rpoA RNA polymerase alpha subunit
Probab=73.23 E-value=4.6 Score=43.79 Aligned_cols=49 Identities=31% Similarity=0.415 Sum_probs=41.6
Q ss_pred CCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHHH
Q psy11423 464 GLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK 513 (655)
Q Consensus 464 GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~ 513 (655)
.|.-....-|-.+| |.++.||...+.++|++++.||+||.+.|.+.++.
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 44555566666666 79999999999999999999999999999999865
No 214
>KOG0966|consensus
Probab=72.77 E-value=1.2e+02 Score=36.66 Aligned_cols=198 Identities=16% Similarity=0.165 Sum_probs=117.3
Q ss_pred CceEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhhhhhh---hcccCCcccccCCCC---ceEEEEEEEEeehhh
Q psy11423 117 NIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIH---IIHKIPLVLNIKYPP---ELLEVRCEVLIYKKD 190 (655)
Q Consensus 117 ~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~---~i~~iP~~l~~~~~p---~~~evRGEv~~~~~~ 190 (655)
.-.|++|-|+||=-|.|.|..|.+ +-.|| -|-|-|.+.. ....+-..|.+. .+ ....+-||...=...
T Consensus 249 ~~~f~lEtK~DGERiQlHk~g~~~-~yfSR----Ng~dyT~~yg~s~~~g~lt~~i~~~-f~~~v~~cILDGEMm~wD~~ 322 (881)
T KOG0966|consen 249 GQDFYLETKFDGERIQLHKDGGEY-KYFSR----NGNDYTYEYGASYAHGTLTQRIHGA-FNKEVESCILDGEMMTWDTK 322 (881)
T ss_pred CCceEEEeeccCceEEEEecCCEE-EEEec----CCcchhhhcCcccccccccHHHHhh-hhhcchheEecceEEEeecc
Confidence 357999999999999999987765 67788 5667775432 112222333221 11 247789998764443
Q ss_pred HHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccceEEEEEecccccCCCC-CCCHHHHHHHHHhCCCCCCCC---
Q psy11423 191 FIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLSICGE--- 266 (655)
Q Consensus 191 F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~GF~~~~~--- 266 (655)
-+++ . +|-..+ .+..+.+.. ..-...++.|++....+..+ ..+..+..+.|+..=-+-...
T Consensus 323 ~~~f----~-----~~G~~~-----dik~~~~~~-~~~qp~yvvfDLLylNgksL~~~~l~qR~e~L~~v~~p~~~~iei 387 (881)
T KOG0966|consen 323 TKRF----C-----PFGSNS-----DIKELSSRD-GSQQPCYVVFDLLYLNGKSLFGAPLHQRLEILKKVIVPKSGRIEI 387 (881)
T ss_pred hhhh----c-----cCCchh-----hHHHhhccc-cCCCceEEEeeeeeecCcccCCccHHHHHHHHHhcccCCCCeeEE
Confidence 2221 1 122222 222222211 22357899999876544433 356777788887764333311
Q ss_pred --ceeeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCcc-------eeeEEEEEE
Q psy11423 267 --YSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSK-------EALTKIKAI 337 (655)
Q Consensus 267 --~~~~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~-------~~~T~v~~I 337 (655)
...+.+.+++.++.++-.+.++ -|||+|--+..++ . ..+.--| +|.-|+ .----|.+.
T Consensus 388 ~~~~~~~~~edi~~~f~~ai~~~~------EGIVlK~~~S~Y~--p--g~R~~gW---~K~KPeYlkg~g~dLD~lIiGg 454 (881)
T KOG0966|consen 388 VRSEVGSTKEDIEQFFEEAIDNGE------EGIVLKKPDSSYV--P--GQRSNGW---IKLKPEYLKGFGEDLDLLIIGG 454 (881)
T ss_pred eehhhcccHHHHHHHHHHHHhcCC------CceEEeccCcccC--c--cccCCCc---EeecHHHHhhcCccccEEEEec
Confidence 2346789999999887766664 6999998876654 1 2335556 454332 233466777
Q ss_pred EEeec-Ccceee
Q psy11423 338 NIQIG-RTGIIT 348 (655)
Q Consensus 338 ~~qvG-RTG~it 348 (655)
.|--| |.|++.
T Consensus 455 y~G~g~rgg~~~ 466 (881)
T KOG0966|consen 455 YYGRGDRGGKVL 466 (881)
T ss_pred ccCCCCCCCeee
Confidence 77777 667654
No 215
>PRK07220 DNA topoisomerase I; Validated
Probab=72.26 E-value=5.7 Score=47.83 Aligned_cols=47 Identities=30% Similarity=0.355 Sum_probs=37.0
Q ss_pred ccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHH
Q psy11423 459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANN 506 (655)
Q Consensus 459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~n 506 (655)
+-+++|+|+++.++|-.++ +.++.+|-..+.+++..--+.+.+..++
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 4679999999999999888 5888999888888887655555555443
No 216
>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=71.54 E-value=5.2 Score=36.39 Aligned_cols=59 Identities=20% Similarity=0.250 Sum_probs=45.0
Q ss_pred hcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCcceeeEEEEEEEEeecCcceeeeEEEE
Q psy11423 287 RFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQIGRTGIITPVALL 353 (655)
Q Consensus 287 r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~~~T~v~~I~~qvGRTG~itPvA~l 353 (655)
|..-+| ++||++|....+. .++++|||.=.|.|+-+ ....|+=+.|..+ .+..+|||.|
T Consensus 21 ~~~ety----V~IKved~~kaRT--r~srnd~WnE~F~i~Vd-k~nEiel~VyDk~-~~~~~Pi~ll 79 (109)
T cd08689 21 KRPETY----VSIKVEDVERART--KPSRNDRWNEDFEIPVE-KNNEEEVIVYDKG-GDQPVPVGLL 79 (109)
T ss_pred cCCCcE----EEEEECCEEEEec--cCCCCCcccceEEEEec-CCcEEEEEEEeCC-CCeecceeee
Confidence 444566 8899999743332 46899999999999985 6777777888875 5678899986
No 217
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=71.26 E-value=4.4 Score=43.43 Aligned_cols=26 Identities=27% Similarity=0.570 Sum_probs=22.7
Q ss_pred CCCCccHHHHHHHHHhCCCHHHHHhc
Q psy11423 527 GIRHVGETTAKELANYFKNLECMFKA 552 (655)
Q Consensus 527 gIpgIG~~~Ak~L~~~fgsl~~l~~a 552 (655)
||||||+++|..|++.|++++.+...
T Consensus 202 GV~GIG~ktA~~Ll~~~gs~e~i~~~ 227 (310)
T COG0258 202 GVKGIGPKTALKLLQEYGSLEGLYEN 227 (310)
T ss_pred CCCCcCHHHHHHHHHHhCCHHHHHHh
Confidence 79999999999999999988888753
No 218
>PRK03352 DNA polymerase IV; Validated
Probab=70.93 E-value=4.8 Score=43.64 Aligned_cols=50 Identities=20% Similarity=0.240 Sum_probs=40.8
Q ss_pred cccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHH
Q psy11423 458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLA 510 (655)
Q Consensus 458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~ 510 (655)
..=.++|+|+++.++|...| |.++.||..+....|... ||.+.++.|.+.
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 45578999999999997766 699999999998888886 997766655544
No 219
>PLN03123 poly [ADP-ribose] polymerase; Provisional
Probab=70.91 E-value=4.2 Score=50.15 Aligned_cols=49 Identities=29% Similarity=0.386 Sum_probs=41.7
Q ss_pred CCCCeEecccccCccEEEecCC---CCchHHHHHHcCCeeeCHHHHHHHHhc
Q psy11423 600 TKGGKVVNFISKNTNYLVKGQK---PGKKLEKAIKLNIKILDEKNFVKIVKG 648 (655)
Q Consensus 600 ~~G~~v~~sVsk~t~ylv~g~~---~g~K~~kA~~lgi~ii~e~~f~~~l~~ 648 (655)
.+||+++.+|++.++.||+-+. .+.|.++|+++||||++++-+.+.+..
T Consensus 418 ~~GG~~s~~v~~~~t~l~tt~e~~k~~~kv~qAk~~~ipIVsedwL~ds~~~ 469 (981)
T PLN03123 418 EAGGVFHATVKKDTNCLVVCGELDDEDAEMRKARRMKIPIVREDYLVDCFKK 469 (981)
T ss_pred hcCCEEeeeccCCceEEEccHHhhhcchHHHHHHhcCCCcccHHHHHHHHhc
Confidence 7899999999999998887653 458899999999999999988776643
No 220
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=70.91 E-value=3.3 Score=50.74 Aligned_cols=25 Identities=36% Similarity=0.697 Sum_probs=18.9
Q ss_pred CCCCccHHHHHHHHHhCCCHHHHHh
Q psy11423 527 GIRHVGETTAKELANYFKNLECMFK 551 (655)
Q Consensus 527 gIpgIG~~~Ak~L~~~fgsl~~l~~ 551 (655)
||||||+++|.+|++.|||+++|..
T Consensus 189 GVpGIG~KtA~kLL~~ygsle~i~~ 213 (887)
T TIGR00593 189 GVKGIGEKTAAKLLQEFGSLENIYE 213 (887)
T ss_pred CCCCcCHHHHHHHHHHcCCHHHHHH
Confidence 6777777777777777777777764
No 221
>KOG1921|consensus
Probab=69.94 E-value=3.9 Score=42.20 Aligned_cols=35 Identities=31% Similarity=0.496 Sum_probs=20.4
Q ss_pred HHHHHHHHhCCC-HHHHHhcCHHHHhcCCCCCHHHHHHHH
Q psy11423 534 TTAKELANYFKN-LECMFKATEEQLLNIPKIGSTTVKAFI 572 (655)
Q Consensus 534 ~~Ak~L~~~fgs-l~~l~~as~eeL~~i~GIG~~~A~~I~ 572 (655)
++|+.|.++|++ +. ++.++|.++||||+++|.-..
T Consensus 141 kta~IL~d~f~gDIP----~~v~dLlsLPGVGPKMa~L~m 176 (286)
T KOG1921|consen 141 KTAKILQDKFDGDIP----DTVEDLLSLPGVGPKMAHLTM 176 (286)
T ss_pred HHHHHHHHHhCCCCc----hhHHHHhcCCCCchHHHHHHH
Confidence 355666666652 21 245667777777777775543
No 222
>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=69.86 E-value=8.3 Score=34.20 Aligned_cols=31 Identities=23% Similarity=0.290 Sum_probs=25.0
Q ss_pred CCCCccHHHHHHHHH-hCCCHHHHHhcCHHHH
Q psy11423 527 GIRHVGETTAKELAN-YFKNLECMFKATEEQL 557 (655)
Q Consensus 527 gIpgIG~~~Ak~L~~-~fgsl~~l~~as~eeL 557 (655)
.||+||+++|+-|.. -+.+++.|...++++|
T Consensus 16 ~iP~IG~a~a~DL~~LGi~s~~~L~g~dP~~L 47 (93)
T PF11731_consen 16 DIPNIGKATAEDLRLLGIRSPADLKGRDPEEL 47 (93)
T ss_pred cCCCccHHHHHHHHHcCCCCHHHHhCCCHHHH
Confidence 789999999987776 4778899998887654
No 223
>PRK03980 flap endonuclease-1; Provisional
Probab=69.82 E-value=4 Score=43.55 Aligned_cols=25 Identities=32% Similarity=0.503 Sum_probs=23.1
Q ss_pred CCCCccHHHHHHHHHhCCCHHHHHh
Q psy11423 527 GIRHVGETTAKELANYFKNLECMFK 551 (655)
Q Consensus 527 gIpgIG~~~Ak~L~~~fgsl~~l~~ 551 (655)
||||||+++|-+|++.|++++.+..
T Consensus 193 GI~GIG~ktA~kLi~~~~sle~i~~ 217 (292)
T PRK03980 193 GIKGIGPKTALKLIKKHGDLEKVLE 217 (292)
T ss_pred CCCCccHHHHHHHHHHCCCHHHHHH
Confidence 8999999999999999999998876
No 224
>KOG2841|consensus
Probab=69.34 E-value=5.4 Score=40.98 Aligned_cols=58 Identities=14% Similarity=0.109 Sum_probs=48.7
Q ss_pred hccccccccccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHHH
Q psy11423 450 GLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK 513 (655)
Q Consensus 450 ~i~~F~sk~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~ 513 (655)
++.+|.. .|+|++..-+..|...= -++..|+..+.++|.+.+|+|+.+|++|++-+..
T Consensus 192 ~~~~~Lt----~i~~VnKtda~~LL~~F--gsLq~~~~AS~~ele~~~G~G~~kak~l~~~l~~ 249 (254)
T KOG2841|consen 192 SLLGFLT----TIPGVNKTDAQLLLQKF--GSLQQISNASEGELEQCPGLGPAKAKRLHKFLHQ 249 (254)
T ss_pred HHHHHHH----hCCCCCcccHHHHHHhc--ccHHHHHhcCHhHHHhCcCcCHHHHHHHHHHHhc
Confidence 6667753 69999999888887653 3888999999999999999999999999987753
No 225
>COG1623 Predicted nucleic-acid-binding protein (contains the HHH domain) [General function prediction only]
Probab=69.10 E-value=7.4 Score=41.20 Aligned_cols=99 Identities=17% Similarity=0.235 Sum_probs=67.4
Q ss_pred EecCCCcCCHHHHHhhccccccccccccCCCCHHHHHHHHHcCCCCChHH-HhcCC-hhhhccccCCcHHHHHHHHHHHH
Q psy11423 435 RCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVD-LYKIN-FKNLLRLDRVSNKLANNILLAIQ 512 (655)
Q Consensus 435 ~C~n~~~~C~~q~~~~i~~F~sk~~l~I~GLG~k~i~~L~~~g~I~~i~D-L~~L~-~~~L~~l~GfG~Ksa~nll~~I~ 512 (655)
||.+... -+....+.|.+|.+++.+| +..|.+++--.-..++.| +..-. .--|.++|++-.+-++||+.++.
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 6666433 7778889999998876654 666777764333333333 11111 23478889999999999998876
Q ss_pred HhcccchhHHHHHh-----CCCCccHHHHHHHHHhCC
Q psy11423 513 KSKLTTFSRFIYAL-----GIRHVGETTAKELANYFK 544 (655)
Q Consensus 513 ~sk~~~l~r~L~al-----gIpgIG~~~Ak~L~~~fg 544 (655)
. +.+++.|. .+.|||+..|+.|.+-.+
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 44555553 689999999998877654
No 226
>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=68.70 E-value=5.8 Score=44.15 Aligned_cols=50 Identities=20% Similarity=0.167 Sum_probs=41.7
Q ss_pred ccccCCCCHHHHHHHHHcCCCCChHHHhcCC--hhhhccccCCcHHHHHHHHHHH
Q psy11423 459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKIN--FKNLLRLDRVSNKLANNILLAI 511 (655)
Q Consensus 459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~--~~~L~~l~GfG~Ksa~nll~~I 511 (655)
.-.|+|+|+++.++|-..| |.++.||..+. ...|... ||.+.++.|++..
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 4578999999999999887 68999999987 7888875 9988777776643
No 227
>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=68.15 E-value=5.8 Score=43.51 Aligned_cols=50 Identities=22% Similarity=0.212 Sum_probs=41.5
Q ss_pred ccccCCCCHHHHHHHHHcCCCCChHHHhcC--ChhhhccccCCcHHHHHHHHHH
Q psy11423 459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKI--NFKNLLRLDRVSNKLANNILLA 510 (655)
Q Consensus 459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L--~~~~L~~l~GfG~Ksa~nll~~ 510 (655)
.-+++|+|+++..+|.+...|.++.||..+ ....|... ||.+..+.|++.
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 457899999999998777778999999999 78888775 888778777654
No 228
>COG2231 Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]
Probab=67.46 E-value=5 Score=40.46 Aligned_cols=39 Identities=36% Similarity=0.589 Sum_probs=31.7
Q ss_pred HHHHHhCCCHHHHHhcC-HHHHhcCCCCCHHHHHHHHHHh
Q psy11423 537 KELANYFKNLECMFKAT-EEQLLNIPKIGSTTVKAFIKFI 575 (655)
Q Consensus 537 k~L~~~fgsl~~l~~as-~eeL~~i~GIG~~~A~~I~~~f 575 (655)
+.|+.+|.+++.+.... .++|.+|.|||+.+|.+|.-|.
T Consensus 96 k~l~~~~~~~~~~~~~~~R~~LL~iKGIG~ETaDsILlYa 135 (215)
T COG2231 96 KNLAKFFINLESFKSEVLREELLSIKGIGKETADSILLYA 135 (215)
T ss_pred HHHHHHhhhhhccchHHHHHHHHccCCcchhhHHHHHHHH
Confidence 34577888888776653 6899999999999999998864
No 229
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=67.36 E-value=14 Score=36.74 Aligned_cols=75 Identities=19% Similarity=0.282 Sum_probs=42.7
Q ss_pred EEEEeeCCCHHHHHhcCCCCCCEEE--EEecCcccceeecccccCCCCCCccccCCCCCCCCCCcceeecCceeEEecCC
Q psy11423 362 TITRATLHNESEIYRKNIQIGDTVV--VHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICNSKIIYIESNLIARCSGS 439 (655)
Q Consensus 362 tVsratLhN~~~i~~~~i~iGd~V~--v~raGdVIP~I~~vv~~~r~~~~~~~~~P~~CP~C~~~l~~~~~~~~~~C~n~ 439 (655)
.||.+.-.-.+.+. -.++|||.|. |..-| =|.-.+... +.- - ++-..|+.|+.+|++ ++..++|+|
T Consensus 103 hvs~~~~~~~~~~~-d~f~~GDivrA~Vis~~--~~~~Lst~~---~dl--G-VI~A~CsrC~~~L~~--~~~~l~Cp~- 170 (188)
T COG1096 103 HVSQVRDGYVEKLS-DAFRIGDIVRARVISTG--DPIQLSTKG---NDL--G-VIYARCSRCRAPLVK--KGNMLKCPN- 170 (188)
T ss_pred EEEecccccccccc-cccccccEEEEEEEecC--CCeEEEecC---Ccc--e-EEEEEccCCCcceEE--cCcEEECCC-
Confidence 34444333333333 4789999886 44444 222222211 111 1 123589999999998 457999998
Q ss_pred CcCCHHHHHhhc
Q psy11423 440 WIECIAQRKAGL 451 (655)
Q Consensus 440 ~~~C~~q~~~~i 451 (655)
|-..-.++|
T Consensus 171 ---Cg~tEkRKi 179 (188)
T COG1096 171 ---CGNTEKRKI 179 (188)
T ss_pred ---CCCEEeeee
Confidence 765555554
No 230
>KOG0442|consensus
Probab=67.25 E-value=5.9 Score=47.35 Aligned_cols=51 Identities=22% Similarity=0.365 Sum_probs=47.5
Q ss_pred hCCCCccHHHHHHHHHhCCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHhcC
Q psy11423 526 LGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQ 577 (655)
Q Consensus 526 lgIpgIG~~~Ak~L~~~fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f~~ 577 (655)
|++|||-...+..+..+|+++..+.+.+.++|..+-|. ...|+.|++||+.
T Consensus 824 l~lPgVs~~n~~~l~~k~ks~~~La~sS~~el~el~~~-~~~a~~LYdFi~~ 874 (892)
T KOG0442|consen 824 LSLPGVSYINYRNLRHKFKSLKELANSSQEELSELLGV-HENAKLLYDFIHT 874 (892)
T ss_pred hcCCCccHHHHHHHHHHhhHHHHHHhCcHHHHHHHhcc-hHHHHHHHHHHHH
Confidence 58999999999999999999999999999999999777 8899999999985
No 231
>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=67.07 E-value=8.9 Score=31.59 Aligned_cols=20 Identities=25% Similarity=0.494 Sum_probs=17.1
Q ss_pred HHhcCCCCCHHHHHHHHHHh
Q psy11423 556 QLLNIPKIGSTTVKAFIKFI 575 (655)
Q Consensus 556 eL~~i~GIG~~~A~~I~~~f 575 (655)
++..+||||+.+|..|.+|+
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 48899999999999988876
No 232
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=66.86 E-value=4.1 Score=37.39 Aligned_cols=24 Identities=21% Similarity=0.832 Sum_probs=18.4
Q ss_pred CCCCCCcceeecCceeEEecCCCcCCHHHHHh
Q psy11423 418 CPICNSKIIYIESNLIARCSGSWIECIAQRKA 449 (655)
Q Consensus 418 CP~C~~~l~~~~~~~~~~C~n~~~~C~~q~~~ 449 (655)
||+||++|+.. .+.|++ |...+.+
T Consensus 1 CPvCg~~l~vt----~l~C~~----C~t~i~G 24 (113)
T PF09862_consen 1 CPVCGGELVVT----RLKCPS----CGTEIEG 24 (113)
T ss_pred CCCCCCceEEE----EEEcCC----CCCEEEe
Confidence 99999999853 688977 7655544
No 233
>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=66.67 E-value=5 Score=43.04 Aligned_cols=25 Identities=28% Similarity=0.433 Sum_probs=20.9
Q ss_pred CCCCccHHHHHHHHHhCCCHHHHHh
Q psy11423 527 GIRHVGETTAKELANYFKNLECMFK 551 (655)
Q Consensus 527 gIpgIG~~~Ak~L~~~fgsl~~l~~ 551 (655)
||||||+++|-+|++.|++++.+..
T Consensus 227 gv~giG~k~A~~li~~~~~~~~~~~ 251 (316)
T cd00128 227 GIPGIGPVTALKLIKKYGDIEKDIE 251 (316)
T ss_pred CCCCccHHHHHHHHHHcCChHHHHH
Confidence 8999999999999999998765543
No 234
>PRK01216 DNA polymerase IV; Validated
Probab=66.62 E-value=7.4 Score=42.60 Aligned_cols=48 Identities=27% Similarity=0.398 Sum_probs=40.0
Q ss_pred ccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHH
Q psy11423 459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILL 509 (655)
Q Consensus 459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~ 509 (655)
.-.++|+|+++.++|...| |.++.||..+....|... ||......|.+
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 4468999999999998776 699999999998888885 99766666655
No 235
>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=65.89 E-value=5.3 Score=43.54 Aligned_cols=26 Identities=35% Similarity=0.521 Sum_probs=23.7
Q ss_pred CCCCccHHHHHHHHHhCCCHHHHHhc
Q psy11423 527 GIRHVGETTAKELANYFKNLECMFKA 552 (655)
Q Consensus 527 gIpgIG~~~Ak~L~~~fgsl~~l~~a 552 (655)
||||||+++|-+|.+.|++++.+...
T Consensus 240 Gv~GIG~ktA~kli~~~gsie~il~~ 265 (338)
T TIGR03674 240 GVKGIGPKTALKLIKEHGDLEKVLKA 265 (338)
T ss_pred CCCCccHHHHHHHHHHcCCHHHHHHh
Confidence 99999999999999999999988753
No 236
>PRK05755 DNA polymerase I; Provisional
Probab=65.48 E-value=4.8 Score=49.38 Aligned_cols=24 Identities=33% Similarity=0.635 Sum_probs=13.5
Q ss_pred CCCCccHHHHHHHHHhCCCHHHHH
Q psy11423 527 GIRHVGETTAKELANYFKNLECMF 550 (655)
Q Consensus 527 gIpgIG~~~Ak~L~~~fgsl~~l~ 550 (655)
||||||+++|..|++.|||+++|.
T Consensus 191 Gv~GiG~ktA~~Ll~~~gsle~i~ 214 (880)
T PRK05755 191 GVPGIGEKTAAKLLQEYGSLEGLY 214 (880)
T ss_pred CCCCccHHHHHHHHHHcCCHHHHH
Confidence 555555555555555555555554
No 237
>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=65.23 E-value=15 Score=39.60 Aligned_cols=21 Identities=19% Similarity=0.433 Sum_probs=17.9
Q ss_pred HHHHhcCCCCCHHHHHHHHHH
Q psy11423 554 EEQLLNIPKIGSTTVKAFIKF 574 (655)
Q Consensus 554 ~eeL~~i~GIG~~~A~~I~~~ 574 (655)
.++|.+++|||+++|+-|.-|
T Consensus 219 ~~~L~~l~GIG~~tAd~vll~ 239 (310)
T TIGR00588 219 REALCELPGVGPKVADCICLM 239 (310)
T ss_pred HHHHHhCCCccHHHHHHHHHH
Confidence 468999999999999998764
No 238
>COG4277 Predicted DNA-binding protein with the Helix-hairpin-helix motif [General function prediction only]
Probab=64.55 E-value=7.3 Score=41.46 Aligned_cols=63 Identities=24% Similarity=0.364 Sum_probs=45.5
Q ss_pred CCccHHHHHHHHH--hCCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHhcChhHHHHHHHHHHcCcccc
Q psy11423 529 RHVGETTAKELAN--YFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYWL 595 (655)
Q Consensus 529 pgIG~~~Ak~L~~--~fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f~~~~n~~li~~L~~~Gi~~~ 595 (655)
|.+.++++.+|.. .|. =.+..|+.++|..+||||.+.|.+|+.--... +-..+.|...|+...
T Consensus 304 ~~lDPK~~wAl~~~d~FP--Vdvn~A~~~~llRVPGiG~ksa~rIv~~Rr~~--rl~~e~Lkk~Gvvlk 368 (404)
T COG4277 304 PDLDPKTAWALKHMDRFP--VDVNKAPYKELLRVPGIGVKSARRIVMTRRRT--RLTLEDLKKLGVVLK 368 (404)
T ss_pred CCCChhhHHHHhcccccc--ccccccCHHHhcccCCCChHHHHHHHHHhhhc--ccCHHHHhhhceeee
Confidence 5677888888864 343 46788999999999999999999998633211 123566777777643
No 239
>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=64.35 E-value=7.6 Score=30.62 Aligned_cols=26 Identities=35% Similarity=0.372 Sum_probs=18.0
Q ss_pred hCCCCccHHHHHHHHH-hCCCHHHHHh
Q psy11423 526 LGIRHVGETTAKELAN-YFKNLECMFK 551 (655)
Q Consensus 526 lgIpgIG~~~Ak~L~~-~fgsl~~l~~ 551 (655)
.+|.|||+++|+++.+ -+.|++.|..
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 3899999999998876 4888888864
No 240
>TIGR00596 rad1 DNA repair protein (rad1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit
Probab=64.18 E-value=7.3 Score=47.31 Aligned_cols=19 Identities=32% Similarity=0.387 Sum_probs=11.4
Q ss_pred hccccCCcHHHHHHHHHHH
Q psy11423 493 LLRLDRVSNKLANNILLAI 511 (655)
Q Consensus 493 L~~l~GfG~Ksa~nll~~I 511 (655)
|..|||+|++.|.+|++..
T Consensus 759 L~~lPgI~~~~a~~ll~~f 777 (814)
T TIGR00596 759 LLKLPGVTKKNYRNLRKKV 777 (814)
T ss_pred HHHCCCCCHHHHHHHHHHc
Confidence 5566666666666666544
No 241
>KOG3084|consensus
Probab=63.78 E-value=3.5 Score=44.01 Aligned_cols=29 Identities=28% Similarity=0.503 Sum_probs=25.3
Q ss_pred CCCCCCCCCcceeecCceeEEecCCCcCCHH
Q psy11423 415 PNICPICNSKIIYIESNLIARCSGSWIECIA 445 (655)
Q Consensus 415 P~~CP~C~~~l~~~~~~~~~~C~n~~~~C~~ 445 (655)
-.+||.||+++..++++...-|.+. . ||.
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 4689999999998888899999985 6 986
No 242
>PRK03858 DNA polymerase IV; Validated
Probab=63.28 E-value=8 Score=42.71 Aligned_cols=49 Identities=16% Similarity=0.217 Sum_probs=40.9
Q ss_pred cccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHH
Q psy11423 458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILL 509 (655)
Q Consensus 458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~ 509 (655)
..-.++|+|+++.++|.+.| |+++.||..+....|... ||....+.|.+
T Consensus 174 pl~~l~Gig~~~~~~L~~~G-i~t~~dl~~l~~~~L~~~--fG~~~~~~l~~ 222 (396)
T PRK03858 174 PVRRLWGVGPVTAAKLRAHG-ITTVGDVAELPESALVSL--LGPAAGRHLHA 222 (396)
T ss_pred ChhhcCCCCHHHHHHHHHhC-CCcHHHHhcCCHHHHHHH--hCcHHHHHHHH
Confidence 34578999999999998776 799999999998888885 88777776655
No 243
>PTZ00217 flap endonuclease-1; Provisional
Probab=62.55 E-value=6.6 Score=43.70 Aligned_cols=25 Identities=28% Similarity=0.503 Sum_probs=20.5
Q ss_pred CCCCccHHHHHHHHHhCCCHHHHHh
Q psy11423 527 GIRHVGETTAKELANYFKNLECMFK 551 (655)
Q Consensus 527 gIpgIG~~~Ak~L~~~fgsl~~l~~ 551 (655)
||||||+++|-.|++.|++++.+..
T Consensus 239 gi~GIG~ktA~~Li~~~gsle~il~ 263 (393)
T PTZ00217 239 TIKGIGPKTAYKLIKKYKSIEEILE 263 (393)
T ss_pred CCCCccHHHHHHHHHHcCCHHHHHH
Confidence 7888888888888888888887764
No 244
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=62.51 E-value=5.2 Score=30.84 Aligned_cols=23 Identities=26% Similarity=0.550 Sum_probs=16.8
Q ss_pred CCCCCCCCcceeecCc--eeEEecC
Q psy11423 416 NICPICNSKIIYIESN--LIARCSG 438 (655)
Q Consensus 416 ~~CP~C~~~l~~~~~~--~~~~C~n 438 (655)
.+||.||+.|...++. ..+.|+.
T Consensus 1 ~FCp~Cg~~l~~~~~~~~~~~vC~~ 25 (52)
T smart00661 1 KFCPKCGNMLIPKEGKEKRRFVCRK 25 (52)
T ss_pred CCCCCCCCccccccCCCCCEEECCc
Confidence 3799999988765443 3778875
No 245
>COG2251 Predicted nuclease (RecB family) [General function prediction only]
Probab=62.49 E-value=10 Score=42.48 Aligned_cols=64 Identities=16% Similarity=0.188 Sum_probs=50.3
Q ss_pred CHHHHHhhccccccccccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHHH
Q psy11423 443 CIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK 513 (655)
Q Consensus 443 C~~q~~~~i~~F~sk~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~ 513 (655)
|.++..+ +++.+=++|++|.+-..|.+.| |+|++||-..+...+..+-|+=.+.+..+.-+...
T Consensus 217 C~~~a~e------~~~L~Lv~Gi~~~r~~~l~~~G-I~Ti~~LA~~~~~~~~~~~ga~~~~~~~l~~qa~~ 280 (474)
T COG2251 217 CESEALE------EDDLSLVPGITPSRYDVLEEVG-ITTIEDLADASLPILELVAGALTALAAQLVLQARA 280 (474)
T ss_pred hhHHHhh------ccceeccCCCCHHHHHHHHHcC-cchHHHHHhccccchhhhhhhHHHHHHHHHHHHHh
Confidence 9887754 5556668999999999999988 69999999988888888866546666666665554
No 246
>PRK03348 DNA polymerase IV; Provisional
Probab=62.15 E-value=9.1 Score=43.36 Aligned_cols=49 Identities=18% Similarity=0.205 Sum_probs=41.0
Q ss_pred ccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHH
Q psy11423 459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLA 510 (655)
Q Consensus 459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~ 510 (655)
.=.++|+|+++.++|...| |+++.||..+....|... ||.+....|.+.
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 4468999999999997766 799999999999899886 898777777553
No 247
>PRK10880 adenine DNA glycosylase; Provisional
Probab=62.07 E-value=15 Score=40.29 Aligned_cols=72 Identities=21% Similarity=0.245 Sum_probs=47.6
Q ss_pred HHHHHcCCCCChHHHhcCChhhhccc-c--CCcHHHHHHHHHHHHHh---cccchhHHHHHh-CCCCccHHHHHHHHH-h
Q psy11423 471 EKLVNANIVVTAVDLYKINFKNLLRL-D--RVSNKLANNILLAIQKS---KLTTFSRFIYAL-GIRHVGETTAKELAN-Y 542 (655)
Q Consensus 471 ~~L~~~g~I~~i~DL~~L~~~~L~~l-~--GfG~Ksa~nll~~I~~s---k~~~l~r~L~al-gIpgIG~~~Ak~L~~-~ 542 (655)
.+|.+. .-++.+|..++.++|..+ . ||- ..|.+|.+..+.. ....+..-...| .+||||+++|..++. .
T Consensus 53 ~rl~~~--fPt~~~La~a~~eel~~~~~glGyy-~RAr~L~~~A~~i~~~~~g~~p~~~~~L~~LpGIG~~TA~aIl~~a 129 (350)
T PRK10880 53 ERFMAR--FPTVTDLANAPLDEVLHLWTGLGYY-ARARNLHKAAQQVATLHGGEFPETFEEVAALPGVGRSTAGAILSLS 129 (350)
T ss_pred HHHHHH--CcCHHHHHCcCHHHHHHHHHcCChH-HHHHHHHHHHHHHHHHhCCCchhhHHHHhcCCCccHHHHHHHHHHH
Confidence 445553 258999999988888753 2 565 3688887766543 122233333343 899999999998876 4
Q ss_pred CCC
Q psy11423 543 FKN 545 (655)
Q Consensus 543 fgs 545 (655)
|+-
T Consensus 130 f~~ 132 (350)
T PRK10880 130 LGK 132 (350)
T ss_pred CCC
Confidence 664
No 248
>PTZ00035 Rad51 protein; Provisional
Probab=61.85 E-value=16 Score=39.88 Aligned_cols=54 Identities=22% Similarity=0.222 Sum_probs=46.0
Q ss_pred HHHhCCCCccHHHHHHHHHh-CCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHhc
Q psy11423 523 IYALGIRHVGETTAKELANY-FKNLECMFKATEEQLLNIPKIGSTTVKAFIKFIN 576 (655)
Q Consensus 523 L~algIpgIG~~~Ak~L~~~-fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f~ 576 (655)
+..|.-+||++...++|.+. |.+++.+..++..+|.++.||++..|++|.+..+
T Consensus 23 ~~~l~~~g~~~~~~~kL~~~g~~t~~~~~~~~~~~L~~~~gis~~~~~~i~~~~~ 77 (337)
T PTZ00035 23 IEKLQSAGINAADIKKLKEAGICTVESVAYATKKDLCNIKGISEAKVEKIKEAAS 77 (337)
T ss_pred HHHHhcCCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHHhhCCCHHHHHHHHHHHH
Confidence 34444588999999998875 9999999999999999999999999999987543
No 249
>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=61.36 E-value=4.8 Score=34.64 Aligned_cols=31 Identities=19% Similarity=0.305 Sum_probs=21.7
Q ss_pred ccccccCCCCHHHHHHHHHcCCCCChHHHhcC
Q psy11423 457 RKAMNIIGLGKKMIEKLVNANIVVTAVDLYKI 488 (655)
Q Consensus 457 k~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L 488 (655)
++.-++|+||++....|.+.| |.|++||-.+
T Consensus 3 ~~l~~LpNig~~~e~~L~~vG-I~t~~~L~~~ 33 (81)
T PF04994_consen 3 NRLKDLPNIGPKSERMLAKVG-IHTVEDLREL 33 (81)
T ss_dssp --GCGSTT--HHHHHHHHHTT---SHHHHHHH
T ss_pred cchhhCCCCCHHHHHHHHHcC-CCCHHHHHHh
Confidence 345689999999999999999 6888888753
No 250
>KOG2534|consensus
Probab=61.36 E-value=15 Score=39.48 Aligned_cols=56 Identities=14% Similarity=0.122 Sum_probs=39.3
Q ss_pred chhHHHHHhCCCCccHHHHHHHHHh--CCCHHHHHhc-------CHHHHhcCCCCCHHHHHHHHH
Q psy11423 518 TFSRFIYALGIRHVGETTAKELANY--FKNLECMFKA-------TEEQLLNIPKIGSTTVKAFIK 573 (655)
Q Consensus 518 ~l~r~L~algIpgIG~~~Ak~L~~~--fgsl~~l~~a-------s~eeL~~i~GIG~~~A~~I~~ 573 (655)
++...-.+-+|||||++.|+++-+- -|.+.++... +..-+.+|-|||.++|+.-+.
T Consensus 51 ~I~S~~ea~~lP~iG~kia~ki~EiletG~l~ele~v~~de~~~~lklFtnifGvG~ktA~~Wy~ 115 (353)
T KOG2534|consen 51 PITSGEEAEKLPGIGPKIAEKIQEILETGVLRELEAVRNDERSQSLKLFTNIFGVGLKTAEKWYR 115 (353)
T ss_pred CcccHHHhcCCCCCCHHHHHHHHHHHHcCCchhHHHHhcchhHHHHHHHHHHhccCHHHHHHHHH
Confidence 3445556679999999999877653 2444444433 235588999999999998654
No 251
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=61.34 E-value=5.4 Score=30.30 Aligned_cols=22 Identities=23% Similarity=0.392 Sum_probs=12.1
Q ss_pred CCCCCCCcceeecCceeEEecC
Q psy11423 417 ICPICNSKIIYIESNLIARCSG 438 (655)
Q Consensus 417 ~CP~C~~~l~~~~~~~~~~C~n 438 (655)
.||.||..+...+....++|++
T Consensus 5 ~C~~CG~~~~~~~~~~~~~Cp~ 26 (46)
T PRK00398 5 KCARCGREVELDEYGTGVRCPY 26 (46)
T ss_pred ECCCCCCEEEECCCCCceECCC
Confidence 4666666655544433556654
No 252
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=60.66 E-value=7.1 Score=35.18 Aligned_cols=29 Identities=34% Similarity=0.813 Sum_probs=21.1
Q ss_pred cCCCCCCCCCCcceeecCceeEEecCCCcCCHHHHHh
Q psy11423 413 KIPNICPICNSKIIYIESNLIARCSGSWIECIAQRKA 449 (655)
Q Consensus 413 ~~P~~CP~C~~~l~~~~~~~~~~C~n~~~~C~~q~~~ 449 (655)
.+|..||.||.++... .++|+| |...+..
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 4678899999987753 689988 5444444
No 253
>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=60.37 E-value=3.5 Score=33.42 Aligned_cols=29 Identities=24% Similarity=0.473 Sum_probs=20.5
Q ss_pred CCCCCCCCCcceeecCceeEEecCCCcCCHHHHHhh
Q psy11423 415 PNICPICNSKIIYIESNLIARCSGSWIECIAQRKAG 450 (655)
Q Consensus 415 P~~CP~C~~~l~~~~~~~~~~C~n~~~~C~~q~~~~ 450 (655)
-.|||.||.++..+ ..+|.. . |.....++
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 36999999998743 458976 3 87655443
No 254
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=59.82 E-value=7.6 Score=33.87 Aligned_cols=24 Identities=21% Similarity=0.575 Sum_probs=20.3
Q ss_pred CCCCCCCCCcceeecCceeEEecC
Q psy11423 415 PNICPICNSKIIYIESNLIARCSG 438 (655)
Q Consensus 415 P~~CP~C~~~l~~~~~~~~~~C~n 438 (655)
+..||+|+++.+.......|.|..
T Consensus 35 ~~~Cp~C~~~~VkR~a~GIW~C~k 58 (89)
T COG1997 35 KHVCPFCGRTTVKRIATGIWKCRK 58 (89)
T ss_pred CCcCCCCCCcceeeeccCeEEcCC
Confidence 557999999988877788999964
No 255
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=59.39 E-value=5.4 Score=30.28 Aligned_cols=26 Identities=19% Similarity=0.443 Sum_probs=20.3
Q ss_pred CCCCCCCCcceeecCceeEEecCCCcCCHHHH
Q psy11423 416 NICPICNSKIIYIESNLIARCSGSWIECIAQR 447 (655)
Q Consensus 416 ~~CP~C~~~l~~~~~~~~~~C~n~~~~C~~q~ 447 (655)
..||.||.- +|...+.|-|. + |+..+
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 479999963 46778999995 6 98655
No 256
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=57.72 E-value=4.4 Score=42.39 Aligned_cols=36 Identities=17% Similarity=0.340 Sum_probs=28.4
Q ss_pred CCCCCCCcceeecCceeEEecCCCcCCHHHHHhhcccccc
Q psy11423 417 ICPICNSKIIYIESNLIARCSGSWIECIAQRKAGLQHFSS 456 (655)
Q Consensus 417 ~CP~C~~~l~~~~~~~~~~C~n~~~~C~~q~~~~i~~F~s 456 (655)
.||.|+++|... +..++|.|. + |.....+...+|..
T Consensus 4 ~CP~C~~~l~~~--~~~~~C~~~-h-~fd~a~~Gy~~ll~ 39 (272)
T PRK11088 4 QCPLCHQPLTLE--ENSWICPQN-H-QFDCAKEGYVNLLP 39 (272)
T ss_pred cCCCCCcchhcC--CCEEEcCCC-C-CCccccCceEEecc
Confidence 599999999753 356999996 7 88777777777763
No 257
>smart00611 SEC63 Domain of unknown function in Sec63p, Brr2p and other proteins.
Probab=57.66 E-value=16 Score=38.74 Aligned_cols=52 Identities=17% Similarity=0.216 Sum_probs=45.9
Q ss_pred hCCCCccHHHHHHHHHh-CCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHhcC
Q psy11423 526 LGIRHVGETTAKELANY-FKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQ 577 (655)
Q Consensus 526 lgIpgIG~~~Ak~L~~~-fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f~~ 577 (655)
+.+||+|+..+++|.+. ..+++.+..++.+++..+-|+++..++.|.++++.
T Consensus 154 ~Qlp~i~~~~~~~l~~~~i~s~~~l~~~~~~~~~~ll~~~~~~~~~i~~~~~~ 206 (312)
T smart00611 154 LQLPHLPEEILKRLEKKKVLSLEDLLELEDEERGELLGLLDAEGERVYKVLSR 206 (312)
T ss_pred ccCCCCCHHHHHHHHhCCCCCHHHHHhcCHHHHHHHHcCCHHHHHHHHHHHHh
Confidence 37899999999999874 67899999999999999999999999999888764
No 258
>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=57.53 E-value=13 Score=40.28 Aligned_cols=48 Identities=19% Similarity=0.266 Sum_probs=38.4
Q ss_pred ccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHH
Q psy11423 459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLA 510 (655)
Q Consensus 459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~ 510 (655)
.-.++|+|+++.++|-..| |+++.||..+..+.|... ||. ...++++.
T Consensus 178 l~~l~gig~~~~~~L~~~G-i~ti~dL~~~~~~~L~~r--fG~-~~~~l~~~ 225 (344)
T cd01700 178 VGDVWGIGRRTAKKLNAMG-IHTAGDLAQADPDLLRKK--FGV-VGERLVRE 225 (344)
T ss_pred hhhcCccCHHHHHHHHHcC-CCcHHHHhcCCHHHHHHH--HHH-HHHHHHHH
Confidence 4468999999999997766 799999999998888874 885 45555554
No 259
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=57.49 E-value=4.4 Score=26.51 Aligned_cols=18 Identities=28% Similarity=0.698 Sum_probs=12.0
Q ss_pred CCCCCCCcceeecCceeEEecC
Q psy11423 417 ICPICNSKIIYIESNLIARCSG 438 (655)
Q Consensus 417 ~CP~C~~~l~~~~~~~~~~C~n 438 (655)
+||.||.++. + ...||++
T Consensus 1 ~Cp~CG~~~~--~--~~~fC~~ 18 (23)
T PF13240_consen 1 YCPNCGAEIE--D--DAKFCPN 18 (23)
T ss_pred CCcccCCCCC--C--cCcchhh
Confidence 5899998775 2 2446766
No 260
>COG3743 Uncharacterized conserved protein [Function unknown]
Probab=57.19 E-value=8.6 Score=36.11 Aligned_cols=41 Identities=17% Similarity=0.246 Sum_probs=33.5
Q ss_pred ccccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccC
Q psy11423 457 RKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDR 498 (655)
Q Consensus 457 k~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~G 498 (655)
-++-.|.|+||+.-..|-+.| |.++++|-..+..++..+++
T Consensus 67 DDLt~I~GIGPk~e~~Ln~~G-I~tfaQIAAwt~~di~~id~ 107 (133)
T COG3743 67 DDLTRISGIGPKLEKVLNELG-IFTFAQIAAWTRADIAWIDD 107 (133)
T ss_pred ccchhhcccCHHHHHHHHHcC-CccHHHHHhcCHHHHHHHHh
Confidence 366789999999999998888 58999999998777665543
No 261
>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=56.67 E-value=10 Score=28.40 Aligned_cols=22 Identities=27% Similarity=0.534 Sum_probs=15.9
Q ss_pred CCCCCCCcc-eeecCceeEEecC
Q psy11423 417 ICPICNSKI-IYIESNLIARCSG 438 (655)
Q Consensus 417 ~CP~C~~~l-~~~~~~~~~~C~n 438 (655)
.||.||+.. +.+.....+.|++
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 599999975 4444556788977
No 262
>PLN03187 meiotic recombination protein DMC1 homolog; Provisional
Probab=56.60 E-value=22 Score=38.90 Aligned_cols=51 Identities=14% Similarity=0.144 Sum_probs=43.9
Q ss_pred HHhCCCCccHHHHHHHHHh-CCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHH
Q psy11423 524 YALGIRHVGETTAKELANY-FKNLECMFKATEEQLLNIPKIGSTTVKAFIKF 574 (655)
Q Consensus 524 ~algIpgIG~~~Ak~L~~~-fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~ 574 (655)
..|.-+||++...++|.+. |.++..+..++..+|.++.|+++..|..|.+-
T Consensus 32 ~~l~~~g~~~~~~~kL~~~g~~tv~~~~~~~~~~L~~~~g~s~~~~~ki~~~ 83 (344)
T PLN03187 32 DKLISQGINAGDVKKLQDAGIYTCNGLMMHTKKNLTGIKGLSEAKVDKICEA 83 (344)
T ss_pred HHHhhCCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHHhcCCCHHHHHHHHHH
Confidence 3344477889999999875 99999999999999999999999999998763
No 263
>PRK10880 adenine DNA glycosylase; Provisional
Probab=55.48 E-value=13 Score=40.66 Aligned_cols=23 Identities=26% Similarity=0.498 Sum_probs=20.4
Q ss_pred cCHHHHhcCCCCCHHHHHHHHHH
Q psy11423 552 ATEEQLLNIPKIGSTTVKAFIKF 574 (655)
Q Consensus 552 as~eeL~~i~GIG~~~A~~I~~~ 574 (655)
.+.++|.++||||+++|..|..|
T Consensus 106 ~~~~~L~~LpGIG~~TA~aIl~~ 128 (350)
T PRK10880 106 ETFEEVAALPGVGRSTAGAILSL 128 (350)
T ss_pred hhHHHHhcCCCccHHHHHHHHHH
Confidence 35689999999999999999875
No 264
>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=55.35 E-value=8.6 Score=25.58 Aligned_cols=21 Identities=24% Similarity=0.483 Sum_probs=12.7
Q ss_pred CCCCCCcceeecCceeEEecC
Q psy11423 418 CPICNSKIIYIESNLIARCSG 438 (655)
Q Consensus 418 CP~C~~~l~~~~~~~~~~C~n 438 (655)
|-+||..|.-.+-.+.+.|+|
T Consensus 1 C~sC~~~i~~r~~~v~f~CPn 21 (24)
T PF07754_consen 1 CTSCGRPIAPREQAVPFPCPN 21 (24)
T ss_pred CccCCCcccCcccCceEeCCC
Confidence 566776666444456666665
No 265
>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=55.30 E-value=21 Score=38.45 Aligned_cols=48 Identities=13% Similarity=0.173 Sum_probs=42.7
Q ss_pred CCccHHHHHHHHHh-CCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHhc
Q psy11423 529 RHVGETTAKELANY-FKNLECMFKATEEQLLNIPKIGSTTVKAFIKFIN 576 (655)
Q Consensus 529 pgIG~~~Ak~L~~~-fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f~ 576 (655)
.|||+...++|.+. |.++..+..++..+|.++.|+++..|++|.+-..
T Consensus 7 ~g~~~~~~~~L~~~g~~t~~~~~~~~~~~L~~~~gls~~~~~~i~~~~~ 55 (313)
T TIGR02238 7 HGINAADIKKLKSAGICTVNGVIMTTRRALCKIKGLSEAKVDKIKEAAS 55 (313)
T ss_pred CCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHHhcCCCHHHHHHHHHHHH
Confidence 56889999988875 9999999999999999999999999999987443
No 266
>TIGR00608 radc DNA repair protein radc. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=55.28 E-value=15 Score=37.66 Aligned_cols=69 Identities=13% Similarity=0.173 Sum_probs=46.5
Q ss_pred HHHHhhccccccccccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHHHhcc
Q psy11423 445 AQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKL 516 (655)
Q Consensus 445 ~q~~~~i~~F~sk~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~sk~ 516 (655)
+-+++-|...+.+..+++..|....+..+.+.| ++.+|+.++.++|.+++|+|+.+|..|...++..+.
T Consensus 17 ~ELLailL~~g~~~~~~~~~lA~~ll~~f~~~g---~l~~l~~a~~~eL~~i~GiG~aka~~l~a~~El~rR 85 (218)
T TIGR00608 17 YELLAIILRTGTPKGLDVLSLSKRLLDVFGRQD---SLGHLLSAPPEELSSVPGIGEAKAIQLKAAVELAKR 85 (218)
T ss_pred HHHHHHHHhCCCCCCCCHHHHHHHHHHHhcccC---CHHHHHhCCHHHHHhCcCCcHHHHHHHHHHHHHHHH
Confidence 445665555544432244444444444322213 788999999999999999999999999998887654
No 267
>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=54.70 E-value=6.8 Score=28.09 Aligned_cols=11 Identities=45% Similarity=1.244 Sum_probs=9.5
Q ss_pred CCCCCCCCCCc
Q psy11423 414 IPNICPICNSK 424 (655)
Q Consensus 414 ~P~~CP~C~~~ 424 (655)
.|+.||.||.+
T Consensus 17 ~p~~CP~Cg~~ 27 (34)
T cd00729 17 APEKCPICGAP 27 (34)
T ss_pred CCCcCcCCCCc
Confidence 68899999975
No 268
>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=54.38 E-value=6.9 Score=33.80 Aligned_cols=21 Identities=24% Similarity=0.278 Sum_probs=9.6
Q ss_pred CCCccHHHHHHHHHhCCCHHH
Q psy11423 528 IRHVGETTAKELANYFKNLEC 548 (655)
Q Consensus 528 IpgIG~~~Ak~L~~~fgsl~~ 548 (655)
|||||+.+|-.|+..+++++.
T Consensus 7 ipGig~~~a~~llaeigd~~r 27 (87)
T PF02371_consen 7 IPGIGPITAATLLAEIGDISR 27 (87)
T ss_pred CCCccHHHHHHHHHHHcCchh
Confidence 444444444444444444433
No 269
>PRK14133 DNA polymerase IV; Provisional
Probab=53.96 E-value=16 Score=39.58 Aligned_cols=49 Identities=31% Similarity=0.424 Sum_probs=39.1
Q ss_pred ccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHH
Q psy11423 459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAI 511 (655)
Q Consensus 459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I 511 (655)
.=.++|+|+++.++|..-| |+++.||..+....|... ||. ....+++..
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 4468999999999997766 799999999998888886 884 555565544
No 270
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=53.67 E-value=8.6 Score=40.24 Aligned_cols=24 Identities=13% Similarity=0.357 Sum_probs=20.4
Q ss_pred CCCCCCCCCcceeecCceeEEecC
Q psy11423 415 PNICPICNSKIIYIESNLIARCSG 438 (655)
Q Consensus 415 P~~CP~C~~~l~~~~~~~~~~C~n 438 (655)
-.+||.||+++...+++...+|++
T Consensus 99 ~~fC~~CG~~~~~~~~~~~~~C~~ 122 (256)
T PRK00241 99 HRFCGYCGHPMHPSKTEWAMLCPH 122 (256)
T ss_pred CccccccCCCCeecCCceeEECCC
Confidence 359999999998777888889965
No 271
>PRK14976 5'-3' exonuclease; Provisional
Probab=53.66 E-value=34 Score=36.31 Aligned_cols=45 Identities=27% Similarity=0.409 Sum_probs=30.4
Q ss_pred cccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHHH
Q psy11423 460 MNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK 513 (655)
Q Consensus 460 l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~ 513 (655)
-+|+|+||||+.+|..+=. +++++|+ .+.++ +.|..++|.++.+.
T Consensus 194 pGVpGIG~KtA~~LL~~~g--sle~i~~----~~~~~---~~~~~~~L~~~~~~ 238 (281)
T PRK14976 194 KGVKGIGPKTAIKLLNKYG--NIENIYE----NIDKI---KKKIKNKLSEAKEK 238 (281)
T ss_pred CCCCcccHHHHHHHHHHcC--CHHHHHH----hHHHH---hHHHHHHHHHhHHH
Confidence 3689999999999998643 7777774 12222 23566667666654
No 272
>PRK13844 recombination protein RecR; Provisional
Probab=53.32 E-value=11 Score=37.90 Aligned_cols=24 Identities=17% Similarity=0.313 Sum_probs=15.4
Q ss_pred hhhccccCCcHHHHHHHHHHHHHh
Q psy11423 491 KNLLRLDRVSNKLANNILLAIQKS 514 (655)
Q Consensus 491 ~~L~~l~GfG~Ksa~nll~~I~~s 514 (655)
+.|..|||+|+|+|++|.-.|=+.
T Consensus 15 ~~l~~LPGIG~KsA~Rla~~lL~~ 38 (200)
T PRK13844 15 ESLRKLPTIGKKSSQRLALYLLDK 38 (200)
T ss_pred HHHHHCCCCCHHHHHHHHHHHHcC
Confidence 446677777777777776555433
No 273
>PRK10445 endonuclease VIII; Provisional
Probab=52.83 E-value=9.1 Score=40.20 Aligned_cols=22 Identities=27% Similarity=0.548 Sum_probs=18.0
Q ss_pred CCCCCCCccee--ecCceeEEecC
Q psy11423 417 ICPICNSKIIY--IESNLIARCSG 438 (655)
Q Consensus 417 ~CP~C~~~l~~--~~~~~~~~C~n 438 (655)
.||.||+++.+ ..+...+||++
T Consensus 237 ~Cp~Cg~~I~~~~~~gR~t~~CP~ 260 (263)
T PRK10445 237 ACERCGGIIEKTTLSSRPFYWCPG 260 (263)
T ss_pred CCCCCCCEeEEEEECCCCcEECCC
Confidence 59999999874 35678899987
No 274
>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=52.30 E-value=6.5 Score=40.56 Aligned_cols=28 Identities=29% Similarity=0.533 Sum_probs=11.3
Q ss_pred CCCCCCCCc-ceeecC---ceeEEecCCCcCCHHHH
Q psy11423 416 NICPICNSK-IIYIES---NLIARCSGSWIECIAQR 447 (655)
Q Consensus 416 ~~CP~C~~~-l~~~~~---~~~~~C~n~~~~C~~q~ 447 (655)
.+||.||+. |..-++ -.+++|++ |-++.
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 389999998 664433 36899988 86654
No 275
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=52.12 E-value=10 Score=38.11 Aligned_cols=31 Identities=13% Similarity=0.171 Sum_probs=22.1
Q ss_pred ccccccCCCCHHHHHHHHHcCCCCChHHHhc
Q psy11423 457 RKAMNIIGLGKKMIEKLVNANIVVTAVDLYK 487 (655)
Q Consensus 457 k~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~ 487 (655)
...+.||-||-+.---=+.+|+|+|+.-++.
T Consensus 86 s~~I~IPELg~~iePG~~s~G~ITtIEGvL~ 116 (201)
T COG1779 86 SATIYIPELGLEIEPGPASEGFITTIEGVLE 116 (201)
T ss_pred CccEEcccCceEeccccccCceEehHHHHHH
Confidence 3567788888766666666788888876665
No 276
>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=52.10 E-value=15 Score=28.17 Aligned_cols=31 Identities=29% Similarity=0.498 Sum_probs=20.6
Q ss_pred CCCCCCCcceeec--------CceeEEecCCCcCCHHHHHh
Q psy11423 417 ICPICNSKIIYIE--------SNLIARCSGSWIECIAQRKA 449 (655)
Q Consensus 417 ~CP~C~~~l~~~~--------~~~~~~C~n~~~~C~~q~~~ 449 (655)
.||.||++..... -+....|.|. . |-...+.
T Consensus 1 ~CP~Cg~~a~ir~S~~~s~~~~~~Y~qC~N~-~-Cg~tfv~ 39 (47)
T PF04606_consen 1 RCPHCGSKARIRTSRQLSPLTRELYCQCTNP-E-CGHTFVA 39 (47)
T ss_pred CcCCCCCeeEEEEchhhCcceEEEEEEECCC-c-CCCEEEE
Confidence 5999999765321 1467889995 5 8655443
No 277
>PLN03186 DNA repair protein RAD51 homolog; Provisional
Probab=52.09 E-value=38 Score=37.07 Aligned_cols=53 Identities=21% Similarity=0.287 Sum_probs=44.5
Q ss_pred HHHhCCCCccHHHHHHHHHh-CCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHh
Q psy11423 523 IYALGIRHVGETTAKELANY-FKNLECMFKATEEQLLNIPKIGSTTVKAFIKFI 575 (655)
Q Consensus 523 L~algIpgIG~~~Ak~L~~~-fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f 575 (655)
|..|.-.||++...++|.+. |.+++.+..++..+|.++.||+...++.+....
T Consensus 28 ~~~l~~~gi~~~~i~kL~~~g~~T~~~~~~~~~~~L~~i~~is~~~~~~~~~~~ 81 (342)
T PLN03186 28 IEQLQASGIAALDIKKLKDAGIHTVESLAYAPKKDLLQIKGISEAKVEKILEAA 81 (342)
T ss_pred HHHHHhCCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHHhcCCCHHHHHHHHHHH
Confidence 34444477889999988775 999999999999999999999999998877654
No 278
>PRK00076 recR recombination protein RecR; Reviewed
Probab=51.64 E-value=13 Score=37.48 Aligned_cols=22 Identities=18% Similarity=0.286 Sum_probs=14.2
Q ss_pred hhhccccCCcHHHHHHHHHHHH
Q psy11423 491 KNLLRLDRVSNKLANNILLAIQ 512 (655)
Q Consensus 491 ~~L~~l~GfG~Ksa~nll~~I~ 512 (655)
+.|..|||+|+|+|++|.-.+=
T Consensus 11 ~~l~~LPGIG~KsA~Rla~~ll 32 (196)
T PRK00076 11 EALRKLPGIGPKSAQRLAFHLL 32 (196)
T ss_pred HHHHHCCCCCHHHHHHHHHHHH
Confidence 4466677777777777665554
No 279
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=51.62 E-value=13 Score=37.44 Aligned_cols=22 Identities=18% Similarity=0.306 Sum_probs=14.3
Q ss_pred hhhccccCCcHHHHHHHHHHHH
Q psy11423 491 KNLLRLDRVSNKLANNILLAIQ 512 (655)
Q Consensus 491 ~~L~~l~GfG~Ksa~nll~~I~ 512 (655)
+.|..|||+|+|+|++|.-.|=
T Consensus 11 ~~l~~LPGIG~KsA~RlA~~ll 32 (195)
T TIGR00615 11 ESLKKLPGIGPKSAQRLAFHLL 32 (195)
T ss_pred HHHHHCCCCCHHHHHHHHHHHH
Confidence 4466777777777777755543
No 280
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=51.37 E-value=22 Score=38.10 Aligned_cols=48 Identities=21% Similarity=0.297 Sum_probs=35.1
Q ss_pred cccccCCCCHHHHHHHHHcCCCCChHHHhc-CChhhhccccCCcHHHHHHHHHHHHHhc
Q psy11423 458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYK-INFKNLLRLDRVSNKLANNILLAIQKSK 515 (655)
Q Consensus 458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~-L~~~~L~~l~GfG~Ksa~nll~~I~~sk 515 (655)
+.-+|+|+|||++.+|.++-. +.+.||. +. ....+..+++.+.++.+.
T Consensus 199 nipGV~GIG~ktA~~Ll~~~g--s~e~i~~~~~--------~~~~~~~~~l~~~~~~af 247 (310)
T COG0258 199 NIPGVKGIGPKTALKLLQEYG--SLEGLYENLD--------IIKKKTREKLLEDKEKAF 247 (310)
T ss_pred CCCCCCCcCHHHHHHHHHHhC--CHHHHHHhhh--------hhcchhhHHHHHHHHHHh
Confidence 344599999999999998754 6666665 32 466777888888777653
No 281
>PRK02406 DNA polymerase IV; Validated
Probab=51.33 E-value=18 Score=39.07 Aligned_cols=48 Identities=27% Similarity=0.389 Sum_probs=38.1
Q ss_pred cccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHH
Q psy11423 458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILL 509 (655)
Q Consensus 458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~ 509 (655)
..-+++|+|+++.++|-..| |.++.||..+....|... ||. ....+++
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 35578999999999997665 799999999988888885 884 4455554
No 282
>KOG2906|consensus
Probab=50.85 E-value=12 Score=33.43 Aligned_cols=26 Identities=23% Similarity=0.543 Sum_probs=18.6
Q ss_pred CCCCCCCCcceeecCce--eEEecCCCcCCHH
Q psy11423 416 NICPICNSKIIYIESNL--IARCSGSWIECIA 445 (655)
Q Consensus 416 ~~CP~C~~~l~~~~~~~--~~~C~n~~~~C~~ 445 (655)
.+||.||.-|+.+.|+. .+.|.- ||-
T Consensus 2 ~FCP~Cgn~Live~g~~~~rf~C~t----CpY 29 (105)
T KOG2906|consen 2 LFCPTCGNMLIVESGESCNRFSCRT----CPY 29 (105)
T ss_pred cccCCCCCEEEEecCCeEeeEEcCC----CCc
Confidence 47999999998877654 455533 773
No 283
>PRK11827 hypothetical protein; Provisional
Probab=50.24 E-value=12 Score=30.45 Aligned_cols=22 Identities=32% Similarity=0.732 Sum_probs=18.1
Q ss_pred CCCCCCCcceeecCceeEEecC
Q psy11423 417 ICPICNSKIIYIESNLIARCSG 438 (655)
Q Consensus 417 ~CP~C~~~l~~~~~~~~~~C~n 438 (655)
.||.|+++|....+...+.|..
T Consensus 10 aCP~ckg~L~~~~~~~~Lic~~ 31 (60)
T PRK11827 10 ACPVCNGKLWYNQEKQELICKL 31 (60)
T ss_pred ECCCCCCcCeEcCCCCeEECCc
Confidence 6999999999776666788866
No 284
>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=49.94 E-value=28 Score=37.49 Aligned_cols=48 Identities=19% Similarity=0.211 Sum_probs=41.7
Q ss_pred CCCccHHHHHHHHH-hCCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHh
Q psy11423 528 IRHVGETTAKELAN-YFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFI 575 (655)
Q Consensus 528 IpgIG~~~Ak~L~~-~fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f 575 (655)
-+|+++...++|.+ .|.+++.+..++..+|.++-||+...++.+....
T Consensus 6 ~~~~~~~~~~~l~~~g~~t~~~~~~~~~~~L~~i~~ls~~~~~~~~~~~ 54 (316)
T TIGR02239 6 GNGITAADIKKLQEAGLHTVESVAYAPKKQLLEIKGISEAKADKILAEA 54 (316)
T ss_pred cCCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 35688999888876 4999999999999999999999999998887744
No 285
>PRK09482 flap endonuclease-like protein; Provisional
Probab=49.90 E-value=20 Score=37.63 Aligned_cols=49 Identities=22% Similarity=0.271 Sum_probs=32.6
Q ss_pred cccccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHHH
Q psy11423 456 SRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK 513 (655)
Q Consensus 456 sk~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~ 513 (655)
|.+.-+|+|+||||+.+|..+=. +++.||+- +..+ +.|..++|.+..+.
T Consensus 181 sDnIpGVpGIG~KtA~~LL~~~g--sle~i~~~----~~~~---~~~~~~~L~~~~~~ 229 (256)
T PRK09482 181 SSKIPGVAGIGPKSAAELLNQFR--SLENIYES----LDAL---PEKWRKKLEEHKEM 229 (256)
T ss_pred ccCCCCCCCcChHHHHHHHHHhC--CHHHHHHh----HHHh---hHHHHHHHHHhHHH
Confidence 33445689999999999998743 77777752 2222 34666677766654
No 286
>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=49.03 E-value=14 Score=33.55 Aligned_cols=21 Identities=33% Similarity=0.730 Sum_probs=16.5
Q ss_pred CCCCCCCcceeecCceeEEecC
Q psy11423 417 ICPICNSKIIYIESNLIARCSG 438 (655)
Q Consensus 417 ~CP~C~~~l~~~~~~~~~~C~n 438 (655)
.||.|+|+.+.++ +..+-|+-
T Consensus 4 ~CP~C~seytY~d-g~~~iCpe 24 (109)
T TIGR00686 4 PCPKCNSEYTYHD-GTQLICPS 24 (109)
T ss_pred cCCcCCCcceEec-CCeeECcc
Confidence 5999999988765 45688865
No 287
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=48.94 E-value=9.5 Score=40.25 Aligned_cols=22 Identities=23% Similarity=0.368 Sum_probs=17.7
Q ss_pred CCCCCCCcceee--cCceeEEecC
Q psy11423 417 ICPICNSKIIYI--ESNLIARCSG 438 (655)
Q Consensus 417 ~CP~C~~~l~~~--~~~~~~~C~n 438 (655)
.||.||+++.+. .+...+||++
T Consensus 247 pC~~Cg~~I~~~~~~gR~t~~CP~ 270 (274)
T PRK01103 247 PCRRCGTPIEKIKQGGRSTFFCPR 270 (274)
T ss_pred CCCCCCCeeEEEEECCCCcEECcC
Confidence 499999998743 4668999987
No 288
>PRK03103 DNA polymerase IV; Reviewed
Probab=48.47 E-value=22 Score=39.52 Aligned_cols=50 Identities=14% Similarity=0.170 Sum_probs=40.1
Q ss_pred ccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHH
Q psy11423 459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQ 512 (655)
Q Consensus 459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~ 512 (655)
.=.++|+|+++.++|-.-| |.++.||..+....|... ||. ....+++...
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 3467999999999998776 799999999998888875 884 4666666543
No 289
>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=48.15 E-value=24 Score=38.21 Aligned_cols=49 Identities=14% Similarity=0.131 Sum_probs=36.1
Q ss_pred ccccCCCCHHHHHHHHHcCCCCChHHHhcCC-hhhhccccCCcHHHHHHHHHHH
Q psy11423 459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKIN-FKNLLRLDRVSNKLANNILLAI 511 (655)
Q Consensus 459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~-~~~L~~l~GfG~Ksa~nll~~I 511 (655)
.=+++|+|+++.++|.+.| |.++.||..+. ...|... || +.+..+++..
T Consensus 175 i~~l~giG~~~~~~L~~~G-i~ti~dl~~~~~~~~l~~~--fg-~~~~~l~~~a 224 (343)
T cd00424 175 LTDLPGIGAVTAKRLEAVG-INPIGDLLAASPDALLALW--GG-VSGERLWYAL 224 (343)
T ss_pred hhhcCCCCHHHHHHHHHcC-CCcHHHHhcCCHHHHHHHH--hh-HHHHHHHHHh
Confidence 3458999999999998777 79999999998 4444443 66 4566666543
No 290
>KOG1921|consensus
Probab=47.99 E-value=63 Score=33.70 Aligned_cols=73 Identities=15% Similarity=0.058 Sum_probs=45.9
Q ss_pred HHHHHHHcCCCCChHHHhcCChhhhccc---cCCcHHHHHHHHHHHHHhcc---cchhHHHHH-hCCCCccHHHHHHHHH
Q psy11423 469 MIEKLVNANIVVTAVDLYKINFKNLLRL---DRVSNKLANNILLAIQKSKL---TTFSRFIYA-LGIRHVGETTAKELAN 541 (655)
Q Consensus 469 ~i~~L~~~g~I~~i~DL~~L~~~~L~~l---~GfG~Ksa~nll~~I~~sk~---~~l~r~L~a-lgIpgIG~~~Ak~L~~ 541 (655)
....|.+.|++ +++++...++..|.+| =||=..+|.+|.+--+-... .++.+=+.. +++||||++.|-..+.
T Consensus 99 Am~rL~~~~gL-T~e~v~~~de~~l~~LI~~VgFy~rKA~ylkkta~IL~d~f~gDIP~~v~dLlsLPGVGPKMa~L~m~ 177 (286)
T KOG1921|consen 99 AMLRLKEYGGL-TLEAVLKIDEPTLNELIYPVGFYTRKAKYLKKTAKILQDKFDGDIPDTVEDLLSLPGVGPKMAHLTMQ 177 (286)
T ss_pred HHHHHHHhcCC-CHHHHhccChHhHHhhhhhccchHHHHHHHHHHHHHHHHHhCCCCchhHHHHhcCCCCchHHHHHHHH
Confidence 44667777754 7888888766544443 58888888777553332221 233344444 4899999999876655
Q ss_pred h
Q psy11423 542 Y 542 (655)
Q Consensus 542 ~ 542 (655)
.
T Consensus 178 ~ 178 (286)
T KOG1921|consen 178 V 178 (286)
T ss_pred H
Confidence 3
No 291
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=47.96 E-value=7.1 Score=31.61 Aligned_cols=25 Identities=24% Similarity=0.506 Sum_probs=19.8
Q ss_pred CCCCCCCCCCcceeecCceeEEecC
Q psy11423 414 IPNICPICNSKIIYIESNLIARCSG 438 (655)
Q Consensus 414 ~P~~CP~C~~~l~~~~~~~~~~C~n 438 (655)
.|..|-|||..|.-.+..+.+-|+|
T Consensus 8 ~~~~CtSCg~~i~p~e~~v~F~CPn 32 (61)
T COG2888 8 DPPVCTSCGREIAPGETAVKFPCPN 32 (61)
T ss_pred CCceeccCCCEeccCCceeEeeCCC
Confidence 3678999998886667778888888
No 292
>KOG2875|consensus
Probab=47.43 E-value=41 Score=35.61 Aligned_cols=39 Identities=23% Similarity=0.348 Sum_probs=23.3
Q ss_pred HHHHHHHhCCCH---HHHHhcCH----HHHhcCCCCCHHHHHHHHH
Q psy11423 535 TAKELANYFKNL---ECMFKATE----EQLLNIPKIGSTTVKAFIK 573 (655)
Q Consensus 535 ~Ak~L~~~fgsl---~~l~~as~----eeL~~i~GIG~~~A~~I~~ 573 (655)
+|+.|.+..+.. ..+..++. +.|..+||||+|+|.-|.-
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 556666666653 33333332 4577777777777777654
No 293
>PRK01810 DNA polymerase IV; Validated
Probab=47.26 E-value=22 Score=39.44 Aligned_cols=50 Identities=22% Similarity=0.169 Sum_probs=39.8
Q ss_pred ccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHH
Q psy11423 459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQ 512 (655)
Q Consensus 459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~ 512 (655)
.-.++|+|+++.++|..-| |.++.||..+....|... ||. ....+++...
T Consensus 181 v~~l~giG~~~~~~L~~~G-i~tigdL~~~~~~~L~~r--fG~-~g~~l~~~a~ 230 (407)
T PRK01810 181 VGEMHGIGEKTAEKLKDIG-IQTIGDLAKADEHILRAK--LGI-NGVRLQRRAN 230 (407)
T ss_pred HhhcCCcCHHHHHHHHHcC-CCcHHHHHhCCHHHHHHH--HhH-HHHHHHHHhc
Confidence 3357999999999998766 799999999998888875 885 5666666543
No 294
>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=47.26 E-value=25 Score=37.60 Aligned_cols=50 Identities=18% Similarity=0.050 Sum_probs=39.0
Q ss_pred cccccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHH
Q psy11423 456 SRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILL 509 (655)
Q Consensus 456 sk~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~ 509 (655)
..--+++.|+|+++.++|-+.| |.++.||.++....|... ||.+ ...+++
T Consensus 169 ~~lp~~~~gig~~~~~~L~~~G-i~t~~dl~~~~~~~l~~r--fG~~-~~~l~~ 218 (335)
T cd03468 169 APLPVAALRLPPETVELLARLG-LRTLGDLAALPRAELARR--FGLA-LLLRLD 218 (335)
T ss_pred CCCChhHhCCCHHHHHHHHHhC-cccHHHHHhCChHHHHhh--cCHH-HHHHHH
Confidence 3334679999999999998776 699999999998888875 9965 444444
No 295
>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=47.09 E-value=24 Score=29.78 Aligned_cols=29 Identities=21% Similarity=0.272 Sum_probs=18.6
Q ss_pred ccccccCCCCHHHHHHHHHcCCCCChHHHhc
Q psy11423 457 RKAMNIIGLGKKMIEKLVNANIVVTAVDLYK 487 (655)
Q Consensus 457 k~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~ 487 (655)
...-.|+|+|+|++.+|+.+- .++..++.
T Consensus 22 D~i~gv~giG~k~A~~ll~~~--~~~~~~~~ 50 (75)
T cd00080 22 DNIPGVPGIGPKTALKLLKEY--GSLENLLE 50 (75)
T ss_pred ccCCCCCcccHHHHHHHHHHh--CCHHHHHH
Confidence 334467788888888877653 35555554
No 296
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=47.04 E-value=15 Score=26.75 Aligned_cols=16 Identities=31% Similarity=0.524 Sum_probs=13.3
Q ss_pred ccCCCCHHHHHHHHHc
Q psy11423 461 NIIGLGKKMIEKLVNA 476 (655)
Q Consensus 461 ~I~GLG~k~i~~L~~~ 476 (655)
.|+|+|+|++.+|+.+
T Consensus 20 Gv~giG~ktA~~ll~~ 35 (36)
T smart00279 20 GVKGIGPKTALKLLRE 35 (36)
T ss_pred CCCcccHHHHHHHHHh
Confidence 5899999999988763
No 297
>PF02643 DUF192: Uncharacterized ACR, COG1430; InterPro: IPR003795 This entry describes proteins of unknown function.; PDB: 3M7A_B 3PJY_B.
Probab=46.67 E-value=55 Score=29.53 Aligned_cols=89 Identities=13% Similarity=0.128 Sum_probs=46.3
Q ss_pred EEECChhhhhhhCC---CCCCCCceEeecCCcceeeE-------EEEEEEEeecCcceeeeEEEEE-EEEECC----EEE
Q psy11423 299 YKINCLSTQKKLGF---TSRAPRFALAYKFLSKEALT-------KIKAINIQIGRTGIITPVALLK-PVLIDG----ITI 363 (655)
Q Consensus 299 ikv~~~~~~~~lG~---ts~~PrwaiA~Kf~~~~~~T-------~v~~I~~qvGRTG~itPvA~le-PV~l~G----~tV 363 (655)
+++-+...++..|- .+-.|.-++=|.||.....| .=.||.| +.+.|+|+=+.... |=...- ..+
T Consensus 4 vevA~t~~~r~~GLm~r~~l~~~~gMLF~~~~~~~~~~~M~~~~~pLDi~f-ld~~g~Vv~i~~~~~P~~~~~~~~~~~a 82 (108)
T PF02643_consen 4 VEVADTFEERARGLMFRRSLPPDEGMLFIFPCPSVHTFWMKNTRFPLDIAF-LDSDGRVVKIERMVPPWRTYPCPSYKPA 82 (108)
T ss_dssp EEEE-SHHHHHHTTTT-----TTEEEEEEECCEEEEEE--TT--S-EEEEE-E-TTSBEEEEEEEE-TT--S-EEECCEE
T ss_pred EEEeCCHHHHHhCCCCCCCCCCCcEEEEecCCCCeEEEEEEccceeEEEEE-ECCCCeEEEEEccCCCCccCCCCCCCcc
Confidence 34444555555552 22244446667766555443 1245555 46788888888887 444322 223
Q ss_pred EEeeCCCHHHHHhcCCCCCCEEEEE
Q psy11423 364 TRATLHNESEIYRKNIQIGDTVVVH 388 (655)
Q Consensus 364 sratLhN~~~i~~~~i~iGd~V~v~ 388 (655)
..|==-|+..++++||++||+|.+.
T Consensus 83 ~~vLE~~aG~~~~~~i~~Gd~v~~~ 107 (108)
T PF02643_consen 83 RYVLELPAGWFEKLGIKVGDRVRIE 107 (108)
T ss_dssp CEEEEEETTHHHHHT--TT-EEE--
T ss_pred CEEEEcCCCchhhcCCCCCCEEEec
Confidence 3344457889999999999999874
No 298
>PRK03760 hypothetical protein; Provisional
Probab=46.60 E-value=25 Score=32.44 Aligned_cols=54 Identities=13% Similarity=0.077 Sum_probs=39.0
Q ss_pred EEEEEeecCcceeeeEEEEEEEEEC--CEEEEEeeCCCHHHHHhcCCCCCCEEEEEe
Q psy11423 335 KAINIQIGRTGIITPVALLKPVLID--GITITRATLHNESEIYRKNIQIGDTVVVHR 389 (655)
Q Consensus 335 ~~I~~qvGRTG~itPvA~lePV~l~--G~tVsratLhN~~~i~~~~i~iGd~V~v~r 389 (655)
+||.| +.+.|+|.=++.+.|-.+- +..+..|==-|+..+.++||.+||+|.+.+
T Consensus 61 LDiiF-ld~~g~Vv~i~~~~P~~~~~~~~~a~~VLEl~aG~~~~~gi~~Gd~v~~~~ 116 (117)
T PRK03760 61 IDVIF-LDSNRRVVDFKTLKPWRIYVPKKPARYIIEGPVGKIRVLKVEVGDEIEWID 116 (117)
T ss_pred eEEEE-ECCCCeEEEEEeCCCccccCCCccceEEEEeCCChHHHcCCCCCCEEEEee
Confidence 45555 4677887777777776542 233445555689999999999999998876
No 299
>PRK02794 DNA polymerase IV; Provisional
Probab=46.59 E-value=21 Score=39.91 Aligned_cols=49 Identities=18% Similarity=0.230 Sum_probs=39.2
Q ss_pred ccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHH
Q psy11423 459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAI 511 (655)
Q Consensus 459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I 511 (655)
.=.++|+|+++.++|...| |.++.||..+....|... ||. ....+++..
T Consensus 211 l~~L~GiG~~~~~~L~~~G-I~tigdL~~l~~~~L~~r--fG~-~g~~l~~~a 259 (419)
T PRK02794 211 VGIIWGVGPATAARLARDG-IRTIGDLQRADEADLMRR--FGS-MGLRLWRLA 259 (419)
T ss_pred hhhhCCCCHHHHHHHHHhc-cchHHHHhhCCHHHHHHH--HhH-HHHHHHHHh
Confidence 4578999999999997766 799999999998888875 886 466665543
No 300
>PF04919 DUF655: Protein of unknown function (DUF655); InterPro: IPR007003 This family includes several uncharacterised archaeal proteins.; PDB: 2I5H_A.
Probab=45.76 E-value=42 Score=33.34 Aligned_cols=55 Identities=15% Similarity=0.189 Sum_probs=32.6
Q ss_pred CChhhhccccCCcHHHHHHHHHHHHHhcccchhHHHHHh-CCCCccHHHHHHHHHh
Q psy11423 488 INFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYAL-GIRHVGETTAKELANY 542 (655)
Q Consensus 488 L~~~~L~~l~GfG~Ksa~nll~~I~~sk~~~l~r~L~al-gIpgIG~~~Ak~L~~~ 542 (655)
+..+.|.-|||+|+|...+|++.-++..=.+|..+-.-. |+++.-+..++++.+.
T Consensus 113 ~RlH~LeLLPGIGKK~m~~ILeERkkkpFeSFeDi~~Rv~gl~~p~~~i~~RIl~E 168 (181)
T PF04919_consen 113 LRLHSLELLPGIGKKTMWKILEERKKKPFESFEDIEERVKGLHDPVKLIVERILEE 168 (181)
T ss_dssp SSSBGGGGSTT--HHHHHHHHHHHHHS---SHHHHHHHSTT---HHHHHHHHHHHH
T ss_pred HHHHHHhhcccccHHHHHHHHHHHccCCCCCHHHHHHHhccCCCHHHHHHHHHHHH
Confidence 456889999999999999999876654334555555555 5666555555555543
No 301
>PTZ00205 DNA polymerase kappa; Provisional
Probab=45.24 E-value=23 Score=41.30 Aligned_cols=47 Identities=23% Similarity=0.294 Sum_probs=37.3
Q ss_pred ccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHH
Q psy11423 459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILL 509 (655)
Q Consensus 459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~ 509 (655)
.=+|+|+|+++..+|-..| |.++.||+....+ |..+ |+++..+.++.
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 4579999999999998776 7999999998753 4444 78887777664
No 302
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=45.01 E-value=12 Score=36.59 Aligned_cols=53 Identities=19% Similarity=0.347 Sum_probs=35.3
Q ss_pred HHHHHhcCCCCCCEEEEEecCcccceeecccccCCCCCCccccCC--CCCCCCCCcceee
Q psy11423 371 ESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIP--NICPICNSKIIYI 428 (655)
Q Consensus 371 ~~~i~~~~i~iGd~V~v~raGdVIP~I~~vv~~~r~~~~~~~~~P--~~CP~C~~~l~~~ 428 (655)
...+++. ..|-.....++-++.-|+..++... +.. +...| +.||.||++|+..
T Consensus 56 r~L~~r~--k~g~~~i~i~~~s~~~Ql~e~~~~~--~l~-~~~~~e~~RCp~CN~~L~~v 110 (165)
T COG1656 56 RELYKRA--KLGIKAILIRSDSIEEQLAEFLARL--GLK-PRLFPEFSRCPECNGELEKV 110 (165)
T ss_pred HHHHHHh--hccCceEEEeCCCHHHHHHHHHHHh--ccc-hhcccccccCcccCCEeccC
Confidence 3445655 5666777888888888888886522 111 22234 6899999998754
No 303
>COG1491 Predicted RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=44.98 E-value=67 Score=32.05 Aligned_cols=23 Identities=22% Similarity=0.154 Sum_probs=16.7
Q ss_pred hhhhccccCCcHHHHHHHHHHHH
Q psy11423 490 FKNLLRLDRVSNKLANNILLAIQ 512 (655)
Q Consensus 490 ~~~L~~l~GfG~Ksa~nll~~I~ 512 (655)
-+.|.-|||+|+|...+||+.-+
T Consensus 129 LH~LELLpGiGkK~m~~ILeERk 151 (202)
T COG1491 129 LHQLELLPGIGKKTMWAILEERK 151 (202)
T ss_pred HHHHHhcccccHHHHHHHHHHHh
Confidence 46777778888888777776544
No 304
>PRK07945 hypothetical protein; Provisional
Probab=44.35 E-value=35 Score=37.13 Aligned_cols=49 Identities=16% Similarity=0.074 Sum_probs=37.9
Q ss_pred hhccccCCcHHHHHHHHHHHHHhcccchhHHHHHhCCCCccHHHHHHHHH
Q psy11423 492 NLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELAN 541 (655)
Q Consensus 492 ~L~~l~GfG~Ksa~nll~~I~~sk~~~l~r~L~algIpgIG~~~Ak~L~~ 541 (655)
+|.++||+|+..|++|.+-++.-+-..+.++....+=-| |+..+.+|.-
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 688999999999999998887554445666666665446 8989888876
No 305
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=44.33 E-value=23 Score=29.00 Aligned_cols=15 Identities=33% Similarity=0.678 Sum_probs=11.2
Q ss_pred CCCCCCCc-ceeecCc
Q psy11423 417 ICPICNSK-IIYIESN 431 (655)
Q Consensus 417 ~CP~C~~~-l~~~~~~ 431 (655)
.||.|||. +..++.|
T Consensus 20 ~CP~Cgs~~~te~W~G 35 (64)
T COG2093 20 ICPVCGSTDLTEEWFG 35 (64)
T ss_pred cCCCCCCcccchhhcc
Confidence 49999998 6655554
No 306
>PF13549 ATP-grasp_5: ATP-grasp domain; PDB: 1WR2_A.
Probab=44.22 E-value=48 Score=33.98 Aligned_cols=48 Identities=15% Similarity=0.216 Sum_probs=32.4
Q ss_pred CCHHHHHHHHHhCCCCCCCCceeeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChh
Q psy11423 247 SSHSELLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLS 305 (655)
Q Consensus 247 ~~~~e~l~~L~~~GF~~~~~~~~~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~ 305 (655)
-+..|..+.|..+|+++++ +.++.+.+++.+..+.+ .|+ +|+|+.+..
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 4678999999999999998 46789999998887765 566 899998743
No 307
>PRK10220 hypothetical protein; Provisional
Probab=44.20 E-value=19 Score=32.77 Aligned_cols=21 Identities=38% Similarity=0.768 Sum_probs=16.5
Q ss_pred CCCCCCCcceeecCceeEEecC
Q psy11423 417 ICPICNSKIIYIESNLIARCSG 438 (655)
Q Consensus 417 ~CP~C~~~l~~~~~~~~~~C~n 438 (655)
.||.|+++.+.++ +..+-|+-
T Consensus 5 ~CP~C~seytY~d-~~~~vCpe 25 (111)
T PRK10220 5 HCPKCNSEYTYED-NGMYICPE 25 (111)
T ss_pred cCCCCCCcceEcC-CCeEECCc
Confidence 5999999988764 46788865
No 308
>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=43.90 E-value=34 Score=35.31 Aligned_cols=43 Identities=16% Similarity=0.281 Sum_probs=28.9
Q ss_pred cccCCCCHHHHHHHHHcCCCCChHHHhc-CChhhhccccCCcHHHHHHHHHHHH
Q psy11423 460 MNIIGLGKKMIEKLVNANIVVTAVDLYK-INFKNLLRLDRVSNKLANNILLAIQ 512 (655)
Q Consensus 460 l~I~GLG~k~i~~L~~~g~I~~i~DL~~-L~~~~L~~l~GfG~Ksa~nll~~I~ 512 (655)
-+|+|+|||++.+|.++= .+++++|. +.. .+.|..++|.++.+
T Consensus 186 pGv~GiG~ktA~~Ll~~~--gsle~i~~~~~~--------~~~~~~~~l~~~~~ 229 (240)
T cd00008 186 PGVPGIGEKTAAKLLKEY--GSLEGILENLDK--------IKGKLREKLEEGKE 229 (240)
T ss_pred CCCCccCHHHHHHHHHHh--CCHHHHHHhHHH--------HhHHHHHHHHHhHH
Confidence 357999999999999874 47888875 222 22355555555544
No 309
>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=43.64 E-value=17 Score=25.57 Aligned_cols=19 Identities=32% Similarity=0.434 Sum_probs=15.0
Q ss_pred ccccCCCCHHHHHHHHHcC
Q psy11423 459 AMNIIGLGKKMIEKLVNAN 477 (655)
Q Consensus 459 ~l~I~GLG~k~i~~L~~~g 477 (655)
.=++.|+|+++.++|.+.|
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 4479999999999997765
No 310
>PRK14182 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=43.36 E-value=78 Score=33.74 Aligned_cols=67 Identities=10% Similarity=0.210 Sum_probs=46.5
Q ss_pred CHHHHHHHHHHhcChhHHHHHHHHHHcCcccccCCCCCCCeEecccccCccEEEecCCCC------chHHHHHHcCCee-
Q psy11423 564 GSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNNPNTKGGKVVNFISKNTNYLVKGQKPG------KKLEKAIKLNIKI- 636 (655)
Q Consensus 564 G~~~A~~I~~~f~~~~n~~li~~L~~~Gi~~~~~~~~~G~~v~~sVsk~t~ylv~g~~~g------~K~~kA~~lgi~i- 636 (655)
|..+|+.|.+.+. +.++.|.+.|+. .+.-.+.+|+.+. .|.+.|+++||..
T Consensus 6 Gk~iA~~i~~~ik-----~~v~~l~~~g~~-----------------P~LaiI~vg~d~as~~Yv~~k~k~a~~~Gi~~~ 63 (282)
T PRK14182 6 GKQIAAKVKGEVA-----TEVRALAARGVQ-----------------TGLTVVRVGDDPASAIYVRGKRKDCEEVGITSV 63 (282)
T ss_pred HHHHHHHHHHHHH-----HHHHHHHhCCCC-----------------CeEEEEEeCCCHHHHHHHHHHHHHHHHcCCEEE
Confidence 6778888877763 346666554443 2344677888754 6778899999885
Q ss_pred -------eCHHHHHHHHhcccCC
Q psy11423 637 -------LDEKNFVKIVKGFSTE 652 (655)
Q Consensus 637 -------i~e~~f~~~l~~~~~~ 652 (655)
++++++.+.+..-+.+
T Consensus 64 ~~~l~~~~t~~~l~~~I~~lN~d 86 (282)
T PRK14182 64 EHHLPATTTQAELLALIARLNAD 86 (282)
T ss_pred EEECCCCCCHHHHHHHHHHHhCC
Confidence 4889999988655444
No 311
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=43.33 E-value=12 Score=36.69 Aligned_cols=12 Identities=42% Similarity=1.317 Sum_probs=9.7
Q ss_pred cCCCCCCCCCCc
Q psy11423 413 KIPNICPICNSK 424 (655)
Q Consensus 413 ~~P~~CP~C~~~ 424 (655)
..|..||+||.+
T Consensus 147 e~P~~CPiCga~ 158 (166)
T COG1592 147 EAPEVCPICGAP 158 (166)
T ss_pred CCCCcCCCCCCh
Confidence 468999999964
No 312
>PRK01229 N-glycosylase/DNA lyase; Provisional
Probab=43.18 E-value=80 Score=32.14 Aligned_cols=20 Identities=35% Similarity=0.566 Sum_probs=17.8
Q ss_pred HHHHh-cCCCCCHHHHHHHHH
Q psy11423 554 EEQLL-NIPKIGSTTVKAFIK 573 (655)
Q Consensus 554 ~eeL~-~i~GIG~~~A~~I~~ 573 (655)
.++|. ++||||+++|..|.-
T Consensus 117 R~~Ll~~lpGIG~KTAd~vL~ 137 (208)
T PRK01229 117 REFLVKNIKGIGYKEASHFLR 137 (208)
T ss_pred HHHHHHcCCCCcHHHHHHHHH
Confidence 47899 999999999999984
No 313
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=43.05 E-value=20 Score=35.95 Aligned_cols=15 Identities=33% Similarity=0.381 Sum_probs=7.8
Q ss_pred hccccCCcHHHHHHH
Q psy11423 493 LLRLDRVSNKLANNI 507 (655)
Q Consensus 493 L~~l~GfG~Ksa~nl 507 (655)
|..|||+|+|+|+++
T Consensus 14 l~kLPGvG~KsA~R~ 28 (198)
T COG0353 14 LKKLPGVGPKSAQRL 28 (198)
T ss_pred HhhCCCCChhHHHHH
Confidence 445555555555554
No 314
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=42.96 E-value=16 Score=28.60 Aligned_cols=22 Identities=27% Similarity=0.505 Sum_probs=15.4
Q ss_pred CCCCCCCCcceeecCceeEEecC
Q psy11423 416 NICPICNSKIIYIESNLIARCSG 438 (655)
Q Consensus 416 ~~CP~C~~~l~~~~~~~~~~C~n 438 (655)
..||.||+. ........+.|..
T Consensus 21 ~fCP~Cg~~-~m~~~~~r~~C~~ 42 (50)
T PRK00432 21 KFCPRCGSG-FMAEHLDRWHCGK 42 (50)
T ss_pred CcCcCCCcc-hheccCCcEECCC
Confidence 489999996 3334446788865
No 315
>PRK03352 DNA polymerase IV; Validated
Probab=42.93 E-value=41 Score=36.37 Aligned_cols=71 Identities=23% Similarity=0.227 Sum_probs=44.1
Q ss_pred HHHHHHHHHHHHhcc------cchhHHHHHh---CCCCccHHHHHHHHHh-CCCHHHHHhcCHHHHhcCCCCCHHHHHHH
Q psy11423 502 KLANNILLAIQKSKL------TTFSRFIYAL---GIRHVGETTAKELANY-FKNLECMFKATEEQLLNIPKIGSTTVKAF 571 (655)
Q Consensus 502 Ksa~nll~~I~~sk~------~~l~r~L~al---gIpgIG~~~Ak~L~~~-fgsl~~l~~as~eeL~~i~GIG~~~A~~I 571 (655)
|.+.++.....+-.. ..+.++|..+ .+||||++++++|.+. +.++..|...+..+|.+. +|...+..+
T Consensus 147 k~lAklaa~~~Kp~g~~~~~~~~~~~~L~~lpl~~l~gig~~~~~~L~~~Gi~ti~dl~~l~~~~L~~~--fG~~~~~~l 224 (346)
T PRK03352 147 KLRAKIATGFAKPAGVFRLTDANWMAVMGDRPTDALWGVGPKTAKRLAALGITTVADLAAADPAELAAT--FGPTTGPWL 224 (346)
T ss_pred HHHHHHHHhhcCCCcEEEECHHHHHHHHhcCCHHHcCCCCHHHHHHHHHcCCccHHHHhcCCHHHHHHH--hChHHHHHH
Confidence 555566555433111 1234566665 5689999998888663 557888888888777776 455455455
Q ss_pred HHH
Q psy11423 572 IKF 574 (655)
Q Consensus 572 ~~~ 574 (655)
...
T Consensus 225 ~~~ 227 (346)
T PRK03352 225 LLL 227 (346)
T ss_pred HHH
Confidence 444
No 316
>PRK01229 N-glycosylase/DNA lyase; Provisional
Probab=42.91 E-value=29 Score=35.31 Aligned_cols=59 Identities=17% Similarity=0.029 Sum_probs=36.6
Q ss_pred cCChhhhccc----c-CCcHHHHHHHHHHHHH------hc--ccchhHHHH-Hh-CCCCccHHHHHHHHHhCCC
Q psy11423 487 KINFKNLLRL----D-RVSNKLANNILLAIQK------SK--LTTFSRFIY-AL-GIRHVGETTAKELANYFKN 545 (655)
Q Consensus 487 ~L~~~~L~~l----~-GfG~Ksa~nll~~I~~------sk--~~~l~r~L~-al-gIpgIG~~~Ak~L~~~fgs 545 (655)
.++.++|..+ - ||-..+|++|.+..+. .. ..+...... -+ .+||||+++|.-++...+.
T Consensus 68 ~~~~eeL~~~Ir~~Gygf~~~KAk~I~~~~~~~~~l~~~~~~~~~~~~~R~~Ll~~lpGIG~KTAd~vL~~~~~ 141 (208)
T PRK01229 68 YLSEEELEEKLKEVGHRFYNKRAEYIVEARKLYGKLKEIIKADKDQFEAREFLVKNIKGIGYKEASHFLRNVGY 141 (208)
T ss_pred CCCHHHHHHHHHHhhcccHHHHHHHHHHHHHHHHHHHHHHhccCCchHHHHHHHHcCCCCcHHHHHHHHHHccC
Confidence 5666665554 2 5889999888766643 11 112112222 24 7999999999988865553
No 317
>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=42.81 E-value=56 Score=25.34 Aligned_cols=44 Identities=23% Similarity=0.224 Sum_probs=33.6
Q ss_pred HHHHHHHHHcCCCCChHHHhcCChhhhccccCCcH-HHHHHHHHHHHH
Q psy11423 467 KKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSN-KLANNILLAIQK 513 (655)
Q Consensus 467 ~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~-Ksa~nll~~I~~ 513 (655)
+.-+..+.++++ +..+|..++.++|..+ |+.. -...+|+.+|+.
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 667777777775 8888999999999877 6654 566777777764
No 318
>KOG1968|consensus
Probab=42.78 E-value=13 Score=45.45 Aligned_cols=42 Identities=31% Similarity=0.294 Sum_probs=40.3
Q ss_pred CCCCCeEecccccCccEEEecCCCC-chHHHHHHcCCeeeCHH
Q psy11423 599 NTKGGKVVNFISKNTNYLVKGQKPG-KKLEKAIKLNIKILDEK 640 (655)
Q Consensus 599 ~~~G~~v~~sVsk~t~ylv~g~~~g-~K~~kA~~lgi~ii~e~ 640 (655)
..+|+.+..+++.+|++++.|++++ .|+.+++++.+++++|+
T Consensus 198 k~~~~~~~~~ls~kt~~s~~~~e~~~~kle~~~~~~~~~~~e~ 240 (871)
T KOG1968|consen 198 KEFGASKTESLSDKTVESCLGDEAIAKKLEKIKELEIPVLLEE 240 (871)
T ss_pred hhccccccccCCCCcceeecCccccchhhcccccccccccchh
Confidence 4899999999999999999999999 89999999999999999
No 319
>PRK12495 hypothetical protein; Provisional
Probab=41.72 E-value=13 Score=37.77 Aligned_cols=23 Identities=17% Similarity=0.374 Sum_probs=18.4
Q ss_pred CCCCCCCCCCcceeecCceeEEecC
Q psy11423 414 IPNICPICNSKIIYIESNLIARCSG 438 (655)
Q Consensus 414 ~P~~CP~C~~~l~~~~~~~~~~C~n 438 (655)
...+||.||.+|-...| ..||+.
T Consensus 41 sa~hC~~CG~PIpa~pG--~~~Cp~ 63 (226)
T PRK12495 41 TNAHCDECGDPIFRHDG--QEFCPT 63 (226)
T ss_pred chhhcccccCcccCCCC--eeECCC
Confidence 45799999999987654 568977
No 320
>PRK14906 DNA-directed RNA polymerase subunit beta'/alpha domain fusion protein; Provisional
Probab=41.39 E-value=31 Score=44.06 Aligned_cols=52 Identities=19% Similarity=0.330 Sum_probs=44.8
Q ss_pred ccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHHH
Q psy11423 461 NIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK 513 (655)
Q Consensus 461 ~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~ 513 (655)
+--+|.-...+.|-.+| |.++.||..+++++|+.+.+||+||.+.|.+.+++
T Consensus 1317 eeL~LSvRs~NcLk~ag-I~tvgdLv~~se~eLlkikN~GkKSl~EIkekL~e 1368 (1460)
T PRK14906 1317 DDLGVSQRWANKFSEAG-IETVGDLIGKTEEDLLRIEGIGAKAIEELKDGLEA 1368 (1460)
T ss_pred cccchhhhHHHHHHHcC-CCcHHHHhhCCHHHHhhccCCCcchHHHHHHHHHH
Confidence 34456667788887777 69999999999999999999999999999988876
No 321
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=41.20 E-value=9.8 Score=30.83 Aligned_cols=24 Identities=25% Similarity=0.477 Sum_probs=16.1
Q ss_pred CCCCCCCCCcceeecCceeEEecC
Q psy11423 415 PNICPICNSKIIYIESNLIARCSG 438 (655)
Q Consensus 415 P~~CP~C~~~l~~~~~~~~~~C~n 438 (655)
|..|-|||..|.-.+..+.+.|+|
T Consensus 7 ~~~CtSCg~~i~~~~~~~~F~CPn 30 (59)
T PRK14890 7 PPKCTSCGIEIAPREKAVKFLCPN 30 (59)
T ss_pred CccccCCCCcccCCCccCEeeCCC
Confidence 446777877776544457777776
No 322
>COG5216 Uncharacterized conserved protein [Function unknown]
Probab=40.76 E-value=27 Score=28.23 Aligned_cols=27 Identities=33% Similarity=0.897 Sum_probs=18.1
Q ss_pred CccccCCCCCCCCCCccee-----ecCceeEEecC
Q psy11423 409 SKIFKIPNICPICNSKIIY-----IESNLIARCSG 438 (655)
Q Consensus 409 ~~~~~~P~~CP~C~~~l~~-----~~~~~~~~C~n 438 (655)
.+.|.+| || ||..... .+|++..+|+.
T Consensus 18 ~~~ftyP--CP-CGDRFeIsLeDl~~GE~VArCPS 49 (67)
T COG5216 18 EKTFTYP--CP-CGDRFEISLEDLRNGEVVARCPS 49 (67)
T ss_pred CceEEec--CC-CCCEeEEEHHHhhCCceEEEcCC
Confidence 3456666 88 8875542 25788889966
No 323
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=40.74 E-value=18 Score=38.10 Aligned_cols=22 Identities=18% Similarity=0.374 Sum_probs=17.8
Q ss_pred CCCCCCCccee--ecCceeEEecC
Q psy11423 417 ICPICNSKIIY--IESNLIARCSG 438 (655)
Q Consensus 417 ~CP~C~~~l~~--~~~~~~~~C~n 438 (655)
.||.||+++.+ ..+...+||++
T Consensus 246 pCprCG~~I~~~~~~gR~t~~CP~ 269 (272)
T PRK14810 246 PCLNCKTPIRRVVVAGRSSHYCPH 269 (272)
T ss_pred cCCCCCCeeEEEEECCCccEECcC
Confidence 59999999874 35678899987
No 324
>PRK03609 umuC DNA polymerase V subunit UmuC; Reviewed
Probab=40.50 E-value=36 Score=38.07 Aligned_cols=48 Identities=19% Similarity=0.323 Sum_probs=37.5
Q ss_pred cccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHH
Q psy11423 458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILL 509 (655)
Q Consensus 458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~ 509 (655)
..=+++|+|+++.++|-..| |+|+.||..+....|... ||. ....+++
T Consensus 180 Pv~~l~GiG~~~~~~L~~lG-i~TigdL~~~~~~~L~~~--fG~-~~~~l~~ 227 (422)
T PRK03609 180 PVEEVWGVGRRISKKLNAMG-IKTALDLADTNIRFIRKH--FNV-VLERTVR 227 (422)
T ss_pred ChhhcCCccHHHHHHHHHcC-CCcHHHHhcCCHHHHHHH--HCH-HHHHHHH
Confidence 34579999999999997766 799999999988888875 774 3444443
No 325
>PRK07945 hypothetical protein; Provisional
Probab=40.37 E-value=44 Score=36.32 Aligned_cols=64 Identities=13% Similarity=0.077 Sum_probs=41.0
Q ss_pred CCCCccHHHHHHHHHh--CCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHhcC--------hhHHHHHHHHHHcCcc
Q psy11423 527 GIRHVGETTAKELANY--FKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQ--------PLHRLLISQLRDVGIY 593 (655)
Q Consensus 527 gIpgIG~~~Ak~L~~~--fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f~~--------~~n~~li~~L~~~Gi~ 593 (655)
.|||||+.+|.+|.+. -|+++.+...- ++.... | |+.++..|.-=+|. ....++++.=.+.|+.
T Consensus 53 ~~~giG~~~a~~i~e~~~tg~~~~l~~l~-~~~~~~-~-g~~l~~~~~~D~H~HT~~Sdg~~~~ee~v~~Ai~~Gl~ 126 (335)
T PRK07945 53 SLPGIGPKTAKVIAQALAGRVPDYLAELR-ADAEPL-G-GGALRAALRGDLHTHSDWSDGGSPIEEMARTAAALGHE 126 (335)
T ss_pred cCCCcCHHHHHHHHHHHhcCCHHHHHHHH-HhhcCC-c-cHHHHHHHhhhcccccCCCCCCCCHHHHHHHHHHCCCC
Confidence 8999999999988874 35555444321 122222 7 99999999874432 1234566666667764
No 326
>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=39.92 E-value=19 Score=37.92 Aligned_cols=22 Identities=23% Similarity=0.356 Sum_probs=17.8
Q ss_pred CCCCCCCcceee--cCceeEEecC
Q psy11423 417 ICPICNSKIIYI--ESNLIARCSG 438 (655)
Q Consensus 417 ~CP~C~~~l~~~--~~~~~~~C~n 438 (655)
.||.||+++.+. .+...+||++
T Consensus 247 pC~~Cg~~I~~~~~~gR~t~~CP~ 270 (272)
T TIGR00577 247 PCRRCGTPIEKIKVGGRGTHFCPQ 270 (272)
T ss_pred CCCCCCCeeEEEEECCCCCEECCC
Confidence 599999998753 4678899976
No 327
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=39.91 E-value=20 Score=38.09 Aligned_cols=22 Identities=18% Similarity=0.439 Sum_probs=17.9
Q ss_pred CCCCCCCccee--ecCceeEEecC
Q psy11423 417 ICPICNSKIIY--IESNLIARCSG 438 (655)
Q Consensus 417 ~CP~C~~~l~~--~~~~~~~~C~n 438 (655)
.||.||+++.+ ..+...+||++
T Consensus 256 pC~~Cg~~I~~~~~~gR~t~~CP~ 279 (282)
T PRK13945 256 PCRKCGTPIERIKLAGRSTHWCPN 279 (282)
T ss_pred CCCcCCCeeEEEEECCCccEECCC
Confidence 59999999874 35678899977
No 328
>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=39.75 E-value=30 Score=29.77 Aligned_cols=40 Identities=28% Similarity=0.267 Sum_probs=27.0
Q ss_pred HHHhcCCCCCHHHHHHHHHHhcChhHHHHHHHHHH-cCccc
Q psy11423 555 EQLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRD-VGIYW 594 (655)
Q Consensus 555 eeL~~i~GIG~~~A~~I~~~f~~~~n~~li~~L~~-~Gi~~ 594 (655)
+-|.+|||||+.+|..|...+.+.....--..|.. .|+.+
T Consensus 2 ~~l~sipGig~~~a~~llaeigd~~rF~~~~~l~~~~Gl~P 42 (87)
T PF02371_consen 2 ELLTSIPGIGPITAATLLAEIGDISRFKSAKQLASYAGLAP 42 (87)
T ss_pred chhcCCCCccHHHHHHHHHHHcCchhcccchhhhhcccccc
Confidence 35889999999999999998766543332333332 36654
No 329
>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=39.64 E-value=10 Score=27.42 Aligned_cols=26 Identities=23% Similarity=0.517 Sum_probs=16.6
Q ss_pred CCCCCCCCcceeecC-ceeEEecCCCcCCHH
Q psy11423 416 NICPICNSKIIYIES-NLIARCSGSWIECIA 445 (655)
Q Consensus 416 ~~CP~C~~~l~~~~~-~~~~~C~n~~~~C~~ 445 (655)
.+||.||+-|...++ .....|.+ |+.
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 479999999875543 22237866 764
No 330
>PTZ00446 vacuolar sorting protein SNF7-like; Provisional
Probab=39.54 E-value=60 Score=32.64 Aligned_cols=52 Identities=13% Similarity=0.160 Sum_probs=42.1
Q ss_pred cCCChhhHHHHHHHHHHHHHHHHHHhhcCCCCCCChHHHHHHHHHHHHHHHh
Q psy11423 7 KKINFSKLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEK 58 (655)
Q Consensus 7 ~~~~~~~~~~~~~~L~~~l~~~~~~Yy~~~~p~isD~~YD~L~~~L~~le~~ 58 (655)
++++.+++..-++++.+++...+.--=..+.|..+|.+-|.|..||.+|+.+
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 5678888877788888888888877666677766888889999999999864
No 331
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=39.33 E-value=19 Score=37.87 Aligned_cols=22 Identities=27% Similarity=0.484 Sum_probs=17.9
Q ss_pred CCCCCCCcceee--cCceeEEecC
Q psy11423 417 ICPICNSKIIYI--ESNLIARCSG 438 (655)
Q Consensus 417 ~CP~C~~~l~~~--~~~~~~~C~n 438 (655)
.||.||+++.+. .+...+||++
T Consensus 237 pC~~Cg~~I~~~~~~gR~ty~Cp~ 260 (269)
T PRK14811 237 PCPRCGTPIEKIVVGGRGTHFCPQ 260 (269)
T ss_pred CCCcCCCeeEEEEECCCCcEECCC
Confidence 599999998743 5678899987
No 332
>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=39.16 E-value=49 Score=36.23 Aligned_cols=67 Identities=10% Similarity=0.021 Sum_probs=38.1
Q ss_pred ceEEEEEecceeEEEEEEe--CCEEeEEEecCCCCccchhhh---h-----hhhcccCCcccccCCCCceEEEEEEEEe
Q psy11423 118 IEYIAELKFDGIAVNLRYE--YGYLKQASTRGDGNIGENITT---N-----IHIIHKIPLVLNIKYPPELLEVRCEVLI 186 (655)
Q Consensus 118 ~~~~~e~KiDGlsi~l~Y~--~G~l~~a~TRGdG~~GeDvT~---n-----~~~i~~iP~~l~~~~~p~~~evRGEv~~ 186 (655)
..|.++.|+||.|+++.|. +|.+- ....|=....-++-. | ++. .+||..|........+.|.||+|=
T Consensus 159 ~~~~~TeKldGss~tv~~~~~~~~~~-~~~~Gvcsr~~~l~~~~~~~~W~~a~~-~~i~~~l~~~~~~~~vaiqGEl~G 235 (341)
T TIGR02306 159 EKVAKTEKLHGTSITVAWVTDEERFL-VLSKGVASRNLVLRENADNKYWKAVEN-YQIVDRAKAAELRMSVAIFGEVMG 235 (341)
T ss_pred ceEEEEEEecceeEEEEEecCCcccc-cccceeecCCcccccCCCchhHHHHHh-cChHHHHhhcccCceEEEEEEEeC
Confidence 5799999999999999874 33321 111221112222111 1 122 346777752113457999999993
No 333
>KOG2875|consensus
Probab=39.00 E-value=37 Score=35.97 Aligned_cols=92 Identities=15% Similarity=0.151 Sum_probs=50.5
Q ss_pred CHHHHHhhccccccc---cccccCCCCHHHHHHHHHcCCCCChHHHhc-CChhhhccccCCcH------HHHHHHHHH--
Q psy11423 443 CIAQRKAGLQHFSSR---KAMNIIGLGKKMIEKLVNANIVVTAVDLYK-INFKNLLRLDRVSN------KLANNILLA-- 510 (655)
Q Consensus 443 C~~q~~~~i~~F~sk---~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~-L~~~~L~~l~GfG~------Ksa~nll~~-- 510 (655)
--+++-+.+.+||+- ..+.|+|+-= .++ .++..|-. -.+++|.++ |||= .+|+.|++.
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 456666666667762 2344555311 111 23322221 235678787 8983 245555432
Q ss_pred ----HHHhcccchhHHHHHh-CCCCccHHHHHHHH-HhCC
Q psy11423 511 ----IQKSKLTTFSRFIYAL-GIRHVGETTAKELA-NYFK 544 (655)
Q Consensus 511 ----I~~sk~~~l~r~L~al-gIpgIG~~~Ak~L~-~~fg 544 (655)
++..+..++.....+| -+||||++.|.=|+ ..++
T Consensus 201 ~~~wLqsl~~~~yeear~~L~~lpGVG~KVADCI~Lm~l~ 240 (323)
T KOG2875|consen 201 GLAWLQSLRKSSYEEAREALCSLPGVGPKVADCICLMSLD 240 (323)
T ss_pred cchHHHHHhcccHHHHHHHHhcCCCCcchHhhhhhhhhcC
Confidence 3333446666777777 68999999987443 3444
No 334
>smart00475 53EXOc 5'-3' exonuclease.
Probab=39.00 E-value=37 Score=35.62 Aligned_cols=27 Identities=19% Similarity=0.292 Sum_probs=20.8
Q ss_pred ccccCCCCHHHHHHHHHcCCCCChHHHhc
Q psy11423 459 AMNIIGLGKKMIEKLVNANIVVTAVDLYK 487 (655)
Q Consensus 459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~ 487 (655)
.-+|+|+|||++.+|+++=. |++.+|.
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 34679999999999998742 7777775
No 335
>PRK14193 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=38.80 E-value=98 Score=33.05 Aligned_cols=67 Identities=15% Similarity=0.320 Sum_probs=45.3
Q ss_pred CHHHHHHHHHHhcChhHHHHHHHHHHcCcccccCCCCCCCeEecccccCccEEEecCCCC------chHHHHHHcCCee-
Q psy11423 564 GSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNNPNTKGGKVVNFISKNTNYLVKGQKPG------KKLEKAIKLNIKI- 636 (655)
Q Consensus 564 G~~~A~~I~~~f~~~~n~~li~~L~~~Gi~~~~~~~~~G~~v~~sVsk~t~ylv~g~~~g------~K~~kA~~lgi~i- 636 (655)
|..+|+.|.+.+. +.++.|.+.|+. .+.-.+.+|+.+. .|.+.|+++||..
T Consensus 8 Gk~va~~i~~~l~-----~~v~~l~~~g~~-----------------P~LaiI~vg~d~as~~Yv~~k~k~a~~~Gi~~~ 65 (284)
T PRK14193 8 GKATADEIKADLA-----ERVAALKEKGIT-----------------PGLGTVLVGDDPGSQAYVRGKHRDCAEVGITSI 65 (284)
T ss_pred HHHHHHHHHHHHH-----HHHHHHHhCCCC-----------------ceEEEEEeCCCHHHHHHHHHHHHHHHHcCCEEE
Confidence 6778888877663 345556544432 2444667787754 6888899999883
Q ss_pred -------eCHHHHHHHHhcccCC
Q psy11423 637 -------LDEKNFVKIVKGFSTE 652 (655)
Q Consensus 637 -------i~e~~f~~~l~~~~~~ 652 (655)
+++++|.+.+..-+.+
T Consensus 66 ~~~l~~~~t~~el~~~I~~lN~D 88 (284)
T PRK14193 66 RRDLPADATQEELNAVIDELNAD 88 (284)
T ss_pred EEECCCCCCHHHHHHHHHHHhCC
Confidence 4689999988655444
No 336
>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=38.70 E-value=17 Score=27.37 Aligned_cols=14 Identities=36% Similarity=0.902 Sum_probs=11.9
Q ss_pred CCCCCCCCCcceee
Q psy11423 415 PNICPICNSKIIYI 428 (655)
Q Consensus 415 P~~CP~C~~~l~~~ 428 (655)
|+.||.||+.|...
T Consensus 2 ~~~C~~Cg~~l~~i 15 (47)
T PF13005_consen 2 PRACPDCGGELKEI 15 (47)
T ss_pred CCcCCCCCceeeEC
Confidence 67899999998854
No 337
>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=38.26 E-value=54 Score=29.99 Aligned_cols=65 Identities=22% Similarity=0.432 Sum_probs=41.1
Q ss_pred CHHHHHHHHHHhcChhHHHHHHHHHHcCcccccCCCCCCCeEecccccCccEEEecCCCC------chHHHHHHcCCee-
Q psy11423 564 GSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNNPNTKGGKVVNFISKNTNYLVKGQKPG------KKLEKAIKLNIKI- 636 (655)
Q Consensus 564 G~~~A~~I~~~f~~~~n~~li~~L~~~Gi~~~~~~~~~G~~v~~sVsk~t~ylv~g~~~g------~K~~kA~~lgi~i- 636 (655)
|..+|+.|.+.+ ++.++.|...|+. ...-.+.+|+.++ +|.+.|+++||..
T Consensus 5 Gk~va~~i~~~l-----~~~i~~l~~~~~~-----------------P~Laii~vg~d~~S~~Y~~~k~k~~~~~Gi~~~ 62 (117)
T PF00763_consen 5 GKPVAKEIKEEL-----KEEIEKLKEKGIT-----------------PKLAIILVGDDPASISYVRSKQKAAEKLGIEFE 62 (117)
T ss_dssp HHHHHHHHHHHH-----HHHHHHHHHCT--------------------EEEEEEES--HHHHHHHHHHHHHHHHHT-EEE
T ss_pred HHHHHHHHHHHH-----HHHHHHHHhcCCC-----------------cEEEEEecCCChhHHHHHHHHHHHHHHcCCceE
Confidence 567788887776 3456667654443 2444677788755 5667799999873
Q ss_pred -------eCHHHHHHHHhccc
Q psy11423 637 -------LDEKNFVKIVKGFS 650 (655)
Q Consensus 637 -------i~e~~f~~~l~~~~ 650 (655)
+++++|.+.+..-+
T Consensus 63 ~~~l~~~~~~~el~~~i~~lN 83 (117)
T PF00763_consen 63 LIELPEDISEEELLELIEKLN 83 (117)
T ss_dssp EEEE-TTSSHHHHHHHHHHHH
T ss_pred EEECCCCcCHHHHHHHHHHHh
Confidence 58999999886443
No 338
>PF09851 SHOCT: Short C-terminal domain; InterPro: IPR018649 This family of hypothetical prokaryotic proteins has no known function.
Probab=38.11 E-value=60 Score=22.68 Aligned_cols=27 Identities=30% Similarity=0.390 Sum_probs=19.7
Q ss_pred HHHHHHHHhhcCCCCCCChHHHHHHHHHHH
Q psy11423 24 ELHRHNIAYYLYDNPIISDNKYDQLLFELK 53 (655)
Q Consensus 24 ~l~~~~~~Yy~~~~p~isD~~YD~L~~~L~ 53 (655)
+|+....+| +.-.||++||.+...+|.
T Consensus 4 ~L~~L~~l~---~~G~IseeEy~~~k~~ll 30 (31)
T PF09851_consen 4 RLEKLKELY---DKGEISEEEYEQKKARLL 30 (31)
T ss_pred HHHHHHHHH---HcCCCCHHHHHHHHHHHh
Confidence 455555555 346999999999988774
No 339
>PRK14171 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=38.07 E-value=1.2e+02 Score=32.50 Aligned_cols=67 Identities=16% Similarity=0.380 Sum_probs=46.0
Q ss_pred CHHHHHHHHHHhcChhHHHHHHHHHHc-CcccccCCCCCCCeEecccccCccEEEecCCCC------chHHHHHHcCCee
Q psy11423 564 GSTTVKAFIKFINQPLHRLLISQLRDV-GIYWLNNPNTKGGKVVNFISKNTNYLVKGQKPG------KKLEKAIKLNIKI 636 (655)
Q Consensus 564 G~~~A~~I~~~f~~~~n~~li~~L~~~-Gi~~~~~~~~~G~~v~~sVsk~t~ylv~g~~~g------~K~~kA~~lgi~i 636 (655)
|..+|+.|.+.+. +.++.|.+. |+ +.+.-.+.+|+.+. .|.+.|+++||..
T Consensus 7 Gk~iA~~i~~~lk-----~~v~~l~~~~g~-----------------~P~LaiI~vg~d~as~~Yv~~k~k~a~~~Gi~~ 64 (288)
T PRK14171 7 GKALANEILADLK-----LEIQELKSQTNA-----------------SPKLAIVLVGDNPASIIYVKNKIKNAHKIGIDT 64 (288)
T ss_pred HHHHHHHHHHHHH-----HHHHHHHhccCC-----------------CCeEEEEEeCCCccHHHHHHHHHHHHHHcCCEE
Confidence 7788888887763 346666543 33 22444677888754 6788899999874
Q ss_pred --------eCHHHHHHHHhcccCC
Q psy11423 637 --------LDEKNFVKIVKGFSTE 652 (655)
Q Consensus 637 --------i~e~~f~~~l~~~~~~ 652 (655)
+++++|.+.+..-+.+
T Consensus 65 ~~~~l~~~~~~~~l~~~I~~LN~D 88 (288)
T PRK14171 65 LLVNLSTTIHTNDLISKINELNLD 88 (288)
T ss_pred EEEECCCCCCHHHHHHHHHHHcCC
Confidence 5789999988755444
No 340
>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=37.97 E-value=49 Score=36.31 Aligned_cols=76 Identities=14% Similarity=0.267 Sum_probs=46.5
Q ss_pred CCcH-HHHHHHHHHHHHhcc------cchhHHHHHh---CCCCccHHHHHHHHHhC--CCHHHHHhc--CHHHHhcCCCC
Q psy11423 498 RVSN-KLANNILLAIQKSKL------TTFSRFIYAL---GIRHVGETTAKELANYF--KNLECMFKA--TEEQLLNIPKI 563 (655)
Q Consensus 498 GfG~-Ksa~nll~~I~~sk~------~~l~r~L~al---gIpgIG~~~Ak~L~~~f--gsl~~l~~a--s~eeL~~i~GI 563 (655)
|+|. |...||.....+-.. ..+..+|..+ .+||||.++++++++.+ .++..|... +..+|.+. +
T Consensus 147 GIa~nk~lAKlAs~~~KP~g~~v~~~~~~~~~L~~lpv~~l~GiG~~~~~~ll~~~Gi~ti~dl~~~~~~~~~L~~~--f 224 (359)
T cd01702 147 GIAHNKMLAKLASGMNKPNAQTILRNDAVASFLSSLPITSIRGLGGKLGEEIIDLLGLPTEGDVAGFRSSESDLQEH--F 224 (359)
T ss_pred eecCCHHHHHHHhcccCCCCeEEECHHHHHHHhhcCcHHHhCCcCHHHHHHHHHHcCCcCHHHHHhccCCHHHHHHH--H
Confidence 4443 555555554432111 1234577666 67999988887776554 477788877 77777764 5
Q ss_pred CHHHHHHHHHHh
Q psy11423 564 GSTTVKAFIKFI 575 (655)
Q Consensus 564 G~~~A~~I~~~f 575 (655)
|.+.++.+++..
T Consensus 225 G~~~g~~l~~~a 236 (359)
T cd01702 225 GEKLGEWLYNLL 236 (359)
T ss_pred HHHHHHHHHHHh
Confidence 666666666554
No 341
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=37.94 E-value=25 Score=28.60 Aligned_cols=22 Identities=27% Similarity=0.773 Sum_probs=19.7
Q ss_pred CCCCCCCcceeecCceeEEecC
Q psy11423 417 ICPICNSKIIYIESNLIARCSG 438 (655)
Q Consensus 417 ~CP~C~~~l~~~~~~~~~~C~n 438 (655)
.||.|..+|...+....++|..
T Consensus 10 aCP~~kg~L~~~~~~~~L~c~~ 31 (60)
T COG2835 10 ACPVCKGPLVYDEEKQELICPR 31 (60)
T ss_pred eccCcCCcceEeccCCEEEecc
Confidence 6999999999888888999977
No 342
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=37.83 E-value=16 Score=26.53 Aligned_cols=23 Identities=22% Similarity=0.566 Sum_probs=16.8
Q ss_pred CCCCCCCCcceeec-----CceeEEecC
Q psy11423 416 NICPICNSKIIYIE-----SNLIARCSG 438 (655)
Q Consensus 416 ~~CP~C~~~l~~~~-----~~~~~~C~n 438 (655)
..||.|++.....+ ++...+|++
T Consensus 3 i~CP~C~~~f~v~~~~l~~~~~~vrC~~ 30 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDDKLPAGGRKVRCPK 30 (37)
T ss_pred EECCCCCceEEcCHHHcccCCcEEECCC
Confidence 46999999765433 367889977
No 343
>PRK00024 hypothetical protein; Reviewed
Probab=37.00 E-value=53 Score=33.72 Aligned_cols=37 Identities=11% Similarity=0.156 Sum_probs=32.1
Q ss_pred CChHHHhcCChhhhccccCCcHHHHHHHHHHHHHhcc
Q psy11423 480 VTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKL 516 (655)
Q Consensus 480 ~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~sk~ 516 (655)
.++.+++.++.++|.+++|+|+.+|..|...++.++.
T Consensus 55 gsL~~l~~as~~eL~~i~GIG~akA~~L~a~~El~~R 91 (224)
T PRK00024 55 GSLRGLLDASLEELQSIKGIGPAKAAQLKAALELARR 91 (224)
T ss_pred CCHHHHHhCCHHHHhhccCccHHHHHHHHHHHHHHHH
Confidence 3788999999999999999999999999888887654
No 344
>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=36.88 E-value=25 Score=35.70 Aligned_cols=61 Identities=15% Similarity=0.039 Sum_probs=30.8
Q ss_pred ceeccccccCCCCCCChHHHHHHHHHHHHhhccCCCceEEEEEecceeEEEEE-EeCCEEeEEEecC
Q psy11423 82 YVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLR-YEYGYLKQASTRG 147 (655)
Q Consensus 82 kv~H~~pMlSL~k~~~~~el~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~-Y~~G~l~~a~TRG 147 (655)
...+.+..-+++|.||..|...+...- +. .....+.+..|+||.=|++. ..+|.+ ...|+|
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 10 01237999999999555244 467876 556665
No 345
>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=36.66 E-value=24 Score=31.83 Aligned_cols=15 Identities=33% Similarity=0.915 Sum_probs=12.1
Q ss_pred CCCCCCCCCcceeec
Q psy11423 415 PNICPICNSKIIYIE 429 (655)
Q Consensus 415 P~~CP~C~~~l~~~~ 429 (655)
|..||.||.+.+...
T Consensus 2 p~~CpYCg~~~~l~~ 16 (102)
T PF11672_consen 2 PIICPYCGGPAELVD 16 (102)
T ss_pred CcccCCCCCeeEEcc
Confidence 789999999876543
No 346
>PHA00626 hypothetical protein
Probab=36.53 E-value=28 Score=27.93 Aligned_cols=36 Identities=28% Similarity=0.425 Sum_probs=21.4
Q ss_pred CCCCCCCc-ceeec---C-ceeEEecCCCcCCHHHHHhhccccccccccccCC
Q psy11423 417 ICPICNSK-IIYIE---S-NLIARCSGSWIECIAQRKAGLQHFSSRKAMNIIG 464 (655)
Q Consensus 417 ~CP~C~~~-l~~~~---~-~~~~~C~n~~~~C~~q~~~~i~~F~sk~~l~I~G 464 (655)
.||.||+. +++.. + .....|.. | -|+++++++.-.|
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 69999995 44321 1 23344533 4 6888888765444
No 347
>PRK14166 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=36.44 E-value=1.1e+02 Score=32.72 Aligned_cols=66 Identities=14% Similarity=0.209 Sum_probs=45.5
Q ss_pred CHHHHHHHHHHhcChhHHHHHHHHHHcCcccccCCCCCCCeEecccccCccEEEecCCCC------chHHHHHHcCCe--
Q psy11423 564 GSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNNPNTKGGKVVNFISKNTNYLVKGQKPG------KKLEKAIKLNIK-- 635 (655)
Q Consensus 564 G~~~A~~I~~~f~~~~n~~li~~L~~~Gi~~~~~~~~~G~~v~~sVsk~t~ylv~g~~~g------~K~~kA~~lgi~-- 635 (655)
|..+|+.|.+.+. +.++.|.+.|+. .+.-.+.+|+.+. .|.+.|+++||.
T Consensus 6 Gk~~a~~i~~~l~-----~~v~~l~~~g~~-----------------P~Laii~vg~d~as~~Yv~~k~k~a~~~Gi~~~ 63 (282)
T PRK14166 6 GKALSAKIKEELK-----EKNQFLKSKGIE-----------------SCLAVILVGDNPASQTYVKSKAKACEECGIKSL 63 (282)
T ss_pred hHHHHHHHHHHHH-----HHHHHHHhCCCC-----------------ceEEEEEeCCCHHHHHHHHHHHHHHHHcCCEEE
Confidence 6788888887763 346666554432 2444577787754 688889999987
Q ss_pred ------eeCHHHHHHHHhcccC
Q psy11423 636 ------ILDEKNFVKIVKGFST 651 (655)
Q Consensus 636 ------ii~e~~f~~~l~~~~~ 651 (655)
-+++++|.+.+..-+.
T Consensus 64 ~~~l~~~~t~~~l~~~I~~lN~ 85 (282)
T PRK14166 64 VYHLNENTTQNELLALINTLNH 85 (282)
T ss_pred EEECCCCCCHHHHHHHHHHHhC
Confidence 2678899998865443
No 348
>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=36.31 E-value=1.3e+02 Score=28.42 Aligned_cols=44 Identities=20% Similarity=0.214 Sum_probs=33.4
Q ss_pred ccCCcccccCCCCceEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcc
Q psy11423 163 HKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPK 223 (655)
Q Consensus 163 ~~iP~~l~~~~~p~~~evRGEv~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~d~~ 223 (655)
++||.-- ..+.++--||+=+.-.+|..+.+.- ..|||-|.+.|-
T Consensus 31 rGvPdG~----v~GdV~aegEiEldt~nf~~l~~aA-------------~~AGSwR~i~~~ 74 (134)
T PF10772_consen 31 RGVPDGY----VDGDVSAEGEIELDTKNFNLLSEAA-------------KSAGSWRGIPPF 74 (134)
T ss_pred CCCCCCc----cccceeeeEEEEEcHHHHHHHHHHH-------------HhcCCccCCCcc
Confidence 4467533 4668999999999999999887652 268888887764
No 349
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=36.17 E-value=31 Score=27.44 Aligned_cols=25 Identities=32% Similarity=0.770 Sum_probs=16.8
Q ss_pred CCCCCCCcceeecC--c------eeEEecCCCcCCHH
Q psy11423 417 ICPICNSKIIYIES--N------LIARCSGSWIECIA 445 (655)
Q Consensus 417 ~CP~C~~~l~~~~~--~------~~~~C~n~~~~C~~ 445 (655)
-||.||++.+.... . ..++|.+ |-+
T Consensus 5 PCPFCG~~~~~~~~~~~~~~~~~~~V~C~~----Cga 37 (61)
T PF14354_consen 5 PCPFCGSADVLIRQDEGFDYGMYYYVECTD----CGA 37 (61)
T ss_pred CCCCCCCcceEeecccCCCCCCEEEEEcCC----CCC
Confidence 39999987654332 1 5677877 755
No 350
>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=35.90 E-value=48 Score=35.07 Aligned_cols=54 Identities=19% Similarity=0.244 Sum_probs=35.8
Q ss_pred ccccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHH
Q psy11423 457 RKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAI 511 (655)
Q Consensus 457 k~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I 511 (655)
-..+.+||+|++.+.+|-..| |.++.||..++.+++..+=+..+..++.+++.+
T Consensus 148 ~~L~Qlp~i~~~~~~~l~~~~-i~~l~~l~~~~~~e~~~ll~~~~~~~~~i~~~~ 201 (314)
T PF02889_consen 148 SPLLQLPHIGEESLKKLEKRG-IKTLQDLRDLSPEELEELLNRNPPFGKEILEVA 201 (314)
T ss_dssp -GGGGSTT--HHHHHHHHHTT---SHHHHHHS-HHHHHHHH-S-HHHHHHHHHHH
T ss_pred ChhhcCCCCCHHHHHHHhccC-CCcHHHHhhCCHHHHHHHHhhhhhhHHHHHHHH
Confidence 357899999999999999866 689999999988877776444445555555544
No 351
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=35.75 E-value=26 Score=35.18 Aligned_cols=26 Identities=31% Similarity=0.405 Sum_probs=17.8
Q ss_pred chhHHHHHh-CCCCccHHHHHHHHHhC
Q psy11423 518 TFSRFIYAL-GIRHVGETTAKELANYF 543 (655)
Q Consensus 518 ~l~r~L~al-gIpgIG~~~Ak~L~~~f 543 (655)
++.+++.+| .+||||++.|++++=+.
T Consensus 6 ~i~~LI~~l~kLPGvG~KsA~R~AfhL 32 (198)
T COG0353 6 PIEKLIDALKKLPGVGPKSAQRLAFHL 32 (198)
T ss_pred HHHHHHHHHhhCCCCChhHHHHHHHHH
Confidence 345566666 57888888888877664
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=35.42 E-value=25 Score=28.70 Aligned_cols=24 Identities=21% Similarity=0.499 Sum_probs=18.5
Q ss_pred CCCCCCCCCcceeecCceeEEecC
Q psy11423 415 PNICPICNSKIIYIESNLIARCSG 438 (655)
Q Consensus 415 P~~CP~C~~~l~~~~~~~~~~C~n 438 (655)
...||.||........+..+.|++
T Consensus 28 Sq~C~~CG~~~~~~~~~r~~~C~~ 51 (69)
T PF07282_consen 28 SQTCPRCGHRNKKRRSGRVFTCPN 51 (69)
T ss_pred ccCccCcccccccccccceEEcCC
Confidence 457999999887634567888986
No 353
>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=35.31 E-value=28 Score=29.31 Aligned_cols=27 Identities=19% Similarity=0.493 Sum_probs=16.2
Q ss_pred ccCCCCCCCCCCcceeec--CceeEEecC
Q psy11423 412 FKIPNICPICNSKIIYIE--SNLIARCSG 438 (655)
Q Consensus 412 ~~~P~~CP~C~~~l~~~~--~~~~~~C~n 438 (655)
|..-..||-|+.+|.+.. |-+++||.+
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 445567999999887543 567889977
No 354
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=35.09 E-value=34 Score=25.30 Aligned_cols=22 Identities=23% Similarity=0.576 Sum_probs=13.3
Q ss_pred CCCCCCCcceee--cCceeEEecC
Q psy11423 417 ICPICNSKIIYI--ESNLIARCSG 438 (655)
Q Consensus 417 ~CP~C~~~l~~~--~~~~~~~C~n 438 (655)
+||.|+..|... .+-..-+|++
T Consensus 1 ~CP~C~~~l~~~~~~~~~id~C~~ 24 (41)
T PF13453_consen 1 KCPRCGTELEPVRLGDVEIDVCPS 24 (41)
T ss_pred CcCCCCcccceEEECCEEEEECCC
Confidence 589998877632 2334445654
No 355
>PRK14189 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=35.08 E-value=1.3e+02 Score=32.06 Aligned_cols=67 Identities=13% Similarity=0.200 Sum_probs=45.3
Q ss_pred CHHHHHHHHHHhcChhHHHHHHHHHHcCcccccCCCCCCCeEecccccCccEEEecCCCC------chHHHHHHcCCee-
Q psy11423 564 GSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNNPNTKGGKVVNFISKNTNYLVKGQKPG------KKLEKAIKLNIKI- 636 (655)
Q Consensus 564 G~~~A~~I~~~f~~~~n~~li~~L~~~Gi~~~~~~~~~G~~v~~sVsk~t~ylv~g~~~g------~K~~kA~~lgi~i- 636 (655)
|..+|++|.+.+. +.++.|...|+. .+.-.+.+|+.+. .|.+.|+++||..
T Consensus 8 Gk~va~~i~~~lk-----~~i~~l~~~g~~-----------------p~Laii~vg~d~as~~Yv~~k~k~~~~~Gi~~~ 65 (285)
T PRK14189 8 GNALSKQLRAEAA-----QRAAALTARGHQ-----------------PGLAVILVGDNPASQVYVRNKVKACEDNGFHSL 65 (285)
T ss_pred HHHHHHHHHHHHH-----HHHHHHHhCCCC-----------------CeEEEEEeCCCchHHHHHHHHHHHHHHcCCEEE
Confidence 6778888877764 335555443432 2444677787754 6777799999875
Q ss_pred -------eCHHHHHHHHhcccCC
Q psy11423 637 -------LDEKNFVKIVKGFSTE 652 (655)
Q Consensus 637 -------i~e~~f~~~l~~~~~~ 652 (655)
+++++|.+.+..-+.+
T Consensus 66 ~~~l~~~~~~~~l~~~I~~lN~d 88 (285)
T PRK14189 66 KDRYPADLSEAELLARIDELNRD 88 (285)
T ss_pred EEECCCCCCHHHHHHHHHHHcCC
Confidence 5689999988654443
No 356
>PRK14185 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=35.00 E-value=1e+02 Score=33.00 Aligned_cols=66 Identities=14% Similarity=0.232 Sum_probs=44.7
Q ss_pred CHHHHHHHHHHhcChhHHHHHHHHHHc-CcccccCCCCCCCeEecccccCccEEEecCCCC------chHHHHHHcCCee
Q psy11423 564 GSTTVKAFIKFINQPLHRLLISQLRDV-GIYWLNNPNTKGGKVVNFISKNTNYLVKGQKPG------KKLEKAIKLNIKI 636 (655)
Q Consensus 564 G~~~A~~I~~~f~~~~n~~li~~L~~~-Gi~~~~~~~~~G~~v~~sVsk~t~ylv~g~~~g------~K~~kA~~lgi~i 636 (655)
|..+|+.|.+.+. +.++.|.+. |+. ...-.+.+|+.+. .|.+.|+++||..
T Consensus 6 Gk~iA~~i~~~l~-----~~v~~l~~~~g~~-----------------P~LaiI~vg~d~as~~Yv~~k~k~a~~~Gi~~ 63 (293)
T PRK14185 6 GKAISAQIKQEIA-----AEVAEIVAKGGKR-----------------PHLAAILVGHDGGSETYVANKVKACEECGFKS 63 (293)
T ss_pred HHHHHHHHHHHHH-----HHHHHHHhccCCC-----------------CeEEEEEeCCCHHHHHHHHHHHHHHHHcCCEE
Confidence 6778888877663 345566543 332 2344577788754 6788899999987
Q ss_pred --------eCHHHHHHHHhcccC
Q psy11423 637 --------LDEKNFVKIVKGFST 651 (655)
Q Consensus 637 --------i~e~~f~~~l~~~~~ 651 (655)
+++++|.+.+..-+.
T Consensus 64 ~~~~l~~~~~~~el~~~I~~lN~ 86 (293)
T PRK14185 64 SLIRYESDVTEEELLAKVRELNQ 86 (293)
T ss_pred EEEECCCCCCHHHHHHHHHHHhC
Confidence 678999988764443
No 357
>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=34.96 E-value=49 Score=35.37 Aligned_cols=48 Identities=29% Similarity=0.333 Sum_probs=36.8
Q ss_pred ccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHH
Q psy11423 459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLA 510 (655)
Q Consensus 459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~ 510 (655)
.-+++|+|+++.++|...| |.++.||..+....|... || +....+++.
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 4578999999999997765 799999999988888773 55 445555443
No 358
>PRK14188 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=34.87 E-value=1.4e+02 Score=32.00 Aligned_cols=67 Identities=9% Similarity=0.266 Sum_probs=45.7
Q ss_pred CHHHHHHHHHHhcChhHHHHHHHHHHc-CcccccCCCCCCCeEecccccCccEEEecCCCC------chHHHHHHcCCe-
Q psy11423 564 GSTTVKAFIKFINQPLHRLLISQLRDV-GIYWLNNPNTKGGKVVNFISKNTNYLVKGQKPG------KKLEKAIKLNIK- 635 (655)
Q Consensus 564 G~~~A~~I~~~f~~~~n~~li~~L~~~-Gi~~~~~~~~~G~~v~~sVsk~t~ylv~g~~~g------~K~~kA~~lgi~- 635 (655)
|..+|++|.+.+. +.++.|.+. |+ +.+.-.+.+|+.+. .|.+.|+++||.
T Consensus 7 Gk~~a~~i~~~i~-----~~v~~l~~~~g~-----------------~p~La~i~vg~~~~s~~Yv~~k~k~a~~~Gi~~ 64 (296)
T PRK14188 7 GKAFAADVRATVA-----AEVARLKAAHGV-----------------TPGLAVVLVGEDPASQVYVRSKGKQTKEAGMAS 64 (296)
T ss_pred HHHHHHHHHHHHH-----HHHHHHHHccCC-----------------CCeEEEEEeCCChhHHHHHHHHHHHHHHcCCEE
Confidence 6778888877663 345555432 22 23555677888754 678889999996
Q ss_pred -e------eCHHHHHHHHhcccCC
Q psy11423 636 -I------LDEKNFVKIVKGFSTE 652 (655)
Q Consensus 636 -i------i~e~~f~~~l~~~~~~ 652 (655)
+ ++++||.+.+..-+.+
T Consensus 65 ~~~~l~~~~~~~el~~~i~~lN~d 88 (296)
T PRK14188 65 FEHKLPADTSQAELLALIARLNAD 88 (296)
T ss_pred EEEECCCCCCHHHHHHHHHHHhCC
Confidence 3 4899999988655444
No 359
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=34.85 E-value=34 Score=28.91 Aligned_cols=41 Identities=20% Similarity=0.408 Sum_probs=28.1
Q ss_pred CCCCCCCcceeecC--------ceeEEecCCCcCCHHHH--Hhhccccccccc
Q psy11423 417 ICPICNSKIIYIES--------NLIARCSGSWIECIAQR--KAGLQHFSSRKA 459 (655)
Q Consensus 417 ~CP~C~~~l~~~~~--------~~~~~C~n~~~~C~~q~--~~~i~~F~sk~~ 459 (655)
+||.||+.-..... +....|.|. + |-..+ ...+.|+.|+.+
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 69999998643321 367789995 5 97766 446677777654
No 360
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=34.58 E-value=35 Score=24.36 Aligned_cols=24 Identities=17% Similarity=0.228 Sum_probs=18.3
Q ss_pred CCCCCCCCCcceeecCceeEEecC
Q psy11423 415 PNICPICNSKIIYIESNLIARCSG 438 (655)
Q Consensus 415 P~~CP~C~~~l~~~~~~~~~~C~n 438 (655)
+..|+.||+.++........+|.+
T Consensus 3 ~~~C~~C~~~~i~~~~~~~~~C~~ 26 (33)
T PF08792_consen 3 LKKCSKCGGNGIVNKEDDYEVCIF 26 (33)
T ss_pred ceEcCCCCCCeEEEecCCeEEccc
Confidence 457999999988744456788976
No 361
>PF03564 DUF1759: Protein of unknown function (DUF1759); InterPro: IPR005312 This is a small family of proteins of unknown function.
Probab=34.45 E-value=1.4e+02 Score=27.80 Aligned_cols=73 Identities=21% Similarity=0.276 Sum_probs=54.3
Q ss_pred hHHHHHhCCCCccHHHHH-HHHHhCCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHhcChhHHHHHHHHHHcCccc
Q psy11423 520 SRFIYALGIRHVGETTAK-ELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYW 594 (655)
Q Consensus 520 ~r~L~algIpgIG~~~Ak-~L~~~fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f~~~~n~~li~~L~~~Gi~~ 594 (655)
.+.+..+.++.-+-..|. .|-++||+-..+..+-.++|.++|.+...-+.++..+...- ...+..|...|...
T Consensus 43 ~~~i~~~~~~~~~Y~~a~~~L~~~yg~~~~i~~~~~~~l~~l~~~~~~d~~~L~~~~~~v--~~~i~~L~~lg~~~ 116 (145)
T PF03564_consen 43 KELIRGLPLSEENYEEAWELLEERYGNPRRIIQALLEELRNLPPISNDDPEALRSLVDKV--NNCIRALKALGVNV 116 (145)
T ss_pred HHHHHcccccchhhHHHHHHHHHHhCCchHHHHHHHHHHhccccccchhHHHHHHHHHHH--HHHHHHHHHcCCCC
Confidence 455666666666666664 55678999999998888999999998888888888877543 34577787777643
No 362
>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=34.42 E-value=29 Score=27.67 Aligned_cols=44 Identities=27% Similarity=0.363 Sum_probs=32.0
Q ss_pred HHHHHHHHcCCCCChHHHhcCChhhhccccCCcH-HHHHHHHHHHHHh
Q psy11423 468 KMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSN-KLANNILLAIQKS 514 (655)
Q Consensus 468 k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~-Ksa~nll~~I~~s 514 (655)
+-+..+ .++.| +-..|..|+.++|..+ |+.. --..+|+.+|+.-
T Consensus 19 ~y~~~F-~~~~i-~g~~L~~lt~~dL~~l-gi~~~ghr~ki~~~i~~L 63 (64)
T PF00536_consen 19 QYAENF-EKNYI-DGEDLLSLTEEDLEEL-GITKLGHRKKILRAIQKL 63 (64)
T ss_dssp GGHHHH-HHTTS-SHHHHTTSCHHHHHHT-T-SSHHHHHHHHHHHHHH
T ss_pred HHHHHH-HcCCc-hHHHHHhcCHHHHHHc-CCCCHHHHHHHHHHHHHh
Confidence 344444 77765 7788999999999997 6654 6778888888764
No 363
>PRK14194 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=34.05 E-value=1.3e+02 Score=32.38 Aligned_cols=67 Identities=13% Similarity=0.314 Sum_probs=46.1
Q ss_pred CHHHHHHHHHHhcChhHHHHHHHHHHcCcccccCCCCCCCeEecccccCccEEEecCCCC------chHHHHHHcCCee-
Q psy11423 564 GSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNNPNTKGGKVVNFISKNTNYLVKGQKPG------KKLEKAIKLNIKI- 636 (655)
Q Consensus 564 G~~~A~~I~~~f~~~~n~~li~~L~~~Gi~~~~~~~~~G~~v~~sVsk~t~ylv~g~~~g------~K~~kA~~lgi~i- 636 (655)
|..+|+.|.+.+. +.++.|.+.|+. .+.-.+.+|+.+. .|.+.|+++||..
T Consensus 9 Gk~iA~~i~~~lk-----~~i~~l~~~g~~-----------------P~LaiI~vg~d~as~~Yv~~k~k~a~~~Gi~~~ 66 (301)
T PRK14194 9 GKAAAARVLAQVR-----EDVRTLKAAGIE-----------------PALAVILVGNDPASQVYVRNKILRAEEAGIRSL 66 (301)
T ss_pred HHHHHHHHHHHHH-----HHHHHHHhCCCC-----------------CeEEEEEeCCChhHHHHHHHHHHHHHHcCCEEE
Confidence 7788888887763 346666544432 2444677787754 6788899999875
Q ss_pred -------eCHHHHHHHHhcccCC
Q psy11423 637 -------LDEKNFVKIVKGFSTE 652 (655)
Q Consensus 637 -------i~e~~f~~~l~~~~~~ 652 (655)
+++++|.+.+..-+.+
T Consensus 67 ~~~l~~~~t~~~l~~~I~~lN~D 89 (301)
T PRK14194 67 EHRLPADTSQARLLALIAELNAD 89 (301)
T ss_pred EEECCCCCCHHHHHHHHHHHcCC
Confidence 3789999988655444
No 364
>PTZ00111 DNA replication licensing factor MCM4; Provisional
Probab=33.74 E-value=29 Score=42.61 Aligned_cols=44 Identities=30% Similarity=0.390 Sum_probs=28.6
Q ss_pred CCCEEE----EEecCcccceeecccccCC------------CC-------CCccccCCCCCCCCCCc
Q psy11423 381 IGDTVV----VHRSGNVIPKITSSILSLR------------PN-------DSKIFKIPNICPICNSK 424 (655)
Q Consensus 381 iGd~V~----v~raGdVIP~I~~vv~~~r------------~~-------~~~~~~~P~~CP~C~~~ 424 (655)
+|-.|. |.|+++|+|++...+..=. .+ ....+..|..||.|++.
T Consensus 226 i~kLV~v~GiV~r~S~v~P~l~~a~f~C~~~~~~~~~~~~~C~~~~~~~~~~g~~~~P~~C~~C~~~ 292 (915)
T PTZ00111 226 ADSLVQFSGTVVRQTWIVPEITMACFRCRGQKKIGLNDYQPCTCEHYEYVIQGEVNEPLLCNECNSK 292 (915)
T ss_pred CCCeEEEEEEEEEccCcchhhEEEEEECCCCCcccCCccccCCccccccccCCcccCCCCCCCCCCC
Confidence 455553 6799999999887654211 11 11246679999999963
No 365
>PLN02616 tetrahydrofolate dehydrogenase/cyclohydrolase, putative
Probab=33.72 E-value=1.3e+02 Score=33.27 Aligned_cols=67 Identities=18% Similarity=0.378 Sum_probs=46.3
Q ss_pred CHHHHHHHHHHhcChhHHHHHHHHHHc-CcccccCCCCCCCeEecccccCccEEEecCCCC------chHHHHHHcCCe-
Q psy11423 564 GSTTVKAFIKFINQPLHRLLISQLRDV-GIYWLNNPNTKGGKVVNFISKNTNYLVKGQKPG------KKLEKAIKLNIK- 635 (655)
Q Consensus 564 G~~~A~~I~~~f~~~~n~~li~~L~~~-Gi~~~~~~~~~G~~v~~sVsk~t~ylv~g~~~g------~K~~kA~~lgi~- 635 (655)
|..+|+.|.+.+. +.++.|.+. |+. .+.-.+.+|+.+. .|.+.|+++||.
T Consensus 78 Gk~iA~~i~~~lk-----~~v~~lk~~~g~~-----------------P~LaiIlvG~dpaS~~Yv~~k~K~~e~~GI~~ 135 (364)
T PLN02616 78 GKAVAKKIRDEIT-----IEVSRMKESIGVV-----------------PGLAVILVGDRKDSATYVRNKKKACDSVGINS 135 (364)
T ss_pred hHHHHHHHHHHHH-----HHHHHHHHcCCCC-----------------CeEEEEEeCCChhHHHHHHHHHHHHHHcCCEE
Confidence 7888998887764 346666543 332 2444677888754 678889999997
Q ss_pred -------eeCHHHHHHHHhcccCC
Q psy11423 636 -------ILDEKNFVKIVKGFSTE 652 (655)
Q Consensus 636 -------ii~e~~f~~~l~~~~~~ 652 (655)
-++|+|+++.+..-..+
T Consensus 136 ~~~~lpe~~te~ell~~I~~LN~D 159 (364)
T PLN02616 136 FEVRLPEDSTEQEVLKFISGFNND 159 (364)
T ss_pred EEEECCCCCCHHHHHHHHHHHcCC
Confidence 46788999988544433
No 366
>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=33.39 E-value=48 Score=25.15 Aligned_cols=22 Identities=18% Similarity=0.297 Sum_probs=19.0
Q ss_pred HHHHHhcCCCCCCEEEEEecCc
Q psy11423 371 ESEIYRKNIQIGDTVVVHRSGN 392 (655)
Q Consensus 371 ~~~i~~~~i~iGd~V~v~raGd 392 (655)
.+..+.++|.+||.|.+.-.|+
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 4556789999999999999887
No 367
>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=33.33 E-value=79 Score=31.83 Aligned_cols=44 Identities=23% Similarity=0.540 Sum_probs=31.4
Q ss_pred HHHHHhCCCCCCCCceeeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhh
Q psy11423 253 LNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLST 306 (655)
Q Consensus 253 l~~L~~~GF~~~~~~~~~~~~~ev~~~~~~~~~~r~~l~y~iDGiVikv~~~~~ 306 (655)
-++|++.|.++.. ...+++.+++.+|++.+ ..|+ +|||.|-++.
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 3578899999995 56788999999999865 3343 7999887543
No 368
>PRK14175 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=33.02 E-value=1.3e+02 Score=32.25 Aligned_cols=67 Identities=13% Similarity=0.249 Sum_probs=45.3
Q ss_pred CHHHHHHHHHHhcChhHHHHHHHHHHcCcccccCCCCCCCeEecccccCccEEEecCCCC------chHHHHHHcCCee-
Q psy11423 564 GSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNNPNTKGGKVVNFISKNTNYLVKGQKPG------KKLEKAIKLNIKI- 636 (655)
Q Consensus 564 G~~~A~~I~~~f~~~~n~~li~~L~~~Gi~~~~~~~~~G~~v~~sVsk~t~ylv~g~~~g------~K~~kA~~lgi~i- 636 (655)
|..+|+.|.+.+. +.++.|.+.|+. .+.-.+.+|+.+. .|.+.|+++||..
T Consensus 8 Gk~ia~~i~~~~~-----~~v~~l~~~g~~-----------------p~Laii~vg~~~as~~Yv~~k~k~a~~~Gi~~~ 65 (286)
T PRK14175 8 GKQIAKDYRQGLQ-----DQVEALKEKGFT-----------------PKLSVILVGNDGASQSYVRSKKKAAEKIGMISE 65 (286)
T ss_pred HHHHHHHHHHHHH-----HHHHHHHhcCCC-----------------CeEEEEEeCCCHHHHHHHHHHHHHHHHcCCEEE
Confidence 6778888877763 345556544432 2344577887754 6888899999874
Q ss_pred -------eCHHHHHHHHhcccCC
Q psy11423 637 -------LDEKNFVKIVKGFSTE 652 (655)
Q Consensus 637 -------i~e~~f~~~l~~~~~~ 652 (655)
+++++|.+.+..-+.+
T Consensus 66 ~~~l~~~~~~~~l~~~I~~lN~d 88 (286)
T PRK14175 66 IVHLEETATEEEVLNELNRLNND 88 (286)
T ss_pred EEECCCCCCHHHHHHHHHHHhCC
Confidence 4678999988655443
No 369
>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=32.61 E-value=62 Score=31.57 Aligned_cols=67 Identities=22% Similarity=0.330 Sum_probs=40.7
Q ss_pred CCCCCCEEEEE--------ecCcccceeecccccCCCCCCccccCCCCCCCCCCcceeecCceeEEecCCCcCCHHHHHh
Q psy11423 378 NIQIGDTVVVH--------RSGNVIPKITSSILSLRPNDSKIFKIPNICPICNSKIIYIESNLIARCSGSWIECIAQRKA 449 (655)
Q Consensus 378 ~i~iGd~V~v~--------raGdVIP~I~~vv~~~r~~~~~~~~~P~~CP~C~~~l~~~~~~~~~~C~n~~~~C~~q~~~ 449 (655)
-|+.||...|= |.++.|== ||+..|+..+. =-+-=+|+.|+..|. ++.+.|.+. . .|+..
T Consensus 73 ~L~eGd~flvP~gvpHsP~r~~~t~~L---vIE~~r~~~~~-d~~~wyc~~c~~~~~----e~~f~~~d~-~---~~~~~ 140 (159)
T TIGR03037 73 PIREGDIFLLPPHVPHSPQRPAGSIGL---VIERKRPQGEL-DGFQWFCPQCGHKLH----RAEVQLENI-V---TDLPP 140 (159)
T ss_pred EECCCCEEEeCCCCCcccccCCCcEEE---EEEeCCCCCCC-cceEEECCCCCCeEE----EEEEEecCh-h---hhhHH
Confidence 46677777753 44444332 33444544331 113348999998776 467899884 3 57878
Q ss_pred hcccccc
Q psy11423 450 GLQHFSS 456 (655)
Q Consensus 450 ~i~~F~s 456 (655)
-+..|.+
T Consensus 141 ~~~~f~~ 147 (159)
T TIGR03037 141 VFEHFYS 147 (159)
T ss_pred HHHHHhC
Confidence 8887765
No 370
>PRK14168 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=32.35 E-value=1.4e+02 Score=32.08 Aligned_cols=67 Identities=15% Similarity=0.367 Sum_probs=46.1
Q ss_pred CHHHHHHHHHHhcChhHHHHHHHHHHc-CcccccCCCCCCCeEecccccCccEEEecCCCC------chHHHHHHcCCee
Q psy11423 564 GSTTVKAFIKFINQPLHRLLISQLRDV-GIYWLNNPNTKGGKVVNFISKNTNYLVKGQKPG------KKLEKAIKLNIKI 636 (655)
Q Consensus 564 G~~~A~~I~~~f~~~~n~~li~~L~~~-Gi~~~~~~~~~G~~v~~sVsk~t~ylv~g~~~g------~K~~kA~~lgi~i 636 (655)
|..+|+.|.+.+. +.++.|.+. |+ +.+.-.+.+|+.+. .|.+.|+++||..
T Consensus 8 Gk~iA~~i~~~lk-----~~v~~l~~~~g~-----------------~P~LaiI~vg~d~as~~Yv~~k~k~~~~~Gi~~ 65 (297)
T PRK14168 8 GTEIREEILEEIR-----GEVAELKEKYGK-----------------VPGLVTILVGESPASLSYVTLKIKTAHRLGFHE 65 (297)
T ss_pred HHHHHHHHHHHHH-----HHHHHHHHcCCC-----------------CCeEEEEEeCCCHHHHHHHHHHHHHHHHcCCEE
Confidence 6778888887764 335556543 33 22444677888754 6777799999874
Q ss_pred --------eCHHHHHHHHhcccCC
Q psy11423 637 --------LDEKNFVKIVKGFSTE 652 (655)
Q Consensus 637 --------i~e~~f~~~l~~~~~~ 652 (655)
+++++|.+.+..-+.+
T Consensus 66 ~~~~l~~~~t~~el~~~I~~lN~D 89 (297)
T PRK14168 66 IQDNQSVDITEEELLALIDKYNND 89 (297)
T ss_pred EEEECCCCCCHHHHHHHHHHHhCC
Confidence 6899999988655544
No 371
>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=31.99 E-value=27 Score=25.28 Aligned_cols=14 Identities=21% Similarity=0.532 Sum_probs=10.3
Q ss_pred CCCCCCCCCCccee
Q psy11423 414 IPNICPICNSKIIY 427 (655)
Q Consensus 414 ~P~~CP~C~~~l~~ 427 (655)
.+..||.||+++.+
T Consensus 25 ~~~~CP~Cg~~~~r 38 (41)
T smart00834 25 PLATCPECGGDVRR 38 (41)
T ss_pred CCCCCCCCCCccee
Confidence 35679999986543
No 372
>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=31.98 E-value=27 Score=25.12 Aligned_cols=22 Identities=23% Similarity=0.637 Sum_probs=14.1
Q ss_pred CCCCCCCcceeec-----CceeEEecC
Q psy11423 417 ICPICNSKIIYIE-----SNLIARCSG 438 (655)
Q Consensus 417 ~CP~C~~~l~~~~-----~~~~~~C~n 438 (655)
.||.|++.....+ ++...+|++
T Consensus 4 ~CP~C~~~~~v~~~~~~~~~~~v~C~~ 30 (38)
T TIGR02098 4 QCPNCKTSFRVVDSQLGANGGKVRCGK 30 (38)
T ss_pred ECCCCCCEEEeCHHHcCCCCCEEECCC
Confidence 5888888654332 234678877
No 373
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=31.82 E-value=16 Score=29.53 Aligned_cols=25 Identities=24% Similarity=0.400 Sum_probs=17.6
Q ss_pred CCCCCCCCCCcceeecCceeEEecCCCcCCHH
Q psy11423 414 IPNICPICNSKIIYIESNLIARCSGSWIECIA 445 (655)
Q Consensus 414 ~P~~CP~C~~~l~~~~~~~~~~C~n~~~~C~~ 445 (655)
+-.|||+||.++.. | ..+|+. . |.+
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 34699999998873 3 347877 2 873
No 374
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=31.80 E-value=23 Score=35.03 Aligned_cols=12 Identities=42% Similarity=1.074 Sum_probs=10.0
Q ss_pred CCCCCCCCccee
Q psy11423 416 NICPICNSKIIY 427 (655)
Q Consensus 416 ~~CP~C~~~l~~ 427 (655)
..||+||+++.+
T Consensus 154 ~~Cp~CG~~~~~ 165 (177)
T COG1439 154 DFCPICGSPLKR 165 (177)
T ss_pred CcCCCCCCceEE
Confidence 589999998764
No 375
>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=31.73 E-value=89 Score=29.51 Aligned_cols=65 Identities=26% Similarity=0.209 Sum_probs=45.0
Q ss_pred HHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCcceeeEEEEEEEEeecCcceeeeEEEEEEEEECCEE
Q psy11423 283 INIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGIT 362 (655)
Q Consensus 283 ~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~~~T~v~~I~~qvGRTG~itPvA~lePV~l~G~t 362 (655)
+..+++.+.-...|.|+|+-.-+. ..|+|-||-+-. + +|.|
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 344667777777999999955321 245566554432 1 2666
Q ss_pred EEEeeCCCHHHHHhcC-CCCCCEEEEE
Q psy11423 363 ITRATLHNESEIYRKN-IQIGDTVVVH 388 (655)
Q Consensus 363 VsratLhN~~~i~~~~-i~iGd~V~v~ 388 (655)
|-=| ||++..-+.. |+.||+|.+.
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 6655 9999998886 9999999886
No 376
>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=31.71 E-value=55 Score=29.26 Aligned_cols=45 Identities=18% Similarity=0.112 Sum_probs=26.4
Q ss_pred CHHHHHHHHHcCCCCChHHHhcC-Ch---hhhccccCCcHHHHHHHHHHH
Q psy11423 466 GKKMIEKLVNANIVVTAVDLYKI-NF---KNLLRLDRVSNKLANNILLAI 511 (655)
Q Consensus 466 G~k~i~~L~~~g~I~~i~DL~~L-~~---~~L~~l~GfG~Ksa~nll~~I 511 (655)
.|..+..|..+| |.|+.||... .. .=-..+||+|.++|..|..=+
T Consensus 22 ~p~va~~L~aaG-i~TL~dL~~~i~~rg~~Wwr~vpglG~~~A~~I~awL 70 (96)
T PF12482_consen 22 PPRVARRLAAAG-IRTLADLVDRINRRGGRWWRAVPGLGAAGARRIEAWL 70 (96)
T ss_pred CHHHHHHHHHcC-CchHHHHHHHHHHccchHHHhCcccchHHHHHHHHHH
Confidence 367778887777 4778777752 11 113455666666665554433
No 377
>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=31.70 E-value=64 Score=25.76 Aligned_cols=48 Identities=23% Similarity=0.348 Sum_probs=34.6
Q ss_pred CCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcH-HHHHHHHHHHHHh
Q psy11423 464 GLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSN-KLANNILLAIQKS 514 (655)
Q Consensus 464 GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~-Ksa~nll~~I~~s 514 (655)
|+ ++-+..+.+.| |.....|..|+.++|.++ |+.. .-..+|+++|+.-
T Consensus 17 gl-~~y~~~f~~~~-i~g~~~L~~l~~~~L~~l-GI~~~~~r~kll~~i~~L 65 (66)
T PF07647_consen 17 GL-EQYADNFRENG-IDGLEDLLQLTEEDLKEL-GITNLGHRRKLLSAIQEL 65 (66)
T ss_dssp TC-GGGHHHHHHTT-CSHHHHHTTSCHHHHHHT-TTTHHHHHHHHHHHHHHH
T ss_pred Cc-HHHHHHHHHcC-CcHHHHHhhCCHHHHHHc-CCCCHHHHHHHHHHHHHc
Confidence 55 55666666666 466688888999999987 7744 4557888888753
No 378
>PRK14184 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=31.66 E-value=1.5e+02 Score=31.68 Aligned_cols=66 Identities=12% Similarity=0.223 Sum_probs=44.5
Q ss_pred CHHHHHHHHHHhcChhHHHHHHHHHHc-CcccccCCCCCCCeEecccccCccEEEecCCCC------chHHHHHHcCCee
Q psy11423 564 GSTTVKAFIKFINQPLHRLLISQLRDV-GIYWLNNPNTKGGKVVNFISKNTNYLVKGQKPG------KKLEKAIKLNIKI 636 (655)
Q Consensus 564 G~~~A~~I~~~f~~~~n~~li~~L~~~-Gi~~~~~~~~~G~~v~~sVsk~t~ylv~g~~~g------~K~~kA~~lgi~i 636 (655)
|..+|+.|.+.+. +.++.|.+. |+ +.+.-.+.+|+.+. .|.+.|+++||..
T Consensus 6 Gk~iA~~i~~~l~-----~~v~~l~~~~g~-----------------~P~Laii~vg~d~as~~Yv~~k~k~~~~~Gi~~ 63 (286)
T PRK14184 6 GKATAATIREELK-----TEVAALTARHGR-----------------APGLAVILVGEDPASQVYVRNKERACEDAGIVS 63 (286)
T ss_pred HHHHHHHHHHHHH-----HHHHHHHhccCC-----------------CCEEEEEEeCCChhHHHHHHHHHHHHHHcCCEE
Confidence 6777888877663 345556543 32 22455677888754 6888899999875
Q ss_pred --------eCHHHHHHHHhcccC
Q psy11423 637 --------LDEKNFVKIVKGFST 651 (655)
Q Consensus 637 --------i~e~~f~~~l~~~~~ 651 (655)
+++++|.+.+..-+.
T Consensus 64 ~~~~l~~~~~~~~l~~~I~~lN~ 86 (286)
T PRK14184 64 EAFRLPADTTQEELEDLIAELNA 86 (286)
T ss_pred EEEECCCCCCHHHHHHHHHHHhC
Confidence 568999998865443
No 379
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=31.45 E-value=30 Score=36.58 Aligned_cols=23 Identities=22% Similarity=0.352 Sum_probs=18.4
Q ss_pred CCCCCCCCcceee--cCceeEEecC
Q psy11423 416 NICPICNSKIIYI--ESNLIARCSG 438 (655)
Q Consensus 416 ~~CP~C~~~l~~~--~~~~~~~C~n 438 (655)
+-|+.||+++++. .+-..+||++
T Consensus 246 epC~~CGt~I~k~~~~gR~t~~CP~ 270 (273)
T COG0266 246 EPCRRCGTPIEKIKLGGRSTFYCPV 270 (273)
T ss_pred CCCCccCCEeEEEEEcCCcCEeCCC
Confidence 3599999998854 5668899987
No 380
>PRK14172 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=31.16 E-value=1.6e+02 Score=31.32 Aligned_cols=67 Identities=13% Similarity=0.288 Sum_probs=44.2
Q ss_pred CHHHHHHHHHHhcChhHHHHHHHHHHcCcccccCCCCCCCeEecccccCccEEEecCCCC------chHHHHHHcCCee-
Q psy11423 564 GSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNNPNTKGGKVVNFISKNTNYLVKGQKPG------KKLEKAIKLNIKI- 636 (655)
Q Consensus 564 G~~~A~~I~~~f~~~~n~~li~~L~~~Gi~~~~~~~~~G~~v~~sVsk~t~ylv~g~~~g------~K~~kA~~lgi~i- 636 (655)
|..+|++|.+.+. +.++.|.+.|.. ..+.-.+.+|+.+. .|.+.|+++||..
T Consensus 7 Gk~iA~~i~~~lk-----~~i~~l~~~g~~----------------~P~Laii~vg~d~as~~Yv~~k~k~a~~~Gi~~~ 65 (278)
T PRK14172 7 GKEVALKIKEEIK-----NFVEERKENGLS----------------IPKIASILVGNDGGSIYYMNNQEKVANSLGIDFK 65 (278)
T ss_pred HHHHHHHHHHHHH-----HHHHHHHhcCCC----------------CceEEEEEeCCCHHHHHHHHHHHHHHHHcCCEEE
Confidence 6778888877663 345556544321 12344667888754 5777799999986
Q ss_pred -------eCHHHHHHHHhcccC
Q psy11423 637 -------LDEKNFVKIVKGFST 651 (655)
Q Consensus 637 -------i~e~~f~~~l~~~~~ 651 (655)
++++++.+.+..-+.
T Consensus 66 ~~~l~~~~~~~el~~~I~~lN~ 87 (278)
T PRK14172 66 KIKLDESISEEDLINEIEELNK 87 (278)
T ss_pred EEECCCCCCHHHHHHHHHHHhC
Confidence 468899988864433
No 381
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=31.15 E-value=20 Score=40.04 Aligned_cols=73 Identities=21% Similarity=0.360 Sum_probs=41.6
Q ss_pred cCCCCCCEEEEEecCcccceeecccccCCCCCCcccc-CCCCCCCCCCcceeecCceeEEecCCCcCCHHHHHhhccccc
Q psy11423 377 KNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFK-IPNICPICNSKIIYIESNLIARCSGSWIECIAQRKAGLQHFS 455 (655)
Q Consensus 377 ~~i~iGd~V~v~raGdVIP~I~~vv~~~r~~~~~~~~-~P~~CP~C~~~l~~~~~~~~~~C~n~~~~C~~q~~~~i~~F~ 455 (655)
..|.+||.|.+. |.|=|+.+.+-+- +.-.-.++. .-..||.||..+.-...+ -++|.. |--+.-....+-+
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 378999999875 6676766444221 000000121 123799999987654334 899975 7655544444433
Q ss_pred cc
Q psy11423 456 SR 457 (655)
Q Consensus 456 sk 457 (655)
-|
T Consensus 386 ~r 387 (421)
T COG1571 386 PR 387 (421)
T ss_pred cc
Confidence 33
No 382
>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=31.10 E-value=46 Score=24.56 Aligned_cols=31 Identities=29% Similarity=0.597 Sum_probs=21.6
Q ss_pred CCCCCCcce------eecCceeEEecCCCcCCHHHHHhhc
Q psy11423 418 CPICNSKII------YIESNLIARCSGSWIECIAQRKAGL 451 (655)
Q Consensus 418 CP~C~~~l~------~~~~~~~~~C~n~~~~C~~q~~~~i 451 (655)
|-.||.++. +..+....+|-+ + |..|+.+++
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 445666543 345678889988 4 999988764
No 383
>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=31.09 E-value=58 Score=28.26 Aligned_cols=29 Identities=28% Similarity=0.408 Sum_probs=21.0
Q ss_pred ccccCCCCHHHHHHHHHc---CCCCChHHHhc
Q psy11423 459 AMNIIGLGKKMIEKLVNA---NIVVTAVDLYK 487 (655)
Q Consensus 459 ~l~I~GLG~k~i~~L~~~---g~I~~i~DL~~ 487 (655)
..-|+|||++.+++++++ |--.++.|++.
T Consensus 29 l~~Ikglg~~~a~~I~~~R~~g~f~s~~df~~ 60 (90)
T PF14579_consen 29 LSAIKGLGEEVAEKIVEERENGPFKSLEDFIQ 60 (90)
T ss_dssp GGGSTTS-HHHHHHHHHHHHCSS-SSHHHHHH
T ss_pred HhhcCCCCHHHHHHHHHhHhcCCCCCHHHHHH
Confidence 456999999999998874 46678888775
No 384
>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=31.04 E-value=26 Score=24.81 Aligned_cols=11 Identities=36% Similarity=1.238 Sum_probs=9.0
Q ss_pred CCCCCCCCCCc
Q psy11423 414 IPNICPICNSK 424 (655)
Q Consensus 414 ~P~~CP~C~~~ 424 (655)
.|..||.||.+
T Consensus 16 ~~~~CP~Cg~~ 26 (33)
T cd00350 16 APWVCPVCGAP 26 (33)
T ss_pred CCCcCcCCCCc
Confidence 57799999974
No 385
>PRK14186 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=31.02 E-value=1.6e+02 Score=31.68 Aligned_cols=67 Identities=12% Similarity=0.179 Sum_probs=44.9
Q ss_pred CHHHHHHHHHHhcChhHHHHHHHHHHc-CcccccCCCCCCCeEecccccCccEEEecCCCC------chHHHHHHcCCee
Q psy11423 564 GSTTVKAFIKFINQPLHRLLISQLRDV-GIYWLNNPNTKGGKVVNFISKNTNYLVKGQKPG------KKLEKAIKLNIKI 636 (655)
Q Consensus 564 G~~~A~~I~~~f~~~~n~~li~~L~~~-Gi~~~~~~~~~G~~v~~sVsk~t~ylv~g~~~g------~K~~kA~~lgi~i 636 (655)
|..+|+.|.+.+. +.++.|.+. |+ ..+.-.+.+|+.+. +|.+.|+++||..
T Consensus 7 Gk~iA~~i~~~lk-----~~v~~l~~~~g~-----------------~p~LaiI~vgdd~as~~Yv~~k~k~a~~~Gi~~ 64 (297)
T PRK14186 7 GKALAAEIEQRLQ-----AQIESNLPKAGR-----------------PPGLAVLRVGDDPASAVYVRNKEKACARVGIAS 64 (297)
T ss_pred hHHHHHHHHHHHH-----HHHHHHHHhcCC-----------------CceEEEEEeCCChHHHHHHHHHHHHHHHcCCEE
Confidence 6778888887763 335555432 32 23444667787754 6888899999876
Q ss_pred --------eCHHHHHHHHhcccCC
Q psy11423 637 --------LDEKNFVKIVKGFSTE 652 (655)
Q Consensus 637 --------i~e~~f~~~l~~~~~~ 652 (655)
+++++|.+.+..-+.+
T Consensus 65 ~~~~l~~~~~~~el~~~I~~lN~D 88 (297)
T PRK14186 65 FGKHLPADTSQAEVEALIAQLNQD 88 (297)
T ss_pred EEEECCCCCCHHHHHHHHHHHhCC
Confidence 3688999988655444
No 386
>PRK08402 replication factor A; Reviewed
Probab=30.85 E-value=26 Score=38.53 Aligned_cols=24 Identities=25% Similarity=0.472 Sum_probs=19.6
Q ss_pred CCCCCCCCCCcceeecCceeEEecC
Q psy11423 414 IPNICPICNSKIIYIESNLIARCSG 438 (655)
Q Consensus 414 ~P~~CP~C~~~l~~~~~~~~~~C~n 438 (655)
+| .||.|+.++...++...++|.+
T Consensus 212 y~-aCp~CnKkv~~~~~~~~~~Ce~ 235 (355)
T PRK08402 212 YD-ACPECRRKVDYDPATDTWICPE 235 (355)
T ss_pred Ee-cCCCCCeEEEEecCCCCEeCCC
Confidence 44 7999999988666677899986
No 387
>PRK14169 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=30.83 E-value=1.7e+02 Score=31.32 Aligned_cols=66 Identities=12% Similarity=0.274 Sum_probs=44.8
Q ss_pred CHHHHHHHHHHhcChhHHHHHHHHHHcCcccccCCCCCCCeEecccccCccEEEecCCCC------chHHHHHHcCCee-
Q psy11423 564 GSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNNPNTKGGKVVNFISKNTNYLVKGQKPG------KKLEKAIKLNIKI- 636 (655)
Q Consensus 564 G~~~A~~I~~~f~~~~n~~li~~L~~~Gi~~~~~~~~~G~~v~~sVsk~t~ylv~g~~~g------~K~~kA~~lgi~i- 636 (655)
|..+|+.|.+.+. +.++.|.+.|+. .+.-.+.+|+.+. .|.+.|+++||..
T Consensus 6 Gk~va~~i~~~l~-----~~v~~l~~~g~~-----------------P~Laii~vg~d~as~~Yv~~k~k~a~~~Gi~~~ 63 (282)
T PRK14169 6 GRAVSKKILADLK-----QTVAKLAQQDVT-----------------PTLAVVLVGSDPASEVYVRNKQRRAEDIGVRSL 63 (282)
T ss_pred hHHHHHHHHHHHH-----HHHHHHHhCCCC-----------------CeEEEEEeCCChhHHHHHHHHHHHHHHcCCEEE
Confidence 6778888887764 346666544432 2344677787654 6788899999874
Q ss_pred -------eCHHHHHHHHhcccC
Q psy11423 637 -------LDEKNFVKIVKGFST 651 (655)
Q Consensus 637 -------i~e~~f~~~l~~~~~ 651 (655)
+++++|.+.+..-+.
T Consensus 64 ~~~l~~~~~~~el~~~I~~lN~ 85 (282)
T PRK14169 64 MFRLPEATTQADLLAKVAELNH 85 (282)
T ss_pred EEECCCCCCHHHHHHHHHHHhC
Confidence 567899998865443
No 388
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=30.75 E-value=41 Score=29.50 Aligned_cols=53 Identities=19% Similarity=0.290 Sum_probs=33.3
Q ss_pred hHHHHHhCCCCccHHHHHHHHHhCCC--HHHHHhcCHHHHhc-CCCCCHHHHHHHHHHhc
Q psy11423 520 SRFIYALGIRHVGETTAKELANYFKN--LECMFKATEEQLLN-IPKIGSTTVKAFIKFIN 576 (655)
Q Consensus 520 ~r~L~algIpgIG~~~Ak~L~~~fgs--l~~l~~as~eeL~~-i~GIG~~~A~~I~~~f~ 576 (655)
..+|..+||+ ...+.+|.+.||+ ++.|.. ++=.|.. ++|||=++|.+|..-+.
T Consensus 12 ~~~L~~~gl~---~~~a~kl~~~yg~~ai~~l~~-nPY~L~~~i~gi~F~~aD~iA~~~g 67 (94)
T PF14490_consen 12 MAFLQEYGLS---PKLAMKLYKKYGDDAIEILKE-NPYRLIEDIDGIGFKTADKIALKLG 67 (94)
T ss_dssp HHHHHHTT-----HHHHHHHHHHH-TTHHHHHHH--STCCCB-SSSSBHHHHHHHHHTTT
T ss_pred HHHHHHcCCC---HHHHHHHHHHHhHHHHHHHHH-ChHHHHHHccCCCHHHHHHHHHHcC
Confidence 3555565665 6889999999885 233332 2223555 89999999999987654
No 389
>PRK00076 recR recombination protein RecR; Reviewed
Probab=30.39 E-value=44 Score=33.69 Aligned_cols=23 Identities=22% Similarity=0.346 Sum_probs=19.7
Q ss_pred HHHHhcCCCCCHHHHHHHHHHhc
Q psy11423 554 EEQLLNIPKIGSTTVKAFIKFIN 576 (655)
Q Consensus 554 ~eeL~~i~GIG~~~A~~I~~~f~ 576 (655)
.+.|.++||||+|.|+++.-|+=
T Consensus 10 i~~l~~LPGIG~KsA~Rla~~ll 32 (196)
T PRK00076 10 IEALRKLPGIGPKSAQRLAFHLL 32 (196)
T ss_pred HHHHHHCCCCCHHHHHHHHHHHH
Confidence 46899999999999999987653
No 390
>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=30.18 E-value=49 Score=27.19 Aligned_cols=20 Identities=20% Similarity=0.326 Sum_probs=16.0
Q ss_pred hhccccCCcHHHHHHHHHHH
Q psy11423 492 NLLRLDRVSNKLANNILLAI 511 (655)
Q Consensus 492 ~L~~l~GfG~Ksa~nll~~I 511 (655)
++..|||+|++.+++|.+-+
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 48899999999888886544
No 391
>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=30.07 E-value=19 Score=28.21 Aligned_cols=10 Identities=30% Similarity=1.029 Sum_probs=5.4
Q ss_pred CCCCCCCcce
Q psy11423 417 ICPICNSKII 426 (655)
Q Consensus 417 ~CP~C~~~l~ 426 (655)
.||.|+++|.
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 8999999875
No 392
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=30.05 E-value=1.7e+02 Score=29.04 Aligned_cols=63 Identities=19% Similarity=0.315 Sum_probs=35.5
Q ss_pred cCCCCCCEEEEE--ecCcccceeecccccCCCCCCccccCCCCCCCCCCcceeecCceeEEecCCCcCCHHHHHhhcc
Q psy11423 377 KNIQIGDTVVVH--RSGNVIPKITSSILSLRPNDSKIFKIPNICPICNSKIIYIESNLIARCSGSWIECIAQRKAGLQ 452 (655)
Q Consensus 377 ~~i~iGd~V~v~--raGdVIP~I~~vv~~~r~~~~~~~~~P~~CP~C~~~l~~~~~~~~~~C~n~~~~C~~q~~~~i~ 452 (655)
..+++||.|.+. ..+ +++.=-+.+ ..-. .+-..|+.||.+++... -..+.|++ |-....+++.
T Consensus 117 ~~~~~GD~V~akV~~i~---~~i~LS~k~---~~lG--vv~a~~~~~g~~~~~~~-~~~~~c~~----~~~~e~rkva 181 (189)
T PRK09521 117 DAFKIGDIVRAKVISYT---DPLQLSTKG---KDLG--VIYAMCSRCRTPLVKKG-ENELKCPN----CGNIETRKLS 181 (189)
T ss_pred hccCCCCEEEEEEEecC---CcEEEEEec---CCce--EEEEEccccCCceEECC-CCEEECCC----CCCEEeeccc
Confidence 358999998765 233 333211211 1111 12348999999998643 25689987 6544444443
No 393
>COG1194 MutY A/G-specific DNA glycosylase [DNA replication, recombination, and repair]
Probab=29.80 E-value=98 Score=33.86 Aligned_cols=73 Identities=18% Similarity=0.069 Sum_probs=47.4
Q ss_pred CChHHHhcCChhh-hccccCCc-HHHHHHHHHHHHHhcc-----cch-hHHHHHhCCCCccHHHHHHHHH-hCCCHHHHH
Q psy11423 480 VTAVDLYKINFKN-LLRLDRVS-NKLANNILLAIQKSKL-----TTF-SRFIYALGIRHVGETTAKELAN-YFKNLECMF 550 (655)
Q Consensus 480 ~~i~DL~~L~~~~-L~~l~GfG-~Ksa~nll~~I~~sk~-----~~l-~r~L~algIpgIG~~~Ak~L~~-~fgsl~~l~ 550 (655)
-++.+|-+...++ |....|.| -..|.||.++-+.-.. .|- ..-|. .+||||..+|..++. .|+....+.
T Consensus 64 Pti~~LA~A~~~evl~~W~gLGYysRArnL~~~A~~v~~~~~G~~P~~~~~l~--~LpGiG~yTa~Ail~~a~~~~~~~l 141 (342)
T COG1194 64 PTIKALAAAPEDEVLKAWEGLGYYSRARNLHKAAQEVVERHGGEFPDDEEELA--ALPGVGPYTAGAILSFAFNQPEPVL 141 (342)
T ss_pred CCHHHHhcCCHHHHHHHHHhcChHHHHHHHHHHHHHHHHHcCCCCCCCHHHHH--hCCCCcHHHHHHHHHHHhCCCCcee
Confidence 5788888876544 55558999 6778888776654221 221 12222 389999999988877 477666666
Q ss_pred hcCH
Q psy11423 551 KATE 554 (655)
Q Consensus 551 ~as~ 554 (655)
.-+.
T Consensus 142 DgNV 145 (342)
T COG1194 142 DGNV 145 (342)
T ss_pred ecch
Confidence 5554
No 394
>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=29.75 E-value=90 Score=26.92 Aligned_cols=44 Identities=18% Similarity=0.299 Sum_probs=26.7
Q ss_pred ChHHHHHHHHHHHHhhccCCCceEEEEEecceeEEEEEEeCCEEe
Q psy11423 97 SDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLK 141 (655)
Q Consensus 97 ~~~el~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y~~G~l~ 141 (655)
+.+++....+.+...+-...+......-|.+|+.|++ |.-|+++
T Consensus 8 ~~~~i~~l~~~y~~~~~~~~~p~~~f~aK~~~~tIt~-Y~SGKV~ 51 (81)
T PF11858_consen 8 TSEQIEKLKKYYKPYLTSSKPPYAVFQAKYNGVTITA-YKSGKVV 51 (81)
T ss_dssp -HHHHHHHHHHSTT-B-SS--TTEEEEEEETTEEEEE-ETTSEEE
T ss_pred CHHHHHHHHHHHHHhcccCCCCCEEEEEeCCCeEEEE-EeCCeEE
Confidence 3445555555543222111244578889999999987 9999864
No 395
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=29.67 E-value=45 Score=24.97 Aligned_cols=14 Identities=36% Similarity=0.747 Sum_probs=11.0
Q ss_pred CCCCCCCCCcceee
Q psy11423 415 PNICPICNSKIIYI 428 (655)
Q Consensus 415 P~~CP~C~~~l~~~ 428 (655)
|..||.||+.-+..
T Consensus 2 ~~~Cp~Cg~~~~~~ 15 (47)
T PF14690_consen 2 PPRCPHCGSPSVHR 15 (47)
T ss_pred CccCCCcCCCceEC
Confidence 67899999886544
No 396
>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=29.54 E-value=37 Score=25.35 Aligned_cols=14 Identities=36% Similarity=0.705 Sum_probs=10.2
Q ss_pred CCCCCCCCCC-ccee
Q psy11423 414 IPNICPICNS-KIIY 427 (655)
Q Consensus 414 ~P~~CP~C~~-~l~~ 427 (655)
.+..||.||+ .+.+
T Consensus 25 ~~~~CP~Cg~~~~~r 39 (42)
T PF09723_consen 25 DPVPCPECGSTEVRR 39 (42)
T ss_pred CCCcCCCCCCCceEE
Confidence 4678999998 4443
No 397
>COG2104 ThiS Sulfur transfer protein involved in thiamine biosynthesis [Coenzyme metabolism]
Probab=29.48 E-value=1e+02 Score=25.69 Aligned_cols=25 Identities=16% Similarity=0.396 Sum_probs=21.9
Q ss_pred HHHHHhcCCCCCCEEEEEecCcccce
Q psy11423 371 ESEIYRKNIQIGDTVVVHRSGNVIPK 396 (655)
Q Consensus 371 ~~~i~~~~i~iGd~V~v~raGdVIP~ 396 (655)
++.+.++++.. ..|.|...|+++|+
T Consensus 21 ~dLL~~l~~~~-~~vav~vNg~iVpr 45 (68)
T COG2104 21 ADLLAQLGLNP-EGVAVAVNGEIVPR 45 (68)
T ss_pred HHHHHHhCCCC-ceEEEEECCEEccc
Confidence 67788888876 89999999999995
No 398
>PRK00366 ispG 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed
Probab=29.39 E-value=33 Score=37.56 Aligned_cols=14 Identities=36% Similarity=0.508 Sum_probs=12.7
Q ss_pred CCCCEEEEEecCcc
Q psy11423 380 QIGDTVVVHRSGNV 393 (655)
Q Consensus 380 ~iGd~V~v~raGdV 393 (655)
+|||||+|+.++|-
T Consensus 232 GIGDTiRVSLt~~P 245 (360)
T PRK00366 232 GIGDTIRVSLTADP 245 (360)
T ss_pred cCCCeEEEeCCCCC
Confidence 58999999999994
No 399
>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=29.11 E-value=49 Score=24.15 Aligned_cols=24 Identities=25% Similarity=0.487 Sum_probs=16.4
Q ss_pred CCCCCCCCCcc-eeec-----CceeEEecC
Q psy11423 415 PNICPICNSKI-IYIE-----SNLIARCSG 438 (655)
Q Consensus 415 P~~CP~C~~~l-~~~~-----~~~~~~C~n 438 (655)
.-+||.|++.- +... |...++|..
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 5433 346777754
No 400
>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=29.09 E-value=1.8e+02 Score=25.81 Aligned_cols=46 Identities=17% Similarity=0.143 Sum_probs=35.3
Q ss_pred ChhhHHHHHHHHHHHHHHHHHHh----------hcCCCCCCChHHHHHHHHHHHHH
Q psy11423 10 NFSKLSFRVTELKKELHRHNIAY----------YLYDNPIISDNKYDQLLFELKKI 55 (655)
Q Consensus 10 ~~~~~~~~~~~L~~~l~~~~~~Y----------y~~~~p~isD~~YD~L~~~L~~l 55 (655)
+.+++.++|+.|+++|+.+...= =-+++=.|+|++++.-++++..-
T Consensus 3 ~~s~I~~eIekLqe~lk~~e~keaERigr~AlKaGL~eieI~d~eL~~~FeeIa~R 58 (92)
T PF07820_consen 3 SSSKIREEIEKLQEQLKQAETKEAERIGRIALKAGLGEIEISDAELQAAFEEIAAR 58 (92)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccCCHHHHHHHHHHHHHH
Confidence 56778889999999888776421 12467799999999999988753
No 401
>PRK12496 hypothetical protein; Provisional
Probab=28.94 E-value=23 Score=34.59 Aligned_cols=15 Identities=7% Similarity=-0.117 Sum_probs=12.2
Q ss_pred EEEEEeehhhHHHHH
Q psy11423 181 RCEVLIYKKDFIKLN 195 (655)
Q Consensus 181 RGEv~~~~~~F~~~n 195 (655)
-||+|++.+.++++.
T Consensus 19 ~~~i~tp~~V~~Ev~ 33 (164)
T PRK12496 19 DGEHYTTPSVVEEVK 33 (164)
T ss_pred CCCEEecHHHHHHHh
Confidence 489999999988754
No 402
>PLN02897 tetrahydrofolate dehydrogenase/cyclohydrolase, putative
Probab=28.90 E-value=1.8e+02 Score=31.96 Aligned_cols=67 Identities=15% Similarity=0.271 Sum_probs=46.0
Q ss_pred CHHHHHHHHHHhcChhHHHHHHHHHHc-CcccccCCCCCCCeEecccccCccEEEecCCCC------chHHHHHHcCCee
Q psy11423 564 GSTTVKAFIKFINQPLHRLLISQLRDV-GIYWLNNPNTKGGKVVNFISKNTNYLVKGQKPG------KKLEKAIKLNIKI 636 (655)
Q Consensus 564 G~~~A~~I~~~f~~~~n~~li~~L~~~-Gi~~~~~~~~~G~~v~~sVsk~t~ylv~g~~~g------~K~~kA~~lgi~i 636 (655)
|..+|+.|.+.+. +.++.|.+. |+ ..+.-.+++|+.+. .|.+.|+++||..
T Consensus 61 Gk~vA~~i~~~lk-----~~v~~l~~~~g~-----------------~P~LaiIlvGddpaS~~Yv~~k~K~a~~~GI~~ 118 (345)
T PLN02897 61 GNVIAEEIRTKIA-----SEVRKMKKAVGK-----------------VPGLAVVLVGQQRDSQTYVRNKIKACEETGIKS 118 (345)
T ss_pred hHHHHHHHHHHHH-----HHHHHHHhccCC-----------------CCeEEEEEeCCChHHHHHHHHHHHHHHhcCCEE
Confidence 7888988887763 345666543 32 22344578888754 6888899999875
Q ss_pred --------eCHHHHHHHHhcccCC
Q psy11423 637 --------LDEKNFVKIVKGFSTE 652 (655)
Q Consensus 637 --------i~e~~f~~~l~~~~~~ 652 (655)
++++++++.+..-..+
T Consensus 119 ~~~~l~~~~te~ell~~I~~lN~D 142 (345)
T PLN02897 119 LLAELPEDCTEGQILSALRKFNED 142 (345)
T ss_pred EEEECCCCCCHHHHHHHHHHHhCC
Confidence 5688999988654433
No 403
>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=28.83 E-value=36 Score=40.19 Aligned_cols=27 Identities=26% Similarity=0.613 Sum_probs=19.6
Q ss_pred CCCCCCCCccee--ecCceeEEecCCCcCC
Q psy11423 416 NICPICNSKIIY--IESNLIARCSGSWIEC 443 (655)
Q Consensus 416 ~~CP~C~~~l~~--~~~~~~~~C~n~~~~C 443 (655)
..||.||..++. ...+..+.|.|.+. |
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 23456799999545 7
No 404
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=28.79 E-value=49 Score=33.32 Aligned_cols=22 Identities=23% Similarity=0.415 Sum_probs=18.9
Q ss_pred HHHHhcCCCCCHHHHHHHHHHh
Q psy11423 554 EEQLLNIPKIGSTTVKAFIKFI 575 (655)
Q Consensus 554 ~eeL~~i~GIG~~~A~~I~~~f 575 (655)
.+.|.++||||++.|+++.-|+
T Consensus 10 i~~l~~LPGIG~KsA~RlA~~l 31 (195)
T TIGR00615 10 IESLKKLPGIGPKSAQRLAFHL 31 (195)
T ss_pred HHHHHHCCCCCHHHHHHHHHHH
Confidence 4689999999999999997655
No 405
>PRK14167 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=28.78 E-value=1.8e+02 Score=31.28 Aligned_cols=67 Identities=12% Similarity=0.234 Sum_probs=44.8
Q ss_pred CHHHHHHHHHHhcChhHHHHHHHHHHcCcccccCCCCCCCeEecccccCccEEEecCCCC------chHHHHHHcCCee-
Q psy11423 564 GSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNNPNTKGGKVVNFISKNTNYLVKGQKPG------KKLEKAIKLNIKI- 636 (655)
Q Consensus 564 G~~~A~~I~~~f~~~~n~~li~~L~~~Gi~~~~~~~~~G~~v~~sVsk~t~ylv~g~~~g------~K~~kA~~lgi~i- 636 (655)
|..+|++|.+.+. +.++.|.+.|+. .+.-.+.+|+.+. .|.+.|+++||..
T Consensus 7 Gk~vA~~i~~~l~-----~~v~~l~~~g~~-----------------P~LaiI~vg~d~as~~Yv~~k~k~~~~~Gi~~~ 64 (297)
T PRK14167 7 GNAVAAQIRDDLT-----DAIETLEDAGVT-----------------PGLATVLMSDDPASETYVSMKQRDCEEVGIEAI 64 (297)
T ss_pred HHHHHHHHHHHHH-----HHHHHHHhCCCC-----------------ceEEEEEeCCCHHHHHHHHHHHHHHHHcCCEEE
Confidence 6778888877764 335556544432 2444667787754 6778899999874
Q ss_pred -------eCHHHHHHHHhcccCC
Q psy11423 637 -------LDEKNFVKIVKGFSTE 652 (655)
Q Consensus 637 -------i~e~~f~~~l~~~~~~ 652 (655)
+++++|.+.+..-+.+
T Consensus 65 ~~~l~~~~~~~el~~~I~~lN~D 87 (297)
T PRK14167 65 DVEIDPDAPAEELYDTIDELNAD 87 (297)
T ss_pred EEECCCCCCHHHHHHHHHHHhCC
Confidence 5688999988655444
No 406
>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=28.51 E-value=33 Score=34.47 Aligned_cols=28 Identities=18% Similarity=0.433 Sum_probs=20.6
Q ss_pred HHhcCCCCCCEEEEEecCcccceeecccc
Q psy11423 374 IYRKNIQIGDTVVVHRSGNVIPKITSSIL 402 (655)
Q Consensus 374 i~~~~i~iGd~V~v~raGdVIP~I~~vv~ 402 (655)
+.-.+|.+||.|.+ ++||+||-=..++.
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 45569999999999 77999996444443
No 407
>smart00746 TRASH metallochaperone-like domain.
Probab=28.45 E-value=51 Score=21.75 Aligned_cols=27 Identities=22% Similarity=0.640 Sum_probs=15.0
Q ss_pred CCCCCCcce--------eecCceeEEecCCCcCCHHHH
Q psy11423 418 CPICNSKII--------YIESNLIARCSGSWIECIAQR 447 (655)
Q Consensus 418 CP~C~~~l~--------~~~~~~~~~C~n~~~~C~~q~ 447 (655)
||.||..+. ..++....||.. . |-+..
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 778887664 223445566665 2 65543
No 408
>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=28.39 E-value=20 Score=33.77 Aligned_cols=27 Identities=33% Similarity=0.585 Sum_probs=20.3
Q ss_pred HHHHHhcCCCCCCEEEEEecCcccceeecccc
Q psy11423 371 ESEIYRKNIQIGDTVVVHRSGNVIPKITSSIL 402 (655)
Q Consensus 371 ~~~i~~~~i~iGd~V~v~raGdVIP~I~~vv~ 402 (655)
...++.|+||+||+|.|.= |++.-+|.
T Consensus 52 ~~dv~~LDlRIGD~Vkv~~-----~k~~yiV~ 78 (131)
T PF08605_consen 52 NEDVKYLDLRIGDTVKVDG-----PKVTYIVV 78 (131)
T ss_pred cccEeeeeeecCCEEEECC-----CCccEEEE
Confidence 4447889999999999975 65555554
No 409
>COG4469 CoiA Competence protein CoiA-like family, contains a predicted nuclease domain [General function prediction only]
Probab=28.37 E-value=28 Score=37.62 Aligned_cols=16 Identities=31% Similarity=0.785 Sum_probs=13.0
Q ss_pred CCCCCCCCCcceeecC
Q psy11423 415 PNICPICNSKIIYIES 430 (655)
Q Consensus 415 P~~CP~C~~~l~~~~~ 430 (655)
+-+||+||++|....|
T Consensus 25 ~ffCPaC~~~l~lK~G 40 (342)
T COG4469 25 RFFCPACGSQLILKQG 40 (342)
T ss_pred ccccCCCCCeeeeecC
Confidence 4589999999986655
No 410
>COG0821 gcpE 1-hydroxy-2-methyl-2-(e)-butenyl 4-diphosphate synthase [Lipid metabolism]
Probab=28.31 E-value=24 Score=38.30 Aligned_cols=14 Identities=36% Similarity=0.508 Sum_probs=12.9
Q ss_pred CCCCEEEEEecCcc
Q psy11423 380 QIGDTVVVHRSGNV 393 (655)
Q Consensus 380 ~iGd~V~v~raGdV 393 (655)
+|||||+|+.++|-
T Consensus 225 GIGDTIRVSLt~~P 238 (361)
T COG0821 225 GIGDTIRVSLTADP 238 (361)
T ss_pred cCCceEEEecCCCc
Confidence 57999999999997
No 411
>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=28.06 E-value=1e+02 Score=34.21 Aligned_cols=33 Identities=18% Similarity=0.202 Sum_probs=20.0
Q ss_pred HHHHHh---CCCCccHHHHHHHHHh-CCCHHHHHhcC
Q psy11423 521 RFIYAL---GIRHVGETTAKELANY-FKNLECMFKAT 553 (655)
Q Consensus 521 r~L~al---gIpgIG~~~Ak~L~~~-fgsl~~l~~as 553 (655)
.||..+ .+||||.+++++|.+. ..++..|...+
T Consensus 167 ~fl~~lpv~~l~GiG~~~~~kL~~~GI~tigdl~~~~ 203 (379)
T cd01703 167 DFMDLHDLRKIPGIGYKTAAKLEAHGISSVRDLQEFS 203 (379)
T ss_pred HHhccCCccccCCcCHHHHHHHHHcCCCcHHHHHhCC
Confidence 355444 5677777777777663 33555665555
No 412
>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=28.04 E-value=43 Score=26.73 Aligned_cols=11 Identities=36% Similarity=0.851 Sum_probs=6.7
Q ss_pred CCCCCCCccee
Q psy11423 417 ICPICNSKIIY 427 (655)
Q Consensus 417 ~CP~C~~~l~~ 427 (655)
.||.||..+..
T Consensus 4 ~CP~CG~~iev 14 (54)
T TIGR01206 4 ECPDCGAEIEL 14 (54)
T ss_pred CCCCCCCEEec
Confidence 46666666553
No 413
>PRK14190 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=27.95 E-value=1.8e+02 Score=31.04 Aligned_cols=67 Identities=18% Similarity=0.337 Sum_probs=44.4
Q ss_pred CHHHHHHHHHHhcChhHHHHHHHHHHcCcccccCCCCCCCeEecccccCccEEEecCCCC------chHHHHHHcCCee-
Q psy11423 564 GSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNNPNTKGGKVVNFISKNTNYLVKGQKPG------KKLEKAIKLNIKI- 636 (655)
Q Consensus 564 G~~~A~~I~~~f~~~~n~~li~~L~~~Gi~~~~~~~~~G~~v~~sVsk~t~ylv~g~~~g------~K~~kA~~lgi~i- 636 (655)
|..+|+.|.+.+. +.++.|.+.|+. .+.-.+.+|+.+. .|.+.|+++||..
T Consensus 8 Gk~vA~~i~~~l~-----~~v~~l~~~g~~-----------------P~Laii~vg~d~as~~Yv~~k~k~a~~~Gi~~~ 65 (284)
T PRK14190 8 GKEVAKEKREQLK-----EEVVKLKEQGIV-----------------PGLAVILVGDDPASHSYVRGKKKAAEKVGIYSE 65 (284)
T ss_pred HHHHHHHHHHHHH-----HHHHHHHhCCCC-----------------CeEEEEEeCCCHHHHHHHHHHHHHHHHcCCEEE
Confidence 6778888877763 345666544432 2333566787754 6788899999875
Q ss_pred -------eCHHHHHHHHhcccCC
Q psy11423 637 -------LDEKNFVKIVKGFSTE 652 (655)
Q Consensus 637 -------i~e~~f~~~l~~~~~~ 652 (655)
+++++|.+.+..-+.+
T Consensus 66 ~~~l~~~~~~~el~~~I~~lN~D 88 (284)
T PRK14190 66 LYEFPADITEEELLALIDRLNAD 88 (284)
T ss_pred EEECCCCCCHHHHHHHHHHHhCC
Confidence 5688999988654433
No 414
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=27.90 E-value=36 Score=36.10 Aligned_cols=23 Identities=22% Similarity=0.431 Sum_probs=20.8
Q ss_pred CCCCCCCCcceeecCceeEEecC
Q psy11423 416 NICPICNSKIIYIESNLIARCSG 438 (655)
Q Consensus 416 ~~CP~C~~~l~~~~~~~~~~C~n 438 (655)
.+||.||+++...+++....|++
T Consensus 112 RFCg~CG~~~~~~~~g~~~~C~~ 134 (279)
T COG2816 112 RFCGRCGTKTYPREGGWARVCPK 134 (279)
T ss_pred cCCCCCCCcCccccCceeeeCCC
Confidence 48999999999888999999988
No 415
>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=27.60 E-value=1.4e+02 Score=25.76 Aligned_cols=47 Identities=15% Similarity=0.302 Sum_probs=27.4
Q ss_pred hccccCCcHHHHHHHHHHHHHhcccchhHHHHHhCCCCccHHHHHHHHH
Q psy11423 493 LLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELAN 541 (655)
Q Consensus 493 L~~l~GfG~Ksa~nll~~I~~sk~~~l~r~L~algIpgIG~~~Ak~L~~ 541 (655)
|..++|+|++.++.|+++-+...=.++..|+..+. ++.....+.|..
T Consensus 29 l~~Ikglg~~~a~~I~~~R~~g~f~s~~df~~R~~--~i~~~~le~Li~ 75 (90)
T PF14579_consen 29 LSAIKGLGEEVAEKIVEERENGPFKSLEDFIQRLP--KINKRQLEALIK 75 (90)
T ss_dssp GGGSTTS-HHHHHHHHHHHHCSS-SSHHHHHHHS---TS-HHHHHHHHH
T ss_pred HhhcCCCCHHHHHHHHHhHhcCCCCCHHHHHHHHh--cCCHHHHHHHHH
Confidence 66778888888888887765222245667777763 444545454444
No 416
>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=27.29 E-value=82 Score=27.51 Aligned_cols=12 Identities=33% Similarity=0.385 Sum_probs=9.6
Q ss_pred cCCCCCCEEEEE
Q psy11423 377 KNIQIGDTVVVH 388 (655)
Q Consensus 377 ~~i~iGd~V~v~ 388 (655)
..+..||.|.|.
T Consensus 46 ~~l~~Gd~V~v~ 57 (91)
T cd04482 46 RLLIPGDEVTVY 57 (91)
T ss_pred CCCCCCCEEEEE
Confidence 478899988876
No 417
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=26.91 E-value=64 Score=34.32 Aligned_cols=21 Identities=29% Similarity=0.297 Sum_probs=17.1
Q ss_pred HHHHhcCCCCCHHHHHHHHHH
Q psy11423 554 EEQLLNIPKIGSTTVKAFIKF 574 (655)
Q Consensus 554 ~eeL~~i~GIG~~~A~~I~~~ 574 (655)
.++|.+++|||+++|+-|.-|
T Consensus 206 ~~~L~~LpGIGpwTA~~vllr 226 (283)
T PRK10308 206 MKTLQTFPGIGRWTANYFALR 226 (283)
T ss_pred HHHHhcCCCcCHHHHHHHHHH
Confidence 468899999999999887654
No 418
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=26.63 E-value=31 Score=31.12 Aligned_cols=11 Identities=27% Similarity=0.773 Sum_probs=9.4
Q ss_pred CCCCCCCCcce
Q psy11423 416 NICPICNSKII 426 (655)
Q Consensus 416 ~~CP~C~~~l~ 426 (655)
+.||.||+++.
T Consensus 50 t~CP~Cg~~~e 60 (115)
T COG1885 50 TSCPKCGEPFE 60 (115)
T ss_pred ccCCCCCCccc
Confidence 58999999875
No 419
>PRK13844 recombination protein RecR; Provisional
Probab=26.62 E-value=56 Score=33.05 Aligned_cols=23 Identities=22% Similarity=0.442 Sum_probs=19.4
Q ss_pred HHHHhcCCCCCHHHHHHHHHHhc
Q psy11423 554 EEQLLNIPKIGSTTVKAFIKFIN 576 (655)
Q Consensus 554 ~eeL~~i~GIG~~~A~~I~~~f~ 576 (655)
.+.|.++||||++.|+++.-|+=
T Consensus 14 I~~l~~LPGIG~KsA~Rla~~lL 36 (200)
T PRK13844 14 IESLRKLPTIGKKSSQRLALYLL 36 (200)
T ss_pred HHHHHHCCCCCHHHHHHHHHHHH
Confidence 36799999999999999987653
No 420
>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=26.56 E-value=56 Score=27.52 Aligned_cols=20 Identities=20% Similarity=0.672 Sum_probs=12.5
Q ss_pred CCCCCCCcceeecCceeEEecC
Q psy11423 417 ICPICNSKIIYIESNLIARCSG 438 (655)
Q Consensus 417 ~CP~C~~~l~~~~~~~~~~C~n 438 (655)
.||.|+++|.+..+ .++|..
T Consensus 3 ~CP~C~~~L~~~~~--~~~C~~ 22 (70)
T PF07191_consen 3 TCPKCQQELEWQGG--HYHCEA 22 (70)
T ss_dssp B-SSS-SBEEEETT--EEEETT
T ss_pred cCCCCCCccEEeCC--EEECcc
Confidence 69999999887753 445544
No 421
>PRK14170 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=26.41 E-value=1.9e+02 Score=30.83 Aligned_cols=67 Identities=13% Similarity=0.266 Sum_probs=45.4
Q ss_pred CHHHHHHHHHHhcChhHHHHHHHHHHcCcccccCCCCCCCeEecccccCccEEEecCCCC------chHHHHHHcCCee-
Q psy11423 564 GSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNNPNTKGGKVVNFISKNTNYLVKGQKPG------KKLEKAIKLNIKI- 636 (655)
Q Consensus 564 G~~~A~~I~~~f~~~~n~~li~~L~~~Gi~~~~~~~~~G~~v~~sVsk~t~ylv~g~~~g------~K~~kA~~lgi~i- 636 (655)
|..+|+.|.+.+. +.++.|.+.|+. .+.-.+.+|+.+. .|.+.|+++||..
T Consensus 7 Gk~iA~~i~~~ik-----~~i~~l~~~g~~-----------------P~Laii~vg~d~as~~Yv~~k~k~a~~~Gi~~~ 64 (284)
T PRK14170 7 GKKLAKEIQEKVT-----REVAELVKEGKK-----------------PGLAVVLVGDNQASRTYVRNKQKRTEEAGMKSV 64 (284)
T ss_pred hHHHHHHHHHHHH-----HHHHHHHhCCCC-----------------CeEEEEEeCCCHHHHHHHHHHHHHHHHcCCEEE
Confidence 6778888877763 346666554432 2444677787754 6888899999874
Q ss_pred -------eCHHHHHHHHhcccCC
Q psy11423 637 -------LDEKNFVKIVKGFSTE 652 (655)
Q Consensus 637 -------i~e~~f~~~l~~~~~~ 652 (655)
+++++|.+.+..-+.+
T Consensus 65 ~~~l~~~~~~~el~~~I~~lN~D 87 (284)
T PRK14170 65 LIELPENVTEEKLLSVVEELNED 87 (284)
T ss_pred EEECCCCCCHHHHHHHHHHHhCC
Confidence 4688999988654443
No 422
>KOG2093|consensus
Probab=26.37 E-value=48 Score=40.15 Aligned_cols=55 Identities=27% Similarity=0.332 Sum_probs=46.9
Q ss_pred cccccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHHH
Q psy11423 456 SRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK 513 (655)
Q Consensus 456 sk~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~ 513 (655)
+-..=+.||+|-.+-.+|...+ |.+--||-..+...|.+. ||+|.+++|+.+..-
T Consensus 548 ~~~v~~LPGVG~sm~~kL~s~~-i~tCgdLq~~T~~kl~k~--~G~Klgq~i~~~CrG 602 (1016)
T KOG2093|consen 548 QLKVDDLPGVGSSMKSKLVSQF-IQTCGDLQLITLIKLRKV--FGPKLGQKIYRGCRG 602 (1016)
T ss_pred hcccccCCCccHHHHHHHHHhc-cchhHHHHHHHHHHHHhh--hcccHHHHHHHhcCC
Confidence 3345579999999999999998 899999988888888876 999999999987653
No 423
>COG1241 MCM2 Predicted ATPase involved in replication control, Cdc46/Mcm family [DNA replication, recombination, and repair]
Probab=26.34 E-value=76 Score=37.95 Aligned_cols=53 Identities=25% Similarity=0.446 Sum_probs=34.4
Q ss_pred EEEEeeCCCHHHHHhcC-CCCCCEEE----EEecCcccceeecccccCCCCCCccccCCCCCCCCCCcceee
Q psy11423 362 TITRATLHNESEIYRKN-IQIGDTVV----VHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICNSKIIYI 428 (655)
Q Consensus 362 tVsratLhN~~~i~~~~-i~iGd~V~----v~raGdVIP~I~~vv~~~r~~~~~~~~~P~~CP~C~~~l~~~ 428 (655)
.++--++++-..|+++. =++|-.|. |+|+.+|.|++..+.- .||.||..+...
T Consensus 85 ~~~~~~~~~~~~iR~l~s~~igkLV~v~GiV~r~s~v~p~~~~~~~--------------~C~~Cg~~~~~~ 142 (682)
T COG1241 85 HVRFKNLPNRLSIRELRSEHIGKLVSVEGIVTRASEVRPRLKKAVF--------------ECPKCGREVEVE 142 (682)
T ss_pred EEEecCCcCCcChhhCchhhCCcEEEEEEEEEecccccceeEEEEE--------------EcCCCCCEEEEE
Confidence 33444444444666665 45788886 6799999999987753 266666655543
No 424
>COG0389 DinP Nucleotidyltransferase/DNA polymerase involved in DNA repair [DNA replication, recombination, and repair]
Probab=26.30 E-value=63 Score=35.35 Aligned_cols=48 Identities=21% Similarity=0.257 Sum_probs=38.9
Q ss_pred cccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHH
Q psy11423 458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILL 509 (655)
Q Consensus 458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~ 509 (655)
...++.|+|+.+..+|...| |.++.||-..+...|... ||... +.|..
T Consensus 177 pv~~~~GvG~~~~~~l~~~G-i~ti~dl~~~~~~~L~~~--~g~~~-~~l~~ 224 (354)
T COG0389 177 PVLEFWGVGKVTAEKLRRLG-ISTIGDLAETDLDALKKR--FGKLG-ERLYR 224 (354)
T ss_pred ChhhhCCCCHHHHHHHHHcC-ChhHHHHHhcCHHHHHHH--HhHhH-HHHHH
Confidence 57889999999999999999 899999999777777665 77655 55553
No 425
>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=26.12 E-value=87 Score=33.09 Aligned_cols=52 Identities=21% Similarity=0.325 Sum_probs=37.2
Q ss_pred hCCCCccHHHHHHHHHh-CCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHhcC
Q psy11423 526 LGIRHVGETTAKELANY-FKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQ 577 (655)
Q Consensus 526 lgIpgIG~~~Ak~L~~~-fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f~~ 577 (655)
+.+||+|+..+++|... ..+++.|..++.+++..+-+..+..++.|.++++.
T Consensus 151 ~Qlp~i~~~~~~~l~~~~i~~l~~l~~~~~~e~~~ll~~~~~~~~~i~~~~~~ 203 (314)
T PF02889_consen 151 LQLPHIGEESLKKLEKRGIKTLQDLRDLSPEELEELLNRNPPFGKEILEVASR 203 (314)
T ss_dssp GGSTT--HHHHHHHHHTT--SHHHHHHS-HHHHHHHH-S-HHHHHHHHHHHCC
T ss_pred hcCCCCCHHHHHHHhccCCCcHHHHhhCCHHHHHHHHhhhhhhHHHHHHHHHH
Confidence 48999999999999985 36899999999998888766666777777777654
No 426
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=26.04 E-value=38 Score=24.56 Aligned_cols=22 Identities=32% Similarity=0.616 Sum_probs=16.1
Q ss_pred CCCCCCCcceeec-----CceeEEecC
Q psy11423 417 ICPICNSKIIYIE-----SNLIARCSG 438 (655)
Q Consensus 417 ~CP~C~~~l~~~~-----~~~~~~C~n 438 (655)
.||.|++.....+ .+..++|++
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 6999998765432 367888977
No 427
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=25.75 E-value=1.5e+02 Score=28.56 Aligned_cols=76 Identities=16% Similarity=0.199 Sum_probs=41.5
Q ss_pred HHHHHHcCCCCC-hHHHhcCChhhhccccCCcHHHHHHHHHHHHHhcccchhHHHH-HhCCCCccHHHHHHHHHhCCCHH
Q psy11423 470 IEKLVNANIVVT-AVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIY-ALGIRHVGETTAKELANYFKNLE 547 (655)
Q Consensus 470 i~~L~~~g~I~~-i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~sk~~~l~r~L~-algIpgIG~~~Ak~L~~~fgsl~ 547 (655)
+++|-+.|+|.- +..-+.|++ .|++.|.+++.. ...+.+||. .+|++ ...+..-+..+.
T Consensus 45 l~rL~~~GlV~~~~y~gi~LT~--------~G~~~a~~~~r~-----hrlle~fL~~~lg~~---~~~~~~ea~~le--- 105 (154)
T COG1321 45 LKRLERLGLVEYEPYGGVTLTE--------KGREKAKELLRK-----HRLLERFLVDVLGLD---WEEAHEEAEGLE--- 105 (154)
T ss_pred HHHHHHCCCeEEecCCCeEECh--------hhHHHHHHHHHH-----HHHHHHHHHHHhCCC---HHHHHHHHHHHh---
Confidence 455666666653 222222333 677777777643 344567776 46666 445554444432
Q ss_pred HHHhcCHHHHhcCCCCCHHHHHHHHHHhcC
Q psy11423 548 CMFKATEEQLLNIPKIGSTTVKAFIKFINQ 577 (655)
Q Consensus 548 ~l~~as~eeL~~i~GIG~~~A~~I~~~f~~ 577 (655)
..+.+.+++.|.+++..
T Consensus 106 -------------h~~s~~~~~rl~~~l~~ 122 (154)
T COG1321 106 -------------HALSDETAERLDELLGF 122 (154)
T ss_pred -------------hcCCHHHHHHHHHHhCC
Confidence 12456667777776654
No 428
>PRK14180 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=25.73 E-value=2.2e+02 Score=30.35 Aligned_cols=67 Identities=12% Similarity=0.301 Sum_probs=44.3
Q ss_pred CHHHHHHHHHHhcChhHHHHHHHHHHc-CcccccCCCCCCCeEecccccCccEEEecCCCC------chHHHHHHcCCee
Q psy11423 564 GSTTVKAFIKFINQPLHRLLISQLRDV-GIYWLNNPNTKGGKVVNFISKNTNYLVKGQKPG------KKLEKAIKLNIKI 636 (655)
Q Consensus 564 G~~~A~~I~~~f~~~~n~~li~~L~~~-Gi~~~~~~~~~G~~v~~sVsk~t~ylv~g~~~g------~K~~kA~~lgi~i 636 (655)
|..+|+.|.+.+. +.++.|.+. |+ +.+.-.+.+|+.+. +|.+.|+++||..
T Consensus 6 Gk~va~~i~~~lk-----~~v~~~~~~~g~-----------------~P~La~I~vg~d~as~~Yv~~k~k~~~~~Gi~~ 63 (282)
T PRK14180 6 GKSLSKDLKERLA-----TQVQEYKHHTAI-----------------TPKLVAIIVGNDPASKTYVASKEKACAQVGIDS 63 (282)
T ss_pred HHHHHHHHHHHHH-----HHHHHHHhccCC-----------------CCeEEEEEeCCCHHHHHHHHHHHHHHHHcCCEE
Confidence 6778888877763 345555443 32 23444667787654 6788899999874
Q ss_pred --------eCHHHHHHHHhcccCC
Q psy11423 637 --------LDEKNFVKIVKGFSTE 652 (655)
Q Consensus 637 --------i~e~~f~~~l~~~~~~ 652 (655)
+++++|.+.+..-+.+
T Consensus 64 ~~~~l~~~~~~~el~~~I~~lN~D 87 (282)
T PRK14180 64 QVITLPEHTTESELLELIDQLNND 87 (282)
T ss_pred EEEECCCCCCHHHHHHHHHHHhCC
Confidence 4578999988654433
No 429
>PRK05179 rpsM 30S ribosomal protein S13; Validated
Probab=25.34 E-value=99 Score=28.80 Aligned_cols=37 Identities=30% Similarity=0.251 Sum_probs=24.5
Q ss_pred HHHh-CCCCccHHHHHHHHHhCC-C-HHHHHhcCHHHHhc
Q psy11423 523 IYAL-GIRHVGETTAKELANYFK-N-LECMFKATEEQLLN 559 (655)
Q Consensus 523 L~al-gIpgIG~~~Ak~L~~~fg-s-l~~l~~as~eeL~~ 559 (655)
..|| .|.|||...|..|++.+| + -..+...+.+++.+
T Consensus 16 ~~aL~~I~GIG~~~a~~i~~~lgi~~~~~~~~L~~~qi~~ 55 (122)
T PRK05179 16 VIALTYIYGIGRTRAKEILAAAGIDPDTRVKDLTDEELDK 55 (122)
T ss_pred EeeecccccccHHHHHHHHHHhCcCcccccccCCHHHHHH
Confidence 3455 799999999999999877 1 12334445555443
No 430
>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=25.14 E-value=35 Score=23.04 Aligned_cols=9 Identities=33% Similarity=1.224 Sum_probs=6.0
Q ss_pred CCCCCCCcc
Q psy11423 417 ICPICNSKI 425 (655)
Q Consensus 417 ~CP~C~~~l 425 (655)
.||.|+..+
T Consensus 2 ~CP~C~~~V 10 (26)
T PF10571_consen 2 TCPECGAEV 10 (26)
T ss_pred cCCCCcCCc
Confidence 577777654
No 431
>PRK14174 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=24.92 E-value=2.3e+02 Score=30.41 Aligned_cols=67 Identities=12% Similarity=0.286 Sum_probs=45.2
Q ss_pred CHHHHHHHHHHhcChhHHHHHHHHHHc-CcccccCCCCCCCeEecccccCccEEEecCCCC------chHHHHHHcCCee
Q psy11423 564 GSTTVKAFIKFINQPLHRLLISQLRDV-GIYWLNNPNTKGGKVVNFISKNTNYLVKGQKPG------KKLEKAIKLNIKI 636 (655)
Q Consensus 564 G~~~A~~I~~~f~~~~n~~li~~L~~~-Gi~~~~~~~~~G~~v~~sVsk~t~ylv~g~~~g------~K~~kA~~lgi~i 636 (655)
|..+|+.|.+.+. +.++.|.+. |+ +.+.-.+.+|+.+. .|.+.|+++||..
T Consensus 6 Gk~iA~~i~~~i~-----~~v~~l~~~~g~-----------------~P~Laii~vg~d~as~~Yv~~k~k~~~~~Gi~~ 63 (295)
T PRK14174 6 GKKVSLDLKNELK-----TRVEAYRAKTGK-----------------VPGLTVIIVGEDPASQVYVRNKAKSCKEIGMNS 63 (295)
T ss_pred HHHHHHHHHHHHH-----HHHHHHHHccCC-----------------CCeEEEEEeCCChHHHHHHHHHHHHHHHcCCEE
Confidence 6778888877763 345556543 22 23455677787754 6778899999874
Q ss_pred --------eCHHHHHHHHhcccCC
Q psy11423 637 --------LDEKNFVKIVKGFSTE 652 (655)
Q Consensus 637 --------i~e~~f~~~l~~~~~~ 652 (655)
+++++|.+.+..-+.+
T Consensus 64 ~~~~l~~~~~~~el~~~I~~lN~D 87 (295)
T PRK14174 64 TVIELPADTTEEHLLKKIEDLNND 87 (295)
T ss_pred EEEECCCCCCHHHHHHHHHHHhCC
Confidence 4688999988655544
No 432
>PF00416 Ribosomal_S13: Ribosomal protein S13/S18; InterPro: IPR001892 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 [, ]. Ribosomal protein S13 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S13 is known to be involved in binding fMet-tRNA and, hence, in the initiation of translation. It is a basic protein of 115 to 177 amino-acid residues that contains thee helices and a beta-hairpin in the core of the protein, forming a helix-two turns-helix (H2TH) motif, and a non-globular C-terminal extension. This family of ribosomal proteins is present in prokaryotes, eukaryotes and archaea [, ].; GO: 0003723 RNA binding, 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3BBN_M 2QBB_M 3I1M_M 3OFP_M 3OFX_M 3OFO_M 1VS5_M 3OAQ_M 2QAL_M 3J18_M ....
Probab=24.88 E-value=99 Score=27.89 Aligned_cols=24 Identities=25% Similarity=0.349 Sum_probs=20.1
Q ss_pred HHHHHh-CCCCccHHHHHHHHHhCC
Q psy11423 521 RFIYAL-GIRHVGETTAKELANYFK 544 (655)
Q Consensus 521 r~L~al-gIpgIG~~~Ak~L~~~fg 544 (655)
.+..|| .|.|||...|..|++.++
T Consensus 12 ~i~~aLt~IyGIG~~~A~~Ic~~lg 36 (107)
T PF00416_consen 12 PIYIALTKIYGIGRRKAKQICKKLG 36 (107)
T ss_dssp BHHHHHTTSTTBCHHHHHHHHHHTT
T ss_pred chHhHHhhhhccCHHHHHHHHHHcC
Confidence 355566 899999999999999877
No 433
>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=24.54 E-value=26 Score=27.68 Aligned_cols=30 Identities=30% Similarity=0.639 Sum_probs=15.4
Q ss_pred cCCCCCCCCCCcceeecCceeEEecCCCcCCHHHHHhhcccccc
Q psy11423 413 KIPNICPICNSKIIYIESNLIARCSGSWIECIAQRKAGLQHFSS 456 (655)
Q Consensus 413 ~~P~~CP~C~~~l~~~~~~~~~~C~n~~~~C~~q~~~~i~~F~s 456 (655)
.-|..||.|+..+ .- + |.-+..-.|.||..
T Consensus 22 ~~PatCP~C~a~~-----------~~--s-rnLrRHle~~H~~k 51 (54)
T PF09237_consen 22 EQPATCPICGAVI-----------RQ--S-RNLRRHLEIRHFKK 51 (54)
T ss_dssp S--EE-TTT--EE-----------SS--H-HHHHHHHHHHTTTS
T ss_pred CCCCCCCcchhhc-----------cc--h-hhHHHHHHHHhccc
Confidence 3577899998532 22 2 44555666888863
No 434
>COG0551 TopA Zn-finger domain associated with topoisomerase type I [DNA replication, recombination, and repair]
Probab=24.52 E-value=63 Score=30.36 Aligned_cols=29 Identities=24% Similarity=0.518 Sum_probs=23.1
Q ss_pred CCCCCCCCcceeecC--ceeEEecCCCcCCHH
Q psy11423 416 NICPICNSKIIYIES--NLIARCSGSWIECIA 445 (655)
Q Consensus 416 ~~CP~C~~~l~~~~~--~~~~~C~n~~~~C~~ 445 (655)
..||.||..++...+ +..+-|.|.+. |..
T Consensus 18 ~~Cp~Cg~~m~~~~~~~g~f~gCs~yP~-C~~ 48 (140)
T COG0551 18 QICPKCGKNMVKKFGKYGIFLGCSNYPK-CDY 48 (140)
T ss_pred ccCCcCCCeeEEEEccCCeEEEeCCCCC-CCC
Confidence 479999999885433 38999999876 975
No 435
>PRK04053 rps13p 30S ribosomal protein S13P; Reviewed
Probab=24.41 E-value=73 Score=30.76 Aligned_cols=24 Identities=38% Similarity=0.617 Sum_probs=19.1
Q ss_pred HHHHHh-CCCCccHHHHHHHHHhCC
Q psy11423 521 RFIYAL-GIRHVGETTAKELANYFK 544 (655)
Q Consensus 521 r~L~al-gIpgIG~~~Ak~L~~~fg 544 (655)
++..|| .|-|||...|..|++..+
T Consensus 22 ~i~~aLt~IyGIG~~~a~~Ic~~lg 46 (149)
T PRK04053 22 PVEYALTGIKGIGRRTARAIARKLG 46 (149)
T ss_pred EEeeeccccccccHHHHHHHHHHcC
Confidence 344555 799999999999999877
No 436
>COG1430 Uncharacterized conserved protein [Function unknown]
Probab=24.39 E-value=3.4e+02 Score=25.49 Aligned_cols=93 Identities=15% Similarity=0.119 Sum_probs=64.8
Q ss_pred EEEECChhhhhhhCC---CCCCCCceEeecCCcceeeE-------EEEEEEEeecCcceeeeEEEEEEEEECC----EEE
Q psy11423 298 VYKINCLSTQKKLGF---TSRAPRFALAYKFLSKEALT-------KIKAINIQIGRTGIITPVALLKPVLIDG----ITI 363 (655)
Q Consensus 298 Vikv~~~~~~~~lG~---ts~~PrwaiA~Kf~~~~~~T-------~v~~I~~qvGRTG~itPvA~lePV~l~G----~tV 363 (655)
++.+-+...++..|. ++-.|..++=|.|+..+... --+||.|= +-.|+|+-+..++|=...- ..+
T Consensus 17 ~vevA~t~~~r~~GLMfR~sl~~d~GMLFv~~~~~~~~~wMknt~lpLDiiFi-d~dg~i~~i~~~~P~~~~~~~~~~~~ 95 (126)
T COG1430 17 AVEVADTFAKRARGLMFRTSLPDDHGMLFVFPETRRVAFWMKNTMLPLDIIFI-DSDGRVVDIVELVPWSTYPCKSYGPV 95 (126)
T ss_pred EEEEeCCHHHHhccccccccCCCCceEEEecCCCceeEEeeecCCcceEEEEE-cCCCCEEEEEeccccccCCCCCCCCc
Confidence 567888888888995 44489999999999433222 23666664 3378888888877754432 122
Q ss_pred EEeeCCCHHHHHhcCCCCCCEEEEEecC
Q psy11423 364 TRATLHNESEIYRKNIQIGDTVVVHRSG 391 (655)
Q Consensus 364 sratLhN~~~i~~~~i~iGd~V~v~raG 391 (655)
..|==-|.+..+++||.+||+|.+...+
T Consensus 96 ~yvLEl~~G~~~~~~i~vGd~v~~~~~~ 123 (126)
T COG1430 96 RYVLELPAGWAARLGIKVGDRVEFRPLG 123 (126)
T ss_pred cEEEEecCCchhhcCCccCCEEEecccC
Confidence 3444456788999999999999987654
No 437
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=24.15 E-value=61 Score=34.33 Aligned_cols=172 Identities=17% Similarity=0.349 Sum_probs=86.5
Q ss_pred CCCCCCCCCCcceeecCc-eeEEecCCCcCCHHHHHhhccccccccccccCCCCHHHHHHHHHcCCCCChHHHhc-CChh
Q psy11423 414 IPNICPICNSKIIYIESN-LIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYK-INFK 491 (655)
Q Consensus 414 ~P~~CP~C~~~l~~~~~~-~~~~C~n~~~~C~~q~~~~i~~F~sk~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~-L~~~ 491 (655)
+=+.||+|+.-+.+.+=+ ....|++ | -|+.- |.- ..+++.|.|+| +..+|.. +...
T Consensus 27 lw~KCp~c~~~~y~~eL~~n~~vcp~----c--------~~h~r-----i~A--~~Ri~~llD~g---sf~el~~~l~~~ 84 (294)
T COG0777 27 LWTKCPSCGEMLYRKELESNLKVCPK----C--------GHHMR-----ISA--RERLEALLDEG---SFEELDSPLEPK 84 (294)
T ss_pred ceeECCCccceeeHHHHHhhhhcccc----c--------Ccccc-----cCH--HHHHHHhhCCC---cceecccCCCcC
Confidence 346899999877654422 3556665 5 33332 221 56888999988 4445665 5555
Q ss_pred hhccccCCcHHHHHHHHHHHHHhcccc--------h---hHHHHHhCCC----CccHHHHHHHHHhCCCHHHHHhcCHHH
Q psy11423 492 NLLRLDRVSNKLANNILLAIQKSKLTT--------F---SRFIYALGIR----HVGETTAKELANYFKNLECMFKATEEQ 556 (655)
Q Consensus 492 ~L~~l~GfG~Ksa~nll~~I~~sk~~~--------l---~r~L~algIp----gIG~~~Ak~L~~~fgsl~~l~~as~ee 556 (655)
|-+..+ =.++-.++|-++-++....+ + .-.+.++... -.|....++|...+ ..|..+
T Consensus 85 dPL~F~-d~k~Y~~rL~~a~~~tg~~davvtg~g~i~G~pvv~av~df~FmgGSmGsVvGeki~ra~------E~A~e~- 156 (294)
T COG0777 85 DPLKFP-DSKKYKDRLEAARKKTGLDDAVVTGEGTINGLPVVLAVMDFAFMGGSMGSVVGEKITRAI------ERAIED- 156 (294)
T ss_pred CcccCC-cchhhHHHHHHHHhhcCCCcceEEEeeEECCeEEEEEEEeccccccchhHHHHHHHHHHH------HHHHHh-
Confidence 555542 22345555544433321110 0 0011111111 12333333333332 111111
Q ss_pred HhcCCCC------CHHHHHHHHHHhcChhHHHHHHHHHHcCcccccC--CCCCCCeEecccccCccEEEe
Q psy11423 557 LLNIPKI------GSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNN--PNTKGGKVVNFISKNTNYLVK 618 (655)
Q Consensus 557 L~~i~GI------G~~~A~~I~~~f~~~~n~~li~~L~~~Gi~~~~~--~~~~G~~v~~sVsk~t~ylv~ 618 (655)
++|-| |..+-+.+..+.+-......+++|.+.|+.+-.. ....|| |+.|.-.--|+.|+
T Consensus 157 --k~P~v~f~aSGGARMQEg~lSLMQMaktsaAl~~l~ea~lpyIsVLt~PTtGG-VsASfA~lGDi~iA 223 (294)
T COG0777 157 --KLPLVLFSASGGARMQEGILSLMQMAKTSAALKRLSEAGLPYISVLTDPTTGG-VSASFAMLGDIIIA 223 (294)
T ss_pred --CCCEEEEecCcchhHhHHHHHHHHHHHHHHHHHHHHhcCCceEEEecCCCccc-hhHhHHhccCeeec
Confidence 12222 6677778888888777778899999988754211 135555 33333334444444
No 438
>PF14066 DUF4256: Protein of unknown function (DUF4256)
Probab=23.89 E-value=66 Score=31.30 Aligned_cols=32 Identities=19% Similarity=0.298 Sum_probs=25.9
Q ss_pred CchHHHHHHcCCeeeCHHHHHHHHhcccCCCC
Q psy11423 623 GKKLEKAIKLNIKILDEKNFVKIVKGFSTETK 654 (655)
Q Consensus 623 g~K~~kA~~lgi~ii~e~~f~~~l~~~~~~~~ 654 (655)
++-++-|.++||++++|+++..|-....-|+|
T Consensus 93 ~sa~d~a~~mGieLLtEeqYr~LQ~lg~FD~K 124 (173)
T PF14066_consen 93 NSAVDMAAEMGIELLTEEQYRELQKLGEFDLK 124 (173)
T ss_pred ccHHHHHHHhhhHhcCHHHHHHHHHhCCCccc
Confidence 47778899999999999999998765555554
No 439
>PRK03348 DNA polymerase IV; Provisional
Probab=23.84 E-value=1.4e+02 Score=33.86 Aligned_cols=53 Identities=17% Similarity=0.340 Sum_probs=37.3
Q ss_pred hHHHHHh---CCCCccHHHHHHHHHh-CCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHH
Q psy11423 520 SRFIYAL---GIRHVGETTAKELANY-FKNLECMFKATEEQLLNIPKIGSTTVKAFIKF 574 (655)
Q Consensus 520 ~r~L~al---gIpgIG~~~Ak~L~~~-fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~ 574 (655)
.++|..| .+||||++++++|.+. +.++..|..++.++|.+. +|...+..+...
T Consensus 174 ~~~L~~LPv~~L~GIG~~t~~~L~~lGI~TigDLa~l~~~~L~~~--fG~~~g~~L~~~ 230 (454)
T PRK03348 174 RELLAPLPVRRLWGIGPVTEEKLHRLGIETIGDLAALSEAEVANL--LGATVGPALHRL 230 (454)
T ss_pred HHHHHhCCccccCCCCHHHHHHHHHcCCccHHHHhcCCHHHHHHH--HCHHHHHHHHHH
Confidence 4567666 5688888888887653 557888888888888776 565566666554
No 440
>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=23.79 E-value=41 Score=29.67 Aligned_cols=24 Identities=21% Similarity=0.491 Sum_probs=18.0
Q ss_pred CCCCCCCCCcceeecCceeEEecC
Q psy11423 415 PNICPICNSKIIYIESNLIARCSG 438 (655)
Q Consensus 415 P~~CP~C~~~l~~~~~~~~~~C~n 438 (655)
.-.||.||..-+....-..|.|..
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 457999999887665556799965
No 441
>TIGR02609 doc_partner putative addiction module antidote. Members of this protein family are putative addiction module antidote proteins that appear recurringly in two-gene operons with members of the Doc (death-on-curing) family TIGR01550. Members of this family contain a SpoVT/AbrB-like domain (pfam04014). Note that the gene pairs with a member of this family tend to be found on bacterial chromosomes, not on plasmids.
Probab=23.74 E-value=80 Score=26.54 Aligned_cols=23 Identities=17% Similarity=0.212 Sum_probs=19.7
Q ss_pred HHHHHhcCCCCCCEEEEEecCcc
Q psy11423 371 ESEIYRKNIQIGDTVVVHRSGNV 393 (655)
Q Consensus 371 ~~~i~~~~i~iGd~V~v~raGdV 393 (655)
.+.++++||.+||.|.|...|+-
T Consensus 16 k~i~~~lgl~~Gd~v~v~~~~~~ 38 (74)
T TIGR02609 16 KEVLESLGLKEGDTLYVDEEEGG 38 (74)
T ss_pred HHHHHHcCcCCCCEEEEEEECCE
Confidence 56789999999999999987763
No 442
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=23.72 E-value=39 Score=33.89 Aligned_cols=22 Identities=32% Similarity=0.732 Sum_probs=14.7
Q ss_pred CCCCCCCc-----ceee-cCceeEEecC
Q psy11423 417 ICPICNSK-----IIYI-ESNLIARCSG 438 (655)
Q Consensus 417 ~CP~C~~~-----l~~~-~~~~~~~C~n 438 (655)
.||+||++ +.+. ..+..++|.|
T Consensus 8 ~Cp~Cg~eev~hEVik~~g~~~lvrC~e 35 (201)
T COG1326 8 ECPSCGSEEVSHEVIKERGREPLVRCEE 35 (201)
T ss_pred ECCCCCcchhhHHHHHhcCCceEEEccC
Confidence 69999942 2232 3457899987
No 443
>PRK09612 rpl2p 50S ribosomal protein L2P; Validated
Probab=23.52 E-value=76 Score=32.98 Aligned_cols=93 Identities=20% Similarity=0.263 Sum_probs=57.5
Q ss_pred eeEEEEEEEEeecCcceeeeEEEEEEEEECCEEEEEeeCCCHHHHHhcCCCCCCEEEEEecCcccceeecccccCCCCCC
Q psy11423 330 ALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDS 409 (655)
Q Consensus 330 ~~T~v~~I~~qvGRTG~itPvA~lePV~l~G~tVsratLhN~~~i~~~~i~iGd~V~v~raGdVIP~I~~vv~~~r~~~~ 409 (655)
...+|.+|+..-+|| .|+|.+. .-+|.. + =.|.-.++.+||.|.. |.-.| ..+++.
T Consensus 39 ~~g~V~~IeyDPnRs---a~IAlv~--~~~g~~-~-------YIiAp~gl~~Gd~I~s---g~~~~--------i~~Gn~ 94 (238)
T PRK09612 39 LRGKVVDILHDPGRN---APVAKVK--FENGEE-F-------LILAPEGLYVGQEIEI---GPSAE--------IKPGNT 94 (238)
T ss_pred eeEEEEEEEECCCCC---CeEEEEE--eCCCCE-E-------EEEccCCCCCCCEEEe---CCCCC--------CCCccc
Confidence 468999999999999 4555554 234432 1 1245569999999996 32211 123444
Q ss_pred ccc-cCCCCCCCCCCcceeecCceeEEecCCCcCCHHHHHhh
Q psy11423 410 KIF-KIPNICPICNSKIIYIESNLIARCSGSWIECIAQRKAG 450 (655)
Q Consensus 410 ~~~-~~P~~CP~C~~~l~~~~~~~~~~C~n~~~~C~~q~~~~ 450 (655)
.++ .+|.-+..|+-++.--+++. +|-.. . |-++++.+
T Consensus 95 lpL~~IP~Gt~I~NIE~~pG~Ggk--l~RSA-G-t~A~Ii~k 132 (238)
T PRK09612 95 LPLGEIPEGTPVCNIESRPGDGGK--FARSS-G-TYALVVGH 132 (238)
T ss_pred cCHhhCCCCCEEEEEEecCCCCcc--eEEcC-C-CeEEEEEe
Confidence 443 57888888887766444444 44442 2 76777664
No 444
>PF11372 DUF3173: Domain of unknown function (DUF3173); InterPro: IPR021512 This family of proteins with unknown function appears to be restricted to Firmicutes.
Probab=23.51 E-value=66 Score=26.19 Aligned_cols=23 Identities=26% Similarity=0.384 Sum_probs=20.0
Q ss_pred CChhhhccccCCcHHHHHHHHHHH
Q psy11423 488 INFKNLLRLDRVSNKLANNILLAI 511 (655)
Q Consensus 488 L~~~~L~~l~GfG~Ksa~nll~~I 511 (655)
.+.+||.+| ||++-+|.+|+.+-
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 99999999998764
No 445
>PF14164 YqzH: YqzH-like protein
Probab=23.49 E-value=2.3e+02 Score=23.52 Aligned_cols=40 Identities=18% Similarity=0.308 Sum_probs=29.6
Q ss_pred HHHHHHHHHHHh-hcCCCCCCChHHHHHHHHHHHHHHHhCC
Q psy11423 21 LKKELHRHNIAY-YLYDNPIISDNKYDQLLFELKKIEEKYP 60 (655)
Q Consensus 21 L~~~l~~~~~~Y-y~~~~p~isD~~YD~L~~~L~~le~~~p 60 (655)
+.+.|.+.=++| |+.....+|+.|+-.|.+.+..--...|
T Consensus 6 I~Kmi~~~l~QYg~d~~~~pls~~E~~~L~~~i~~~~~~~~ 46 (64)
T PF14164_consen 6 IEKMIINCLRQYGYDVECMPLSDEEWEELCKHIQERKNEEP 46 (64)
T ss_pred HHHHHHHHHHHhCCcccCCCCCHHHHHHHHHHHHHHHhcCC
Confidence 344555555566 6667889999999999999987665554
No 446
>PRK03858 DNA polymerase IV; Validated
Probab=23.48 E-value=1.3e+02 Score=33.12 Aligned_cols=34 Identities=21% Similarity=0.264 Sum_probs=18.6
Q ss_pred CCCCccHHHHHHHHHh-CCCHHHHHhcCHHHHhcC
Q psy11423 527 GIRHVGETTAKELANY-FKNLECMFKATEEQLLNI 560 (655)
Q Consensus 527 gIpgIG~~~Ak~L~~~-fgsl~~l~~as~eeL~~i 560 (655)
.+||||++++++|.+. +.++..|...+.+.|.+.
T Consensus 177 ~l~Gig~~~~~~L~~~Gi~t~~dl~~l~~~~L~~~ 211 (396)
T PRK03858 177 RLWGVGPVTAAKLRAHGITTVGDVAELPESALVSL 211 (396)
T ss_pred hcCCCCHHHHHHHHHhCCCcHHHHhcCCHHHHHHH
Confidence 3456666666665442 345555555555555554
No 447
>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=23.38 E-value=1.2e+02 Score=33.69 Aligned_cols=14 Identities=29% Similarity=0.294 Sum_probs=6.3
Q ss_pred hccccCCcHHHHHH
Q psy11423 493 LLRLDRVSNKLANN 506 (655)
Q Consensus 493 L~~l~GfG~Ksa~n 506 (655)
+..|+|+|.+++++
T Consensus 224 v~~l~GIG~~~~~~ 237 (404)
T cd01701 224 VGDLPGVGSSLAEK 237 (404)
T ss_pred HhHhCCCCHHHHHH
Confidence 34444555444433
No 448
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=23.33 E-value=54 Score=30.15 Aligned_cols=80 Identities=16% Similarity=0.211 Sum_probs=43.2
Q ss_pred ceeeEEEEEEEEeecCcceeeeEEEEEEEEECCEEEEEeeCCCHHHHHhcC-CCCCCEEEEEecCcccceeecccccCCC
Q psy11423 328 KEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYRKN-IQIGDTVVVHRSGNVIPKITSSILSLRP 406 (655)
Q Consensus 328 ~~~~T~v~~I~~qvGRTG~itPvA~lePV~l~G~tVsratLhN~~~i~~~~-i~iGd~V~v~raGdVIP~I~~vv~~~r~ 406 (655)
....++|+.|.+.||+- +|+.-.... +=++.+.+-- +-.|+++.|.+ +|-.. .-...
T Consensus 20 ~~~~~~V~~V~l~IG~l--------------s~V~pe~L~-faf~~~~~~T~~~ega~L~Ie~----vp~~~---~C~~C 77 (117)
T PRK00564 20 KNQAHKIEKVVVGIGER--------------SGMDKSLFV-SAFETFREESLVCKDAILDIVD----EKVEL---ECKDC 77 (117)
T ss_pred HcCCCeEEEEEEEEccc--------------cCcCHHHHH-HHHHHHhcCCcccCCCEEEEEe----cCCEE---EhhhC
Confidence 33456899999999963 222211111 1245566666 78899998875 33222 22223
Q ss_pred CCCccccCC---C-CCCCCCCcceeecCc
Q psy11423 407 NDSKIFKIP---N-ICPICNSKIIYIESN 431 (655)
Q Consensus 407 ~~~~~~~~P---~-~CP~C~~~l~~~~~~ 431 (655)
+. .|.++ . .||.||++-....+|
T Consensus 78 g~--~~~~~~~~~~~CP~Cgs~~~~i~~G 104 (117)
T PRK00564 78 SH--VFKPNALDYGVCEKCHSKNVIITQG 104 (117)
T ss_pred CC--ccccCCccCCcCcCCCCCceEEecC
Confidence 32 22222 1 399999875543333
No 449
>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=23.26 E-value=39 Score=37.02 Aligned_cols=38 Identities=21% Similarity=0.139 Sum_probs=22.8
Q ss_pred CHHHHHHHHHhCCCCCCCCceeeCCHHHHHHHHHHHHH
Q psy11423 248 SHSELLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINI 285 (655)
Q Consensus 248 ~~~e~l~~L~~~GF~~~~~~~~~~~~~ev~~~~~~~~~ 285 (655)
+-.+.++.|.++||.-.--+...++.....+.|+.+.+
T Consensus 161 sA~~~~~~le~~~f~~iviSlKsSdv~~~i~ayr~la~ 198 (359)
T PF04551_consen 161 SALEHVRILEELGFDDIVISLKSSDVPETIEAYRLLAE 198 (359)
T ss_dssp HHHHHHHHHHHCT-GGEEEEEEBSSHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHCCCCcEEEEEEeCChHHHHHHHHHHHH
Confidence 44567778888888543333345677776666666643
No 450
>PRK14183 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=22.90 E-value=2.6e+02 Score=29.81 Aligned_cols=66 Identities=12% Similarity=0.228 Sum_probs=44.0
Q ss_pred CHHHHHHHHHHhcChhHHHHHHHHHH-cCcccccCCCCCCCeEecccccCccEEEecCCCC------chHHHHHHcCCee
Q psy11423 564 GSTTVKAFIKFINQPLHRLLISQLRD-VGIYWLNNPNTKGGKVVNFISKNTNYLVKGQKPG------KKLEKAIKLNIKI 636 (655)
Q Consensus 564 G~~~A~~I~~~f~~~~n~~li~~L~~-~Gi~~~~~~~~~G~~v~~sVsk~t~ylv~g~~~g------~K~~kA~~lgi~i 636 (655)
|..+|+.|.+.+. +.++.|.+ .|+ +.+.-.+.+|+.+. .|.+.|+++||..
T Consensus 6 Gk~iA~~i~~~l~-----~~v~~l~~~~g~-----------------~P~Laii~vgdd~as~~Yv~~k~k~a~~~Gi~~ 63 (281)
T PRK14183 6 GKALSDKIKENVK-----KEVDELKLVKNI-----------------VPGLAVILVGDDPASHTYVKMKAKACDRVGIYS 63 (281)
T ss_pred hHHHHHHHHHHHH-----HHHHHHHhcCCC-----------------CCeEEEEEeCCCHHHHHHHHHHHHHHHHcCCEE
Confidence 6778888877763 34555543 232 23445667787754 6778899999874
Q ss_pred --------eCHHHHHHHHhcccC
Q psy11423 637 --------LDEKNFVKIVKGFST 651 (655)
Q Consensus 637 --------i~e~~f~~~l~~~~~ 651 (655)
++++++.+.+..-+.
T Consensus 64 ~~~~l~~~~~~~~l~~~I~~lN~ 86 (281)
T PRK14183 64 ITHEMPSTISQKEILETIAMMNN 86 (281)
T ss_pred EEEECCCCCCHHHHHHHHHHHhC
Confidence 478899998864443
No 451
>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=22.88 E-value=53 Score=23.89 Aligned_cols=18 Identities=17% Similarity=0.556 Sum_probs=13.1
Q ss_pred ccCCCCCCCCCCcceeec
Q psy11423 412 FKIPNICPICNSKIIYIE 429 (655)
Q Consensus 412 ~~~P~~CP~C~~~l~~~~ 429 (655)
...+..|..||++|++..
T Consensus 18 P~~~~~Cd~cg~~L~qR~ 35 (36)
T PF05191_consen 18 PKVEGVCDNCGGELVQRK 35 (36)
T ss_dssp -SSTTBCTTTTEBEBEEG
T ss_pred CCCCCccCCCCCeeEeCC
Confidence 345679999999988653
No 452
>PRK07726 DNA topoisomerase III; Provisional
Probab=22.75 E-value=50 Score=39.32 Aligned_cols=27 Identities=19% Similarity=0.470 Sum_probs=19.2
Q ss_pred CCCCCCCCccee--ecCceeEEecCCCcCCH
Q psy11423 416 NICPICNSKIIY--IESNLIARCSGSWIECI 444 (655)
Q Consensus 416 ~~CP~C~~~l~~--~~~~~~~~C~n~~~~C~ 444 (655)
..||.||..++. ...+..+.|+|. . |.
T Consensus 611 ~~CP~C~~~~~~~~~~~~~f~~Cs~~-~-~~ 639 (658)
T PRK07726 611 PKCPDCGKPMLKVKGKNGKMLVCQDR-E-CG 639 (658)
T ss_pred ccccccCccceeecccCCeeEecCCC-c-cc
Confidence 469999998763 234567999995 4 53
No 453
>PRK14724 DNA topoisomerase III; Provisional
Probab=22.68 E-value=1e+02 Score=38.60 Aligned_cols=52 Identities=17% Similarity=0.322 Sum_probs=34.2
Q ss_pred CCCCCCCcceeecCceeEEecCC-C-------cCCHHHHHhhccccccccccccCCCCHHHHHHHHHcCCCC
Q psy11423 417 ICPICNSKIIYIESNLIARCSGS-W-------IECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVV 480 (655)
Q Consensus 417 ~CP~C~~~l~~~~~~~~~~C~n~-~-------~~C~~q~~~~i~~F~sk~~l~I~GLG~k~i~~L~~~g~I~ 480 (655)
.||.||+.+. +.+..+.|.|. . . |.-..-+ .+++| + +..+.+.+|+..|-..
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 35678999983 1 4 8543211 12232 2 5888999999887643
No 454
>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=22.62 E-value=73 Score=26.51 Aligned_cols=15 Identities=27% Similarity=0.390 Sum_probs=12.0
Q ss_pred HHhcCCCCCCEEEEE
Q psy11423 374 IYRKNIQIGDTVVVH 388 (655)
Q Consensus 374 i~~~~i~iGd~V~v~ 388 (655)
++++|+..||+|.|.
T Consensus 49 L~~~G~~~GD~V~Ig 63 (69)
T TIGR03595 49 LRKAGAKDGDTVRIG 63 (69)
T ss_pred HHHcCCCCCCEEEEc
Confidence 467899999999874
No 455
>PRK12278 50S ribosomal protein L21/unknown domain fusion protein; Provisional
Probab=22.58 E-value=75 Score=32.66 Aligned_cols=40 Identities=23% Similarity=0.382 Sum_probs=33.2
Q ss_pred ccccccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhcccc
Q psy11423 457 RKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLD 497 (655)
Q Consensus 457 k~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~ 497 (655)
-+.-.|+|+||+...+|.+.| |.+.++|=.++.+++..++
T Consensus 158 DDL~~I~GIGp~~a~~L~eaG-i~tfaQIAa~t~a~ia~id 197 (221)
T PRK12278 158 DDLTKITGVGPALAKKLNEAG-VTTFAQIAALTDADIAKID 197 (221)
T ss_pred chheeccccChHHHHHHHHcC-CCCHHHhhCCChhhhhhhh
Confidence 355679999999999999999 5899999888887766554
No 456
>PRK14176 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=22.36 E-value=3e+02 Score=29.43 Aligned_cols=67 Identities=13% Similarity=0.316 Sum_probs=44.9
Q ss_pred CHHHHHHHHHHhcChhHHHHHHHHHHc-CcccccCCCCCCCeEecccccCccEEEecCCCC------chHHHHHHcCCee
Q psy11423 564 GSTTVKAFIKFINQPLHRLLISQLRDV-GIYWLNNPNTKGGKVVNFISKNTNYLVKGQKPG------KKLEKAIKLNIKI 636 (655)
Q Consensus 564 G~~~A~~I~~~f~~~~n~~li~~L~~~-Gi~~~~~~~~~G~~v~~sVsk~t~ylv~g~~~g------~K~~kA~~lgi~i 636 (655)
|..+|+.|.+.+. +.++.|.+. |+ +.+.-.+.+|+.+. .|.+.|+++||..
T Consensus 13 Gk~iA~~i~~~l~-----~~i~~l~~~~g~-----------------~P~Laii~vg~d~aS~~Yv~~k~k~~~~~Gi~~ 70 (287)
T PRK14176 13 GKALAKKIEAEVR-----SGVERLKSNRGI-----------------TPGLATILVGDDPASKMYVRLKHKACERVGIRA 70 (287)
T ss_pred hHHHHHHHHHHHH-----HHHHHHHhccCC-----------------CCeEEEEEECCCcchHHHHHHHHHHHHHcCCEE
Confidence 7788888887663 345555443 22 23455677887754 6777899999863
Q ss_pred --------eCHHHHHHHHhcccCC
Q psy11423 637 --------LDEKNFVKIVKGFSTE 652 (655)
Q Consensus 637 --------i~e~~f~~~l~~~~~~ 652 (655)
+++++|.+.+..-+.+
T Consensus 71 ~~~~l~~~~~~~el~~~I~~LN~D 94 (287)
T PRK14176 71 EDQFLPADTTQEELLELIDSLNKR 94 (287)
T ss_pred EEEECCCCCCHHHHHHHHHHHhCC
Confidence 4688999988654443
No 457
>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=22.30 E-value=59 Score=24.64 Aligned_cols=22 Identities=27% Similarity=0.632 Sum_probs=14.0
Q ss_pred CCCCCCCcce-eecCceeEEecC
Q psy11423 417 ICPICNSKII-YIESNLIARCSG 438 (655)
Q Consensus 417 ~CP~C~~~l~-~~~~~~~~~C~n 438 (655)
.||.||+.-. ...+...+.|.+
T Consensus 20 ~CP~Cg~~~~~~~~~~~~~~C~~ 42 (46)
T PF12760_consen 20 VCPHCGSTKHYRLKTRGRYRCKA 42 (46)
T ss_pred CCCCCCCeeeEEeCCCCeEECCC
Confidence 5999999522 333446677754
No 458
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=22.25 E-value=3.7e+02 Score=34.46 Aligned_cols=174 Identities=18% Similarity=0.286 Sum_probs=0.0
Q ss_pred CHHHHHHHHHhCCCCCCCCceee---CCHHHHHHHHHHHHH-hhcCCCCccce-EEEEECCh------------------
Q psy11423 248 SHSELLNWYQKIGLSICGEYSVL---SGVNKLIEFYKKINI-KRFNLPYEIDG-VVYKINCL------------------ 304 (655)
Q Consensus 248 ~~~e~l~~L~~~GF~~~~~~~~~---~~~~ev~~~~~~~~~-~r~~l~y~iDG-iVikv~~~------------------ 304 (655)
+..+.+.+-...|-|..|.+... -+.+++....+.+.. .........|| +++..+..
T Consensus 475 ~~~eA~~~s~~~~~pLHP~yty~W~dis~e~~~~L~~~~~~~~~~~~~~~~~~~l~~~~~~~~k~~LE~L~v~H~~~~~~ 554 (1337)
T PRK14714 475 TVEEAAHWATEYGAPLHPYYTYLWHDISVEQVRALADAVADAETRGIGFADDGVLVLPLTPTVKRTLELLLVPHTVREDR 554 (1337)
T ss_pred CHHHHHHHHHHhCCCCCCCeeeeeccCCHHHHHHHHHHHHhcccccccccccceEEeeCcHHHHHHHHHhCCceEecCCe
Q ss_pred -------hhhhhhCCCCCCCCceEeecCCcceeeEEE----------------EEEEEeecCcceeeeEEEEEEEEE---
Q psy11423 305 -------STQKKLGFTSRAPRFALAYKFLSKEALTKI----------------KAINIQIGRTGIITPVALLKPVLI--- 358 (655)
Q Consensus 305 -------~~~~~lG~ts~~PrwaiA~Kf~~~~~~T~v----------------~~I~~qvGRTG~itPvA~lePV~l--- 358 (655)
.+-..||++.+.++ +-.|++.+....+.+ +.|=-.+||-++-.|.-.=-||..
T Consensus 555 i~i~~~~~l~~~Lg~~~~~~~-~~~~~~~~~~~~~~~~~vn~~s~~~ir~ra~trIG~RmGRPeKs~~R~mkP~~h~LFP 633 (1337)
T PRK14714 555 IRIPDWRPLLRSLGLDLSSEA-ALEWEFAPKDGHNAIDLINELAPFKVRERAPTRIGNRMGRPEKSKPRKMKPPVHTLFP 633 (1337)
T ss_pred EEecchHHHHHhcCCCccccc-cccccccccccccHHHHHHhhCCcEEeccCcceeecccCCcccccccccCCCCccccc
Q ss_pred -CCEEEEEeeCCCHHHHHhcCCCCCCEEEEEecCcccceeecccccCCCCCCccccCCCCCCCCCCcceeecCceeEEec
Q psy11423 359 -DGITITRATLHNESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICNSKIIYIESNLIARCS 437 (655)
Q Consensus 359 -~G~tVsratLhN~~~i~~~~i~iGd~V~v~raGdVIP~I~~vv~~~r~~~~~~~~~P~~CP~C~~~l~~~~~~~~~~C~ 437 (655)
+..==++=++-.+..........+=.+.|+-+ ..+.+.-....+...||.||+.+. ....|+
T Consensus 634 ig~aGG~qR~I~kAa~~a~~~~d~~G~ieVEV~------------~rkCPkCG~~t~~~fCP~CGs~te-----~vy~CP 696 (1337)
T PRK14714 634 IGEAGGAQRDVAKAAKHAPDMSDEGGVIEVEVG------------RRRCPSCGTETYENRCPDCGTHTE-----PVYVCP 696 (1337)
T ss_pred ccccCcccccHHHHHHhhhhccccCCeEEEEEE------------EEECCCCCCccccccCcccCCcCC-----CceeCc
Q ss_pred CCCcCC
Q psy11423 438 GSWIEC 443 (655)
Q Consensus 438 n~~~~C 443 (655)
+ |
T Consensus 697 s----C 698 (1337)
T PRK14714 697 D----C 698 (1337)
T ss_pred c----C
No 459
>PRK14177 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=22.22 E-value=3.1e+02 Score=29.33 Aligned_cols=68 Identities=10% Similarity=0.181 Sum_probs=45.2
Q ss_pred CHHHHHHHHHHhcChhHHHHHHHHHHcCcccccCCCCCCCeEecccccCccEEEecCCCC------chHHHHHHcCCee-
Q psy11423 564 GSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNNPNTKGGKVVNFISKNTNYLVKGQKPG------KKLEKAIKLNIKI- 636 (655)
Q Consensus 564 G~~~A~~I~~~f~~~~n~~li~~L~~~Gi~~~~~~~~~G~~v~~sVsk~t~ylv~g~~~g------~K~~kA~~lgi~i- 636 (655)
|..+|+.|.+.+. +.++.|.+.|- ...+.-.+.+|+++. +|.+.|+++||..
T Consensus 8 Gk~ia~~i~~~lk-----~~i~~l~~~~~----------------~~P~Laii~vg~d~as~~Yv~~k~k~~~~~Gi~~~ 66 (284)
T PRK14177 8 GKKLSEKIRNEIR-----ETIEERKTKNK----------------RIPKLATILVGNNPASETYVSMKVKACHKVGMGSE 66 (284)
T ss_pred hHHHHHHHHHHHH-----HHHHHHHhcCC----------------CCCeEEEEEeCCChhHHHHHHHHHHHHHHcCCEEE
Confidence 6778888877763 34666654321 112444677888754 6777899999872
Q ss_pred -------eCHHHHHHHHhcccCC
Q psy11423 637 -------LDEKNFVKIVKGFSTE 652 (655)
Q Consensus 637 -------i~e~~f~~~l~~~~~~ 652 (655)
+++++|.+.+..-+.+
T Consensus 67 ~~~l~~~~s~~el~~~I~~lN~D 89 (284)
T PRK14177 67 MIRLKEQTTTEELLGVIDKLNLD 89 (284)
T ss_pred EEECCCCCCHHHHHHHHHHHhCC
Confidence 4889999988655443
No 460
>PF00730 HhH-GPD: HhH-GPD superfamily base excision DNA repair protein This entry corresponds to Endonuclease III This entry corresponds to Alkylbase DNA glycosidase; InterPro: IPR003265 Endonuclease III (4.2.99.18 from EC) is a DNA repair enzyme which removes a number of damaged pyrimidines from DNA via its glycosylase activity and also cleaves the phosphodiester backbone at apurinic / apyrimidinic sites via a beta-elimination mechanism [, ]. The structurally related DNA glycosylase MutY recognises and excises the mutational intermediate 8-oxoguanine-adenine mispair []. The 3-D structures of Escherichia coli endonuclease III [] and catalytic domain of MutY [] have been determined. The structures contain two all-alpha domains: a sequence-continuous, six-helix domain (residues 22-132) and a Greek-key, four-helix domain formed by one N-terminal and three C-terminal helices (residues 1-21 and 133-211) together with the [Fe4S4] cluster. The cluster is bound entirely within the C-terminal loop by four cysteine residues with a ligation pattern Cys-(Xaa)6-Cys-(Xaa)2-Cys-(Xaa)5-Cys which is distinct from all other known Fe4S4 proteins. This structural motif is referred to as a [Fe4S4] cluster loop (FCL) []. Two DNA-binding motifs have been proposed, one at either end of the interdomain groove: the helix-hairpin-helix (HhH) and FCL motifs (see IPR003651 from INTERPRO). The primary role of the iron-sulphur cluster appears to involve positioning conserved basic residues for interaction with the DNA phosphate backbone by forming the loop of the FCL motif [, ]. The HhH-GPD domain gets its name from its hallmark helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate. This domain is found in a diverse range of structurally related DNA repair proteins that include: endonuclease III, 4.2.99.18 from EC and DNA glycosylase MutY, an A/G-specific adenine glycosylase. Both of these enzymes have a C-terminal iron-sulphur cluster loop (FCL). The methyl-CPG binding protein (MBD4) also contain a related domain that is a thymine DNA glycosylase. The family also includes DNA-3-methyladenine glycosylase II 3.2.2.21 from EC, 8-oxoguanine DNA glycosylases and other members of the AlkA family.; GO: 0006284 base-excision repair; PDB: 3F0Z_A 3I0X_A 3F10_A 3I0W_A 3S6I_D 3N5N_Y 1PU7_A 1PU8_B 1PU6_B 1NGN_A ....
Probab=22.07 E-value=85 Score=27.61 Aligned_cols=39 Identities=21% Similarity=0.317 Sum_probs=30.1
Q ss_pred HHHHHhC--CCHHHHHhcCHHHHhcC---CCCCHHHHHHHHHHh
Q psy11423 537 KELANYF--KNLECMFKATEEQLLNI---PKIGSTTVKAFIKFI 575 (655)
Q Consensus 537 k~L~~~f--gsl~~l~~as~eeL~~i---~GIG~~~A~~I~~~f 575 (655)
.+|.+.| .+++.|..++.++|.++ -|++...|+.|.+..
T Consensus 19 ~~l~~~~g~pt~~~l~~~~~~el~~~i~~~G~~~~ka~~i~~~a 62 (108)
T PF00730_consen 19 RRLFERYGFPTPEALAEASEEELRELIRPLGFSRRKAKYIIELA 62 (108)
T ss_dssp HHHHHHHSCSSHHHHHCSHHHHHHHHHTTSTSHHHHHHHHHHHH
T ss_pred HHHHHHhcCCCHHHHHhCCHHHHHHHhhccCCCHHHHHHHHHHH
Confidence 4555554 59999999998888665 789988898887743
No 461
>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=22.02 E-value=41 Score=32.60 Aligned_cols=13 Identities=31% Similarity=1.025 Sum_probs=9.6
Q ss_pred CCCCCCCcceeec
Q psy11423 417 ICPICNSKIIYIE 429 (655)
Q Consensus 417 ~CP~C~~~l~~~~ 429 (655)
.||.||++|+..+
T Consensus 130 ~Cp~Cg~~L~~~d 142 (158)
T TIGR00373 130 TCPRCGAMLDYLD 142 (158)
T ss_pred cCCCCCCEeeecc
Confidence 6888888877543
No 462
>PHA02325 hypothetical protein
Probab=21.95 E-value=78 Score=26.12 Aligned_cols=22 Identities=23% Similarity=0.727 Sum_probs=13.0
Q ss_pred CCCCCCCCCcceeecCceeEEecC
Q psy11423 415 PNICPICNSKIIYIESNLIARCSG 438 (655)
Q Consensus 415 P~~CP~C~~~l~~~~~~~~~~C~n 438 (655)
|+.||.|+.. +.+|.-.|.=++
T Consensus 3 ~k~CPkC~A~--WldgqhYWsgTg 24 (72)
T PHA02325 3 TKICPKCGAR--WLDGQHYWSGTG 24 (72)
T ss_pred ccccCccCCE--eEcceeeeccCC
Confidence 5789999973 444443333333
No 463
>PF08443 RimK: RimK-like ATP-grasp domain; InterPro: IPR013651 This ATP-grasp domain is found in the ribosomal S6 modification enzyme RimK []. It has an unusual nucleotide-binding fold referred to as palmate, or ATP-grasp fold. This domain is found in a number of enzymes of known structure as well as in urea amidolyase, tubulin-tyrosine ligase, and three enzymes of purine biosynthesis.; PDB: 1UC8_B 1UC9_A.
Probab=21.95 E-value=1.6e+02 Score=28.94 Aligned_cols=34 Identities=18% Similarity=0.225 Sum_probs=23.5
Q ss_pred HHHHHHHHhCCCCCCCCceeeCCHHHHHHHHHHHH
Q psy11423 250 SELLNWYQKIGLSICGEYSVLSGVNKLIEFYKKIN 284 (655)
Q Consensus 250 ~e~l~~L~~~GF~~~~~~~~~~~~~ev~~~~~~~~ 284 (655)
.-+++.|++.|+++++ +.++.+.+++.++++.+.
T Consensus 5 ~~~~~~l~~~gipvP~-t~~~~~~~~~~~~~~~~~ 38 (190)
T PF08443_consen 5 LLTLQLLAKAGIPVPE-TRVTNSPEEAKEFIEELG 38 (190)
T ss_dssp HHHHHHHHHTT------EEEESSHHHHHHHHHHH-
T ss_pred HHHHHHHHHCCcCCCC-EEEECCHHHHHHHHHHhc
Confidence 4567889999999976 667888999999998874
No 464
>PRK10792 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=21.80 E-value=2.5e+02 Score=30.08 Aligned_cols=68 Identities=10% Similarity=0.185 Sum_probs=45.2
Q ss_pred CHHHHHHHHHHhcChhHHHHHHHHHHcCcccccCCCCCCCeEecccccCccEEEecCCCC------chHHHHHHcCCe--
Q psy11423 564 GSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNNPNTKGGKVVNFISKNTNYLVKGQKPG------KKLEKAIKLNIK-- 635 (655)
Q Consensus 564 G~~~A~~I~~~f~~~~n~~li~~L~~~Gi~~~~~~~~~G~~v~~sVsk~t~ylv~g~~~g------~K~~kA~~lgi~-- 635 (655)
|..+|++|.+.+. +.++.|.+.| + ++.+.-.+.+|+.+. .|.+.|+++||.
T Consensus 8 Gk~va~~i~~~lk-----~~v~~l~~~~-----------~-----~~P~Laii~vg~d~as~~Yv~~k~k~a~~~Gi~~~ 66 (285)
T PRK10792 8 GKTIAQQVRSEVA-----QKVQARVAAG-----------L-----RAPGLAVVLVGSDPASQVYVASKRKACEEVGFVSR 66 (285)
T ss_pred HHHHHHHHHHHHH-----HHHHHHHHcC-----------C-----CCceEEEEEeCCCHHHHHHHHHHHHHHHHcCCEEE
Confidence 6778888887763 3466665432 1 122444567787753 688889999988
Q ss_pred ------eeCHHHHHHHHhcccCC
Q psy11423 636 ------ILDEKNFVKIVKGFSTE 652 (655)
Q Consensus 636 ------ii~e~~f~~~l~~~~~~ 652 (655)
-+++++|.+.+..-+.+
T Consensus 67 ~~~l~~~~s~~el~~~I~~lN~d 89 (285)
T PRK10792 67 SYDLPETTSEAELLALIDELNAD 89 (285)
T ss_pred EEECCCCCCHHHHHHHHHHHhCC
Confidence 35889999988654433
No 465
>PF04919 DUF655: Protein of unknown function (DUF655); InterPro: IPR007003 This family includes several uncharacterised archaeal proteins.; PDB: 2I5H_A.
Probab=21.70 E-value=95 Score=30.90 Aligned_cols=49 Identities=12% Similarity=0.165 Sum_probs=26.2
Q ss_pred Hh-CCCCccHHHHHHHHH-----hCCCHHHHHhcCHHHHhcCCCCCHHHHHHHHHHhcC
Q psy11423 525 AL-GIRHVGETTAKELAN-----YFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQ 577 (655)
Q Consensus 525 al-gIpgIG~~~Ak~L~~-----~fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~~f~~ 577 (655)
+| =+||||+++...|++ .|.|++.|... ...+...-+.+++.|..-+++
T Consensus 117 ~LeLLPGIGKK~m~~ILeERkkkpFeSFeDi~~R----v~gl~~p~~~i~~RIl~EL~~ 171 (181)
T PF04919_consen 117 SLELLPGIGKKTMWKILEERKKKPFESFEDIEER----VKGLHDPVKLIVERILEELQG 171 (181)
T ss_dssp GGGGSTT--HHHHHHHHHHHHHS---SHHHHHHH----STT---HHHHHHHHHHHHHH-
T ss_pred HHhhcccccHHHHHHHHHHHccCCCCCHHHHHHH----hccCCCHHHHHHHHHHHHHcC
Confidence 44 469999999988875 48888777652 222333345666666665543
No 466
>PRK00419 DNA primase small subunit; Reviewed
Probab=21.62 E-value=42 Score=37.21 Aligned_cols=77 Identities=17% Similarity=0.193 Sum_probs=42.4
Q ss_pred HHHhcCChhhhccccCCcHHHHHHHHHHHHHhcccchhH-HHHHhCCCCccHHHHHHHHHhC-----CCHHHHHhcCHHH
Q psy11423 483 VDLYKINFKNLLRLDRVSNKLANNILLAIQKSKLTTFSR-FIYALGIRHVGETTAKELANYF-----KNLECMFKATEEQ 556 (655)
Q Consensus 483 ~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~sk~~~l~r-~L~algIpgIG~~~Ak~L~~~f-----gsl~~l~~as~ee 556 (655)
.+|.....+.|..++|+|++.+.++++.+...... +.. .+.+ + .++|....+.|.+.. -.+|+-..++...
T Consensus 213 ~~l~~~~~~~l~~~~gi~~~~~~~~l~~~~~~~~~-~~~g~~~~-~-~~~~~~~~~~l~~~~~~~~~~~iDe~VT~DikR 289 (376)
T PRK00419 213 DHLRELALERLEEFDGIGEGTAKKILKAARDNTEF-LRKGNLDA-F-HGIGPRLAARLFAESVRFSKAPIDEPVTIDIKR 289 (376)
T ss_pred HHHhhhhhhhhhhhcccchhHHHHHHHHhhhhhhh-hhccchhh-c-cchhHHHHHHHHHHhhHhhcCcCCCCccccchh
Confidence 34444444478888899999999988876541100 001 1111 1 344555555554432 1245555566677
Q ss_pred HhcCCC
Q psy11423 557 LLNIPK 562 (655)
Q Consensus 557 L~~i~G 562 (655)
|..+||
T Consensus 290 LiRlPg 295 (376)
T PRK00419 290 LIRLPG 295 (376)
T ss_pred hhhCCC
Confidence 777776
No 467
>PRK07194 fliG flagellar motor switch protein G; Reviewed
Probab=21.59 E-value=5e+02 Score=28.23 Aligned_cols=26 Identities=8% Similarity=0.275 Sum_probs=14.5
Q ss_pred CCHHHHHHHHHHhcChhHHHHHHHHH
Q psy11423 563 IGSTTVKAFIKFINQPLHRLLISQLR 588 (655)
Q Consensus 563 IG~~~A~~I~~~f~~~~n~~li~~L~ 588 (655)
+++..|..|..+|......+++.++.
T Consensus 139 L~~e~AA~VL~~Lpe~~~~~v~~ria 164 (334)
T PRK07194 139 LPPESAAAVLKYLPEDRQDDILYRIA 164 (334)
T ss_pred cCHHHHHHHHHhCCHHHHHHHHHHHH
Confidence 46666666666666544444444443
No 468
>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=21.42 E-value=59 Score=29.80 Aligned_cols=77 Identities=10% Similarity=0.175 Sum_probs=39.7
Q ss_pred eeEEEEEEEEeecCcceeeeEEEEEEEEECCEEEEEeeCCCHHHHHhcCCCCCCEEEEEecCcccceeecccccCCCCCC
Q psy11423 330 ALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDS 409 (655)
Q Consensus 330 ~~T~v~~I~~qvGRTG~itPvA~lePV~l~G~tVsratLhN~~~i~~~~i~iGd~V~v~raGdVIP~I~~vv~~~r~~~~ 409 (655)
..++|+.|..+||+- +|+.-..... =++-+.+-.+-.|+.+.|.. +|-. ..-...+..
T Consensus 22 ~~~~V~~V~l~iG~l--------------s~V~p~~L~f-af~~~~~~t~~ega~L~I~~----~p~~---~~C~~Cg~~ 79 (115)
T TIGR00100 22 QAKKVTRVTLEIGEL--------------SCVNPSQLQF-AFEVVREGTVAEGAKLNIED----EPVE---CECEDCSEE 79 (115)
T ss_pred CCCeEEEEEEEEccc--------------cccCHHHHHH-HHHHHhCCCccCCCEEEEEe----eCcE---EEcccCCCE
Confidence 346899999999963 2222111111 13445666677788887765 3322 222223222
Q ss_pred ccc-cCCCCCCCCCCcceee
Q psy11423 410 KIF-KIPNICPICNSKIIYI 428 (655)
Q Consensus 410 ~~~-~~P~~CP~C~~~l~~~ 428 (655)
.+. ..-..||.||+.-...
T Consensus 80 ~~~~~~~~~CP~Cgs~~~~i 99 (115)
T TIGR00100 80 VSPEIDLYRCPKCHGIMLQV 99 (115)
T ss_pred EecCCcCccCcCCcCCCcEE
Confidence 111 1123599998865433
No 469
>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=21.40 E-value=54 Score=34.79 Aligned_cols=24 Identities=25% Similarity=0.485 Sum_probs=10.5
Q ss_pred CCCCCCCCCcce----eec---CceeEEecC
Q psy11423 415 PNICPICNSKII----YIE---SNLIARCSG 438 (655)
Q Consensus 415 P~~CP~C~~~l~----~~~---~~~~~~C~n 438 (655)
..+||+||+.=+ ..+ |...++|.-
T Consensus 172 ~g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~ 202 (290)
T PF04216_consen 172 RGYCPVCGSPPVLSVLRGGEREGKRYLHCSL 202 (290)
T ss_dssp -SS-TTT---EEEEEEE------EEEEEETT
T ss_pred CCcCCCCCCcCceEEEecCCCCccEEEEcCC
Confidence 358999999622 222 457788743
No 470
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=21.30 E-value=1.3e+02 Score=37.21 Aligned_cols=46 Identities=20% Similarity=0.374 Sum_probs=30.1
Q ss_pred cccCCCCHHHHHHHHHcCCCCChHHHhcCChhhhccccCCcHHHHHHHHHHHHH
Q psy11423 460 MNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK 513 (655)
Q Consensus 460 l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~GfG~Ksa~nll~~I~~ 513 (655)
-+|+|+||||+.+|..+=. |+++||. .+..++| +|..++|.+..+.
T Consensus 188 pGVpGIG~KtA~kLL~~yg--sle~i~~----~~~~i~~--~k~~~~L~~~~e~ 233 (887)
T TIGR00593 188 PGVKGIGEKTAAKLLQEFG--SLENIYE----NLDQIKS--AKMREKLIAHKED 233 (887)
T ss_pred CCCCCcCHHHHHHHHHHcC--CHHHHHH----HHHHhcc--HHHHHHHHHhHHH
Confidence 3689999999999998642 7778875 1222322 2455666665543
No 471
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=21.07 E-value=69 Score=29.11 Aligned_cols=21 Identities=33% Similarity=0.730 Sum_probs=17.0
Q ss_pred CCCCCCCcceeecCceeEEecC
Q psy11423 417 ICPICNSKIIYIESNLIARCSG 438 (655)
Q Consensus 417 ~CP~C~~~l~~~~~~~~~~C~n 438 (655)
.||.|+++-+.+++. .+.|+.
T Consensus 5 ~cp~c~sEytYed~~-~~~cpe 25 (112)
T COG2824 5 PCPKCNSEYTYEDGG-QLICPE 25 (112)
T ss_pred CCCccCCceEEecCc-eEeCch
Confidence 499999998887655 788865
No 472
>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=20.91 E-value=61 Score=28.76 Aligned_cols=26 Identities=23% Similarity=0.575 Sum_probs=19.3
Q ss_pred CCCCCCCcceeecCceeEEecCCCcCCHHHHH
Q psy11423 417 ICPICNSKIIYIESNLIARCSGSWIECIAQRK 448 (655)
Q Consensus 417 ~CP~C~~~l~~~~~~~~~~C~n~~~~C~~q~~ 448 (655)
+||.||+.|...+ ..+.|.+ |.....
T Consensus 2 fC~~Cg~~l~~~~--~~~~C~~----C~~~~~ 27 (104)
T TIGR01384 2 FCPKCGSLMTPKN--GVYVCPS----CGYEKE 27 (104)
T ss_pred CCcccCcccccCC--CeEECcC----CCCccc
Confidence 7999999997543 4789976 875543
No 473
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=20.81 E-value=47 Score=32.91 Aligned_cols=12 Identities=25% Similarity=0.617 Sum_probs=9.7
Q ss_pred CCCCCCCcceee
Q psy11423 417 ICPICNSKIIYI 428 (655)
Q Consensus 417 ~CP~C~~~l~~~ 428 (655)
.||.||++|+..
T Consensus 138 ~Cp~Cg~~L~~~ 149 (178)
T PRK06266 138 RCPQCGEMLEEY 149 (178)
T ss_pred cCCCCCCCCeec
Confidence 799999988753
No 474
>PF04475 DUF555: Protein of unknown function (DUF555); InterPro: IPR007564 This is a family of uncharacterised, hypothetical archaeal proteins.
Probab=20.79 E-value=45 Score=29.87 Aligned_cols=11 Identities=36% Similarity=1.023 Sum_probs=9.2
Q ss_pred CCCCCCCCcce
Q psy11423 416 NICPICNSKII 426 (655)
Q Consensus 416 ~~CP~C~~~l~ 426 (655)
..||+||.++.
T Consensus 48 ~~cP~Cge~~~ 58 (102)
T PF04475_consen 48 TICPKCGEELD 58 (102)
T ss_pred ccCCCCCCccC
Confidence 58999999874
No 475
>KOG2041|consensus
Probab=20.67 E-value=1.5e+02 Score=35.42 Aligned_cols=52 Identities=19% Similarity=0.330 Sum_probs=41.9
Q ss_pred HHHHHHHHhhccCCCceEEEEEecceeEEEEEEeCCEEeEEEecCCCCccchhh
Q psy11423 103 IFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENIT 156 (655)
Q Consensus 103 ~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT 156 (655)
.|.+.+-..- ..++...++|-.||--|-++|+||-.+-.+--||-..|.++-
T Consensus 104 sW~EEMiNnR--nKSvV~SmsWn~dG~kIcIvYeDGavIVGsvdGNRIwgKeLk 155 (1189)
T KOG2041|consen 104 SWCEEMINNR--NKSVVVSMSWNLDGTKICIVYEDGAVIVGSVDGNRIWGKELK 155 (1189)
T ss_pred cHHHHHhhCc--CccEEEEEEEcCCCcEEEEEEccCCEEEEeeccceecchhcc
Confidence 4666653321 235778999999999999999999999999999999998864
No 476
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=20.60 E-value=62 Score=34.87 Aligned_cols=10 Identities=40% Similarity=1.139 Sum_probs=8.2
Q ss_pred CCCCCCCCCc
Q psy11423 415 PNICPICNSK 424 (655)
Q Consensus 415 P~~CP~C~~~ 424 (655)
..+||+||+.
T Consensus 184 ~~~CPvCGs~ 193 (305)
T TIGR01562 184 RTLCPACGSP 193 (305)
T ss_pred CCcCCCCCCh
Confidence 3489999996
No 477
>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=20.56 E-value=97 Score=30.77 Aligned_cols=23 Identities=22% Similarity=0.224 Sum_probs=16.5
Q ss_pred hhhccccCCcHHHHHHHHHHHHH
Q psy11423 491 KNLLRLDRVSNKLANNILLAIQK 513 (655)
Q Consensus 491 ~~L~~l~GfG~Ksa~nll~~I~~ 513 (655)
++|+.|||+|+|+|+=++.-+.+
T Consensus 115 e~Ll~LpGVG~KTAnvVL~~l~~ 137 (177)
T TIGR03252 115 RRLKALPGFGKQKAKIFLALLGK 137 (177)
T ss_pred HHHHcCCCCCHHHHHHHHHHHHH
Confidence 46788888888888777665544
No 478
>COG0099 RpsM Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=20.46 E-value=1.1e+02 Score=28.45 Aligned_cols=39 Identities=26% Similarity=0.284 Sum_probs=27.2
Q ss_pred HHHHh-CCCCccHHHHHHHHHhCC-CH-HHHHhcCHHHHhcC
Q psy11423 522 FIYAL-GIRHVGETTAKELANYFK-NL-ECMFKATEEQLLNI 560 (655)
Q Consensus 522 ~L~al-gIpgIG~~~Ak~L~~~fg-sl-~~l~~as~eeL~~i 560 (655)
+..|| .|.|||..+|+.+++..+ +. ..+...+.+|+.++
T Consensus 15 v~iALt~IyGIG~~~a~~I~~~~gi~~~~r~~eLteeei~~i 56 (121)
T COG0099 15 VVIALTYIYGIGRRRAKEICKKAGIDPDKRVGELTEEEIERL 56 (121)
T ss_pred EeehhhhhccccHHHHHHHHHHcCCCHhHhhccCCHHHHHHH
Confidence 34455 699999999999999866 22 24445666776653
No 479
>COG2336 MazE Growth regulator [Signal transduction mechanisms]
Probab=20.45 E-value=1.1e+02 Score=26.68 Aligned_cols=22 Identities=27% Similarity=0.403 Sum_probs=20.0
Q ss_pred HHHHHhcCCCCCCEEEEEecCc
Q psy11423 371 ESEIYRKNIQIGDTVVVHRSGN 392 (655)
Q Consensus 371 ~~~i~~~~i~iGd~V~v~raGd 392 (655)
...++++++.+||.|.|...||
T Consensus 18 ~~l~kql~l~~g~~v~v~v~n~ 39 (82)
T COG2336 18 AALLKQLNLTIGDEVEVEVGND 39 (82)
T ss_pred HHHHHHhCCCcCceEEEEEcCC
Confidence 4578999999999999999987
No 480
>PRK14187 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=20.45 E-value=3.6e+02 Score=28.97 Aligned_cols=67 Identities=15% Similarity=0.324 Sum_probs=45.4
Q ss_pred CHHHHHHHHHHhcChhHHHHHHHHHHc-CcccccCCCCCCCeEecccccCccEEEecCCCC------chHHHHHHcCCee
Q psy11423 564 GSTTVKAFIKFINQPLHRLLISQLRDV-GIYWLNNPNTKGGKVVNFISKNTNYLVKGQKPG------KKLEKAIKLNIKI 636 (655)
Q Consensus 564 G~~~A~~I~~~f~~~~n~~li~~L~~~-Gi~~~~~~~~~G~~v~~sVsk~t~ylv~g~~~g------~K~~kA~~lgi~i 636 (655)
|..+|+.|.+.+. +.++.|.+. |+ +.+.-.+.+|+.+. .|.+.|+++||..
T Consensus 7 Gk~va~~i~~~lk-----~~v~~l~~~~g~-----------------~P~LaiI~vg~d~as~~Yv~~k~k~a~~~Gi~~ 64 (294)
T PRK14187 7 GKKIANDITEILA-----TCIDDLKRQHNL-----------------FPCLIVILVGDDPASQLYVRNKQRKAEMLGLRS 64 (294)
T ss_pred hHHHHHHHHHHHH-----HHHHHHHHccCC-----------------CCeEEEEEeCCChhHHHHHHHHHHHHHHcCCEE
Confidence 7788888887763 345555443 33 23455677888754 6788899999874
Q ss_pred --------eCHHHHHHHHhcccCC
Q psy11423 637 --------LDEKNFVKIVKGFSTE 652 (655)
Q Consensus 637 --------i~e~~f~~~l~~~~~~ 652 (655)
+++++|.+.+..-+.+
T Consensus 65 ~~~~l~~~~~e~~l~~~I~~lN~d 88 (294)
T PRK14187 65 ETILLPSTISESSLIEKINELNND 88 (294)
T ss_pred EEEECCCCCCHHHHHHHHHHHhCC
Confidence 3688998888654443
No 481
>PHA00439 exonuclease
Probab=20.33 E-value=73 Score=34.01 Aligned_cols=15 Identities=33% Similarity=0.417 Sum_probs=7.4
Q ss_pred CCCCccHHHHHHHHHh
Q psy11423 527 GIRHVGETTAKELANY 542 (655)
Q Consensus 527 gIpgIG~~~Ak~L~~~ 542 (655)
|+|||| ++|.+|++.
T Consensus 192 GVpGIG-KTA~kLL~~ 206 (286)
T PHA00439 192 GIPGWG-DTAEAFLEN 206 (286)
T ss_pred CCCCcC-HHHHHHHhC
Confidence 455555 555444443
No 482
>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=20.29 E-value=64 Score=24.79 Aligned_cols=10 Identities=30% Similarity=0.763 Sum_probs=8.0
Q ss_pred CCCCCCCCCC
Q psy11423 414 IPNICPICNS 423 (655)
Q Consensus 414 ~P~~CP~C~~ 423 (655)
.+..||.||+
T Consensus 25 ~~~~CP~Cg~ 34 (52)
T TIGR02605 25 PLATCPECGG 34 (52)
T ss_pred CCCCCCCCCC
Confidence 3557999998
No 483
>PRK03922 hypothetical protein; Provisional
Probab=20.25 E-value=46 Score=30.32 Aligned_cols=11 Identities=36% Similarity=0.914 Sum_probs=9.3
Q ss_pred CCCCCCCCcce
Q psy11423 416 NICPICNSKII 426 (655)
Q Consensus 416 ~~CP~C~~~l~ 426 (655)
+.||.||.++.
T Consensus 50 ~~cP~cge~~~ 60 (113)
T PRK03922 50 TICPKCGEPFD 60 (113)
T ss_pred ccCCCCCCcCC
Confidence 58999999874
No 484
>PRK01216 DNA polymerase IV; Validated
Probab=20.21 E-value=1.7e+02 Score=31.97 Aligned_cols=52 Identities=29% Similarity=0.450 Sum_probs=32.8
Q ss_pred hHHHHHh---CCCCccHHHHHHHHHh-CCCHHHHHhcCHHHHhcCCCCCHHHHHHHHH
Q psy11423 520 SRFIYAL---GIRHVGETTAKELANY-FKNLECMFKATEEQLLNIPKIGSTTVKAFIK 573 (655)
Q Consensus 520 ~r~L~al---gIpgIG~~~Ak~L~~~-fgsl~~l~~as~eeL~~i~GIG~~~A~~I~~ 573 (655)
..+|..| .+||||++++++|.+. +.++..|...+.++|.+. +|+..+..+..
T Consensus 172 ~~~L~~LPi~~l~giG~~~~~~L~~~Gi~TigdL~~~~~~~L~~r--fG~~~~~~L~~ 227 (351)
T PRK01216 172 KRFINELDIADIPGIGDITAEKLKKLGVNKLVDTLRIEFDELKGI--IGEAKAKYLFS 227 (351)
T ss_pred HHHHhcCCcccccCCCHHHHHHHHHcCCCcHHHHhcCCHHHHHHH--HCHHHHHHHHH
Confidence 4566655 4578887777777653 557777777777777765 45544545544
No 485
>PRK14191 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=20.16 E-value=3.2e+02 Score=29.19 Aligned_cols=67 Identities=16% Similarity=0.285 Sum_probs=44.8
Q ss_pred CHHHHHHHHHHhcChhHHHHHHHHHHc-CcccccCCCCCCCeEecccccCccEEEecCCCC------chHHHHHHcCCee
Q psy11423 564 GSTTVKAFIKFINQPLHRLLISQLRDV-GIYWLNNPNTKGGKVVNFISKNTNYLVKGQKPG------KKLEKAIKLNIKI 636 (655)
Q Consensus 564 G~~~A~~I~~~f~~~~n~~li~~L~~~-Gi~~~~~~~~~G~~v~~sVsk~t~ylv~g~~~g------~K~~kA~~lgi~i 636 (655)
|..+|+.|.+.+. +.++.|.+. |+ +.+.-.+.+|+.+. +|.+.|+++||..
T Consensus 6 Gk~~A~~i~~~l~-----~~v~~l~~~~g~-----------------~P~LaiI~vg~d~as~~Yv~~k~k~a~~~Gi~~ 63 (285)
T PRK14191 6 GKALSYKIEKDLK-----NKIQILTAQTGK-----------------RPKLAVILVGKDPASQTYVNMKIKACERVGMDS 63 (285)
T ss_pred hHHHHHHHHHHHH-----HHHHHHHhcCCC-----------------CCeEEEEEeCCCHHHHHHHHHHHHHHHHcCCEE
Confidence 6778888877663 335555432 22 23455677887754 6788899999874
Q ss_pred --------eCHHHHHHHHhcccCC
Q psy11423 637 --------LDEKNFVKIVKGFSTE 652 (655)
Q Consensus 637 --------i~e~~f~~~l~~~~~~ 652 (655)
+++++|.+.+..-+.+
T Consensus 64 ~~~~l~~~~~~~el~~~I~~lN~D 87 (285)
T PRK14191 64 DLHTLQENTTEAELLSLIKDLNTD 87 (285)
T ss_pred EEEECCCCCCHHHHHHHHHHHhCC
Confidence 4688999988654443
No 486
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=20.14 E-value=61 Score=25.44 Aligned_cols=24 Identities=17% Similarity=0.486 Sum_probs=16.4
Q ss_pred CCCCCCCCCcceeecCceeEEecC
Q psy11423 415 PNICPICNSKIIYIESNLIARCSG 438 (655)
Q Consensus 415 P~~CP~C~~~l~~~~~~~~~~C~n 438 (655)
-..||.||..+.+.+-...+.|-.
T Consensus 19 ~~~CPrCG~gvfmA~H~dR~~CGk 42 (51)
T COG1998 19 NRFCPRCGPGVFMADHKDRWACGK 42 (51)
T ss_pred cccCCCCCCcchhhhcCceeEecc
Confidence 457999997655555455777854
Done!