Query gi|254781172|ref|YP_003065585.1| NAD-dependent DNA ligase LigA [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 731
No_of_seqs 179 out of 2993
Neff 6.4
Searched_HMMs 39220
Date Mon May 30 08:29:17 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254781172.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR00575 dnlj DNA ligase, NAD 100.0 0 0 1781.7 46.4 663 24-714 1-706 (706)
2 PRK07956 ligA NAD-dependent DN 100.0 0 0 1659.2 62.7 666 13-721 1-668 (668)
3 COG0272 Lig NAD-dependent DNA 100.0 0 0 1632.5 56.2 663 12-719 2-667 (667)
4 PRK08097 ligB NAD-dependent DN 100.0 0 0 1232.1 42.9 535 9-635 23-560 (563)
5 smart00532 LIGANc Ligase N fam 100.0 0 0 1127.9 40.3 439 17-480 1-441 (441)
6 pfam01653 DNA_ligase_aden NAD- 100.0 0 0 747.0 28.2 312 15-333 1-315 (315)
7 cd00114 LIGANc NAD+ dependent 100.0 0 0 725.0 26.1 306 19-332 1-307 (307)
8 pfam03120 DNA_ligase_OB NAD-de 99.9 1.3E-24 3.3E-29 209.5 8.4 82 335-427 1-82 (82)
9 PRK06195 DNA polymerase III su 99.8 1.3E-18 3.3E-23 163.1 8.7 77 644-720 218-308 (309)
10 COG5275 BRCT domain type II [G 99.5 1.8E-14 4.7E-19 131.0 6.6 114 598-725 122-236 (276)
11 PRK06063 DNA polymerase III su 99.4 2.7E-12 6.8E-17 114.3 8.2 75 646-721 232-308 (313)
12 PHA00454 ATP-dependent DNA lig 98.8 5.1E-06 1.3E-10 65.7 19.7 240 125-404 26-291 (312)
13 PRK05601 DNA polymerase III su 98.7 6.4E-08 1.6E-12 80.4 7.6 78 645-723 293-372 (377)
14 LOAD_ligase consensus 98.7 3.4E-07 8.7E-12 74.8 10.9 155 127-311 1-166 (184)
15 pfam00533 BRCT BRCA1 C Terminu 98.7 1.7E-07 4.3E-12 77.2 8.9 74 644-718 3-77 (77)
16 PRK09125 DNA ligase; Provision 98.6 3.1E-05 7.9E-10 59.7 17.8 213 124-405 36-256 (277)
17 cd07898 Adenylation_DNA_ligase 98.5 4.3E-06 1.1E-10 66.3 13.2 161 124-311 19-186 (201)
18 smart00292 BRCT breast cancer 98.5 1.4E-06 3.6E-11 70.0 8.9 76 645-720 1-79 (80)
19 cd07901 Adenylation_DNA_ligase 98.5 1.9E-05 4.8E-10 61.3 14.7 177 92-311 5-192 (207)
20 COG1793 CDC9 ATP-dependent DNA 98.4 0.00015 3.8E-09 54.4 17.6 216 125-382 132-367 (444)
21 cd07906 Adenylation_DNA_ligase 98.4 2.1E-05 5.5E-10 60.9 13.0 151 124-311 14-171 (186)
22 cd07903 Adenylation_DNA_ligase 98.3 6.2E-05 1.6E-09 57.3 14.1 172 125-324 32-218 (227)
23 pfam01068 DNA_ligase_A_M ATP d 98.2 3E-05 7.6E-10 59.8 11.5 155 124-312 16-178 (190)
24 cd07900 Adenylation_DNA_ligase 98.2 8.5E-05 2.2E-09 56.3 13.8 173 92-306 10-196 (219)
25 PRK03180 ligB ATP-dependent DN 98.2 0.00023 5.9E-09 52.9 15.8 239 91-380 182-434 (509)
26 cd07907 Adenylation_DNA_ligase 98.2 0.00013 3.3E-09 54.8 14.5 153 124-311 31-197 (213)
27 PRK07636 ligB ATP-dependent DN 98.2 7.8E-05 2E-09 56.5 13.1 160 123-326 15-181 (269)
28 cd07896 Adenylation_kDNA_ligas 98.2 1.8E-05 4.7E-10 61.4 9.6 142 124-313 14-163 (174)
29 PRK01109 ATP-dependent DNA lig 98.2 0.00089 2.3E-08 48.4 18.1 237 93-382 228-491 (589)
30 cd00027 BRCT Breast Cancer Sup 98.2 1.1E-05 2.9E-10 63.0 8.2 70 649-718 1-71 (72)
31 cd06846 Adenylation_DNA_ligase 98.1 9.1E-05 2.3E-09 56.0 11.3 158 124-324 19-182 (187)
32 cd07897 Adenylation_DNA_ligase 98.1 0.00015 3.8E-09 54.4 12.1 154 125-312 23-192 (208)
33 PRK09633 ligD ATP-dependent DN 98.0 0.00055 1.4E-08 50.0 13.8 195 123-353 10-224 (604)
34 cd07905 Adenylation_DNA_ligase 97.9 0.00041 1.1E-08 50.9 11.8 160 124-312 14-181 (194)
35 PRK09247 ATP-dependent DNA lig 97.9 0.00087 2.2E-08 48.5 13.2 218 126-382 225-463 (537)
36 KOG1968 consensus 97.8 1.7E-05 4.3E-10 61.7 3.9 20 349-368 495-514 (871)
37 cd07902 Adenylation_DNA_ligase 97.8 0.00074 1.9E-08 49.0 12.1 176 92-311 14-199 (213)
38 PRK13766 Hef nuclease; Provisi 97.8 4.2E-05 1.1E-09 58.6 5.1 52 558-619 710-761 (764)
39 PRK00558 uvrC excinuclease ABC 97.7 8.5E-05 2.2E-09 56.3 5.6 52 557-618 557-608 (609)
40 PRK08224 ligC ATP-dependent DN 97.7 0.0015 3.8E-08 46.7 11.7 217 124-382 22-251 (345)
41 KOG2841 consensus 97.6 0.00012 3E-09 55.2 5.4 78 530-620 173-251 (254)
42 cd07894 Adenylation_RNA_ligase 97.6 0.0015 3.8E-08 46.6 10.7 169 81-308 24-194 (340)
43 TIGR02776 NHEJ_ligase_prk DNA 97.6 0.0011 2.9E-08 47.6 10.0 165 125-325 4-194 (645)
44 PRK08609 hypothetical protein; 97.6 0.00026 6.7E-09 52.5 6.6 22 217-240 177-198 (570)
45 PRK09632 ATP-dependent DNA lig 97.4 0.0046 1.2E-07 42.8 11.5 26 128-154 470-495 (753)
46 PHA02142 putative RNA ligase 97.4 0.0027 6.8E-08 44.7 9.7 148 124-308 167-344 (366)
47 TIGR02779 NHEJ_ligase_lig DNA 97.4 0.015 3.9E-07 38.8 13.5 171 123-326 12-205 (328)
48 PRK05972 ligD ATP-dependent DN 97.3 0.011 2.9E-07 39.8 12.5 161 123-325 216-384 (832)
49 cd08039 Adenylation_DNA_ligase 97.3 0.024 6.1E-07 37.3 14.6 163 125-311 21-214 (235)
50 cd00141 NT_POLXc Nucleotidyltr 97.3 0.00085 2.2E-08 48.5 6.1 81 529-614 21-103 (307)
51 COG1423 ATP-dependent DNA liga 97.2 0.012 3.1E-07 39.6 11.8 174 90-320 69-246 (382)
52 pfam09414 RNA_ligase RNA ligas 97.2 0.01 2.6E-07 40.2 11.4 150 127-308 2-168 (183)
53 smart00483 POLXc DNA polymeras 97.2 0.0024 6E-08 45.1 7.8 83 522-614 48-140 (334)
54 TIGR00574 dnl1 DNA ligase I, A 96.8 0.038 9.8E-07 35.7 11.3 221 92-343 196-451 (705)
55 PRK00116 ruvA Holliday junctio 96.7 0.037 9.4E-07 35.9 10.6 73 523-616 56-128 (198)
56 COG1948 MUS81 ERCC4-type nucle 96.7 0.0036 9.1E-08 43.7 5.1 54 556-619 184-237 (254)
57 COG0322 UvrC Nuclease subunit 96.7 0.0054 1.4E-07 42.3 6.0 49 557-616 533-581 (581)
58 pfam03119 DNA_ligase_ZBD NAD-d 96.6 0.00092 2.3E-08 48.3 1.7 27 433-466 1-27 (27)
59 TIGR00084 ruvA Holliday juncti 96.6 0.016 4.1E-07 38.7 8.1 138 467-678 49-187 (217)
60 TIGR00575 dnlj DNA ligase, NAD 96.5 0.00035 8.9E-09 51.5 -1.3 161 525-724 455-627 (706)
61 PRK01172 ski2-like helicase; P 96.5 0.018 4.5E-07 38.4 7.4 51 554-614 612-663 (674)
62 PRK07997 consensus 96.4 0.027 6.9E-07 36.9 8.2 83 31-115 18-125 (928)
63 COG0632 RuvA Holliday junction 96.2 0.025 6.5E-07 37.1 7.1 53 558-617 77-129 (201)
64 PRK08609 hypothetical protein; 96.1 0.0025 6.5E-08 44.9 1.8 10 698-707 511-520 (570)
65 PRK13901 ruvA Holliday junctio 96.1 0.024 6E-07 37.4 6.5 74 522-616 54-127 (196)
66 PRK07898 consensus 96.0 0.019 4.9E-07 38.1 5.5 48 31-78 26-81 (902)
67 smart00483 POLXc DNA polymeras 95.9 0.018 4.5E-07 38.3 5.3 56 556-614 50-107 (334)
68 PRK13482 DNA integrity scannin 95.6 0.036 9.2E-07 35.9 5.8 58 559-626 292-349 (352)
69 TIGR01448 recD_rel helicase, R 95.6 0.057 1.5E-06 34.4 6.8 129 467-616 84-215 (769)
70 PRK08928 consensus 95.6 0.057 1.4E-06 34.4 6.8 47 31-78 16-69 (861)
71 COG1796 POL4 DNA polymerase IV 95.6 0.0091 2.3E-07 40.6 2.6 58 479-545 94-151 (326)
72 pfam09513 consensus 95.5 0.24 6.2E-06 29.6 11.2 156 124-311 164-341 (356)
73 KOG1929 consensus 95.5 0.036 9.1E-07 36.0 5.4 79 643-722 490-568 (811)
74 PRK00254 ski2-like helicase; P 95.4 0.024 6E-07 37.4 4.1 50 557-616 647-697 (717)
75 PRK05797 consensus 95.2 0.12 3E-06 32.0 7.4 46 32-78 15-67 (869)
76 TIGR02236 recomb_radA DNA repa 95.0 0.025 6.5E-07 37.1 3.5 153 482-674 4-167 (333)
77 PRK08076 consensus 94.9 0.1 2.6E-06 32.5 6.3 45 32-78 15-67 (877)
78 TIGR01259 comE comEA protein; 94.9 0.034 8.6E-07 36.2 3.8 57 542-616 66-122 (124)
79 pfam01367 5_3_exonuc 5'-3' exo 94.8 0.052 1.3E-06 34.7 4.7 44 557-617 21-64 (100)
80 PRK09482 xni exonuclease IX; P 94.8 0.042 1.1E-06 35.4 4.1 41 557-614 185-225 (256)
81 PRK05929 consensus 94.8 0.042 1.1E-06 35.4 4.1 46 31-78 13-67 (870)
82 PRK07456 consensus 94.7 0.1 2.6E-06 32.4 5.9 83 31-114 19-131 (975)
83 PRK07300 consensus 94.7 0.06 1.5E-06 34.2 4.6 84 31-115 16-127 (880)
84 PRK05755 DNA polymerase I; Pro 94.6 0.065 1.7E-06 34.0 4.7 47 31-78 16-69 (889)
85 PRK00254 ski2-like helicase; P 94.6 0.02 5.2E-07 37.8 2.0 66 590-680 638-704 (717)
86 PRK07956 ligA NAD-dependent DN 94.6 0.035 9E-07 36.0 3.2 86 479-579 480-568 (668)
87 PRK06887 consensus 94.5 0.17 4.3E-06 30.8 6.6 47 31-78 18-71 (954)
88 PRK07556 consensus 94.4 0.078 2E-06 33.3 4.6 47 31-78 19-77 (977)
89 PRK07625 consensus 94.2 0.076 1.9E-06 33.5 4.3 46 31-78 17-70 (922)
90 COG1796 POL4 DNA polymerase IV 94.2 0.51 1.3E-05 27.1 13.5 53 554-615 93-147 (326)
91 PRK08835 consensus 94.2 0.11 2.7E-06 32.3 5.0 83 31-114 18-124 (931)
92 PRK08786 consensus 94.1 0.066 1.7E-06 33.9 3.9 46 31-78 13-65 (927)
93 TIGR01448 recD_rel helicase, R 94.1 0.16 4E-06 31.0 5.7 67 254-324 152-224 (769)
94 PRK08434 consensus 93.9 0.07 1.8E-06 33.7 3.7 83 31-115 13-120 (887)
95 smart00475 53EXOc 5'-3' exonuc 93.5 0.11 2.9E-06 32.1 4.1 42 557-615 189-230 (259)
96 COG2231 Uncharacterized protei 93.5 0.17 4.4E-06 30.7 5.1 40 568-616 96-135 (215)
97 TIGR02236 recomb_radA DNA repa 93.5 0.039 9.9E-07 35.7 1.8 46 559-614 5-51 (333)
98 PRK02362 ski2-like helicase; P 93.4 0.29 7.4E-06 29.0 6.1 67 35-110 16-87 (736)
99 cd00008 53EXOc 5'-3' exonuclea 93.4 0.2 5E-06 30.3 5.2 29 557-585 186-214 (240)
100 PRK01172 ski2-like helicase; P 93.4 0.056 1.4E-06 34.5 2.4 30 590-619 606-636 (674)
101 KOG2534 consensus 93.1 0.77 2E-05 25.7 8.4 62 521-582 55-126 (353)
102 TIGR00593 pola DNA polymerase 92.9 0.076 1.9E-06 33.4 2.5 46 33-78 12-68 (1005)
103 PRK08097 ligB NAD-dependent DN 92.6 0.13 3.3E-06 31.7 3.3 109 555-681 427-537 (563)
104 KOG3226 consensus 92.5 0.35 8.9E-06 28.3 5.4 67 646-713 317-383 (508)
105 PRK13913 3-methyladenine DNA g 92.4 0.33 8.3E-06 28.6 5.1 23 593-615 118-140 (218)
106 pfam00763 THF_DHG_CYH Tetrahyd 92.3 0.5 1.3E-05 27.1 6.0 61 664-727 14-88 (117)
107 KOG0966 consensus 92.2 0.98 2.5E-05 24.9 8.8 198 124-353 248-466 (881)
108 KOG0967 consensus 92.2 0.99 2.5E-05 24.8 13.7 178 92-308 344-532 (714)
109 PRK07220 DNA topoisomerase I; 92.1 0.24 6.2E-06 29.5 4.2 21 479-499 476-501 (740)
110 PRK00558 uvrC excinuclease ABC 92.1 0.088 2.2E-06 33.0 1.9 24 42-65 70-93 (609)
111 COG0190 FolD 5,10-methylene-te 91.3 0.6 1.5E-05 26.5 5.5 13 485-497 259-271 (283)
112 COG1623 Predicted nucleic-acid 91.1 0.38 9.7E-06 28.0 4.3 50 558-617 297-346 (349)
113 PRK00116 ruvA Holliday junctio 91.1 0.62 1.6E-05 26.4 5.4 55 480-543 75-129 (198)
114 smart00478 ENDO3c endonuclease 91.1 0.96 2.5E-05 24.9 6.4 23 593-615 69-91 (149)
115 COG0177 Nth Predicted EndoIII- 91.0 0.55 1.4E-05 26.8 5.1 45 487-540 47-91 (211)
116 COG0272 Lig NAD-dependent DNA 90.8 0.25 6.3E-06 29.5 3.1 82 478-577 479-566 (667)
117 PRK10702 endonuclease III; Pro 90.6 0.79 2E-05 25.6 5.5 22 594-615 107-128 (211)
118 cd00056 ENDO3c endonuclease II 90.5 0.86 2.2E-05 25.3 5.7 24 593-616 80-103 (158)
119 TIGR01083 nth endonuclease III 90.5 0.6 1.5E-05 26.5 4.9 74 489-614 47-125 (192)
120 cd00141 NT_POLXc Nucleotidyltr 90.3 0.55 1.4E-05 26.8 4.6 60 523-582 46-114 (307)
121 PRK00024 radC DNA repair prote 90.2 1.5 3.8E-05 23.5 11.8 144 547-710 26-206 (224)
122 TIGR01239 galT_2 galactose-1-p 90.0 0.29 7.5E-06 28.9 3.0 46 306-351 232-278 (502)
123 COG0632 RuvA Holliday junction 89.7 0.1 2.6E-06 32.4 0.4 53 520-573 71-127 (201)
124 cd00128 XPG Xeroderma pigmento 89.5 0.94 2.4E-05 25.0 5.2 29 557-585 226-254 (316)
125 TIGR00084 ruvA Holliday juncti 89.5 0.28 7.1E-06 29.1 2.5 68 467-543 65-140 (217)
126 cd07895 Adenylation_mRNA_cappi 89.3 1.7 4.4E-05 23.0 12.4 154 126-332 40-214 (216)
127 cd00080 HhH2_motif Helix-hairp 89.3 0.44 1.1E-05 27.6 3.4 29 557-585 25-53 (75)
128 PRK10792 bifunctional 5,10-met 89.2 0.96 2.4E-05 24.9 5.1 14 484-497 261-274 (288)
129 COG1555 ComEA DNA uptake prote 88.9 0.87 2.2E-05 25.3 4.7 46 559-616 102-147 (149)
130 PRK04301 radA DNA repair and r 88.8 0.21 5.3E-06 30.0 1.5 18 1-18 4-21 (318)
131 COG2003 RadC DNA repair protei 88.3 2 5.1E-05 22.5 10.7 116 547-674 26-166 (224)
132 TIGR00354 polC DNA polymerase 88.0 0.16 4.2E-06 30.9 0.5 51 133-203 389-439 (1173)
133 pfam00633 HHH Helix-hairpin-he 88.0 0.31 7.9E-06 28.7 1.9 25 591-615 6-30 (30)
134 KOG1921 consensus 87.1 1.3 3.2E-05 24.0 4.6 36 564-613 140-176 (286)
135 TIGR01259 comE comEA protein; 86.4 0.44 1.1E-05 27.6 1.9 98 524-630 8-106 (124)
136 pfam00730 HhH-GPD HhH-GPD supe 86.1 2.4 6.2E-05 21.8 5.7 22 594-615 79-100 (144)
137 PRK00420 hypothetical protein; 85.8 0.36 9.1E-06 28.3 1.3 25 429-460 17-41 (107)
138 PRK02362 ski2-like helicase; P 85.7 0.42 1.1E-05 27.7 1.5 48 557-616 655-703 (736)
139 TIGR02317 prpB methylisocitrat 85.2 1.3 3.3E-05 24.0 3.9 131 519-691 9-151 (287)
140 PRK00421 murC UDP-N-acetylmura 84.3 3.1 7.9E-05 21.0 6.4 13 302-314 215-227 (459)
141 pfam03118 RNA_pol_A_CTD Bacter 84.1 0.6 1.5E-05 26.5 1.8 50 483-543 12-61 (62)
142 KOG2043 consensus 84.1 2.2 5.7E-05 22.1 4.7 68 651-721 661-728 (896)
143 PRK13766 Hef nuclease; Provisi 83.8 0.53 1.4E-05 26.9 1.4 28 597-624 707-734 (764)
144 PRK11088 rrmA 23S rRNA methylt 82.9 0.39 9.9E-06 28.0 0.4 35 433-476 4-38 (272)
145 pfam06044 DRP Dam-replacing fa 81.3 0.82 2.1E-05 25.5 1.6 49 411-471 17-66 (254)
146 TIGR00600 rad2 DNA excision re 81.0 4.1 0.0001 20.1 5.5 25 39-63 188-212 (1127)
147 COG0258 Exo 5'-3' exonuclease 80.9 1.7 4.3E-05 23.0 3.1 15 214-228 38-52 (310)
148 TIGR01497 kdpB K+-transporting 80.7 0.85 2.2E-05 25.4 1.5 157 547-709 262-466 (675)
149 PRK07726 DNA topoisomerase III 80.6 0.84 2.1E-05 25.4 1.4 18 482-499 511-533 (716)
150 TIGR01265 tyr_nico_aTase tyros 80.4 0.81 2.1E-05 25.5 1.3 107 534-656 282-404 (424)
151 COG1110 Reverse gyrase [DNA re 79.9 1.4 3.4E-05 23.8 2.3 40 402-442 680-719 (1187)
152 PTZ00111 DNA replication licen 79.8 1.3 3.4E-05 23.8 2.3 41 11-52 82-122 (916)
153 TIGR01954 nusA_Cterm_rpt trans 79.6 3.7 9.4E-05 20.4 4.5 42 563-614 2-46 (52)
154 TIGR00608 radc DNA repair prot 79.4 4.5 0.00011 19.7 7.1 126 565-710 37-205 (223)
155 TIGR03674 fen_arch flap struct 79.4 2.6 6.8E-05 21.5 3.7 27 557-583 239-265 (338)
156 PRK07219 DNA topoisomerase I; 79.3 0.89 2.3E-05 25.2 1.2 15 21-35 91-105 (769)
157 COG1645 Uncharacterized Zn-fin 79.1 0.82 2.1E-05 25.5 1.0 23 430-460 27-49 (131)
158 TIGR00426 TIGR00426 competence 78.6 0.85 2.2E-05 25.3 0.9 40 560-614 24-66 (70)
159 TIGR01057 topA_arch DNA topois 77.9 1.1 2.8E-05 24.4 1.4 63 88-162 186-249 (637)
160 PRK08620 DNA topoisomerase III 77.7 1.1 2.9E-05 24.4 1.4 51 674-724 655-709 (726)
161 PRK06398 aldose dehydrogenase; 77.6 3.6 9.3E-05 20.5 3.9 16 644-659 231-246 (256)
162 TIGR01209 TIGR01209 conserved 76.4 5.4 0.00014 19.1 8.4 153 124-308 78-237 (388)
163 PRK12766 50S ribosomal protein 76.2 3.5 8.9E-05 20.6 3.5 48 481-539 13-60 (238)
164 PRK01438 murD UDP-N-acetylmura 75.8 5.6 0.00014 19.0 8.5 14 300-313 226-239 (481)
165 TIGR01862 N2-ase-Ialpha nitrog 75.8 5.6 0.00014 19.0 5.8 120 535-680 237-361 (510)
166 smart00278 HhH1 Helix-hairpin- 75.8 1.4 3.7E-05 23.6 1.5 20 597-616 2-21 (26)
167 CHL00013 rpoA RNA polymerase a 75.0 2.1 5.3E-05 22.3 2.1 50 485-545 278-327 (333)
168 KOG0442 consensus 74.6 4.3 0.00011 19.9 3.6 52 556-618 823-874 (892)
169 PRK09137 DNA topoisomerase I; 74.6 1.6 4E-05 23.3 1.4 22 16-37 58-79 (761)
170 pfam02571 CbiJ Precorrin-6x re 74.4 6.1 0.00015 18.7 5.8 53 645-710 164-220 (246)
171 COG4469 CoiA Competence protei 74.3 0.84 2.1E-05 25.4 -0.0 17 431-447 25-41 (342)
172 PTZ00217 flap endonuclease-1; 73.8 3.3 8.3E-05 20.8 2.9 26 558-583 239-264 (394)
173 TIGR00615 recR recombination p 73.1 3.4 8.7E-05 20.7 2.8 35 645-679 101-140 (205)
174 TIGR00336 pyrE orotate phospho 72.3 6.7 0.00017 18.4 5.1 66 642-711 109-181 (187)
175 pfam06677 Auto_anti-p27 Sjogre 72.2 1.9 4.8E-05 22.7 1.3 24 430-460 16-39 (41)
176 TIGR03190 benz_CoA_bzdN benzoy 72.1 6.8 0.00017 18.4 7.9 98 619-725 206-316 (377)
177 COG1096 Predicted RNA-binding 71.7 6.9 0.00018 18.3 4.7 62 393-473 117-180 (188)
178 pfam09511 RNA_lig_T4_1 RNA lig 71.1 5.6 0.00014 19.0 3.5 56 92-156 15-70 (212)
179 PRK03980 flap endonuclease-1; 70.9 7.2 0.00018 18.2 6.2 28 557-584 192-219 (295)
180 PRK08173 DNA topoisomerase III 70.7 2.5 6.3E-05 21.7 1.7 21 479-499 513-538 (857)
181 COG5241 RAD10 Nucleotide excis 70.7 2.9 7.3E-05 21.3 2.0 52 558-619 171-222 (224)
182 PRK09521 exosome complex RNA-b 70.6 5.4 0.00014 19.1 3.4 61 393-472 118-180 (187)
183 PRK13844 recombination protein 70.5 3.7 9.4E-05 20.4 2.5 16 644-659 100-115 (200)
184 pfam01331 mRNA_cap_enzyme mRNA 70.3 7.4 0.00019 18.1 11.7 143 126-311 16-178 (190)
185 pfam08304 consensus 70.0 7.5 0.00019 18.0 5.2 218 73-332 55-283 (378)
186 PRK00076 recR recombination pr 69.9 3.8 9.7E-05 20.3 2.5 16 644-659 96-111 (197)
187 PRK05182 DNA-directed RNA poly 69.8 3.7 9.5E-05 20.4 2.4 50 484-544 250-299 (306)
188 COG1656 Uncharacterized conser 69.5 3.9 0.0001 20.2 2.5 60 398-460 65-135 (165)
189 COG0122 AlkA 3-methyladenine D 69.3 7.8 0.0002 17.9 4.2 23 593-615 195-217 (285)
190 pfam03811 Ins_element1 Inserti 69.2 3.5 9E-05 20.6 2.2 65 432-510 6-72 (88)
191 pfam04551 GcpE GcpE protein. I 68.4 5.2 0.00013 19.3 2.9 42 395-440 219-265 (345)
192 TIGR01405 polC_Gram_pos DNA po 68.4 2 5.2E-05 22.4 0.9 29 23-52 419-447 (1264)
193 TIGR03491 RecB family nuclease 68.4 5.5 0.00014 19.1 3.0 12 257-268 219-230 (457)
194 PRK08057 cobalt-precorrin-6x r 68.2 8.1 0.00021 17.8 5.8 50 648-710 165-218 (241)
195 PRK09401 reverse gyrase; Revie 68.0 2.3 5.8E-05 22.0 1.0 45 398-443 659-703 (1176)
196 KOG3123 consensus 68.0 4.6 0.00012 19.7 2.6 11 257-267 233-243 (272)
197 PTZ00035 Rad51; Provisional 67.7 4.7 0.00012 19.6 2.6 16 524-539 70-85 (350)
198 PRK03369 murD UDP-N-acetylmura 67.6 8.3 0.00021 17.7 9.2 15 300-314 217-231 (487)
199 COG0052 RpsB Ribosomal protein 67.5 8.4 0.00021 17.7 4.2 32 662-693 165-203 (252)
200 PRK08938 DNA topoisomerase I; 67.5 2.9 7.4E-05 21.2 1.5 20 479-498 468-492 (692)
201 TIGR02770 nickel_nikD nickel i 66.5 8.7 0.00022 17.5 5.0 75 134-220 2-81 (239)
202 pfam02371 Transposase_20 Trans 66.2 7.6 0.00019 18.0 3.4 39 597-635 3-41 (87)
203 COG1241 MCM2 Predicted ATPase 66.1 2.8 7.1E-05 21.3 1.2 19 708-726 652-670 (682)
204 pfam09151 DUF1936 Domain of un 65.8 3.4 8.6E-05 20.7 1.5 31 433-466 3-34 (36)
205 COG0821 gcpE 1-hydroxy-2-methy 65.2 6.2 0.00016 18.6 2.8 77 395-494 224-312 (361)
206 pfam01927 DUF82 Protein of unk 64.9 5.8 0.00015 18.9 2.6 40 404-444 64-103 (146)
207 COG4468 GalT Galactose-1-phosp 64.9 7 0.00018 18.2 3.0 12 262-273 207-218 (503)
208 PRK02472 murD UDP-N-acetylmura 64.7 9.4 0.00024 17.3 8.3 10 666-675 440-449 (450)
209 PRK00366 ispG 4-hydroxy-3-meth 64.7 6.5 0.00017 18.5 2.8 42 395-440 230-276 (367)
210 KOG3084 consensus 64.7 3.2 8.1E-05 20.9 1.2 29 431-466 150-178 (345)
211 PRK08115 ribonucleotide-diphos 63.5 3.4 8.7E-05 20.7 1.2 22 549-571 553-574 (857)
212 PRK09536 btuD corrinoid ABC tr 62.7 9 0.00023 17.4 3.2 30 365-410 188-217 (409)
213 PRK06196 oxidoreductase; Provi 62.4 8.3 0.00021 17.7 3.0 14 152-165 31-44 (316)
214 PRK12481 2-deoxy-D-gluconate 3 62.3 10 0.00026 17.0 6.4 14 644-657 234-247 (251)
215 COG1439 Predicted nucleic acid 62.2 2.9 7.3E-05 21.2 0.6 14 431-444 153-166 (177)
216 COG0353 RecR Recombinational D 61.2 7.8 0.0002 17.9 2.7 17 645-661 98-114 (198)
217 TIGR02707 butyr_kinase butyrat 61.0 4 0.0001 20.1 1.2 76 257-364 52-132 (353)
218 PRK03806 murD UDP-N-acetylmura 61.0 11 0.00028 16.8 8.2 26 649-674 405-438 (438)
219 COG1198 PriA Primosomal protei 61.0 3 7.7E-05 21.1 0.6 54 432-497 445-502 (730)
220 pfam03786 UxuA D-mannonate deh 60.6 5.7 0.00014 19.0 1.9 81 91-200 34-114 (350)
221 COG3877 Uncharacterized protei 60.4 3.7 9.5E-05 20.4 1.0 24 428-461 3-26 (122)
222 PRK08305 spoVFB dipicolinate s 60.1 11 0.00028 16.7 4.9 27 213-247 135-161 (195)
223 KOG4362 consensus 60.0 11 0.00029 16.7 4.2 62 644-705 585-658 (684)
224 pfam09862 DUF2089 Protein of u 59.7 4.3 0.00011 19.9 1.2 26 434-472 1-26 (113)
225 TIGR02644 Y_phosphoryl pyrimid 59.6 11 0.00029 16.6 3.6 44 102-165 49-92 (425)
226 KOG2703 consensus 59.6 4.8 0.00012 19.5 1.4 58 555-617 333-391 (460)
227 KOG2875 consensus 59.2 12 0.00029 16.6 3.9 43 566-614 191-236 (323)
228 PRK08174 DNA topoisomerase III 59.1 5.5 0.00014 19.1 1.6 21 16-36 78-98 (670)
229 pfam10391 DNA_pol_lambd_f Fing 58.9 3.5 8.8E-05 20.6 0.6 25 481-510 5-29 (52)
230 PRK07141 DNA topoisomerase I; 58.9 4.1 0.0001 20.1 0.9 21 479-499 456-481 (622)
231 PRK06139 short chain dehydroge 58.9 7.9 0.0002 17.9 2.4 13 533-545 216-228 (324)
232 TIGR01588 citE citrate lyase, 58.5 7.9 0.0002 17.8 2.4 15 485-499 72-86 (288)
233 KOG2379 consensus 58.4 12 0.0003 16.5 7.4 29 557-585 433-461 (501)
234 TIGR01203 HGPRTase hypoxanthin 58.4 11 0.00029 16.6 3.2 20 12-31 3-22 (183)
235 KOG0323 consensus 58.3 7.3 0.00019 18.1 2.2 81 644-725 439-524 (635)
236 COG2176 PolC DNA polymerase II 58.1 4 0.0001 20.1 0.8 35 233-268 334-368 (1444)
237 TIGR02605 CxxC_CxxC_SSSS putat 58.0 4.1 0.0001 20.1 0.8 15 430-444 26-41 (43)
238 PRK10246 exonuclease subunit S 57.8 3.6 9.3E-05 20.5 0.5 13 429-441 501-513 (1047)
239 PRK02048 4-hydroxy-3-methylbut 57.4 8.6 0.00022 17.6 2.4 63 644-723 542-609 (613)
240 KOG0477 consensus 56.3 6.9 0.00018 18.3 1.8 65 646-710 543-621 (854)
241 PRK06200 2,3-dihydroxy-2,3-dih 56.1 12 0.00031 16.4 3.0 13 646-658 245-257 (263)
242 PRK07239 bifunctional uroporph 56.1 13 0.00033 16.2 4.7 163 93-305 39-208 (381)
243 PRK06556 vitamin B12-dependent 55.7 5.7 0.00015 18.9 1.3 87 16-117 95-182 (957)
244 PRK12496 hypothetical protein; 55.7 3.6 9.3E-05 20.5 0.2 21 294-315 87-107 (166)
245 COG1571 Predicted DNA-binding 55.6 8.1 0.00021 17.8 2.0 68 394-474 315-383 (421)
246 TIGR01054 rgy reverse gyrase; 55.5 13 0.00034 16.1 3.2 232 19-308 599-877 (1843)
247 PRK06319 DNA topoisomerase I/S 54.8 6.2 0.00016 18.6 1.3 21 16-36 59-79 (864)
248 COG3743 Uncharacterized conser 54.7 5.7 0.00015 18.9 1.1 43 482-529 71-113 (133)
249 TIGR00679 hpr-ser HPr(Ser) kin 54.7 8.7 0.00022 17.5 2.0 61 441-510 168-229 (309)
250 cd01075 NAD_bind_Leu_Phe_Val_D 54.6 14 0.00035 16.0 5.5 27 235-268 28-54 (200)
251 PRK06599 DNA topoisomerase I; 54.5 9.1 0.00023 17.4 2.1 36 15-51 56-96 (776)
252 PRK01390 murD UDP-N-acetylmura 54.4 14 0.00035 16.0 8.2 10 300-309 216-225 (457)
253 PRK03564 formate dehydrogenase 54.4 6.5 0.00017 18.5 1.4 10 431-440 187-196 (307)
254 KOG2906 consensus 53.9 4.9 0.00013 19.4 0.7 16 432-447 2-17 (105)
255 PRK05823 consensus 53.9 10 0.00025 17.1 2.3 20 17-36 72-91 (691)
256 smart00350 MCM minichromosome 53.6 5.4 0.00014 19.1 0.9 15 560-574 436-450 (509)
257 COG1458 Predicted DNA-binding 53.5 14 0.00036 15.9 5.9 55 656-723 157-211 (221)
258 pfam00122 E1-E2_ATPase E1-E2 A 53.1 5.3 0.00013 19.2 0.7 24 393-418 50-73 (222)
259 TIGR01647 ATPase-IIIA_H plasma 53.1 7.7 0.0002 17.9 1.6 16 395-411 117-132 (835)
260 PRK06197 short chain dehydroge 53.0 13 0.00033 16.2 2.7 14 152-165 21-34 (306)
261 cd00729 rubredoxin_SM Rubredox 52.9 4.7 0.00012 19.6 0.4 12 430-441 17-28 (34)
262 PRK10355 xylF D-xylose transpo 52.5 12 0.00032 16.3 2.6 45 257-308 47-91 (330)
263 PRK06500 short chain dehydroge 52.5 15 0.00037 15.8 3.2 15 644-658 232-246 (249)
264 PRK09001 DNA topoisomerase I; 52.4 6.8 0.00017 18.3 1.2 17 19-35 96-112 (869)
265 PRK12825 fabG 3-ketoacyl-(acyl 52.3 15 0.00037 15.8 2.9 16 644-659 233-248 (250)
266 COG4277 Predicted DNA-binding 52.2 12 0.00031 16.4 2.4 87 519-634 278-366 (404)
267 smart00279 HhH2 Helix-hairpin- 52.0 8.3 0.00021 17.7 1.6 19 596-614 16-34 (36)
268 TIGR02027 rpoA DNA-directed RN 51.8 13 0.00034 16.1 2.6 56 481-547 261-318 (324)
269 pfam09538 FYDLN_acid Protein o 51.7 5.8 0.00015 18.9 0.8 11 431-441 26-36 (104)
270 TIGR02354 thiF_fam2 thiamine b 51.4 6.8 0.00017 18.4 1.1 121 532-672 9-129 (200)
271 TIGR00143 hypF [NiFe] hydrogen 51.1 4.4 0.00011 19.8 0.1 28 650-677 748-777 (799)
272 PRK09202 nusA transcription el 50.8 9.1 0.00023 17.4 1.6 48 557-614 377-425 (428)
273 PRK00141 murD UDP-N-acetylmura 50.8 15 0.00039 15.6 8.5 12 300-311 225-236 (476)
274 PRK08628 short chain dehydroge 50.6 15 0.00039 15.6 2.8 16 644-659 236-251 (258)
275 COG2099 CobK Precorrin-6x redu 50.3 16 0.0004 15.6 5.5 48 649-709 174-226 (257)
276 pfam11672 DUF3268 Protein of u 50.3 6 0.00015 18.8 0.7 15 430-444 1-15 (102)
277 TIGR01900 dapE-gram_pos succin 50.2 9.7 0.00025 17.2 1.7 105 405-562 243-355 (373)
278 PRK03906 mannonate dehydratase 50.0 8.9 0.00023 17.4 1.5 83 89-200 30-112 (389)
279 TIGR01186 proV glycine betaine 49.9 7.5 0.00019 18.0 1.1 30 365-410 181-210 (372)
280 pfam06054 CoiA Competence prot 49.7 7 0.00018 18.3 0.9 18 251-268 66-83 (348)
281 pfam10941 DUF2620 Protein of u 49.6 16 0.00041 15.5 3.4 72 650-724 1-97 (117)
282 TIGR00789 flhB_rel FlhB domain 49.5 13 0.00033 16.2 2.3 24 699-722 34-57 (84)
283 TIGR02634 xylF D-xylose ABC tr 49.5 16 0.00041 15.5 3.3 13 530-542 165-177 (307)
284 TIGR00340 zpr1_rel zinc finger 49.3 5.9 0.00015 18.9 0.5 37 596-632 92-134 (168)
285 KOG0478 consensus 49.0 12 0.0003 16.5 2.0 44 657-700 534-585 (804)
286 COG1326 Uncharacterized archae 48.5 5.9 0.00015 18.8 0.4 15 358-372 90-105 (201)
287 PRK00080 ruvB Holliday junctio 48.3 13 0.00033 16.2 2.1 21 353-373 143-163 (328)
288 COG0474 MgtA Cation transport 48.3 8.2 0.00021 17.7 1.1 48 524-575 538-585 (917)
289 PRK05876 short chain dehydroge 48.2 17 0.00043 15.3 2.8 16 481-496 224-239 (275)
290 COG3845 ABC-type uncharacteriz 48.1 9.8 0.00025 17.1 1.5 43 354-412 167-221 (501)
291 pfam05876 Terminase_GpA Phage 48.1 15 0.00039 15.7 2.4 19 49-67 77-95 (552)
292 PRK00349 uvrA excinuclease ABC 47.7 17 0.00043 15.3 4.7 26 367-404 616-641 (944)
293 PRK05866 short chain dehydroge 47.6 17 0.00043 15.3 2.6 13 532-544 245-257 (290)
294 PRK05582 DNA topoisomerase I; 47.6 10 0.00026 17.0 1.5 22 15-36 57-78 (692)
295 PRK12823 benD 1,6-dihydroxycyc 47.3 17 0.00044 15.2 3.1 12 645-656 245-256 (260)
296 PRK09783 copper/silver efflux 47.3 7.3 0.00019 18.1 0.7 95 294-406 209-318 (407)
297 PRK13812 orotate phosphoribosy 47.2 17 0.00044 15.2 5.1 62 648-720 106-173 (174)
298 COG1997 RPL43A Ribosomal prote 47.1 9.6 0.00024 17.2 1.3 28 431-467 35-62 (89)
299 PRK09138 DNA topoisomerase I; 47.1 8.7 0.00022 17.5 1.1 35 430-467 601-635 (887)
300 pfam08745 UPF0278 UPF0278 fami 47.0 17 0.00044 15.2 3.5 52 656-722 150-203 (206)
301 TIGR01701 Fdhalpha-like oxidor 47.0 17 0.00045 15.2 3.2 81 648-729 502-596 (824)
302 TIGR01525 ATPase-IB_hvy heavy 47.0 11 0.00028 16.8 1.5 39 663-708 452-493 (639)
303 pfam11382 DUF3186 Protein of u 46.8 18 0.00045 15.2 5.7 14 130-143 77-90 (307)
304 PRK12278 50S ribosomal protein 46.6 8.4 0.00022 17.6 0.9 21 594-614 151-171 (216)
305 COG0773 MurC UDP-N-acetylmuram 46.6 18 0.00045 15.1 5.5 67 302-376 214-282 (459)
306 COG1885 Uncharacterized protei 46.6 7.6 0.00019 18.0 0.7 11 432-442 50-60 (115)
307 PRK00448 polC DNA polymerase I 46.4 8.4 0.00021 17.7 0.9 45 672-717 1345-1406(1436)
308 PRK08413 consensus 46.4 11 0.00029 16.6 1.6 21 16-36 59-79 (733)
309 PRK01710 murD UDP-N-acetylmura 46.3 18 0.00045 15.1 8.7 15 705-719 403-417 (458)
310 PRK13130 H/ACA RNA-protein com 46.3 8.6 0.00022 17.6 0.9 21 424-444 10-30 (54)
311 TIGR00588 ogg 8-oxoguanine DNA 46.0 11 0.00028 16.7 1.5 91 520-614 191-292 (379)
312 PRK08324 short chain dehydroge 45.8 18 0.00046 15.1 5.1 56 41-108 90-149 (676)
313 TIGR01523 ATPase-IID_K-Na pota 45.8 12 0.0003 16.5 1.6 40 313-354 329-368 (1001)
314 TIGR02194 GlrX_NrdH Glutaredox 45.8 13 0.00034 16.1 1.8 30 239-273 24-53 (72)
315 pfam04606 Ogr_Delta Ogr/Delta- 45.6 7.8 0.0002 17.9 0.6 37 433-470 1-39 (47)
316 PRK01216 DNA polymerase IV; Va 45.5 11 0.00029 16.6 1.5 49 479-540 179-227 (351)
317 TIGR00596 rad1 DNA repair prot 45.4 18 0.00047 15.0 3.8 50 557-618 884-935 (939)
318 cd00513 Ribosomal_L32_L32e Rib 45.3 3.7 9.3E-05 20.4 -1.1 36 479-514 36-72 (107)
319 COG0419 SbcC ATPase involved i 45.2 8.3 0.00021 17.7 0.7 14 431-444 457-470 (908)
320 COG1312 UxuA D-mannonate dehyd 45.1 14 0.00036 15.9 1.9 82 90-200 31-112 (362)
321 TIGR01562 FdhE formate dehydro 45.0 7.8 0.0002 17.9 0.6 80 167-271 15-94 (312)
322 smart00661 RPOL9 RNA polymeras 44.9 11 0.00029 16.6 1.4 29 432-467 1-29 (52)
323 pfam05559 DUF763 Protein of un 44.7 19 0.00048 14.9 4.3 32 581-612 254-285 (319)
324 PRK13809 orotate phosphoribosy 44.6 19 0.00048 14.9 5.8 68 648-726 117-190 (206)
325 PRK12859 3-ketoacyl-(acyl-carr 44.6 19 0.00048 14.9 4.9 14 644-657 241-254 (257)
326 TIGR00375 TIGR00375 conserved 44.4 19 0.00048 14.9 3.7 118 430-615 246-366 (384)
327 TIGR02339 thermosome_arch ther 44.4 19 0.00048 14.9 3.2 22 535-556 375-396 (522)
328 pfam01396 zf-C4_Topoisom Topoi 44.3 13 0.00033 16.2 1.6 30 433-466 3-32 (39)
329 PRK07062 short chain dehydroge 44.3 19 0.00049 14.9 2.9 15 644-658 247-261 (265)
330 PRK05867 short chain dehydroge 44.2 19 0.00049 14.9 2.9 14 644-657 236-249 (253)
331 PRK13945 formamidopyrimidine-D 44.0 8.7 0.00022 17.5 0.7 24 433-460 257-280 (283)
332 PRK06988 putative formyltransf 44.0 19 0.00049 14.9 5.9 15 704-718 293-307 (313)
333 PRK07677 short chain dehydroge 44.0 19 0.00049 14.9 3.0 14 644-657 233-246 (254)
334 PRK06701 short chain dehydroge 43.9 19 0.00049 14.8 3.9 15 152-166 50-64 (289)
335 TIGR03655 anti_R_Lar restricti 43.8 13 0.00032 16.3 1.5 10 433-442 3-12 (53)
336 PRK04358 hypothetical protein; 43.6 19 0.0005 14.8 3.4 55 656-725 163-219 (223)
337 PRK03922 hypothetical protein; 43.3 8.8 0.00023 17.5 0.6 11 432-442 50-60 (113)
338 pfam08442 ATP-grasp_2 ATP-gras 43.3 20 0.0005 14.8 3.4 43 254-306 4-46 (202)
339 COG5222 Uncharacterized conser 43.2 13 0.00033 16.2 1.5 112 362-490 199-330 (427)
340 TIGR01652 ATPase-Plipid phosph 43.2 9.9 0.00025 17.1 0.9 39 308-369 468-507 (1249)
341 PRK06128 oxidoreductase; Provi 43.2 20 0.0005 14.8 3.1 15 152-166 60-74 (300)
342 cd00528 MoaC MoaC family. Memb 43.1 20 0.0005 14.8 2.5 53 338-408 84-136 (136)
343 pfam04475 DUF555 Protein of un 43.1 8.9 0.00023 17.5 0.6 11 432-442 48-58 (102)
344 TIGR00715 precor6x_red precorr 43.1 20 0.00051 14.8 3.1 43 159-203 78-123 (260)
345 PRK07063 short chain dehydroge 43.0 20 0.00051 14.8 3.0 15 644-658 239-253 (259)
346 TIGR01367 pyrE_Therm orotate p 42.9 20 0.00051 14.7 3.5 27 649-679 111-143 (205)
347 PRK06194 hypothetical protein; 42.9 20 0.00051 14.7 2.6 20 473-494 160-179 (301)
348 TIGR02397 dnaX_nterm DNA polym 42.8 16 0.0004 15.5 1.9 20 465-484 177-196 (363)
349 COG3024 Uncharacterized protei 42.7 9.7 0.00025 17.1 0.8 34 431-488 7-40 (65)
350 PRK08277 D-mannonate oxidoredu 42.7 20 0.00051 14.7 3.1 15 645-659 259-273 (278)
351 PRK06079 enoyl-(acyl carrier p 42.5 20 0.00051 14.7 3.4 12 645-656 236-247 (252)
352 PRK07168 bifunctional uroporph 42.4 20 0.00052 14.7 6.4 130 335-498 207-348 (474)
353 PRK12495 hypothetical protein; 42.3 11 0.00027 16.8 0.9 13 432-444 43-55 (221)
354 PRK06550 fabG 3-ketoacyl-(acyl 42.3 20 0.00052 14.7 2.8 15 644-658 220-234 (237)
355 KOG4236 consensus 42.3 6.5 0.00017 18.5 -0.2 86 338-438 395-482 (888)
356 PRK08226 short chain dehydroge 42.3 20 0.00052 14.7 3.1 15 644-658 239-253 (263)
357 COG1579 Zn-ribbon protein, pos 42.3 7.6 0.00019 18.0 0.2 14 431-444 221-234 (239)
358 COG1327 Predicted transcriptio 42.1 11 0.00027 16.9 0.9 36 595-630 113-149 (156)
359 smart00834 CxxC_CXXC_SSSS Puta 42.0 11 0.00028 16.8 0.9 14 430-443 25-38 (41)
360 TIGR01512 ATPase-IB2_Cd cadmiu 41.8 14 0.00035 16.0 1.4 54 316-375 268-324 (494)
361 PRK10517 magnesium-transportin 41.8 12 0.0003 16.5 1.0 15 365-379 564-578 (900)
362 COG4213 XylF ABC-type xylose t 41.8 13 0.00033 16.2 1.3 20 465-484 200-219 (341)
363 PRK07758 hypothetical protein; 41.7 19 0.00048 15.0 2.1 24 522-545 67-90 (95)
364 COG3791 Uncharacterized conser 41.6 10 0.00026 17.0 0.7 42 433-477 71-112 (133)
365 PRK13810 orotate phosphoribosy 41.4 21 0.00053 14.6 5.5 60 648-718 121-186 (187)
366 PRK08217 fabG 3-ketoacyl-(acyl 41.3 21 0.00053 14.6 3.1 11 646-656 239-249 (253)
367 PRK06227 consensus 41.3 21 0.00054 14.6 2.9 15 644-658 234-248 (256)
368 PRK05855 short chain dehydroge 41.3 21 0.00054 14.6 3.2 26 474-499 312-340 (582)
369 COG2100 Predicted Fe-S oxidore 41.2 21 0.00054 14.6 4.9 15 601-615 265-279 (414)
370 PRK01103 formamidopyrimidine-D 41.2 11 0.00028 16.7 0.8 24 433-460 246-269 (273)
371 PRK06171 sorbitol-6-phosphate 41.2 21 0.00054 14.6 2.9 15 644-658 249-263 (266)
372 TIGR01082 murC UDP-N-acetylmur 41.1 21 0.00054 14.5 4.4 66 276-346 198-265 (491)
373 COG2216 KdpB High-affinity K+ 40.9 19 0.00048 15.0 2.0 16 217-232 201-216 (681)
374 cd00350 rubredoxin_like Rubred 40.7 10 0.00027 16.9 0.7 12 430-441 16-27 (33)
375 PRK04690 murD UDP-N-acetylmura 40.6 21 0.00055 14.5 8.1 14 592-605 453-466 (468)
376 COG2260 Predicted Zn-ribbon RN 40.6 13 0.00034 16.1 1.2 20 425-444 11-30 (59)
377 PRK07231 fabG 3-ketoacyl-(acyl 40.6 21 0.00055 14.5 2.8 14 644-657 234-247 (250)
378 PRK00464 nrdR transcriptional 40.6 14 0.00035 16.0 1.2 34 595-628 113-147 (149)
379 PRK07985 oxidoreductase; Provi 40.4 22 0.00055 14.5 3.1 14 153-166 55-68 (294)
380 TIGR02109 PQQ_syn_pqqE coenzym 40.4 10 0.00026 17.0 0.6 74 485-585 92-167 (363)
381 PRK06057 short chain dehydroge 40.3 22 0.00055 14.5 5.8 15 644-658 233-247 (255)
382 PRK08220 2,3-dihydroxybenzoate 40.3 22 0.00055 14.5 3.1 14 644-657 235-248 (253)
383 PRK08063 enoyl-(acyl carrier p 40.1 22 0.00056 14.4 2.6 14 644-657 232-245 (250)
384 PRK08993 2-deoxy-D-gluconate 3 40.0 22 0.00056 14.4 6.5 13 645-657 237-249 (253)
385 PRK05854 short chain dehydroge 39.9 22 0.00056 14.4 3.5 14 152-165 19-32 (314)
386 PTZ00159 60S ribosomal protein 39.8 8.1 0.00021 17.8 -0.0 55 454-513 32-87 (134)
387 PRK10445 endonuclease VIII; Pr 39.7 12 0.0003 16.5 0.8 24 433-460 237-260 (263)
388 pfam11290 DUF3090 Protein of u 39.4 19 0.00049 14.9 1.9 24 411-444 144-167 (171)
389 TIGR02187 GlrX_arch Glutaredox 39.4 14 0.00035 16.0 1.1 14 398-411 121-134 (237)
390 PRK08351 DNA-directed RNA poly 39.4 12 0.0003 16.5 0.8 18 429-446 13-31 (61)
391 PRK07889 enoyl-(acyl carrier p 39.3 22 0.00057 14.3 3.1 13 645-657 238-250 (256)
392 PRK06172 short chain dehydroge 39.2 22 0.00057 14.3 2.8 15 644-658 236-250 (253)
393 COG2093 DNA-directed RNA polym 39.1 10 0.00027 16.9 0.4 18 428-445 13-33 (64)
394 PRK06463 fabG 3-ketoacyl-(acyl 39.0 23 0.00058 14.3 7.2 14 644-657 232-245 (254)
395 PRK07791 short chain dehydroge 38.7 23 0.00058 14.3 3.2 14 644-657 242-255 (285)
396 PRK07109 short chain dehydroge 38.7 23 0.00058 14.3 2.9 12 153-164 14-25 (338)
397 cd01701 Pol_zeta Pol_zeta, a m 38.7 18 0.00046 15.1 1.6 16 482-497 228-243 (405)
398 PRK02406 DNA polymerase IV; Va 38.6 18 0.00045 15.1 1.6 27 482-513 184-210 (355)
399 PRK05270 galactose-1-phosphate 38.4 23 0.00059 14.3 3.4 12 262-273 205-216 (496)
400 PRK08936 glucose-1-dehydrogena 38.3 23 0.00059 14.2 3.1 15 645-659 237-251 (261)
401 cd02173 ECT CTP:phosphoethanol 38.2 23 0.00059 14.2 5.6 29 524-552 119-147 (152)
402 PRK06603 enoyl-(acyl carrier p 38.2 23 0.00059 14.2 4.5 15 644-658 238-252 (260)
403 PRK07825 short chain dehydroge 38.1 23 0.0006 14.2 2.8 15 532-546 203-217 (273)
404 TIGR02869 spore_SleB spore cor 37.9 17 0.00044 15.2 1.4 31 467-497 40-71 (232)
405 PRK08562 rpl32e 50S ribosomal 37.9 5.5 0.00014 19.0 -1.1 26 488-513 67-92 (127)
406 pfam08394 Arc_trans_TRASH Arch 37.7 16 0.0004 15.6 1.1 37 434-472 1-37 (37)
407 TIGR00577 fpg formamidopyrimid 36.9 16 0.0004 15.5 1.1 27 432-460 260-290 (292)
408 COG3058 FdhE Uncharacterized p 36.8 12 0.00032 16.3 0.6 12 431-442 185-196 (308)
409 COG0266 Nei Formamidopyrimidin 36.7 13 0.00034 16.1 0.7 24 433-460 247-270 (273)
410 PRK11827 hypothetical protein; 36.6 17 0.00042 15.4 1.2 15 433-447 10-24 (60)
411 pfam01655 Ribosomal_L32e Ribos 36.6 5.3 0.00013 19.2 -1.4 27 487-513 47-73 (110)
412 PRK03754 DNA-directed RNA poly 36.5 13 0.00034 16.1 0.7 13 433-445 26-38 (49)
413 PRK07060 short chain dehydroge 36.4 25 0.00063 14.0 3.1 15 644-658 228-242 (245)
414 PRK07792 fabG 3-ketoacyl-(acyl 36.4 25 0.00063 14.0 2.9 14 644-657 237-250 (303)
415 TIGR02098 MJ0042_CXXC MJ0042 f 36.3 19 0.00048 14.9 1.4 30 431-460 2-32 (40)
416 pfam08645 PNK3P Polynucleotide 36.2 25 0.00063 14.0 2.7 46 666-714 102-157 (158)
417 PRK03352 DNA polymerase IV; Va 36.2 21 0.00052 14.6 1.6 27 482-513 181-207 (345)
418 cd01703 Pol_iota Pol iota is m 36.1 21 0.00053 14.6 1.6 49 482-542 214-262 (394)
419 PRK02794 DNA polymerase IV; Pr 35.8 22 0.00055 14.5 1.6 31 481-516 212-242 (417)
420 COG4888 Uncharacterized Zn rib 35.8 14 0.00037 15.8 0.7 11 433-443 24-34 (104)
421 pfam06750 DiS_P_DiS Bacterial 35.8 13 0.00034 16.1 0.6 19 428-446 24-42 (86)
422 KOG1247 consensus 35.7 9.5 0.00024 17.2 -0.2 49 189-237 198-250 (567)
423 PRK00241 nudC NADH pyrophospha 35.6 17 0.00043 15.3 1.1 13 432-444 101-113 (257)
424 PRK13638 cbiO cobalt transport 35.6 23 0.00059 14.3 1.7 31 365-411 186-216 (271)
425 LOAD_Hrd consensus 35.4 26 0.00065 13.9 4.1 26 591-616 42-67 (77)
426 TIGR02311 HpaI 2,4-dihydroxyhe 35.3 24 0.0006 14.2 1.8 68 557-629 111-194 (249)
427 PRK12367 short chain dehydroge 35.3 26 0.00065 13.9 4.4 23 145-168 16-38 (250)
428 TIGR02390 RNA_pol_rpoA1 DNA-di 35.3 14 0.00036 15.9 0.6 63 39-115 124-195 (901)
429 KOG4169 consensus 35.2 26 0.00066 13.9 2.6 17 151-167 9-25 (261)
430 PRK03918 chromosome segregatio 35.1 14 0.00036 15.9 0.6 12 432-443 439-450 (882)
431 cd01403 Cyt_c_Oxidase_VIIb Cyt 35.1 22 0.00055 14.5 1.5 21 335-355 27-47 (51)
432 PTZ00180 60S ribosomal protein 35.1 26 0.00066 13.9 4.7 87 328-443 34-120 (260)
433 PRK12829 short chain dehydroge 35.1 26 0.00066 13.9 2.9 16 644-659 247-262 (264)
434 pfam04423 Rad50_zn_hook Rad50 35.0 14 0.00035 16.0 0.5 10 433-442 22-31 (54)
435 COG1570 XseA Exonuclease VII, 35.0 26 0.00066 13.9 3.1 16 99-114 3-18 (440)
436 PRK08416 7-alpha-hydroxysteroi 35.0 26 0.00066 13.9 3.1 13 645-657 244-256 (260)
437 PRK09242 tropinone reductase; 34.5 26 0.00067 13.8 3.1 15 644-658 239-253 (258)
438 PRK01122 potassium-transportin 34.5 17 0.00043 15.3 0.9 56 648-708 511-570 (684)
439 PRK13811 orotate phosphoribosy 34.5 26 0.00067 13.8 6.6 63 645-718 100-168 (170)
440 PRK12826 3-ketoacyl-(acyl-carr 34.5 26 0.00067 13.8 2.9 13 645-657 236-248 (253)
441 pfam11376 DUF3179 Protein of u 34.5 14 0.00035 16.0 0.5 11 133-143 54-64 (261)
442 TIGR02487 NrdD anaerobic ribon 34.5 15 0.00038 15.7 0.6 86 479-607 414-508 (655)
443 COG1569 Predicted nucleic acid 34.4 25 0.00063 14.0 1.7 38 681-720 101-139 (142)
444 PRK06997 enoyl-(acyl carrier p 34.4 26 0.00067 13.8 3.2 15 644-658 237-251 (260)
445 PRK08245 hypothetical protein; 34.4 26 0.00067 13.8 4.0 21 349-369 149-169 (239)
446 PRK12429 3-hydroxybutyrate deh 34.4 26 0.00067 13.8 3.0 14 645-658 242-255 (258)
447 PRK11281 potassium efflux prot 34.2 18 0.00047 15.0 1.1 45 659-705 964-1014(1107)
448 COG1137 YhbG ABC-type (unclass 34.1 17 0.00043 15.3 0.8 10 603-612 169-178 (243)
449 PRK07562 ribonucleotide-diphos 34.1 21 0.00053 14.6 1.4 94 14-118 103-225 (1177)
450 pfam00406 ADK Adenylate kinase 33.9 26 0.00065 13.9 1.8 34 428-477 139-172 (186)
451 pfam01967 MoaC MoaC family. Me 33.7 27 0.00069 13.7 2.9 52 339-408 85-136 (136)
452 KOG2661 consensus 33.7 23 0.00059 14.2 1.5 16 424-439 256-271 (424)
453 PRK00724 formate dehydrogenase 33.7 27 0.00069 13.7 4.6 52 646-710 196-247 (262)
454 COG1717 RPL32 Ribosomal protei 33.6 21 0.00055 14.5 1.3 28 488-515 68-95 (133)
455 TIGR01011 rpsB_bact ribosomal 33.5 22 0.00057 14.4 1.4 24 533-556 74-99 (227)
456 pfam05129 Elf1 Transcription e 33.4 10 0.00027 16.9 -0.3 30 430-459 14-45 (74)
457 PRK11033 zntA zinc/cadmium/mer 33.2 19 0.00048 14.9 1.0 25 393-419 256-280 (739)
458 TIGR01051 topA_bact DNA topois 33.2 16 0.00041 15.5 0.6 18 560-577 562-579 (688)
459 PRK08589 short chain dehydroge 33.1 28 0.0007 13.7 3.0 18 644-661 238-255 (272)
460 pfam01215 COX5B Cytochrome c o 33.1 16 0.0004 15.5 0.6 10 431-440 81-90 (99)
461 PRK07523 gluconate 5-dehydroge 33.1 28 0.0007 13.6 2.7 15 644-658 233-247 (251)
462 PRK13646 cbiO cobalt transport 32.9 28 0.00071 13.6 1.8 31 365-411 196-226 (286)
463 PRK00694 4-hydroxy-3-methylbut 32.9 13 0.00033 16.2 0.1 66 644-726 534-604 (606)
464 PRK10671 copA copper exporting 32.8 20 0.00051 14.7 1.1 24 394-419 340-363 (834)
465 PRK08690 enoyl-(acyl carrier p 32.5 28 0.00072 13.6 3.2 13 645-657 239-251 (261)
466 pfam09889 DUF2116 Uncharacteri 32.4 20 0.0005 14.8 1.0 30 430-471 2-31 (59)
467 TIGR01161 purK phosphoribosyla 32.4 28 0.00072 13.6 3.8 54 251-320 100-154 (386)
468 COG4068 Uncharacterized protei 32.4 14 0.00035 16.0 0.2 16 429-444 6-21 (64)
469 KOG4450 consensus 32.3 23 0.00058 14.3 1.3 21 172-194 54-75 (168)
470 PRK07041 short chain dehydroge 32.1 29 0.00073 13.5 3.1 15 152-166 12-26 (240)
471 PRK06523 short chain dehydroge 32.1 29 0.00073 13.5 3.6 15 643-657 241-255 (260)
472 TIGR00705 SppA_67K signal pept 32.0 29 0.00073 13.5 4.0 36 139-174 322-358 (614)
473 PRK08270 anaerobic ribonucleos 32.0 17 0.00044 15.2 0.7 10 359-368 283-292 (681)
474 PRK09072 short chain dehydroge 31.9 29 0.00073 13.5 2.8 16 532-547 208-223 (262)
475 pfam08996 zf-DNA_Pol DNA Polym 31.9 29 0.00073 13.5 1.8 25 420-446 9-33 (186)
476 PRK06138 short chain dehydroge 31.9 29 0.00074 13.5 2.9 31 647-678 3-33 (252)
477 TIGR00463 gltX_arch glutamyl-t 31.8 29 0.00073 13.5 1.7 20 184-203 454-473 (600)
478 TIGR02870 spore_II_D stage II 31.7 15 0.00037 15.8 0.2 73 320-410 227-314 (358)
479 TIGR01966 RNasePH ribonuclease 31.6 29 0.00074 13.5 2.6 22 649-670 186-218 (237)
480 PRK12828 short chain dehydroge 31.6 29 0.00074 13.5 3.3 34 644-678 2-35 (239)
481 COG2816 NPY1 NTP pyrophosphohy 31.5 26 0.00066 13.8 1.5 22 433-460 113-134 (279)
482 pfam03129 HGTP_anticodon Antic 31.4 29 0.00075 13.4 3.6 43 664-714 18-63 (93)
483 PRK06720 hypothetical protein; 31.3 29 0.00075 13.4 3.1 31 647-678 14-44 (169)
484 PRK07890 short chain dehydroge 31.3 29 0.00075 13.4 3.1 31 647-678 3-33 (258)
485 KOG2463 consensus 31.3 16 0.00041 15.4 0.4 10 432-441 258-267 (376)
486 pfam06676 DUF1178 Protein of u 31.3 18 0.00045 15.1 0.6 9 434-442 35-43 (145)
487 PRK12428 3-alpha-hydroxysteroi 31.2 29 0.00075 13.4 2.9 31 647-678 3-33 (261)
488 TIGR00515 accD acetyl-CoA carb 31.1 20 0.00051 14.7 0.8 41 432-476 34-74 (292)
489 PHA00439 exonuclease 31.1 23 0.00058 14.3 1.1 15 558-572 191-205 (288)
490 PHA00732 hypothetical protein 31.0 27 0.00068 13.8 1.5 49 433-486 3-53 (79)
491 COG1888 Uncharacterized protei 31.0 30 0.00076 13.4 4.1 29 649-679 50-78 (97)
492 PRK07577 short chain dehydroge 31.0 30 0.00076 13.4 2.7 31 647-678 1-31 (234)
493 PRK06935 2-deoxy-D-gluconate 3 30.9 30 0.00076 13.4 2.8 31 647-678 13-43 (258)
494 PRK10348 ribosome-associated h 30.8 30 0.00076 13.4 2.6 28 361-409 36-63 (133)
495 PRK07776 consensus 30.7 30 0.00076 13.4 2.9 31 647-678 6-36 (252)
496 pfam09297 zf-NADH-PPase NADH p 30.7 26 0.00067 13.8 1.4 22 433-460 5-26 (32)
497 PRK12742 oxidoreductase; Provi 30.7 30 0.00077 13.4 3.1 33 645-678 2-34 (237)
498 pfam08605 Rad9_Rad53_bind Fung 30.7 13 0.00032 16.3 -0.2 42 375-429 51-92 (131)
499 pfam02680 DUF211 Uncharacteriz 30.7 30 0.00077 13.4 5.2 61 617-679 15-76 (91)
500 TIGR02389 RNA_pol_rpoA2 DNA-di 30.6 24 0.00061 14.1 1.2 78 604-687 48-140 (397)
No 1
>TIGR00575 dnlj DNA ligase, NAD-dependent; InterPro: IPR001679 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 family is predominantly composed of NAD-dependent bacterial DNA ligases. They 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.; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair.
Probab=100.00 E-value=0 Score=1781.73 Aligned_cols=663 Identities=42% Similarity=0.733 Sum_probs=619.6
Q ss_pred HHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCHHHCCCCCCCCCCCCCCCCCCC-CCEEECCCCCCCHHHCC
Q ss_conf 99999999984331779820878999999999999897720311589999620036432357-75045166425702159
Q gi|254781172|r 24 LEQEISYHDDCYYQYSKPIILDSEYDALKRRCDAIAHAFPDLARSEDPNGPLNKIGGEMNLS-LFKVTHSIPTLSLEKIW 102 (731)
Q Consensus 24 L~~~i~~~~~~Yy~~~~p~isD~eYD~L~~~L~~le~~~p~~~~~~~p~spt~~Vg~~~~~~-~~kv~H~~pMlSL~k~~ 102 (731)
|++.|++|+|.||++++|.|||++||+|+++|++||++||+|+ +|||||||||+.+.+. |.||+|..|||||||+|
T Consensus 1 L~~~i~~h~y~YYVld~P~i~D~~YD~L~~~L~~LE~~~PeL~---~pDSPTqrVG~~~~~~~F~~v~H~~PMLSLdNAF 77 (706)
T TIGR00575 1 LRKLIRKHDYRYYVLDEPSISDAEYDRLMRELQELEEKHPELI---TPDSPTQRVGAAPLSADFPKVRHSTPMLSLDNAF 77 (706)
T ss_pred CHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCC---CCCCCCCCCCCHHHCCCCCCCCCCCCCCCHHHCC
T ss_conf 9467776755134657798882888899999999865488853---6898642137600215787267776520132214
Q ss_pred CHHHHHHHHHHHHHHHCCCCC--CCCEEEEEEECCEEEEEEEEECCEEEEEEECCCCHHHHHHHHHHHHHCCCCCCCCC-
Q ss_conf 999999999999986124677--76119999415818999998599899888659865566699977531024322335-
Q gi|254781172|r 103 NIEDLRKFITRIYRFWQKKDD--NSIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPTIPRVLSL- 179 (731)
Q Consensus 103 ~~~el~~w~~~~~~~~~~~~~--~~~~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n~~~i~~iP~~l~~- 179 (731)
+.+||.+|.+|+.+.+..... ....|+|||||||+||+|+||||.|++|+|||||.+|||||.|+|||++||++|..
T Consensus 78 ~~~el~~f~~R~~~~~~~~~~~~~~~~~~~EpKiDG~s~~L~Ye~G~L~~A~TRGDG~~GEDvT~NvrTI~~IP~~~~~~ 157 (706)
T TIGR00575 78 DEDELRAFIKRIRRALGSKEKQEEKVEYVVEPKIDGLSISLTYENGVLVRAATRGDGTTGEDVTANVRTIRSIPLRLAGD 157 (706)
T ss_pred CHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCEEEEEEEECCEEEEEEECCCCCCCCCHHCCCHHHCCCCCCCCCC
T ss_conf 88899999999998603335755460689702427157889983765898667488833751211302100244413588
Q ss_pred ---CCCCEEEEEEEEEEECHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCHHHH-HCCCEEEEEEEC--CCCCCC---
Q ss_conf ---44550489999998520212345564314854334234567777523455553-011105664102--454332---
Q gi|254781172|r 180 ---NIPEIIEVRGEVYISKNDFLALNDEMIAVGRKPYANPRNAASGILRRLNPTDI-TRYLNFFVHGLG--KTSEIF--- 250 (731)
Q Consensus 180 ---~~~~~ieiRGEv~m~~~~F~~lN~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~-~r~L~f~ay~~~--~~~~~~--- 250 (731)
+.|..+||||||||++++|++||+++.+.|+++|||||||||||||||||+++ .|+|+|++|+++ ......
T Consensus 158 ~~~n~p~~~EvRGEVf~~k~~F~~lN~~~~~~ge~~FANPRNaAAGsLRqlDp~ita~R~L~~~~Y~~G~~~~~~~~~~L 237 (706)
T TIGR00575 158 GVGNPPERLEVRGEVFMPKEDFEALNEERLEEGEKPFANPRNAAAGSLRQLDPRITAKRKLRFFAYGLGNAEGLELKGSL 237 (706)
T ss_pred CCCCCCCEEEEEEEEEECHHHHHHHHHHHHHCCCCCCCCCCHHHCCCEECCCCCCEECCCCEEEEEECCCCCCCCCCCCC
T ss_conf 87664325898436885658999999999970889666841333130000473111116636898762554577777657
Q ss_pred -CCCCHHHHHHHHHCCCC-CCCCEEEEE--CCCCHHHHHHHHHHHHCCCCCCCCCEEEEECCHHCCCCCCCCCCCCCCEE
Q ss_conf -10000368999975996-654148874--03211345566553100112343763777311000111587656866312
Q gi|254781172|r 251 -AKGQYEMLQKMRCLGFP-VNNGVRQAN--TFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSLQKQLGERARSPRWMI 326 (731)
Q Consensus 251 -~~~~~e~l~~L~~~GF~-v~~~~~~~~--~~~~~~~~~~~~~~~r~~l~y~iDGiVikvn~~~~q~~lG~ts~~Prwai 326 (731)
+.||++.|++|++|||+ |+++...|. +.++|++++++|.+.|+.|||+|||+|||||++++|+.||+|||+|||||
T Consensus 238 ~~~t~~~~L~~L~~~GF~TV~~~~~~~~ln~~~eV~~~~~~~~~~R~~L~y~IDGvV~Kvd~l~~Q~~LG~t~k~PRWAi 317 (706)
T TIGR00575 238 PFRTQYEALAWLKKLGFPTVNPHIRLCKLNSIEEVLEYYEEIEKKRDSLPYEIDGVVVKVDDLALQEELGFTSKAPRWAI 317 (706)
T ss_pred CCCCHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCHHHHHHHCHHCCCCCHHH
T ss_conf 86778999999986388420125776303898899999999998752078730437898378799987111027860010
Q ss_pred EECCCCCEEEEEEEEEEEEECCCCEEEEEEEEEEEEECCCEEEEECCCCHHHHHHHCCCCCCCCCCCCCCCCCEEEEEEC
Q ss_conf 31145621589987889940356225899997433302640001014898999750234543222468440768999835
Q gi|254781172|r 327 SHKFAEKQASTRLLDIDIQIGRTGILTPVARLEPVNIGGALITNATLHNEDYIKGLDASGKVMRGGRDIRVGDRVLVKRA 406 (731)
Q Consensus 327 A~Kf~~e~~~T~v~~I~wqvgRtG~itPva~~ePV~l~G~~V~ratlhN~~~I~~l~~~~~~~~~~~~I~iGd~V~I~Ra 406 (731)
||||||+++.|+|+||+|||||||+|||||.||||.|+|||||||||||.|||++ +||||||+|+|.||
T Consensus 318 AYKFpa~e~~T~L~dv~~qVGRTG~iTPvA~LePV~vaG~~Vs~ATLHN~D~I~~-----------kdiriGD~Vvv~kA 386 (706)
T TIGR00575 318 AYKFPAEEAQTKLLDVVVQVGRTGAITPVAKLEPVFVAGTTVSRATLHNEDEIEE-----------KDIRIGDTVVVRKA 386 (706)
T ss_pred CCCCCCCCCCEEEEEEEEEECCEEEECCEEEECCEEECCEEEEEEEECCHHHHHC-----------CCCCCCCEEEEEEC
T ss_conf 2366743010089878998465677600367565587207862344016002420-----------27665888999844
Q ss_pred CCCHHHHHHHCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCHHHHHHHHHHHHHCCCCCHHHH
Q ss_conf 87025665410123578730477704326577501033786544521010035434411446655332130123103541
Q gi|254781172|r 407 GEVIPKVVDIIVNERHPDAQPFSFPSFCPICQSRVVRDLNPKTGKLVAAHRCTGGLACSAQQLERLKHFVSRDAFNIEGL 486 (731)
Q Consensus 407 GdVIP~I~~Vi~~~r~~~~~~~~~P~~CP~Cgs~l~~~~~~~~~~~~~~~rC~n~~~Cpaq~~~~i~hF~SK~aldI~GL 486 (731)
|||||+|++|+.++|++++++|.||++||+|||+|++..++ +++||+|+.+||+|..++|.|||||+||||+||
T Consensus 387 GdVIP~vv~v~~~~R~~~~~~~~~P~~CP~C~s~lv~~~~e------~~~rC~Ng~~Cpa~~~e~i~hFaSr~AmdI~GL 460 (706)
T TIGR00575 387 GDVIPKVVEVLLEKRTGEERPIKFPTHCPSCGSPLVRIEEE------VDIRCTNGLNCPAQLVERIKHFASRNAMDIDGL 460 (706)
T ss_pred CCCCHHHHHCCCCCCCCCCCEEECCCCCCCCCCEEECCCCC------EEEECCCCCCCHHHHHHHEEEEEEECCCCCCCC
T ss_conf 86253554102357888887034287188888331115787------216538876653676511023454110332222
Q ss_pred HHHHHHHHHCCCCCCEEEEEHHHHCCHHHHHHHHCCCCCCCCC-CCCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHH
Q ss_conf 0355556530576540454101101067775310001000134-210014568999987522346667763010111168
Q gi|254781172|r 487 GKQQLDFFFKSEDPAFSIRIPADIFTLQRRQQTSTTKIENILG-FGDVSVTNLYDSINKRRNISLERFIFSLGIRHVGAE 565 (731)
Q Consensus 487 G~k~Ie~L~e~~~~~g~I~~~~DLy~L~~~~~~~~~~l~~l~G-fgeKsa~nL~~sIe~sK~~~L~r~L~ALGI~~vG~~ 565 (731)
|+++|++|+|++ +|++++|||+|+.+ .++|+++|| ||+|||+||++||++||+.||+|||+||||||||+.
T Consensus 461 G~~~I~~LfE~~----Lv~~~~DLY~L~~k----~~~Ll~le~~~g~~sa~nLl~aIe~sK~~pl~RlL~aLGIr~VG~~ 532 (706)
T TIGR00575 461 GEKVIEQLFEEK----LVRSVADLYALKEK----LEDLLELEGKFGEKSAQNLLSAIEKSKKKPLARLLFALGIRHVGEV 532 (706)
T ss_pred CHHHHHHHHHCC----CCCCHHHHHHHHHH----HHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHH
T ss_conf 389999998726----66785666577889----9998706403556889999999998521048999986286035799
Q ss_pred HHHHHHHHCCCHHHHHHHHHH-HHHCCCCCHHHHHCCCCCCHHHHHHHHHHHCCHHHH--------HHHHHHHHHCCCCC
Q ss_conf 999999882998999997897-761251177876138886789999999996697999--------99999997338776
Q gi|254781172|r 566 IARSLAKYYLSYQNFAQEINN-IIAHNNDDWLSLIRVPLVGDIIAQAIVEFYQNPRNI--------CAVEALLKEVSPSI 636 (731)
Q Consensus 566 ~Ak~La~~f~si~~l~~~~~~-~~~~~~~~~e~L~~I~GiG~~~A~si~~ff~~~~n~--------~~i~~L~~~~~~~~ 636 (731)
+|+.|+++|.|++++.++..+ +-.....+..+|++|+|||+++|++|++||+++.|. +++++|...++...
T Consensus 533 ~A~~La~~f~tl~~L~~A~~e~~~~~~~f~~s~L~~~~g~G~~vA~~~~~~F~~~~~~~~qPYRta~~~~~L~~~gv~~~ 612 (706)
T TIGR00575 533 TAKLLAKHFGTLDKLKAASLETLESIYQFDRSELLSVEGVGPKVAESIVNFFHDPNNLSLQPYRTAELIEKLEELGVNME 612 (706)
T ss_pred HHHHHHHHCCCHHHHHHCCHHHHHHHHHHCCHHHHHCCCCHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHCCCH
T ss_conf 99999985588689985082167788751605564101402789999999871200013560468999999988316310
Q ss_pred C----------CCC-----CCCCCCCCCCEEEEECCCCCCCHHHHHHHHHHCCCEEEEEEECCEEEEEECCCCCC-HHHH
Q ss_conf 5----------432-----24688216866999725889987899999998298499811163217997788886-3798
Q gi|254781172|r 637 G----------RHE-----KNVSSEIENKKLVFTGTLQKIQRHKAQEYVTQLGAVVSAILSRKTDIIIVGDNPGS-KLEK 700 (731)
Q Consensus 637 ~----------~~~-----~~~~~~l~gk~vV~TGtl~~~~R~e~~~~ie~~Ggkv~sSVSkkT~~LI~ge~~gS-Kl~K 700 (731)
. ... ...+++|+||+|||||+|++|||++++++|+++||||+||||+||||||+|++||| |++|
T Consensus 613 ~~D~~~~LL~~~~~~~~~~~~~~~~~~GK~fVlTG~L~~~sR~~a~~~~~~lGgkv~sSVS~kTD~viaG~~aGs~Kl~k 692 (706)
T TIGR00575 613 SEDEFCRLLDQALKEKVEAELAGSPLAGKTFVLTGTLSQMSRDEAKELLEALGGKVASSVSKKTDYVIAGEKAGSRKLAK 692 (706)
T ss_pred HHHHHHHHHHHHHHHHCCCCCCCCCCCCCEEEEECCCCCCCHHHHHHHHHHHCCEEECCCEEEEEEEEEECCCCHHHHHH
T ss_conf 11357877764201100100057520277689951568888899999999809978004000440789855855468999
Q ss_pred HHHCCCEEECHHHH
Q ss_conf 99749917379999
Q gi|254781172|r 701 AQQLGVKIMNEEQF 714 (731)
Q Consensus 701 A~~LgI~Ii~e~ef 714 (731)
|++|||+||||++|
T Consensus 693 A~~Lgi~il~Ee~l 706 (706)
T TIGR00575 693 AQELGIPILNEEEL 706 (706)
T ss_pred HHHCCCCCCCCCCC
T ss_conf 99718942343149
No 2
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=100.00 E-value=0 Score=1659.17 Aligned_cols=666 Identities=42% Similarity=0.732 Sum_probs=637.3
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCHHHCCCCCCCCCCCCCCCCCCCCCEEECC
Q ss_conf 99999999999999999999843317798208789999999999998977203115899996200364323577504516
Q gi|254781172|r 13 SIEQARKELSSLEQEISYHDDCYYQYSKPIILDSEYDALKRRCDAIAHAFPDLARSEDPNGPLNKIGGEMNLSLFKVTHS 92 (731)
Q Consensus 13 s~~~~~~~i~~L~~~i~~~~~~Yy~~~~p~isD~eYD~L~~~L~~le~~~p~~~~~~~p~spt~~Vg~~~~~~~~kv~H~ 92 (731)
+|+++++||.+|+++|++||++||++++|+|||+|||+|+++|+.||++||++. +||||||+||+.+..+|.||+|+
T Consensus 1 ~m~~~~~~i~~L~~~i~~~n~~YY~~~~p~isD~eYD~L~~eL~~lE~~~P~~~---~~~SPt~~VG~~~~~~f~kv~H~ 77 (668)
T PRK07956 1 TMEEAKKRIEELREELNHHAYAYYVLDNPEISDAEYDRLYRELLALEAEHPELI---TPDSPTQRVGGAPLDGFEKVRHL 77 (668)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHCCCCC---CCCCCCCCCCCCCCCCCCCCCCC
T ss_conf 977999999999999999999864389987888999999999999998690555---89998443366612478733689
Q ss_pred CCCCCHHHCCCHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCEEEEEEEEECCEEEEEEECCCCHHHHHHHHHHHHHCC
Q ss_conf 64257021599999999999999861246777611999941581899999859989988865986556669997753102
Q gi|254781172|r 93 IPTLSLEKIWNIEDLRKFITRIYRFWQKKDDNSIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPT 172 (731)
Q Consensus 93 ~pMlSL~k~~~~~el~~w~~~~~~~~~~~~~~~~~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n~~~i~~ 172 (731)
.|||||+|+|+.+||.+|++|+.+.+. .....|+||||+||+|++|+|++|+|++|+|||||.+|||||+|+++|++
T Consensus 78 ~pMlSL~k~~~~~el~~~~~r~~k~l~---~~~~~~~~epKiDGlsisL~Ye~G~L~~a~TRGdG~~GeDVT~nv~~I~~ 154 (668)
T PRK07956 78 VPMLSLDNAFSEEELRAFDKRVRKRLS---GPSLTYVCELKIDGLAVSLLYENGVLVRAATRGDGTTGEDITANVRTIRS 154 (668)
T ss_pred CCCCCCCCCCCHHHHHHHHHHHHHHCC---CCCCCEEEEEECCCEEEEEEEECCEEEEEECCCCCCCHHHHHHHHHHHCC
T ss_conf 877460133999999999999998618---88865798860461689999989999887615899731338788876526
Q ss_pred CCCCCCCCCCCEEEEEEEEEEECHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCHHHH-HCCCEEEEEEECCCC-CCC
Q ss_conf 432233544550489999998520212345564314854334234567777523455553-011105664102454-332
Q gi|254781172|r 173 IPRVLSLNIPEIIEVRGEVYISKNDFLALNDEMIAVGRKPYANPRNAASGILRRLNPTDI-TRYLNFFVHGLGKTS-EIF 250 (731)
Q Consensus 173 iP~~l~~~~~~~ieiRGEv~m~~~~F~~lN~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~-~r~L~f~ay~~~~~~-~~~ 250 (731)
||++|..++|+.+|||||+||++++|+++|+++.+.|+++|+||||+|||+|||+||..+ .|+|+||+|+++... ...
T Consensus 155 iP~~l~~~~p~~leiRGEv~~~~~~F~~lN~~~~~~g~~~faNpRNaaAGslrqld~~~~~~R~L~~~~y~~~~~~~~~~ 234 (668)
T PRK07956 155 IPLRLQDNVPEVLEVRGEVFMPKADFEALNEERREAGEKPFANPRNAAAGSLRQLDPKITAKRPLSFFAYGVGVLEGGEL 234 (668)
T ss_pred CCCCCCCCCCCEEEEEEEEEEEHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCCHHCCCCCEEEEEECCCCCCCCC
T ss_conf 64312246886599988999986689999899997178766784889877977589311203776699997013478888
Q ss_pred CCCCHHHHHHHHHCCCCCCCCEEEEECCCCHHHHHHHHHHHHCCCCCCCCCEEEEECCHHCCCCCCCCCCCCCCEEEECC
Q ss_conf 10000368999975996654148874032113455665531001123437637773110001115876568663123114
Q gi|254781172|r 251 AKGQYEMLQKMRCLGFPVNNGVRQANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSLQKQLGERARSPRWMISHKF 330 (731)
Q Consensus 251 ~~~~~e~l~~L~~~GF~v~~~~~~~~~~~~~~~~~~~~~~~r~~l~y~iDGiVikvn~~~~q~~lG~ts~~PrwaiA~Kf 330 (731)
+.+|++.|++|+.|||+|+++...|.+++++.+++++|.+.|+.+||+|||+||||||+.+|+.||+|+|+|||||||||
T Consensus 235 ~~t~~e~l~~l~~~GF~v~~~~~~~~~~~ev~~~~~~~~~~R~~l~y~iDGiViKvn~~~~q~~LG~tsk~PrwAiA~Kf 314 (668)
T PRK07956 235 PDSQSEALEFLKAWGFPVNPYTKLCSSIEEVLAFYEYIEEERHDLPYDIDGVVIKVDDLALQEELGFTSKAPRWAIAYKF 314 (668)
T ss_pred CCCHHHHHHHHHHCCCCCCCCEEEECCHHHHHHHHHHHHHHHHHCCCCCCCEEEEECCHHHHHHCCCCCCCCCEEEEECC
T ss_conf 66799999999977998886759958899999999999987751776667469995538878753976689780478747
Q ss_pred CCCEEEEEEEEEEEEECCCCEEEEEEEEEEEEECCCEEEEECCCCHHHHHHHCCCCCCCCCCCCCCCCCEEEEEECCCCH
Q ss_conf 56215899878899403562258999974333026400010148989997502345432224684407689998358702
Q gi|254781172|r 331 AEKQASTRLLDIDIQIGRTGILTPVARLEPVNIGGALITNATLHNEDYIKGLDASGKVMRGGRDIRVGDRVLVKRAGEVI 410 (731)
Q Consensus 331 ~~e~~~T~v~~I~wqvgRtG~itPva~~ePV~l~G~~V~ratlhN~~~I~~l~~~~~~~~~~~~I~iGd~V~I~RaGdVI 410 (731)
|+++++|+|.+|+|||||||+|||||+|+||.|+|++|+||||||+++|++ +||+|||+|.|+||||||
T Consensus 315 ~~e~~~T~l~~I~~qVGRTG~iTPvA~l~PV~l~G~~VsrATLHN~~~I~~-----------~~i~iGd~V~v~raGdVI 383 (668)
T PRK07956 315 PAEEATTKLLDIEVQVGRTGAVTPVARLEPVEVAGVTVSRATLHNADEIER-----------KDIRIGDTVVVRRAGDVI 383 (668)
T ss_pred CCCEEEEEEEEEEEEECCCCEEEEEEEEEEEEECCEEEEECCCCCHHHHHH-----------CCCCCCCEEEEEECCCCC
T ss_conf 736799997777997347635626999987871560675236478899997-----------078999989999888887
Q ss_pred HHHHHHCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHH
Q ss_conf 56654101235787304777043265775010337865445210100354344114466553321301231035410355
Q gi|254781172|r 411 PKVVDIIVNERHPDAQPFSFPSFCPICQSRVVRDLNPKTGKLVAAHRCTGGLACSAQQLERLKHFVSRDAFNIEGLGKQQ 490 (731)
Q Consensus 411 P~I~~Vi~~~r~~~~~~~~~P~~CP~Cgs~l~~~~~~~~~~~~~~~rC~n~~~Cpaq~~~~i~hF~SK~aldI~GLG~k~ 490 (731)
|+|++|+.++|++++++|.||++||+||+++++..+. +++||+|+.+||+|++++|.|||||+||||+|||+++
T Consensus 384 P~I~~v~~~~r~~~~~~~~~P~~CP~C~s~l~~~~~~------~~~~C~N~~~Cpaq~~~~i~hF~Sr~amdI~GlG~~~ 457 (668)
T PRK07956 384 PEVVGVVLEKRPGDEREIVMPTHCPVCGSELVREEGE------AVLRCTNGLSCPAQLKERLIHFVSRNAMDIDGLGEKI 457 (668)
T ss_pred CCEEEECCCCCCCCCCCCCCCCCCCCCCCEEEEECCC------EEEECCCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHH
T ss_conf 2004641301899887543677876779857993696------3787789989989999988865244531646659999
Q ss_pred HHHHHCCCCCCEEEEEHHHHCCHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHH
Q ss_conf 55653057654045410110106777531000100013421001456899998752234666776301011116899999
Q gi|254781172|r 491 LDFFFKSEDPAFSIRIPADIFTLQRRQQTSTTKIENILGFGDVSVTNLYDSINKRRNISLERFIFSLGIRHVGAEIARSL 570 (731)
Q Consensus 491 Ie~L~e~~~~~g~I~~~~DLy~L~~~~~~~~~~l~~l~GfgeKsa~nL~~sIe~sK~~~L~r~L~ALGI~~vG~~~Ak~L 570 (731)
|++|+++ |+|++++|||.|+.+ +|++++|||+|||+||+++|++||+++|+|||+||||||||+++|++|
T Consensus 458 i~~L~~~----g~i~~~~Diy~L~~~------~L~~l~gfgeKsa~nLl~aIe~SK~~~l~r~L~ALGI~~VG~~~Ak~L 527 (668)
T PRK07956 458 IEQLFEK----GLIHTPADLFKLTEE------DLLQLEGFGEKSAQNLLDAIEKSKETPLARFLYALGIRHVGEKAAKAL 527 (668)
T ss_pred HHHHHHC----CCCCCHHHHHCCCHH------HHHCCCCHHHHHHHHHHHHHHHHCCCCHHHHHHHCCCCCCCHHHHHHH
T ss_conf 9999876----876658999728854------540212355669999999999854775888998627864129999999
Q ss_pred HHHCCCHHHHHHHHHHHHHCCCCCHHHHHCCCCCCHHHHHHHHHHHCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCC
Q ss_conf 98829989999978977612511778761388867899999999966979999999999733877654322468821686
Q gi|254781172|r 571 AKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVEFYQNPRNICAVEALLKEVSPSIGRHEKNVSSEIENK 650 (731)
Q Consensus 571 a~~f~si~~l~~~~~~~~~~~~~~~e~L~~I~GiG~~~A~si~~ff~~~~n~~~i~~L~~~~~~~~~~~~~~~~~~l~gk 650 (731)
+++|++++++..+ +.++|.+|+|||+++|+||++||+++.|++++++|.+.+...........+++|+||
T Consensus 528 a~~f~sl~~l~~a----------s~e~L~~I~giG~~~A~si~~ff~~~~n~~~i~~L~~~g~~~~~~~~~~~~~~l~Gk 597 (668)
T PRK07956 528 ARHFGSLEALEAA----------SEEELAAVEGIGEEVAQSIVEFFAVEHNRELIDELLEEGLGPEDEKEEAADSPLAGK 597 (668)
T ss_pred HHHHCCHHHHHHC----------CHHHHHCCCCCCHHHHHHHHHHHCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCC
T ss_conf 9996689999708----------999985768844999999999970976899999999837986655444668865898
Q ss_pred EEEEECCCCCCCHHHHHHHHHHCCCEEEEEEECCEEEEEECCCCCCHHHHHHHCCCEEECHHHHHHHHHHH
Q ss_conf 69997258899878999999982984998111632179977888863798997499173799999999882
Q gi|254781172|r 651 KLVFTGTLQKIQRHKAQEYVTQLGAVVSAILSRKTDIIIVGDNPGSKLEKAQQLGVKIMNEEQFLFLLQQY 721 (731)
Q Consensus 651 ~vV~TGtl~~~~R~e~~~~ie~~Ggkv~sSVSkkT~~LI~ge~~gSKl~KA~~LgI~Ii~e~ef~~ll~~~ 721 (731)
+|||||+|++|+|++++++||++||+|+|||||||||||+|+++|||++||++|||+||+|+||++||++.
T Consensus 598 t~ViTGtl~~~sR~e~k~~ie~~Ggkv~sSVSkkTd~LV~Ge~~GSKl~KA~~LGI~Ii~E~ef~~ll~~g 668 (668)
T PRK07956 598 TVVLTGTLEQLSRDEAKEKLEALGAKVSGSVSKKTDYVVAGEAAGSKLAKAQELGVKVLDEEEFLRLLGEG 668 (668)
T ss_pred EEEEEECCCCCCHHHHHHHHHHCCCEECCCCCCCCEEEEECCCCCCHHHHHHHCCCEEECHHHHHHHHHCC
T ss_conf 89998069998989999999987999946401675299988998858999998699083499999998478
No 3
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=100.00 E-value=0 Score=1632.49 Aligned_cols=663 Identities=42% Similarity=0.750 Sum_probs=630.9
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCHHHCCCCCCCCCCCCCCCCCCCCCEEEC
Q ss_conf 89999999999999999999984331779820878999999999999897720311589999620036432357750451
Q gi|254781172|r 12 LSIEQARKELSSLEQEISYHDDCYYQYSKPIILDSEYDALKRRCDAIAHAFPDLARSEDPNGPLNKIGGEMNLSLFKVTH 91 (731)
Q Consensus 12 ~s~~~~~~~i~~L~~~i~~~~~~Yy~~~~p~isD~eYD~L~~~L~~le~~~p~~~~~~~p~spt~~Vg~~~~~~~~kv~H 91 (731)
+++.+++++|.+|+++|++|+|.||++++|+|||+|||+|+++|.+||++||++++ ||||||+||+.++.+|.||+|
T Consensus 2 ~~~~~~~~~i~~L~~~L~~~~~~Yyv~d~P~VsD~eYD~L~reL~~lE~~~Pel~~---~dSPtqrVG~~~~~~F~kv~H 78 (667)
T COG0272 2 WSMAEAQEEIEELRELLNKHDYRYYVLDAPSVSDAEYDQLYRELQELEEKHPELIT---PDSPTQRVGAAPLNAFKKVRH 78 (667)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCC---CCCCCCCCCCCCHHCCCCCCC
T ss_conf 53678999999999999997788722699979858999999999999986877678---999965557430100453347
Q ss_pred CCCCCCHHHCCCHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCEEEEEEEEECCEEEEEEECCCCHHHHHHHHHHHHHC
Q ss_conf 66425702159999999999999986124677761199994158189999985998998886598655666999775310
Q gi|254781172|r 92 SIPTLSLEKIWNIEDLRKFITRIYRFWQKKDDNSIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIP 171 (731)
Q Consensus 92 ~~pMlSL~k~~~~~el~~w~~~~~~~~~~~~~~~~~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n~~~i~ 171 (731)
..|||||+|+||.+||.+|++|+.+.+.. ...|+|||||||+|+||+|+||+|++|+|||||.+|||||+|+|||+
T Consensus 79 ~~pMlSL~naf~~~el~~f~~ri~~~~~~----~~~y~~EpKiDGlsisL~YenG~Lv~aaTRGdG~~GEDiT~NvrtI~ 154 (667)
T COG0272 79 PVPMLSLDNAFDEEELRAFDRRIRKFLGD----SVEYVVEPKIDGLAISLVYENGKLVRAATRGDGTTGEDITANVRTIR 154 (667)
T ss_pred CCCCCCHHHCCCHHHHHHHHHHHHHHCCC----CCCEEEEEECCEEEEEEEEECCEEEEEECCCCCCCCCCHHHHHHHHH
T ss_conf 87554344227989999999999875178----86568886236189999997899988624679962642222140265
Q ss_pred CCCCCCCCCCCCEEEEEEEEEEECHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCHHHH-HCCCEEEEEEECCCCC-C
Q ss_conf 2432233544550489999998520212345564314854334234567777523455553-0111056641024543-3
Q gi|254781172|r 172 TIPRVLSLNIPEIIEVRGEVYISKNDFLALNDEMIAVGRKPYANPRNAASGILRRLNPTDI-TRYLNFFVHGLGKTSE-I 249 (731)
Q Consensus 172 ~iP~~l~~~~~~~ieiRGEv~m~~~~F~~lN~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~-~r~L~f~ay~~~~~~~-~ 249 (731)
+||++|.. .|..+|||||+||++++|+++|+++.+.|+++|+||||+|||+|||+||+.+ .|+|.||+|+|+.... .
T Consensus 155 ~IP~~l~~-~p~~lEVRGEvfm~k~~F~~lN~~~~~~g~~~faNpRNaAAGsLRqlD~~ita~R~L~~f~y~~~~~~~~~ 233 (667)
T COG0272 155 SIPLKLPG-APAVLEVRGEVFMPKEDFEALNEEREEEGEKPFANPRNAAAGSLRQLDPKITAKRKLGFFIYAVGDGEEGL 233 (667)
T ss_pred HHHHHCCC-CCCEEEEEEEEEEEHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCHHHHHCCCCEEEEEECCCCCCCC
T ss_conf 54333257-88538997689977899999999999847988678044555466536968774177359998677667677
Q ss_pred CCCCCHHHHHHHHHCCCCCCCCEEEEECCCCHHHHHHHHHHHHCCCCCCCCCEEEEECCHHCCCCCCCCCCCCCCEEEEC
Q ss_conf 21000036899997599665414887403211345566553100112343763777311000111587656866312311
Q gi|254781172|r 250 FAKGQYEMLQKMRCLGFPVNNGVRQANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSLQKQLGERARSPRWMISHK 329 (731)
Q Consensus 250 ~~~~~~e~l~~L~~~GF~v~~~~~~~~~~~~~~~~~~~~~~~r~~l~y~iDGiVikvn~~~~q~~lG~ts~~PrwaiA~K 329 (731)
.+.||++.|++|+.|||+|+++...|.+.+++.++|++|...|++|||+|||+|||+||+++|+.||+|+|+||||||||
T Consensus 234 ~~~t~~e~l~~L~~~GF~v~~~~~~~~~~~ev~~~~~~~~~~R~~L~y~IDGvViKvn~l~~q~~lG~tsk~PrWAiAyK 313 (667)
T COG0272 234 LADTQSERLAFLKAWGFPVNPYTRLCKNADEVLAFYEEWEKKRASLPYDIDGVVIKVNDLALQRELGFTSKAPRWAIAYK 313 (667)
T ss_pred CCCCHHHHHHHHHHCCCCCCCHHHHCCCHHHHHHHHHHHHHHHHCCCCCCCEEEEEECCHHHHHHHCCCCCCCCEEEEEC
T ss_conf 74579999999997599988076660899999999999986322289766438999676888987097068986323553
Q ss_pred CCCCEEEEEEEEEEEEECCCCEEEEEEEEEEEEECCCEEEEECCCCHHHHHHHCCCCCCCCCCCCCCCCCEEEEEECCCC
Q ss_conf 45621589987889940356225899997433302640001014898999750234543222468440768999835870
Q gi|254781172|r 330 FAEKQASTRLLDIDIQIGRTGILTPVARLEPVNIGGALITNATLHNEDYIKGLDASGKVMRGGRDIRVGDRVLVKRAGEV 409 (731)
Q Consensus 330 f~~e~~~T~v~~I~wqvgRtG~itPva~~ePV~l~G~~V~ratlhN~~~I~~l~~~~~~~~~~~~I~iGd~V~I~RaGdV 409 (731)
|||+++.|+|.||+|||||||+|||||.++||.|+|++|+||||||.|+|++ +||+|||+|.|.|||||
T Consensus 314 Fpa~e~~T~l~dI~~qVGRTG~iTPvA~L~PV~laG~~VsrATLHN~d~I~r-----------kdIrIGDtV~V~kAGdV 382 (667)
T COG0272 314 FPAEEAVTKLLDIEVQVGRTGAITPVARLEPVELAGVTVSRATLHNVDEIKR-----------KDIRIGDTVVVRKAGDV 382 (667)
T ss_pred CCCHHEEEEEEEEEEECCCCEEEEEEEEEEEEEECCEEEEEEECCCHHHHHH-----------CCCCCCCEEEEEECCCC
T ss_conf 7732214689999995268536413379776998798999762388888986-----------38787999999736887
Q ss_pred HHHHHHHCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHH
Q ss_conf 25665410123578730477704326577501033786544521010035434411446655332130123103541035
Q gi|254781172|r 410 IPKVVDIIVNERHPDAQPFSFPSFCPICQSRVVRDLNPKTGKLVAAHRCTGGLACSAQQLERLKHFVSRDAFNIEGLGKQ 489 (731)
Q Consensus 410 IP~I~~Vi~~~r~~~~~~~~~P~~CP~Cgs~l~~~~~~~~~~~~~~~rC~n~~~Cpaq~~~~i~hF~SK~aldI~GLG~k 489 (731)
||+|++|+.++|++++++|.||++||+|||++++..++ +++||+|+.+||+|.+++|.||+||+||||+|||++
T Consensus 383 IP~V~~Vv~e~R~~~~~~~~~P~~CP~C~s~l~r~~~e------~~~rC~n~~~C~aq~~e~l~hfvSr~AmdI~GLG~k 456 (667)
T COG0272 383 IPQVVGVVLEKRPGNEKPIPFPTHCPVCGSELVREEGE------VVIRCTNGLNCPAQLKERLIHFVSRNALDIDGLGEK 456 (667)
T ss_pred CCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEECCCC------EEEECCCCCCCHHHHHHHEEEEECCCCCCCCCCCHH
T ss_conf 77323554344779998888999798899976742675------568668987885888623346744786577776799
Q ss_pred HHHHHHCCCCCCEEEEEHHHHCCHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHH
Q ss_conf 55565305765404541011010677753100010001342100145689999875223466677630101111689999
Q gi|254781172|r 490 QLDFFFKSEDPAFSIRIPADIFTLQRRQQTSTTKIENILGFGDVSVTNLYDSINKRRNISLERFIFSLGIRHVGAEIARS 569 (731)
Q Consensus 490 ~Ie~L~e~~~~~g~I~~~~DLy~L~~~~~~~~~~l~~l~GfgeKsa~nL~~sIe~sK~~~L~r~L~ALGI~~vG~~~Ak~ 569 (731)
+|++|++++ +|++++|||+|+.++ ++.++||++||++||+++|++||+++|+|||+||||||||+++|+.
T Consensus 457 ~i~~L~e~~----lI~~~~Dly~Lt~~~------l~~l~~~~~ks~~nLl~aIe~sK~~~l~r~l~aLGIr~VG~~~Ak~ 526 (667)
T COG0272 457 IIEQLFEKG----LIKDIADLYTLTEED------LLSLEGFGEKSAENLLNAIEKSKKQPLARFLYALGIRHVGETTAKS 526 (667)
T ss_pred HHHHHHHCC----CCCCHHHHHHCCHHH------HHHCCCHHHHHHHHHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHH
T ss_conf 999999737----537879877378988------8416224465799999999986049899999987971140899999
Q ss_pred HHHHCCCHHHHHHHHHHHHHCCCCCHHHHHCCCCCCHHHHHHHHHHHCCHHHHHHHHHHHHHCCCCCCCCCCCC-CCCCC
Q ss_conf 99882998999997897761251177876138886789999999996697999999999973387765432246-88216
Q gi|254781172|r 570 LAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVEFYQNPRNICAVEALLKEVSPSIGRHEKNV-SSEIE 648 (731)
Q Consensus 570 La~~f~si~~l~~~~~~~~~~~~~~~e~L~~I~GiG~~~A~si~~ff~~~~n~~~i~~L~~~~~~~~~~~~~~~-~~~l~ 648 (731)
|+++|++++++..+ +.++|..|+|||+++|.||++||+++.|++++++|...+........... .++|+
T Consensus 527 La~~f~sl~~l~~a----------~~e~l~~i~giG~~vA~si~~ff~~~~~~~li~~L~~~g~~~~~~~~~~~~~~~l~ 596 (667)
T COG0272 527 LARHFGTLEALLAA----------SEEELASIPGIGEVVARSIIEFFANEENRELIDELLAAGVKWEEEEKISIETSPLA 596 (667)
T ss_pred HHHHHHHHHHHHHC----------CHHHHHHCCCHHHHHHHHHHHHHCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCC
T ss_conf 99876029999842----------99999506661289999999997277789999999971787221002333444457
Q ss_pred CCEEEEECCCCCCCHHHHHHHHHHCCCEEEEEEECCEEEEEECCCCCCHHHHHHHCCCEEECHHHHHHHHH
Q ss_conf 86699972588998789999999829849981116321799778888637989974991737999999998
Q gi|254781172|r 649 NKKLVFTGTLQKIQRHKAQEYVTQLGAVVSAILSRKTDIIIVGDNPGSKLEKAQQLGVKIMNEEQFLFLLQ 719 (731)
Q Consensus 649 gk~vV~TGtl~~~~R~e~~~~ie~~Ggkv~sSVSkkT~~LI~ge~~gSKl~KA~~LgI~Ii~e~ef~~ll~ 719 (731)
||||||||+|++|+|++++++|+++||||++||||||||||+|++||||++||++|||+||||++|++||+
T Consensus 597 gkt~V~TGtL~~~sR~eak~~le~lGakv~~SVSkktD~vvaG~~aGSKl~kA~eLgv~i~~E~~~~~ll~ 667 (667)
T COG0272 597 GKTFVLTGTLEGMSRDEAKALLEALGAKVSGSVSKKTDYVVAGENAGSKLAKAQELGVKIIDEEEFLALLG 667 (667)
T ss_pred CCEEEEECCCCCCCHHHHHHHHHHCCCEEECEECCCCEEEEECCCCCHHHHHHHHCCCEEECHHHHHHHHC
T ss_conf 97799966678789999999999869999210415410899758977078889974986745999998649
No 4
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=100.00 E-value=0 Score=1232.11 Aligned_cols=535 Identities=23% Similarity=0.389 Sum_probs=482.9
Q ss_pred HHHCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCHHHCCCCCCCCCCCCCCCCCCCCCE
Q ss_conf 46889999999999999999999984331779820878999999999999897720311589999620036432357750
Q gi|254781172|r 9 IEALSIEQARKELSSLEQEISYHDDCYYQYSKPIILDSEYDALKRRCDAIAHAFPDLARSEDPNGPLNKIGGEMNLSLFK 88 (731)
Q Consensus 9 ~~~~s~~~~~~~i~~L~~~i~~~~~~Yy~~~~p~isD~eYD~L~~~L~~le~~~p~~~~~~~p~spt~~Vg~~~~~~~~k 88 (731)
-.+||.++||++|++|+++|++||++||++++|+|||+|||+|+++|..||++||++. +|+|||++||+ |
T Consensus 23 ~~~~~p~~ak~~I~~Lr~~i~~hn~~YY~~d~P~IsD~eYD~L~~eL~~LE~~~p~~~---~~~SPt~~vgg-------k 92 (563)
T PRK08097 23 CPDWSPARAQEEISALQQQLAQWDDAYWRQGKSPVDDEVYDQLRARLTQWQRCFGLPV---PRDPPLPPANG-------P 92 (563)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCCCC---CCCCCCCCCCC-------C
T ss_conf 9698989999999999999999999875289997888999999999999998686767---99999789998-------5
Q ss_pred EECCCCCCCHHHCCCHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCEEEEEEEEECCEEEEEEECCCCHHHHHHHHHHH
Q ss_conf 45166425702159999999999999986124677761199994158189999985998998886598655666999775
Q gi|254781172|r 89 VTHSIPTLSLEKIWNIEDLRKFITRIYRFWQKKDDNSIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIR 168 (731)
Q Consensus 89 v~H~~pMlSL~k~~~~~el~~w~~~~~~~~~~~~~~~~~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n~~ 168 (731)
|+|++|||||+|+|+.+|+.+|.++. ..|+||||+||+|++|+|+||+|++|+|||||.+|||||+|++
T Consensus 93 v~H~~pMlSL~n~~~~~el~~~~~~~-----------~~~~vEpKiDGlaisL~YenG~Lv~A~TRGDG~~GEDVT~Nv~ 161 (563)
T PRK08097 93 VMHPVAHTGVRKLADKQALARWMRGR-----------SDLWVQPKVDGVAVTLVYRDGKLVQAISRGNGLKGEDWTAKAR 161 (563)
T ss_pred CCCCCCCCCHHHCCCHHHHHHHHHCC-----------CCCEEEEECCCEEEEEEEECCEEEEEECCCCCCCCEEHHHHHH
T ss_conf 25898764711118989999998413-----------0617622056468999998998988871379976504888777
Q ss_pred HHCCCCCCCCCCCCCEEEEEEEEEEECHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCHHHHHCCCEEEEEEECCCCC
Q ss_conf 31024322335445504899999985202123455643148543342345677775234555530111056641024543
Q gi|254781172|r 169 AIPTIPRVLSLNIPEIIEVRGEVYISKNDFLALNDEMIAVGRKPYANPRNAASGILRRLNPTDITRYLNFFVHGLGKTSE 248 (731)
Q Consensus 169 ~i~~iP~~l~~~~~~~ieiRGEv~m~~~~F~~lN~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~r~L~f~ay~~~~~~~ 248 (731)
+|++||++|+.. |..+|||||+||++++|.+. ...|+||||+|||+||++++..+.|+|.||+|++..
T Consensus 162 tI~~IP~~L~~~-p~~levRGEv~~~~~~~~~~--------~~~~aNPRNaAAGsLr~~~~~~~~~~l~~f~y~~~~--- 229 (563)
T PRK08097 162 LIPAIPQTLPGA-PANLVLQGELFLRREGHIQA--------QMGGINARSKVAGLMMRKDLSPALNSIGLFVWAWPD--- 229 (563)
T ss_pred HHCCCCHHHCCC-CCEEEEEEEEEEECCHHHHH--------HCCCCCCCHHHHHHHHHCCCHHHHHCCCEEEEECCC---
T ss_conf 770603221799-96479977999861458887--------437889734552045523848777416779994588---
Q ss_pred CCCCCCHHHHHHHHHCCCCCCC-CEEEEECCCCHHHHHHHHHHHHCCCCCCCCCEEEEECCHHCCCCCCCCCCCCCCEEE
Q ss_conf 3210000368999975996654-148874032113455665531001123437637773110001115876568663123
Q gi|254781172|r 249 IFAKGQYEMLQKMRCLGFPVNN-GVRQANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSLQKQLGERARSPRWMIS 327 (731)
Q Consensus 249 ~~~~~~~e~l~~L~~~GF~v~~-~~~~~~~~~~~~~~~~~~~~~r~~l~y~iDGiVikvn~~~~q~~lG~ts~~PrwaiA 327 (731)
.+.+|++.|++|+.|||++++ +...+.+++++.+++++| .|+.|||+|||+|||+|+..+|+. +|+|+||||||
T Consensus 230 -g~~~~~e~l~~L~~~GF~v~~~~~~~~~~~~ev~~~~~~~--~R~~L~y~iDGiViK~~~~~~~~~--~tsk~PRWAIA 304 (563)
T PRK08097 230 -GPATMPERLAQLATAGFPLTQKYSHAVKNADEVARWRQHW--YRSPLPFVTDGVVVRQAKEPPGRR--WQPGQGEWLVA 304 (563)
T ss_pred -CCCCHHHHHHHHHHCCCCCCHHHCEECCCHHHHHHHHHHH--HHCCCCCCCCEEEEEECCHHHHHH--HCCCCCCCEEE
T ss_conf -9779999999999779998856612048899999999997--533588777538998356888875--25689873146
Q ss_pred ECCCCCEEEEEEEEEEEEECCCCEEEEEEEEEEEEECCCEEEEECCCCHHHHHHHCCCCCCCCCCCCCCCCCEEEEEECC
Q ss_conf 11456215899878899403562258999974333026400010148989997502345432224684407689998358
Q gi|254781172|r 328 HKFAEKQASTRLLDIDIQIGRTGILTPVARLEPVNIGGALITNATLHNEDYIKGLDASGKVMRGGRDIRVGDRVLVKRAG 407 (731)
Q Consensus 328 ~Kf~~e~~~T~v~~I~wqvgRtG~itPva~~ePV~l~G~~V~ratlhN~~~I~~l~~~~~~~~~~~~I~iGd~V~I~RaG 407 (731)
||||+++++|+|++|+|||||||+|||||+|+||.|+|+|||||||||+++|++ +||+|||+|.|+|||
T Consensus 305 yKF~ae~~~T~l~~I~~qVGRTG~iTPVA~lePV~l~G~tVsrATLHN~d~I~r-----------~diriGD~V~V~rAG 373 (563)
T PRK08097 305 WKYPPVQQVAEVRAIQFAVGRTGKITVVLSLAPVMLDDKRVQRVNIGSVRRWQQ-----------WDIAPGDQILVSLAG 373 (563)
T ss_pred ECCCCCCCEEEEEEEEEEECCCCEEEEEEEEEEEEECCEEEEECCCCCHHHHHH-----------CCCCCCCEEEEEECC
T ss_conf 657510307999888998667511325899887887789998403578889987-----------499989999999678
Q ss_pred CCHHHHHHHCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCEEECC--CCCCCCHHHHHHHHHHHHHCCCCCHHH
Q ss_conf 702566541012357873047770432657750103378654452101003--543441144665533213012310354
Q gi|254781172|r 408 EVIPKVVDIIVNERHPDAQPFSFPSFCPICQSRVVRDLNPKTGKLVAAHRC--TGGLACSAQQLERLKHFVSRDAFNIEG 485 (731)
Q Consensus 408 dVIP~I~~Vi~~~r~~~~~~~~~P~~CP~Cgs~l~~~~~~~~~~~~~~~rC--~n~~~Cpaq~~~~i~hF~SK~aldI~G 485 (731)
||||+|++|+. |.+...++.+|..|+. ..++| +|. +||+|.+++|.||+||+||||+|
T Consensus 374 dVIP~V~~Vv~--r~~~~~~~~~P~~~~~-----------------~~~~C~~~~~-~C~aq~~~rl~hF~Sr~amdI~G 433 (563)
T PRK08097 374 QGIPRLDEVVW--RGAERAKPTPPDADRF-----------------HSLSCFQASP-GCQEQFIARLVWLGGKQGLGLDG 433 (563)
T ss_pred CCCCCCCEECC--CCCCCCCCCCCCCCCC-----------------CCCEECCCCC-CCHHHHHHHHHHHHCCCCCCCCC
T ss_conf 86787044126--6778899889987788-----------------8852178999-99799999978600234158567
Q ss_pred HHHHHHHHHHCCCCCCEEEEEHHHHCCHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHH
Q ss_conf 10355556530576540454101101067775310001000134210014568999987522346667763010111168
Q gi|254781172|r 486 LGKQQLDFFFKSEDPAFSIRIPADIFTLQRRQQTSTTKIENILGFGDVSVTNLYDSINKRRNISLERFIFSLGIRHVGAE 565 (731)
Q Consensus 486 LG~k~Ie~L~e~~~~~g~I~~~~DLy~L~~~~~~~~~~l~~l~GfgeKsa~nL~~sIe~sK~~~L~r~L~ALGI~~vG~~ 565 (731)
||+++|++|+++ |+|++++|||+|+.+ +|.+++|||+|||+||+++|++||+++|+|||+|||||+||+.
T Consensus 434 LGek~i~~L~~~----gli~~~~Dly~L~~~------~L~~l~g~geKsa~nLl~aIe~SK~~~l~r~l~aLGI~~vG~~ 503 (563)
T PRK08097 434 IGEGTWRALHQT----GRFEHLFSWLALTPE------QLANTPGIGKARAAQLWHQFNLARQQPFTRWLKALGIPLTQAA 503 (563)
T ss_pred CCHHHHHHHHHC----CCCCCHHHHHHCCHH------HHHCCCCHHHHHHHHHHHHHHHHCCCCHHHHHHHCCCCCHHHH
T ss_conf 699999999975----888997997508999------9855898578999999999999728999999998699508999
Q ss_pred HHHHHHHHCCCHHHHHHHHHHHHHCCCCCHHHHHCCCCCCHHHHHHHHHHHCCHHHHHHHHHHHHHCCCC
Q ss_conf 9999998829989999978977612511778761388867899999999966979999999999733877
Q gi|254781172|r 566 IARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVEFYQNPRNICAVEALLKEVSPS 635 (731)
Q Consensus 566 ~Ak~La~~f~si~~l~~~~~~~~~~~~~~~e~L~~I~GiG~~~A~si~~ff~~~~n~~~i~~L~~~~~~~ 635 (731)
+|+.|+.+| +.++ ..+.++|.+|+|||+++|+||++||+++.|++++++|.+.|...
T Consensus 504 ~a~~l~~~~---~~L~----------~as~e~l~~i~gIG~~~A~si~~fF~~~~n~~li~~L~~~Gvn~ 560 (563)
T PRK08097 504 LNASLDRSW---QQLL----------SRTEQQWQQLPGIGEGRARQLIAFFDHPQVQALAEWLAAQGITG 560 (563)
T ss_pred HHHHHHCCH---HHHH----------CCCHHHHHCCCCCCHHHHHHHHHHHCCHHHHHHHHHHHHCCCCC
T ss_conf 999986199---9997----------39998995579848999999999985988999999999769998
No 5
>smart00532 LIGANc Ligase N family.
Probab=100.00 E-value=0 Score=1127.94 Aligned_cols=439 Identities=45% Similarity=0.784 Sum_probs=421.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCHHHCCCCCCCCCCCCCCCCCCCCCEEECCCCCC
Q ss_conf 99999999999999998433177982087899999999999989772031158999962003643235775045166425
Q gi|254781172|r 17 ARKELSSLEQEISYHDDCYYQYSKPIILDSEYDALKRRCDAIAHAFPDLARSEDPNGPLNKIGGEMNLSLFKVTHSIPTL 96 (731)
Q Consensus 17 ~~~~i~~L~~~i~~~~~~Yy~~~~p~isD~eYD~L~~~L~~le~~~p~~~~~~~p~spt~~Vg~~~~~~~~kv~H~~pMl 96 (731)
|++||.+|+++|++||++||+.++|+|||++||+|+++|..||++||++. +|+||||+||+++...|.||+|+.|||
T Consensus 1 ak~~i~~L~~~I~~~n~~YY~~~~p~ISD~eYD~L~~eL~~Le~~~P~l~---~~~SPt~~VG~~~~~~f~kv~H~~pMl 77 (441)
T smart00532 1 AQKEISELRKLLNKHDYRYYVLDAPIISDAEYDRLMRELKELEEKHPELK---TPDSPTQRVGGKPLEGFNKVRHPVPML 77 (441)
T ss_pred CHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHCCCCC---CCCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf 97899999999999999876189987998999999999999998691446---899985455766166886217898675
Q ss_pred CHHHCCCHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCEEEEEEEEECCEEEEEEECCCCHHHHHHHHHHHHHCCCCCC
Q ss_conf 70215999999999999998612467776119999415818999998599899888659865566699977531024322
Q gi|254781172|r 97 SLEKIWNIEDLRKFITRIYRFWQKKDDNSIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPTIPRV 176 (731)
Q Consensus 97 SL~k~~~~~el~~w~~~~~~~~~~~~~~~~~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n~~~i~~iP~~ 176 (731)
||+|+|+.+||.+|++|+.+.+. ....|+|||||||+|++|+|++|+|++|+|||||.+|||||+|+++|++||++
T Consensus 78 SL~k~~~~~el~~w~~r~~k~l~----~~~~~~~epKiDGlsisL~Y~~G~L~~a~TRGDG~~GeDVT~nv~~I~~iP~~ 153 (441)
T smart00532 78 SLDNAFDEDELRAFDERIEKALG----SPFAYVVEPKIDGLSVSLLYENGKLVQAATRGDGTVGEDVTQNVKTIRSIPLR 153 (441)
T ss_pred CCCCCCCHHHHHHHHHHHHHHHC----CCCCEEEEECCCCEEEEEEEECCEEEEEEECCCCCHHHHHHHHHHHCCCCCHH
T ss_conf 70334899999999999998624----66435787614752689999799998887247982555455555311578532
Q ss_pred CCCCCCCEEEEEEEEEEECHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCHHHH-HCCCEEEEEEECCCCCC-CCCCC
Q ss_conf 33544550489999998520212345564314854334234567777523455553-01110566410245433-21000
Q gi|254781172|r 177 LSLNIPEIIEVRGEVYISKNDFLALNDEMIAVGRKPYANPRNAASGILRRLNPTDI-TRYLNFFVHGLGKTSEI-FAKGQ 254 (731)
Q Consensus 177 l~~~~~~~ieiRGEv~m~~~~F~~lN~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~-~r~L~f~ay~~~~~~~~-~~~~~ 254 (731)
|..+.|+.+|||||+||++++|++||+++.+.|+++|+||||+|||+|||+||..+ .|+|+||+|+|+..+.. .+.+|
T Consensus 154 l~~~~p~~leiRGEv~~~~~~F~~lN~~~~~~~~~~faNpRNaaAGslrqld~~~~~~r~L~f~~y~~~~~~~~~~~~t~ 233 (441)
T smart00532 154 LSGDVPERLEVRGEVFMPKEDFLALNEELEEEGEKPFANPRNAAAGSLRQLDPRITAKRKLRAFFYGLGTGEELFLPKTQ 233 (441)
T ss_pred HCCCCCCEEEEEEEEEEEHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCCCHHHHCCCEEEEEEECCCCCCCCCCCH
T ss_conf 14788863899889998721344788999864887667837898899876793015425516999980246777785689
Q ss_pred HHHHHHHHHCCCCCCCCEEEEECCCCHHHHHHHHHHHHCCCCCCCCCEEEEECCHHCCCCCCCCCCCCCCEEEECCCCCE
Q ss_conf 03689999759966541488740321134556655310011234376377731100011158765686631231145621
Q gi|254781172|r 255 YEMLQKMRCLGFPVNNGVRQANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSLQKQLGERARSPRWMISHKFAEKQ 334 (731)
Q Consensus 255 ~e~l~~L~~~GF~v~~~~~~~~~~~~~~~~~~~~~~~r~~l~y~iDGiVikvn~~~~q~~lG~ts~~PrwaiA~Kf~~e~ 334 (731)
++.|++|+.|||+|+++...+.+.+++..++++|.+.|+.+||+|||+|||+||+.+|+.||+|+|+|||||||||++++
T Consensus 234 ~e~l~~L~~~GF~v~~~~~~~~~~~ev~~~~~~~~~~R~~l~y~iDGiVikvn~~~~q~~lG~ts~~PrwAiA~Kf~~e~ 313 (441)
T smart00532 234 SEALKWLKELGFPVSPHTRLCKNADEVIEYYEEWEEKRAELPYEIDGVVVKVDDLALQRELGFTSKAPRWAIAYKFPAEE 313 (441)
T ss_pred HHHHHHHHHCCCCCCCCEEEECCHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCHHHHHHCCCCCCCCCEEEEECCCCCE
T ss_conf 99999999779924876199689999999999999665629988772699985889875428546898834897688665
Q ss_pred EEEEEEEEEEEECCCCEEEEEEEEEEEEECCCEEEEECCCCHHHHHHHCCCCCCCCCCCCCCCCCEEEEEECCCCHHHHH
Q ss_conf 58998788994035622589999743330264000101489899975023454322246844076899983587025665
Q gi|254781172|r 335 ASTRLLDIDIQIGRTGILTPVARLEPVNIGGALITNATLHNEDYIKGLDASGKVMRGGRDIRVGDRVLVKRAGEVIPKVV 414 (731)
Q Consensus 335 ~~T~v~~I~wqvgRtG~itPva~~ePV~l~G~~V~ratlhN~~~I~~l~~~~~~~~~~~~I~iGd~V~I~RaGdVIP~I~ 414 (731)
++|+|++|+|||||||+|||||+|+||.|+|+||+||||||+++|+++ ||+|||+|.|+|||||||+|+
T Consensus 314 ~~T~l~~I~~qVGRtG~itPva~lePV~l~G~~Vs~aTLhN~~~i~~~-----------~i~iGd~V~i~raGdVIPkI~ 382 (441)
T smart00532 314 AETKLLDIIVQVGRTGKITPVAELEPVFLAGSTVSRATLHNEDEIEEK-----------DIRIGDTVVVRKAGDVIPKVV 382 (441)
T ss_pred EEEEEEEEEEECCCCEEEEEEEEEEEEEECCEEEEEECCCCHHHHHHC-----------CCCCCCEEEEEECCCCCCCEE
T ss_conf 789999999973786287689999768867869997056898999975-----------999999999997788887431
Q ss_pred HHCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCHHHHHHHHHHHHHCCC
Q ss_conf 410123578730477704326577501033786544521010035434411446655332130123
Q gi|254781172|r 415 DIIVNERHPDAQPFSFPSFCPICQSRVVRDLNPKTGKLVAAHRCTGGLACSAQQLERLKHFVSRDA 480 (731)
Q Consensus 415 ~Vi~~~r~~~~~~~~~P~~CP~Cgs~l~~~~~~~~~~~~~~~rC~n~~~Cpaq~~~~i~hF~SK~a 480 (731)
+|++++|++++++|.+|+.||+||+++++..++ +++||+|. +||+|+.++|.|||||+|
T Consensus 383 ~vv~~~r~~~~~~~~~P~~CP~C~s~l~~~~~~------~~~~C~n~-~C~aq~~~~i~hf~Sr~A 441 (441)
T smart00532 383 GVVKEKRPGDEREIEMPTHCPSCGSELVREEGE------VDIRCPNP-LCPAQLIERIIHFASRKA 441 (441)
T ss_pred ECCCCCCCCCCCCCCCCCCCCCCCCEEEECCCC------EEEECCCC-CCHHHHHHHEEEEECCCC
T ss_conf 411023899885655899898997983843898------78988999-898999701148756799
No 6
>pfam01653 DNA_ligase_aden NAD-dependent DNA ligase adenylation domain. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilising either ATP or NAD(+) as a cofactor. This domain is the catalytic adenylation domain. The NAD+ group is covalently attached to this domain at the lysine in the KXDG motif of this domain. This enzyme- adenylate intermediate is an important feature of the proposed catalytic mechanism.
Probab=100.00 E-value=0 Score=747.00 Aligned_cols=312 Identities=41% Similarity=0.725 Sum_probs=296.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCHHHCCCCCCCCCCCCCCCCCCCCCEEECCCC
Q ss_conf 99999999999999999984331779820878999999999999897720311589999620036432357750451664
Q gi|254781172|r 15 EQARKELSSLEQEISYHDDCYYQYSKPIILDSEYDALKRRCDAIAHAFPDLARSEDPNGPLNKIGGEMNLSLFKVTHSIP 94 (731)
Q Consensus 15 ~~~~~~i~~L~~~i~~~~~~Yy~~~~p~isD~eYD~L~~~L~~le~~~p~~~~~~~p~spt~~Vg~~~~~~~~kv~H~~p 94 (731)
++||+||++|+++|++||++||+.++|+|||++||+|+++|+.||++||++. +|+|||++||+++.++|.||+|+.|
T Consensus 1 e~~k~~i~~L~~~I~~~n~~YY~~~~p~ISD~eYD~L~~eL~~le~~~P~l~---~~~spt~~VG~~~~~~f~kv~H~~p 77 (315)
T pfam01653 1 EEAQQEIARLRELIRQYDYHYYVLDNPEVPDAEYDRLYRRLQALEEKFPELI---TPDSPTQRVGAPLLGDFKKVRHPAP 77 (315)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHCHHCC---CCCCCCCCCCCCCCCCCCCEECCCC
T ss_conf 9589999999999999999986489997999999999999999998691004---8999522358765577750036875
Q ss_pred CCCHHHCCCHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCEEEEEEEEECCEEEEEEECCCCHHHHHHHHHHHHHCCCC
Q ss_conf 25702159999999999999986124677761199994158189999985998998886598655666999775310243
Q gi|254781172|r 95 TLSLEKIWNIEDLRKFITRIYRFWQKKDDNSIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPTIP 174 (731)
Q Consensus 95 MlSL~k~~~~~el~~w~~~~~~~~~~~~~~~~~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n~~~i~~iP 174 (731)
||||+|+|+.+||.+|++|+.+.+.. ....|+|||||||+|++|+|++|+|++|+|||||.+|||||+|+++|++||
T Consensus 78 MlSL~k~~~~~el~~w~~r~~~~~~~---~~~~~~~e~KiDGlsisL~Y~~G~L~~a~TRGDG~~GeDIT~nv~~I~~iP 154 (315)
T pfam01653 78 MLSLDNAFDEDELAAWIRRIRRRLGN---SEKAYVVEPKIDGVAVSLTYEDGVLVRAATRGDGTTGEDVTQNVKTIRAIP 154 (315)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHHCCC---CCCCEEEEECCCCCEEEEEEECCEEEEEEECCCCCCCCCHHHHHHHHCCCH
T ss_conf 65521115667799999999875188---875358876247710478980890568875589864217176564333660
Q ss_pred CCCCCCCCCEEEEEEEEEEECHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCHHHH-HCCCEEEEEEECCCCC--CCC
Q ss_conf 2233544550489999998520212345564314854334234567777523455553-0111056641024543--321
Q gi|254781172|r 175 RVLSLNIPEIIEVRGEVYISKNDFLALNDEMIAVGRKPYANPRNAASGILRRLNPTDI-TRYLNFFVHGLGKTSE--IFA 251 (731)
Q Consensus 175 ~~l~~~~~~~ieiRGEv~m~~~~F~~lN~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~-~r~L~f~ay~~~~~~~--~~~ 251 (731)
++|+.+ |+.+|||||+||++++|+++|+++.+.|+++|+||||+|||+||++||..+ .|+|+||||+|+.... ..+
T Consensus 155 ~~l~~~-~~~ievRGEv~i~~~~F~~lN~~~~~~~~~~faNpRN~aaG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~~~ 233 (315)
T pfam01653 155 LTLPGD-PARLEVRGEVFMPKEDFEALNEEREEEGEKPFANPRNAAAGSLRQLDPEITAKRKLRFFVYGLGLPEGLELGP 233 (315)
T ss_pred HHCCCC-CCEEEEEEEEEEEHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCCCHHHCCCCEEEEEECCCCCCCCCCC
T ss_conf 211799-8728999999964789889889999727886778289999998625951221687779998676666677785
Q ss_pred CCCHHHHHHHHHCCCCCCCCEEEEECCCCHHHHHHHHHHHHCCCCCCCCCEEEEECCHHCCCCCCCCCCCCCCEEEECCC
Q ss_conf 00003689999759966541488740321134556655310011234376377731100011158765686631231145
Q gi|254781172|r 252 KGQYEMLQKMRCLGFPVNNGVRQANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSLQKQLGERARSPRWMISHKFA 331 (731)
Q Consensus 252 ~~~~e~l~~L~~~GF~v~~~~~~~~~~~~~~~~~~~~~~~r~~l~y~iDGiVikvn~~~~q~~lG~ts~~PrwaiA~Kf~ 331 (731)
.+|++.|++|+.|||+|+++...+.+++++.+++++|.+.|+.++|+|||||||+||+.+|+.||+|+|+||||||||||
T Consensus 234 ~t~~e~l~~L~~~GF~~~~~~~~~~~~~~v~~~~~~~~~~R~~l~y~iDGiVikvn~~~~q~~LG~ts~~PrwAiA~Kf~ 313 (315)
T pfam01653 234 QTQSEALKQLKSLGFPVSPHTRLCKNIDEVLDYYAEWEKKRDELPFEIDGVVVKVNELPLQRELGFTSKAPRWAIAYKFP 313 (315)
T ss_pred CCHHHHHHHHHHCCCCCCCCCEEECCHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCHHHHHHHCCCCCCCCCEEEECCC
T ss_conf 68999999999779976871178799999999999999777629988874799980989999828767998843786768
Q ss_pred CC
Q ss_conf 62
Q gi|254781172|r 332 EK 333 (731)
Q Consensus 332 ~e 333 (731)
||
T Consensus 314 ~E 315 (315)
T pfam01653 314 AE 315 (315)
T ss_pred CC
T ss_conf 99
No 7
>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=0 Score=724.98 Aligned_cols=306 Identities=42% Similarity=0.750 Sum_probs=293.2
Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCHHHCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCH
Q ss_conf 99999999999999843317798208789999999999998977203115899996200364323577504516642570
Q gi|254781172|r 19 KELSSLEQEISYHDDCYYQYSKPIILDSEYDALKRRCDAIAHAFPDLARSEDPNGPLNKIGGEMNLSLFKVTHSIPTLSL 98 (731)
Q Consensus 19 ~~i~~L~~~i~~~~~~Yy~~~~p~isD~eYD~L~~~L~~le~~~p~~~~~~~p~spt~~Vg~~~~~~~~kv~H~~pMlSL 98 (731)
+||.+|+++|++||++||+.++|+|||++||+|+++|+.||++||++. .++|||++||+++..+|.||+|+.|||||
T Consensus 1 ~ri~~L~~~I~~~n~~Yy~~~~p~ISD~eYD~L~~eL~~le~~~p~l~---~~~spt~~VG~~~~~~~~kv~H~~pMlSL 77 (307)
T cd00114 1 ERIAELRELLNKHDYRYYVLDEPSVSDAEYDRLYRELRALEEEHPELK---TPDSPTQRVGGTPLSGFKKVRHPVPMLSL 77 (307)
T ss_pred CHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHCCCCC---CCCCCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf 979999999999999986489997988999999999999998682336---89998655587525667642178655453
Q ss_pred HHCCCHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCEEEEEEEEECCEEEEEEECCCCHHHHHHHHHHHHHCCCCCCCC
Q ss_conf 21599999999999999861246777611999941581899999859989988865986556669997753102432233
Q gi|254781172|r 99 EKIWNIEDLRKFITRIYRFWQKKDDNSIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPTIPRVLS 178 (731)
Q Consensus 99 ~k~~~~~el~~w~~~~~~~~~~~~~~~~~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n~~~i~~iP~~l~ 178 (731)
+|+|+++||.+|++|+.+.+. ....|+|||||||+|++|+|++|+|++|+|||||.+|||||+|+++|++||++|+
T Consensus 78 ~k~~~~~el~~w~~r~~~~~~----~~~~~~vepKlDGlaisl~Y~~G~L~~a~TRGDG~~GeDIT~nv~~i~~iP~~l~ 153 (307)
T cd00114 78 DNAFDEEELRAFDERIKRFLG----EEPAYVVEPKIDGLSISLRYENGVLVQAATRGDGTTGEDVTENVRTIRSIPLTLA 153 (307)
T ss_pred CCCCCHHHHHHHHHHHHHHHC----CCCCEEEEECCCCEEEEEEEECCEEEEEEECCCCCCCCCCCCCHHHHCCCHHHCC
T ss_conf 443889999999999998515----6744588761376368999809966676625898655483023212227313237
Q ss_pred CCCCCEEEEEEEEEEECHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCHHHH-HCCCEEEEEEECCCCCCCCCCCHHH
Q ss_conf 544550489999998520212345564314854334234567777523455553-0111056641024543321000036
Q gi|254781172|r 179 LNIPEIIEVRGEVYISKNDFLALNDEMIAVGRKPYANPRNAASGILRRLNPTDI-TRYLNFFVHGLGKTSEIFAKGQYEM 257 (731)
Q Consensus 179 ~~~~~~ieiRGEv~m~~~~F~~lN~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~-~r~L~f~ay~~~~~~~~~~~~~~e~ 257 (731)
. .|+.+|||||+||++++|+++|+++.+.|+++|+||||+|||+||++||..+ .|+|+||+|+|+.+....+.+|++.
T Consensus 154 ~-~~~~levRGEi~~~~~~F~~~n~~~~~~~~~~f~NpRN~aAG~lr~~d~~~~~~r~L~f~~y~~~~~~~~~~~t~~e~ 232 (307)
T cd00114 154 G-APETLEVRGEVFMPKADFEALNKEREERGEKPFANPRNAAAGSLRQLDPKITAKRPLRFFIYGLGEAEGLGPKTQSEA 232 (307)
T ss_pred C-CCCEEEEEEEEEECHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCHHHHCCCCEEEEEEECCCCCCCCCHHHH
T ss_conf 9-986299999997528879999999998178866573378761656248532440766178998552578886778999
Q ss_pred HHHHHHCCCCCCCCEEEEECCCCHHHHHHHHHHHHCCCCCCCCCEEEEECCHHCCCCCCCCCCCCCCEEEECCCC
Q ss_conf 899997599665414887403211345566553100112343763777311000111587656866312311456
Q gi|254781172|r 258 LQKMRCLGFPVNNGVRQANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSLQKQLGERARSPRWMISHKFAE 332 (731)
Q Consensus 258 l~~L~~~GF~v~~~~~~~~~~~~~~~~~~~~~~~r~~l~y~iDGiVikvn~~~~q~~lG~ts~~PrwaiA~Kf~~ 332 (731)
|++|+.|||+|+++...+.+.+++..++++|...|..++|+|||||||+||+.+|+.||+|+|+|||||||||||
T Consensus 233 l~~L~~~GF~~~~~~~~~~~~~~~~~~~~~~~~~r~~l~y~iDGiVvkvn~~~~~~~lG~ts~~PrwAiA~KfpA 307 (307)
T cd00114 233 LAFLKEWGFPVSPETRLCKNIEEVLAFYDEIEAKRDSLPYEIDGVVVKVDDLALQRELGFTSKAPRWAIAYKFPA 307 (307)
T ss_pred HHHHHHCCCCCCCCCEEECCHHHHHHHHHHHHHHHHCCCCCCCCEEEEEECHHHHHHHCCCCCCCCCEEEECCCC
T ss_conf 999997799668861897999999999999997642399887737999829899998487678987606856369
No 8
>pfam03120 DNA_ligase_OB NAD-dependent DNA ligase OB-fold domain. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilising either ATP or NAD(+) as a cofactor. This family is a small domain found after the adenylation domain pfam01653 in NAD dependent ligases. OB-fold domains generally are involved in nucleic acid binding.
Probab=99.91 E-value=1.3e-24 Score=209.54 Aligned_cols=82 Identities=55% Similarity=0.973 Sum_probs=78.7
Q ss_pred EEEEEEEEEEEECCCCEEEEEEEEEEEEECCCEEEEECCCCHHHHHHHCCCCCCCCCCCCCCCCCEEEEEECCCCHHHHH
Q ss_conf 58998788994035622589999743330264000101489899975023454322246844076899983587025665
Q gi|254781172|r 335 ASTRLLDIDIQIGRTGILTPVARLEPVNIGGALITNATLHNEDYIKGLDASGKVMRGGRDIRVGDRVLVKRAGEVIPKVV 414 (731)
Q Consensus 335 ~~T~v~~I~wqvgRtG~itPva~~ePV~l~G~~V~ratlhN~~~I~~l~~~~~~~~~~~~I~iGd~V~I~RaGdVIP~I~ 414 (731)
|+|+|++|+|||||||++||||+|+||.|+|++|+||||||++||+++ ||++||.|.|.|||||||+|+
T Consensus 1 A~T~v~~I~~~vgRtG~itPva~~ePV~l~G~~V~~atlhN~~~i~~~-----------~i~~Gd~V~I~raGdVIP~I~ 69 (82)
T pfam03120 1 AVTKLLDIEVQVGRTGVITPVAILEPVELAGTTVSRATLHNEDEIEEK-----------DIRIGDTVVVRKAGDVIPKIV 69 (82)
T ss_pred CEEEEEEEEEECCCCEEEEEEEEEEEEEECCEEEEEEECCCHHHHHHC-----------CCCCCCEEEEEECCCCCCCEE
T ss_conf 958999999955887088699999989989999999975798998645-----------999899999999788766673
Q ss_pred HHCCCCCCCCCCE
Q ss_conf 4101235787304
Q gi|254781172|r 415 DIIVNERHPDAQP 427 (731)
Q Consensus 415 ~Vi~~~r~~~~~~ 427 (731)
+|++++|+++++|
T Consensus 70 ~Vi~~~R~~~~~p 82 (82)
T pfam03120 70 GVVLEKRPGDTRP 82 (82)
T ss_pred EEEHHHCCCCCCC
T ss_conf 8786238998999
No 9
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=99.77 E-value=1.3e-18 Score=163.09 Aligned_cols=77 Identities=31% Similarity=0.531 Sum_probs=73.2
Q ss_pred CCCCCCCEEEEECCCCCCCHHHHHHHHHHCCCEEEEEEECCEEEEEECC---------CCCCHHHHHHHC-----CCEEE
Q ss_conf 8821686699972588998789999999829849981116321799778---------888637989974-----99173
Q gi|254781172|r 644 SSEIENKKLVFTGTLQKIQRHKAQEYVTQLGAVVSAILSRKTDIIIVGD---------NPGSKLEKAQQL-----GVKIM 709 (731)
Q Consensus 644 ~~~l~gk~vV~TGtl~~~~R~e~~~~ie~~Ggkv~sSVSkkT~~LI~ge---------~~gSKl~KA~~L-----gI~Ii 709 (731)
..+|+||+|||||+|+.|+|+|++++++++||+|.+||||+|||||+|+ .+|||++||++| +|+||
T Consensus 218 ~~~~~g~~vvfTG~l~~~~R~ea~~~~~~~Gg~v~~sVskkT~~lV~G~~d~~~~~~~~~~sK~~kA~~L~~~G~~I~ii 297 (309)
T PRK06195 218 FTAFKEEVVVFTGGLASMTRDEAIGLVRRLGGTVGSSVTKKTTYLVTNTKDIEDLNREEMSNKLKKAIDLKKEGQNIKFL 297 (309)
T ss_pred CCCCCCCEEEEECCCCCCCHHHHHHHHHHCCCEECCCCCCCCCEEEECCCCHHHCCCCCCCHHHHHHHHHHHCCCCCEEE
T ss_conf 89878998999457997799999999998599966871677778998886311003677766999999998479996796
Q ss_pred CHHHHHHHHHH
Q ss_conf 79999999988
Q gi|254781172|r 710 NEEQFLFLLQQ 720 (731)
Q Consensus 710 ~e~ef~~ll~~ 720 (731)
+|++|++||++
T Consensus 298 ~E~~fl~~i~~ 308 (309)
T PRK06195 298 NEEEFLQKIKE 308 (309)
T ss_pred CHHHHHHHHHC
T ss_conf 59999998741
No 10
>COG5275 BRCT domain type II [General function prediction only]
Probab=99.53 E-value=1.8e-14 Score=130.98 Aligned_cols=114 Identities=31% Similarity=0.447 Sum_probs=89.6
Q ss_pred HHCCCCCCHHHHHHHHHHHCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCHHHHHHHHHHCCCEE
Q ss_conf 61388867899999999966979999999999733877654322468821686699972588998789999999829849
Q gi|254781172|r 598 LIRVPLVGDIIAQAIVEFYQNPRNICAVEALLKEVSPSIGRHEKNVSSEIENKKLVFTGTLQKIQRHKAQEYVTQLGAVV 677 (731)
Q Consensus 598 L~~I~GiG~~~A~si~~ff~~~~n~~~i~~L~~~~~~~~~~~~~~~~~~l~gk~vV~TGtl~~~~R~e~~~~ie~~Ggkv 677 (731)
|.+++-||-..+.++.+ +. ... ...+ .-..-....|.|++|||||-|...+|++++.+++.+||+|
T Consensus 122 ~~d~~~~~~~a~~t~~e----~~--~~~----~~~G----S~peg~~~cL~G~~fVfTG~l~TlsR~~a~~lvk~yGgrv 187 (276)
T COG5275 122 LIDVDSMGVMAPGTFYE----RA--ATT----QTPG----SVPEGERECLKGKVFVFTGDLKTLSRDDAKTLVKVYGGRV 187 (276)
T ss_pred CEECCCCCCCCCCCCCC----HH--HHH----CCCC----CCCCCCCCCCCCCEEEEECCCCCCCCHHHHHHHHHHCCEE
T ss_conf 12102235226876567----25--441----4777----7788986432561799942430003203888999868734
Q ss_pred EEEEECCEEEEEECCCCC-CHHHHHHHCCCEEECHHHHHHHHHHHCCCC
Q ss_conf 981116321799778888-637989974991737999999998828656
Q gi|254781172|r 678 SAILSRKTDIIIVGDNPG-SKLEKAQQLGVKIMNEEQFLFLLQQYNTTL 725 (731)
Q Consensus 678 ~sSVSkkT~~LI~ge~~g-SKl~KA~~LgI~Ii~e~ef~~ll~~~~~~~ 725 (731)
+.+.|.+|+|||.||++| +|++|+++|+|+.|+|++|..||+..-.++
T Consensus 188 T~~pSskTtflvlGdnaGP~K~ekiKqlkIkaidEegf~~LI~~~pa~g 236 (276)
T COG5275 188 TAVPSSKTTFLVLGDNAGPSKMEKIKQLKIKAIDEEGFDSLIKDTPAAG 236 (276)
T ss_pred ECCCCCCEEEEEECCCCCHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCC
T ss_conf 4056654158996588881787889872875016778899973585347
No 11
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=99.37 E-value=2.7e-12 Score=114.29 Aligned_cols=75 Identities=23% Similarity=0.362 Sum_probs=68.9
Q ss_pred CCCCCEEEEECCCCCCCHHHHHHHHHHCCCEEEEEEECCEEEEEECCCC--CCHHHHHHHCCCEEECHHHHHHHHHHH
Q ss_conf 2168669997258899878999999982984998111632179977888--863798997499173799999999882
Q gi|254781172|r 646 EIENKKLVFTGTLQKIQRHKAQEYVTQLGAVVSAILSRKTDIIIVGDNP--GSKLEKAQQLGVKIMNEEQFLFLLQQY 721 (731)
Q Consensus 646 ~l~gk~vV~TGtl~~~~R~e~~~~ie~~Ggkv~sSVSkkT~~LI~ge~~--gSKl~KA~~LgI~Ii~e~ef~~ll~~~ 721 (731)
.++|++|||||.++ +.|+++++.+...|..+++|||++|++||+|+.. +.|..||+++|||||+|.+|++||+.-
T Consensus 232 L~~Gm~VVfTGel~-~~r~e~~~~a~~aGl~~~~sVTr~TsllV~nd~~~~~gKa~~A~~~giPv~~e~~Fl~~l~~v 308 (313)
T PRK06063 232 LVQGMRVALSAEVS-RTHEELVERILHAGLAYSDSVDRETSLVVCNDPAPEQGKGYHARQLGVPVLPEAAFLELLRAV 308 (313)
T ss_pred CCCCCEEEEECCCC-CCHHHHHHHHHHCCCCCCCCCCCCEEEEEECCCCCCCHHHHHHHHCCCCCCCHHHHHHHHHHC
T ss_conf 50688899958976-798999999997298304763476369995799986427787887199725899999999751
No 12
>PHA00454 ATP-dependent DNA ligase
Probab=98.80 E-value=5.1e-06 Score=65.70 Aligned_cols=240 Identities=16% Similarity=0.117 Sum_probs=118.0
Q ss_pred CCEEEEEEECCEEEEEEEEECCEEEEEEECCCCHHHHHHHHHHHHHCCCCCCCC---CCCCCEEEEEEEEEEECHHHHHH
Q ss_conf 611999941581899999859989988865986556669997753102432233---54455048999999852021234
Q gi|254781172|r 125 SIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPTIPRVLS---LNIPEIIEVRGEVYISKNDFLAL 201 (731)
Q Consensus 125 ~~~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n~~~i~~iP~~l~---~~~~~~ieiRGEv~m~~~~F~~l 201 (731)
...+.||||+||+=+-++..+..-+..++| .|..=..+.|.... ..++..+. .-+|..+.+=||+++.--+|+
T Consensus 26 ~G~~ivE~KyDGvRvqi~~~g~~~~~~~SR-~gk~~p~L~hi~~~-~~~~~l~~~~~~~~~~g~VLDGEv~~~~~dFq-- 101 (312)
T PHA00454 26 AGYLIADVKYDGVRGNIVVDGTADSVWLSR-VSKRIPALEHLNGD-RRWRKLLNDDRCIFPDGFMLDGELMVKGVDFN-- 101 (312)
T ss_pred CCCEEEEECCCEEEEEEEEECCEEEEEEEC-CCCCCCCCHHHHHH-HHHHHHHCHHHHHCCCCEEEEEEEECCCCCHH--
T ss_conf 894899966350799999948914999944-88765441556666-66787614255516898799848965889988--
Q ss_pred HHHHHHCCCCCCCCHHHHHHHHHHCCCHHH-H-HCCCEEEEEEECCCCC------C-----CCCCCHHHHHHHHHCCCCC
Q ss_conf 556431485433423456777752345555-3-0111056641024543------3-----2100003689999759966
Q gi|254781172|r 202 NDEMIAVGRKPYANPRNAASGILRRLNPTD-I-TRYLNFFVHGLGKTSE------I-----FAKGQYEMLQKMRCLGFPV 268 (731)
Q Consensus 202 N~~~~~~g~~~f~NpRN~aaG~lr~~d~~~-~-~r~L~f~ay~~~~~~~------~-----~~~~~~e~l~~L~~~GF~v 268 (731)
..+|.+|++.+.. . ..++.|++|++..... . ....+...+..+-.-.|+.
T Consensus 102 -----------------~i~~rvRrK~~~~~~~~~~l~~~~FDil~l~~~~~g~~~~~~~~~~~err~~l~~~l~~~~~~ 164 (312)
T PHA00454 102 -----------------TGSGLLRTKKVLFKLHLKKLHVVVYDVTPLDVIESGEDYDVMHLVMREHVEAMRPLLEEYFPE 164 (312)
T ss_pred -----------------HHHHHHEECCCCCCCCCCCEEEEEEEEEEHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCC
T ss_conf -----------------998876017786211000638999778831110356543200121399999999988760886
Q ss_pred CCCE----EEEECCCCHHHHHHHHHHHHCCCCCCCCCEEEEECCHHCCCCCCCCCCCCCCEEEECCCCC-EEEEEEEEEE
Q ss_conf 5414----8874032113455665531001123437637773110001115876568663123114562-1589987889
Q gi|254781172|r 269 NNGV----RQANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSLQKQLGERARSPRWMISHKFAEK-QASTRLLDID 343 (731)
Q Consensus 269 ~~~~----~~~~~~~~~~~~~~~~~~~r~~l~y~iDGiVikvn~~~~q~~lG~ts~~PrwaiA~Kf~~e-~~~T~v~~I~ 343 (731)
.... ..+.+.+++..++++. +.=.-+|+++|--+..++ -| |... -||+.+. ++.-+|.+++
T Consensus 165 i~~~~~e~~~v~~~~~l~~l~~~a------l~~g~EG~m~k~~~~~y~--~g---r~~~---~~K~Kp~~~~d~~v~~~~ 230 (312)
T PHA00454 165 IDWVLAESYEVYDMESLQELYEKK------RAEGHEGLVVKDPLLIYK--RG---KKSG---WWKMKPECEADGIIVGVV 230 (312)
T ss_pred CCEEEEEEECCCCHHHHHHHHHHH------HHCCCCEEEEECCCCCCC--CC---CCCC---EEEECCCCEEEEEEEEEE
T ss_conf 526985203368999999999999------857984688867998755--88---7265---088655604579999887
Q ss_pred EEECCC---CEEE-EEEEEEEEEECCCEEEEECCCCHHHHHHHCCC-CCCCCCCCCCCCCCEEEEE
Q ss_conf 940356---2258-99997433302640001014898999750234-5432224684407689998
Q gi|254781172|r 344 IQIGRT---GILT-PVARLEPVNIGGALITNATLHNEDYIKGLDAS-GKVMRGGRDIRVGDRVLVK 404 (731)
Q Consensus 344 wqvgRt---G~it-Pva~~ePV~l~G~~V~ratlhN~~~I~~l~~~-~~~~~~~~~I~iGd~V~I~ 404 (731)
|-.|+. |++- -.+.++ +|.. -.++......+..+.-. ....|...+.-+|-.|.|.
T Consensus 231 ~G~~~~~~~Gk~~~f~v~~e----dg~~-~~~~g~~~~~~~~~t~~~~~~~~~~~~~~~G~~~ei~ 291 (312)
T PHA00454 231 WGTPGLANEGKVIGFRVLLE----DGRV-VNATGISRALMDEFTANVKEHHIDEPMPYNGWACQVS 291 (312)
T ss_pred ECCCCCCCCCCEEEEEEEEC----CCCE-EECCCCCHHHHHHHHHHHHHHHCCCCCCCCCEEEEEE
T ss_conf 04677666564688999956----8977-8636776667656308788650124566465599999
No 13
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=98.71 E-value=6.4e-08 Score=80.41 Aligned_cols=78 Identities=15% Similarity=0.283 Sum_probs=70.1
Q ss_pred CCCCCCEEEEECCCCCCCHHHHHHHHHHCCCEEEEEEECCEEEEEECCCCC--CHHHHHHHCCCEEECHHHHHHHHHHHC
Q ss_conf 821686699972588998789999999829849981116321799778888--637989974991737999999998828
Q gi|254781172|r 645 SEIENKKLVFTGTLQKIQRHKAQEYVTQLGAVVSAILSRKTDIIIVGDNPG--SKLEKAQQLGVKIMNEEQFLFLLQQYN 722 (731)
Q Consensus 645 ~~l~gk~vV~TGtl~~~~R~e~~~~ie~~Ggkv~sSVSkkT~~LI~ge~~g--SKl~KA~~LgI~Ii~e~ef~~ll~~~~ 722 (731)
...+||.|||||..+ ..|+++.+.+...|=.++.|||..|+.||+++..+ +|...|..+|||+|++.+|+++|+.-.
T Consensus 293 ~LvqGMrVvvage~~-~~rd~Li~rav~AGL~ysesvsR~TSLVVcN~~~~~~GKa~hA~r~GIPlv~d~~Fl~ll~~V~ 371 (377)
T PRK05601 293 GLVAGMEVVVAPEIE-MDPDIIIQAGVDAGLSYSEKLTRQTSVVVCNQTRDIDGKAMHAQRKGIPLLSDVAFLAAVERVK 371 (377)
T ss_pred CCCCCCEEEEECCCC-CCHHHHHHHHHHHCCHHHHCCCCCEEEEEECCCCCCCHHHHHHHHCCCCCCCHHHHHHHHHHCC
T ss_conf 565788899817877-8989999999870620200204542279957998763066777761998468899999998577
Q ss_pred C
Q ss_conf 6
Q gi|254781172|r 723 T 723 (731)
Q Consensus 723 ~ 723 (731)
.
T Consensus 372 p 372 (377)
T PRK05601 372 E 372 (377)
T ss_pred C
T ss_conf 5
No 14
>LOAD_ligase consensus
Probab=98.69 E-value=3.4e-07 Score=74.80 Aligned_cols=155 Identities=21% Similarity=0.278 Sum_probs=88.7
Q ss_pred EEEEEEECCEEEEEEEEECCEEEEEEECCCCHHHHHHHHH---HHHHCCCCCCCCCCCCCEEEEEEEEEEECHHHHHHHH
Q ss_conf 1999941581899999859989988865986556669997---7531024322335445504899999985202123455
Q gi|254781172|r 127 FFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSAC---IRAIPTIPRVLSLNIPEIIEVRGEVYISKNDFLALND 203 (731)
Q Consensus 127 ~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n---~~~i~~iP~~l~~~~~~~ieiRGEv~m~~~~F~~lN~ 203 (731)
+|++|+|+||+-+.+++.+|. +.+.|| .|.++|+. +......+. ....+..+.+-||++.....+
T Consensus 1 e~~~e~K~DG~R~~~~~~~~~-v~~~SR----~g~~~t~~f~~~~~~~~~~~--~~~~~~~~iLDGEl~~~~~~~----- 68 (184)
T LOAD_ligase 1 EYYVEEKYDGERVQIHKDGDG-VYFFSR----NGEDITDYFPDVKTALKIPL--KLSGLKNLILDGELVVDDVDF----- 68 (184)
T ss_pred CCEEEEEECEEEEEEEEECCE-EEEECC----CCCCCCCCCCHHHHHHHHHH--HCCCCCCEEEEEEEEEECCCC-----
T ss_conf 936898886089999998999-999979----99876100417899987665--025788779987999736999-----
Q ss_pred HHHHCCCCCCCCHHHHHHHHHHCCCHH-HHHCCCEEEEEEECCCCCCCC--CCCHHHHHHHHHCCCCCCCC-----EEEE
Q ss_conf 643148543342345677775234555-530111056641024543321--00003689999759966541-----4887
Q gi|254781172|r 204 EMIAVGRKPYANPRNAASGILRRLNPT-DITRYLNFFVHGLGKTSEIFA--KGQYEMLQKMRCLGFPVNNG-----VRQA 275 (731)
Q Consensus 204 ~~~~~g~~~f~NpRN~aaG~lr~~d~~-~~~r~L~f~ay~~~~~~~~~~--~~~~e~l~~L~~~GF~v~~~-----~~~~ 275 (731)
+|...++.+ +...+. ....++.|++|++...++... ....+..+.|..+--.+... ....
T Consensus 69 --------~f~~~~~~~----~~~~~~~~~~~~~~~~vFDil~~~g~~~~~~~~~~R~~~L~~~~~~~~~~~~~~~~~~~ 136 (184)
T LOAD_ligase 69 --------PFQLLRNRK----RKSVRVKDMKEPLEYFVFDILYLNGEDLTDLPLEERRKILEKLIKEIKDVRAIKNITVI 136 (184)
T ss_pred --------CHHHHHHHH----CCCCCCHHHCCCEEEEEEEEECCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEEEEEEC
T ss_conf --------989998775----33665122215618999996364898154588999999999974125883598789954
Q ss_pred ECCCCHHHHHHHHHHHHCCCCCCCCCEEEEECCHHC
Q ss_conf 403211345566553100112343763777311000
Q gi|254781172|r 276 NTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSL 311 (731)
Q Consensus 276 ~~~~~~~~~~~~~~~~r~~l~y~iDGiVikvn~~~~ 311 (731)
.+.+++.++++... ....+|+|+|-.+..+
T Consensus 137 ~~~~~~~~~~~~~~------~~g~EGimiK~~~s~Y 166 (184)
T LOAD_ligase 137 DDVEELNKFLEKAL------GEGIEGLVIKDPDSPY 166 (184)
T ss_pred CCHHHHHHHHHHHH------HCCCCEEEEECCCCCC
T ss_conf 99999999999998------6899679987899978
No 15
>pfam00533 BRCT BRCA1 C Terminus (BRCT) domain. The BRCT domain is found predominantly in proteins involved in cell cycle checkpoint functions responsive to DNA damage. The BRCT domain of XRCC1 forms a homodimer in the crystal structure. This suggests that pairs of BRCT domains associate as homo- or heterodimers. BRCT domains are often found as tandem-repeat pairs. Structures of the BRCA1 BRCT domains revealed a basis for a widely utilized head-to-tail BRCT-BRCT oligomerisation mode. This conserved tandem BRCT architecture facilitates formation of the canonical BRCT phospho-peptide interaction cleft at a groove between the BRCT domains. Disease associated missense and nonsense mutations in the BRCA1 BRCT domains disrupt peptide binding by directly occluding this peptide binding groove, or by disrupting key conserved BRCT core folding determinants.
Probab=98.67 E-value=1.7e-07 Score=77.19 Aligned_cols=74 Identities=39% Similarity=0.589 Sum_probs=67.2
Q ss_pred CCCCCCCEEEEECCCCCCCHHHHHHHHHHCCCEEEEEEECCEEEEEECCCCC-CHHHHHHHCCCEEECHHHHHHHH
Q ss_conf 8821686699972588998789999999829849981116321799778888-63798997499173799999999
Q gi|254781172|r 644 SSEIENKKLVFTGTLQKIQRHKAQEYVTQLGAVVSAILSRKTDIIIVGDNPG-SKLEKAQQLGVKIMNEEQFLFLL 718 (731)
Q Consensus 644 ~~~l~gk~vV~TGtl~~~~R~e~~~~ie~~Ggkv~sSVSkkT~~LI~ge~~g-SKl~KA~~LgI~Ii~e~ef~~ll 718 (731)
...|.|.+|++|| +..+.|++++++|+.+||++..++++.|++||+++..+ .|..+|...|++|++++.+.+.+
T Consensus 3 ~~~f~~~~~~i~~-~~~~~r~~l~~~i~~~Gg~~~~~~~~~~thli~~~~~~~~k~~~a~~~~i~iV~~~Wi~~ci 77 (77)
T pfam00533 3 EKLFKGKTFVITG-LDSLEREELEELIEKLGGKVTDSLSKKTTHVIVGENAGTLKLLKAIALGIPIVTEEWLLDCI 77 (77)
T ss_pred CCCCCCCEEEEEC-CCCCCHHHHHHHHHHHCCEEECCCCCCEEEEEECCCCCCHHHHHHHHCCCEEECHHHHHHHC
T ss_conf 8537996899979-49849999999999959947164346678999828988479998886896795399999869
No 16
>PRK09125 DNA ligase; Provisional
Probab=98.56 E-value=3.1e-05 Score=59.66 Aligned_cols=213 Identities=19% Similarity=0.268 Sum_probs=125.3
Q ss_pred CCCEEEEEEECCEEEEEEEEECCEEEEEEECCCCHHHHHHHHHHHHHCCCCCCCCCCCCCEEEEEEEEEEECHHHHHHHH
Q ss_conf 76119999415818999998599899888659865566699977531024322335445504899999985202123455
Q gi|254781172|r 124 NSIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPTIPRVLSLNIPEIIEVRGEVYISKNDFLALND 203 (731)
Q Consensus 124 ~~~~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n~~~i~~iP~~l~~~~~~~ieiRGEv~m~~~~F~~lN~ 203 (731)
....|.++.|+||+=+ |=+|+ +..||. |..+.. |.......|. +.+=||+++.+.+|++
T Consensus 36 ~~~~w~~SeKlDGvRa---~wdG~--~l~SR~----G~~~~a--------P~wf~~~lP~-~~LDGELw~gR~~Fe~--- 94 (277)
T PRK09125 36 DISGYLVSEKLDGVRA---YWDGK--QLLTRQ----GNPIAA--------PAWFTAGFPP-FALDGELWAGRGQFEQ--- 94 (277)
T ss_pred CCCCEEEEEEEEEEEE---EEECC--EEECCC----CCCCCC--------CHHHHHCCCC-CCEEEEEEECCCCHHH---
T ss_conf 8423589874137999---99789--888069----977789--------7788830999-6542468707788999---
Q ss_pred HHHHCCCCCCCCHHHHHHHHHHCCCHHHHH-CCCEEEEEEECCCCCCCCCCCHHHHHHHHHC----CCCCCCC--EEEEE
Q ss_conf 643148543342345677775234555530-1110566410245433210000368999975----9966541--48874
Q gi|254781172|r 204 EMIAVGRKPYANPRNAASGILRRLNPTDIT-RYLNFFVHGLGKTSEIFAKGQYEMLQKMRCL----GFPVNNG--VRQAN 276 (731)
Q Consensus 204 ~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~-r~L~f~ay~~~~~~~~~~~~~~e~l~~L~~~----GF~v~~~--~~~~~ 276 (731)
.++++|++.|.... +.+.|++|++....+ + ..+.++.|+.+ .-+.... ...+.
T Consensus 95 ----------------l~s~Vr~~~p~d~~W~~I~y~VFDlP~~~g-p---f~eR~~~L~~ll~~~~~~~l~~v~q~~v~ 154 (277)
T PRK09125 95 ----------------ISSTVRDQTPDDAEWRKVRFMVFDLPDAGG-D---FEERLAVLRKLLAKLPSPYLKIIEQIPVD 154 (277)
T ss_pred ----------------HHHHHHCCCCCHHHHHEEEEEEEECCCCCC-C---HHHHHHHHHHHHHHCCCCCEEEEEEEEEC
T ss_conf ----------------987883589980443204899986788899-9---99999999999965899718998458979
Q ss_pred CCCCHHHHHHHHHHHHCCCCCCCCCEEEEECCHHCCCCCCCCCCCCCCEEEECCCCCEEEEEEEEEEEEECC-CCEEEEE
Q ss_conf 032113455665531001123437637773110001115876568663123114562158998788994035-6225899
Q gi|254781172|r 277 TFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSLQKQLGERARSPRWMISHKFAEKQASTRLLDIDIQIGR-TGILTPV 355 (731)
Q Consensus 277 ~~~~~~~~~~~~~~~r~~l~y~iDGiVikvn~~~~q~~lG~ts~~PrwaiA~Kf~~e~~~T~v~~I~wqvgR-tG~itPv 355 (731)
+.+++..+++++.+ -.--|+++|-.+..++. |. + +.-+=+| +-..++.+|.+..--.|| .|.+--
T Consensus 155 ~~~~l~~~l~~~~~------~G~EGlmlr~~~~~Y~~--gR---s-~~llK~K-~~~d~E~~Vvg~~~G~Gk~~g~lGa- 220 (277)
T PRK09125 155 SEEALLQFLDQIVA------AGGEGLMLHRPDAPYEA--GR---S-DDLLKLK-PYQDAEATVIGHLPGKGKFAGMLGA- 220 (277)
T ss_pred CHHHHHHHHHHHHH------CCCCEEEEECCCCCCCC--CC---C-CCCEEEE-CCCCEEEEEEEEECCCCCCCCCEEE-
T ss_conf 99999999999996------79838778879996578--89---8-5427873-2364799999677599864684579-
Q ss_pred EEEEEEEECCCEEEEECCCCHHHHHHHCCCCCCCCCCCCCCCCCEEEEEE
Q ss_conf 99743330264000101489899975023454322246844076899983
Q gi|254781172|r 356 ARLEPVNIGGALITNATLHNEDYIKGLDASGKVMRGGRDIRVGDRVLVKR 405 (731)
Q Consensus 356 a~~ePV~l~G~~V~ratlhN~~~I~~l~~~~~~~~~~~~I~iGd~V~I~R 405 (731)
+.=..-+|.+.+--|+.+-..= ++.--||..|++.-
T Consensus 221 --l~~~~~~G~~f~vGsGfsd~~R------------~~pp~iG~~it~ky 256 (277)
T PRK09125 221 --LLVETPDGREFKIGSGFSDEER------------ENPPKIGSIITYKY 256 (277)
T ss_pred --EEEEECCCCEEEECCCCCHHHH------------CCCCCCCCEEEEEE
T ss_conf --9999689978985899998997------------59976898999998
No 17
>cd07898 Adenylation_DNA_ligase The Adenylation domain of ATP-dependent DNA Ligases is a component of the catalytic core unit. 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 a specific function. 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-sit
Probab=98.55 E-value=4.3e-06 Score=66.32 Aligned_cols=161 Identities=15% Similarity=0.134 Sum_probs=89.7
Q ss_pred CCCEEEEEEECCEEEEEEEEECCEEEEEEECCCCHHHHHHHHHHHHHCCCCCCCCCCCCCEEEEEEEEEEECHHHHHHHH
Q ss_conf 76119999415818999998599899888659865566699977531024322335445504899999985202123455
Q gi|254781172|r 124 NSIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPTIPRVLSLNIPEIIEVRGEVYISKNDFLALND 203 (731)
Q Consensus 124 ~~~~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n~~~i~~iP~~l~~~~~~~ieiRGEv~m~~~~F~~lN~ 203 (731)
.+..|++|||+||+=+-+++.+|. ++..|| .|.++|++...|......+ ..+..+.+=||++.-.....
T Consensus 19 ~~~~~~~E~K~DG~R~~~~~~~~~-v~l~SR----~gk~~t~~fpei~~~~~~~--~~~~~~IlDGElv~~d~~~~---- 87 (201)
T cd07898 19 GPREMSFEIKYDGERCQVHKDGDR-VKLFSR----SGKDVTDDFPELAAAAKDC--ALPHSCILDGEIVAWDDNGG---- 87 (201)
T ss_pred CCCCEEEEEEECCEEEEEEEECCE-EEEEEC----CCCCCHHHHHHHHHHHHHC--CCCCCEEEEEEEEEECCCCC----
T ss_conf 898489998887189999998999-999958----9870012358899999854--68744599506999728999----
Q ss_pred HHHHCCCCCCCCHHHHHHHHHHCCCHHHHHCCCEEEEEEECCCCCCCC--CCCHHHHHHHHHCCCCCCCCE-----EEEE
Q ss_conf 643148543342345677775234555530111056641024543321--000036899997599665414-----8874
Q gi|254781172|r 204 EMIAVGRKPYANPRNAASGILRRLNPTDITRYLNFFVHGLGKTSEIFA--KGQYEMLQKMRCLGFPVNNGV-----RQAN 276 (731)
Q Consensus 204 ~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~r~L~f~ay~~~~~~~~~~--~~~~e~l~~L~~~GF~v~~~~-----~~~~ 276 (731)
+.-+-.......+.+. ....-++.|++|++....+... ....+..+.|+.+-=+..+.. ..+.
T Consensus 88 ---------~~~~f~~~~~~~~~~~-~~~~~~~~~~vFDil~l~g~~l~~~pl~eR~~~L~~~~~~~~~~i~~~~~~~~~ 157 (201)
T cd07898 88 ---------KPLPFKALGRRFRGKR-LDEDVPVCLYAFDLLYLNGESLLDRPLSERRALLEDLVKEIPGRIRVAEQLIVD 157 (201)
T ss_pred ---------CCCCHHHHHHHCCCCC-CCCCCCCEEEEEEEEEECCCCCCCCCHHHHHHHHHHHHHCCCCCEEEEEEEECC
T ss_conf ---------7769999852355432-110378289999765188850112879999999998751289838999999759
Q ss_pred CCCCHHHHHHHHHHHHCCCCCCCCCEEEEECCHHC
Q ss_conf 03211345566553100112343763777311000
Q gi|254781172|r 277 TFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSL 311 (731)
Q Consensus 277 ~~~~~~~~~~~~~~~r~~l~y~iDGiVikvn~~~~ 311 (731)
+.+++.++++.+.+ -.-.|+|+|--|-.+
T Consensus 158 ~~~~i~~~~~~~~~------~G~EGimiK~~ds~Y 186 (201)
T cd07898 158 SIEELATAFSEARK------EGWEGLMLKRPDSTY 186 (201)
T ss_pred CHHHHHHHHHHHHH------CCCCEEEEECCCCCC
T ss_conf 89999999999997------899779973799962
No 18
>smart00292 BRCT breast cancer carboxy-terminal domain.
Probab=98.46 E-value=1.4e-06 Score=70.00 Aligned_cols=76 Identities=34% Similarity=0.479 Sum_probs=67.4
Q ss_pred CCCCCCEEEEECCCCCCCHHHHHHHHHHCCCEEEEEEEC-CEEEEEECCCCCCH--HHHHHHCCCEEECHHHHHHHHHH
Q ss_conf 821686699972588998789999999829849981116-32179977888863--79899749917379999999988
Q gi|254781172|r 645 SEIENKKLVFTGTLQKIQRHKAQEYVTQLGAVVSAILSR-KTDIIIVGDNPGSK--LEKAQQLGVKIMNEEQFLFLLQQ 720 (731)
Q Consensus 645 ~~l~gk~vV~TGtl~~~~R~e~~~~ie~~Ggkv~sSVSk-kT~~LI~ge~~gSK--l~KA~~LgI~Ii~e~ef~~ll~~ 720 (731)
..|.|++|++||.+....|++++++|+.+||++..++++ .++++|+++..+.+ +..|...|++|++++.+.+.+..
T Consensus 1 ~~f~~~~~~i~g~~~~~~~~~l~~~i~~~Gg~v~~~~~~~~~th~I~~~~~~~~~~~~~~~~~~~~iV~~~Wi~~c~~~ 79 (80)
T smart00292 1 KLFKGKVFVITGKFDKNERDELKELIEALGGKVTSSLSSKTTTHVIVGSPEGGKLELLLAIALGIPIVTEDWLLDCLKA 79 (80)
T ss_pred CCCCCCEEEEEEECCCCCHHHHHHHHHHHCCEECCCCCCCCEEEEEEECCCCCCHHHHHHHHCCCCEECHHHHHHHHHC
T ss_conf 9579989999861698899999999998399250432577507999837988607789999809928759999999977
No 19
>cd07901 Adenylation_DNA_ligase_Arch_LigB The Adenylation domain of archaeal and bacterial LigB-like DNA ligases is a component of the catalytic core unit. 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, bacteriohages, 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 tuberculo
Probab=98.46 E-value=1.9e-05 Score=61.34 Aligned_cols=177 Identities=16% Similarity=0.136 Sum_probs=96.2
Q ss_pred CCCCCCHHHCCCHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCEEEEEEEEECCEEEEEEECCCCHHHHHHHHHHHHHC
Q ss_conf 66425702159999999999999986124677761199994158189999985998998886598655666999775310
Q gi|254781172|r 92 SIPTLSLEKIWNIEDLRKFITRIYRFWQKKDDNSIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIP 171 (731)
Q Consensus 92 ~~pMlSL~k~~~~~el~~w~~~~~~~~~~~~~~~~~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n~~~i~ 171 (731)
-.|||.-- +.+.+++... ....|.+|+|+||.=+-+.+.+|. ++..|| -|+|+|+..-.|.
T Consensus 5 i~PMLA~~-~~~~~~~~~~-------------~~~~~~~E~K~DG~R~~i~~~~~~-v~l~SR----~g~~~t~~fPei~ 65 (207)
T cd07901 5 VRPMLAQR-ASSVEEALEK-------------EGGPAAVEYKYDGARVQIHKDGDK-VRIFSR----RLEDVTNALPDVV 65 (207)
T ss_pred CCCCCCCC-CCCHHHHHHH-------------CCCCEEEEEEECEEEEEEEEECCE-EEEEEC----CCCCCCCCCHHHH
T ss_conf 74415898-7997899863-------------089669998588188999998999-999973----6860223466899
Q ss_pred C-CCCCCCCCCCCEEEEEEEEEEECHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCHH-H--HHCCCEEEEEEECCCC
Q ss_conf 2-4322335445504899999985202123455643148543342345677775234555-5--3011105664102454
Q gi|254781172|r 172 T-IPRVLSLNIPEIIEVRGEVYISKNDFLALNDEMIAVGRKPYANPRNAASGILRRLNPT-D--ITRYLNFFVHGLGKTS 247 (731)
Q Consensus 172 ~-iP~~l~~~~~~~ieiRGEv~m~~~~F~~lN~~~~~~g~~~f~NpRN~aaG~lr~~d~~-~--~~r~L~f~ay~~~~~~ 247 (731)
. +.. ......+.+=||++.-..+ |.. .|-....+-++++++. . ...++.|++|++...+
T Consensus 66 ~~~~~---~~~~~~~ILDGElv~~d~~-----------g~~---~~F~~l~~r~~~~~~~~~~~~~~p~~~~vFDiL~l~ 128 (207)
T cd07901 66 EAVRE---AVKADEAILDGEAVAYDPD-----------GRP---LPFQETLRRFRRKYDVAEAAEEIPLTLFLFDILYLD 128 (207)
T ss_pred HHHHH---CCCCCCEEEEEEEEEECCC-----------CCC---CCHHHHHHHHCCCCCHHHHHHCCCEEEEEEEEEEEC
T ss_conf 99985---4898877985599998899-----------998---789999977533653556542087489998776688
Q ss_pred CCCC--CCCHHHHHHHHHCCCCCCCCEE-----EEECCCCHHHHHHHHHHHHCCCCCCCCCEEEEECCHHC
Q ss_conf 3321--0000368999975996654148-----87403211345566553100112343763777311000
Q gi|254781172|r 248 EIFA--KGQYEMLQKMRCLGFPVNNGVR-----QANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSL 311 (731)
Q Consensus 248 ~~~~--~~~~e~l~~L~~~GF~v~~~~~-----~~~~~~~~~~~~~~~~~~r~~l~y~iDGiVikvn~~~~ 311 (731)
+... ....+..+.|+.+ |+..+... .+++.+++.++++...+ -..-|||+|--+-.+
T Consensus 129 g~~l~~~pl~eRr~~L~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~g~EGiv~K~~~s~Y 192 (207)
T cd07901 129 GEDLLDLPLEERRKILEEI-VPESEEISLAPRLVTDDPEEAEEFFEEALE------AGHEGVMVKSLDSPY 192 (207)
T ss_pred CCCHHCCCHHHHHHHHHHH-CCCCCCEEEEEEEECCCHHHHHHHHHHHHH------CCCCEEEEECCCCCC
T ss_conf 7214208799999999975-265797388304865999999999999997------899769985799976
No 20
>COG1793 CDC9 ATP-dependent DNA ligase [DNA replication, recombination, and repair]
Probab=98.38 E-value=0.00015 Score=54.37 Aligned_cols=216 Identities=19% Similarity=0.198 Sum_probs=125.0
Q ss_pred CCEEEEEEECCEEEEEEEEECCEEEEEEECCCCHHHHHHHHHHH-HHCCCCCCCCCCCCCEEEEEEEEEEE----CHHHH
Q ss_conf 61199994158189999985998998886598655666999775-31024322335445504899999985----20212
Q gi|254781172|r 125 SIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIR-AIPTIPRVLSLNIPEIIEVRGEVYIS----KNDFL 199 (731)
Q Consensus 125 ~~~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n~~-~i~~iP~~l~~~~~~~ieiRGEv~m~----~~~F~ 199 (731)
...|.+|.|+||.=+-++..+|. ++.+|| -|+|||+... .+..+-..++ +..+.+-||+++- ..+|+
T Consensus 132 ~~~w~~E~K~DG~R~q~h~~~~~-vrl~SR----~g~d~T~~fP~~~~~~~~~l~---~~~~iiDGE~V~~~~~~~~~F~ 203 (444)
T COG1793 132 GGDWAYEEKFDGYRVQIHIDGGK-VRLYSR----NGEDWTGRFPDILEAAAEALP---ADDFILDGEIVVLDEEGRLDFQ 203 (444)
T ss_pred CCCEEEEEEECEEEEEEEECCCE-EEEEEC----CCCCCHHHCCHHHHHHHHCCC---CCCEEEECEEEEECCCCCCCHH
T ss_conf 67779998635699999976987-999957----984124458288999863278---7776896769987888889989
Q ss_pred HHHHHHHHCCCCCCCCHHHHHHHHHHCCCHHH---HHCCCEEEEEEECCCCCCCCC--CCHHHHHHHHHC-----CCCCC
Q ss_conf 34556431485433423456777752345555---301110566410245433210--000368999975-----99665
Q gi|254781172|r 200 ALNDEMIAVGRKPYANPRNAASGILRRLNPTD---ITRYLNFFVHGLGKTSEIFAK--GQYEMLQKMRCL-----GFPVN 269 (731)
Q Consensus 200 ~lN~~~~~~g~~~f~NpRN~aaG~lr~~d~~~---~~r~L~f~ay~~~~~~~~~~~--~~~e~l~~L~~~-----GF~v~ 269 (731)
.|-. .+|++.+.. ..-++.|++|++.+.++.... .-.+.-+.|..+ -|...
T Consensus 204 ~Lq~-------------------r~~~~~~v~~~~~~~~~~~~aFDlL~~dG~dL~~~pl~eRr~~Le~lv~~~~~~~~~ 264 (444)
T COG1793 204 ALQQ-------------------RLRRKYDVAKLRRETPLVLFAFDLLYLDGEDLRGLPLEERRALLEELVKSSDKIEIA 264 (444)
T ss_pred HHHH-------------------HHHHCCCHHHHCCCCCEEEEEEEEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCC
T ss_conf 9998-------------------751044334414677617999977401675402287899999999985523543424
Q ss_pred CCEEEEECCCCHHHHHHHHHHHHCCCCCCCCCEEEEECCHHCCCCCCCCCCCCCCEEEECCCCCEEEEEEEEEEEEECCC
Q ss_conf 41488740321134556655310011234376377731100011158765686631231145621589987889940356
Q gi|254781172|r 270 NGVRQANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSLQKQLGERARSPRWMISHKFAEKQASTRLLDIDIQIGRT 349 (731)
Q Consensus 270 ~~~~~~~~~~~~~~~~~~~~~~r~~l~y~iDGiVikvn~~~~q~~lG~ts~~PrwaiA~Kf~~e~~~T~v~~I~wqvgRt 349 (731)
+.... .+.++...+++...+ ..+.|||+|--|-.++.. .+.-.| +=+| +.++..-+|.+..|+-|+-
T Consensus 265 ~~i~~-~~~~~~~~~~~~a~~------~g~EGvv~K~~ds~Y~~g----~R~~~W-~K~K-~~~~~d~vv~G~~~g~Gkr 331 (444)
T COG1793 265 ERIPF-SDAEEGEAFLEAAIE------LGLEGVVAKRPDSPYRAG----GRSNKW-LKVK-RDETLDLVVVGAEYGKGKR 331 (444)
T ss_pred CCEEE-CCHHHHHHHHHHHHH------CCCEEEEEECCCCCCCCC----CCCCCC-EEEC-CCCCEEEEEEEEEECCCCC
T ss_conf 51451-776789999998886------396689970799986789----988774-5651-4775008999788468854
Q ss_pred CEEEEEEEEEEEEECCC-----EEEEECCCCHHHHHHH
Q ss_conf 22589999743330264-----0001014898999750
Q gi|254781172|r 350 GILTPVARLEPVNIGGA-----LITNATLHNEDYIKGL 382 (731)
Q Consensus 350 G~itPva~~ePV~l~G~-----~V~ratlhN~~~I~~l 382 (731)
+ .--+.+-.+.-++. .++=.|++..++.+.|
T Consensus 332 ~--~~~slll~~~~~~~~~~~~v~kVgtGf~~~~l~~l 367 (444)
T COG1793 332 S--LYGSLLLGVYDGDGGGLLYVGKVGTGFSDAELEEL 367 (444)
T ss_pred C--CCCCEEEEEEECCCCEEEEEEEECCCCCHHHHHHH
T ss_conf 5--52206999980898638999874477798999999
No 21
>cd07906 Adenylation_DNA_ligase_LigD The Adenylation domain of Mycobacterium tuberculosis LigD-like ATP-dependent DNA ligases is a component of the catalytic core unit. 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 oligouncleotide/oligosaccharide binding (OB)-fold dom
Probab=98.37 E-value=2.1e-05 Score=60.89 Aligned_cols=151 Identities=19% Similarity=0.158 Sum_probs=86.8
Q ss_pred CCCEEEEEEECCEEEEEEEEECCEEEEEEECCCCHHHHHHHHHHHHHCCCCCCCCCCCCCEEEEEEEEEEECH----HHH
Q ss_conf 7611999941581899999859989988865986556669997753102432233544550489999998520----212
Q gi|254781172|r 124 NSIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPTIPRVLSLNIPEIIEVRGEVYISKN----DFL 199 (731)
Q Consensus 124 ~~~~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n~~~i~~iP~~l~~~~~~~ieiRGEv~m~~~----~F~ 199 (731)
.+..|++|+|+||+=+-+++.+|. ++..|| .|+|+|+....|......+ .+..+.+=||++.-.. +|+
T Consensus 14 ~~~~~~~E~K~DG~R~~~~~~~~~-v~l~SR----~g~~~t~~fp~i~~~~~~~---~~~~~ILDGElv~~~~~~~~~F~ 85 (186)
T cd07906 14 DGEDWLYEIKWDGYRALARVDGGR-VRLYSR----NGLDWTARFPELADALAAL---PVRSAVLDGEIVVLDEGGRPDFQ 85 (186)
T ss_pred CCCCEEEEEEECCEEEEEEEECCE-EEEEEC----CCCCCCHHCHHHHHHHHHC---CCCCEEEEEEEEEECCCCCCCHH
T ss_conf 999768998478199999998999-999969----9984410167899999847---98758994369986799888989
Q ss_pred HHHHHHHHCCCCCCCCHHHHHHHHHHCCCHHHHHCCCEEEEEEECCCCCCCC--CCCHHHHHHHHHCCCCCCCCEEEEEC
Q ss_conf 3455643148543342345677775234555530111056641024543321--00003689999759966541488740
Q gi|254781172|r 200 ALNDEMIAVGRKPYANPRNAASGILRRLNPTDITRYLNFFVHGLGKTSEIFA--KGQYEMLQKMRCLGFPVNNGVRQANT 277 (731)
Q Consensus 200 ~lN~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~r~L~f~ay~~~~~~~~~~--~~~~e~l~~L~~~GF~v~~~~~~~~~ 277 (731)
.+... .+. ....++.|++|++...++... ....+..+.|+.+--+..+....+..
T Consensus 86 ~l~~r-------------------~~~----~~~~~v~~~vFDiL~l~g~~l~~~pl~eR~~~L~~l~~~~~~~i~~~~~ 142 (186)
T cd07906 86 ALQNR-------------------LRL----ARTVPVVYYAFDLLYLDGEDLRGLPLLERKELLEELLPAASPRLRFSEH 142 (186)
T ss_pred HHHHH-------------------HHC----CCCCCEEEEEEEEEEECCCCHHHCCHHHHHHHHHHHHCCCCCCEEECCC
T ss_conf 99867-------------------512----6777749999960028871500088999999999874247995897872
Q ss_pred C-CCHHHHHHHHHHHHCCCCCCCCCEEEEECCHHC
Q ss_conf 3-211345566553100112343763777311000
Q gi|254781172|r 278 F-HGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSL 311 (731)
Q Consensus 278 ~-~~~~~~~~~~~~~r~~l~y~iDGiVikvn~~~~ 311 (731)
. ++...+++...+ -...|||+|--+-.+
T Consensus 143 ~~~~~~~~~~~~~~------~g~EGimiK~~~s~Y 171 (186)
T cd07906 143 FEGDGAALLEAACE------LGLEGIVAKRADSPY 171 (186)
T ss_pred CCCCHHHHHHHHHH------CCCCEEEEECCCCCC
T ss_conf 55649999999997------799569986799941
No 22
>cd07903 Adenylation_DNA_ligase_IV The Adenylation domain of DNA Ligase IV is a component of the catalytic core unit. 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, bacteriohages, 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 consist
Probab=98.30 E-value=6.2e-05 Score=57.33 Aligned_cols=172 Identities=18% Similarity=0.166 Sum_probs=92.9
Q ss_pred CCEEEEEEECCEEEEEEEEECCEEEEEEECCCCHHHHHHHHHHH----HHCCCCCCCC--CCCCCEEEEEEEEEEECHHH
Q ss_conf 61199994158189999985998998886598655666999775----3102432233--54455048999999852021
Q gi|254781172|r 125 SIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIR----AIPTIPRVLS--LNIPEIIEVRGEVYISKNDF 198 (731)
Q Consensus 125 ~~~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n~~----~i~~iP~~l~--~~~~~~ieiRGEv~m~~~~F 198 (731)
...|.+|+|+||+=+-+++.+|. ++..|| -|+|+|+.-. .+...|.... ...+..+.+=||++.-...-
T Consensus 32 ~~~~~~E~K~DG~R~~~h~~~~~-v~l~SR----ng~d~t~~fpe~~~~~~~~~~~~~~~~~~~~~~ILDGElv~~d~~~ 106 (227)
T cd07903 32 GDPFYIETKFDGERIQLHKDGEE-FKYFSR----NGNDYTYLYGESLDEGSLTPYIHLAFAKSVKSCILDGEMMVWDKET 106 (227)
T ss_pred CCCEEEEEEECEEEEEEEEECCE-EEEEEC----CCCCCHHHCCCHHHHHHHCHHHHHHHHCCCCCEEEEEEEEEEECCC
T ss_conf 98469998775189999995999-999977----8870023253056553202556777513688689960598873677
Q ss_pred HHHHHHHHHCCCCCCCCHHHHHHHHHHCCCH--HHHHCCCEEEEEEECCCCCCC--CCCCHHHHHHHHHCCCCCCCCE--
Q ss_conf 2345564314854334234567777523455--553011105664102454332--1000036899997599665414--
Q gi|254781172|r 199 LALNDEMIAVGRKPYANPRNAASGILRRLNP--TDITRYLNFFVHGLGKTSEIF--AKGQYEMLQKMRCLGFPVNNGV-- 272 (731)
Q Consensus 199 ~~lN~~~~~~g~~~f~NpRN~aaG~lr~~d~--~~~~r~L~f~ay~~~~~~~~~--~~~~~e~l~~L~~~GF~v~~~~-- 272 (731)
.+ --+|.--+. ..+.... ......+.|++|++...++.. -....+..+.|+.+--+.....
T Consensus 107 ~~---------~~~f~~l~~----~~~~~~~~~~~~~~~~~~~~FDiL~l~g~~l~~~p~~eR~~~L~~~~~~~~~~i~~ 173 (227)
T cd07903 107 KR---------FLPFGTLKD----VAALRESRLEDSNLQPCFVVFDILYLNGKSLTNLPLHERKELLRKIITPVPGRIEI 173 (227)
T ss_pred CC---------CCCCCHHHH----HHHHCCCCCCCCCCCEEEEEEEEEEECCHHHHHHHHHHHHHHHHHHHCCCCCCEEE
T ss_conf 75---------255303667----98742344333455427999877515883165437899999999862568982798
Q ss_pred ---EEEECCCCHHHHHHHHHHHHCCCCCCCCCEEEEECCHHCCCCCCCCCCCCCC
Q ss_conf ---8874032113455665531001123437637773110001115876568663
Q gi|254781172|r 273 ---RQANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSLQKQLGERARSPRW 324 (731)
Q Consensus 273 ---~~~~~~~~~~~~~~~~~~~r~~l~y~iDGiVikvn~~~~q~~lG~ts~~Prw 324 (731)
..+.+.+++..+++...+. .-.|||+|--+-.++- | .|+..|
T Consensus 174 ~~~~~~~~~~~i~~~~~~~~~~------g~EGimiK~~~s~Y~~--g--kRs~~W 218 (227)
T cd07903 174 VKRKEASTKEDIEEALNEAIDN------REEGIVVKDLDSKYRP--G--KRGDGW 218 (227)
T ss_pred EEEEECCCHHHHHHHHHHHHHC------CCCEEEEECCCCCCCC--C--CCCCCC
T ss_conf 7778739999999999999987------9978998179996479--9--989982
No 23
>pfam01068 DNA_ligase_A_M ATP dependent DNA ligase domain. This domain belongs to a more diverse superfamily, including pfam01331 and pfam01653.
Probab=98.25 E-value=3e-05 Score=59.80 Aligned_cols=155 Identities=17% Similarity=0.146 Sum_probs=89.0
Q ss_pred CCCEEEEEEECCEEEEEEEEECCEEEEEEECCCCHHHHHHHHHHHHHCC-CCCCCCCCCCCEEEEEEEEEEECHHHHHHH
Q ss_conf 7611999941581899999859989988865986556669997753102-432233544550489999998520212345
Q gi|254781172|r 124 NSIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPT-IPRVLSLNIPEIIEVRGEVYISKNDFLALN 202 (731)
Q Consensus 124 ~~~~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n~~~i~~-iP~~l~~~~~~~ieiRGEv~m~~~~F~~lN 202 (731)
....|++|||+||+=+-+++.+|. +++.|| .|.++|+....|.. +...+... ...+.+=||++.......
T Consensus 16 ~~~~~~~E~K~DG~R~~i~~~~~~-v~~~SR----~gk~~t~~~p~l~~~~~~~~~~~-~~~~iLDGElv~~~~~~~--- 86 (190)
T pfam01068 16 GGGAFIVEEKYDGERVQIHKDGGE-VKLLSR----NGKPITATYPELLEFLLEAFFPD-VKSFILDGEIVAIPETGR--- 86 (190)
T ss_pred CCCCEEEEEEECEEEEEEEEECCE-EEEECC----CCCCCCCCCHHHHHHHHHHHCCC-CCCEEEEEEEEEECCCCC---
T ss_conf 799689999886099999998999-999929----99886101689999998763467-875799868998768998---
Q ss_pred HHHHHCCCCCCCCHHHHHHHHHHCCCHHHHHCCCEEEEEEECCCCCC--CCCCCHHHHHHHHHCCCCCCCCE-----EEE
Q ss_conf 56431485433423456777752345555301110566410245433--21000036899997599665414-----887
Q gi|254781172|r 203 DEMIAVGRKPYANPRNAASGILRRLNPTDITRYLNFFVHGLGKTSEI--FAKGQYEMLQKMRCLGFPVNNGV-----RQA 275 (731)
Q Consensus 203 ~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~r~L~f~ay~~~~~~~~--~~~~~~e~l~~L~~~GF~v~~~~-----~~~ 275 (731)
.++....+ ++. ...++.|++|++...++. .-....+..+.|..+--+ .+.. ..+
T Consensus 87 -----------~~~~~~~~---~~~----~~~~~~~~vFDil~~~~~~l~~~p~~~R~~~L~~~~~~-~~~i~~~~~~~~ 147 (190)
T pfam01068 87 -----------ILPFQTLA---VRK----KKEPLCFFVFDVLYLDGESLTDKPLKERRELLEEYFKI-PVRIEIAETIET 147 (190)
T ss_pred -----------CCCHHHHH---HHC----CCCCEEEEEEEEEEECCCCHHCCCHHHHHHHHHHHHCC-CCCEEEEEEEEC
T ss_conf -----------36167765---222----35772899998767887532108899999999986076-883599899862
Q ss_pred ECCCCHHHHHHHHHHHHCCCCCCCCCEEEEECCHHCC
Q ss_conf 4032113455665531001123437637773110001
Q gi|254781172|r 276 NTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSLQ 312 (731)
Q Consensus 276 ~~~~~~~~~~~~~~~~r~~l~y~iDGiVikvn~~~~q 312 (731)
.+.+++.++++++.+. .--|+|+|--+-.+.
T Consensus 148 ~~~~~~~~~~~~~~~~------G~EGim~K~~~s~Y~ 178 (190)
T pfam01068 148 NDIEELAEFLEEAIKE------GLEGVVVKDPDSRYE 178 (190)
T ss_pred CCHHHHHHHHHHHHHC------CCCEEEEECCCCCCC
T ss_conf 9999999999999878------997899968999646
No 24
>cd07900 Adenylation_DNA_ligase_I_Euk The Adenylation domain of eukaryotic DNA Ligase I is a component of the catalytic core unit. 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, bacteriohages, eukarya, archaea and bacteria. Some organisms express a variety of different ligases which appear to be targeted to a specific function. 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 ad
Probab=98.24 E-value=8.5e-05 Score=56.26 Aligned_cols=173 Identities=20% Similarity=0.146 Sum_probs=90.8
Q ss_pred CCCCCCHHHCCCHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCEEEEEEEEE-CCEEEEEEECCCCHHHHHHHHHHHHH
Q ss_conf 66425702159999999999999986124677761199994158189999985-99899888659865566699977531
Q gi|254781172|r 92 SIPTLSLEKIWNIEDLRKFITRIYRFWQKKDDNSIFFTLEPKIDGTMITIRYE-KGKFVYAALRGDGHSGEDVSACIRAI 170 (731)
Q Consensus 92 ~~pMlSL~k~~~~~el~~w~~~~~~~~~~~~~~~~~~~vepKiDG~sisl~Y~-~G~L~~a~TRGdG~~GeDVT~n~~~i 170 (731)
-.|||.- -+.+.+|+.+ + .....|++|+|+||.=+-+.+. +|. ++..|| -|+|+|+.--.|
T Consensus 10 i~PMLA~-~~~~~~~~~~---~---------~~~~~~~~E~K~DG~R~qih~~~~~~-v~l~SR----ng~d~T~~fPel 71 (219)
T cd07900 10 LKPMLAK-PTKGISEVLK---R---------FEDKAFTCEYKYDGERAQIHLLEDGK-VKIFSR----NLENMTEKYPDV 71 (219)
T ss_pred CCCEECC-CCCCHHHHHH---H---------CCCCCEEEEEEECCEEEEEEEECCCE-EEEEEC----CCCCCCCCCHHH
T ss_conf 7871279-8898689997---3---------58981689960980579999908997-999957----997341104579
Q ss_pred CCCCCCCCCCCCCEEEEEEEEEEECH------HHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCHHHHHCCCEEEEEEEC
Q ss_conf 02432233544550489999998520------212345564314854334234567777523455553011105664102
Q gi|254781172|r 171 PTIPRVLSLNIPEIIEVRGEVYISKN------DFLALNDEMIAVGRKPYANPRNAASGILRRLNPTDITRYLNFFVHGLG 244 (731)
Q Consensus 171 ~~iP~~l~~~~~~~ieiRGEv~m~~~------~F~~lN~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~r~L~f~ay~~~ 244 (731)
.+.-..+.......+.+=||++.-.. .|+.+-.+. | .. .+.....-++.|++|++.
T Consensus 72 ~~~~~~~~~~~~~~~ILDGEiv~~d~~~~~~~~Fq~l~~r~-----------r----~~---~~~~~~~~~~~~~~FDiL 133 (219)
T cd07900 72 IEIIKESLKPNVKSFILDCEVVAYDRETGKILPFQVLSTRK-----------R----KD---VDANDIKVQVCVFAFDLL 133 (219)
T ss_pred HHHHHHHHCCCCCEEEEEEEEEEEECCCCCCCCHHHHHHHH-----------H----CC---CCHHHCCCCEEEEEEEEE
T ss_conf 99999862477630799637987607999605788985553-----------3----23---341321476689998540
Q ss_pred CCCCCC--CCCCHHHHHHHHHCCCCCCCCE-----EEEECCCCHHHHHHHHHHHHCCCCCCCCCEEEEE
Q ss_conf 454332--1000036899997599665414-----8874032113455665531001123437637773
Q gi|254781172|r 245 KTSEIF--AKGQYEMLQKMRCLGFPVNNGV-----RQANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKV 306 (731)
Q Consensus 245 ~~~~~~--~~~~~e~l~~L~~~GF~v~~~~-----~~~~~~~~~~~~~~~~~~~r~~l~y~iDGiVikv 306 (731)
+.++.. -....+..+.|+.+-=++.... ..+.+.+++.++++...+ -...|||+|-
T Consensus 134 ~l~g~~l~~~pl~eRr~~L~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~a~~------~g~EGiv~K~ 196 (219)
T cd07900 134 YLNGESLLDKPLRERRELLHSSFKEVPGEFQFATSKDSEDIEEIQEFLEEAVK------NNCEGLMVKT 196 (219)
T ss_pred CCCCCCHHHCCHHHHHHHHHHHHCCCCCEEEEEEEEECCCHHHHHHHHHHHHH------CCCCEEEEEC
T ss_conf 03883443281999999999864338981898876754999999999999998------6993699966
No 25
>PRK03180 ligB ATP-dependent DNA ligase; Reviewed
Probab=98.23 E-value=0.00023 Score=52.90 Aligned_cols=239 Identities=18% Similarity=0.220 Sum_probs=126.1
Q ss_pred CCC-CCCCHHHCCCHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCEEEEEEEEECCEEEEEEECCCCHHHHHHHHHHHH
Q ss_conf 166-4257021599999999999999861246777611999941581899999859989988865986556669997753
Q gi|254781172|r 91 HSI-PTLSLEKIWNIEDLRKFITRIYRFWQKKDDNSIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRA 169 (731)
Q Consensus 91 H~~-pMlSL~k~~~~~el~~w~~~~~~~~~~~~~~~~~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n~~~ 169 (731)
+|+ |||.-. +.+.+|+..-+ ...+.+|.|.||.=+-+++++|. ++..|| -|+|||+..--
T Consensus 182 ~Pv~pmLA~~-~~~~~~~~~~~-------------~~~~~~E~K~DG~R~Qih~~g~~-v~l~SR----~~ediT~~fPe 242 (509)
T PRK03180 182 RPVGPMLAQT-ATSVAEALERL-------------GGTAAVEAKLDGARVQIHRDGDD-VRVYTR----SLDDVTARLPE 242 (509)
T ss_pred CCCCCEECCC-CCCHHHHHHHC-------------CCCEEEEEEECEEEEEEEEECCE-EEEECC----CCCCCHHHHHH
T ss_conf 9867630897-99989999864-------------98747997305189999997999-999858----98602345579
Q ss_pred HCCCCCCCCCCCCCEEEEEEEEEEECHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHCC-CHHH--HHCCCEEEEEEECCC
Q ss_conf 1024322335445504899999985202123455643148543342345677775234-5555--301110566410245
Q gi|254781172|r 170 IPTIPRVLSLNIPEIIEVRGEVYISKNDFLALNDEMIAVGRKPYANPRNAASGILRRL-NPTD--ITRYLNFFVHGLGKT 246 (731)
Q Consensus 170 i~~iP~~l~~~~~~~ieiRGEv~m~~~~F~~lN~~~~~~g~~~f~NpRN~aaG~lr~~-d~~~--~~r~L~f~ay~~~~~ 246 (731)
|-..-..++ ...+.+=||++.-..+ |.. .|=+.-..-++++ +... ..-++.+++|++.+.
T Consensus 243 iv~~~~~~~---~~~~ILDGEiva~~~~-----------G~~---~~Fq~l~~R~~rk~~~~~~~~~~pv~~~~FDlL~~ 305 (509)
T PRK03180 243 VVEAVLALP---VRSLVLDGEAIALRPD-----------GRP---RPFQVTASRFGRSVDVAAAAATQPLSVFFFDILHL 305 (509)
T ss_pred HHHHHHHCC---CCCEEECCEEEEECCC-----------CCC---CCHHHHHHHHCCCCCHHHHHHCCCEEEEEEEEEEE
T ss_conf 999998479---8534675479998899-----------988---73799987641255067775308859998745203
Q ss_pred CCCC--CCCCHHHHHHHHHCC---CCCCCCEEEEECCCCHHHHHHHHHHHHCCCCCCCCCEEEEECCHHCCCCCCCCCCC
Q ss_conf 4332--100003689999759---96654148874032113455665531001123437637773110001115876568
Q gi|254781172|r 247 SEIF--AKGQYEMLQKMRCLG---FPVNNGVRQANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSLQKQLGERARS 321 (731)
Q Consensus 247 ~~~~--~~~~~e~l~~L~~~G---F~v~~~~~~~~~~~~~~~~~~~~~~~r~~l~y~iDGiVikvn~~~~q~~lG~ts~~ 321 (731)
++.. -....+..+.|.++= ..+ + .....+.+++..+++. ...-...|+|+|--|-.++- ..+.
T Consensus 306 ~G~dl~~~Pl~eRR~~Le~~~~~~~~~-~-~~~~~~~~~~~~~~~~------a~~~g~EGlm~K~~dS~Y~p----GrR~ 373 (509)
T PRK03180 306 DGRDLLDAPTTERLAALDALVPARHRV-P-RLVTADPAAAAAFLDA------TLAAGHEGVMAKSLAAPYEA----GRRG 373 (509)
T ss_pred CCCCHHHCCHHHHHHHHHHHCCCCCCC-C-CEECCCHHHHHHHHHH------HHHCCCEEEEEECCCCCCCC----CCCC
T ss_conf 884033187999999999844631356-7-1224899999999999------98669806898269998789----9878
Q ss_pred CCCEEEECCCC-CEEEEEEEEEEEEECC-CCEEEE--EEEEEEEEECCCEEEEE-CCCCHHHHH
Q ss_conf 66312311456-2158998788994035-622589--99974333026400010-148989997
Q gi|254781172|r 322 PRWMISHKFAE-KQASTRLLDIDIQIGR-TGILTP--VARLEPVNIGGALITNA-TLHNEDYIK 380 (731)
Q Consensus 322 PrwaiA~Kf~~-e~~~T~v~~I~wqvgR-tG~itP--va~~ePV~l~G~~V~ra-tlhN~~~I~ 380 (731)
..| +|+.. .+...+|..-.|--|| +|.+.. .|..+|-.-.=++|.++ |++.-.+++
T Consensus 374 ~~W---~K~K~~~tlD~ViiGa~~G~GkR~g~~s~~llg~~d~~~~~~~~vgKvgsGftD~~l~ 434 (509)
T PRK03180 374 AGW---LKVKPVHTLDLVVLAVEWGSGRRRGKLSNLHLGARDPATGGFVMLGKTFKGMTDAMLA 434 (509)
T ss_pred CCC---EEECCCCCCEEEEEEEECCCCCCCCCCCCEEEEEECCCCCCEEEEEEECCCCCHHHHH
T ss_conf 772---6644776540899963518888788744259998838999589997636789989999
No 26
>cd07907 Adenylation_DNA_ligase_Bac2 The Adenylation domain of putative bacterial ATP-dependent DNA ligases is inferred by similarity to be a component of the catalytic core unit. 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 oligouncleotide/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 adenyl
Probab=98.23 E-value=0.00013 Score=54.82 Aligned_cols=153 Identities=20% Similarity=0.154 Sum_probs=87.0
Q ss_pred CCCEEEEEEECCEEEEEEEEECCEEEEEEECCCCHHHHHHHHHHHHHCCCCCCCCCCCCCEEEEEEEEEEECH----HHH
Q ss_conf 7611999941581899999859989988865986556669997753102432233544550489999998520----212
Q gi|254781172|r 124 NSIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPTIPRVLSLNIPEIIEVRGEVYISKN----DFL 199 (731)
Q Consensus 124 ~~~~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n~~~i~~iP~~l~~~~~~~ieiRGEv~m~~~----~F~ 199 (731)
++..|.+|+|+||.=+-+++.+|. ++..|| -|+|+|+.---|...=. ..++.+.+=||++.-.. .|.
T Consensus 31 ~~~~~~~E~K~DG~R~qih~~~~~-v~l~SR----ng~d~T~~fPel~~~~~----~l~~~~ILDGEiv~~~~~~~~~F~ 101 (213)
T cd07907 31 APPAAWLEDKYDGIRAQLHKSEGR-VELYSR----DLEDITEQFPELADAAR----ALPHEFILDGEILAWRYGRALPFS 101 (213)
T ss_pred CCCCCEEEECCCCEEEEEEEECCE-EEEEEC----CCCCCHHHHHHHHHHHH----HCCCCEEEEEEEEEECCCCCCCHH
T ss_conf 999887996438078999998999-999918----98704335578999998----279985998078997389879889
Q ss_pred HHHHHHHHCCCCCCCCHHHHHHHHHHCCCHH-H--HHCCCEEEEEEECCCCCCCC--CCCHHHHHHHHHCCCCCCCCE--
Q ss_conf 3455643148543342345677775234555-5--30111056641024543321--000036899997599665414--
Q gi|254781172|r 200 ALNDEMIAVGRKPYANPRNAASGILRRLNPT-D--ITRYLNFFVHGLGKTSEIFA--KGQYEMLQKMRCLGFPVNNGV-- 272 (731)
Q Consensus 200 ~lN~~~~~~g~~~f~NpRN~aaG~lr~~d~~-~--~~r~L~f~ay~~~~~~~~~~--~~~~e~l~~L~~~GF~v~~~~-- 272 (731)
.+.. -++++.+. . ...++.|++|++...++... ....+..+.|..+--+. +..
T Consensus 102 ~lq~-------------------r~~~k~~~~~~~~~~pv~~~~FDiL~lng~~L~~~pl~eRr~~L~~l~~~~-~~~~l 161 (213)
T cd07907 102 ELQK-------------------RLGRKAEDDFMQEEIPVVYVAFDLLWLNGELLLDRPLEERRQKLESLLSPP-PKLRL 161 (213)
T ss_pred HHHH-------------------HHHCCCCCHHHHHHCCEEEEEEEEEEECCCCHHHCCHHHHHHHHHHHCCCC-CCEEE
T ss_conf 9998-------------------752046416667317838999764116871732189999999999733788-87596
Q ss_pred ---EEEECCCCHHHHHHHHHHHHCCCCCCCCCEEEEECCHHC
Q ss_conf ---887403211345566553100112343763777311000
Q gi|254781172|r 273 ---RQANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSL 311 (731)
Q Consensus 273 ---~~~~~~~~~~~~~~~~~~~r~~l~y~iDGiVikvn~~~~ 311 (731)
..+.+.+++.+.++.. ..-...|||+|--+-.+
T Consensus 162 ~~~~~~~~~~~~~~~~~~a------~~~g~EGIv~K~~dS~Y 197 (213)
T cd07907 162 APATQASSAEQIEAAFAAA------RERGNEGLMIKDPASPY 197 (213)
T ss_pred CCEEECCCHHHHHHHHHHH------HHCCCCEEEECCCCCCC
T ss_conf 3448579999999999999------97699559972799987
No 27
>PRK07636 ligB ATP-dependent DNA ligase; Reviewed
Probab=98.21 E-value=7.8e-05 Score=56.55 Aligned_cols=160 Identities=21% Similarity=0.282 Sum_probs=96.3
Q ss_pred CCCCEEEEEEECCEEEEEEEEECCEEEEEEECCCCHHHHHHHHHHHHHCCCCCCCCCCCCCEEEEEEEEEEECH----HH
Q ss_conf 77611999941581899999859989988865986556669997753102432233544550489999998520----21
Q gi|254781172|r 123 DNSIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPTIPRVLSLNIPEIIEVRGEVYISKN----DF 198 (731)
Q Consensus 123 ~~~~~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n~~~i~~iP~~l~~~~~~~ieiRGEv~m~~~----~F 198 (731)
...-.|+.|.|+||.=+-+.+.+|. ++..|| -|.|+|+..-.+- ....|....+=||++.... +|
T Consensus 15 ~~~~~W~~E~K~DG~R~~~~~~~g~-v~l~SR----ng~d~t~~fPel~------~~~~~~~~iLDGEiVv~~~~g~~~F 83 (269)
T PRK07636 15 FNSDNYITELKFDGIRLIASKNDGL-IRLYTR----HNNEVTAKFPELL------TLDIPDGTILDGELIVPGSTGAPDF 83 (269)
T ss_pred CCCCCEEEEEEECEEEEEEEEECCE-EEEEEC----CCCCCHHHCHHHH------HHCCCCCEEEECEEEEECCCCCCCH
T ss_conf 8999747885277099999998999-999908----9988333476889------7348854088245899888988898
Q ss_pred HHHHHHHHHCCCCCCCCHHHHHHHHHHCCCHHHHHCCCEEEEEEECCCCCCC--CCCCHHHHHHHHHCCCCCCCCEEEEE
Q ss_conf 2345564314854334234567777523455553011105664102454332--10000368999975996654148874
Q gi|254781172|r 199 LALNDEMIAVGRKPYANPRNAASGILRRLNPTDITRYLNFFVHGLGKTSEIF--AKGQYEMLQKMRCLGFPVNNGVRQAN 276 (731)
Q Consensus 199 ~~lN~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~r~L~f~ay~~~~~~~~~--~~~~~e~l~~L~~~GF~v~~~~~~~~ 276 (731)
+.+... ++.. ....++.|++|++...++.. -....+..+.|+.+--+. ++...+.
T Consensus 84 ~~lq~r-------------------~~~~---~~~~pv~y~vFDlL~l~G~~L~~~Pl~eRr~~L~~l~~~~-~~~~~~~ 140 (269)
T PRK07636 84 EAVMER-------------------FQSR---KSFYPIVFCVFDVIRIEGVSVTAKPLSERKELLAGLKLDH-PNVKIIE 140 (269)
T ss_pred HHHHHH-------------------HHCC---CCCCCEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHCCCC-CCEEECC
T ss_conf 999754-------------------5405---8766359999957345864300378999999998643579-9658756
Q ss_pred CCC-CHHHHHHHHHHHHCCCCCCCCCEEEEECCHHCCCCCCCCCCCCCCEE
Q ss_conf 032-11345566553100112343763777311000111587656866312
Q gi|254781172|r 277 TFH-GIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSLQKQLGERARSPRWMI 326 (731)
Q Consensus 277 ~~~-~~~~~~~~~~~~r~~l~y~iDGiVikvn~~~~q~~lG~ts~~Prwai 326 (731)
..+ +..++++...+ -...|||.|--|..++. ..|++.|--
T Consensus 141 ~~~~~~~~~~~~a~~------~glEGIvaKr~dS~Y~~----G~Rs~~WlK 181 (269)
T PRK07636 141 GVRGHATAYFELVKE------NKLEGIVIKQANSPYAI----NKRSDRWLK 181 (269)
T ss_pred CCCCHHHHHHHHHHH------CCCCEEEECCCCCCCCC----CCCCCCEEE
T ss_conf 554519999999997------69924785179998679----998735089
No 28
>cd07896 Adenylation_kDNA_ligase_like The Adenylation domain of kDNA ligase and similar proteins, which is involved in kDNA replication or repair, is a component of the catalytic core unit. The mitochondrial DNA of parasitic protozoan 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 oligouncleotide/olig
Probab=98.20 E-value=1.8e-05 Score=61.42 Aligned_cols=142 Identities=23% Similarity=0.365 Sum_probs=85.0
Q ss_pred CCCEEEEEEECCEEEEEEEEECCEEEEEEECCCCHHHHHHHHHHHHHCCCCCCCCCCCCCEEEEEEEEEEECHHHHHHHH
Q ss_conf 76119999415818999998599899888659865566699977531024322335445504899999985202123455
Q gi|254781172|r 124 NSIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPTIPRVLSLNIPEIIEVRGEVYISKNDFLALND 203 (731)
Q Consensus 124 ~~~~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n~~~i~~iP~~l~~~~~~~ieiRGEv~m~~~~F~~lN~ 203 (731)
....|.+|||+||+=+- . +|. +..|| .|.+++.. + .+....| .+++=||+|....+|+.+
T Consensus 14 ~~~~w~~e~K~DG~R~~--~-~~~--~l~SR----~G~~~~~~-------~-~~~~~~~-~~vlDGEl~~~~~~F~~l-- 73 (174)
T cd07896 14 DISGYLVSEKLDGVRAY--W-DGK--QLLSR----SGKPIAAP-------D-WFTAGLP-PFPLDGELWIGRGQFEQL-- 73 (174)
T ss_pred CCCCEEEEEEECEEEEE--E-ECC--EEEEC----CCCCCCCH-------H-HHHHHCC-CCCEEEEEEECCCCHHHH--
T ss_conf 94043876511479999--9-889--99966----99867894-------9-9995498-851745886078987999--
Q ss_pred HHHHCCCCCCCCHHHHHHHHHHCCCHHH-HHCCCEEEEEEECCCCCCCCCCCHHHHHHHHHC----CCC---CCCCEEEE
Q ss_conf 6431485433423456777752345555-301110566410245433210000368999975----996---65414887
Q gi|254781172|r 204 EMIAVGRKPYANPRNAASGILRRLNPTD-ITRYLNFFVHGLGKTSEIFAKGQYEMLQKMRCL----GFP---VNNGVRQA 275 (731)
Q Consensus 204 ~~~~~g~~~f~NpRN~aaG~lr~~d~~~-~~r~L~f~ay~~~~~~~~~~~~~~e~l~~L~~~----GF~---v~~~~~~~ 275 (731)
.|.+|++.+.. ....+.|++|++...++ + ..+..+.|..+ ..+ +++ ...+
T Consensus 74 -----------------~~~~~~~~~~~~~~~~l~y~vFDll~~~~-p---~~~R~~~L~~~~~~~~~~~v~~v~-~~~v 131 (174)
T cd07896 74 -----------------SSIVRRKGPDDEAWRKVKYMVFDLPSADG-P---FEERLERLKNLLEKAPNPHIKIVP-QIRV 131 (174)
T ss_pred -----------------HHHHHCCCCCHHHCCCCEEEEEECCCCCC-C---HHHHHHHHHHHHHHCCCCEEEEEC-EEEE
T ss_conf -----------------99986169883330341599987245689-9---999999999998657998099736-1880
Q ss_pred ECCCCHHHHHHHHHHHHCCCCCCCCCEEEEECCHHCCC
Q ss_conf 40321134556655310011234376377731100011
Q gi|254781172|r 276 NTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSLQK 313 (731)
Q Consensus 276 ~~~~~~~~~~~~~~~~r~~l~y~iDGiVikvn~~~~q~ 313 (731)
.+.+++..++++..+. .-.|+|+|-.+..++.
T Consensus 132 ~~~~el~~~~~~~~~~------G~EGimlK~~~s~Y~~ 163 (174)
T cd07896 132 KSNAHLDSYLDEVVAQ------GGEGLMLRRPDAPYEA 163 (174)
T ss_pred CCHHHHHHHHHHHHHC------CCCEEEEECCCCCCCC
T ss_conf 9999999999999877------9876478889995789
No 29
>PRK01109 ATP-dependent DNA ligase; Provisional
Probab=98.19 E-value=0.00089 Score=48.37 Aligned_cols=237 Identities=17% Similarity=0.181 Sum_probs=127.1
Q ss_pred CCCCCHHHCCCHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCEEEEEEEEECCEEEEEEECCCCHHHHHHHHHHHHHCC
Q ss_conf 64257021599999999999999861246777611999941581899999859989988865986556669997753102
Q gi|254781172|r 93 IPTLSLEKIWNIEDLRKFITRIYRFWQKKDDNSIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPT 172 (731)
Q Consensus 93 ~pMlSL~k~~~~~el~~w~~~~~~~~~~~~~~~~~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n~~~i~~ 172 (731)
.|||.- .+.+.+|+ .+++ ...+.+|.|+||.=+-+++.+|. ++..|| -|||+|+..--|-.
T Consensus 228 ~PMLA~-~~~~~~e~---~~~~----------~~~~~~E~K~DG~R~QiH~~~~~-v~~fSR----~~ed~T~~fPel~~ 288 (589)
T PRK01109 228 RPMLAE-RLSSPKEI---LAKM----------GGKAIFEYKYDGERAQIHKKGDK-VKIFSR----RLENITHQYPDVVE 288 (589)
T ss_pred CCCCCC-CCCCHHHH---HHHC----------CCCEEEEEEECCEEEEEEEECCE-EEEEEC----CCHHHHHHHHHHHH
T ss_conf 642489-88998999---9755----------98679999873568999981998-999836----84231344448999
Q ss_pred -CCCCCCCCCCCEEEEEEEEEEECH------HHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCHHHH--HCCCEEEEEEE
Q ss_conf -432233544550489999998520------212345564314854334234567777523455553--01110566410
Q gi|254781172|r 173 -IPRVLSLNIPEIIEVRGEVYISKN------DFLALNDEMIAVGRKPYANPRNAASGILRRLNPTDI--TRYLNFFVHGL 243 (731)
Q Consensus 173 -iP~~l~~~~~~~ieiRGEv~m~~~------~F~~lN~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~--~r~L~f~ay~~ 243 (731)
+...+ .+..+.+=||++.-.. .|+.+-.+ .|..+.... .-++.|++|++
T Consensus 289 ~~~~~~---~~~~~ILDGEiv~~d~~~g~~~pFq~l~~R-------------------~rk~~~~~~~~~~pv~~~~FDi 346 (589)
T PRK01109 289 AAKEAI---KAEEAIVEGEIVAVDPETGEMRPFQELMHR-------------------KRKHDIAEAIEEYPVNVFLFDV 346 (589)
T ss_pred HHHHHC---CCCCEEEEEEEEEECCCCCCCCCHHHHHHH-------------------CCCCCHHHHHHHCCEEEEEEEE
T ss_conf 999627---877669844799872888964576899863-------------------3143356676408748999988
Q ss_pred CCCCCCC--CCCCHHHHHHHHHCCCCCCCCE-----EEEECCCCHHHHHHHHHHHHCCCCCCCCCEEEEE-C-CHHCCCC
Q ss_conf 2454332--1000036899997599665414-----8874032113455665531001123437637773-1-1000111
Q gi|254781172|r 244 GKTSEIF--AKGQYEMLQKMRCLGFPVNNGV-----RQANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKV-D-EFSLQKQ 314 (731)
Q Consensus 244 ~~~~~~~--~~~~~e~l~~L~~~GF~v~~~~-----~~~~~~~~~~~~~~~~~~~r~~l~y~iDGiVikv-n-~~~~q~~ 314 (731)
.+.++.. .....+..+.|..+ |...+.. ..+.+.+++.+++++- ..-...|+|+|- | +..++
T Consensus 347 L~~ng~~l~~~pl~eRr~~L~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~a------~~~~~EGlmiK~l~~~s~Y~-- 417 (589)
T PRK01109 347 LYVDGEDLTDKPLPERRKKLEEI-VKENDKVKLAERIITDDVEELEKFFHQA------IEEGCEGLMAKSLGPDSIYQ-- 417 (589)
T ss_pred EEECCCCHHCCCHHHHHHHHHHH-CCCCCCEEEEEEEECCCHHHHHHHHHHH------HHCCCCCEEEECCCCCCCCC--
T ss_conf 40377371107899999999985-1878856984147559999999999999------86476523630378877656--
Q ss_pred CCCCCCCCCCEEEEC--C--C-CCEEEEEEEEEEEEECCCCE-EE--EEEEEEEEEECCCEEEEE-CCCCHHHHHHH
Q ss_conf 587656866312311--4--5-62158998788994035622-58--999974333026400010-14898999750
Q gi|254781172|r 315 LGERARSPRWMISHK--F--A-EKQASTRLLDIDIQIGRTGI-LT--PVARLEPVNIGGALITNA-TLHNEDYIKGL 382 (731)
Q Consensus 315 lG~ts~~PrwaiA~K--f--~-~e~~~T~v~~I~wqvgRtG~-it--Pva~~ePV~l~G~~V~ra-tlhN~~~I~~l 382 (731)
-| .|.-.| +=+| | + .++..-+|.+=.|-.||-+- ++ -+|..+|-.=.=.+|.+| |+++-.+++.|
T Consensus 418 pg--~R~~~W-~K~K~dy~~~~~dtlDlVviga~~G~GrR~~~~s~fl~a~~d~~~~~~~~v~KvgsGftd~~l~~l 491 (589)
T PRK01109 418 AG--ARGWLW-IKYKRDYKSEMMDTVDLVVVGAFYGRGRRAGLYGALLLAAYDPETDTFETVCKVGSGFTDEDLDEL 491 (589)
T ss_pred CC--CCCCCE-EEEEECCCCCCCCCCCEEEEEEEECCCCCCCCCCCEEEEEECCCCCEEEEEEEECCCCCHHHHHHH
T ss_conf 88--747870-687421045655520179998674798766753423788872899879999996889999999999
No 30
>cd00027 BRCT Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo/hetero BRCT multimers, BRCT-non-BRCT interactions, and interactions within DNA strand breaks.
Probab=98.18 E-value=1.1e-05 Score=63.02 Aligned_cols=70 Identities=37% Similarity=0.551 Sum_probs=63.0
Q ss_pred CCEEEEECCCCCCCHHHHHHHHHHCCCEEEEEEECCEEEEEECCCCCC-HHHHHHHCCCEEECHHHHHHHH
Q ss_conf 866999725889987899999998298499811163217997788886-3798997499173799999999
Q gi|254781172|r 649 NKKLVFTGTLQKIQRHKAQEYVTQLGAVVSAILSRKTDIIIVGDNPGS-KLEKAQQLGVKIMNEEQFLFLL 718 (731)
Q Consensus 649 gk~vV~TGtl~~~~R~e~~~~ie~~Ggkv~sSVSkkT~~LI~ge~~gS-Kl~KA~~LgI~Ii~e~ef~~ll 718 (731)
|+.|++||.+....|++++++|+.+||++..+++.+++++|++...+. ++..|...|++|++++.+.+.+
T Consensus 1 ~~~~~i~~~~~~~~~~~l~~~i~~~Gg~v~~~~~~~~thvI~~~~~~~~~~~~~~~~~~~iV~~~Wi~~~~ 71 (72)
T cd00027 1 GLTFVITGDLPSEERDELKELIEKLGGKVTSSVSKKTTHVIVGSDAGPKKLLKAIKLGIPIVTPEWLLDCL 71 (72)
T ss_pred CCEEEEEECCCCCCHHHHHHHHHHCCCEEECCCCCCCCEEEECCCCCCHHHHHHHHCCCCCCCHHHHHHHH
T ss_conf 98999950489889999999999849989581558855999868778289999997599573799999985
No 31
>cd06846 Adenylation_DNA_ligase_family The Adenylation domain of proteins from the ATP-dependent polynucleotide ligase family is the minimal catalytic unit that is common to all family members. 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 A
Probab=98.09 E-value=9.1e-05 Score=56.05 Aligned_cols=158 Identities=13% Similarity=0.092 Sum_probs=88.9
Q ss_pred CCCEEEEEEECCEEEEEEEEECCEEEEEEECCCCHHHHHHHHHHHHHCCCCCCCCCCCCCEEEEEEEEEEECHHHHHHHH
Q ss_conf 76119999415818999998599899888659865566699977531024322335445504899999985202123455
Q gi|254781172|r 124 NSIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPTIPRVLSLNIPEIIEVRGEVYISKNDFLALND 203 (731)
Q Consensus 124 ~~~~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n~~~i~~iP~~l~~~~~~~ieiRGEv~m~~~~F~~lN~ 203 (731)
.+-.|++|+|+||.=+-+.+.+|. ++..|| -|+|+|+.--. ++.... ..+..+.+=||+++....+.
T Consensus 19 ~~~~w~~E~K~DG~R~~~~~~~~~-v~l~SR----~g~~~t~~~p~---~~~~~~-~~~~~~iLDGElv~~~~~~~---- 85 (187)
T cd06846 19 EDDGYYAQEKADGERALLSVLNGG-VFGISR----TGLEVPLPTII---ILAAKL-KLLPGFILDGEAVGERRGVK---- 85 (187)
T ss_pred CCCCEEEEEEECCEEEEEEEECCE-EEEEEC----CCCCCCCCCHH---HHHHHH-HCCCCCEEEEEEEEECCCCC----
T ss_conf 899789998073279999998999-999969----89985553877---999986-44898158989998758765----
Q ss_pred HHHHCCCCCCCCHHHHHHHHHHCCCHHHHHCCCEEEEEEECCCCCC--CCCCCHHHHHHHHHCCCCCC----CCEEEEEC
Q ss_conf 6431485433423456777752345555301110566410245433--21000036899997599665----41488740
Q gi|254781172|r 204 EMIAVGRKPYANPRNAASGILRRLNPTDITRYLNFFVHGLGKTSEI--FAKGQYEMLQKMRCLGFPVN----NGVRQANT 277 (731)
Q Consensus 204 ~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~r~L~f~ay~~~~~~~~--~~~~~~e~l~~L~~~GF~v~----~~~~~~~~ 277 (731)
.++- .....++.|++|++...++. ......+..+.|.++.=... +.......
T Consensus 86 -----------~~~~-----------~~~~~~~~~~~FDiL~l~g~~l~~~pl~~R~~~L~~~~~~~~~~~~~~~~~~~~ 143 (187)
T cd06846 86 -----------LIRP-----------FEANPKLQYYAFDVLELEGKDLRLLPYSRRLAYLKELGEEFAVKIVPLISAGKV 143 (187)
T ss_pred -----------CCCH-----------HHHCCCCEEEEECCCCCCCCCHHHCCHHHHHHHHHHHHHHCCCCEEEEEECCCC
T ss_conf -----------6330-----------342268479998334689835245619999999999762168752675550457
Q ss_pred CCCHHHHHHHHHHHHCCCCCCCCCEEEEECCHHCCCCCCCCCCCCCC
Q ss_conf 32113455665531001123437637773110001115876568663
Q gi|254781172|r 278 FHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSLQKQLGERARSPRW 324 (731)
Q Consensus 278 ~~~~~~~~~~~~~~r~~l~y~iDGiVikvn~~~~q~~lG~ts~~Prw 324 (731)
..++.++++...+ -...|||+|--|-.++ .|.+++.+.|
T Consensus 144 ~~~~~~~~~~~~~------~G~EGiv~K~~ds~Y~--~Gr~~~~~~W 182 (187)
T cd06846 144 DSPLDQLLARLDK------KGKEGIVFKHPDAPYK--AGRPGSGGTQ 182 (187)
T ss_pred HHHHHHHHHHHHH------CCCCEEEEECCCCCCC--CCCCCCCCCE
T ss_conf 0589999999987------6996278748999658--9987999987
No 32
>cd07897 Adenylation_DNA_ligase_Bac1 The Adenylation domain of putative bacterial ATP-dependent DNA ligases is inferred by similarity to be a component of the catalytic core unit. 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 oligouncleotide/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 adenyl
Probab=98.07 E-value=0.00015 Score=54.36 Aligned_cols=154 Identities=16% Similarity=0.122 Sum_probs=87.2
Q ss_pred CCEEEEEEECCEEEEEEEEECCEEEEEEECCCCHHHHHHHHHHHHHCCCCCCCCCCCCCEEEEEEEEEEECH-----HHH
Q ss_conf 611999941581899999859989988865986556669997753102432233544550489999998520-----212
Q gi|254781172|r 125 SIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPTIPRVLSLNIPEIIEVRGEVYISKN-----DFL 199 (731)
Q Consensus 125 ~~~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n~~~i~~iP~~l~~~~~~~ieiRGEv~m~~~-----~F~ 199 (731)
...|++|+|+||.=+-++..+|. ++..|| -|+|+|+.--.|..+...+ |....+=||++.-.. .|.
T Consensus 23 ~~dw~~E~K~DG~R~~~~~~~~~-v~l~SR----ng~~~t~~fPei~~~~~~~----~~~~ILDGEiv~~~~~g~~~~F~ 93 (208)
T cd07897 23 PSDWQAEWKWDGIRGQLVRRGGE-VFLWSR----GEELISGSFPELLAAAEAL----PDGTVLDGELLVWRDGGEPLPFN 93 (208)
T ss_pred CCCEEEEEEECCEEEEEEEECCE-EEEEEC----CCCCCCHHCHHHHHHHHHC----CCCEEEEEEEEEECCCCCCCCHH
T ss_conf 67679995376188999997999-999948----9870210164789999848----87859985899973899845889
Q ss_pred HHHHHHHHCCCCCCCCHHHHHHHHHHCCCHH--H-HHCCCEEEEEEECCCCCCCC--CCCHHHHHHHHHCCCCCC-CCE-
Q ss_conf 3455643148543342345677775234555--5-30111056641024543321--000036899997599665-414-
Q gi|254781172|r 200 ALNDEMIAVGRKPYANPRNAASGILRRLNPT--D-ITRYLNFFVHGLGKTSEIFA--KGQYEMLQKMRCLGFPVN-NGV- 272 (731)
Q Consensus 200 ~lN~~~~~~g~~~f~NpRN~aaG~lr~~d~~--~-~~r~L~f~ay~~~~~~~~~~--~~~~e~l~~L~~~GF~v~-~~~- 272 (731)
.+-.+ ++++.+. . ...++.|++|++.+..+... ....+..+.|..+==++. +..
T Consensus 94 ~l~~r-------------------~~rk~~~~~~~~~~p~~~~vFDiL~l~g~~l~~~pl~eRk~~L~~l~~~~~~~~i~ 154 (208)
T cd07897 94 DLQQR-------------------LGRKTVGKKLLADAPAAFRAYDLLELNGEDLRALPLRERRARLEALLAELPPPRLD 154 (208)
T ss_pred HHHHH-------------------HCCCCCCHHHHHCCCEEEEEEEEEEECCCCCCCCCHHHHHHHHHHHHHCCCCCEEE
T ss_conf 99977-------------------53357426677318759999875303797201187999999999987315898299
Q ss_pred ----EEEECCCCHHHHHHHHHHHHCCCCCCCCCEEEEECCHHCC
Q ss_conf ----8874032113455665531001123437637773110001
Q gi|254781172|r 273 ----RQANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSLQ 312 (731)
Q Consensus 273 ----~~~~~~~~~~~~~~~~~~~r~~l~y~iDGiVikvn~~~~q 312 (731)
..+.+.+++.++++.. ......|||+|--|-.++
T Consensus 155 ~s~~~~~~~~~~~~~l~~~a------~~~G~EGIm~K~~dS~Y~ 192 (208)
T cd07897 155 LSPLVPFSSWEELAALRAES------RERGVEGLMLKRRDSPYL 192 (208)
T ss_pred EECEEECCCHHHHHHHHHHH------HHCCCCEEEECCCCCCCC
T ss_conf 81407369999999999999------876995299728999668
No 33
>PRK09633 ligD ATP-dependent DNA ligase; Reviewed
Probab=97.99 E-value=0.00055 Score=49.97 Aligned_cols=195 Identities=15% Similarity=0.200 Sum_probs=103.1
Q ss_pred CCCCEEEEEEECCEEEEEEEEECCEEEEEEECCCCHHHHHHHHHHHHHCCCCCCC----CCCCCCEEEEEEEEEEE----
Q ss_conf 7761199994158189999985998998886598655666999775310243223----35445504899999985----
Q gi|254781172|r 123 DNSIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPTIPRVL----SLNIPEIIEVRGEVYIS---- 194 (731)
Q Consensus 123 ~~~~~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n~~~i~~iP~~l----~~~~~~~ieiRGEv~m~---- 194 (731)
...-.|+-|.|+||.=+.+...+|. ++..|| -|+|+|+..-.|...-..+ ....| +++=||++.-
T Consensus 10 P~G~dWiyEiK~DG~R~la~~~~~~-VrL~SR----ng~d~T~~fPEl~~a~~~l~~~~~~~lp--~VLDGEiVald~~g 82 (604)
T PRK09633 10 PTGDEWRYEVKYDGFRCLLIIDETG-ITLISR----NGRNLNNQFPEIIEFCEQIREHLKAELP--LTFDGELVCLLNPY 82 (604)
T ss_pred CCCCCEEEEEEECEEEEEEEEECCE-EEEEEC----CCCCCHHHHHHHHHHHHHHHHHHCCCCC--CEEEEEEEEECCCC
T ss_conf 6999666874266068999998999-999928----9987376759999999975542102467--34764799888999
Q ss_pred CHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCHHHHHCCCEEEEEEECCCCCCC-----CCCCHHHHHHH-HHCCCCC
Q ss_conf 20212345564314854334234567777523455553011105664102454332-----10000368999-9759966
Q gi|254781172|r 195 KNDFLALNDEMIAVGRKPYANPRNAASGILRRLNPTDITRYLNFFVHGLGKTSEIF-----AKGQYEMLQKM-RCLGFPV 268 (731)
Q Consensus 195 ~~~F~~lN~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~r~L~f~ay~~~~~~~~~-----~~~~~e~l~~L-~~~GF~v 268 (731)
+.+|..|..... ..++.+.+. ....+++.|++|++...++.. .....+.|+.| +..+.+.
T Consensus 83 ~p~F~~LQ~R~~------~~~~~~i~~--------~~~~~Pv~y~vFDLL~LdG~dL~~lPL~eRK~~L~~ll~~~~~p~ 148 (604)
T PRK09633 83 RSDFAHVQTRGR------LKNTEVIAK--------SANKRPCQLLAFDLLVLKGESLTSLPYTERKKQLFQLMKAAKLPA 148 (604)
T ss_pred CCCHHHHHHHHH------CCCCHHHHH--------HHHCCCCEEEEEEEEEECCCCCCCCCHHHHHHHHHHHHHHCCCCC
T ss_conf 999899997642------367146666--------532277479999702078714000879999999999986434666
Q ss_pred CC------CEEEEECCCCHHHHHHHHHHHHCCCCCCCCCEEEEECCHHCCCCCCCCCCCCCCEEEECCCCCEEEEEEEEE
Q ss_conf 54------148874032113455665531001123437637773110001115876568663123114562158998788
Q gi|254781172|r 269 NN------GVRQANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSLQKQLGERARSPRWMISHKFAEKQASTRLLDI 342 (731)
Q Consensus 269 ~~------~~~~~~~~~~~~~~~~~~~~~r~~l~y~iDGiVikvn~~~~q~~lG~ts~~PrwaiA~Kf~~e~~~T~v~~I 342 (731)
.+ .........+..++++...+ -...|||.|--|..++. ..|++.| +=.|.. ..++.+|-
T Consensus 149 ~~~~~~~~~~~~~~~~~dg~~l~~~A~~------~glEGIVaKR~DS~Y~~----GrRs~~W-lKiK~~-~~qe~VIg-- 214 (604)
T PRK09633 149 SPDPMGKARIQYIPSTTDFQALWKAVKR------YDGEGIVAKKKTSKWAE----NKRSKDW-LKLKNW-RLVHVIVT-- 214 (604)
T ss_pred CCCCCCCCEEEECCCCCCHHHHHHHHHH------CCCCEEEEECCCCCCCC----CCCCCCE-EEEEEC-CCCEEEEE--
T ss_conf 6665677606733672429999999998------49970686269998789----9998660-786204-63029999--
Q ss_pred EEEECCCCEEE
Q ss_conf 99403562258
Q gi|254781172|r 343 DIQIGRTGILT 353 (731)
Q Consensus 343 ~wqvgRtG~it 353 (731)
=|..+ .|.+.
T Consensus 215 Gy~~~-~G~l~ 224 (604)
T PRK09633 215 GYNPS-NGYFT 224 (604)
T ss_pred EEECC-CCCEE
T ss_conf 87279-98178
No 34
>cd07905 Adenylation_DNA_ligase_LigC The Adenylation domain of Mycobacterium tuberculosis LigC-like ATP-dependent DNA ligases is a component of the catalytic core unit. 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 oligouncleotide/oligosaccharide binding (OB)-fold dom
Probab=97.90 E-value=0.00041 Score=50.95 Aligned_cols=160 Identities=18% Similarity=0.155 Sum_probs=85.1
Q ss_pred CCCEEEEEEECCEEEEEEEEECCEEEEEEECCCCHHHHHHHHHHHHHCCCCCCCCCCCCCEEEEEEEEEEEC---HHHHH
Q ss_conf 761199994158189999985998998886598655666999775310243223354455048999999852---02123
Q gi|254781172|r 124 NSIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPTIPRVLSLNIPEIIEVRGEVYISK---NDFLA 200 (731)
Q Consensus 124 ~~~~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n~~~i~~iP~~l~~~~~~~ieiRGEv~m~~---~~F~~ 200 (731)
..-.|++|+|+||.=+-++..+|. ++..|| -|+|+|+..--|... +....+..+.+=||++.-. .+|..
T Consensus 14 ~~~~w~~E~K~DG~R~~~h~~~~~-v~l~SR----~g~~~t~~fpei~~~---~~~~~~~~~ILDGElv~~~~~~~~F~~ 85 (194)
T cd07905 14 LGGGWLYEPKWDGFRCLVFRDGDE-VELQSR----SGKPLTRYFPELVAA---ARALLPERCVLDGELVVWRGGRLDFDA 85 (194)
T ss_pred CCCCEEEEEEECCEEEEEEEECCE-EEEEEC----CCCHHHHHCHHHHHH---HHHHCCCCEEEEEEEEEECCCCCCHHH
T ss_conf 999669998177299999998999-999949----998234557699999---987388656997479984599889899
Q ss_pred HHHHHHHCCCCCCCCHHHHHHHHHHCCCHHHHHCCCEEEEEEECCCCCCC--CCCCHHHHHHHHHCCCCCCCCEEEE---
Q ss_conf 45564314854334234567777523455553011105664102454332--1000036899997599665414887---
Q gi|254781172|r 201 LNDEMIAVGRKPYANPRNAASGILRRLNPTDITRYLNFFVHGLGKTSEIF--AKGQYEMLQKMRCLGFPVNNGVRQA--- 275 (731)
Q Consensus 201 lN~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~r~L~f~ay~~~~~~~~~--~~~~~e~l~~L~~~GF~v~~~~~~~--- 275 (731)
+..+.. +| .+ .........++.|++|++...++.. -....+..+.|+.+-=++......+
T Consensus 86 l~~r~~---------~~--~~----~~~~~~~~~p~~~~vFDiL~l~g~~l~~~pl~eRr~~L~~~~~~~~~~~~~~~~~ 150 (194)
T cd07905 86 LQQRIH---------PA--AS----RVRKLAEETPASFVAFDLLALGGVDLRGRPLRERRARLEELLAGWGPPLQLSPAT 150 (194)
T ss_pred HHHHHH---------HC--CC----CHHHHHHCCCEEEEEEEEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCEEEEEEE
T ss_conf 998865---------13--43----0556542288079998888889715223889999999999862589958997443
Q ss_pred ECCCCHHHHHHHHHHHHCCCCCCCCCEEEEECCHHCC
Q ss_conf 4032113455665531001123437637773110001
Q gi|254781172|r 276 NTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSLQ 312 (731)
Q Consensus 276 ~~~~~~~~~~~~~~~~r~~l~y~iDGiVikvn~~~~q 312 (731)
.+.+++..++++..+ -..-|||+|--|-.++
T Consensus 151 ~~~~~~~~~~~~a~~------~g~EGiv~K~~dS~Y~ 181 (194)
T cd07905 151 TDPAEAEEWLEAFEG------AGLDGVVAKRLDGRYR 181 (194)
T ss_pred CCHHHHHHHHHHHHH------CCCCEEEECCCCCCCC
T ss_conf 898999999999987------7995699718999718
No 35
>PRK09247 ATP-dependent DNA ligase; Validated
Probab=97.89 E-value=0.00087 Score=48.46 Aligned_cols=218 Identities=14% Similarity=0.095 Sum_probs=116.7
Q ss_pred CEEEEEEECCEEEEEEEEECCEEEEEEECCCCHHHHHHHHHHHHHCCCCCCCCCCCCCEEEEEEEEEEECH----HHHHH
Q ss_conf 11999941581899999859989988865986556669997753102432233544550489999998520----21234
Q gi|254781172|r 126 IFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPTIPRVLSLNIPEIIEVRGEVYISKN----DFLAL 201 (731)
Q Consensus 126 ~~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n~~~i~~iP~~l~~~~~~~ieiRGEv~m~~~----~F~~l 201 (731)
..|.+|.|+||.=+-++..+|. ++..|| -|||||+..--|-.. + ...|....+-||++.-.. .|+.|
T Consensus 225 ~~~~~E~K~DG~R~Qih~~~~~-v~l~SR----~~e~it~~fPei~~~---~-~~~~~~~ilDGEiv~~~~~~~~~F~~l 295 (537)
T PRK09247 225 ADWQAEWKWDGIRVQLVRRGGE-VRLWSR----GEELITERFPELVEA---A-EALPDGTVLDGELLVWRPGRVQPFAAL 295 (537)
T ss_pred HCCEEEECCCCEEEEEEEECCE-EEEEEC----CCCCCHHHHHHHHHH---H-HHCCCCEEEEEEEEEECCCCCCCHHHH
T ss_conf 0065461148268999995999-999937----986031242889999---9-838988478768997359986888999
Q ss_pred HHHHHHCCCCCCCCHHHHHHHHHHCCCHH--HH-HCCCEEEEEEECCCCCCC--CCCCHHHHHHHHHCCCCCC-CCE---
Q ss_conf 55643148543342345677775234555--53-011105664102454332--1000036899997599665-414---
Q gi|254781172|r 202 NDEMIAVGRKPYANPRNAASGILRRLNPT--DI-TRYLNFFVHGLGKTSEIF--AKGQYEMLQKMRCLGFPVN-NGV--- 272 (731)
Q Consensus 202 N~~~~~~g~~~f~NpRN~aaG~lr~~d~~--~~-~r~L~f~ay~~~~~~~~~--~~~~~e~l~~L~~~GF~v~-~~~--- 272 (731)
.--++++.+. .. .-++.|++|++.+.++.. -....+..+.|..+=-.+. +..
T Consensus 296 -------------------q~Rl~rk~~~~~~~~~~Pv~~~~FDlL~~~G~dl~~~pl~eRR~~L~~~~~~~~~~~~~~s 356 (537)
T PRK09247 296 -------------------QQRIGRKTVGKKLLAEYPAFLRAYDLLEDGGEDLRELPLAERRARLEALIARLPDPRLDLS 356 (537)
T ss_pred -------------------HHHHCCCCCCHHHHHCCCEEEEEEEHHHHCCCCHHHCCHHHHHHHHHHHHHHCCCCEEEEE
T ss_conf -------------------8774236753767514886999862044278614438899999999998733689849960
Q ss_pred --EEEECCCCHHHHHHHHHHHHCCCCCCCCCEEEEECCHHCCCCCCCCCCCCCCEEEECCCCCEEEEEEEEEEEEEC-CC
Q ss_conf --887403211345566553100112343763777311000111587656866312311456215899878899403-56
Q gi|254781172|r 273 --RQANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSLQKQLGERARSPRWMISHKFAEKQASTRLLDIDIQIG-RT 349 (731)
Q Consensus 273 --~~~~~~~~~~~~~~~~~~~r~~l~y~iDGiVikvn~~~~q~~lG~ts~~PrwaiA~Kf~~e~~~T~v~~I~wqvg-Rt 349 (731)
...++.+++..++++ ...-...|||+|--|-.++- | .+.-.| +=+|-.+.+...+|..-.|--| |+
T Consensus 357 ~~~~~~~~~e~~~~~~~------a~~~g~EGlm~K~~ds~Y~p--G--rR~~~W-~K~K~d~~tlDlVviga~~G~GrR~ 425 (537)
T PRK09247 357 PLVPFSDWDELAALRAA------ARERGVEGLMLKRRDSPYLV--G--RKKGDW-WKWKRDPLTIDAVLIYAQRGHGRRA 425 (537)
T ss_pred CCCCCCCHHHHHHHHHH------HHHCCCEEEEEECCCCCCCC--C--CCCCCE-EEECCCCCCCEEEEEECCCCCCCCC
T ss_conf 51406999999999998------87538704798458998679--9--878974-7880575310048972245876645
Q ss_pred CEEEE--EEEEEEEEECCC--EEEE-ECCCCHHHHHHH
Q ss_conf 22589--999743330264--0001-014898999750
Q gi|254781172|r 350 GILTP--VARLEPVNIGGA--LITN-ATLHNEDYIKGL 382 (731)
Q Consensus 350 G~itP--va~~ePV~l~G~--~V~r-atlhN~~~I~~l 382 (731)
|.++. .|..++-.-... +|.+ .|++.-.++++|
T Consensus 426 ~~~~~~~la~~~~~~~~~~l~~v~K~~sG~td~el~~l 463 (537)
T PRK09247 426 SLYTDYTFGVWDGGEGGRQLVPFAKAYSGLTDEEILQL 463 (537)
T ss_pred CCCCCEEEEEEECCCCCCEEEEEEEECCCCCHHHHHHH
T ss_conf 54244579998079986168887886478999999999
No 36
>KOG1968 consensus
Probab=97.85 E-value=1.7e-05 Score=61.70 Aligned_cols=20 Identities=10% Similarity=0.323 Sum_probs=11.2
Q ss_pred CCEEEEEEEEEEEEECCCEE
Q ss_conf 62258999974333026400
Q gi|254781172|r 349 TGILTPVARLEPVNIGGALI 368 (731)
Q Consensus 349 tG~itPva~~ePV~l~G~~V 368 (731)
+++|++++.-|-+.|++.-+
T Consensus 495 ~~ri~si~~se~~ki~~~~l 514 (871)
T KOG1968 495 RSRIMSICKSEGIKISDDVL 514 (871)
T ss_pred HHHHHHHHCCCCEECCCHHH
T ss_conf 76665330246424172788
No 37
>cd07902 Adenylation_DNA_ligase_III The Adenylation domain of DNA Ligase III is a component of the catalytic core unit. 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, bacteriohages, 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
Probab=97.83 E-value=0.00074 Score=48.98 Aligned_cols=176 Identities=15% Similarity=0.131 Sum_probs=90.4
Q ss_pred CCCCCCHHHCCCHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCEEEEEEEEECCEEEEEEECCCCHHHHHHHHH-HHHH
Q ss_conf 664257021599999999999999861246777611999941581899999859989988865986556669997-7531
Q gi|254781172|r 92 SIPTLSLEKIWNIEDLRKFITRIYRFWQKKDDNSIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSAC-IRAI 170 (731)
Q Consensus 92 ~~pMlSL~k~~~~~el~~w~~~~~~~~~~~~~~~~~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n-~~~i 170 (731)
-.|||-- -+.+.++... + .+..|.+|+|+||.=+-+++.+|. ++..|| -|+|+|.. ...+
T Consensus 14 i~PMLA~-~~~~~~~~~~---~----------~~~~~~~E~K~DG~R~qih~~~~~-v~l~SR----n~~d~~~~~~~~~ 74 (213)
T cd07902 14 VKPMLAE-ACKSVEYAMK---K----------CPNGMYAEIKYDGERVQLHKQGDN-FSFFSR----SLKPVLPHKVSHF 74 (213)
T ss_pred CCCEECC-CCCCHHHHHH---H----------CCCCEEEEEEECEEEEEEEECCCE-EEEEEC----CCCCCCCCHHHHH
T ss_conf 8243589-8799799997---5----------799759997158189999982999-999927----8830364217789
Q ss_pred C-CCCCCCCCCCCCEEEEEEEEEEECHHHHHHHHHHHHCCCC-CCCCHHHHHHHHHHCCCHHHHHCCCEEEEEEECCCCC
Q ss_conf 0-2432233544550489999998520212345564314854-3342345677775234555530111056641024543
Q gi|254781172|r 171 P-TIPRVLSLNIPEIIEVRGEVYISKNDFLALNDEMIAVGRK-PYANPRNAASGILRRLNPTDITRYLNFFVHGLGKTSE 248 (731)
Q Consensus 171 ~-~iP~~l~~~~~~~ieiRGEv~m~~~~F~~lN~~~~~~g~~-~f~NpRN~aaG~lr~~d~~~~~r~L~f~ay~~~~~~~ 248 (731)
. -||..++ ....+.+=||++.-... .|.. +|..- + ++++.. ....++.+++|++.+.++
T Consensus 75 ~~~i~~~~~--~~~~~ILDGEiv~~d~~----------~g~~~~f~~l-----~-~~~~~~-~~~~~~~~~vFDlL~l~g 135 (213)
T cd07902 75 KDYIPKAFP--HGHSMILDSEVLLVDTK----------TGKPLPFGTL-----G-IHKKSA-FKDANVCLFVFDCLYFNG 135 (213)
T ss_pred HHHHHHHCC--CCCCEEEEEEEEEEECC----------CCCCCCCHHH-----H-HHHHHH-CCCCCEEEEEEEEEEECC
T ss_conf 999998647--78747997047998668----------9975503004-----4-554541-245781699997700598
Q ss_pred C--CCCCCHHHHHHHHHCCCCCCCCEEE-----EECCCCHHHHHHHHHHHHCCCCCCCCCEEEEECCHHC
Q ss_conf 3--2100003689999759966541488-----7403211345566553100112343763777311000
Q gi|254781172|r 249 I--FAKGQYEMLQKMRCLGFPVNNGVRQ-----ANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSL 311 (731)
Q Consensus 249 ~--~~~~~~e~l~~L~~~GF~v~~~~~~-----~~~~~~~~~~~~~~~~~r~~l~y~iDGiVikvn~~~~ 311 (731)
. .-....+..+.|..+--++...... ..+.+++.+++++..+ -...|||+|--+-.+
T Consensus 136 ~~l~~~pl~eRr~~L~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~a~~------~g~EGiv~K~~~S~Y 199 (213)
T cd07902 136 ESLMDKPLRERRKILEDNMVEIPNRIMFSEMKFVKKADDLAALITRVIR------EGLEGLVLKDIKSVY 199 (213)
T ss_pred EEHHHCCHHHHHHHHHHHHCCCCCCEEEEEEEECCCHHHHHHHHHHHHH------CCCEEEEEECCCCCC
T ss_conf 1833088999999999740568984798744755999999999999997------698389975898976
No 38
>PRK13766 Hef nuclease; Provisional
Probab=97.78 E-value=4.2e-05 Score=58.62 Aligned_cols=52 Identities=25% Similarity=0.264 Sum_probs=46.8
Q ss_pred CHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCHHHHHCCCCCCHHHHHHHHHHHCCH
Q ss_conf 10111168999999882998999997897761251177876138886789999999996697
Q gi|254781172|r 558 GIRHVGAEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVEFYQNP 619 (731)
Q Consensus 558 GI~~vG~~~Ak~La~~f~si~~l~~~~~~~~~~~~~~~e~L~~I~GiG~~~A~si~~ff~~~ 619 (731)
+|||||.++|+.|..+|+|+..+.. ++.++|.+|+|||+++|+.|.+++..+
T Consensus 710 ~~pgvg~~~a~~ll~~fgsi~~i~~----------a~~~eL~~v~giG~~~A~~i~~~~~~~ 761 (764)
T PRK13766 710 SLPDVGPVLARNLLDHFGSVENVMT----------ASEEELKAVEGIGEKTAKKIREVVTSE 761 (764)
T ss_pred HCCCCCHHHHHHHHHHCCCHHHHHC----------CCHHHHHHCCCCCHHHHHHHHHHHCCC
T ss_conf 3899999999999997199999965----------999999547496999999999985251
No 39
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=97.70 E-value=8.5e-05 Score=56.26 Aligned_cols=52 Identities=21% Similarity=0.273 Sum_probs=47.9
Q ss_pred CCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCHHHHHCCCCCCHHHHHHHHHHHCC
Q ss_conf 01011116899999988299899999789776125117787613888678999999999669
Q gi|254781172|r 557 LGIRHVGAEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVEFYQN 618 (731)
Q Consensus 557 LGI~~vG~~~Ak~La~~f~si~~l~~~~~~~~~~~~~~~e~L~~I~GiG~~~A~si~~ff~~ 618 (731)
..|||||+++.+.|.++|+|++++..+ +.++|..++|||.++|+.|.++|+.
T Consensus 557 d~I~GIG~kr~~~Ll~~Fgs~~~i~~A----------s~eeL~~v~Gi~~~~A~~I~~~l~~ 608 (609)
T PRK00558 557 DDIPGIGPKRRKALLKHFGSLKAIKEA----------SVEELAKVPGISKKLAEKIYEALHK 608 (609)
T ss_pred CCCCCCCHHHHHHHHHHCCCHHHHHHC----------CHHHHHHCCCCCHHHHHHHHHHHHC
T ss_conf 478997999999999970799999738----------9999964899899999999999705
No 40
>PRK08224 ligC ATP-dependent DNA ligase; Reviewed
Probab=97.68 E-value=0.0015 Score=46.69 Aligned_cols=217 Identities=17% Similarity=0.194 Sum_probs=104.7
Q ss_pred CCCEEEEEEECCEEEEEEEEECCEEEEEEECCCCHHHHHHHHHHHHHCCCCCCCCCCCCCEEEEEEEEEEECH---HHHH
Q ss_conf 7611999941581899999859989988865986556669997753102432233544550489999998520---2123
Q gi|254781172|r 124 NSIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPTIPRVLSLNIPEIIEVRGEVYISKN---DFLA 200 (731)
Q Consensus 124 ~~~~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n~~~i~~iP~~l~~~~~~~ieiRGEv~m~~~---~F~~ 200 (731)
....|..|.|+||.=+-+...+|. ++..|| -|+|+|+.---|...-..+ .+....+=||+++... +|..
T Consensus 22 ~~~~w~~E~K~DG~R~~~~~~~~~-v~L~SR----~g~d~T~~fPel~~~~~~~---~~~~~VLDGEiV~~~~~~~~F~~ 93 (345)
T PRK08224 22 PGGGWSYEPKWDGFRCLVFRDGDE-VELGSR----NGKPLTRYFPELVAALRAE---LPERCVLDGEIVIATDGGLDFEA 93 (345)
T ss_pred CCCCEEEEEEECCEEEEEEEECCE-EEEECC----CCCCCHHHCHHHHHHHHHC---CCCCEEEEEEEEECCCCCCCHHH
T ss_conf 999758996277099999998999-999938----9752034578999999752---78657985069960699789899
Q ss_pred HHHHHHHCCCCCCCCHHHHHHHHHHCCCHHHHHCCCEEEEEEECCCCCCCC--CCCHHHHHHHHHCCCCCCCCEEEE---
Q ss_conf 455643148543342345677775234555530111056641024543321--000036899997599665414887---
Q gi|254781172|r 201 LNDEMIAVGRKPYANPRNAASGILRRLNPTDITRYLNFFVHGLGKTSEIFA--KGQYEMLQKMRCLGFPVNNGVRQA--- 275 (731)
Q Consensus 201 lN~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~r~L~f~ay~~~~~~~~~~--~~~~e~l~~L~~~GF~v~~~~~~~--- 275 (731)
|..+. +| +++..+.+ ....++.|++|++.+.++... ....+.-+.|..+-=...+....+
T Consensus 94 Lq~R~---------~~---~~~r~~~l---~~~~Pv~~~~FDlL~l~G~dL~~~Pl~eRr~~L~~ll~~~~~~~~~~~~~ 158 (345)
T PRK08224 94 LQQRI---------HP---AASRVRKL---AEETPASFVAFDLLALGDEDLTGRPFAERRAALEAALAGAGPPVHLTPAT 158 (345)
T ss_pred HHHHC---------CC---CCCHHHHH---HHHCCCEEEEEEEEEECCEEHHHCCHHHHHHHHHHHHCCCCCCEEECCCC
T ss_conf 96452---------22---33137776---43078479999775599637454879999999998752479857974520
Q ss_pred ECCCCHHHHHHHHHHHHCCCCCCCCCEEEEECCHHCCCCCCCCCCCCCCEEEECCCC-CEEEEEEEEEEEEECCCCEE--
Q ss_conf 403211345566553100112343763777311000111587656866312311456-21589987889940356225--
Q gi|254781172|r 276 NTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSLQKQLGERARSPRWMISHKFAE-KQASTRLLDIDIQIGRTGIL-- 352 (731)
Q Consensus 276 ~~~~~~~~~~~~~~~~r~~l~y~iDGiVikvn~~~~q~~lG~ts~~PrwaiA~Kf~~-e~~~T~v~~I~wqvgRtG~i-- 352 (731)
.+.++...+++...+ -...|||.|--|..++- |. + .| .|... .+++.+|.+- ..|+.+..
T Consensus 159 ~~~~~~~~~~~~a~~------~G~EGIvaKr~dS~Y~~--Gr--R--~w---lKiK~~~~~d~VI~G~--~~~~~~~~~g 221 (345)
T PRK08224 159 TDLATARRWFEEFEG------AGLDGVIAKPLDGPYQP--GK--R--VM---FKVKHERTADCVVAGF--RYHKSGDAVG 221 (345)
T ss_pred CCHHHHHHHHHHHHH------CCCCEEEEECCCCCCCC--CC--C--CC---EEECCCCEEEEEEEEE--ECCCCCCCCC
T ss_conf 788899999999997------69932798669997678--98--6--66---7963446031999956--7489877544
Q ss_pred -EEEEEEEEE-EECCCEEEEECCCCHHHHHHH
Q ss_conf -899997433-302640001014898999750
Q gi|254781172|r 353 -TPVARLEPV-NIGGALITNATLHNEDYIKGL 382 (731)
Q Consensus 353 -tPva~~ePV-~l~G~~V~ratlhN~~~I~~l 382 (731)
-=++..++- .| ..|..+|.++....++|
T Consensus 222 slllG~y~~~g~l--~~vGv~tgf~~~~~~~L 251 (345)
T PRK08224 222 SLLLGLYDDDGLL--HHVGVTSAFPMAERRAL 251 (345)
T ss_pred CEEEEEECCCCCE--EEEEEECCCCHHHHHHH
T ss_conf 0789998599758--99753068798999999
No 41
>KOG2841 consensus
Probab=97.62 E-value=0.00012 Score=55.16 Aligned_cols=78 Identities=18% Similarity=0.209 Sum_probs=58.3
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHC-CHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCHHHHHCCCCCCHHH
Q ss_conf 2100145689999875223466677630-101111689999998829989999978977612511778761388867899
Q gi|254781172|r 530 FGDVSVTNLYDSINKRRNISLERFIFSL-GIRHVGAEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDII 608 (731)
Q Consensus 530 fgeKsa~nL~~sIe~sK~~~L~r~L~AL-GI~~vG~~~Ak~La~~f~si~~l~~~~~~~~~~~~~~~e~L~~I~GiG~~~ 608 (731)
+..|+++++...++.. .+.+++..| .||+|+++-|-.|..+|++++.+..+ +.++|..++|+|+..
T Consensus 173 ~ek~p~dli~~~~~~d---~ls~~~~~Lt~i~~VnKtda~~LL~~FgsLq~~~~A----------S~~ele~~~G~G~~k 239 (254)
T KOG2841 173 YEKKPIDLIMERKDRD---LLSSLLGFLTTIPGVNKTDAQLLLQKFGSLQQISNA----------SEGELEQCPGLGPAK 239 (254)
T ss_pred HHCCCCHHHHHCCCCC---HHHHHHHHHHHCCCCCCCCHHHHHHHCCCHHHHHHC----------CHHHHHHCCCCCHHH
T ss_conf 6038804555333530---889999998817897700189998855359998741----------776798675737899
Q ss_pred HHHHHHHHCCHH
Q ss_conf 999999966979
Q gi|254781172|r 609 AQAIVEFYQNPR 620 (731)
Q Consensus 609 A~si~~ff~~~~ 620 (731)
|+.|.+||+.+.
T Consensus 240 ak~l~~~l~~pf 251 (254)
T KOG2841 240 AKRLHKFLHQPF 251 (254)
T ss_pred HHHHHHHHHCCC
T ss_conf 999999984511
No 42
>cd07894 Adenylation_RNA_ligase The Adenylation domain of RNA circularization protein, which catalyzes the circularization of RNA molecules in an ATP-dependent reaction, comprises the enzyme's catalytic unit. RNA circularization protein is 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=97.59 E-value=0.0015 Score=46.63 Aligned_cols=169 Identities=20% Similarity=0.164 Sum_probs=105.6
Q ss_pred CCCCCCCEEECCCCCCCHHHCCCHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCEEEEEEEEECCEEEEEEECCCCHHH
Q ss_conf 32357750451664257021599999999999999861246777611999941581899999859989988865986556
Q gi|254781172|r 81 EMNLSLFKVTHSIPTLSLEKIWNIEDLRKFITRIYRFWQKKDDNSIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSG 160 (731)
Q Consensus 81 ~~~~~~~kv~H~~pMlSL~k~~~~~el~~w~~~~~~~~~~~~~~~~~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~G 160 (731)
.+..+|.| -..++.|+.. |..++ ...++||-|+||--+-+..-+|+ +.|+||| |.+=
T Consensus 24 ~vV~GyP~---I~R~~~L~~g-----i~~~F-------------~~~v~vEEK~dGYNVRI~~~~g~-vlA~TRG-G~IC 80 (340)
T cd07894 24 RVVPGYPK---IRRALLLEPG-----LKRHF-------------IDPVAVEEKMNGYNVRIVRVGGE-VLAFTRG-GFIC 80 (340)
T ss_pred CEECCCCC---CCEEECCCCC-----HHHHC-------------CCCEEEEEECCCCEEEEEEECCE-EEEEECC-CEEC
T ss_conf 68837997---1245403420-----69776-------------89858998216706999999999-9999058-7207
Q ss_pred HHHHHHHHHHCCCCCCCCCCCCCEEEEEEEEEEECHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCHHHHHCCCEEEE
Q ss_conf 66999775310243223354455048999999852021234556431485433423456777752345555301110566
Q gi|254781172|r 161 EDVSACIRAIPTIPRVLSLNIPEIIEVRGEVYISKNDFLALNDEMIAVGRKPYANPRNAASGILRRLNPTDITRYLNFFV 240 (731)
Q Consensus 161 eDVT~n~~~i~~iP~~l~~~~~~~ieiRGEv~m~~~~F~~lN~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~r~L~f~a 240 (731)
-=-|+.++. -++..+-.++|+ +.+=||++=+. ||= +.+ ++- ...++.||+
T Consensus 81 PfTT~r~~~--~~~~~fF~d~P~-lvLCgE~~Gpe-------------------NPY--v~~-----~~p-~~edi~ffv 130 (340)
T cd07894 81 PFTTDRLRE--LDLPEFFDDYPD-LMLCGEVVGPE-------------------NPY--VPY-----DYP-VAEDVGFFV 130 (340)
T ss_pred CCCHHHHHH--HHHHHHHHHCCC-CEEEEEEECCC-------------------CCC--CCC-----CCC-CCCCCEEEE
T ss_conf 873478776--400777865898-68999860689-------------------999--789-----998-757731899
Q ss_pred EEECCCCCCCCCCCHHHHHHHHHCCCCCCCCEEEEECC--CCHHHHHHHHHHHHCCCCCCCCCEEEEECC
Q ss_conf 41024543321000036899997599665414887403--211345566553100112343763777311
Q gi|254781172|r 241 HGLGKTSEIFAKGQYEMLQKMRCLGFPVNNGVRQANTF--HGIVSYYNEMKSIRSTLPYDIDGLVYKVDE 308 (731)
Q Consensus 241 y~~~~~~~~~~~~~~e~l~~L~~~GF~v~~~~~~~~~~--~~~~~~~~~~~~~r~~l~y~iDGiVikvn~ 308 (731)
|++-......+-.+.+.++.+.+.|++.++..-.+..- +++.+.+.++.+ =.--|+|+|-.+
T Consensus 131 FDi~~k~t~~~Lpv~er~~L~e~Yglp~V~~fg~~~~~~~~~l~eiI~~L~~------egrEGVVlKdp~ 194 (340)
T cd07894 131 FDIRKKNTGKPLPVEERRELLEEYGLPHVRLFGTFTVDEVEELKEIIRELDK------EGREGVVLKDPD 194 (340)
T ss_pred EEEEECCCCCCCCHHHHHHHHHHCCCCCCCCCCEECHHHHHHHHHHHHHHHH------CCCCEEEECCCC
T ss_conf 9866879898579999999999739997644127839999999999998735------488318974866
No 43
>TIGR02776 NHEJ_ligase_prk DNA ligase D; InterPro: IPR014143 Members of this entry 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 (IPR009187 from INTERPRO) plus this DNA ligase is seen in about 200f bacterial genomes to date and at least one archaeon (Archeoglobus fulgidus). This entry describes a central and C-terminal domain. These two domains may be permuted, as in genus Mycobacterium, or divided into tandem ORFs. An additional N-terminal 3 -phosphoesterase (PE) domain (IPR014144 from INTERPRO) is present in some members of this ligase. Most examples of genes for this ligase are adjacent to the gene for Ku..
Probab=97.59 E-value=0.0011 Score=47.58 Aligned_cols=165 Identities=20% Similarity=0.212 Sum_probs=98.1
Q ss_pred CCEEEEEEECCEEEEEEEEECCEEEEEEECCCCHHHHHHHHHHHHHCCCCCCCC-----CCCCCEEEEEEEEEEEC----
Q ss_conf 611999941581899999859989988865986556669997753102432233-----54455048999999852----
Q gi|254781172|r 125 SIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPTIPRVLS-----LNIPEIIEVRGEVYISK---- 195 (731)
Q Consensus 125 ~~~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n~~~i~~iP~~l~-----~~~~~~ieiRGEv~m~~---- 195 (731)
..+|+-|.|+||-=+-++-++|. |+.+|| -|.|+|+..-. |+.-+. ...-..+.|=||||+-.
T Consensus 4 G~~W~yEvKyDGYR~~~~i~~g~-vrL~tR----nG~dwt~~fp~---i~~~~~~~~~~~l~~~~~~lDGEiVvL~~~g~ 75 (645)
T TIGR02776 4 GDGWLYEVKYDGYRCLLRIEDGD-VRLITR----NGHDWTERFPE---IVKALAEIIEKLLKLLPAWLDGEIVVLDERGR 75 (645)
T ss_pred CCCCEEEECCCCCEEEEEEECCE-EEEEEC----CCCCHHHHHHH---HHHHHHHHHHHHHHCCCEEECCEEEEECCCCC
T ss_conf 88843763124223566785481-799852----88785552068---99999999986520563121335797278898
Q ss_pred HHHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCHH---HHHCCCEEEEEEECCCCCC-----CCCCCHHHH-HHHHHCCC
Q ss_conf 02123455643148543342345677775234555---5301110566410245433-----210000368-99997599
Q gi|254781172|r 196 NDFLALNDEMIAVGRKPYANPRNAASGILRRLNPT---DITRYLNFFVHGLGKTSEI-----FAKGQYEML-QKMRCLGF 266 (731)
Q Consensus 196 ~~F~~lN~~~~~~g~~~f~NpRN~aaG~lr~~d~~---~~~r~L~f~ay~~~~~~~~-----~~~~~~e~l-~~L~~~GF 266 (731)
++|+.|..+ |-|++-|-. ...+++.|+||++..-++. +....-..| +.|+....
T Consensus 76 ~~F~~LQ~R-----------------gr~~~~~~a~~~~~~~~~~~~aFDLl~l~G~dL~~lPL~~RK~~L~~LL~~~~~ 138 (645)
T TIGR02776 76 ADFAALQNR-----------------GRLKKTDRALSEGASEPLLYYAFDLLFLSGEDLRALPLEERKKRLKELLKAQDG 138 (645)
T ss_pred CCHHHHHCC-----------------HHCCCHHHHHHHHCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf 781886202-----------------001334589997218980899971566880677862489999999999984468
Q ss_pred C-----CCCCEEE--EECCCCHHHHHHHHHHHHCCCCCCCCCEEEEECCHHCCCCCCCCC-CCCCCE
Q ss_conf 6-----6541488--740321134556655310011234376377731100011158765-686631
Q gi|254781172|r 267 P-----VNNGVRQ--ANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSLQKQLGERA-RSPRWM 325 (731)
Q Consensus 267 ~-----v~~~~~~--~~~~~~~~~~~~~~~~~r~~l~y~iDGiVikvn~~~~q~~lG~ts-~~Prwa 325 (731)
+ ...++.. +.+..++.+.++.-.. |.--|||-|=-+-.++. . |++.|-
T Consensus 139 ~~~~~~~~~~~~~r~~~~~~~~~~ll~~a~~------~~lEGvv~Kr~~s~Y~s-----gkRs~~W~ 194 (645)
T TIGR02776 139 PAEPDPAIRYSDHRVFEEDGDGQALLESACR------LGLEGVVSKRLDSPYRS-----GKRSKDWL 194 (645)
T ss_pred CCCCCCCCCCEECCCCCCCCHHHHHHHHHHH------HCCCEEEEECCCCCCCC-----CCCCCCHH
T ss_conf 7567741200001100685158999999998------57973898547773016-----77686024
No 44
>PRK08609 hypothetical protein; Provisional
Probab=97.57 E-value=0.00026 Score=52.47 Aligned_cols=22 Identities=32% Similarity=0.604 Sum_probs=9.2
Q ss_pred HHHHHHHHHCCCHHHHHCCCEEEE
Q ss_conf 456777752345555301110566
Q gi|254781172|r 217 RNAASGILRRLNPTDITRYLNFFV 240 (731)
Q Consensus 217 RN~aaG~lr~~d~~~~~r~L~f~a 240 (731)
|-.+|||+|+.- +...++++++
T Consensus 177 ~veiaGS~RR~k--etvGDIDiLv 198 (570)
T PRK08609 177 RFSRAGSLRRAR--ETVKDLDFII 198 (570)
T ss_pred EEEEECHHHHCC--CCCCCEEEEE
T ss_conf 798602023146--6546734899
No 45
>PRK09632 ATP-dependent DNA ligase; Reviewed
Probab=97.44 E-value=0.0046 Score=42.85 Aligned_cols=26 Identities=23% Similarity=0.391 Sum_probs=9.4
Q ss_pred EEEEEECCEEEEEEEEECCEEEEEEEC
Q ss_conf 999941581899999859989988865
Q gi|254781172|r 128 FTLEPKIDGTMITIRYEKGKFVYAALR 154 (731)
Q Consensus 128 ~~vepKiDG~sisl~Y~~G~L~~a~TR 154 (731)
|+.|+|.||.=+-+..++|. ++..||
T Consensus 470 W~yEiKwDGyR~la~~~~g~-VrL~SR 495 (753)
T PRK09632 470 WAFEGKWDGYRLLVEADHGA-LRLRSR 495 (753)
T ss_pred EEEECCCCEEEEEEEEECCE-EEEECC
T ss_conf 56770075399999998999-999818
No 46
>PHA02142 putative RNA ligase
Probab=97.37 E-value=0.0027 Score=44.70 Aligned_cols=148 Identities=18% Similarity=0.119 Sum_probs=80.5
Q ss_pred CCCEEEEEEECCEEEEEEEEE---------------------CCEEEEEEECCCCHHHHH---HHHHHHHHCCCCCCCCC
Q ss_conf 761199994158189999985---------------------998998886598655666---99977531024322335
Q gi|254781172|r 124 NSIFFTLEPKIDGTMITIRYE---------------------KGKFVYAALRGDGHSGED---VSACIRAIPTIPRVLSL 179 (731)
Q Consensus 124 ~~~~~~vepKiDG~sisl~Y~---------------------~G~L~~a~TRGdG~~GeD---VT~n~~~i~~iP~~l~~ 179 (731)
....|.++-|+||.|+++.|- +|++ ++.+.|-..=+| .-..+-.--+||.+|.
T Consensus 167 ~~~~~~vTeKLDGsS~tvy~v~~~~~~~~~g~~~~~~~~~~~~~~f--gvcsrn~~L~~~~~n~yW~~a~~~~i~~~l~- 243 (366)
T PHA02142 167 ADVKFAKSLKLDGSSITMAWVTDPDLFLDLGTEDEPYAHDYDDAQF--IVASRNQVLRYNADSKWWKGVENYQIVDRLK- 243 (366)
T ss_pred CCCEEEEEEEECCEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCE--EEECCCEEEEECCCCHHHHHHHHCCCHHHHH-
T ss_conf 7926999997525358999814774000134235665444456640--6861642563178872999988758288997-
Q ss_pred CCCCEEEEEEEEEEECHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCHHHHHCCCEEEEEEECCCCCCCCCCCHHHHH
Q ss_conf 44550489999998520212345564314854334234567777523455553011105664102454332100003689
Q gi|254781172|r 180 NIPEIIEVRGEVYISKNDFLALNDEMIAVGRKPYANPRNAASGILRRLNPTDITRYLNFFVHGLGKTSEIFAKGQYEMLQ 259 (731)
Q Consensus 180 ~~~~~ieiRGEv~m~~~~F~~lN~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~r~L~f~ay~~~~~~~~~~~~~~e~l~ 259 (731)
.....+-|+||++=+.= =.|+-++ ..-.|++|++-..+....-++.++..
T Consensus 244 klg~nIAIQGEliGpgI----------------QgN~y~l--------------~~~~f~vF~v~dId~~ryl~~~e~~~ 293 (366)
T PHA02142 244 ELGMSVAIQGELMGPGI----------------QKNRENF--------------DKYRIFAFRAWFIDEQRFATDEEFQD 293 (366)
T ss_pred HCCCCEEEEEEEECCCC----------------CCCCCCC--------------CCCEEEEEEEEECCCCEECCHHHHHH
T ss_conf 54872799888876543----------------5764457--------------88669999999828867778899999
Q ss_pred HHHHCCCCCCCCEEE------EECCCCHHHHHHHHHHHHCCCCCCCCCEEEEECC
Q ss_conf 999759966541488------7403211345566553100112343763777311
Q gi|254781172|r 260 KMRCLGFPVNNGVRQ------ANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDE 308 (731)
Q Consensus 260 ~L~~~GF~v~~~~~~------~~~~~~~~~~~~~~~~~r~~l~y~iDGiVikvn~ 308 (731)
+++.+|.+.+|..-. ..+.++++++-+ ......-.=-|+|+|-.+
T Consensus 294 ~~~~lgl~~VPvlgy~~~~~~~~sv~ell~~Ae----~~~~~~~~REGiV~rs~~ 344 (366)
T PHA02142 294 LCRTLGMEIVPQLGYSYPFQEFTNVKEMLAAAD----IPSINHKIAEGVVYKSVE 344 (366)
T ss_pred HHHHCCCCEEEECCCCCCCCCCCCHHHHHHHCC----CCCCCCCCCCEEEEEECC
T ss_conf 998769962404265454343212999975422----788788611329996326
No 47
>TIGR02779 NHEJ_ligase_lig DNA polymerase LigD, ligase domain; InterPro: IPR014146 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 IPR009187 from INTERPRO), 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 region represents the central ligase domain..
Probab=97.36 E-value=0.015 Score=38.82 Aligned_cols=171 Identities=19% Similarity=0.265 Sum_probs=101.5
Q ss_pred CCCCEEEEEEECCEEEEEEEEE-CCEEEEEEECCCCHHHHHHHHHH-HHHCCC----CCCCCCCCCCEEEEEEEEEEEC-
Q ss_conf 7761199994158189999985-99899888659865566699977-531024----3223354455048999999852-
Q gi|254781172|r 123 DNSIFFTLEPKIDGTMITIRYE-KGKFVYAALRGDGHSGEDVSACI-RAIPTI----PRVLSLNIPEIIEVRGEVYISK- 195 (731)
Q Consensus 123 ~~~~~~~vepKiDG~sisl~Y~-~G~L~~a~TRGdG~~GeDVT~n~-~~i~~i----P~~l~~~~~~~ieiRGEv~m~~- 195 (731)
+..-.|+-|.|+||-=+-+.-+ .|+ |+..|| -|.|+|+.- -.|.-. -..++. ....+=||||+-.
T Consensus 12 P~G~~W~yEvK~DGYR~l~~i~~~g~-vrL~sR----ng~dwT~~fP~~~~~~~~~~~~~l~~---~~~~lDGE~VvL~~ 83 (328)
T TIGR02779 12 PTGDDWLYEVKFDGYRLLARIEEGGK-VRLISR----NGHDWTEKFPPELAAAEEIILAALPI---LPAILDGEIVVLDE 83 (328)
T ss_pred CCCCCCEEEEEECCEEEEEEEECCCC-EEEEEC----CCCCHHHHCCHHHHHHHHHHHHHCCC---CEEEEEEEEEEECC
T ss_conf 88678127851124047888840883-899735----88551442686689999999875478---80677037999468
Q ss_pred ---HHHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCHHHHHCCCEEEEEEECCCCCCC-----CCCCHHHHHH-HHHCCC
Q ss_conf ---0212345564314854334234567777523455553011105664102454332-----1000036899-997599
Q gi|254781172|r 196 ---NDFLALNDEMIAVGRKPYANPRNAASGILRRLNPTDITRYLNFFVHGLGKTSEIF-----AKGQYEMLQK-MRCLGF 266 (731)
Q Consensus 196 ---~~F~~lN~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~r~L~f~ay~~~~~~~~~-----~~~~~e~l~~-L~~~GF 266 (731)
++|..|...... -.+...+. .-..+++.|+||++.+.++.. ....-..|+. |+.++-
T Consensus 84 ~G~~~F~~LQ~~~~~-------~~~~~I~~-------~~~~~~~~y~aFDLL~~~G~dL~~~pL~eRk~~L~~Ll~~~~~ 149 (328)
T TIGR02779 84 SGRSDFQALQNRLDA-------GKAEKIEK-------AAAKRPLTYYAFDLLYLDGEDLRDLPLSERKKLLEELLKAQKG 149 (328)
T ss_pred CCCCCHHHHHHHHHC-------CCHHHHHH-------HHHCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf 898787999776414-------76257899-------9722993799970456782476620289999999998611578
Q ss_pred CCCC-----CEEEEECC-CCHHHHHHHHHHHHCCCCCCCCCEEEEECCHHCCCCCCCCCC-CCCCEE
Q ss_conf 6654-----14887403-211345566553100112343763777311000111587656-866312
Q gi|254781172|r 267 PVNN-----GVRQANTF-HGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSLQKQLGERAR-SPRWMI 326 (731)
Q Consensus 267 ~v~~-----~~~~~~~~-~~~~~~~~~~~~~r~~l~y~iDGiVikvn~~~~q~~lG~ts~-~Prwai 326 (731)
+.++ .+..+..+ .+..+.++.-. .+.-=|||=|--|-.++. .| ++.|-=
T Consensus 150 ~~~p~~~~~~~~~s~~~~~~g~~l~~~a~------~~glEGvvaKr~dS~Y~~-----GrR~~~W~K 205 (328)
T TIGR02779 150 PLAPDPQAKAIRYSEHFEGDGQALLEAAC------RLGLEGVVAKRRDSPYRS-----GRRSADWLK 205 (328)
T ss_pred CCCCCCCCCEEEEEEECCCCHHHHHHHHH------HHCCCEEEEECCCCCCCC-----CCCCCCCCE
T ss_conf 87878775404788753675789999999------828962799527787678-----861565401
No 48
>PRK05972 ligD ATP-dependent DNA ligase; Reviewed
Probab=97.33 E-value=0.011 Score=39.84 Aligned_cols=161 Identities=23% Similarity=0.251 Sum_probs=91.9
Q ss_pred CCCCEEEEEEECCEEEEEEEEECCEEEEEEECCCCHHHHHHHHHHHHHCCCCCCCCCCCCCEEEEEEEEEEE----CHHH
Q ss_conf 776119999415818999998599899888659865566699977531024322335445504899999985----2021
Q gi|254781172|r 123 DNSIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPTIPRVLSLNIPEIIEVRGEVYIS----KNDF 198 (731)
Q Consensus 123 ~~~~~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n~~~i~~iP~~l~~~~~~~ieiRGEv~m~----~~~F 198 (731)
...-.|+-|.|+||.=+-+..++|. ++..|| -|.|+|+.--.|...-..|+. ....+=|||+.- +.+|
T Consensus 216 P~g~~W~~EiK~DGyR~la~i~~g~-v~L~SR----nG~D~T~~fPel~~a~~~l~~---~~avLDGEIVald~~Grp~F 287 (832)
T PRK05972 216 PSGDGWIYEIKFDGYRILARIEGGE-VRLFTR----NGLDWTAKLPALAKAAAALGL---PDAWLDGEIVVLDENGVPDF 287 (832)
T ss_pred CCCCCEEEEEEECEEEEEEEEECCE-EEEEEC----CCCCCHHHHHHHHHHHHHCCC---CCEEEEEEEEEECCCCCCCH
T ss_conf 9999725886554288999980998-899816----998534455999999984688---76356206998679998798
Q ss_pred HHHHHHHHHCCCCCCCCHHHHHHHHHHCCCHHHHHCCCEEEEEEECCCCCCCCC--CCHHHHHHHHHCCCCC-CCCEEEE
Q ss_conf 234556431485433423456777752345555301110566410245433210--0003689999759966-5414887
Q gi|254781172|r 199 LALNDEMIAVGRKPYANPRNAASGILRRLNPTDITRYLNFFVHGLGKTSEIFAK--GQYEMLQKMRCLGFPV-NNGVRQA 275 (731)
Q Consensus 199 ~~lN~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~r~L~f~ay~~~~~~~~~~~--~~~e~l~~L~~~GF~v-~~~~~~~ 275 (731)
..|.... + ......+.|++|++...++.... ...+.-+.|+.+-=.. .+....+
T Consensus 288 ~~LQ~~~---------------~--------~~~~~~l~y~~FDLL~ldG~dL~~~Pl~eRk~~L~~Ll~~~~~~~ir~s 344 (832)
T PRK05972 288 QALQNAF---------------D--------EGRTEDLVYFAFDLPFLEGEDLRALPLEERRARLRALLEAARSDRLRFS 344 (832)
T ss_pred HHHHHHH---------------H--------CCCCCCEEEEEEEECCCCCCCCHHCCHHHHHHHHHHHHCCCCCCCEECC
T ss_conf 9999887---------------4--------4787753899962103388510007899999999987502689837637
Q ss_pred ECCC-CHHHHHHHHHHHHCCCCCCCCCEEEEECCHHCCCCCCCCCCCCCCE
Q ss_conf 4032-1134556655310011234376377731100011158765686631
Q gi|254781172|r 276 NTFH-GIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSLQKQLGERARSPRWM 325 (731)
Q Consensus 276 ~~~~-~~~~~~~~~~~~r~~l~y~iDGiVikvn~~~~q~~lG~ts~~Prwa 325 (731)
..++ +-.+.++.-.+ ...-|||-|--|-.++ - .|++.|-
T Consensus 345 ~~~~~~g~~~~~~a~~------~glEGIVaKr~dS~Y~--~---gRS~~Wl 384 (832)
T PRK05972 345 EHFDAGGDAVLASACR------LGLEGVIGKRADSPYV--S---GRSEDWI 384 (832)
T ss_pred CCCCCCHHHHHHHHHH------CCCCCEEEECCCCCCC--C---CCCHHHH
T ss_conf 5405799999999987------1885326513788656--8---8864334
No 49
>cd08039 Adenylation_DNA_ligase_Fungal The Adenylation domain of uncharacterized fungal ATP-dependent DNA ligase-like proteins is inferred by similarity to be a component of the catalytic core unit. 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
Probab=97.28 E-value=0.024 Score=37.32 Aligned_cols=163 Identities=18% Similarity=0.185 Sum_probs=84.9
Q ss_pred CCEEEEEEECCEEEEEEEE---ECCEEEEEEECCCCHHHHHHHHHHH----HHCCCCCC--CCCCCCCEEEEEEEEEEEC
Q ss_conf 6119999415818999998---5998998886598655666999775----31024322--3354455048999999852
Q gi|254781172|r 125 SIFFTLEPKIDGTMITIRY---EKGKFVYAALRGDGHSGEDVSACIR----AIPTIPRV--LSLNIPEIIEVRGEVYISK 195 (731)
Q Consensus 125 ~~~~~vepKiDG~sisl~Y---~~G~L~~a~TRGdG~~GeDVT~n~~----~i~~iP~~--l~~~~~~~ieiRGEv~m~~ 195 (731)
.-.|++|.|+||-=+-++| +.|.=++..|| -|+|+|...- .+..-... ........+.+=||++.=.
T Consensus 21 ~~~f~~E~KyDGeR~QiH~~~~k~~~~irifSR----n~ed~T~~~p~~~~~i~~~l~~~~~~~~~~~~~ILDGE~va~d 96 (235)
T cd08039 21 RRRMSAERKYDGEYCQIHVDLSKGPNPIRIFSK----SGKDSTADRHGIHDVIRKSLRIGKPDCKFKKNCILEGEMLVWN 96 (235)
T ss_pred CCEEEEEEEECEEEEEEEECCCCCCCEEEEECC----CCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCCEEEEEEEEEEE
T ss_conf 984999980380359999721478999999889----8641545432267999986411566544652079971589986
Q ss_pred H------HHHHHHHHHHHCCCCCCCCHHHHHHHHHH-CC-C-HHHHHCCCEEEEEEECCCCCC--CCCCCHHHHHHHHHC
Q ss_conf 0------21234556431485433423456777752-34-5-555301110566410245433--210000368999975
Q gi|254781172|r 196 N------DFLALNDEMIAVGRKPYANPRNAASGILR-RL-N-PTDITRYLNFFVHGLGKTSEI--FAKGQYEMLQKMRCL 264 (731)
Q Consensus 196 ~------~F~~lN~~~~~~g~~~f~NpRN~aaG~lr-~~-d-~~~~~r~L~f~ay~~~~~~~~--~~~~~~e~l~~L~~~ 264 (731)
. .|+.+...... ++..+ .+ + +....+++.+++|++.+.++. .-....+..+.|..+
T Consensus 97 ~~~~~~lpFq~l~~~~~r-------------~~~~~~~~~~~~~~~~~~~~~~~FDiLylnG~~L~~~Pl~eRR~~Le~l 163 (235)
T cd08039 97 DRKSDILPFHKLRKHISR-------------SGSFIGTDNDSPPHPYEHLMIVFFDVLLLDDDSLLSKPYRERRDLLESL 163 (235)
T ss_pred CCCCCCCCHHHHHHHHHC-------------CCCHHHHHHCCCCCCCCEEEEEEEEEEEECCHHHHCCCHHHHHHHHHHH
T ss_conf 788960777888767520-------------3210222212644464127999988998988534308799999999986
Q ss_pred CCCCCCC-EEEE----------ECCCCHHHHHHHHHHHHCCCCCCCCCEEEEECCHHC
Q ss_conf 9966541-4887----------403211345566553100112343763777311000
Q gi|254781172|r 265 GFPVNNG-VRQA----------NTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSL 311 (731)
Q Consensus 265 GF~v~~~-~~~~----------~~~~~~~~~~~~~~~~r~~l~y~iDGiVikvn~~~~ 311 (731)
|...+. ...+ .+.+++..+.++- +.=..-|||+|--+-.+
T Consensus 164 -~~~~~g~~~~~~~~~i~~~~~~~~~~i~~~~~~a------i~~~~EGlmiK~~~S~Y 214 (235)
T cd08039 164 -VSPIPGRAILAEQFPIDFSHPDAYSRLRTIFARA------IAEHQEGLVLKASEEPY 214 (235)
T ss_pred -HCCCCCEEEEEEEEEECCCCCCCHHHHHHHHHHH------HHCCCCEEEECCCCCCC
T ss_conf -2657881788888742367778899999999999------98699879972699977
No 50
>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=97.26 E-value=0.00085 Score=48.53 Aligned_cols=81 Identities=17% Similarity=0.205 Sum_probs=44.7
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHHCCCCCHHHHHCCCCCCH
Q ss_conf 4210014568999987522346667763010111168999999882--99899999789776125117787613888678
Q gi|254781172|r 529 GFGDVSVTNLYDSINKRRNISLERFIFSLGIRHVGAEIARSLAKYY--LSYQNFAQEINNIIAHNNDDWLSLIRVPLVGD 606 (731)
Q Consensus 529 GfgeKsa~nL~~sIe~sK~~~L~r~L~ALGI~~vG~~~Ak~La~~f--~si~~l~~~~~~~~~~~~~~~e~L~~I~GiG~ 606 (731)
-|+-++-.+-..+|++- ..++..+--...|||||.+.+..|.... +++..+. .+.........+|++|+|+||
T Consensus 21 ~fr~rAY~~Aa~~l~~~-~~~i~~~~~~~~lpGIG~~ia~kI~Eil~tG~~~~le----~l~~~~p~~l~~l~~I~GiGp 95 (307)
T cd00141 21 PFRVRAYRKAARALESL-PEPIESLEEAKKLPGIGKKIAEKIEEILETGKLRKLE----ELREDVPPGLLLLLRVPGVGP 95 (307)
T ss_pred CHHHHHHHHHHHHHHHC-CCCCCCHHHHCCCCCCCHHHHHHHHHHHHHCCHHHHH----HHHCCCCHHHHHHHCCCCCCH
T ss_conf 26699999999999869-9564789987179996489999999999979808999----986656378999964788788
Q ss_pred HHHHHHHH
Q ss_conf 99999999
Q gi|254781172|r 607 IIAQAIVE 614 (731)
Q Consensus 607 ~~A~si~~ 614 (731)
++|..+.+
T Consensus 96 k~a~~l~~ 103 (307)
T cd00141 96 KTARKLYE 103 (307)
T ss_pred HHHHHHHH
T ss_conf 99999998
No 51
>COG1423 ATP-dependent DNA ligase, homolog of eukaryotic ligase III [DNA replication, recombination, and repair]
Probab=97.24 E-value=0.012 Score=39.63 Aligned_cols=174 Identities=18% Similarity=0.184 Sum_probs=105.7
Q ss_pred ECCCCCCCHHHCCCHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCEEEEEEEEECCEEEEEEECCCCHHHHHHHHHHHH
Q ss_conf 51664257021599999999999999861246777611999941581899999859989988865986556669997753
Q gi|254781172|r 90 THSIPTLSLEKIWNIEDLRKFITRIYRFWQKKDDNSIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRA 169 (731)
Q Consensus 90 ~H~~pMlSL~k~~~~~el~~w~~~~~~~~~~~~~~~~~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n~~~ 169 (731)
.|-..|+-|+.+ |..|. +...++||-|+||--+-+.--+|. +.|+||| |.+--=-|+.++.
T Consensus 69 PkI~R~llL~p~-----ik~~F------------~~~~v~VEEKmnGYNVRV~k~~g~-vyAiTRg-G~ICPfTT~r~~~ 129 (382)
T COG1423 69 PKIRRALLLEPT-----IKKHF------------GRGKVVVEEKMNGYNVRVVKLGGE-VYAITRG-GLICPFTTERLRD 129 (382)
T ss_pred CHHHEEECCCHH-----HHHHC------------CCCCEEEEEECCCCEEEEEEECCE-EEEEECC-CEECCCHHHHHHH
T ss_conf 404213226633-----68654------------898479997226715899998899-9998148-5246760677776
Q ss_pred HCCCCCCCCCCCCCEEEEEEEEEEECHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCHHHHHCCCEEEEEEECCCCCC
Q ss_conf 10243223354455048999999852021234556431485433423456777752345555301110566410245433
Q gi|254781172|r 170 IPTIPRVLSLNIPEIIEVRGEVYISKNDFLALNDEMIAVGRKPYANPRNAASGILRRLNPTDITRYLNFFVHGLGKTSEI 249 (731)
Q Consensus 170 i~~iP~~l~~~~~~~ieiRGEv~m~~~~F~~lN~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~r~L~f~ay~~~~~~~~ 249 (731)
. +|+.+-.++|+ +.+=||.+=+. ||= +. .++ -..+++.||.|++-+-...
T Consensus 130 l--~~~eff~d~p~-lvlcgEmvG~e-------------------nPY--v~-----~~~-y~~e~v~fFvFDire~~tg 179 (382)
T COG1423 130 L--IDLEFFDDYPD-LVLCGEMVGPE-------------------NPY--VP-----GPY-YEKEDVGFFVFDIREKNTG 179 (382)
T ss_pred H--CCHHHHHHCCC-CEEEEEECCCC-------------------CCC--CC-----CCC-CCCCCCEEEEEEEEECCCC
T ss_conf 4--35456763898-58999750678-------------------998--77-----898-7657740899998755889
Q ss_pred CCCCCHHHHHHHHHCCCCCCCCEEEEECCCCH----HHHHHHHHHHHCCCCCCCCCEEEEECCHHCCCCCCCCCC
Q ss_conf 21000036899997599665414887403211----345566553100112343763777311000111587656
Q gi|254781172|r 250 FAKGQYEMLQKMRCLGFPVNNGVRQANTFHGI----VSYYNEMKSIRSTLPYDIDGLVYKVDEFSLQKQLGERAR 320 (731)
Q Consensus 250 ~~~~~~e~l~~L~~~GF~v~~~~~~~~~~~~~----~~~~~~~~~~r~~l~y~iDGiVikvn~~~~q~~lG~ts~ 320 (731)
.+-.+.+.++.+.+.||+.+...-.. ..+++ ..-+.++.+ =.=.|+|+|-.|... ..|-+|++
T Consensus 180 r~Lp~eer~~l~ekYgl~~V~~fg~~-~~~e~~eei~eIve~L~k------eGREGVV~Kdpdm~~-~plKYtTs 246 (382)
T COG1423 180 RPLPVEERLELAEKYGLPHVEIFGEF-PADEAGEEIYEIVERLNK------EGREGVVMKDPDMRV-PPLKYTTS 246 (382)
T ss_pred CCCCHHHHHHHHHHCCCCCEEEEEEE-CHHHHHHHHHHHHHHHHH------CCCCCEEECCCCCCC-CCCEEECC
T ss_conf 97899999978987098706774266-366768999999999735------577535863813356-86331125
No 52
>pfam09414 RNA_ligase RNA ligase. This is a family of RNA ligases. The enzyme repairs RNA strand breaks in nicked DNA:RNA and RNA:RNA but not in DNA:DNA duplexes.
Probab=97.24 E-value=0.01 Score=40.18 Aligned_cols=150 Identities=19% Similarity=0.168 Sum_probs=81.3
Q ss_pred EEEEEEECCEEEEEEEEECCE-EEEEEECCCCHHHH----------HHHHHHHHHCCCCCCCCCCCCCEEEEEEEEEEEC
Q ss_conf 199994158189999985998-99888659865566----------6999775310243223354455048999999852
Q gi|254781172|r 127 FFTLEPKIDGTMITIRYEKGK-FVYAALRGDGHSGE----------DVSACIRAIPTIPRVLSLNIPEIIEVRGEVYISK 195 (731)
Q Consensus 127 ~~~vepKiDG~sisl~Y~~G~-L~~a~TRGdG~~Ge----------DVT~n~~~i~~iP~~l~~~~~~~ieiRGEv~m~~ 195 (731)
+|+++-||||.++++.+.++. .+...+|+=|...+ .-+..++.. .++.++....+..+.|.||+|=+.
T Consensus 2 e~vvTEKLhGtn~~~~~~~~~~~~~~r~~~~g~~~~~~~~~~~~~n~~~~~~~~~-~~~~~~~~~~~~~v~i~GEl~Gp~ 80 (183)
T pfam09414 2 EWVATEKLHGTNFSVYIVRDESQFAKRKRLVGVPAEDFFGYEILDNIYWAAIEAL-QILLRLAYLIPESVAVYGELFGPG 80 (183)
T ss_pred CEEEEEEECCEEEEEEEECCCCEEEEEEECCCCCCCCCCCCCCCHHHHHHHHHHH-HHHHHHHCCCCCEEEEEEEEECCC
T ss_conf 2899983747658999989821588732001345556310323115899999971-278775303875189998883475
Q ss_pred HHHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCHHHHHCCCEEEEEEECCCCC--CCCCCCHHHHHHHHHCCCCCCCCEE
Q ss_conf 02123455643148543342345677775234555530111056641024543--3210000368999975996654148
Q gi|254781172|r 196 NDFLALNDEMIAVGRKPYANPRNAASGILRRLNPTDITRYLNFFVHGLGKTSE--IFAKGQYEMLQKMRCLGFPVNNGVR 273 (731)
Q Consensus 196 ~~F~~lN~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~r~L~f~ay~~~~~~~--~~~~~~~e~l~~L~~~GF~v~~~~~ 273 (731)
-|.+.- ....+.|++|++-.... ...-++.+...+++.+|++++|-..
T Consensus 81 -----------------------------IQ~~~y-~~~~~~fy~Fdi~~~~~~~~~~l~~d~~~~~~~~lgl~~vP~L~ 130 (183)
T pfam09414 81 -----------------------------IQKNTY-YQGDLHFYVFDIWYIDAQETRFLDDDEVEAFCKTLGLKTVPVLG 130 (183)
T ss_pred -----------------------------CCCCCC-CCCCCEEEEEEEEECCCCCEEECCHHHHHHHHHHCCCCCCCEEE
T ss_conf -----------------------------357632-58876599999998169916978889999999876998178895
Q ss_pred EEECCCCHHHHHHHHHHH----HCCCCCCCCCEEEEECC
Q ss_conf 874032113455665531----00112343763777311
Q gi|254781172|r 274 QANTFHGIVSYYNEMKSI----RSTLPYDIDGLVYKVDE 308 (731)
Q Consensus 274 ~~~~~~~~~~~~~~~~~~----r~~l~y~iDGiVikvn~ 308 (731)
-..++++..+-...... -..-+----|+|||-..
T Consensus 131 -rG~~~e~~~~~~~~~~~~~~~~~~~~~i~EGvVikp~~ 168 (183)
T pfam09414 131 -RGPFDELKAFDVELEMLAGALLGLEGNLAEGVVLKPVR 168 (183)
T ss_pred -EECHHHHHCCCHHCCCCCCCCCCCCCCEEEEEEEEECC
T ss_conf -98079952040112544577788888566369971144
No 53
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=97.19 E-value=0.0024 Score=45.11 Aligned_cols=83 Identities=13% Similarity=0.200 Sum_probs=48.9
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHH--------HHH-CCHHHHHHHHHHHHHHH-CCCHHHHHHHHHHHHHCC
Q ss_conf 01000134210014568999987522346667--------763-01011116899999988-299899999789776125
Q gi|254781172|r 522 TKIENILGFGDVSVTNLYDSINKRRNISLERF--------IFS-LGIRHVGAEIARSLAKY-YLSYQNFAQEINNIIAHN 591 (731)
Q Consensus 522 ~~l~~l~GfgeKsa~nL~~sIe~sK~~~L~r~--------L~A-LGI~~vG~~~Ak~La~~-f~si~~l~~~~~~~~~~~ 591 (731)
+++.+++|+|++.+++|.+=++.-+-..+..+ |.- ++|+|||.++|+.+-+. +.|++.+..+-+
T Consensus 48 ~~l~~ipGIG~~ia~kI~Eil~TG~~~~~e~~~~~~~~~~l~el~~I~GvGpk~a~~l~~~Gi~tl~dL~~a~~------ 121 (334)
T smart00483 48 KDLKGLPGIGDKIKKKIEEIIETGKSSKVLEILNDEVYKSLKLFTNVFGVGPKTAAKWYRKGIRTLEELKKNKE------ 121 (334)
T ss_pred HHHCCCCCCCHHHHHHHHHHHHCCCCHHHHHHHCCCCCHHHHHHHCCCCCCHHHHHHHHHCCCCCHHHHHHHHH------
T ss_conf 99727999878999999999984994899998728651689998538887789999999849887999998788------
Q ss_pred CCCHHHHHCCCCCCHHHHHHHHH
Q ss_conf 11778761388867899999999
Q gi|254781172|r 592 NDDWLSLIRVPLVGDIIAQAIVE 614 (731)
Q Consensus 592 ~~~~e~L~~I~GiG~~~A~si~~ 614 (731)
..|....++|-+.-+.+..
T Consensus 122 ----~~l~~~q~~Glk~~ed~~~ 140 (334)
T smart00483 122 ----LKLTKQQKAGLKYYEDILK 140 (334)
T ss_pred ----HHHHHHHHHHHHHHHHHHC
T ss_conf ----7678898876999999972
No 54
>TIGR00574 dnl1 DNA ligase I, ATP-dependent (dnl1); InterPro: IPR000977 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 , . ; GO: 0003910 DNA ligase (ATP) activity, 0005524 ATP binding, 0006260 DNA replication, 0006281 DNA repair, 0006310 DNA recombination.
Probab=96.83 E-value=0.038 Score=35.75 Aligned_cols=221 Identities=18% Similarity=0.145 Sum_probs=123.1
Q ss_pred CCCCCCHHHCCCHHHHHHHHHHHH-------HHHCCCCCCCCEEEEEEECCEEEEEEEE-ECCEEEEEEECCCCHHHHHH
Q ss_conf 664257021599999999999999-------8612467776119999415818999998-59989988865986556669
Q gi|254781172|r 92 SIPTLSLEKIWNIEDLRKFITRIY-------RFWQKKDDNSIFFTLEPKIDGTMITIRY-EKGKFVYAALRGDGHSGEDV 163 (731)
Q Consensus 92 ~~pMlSL~k~~~~~el~~w~~~~~-------~~~~~~~~~~~~~~vepKiDG~sisl~Y-~~G~L~~a~TRGdG~~GeDV 163 (731)
..|||+-.=.-..+.|..+.+|-. +-.+..+. .-.|.+|-|+||-=+-+++ .++. +.-.+| -||||
T Consensus 196 ~kPMLA~~~~~~~e~l~~~~~RkhemDPPYekkfqeLGL-e~~~~~E~KYDGeR~Q~Hkl~Gd~-~~~FSR----rlen~ 269 (705)
T TIGR00574 196 LKPMLAERAKSIEEALKKLGNRKHEMDPPYEKKFQELGL-EDKFLVEYKYDGERVQIHKLDGDE-VKIFSR----RLENI 269 (705)
T ss_pred CCCHHHHHCCCHHHHHHHCCCCCCCCCCCHHHHHHHCCC-CCCEEEEEECCCHHEEEEEEECCE-EEEEEE----CCCCH
T ss_conf 662047445774799984588724688853234655177-451587640451010012331884-899873----78640
Q ss_pred HHHHHHHC----C--CCCCCCCCCCCEEEEEEEEEEECHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHCC-C-----HHH
Q ss_conf 99775310----2--4322335445504899999985202123455643148543342345677775234-5-----555
Q gi|254781172|r 164 SACIRAIP----T--IPRVLSLNIPEIIEVRGEVYISKNDFLALNDEMIAVGRKPYANPRNAASGILRRL-N-----PTD 231 (731)
Q Consensus 164 T~n~~~i~----~--iP~~l~~~~~~~ieiRGEv~m~~~~F~~lN~~~~~~g~~~f~NpRN~aaG~lr~~-d-----~~~ 231 (731)
|+..-.+. . |+..++.+ ...+.|=||++.-...= |+.. |=-.....+|++ | -..
T Consensus 270 T~~~p~~~~~s~~~~~~~a~~~~-~~~~IldGE~va~D~~~----------g~~l---PFq~l~~r~~~k~dRqftt~~~ 335 (705)
T TIGR00574 270 TYQYPEILSESLTEFIKKAFPGD-IKSCILDGEMVAIDPET----------GKIL---PFQTLLTRAKRKYDRQFTTIDS 335 (705)
T ss_pred HHHCCCHHHHHHHHHHHHHCCCC-CCEEEEEEEEEEECCCC----------CCCC---CCCHHHHHHHHHHHHHHHHHHH
T ss_conf 22304214564488899745888-66179714678731145----------8216---6413301311112001355676
Q ss_pred --HHCCCEEE-EEEECCCCCCC--CCCCHHHHHHHHHCCCCCCC-CE-----EEE-ECCCCHHHHHHHHHHHHCCCCCCC
Q ss_conf --30111056-64102454332--10000368999975996654-14-----887-403211345566553100112343
Q gi|254781172|r 232 --ITRYLNFF-VHGLGKTSEIF--AKGQYEMLQKMRCLGFPVNN-GV-----RQA-NTFHGIVSYYNEMKSIRSTLPYDI 299 (731)
Q Consensus 232 --~~r~L~f~-ay~~~~~~~~~--~~~~~e~l~~L~~~GF~v~~-~~-----~~~-~~~~~~~~~~~~~~~~r~~l~y~i 299 (731)
..-.+.+| +|++.+.++.. ...-.++-+.|...==++.. .. ..+ ++.+++.+++++- +.-.+
T Consensus 336 ~~~~~~~~~fl~FD~LY~ng~~L~~~pL~~RR~~L~~i~~~~~nWr~~~~~~~~~~~~~ee~~~~l~~a------i~~g~ 409 (705)
T TIGR00574 336 MEKKVPVCLFLVFDILYLNGESLIDEPLIERREILESIVKPIPNWRIEIAEMIDVSDNVEELEKFLNEA------ISEGC 409 (705)
T ss_pred HHHHCCCEEEEEEEEEEECCCCCCCCCHHHHHHHHHHHCCCCCCEEEEEEEEEECCCCHHHHHHHHHHH------HHCCC
T ss_conf 752014024444656232780355677388999988753528881799974463127989999999999------96389
Q ss_pred CCEEEEECC---HHCCCCCCCCCCCCCCEEEECCCCCEEEEEEEEEE
Q ss_conf 763777311---00011158765686631231145621589987889
Q gi|254781172|r 300 DGLVYKVDE---FSLQKQLGERARSPRWMISHKFAEKQASTRLLDID 343 (731)
Q Consensus 300 DGiVikvn~---~~~q~~lG~ts~~PrwaiA~Kf~~e~~~T~v~~I~ 343 (731)
=|+|+|--. -.++- .+|.+.| +=+|..-.+...-=.|++
T Consensus 410 EGlm~K~~~p~~~~Y~p----g~R~~~w-~K~K~~Y~~~~~d~LDLv 451 (705)
T TIGR00574 410 EGLMVKDLEPDEAIYEP----GKRGWLW-LKFKPDYLEGMGDTLDLV 451 (705)
T ss_pred CEEEECCCCCCCCCCCC----CCCCCCC-EEEECCCCCCCCCEEEEE
T ss_conf 73897046879863147----7778875-033002366567510168
No 55
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=96.74 E-value=0.037 Score=35.89 Aligned_cols=73 Identities=27% Similarity=0.358 Sum_probs=51.5
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCHHHHHCCC
Q ss_conf 10001342100145689999875223466677630101111689999998829989999978977612511778761388
Q gi|254781172|r 523 KIENILGFGDVSVTNLYDSINKRRNISLERFIFSLGIRHVGAEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVP 602 (731)
Q Consensus 523 ~l~~l~GfgeKsa~nL~~sIe~sK~~~L~r~L~ALGI~~vG~~~Ak~La~~f~si~~l~~~~~~~~~~~~~~~e~L~~I~ 602 (731)
+-..|-||....-..++..+ +++.|||.++|-.+...+ +.+.+..++. +.+...|..++
T Consensus 56 d~~~LyGF~~~~Er~~F~~L--------------i~V~GIGpK~AL~ILs~~-~~~~l~~aI~------~~D~~~L~~vp 114 (198)
T PRK00116 56 DAQLLYGFLTKEERELFRLL--------------ISVSGVGPKLALAILSGL-SPEELAQAIA------NGDIKALTKVP 114 (198)
T ss_pred CCCEEEEECCHHHHHHHHHH--------------HCCCCCCHHHHHHHHCCC-CHHHHHHHHH------HCCHHHHCCCC
T ss_conf 88757840888999999998--------------566885789999887029-9999999998------58999970688
Q ss_pred CCCHHHHHHHHHHH
Q ss_conf 86789999999996
Q gi|254781172|r 603 LVGDIIAQAIVEFY 616 (731)
Q Consensus 603 GiG~~~A~si~~ff 616 (731)
|||+++|+.|+--+
T Consensus 115 GIG~KtA~rIi~EL 128 (198)
T PRK00116 115 GVGKKTAERIVLEL 128 (198)
T ss_pred CCCHHHHHHHHHHH
T ss_conf 97889999999999
No 56
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=96.69 E-value=0.0036 Score=43.71 Aligned_cols=54 Identities=22% Similarity=0.294 Sum_probs=48.0
Q ss_pred HCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCHHHHHCCCCCCHHHHHHHHHHHCCH
Q ss_conf 3010111168999999882998999997897761251177876138886789999999996697
Q gi|254781172|r 556 SLGIRHVGAEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVEFYQNP 619 (731)
Q Consensus 556 ALGI~~vG~~~Ak~La~~f~si~~l~~~~~~~~~~~~~~~e~L~~I~GiG~~~A~si~~ff~~~ 619 (731)
=.+||+||...|..|..+|+++.++..+ +..+|+.++|||++.|.-|..||..+
T Consensus 184 l~s~pgig~~~a~~ll~~fgS~~~~~ta----------s~~eL~~v~gig~k~A~~I~~~~~t~ 237 (254)
T COG1948 184 LESIPGIGPKLAERLLKKFGSVEDVLTA----------SEEELMKVKGIGEKKAREIYRFLRTE 237 (254)
T ss_pred HHCCCCCCHHHHHHHHHHHCCHHHHHHC----------CHHHHHHHCCCCHHHHHHHHHHHHCH
T ss_conf 9708996489999999985688877655----------99999774484688999999998344
No 57
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]
Probab=96.68 E-value=0.0054 Score=42.31 Aligned_cols=49 Identities=20% Similarity=0.219 Sum_probs=44.3
Q ss_pred CCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCHHHHHCCCCCCHHHHHHHHHHH
Q ss_conf 010111168999999882998999997897761251177876138886789999999996
Q gi|254781172|r 557 LGIRHVGAEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVEFY 616 (731)
Q Consensus 557 LGI~~vG~~~Ak~La~~f~si~~l~~~~~~~~~~~~~~~e~L~~I~GiG~~~A~si~~ff 616 (731)
.+|||||++..+.|.+||+++..+..+ +.++|..+ ||+...|+.|.++|
T Consensus 533 d~I~GiG~~r~~~LL~~Fgs~~~i~~A----------s~eel~~v-gi~~~~a~~i~~~~ 581 (581)
T COG0322 533 DDIPGIGPKRRKALLKHFGSLKGIKSA----------SVEELAKV-GISKKLAEKIYEAL 581 (581)
T ss_pred CCCCCCCHHHHHHHHHHHHCHHHHHHC----------CHHHHHHC-CCCHHHHHHHHHHC
T ss_conf 048886889999999983178888855----------99999874-99999999998529
No 58
>pfam03119 DNA_ligase_ZBD NAD-dependent DNA ligase C4 zinc finger domain. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilising either ATP or NAD(+) as a cofactor. This family is a small zinc binding motif that is presumably DNA binding. IT is found only in NAD dependent DNA ligases.
Probab=96.62 E-value=0.00092 Score=48.27 Aligned_cols=27 Identities=44% Similarity=1.015 Sum_probs=23.9
Q ss_pred CCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCHH
Q ss_conf 3265775010337865445210100354344114
Q gi|254781172|r 433 FCPICQSRVVRDLNPKTGKLVAAHRCTGGLACSA 466 (731)
Q Consensus 433 ~CP~Cgs~l~~~~~~~~~~~~~~~rC~n~~~Cpa 466 (731)
+||+||+++++..++ +++||+|. .|||
T Consensus 1 ~CP~C~s~l~r~~~e------v~~rC~n~-~CpA 27 (27)
T pfam03119 1 HCPVCGSPLVREEGE------VDIRCTNG-SCPA 27 (27)
T ss_pred CCCCCCCEEECCCCC------EEEECCCC-CCCC
T ss_conf 988898974856897------86888898-8879
No 59
>TIGR00084 ruvA Holliday junction DNA helicase RuvA; InterPro: IPR000085 In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction. The tetrameric DNA helicase RuvA specifically binds to the Holliday junction and facilitates the isomerization of the junction from the stacked folded configuration to the square-planar structure . In the RuvA tetramer, each subunit consists of three domains, I, II and III, where I and II form the major core that is responsible for Holliday junction binding and base pair rearrangements of Holliday junction executed at the crossover point, whereas domain III regulates branch migration through direct contact with RuvB.; GO: 0003678 DNA helicase activity, 0006281 DNA repair, 0006310 DNA recombination.
Probab=96.62 E-value=0.016 Score=38.66 Aligned_cols=138 Identities=17% Similarity=0.233 Sum_probs=71.6
Q ss_pred HHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCCCEEEEEHHHHCCHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHH
Q ss_conf 46655332130123103541035555653057654045410110106777531000100013421001456899998752
Q gi|254781172|r 467 QQLERLKHFVSRDAFNIEGLGKQQLDFFFKSEDPAFSIRIPADIFTLQRRQQTSTTKIENILGFGDVSVTNLYDSINKRR 546 (731)
Q Consensus 467 q~~~~i~hF~SK~aldI~GLG~k~Ie~L~e~~~~~g~I~~~~DLy~L~~~~~~~~~~l~~l~GfgeKsa~nL~~sIe~sK 546 (731)
|-.+-++|++-| .| -..++..||- + ++.....-+.+|+++.|.|.|.|=+|++++.
T Consensus 49 ~~~~~Ft~~~~R--ed----aNQi~~~LfG------F---------~~~~Er~lF~~Li~~nGvGpk~ALaiL~~~~--- 104 (217)
T TIGR00084 49 QKAQLFTHLVVR--ED----ANQILHLLFG------F---------NTLEERELFKELIKVNGVGPKLALAILSNMS--- 104 (217)
T ss_pred CCCEEEEEEEEE--CC----HHHHHHHHHC------C---------CCHHHHHHHHHHHHCCCCHHHHHHHHHCCCC---
T ss_conf 863467877776--04----6789999734------7---------9877899999985148802899999866788---
Q ss_pred HHHHHHHHHHCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCHHHHHCCCCCCHHHHHHHHHHHCCHHHHHHHH
Q ss_conf 23466677630101111689999998829989999978977612511778761388867899999999966979999999
Q gi|254781172|r 547 NISLERFIFSLGIRHVGAEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVEFYQNPRNICAVE 626 (731)
Q Consensus 547 ~~~L~r~L~ALGI~~vG~~~Ak~La~~f~si~~l~~~~~~~~~~~~~~~e~L~~I~GiG~~~A~si~~ff~~~~n~~~i~ 626 (731)
.+.+..+++ ..+...|.+++|||.|+|+.+.. .++..
T Consensus 105 ------------------------------~~~~~~ai~------~~~~~~L~k~pGvGKK~A~~l~~-------leL~g 141 (217)
T TIGR00084 105 ------------------------------PEEFVQAIE------TEEVKALVKIPGVGKKTAERLLA-------LELKG 141 (217)
T ss_pred ------------------------------HHHHHHHHH------HHHHHHHHCCCCCCHHHHHHHHH-------HHHHH
T ss_conf ------------------------------758988886------41044420458857378999987-------77545
Q ss_pred HHHHHCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCH-HHHHHHHHHCCCEEE
Q ss_conf 9997338776543224688216866999725889987-899999998298499
Q gi|254781172|r 627 ALLKEVSPSIGRHEKNVSSEIENKKLVFTGTLQKIQR-HKAQEYVTQLGAVVS 678 (731)
Q Consensus 627 ~L~~~~~~~~~~~~~~~~~~l~gk~vV~TGtl~~~~R-~e~~~~ie~~Ggkv~ 678 (731)
++........... ..+ ++.-..=-.|- -.| +|+.+.|.++|++-.
T Consensus 142 k~~~~~~~~~~~~--~~~-~~~~~~~~~~~----~~~y~E~~~aL~sLGY~~~ 187 (217)
T TIGR00084 142 KLKGVKNLEMFTN--LAN-HLETDEKLTAE----AARYDELFEALVSLGYKPQ 187 (217)
T ss_pred HHCCCCCCCCCCC--CCC-CCCCCCHHHHH----HHHHHHHHHHHHHCCCCHH
T ss_conf 4405521124554--335-33554101210----2118899999997298888
No 60
>TIGR00575 dnlj DNA ligase, NAD-dependent; InterPro: IPR001679 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 family is predominantly composed of NAD-dependent bacterial DNA ligases. They 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.; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair.
Probab=96.46 E-value=0.00035 Score=51.51 Aligned_cols=161 Identities=19% Similarity=0.262 Sum_probs=76.4
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHHHHHHHHH--HH--CCHHH-HHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCHHHH-
Q ss_conf 001342100145689999875223466677--63--01011-1168999999882998999997897761251177876-
Q gi|254781172|r 525 ENILGFGDVSVTNLYDSINKRRNISLERFI--FS--LGIRH-VGAEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSL- 598 (731)
Q Consensus 525 ~~l~GfgeKsa~nL~~sIe~sK~~~L~r~L--~A--LGI~~-vG~~~Ak~La~~f~si~~l~~~~~~~~~~~~~~~e~L- 598 (731)
+.++|+|+|.++.|++.=--..-.+|.+|= .. |++++ +|++.|+.|.+. |+ ..+...+.+|
T Consensus 455 mdI~GLG~~~I~~LfE~~Lv~~~~DLY~L~~k~~~Ll~le~~~g~~sa~nLl~a----------Ie---~sK~~pl~RlL 521 (706)
T TIGR00575 455 MDIDGLGEKVIEQLFEEKLVRSVADLYALKEKLEDLLELEGKFGEKSAQNLLSA----------IE---KSKKKPLARLL 521 (706)
T ss_pred CCCCCCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH----------HH---HHHHHHHHHHH
T ss_conf 332222389999998726667856665778899998706403556889999999----------99---85210489999
Q ss_pred --HCCCCCCHHHHHHHHHHHCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCHHHHHHHHHHCCCE
Q ss_conf --138886789999999996697999999999973387765432246882168669997258899878999999982984
Q gi|254781172|r 599 --IRVPLVGDIIAQAIVEFYQNPRNICAVEALLKEVSPSIGRHEKNVSSEIENKKLVFTGTLQKIQRHKAQEYVTQLGAV 676 (731)
Q Consensus 599 --~~I~GiG~~~A~si~~ff~~~~n~~~i~~L~~~~~~~~~~~~~~~~~~l~gk~vV~TGtl~~~~R~e~~~~ie~~Ggk 676 (731)
+.|++||+.+|+.+...|.. +++|.++..- . ..+ +| .|.|.++. .++..|.+
T Consensus 522 ~aLGIr~VG~~~A~~La~~f~t------l~~L~~A~~e------~-~~~--------~~----~f~~s~L~-~~~g~G~~ 575 (706)
T TIGR00575 522 FALGIRHVGEVTAKLLAKHFGT------LDKLKAASLE------T-LES--------IY----QFDRSELL-SVEGVGPK 575 (706)
T ss_pred HHCCCHHHHHHHHHHHHHHCCC------HHHHHHCCHH------H-HHH--------HH----HHCCHHHH-HCCCCHHH
T ss_conf 8628603579999999985588------6899850821------6-778--------87----51605564-10140278
Q ss_pred EEEEEECCEEEEEEC----CCCCCHHHHHHHCCCEEECHHHHHHHHHHHCCC
Q ss_conf 998111632179977----888863798997499173799999999882865
Q gi|254781172|r 677 VSAILSRKTDIIIVG----DNPGSKLEKAQQLGVKIMNEEQFLFLLQQYNTT 724 (731)
Q Consensus 677 v~sSVSkkT~~LI~g----e~~gSKl~KA~~LgI~Ii~e~ef~~ll~~~~~~ 724 (731)
|..||..-=..-... =.+..++++=+++|+.+.++++|.+||.+-..+
T Consensus 576 vA~~~~~~F~~~~~~~~qPYRta~~~~~L~~~gv~~~~~D~~~~LL~~~~~~ 627 (706)
T TIGR00575 576 VAESIVNFFHDPNNLSLQPYRTAELIEKLEELGVNMESEDEFCRLLDQALKE 627 (706)
T ss_pred HHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 9999999871200013560468999999988316310113578777642011
No 61
>PRK01172 ski2-like helicase; Provisional
Probab=96.45 E-value=0.018 Score=38.37 Aligned_cols=51 Identities=25% Similarity=0.232 Sum_probs=39.2
Q ss_pred HHHCCHHHHHHHHHHHHHHH-CCCHHHHHHHHHHHHHCCCCCHHHHHCCCCCCHHHHHHHHH
Q ss_conf 76301011116899999988-29989999978977612511778761388867899999999
Q gi|254781172|r 554 IFSLGIRHVGAEIARSLAKY-YLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVE 614 (731)
Q Consensus 554 L~ALGI~~vG~~~Ak~La~~-f~si~~l~~~~~~~~~~~~~~~e~L~~I~GiG~~~A~si~~ 614 (731)
+-=.-||+||...|+.|.++ |.|+..+.. ++.++|..|.|+|++.|++|++
T Consensus 612 l~L~~I~gigr~RAR~Ly~aG~~s~~dia~----------a~~~~L~~i~g~~~~~A~~Ii~ 663 (674)
T PRK01172 612 IDLVLIPKVGRVRARRLYDAGFKTVDDIAR----------SSPERIKKIYGFSDTLANAIVN 663 (674)
T ss_pred HHHCCCCCCCHHHHHHHHHCCCCCHHHHHH----------CCHHHHHHCCCCCHHHHHHHHH
T ss_conf 977188999989999999869999999970----------9998987641989999999999
No 62
>PRK07997 consensus
Probab=96.41 E-value=0.027 Score=36.90 Aligned_cols=83 Identities=16% Similarity=0.117 Sum_probs=40.1
Q ss_pred HHHHHHHCCCCC------CCHHHHHHHHHHHHHHHHHCCHHHC-CCCCCCCCCCCCCCC---------CCC----CCEE-
Q ss_conf 998433177982------0878999999999999897720311-589999620036432---------357----7504-
Q gi|254781172|r 31 HDDCYYQYSKPI------ILDSEYDALKRRCDAIAHAFPDLAR-SEDPNGPLNKIGGEM---------NLS----LFKV- 89 (731)
Q Consensus 31 ~~~~Yy~~~~p~------isD~eYD~L~~~L~~le~~~p~~~~-~~~p~spt~~Vg~~~---------~~~----~~kv- 89 (731)
.-++||.. .|. =+.+.|-.+---++.++...|+++. ..|...||.|----+ ..+ +.-+
T Consensus 18 ifRAfyAl-~~l~~s~G~pTnAi~GF~~mL~kli~~~~P~~iavaFD~~~~TFR~e~y~~YKA~R~~~PedL~~Qip~i~ 96 (928)
T PRK07997 18 LYRAYHAF-PPLTNSAGEPTGAMYGVLNMLRSLIMQYKPTHAAVVFDAKGKTFRDELFEHYKSHRPPMPDDLRAQIEPLH 96 (928)
T ss_pred HHHHHCCC-CCCCCCCCCEECHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCCCHHHHHHHCCCCCCCCHHHHHHHHHHH
T ss_conf 99998078-86779989662079999999999998649987999980889960343305652899999878999999999
Q ss_pred ----ECCCCCCCHHHCCCHHHHHHHHHHHH
Q ss_conf ----51664257021599999999999999
Q gi|254781172|r 90 ----THSIPTLSLEKIWNIEDLRKFITRIY 115 (731)
Q Consensus 90 ----~H~~pMlSL~k~~~~~el~~w~~~~~ 115 (731)
..-+|.++++. |--||+..=+.+..
T Consensus 97 e~l~a~gIp~~~~~G-yEADDiIgTla~~~ 125 (928)
T PRK07997 97 AMVKAMGLPLLAVSG-VEADDVIGTLAREA 125 (928)
T ss_pred HHHHHCCCCEECCCC-CCHHHHHHHHHHHH
T ss_conf 999987998855589-24999999999999
No 63
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=96.21 E-value=0.025 Score=37.13 Aligned_cols=53 Identities=25% Similarity=0.384 Sum_probs=35.1
Q ss_pred CHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCHHHHHCCCCCCHHHHHHHHHHHC
Q ss_conf 101111689999998829989999978977612511778761388867899999999966
Q gi|254781172|r 558 GIRHVGAEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVEFYQ 617 (731)
Q Consensus 558 GI~~vG~~~Ak~La~~f~si~~l~~~~~~~~~~~~~~~e~L~~I~GiG~~~A~si~~ff~ 617 (731)
++.|||.++|-.|.+.+ +.+.+..++. ..++..|.++||||.|+|+.++--+.
T Consensus 77 sVnGIGpK~ALaiLs~~-~~~~l~~aI~------~~d~~~L~k~PGIGkKtAerivleLk 129 (201)
T COG0632 77 SVNGIGPKLALAILSNL-DPEELAQAIA------NEDVKALSKIPGIGKKTAERIVLELK 129 (201)
T ss_pred CCCCCCHHHHHHHHCCC-CHHHHHHHHH------HCCHHHHHCCCCCCHHHHHHHHHHHH
T ss_conf 11880589999998489-9999999998------32867644189877889999999976
No 64
>PRK08609 hypothetical protein; Provisional
Probab=96.15 E-value=0.0025 Score=44.85 Aligned_cols=10 Identities=70% Similarity=0.843 Sum_probs=3.8
Q ss_pred HHHHHHCCCE
Q ss_conf 7989974991
Q gi|254781172|r 698 LEKAQQLGVK 707 (731)
Q Consensus 698 l~KA~~LgI~ 707 (731)
+..|++.|++
T Consensus 511 ~~~A~~~gv~ 520 (570)
T PRK08609 511 LKKAQAAGVK 520 (570)
T ss_pred HHHHHHCCCE
T ss_conf 9999986996
No 65
>PRK13901 ruvA Holliday junction DNA helicase motor protein; Provisional
Probab=96.08 E-value=0.024 Score=37.36 Aligned_cols=74 Identities=19% Similarity=0.354 Sum_probs=52.0
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCHHHHHCC
Q ss_conf 01000134210014568999987522346667763010111168999999882998999997897761251177876138
Q gi|254781172|r 522 TKIENILGFGDVSVTNLYDSINKRRNISLERFIFSLGIRHVGAEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRV 601 (731)
Q Consensus 522 ~~l~~l~GfgeKsa~nL~~sIe~sK~~~L~r~L~ALGI~~vG~~~Ak~La~~f~si~~l~~~~~~~~~~~~~~~e~L~~I 601 (731)
++-..|-||..+.-..++..+ +.+.|||.++|-.+...+ +.+.+..++. ..+...|..+
T Consensus 54 Ed~~~LyGF~~~~Er~~F~~L--------------isVsGIGpk~Al~iLs~~-~~~~l~~aI~------~~D~~~L~~v 112 (196)
T PRK13901 54 EDELKLFGFLNSSEREVFEEL--------------IGVDGIGPRAALRVLSGI-KYNEFRDAID------REDIELISKV 112 (196)
T ss_pred ECCCEEECCCCHHHHHHHHHH--------------HCCCCCCHHHHHHHHCCC-CHHHHHHHHH------HCCHHHHHHC
T ss_conf 167713365988999999998--------------765882689999997579-9999999999------2899998319
Q ss_pred CCCCHHHHHHHHHHH
Q ss_conf 886789999999996
Q gi|254781172|r 602 PLVGDIIAQAIVEFY 616 (731)
Q Consensus 602 ~GiG~~~A~si~~ff 616 (731)
+|||+++|+.|+--+
T Consensus 113 pGIG~KtA~rIi~EL 127 (196)
T PRK13901 113 KGIGNKMAGKIFLKL 127 (196)
T ss_pred CCCCHHHHHHHHHHH
T ss_conf 995899999999999
No 66
>PRK07898 consensus
Probab=95.96 E-value=0.019 Score=38.07 Aligned_cols=48 Identities=8% Similarity=0.081 Sum_probs=26.4
Q ss_pred HHHHHHHCC-CCC------CCHHHHHHHHHHHHHHHHHCCHHHC-CCCCCCCCCCC
Q ss_conf 998433177-982------0878999999999999897720311-58999962003
Q gi|254781172|r 31 HDDCYYQYS-KPI------ILDSEYDALKRRCDAIAHAFPDLAR-SEDPNGPLNKI 78 (731)
Q Consensus 31 ~~~~Yy~~~-~p~------isD~eYD~L~~~L~~le~~~p~~~~-~~~p~spt~~V 78 (731)
.-++||..- .|. =+.+.|-.+---++.++...|+++. ..|.-.||.|-
T Consensus 26 ~fRAy~Al~~~~l~~~~G~pTnAi~GF~~ml~kli~~~~P~~iavaFD~~~~TFRh 81 (902)
T PRK07898 26 AFRAFYALPAENFSTSGGQTTNAVYGFTAMLINLLRDEQPTHVAVAFDVSRQTFRT 81 (902)
T ss_pred HHHHHCCCCCCCCCCCCCCEECHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCCCH
T ss_conf 99997169976683999987025999999999999873998899999795996031
No 67
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=95.94 E-value=0.018 Score=38.34 Aligned_cols=56 Identities=13% Similarity=0.075 Sum_probs=29.4
Q ss_pred HCCHHHHHHHHHHHHHHHCC--CHHHHHHHHHHHHHCCCCCHHHHHCCCCCCHHHHHHHHH
Q ss_conf 30101111689999998829--989999978977612511778761388867899999999
Q gi|254781172|r 556 SLGIRHVGAEIARSLAKYYL--SYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVE 614 (731)
Q Consensus 556 ALGI~~vG~~~Ak~La~~f~--si~~l~~~~~~~~~~~~~~~e~L~~I~GiG~~~A~si~~ 614 (731)
..+|||||++.|+.|...+. .+..+... +.......+.+|++|+|+||++|..+.+
T Consensus 50 l~~ipGIG~~ia~kI~Eil~TG~~~~~e~~---~~~~~~~~l~el~~I~GvGpk~a~~l~~ 107 (334)
T smart00483 50 LKGLPGIGDKIKKKIEEIIETGKSSKVLEI---LNDEVYKSLKLFTNVFGVGPKTAAKWYR 107 (334)
T ss_pred HCCCCCCCHHHHHHHHHHHHCCCCHHHHHH---HCCCCCHHHHHHHCCCCCCHHHHHHHHH
T ss_conf 727999878999999999984994899998---7286516899985388877899999998
No 68
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=95.63 E-value=0.036 Score=35.93 Aligned_cols=58 Identities=19% Similarity=0.202 Sum_probs=47.4
Q ss_pred HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCHHHHHCCCCCCHHHHHHHHHHHCCHHHHHHHH
Q ss_conf 01111689999998829989999978977612511778761388867899999999966979999999
Q gi|254781172|r 559 IRHVGAEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVEFYQNPRNICAVE 626 (731)
Q Consensus 559 I~~vG~~~Ak~La~~f~si~~l~~~~~~~~~~~~~~~e~L~~I~GiG~~~A~si~~ff~~~~n~~~i~ 626 (731)
||.+-......|.++|+++++++.+ +.++|.+|+|||+.-|.+|.+.++--.+...++
T Consensus 292 iprlp~~vie~lV~~Fg~L~~ll~A----------s~eeL~~VeGIGe~RAr~IregL~Rl~e~~~~~ 349 (352)
T PRK13482 292 IPRLPSAVIENLVKHFGTLQGLLEA----------SIEDLDDVEGIGEVRARAIREGLSRLAEQLILD 349 (352)
T ss_pred CCCCCHHHHHHHHHHHCCHHHHHHC----------CHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf 9999999999999985279999868----------998886567967999999999999999988776
No 69
>TIGR01448 recD_rel helicase, RecD/TraA family; InterPro: IPR006345 These sequences represent a family similar to RecD, the exodeoxyribonuclease V alpha chain of IPR006344 from INTERPRO. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD. .
Probab=95.61 E-value=0.057 Score=34.39 Aligned_cols=129 Identities=18% Similarity=0.216 Sum_probs=81.2
Q ss_pred HHHHH-HHHHHHCCCCCHHHHHHHHHHHHHCCCCCCEEEEEHHHHCCHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHH
Q ss_conf 46655-33213012310354103555565305765404541011010677753100010001342100145689999875
Q gi|254781172|r 467 QQLER-LKHFVSRDAFNIEGLGKQQLDFFFKSEDPAFSIRIPADIFTLQRRQQTSTTKIENILGFGDVSVTNLYDSINKR 545 (731)
Q Consensus 467 q~~~~-i~hF~SK~aldI~GLG~k~Ie~L~e~~~~~g~I~~~~DLy~L~~~~~~~~~~l~~l~GfgeKsa~nL~~sIe~s 545 (731)
+..+. +.||-| =.|+|+|+++..++++.- | =..+.+| ...-+.|.+++|.+++.-..+..++.+.
T Consensus 84 ~~~~gi~~Yl~S---~~~KGvGk~~Aq~Iv~Tf---G-e~~~~~l-------~~~P~kL~~V~G~s~~~~~~~~~~~~~~ 149 (769)
T TIGR01448 84 TSKEGIVAYLSS---SSIKGVGKKLAQRIVETF---G-EAAIDVL-------DDDPEKLLEVSGISKANLEKIVSQLSKQ 149 (769)
T ss_pred CHHHHHHHHHHC---CCCCCCCHHHHHHHHHHH---H-HHHHHHH-------HCCCHHEEEECCCCHHHHHHHHHHHHHH
T ss_conf 506787655522---541672057789999987---6-9999887-------4086010330775667789999999975
Q ss_pred HH-HHHHHHHHHCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCHHHHHC-CCCCCHHHHHHHHHHH
Q ss_conf 22-34666776301011116899999988299899999789776125117787613-8886789999999996
Q gi|254781172|r 546 RN-ISLERFIFSLGIRHVGAEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIR-VPLVGDIIAQAIVEFY 616 (731)
Q Consensus 546 K~-~~L~r~L~ALGI~~vG~~~Ak~La~~f~si~~l~~~~~~~~~~~~~~~e~L~~-I~GiG~~~A~si~~ff 616 (731)
+. ..+=-+|+.|| +|..-|..+.++|..-+-..+.++. -..+.-.|.+ |.|||=.+|+++-.-+
T Consensus 150 ~~~~~~l~~L~~lG---~~~~l~~~~~k~y~eadP~~dtLd~----v~~~Py~L~~d~~GiGF~~AD~lA~~l 215 (769)
T TIGR01448 150 KDERKLLLKLQQLG---IGIKLALRIYKFYREADPQADTLDV----VEKDPYLLAEDVKGIGFKTADQLAEEL 215 (769)
T ss_pred HHHHHHHHHHHHCC---CCHHHHHHHHHHHCCCCCCCCHHHH----HHCCHHHHHHHHCCCCHHHHHHHHHHC
T ss_conf 58999999998538---7678999999984035872116888----621720136751374056899999971
No 70
>PRK08928 consensus
Probab=95.61 E-value=0.057 Score=34.43 Aligned_cols=47 Identities=17% Similarity=0.228 Sum_probs=24.0
Q ss_pred HHHHHHHCCCCC------CCHHHHHHHHHHHHHHHHHCCHHHC-CCCCCCCCCCC
Q ss_conf 998433177982------0878999999999999897720311-58999962003
Q gi|254781172|r 31 HDDCYYQYSKPI------ILDSEYDALKRRCDAIAHAFPDLAR-SEDPNGPLNKI 78 (731)
Q Consensus 31 ~~~~Yy~~~~p~------isD~eYD~L~~~L~~le~~~p~~~~-~~~p~spt~~V 78 (731)
.-++||... |. -+.+.|-.+---++.+....|+++. ..|...||.|-
T Consensus 16 ~fRAf~Al~-~l~t~~G~pTnAi~GF~~mL~~~~~~~~P~~~~v~fD~~~~TFR~ 69 (861)
T PRK08928 16 LFRAYYALQ-PLTTSKGEPIGGVYGFINMLLKLLSDFKPDYLAVVFDSGGKNFRH 69 (861)
T ss_pred HHHHHCCCC-CCCCCCCCEECHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCCCH
T ss_conf 999980799-887999988244999999999999863998899999795996224
No 71
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=95.56 E-value=0.0091 Score=40.56 Aligned_cols=58 Identities=21% Similarity=0.388 Sum_probs=43.1
Q ss_pred CCCCHHHHHHHHHHHHHCCCCCCEEEEEHHHHCCHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHH
Q ss_conf 2310354103555565305765404541011010677753100010001342100145689999875
Q gi|254781172|r 479 DAFNIEGLGKQQLDFFFKSEDPAFSIRIPADIFTLQRRQQTSTTKIENILGFGDVSVTNLYDSINKR 545 (731)
Q Consensus 479 ~aldI~GLG~k~Ie~L~e~~~~~g~I~~~~DLy~L~~~~~~~~~~l~~l~GfgeKsa~nL~~sIe~s 545 (731)
.-|.+.|+|++.|..||..- .|++..+|-. .-. .-.+..+.|||+||+.+|+.+|...
T Consensus 94 ~Ll~v~GlGpkKi~~Ly~el----gi~~~e~l~~---a~~--~~~~~~l~GfG~kse~~il~~i~~~ 151 (326)
T COG1796 94 PLLKVPGLGPKKIVSLYKEL----GIKDLEELQE---ALE--NGKIRGLRGFGKKSEAKILENIEFA 151 (326)
T ss_pred HHHHCCCCCCHHHHHHHHHH----CCCCHHHHHH---HHH--HCCCCCCCCCCCHHHHHHHHHHHHH
T ss_conf 78607798928899999997----8664999999---998--4770326785602199999999997
No 72
>pfam09513 consensus
Probab=95.54 E-value=0.24 Score=29.56 Aligned_cols=156 Identities=17% Similarity=0.045 Sum_probs=73.2
Q ss_pred CCCEEEEEEECCEEEEEEEE-------ECCEEEEEEECCCCHHH---HHHHHHHHHHCCCC-------CCCCCCCCCEEE
Q ss_conf 76119999415818999998-------59989988865986556---66999775310243-------223354455048
Q gi|254781172|r 124 NSIFFTLEPKIDGTMITIRY-------EKGKFVYAALRGDGHSG---EDVSACIRAIPTIP-------RVLSLNIPEIIE 186 (731)
Q Consensus 124 ~~~~~~vepKiDG~sisl~Y-------~~G~L~~a~TRGdG~~G---eDVT~n~~~i~~iP-------~~l~~~~~~~ie 186 (731)
....|.++-|+||.|++.-| ..|+.-- -+|. =..- .++=..+....++| .++.. ....+.
T Consensus 164 ~~~~~~vTeKLdGtS~tvy~v~~~~~~~~g~~Gv-csrn-l~l~~~~~n~~W~~a~~~~i~~~~~~l~~~l~~-~~~nia 240 (356)
T pfam09513 164 IGEEVVVTEKLHGTSITVFNTPERRKVLVWSKGV-CSRN-LVLPEDADNVYWKAAENKNLKAQANHLQRRLKL-IDGGVA 240 (356)
T ss_pred CCCEEEEEEEECCEEEEEEEECCCCCCCCCEEEE-EECC-EECCCCCCCHHHHHHHHCCHHHHHHHHHHHHHH-CCCCEE
T ss_conf 9947999997547158999945755542433676-0166-771468875799998860617788777777640-388569
Q ss_pred EEEEEEEECHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCHHHHHCCCEEEEEEECCCCCCCCCCCHHHHH-HHHHCC
Q ss_conf 9999998520212345564314854334234567777523455553011105664102454332100003689-999759
Q gi|254781172|r 187 VRGEVYISKNDFLALNDEMIAVGRKPYANPRNAASGILRRLNPTDITRYLNFFVHGLGKTSEIFAKGQYEMLQ-KMRCLG 265 (731)
Q Consensus 187 iRGEv~m~~~~F~~lN~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~r~L~f~ay~~~~~~~~~~~~~~e~l~-~L~~~G 265 (731)
|.||+|=+.= =.|+=++. ..+...|++|.+-..+....-++.+.+. +.+.+|
T Consensus 241 iQGElvGpgI----------------QgN~~~~~-----------~~~~~~f~~F~v~dI~~~~~~~~~~~~~~~~~~lg 293 (356)
T pfam09513 241 IQGELVGPGI----------------QGNYLNYG-----------KNGDAHFLVFRVFDIDSQRRATDLEWGDALCRQLG 293 (356)
T ss_pred EEEEEECCCC----------------CCCCCCCC-----------CCCCCEEEEEEEEECCCCCCCCHHHHHHHHHHHCC
T ss_conf 9988867776----------------67753466-----------67884179999998247653584899999998679
Q ss_pred CCCCCCEEEEECCCCHHHHHHHHHHHHCCC----CCCCCCEEEEECCHHC
Q ss_conf 966541488740321134556655310011----2343763777311000
Q gi|254781172|r 266 FPVNNGVRQANTFHGIVSYYNEMKSIRSTL----PYDIDGLVYKVDEFSL 311 (731)
Q Consensus 266 F~v~~~~~~~~~~~~~~~~~~~~~~~r~~l----~y~iDGiVikvn~~~~ 311 (731)
.+++|..- .....++...+..+.. +.+. .+.=-|||+|-.+-..
T Consensus 294 l~~VPvlg-y~~~~~~~~~~~~~~~-~~~~~~~~~~~REGiVirs~~~~~ 341 (356)
T pfam09513 294 LKTVPVLG-YSGPFDIARVREDMGG-GATVSGSGKHIREGVVIKSVDTRF 341 (356)
T ss_pred CCEEEECC-CCCCCHHHHHHHHHHC-CCCCCCCCCCEEEEEEEEECCCCC
T ss_conf 86024646-2246228789987534-454358887332149983255554
No 73
>KOG1929 consensus
Probab=95.50 E-value=0.036 Score=35.99 Aligned_cols=79 Identities=22% Similarity=0.309 Sum_probs=63.2
Q ss_pred CCCCCCCCEEEEECCCCCCCHHHHHHHHHHCCCEEEEEEECCEEEEEECCCCCCHHHHHHHCCCEEECHHHHHHHHHHHC
Q ss_conf 68821686699972588998789999999829849981116321799778888637989974991737999999998828
Q gi|254781172|r 643 VSSEIENKKLVFTGTLQKIQRHKAQEYVTQLGAVVSAILSRKTDIIIVGDNPGSKLEKAQQLGVKIMNEEQFLFLLQQYN 722 (731)
Q Consensus 643 ~~~~l~gk~vV~TGtl~~~~R~e~~~~ie~~Ggkv~sSVSkkT~~LI~ge~~gSKl~KA~~LgI~Ii~e~ef~~ll~~~~ 722 (731)
...+|.|.+|++.+.=. ..|+-+-..+...|+.+......+...|+.....|||+.-|.+-+||+.+.+.+.......+
T Consensus 490 l~~~~e~~~~~~s~~~~-~~~e~ln~~~~~~gas~~~~f~r~~~~l~~~~~k~s~~~~~~kw~ip~vT~~wL~e~~rq~~ 568 (811)
T KOG1929 490 LSQPFENLTISNSQSAE-AEREKLNNLANDLGASNVKTFTRKSTTLLTTSAKGSKYEIAGKWSIPIVTPDWLYECVRQNK 568 (811)
T ss_pred CCCCCCCCEEEEEECHH-HHHHHHHHHHHHCCCCCCCEEEECCCEEECCCCCCCHHHHCCCCCCCCCCHHHHHHHCCCCC
T ss_conf 66666672688651518-88888767666506652330121441786344455543313666787557558875033567
No 74
>PRK00254 ski2-like helicase; Provisional
Probab=95.36 E-value=0.024 Score=37.37 Aligned_cols=50 Identities=20% Similarity=0.317 Sum_probs=38.8
Q ss_pred CCHHHHHHHHHHHHHHH-CCCHHHHHHHHHHHHHCCCCCHHHHHCCCCCCHHHHHHHHHHH
Q ss_conf 01011116899999988-2998999997897761251177876138886789999999996
Q gi|254781172|r 557 LGIRHVGAEIARSLAKY-YLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVEFY 616 (731)
Q Consensus 557 LGI~~vG~~~Ak~La~~-f~si~~l~~~~~~~~~~~~~~~e~L~~I~GiG~~~A~si~~ff 616 (731)
..||+||...|+.|-++ |.|+..+. +++..+|..|+|||+++|++|.+..
T Consensus 647 ~~I~gvgr~RAR~Ly~aGi~s~~~ia----------~A~p~~l~~i~g~g~~~a~~i~~~~ 697 (717)
T PRK00254 647 MELPMIGRKRARALYNAGFRDLEDIM----------NAKPSELLAVEGIGAKIVEGIFKHL 697 (717)
T ss_pred CCCCCCCHHHHHHHHHCCCCCHHHHH----------CCCHHHEECCCCCCHHHHHHHHHHH
T ss_conf 64899898999999986999999996----------5999990302372789999999983
No 75
>PRK05797 consensus
Probab=95.23 E-value=0.12 Score=31.95 Aligned_cols=46 Identities=15% Similarity=0.237 Sum_probs=24.2
Q ss_pred HHHHHHCCCCC------CCHHHHHHHHHHHHHHHHHCCHHHC-CCCCCCCCCCC
Q ss_conf 98433177982------0878999999999999897720311-58999962003
Q gi|254781172|r 32 DDCYYQYSKPI------ILDSEYDALKRRCDAIAHAFPDLAR-SEDPNGPLNKI 78 (731)
Q Consensus 32 ~~~Yy~~~~p~------isD~eYD~L~~~L~~le~~~p~~~~-~~~p~spt~~V 78 (731)
-++||... |. -+-+.|-.+---++.++...|+++. ..|...||.|-
T Consensus 15 ~Ra~~a~~-~l~~~~G~pt~ai~Gf~~~l~~~~~~~~p~~~~v~fD~~~~tfR~ 67 (869)
T PRK05797 15 NRAFYALP-PLTNSEGIHTNAIYGFTNMLLKMKEEIKPDYIVVAFDKKAPTFRH 67 (869)
T ss_pred HHHHCCCC-CCCCCCCCEECHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCCCH
T ss_conf 99980799-888998987054999999999999873998899998593996042
No 76
>TIGR02236 recomb_radA DNA repair and recombination protein RadA; InterPro: IPR011938 This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA, eukaryotic RAD51 (IPR011941 from INTERPRO), and archaeal RadB (IPR011939 from INTERPRO). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein .; GO: 0003684 damaged DNA binding, 0005524 ATP binding, 0008094 DNA-dependent ATPase activity, 0006281 DNA repair, 0006310 DNA recombination.
Probab=95.04 E-value=0.025 Score=37.14 Aligned_cols=153 Identities=16% Similarity=0.219 Sum_probs=85.9
Q ss_pred CHHHHHHHHHHHHHCCCCCCEEEEEHHHHCCHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHH-HHHHHHHHHCCHH
Q ss_conf 035410355556530576540454101101067775310001000134210014568999987522-3466677630101
Q gi|254781172|r 482 NIEGLGKQQLDFFFKSEDPAFSIRIPADIFTLQRRQQTSTTKIENILGFGDVSVTNLYDSINKRRN-ISLERFIFSLGIR 560 (731)
Q Consensus 482 dI~GLG~k~Ie~L~e~~~~~g~I~~~~DLy~L~~~~~~~~~~l~~l~GfgeKsa~nL~~sIe~sK~-~~L~r~L~ALGI~ 560 (731)
|+.|+||.|-+||-|+||. ++...=-.+..+|....|.+|..|.+++++ +|. ..+..|..|.-.-
T Consensus 4 dLPGVGp~TA~KL~EaGy~-----------t~~~iA~A~~~EL~~~~gI~E~~A~kiI~A---AR~a~~~~~F~~a~~vl 69 (333)
T TIGR02236 4 DLPGVGPATAEKLREAGYD-----------TLEAIAVASPKELSEIAGIGEGTAAKIIQA---ARKAADLGGFETADDVL 69 (333)
T ss_pred CCCCCCHHHHHHHHHHHHH-----------HHHHHHCCCHHHHHHHCCCCHHHHHHHHHH---HHHHHCCCCCHHHHHHH
T ss_conf 5789757688998861078-----------899984458579532037877789999999---99984676721489999
Q ss_pred HHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCHHHHHCCCCCCHHHHHHHHHHHC---CHHHHHHHHHHHHHCCCC--
Q ss_conf 111689999998829989999978977612511778761388867899999999966---979999999999733877--
Q gi|254781172|r 561 HVGAEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVEFYQ---NPRNICAVEALLKEVSPS-- 635 (731)
Q Consensus 561 ~vG~~~Ak~La~~f~si~~l~~~~~~~~~~~~~~~e~L~~I~GiG~~~A~si~~ff~---~~~n~~~i~~L~~~~~~~-- 635 (731)
-=++.-+.|+.-..++|.++ | |-+=.++|-++|- .=+ .++..+| ++.++
T Consensus 70 -~rR~~v~kitTgs~~LDeLL---------------------G-GGiETqaiTE~~GEFGSGK-TQ~~HqL--AVnVQlP 123 (333)
T TIGR02236 70 -ERRKSVGKITTGSKELDELL---------------------G-GGIETQAITEVFGEFGSGK-TQICHQL--AVNVQLP 123 (333)
T ss_pred -HHHHCCCEEECCCHHHHHHC---------------------C-CCCCCEEEEEEEEEECCCH-HHHHHHH--HHHHCCC
T ss_conf -98720750444863676560---------------------7-9600005888771007865-7876676--5532287
Q ss_pred ---CCCCCCCCCCCCCCCEEEEECCCCCCCHHHHHHHHH--HCC
Q ss_conf ---654322468821686699972588998789999999--829
Q gi|254781172|r 636 ---IGRHEKNVSSEIENKKLVFTGTLQKIQRHKAQEYVT--QLG 674 (731)
Q Consensus 636 ---~~~~~~~~~~~l~gk~vV~TGtl~~~~R~e~~~~ie--~~G 674 (731)
+..++....+-|.|-++||==|=..||=.-++++.+ ..|
T Consensus 124 ~flfydeeave~GGL~gp~av~IDTEnTFRPERI~qmA~GL~~g 167 (333)
T TIGR02236 124 EFLFYDEEAVEKGGLEGPKAVYIDTENTFRPERIEQMAKGLARG 167 (333)
T ss_pred CHHHCCCHHHCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHH
T ss_conf 11210110001477678768998559798625799999863111
No 77
>PRK08076 consensus
Probab=94.93 E-value=0.1 Score=32.50 Aligned_cols=45 Identities=9% Similarity=0.142 Sum_probs=23.7
Q ss_pred HHHHHHCCCCCC-------CHHHHHHHHHHHHHHHHHCCHHHC-CCCCCCCCCCC
Q ss_conf 984331779820-------878999999999999897720311-58999962003
Q gi|254781172|r 32 DDCYYQYSKPII-------LDSEYDALKRRCDAIAHAFPDLAR-SEDPNGPLNKI 78 (731)
Q Consensus 32 ~~~Yy~~~~p~i-------sD~eYD~L~~~L~~le~~~p~~~~-~~~p~spt~~V 78 (731)
-++||.. |.+ +.+.|-.+---++.+....|+.+. ..|...||.|-
T Consensus 15 ~Ra~~a~--p~l~~~~G~~t~ai~Gf~~~l~k~~~~~~p~~~~v~fD~~~~tfR~ 67 (877)
T PRK08076 15 YRAFFAL--PLLNNDKGIHTNAVYGFTMMLMKILEEEKPTHMLVAFDAGKTTFRH 67 (877)
T ss_pred HHHHCCC--CCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCCCH
T ss_conf 9998189--8787999987134999999999999864998899998694896322
No 78
>TIGR01259 comE comEA protein; InterPro: IPR004787 The comE locus is obligatory for bacterial cell competence - the process of internalizing the exogenous added DNA. comEA and comEC are required for transformability, whereas the products of comEB and of the overlapping comER, which is transcribed in the reverse direction, are dispensable . ComEA has been shown to be an integral membrane protein, as predicted from hydropathy analysis, with its C-terminal domain outside the cytoplasmic membrane. This C-terminal domain possesses a sequence with similarity to those of several proteins known to be involved in nucleic acid transactions including UvrC and a human protein that binds to the replication origin of the Human herpesvirus 4 (Epstein-Barr virus) ..
Probab=94.89 E-value=0.034 Score=36.19 Aligned_cols=57 Identities=16% Similarity=0.256 Sum_probs=37.9
Q ss_pred HHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCHHHHHCCCCCCHHHHHHHHHHH
Q ss_conf 987522346667763010111168999999882998999997897761251177876138886789999999996
Q gi|254781172|r 542 INKRRNISLERFIFSLGIRHVGAEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVEFY 616 (731)
Q Consensus 542 Ie~sK~~~L~r~L~ALGI~~vG~~~Ak~La~~f~si~~l~~~~~~~~~~~~~~~e~L~~I~GiG~~~A~si~~ff 616 (731)
|+++....|..+ ||||...|+.|..| ++ ..-.-.+.++|+++.|||+++-+.|.++.
T Consensus 66 lN~As~~EL~~l------~GiGP~kA~aIi~Y-------Re-----~nG~F~SvddL~kVsGIG~k~~eKLk~~~ 122 (124)
T TIGR01259 66 LNKASLEELQAL------PGIGPAKAKAIIEY-------RE-----ENGAFKSVDDLTKVSGIGEKSLEKLKDYV 122 (124)
T ss_pred HHHHHHHHHHHC------CCCCCHHHHHHHHH-------HH-----HCCCCCCHHHHHCCCCCCHHHHHHHHHCC
T ss_conf 406789998636------99981337999999-------98-----56997775550035788546687420003
No 79
>pfam01367 5_3_exonuc 5'-3' exonuclease, C-terminal SAM fold.
Probab=94.84 E-value=0.052 Score=34.70 Aligned_cols=44 Identities=18% Similarity=0.290 Sum_probs=32.6
Q ss_pred CCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCHHHHHCCCCCCHHHHHHHHHHHC
Q ss_conf 0101111689999998829989999978977612511778761388867899999999966
Q gi|254781172|r 557 LGIRHVGAEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVEFYQ 617 (731)
Q Consensus 557 LGI~~vG~~~Ak~La~~f~si~~l~~~~~~~~~~~~~~~e~L~~I~GiG~~~A~si~~ff~ 617 (731)
=|+||||+++|..|.+.|++++++....+ .+-.+..+.|.++..
T Consensus 21 PGv~GiG~KtA~~Ll~~~gsle~i~~n~d-----------------~i~~k~~~~l~~~~~ 64 (100)
T pfam01367 21 PGVPGIGEKTAAKLLKEYGSLENIYENLD-----------------KLKGKLREKLLNGKE 64 (100)
T ss_pred CCCCCCCCHHHHHHHHHCCCHHHHHHHHH-----------------HCCHHHHHHHHHHHH
T ss_conf 99999881689999998198999998198-----------------717999999997899
No 80
>PRK09482 xni exonuclease IX; Provisional
Probab=94.82 E-value=0.042 Score=35.44 Aligned_cols=41 Identities=15% Similarity=0.281 Sum_probs=29.9
Q ss_pred CCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCHHHHHCCCCCCHHHHHHHHH
Q ss_conf 0101111689999998829989999978977612511778761388867899999999
Q gi|254781172|r 557 LGIRHVGAEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVE 614 (731)
Q Consensus 557 LGI~~vG~~~Ak~La~~f~si~~l~~~~~~~~~~~~~~~e~L~~I~GiG~~~A~si~~ 614 (731)
=||||||+++|..|.+.|++++++.+.++ .++++..+.+.+
T Consensus 185 PGV~GIG~KtA~~LL~~fgsle~i~~n~d-----------------~i~~k~~~~l~~ 225 (256)
T PRK09482 185 PGVAGIGPKSAAELLNQFRSLEGIYESLD-----------------ALPEKWRKKLEE 225 (256)
T ss_pred CCCCCCCHHHHHHHHHHHCCHHHHHHHHH-----------------HCCHHHHHHHHH
T ss_conf 99998588899999998550999998377-----------------556899999996
No 81
>PRK05929 consensus
Probab=94.80 E-value=0.042 Score=35.42 Aligned_cols=46 Identities=15% Similarity=0.246 Sum_probs=24.6
Q ss_pred HHHHHHHCCCCCC-------CHHHHHHHHHHHHHHHHHCCHHHC-CCC-CCCCCCCC
Q ss_conf 9984331779820-------878999999999999897720311-589-99962003
Q gi|254781172|r 31 HDDCYYQYSKPII-------LDSEYDALKRRCDAIAHAFPDLAR-SED-PNGPLNKI 78 (731)
Q Consensus 31 ~~~~Yy~~~~p~i-------sD~eYD~L~~~L~~le~~~p~~~~-~~~-p~spt~~V 78 (731)
.-++||.. |.+ +-+.|-.+---++.++...|..+. ..| |..||.|-
T Consensus 13 ~fRAy~Al--p~l~~s~G~pTnAv~GF~~mL~kll~~~~p~~~avaFD~~~~~tfRh 67 (870)
T PRK05929 13 VFRAYFAL--PEMKNPNGESTQAVFGFIRSLNKLIKEFSPEYMVAVFDGPNNKQSRQ 67 (870)
T ss_pred HHHHHCCC--CCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCEEEEEEECCCCCCCHH
T ss_conf 99998079--98879999870509999999999998659988999987979997164
No 82
>PRK07456 consensus
Probab=94.71 E-value=0.1 Score=32.43 Aligned_cols=83 Identities=16% Similarity=0.185 Sum_probs=39.6
Q ss_pred HHHHHHHCCC----CC------CCHHHHHHHHHHHHHHHHHCCHHHC-CCCCCCCCCCCCCCC---------CCC----C
Q ss_conf 9984331779----82------0878999999999999897720311-589999620036432---------357----7
Q gi|254781172|r 31 HDDCYYQYSK----PI------ILDSEYDALKRRCDAIAHAFPDLAR-SEDPNGPLNKIGGEM---------NLS----L 86 (731)
Q Consensus 31 ~~~~Yy~~~~----p~------isD~eYD~L~~~L~~le~~~p~~~~-~~~p~spt~~Vg~~~---------~~~----~ 86 (731)
.-++||.... |. -+.+.|-.+---++.++...|+++. ..|.-.||.|----+ ..+ +
T Consensus 19 ~fRay~A~~~~~~~pl~~~~G~~tnAv~GF~~~l~kli~~~~P~~iavaFD~~~~TFR~e~y~~YKA~R~~~PedL~~Qi 98 (975)
T PRK07456 19 AFRSFYAFSKGGEGGLRTKTGIPTSVTYGFLKSLLDNCKTQKPQGVAIAFDTAEPTFRHEADPNYKANRDVAPDDFFQDL 98 (975)
T ss_pred HHHHHHCCCCCCCCCCCCCCCCEECHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCCCHHHHHHHHCCCCCCCHHHHHHH
T ss_conf 99998077867888864899987214999999999999863998899998288995254231364079999988899999
Q ss_pred ---CE-EE--CCCCCCCHHHCCCHHHHHHHHHHH
Q ss_conf ---50-45--166425702159999999999999
Q gi|254781172|r 87 ---FK-VT--HSIPTLSLEKIWNIEDLRKFITRI 114 (731)
Q Consensus 87 ---~k-v~--H~~pMlSL~k~~~~~el~~w~~~~ 114 (731)
.+ ++ .-+|.++++. |--|++..=+.+.
T Consensus 99 p~i~e~l~~algIp~~e~~G-yEADDiIaTla~~ 131 (975)
T PRK07456 99 EQLQEILEEALNLPICTAPG-YEADDVLGTLANR 131 (975)
T ss_pred HHHHHHHHHHCCCCEEEECC-CCHHHHHHHHHHH
T ss_conf 99999999836998741788-0199999999999
No 83
>PRK07300 consensus
Probab=94.65 E-value=0.06 Score=34.23 Aligned_cols=84 Identities=8% Similarity=0.057 Sum_probs=40.8
Q ss_pred HHHHHHHCCC--CCC-------CHHHHHHHHHHHHHHHHHCCHHHC-CCCCCCCCCCCCCCCC-------------CCCC
Q ss_conf 9984331779--820-------878999999999999897720311-5899996200364323-------------5775
Q gi|254781172|r 31 HDDCYYQYSK--PII-------LDSEYDALKRRCDAIAHAFPDLAR-SEDPNGPLNKIGGEMN-------------LSLF 87 (731)
Q Consensus 31 ~~~~Yy~~~~--p~i-------sD~eYD~L~~~L~~le~~~p~~~~-~~~p~spt~~Vg~~~~-------------~~~~ 87 (731)
.-++||..-. |.+ +-+.|-.+---++.++...|+.+. ..|...||.|----+. ..+.
T Consensus 16 ifRAfyAl~~~~~~l~ts~G~pTnAi~GF~~mL~kli~~~~P~~iavaFD~~~~TFR~~~~~~YKa~R~~~P~~l~~Q~~ 95 (880)
T PRK07300 16 AFRAFFALYNQIDRFKNHSGLHTNAIYGFHLMLDHMMKRVQPTHVLVAFDAGKTTFRTEMYADYKAGRAKTPDEFREQFP 95 (880)
T ss_pred HHHHHCCCCCCCCCCCCCCCCEECHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCCCHHHHHHHCCCCCCCCHHHHHHHH
T ss_conf 99987178877788729999882359999999999998649988999996959960142315752799999889999999
Q ss_pred EE-----ECCCCCCCHHHCCCHHHHHHHHHHHH
Q ss_conf 04-----51664257021599999999999999
Q gi|254781172|r 88 KV-----THSIPTLSLEKIWNIEDLRKFITRIY 115 (731)
Q Consensus 88 kv-----~H~~pMlSL~k~~~~~el~~w~~~~~ 115 (731)
-+ .+-+|+++.+. |--|++..=+.+..
T Consensus 96 ~i~~~~~~~~i~~~~~~g-~EADDvi~tlak~a 127 (880)
T PRK07300 96 YIREMLTALGIAYYELEH-YEADDIIGTLDKMA 127 (880)
T ss_pred HHHHHHHHCCCCEECCCC-CCHHHHHHHHHHHH
T ss_conf 999999987998825289-14999999999999
No 84
>PRK05755 DNA polymerase I; Provisional
Probab=94.63 E-value=0.065 Score=33.98 Aligned_cols=47 Identities=15% Similarity=0.176 Sum_probs=25.7
Q ss_pred HHHHHHHCCCC------CCCHHHHHHHHHHHHHHHHHCCHHH-CCCCCCCCCCCC
Q ss_conf 99843317798------2087899999999999989772031-158999962003
Q gi|254781172|r 31 HDDCYYQYSKP------IILDSEYDALKRRCDAIAHAFPDLA-RSEDPNGPLNKI 78 (731)
Q Consensus 31 ~~~~Yy~~~~p------~isD~eYD~L~~~L~~le~~~p~~~-~~~~p~spt~~V 78 (731)
.-++||.. .| .-+.+.|-.+---++.++...|+.+ -..|...||.|-
T Consensus 16 ~~Ra~~a~-~~l~~~~G~~tnai~Gf~~~l~~~~~~~~p~~~~v~fD~~~~tfR~ 69 (889)
T PRK05755 16 AFRAFYAL-PPLTNSDGLPTGAVYGFLNMLLKLLKDEKPTHIAVAFDAKGKTFRH 69 (889)
T ss_pred HHHHHCCC-CCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCEEEEEECCCCCCCCC
T ss_conf 99998078-9887999987252999999999999862998899996398996352
No 85
>PRK00254 ski2-like helicase; Provisional
Probab=94.57 E-value=0.02 Score=37.85 Aligned_cols=66 Identities=18% Similarity=0.350 Sum_probs=37.4
Q ss_pred CCCCCHHHHHCCCCCCHHHHHHHHHH-HCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCHHHHHH
Q ss_conf 25117787613888678999999999-66979999999999733877654322468821686699972588998789999
Q gi|254781172|r 590 HNNDDWLSLIRVPLVGDIIAQAIVEF-YQNPRNICAVEALLKEVSPSIGRHEKNVSSEIENKKLVFTGTLQKIQRHKAQE 668 (731)
Q Consensus 590 ~~~~~~e~L~~I~GiG~~~A~si~~f-f~~~~n~~~i~~L~~~~~~~~~~~~~~~~~~l~gk~vV~TGtl~~~~R~e~~~ 668 (731)
.-..+..+|++|+|||...|..+.+. |..+. .+..+ ... .-.-+.| +..+-+++
T Consensus 638 Gv~~ELl~L~~I~gvgr~RAR~Ly~aGi~s~~------~ia~A-----------~p~----~l~~i~g----~g~~~a~~ 692 (717)
T PRK00254 638 GIREELIPLMELPMIGRKRARALYNAGFRDLE------DIMNA-----------KPS----ELLAVEG----IGAKIVEG 692 (717)
T ss_pred CCCHHHHHHCCCCCCCHHHHHHHHHCCCCCHH------HHHCC-----------CHH----HEECCCC----CCHHHHHH
T ss_conf 99765683564899898999999986999999------99659-----------999----9030237----27899999
Q ss_pred HHHHCCCEEEEE
Q ss_conf 999829849981
Q gi|254781172|r 669 YVTQLGAVVSAI 680 (731)
Q Consensus 669 ~ie~~Ggkv~sS 680 (731)
++++.|-+|.=+
T Consensus 693 i~~~~~~~~~~~ 704 (717)
T PRK00254 693 IFKHLGKEVKIN 704 (717)
T ss_pred HHHHHCCEEEHH
T ss_conf 999838644300
No 86
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=94.56 E-value=0.035 Score=36.01 Aligned_cols=86 Identities=20% Similarity=0.351 Sum_probs=52.1
Q ss_pred CCCCHHHHHHHHHHHHHCCCCCCEEEEEHHHHCCHHHHHHHHCCCCCCCCCCCCCHHHHHHHH---HHHHHHHHHHHHHH
Q ss_conf 231035410355556530576540454101101067775310001000134210014568999---98752234666776
Q gi|254781172|r 479 DAFNIEGLGKQQLDFFFKSEDPAFSIRIPADIFTLQRRQQTSTTKIENILGFGDVSVTNLYDS---INKRRNISLERFIF 555 (731)
Q Consensus 479 ~aldI~GLG~k~Ie~L~e~~~~~g~I~~~~DLy~L~~~~~~~~~~l~~l~GfgeKsa~nL~~s---Ie~sK~~~L~r~L~ 555 (731)
+-+.++|+|++.++.|+++ |..--.. .|.... -=+.+++.|++.|..|.+. |++-.+.+...+
T Consensus 480 ~L~~l~gfgeKsa~nLl~a------Ie~SK~~-~l~r~L-----~ALGI~~VG~~~Ak~La~~f~sl~~l~~as~e~L-- 545 (668)
T PRK07956 480 DLLQLEGFGEKSAQNLLDA------IEKSKET-PLARFL-----YALGIRHVGEKAAKALARHFGSLEALEAASEEEL-- 545 (668)
T ss_pred HHHCCCCHHHHHHHHHHHH------HHHHCCC-CHHHHH-----HHCCCCCCCHHHHHHHHHHHCCHHHHHHCCHHHH--
T ss_conf 5402123556699999999------9985477-588899-----8627864129999999999668999970899998--
Q ss_pred HCCHHHHHHHHHHHHHHHCCCHHH
Q ss_conf 301011116899999988299899
Q gi|254781172|r 556 SLGIRHVGAEIARSLAKYYLSYQN 579 (731)
Q Consensus 556 ALGI~~vG~~~Ak~La~~f~si~~ 579 (731)
+.|++||+.+|..|...|.+-.+
T Consensus 546 -~~I~giG~~~A~si~~ff~~~~n 568 (668)
T PRK07956 546 -AAVEGIGEEVAQSIVEFFAVEHN 568 (668)
T ss_pred -HCCCCCCHHHHHHHHHHHCCHHH
T ss_conf -57688449999999999709768
No 87
>PRK06887 consensus
Probab=94.52 E-value=0.17 Score=30.76 Aligned_cols=47 Identities=15% Similarity=0.171 Sum_probs=24.1
Q ss_pred HHHHHHHCCCCC------CCHHHHHHHHHHHHHHHHHCCHHHC-CCCCCCCCCCC
Q ss_conf 998433177982------0878999999999999897720311-58999962003
Q gi|254781172|r 31 HDDCYYQYSKPI------ILDSEYDALKRRCDAIAHAFPDLAR-SEDPNGPLNKI 78 (731)
Q Consensus 31 ~~~~Yy~~~~p~------isD~eYD~L~~~L~~le~~~p~~~~-~~~p~spt~~V 78 (731)
.-++||.. .|. =+.+.|-.+---++.++..-|+.+. ..|...||.|-
T Consensus 18 ~fRAfyAl-~~l~ts~G~pTnAi~GF~~ml~kli~~~kP~~iavaFD~~~~TFR~ 71 (954)
T PRK06887 18 LYRAFHAF-PPLTNSAGEPTGAMYGVLNMLKSLISQVQPSHIAVVFDAKGKTFRD 71 (954)
T ss_pred HHHHHCCC-CCCCCCCCCEECHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCCCH
T ss_conf 99998078-8675998987335999999999999871998899998088996033
No 88
>PRK07556 consensus
Probab=94.37 E-value=0.078 Score=33.35 Aligned_cols=47 Identities=11% Similarity=-0.032 Sum_probs=22.0
Q ss_pred HHHHHHHCCCCCC-------CHHHHHHHHHHHHHHHHHC----CHHH-CCCCCCCCCCCC
Q ss_conf 9984331779820-------8789999999999998977----2031-158999962003
Q gi|254781172|r 31 HDDCYYQYSKPII-------LDSEYDALKRRCDAIAHAF----PDLA-RSEDPNGPLNKI 78 (731)
Q Consensus 31 ~~~~Yy~~~~p~i-------sD~eYD~L~~~L~~le~~~----p~~~-~~~~p~spt~~V 78 (731)
.-++||.. .|+. +-+.|-.+---++.++... |.++ -..|...||.|-
T Consensus 19 ~fRAyyAl-p~l~~~s~G~pTnAvyGF~~mL~kll~~~~~~~~p~~iavaFD~~~~TFRh 77 (977)
T PRK07556 19 IFRAYHAL-PPLTRKSDGLPVGAVSGFCNMLWKLLRDARNTDVPTHLAVIFDYSSKTFRN 77 (977)
T ss_pred HHHHHCCC-CCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCCCCCCH
T ss_conf 99998179-976779999471369999999999998623567998899998088996012
No 89
>PRK07625 consensus
Probab=94.24 E-value=0.076 Score=33.46 Aligned_cols=46 Identities=11% Similarity=0.052 Sum_probs=25.7
Q ss_pred HHHHHHHCCCCCC-------CHHHHHHHHHHHHHHHHHCCHHHC-CCCCCCCCCCC
Q ss_conf 9984331779820-------878999999999999897720311-58999962003
Q gi|254781172|r 31 HDDCYYQYSKPII-------LDSEYDALKRRCDAIAHAFPDLAR-SEDPNGPLNKI 78 (731)
Q Consensus 31 ~~~~Yy~~~~p~i-------sD~eYD~L~~~L~~le~~~p~~~~-~~~p~spt~~V 78 (731)
.-++||.. |.+ +.+.|-.+---++.++..-|+++. ..|...||.|-
T Consensus 17 ifRAfyAl--p~l~ts~G~pTnAi~GF~~mL~kli~e~~P~~iavaFD~~~~TFR~ 70 (922)
T PRK07625 17 LYRAYHAM--PDLRGPGGEPTGALYGIVNMLRRMRKDVSAEYSACVFDAKGKTFRD 70 (922)
T ss_pred HHHHHHCC--CCCCCCCCCEECHHHHHHHHHHHHHHHCCCCEEEEEECCCCCCCCH
T ss_conf 99998278--8887998987117999999999999865998899997198996340
No 90
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=94.23 E-value=0.51 Score=27.07 Aligned_cols=53 Identities=17% Similarity=0.110 Sum_probs=30.4
Q ss_pred HHHCCHHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHHCCCCCHHHHHCCCCCCHHHHHHHHHH
Q ss_conf 763010111168999999882--99899999789776125117787613888678999999999
Q gi|254781172|r 554 IFSLGIRHVGAEIARSLAKYY--LSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVEF 615 (731)
Q Consensus 554 L~ALGI~~vG~~~Ak~La~~f--~si~~l~~~~~~~~~~~~~~~e~L~~I~GiG~~~A~si~~f 615 (731)
+.=|.+|++|.+.-+.|-+.+ .+++.+.++..+ -.+..+.|||.+.+..|..+
T Consensus 93 ~~Ll~v~GlGpkKi~~Ly~elgi~~~e~l~~a~~~---------~~~~~l~GfG~kse~~il~~ 147 (326)
T COG1796 93 EPLLKVPGLGPKKIVSLYKELGIKDLEELQEALEN---------GKIRGLRGFGKKSEAKILEN 147 (326)
T ss_pred HHHHHCCCCCCHHHHHHHHHHCCCCHHHHHHHHHH---------CCCCCCCCCCCHHHHHHHHH
T ss_conf 87860779892889999999786649999999984---------77032678560219999999
No 91
>PRK08835 consensus
Probab=94.18 E-value=0.11 Score=32.27 Aligned_cols=83 Identities=11% Similarity=0.089 Sum_probs=37.5
Q ss_pred HHHHHHHCCCC-----CCCHHHHHHHHHHHHHHHHHCCHHHC-CCCCCCCCCCCCCCCC-------------CCCCEE--
Q ss_conf 99843317798-----20878999999999999897720311-5899996200364323-------------577504--
Q gi|254781172|r 31 HDDCYYQYSKP-----IILDSEYDALKRRCDAIAHAFPDLAR-SEDPNGPLNKIGGEMN-------------LSLFKV-- 89 (731)
Q Consensus 31 ~~~~Yy~~~~p-----~isD~eYD~L~~~L~~le~~~p~~~~-~~~p~spt~~Vg~~~~-------------~~~~kv-- 89 (731)
.-++||....- .-+.+.|-.+---++.++...|+++. ..|...||.|----+. ..|.-+
T Consensus 18 ifRAfyA~p~l~ts~G~pTnAv~GF~~mL~kli~~~~P~~iavaFD~~~~TfR~~~y~~YKa~R~~~pedL~~Q~p~i~e 97 (931)
T PRK08835 18 LYRAFHAYPGTMSNGEIPTNAVYGVVNMLRSMMRQFASDRIAVIFDAKGKTFRDDMYPEYKANRPPMPDDLRCQIEPLHQ 97 (931)
T ss_pred HHHHHHCCCCCCCCCCCEECHHHHHHHHHHHHHHHCCCCEEEEEECCCCCCCCHHHHHHHCCCCCCCCHHHHHHHHHHHH
T ss_conf 99998279987899998830699999999999986499879999749899623434057517999998789999999999
Q ss_pred ---ECCCCCCCHHHCCCHHHHHHHHHHH
Q ss_conf ---5166425702159999999999999
Q gi|254781172|r 90 ---THSIPTLSLEKIWNIEDLRKFITRI 114 (731)
Q Consensus 90 ---~H~~pMlSL~k~~~~~el~~w~~~~ 114 (731)
.+-+|.++++. |--|++..=+.+.
T Consensus 98 ~l~a~gIp~~~~~G-yEADDiIgTla~~ 124 (931)
T PRK08835 98 VIKAMGLPLIAIEG-VEADDVIGTLAYQ 124 (931)
T ss_pred HHHHCCCCEEEECC-CCHHHHHHHHHHH
T ss_conf 99987998844589-1499999999999
No 92
>PRK08786 consensus
Probab=94.15 E-value=0.066 Score=33.93 Aligned_cols=46 Identities=11% Similarity=0.114 Sum_probs=21.8
Q ss_pred HHHHHHHCCCCCC------CHHHHHHHHHHHHHHHHHCCHHHC-CCCCCCCCCCC
Q ss_conf 9984331779820------878999999999999897720311-58999962003
Q gi|254781172|r 31 HDDCYYQYSKPII------LDSEYDALKRRCDAIAHAFPDLAR-SEDPNGPLNKI 78 (731)
Q Consensus 31 ~~~~Yy~~~~p~i------sD~eYD~L~~~L~~le~~~p~~~~-~~~p~spt~~V 78 (731)
.-++||.. .|.. +-+.|-.+- -|..+-...|.++. ..|...||.|-
T Consensus 13 ifRAy~A~-~~l~~~~G~pTnAv~GF~~-mL~kl~~e~p~~~~v~fD~~~~tfR~ 65 (927)
T PRK08786 13 LYRAFHAL-PPLTNAQGEPTGALFGVVN-MLRATLKERPAYVAFVVDAPGKTFRD 65 (927)
T ss_pred HHHHHCCC-CCCCCCCCCEECHHHHHHH-HHHHHHHHCCCEEEEEEECCCCCCCC
T ss_conf 99998079-9887999988207999999-99999987889899999695997451
No 93
>TIGR01448 recD_rel helicase, RecD/TraA family; InterPro: IPR006345 These sequences represent a family similar to RecD, the exodeoxyribonuclease V alpha chain of IPR006344 from INTERPRO. 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=94.10 E-value=0.16 Score=30.98 Aligned_cols=67 Identities=22% Similarity=0.357 Sum_probs=38.5
Q ss_pred CHHHHHHHHHCCCCCC------CCEEEEECCCCHHHHHHHHHHHHCCCCCCCCCEEEEECCHHCCCCCCCCCCCCCC
Q ss_conf 0036899997599665------4148874032113455665531001123437637773110001115876568663
Q gi|254781172|r 254 QYEMLQKMRCLGFPVN------NGVRQANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSLQKQLGERARSPRW 324 (731)
Q Consensus 254 ~~e~l~~L~~~GF~v~------~~~~~~~~~~~~~~~~~~~~~~r~~l~y~iDGiVikvn~~~~q~~lG~ts~~Prw 324 (731)
....|..|..+||+.. .++...+-..+-++..+ +-=-.|-+||-||=++--| .+...||--...||-
T Consensus 152 ~~~~l~~L~~lG~~~~l~~~~~k~y~eadP~~dtLd~v~---~~Py~L~~d~~GiGF~~AD-~lA~~lG~~~~dP~R 224 (769)
T TIGR01448 152 ERKLLLKLQQLGIGIKLALRIYKFYREADPQADTLDVVE---KDPYLLAEDVKGIGFKTAD-QLAEELGIALNDPRR 224 (769)
T ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCHHHHHH---CCHHHHHHHHCCCCHHHHH-HHHHHCCCCCCCCHH
T ss_conf 999999998538767899999998403587211688862---1720136751374056899-999971862358447
No 94
>PRK08434 consensus
Probab=93.93 E-value=0.07 Score=33.72 Aligned_cols=83 Identities=14% Similarity=0.050 Sum_probs=42.9
Q ss_pred HHHHHHHCCCCC------CCHHHHHHHHHHHHHHHHHCCHHHCC-CCCCCCCCCCCCCCC---------CC----CCEE-
Q ss_conf 998433177982------08789999999999998977203115-899996200364323---------57----7504-
Q gi|254781172|r 31 HDDCYYQYSKPI------ILDSEYDALKRRCDAIAHAFPDLARS-EDPNGPLNKIGGEMN---------LS----LFKV- 89 (731)
Q Consensus 31 ~~~~Yy~~~~p~------isD~eYD~L~~~L~~le~~~p~~~~~-~~p~spt~~Vg~~~~---------~~----~~kv- 89 (731)
.-++||.. .|. -+.+.|-.+---++.++...|+++.. .|...||.|----+. .+ +.-+
T Consensus 13 ~fRAy~A~-~~l~t~~G~pTnAv~GF~~mL~kli~~~~P~~iavaFD~~~~TFRhe~y~~YKAnR~~~PedL~~Qip~i~ 91 (887)
T PRK08434 13 FFRSYYAL-PPLKNSQGFPTGLLSGFANFIYSLKNEFKSDYIVFALDSKGKTFRSEIDPNYKANRPPPPEELLEQLPIAI 91 (887)
T ss_pred HHHHHCCC-CCCCCCCCCEECHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCCCHHHHHHHCCCCCCCCHHHHHHHHHHH
T ss_conf 99997079-99879999880359999999999998659988999984959962210205752899999989999999999
Q ss_pred ----ECCCCCCCHHHCCCHHHHHHHHHHHH
Q ss_conf ----51664257021599999999999999
Q gi|254781172|r 90 ----THSIPTLSLEKIWNIEDLRKFITRIY 115 (731)
Q Consensus 90 ----~H~~pMlSL~k~~~~~el~~w~~~~~ 115 (731)
..-+|.++++. |--|++..=+.+..
T Consensus 92 e~l~algIp~~e~~G-yEADDiIgTla~~a 120 (887)
T PRK08434 92 EWIEKMGFKSLSQEG-YEADDIIASFVKFA 120 (887)
T ss_pred HHHHHCCCCEECCCC-CCHHHHHHHHHHHH
T ss_conf 999987998845589-24999999999999
No 95
>smart00475 53EXOc 5'-3' exonuclease.
Probab=93.54 E-value=0.11 Score=32.12 Aligned_cols=42 Identities=17% Similarity=0.353 Sum_probs=30.7
Q ss_pred CCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCHHHHHCCCCCCHHHHHHHHHH
Q ss_conf 01011116899999988299899999789776125117787613888678999999999
Q gi|254781172|r 557 LGIRHVGAEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVEF 615 (731)
Q Consensus 557 LGI~~vG~~~Ak~La~~f~si~~l~~~~~~~~~~~~~~~e~L~~I~GiG~~~A~si~~f 615 (731)
=||||||+++|..|.+.|++++++++.++. +.++..+.+.+.
T Consensus 189 pGV~GIG~KtA~kLL~~ygsle~i~~~~d~-----------------i~~k~~~~l~~~ 230 (259)
T smart00475 189 PGVPGIGEKTAAKLLKEFGSLENILENLDK-----------------LKKKLREKLLAH 230 (259)
T ss_pred CCCCCCCHHHHHHHHHHCCCHHHHHHHHHH-----------------CCHHHHHHHHHH
T ss_conf 999984789999999983999999983985-----------------488999999977
No 96
>COG2231 Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]
Probab=93.54 E-value=0.17 Score=30.70 Aligned_cols=40 Identities=23% Similarity=0.475 Sum_probs=27.6
Q ss_pred HHHHHHCCCHHHHHHHHHHHHHCCCCCHHHHHCCCCCCHHHHHHHHHHH
Q ss_conf 9999882998999997897761251177876138886789999999996
Q gi|254781172|r 568 RSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVEFY 616 (731)
Q Consensus 568 k~La~~f~si~~l~~~~~~~~~~~~~~~e~L~~I~GiG~~~A~si~~ff 616 (731)
+.|+.+|.+++.+.+.. ..++|..|+|||+.+|++|.-|-
T Consensus 96 k~l~~~~~~~~~~~~~~---------~R~~LL~iKGIG~ETaDsILlYa 135 (215)
T COG2231 96 KNLAKFFINLESFKSEV---------LREELLSIKGIGKETADSILLYA 135 (215)
T ss_pred HHHHHHHHHHHCCCHHH---------HHHHHHCCCCCCHHHHHHHHHHH
T ss_conf 99999864231115188---------99998726886622399999998
No 97
>TIGR02236 recomb_radA DNA repair and recombination protein RadA; InterPro: IPR011938 This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA, eukaryotic RAD51 (IPR011941 from INTERPRO), and archaeal RadB (IPR011939 from INTERPRO). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein .; GO: 0003684 damaged DNA binding, 0005524 ATP binding, 0008094 DNA-dependent ATPase activity, 0006281 DNA repair, 0006310 DNA recombination.
Probab=93.52 E-value=0.039 Score=35.70 Aligned_cols=46 Identities=22% Similarity=0.264 Sum_probs=35.3
Q ss_pred HHHHHHHHHHHHHHH-CCCHHHHHHHHHHHHHCCCCCHHHHHCCCCCCHHHHHHHHH
Q ss_conf 011116899999988-29989999978977612511778761388867899999999
Q gi|254781172|r 559 IRHVGAEIARSLAKY-YLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVE 614 (731)
Q Consensus 559 I~~vG~~~Ak~La~~-f~si~~l~~~~~~~~~~~~~~~e~L~~I~GiG~~~A~si~~ 614 (731)
+||||..||.+|-.+ |.+++.+. .++..+|.++.|||+.+|..|++
T Consensus 5 LPGVGp~TA~KL~EaGy~t~~~iA----------~A~~~EL~~~~gI~E~~A~kiI~ 51 (333)
T TIGR02236 5 LPGVGPATAEKLREAGYDTLEAIA----------VASPKELSEIAGIGEGTAAKIIQ 51 (333)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHH----------CCCHHHHHHHCCCCHHHHHHHHH
T ss_conf 789757688998861078899984----------45857953203787778999999
No 98
>PRK02362 ski2-like helicase; Provisional
Probab=93.44 E-value=0.29 Score=28.97 Aligned_cols=67 Identities=16% Similarity=0.123 Sum_probs=30.3
Q ss_pred HHHCCCCCCCHHHHHHHHHHHHHHHHHCCHHHCCCCCCCCCCCCCCCC-----CCCCCEEECCCCCCCHHHCCCHHHHHH
Q ss_conf 331779820878999999999999897720311589999620036432-----357750451664257021599999999
Q gi|254781172|r 35 YYQYSKPIILDSEYDALKRRCDAIAHAFPDLARSEDPNGPLNKIGGEM-----NLSLFKVTHSIPTLSLEKIWNIEDLRK 109 (731)
Q Consensus 35 Yy~~~~p~isD~eYD~L~~~L~~le~~~p~~~~~~~p~spt~~Vg~~~-----~~~~~kv~H~~pMlSL~k~~~~~el~~ 109 (731)
|-..|-..+-+.+.+++..-+ ++-++- ++. .|+|-=..+-++. .....|+--..|+-||.+ |-+..
T Consensus 16 ~~~~gI~~Lyp~Q~eal~~gl--~~g~Nl-vvs--aPTgsGKTlvAElail~~l~~g~k~vYi~P~kALa~----EK~~~ 86 (736)
T PRK02362 16 YEGSGIEELYPPQAEAVEAGL--LEGKNL-LAA--IPTASGKTLLAELAMLKAIAEGGKALYIVPLRALAS----EKFEE 86 (736)
T ss_pred HHHCCCCCCCHHHHHHHHHHH--CCCCCE-EEE--CCCCCCHHHHHHHHHHHHHHHCCEEEEECCHHHHHH----HHHHH
T ss_conf 997699757899999998643--569818-997--999985899999999999983997999858799999----99999
Q ss_pred H
Q ss_conf 9
Q gi|254781172|r 110 F 110 (731)
Q Consensus 110 w 110 (731)
|
T Consensus 87 ~ 87 (736)
T PRK02362 87 F 87 (736)
T ss_pred H
T ss_conf 9
No 99
>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=93.41 E-value=0.2 Score=30.28 Aligned_cols=29 Identities=24% Similarity=0.412 Sum_probs=24.3
Q ss_pred CCHHHHHHHHHHHHHHHCCCHHHHHHHHH
Q ss_conf 01011116899999988299899999789
Q gi|254781172|r 557 LGIRHVGAEIARSLAKYYLSYQNFAQEIN 585 (731)
Q Consensus 557 LGI~~vG~~~Ak~La~~f~si~~l~~~~~ 585 (731)
=||||||.++|..|.+.|++++++.+..+
T Consensus 186 pGV~GiG~KtA~kLl~~~gsle~i~~~~~ 214 (240)
T cd00008 186 PGVPGIGEKTAAKLLKEYGSLEGILENLD 214 (240)
T ss_pred CCCCCCCHHHHHHHHHHHCCHHHHHHHHH
T ss_conf 99998578999999998099999998298
No 100
>PRK01172 ski2-like helicase; Provisional
Probab=93.39 E-value=0.056 Score=34.49 Aligned_cols=30 Identities=20% Similarity=0.453 Sum_probs=19.4
Q ss_pred CCCCCHHHHHCCCCCCHHHHHHHHHH-HCCH
Q ss_conf 25117787613888678999999999-6697
Q gi|254781172|r 590 HNNDDWLSLIRVPLVGDIIAQAIVEF-YQNP 619 (731)
Q Consensus 590 ~~~~~~e~L~~I~GiG~~~A~si~~f-f~~~ 619 (731)
.-..+..+|++|+|||.+.|..+.+. |..+
T Consensus 606 Gv~~eLl~L~~I~gigr~RAR~Ly~aG~~s~ 636 (674)
T PRK01172 606 GIREDLIDLVLIPKVGRVRARRLYDAGFKTV 636 (674)
T ss_pred CCHHHHHHHCCCCCCCHHHHHHHHHCCCCCH
T ss_conf 9868889771889999899999998699999
No 101
>KOG2534 consensus
Probab=93.10 E-value=0.77 Score=25.68 Aligned_cols=62 Identities=15% Similarity=0.187 Sum_probs=35.3
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHH---------HHHHCCHHHHHHHHHHHHHH-HCCCHHHHHH
Q ss_conf 00100013421001456899998752234666---------77630101111689999998-8299899999
Q gi|254781172|r 521 TTKIENILGFGDVSVTNLYDSINKRRNISLER---------FIFSLGIRHVGAEIARSLAK-YYLSYQNFAQ 582 (731)
Q Consensus 521 ~~~l~~l~GfgeKsa~nL~~sIe~sK~~~L~r---------~L~ALGI~~vG~~~Ak~La~-~f~si~~l~~ 582 (731)
.+++.+|+|+|+|.|.++..=++.-.-..+.+ +.+=-.|-|||.++|+.--+ .|.+++.+++
T Consensus 55 ~~ea~~lP~iG~kia~ki~EiletG~l~ele~v~~de~~~~lklFtnifGvG~ktA~~Wy~~GfrTled~Rk 126 (353)
T KOG2534 55 GEEAEKLPGIGPKIAEKIQEILETGVLRELEAVRNDERSQSLKLFTNIFGVGLKTAEKWYREGFRTLEDVRK 126 (353)
T ss_pred HHHHCCCCCCCHHHHHHHHHHHHCCCCHHHHHHHCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf 788557999777799999999970873667877545067899999987255778999999951467999875
No 102
>TIGR00593 pola DNA polymerase I; InterPro: IPR002298 DNA carries the biological information that instructs cells how to exist in an ordered fashion. Accurate replication is thus one of the most important events in the cell life cycle. This function is mediated by DNA-directed DNA polymerases, which add nucleotide triphosphate (dNTP) residues to the 5'-end of the growing DNA chain, using a complementary DNA as template. Small RNA molecules are generally used as primers for chain elongation, although terminal proteins may also be used. DNA-dependent DNA polymerases have been grouped into families, denoted A, B and X, on the basis of sequence similarities , . Members of family A, which includes bacterial and bacteriophage polymerases, share significant similarity to Escherichia coli polymerase I; hence family A is also known as the pol I family. The bacterial polymerases also contain an exonuclease activity, which is coded for in the N-terminal portion. Three motifs, A, B and C , are seen to be conserved across all DNA polymerases, with motifs A and C also seen in RNA polymerases. They are centred on invariant residues, and their structural significance was implied from the Klenow (E. coli) structure. Motif A contains a strictly-conserved aspartate at the junction of a beta-strand and an alpha-helix; motif B contains an alpha-helix with positive charges; and motif C has a doublet of negative charges, located in a beta-turn-beta secondary structure .; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication.
Probab=92.92 E-value=0.076 Score=33.43 Aligned_cols=46 Identities=13% Similarity=0.188 Sum_probs=23.9
Q ss_pred HHHHHCCC---CC------CCHHHHHHHHHHHHHHHHHCC-HHH-CCCCCCCCCCCC
Q ss_conf 84331779---82------087899999999999989772-031-158999962003
Q gi|254781172|r 33 DCYYQYSK---PI------ILDSEYDALKRRCDAIAHAFP-DLA-RSEDPNGPLNKI 78 (731)
Q Consensus 33 ~~Yy~~~~---p~------isD~eYD~L~~~L~~le~~~p-~~~-~~~~p~spt~~V 78 (731)
++||.... |+ -+++.|=...-=+..|++.-| .++ -..|...||.|-
T Consensus 12 RayfAl~~~~~~L~~~~G~~t~A~yGF~~~L~~~l~~~~Pm~~~~~aFD~~~~TFR~ 68 (1005)
T TIGR00593 12 RAYFALPNNKKPLTNSKGEPTNAVYGFTKMLLKLLKEEKPMTYVAVAFDSGTKTFRH 68 (1005)
T ss_pred HHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCEEEEEEECCCCCCHHH
T ss_conf 998862211466666788711677888999999997418951699887688885166
No 103
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=92.63 E-value=0.13 Score=31.68 Aligned_cols=109 Identities=15% Similarity=0.164 Sum_probs=61.3
Q ss_pred HHCCHHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHHCCCCCHHHHHCCCCCCHHHHHHHHHHHCCHHHHHHHHHHHHHC
Q ss_conf 63010111168999999882--9989999978977612511778761388867899999999966979999999999733
Q gi|254781172|r 555 FSLGIRHVGAEIARSLAKYY--LSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVEFYQNPRNICAVEALLKEV 632 (731)
Q Consensus 555 ~ALGI~~vG~~~Ak~La~~f--~si~~l~~~~~~~~~~~~~~~e~L~~I~GiG~~~A~si~~ff~~~~n~~~i~~L~~~~ 632 (731)
-||.|.|+|+++...|.... .++..++. .+.++|.+++|||++.|+++++-+...++ ..+.+++..+
T Consensus 427 ~amdI~GLGek~i~~L~~~gli~~~~Dly~----------L~~~~L~~l~g~geKsa~nLl~aIe~SK~-~~l~r~l~aL 495 (563)
T PRK08097 427 QGLGLDGIGEGTWRALHQTGRFEHLFSWLA----------LTPEQLANTPGIGKARAAQLWHQFNLARQ-QPFTRWLKAL 495 (563)
T ss_pred CCCCCCCCCHHHHHHHHHCCCCCCHHHHHH----------CCHHHHHCCCCHHHHHHHHHHHHHHHHCC-CCHHHHHHHC
T ss_conf 415856769999999997588899799750----------89999855898578999999999999728-9999999986
Q ss_pred CCCCCCCCCCCCCCCCCCEEEEECCCCCCCHHHHHHHHHHCCCEEEEEE
Q ss_conf 8776543224688216866999725889987899999998298499811
Q gi|254781172|r 633 SPSIGRHEKNVSSEIENKKLVFTGTLQKIQRHKAQEYVTQLGAVVSAIL 681 (731)
Q Consensus 633 ~~~~~~~~~~~~~~l~gk~vV~TGtl~~~~R~e~~~~ie~~Ggkv~sSV 681 (731)
++...-.. ....+.+ .| .+|...+.+++.+ |+..|-+++.||
T Consensus 496 GI~~vG~~--~a~~l~~-~~---~~L~~as~e~l~~-i~gIG~~~A~si 537 (563)
T PRK08097 496 GIPLTQAA--LNASLDR-SW---QQLLSRTEQQWQQ-LPGIGEGRARQL 537 (563)
T ss_pred CCCCHHHH--HHHHHHC-CH---HHHHCCCHHHHHC-CCCCCHHHHHHH
T ss_conf 99508999--9999861-99---9997399989955-798489999999
No 104
>KOG3226 consensus
Probab=92.48 E-value=0.35 Score=28.32 Aligned_cols=67 Identities=19% Similarity=0.213 Sum_probs=32.6
Q ss_pred CCCCCEEEEECCCCCCCHHHHHHHHHHCCCEEEEEEECCEEEEEECCCCCCHHHHHHHCCCEEECHHH
Q ss_conf 21686699972588998789999999829849981116321799778888637989974991737999
Q gi|254781172|r 646 EIENKKLVFTGTLQKIQRHKAQEYVTQLGAVVSAILSRKTDIIIVGDNPGSKLEKAQQLGVKIMNEEQ 713 (731)
Q Consensus 646 ~l~gk~vV~TGtl~~~~R~e~~~~ie~~Ggkv~sSVSkkT~~LI~ge~~gSKl~KA~~LgI~Ii~e~e 713 (731)
.|.|-.||++| |++-.|.++-.+.-.+|+|-.-..+...++||+.-.-.-|+..-+-+|=.|++.+.
T Consensus 317 lL~GVV~VlSG-fqNP~Rs~LRskAl~LGAkY~pDW~~gsThLICAF~NTPKy~QV~g~Gg~IV~keW 383 (508)
T KOG3226 317 LLEGVVFVLSG-FQNPERSTLRSKALTLGAKYQPDWNAGSTHLICAFPNTPKYRQVEGNGGTIVSKEW 383 (508)
T ss_pred HHHCEEEEEEC-CCCCHHHHHHHHHHHHCCCCCCCCCCCCEEEEEECCCCCCHHHCCCCCCEEEEHHH
T ss_conf 65114899725-66810777888887616602677678963689723899515320157854864899
No 105
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=92.38 E-value=0.33 Score=28.56 Aligned_cols=23 Identities=22% Similarity=0.128 Sum_probs=18.9
Q ss_pred CCHHHHHCCCCCCHHHHHHHHHH
Q ss_conf 17787613888678999999999
Q gi|254781172|r 593 DDWLSLIRVPLVGDIIAQAIVEF 615 (731)
Q Consensus 593 ~~~e~L~~I~GiG~~~A~si~~f 615 (731)
...++|..++|||++||++|.-|
T Consensus 118 ~~Re~LL~lkGIG~ETADsILlY 140 (218)
T PRK13913 118 VTREWLLDQKGIGKESADAILCY 140 (218)
T ss_pred HHHHHHHCCCCCCHHHHHHHHHH
T ss_conf 58999974898663339999999
No 106
>pfam00763 THF_DHG_CYH Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain.
Probab=92.28 E-value=0.5 Score=27.13 Aligned_cols=61 Identities=31% Similarity=0.533 Sum_probs=33.0
Q ss_pred HHHHHHHHHCCCEEEEEEECCEEEEEECCCCCC------HHHHHHHCCCEE--------ECHHHHHHHHHHHCCCCCC
Q ss_conf 899999998298499811163217997788886------379899749917--------3799999999882865687
Q gi|254781172|r 664 HKAQEYVTQLGAVVSAILSRKTDIIIVGDNPGS------KLEKAQQLGVKI--------MNEEQFLFLLQQYNTTLRI 727 (731)
Q Consensus 664 ~e~~~~ie~~Ggkv~sSVSkkT~~LI~ge~~gS------Kl~KA~~LgI~I--------i~e~ef~~ll~~~~~~~~~ 727 (731)
.++++.++.+..+ .+.-+...+.+|++++| |.+.|+++||.. ++++++++.|.+.|.+...
T Consensus 14 ~~l~~~i~~l~~~---g~~P~Laii~vg~~~~s~~Yv~~k~k~~~~~Gi~~~~~~l~~~~s~~~l~~~I~~lN~D~~V 88 (117)
T pfam00763 14 EELKEEVAKLKEK---GVTPKLAVILVGDDPASQVYVRSKRKAAEELGIESELIRLPEDITEEELLALIEKLNADPSV 88 (117)
T ss_pred HHHHHHHHHHHHC---CCCCEEEEEEECCCHHHHHHHHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHHHCCCCC
T ss_conf 9999999999857---99971899984897567999999999999728716998777633499999999999678878
No 107
>KOG0966 consensus
Probab=92.23 E-value=0.98 Score=24.87 Aligned_cols=198 Identities=19% Similarity=0.228 Sum_probs=105.0
Q ss_pred CCCEEEEEEECCEEEEEEEEECCEEEEEEECCCCHHHHHHHHHHH---HHCCCCCCCCCCCC---CEEEEEEEEEEECHH
Q ss_conf 761199994158189999985998998886598655666999775---31024322335445---504899999985202
Q gi|254781172|r 124 NSIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIR---AIPTIPRVLSLNIP---EIIEVRGEVYISKND 197 (731)
Q Consensus 124 ~~~~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n~~---~i~~iP~~l~~~~~---~~ieiRGEv~m~~~~ 197 (731)
....|.+|-|+||=-+-|+|..|.. +=.|| -|-|-|.+.- ....+-.+|-...+ +....-||.+.=...
T Consensus 248 ~~~~f~lEtK~DGERiQlHk~g~~~-~yfSR----Ng~dyT~~yg~s~~~g~lt~~i~~~f~~~v~~cILDGEMm~wD~~ 322 (881)
T KOG0966 248 GGQDFYLETKFDGERIQLHKDGGEY-KYFSR----NGNDYTYEYGASYAHGTLTQRIHGAFNKEVESCILDGEMMTWDTK 322 (881)
T ss_pred CCCCEEEEEECCCCEEEEEECCCEE-EEEEC----CCCCHHHHCCCCCCCCCCCHHHHHHHHHCCHHEEECCEEEEEECC
T ss_conf 5993699862167057998438778-99832----775315440765111420188876413102401734647886053
Q ss_pred HHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCHHHHHCCCEEEEEEECCCCCC--CCCCCHHHHHHHHHCCCCCCCCE---
Q ss_conf 1234556431485433423456777752345555301110566410245433--21000036899997599665414---
Q gi|254781172|r 198 FLALNDEMIAVGRKPYANPRNAASGILRRLNPTDITRYLNFFVHGLGKTSEI--FAKGQYEMLQKMRCLGFPVNNGV--- 272 (731)
Q Consensus 198 F~~lN~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~r~L~f~ay~~~~~~~~--~~~~~~e~l~~L~~~GF~v~~~~--- 272 (731)
-+++ ...|. .+.+ ....+.+..-+..++.|++.+..+. ...+-.+..+.|+..--+...-.
T Consensus 323 ~~~f----~~~G~-----~~di-----k~~~~~~~~~qp~yvvfDLLylNgksL~~~~l~qR~e~L~~v~~p~~~~iei~ 388 (881)
T KOG0966 323 TKRF----CPFGS-----NSDI-----KELSSRDGSQQPCYVVFDLLYLNGKSLFGAPLHQRLEILKKVIVPKSGRIEIV 388 (881)
T ss_pred HHHH----CCCCC-----HHHH-----HHHHCCCCCCCCEEEEEEEEEECCCCCCCCCHHHHHHHHHHCCCCCCCEEEEE
T ss_conf 1121----14786-----2568-----87520256777317886550015853677528999999874246778705886
Q ss_pred --EEEECCCCHHHHHHHHHHHHCCCCCCCCCEEEEECCHHCCCCCCCCCCCCCCEEEECCCC-------CEEEEEEEEEE
Q ss_conf --887403211345566553100112343763777311000111587656866312311456-------21589987889
Q gi|254781172|r 273 --RQANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSLQKQLGERARSPRWMISHKFAE-------KQASTRLLDID 343 (731)
Q Consensus 273 --~~~~~~~~~~~~~~~~~~~r~~l~y~iDGiVikvn~~~~q~~lG~ts~~PrwaiA~Kf~~-------e~~~T~v~~I~ 343 (731)
..+...+++.++.++--+ -.-.|||+|--+-.++- ..|.-.| +|..| +.-.--|.+.-
T Consensus 389 ~~~~~~~~edi~~~f~~ai~------~~~EGIVlK~~~S~Y~p----g~R~~gW---~K~KPeYlkg~g~dLD~lIiGgy 455 (881)
T KOG0966 389 RSEVGSTKEDIEQFFEEAID------NGEEGIVLKKPDSSYVP----GQRSNGW---IKLKPEYLKGFGEDLDLLIIGGY 455 (881)
T ss_pred EHHHCCCHHHHHHHHHHHHH------CCCCCEEEECCCCCCCC----CCCCCCC---EEECHHHHHHCCCCCCEEEEECC
T ss_conf 24301529999999999985------68872598456764475----5457983---76468998423766537999324
Q ss_pred EEEC-CCCEEE
Q ss_conf 9403-562258
Q gi|254781172|r 344 IQIG-RTGILT 353 (731)
Q Consensus 344 wqvg-RtG~it 353 (731)
|.-| |.|.+.
T Consensus 456 ~G~g~rgg~~~ 466 (881)
T KOG0966 456 YGRGDRGGKVL 466 (881)
T ss_pred CCCCCCCCEEE
T ss_conf 58777787121
No 108
>KOG0967 consensus
Probab=92.17 E-value=0.99 Score=24.81 Aligned_cols=178 Identities=19% Similarity=0.172 Sum_probs=92.9
Q ss_pred CCCCCCHHHCCCHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCEEEEEEEE-ECCEEEEEEECCCCHHHHHHHHHHHH-
Q ss_conf 6642570215999999999999998612467776119999415818999998-59989988865986556669997753-
Q gi|254781172|r 92 SIPTLSLEKIWNIEDLRKFITRIYRFWQKKDDNSIFFTLEPKIDGTMITIRY-EKGKFVYAALRGDGHSGEDVSACIRA- 169 (731)
Q Consensus 92 ~~pMlSL~k~~~~~el~~w~~~~~~~~~~~~~~~~~~~vepKiDG~sisl~Y-~~G~L~~a~TRGdG~~GeDVT~n~~~- 169 (731)
..|||.-- ++. +...++|. .+..|+||.|+||=-.-+++ ++|. +...+| -+|+.|...--
T Consensus 344 lKPMLAkp-TK~---i~evl~rf---------~~~~FTCEyKYDGeRAQIH~~edG~-v~IfSR----N~E~~T~kYPDi 405 (714)
T KOG0967 344 LKPMLAKP-TKG---IQEVLERF---------QDKAFTCEYKYDGERAQIHKLEDGT-VEIFSR----NSENNTGKYPDI 405 (714)
T ss_pred CCCHHCCC-CHH---HHHHHHHH---------HCCEEEEEEECCCEEEEEEECCCCC-EEEEEC----CCCCCCCCCCCH
T ss_conf 74000375-210---99999985---------3751688863076022568726885-899833----653356658539
Q ss_pred HCCCCCCCCCCCCCEEEEEEEEEEECHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCH--HHHHCCCEEEEEEECCCC
Q ss_conf 102432233544550489999998520212345564314854334234567777523455--553011105664102454
Q gi|254781172|r 170 IPTIPRVLSLNIPEIIEVRGEVYISKNDFLALNDEMIAVGRKPYANPRNAASGILRRLNP--TDITRYLNFFVHGLGKTS 247 (731)
Q Consensus 170 i~~iP~~l~~~~~~~ieiRGEv~m~~~~F~~lN~~~~~~g~~~f~NpRN~aaG~lr~~d~--~~~~r~L~f~ay~~~~~~ 247 (731)
|..++...... -..+.+-||++--.. -|.+ --||. +.-+=++++. ..+.-.+..|+|++.+..
T Consensus 406 ~~~~~~~~kp~-v~sFIlD~EvVA~Dr----~~~~-----IlpFQ-----vLSTRkRk~v~v~dikV~Vcvf~FDily~n 470 (714)
T KOG0967 406 IEVISKLKKPS-VKSFILDCEVVAWDR----EKGK-----ILPFQ-----VLSTRKRKNVDVNDIKVKVCVFVFDILYLN 470 (714)
T ss_pred HHHHHHHHCCC-CCEEEEEEEEEEEEC----CCCC-----CCCHH-----HHHHHHCCCCCHHHCEEEEEEEEEEEEEEC
T ss_conf 99988752775-211577415899714----4780-----47435-----442453045306354588999998546667
Q ss_pred CCCC--CCCHHHHHHHHHCCCCCCCCEEEE-----ECCCCHHHHHHHHHHHHCCCCCCCCCEEEEECC
Q ss_conf 3321--000036899997599665414887-----403211345566553100112343763777311
Q gi|254781172|r 248 EIFA--KGQYEMLQKMRCLGFPVNNGVRQA-----NTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDE 308 (731)
Q Consensus 248 ~~~~--~~~~e~l~~L~~~GF~v~~~~~~~-----~~~~~~~~~~~~~~~~r~~l~y~iDGiVikvn~ 308 (731)
+... ..-.+.-++|.+-.=.+..+.... ++++++..+.++ +.+--+-|+-||+=|
T Consensus 471 g~~Li~~pL~eRR~~l~e~f~e~~g~f~fat~~~tn~~~eiq~Fl~~------sv~~~cEGlMvKtLd 532 (714)
T KOG0967 471 GESLIQEPLRERRELLHESFKEIPGEFQFATSLDTNDIDEIQEFLEE------SVQNSCEGLMVKTLD 532 (714)
T ss_pred CHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCCHHHHHHHHHH------HHCCCCCEEEEEEEC
T ss_conf 74565421999999877514567880667653034789999999998------632576436887506
No 109
>PRK07220 DNA topoisomerase I; Validated
Probab=92.07 E-value=0.24 Score=29.52 Aligned_cols=21 Identities=14% Similarity=0.272 Sum_probs=12.9
Q ss_pred CCCCHHHHH-----HHHHHHHHCCCC
Q ss_conf 231035410-----355556530576
Q gi|254781172|r 479 DAFNIEGLG-----KQQLDFFFKSED 499 (731)
Q Consensus 479 ~aldI~GLG-----~k~Ie~L~e~~~ 499 (731)
++|+=.||| ..+|+.|++.+|
T Consensus 476 k~ME~~GIGtpATrA~iIe~L~~R~Y 501 (740)
T PRK07220 476 KLMEDLGLGTKATRHEIISKLYSRAY 501 (740)
T ss_pred HHHHHCCCCCCCCHHHHHHHHHHCCC
T ss_conf 99973899850049999999986188
No 110
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=92.06 E-value=0.088 Score=32.95 Aligned_cols=24 Identities=29% Similarity=0.277 Sum_probs=13.8
Q ss_pred CCCHHHHHHHHHHHHHHHHHCCHH
Q ss_conf 208789999999999998977203
Q gi|254781172|r 42 IILDSEYDALKRRCDAIAHAFPDL 65 (731)
Q Consensus 42 ~isD~eYD~L~~~L~~le~~~p~~ 65 (731)
++++.|.|+|.-|-..+-+--|.+
T Consensus 70 ivt~sE~EALlLE~~LIK~~kP~Y 93 (609)
T PRK00558 70 IVTRSETEALLLENNLIKKYKPRY 93 (609)
T ss_pred EEECCHHHHHHHHHHHHHHHCCCC
T ss_conf 996998999999999986758985
No 111
>COG0190 FolD 5,10-methylene-tetrahydrofolate dehydrogenase/Methenyl tetrahydrofolate cyclohydrolase [Coenzyme metabolism]
Probab=91.35 E-value=0.6 Score=26.53 Aligned_cols=13 Identities=15% Similarity=0.580 Sum_probs=6.6
Q ss_pred HHHHHHHHHHHCC
Q ss_conf 4103555565305
Q gi|254781172|r 485 GLGKQQLDFFFKS 497 (731)
Q Consensus 485 GLG~k~Ie~L~e~ 497 (731)
|+||-|+.-|+++
T Consensus 259 GVGPmTvamLl~N 271 (283)
T COG0190 259 GVGPMTVAMLLEN 271 (283)
T ss_pred CCCHHHHHHHHHH
T ss_conf 6479999999999
No 112
>COG1623 Predicted nucleic-acid-binding protein (contains the HHH domain) [General function prediction only]
Probab=91.09 E-value=0.38 Score=28.05 Aligned_cols=50 Identities=20% Similarity=0.166 Sum_probs=40.8
Q ss_pred CHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCHHHHHCCCCCCHHHHHHHHHHHC
Q ss_conf 101111689999998829989999978977612511778761388867899999999966
Q gi|254781172|r 558 GIRHVGAEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVEFYQ 617 (731)
Q Consensus 558 GI~~vG~~~Ak~La~~f~si~~l~~~~~~~~~~~~~~~e~L~~I~GiG~~~A~si~~ff~ 617 (731)
.||-+-......|.+.|++++.+.++ +.++|.+++|||+.-|..|.+.++
T Consensus 297 kIpRlp~~iv~nlV~~F~~l~~il~A----------s~edL~~VeGIGe~rAr~i~~Gl~ 346 (349)
T COG1623 297 KIPRLPFAIVENLVRAFGTLDGILEA----------SAEDLDAVEGIGEARARAIKEGLS 346 (349)
T ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHH----------CHHHHHHHCCHHHHHHHHHHHHHH
T ss_conf 17676378999999997528999871----------476776621366999999997675
No 113
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=91.08 E-value=0.62 Score=26.41 Aligned_cols=55 Identities=9% Similarity=0.222 Sum_probs=23.8
Q ss_pred CCCHHHHHHHHHHHHHCCCCCCEEEEEHHHHCCHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHH
Q ss_conf 3103541035555653057654045410110106777531000100013421001456899998
Q gi|254781172|r 480 AFNIEGLGKQQLDFFFKSEDPAFSIRIPADIFTLQRRQQTSTTKIENILGFGDVSVTNLYDSIN 543 (731)
Q Consensus 480 aldI~GLG~k~Ie~L~e~~~~~g~I~~~~DLy~L~~~~~~~~~~l~~l~GfgeKsa~nL~~sIe 543 (731)
-+.|.|+||++.-.+... -++.+|...=. .-+...|.+++|.|.|+|++|+-+++
T Consensus 75 Li~V~GIGpK~AL~ILs~-------~~~~~l~~aI~--~~D~~~L~~vpGIG~KtA~rIi~ELk 129 (198)
T PRK00116 75 LISVSGVGPKLALAILSG-------LSPEELAQAIA--NGDIKALTKVPGVGKKTAERIVLELK 129 (198)
T ss_pred HHCCCCCCHHHHHHHHCC-------CCHHHHHHHHH--HCCHHHHCCCCCCCHHHHHHHHHHHH
T ss_conf 856688578999988702-------99999999998--58999970688978899999999999
No 114
>smart00478 ENDO3c endonuclease III. includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=91.06 E-value=0.96 Score=24.92 Aligned_cols=23 Identities=39% Similarity=0.642 Sum_probs=19.8
Q ss_pred CCHHHHHCCCCCCHHHHHHHHHH
Q ss_conf 17787613888678999999999
Q gi|254781172|r 593 DDWLSLIRVPLVGDIIAQAIVEF 615 (731)
Q Consensus 593 ~~~e~L~~I~GiG~~~A~si~~f 615 (731)
.+.++|.+++|||+++|..+..|
T Consensus 69 ~~~~~L~~lpGVG~~tA~~vl~~ 91 (149)
T smart00478 69 DDREELLKLPGVGRKTANAVLSF 91 (149)
T ss_pred CHHHHHHCCCCCCHHHHHHHHHH
T ss_conf 55999875898659999999999
No 115
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=91.01 E-value=0.55 Score=26.78 Aligned_cols=45 Identities=13% Similarity=0.264 Sum_probs=22.0
Q ss_pred HHHHHHHHHCCCCCCEEEEEHHHHCCHHHHHHHHCCCCCCCCCCCCCHHHHHHH
Q ss_conf 035555653057654045410110106777531000100013421001456899
Q gi|254781172|r 487 GKQQLDFFFKSEDPAFSIRIPADIFTLQRRQQTSTTKIENILGFGDVSVTNLYD 540 (731)
Q Consensus 487 G~k~Ie~L~e~~~~~g~I~~~~DLy~L~~~~~~~~~~l~~l~GfgeKsa~nL~~ 540 (731)
-.+.-..|++. ..+|.|+..+..+. ++++++-=||-..+|.||+.
T Consensus 47 vn~at~~Lf~~------~~t~e~l~~a~~~~---l~~~I~~iGlyr~KAk~I~~ 91 (211)
T COG0177 47 VNKATPALFKR------YPTPEDLLNADEEE---LEELIKSIGLYRNKAKNIKE 91 (211)
T ss_pred HHHHHHHHHHH------CCCHHHHHCCCHHH---HHHHHHHCCCCHHHHHHHHH
T ss_conf 99999999997------59999997499999---99999863871899999999
No 116
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=90.75 E-value=0.25 Score=29.47 Aligned_cols=82 Identities=17% Similarity=0.373 Sum_probs=42.1
Q ss_pred CCCCCHHHHHHHHHHHHHCCCCCCEEEEEHHHHCCHHHHHHHHCCC---CCCCCCCCCCHHHHHHHHH---HHHHHHHHH
Q ss_conf 1231035410355556530576540454101101067775310001---0001342100145689999---875223466
Q gi|254781172|r 478 RDAFNIEGLGKQQLDFFFKSEDPAFSIRIPADIFTLQRRQQTSTTK---IENILGFGDVSVTNLYDSI---NKRRNISLE 551 (731)
Q Consensus 478 K~aldI~GLG~k~Ie~L~e~~~~~g~I~~~~DLy~L~~~~~~~~~~---l~~l~GfgeKsa~nL~~sI---e~sK~~~L~ 551 (731)
.+-+.++++|++.+++|+++ +...+...... =+.++..|++.|.+|.... ++-...+++
T Consensus 479 ~~l~~l~~~~~ks~~nLl~a---------------Ie~sK~~~l~r~l~aLGIr~VG~~~Ak~La~~f~sl~~l~~a~~e 543 (667)
T COG0272 479 EDLLSLEGFGEKSAENLLNA---------------IEKSKKQPLARFLYALGIRHVGETTAKSLARHFGTLEALLAASEE 543 (667)
T ss_pred HHHHHCCCHHHHHHHHHHHH---------------HHHHCCCCHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHCCHH
T ss_conf 88841622446579999999---------------998604989999998797114089999999876029999842999
Q ss_pred HHHHHCCHHHHHHHHHHHHHHHCCCH
Q ss_conf 67763010111168999999882998
Q gi|254781172|r 552 RFIFSLGIRHVGAEIARSLAKYYLSY 577 (731)
Q Consensus 552 r~L~ALGI~~vG~~~Ak~La~~f~si 577 (731)
.+ ..|++||...|+.|...|..-
T Consensus 544 ~l---~~i~giG~~vA~si~~ff~~~ 566 (667)
T COG0272 544 EL---ASIPGIGEVVARSIIEFFANE 566 (667)
T ss_pred HH---HHCCCHHHHHHHHHHHHHCCH
T ss_conf 99---506661289999999997277
No 117
>PRK10702 endonuclease III; Provisional
Probab=90.55 E-value=0.79 Score=25.58 Aligned_cols=22 Identities=27% Similarity=0.342 Sum_probs=18.5
Q ss_pred CHHHHHCCCCCCHHHHHHHHHH
Q ss_conf 7787613888678999999999
Q gi|254781172|r 594 DWLSLIRVPLVGDIIAQAIVEF 615 (731)
Q Consensus 594 ~~e~L~~I~GiG~~~A~si~~f 615 (731)
+.++|+.++|||+++|..|..|
T Consensus 107 ~~~~L~~LpGIG~kTA~aIl~~ 128 (211)
T PRK10702 107 DRAALEALPGVGRKTANVVLNT 128 (211)
T ss_pred HHHHHHHHHCCCHHHHHHHHHH
T ss_conf 6999998766358899999999
No 118
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=90.51 E-value=0.86 Score=25.28 Aligned_cols=24 Identities=29% Similarity=0.397 Sum_probs=20.3
Q ss_pred CCHHHHHCCCCCCHHHHHHHHHHH
Q ss_conf 177876138886789999999996
Q gi|254781172|r 593 DDWLSLIRVPLVGDIIAQAIVEFY 616 (731)
Q Consensus 593 ~~~e~L~~I~GiG~~~A~si~~ff 616 (731)
...++|+.++|||+++|+.+.-|-
T Consensus 80 ~~~~~L~~l~GIG~~TA~~vl~~~ 103 (158)
T cd00056 80 DAREELLALPGVGRKTANVVLLFA 103 (158)
T ss_pred HHHHHHHCCCCCCHHHHHHHHHHH
T ss_conf 899998758982899999999998
No 119
>TIGR01083 nth endonuclease III; InterPro: IPR005759 The spectrum of DNA damage caused by reactive oxygen species includes a wide variety of modifications of purine and pyrimidine bases. Among these modified bases, 7,8-dihydro-8-oxoguanine (8-oxoG) is an important mutagenic lesion. Base excision repair is a critical mechanism for preventing mutations by removing the oxidative lesion from the DNA. Escherichia coli Nth protein (endonuclease III) has an 8-oxoG DNA glycosylase/AP lyase activity which removes 8-oxoG preferentially from 8-oxoG/G mispairs. Human hNTH1 protein, a homolog of E. coli Nth protein, has similar DNA glycosylase/AP lyase activity that removes 8-oxoG from 8-oxoG/G mispairs . ; GO: 0003906 DNA-(apurinic or apyrimidinic site) lyase activity, 0006284 base-excision repair, 0005622 intracellular.
Probab=90.50 E-value=0.6 Score=26.52 Aligned_cols=74 Identities=23% Similarity=0.355 Sum_probs=42.4
Q ss_pred HHHHHHHCCCCCCEEEEEHHHHCCHHHHHHHHCCCCCCCCCCCCCHHHHHHHHH----HHHHHHHHHHHHHHCCHHHHHH
Q ss_conf 555565305765404541011010677753100010001342100145689999----8752234666776301011116
Q gi|254781172|r 489 QQLDFFFKSEDPAFSIRIPADIFTLQRRQQTSTTKIENILGFGDVSVTNLYDSI----NKRRNISLERFIFSLGIRHVGA 564 (731)
Q Consensus 489 k~Ie~L~e~~~~~g~I~~~~DLy~L~~~~~~~~~~l~~l~GfgeKsa~nL~~sI----e~sK~~~L~r~L~ALGI~~vG~ 564 (731)
+.=.+||+. =.+|.|+-.+..+.+ +.++.+| .|||++ .
T Consensus 47 kaT~~LF~~------Y~tp~~~a~a~~eel-----------------~~~Ik~iGlYr~KAk~I---------------~ 88 (192)
T TIGR01083 47 KATKKLFEV------YPTPQALAAAGLEEL-----------------EEYIKSIGLYRNKAKNI---------------I 88 (192)
T ss_pred HCCHHHHHC------CCCHHHHHCCCHHHH-----------------HHHHHCCCCCHHHHHHH---------------H
T ss_conf 316786512------778689960893134-----------------77642258645689999---------------9
Q ss_pred HHHHHHHHHCC-CHHHHHHHHHHHHHCCCCCHHHHHCCCCCCHHHHHHHHH
Q ss_conf 89999998829-989999978977612511778761388867899999999
Q gi|254781172|r 565 EIARSLAKYYL-SYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVE 614 (731)
Q Consensus 565 ~~Ak~La~~f~-si~~l~~~~~~~~~~~~~~~e~L~~I~GiG~~~A~si~~ 614 (731)
..|+.|...|+ .+ -.+.++|++.||+|-|||+-+..
T Consensus 89 ~~~~~LvE~y~GeV--------------P~~~~eL~~LPGVGRKTANVVL~ 125 (192)
T TIGR01083 89 ALCRKLVERYGGEV--------------PEDREELVKLPGVGRKTANVVLN 125 (192)
T ss_pred HHHHHHHHHHCCCC--------------CCCHHHHHCCCCCCCHHHHHHHH
T ss_conf 99999999818987--------------75537661789987114562433
No 120
>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=90.26 E-value=0.55 Score=26.77 Aligned_cols=60 Identities=17% Similarity=0.330 Sum_probs=30.8
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHHHHHHHH--------HHHHCCHHHHHHHHHHHHHHH-CCCHHHHHH
Q ss_conf 100013421001456899998752234666--------776301011116899999988-299899999
Q gi|254781172|r 523 KIENILGFGDVSVTNLYDSINKRRNISLER--------FIFSLGIRHVGAEIARSLAKY-YLSYQNFAQ 582 (731)
Q Consensus 523 ~l~~l~GfgeKsa~nL~~sIe~sK~~~L~r--------~L~ALGI~~vG~~~Ak~La~~-f~si~~l~~ 582 (731)
++.+++|+|++.+++|.+=++.=+-..+.. ++.=+.|+|||.++|+.|-+. +.|++.+..
T Consensus 46 ~~~~lpGIG~~ia~kI~Eil~tG~~~~le~l~~~~p~~l~~l~~I~GiGpk~a~~l~~~Gi~sl~dL~~ 114 (307)
T cd00141 46 EAKKLPGIGKKIAEKIEEILETGKLRKLEELREDVPPGLLLLLRVPGVGPKTARKLYELGIRTLEDLRK 114 (307)
T ss_pred HHCCCCCCCHHHHHHHHHHHHHCCHHHHHHHHCCCCHHHHHHHCCCCCCHHHHHHHHHCCCCCHHHHHH
T ss_conf 871799964899999999999798089999866563789999647887889999999829997999997
No 121
>PRK00024 radC DNA repair protein RadC; Reviewed
Probab=90.23 E-value=1.5 Score=23.46 Aligned_cols=144 Identities=18% Similarity=0.299 Sum_probs=76.9
Q ss_pred HHHHHHHHHHCCHHHHH-HHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCHHHHHCCCCCCHHHHHHHHHHHCCHH-----
Q ss_conf 23466677630101111-689999998829989999978977612511778761388867899999999966979-----
Q gi|254781172|r 547 NISLERFIFSLGIRHVG-AEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVEFYQNPR----- 620 (731)
Q Consensus 547 ~~~L~r~L~ALGI~~vG-~~~Ak~La~~f~si~~l~~~~~~~~~~~~~~~e~L~~I~GiG~~~A~si~~ff~~~~----- 620 (731)
+.+|=-+|-..|.|+-- ...|+.|.+.|+++..+..+ +.++|.+|+|||+..|..|.--+.--+
T Consensus 26 D~ELLallL~~g~~~~d~~~lA~~ll~~~g~l~~l~~a----------~~~eL~~i~GiG~~kA~~l~a~~El~rR~~~~ 95 (224)
T PRK00024 26 DAELLAILLRTGTKGKSVLDLARELLERFGSLRGLLDA----------SLEELQEIKGIGPAKAAQLKAALELARRILAE 95 (224)
T ss_pred HHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHHC----------CHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHC
T ss_conf 79999999846999999899999999985999999870----------88988447898899999999999999999752
Q ss_pred ---------HHHHHHHHHH-HCCCCCCCC----CCCCCCCCCCCEEEEECCCCCC---CHHHHHHHHHHCCCEEEEEEEC
Q ss_conf ---------9999999997-338776543----2246882168669997258899---8789999999829849981116
Q gi|254781172|r 621 ---------NICAVEALLK-EVSPSIGRH----EKNVSSEIENKKLVFTGTLQKI---QRHKAQEYVTQLGAVVSAILSR 683 (731)
Q Consensus 621 ---------n~~~i~~L~~-~~~~~~~~~----~~~~~~~l~gk~vV~TGtl~~~---~R~e~~~~ie~~Ggkv~sSVSk 683 (731)
+.+.+.+++. .......+. --+..+.+-....++.|++..- .|+-++..|....
T Consensus 96 ~~~~~~~l~s~~~v~~~~~~~l~~~~~E~f~vl~Ld~~n~li~~~~i~~Gt~~~~~v~pReI~~~Al~~~A--------- 166 (224)
T PRK00024 96 RLREREVLTSPEDVADYLQAELRDEEQEVFVVLFLDTKNRLIADEELFIGTLNSSIVHPREIVKEALKLNA--------- 166 (224)
T ss_pred CCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEEEEECCCCCEEEEEEEECCCCCEEEECHHHHHHHHHHHCC---------
T ss_conf 10469874899999999999865667867999998787775568997047886467628999999998278---------
Q ss_pred CEEEEEE-----CC-CCCC-------HHHH-HHHCCCEEEC
Q ss_conf 3217997-----78-8886-------3798-9974991737
Q gi|254781172|r 684 KTDIIIV-----GD-NPGS-------KLEK-AQQLGVKIMN 710 (731)
Q Consensus 684 kT~~LI~-----ge-~~gS-------Kl~K-A~~LgI~Ii~ 710 (731)
+.++++ |+ .||. ++.+ ++.+||+++|
T Consensus 167 -~~iIl~HNHPSG~~~PS~~Di~~T~~l~~a~~~lgI~llD 206 (224)
T PRK00024 167 -AALILAHNHPSGDPEPSQADILITKRLKEAGELLGIRLLD 206 (224)
T ss_pred -CEEEEEEECCCCCCCCCHHHHHHHHHHHHHHHHCCCEEEE
T ss_conf -8799995469999998988999999999999768986861
No 122
>TIGR01239 galT_2 galactose-1-phosphate uridylyltransferase; InterPro: IPR000766 Galactose-1-phosphate uridyl transferase 2.7.7.12 from EC (galT) catalyzes the transfer of an uridyldiphosphate group on galactose (or glucose) 1-phosphate. During the reaction, the uridyl moiety links to a histidine residue. In the Escherichia coli enzyme, it has been shown that two histidine residues separated by a single proline residue are essential for enzyme activity. On the basis of sequence similarities, two apparently unrelated families seem to exist. Class-I enzymes are found in eukaryotes as well as some bacteria such as E. coli or Streptomyces lividans, while class-II enzymes have been found so far only in bacteria such as Bacillus subtilis or Lactobacillus helveticus .; GO: 0008108 UDP-glucose:hexose-1-phosphate uridylyltransferase activity, 0006012 galactose metabolic process, 0005737 cytoplasm.
Probab=90.01 E-value=0.29 Score=28.91 Aligned_cols=46 Identities=15% Similarity=0.195 Sum_probs=26.6
Q ss_pred ECCHHCCCCCCCCCCCCCCEEEECCC-CCEEEEEEEEEEEEECCCCE
Q ss_conf 31100011158765686631231145-62158998788994035622
Q gi|254781172|r 306 VDEFSLQKQLGERARSPRWMISHKFA-EKQASTRLLDIDIQIGRTGI 351 (731)
Q Consensus 306 vn~~~~q~~lG~ts~~PrwaiA~Kf~-~e~~~T~v~~I~wqvgRtG~ 351 (731)
++.....+.|+...++|.|-+====- |.-.=|.|..=.+|.||.--
T Consensus 232 I~k~tF~~LL~fl~~FP~Yf~GSNADLPIVGGsILsHdHYQ~GrH~F 278 (502)
T TIGR01239 232 ISKKTFERLLSFLEKFPHYFIGSNADLPIVGGSILSHDHYQGGRHDF 278 (502)
T ss_pred CCHHHHHHHHHHHHHCCCCEECCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf 28476888998975258750214566665577215634446888887
No 123
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=89.67 E-value=0.1 Score=32.40 Aligned_cols=53 Identities=13% Similarity=0.173 Sum_probs=32.5
Q ss_pred HCCCCCCCCCCCCCHHHHHHHHHHHH--HH-HHHHHHHHH-CCHHHHHHHHHHHHHHH
Q ss_conf 00010001342100145689999875--22-346667763-01011116899999988
Q gi|254781172|r 520 STTKIENILGFGDVSVTNLYDSINKR--RN-ISLERFIFS-LGIRHVGAEIARSLAKY 573 (731)
Q Consensus 520 ~~~~l~~l~GfgeKsa~nL~~sIe~s--K~-~~L~r~L~A-LGI~~vG~~~Ak~La~~ 573 (731)
.+..|+++.|.|.|+|-++++++.-. .+ +.... +.+ -.+||||+++|+.|.-.
T Consensus 71 lF~~LisVnGIGpK~ALaiLs~~~~~~l~~aI~~~d-~~~L~k~PGIGkKtAerivle 127 (201)
T COG0632 71 LFRLLISVNGIGPKLALAILSNLDPEELAQAIANED-VKALSKIPGIGKKTAERIVLE 127 (201)
T ss_pred HHHHHHCCCCCCHHHHHHHHCCCCHHHHHHHHHHCC-HHHHHCCCCCCHHHHHHHHHH
T ss_conf 999987118805899999984899999999998328-676441898778899999999
No 124
>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=89.46 E-value=0.94 Score=25.01 Aligned_cols=29 Identities=24% Similarity=0.274 Sum_probs=21.3
Q ss_pred CCHHHHHHHHHHHHHHHCCCHHHHHHHHH
Q ss_conf 01011116899999988299899999789
Q gi|254781172|r 557 LGIRHVGAEIARSLAKYYLSYQNFAQEIN 585 (731)
Q Consensus 557 LGI~~vG~~~Ak~La~~f~si~~l~~~~~ 585 (731)
=|||+||.++|-.|.+.|++++++...+.
T Consensus 226 ~gi~giG~k~A~kli~~~~~~e~~~~~l~ 254 (316)
T cd00128 226 EGIPGIGPVTALKLIKKYGDIEKDIERLK 254 (316)
T ss_pred CCCCCCCHHHHHHHHHHHCCHHHHHHHHH
T ss_conf 99997359999999999199999999998
No 125
>TIGR00084 ruvA Holliday junction DNA helicase RuvA; InterPro: IPR000085 In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction. The tetrameric DNA helicase RuvA specifically binds to the Holliday junction and facilitates the isomerization of the junction from the stacked folded configuration to the square-planar structure . In the RuvA tetramer, each subunit consists of three domains, I, II and III, where I and II form the major core that is responsible for Holliday junction binding and base pair rearrangements of Holliday junction executed at the crossover point, whereas domain III regulates branch migration through direct contact with RuvB.; GO: 0003678 DNA helicase activity, 0006281 DNA repair, 0006310 DNA recombination.
Probab=89.45 E-value=0.28 Score=29.10 Aligned_cols=68 Identities=16% Similarity=0.287 Sum_probs=39.6
Q ss_pred HHHHHHHHHHH-------CCCCCHHHHHHHHHHHHHCCCCCCEEEEEHHHHCCHHHHHHHHCCCCCCCCCCCCCHHHHHH
Q ss_conf 46655332130-------12310354103555565305765404541011010677753100010001342100145689
Q gi|254781172|r 467 QQLERLKHFVS-------RDAFNIEGLGKQQLDFFFKSEDPAFSIRIPADIFTLQRRQQTSTTKIENILGFGDVSVTNLY 539 (731)
Q Consensus 467 q~~~~i~hF~S-------K~aldI~GLG~k~Ie~L~e~~~~~g~I~~~~DLy~L~~~~~~~~~~l~~l~GfgeKsa~nL~ 539 (731)
|++..+-=|.. ++=|++.|+|+++.=.+.++... . .=-|.+... .+..|.+++|.|.|.|++|+
T Consensus 65 Qi~~~LfGF~~~~Er~lF~~Li~~nGvGpk~ALaiL~~~~~----~--~~~~ai~~~---~~~~L~k~pGvGKK~A~~l~ 135 (217)
T TIGR00084 65 QILHLLFGFNTLEERELFKELIKVNGVGPKLALAILSNMSP----E--EFVQAIETE---EVKALVKIPGVGKKTAERLL 135 (217)
T ss_pred HHHHHHHCCCCHHHHHHHHHHHHCCCCHHHHHHHHHCCCCH----H--HHHHHHHHH---HHHHHHCCCCCCHHHHHHHH
T ss_conf 89999734798778999999851488028999998667887----5--898888641---04442045885737899998
Q ss_pred -HHHH
Q ss_conf -9998
Q gi|254781172|r 540 -DSIN 543 (731)
Q Consensus 540 -~sIe 543 (731)
=.+.
T Consensus 136 ~leL~ 140 (217)
T TIGR00084 136 ALELK 140 (217)
T ss_pred HHHHH
T ss_conf 77754
No 126
>cd07895 Adenylation_mRNA_capping The Adenylation domain of GTP-dependent mRNA capping enzyme is a component of the catalytic core unit. 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=89.35 E-value=1.7 Score=22.97 Aligned_cols=154 Identities=18% Similarity=0.225 Sum_probs=71.6
Q ss_pred CEEEEEEECCEEEEEEEEE-CCEEEEEEECCCCHHHHHHHHHHHHHCC--CCC--CCCCCCCCEEEEEEEEEEECHHHHH
Q ss_conf 1199994158189999985-9989988865986556669997753102--432--2335445504899999985202123
Q gi|254781172|r 126 IFFTLEPKIDGTMITIRYE-KGKFVYAALRGDGHSGEDVSACIRAIPT--IPR--VLSLNIPEIIEVRGEVYISKNDFLA 200 (731)
Q Consensus 126 ~~~~vepKiDG~sisl~Y~-~G~L~~a~TRGdG~~GeDVT~n~~~i~~--iP~--~l~~~~~~~ieiRGEv~m~~~~F~~ 200 (731)
-.|+|..|-||+=.-|.-- +|. +-.++|-+-. ..+.. .|. .......+.+ +=||++.....
T Consensus 40 ~~Y~VteKaDG~R~lL~i~~~~~-~yLidR~~~~---------~~~~~~~~~~~~~~~~~~~~Tl-lDGElV~~~~~--- 105 (216)
T cd07895 40 KDYYVCEKSDGVRYLLLIDGRGE-VYLIDRNNEF---------FKVPGLFFPRPKNLKEHHQNTL-LDGELVIDKDP--- 105 (216)
T ss_pred CCEEEEECCCCEEEEEEEECCCE-EEEEECCCEE---------EECCCCCCCCCCCCCCCCCCEE-EEEEEEEECCC---
T ss_conf 98699985576599999957985-9999689817---------9844424565566765447888-96479987479---
Q ss_pred HHHHHHHCCCCCCCCHHHHHHHHHHCCCHHHHHCCCEEEEEEECCCCCCC--CCCCHHHHHHHHHC-----------CCC
Q ss_conf 45564314854334234567777523455553011105664102454332--10000368999975-----------996
Q gi|254781172|r 201 LNDEMIAVGRKPYANPRNAASGILRRLNPTDITRYLNFFVHGLGKTSEIF--AKGQYEMLQKMRCL-----------GFP 267 (731)
Q Consensus 201 lN~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~r~L~f~ay~~~~~~~~~--~~~~~e~l~~L~~~-----------GF~ 267 (731)
+ + ....|++|++....+.. .....+++..++.+ +..
T Consensus 106 --------~-----~------------------~~~~ylifDi~~~~g~~v~~~~~~~Rl~~l~~~v~~~~~~~~~~~~~ 154 (216)
T cd07895 106 --------G-----K------------------KVPRYLIFDILAFNGEPVTNRPLSERLGCLQKEVIKPRKNLKKKGPI 154 (216)
T ss_pred --------C-----C------------------EEEEEEEEEEEEECCEECCCCCHHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf --------9-----7------------------87888999999999918455987999999999877778887752533
Q ss_pred ---CCCCEEEEECCCCHHHHHHHHHHHHCCCCCCCCCEEEEECCHHCCCCCCCCCCCCCCEEEECCCC
Q ss_conf ---65414887403211345566553100112343763777311000111587656866312311456
Q gi|254781172|r 268 ---VNNGVRQANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSLQKQLGERARSPRWMISHKFAE 332 (731)
Q Consensus 268 ---v~~~~~~~~~~~~~~~~~~~~~~~r~~l~y~iDGiVikvn~~~~q~~lG~ts~~PrwaiA~Kf~~ 332 (731)
..+......++-.+.....-+......++|++||+|+.-++..+. .| +|.-.|||.+
T Consensus 155 ~~~~~~f~i~~K~f~~~~~~~~i~~~~~~~l~h~~DGLIFtP~~~py~--~G------t~~~~~KWKP 214 (216)
T cd07895 155 DKPKEPFSVRLKDFFPLYGIEKLLEKIPRSLPHENDGLIFTPNDEPYV--PG------TDKGLLKWKP 214 (216)
T ss_pred CCCCCCEEEEECCCEEHHHHHHHHHHHHCCCCCCCCEEEECCCCCCCC--CC------CCCCCEEECC
T ss_conf 366777499975728777689999866440888898599868999897--78------6776675588
No 127
>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=89.32 E-value=0.44 Score=27.57 Aligned_cols=29 Identities=28% Similarity=0.447 Sum_probs=24.0
Q ss_pred CCHHHHHHHHHHHHHHHCCCHHHHHHHHH
Q ss_conf 01011116899999988299899999789
Q gi|254781172|r 557 LGIRHVGAEIARSLAKYYLSYQNFAQEIN 585 (731)
Q Consensus 557 LGI~~vG~~~Ak~La~~f~si~~l~~~~~ 585 (731)
=|||+||.++|..|.+.|++++.+....+
T Consensus 25 pGV~GIG~ktA~~ll~~~~~l~~i~~~~~ 53 (75)
T cd00080 25 PGVPGIGPKTALKLLKEYGSLENLLENLD 53 (75)
T ss_pred CCCCCCCHHHHHHHHHHCCCHHHHHHHHH
T ss_conf 77586379999999999099999998387
No 128
>PRK10792 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=89.16 E-value=0.96 Score=24.93 Aligned_cols=14 Identities=14% Similarity=0.406 Sum_probs=8.8
Q ss_pred HHHHHHHHHHHHCC
Q ss_conf 54103555565305
Q gi|254781172|r 484 EGLGKQQLDFFFKS 497 (731)
Q Consensus 484 ~GLG~k~Ie~L~e~ 497 (731)
-|+||-|+..|+++
T Consensus 261 GGVGP~Tva~L~~N 274 (288)
T PRK10792 261 GGVGPMTVATLIEN 274 (288)
T ss_pred CCCCHHHHHHHHHH
T ss_conf 96169999999999
No 129
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=88.88 E-value=0.87 Score=25.26 Aligned_cols=46 Identities=15% Similarity=0.266 Sum_probs=27.9
Q ss_pred HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCHHHHHCCCCCCHHHHHHHHHHH
Q ss_conf 0111168999999882998999997897761251177876138886789999999996
Q gi|254781172|r 559 IRHVGAEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVEFY 616 (731)
Q Consensus 559 I~~vG~~~Ak~La~~f~si~~l~~~~~~~~~~~~~~~e~L~~I~GiG~~~A~si~~ff 616 (731)
+||||.+.|+.|..+= +. ...-.++++|..++|||+++-+.+.+++
T Consensus 102 lpgIG~~kA~aIi~yR-------e~-----~G~f~sv~dL~~v~GiG~~~~ekl~~~i 147 (149)
T COG1555 102 LPGIGPKKAQAIIDYR-------EE-----NGPFKSVDDLAKVKGIGPKTLEKLKDYI 147 (149)
T ss_pred CCCCCHHHHHHHHHHH-------HH-----CCCCCCHHHHCCCCCCCHHHHHHHHHHC
T ss_conf 6798999999999999-------97-----3997657887107777899999877561
No 130
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=88.75 E-value=0.21 Score=30.05 Aligned_cols=18 Identities=22% Similarity=0.337 Sum_probs=10.2
Q ss_pred CCCCCCCCHHHCCHHHHH
Q ss_conf 997779994688999999
Q gi|254781172|r 1 MKKRQLIPIEALSIEQAR 18 (731)
Q Consensus 1 ~~~~~~~~~~~~s~~~~~ 18 (731)
|+.+++..++-++...++
T Consensus 4 ~~~~~l~~lpGv~~~~~~ 21 (318)
T PRK04301 4 MKEKDLEDLPGVGPATAE 21 (318)
T ss_pred CCCCCCCCCCCCCHHHHH
T ss_conf 554774558998999999
No 131
>COG2003 RadC DNA repair proteins [DNA replication, recombination, and repair]
Probab=88.31 E-value=2 Score=22.47 Aligned_cols=116 Identities=18% Similarity=0.185 Sum_probs=63.1
Q ss_pred HHHHHHHHHHCCHHHHH-HHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCHHHHHCCCCCCHHHHHHHHHHHC--------
Q ss_conf 23466677630101111-689999998829989999978977612511778761388867899999999966--------
Q gi|254781172|r 547 NISLERFIFSLGIRHVG-AEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVEFYQ-------- 617 (731)
Q Consensus 547 ~~~L~r~L~ALGI~~vG-~~~Ak~La~~f~si~~l~~~~~~~~~~~~~~~e~L~~I~GiG~~~A~si~~ff~-------- 617 (731)
+..|--++-.-|+|+-- ...|+.|.++|+++..+..+ +.++|+.++|+|...|-++..-..
T Consensus 26 d~ELLailLrtG~~~~~~~~la~~lL~~fg~L~~l~~a----------~~~el~~v~GiG~aka~~l~a~~El~~R~~~~ 95 (224)
T COG2003 26 DAELLAILLRTGTKGESVLDLAKELLQEFGSLAELLKA----------SVEELSSVKGIGLAKAIQIKAAIELGKRILAE 95 (224)
T ss_pred HHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHHC----------CHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf 68999999962899987899999999973258888737----------99999517883388999999999999999998
Q ss_pred ---------CHHHHHHHHHHHHHCCCCCCCCC----CCCCCCCCCCEEEEECCCCC---CCHHHHHHHHHHCC
Q ss_conf ---------97999999999973387765432----24688216866999725889---98789999999829
Q gi|254781172|r 618 ---------NPRNICAVEALLKEVSPSIGRHE----KNVSSEIENKKLVFTGTLQK---IQRHKAQEYVTQLG 674 (731)
Q Consensus 618 ---------~~~n~~~i~~L~~~~~~~~~~~~----~~~~~~l~gk~vV~TGtl~~---~~R~e~~~~ie~~G 674 (731)
++.. ..+-+.........+.- -+..+.+-....+|+||+.. +.|.-++..+..+-
T Consensus 96 ~~~~~~~i~sp~~--~~~~l~~~l~~~~~E~f~vL~Ld~qnrlI~~e~lf~GTi~~s~V~PREI~k~Al~~nA 166 (224)
T COG2003 96 RLREGVVITSPEA--VAEYLRAELGGEEREHFVVLYLDSQNRLIATETLFIGTLNVSEVHPREIFKEALKYNA 166 (224)
T ss_pred HHCCCCCCCCHHH--HHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEEEEEECCCCEECHHHHHHHHHHHCC
T ss_conf 7505775489999--9999999861348899999995476843310037752014504337999999998221
No 132
>TIGR00354 polC DNA polymerase II, large subunit DP2; InterPro: IPR004475 This family represents the large subunit, DP2, of a two subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit.; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication, 0006308 DNA catabolic process.
Probab=88.03 E-value=0.16 Score=30.87 Aligned_cols=51 Identities=24% Similarity=0.507 Sum_probs=30.3
Q ss_pred ECCEEEEEEEEECCEEEEEEECCCCHHHHHHHHHHHHHCCCCCCCCCCCCCEEEEEEEEEEECHHHHHHHH
Q ss_conf 15818999998599899888659865566699977531024322335445504899999985202123455
Q gi|254781172|r 133 KIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPTIPRVLSLNIPEIIEVRGEVYISKNDFLALND 203 (731)
Q Consensus 133 KiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n~~~i~~iP~~l~~~~~~~ieiRGEv~m~~~~F~~lN~ 203 (731)
-|||=.+-| +||--++.-|= +.-.+|-..+-.| | .| ||+.+.+.+|-+=|+
T Consensus 389 tIegP~VkL--kNGDViri~t~---e~A~~vr~eVeeI------L------fL---Gd~LvnyGdFLeNNH 439 (1173)
T TIGR00354 389 TIEGPVVKL--KNGDVIRIDTL---EKAKAVRSEVEEI------L------FL---GDVLVNYGDFLENNH 439 (1173)
T ss_pred CCCCCEEEE--ECCCEEEECCH---HHHHHHHHHHHHH------H------HH---HHHHHHHHHHHHCCC
T ss_conf 588786584--17887882576---8888887789988------8------76---578876300432475
No 133
>pfam00633 HHH Helix-hairpin-helix motif. The helix-hairpin-helix DNA-binding motif is found to be duplicated in the central domain of RuvA. The HhH domain of DisA, a bacterial checkpoint control protein, is a DNA-binding domain.
Probab=87.96 E-value=0.31 Score=28.72 Aligned_cols=25 Identities=28% Similarity=0.371 Sum_probs=21.1
Q ss_pred CCCCHHHHHCCCCCCHHHHHHHHHH
Q ss_conf 5117787613888678999999999
Q gi|254781172|r 591 NNDDWLSLIRVPLVGDIIAQAIVEF 615 (731)
Q Consensus 591 ~~~~~e~L~~I~GiG~~~A~si~~f 615 (731)
...+.++|..++|||+++|+.|.+|
T Consensus 6 ~~as~eeL~~lpGVG~~tA~~I~~~ 30 (30)
T pfam00633 6 IPASREELLALPGVGPKTAEAILSY 30 (30)
T ss_pred CCCCHHHHHHCCCCCHHHHHHHHCC
T ss_conf 5235999972889776889988539
No 134
>KOG1921 consensus
Probab=87.07 E-value=1.3 Score=24.00 Aligned_cols=36 Identities=22% Similarity=0.280 Sum_probs=23.7
Q ss_pred HHHHHHHHHHCCC-HHHHHHHHHHHHHCCCCCHHHHHCCCCCCHHHHHHHH
Q ss_conf 6899999988299-8999997897761251177876138886789999999
Q gi|254781172|r 564 AEIARSLAKYYLS-YQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIV 613 (731)
Q Consensus 564 ~~~Ak~La~~f~s-i~~l~~~~~~~~~~~~~~~e~L~~I~GiG~~~A~si~ 613 (731)
.++|+.|..+|.+ + -.+.++|..++|+||++|--..
T Consensus 140 kkta~IL~d~f~gDI--------------P~~v~dLlsLPGVGPKMa~L~m 176 (286)
T KOG1921 140 KKTAKILQDKFDGDI--------------PDTVEDLLSLPGVGPKMAHLTM 176 (286)
T ss_pred HHHHHHHHHHHCCCC--------------CHHHHHHHCCCCCCHHHHHHHH
T ss_conf 999999998707997--------------5559988558997659999999
No 135
>TIGR01259 comE comEA protein; InterPro: IPR004787 The comE locus is obligatory for bacterial cell competence - the process of internalizing the exogenous added DNA. comEA and comEC are required for transformability, whereas the products of comEB and of the overlapping comER, which is transcribed in the reverse direction, are dispensable . ComEA has been shown to be an integral membrane protein, as predicted from hydropathy analysis, with its C-terminal domain outside the cytoplasmic membrane. This C-terminal domain possesses a sequence with similarity to those of several proteins known to be involved in nucleic acid transactions including UvrC and a human protein that binds to the replication origin of the Human herpesvirus 4 (Epstein-Barr virus) ..
Probab=86.36 E-value=0.44 Score=27.57 Aligned_cols=98 Identities=20% Similarity=0.289 Sum_probs=50.2
Q ss_pred CCCCCCCCCCHHHHHHHHHHHH-HHHHHHHHHHHCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCHHHHHCCC
Q ss_conf 0001342100145689999875-223466677630101111689999998829989999978977612511778761388
Q gi|254781172|r 524 IENILGFGDVSVTNLYDSINKR-RNISLERFIFSLGIRHVGAEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVP 602 (731)
Q Consensus 524 l~~l~GfgeKsa~nL~~sIe~s-K~~~L~r~L~ALGI~~vG~~~Ak~La~~f~si~~l~~~~~~~~~~~~~~~e~L~~I~ 602 (731)
+.+.-||-++.+...++.+... .+-. |+| ||.-|+.++-.- ....... .........+|.++.++|..|+
T Consensus 8 ~~kagg~~e~a~~~~~ntLa~k~~d~~---~vy---~P~~Ge~~~s~q--~G~~~~s-~~~~~~~VnlN~As~~EL~~l~ 78 (124)
T TIGR01259 8 IEKAGGLTEQADEKSVNTLAEKLSDEM---FVY---VPKKGEEEASQQ--TGLEVQS-EAGKEAAVNLNKASLEELQALP 78 (124)
T ss_pred HHHHCCHHHHHHHHHHHHHHHHHCCCC---EEE---CCCCCCCCCCCC--CCCCCCC-CCCCCCHHHHHHHHHHHHHHCC
T ss_conf 986133389998999999988750781---575---027652000026--7731010-0115001344067899986369
Q ss_pred CCCHHHHHHHHHHHCCHHHHHHHHHHHH
Q ss_conf 8678999999999669799999999997
Q gi|254781172|r 603 LVGDIIAQAIVEFYQNPRNICAVEALLK 630 (731)
Q Consensus 603 GiG~~~A~si~~ff~~~~n~~~i~~L~~ 630 (731)
||||..|+.|++|=..-=-...+++|.+
T Consensus 79 GiGP~kA~aIi~YRe~nG~F~SvddL~k 106 (124)
T TIGR01259 79 GIGPAKAKAIIEYREENGAFKSVDDLTK 106 (124)
T ss_pred CCCCHHHHHHHHHHHHCCCCCCHHHHHC
T ss_conf 9981337999999985699777555003
No 136
>pfam00730 HhH-GPD HhH-GPD superfamily base excision DNA repair protein. This family contains a diverse range of structurally related DNA repair proteins. The superfamily is called the HhH-GPD family after its hallmark Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate. This includes endonuclease III, EC:4.2.99.18 and MutY an A/G-specific adenine glycosylase, both have a C terminal 4Fe-4S cluster. The family also includes 8-oxoguanine DNA glycosylases. The methyl-CPG binding protein MBD4 also contains a related domain that is a thymine DNA glycosylase. The family also includes DNA-3-methyladenine glycosylase II EC:3.2.2.21 and other members of the AlkA family.
Probab=86.14 E-value=2.4 Score=21.81 Aligned_cols=22 Identities=32% Similarity=0.522 Sum_probs=18.2
Q ss_pred CHHHHHCCCCCCHHHHHHHHHH
Q ss_conf 7787613888678999999999
Q gi|254781172|r 594 DWLSLIRVPLVGDIIAQAIVEF 615 (731)
Q Consensus 594 ~~e~L~~I~GiG~~~A~si~~f 615 (731)
..++|+.++|||+.+|+.+.-|
T Consensus 79 ~~~~L~~l~GIG~~ta~~~l~~ 100 (144)
T pfam00730 79 ELEALLALPGVGRWTAEAVLLF 100 (144)
T ss_pred HHHHHHCCCCCCHHHHHHHHHH
T ss_conf 6999860889769999999999
No 137
>PRK00420 hypothetical protein; Validated
Probab=85.82 E-value=0.36 Score=28.27 Aligned_cols=25 Identities=16% Similarity=0.460 Sum_probs=17.9
Q ss_pred EECCCCCCCCCCCCCCCCCCCCCCCEEECCCC
Q ss_conf 77043265775010337865445210100354
Q gi|254781172|r 429 SFPSFCPICQSRVVRDLNPKTGKLVAAHRCTG 460 (731)
Q Consensus 429 ~~P~~CP~Cgs~l~~~~~~~~~~~~~~~rC~n 460 (731)
-.+.+||.||+|+.+..+. ..+|++
T Consensus 17 ml~~~C~~Cg~plf~~k~G-------~~~Cp~ 41 (107)
T PRK00420 17 MLDKHCPVCGLPLFELKDG-------EVVCPN 41 (107)
T ss_pred HHHHHCCCCCCCEEECCCC-------CEECCC
T ss_conf 6351376579840574898-------776898
No 138
>PRK02362 ski2-like helicase; Provisional
Probab=85.66 E-value=0.42 Score=27.72 Aligned_cols=48 Identities=25% Similarity=0.333 Sum_probs=26.2
Q ss_pred CCHHHHHHHHHHHHHHH-CCCHHHHHHHHHHHHHCCCCCHHHHHCCCCCCHHHHHHHHHHH
Q ss_conf 01011116899999988-2998999997897761251177876138886789999999996
Q gi|254781172|r 557 LGIRHVGAEIARSLAKY-YLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVEFY 616 (731)
Q Consensus 557 LGI~~vG~~~Ak~La~~-f~si~~l~~~~~~~~~~~~~~~e~L~~I~GiG~~~A~si~~ff 616 (731)
+.||+||...|+.|-++ |.|+..+.. ++.++|..| +|+++|++|.+.+
T Consensus 655 ~~I~gvgr~RAR~Ly~aGi~s~~dla~----------A~p~~l~~i--lg~~~a~~i~~~~ 703 (736)
T PRK02362 655 VGLRGIGRVRARRLYNAGITSRADLRA----------ADKEVVAAI--LGPKIAERVLEQL 703 (736)
T ss_pred CCCCCCCHHHHHHHHHCCCCCHHHHHH----------CCHHHHHHH--HHHHHHHHHHHHH
T ss_conf 088999989999999879999999970----------999999999--7778999999983
No 139
>TIGR02317 prpB methylisocitrate lyase; InterPro: IPR012695 Propionate is the second most abundant low molecular mass carbon source found in soil, being generated by the degradation of several amino acids, fementation of crabohydrates and the oxidation of odd-chain fatty acids. Many different organisms are capable of metabolising propionate and several distinct pathways for utilising this compound exist, all of which begin with its activation to propionyl-CoA . Many bacteria metabolise propionate to pyruvate by the 2-methylcitric acid cycle. In the first step, catalysed by methycitrate synthase, oxaloacetate and propionyl-CoA are condensed to form 2-methylcitrate and CoA. The 2-methylcitrate is subsequently converted to 2-methylisocitrate by the combined actions of a dehydratase and an aconitase. In the final step, 2-methylisocitrate lyase cleaves a C-C bond within this compound to form succinate and pyruvate. The succinate is further oxidised to oxaloacetate which re-enters the cycle, while the pyruvate can be used further for either energy generation or biomass synthesis. Proteins in this entry are mostly 2-methylisocitrate lyases. Some of them have been annotated (incorrectly it seems) as the related protein carboxyphosphoenolpyruvate phosphomutase, which is involved in synthesizing the antibiotic bialaphos in Streptomyces hygroscopicus. Structural studies indicate that these enzymes belong to the isocitrate lyase family, binding a Mg(2+) cofactor and forming a TIM barrel fold , . As with other enzymes in this family, substrate-binding induces a conformational change that prevents solvent access to the active site and which is important for catalysis. .
Probab=85.21 E-value=1.3 Score=23.96 Aligned_cols=131 Identities=19% Similarity=0.237 Sum_probs=73.7
Q ss_pred HHCCCCCCCCCCCCCHHHHHHHHH--HHH--HHHHHH--HHHH-HCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCC
Q ss_conf 100010001342100145689999--875--223466--6776-301011116899999988299899999789776125
Q gi|254781172|r 519 TSTTKIENILGFGDVSVTNLYDSI--NKR--RNISLE--RFIF-SLGIRHVGAEIARSLAKYYLSYQNFAQEINNIIAHN 591 (731)
Q Consensus 519 ~~~~~l~~l~GfgeKsa~nL~~sI--e~s--K~~~L~--r~L~-ALGI~~vG~~~Ak~La~~f~si~~l~~~~~~~~~~~ 591 (731)
+...++++++| +=|=+-|+ |++ +-+-|+ =+=. +||+|.+|-++..-++..-..|-.. .
T Consensus 9 ~~~~~ilq~pG-----a~n~~~AL~Ae~aGF~A~YLSGaa~aa~sLGlPDLG~~tL~Eva~~~r~Itr~----------~ 73 (287)
T TIGR02317 9 IAKEDILQIPG-----AINGLVALLAERAGFEAIYLSGAAVAAGSLGLPDLGITTLTEVAERARRITRV----------T 73 (287)
T ss_pred HHCCCCEEECC-----HHHHHHHHHHHHCCCCEEEEHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHH----------C
T ss_conf 85689748714-----06189999998637556610168774132067767667878999998877753----------0
Q ss_pred CCCHHHHHCCC-CCCHHH--HHHHHHHHCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCHHHHHH
Q ss_conf 11778761388-867899--999999966979999999999733877654322468821686699972588998789999
Q gi|254781172|r 592 NDDWLSLIRVP-LVGDII--AQAIVEFYQNPRNICAVEALLKEVSPSIGRHEKNVSSEIENKKLVFTGTLQKIQRHKAQE 668 (731)
Q Consensus 592 ~~~~e~L~~I~-GiG~~~--A~si~~ff~~~~n~~~i~~L~~~~~~~~~~~~~~~~~~l~gk~vV~TGtl~~~~R~e~~~ 668 (731)
+.--|..+| |||+-. +..+.+ +.+--...+.++....++. =++|.||.+| +++|+.+
T Consensus 74 --~LPlLVD~DTGFGea~nvaRTVre---------me~AGaAa~HiEDQv~pKr-CGHL~gK~lv--------~~~eMv~ 133 (287)
T TIGR02317 74 --DLPLLVDADTGFGEALNVARTVRE---------MEDAGAAAVHIEDQVLPKR-CGHLNGKELV--------SRDEMVR 133 (287)
T ss_pred --CCCEEEEEECCCCCHHHHHHHHHH---------HHHHHHHHCCHHHHCCCCC-CCCCCCCCCC--------CHHHHHH
T ss_conf --487278633289835449999999---------9984454004677425442-6789887404--------8877999
Q ss_pred HHHHCCCEEEEEEECCE--EEEEEC
Q ss_conf 99982984998111632--179977
Q gi|254781172|r 669 YVTQLGAVVSAILSRKT--DIIIVG 691 (731)
Q Consensus 669 ~ie~~Ggkv~sSVSkkT--~~LI~g 691 (731)
+|.+. |+.+. |++|+-
T Consensus 134 kI~AA-------v~Ar~De~f~iiA 151 (287)
T TIGR02317 134 KIKAA-------VDARRDEDFVIIA 151 (287)
T ss_pred HHHHH-------HCCCCCCCCEEEE
T ss_conf 99997-------1478999727753
No 140
>PRK00421 murC UDP-N-acetylmuramate--L-alanine ligase; Provisional
Probab=84.28 E-value=3.1 Score=20.98 Aligned_cols=13 Identities=31% Similarity=0.207 Sum_probs=5.6
Q ss_pred EEEEECCHHCCCC
Q ss_conf 3777311000111
Q gi|254781172|r 302 LVYKVDEFSLQKQ 314 (731)
Q Consensus 302 iVikvn~~~~q~~ 314 (731)
+|+-.||...+..
T Consensus 215 ~ViN~DD~~~~~l 227 (459)
T PRK00421 215 LVACGDDPELREL 227 (459)
T ss_pred EECCCCCHHHHHH
T ss_conf 1146879899998
No 141
>pfam03118 RNA_pol_A_CTD Bacterial RNA polymerase, alpha chain C terminal domain. The alpha subunit of RNA polymerase consists of two independently folded domains, referred to as amino-terminal and carboxyl terminal domains. The amino terminal domain is involved in the interaction with the other subunits of the RNA polymerase. The carboxyl-terminal domain interacts with the DNA and activators. The amino acid sequence of the alpha subunit is conserved in prokaryotic and chloroplast RNA polymerases. There are three regions of particularly strong conservation, two in the amino-terminal and one in the carboxyl- terminal.
Probab=84.07 E-value=0.6 Score=26.49 Aligned_cols=50 Identities=14% Similarity=0.278 Sum_probs=35.9
Q ss_pred HHHHHHHHHHHHHCCCCCCEEEEEHHHHCCHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHH
Q ss_conf 3541035555653057654045410110106777531000100013421001456899998
Q gi|254781172|r 483 IEGLGKQQLDFFFKSEDPAFSIRIPADIFTLQRRQQTSTTKIENILGFGDVSVTNLYDSIN 543 (731)
Q Consensus 483 I~GLG~k~Ie~L~e~~~~~g~I~~~~DLy~L~~~~~~~~~~l~~l~GfgeKsa~nL~~sIe 543 (731)
--+|+..+...|-.++ |.++.||..++.. +|.++++||.||.+-+.+.++
T Consensus 12 ~L~LS~R~~N~Lk~~~-----I~tv~dL~~~s~~------dLl~i~N~G~kSl~EI~~~L~ 61 (62)
T pfam03118 12 ELELSVRSYNCLKRAG-----INTVGDLLSKSEE------DLLKIKNFGKKSLEEIKEKLE 61 (62)
T ss_pred HHCCCHHHHHHHHHCC-----CCCHHHHHHCCHH------HHHHCCCCCHHHHHHHHHHHC
T ss_conf 8168689999998949-----9679999858999------997488986857999999982
No 142
>KOG2043 consensus
Probab=84.07 E-value=2.2 Score=22.08 Aligned_cols=68 Identities=16% Similarity=0.101 Sum_probs=51.7
Q ss_pred EEEEECCCCCCCHHHHHHHHHHCCCEEEEEEECCEEEEEECCCCCCHHHHHHHCCCEEECHHHHHHHHHHH
Q ss_conf 69997258899878999999982984998111632179977888863798997499173799999999882
Q gi|254781172|r 651 KLVFTGTLQKIQRHKAQEYVTQLGAVVSAILSRKTDIIIVGDNPGSKLEKAQQLGVKIMNEEQFLFLLQQY 721 (731)
Q Consensus 651 ~vV~TGtl~~~~R~e~~~~ie~~Ggkv~sSVSkkT~~LI~ge~~gSKl~KA~~LgI~Ii~e~ef~~ll~~~ 721 (731)
.++|+|.+ .+.-++.+++.+||.+.+|.+.-|++++-.---..|+--|-.+|++|++++.+.+.+...
T Consensus 661 ~~lfs~~~---~~~~~k~~~k~lg~s~~ss~~e~Th~i~~rirRT~k~Leai~~G~~ivT~~wL~s~~k~g 728 (896)
T KOG2043 661 EVLFSDKN---DGKNYKLAKKFLGGSVASSDSEATHFIADRIRRTLKFLEAISSGKPLVTPQWLVSSLKSG 728 (896)
T ss_pred EEEEEECC---CCHHHHHHHHHCCCEEECCCCCCEEEEEHHHHCCHHHHHHHCCCCCCCCHHHHHHHHHCC
T ss_conf 36665135---754555677650650103530100243020221178775022487412548988776416
No 143
>PRK13766 Hef nuclease; Provisional
Probab=83.83 E-value=0.53 Score=26.91 Aligned_cols=28 Identities=18% Similarity=0.472 Sum_probs=22.5
Q ss_pred HHHCCCCCCHHHHHHHHHHHCCHHHHHH
Q ss_conf 7613888678999999999669799999
Q gi|254781172|r 597 SLIRVPLVGDIIAQAIVEFYQNPRNICA 624 (731)
Q Consensus 597 ~L~~I~GiG~~~A~si~~ff~~~~n~~~ 624 (731)
-|..+|||||+.|..+.+-|...+++..
T Consensus 707 ~l~~~pgvg~~~a~~ll~~fgsi~~i~~ 734 (764)
T PRK13766 707 IVSSLPDVGPVLARNLLDHFGSVENVMT 734 (764)
T ss_pred HHHHCCCCCHHHHHHHHHHCCCHHHHHC
T ss_conf 9983899999999999997199999965
No 144
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=82.85 E-value=0.39 Score=27.96 Aligned_cols=35 Identities=14% Similarity=0.328 Sum_probs=28.2
Q ss_pred CCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCHHHHHHHHHHHH
Q ss_conf 32657750103378654452101003543441144665533213
Q gi|254781172|r 433 FCPICQSRVVRDLNPKTGKLVAAHRCTGGLACSAQQLERLKHFV 476 (731)
Q Consensus 433 ~CP~Cgs~l~~~~~~~~~~~~~~~rC~n~~~Cpaq~~~~i~hF~ 476 (731)
.||.|+.++.... ..++|.|+ .|.....+-..++-
T Consensus 4 ~CPvC~~~L~~~~--------~sl~C~~~-H~FD~AkqGYvnLL 38 (272)
T PRK11088 4 QCPLCHQPLTLEE--------NSWICPQN-HQFDCAKEGYVNLL 38 (272)
T ss_pred ECCCCCCCCEECC--------CEEECCCC-CCCCCCCCCEEEEC
T ss_conf 0899991201079--------68885899-88745678467703
No 145
>pfam06044 DRP Dam-replacing family. Dam-replacing protein (DRP) is an 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.
Probab=81.33 E-value=0.82 Score=25.46 Aligned_cols=49 Identities=20% Similarity=0.490 Sum_probs=28.6
Q ss_pred HHHHHHCCCCCCCCCCEEEECCCCCCCCCC-CCCCCCCCCCCCCEEECCCCCCCCHHHHHHH
Q ss_conf 566541012357873047770432657750-1033786544521010035434411446655
Q gi|254781172|r 411 PKVVDIIVNERHPDAQPFSFPSFCPICQSR-VVRDLNPKTGKLVAAHRCTGGLACSAQQLER 471 (731)
Q Consensus 411 P~I~~Vi~~~r~~~~~~~~~P~~CP~Cgs~-l~~~~~~~~~~~~~~~rC~n~~~Cpaq~~~~ 471 (731)
+++++|+.+.=- .--..||.||+. +..-.+... .+|.+|+ +|.++..=+
T Consensus 17 sQi~RVLsE~Wv------~~n~yCP~Cg~~~l~~~~NN~P---VaDFyC~---~C~e~yELK 66 (254)
T pfam06044 17 SQIIRVLSEDWV------AKQGYCPNCGSNPLSRFANNQP---VADFYCP---NCHEDYELK 66 (254)
T ss_pred CCEEEECCHHHH------HHCCCCCCCCCCHHHHCCCCCC---CCEEECC---CCCHHHHHH
T ss_conf 044564037789------8668799889722122337992---3303547---740666003
No 146
>TIGR00600 rad2 DNA excision repair protein (rad2); InterPro: IPR001044 Xeroderma pigmentosum (XP) is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. People's skin cells with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-G is one of the most rare and phenotypically heterogeneous of XP, showing anything from slight to extreme dysfunction in DNA excision repair , . XP-G can be corrected by a 133 Kd nuclear protein, XPGC . XPGC is an acidic protein that confers normal UV resistance in expressing cells . It is a magnesium-dependent, single-strand DNA endonuclease that makes structure-specific endonucleolytic incisions in a DNA substrate containing a duplex region and single-stranded arms , . XPGC cleaves one strand of the duplex at the border with the single-stranded region . XPG belongs to a family of proteins that includes RAD2 from Saccharomyces cerevisiae (Baker's yeast) and rad13 from Schizosaccharomyces pombe (Fission yeast), which are single-stranded DNA endonucleases , ; mouse and human FEN-1, a structure-specific endonuclease; RAD2 from fission yeast and RAD27 from budding yeast; fission yeast exo1, a 5'-3' double-stranded DNA exonuclease that may act in a pathway that corrects mismatched base pairs; yeast DHS1, and yeast DIN7. Sequence alignment of this family of proteins reveals that similarities are largely confined to two regions. The first is located at the N-terminal extremity (N-region) and corresponds to the first 95 to 105 amino acids. The second region is internal (I-region) and found towards the C-terminus; it spans about 140 residues and contains a highly conserved core of 27 amino acids that includes a conserved pentapeptide (E-A-[DE]-A-[QS]). It is possible that the conserved acidic residues are involved in the catalytic mechanism of DNA excision repair in XPG. The amino acids linking the N- and I-regions are not conserved. This entry represents XPGC, an acidic protein that confers normal UV resistance in expressing cells, can correct XP-G. It is a magnesium-dependent, single-strand DNA endonuclease that makes structure-specific endonucleolytic incisions in a DNA substrate containing a duplex region and single-stranded arms. XPGC cleaves one strand of the duplex at the border with the single-stranded region , .; GO: 0003697 single-stranded DNA binding, 0004519 endonuclease activity, 0006289 nucleotide-excision repair, 0005634 nucleus.
Probab=80.98 E-value=4.1 Score=20.09 Aligned_cols=25 Identities=8% Similarity=0.108 Sum_probs=17.2
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHCC
Q ss_conf 7982087899999999999989772
Q gi|254781172|r 39 SKPIILDSEYDALKRRCDAIAHAFP 63 (731)
Q Consensus 39 ~~p~isD~eYD~L~~~L~~le~~~p 63 (731)
+.-+.|..+|..++.+...|+..+-
T Consensus 188 ~s~~~~~~~~~~~mn~~q~~~~~~~ 212 (1127)
T TIGR00600 188 DSEEESEKEWEERMNQKQKLQEEFF 212 (1127)
T ss_pred CCCCCCHHHHHHHHHHHHHCCCCCC
T ss_conf 7331224899999888852043103
No 147
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=80.89 E-value=1.7 Score=23.01 Aligned_cols=15 Identities=40% Similarity=0.594 Sum_probs=7.7
Q ss_pred CCHHHHHHHHHHCCC
Q ss_conf 423456777752345
Q gi|254781172|r 214 ANPRNAASGILRRLN 228 (731)
Q Consensus 214 ~NpRN~aaG~lr~~d 228 (731)
-.|.|++.|.++.+.
T Consensus 38 g~~~~~~~~~~~~l~ 52 (310)
T COG0258 38 GDPTGAVSGFLGMLY 52 (310)
T ss_pred CCCCCHHHHHHHHHH
T ss_conf 784449999999999
No 148
>TIGR01497 kdpB K+-transporting ATPase, B subunit; InterPro: IPR006391 These sequences describe the P-type ATPase subunit of the complex responsible for translocating potassium ions across biological membranes in microbes. In Escherichia coli and other species, this complex consists of the proteins KdpA, KdpB, KdpC and KdpF. KdpB is the ATPase subunit, while KdpA is the potassium-ion translocating subunit . The function of KdpC is unclear, although it has been suggested to couple the ATPase subunit to the ion-translocating subunit , while KdpF serves to stabilize the complex . The potassium P-type ATPases have been characterised as Type IA based on a phylogenetic analysis which places this clade closest to the heavy-metal translocating ATPases (Type IB) . Others place this clade closer to the Na+/K+ antiporter type (Type IIC) based on physical characteristics . ; GO: 0008556 potassium-transporting ATPase activity, 0006813 potassium ion transport, 0016021 integral to membrane.
Probab=80.67 E-value=0.85 Score=25.35 Aligned_cols=157 Identities=15% Similarity=0.261 Sum_probs=72.8
Q ss_pred HHHHHHHHHHCCHHHHHHHHH-HHHHH------HCCCHHHHHHHHHHHHHCCCCCHHHHHCCCCCCHHHHHHHH---HHH
Q ss_conf 234666776301011116899-99998------82998999997897761251177876138886789999999---996
Q gi|254781172|r 547 NISLERFIFSLGIRHVGAEIA-RSLAK------YYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIV---EFY 616 (731)
Q Consensus 547 ~~~L~r~L~ALGI~~vG~~~A-k~La~------~f~si~~l~~~~~~~~~~~~~~~e~L~~I~GiG~~~A~si~---~ff 616 (731)
..+.-=+|.|.||-|.-+-+- ..||. +.++.+.+.=+-...+-..|...+++.-+.|...+.--+.- .-+
T Consensus 262 PTTIGGLLSAIGiAGMdRv~~fNVIAtSGrAVEAcGDVdtl~LDKTGTITlGNRlA~eFIp~~G~d~~~lad~a~~aSl~ 341 (675)
T TIGR01497 262 PTTIGGLLSAIGIAGMDRVLRFNVIATSGRAVEACGDVDTLVLDKTGTITLGNRLAEEFIPVQGVDKKKLADVAVLASLA 341 (675)
T ss_pred HHHHHHHHHHHHHHHHHHHHHCCEEEECCCEEEECCCCCEEEECCCCCCCCCCHHHHHCCCCCCCCHHHHHHHHHHHCCC
T ss_conf 00033688886542355673055245246402412872347764657403321105334455883488898588760113
Q ss_pred CC-HHHHHHHHHHHHHCCCCCCCCCCC-C-------CC-----CCCCCEEEEECCCCCCCHHHHHHHHHHCCCEEEEEEE
Q ss_conf 69-799999999997338776543224-6-------88-----2168669997258899878999999982984998111
Q gi|254781172|r 617 QN-PRNICAVEALLKEVSPSIGRHEKN-V-------SS-----EIENKKLVFTGTLQKIQRHKAQEYVTQLGAVVSAILS 682 (731)
Q Consensus 617 ~~-~~n~~~i~~L~~~~~~~~~~~~~~-~-------~~-----~l~gk~vV~TGtl~~~~R~e~~~~ie~~Ggkv~sSVS 682 (731)
.+ |+-+..+ +|-+++++.....+.. . .+ .|.|=+-+==| +=+-++..+++++|.+...+-
T Consensus 342 DdTPEGkSIV-~Lakqlgir~d~~~~~~a~fveFtAqtRMSGinl~nGr~~rKG-----avdAIk~~V~~~~G~ip~dlD 415 (675)
T TIGR01497 342 DDTPEGKSIV-ELAKQLGIRIDDKKSESAEFVEFTAQTRMSGINLDNGREVRKG-----AVDAIKKFVEERKGRIPKDLD 415 (675)
T ss_pred CCCCCCHHHH-HHHHHHCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCEEECC-----CHHHHHHHHHHCCCCCCHHHH
T ss_conf 5898836888-8887808610147453232101323333454438988436227-----617887898763797783767
Q ss_pred CC---------EEEEEE-----------CC--CCC--CHHHHHHHCCCEEE
Q ss_conf 63---------217997-----------78--888--63798997499173
Q gi|254781172|r 683 RK---------TDIIIV-----------GD--NPG--SKLEKAQQLGVKIM 709 (731)
Q Consensus 683 kk---------T~~LI~-----------ge--~~g--SKl~KA~~LgI~Ii 709 (731)
.+ |=++|+ +| |+| -..++=++.||+-|
T Consensus 416 ~av~qVa~~GgTPLvVc~dn~iyGVIyLKDiVK~Gi~ERF~qLR~~GikTi 466 (675)
T TIGR01497 416 EAVDQVAKQGGTPLVVCVDNKIYGVIYLKDIVKSGIKERFEQLRKMGIKTI 466 (675)
T ss_pred HHHHHHHHCCCCCEEEEECCEEEEEEEEECCCCCCHHHHHHHHHHCCCEEE
T ss_conf 889998732898479997577898898730137860457888722586689
No 149
>PRK07726 DNA topoisomerase III; Provisional
Probab=80.56 E-value=0.84 Score=25.40 Aligned_cols=18 Identities=22% Similarity=0.362 Sum_probs=12.3
Q ss_pred CHHHHH-----HHHHHHHHCCCC
Q ss_conf 035410-----355556530576
Q gi|254781172|r 482 NIEGLG-----KQQLDFFFKSED 499 (731)
Q Consensus 482 dI~GLG-----~k~Ie~L~e~~~ 499 (731)
+.+||| ..+|+.|++.+|
T Consensus 511 ~~~GIGTpATRA~IIe~L~~r~Y 533 (716)
T PRK07726 511 KTEGLGTEATRAGIITMLKDRKY 533 (716)
T ss_pred HCCCCCCCCCHHHHHHHHHHCCC
T ss_conf 45688884108999999874571
No 150
>TIGR01265 tyr_nico_aTase tyrosine/nicotianamine aminotransferases; InterPro: IPR005958 This entry describes tyrosine aminotransferase (2.6.1.5 from EC) as found in animals and Trypanosoma cruzi (Euglenozoa). It is the first enzyme of a pathway of tyrosine degradation via homogentisate. L-tyrosine + 2-oxoglutarate = 4-hydroxyphenylpyruvate + L-glutamate. Several plant enzyme designated as probable tyrosine aminotransferases are very closely related to an experimentally demonstrated nicotianamine aminotransferase, an enzyme in a siderophore (iron uptake chelator) biosynthesis pathway are included in this family. ; GO: 0008483 transaminase activity, 0030170 pyridoxal phosphate binding, 0006519 amino acid and derivative metabolic process.
Probab=80.43 E-value=0.81 Score=25.50 Aligned_cols=107 Identities=12% Similarity=0.097 Sum_probs=48.1
Q ss_pred HHHHHHHHHHHHHH--HHHHHHHHHCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHH-HCCCCCHHHHHCCCCCCHHH-H
Q ss_conf 14568999987522--34666776301011116899999988299899999789776-12511778761388867899-9
Q gi|254781172|r 534 SVTNLYDSINKRRN--ISLERFIFSLGIRHVGAEIARSLAKYYLSYQNFAQEINNII-AHNNDDWLSLIRVPLVGDII-A 609 (731)
Q Consensus 534 sa~nL~~sIe~sK~--~~L~r~L~ALGI~~vG~~~Ak~La~~f~si~~l~~~~~~~~-~~~~~~~e~L~~I~GiG~~~-A 609 (731)
.-++++++|.+--+ ..-..|+-| -.-+.|.+ |-++|.+.+-+.+ ...+.-+++|.+|+|+-+.. =
T Consensus 282 ~~~k~~~gl~~~~~~~~gP~Ti~Qg--------ALP~IL~~---Tp~efF~~~~~~lk~na~l~y~~L~~ipg~~c~~KP 350 (424)
T TIGR01265 282 RDTKVLQGLKNVLQLILGPATIVQG--------ALPDILEN---TPQEFFDKKISVLKENAELCYEELKDIPGLTCPKKP 350 (424)
T ss_pred CCCCHHHHHHHHHCCCCCCHHHHHH--------HHHHHHHH---CCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCC
T ss_conf 4440338989984234781578999--------99999851---687688999999885188999997348876476488
Q ss_pred -----------HHHHHHHCCHHHHHHHHHHHHHCCCCCCCC-CCCCCCCCCCCEEEEEC
Q ss_conf -----------999999669799999999997338776543-22468821686699972
Q gi|254781172|r 610 -----------QAIVEFYQNPRNICAVEALLKEVSPSIGRH-EKNVSSEIENKKLVFTG 656 (731)
Q Consensus 610 -----------~si~~ff~~~~n~~~i~~L~~~~~~~~~~~-~~~~~~~l~gk~vV~TG 656 (731)
-+..+-|++ ..++.++|.++=....-+- .-...+- ..||||=
T Consensus 351 ~G~MY~mvkl~~~~~~~ikd--D~dFc~kL~~EESv~~LPG~~f~~pnw---~Rit~t~ 404 (424)
T TIGR01265 351 EGSMYLMVKLELELLEEIKD--DVDFCEKLVKEESVICLPGSAFGLPNW---VRITITV 404 (424)
T ss_pred CCCEEEHHHCCHHHCCCCCC--CHHHHHHHHHHCCCEECCCEEECCCCC---EEEEECC
T ss_conf 87500020101653446464--189999998737633546002559984---7998527
No 151
>COG1110 Reverse gyrase [DNA replication, recombination, and repair]
Probab=79.85 E-value=1.4 Score=23.78 Aligned_cols=40 Identities=33% Similarity=0.488 Sum_probs=27.4
Q ss_pred EEEECCCCHHHHHHHCCCCCCCCCCEEEECCCCCCCCCCCC
Q ss_conf 99835870256654101235787304777043265775010
Q gi|254781172|r 402 LVKRAGEVIPKVVDIIVNERHPDAQPFSFPSFCPICQSRVV 442 (731)
Q Consensus 402 ~I~RaGdVIP~I~~Vi~~~r~~~~~~~~~P~~CP~Cgs~l~ 442 (731)
++...|.-+| |..+++..|..+.+-...-..||-||+.-+
T Consensus 680 vl~~~~~~vP-vY~tIKrC~dcg~q~~~~~~~cP~Cgs~~v 719 (1187)
T COG1110 680 VLVKDGKYVP-VYDTIKRCRDCGEQFVDSEDKCPRCGSRNV 719 (1187)
T ss_pred EECCCCCEEE-HHHHHHHHHHCCCEECCCCCCCCCCCCCCC
T ss_conf 5605870686-278888885158440443235988788320
No 152
>PTZ00111 DNA replication licensing factor MCM4; Provisional
Probab=79.85 E-value=1.3 Score=23.85 Aligned_cols=41 Identities=7% Similarity=0.041 Sum_probs=17.3
Q ss_pred HCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHH
Q ss_conf 889999999999999999999984331779820878999999
Q gi|254781172|r 11 ALSIEQARKELSSLEQEISYHDDCYYQYSKPIILDSEYDALK 52 (731)
Q Consensus 11 ~~s~~~~~~~i~~L~~~i~~~~~~Yy~~~~p~isD~eYD~L~ 52 (731)
+-.+++.+++......+...++.-| ..-+.-++-.+|+.|+
T Consensus 82 d~~~e~~~e~f~~f~~~ft~~~~~~-~~~d~~~~~~~~~~ly 122 (916)
T PTZ00111 82 DNRLEELSERFTNFLKNFTEFDANS-EDKDEQQNKPANTELY 122 (916)
T ss_pred HCCHHHHHHHHHHHHHHCCCCCCHH-HHHHHHHCCHHHHHHH
T ss_conf 4309999999999998426643012-2346542212678899
No 153
>TIGR01954 nusA_Cterm_rpt transcription termination factor NusA, C-terminal duplication; InterPro: IPR010214 NusA, or N utilisation substance protein A, is a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in Escherichia coli of phage lambda antitermination protein N with the N-utilisation substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and NusG . This entry 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 ; GO: 0030528 transcription regulator activity.
Probab=79.56 E-value=3.7 Score=20.40 Aligned_cols=42 Identities=17% Similarity=0.237 Sum_probs=29.1
Q ss_pred HHHHHHHHHHH-CCCHHHHHHHHHHHHHCCCCCHHHHHC--CCCCCHHHHHHHHH
Q ss_conf 16899999988-299899999789776125117787613--88867899999999
Q gi|254781172|r 563 GAEIARSLAKY-YLSYQNFAQEINNIIAHNNDDWLSLIR--VPLVGDIIAQAIVE 614 (731)
Q Consensus 563 G~~~Ak~La~~-f~si~~l~~~~~~~~~~~~~~~e~L~~--I~GiG~~~A~si~~ 614 (731)
.+..|+.|+.+ |.|++.+.. ..+.+|.. |+|+-+.+|+.+..
T Consensus 2 ~e~~a~~Lv~eGf~t~EdlAy----------~~~~EL~~fGIeG~~Ee~A~~L~~ 46 (52)
T TIGR01954 2 DEEIAQLLVEEGFTTVEDLAY----------VPVDELLSFGIEGLDEETAKELIN 46 (52)
T ss_pred CHHHHHHHHHHCCCHHHHHHC----------CCHHHHHHHCCCCCCHHHHHHHHH
T ss_conf 578899999736731788750----------455668863589988788999999
No 154
>TIGR00608 radc DNA repair protein RadC; InterPro: IPR001405 RadC is a DNA repair protein found in many bacteria. They share a region of similarity at the C-terminus that contains two perfectly conserved histidine residues.; GO: 0006281 DNA repair.
Probab=79.45 E-value=4.5 Score=19.74 Aligned_cols=126 Identities=21% Similarity=0.363 Sum_probs=65.3
Q ss_pred HHHHHHHHHCC--CHHHHHHHHHHHHHCCCCCHHHHHCCCCCCHHHHHHHHH-------HH----------CCHHHHHHH
Q ss_conf 89999998829--989999978977612511778761388867899999999-------96----------697999999
Q gi|254781172|r 565 EIARSLAKYYL--SYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVE-------FY----------QNPRNICAV 625 (731)
Q Consensus 565 ~~Ak~La~~f~--si~~l~~~~~~~~~~~~~~~e~L~~I~GiG~~~A~si~~-------ff----------~~~~n~~~i 625 (731)
.-||.|.++|+ .++.+. .....+.++|.+|+|||...|.++.- ++ .+|+ ..
T Consensus 37 ~Lsk~lL~~fG~~~~d~l~-------~L~~~~~~~L~~v~GiG~ak~~qlka~~El~~R~~~~~~~~~~~i~sPe---~~ 106 (223)
T TIGR00608 37 SLSKELLKQFGQEELDSLD-------LLLSAEPEELSSVPGIGLAKAIQLKAIVELAKRYAKSRMLERPVIRSPE---AA 106 (223)
T ss_pred HHHHHHHHHHCHHCCCCHH-------HHHCCCHHHHHCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHH---HH
T ss_conf 7899999870700013001-------4321585785046885088999999999998677524421466648989---99
Q ss_pred HHHH-HHCCCCCCCCC----CCCCCCCCCCEEEEECCCCC---CCHHHHHHHHHHCCCEEEEEEECCEEEEEE-----C-
Q ss_conf 9999-73387765432----24688216866999725889---987899999998298499811163217997-----7-
Q gi|254781172|r 626 EALL-KEVSPSIGRHE----KNVSSEIENKKLVFTGTLQK---IQRHKAQEYVTQLGAVVSAILSRKTDIIIV-----G- 691 (731)
Q Consensus 626 ~~L~-~~~~~~~~~~~----~~~~~~l~gk~vV~TGtl~~---~~R~e~~~~ie~~Ggkv~sSVSkkT~~LI~-----g- 691 (731)
..++ +.......+.- =+..+.|=-+..||.||+.. +.|+=+++.|+.. -+.+.+| |
T Consensus 107 ~~~l~~~l~~~~~E~F~vlfLD~~nrli~~~~~~~Gt~~~v~v~PREi~keA~k~~----------A~alI~aHNHPSGG 176 (223)
T TIGR00608 107 AEFLSTDLAHEEREHFMVLFLDLKNRLIAKEVVFIGTVNHVLVHPREIIKEALKLS----------ASALILAHNHPSGG 176 (223)
T ss_pred HHHHHHHHCCCCCEEEEEEEECCCCCEECCEEEEEEEEEEEEECCCHHHHHHHHHC----------CCCEEEEEECCCCC
T ss_conf 99999863347642678887168541010024565412422366507877887617----------43025565375529
Q ss_pred -C-CCC-------CHHHH-HHHCCCEEEC
Q ss_conf -8-888-------63798-9974991737
Q gi|254781172|r 692 -D-NPG-------SKLEK-AQQLGVKIMN 710 (731)
Q Consensus 692 -e-~~g-------SKl~K-A~~LgI~Ii~ 710 (731)
+ +|| -++.+ |+=+||+++|
T Consensus 177 l~p~PS~~D~~~T~~l~~aae~l~i~lLD 205 (223)
T TIGR00608 177 LEPSPSKEDILITERLLKAAELLGIELLD 205 (223)
T ss_pred CCCCCCHHHHHHHHHHHHHHHHCCCEEEE
T ss_conf 89986877799999999888662862411
No 155
>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=79.37 E-value=2.6 Score=21.52 Aligned_cols=27 Identities=19% Similarity=0.244 Sum_probs=23.3
Q ss_pred CCHHHHHHHHHHHHHHHCCCHHHHHHH
Q ss_conf 010111168999999882998999997
Q gi|254781172|r 557 LGIRHVGAEIARSLAKYYLSYQNFAQE 583 (731)
Q Consensus 557 LGI~~vG~~~Ak~La~~f~si~~l~~~ 583 (731)
=||||||.++|-.|.+.|++++++.+.
T Consensus 239 ~gI~GIG~k~A~klIkk~~~ie~i~~~ 265 (338)
T TIGR03674 239 EGVKGIGPKTALKLIKEHGDLEKVLKA 265 (338)
T ss_pred CCCCCCCHHHHHHHHHHHCCHHHHHHH
T ss_conf 899985689999999985999999986
No 156
>PRK07219 DNA topoisomerase I; Validated
Probab=79.34 E-value=0.89 Score=25.20 Aligned_cols=15 Identities=13% Similarity=0.107 Sum_probs=5.6
Q ss_pred HHHHHHHHHHHHHHH
Q ss_conf 999999999999843
Q gi|254781172|r 21 LSSLEQEISYHDDCY 35 (731)
Q Consensus 21 i~~L~~~i~~~~~~Y 35 (731)
+..|.+....++..|
T Consensus 91 ~~~Lk~lak~ad~Ii 105 (769)
T PRK07219 91 YQTLKNFKGKADEII 105 (769)
T ss_pred HHHHHHHHHCCCEEE
T ss_conf 999999981699999
No 157
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=79.06 E-value=0.82 Score=25.48 Aligned_cols=23 Identities=22% Similarity=0.628 Sum_probs=16.8
Q ss_pred ECCCCCCCCCCCCCCCCCCCCCCCEEECCCC
Q ss_conf 7043265775010337865445210100354
Q gi|254781172|r 430 FPSFCPICQSRVVRDLNPKTGKLVAAHRCTG 460 (731)
Q Consensus 430 ~P~~CP~Cgs~l~~~~~~~~~~~~~~~rC~n 460 (731)
.-++||.||++|.+. + ..++|++
T Consensus 27 L~~hCp~Cg~PLF~K-d-------G~v~CPv 49 (131)
T COG1645 27 LAKHCPKCGTPLFRK-D-------GEVFCPV 49 (131)
T ss_pred HHHHCCCCCCCCEEE-C-------CEEECCC
T ss_conf 874486558831630-8-------9587777
No 158
>TIGR00426 TIGR00426 competence protein ComEA helix-hairpin-helix repeat region; InterPro: IPR004509 This domain is found in 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 domain represents a region of two tandem copies of a helix-hairpin-helix domain, each about 30 residues in length. Limited sequence similarity can be found among some members of this family N-terminal to this domain..
Probab=78.60 E-value=0.85 Score=25.34 Aligned_cols=40 Identities=23% Similarity=0.341 Sum_probs=21.7
Q ss_pred HHHHHHHHHHHHHH---CCCHHHHHHHHHHHHHCCCCCHHHHHCCCCCCHHHHHHHHH
Q ss_conf 11116899999988---29989999978977612511778761388867899999999
Q gi|254781172|r 560 RHVGAEIARSLAKY---YLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVE 614 (731)
Q Consensus 560 ~~vG~~~Ak~La~~---f~si~~l~~~~~~~~~~~~~~~e~L~~I~GiG~~~A~si~~ 614 (731)
.|||.+.|..|.++ ++.+ ...|+|.+++|||..+-+...+
T Consensus 24 ~GvG~kKAeAIv~YREe~G~F---------------~t~Edl~~V~GiG~~~~Ek~~~ 66 (70)
T TIGR00426 24 SGVGAKKAEAIVAYREEYGRF---------------KTVEDLKKVSGIGEKLLEKNKA 66 (70)
T ss_pred CCCCHHHHHHHHHHHHCCCCC---------------CCHHHHHHCCCCCHHHHHHHHH
T ss_conf 288723789998875327795---------------7622232147876245555644
No 159
>TIGR01057 topA_arch DNA topoisomerase I; InterPro: IPR005739 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 describes topoisomerase I from archaea, which is more closely related to bacterial than to eukaryotic topoisomerase I . Topoisomerase I is the major enzyme for relaxing negatively supercoiled DNA, and its presence is balanced by reverse gyrase, which can introduce negative supercoils. 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, 0006268 DNA unwinding during replication, 0005694 chromosome.
Probab=77.93 E-value=1.1 Score=24.44 Aligned_cols=63 Identities=11% Similarity=0.056 Sum_probs=28.8
Q ss_pred EEECCCCCCCHHHCCCHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCEEEEEEEE-ECCEEEEEEECCCCHHHHH
Q ss_conf 04516642570215999999999999998612467776119999415818999998-5998998886598655666
Q gi|254781172|r 88 KVTHSIPTLSLEKIWNIEDLRKFITRIYRFWQKKDDNSIFFTLEPKIDGTMITIRY-EKGKFVYAALRGDGHSGED 162 (731)
Q Consensus 88 kv~H~~pMlSL~k~~~~~el~~w~~~~~~~~~~~~~~~~~~~vepKiDG~sisl~Y-~~G~L~~a~TRGdG~~GeD 162 (731)
++.-..-.||-.-|.+.. |.--++|-++.-.-. |...|++. ++. +||.-..|...++=.+-+.
T Consensus 186 ~a~gr~v~LS~GRVQ~Pt-L~~l~eRe~EI~~F~--P~pywvi~---------~~~~~gG~~~~A~~~~~K~~~~e 249 (637)
T TIGR01057 186 AAAGRWVILSAGRVQGPT-LAFLVEREREIKKFV--PKPYWVIK---------ALLEKGGGVFKAESEKEKIWKEE 249 (637)
T ss_pred HHHCCEEEEECCCCCCHH-HHHHHHHHHHHHCCC--CCCEEEEE---------EEEECCCCEEEEECCCCCCCHHH
T ss_conf 972998999517652079-999998899985289--98302677---------85406885587522578741246
No 160
>PRK08620 DNA topoisomerase III; Provisional
Probab=77.72 E-value=1.1 Score=24.39 Aligned_cols=51 Identities=8% Similarity=0.031 Sum_probs=20.8
Q ss_pred CCEEEEEEECCEEEEEECCCCCCHH---HHH-HHCCCEEECHHHHHHHHHHHCCC
Q ss_conf 9849981116321799778888637---989-97499173799999999882865
Q gi|254781172|r 674 GAVVSAILSRKTDIIIVGDNPGSKL---EKA-QQLGVKIMNEEQFLFLLQQYNTT 724 (731)
Q Consensus 674 Ggkv~sSVSkkT~~LI~ge~~gSKl---~KA-~~LgI~Ii~e~ef~~ll~~~~~~ 724 (731)
|++..---+++--+.++.-+---|+ +|- ++-+=.=++..|-.+.+++.+..
T Consensus 655 ~~~~~~~~~~~g~~~~c~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 709 (726)
T PRK08620 655 KKKLELRGEGEGQIFVCVCGHREKLSQFQKRRKKESSGKVSKREVKKYMKKQKKE 709 (726)
T ss_pred CCEEEEEECCCCCEEEECCCCHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHCC
T ss_conf 9856898567787899738988788889998764026888889999999873302
No 161
>PRK06398 aldose dehydrogenase; Validated
Probab=77.56 E-value=3.6 Score=20.45 Aligned_cols=16 Identities=38% Similarity=0.310 Sum_probs=11.2
Q ss_pred CCCCCCCEEEEECCCC
Q ss_conf 8821686699972588
Q gi|254781172|r 644 SSEIENKKLVFTGTLQ 659 (731)
Q Consensus 644 ~~~l~gk~vV~TGtl~ 659 (731)
++..+|.++++-|-++
T Consensus 231 as~iTG~~i~VDGG~t 246 (256)
T PRK06398 231 SSFITGTCLYVDGGLS 246 (256)
T ss_pred HCCCCCCEEEECCCHH
T ss_conf 3383386177893932
No 162
>TIGR01209 TIGR01209 conserved hypothetical protein TIGR01209; InterPro: IPR001072 The uncharacterised protein MJ0414 from Methanococcus jannaschii belongs to a conserved family that includes proteins from other archaea and from the thermophilic bacterium Aquifex aeolicus . Nothing is known about the function of this conserved family..
Probab=76.42 E-value=5.4 Score=19.11 Aligned_cols=153 Identities=20% Similarity=0.211 Sum_probs=90.5
Q ss_pred CCCEEEEEEECCEEEEEEEEECCEEEEEEECCCCHHHHHHHHHHHHHCC--CCCCCCCCC--CCEEEEEEEEEEECHHHH
Q ss_conf 7611999941581899999859989988865986556669997753102--432233544--550489999998520212
Q gi|254781172|r 124 NSIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPT--IPRVLSLNI--PEIIEVRGEVYISKNDFL 199 (731)
Q Consensus 124 ~~~~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n~~~i~~--iP~~l~~~~--~~~ieiRGEv~m~~~~F~ 199 (731)
....++++.|+||..+.+.--.|.+ .++||| |.+---.|..++.+-+ +. .+-.+. |. +.+-||+.-+.+-+-
T Consensus 78 ~~~~~~~~~~~~g~~~~~~~~~~~~-~~~~~~-g~~cp~~~~~~~~~~~g~~~-~~~~~~g~~~-~~~~~~~~g~~~p~~ 153 (388)
T TIGR01209 78 KDPEVLVEEKLNGYNVRIVKLGGEL-YALTRG-GLICPFTTERLPDLLDGALS-EFLDDYGAPD-LVLCGEVVGPENPYL 153 (388)
T ss_pred CCCCEEEEECCCCCEEEEEEECCEE-EEEECC-CEECCCCHHHHHHHHCHHHH-HHHHHHCCCC-EEEEEHHCCCCCCCC
T ss_conf 7760577421476225789863706-653137-50133204556665143577-8887508864-054200105667743
Q ss_pred HHHHHHHHCCCCCCCCHHHHHHHHHHCCCHHHHH---CCCEEEEEEECCCCCCCCCCCHHHHHHHHHCCCCCCCCEEEEE
Q ss_conf 3455643148543342345677775234555530---1110566410245433210000368999975996654148874
Q gi|254781172|r 200 ALNDEMIAVGRKPYANPRNAASGILRRLNPTDIT---RYLNFFVHGLGKTSEIFAKGQYEMLQKMRCLGFPVNNGVRQAN 276 (731)
Q Consensus 200 ~lN~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~---r~L~f~ay~~~~~~~~~~~~~~e~l~~L~~~GF~v~~~~~~~~ 276 (731)
. .++..+. ..+.|+.|++........-...+.+......|++.........
T Consensus 154 ~--------------------------~~~~~~~~g~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 207 (388)
T TIGR01209 154 P--------------------------EDPPEVKRGFEDLGFFLFDLREGNTGRPLPVEEKLELAEKYGLPHVELLGKFP 207 (388)
T ss_pred C--------------------------CCCCHHCCCCCCCCEEEEEEEECCCCCCCCHHHHHHHHHHHCCCCHHHHCCCC
T ss_conf 3--------------------------45310014533220345542113567656677888776650774101110025
Q ss_pred CCCCHHHHHHHHHHHHCCCCCCCCCEEEEECC
Q ss_conf 03211345566553100112343763777311
Q gi|254781172|r 277 TFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDE 308 (731)
Q Consensus 277 ~~~~~~~~~~~~~~~r~~l~y~iDGiVikvn~ 308 (731)
..++....+.++-+. .-.-.-+|+|++-.+
T Consensus 208 ~~~~~~~~~~~~~~~--~~~~g~~g~~~~~~~ 237 (388)
T TIGR01209 208 ADEEGVEELYEIVER--LNKEGREGVVLKDPE 237 (388)
T ss_pred CCHHHHHHHHHHHHH--HHCCCCCCEEEECCH
T ss_conf 304578999999998--520344530330741
No 163
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=76.16 E-value=3.5 Score=20.61 Aligned_cols=48 Identities=13% Similarity=0.272 Sum_probs=33.3
Q ss_pred CCHHHHHHHHHHHHHCCCCCCEEEEEHHHHCCHHHHHHHHCCCCCCCCCCCCCHHHHHH
Q ss_conf 10354103555565305765404541011010677753100010001342100145689
Q gi|254781172|r 481 FNIEGLGKQQLDFFFKSEDPAFSIRIPADIFTLQRRQQTSTTKIENILGFGDVSVTNLY 539 (731)
Q Consensus 481 ldI~GLG~k~Ie~L~e~~~~~g~I~~~~DLy~L~~~~~~~~~~l~~l~GfgeKsa~nL~ 539 (731)
-||.|+|+...+.|-++|| .++.|+-.- .-++|...+|.|-..|..|-
T Consensus 13 ~disgvg~~~a~~l~~ag~-----e~~~d~~~a------~q~~l~~~~gignalaarik 60 (238)
T PRK12766 13 TDISGVGPSKAESLREAGF-----ESVEDVRAA------DQSELADVDGIGNALAARIK 60 (238)
T ss_pred HCCCCCCHHHHHHHHHCCC-----CHHHHHHHH------HHHHHHHCCCHHHHHHHHHH
T ss_conf 4123668003678887040-----128989764------27766420131389999874
No 164
>PRK01438 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=75.82 E-value=5.6 Score=19.00 Aligned_cols=14 Identities=21% Similarity=0.290 Sum_probs=5.6
Q ss_pred CCEEEEECCHHCCC
Q ss_conf 76377731100011
Q gi|254781172|r 300 DGLVYKVDEFSLQK 313 (731)
Q Consensus 300 DGiVikvn~~~~q~ 313 (731)
+.+|+-.+|...++
T Consensus 226 ~~~v~n~dD~~~~~ 239 (481)
T PRK01438 226 VACVYNVADPATED 239 (481)
T ss_pred EEEEEECCCHHHHH
T ss_conf 14997057788999
No 165
>TIGR01862 N2-ase-Ialpha nitrogenase component I, alpha chain; InterPro: IPR010143 This entry represents all three varieties (Fe-Fe, Mo-Fe and V-Fe) of the component I alpha chain of nitrogenase. Nitrogenase (1.18.6.1 from EC) is the enzyme system responsible for biological nitrogen fixation. Nitrogenase is an oligomeric complex which consists of two components: component 2 is an homodimer of an iron-sulphur protein, while component 1 which contains the active site for the reduction of nitrogen to ammonia exists in three different forms: the molybdenum-iron containing protein (MoFe) is a hetero-tetramer consisting of two pairs of alpha (nifD) and beta (nifK) subunits; the vanadium-iron containing protein (VFe) is a hexamer of two pairs each of alpha (vnfD), beta (vnfK), and delta (vnfG) subunits; the third form seems to only contain iron and is a hexamer composed of alpha (anfD), beta (anfK), and delta (anfG) subunits. The alpha and beta chains of the three types of component 1 are evolutionary related and they are also related to proteins nifE and nifN, which are most probably involved in the iron-molybdenum cofactor biosynthesis .; GO: 0016163 nitrogenase activity, 0051536 iron-sulfur cluster binding, 0009399 nitrogen fixation.
Probab=75.80 E-value=5.6 Score=19.00 Aligned_cols=120 Identities=18% Similarity=0.233 Sum_probs=71.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCHHHHHCCCCCCHH-HHHHHH
Q ss_conf 4568999987522346667763010111168999999882998999997897761251177876138886789-999999
Q gi|254781172|r 535 VTNLYDSINKRRNISLERFIFSLGIRHVGAEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDI-IAQAIV 613 (731)
Q Consensus 535 a~nL~~sIe~sK~~~L~r~L~ALGI~~vG~~~Ak~La~~f~si~~l~~~~~~~~~~~~~~~e~L~~I~GiG~~-~A~si~ 613 (731)
-+-.++.|+..-.+.|.-+=++=++- -.|+.|-.+|+ + --+++++||.. ++++|.
T Consensus 237 Gdg~yd~~~~mh~A~LNlV~C~RS~n----YIa~~le~rYG--------I------------P~~~~dffG~~~~~e~LR 292 (510)
T TIGR01862 237 GDGTYDEIRLMHKAKLNLVECARSAN----YIANELEERYG--------I------------PWLKIDFFGFEYIAESLR 292 (510)
T ss_pred CCCCHHHHHCCCCCCCCCEEECCHHH----HHHHHHHHCCC--------C------------CEEEECCCCCHHHHHHHH
T ss_conf 44222663126621101111014057----99998553078--------7------------537754657037899899
Q ss_pred ---HHHCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEEE-ECCCCCCCHHHHHHHHHHCCCEEEEE
Q ss_conf ---99669799999999997338776543224688216866999-72588998789999999829849981
Q gi|254781172|r 614 ---EFYQNPRNICAVEALLKEVSPSIGRHEKNVSSEIENKKLVF-TGTLQKIQRHKAQEYVTQLGAVVSAI 680 (731)
Q Consensus 614 ---~ff~~~~n~~~i~~L~~~~~~~~~~~~~~~~~~l~gk~vV~-TGtl~~~~R~e~~~~ie~~Ggkv~sS 680 (731)
.||.+++-.+--+++...-.....+.-.-=...|.||++|+ +|-.. .|--+..+.+++|=.|++.
T Consensus 293 ~I~~~Fg~~eI~~r~EevIae~~a~w~p~ld~yKerL~GK~v~ly~GG~r--~wH~~~~~~~~lG~~VV~~ 361 (510)
T TIGR01862 293 AIAAFFGDSEIEKRAEEVIAEEIAKWKPELDYYKERLQGKRVCLYVGGSR--LWHWIKSLEEDLGVEVVAV 361 (510)
T ss_pred HHHHHCCCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHCCCEEEEECCCCC--HHHHHHHHHHHCCCEEEEE
T ss_conf 99964588542268888778744210412454113114988999758880--0111125777639459997
No 166
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=75.78 E-value=1.4 Score=23.55 Aligned_cols=20 Identities=35% Similarity=0.557 Sum_probs=13.1
Q ss_pred HHHCCCCCCHHHHHHHHHHH
Q ss_conf 76138886789999999996
Q gi|254781172|r 597 SLIRVPLVGDIIAQAIVEFY 616 (731)
Q Consensus 597 ~L~~I~GiG~~~A~si~~ff 616 (731)
+|++|+|||+++|+++.++.
T Consensus 2 ~L~~v~GIG~k~A~~ll~~~ 21 (26)
T smart00278 2 ELLKVPGIGPKTAEKILEAX 21 (26)
T ss_pred CCCCCCCCCCHHHHHHHHHH
T ss_conf 21017998811599999976
No 167
>CHL00013 rpoA RNA polymerase alpha subunit
Probab=74.98 E-value=2.1 Score=22.32 Aligned_cols=50 Identities=22% Similarity=0.418 Sum_probs=37.7
Q ss_pred HHHHHHHHHHHCCCCCCEEEEEHHHHCCHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHH
Q ss_conf 4103555565305765404541011010677753100010001342100145689999875
Q gi|254781172|r 485 GLGKQQLDFFFKSEDPAFSIRIPADIFTLQRRQQTSTTKIENILGFGDVSVTNLYDSINKR 545 (731)
Q Consensus 485 GLG~k~Ie~L~e~~~~~g~I~~~~DLy~L~~~~~~~~~~l~~l~GfgeKsa~nL~~sIe~s 545 (731)
.|+-....-|=.++ |.++.||...+.. +|+++..||.||.+-+.+.+++.
T Consensus 278 eLSvRs~NCLKra~-----I~tvgdLv~~se~------dLl~ikNfGkKSl~EI~ekL~e~ 327 (333)
T CHL00013 278 ELSVRAYNCLKRAN-----IHTLLDLLNYSQE------DLLKIKNFGQKSVKQVLDALEKR 327 (333)
T ss_pred CCCHHHHHHHHHCC-----CCCHHHHHHCCHH------HHHCCCCCCHHHHHHHHHHHHHH
T ss_conf 18788774363738-----9379998638999------99418998630299999999886
No 168
>KOG0442 consensus
Probab=74.62 E-value=4.3 Score=19.91 Aligned_cols=52 Identities=19% Similarity=0.152 Sum_probs=41.4
Q ss_pred HCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCHHHHHCCCCCCHHHHHHHHHHHCC
Q ss_conf 301011116899999988299899999789776125117787613888678999999999669
Q gi|254781172|r 556 SLGIRHVGAEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVEFYQN 618 (731)
Q Consensus 556 ALGI~~vG~~~Ak~La~~f~si~~l~~~~~~~~~~~~~~~e~L~~I~GiG~~~A~si~~ff~~ 618 (731)
=|++|||-..++..+..+|+++..+... ++++|..+=|. ...|+.|.+||+.
T Consensus 823 ll~lPgVs~~n~~~l~~k~ks~~~La~s----------S~~el~el~~~-~~~a~~LYdFi~~ 874 (892)
T KOG0442 823 LLSLPGVSYINYRNLRHKFKSLKELANS----------SQEELSELLGV-HENAKLLYDFIHT 874 (892)
T ss_pred HHCCCCCCHHHHHHHHHHHHHHHHHHHC----------CHHHHHHHHCC-HHHHHHHHHHHHH
T ss_conf 7518980088899999986679999867----------39999999665-6779999999988
No 169
>PRK09137 DNA topoisomerase I; Validated
Probab=74.61 E-value=1.6 Score=23.25 Aligned_cols=22 Identities=14% Similarity=0.418 Sum_probs=16.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 9999999999999999984331
Q gi|254781172|r 16 QARKELSSLEQEISYHDDCYYQ 37 (731)
Q Consensus 16 ~~~~~i~~L~~~i~~~~~~Yy~ 37 (731)
..++.+..|.+.++.++..|-.
T Consensus 58 ~~kk~i~~lk~l~k~ad~IilA 79 (761)
T PRK09137 58 RSKKHIDAIKKAAKDADNLYLA 79 (761)
T ss_pred CHHHHHHHHHHHHHCCCEEEEC
T ss_conf 4789999999998389989989
No 170
>pfam02571 CbiJ Precorrin-6x reductase CbiJ/CobK. This family consists of Precorrin-6x reductase EC:1.3.1.54. This enzyme catalyses the reaction: precorrin-6Y + NADP(+) <= precorrin-6X + NADPH. CbiJ and CobK both catalyse the reduction of macocycle in the colbalmin biosynthesis pathway.
Probab=74.36 E-value=6.1 Score=18.73 Aligned_cols=53 Identities=17% Similarity=0.353 Sum_probs=37.8
Q ss_pred CCCCCCEEEEECCCCCCCHHHHHHHHHHCCCEEEEEEECCEEEEEECCCC--C--CHHHHHHHCCCEEEC
Q ss_conf 82168669997258899878999999982984998111632179977888--8--637989974991737
Q gi|254781172|r 645 SEIENKKLVFTGTLQKIQRHKAQEYVTQLGAVVSAILSRKTDIIIVGDNP--G--SKLEKAQQLGVKIMN 710 (731)
Q Consensus 645 ~~l~gk~vV~TGtl~~~~R~e~~~~ie~~Ggkv~sSVSkkT~~LI~ge~~--g--SKl~KA~~LgI~Ii~ 710 (731)
+.-....+.+.|- ||...-.+++++.+. ++||.+++. | .|+.-|+++||+||-
T Consensus 164 g~~~~~iIa~~gP---fs~e~n~al~~~~~i----------~~lVtK~SG~~g~~~Ki~AA~~lgi~viv 220 (246)
T pfam02571 164 GFPNAEIIAARGP---FSLELERALLRRHGI----------DVLVTKNSGGAGTYAKLAAARELGLPVIM 220 (246)
T ss_pred CCCHHCEEEECCC---CCHHHHHHHHHHCCC----------CEEEEECCCCHHHHHHHHHHHHCCCEEEE
T ss_conf 9980018990499---998999999997099----------99999288865069999999984992999
No 171
>COG4469 CoiA Competence protein CoiA-like family, contains a predicted nuclease domain [General function prediction only]
Probab=74.35 E-value=0.84 Score=25.39 Aligned_cols=17 Identities=29% Similarity=0.696 Sum_probs=12.9
Q ss_pred CCCCCCCCCCCCCCCCC
Q ss_conf 04326577501033786
Q gi|254781172|r 431 PSFCPICQSRVVRDLNP 447 (731)
Q Consensus 431 P~~CP~Cgs~l~~~~~~ 447 (731)
+=+||+||++|....+.
T Consensus 25 ~ffCPaC~~~l~lK~G~ 41 (342)
T COG4469 25 RFFCPACGSQLILKQGL 41 (342)
T ss_pred CCCCCCCCCEEEEECCC
T ss_conf 40267789841453375
No 172
>PTZ00217 flap endonuclease-1; Provisional
Probab=73.76 E-value=3.3 Score=20.82 Aligned_cols=26 Identities=27% Similarity=0.347 Sum_probs=14.1
Q ss_pred CHHHHHHHHHHHHHHHCCCHHHHHHH
Q ss_conf 10111168999999882998999997
Q gi|254781172|r 558 GIRHVGAEIARSLAKYYLSYQNFAQE 583 (731)
Q Consensus 558 GI~~vG~~~Ak~La~~f~si~~l~~~ 583 (731)
||||||.++|-.|.+.|++++++.+.
T Consensus 239 ~I~GIGpk~A~klIk~~~sie~il~~ 264 (394)
T PTZ00217 239 TIEGIGPKTAYELIKKYGSIEEILEH 264 (394)
T ss_pred CCCCCCHHHHHHHHHHHCCHHHHHHH
T ss_conf 99874889999999995999999987
No 173
>TIGR00615 recR recombination protein RecR; InterPro: IPR000093 The bacterial protein recR seems to play a role in a recombinational process of DNA repair . It may act with recF and recO. RecR is a protein of about 200 amino acid residues. This protein contains a putative C4-type zinc finger in the N-terminal section.; GO: 0006281 DNA repair, 0006310 DNA recombination.
Probab=73.13 E-value=3.4 Score=20.69 Aligned_cols=35 Identities=14% Similarity=0.329 Sum_probs=17.5
Q ss_pred CCCCCCEEEEECCCCCCC---HH--HHHHHHHHCCCEEEE
Q ss_conf 821686699972588998---78--999999982984998
Q gi|254781172|r 645 SEIENKKLVFTGTLQKIQ---RH--KAQEYVTQLGAVVSA 679 (731)
Q Consensus 645 ~~l~gk~vV~TGtl~~~~---R~--e~~~~ie~~Ggkv~s 679 (731)
..|.|+-+|.-|.++=+. =+ .+..+++..|-++..
T Consensus 101 ~~f~G~YhVL~G~isPl~Gigp~~~~i~~L~~riGeRl~~ 140 (205)
T TIGR00615 101 KEFRGRYHVLGGLISPLDGIGPEDLKIAALLKRIGERLQE 140 (205)
T ss_pred HHHCCCEEEECCEECCCCCCCCCCCCHHHHHHHHHCCCCC
T ss_conf 4216601431564176457683221468899886000000
No 174
>TIGR00336 pyrE orotate phosphoribosyltransferase; InterPro: IPR004467 Orotate phosphoribosyl transferase (OPRTase) is involved in the biosynthesis of pyrimidine nucleotides. Alpha-D-ribosyldiphosphate 5-phosphate (PRPP) and orotate are utilised to form pyrophosphate and orotidine 5 -monophosphate (OMP) in the presence of divalent cations, preferably Mg2+. In a number of eukaryotes, this protein is fused to a domain that catalyses the reaction (4.1.1.23 from EC). The combined activity of 2.4.2.10 from EC and 4.1.1.23 from EC is termed uridine 5 -monophosphate synthase. The conserved Lys (K) residue at position 101 of the seed alignment has been proposed as the active site for the enzyme.; GO: 0004588 orotate phosphoribosyltransferase activity, 0006221 pyrimidine nucleotide biosynthetic process.
Probab=72.28 E-value=6.7 Score=18.38 Aligned_cols=66 Identities=17% Similarity=0.161 Sum_probs=46.0
Q ss_pred CCC-CCCCCCEEEE------ECCCCCCCHHHHHHHHHHCCCEEEEEEECCEEEEEECCCCCCHHHHHHHCCCEEECH
Q ss_conf 468-8216866999------725889987899999998298499811163217997788886379899749917379
Q gi|254781172|r 642 NVS-SEIENKKLVF------TGTLQKIQRHKAQEYVTQLGAVVSAILSRKTDIIIVGDNPGSKLEKAQQLGVKIMNE 711 (731)
Q Consensus 642 ~~~-~~l~gk~vV~------TGtl~~~~R~e~~~~ie~~Ggkv~sSVSkkT~~LI~ge~~gSKl~KA~~LgI~Ii~e 711 (731)
-.. ..+.|+++|+ ||+ +=-++.+.|.++||.|.+.++-=+--.......|+.-+=.++.|+++++.
T Consensus 109 i~GP~~~eG~kvvvveDV~TtG~----s~~~A~~~i~~ag~~V~~v~~~vDR~e~~~~E~~A~~~f~~~y~~~~~sl 181 (187)
T TIGR00336 109 IEGPELLEGDKVVVVEDVITTGG----SILEAVEAIQEAGGEVAGVIVIVDRQERGKGELSAGQEFEKEYGLPLISL 181 (187)
T ss_pred EECCCCCCCCEEEEEECCCCHHH----HHHHHHHHHHHCCCEEEEEEEEEECCCCCCCCCCHHHHHHHHHCCEEEEE
T ss_conf 45676578963899951434247----99999999986188899999998267243310133455465528644323
No 175
>pfam06677 Auto_anti-p27 Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). This family consists of several Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27) sequences. 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=72.16 E-value=1.9 Score=22.69 Aligned_cols=24 Identities=21% Similarity=0.515 Sum_probs=17.3
Q ss_pred ECCCCCCCCCCCCCCCCCCCCCCCEEECCCC
Q ss_conf 7043265775010337865445210100354
Q gi|254781172|r 430 FPSFCPICQSRVVRDLNPKTGKLVAAHRCTG 460 (731)
Q Consensus 430 ~P~~CP~Cgs~l~~~~~~~~~~~~~~~rC~n 460 (731)
..++||.||+++.++.+. ..+|++
T Consensus 16 L~~~C~~Cg~pLf~~k~g-------~~~Cp~ 39 (41)
T pfam06677 16 LDEHCPKCGTPLFRLKDG-------KVFCPS 39 (41)
T ss_pred HHCCCCCCCCEEEECCCC-------CEECCC
T ss_conf 543254569830584899-------995787
No 176
>TIGR03190 benz_CoA_bzdN benzoyl-CoA reductase, bzd-type, N subunit. Members of this family are the N subunit of one of two related types of four-subunit ATP-dependent benzoyl-CoA reductase. This enzyme system catalyzes the dearomatization of benzoyl-CoA, a common intermediate in pathways for the degradation for a number of different aromatic compounds, such as phenol and toluene.
Probab=72.14 E-value=6.8 Score=18.36 Aligned_cols=98 Identities=11% Similarity=0.101 Sum_probs=49.8
Q ss_pred HHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCHHHHHHHHHHCCCEEEE--EEECCEEEEEECCCCCC
Q ss_conf 7999999999973387765432246882168669997258899878999999982984998--11163217997788886
Q gi|254781172|r 619 PRNICAVEALLKEVSPSIGRHEKNVSSEIENKKLVFTGTLQKIQRHKAQEYVTQLGAVVSA--ILSRKTDIIIVGDNPGS 696 (731)
Q Consensus 619 ~~n~~~i~~L~~~~~~~~~~~~~~~~~~l~gk~vV~TGtl~~~~R~e~~~~ie~~Ggkv~s--SVSkkT~~LI~ge~~gS 696 (731)
.+....+.+++..+.... ...-.|+.|++||+.. ..-.+.++||.+||.|+. +-|.-=.+.-.-+..+.
T Consensus 206 ~e~~~~l~~ll~~l~~~~-------~~~~~~~RIlvtG~~~--~~~kl~~iIEe~G~~VV~de~C~G~R~~~~~~~~~~d 276 (377)
T TIGR03190 206 REHNEMLKKVLAALPSRK-------VERKTGARFMTIGSEN--DDIAFMAMVESVGATIVIDDQCSGTRYFWNASKPEDD 276 (377)
T ss_pred HHHHHHHHHHHHHHHCCC-------CCCCCCCEEEEECCCC--CCCHHHHHHHHCCCEEEEECCCCCCCCCCCCCCCCCC
T ss_conf 999999999999986065-------5467997799978999--9735999999869989997777751200578887777
Q ss_pred HH-HHHHHC----CCEEEC------HHHHHHHHHHHCCCC
Q ss_conf 37-989974----991737------999999998828656
Q gi|254781172|r 697 KL-EKAQQL----GVKIMN------EEQFLFLLQQYNTTL 725 (731)
Q Consensus 697 Kl-~KA~~L----gI~Ii~------e~ef~~ll~~~~~~~ 725 (731)
-+ .=|+.+ +-++++ -+.+.+|+++|+.+.
T Consensus 277 pl~alA~rYl~~~~C~~~~~pn~~R~~~i~~lvke~~aDG 316 (377)
T TIGR03190 277 VIKAIAERYCDRPACPTKDYPVHTRYDHVLGLAKEYNVQG 316 (377)
T ss_pred HHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHCCCE
T ss_conf 9999999982789987888880458999999999968899
No 177
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=71.68 E-value=6.9 Score=18.29 Aligned_cols=62 Identities=23% Similarity=0.466 Sum_probs=35.3
Q ss_pred CCCCCCCEEE--EEECCCCHHHHHHHCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCHHHHHH
Q ss_conf 6844076899--98358702566541012357873047770432657750103378654452101003543441144665
Q gi|254781172|r 393 RDIRVGDRVL--VKRAGEVIPKVVDIIVNERHPDAQPFSFPSFCPICQSRVVRDLNPKTGKLVAAHRCTGGLACSAQQLE 470 (731)
Q Consensus 393 ~~I~iGd~V~--I~RaGdVIP~I~~Vi~~~r~~~~~~~~~P~~CP~Cgs~l~~~~~~~~~~~~~~~rC~n~~~Cpaq~~~ 470 (731)
..++|||.|. |.+-| =|.-++. .++ +-. ++-..|+-|++++++... .++|+| |-..-.+
T Consensus 117 d~f~~GDivrA~Vis~~--~~~~Lst---~~~-dlG--VI~A~CsrC~~~L~~~~~--------~l~Cp~---Cg~tEkR 177 (188)
T COG1096 117 DAFRIGDIVRARVISTG--DPIQLST---KGN-DLG--VIYARCSRCRAPLVKKGN--------MLKCPN---CGNTEKR 177 (188)
T ss_pred CCCCCCCEEEEEEEECC--CCEEEEE---CCC-CCE--EEEEECCCCCCCEEECCC--------EEECCC---CCCEEEE
T ss_conf 34464617999998617--8718985---278-616--999983677762088475--------998887---7987766
Q ss_pred HHH
Q ss_conf 533
Q gi|254781172|r 471 RLK 473 (731)
Q Consensus 471 ~i~ 473 (731)
+|.
T Consensus 178 Kia 180 (188)
T COG1096 178 KIA 180 (188)
T ss_pred EEC
T ss_conf 422
No 178
>pfam09511 RNA_lig_T4_1 RNA ligase. 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.
Probab=71.08 E-value=5.6 Score=19.03 Aligned_cols=56 Identities=21% Similarity=0.406 Sum_probs=37.2
Q ss_pred CCCCCCHHHCCCHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCEEEEEEEEECCEEEEEEECCC
Q ss_conf 66425702159999999999999986124677761199994158189999985998998886598
Q gi|254781172|r 92 SIPTLSLEKIWNIEDLRKFITRIYRFWQKKDDNSIFFTLEPKIDGTMITIRYEKGKFVYAALRGD 156 (731)
Q Consensus 92 ~~pMlSL~k~~~~~el~~w~~~~~~~~~~~~~~~~~~~vepKiDG~sisl~Y~~G~L~~a~TRGd 156 (731)
.+...|.+|-|+.+|... .+ +. ......|.+.-|+||.=+.+.+.+|++ ...|||.
T Consensus 15 ~Iv~R~f~KFFN~~E~~~-t~-----~~--~l~~~p~~v~~K~dGsLi~~~~~~g~~-~~~SK~s 70 (212)
T pfam09511 15 RIVSRSYDKFFNVNEVPE-TK-----WD--DLERGPYEVYEKEDGSLIISYLDDGKL-VVCSKHS 70 (212)
T ss_pred EEEECCCCCCEECCCCCC-CC-----CC--CCCCCCEEEEEECCCEEEEEEEECCEE-EEEECCC
T ss_conf 399877887367797645-66-----44--245788899995198899999879999-9997787
No 179
>PRK03980 flap endonuclease-1; Provisional
Probab=70.89 E-value=7.2 Score=18.16 Aligned_cols=28 Identities=18% Similarity=0.287 Sum_probs=22.8
Q ss_pred CCHHHHHHHHHHHHHHHCCCHHHHHHHH
Q ss_conf 0101111689999998829989999978
Q gi|254781172|r 557 LGIRHVGAEIARSLAKYYLSYQNFAQEI 584 (731)
Q Consensus 557 LGI~~vG~~~Ak~La~~f~si~~l~~~~ 584 (731)
=|||+||.++|-.|.+.|++++++.+.+
T Consensus 192 ~gI~gIGpk~Alklikk~~~ie~il~~~ 219 (295)
T PRK03980 192 PGVKGIGPKTALKLIKKHGDLEKVLEAV 219 (295)
T ss_pred CCCCCCCHHHHHHHHHHHCCHHHHHHHC
T ss_conf 9999842999999999969999999863
No 180
>PRK08173 DNA topoisomerase III; Validated
Probab=70.71 E-value=2.5 Score=21.74 Aligned_cols=21 Identities=19% Similarity=0.371 Sum_probs=13.2
Q ss_pred CCCCHHHHH-----HHHHHHHHCCCC
Q ss_conf 231035410-----355556530576
Q gi|254781172|r 479 DAFNIEGLG-----KQQLDFFFKSED 499 (731)
Q Consensus 479 ~aldI~GLG-----~k~Ie~L~e~~~ 499 (731)
++|.=.||| ..+|+.|++.+|
T Consensus 513 ~~lk~~GiGTpATRA~IIe~L~~r~Y 538 (857)
T PRK08173 513 EAMAAKGLGTPATRAAIIEGLLGEKY 538 (857)
T ss_pred HHHHHCCCCCCCHHHHHHHHHHHCCC
T ss_conf 99864789985108899999975786
No 181
>COG5241 RAD10 Nucleotide excision repair endonuclease NEF1, RAD10 subunit [DNA replication, recombination, and repair]
Probab=70.66 E-value=2.9 Score=21.26 Aligned_cols=52 Identities=13% Similarity=-0.044 Sum_probs=42.4
Q ss_pred CHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCHHHHHCCCCCCHHHHHHHHHHHCCH
Q ss_conf 10111168999999882998999997897761251177876138886789999999996697
Q gi|254781172|r 558 GIRHVGAEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVEFYQNP 619 (731)
Q Consensus 558 GI~~vG~~~Ak~La~~f~si~~l~~~~~~~~~~~~~~~e~L~~I~GiG~~~A~si~~ff~~~ 619 (731)
-||.|-...|..+...|+++..+.. ++..++..+.|+|+..|+.++++++.+
T Consensus 171 ~i~~Vnksds~~~L~d~g~L~rf~g----------aSrdE~e~l~g~g~~ka~~~ieyln~p 222 (224)
T COG5241 171 LIFIVNKSDSEDTLNDIGKLCRFNG----------ASRDEFELLLGFGFEKAAKYIEYLNLP 222 (224)
T ss_pred EEEEECCCCHHHHHHHHHHHHHHHC----------CCHHHHHHHHCCCHHHHHHHHHHHCCC
T ss_conf 8984446418989988878999856----------461588999700888999999985466
No 182
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=70.60 E-value=5.4 Score=19.14 Aligned_cols=61 Identities=20% Similarity=0.452 Sum_probs=34.5
Q ss_pred CCCCCCCEEE--EEECCCCHHHHHHHCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCHHHHHH
Q ss_conf 6844076899--98358702566541012357873047770432657750103378654452101003543441144665
Q gi|254781172|r 393 RDIRVGDRVL--VKRAGEVIPKVVDIIVNERHPDAQPFSFPSFCPICQSRVVRDLNPKTGKLVAAHRCTGGLACSAQQLE 470 (731)
Q Consensus 393 ~~I~iGd~V~--I~RaGdVIP~I~~Vi~~~r~~~~~~~~~P~~CP~Cgs~l~~~~~~~~~~~~~~~rC~n~~~Cpaq~~~ 470 (731)
.-.|+||.|. |...||. .- +.-. .++-- +.-..||.||.++...++ .+.|++ |-..-.+
T Consensus 118 d~fr~gDIVrAkVis~~~~--~~---Lst~-~~eLG--Vv~A~C~~cg~~m~~~~~--------~~~Cp~---cg~~e~R 178 (187)
T PRK09521 118 DAFKIGDIVRAKVISTTDP--IQ---LSTK-GKDLG--VIKALCSRCRTPLVKKGN--------TLKCPN---CGNVETR 178 (187)
T ss_pred HHCCCCCEEEEEEEECCCC--EE---EEEC-CCCCE--EEEEECCCCCCCEEEECC--------EEECCC---CCCEEEE
T ss_conf 5248786899999735984--69---9953-88844--999957767885867399--------999999---9998967
Q ss_pred HH
Q ss_conf 53
Q gi|254781172|r 471 RL 472 (731)
Q Consensus 471 ~i 472 (731)
++
T Consensus 179 Kv 180 (187)
T PRK09521 179 KL 180 (187)
T ss_pred EE
T ss_conf 01
No 183
>PRK13844 recombination protein RecR; Provisional
Probab=70.49 E-value=3.7 Score=20.41 Aligned_cols=16 Identities=19% Similarity=0.362 Sum_probs=8.8
Q ss_pred CCCCCCCEEEEECCCC
Q ss_conf 8821686699972588
Q gi|254781172|r 644 SSEIENKKLVFTGTLQ 659 (731)
Q Consensus 644 ~~~l~gk~vV~TGtl~ 659 (731)
++.+.|.-+|+-|.++
T Consensus 100 s~~y~G~YhVL~G~iS 115 (200)
T PRK13844 100 AGIYRGKYFVLNGRIS 115 (200)
T ss_pred HCCCCEEEEECCCCCC
T ss_conf 4410668887487447
No 184
>pfam01331 mRNA_cap_enzyme mRNA capping enzyme, catalytic domain. This family represents the ATP binding catalytic domain of the mRNA capping enzyme.
Probab=70.26 E-value=7.4 Score=18.06 Aligned_cols=143 Identities=16% Similarity=0.166 Sum_probs=64.5
Q ss_pred CEEEEEEECCEEEEEEEEECCEEEEEEECCCCHHHHHHHHHHHHHCCCCCCCC--CCCCCEEEEEEEEEEECHHHHHHHH
Q ss_conf 11999941581899999859989988865986556669997753102432233--5445504899999985202123455
Q gi|254781172|r 126 IFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPTIPRVLS--LNIPEIIEVRGEVYISKNDFLALND 203 (731)
Q Consensus 126 ~~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n~~~i~~iP~~l~--~~~~~~ieiRGEv~m~~~~F~~lN~ 203 (731)
-.|+|..|-||+=.-|.--++. +-.+.|.+=.. .|+ ++ ..|.... ....+++ +=||+++....
T Consensus 16 ~~Y~V~eKaDG~R~lL~i~~~~-~ylidr~~~~~--~~~-~~----~~p~~~~~~~~~~~Tl-lDGElv~d~~~------ 80 (190)
T pfam01331 16 NDYYVCEKADGIRYMMLITDDG-VYLIDRDNEYF--LVE-NL----RFPLKLNKSKVHHGTL-LDGELVIDTVP------ 80 (190)
T ss_pred CCEEEEECCCCEEEEEEEECCE-EEEEECCCCEE--ECC-CC----CCCCCCCCCCCCCCEE-EEEEEEEEECC------
T ss_conf 9869988757779999995884-99997898369--813-40----0455465543014268-73589974047------
Q ss_pred HHHHCCCCCCCCHHHHHHHHHHCCCHHHHHCCCEEEEEEECCCCCCCC--CCCHHHHHHHHHC----------CCCC---
Q ss_conf 643148543342345677775234555530111056641024543321--0000368999975----------9966---
Q gi|254781172|r 204 EMIAVGRKPYANPRNAASGILRRLNPTDITRYLNFFVHGLGKTSEIFA--KGQYEMLQKMRCL----------GFPV--- 268 (731)
Q Consensus 204 ~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~r~L~f~ay~~~~~~~~~~--~~~~e~l~~L~~~----------GF~v--- 268 (731)
+ -...+.|++|++....+... ....++|..+... ..+.
T Consensus 81 -----~----------------------~~~~~~yl~fD~l~~~g~~v~~~~l~~Rl~~l~~~i~~~~~~~~~~~~~~~~ 133 (190)
T pfam01331 81 -----G----------------------TQAKLRYLIYDIVAINGVSVSQRPFSKRLEILKKEIIKPRNANKKRSHIRYD 133 (190)
T ss_pred -----C----------------------CCCEEEEEEEEEEEECCEEECCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCC
T ss_conf -----8----------------------8741789999899999978446998999999998764245565431554346
Q ss_pred -CCCEEEEECCCCHHHHHHHH--HHHHCCCCCCCCCEEEEECCHHC
Q ss_conf -54148874032113455665--53100112343763777311000
Q gi|254781172|r 269 -NNGVRQANTFHGIVSYYNEM--KSIRSTLPYDIDGLVYKVDEFSL 311 (731)
Q Consensus 269 -~~~~~~~~~~~~~~~~~~~~--~~~r~~l~y~iDGiVikvn~~~~ 311 (731)
.|.......+-.+.. .+.+ ......++|++||+++.-.+.++
T Consensus 134 ~~pf~i~~K~f~~~~~-~~~~~~~~~~~~l~h~~DGLIFTP~~~py 178 (190)
T pfam01331 134 LFPFIVRFKSFWLLSA-SEKLLSKKKIKTLSHEIDGLIFQPWDTPY 178 (190)
T ss_pred CCCEEEEEECCHHHHH-HHHHHHHHHCCCCCCCCCEEEECCCCCCC
T ss_conf 6765999402065677-89887676348778879869989999889
No 185
>pfam08304 consensus
Probab=69.95 E-value=7.5 Score=18.02 Aligned_cols=218 Identities=17% Similarity=0.204 Sum_probs=109.8
Q ss_pred CCCCCCCCCCCCCCCEEECCCCCCCHHHCCCHHHHH--HHHHHHHHHHCCCCCCCCEEEEEEECCEEEEEEEE-ECCEEE
Q ss_conf 962003643235775045166425702159999999--99999998612467776119999415818999998-599899
Q gi|254781172|r 73 GPLNKIGGEMNLSLFKVTHSIPTLSLEKIWNIEDLR--KFITRIYRFWQKKDDNSIFFTLEPKIDGTMITIRY-EKGKFV 149 (731)
Q Consensus 73 spt~~Vg~~~~~~~~kv~H~~pMlSL~k~~~~~el~--~w~~~~~~~~~~~~~~~~~~~vepKiDG~sisl~Y-~~G~L~ 149 (731)
-||.-=|--.... +-.|.+-.-.-||-|+.+|+. +|.. + ......+|-++.|=-||-|=+.= ++|.|+
T Consensus 55 LPt~ARGLFt~~~--~~~~~IvvRGYDKFFNv~EV~~Tkw~~-i------~~~T~GPYeltlKENGCIIFISgL~dgtLl 125 (378)
T pfam08304 55 LPCNARGLFITND--KDNPEIVARGYDKFFNVDEVPFTKWDN-L------ENNTEGPYEVTLKENGCIIFISGLADGTLV 125 (378)
T ss_pred CCCCCCCCEEECC--CCCCEEEEECCCCCCCCCCCCCCCHHH-H------HHCCCCCEEEEECCCCEEEEEECCCCCCEE
T ss_conf 8650342334358--999559984156654478766776788-9------735878818886057609998307999789
Q ss_pred EEEECCCCHHH-HHHHHHHHHHCCCCCCCCCCCCCEEEEEEEEEEECHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCC
Q ss_conf 88865986556-66999775310243223354455048999999852021234556431485433423456777752345
Q gi|254781172|r 150 YAALRGDGHSG-EDVSACIRAIPTIPRVLSLNIPEIIEVRGEVYISKNDFLALNDEMIAVGRKPYANPRNAASGILRRLN 228 (731)
Q Consensus 150 ~a~TRGdG~~G-eDVT~n~~~i~~iP~~l~~~~~~~ieiRGEv~m~~~~F~~lN~~~~~~g~~~f~NpRN~aaG~lr~~d 228 (731)
--+----|..+ .+.+|....=.-+-.+|... | .+..++.+ .++ .+|+.|=+=-..|
T Consensus 126 VcSKHStG~r~d~~~sHA~aGe~~l~~~l~~~--------g---kt~~dLA~----------~L~--~~N~TAVaElCDD 182 (378)
T pfam08304 126 VCSKHSTGPRDDVDRNHAEAGEQFLEQQLAEI--------G---KSKKDLAR----------ELY--ENNVTAVAEYCDD 182 (378)
T ss_pred EECCCCCCCCCCCCCHHHHHHHHHHHHHHHHC--------C---CCHHHHHH----------HHH--HCCHHHHHHHCCC
T ss_conf 96377688888754038999999999999980--------9---98999999----------999--7371466776075
Q ss_pred H-HH----HH-CCCEEEEEEECCC-CCCCCCCCHHHHHHHHHCCCCCCCCEEEEECCCCHHHHHHHHHHHHCCCCCCCCC
Q ss_conf 5-55----30-1110566410245-4332100003689999759966541488740321134556655310011234376
Q gi|254781172|r 229 P-TD----IT-RYLNFFVHGLGKT-SEIFAKGQYEMLQKMRCLGFPVNNGVRQANTFHGIVSYYNEMKSIRSTLPYDIDG 301 (731)
Q Consensus 229 ~-~~----~~-r~L~f~ay~~~~~-~~~~~~~~~e~l~~L~~~GF~v~~~~~~~~~~~~~~~~~~~~~~~r~~l~y~iDG 301 (731)
. .+ .. ..-..+.+|+-.. .....-...+.-++-.+|||.-..+ ...++++++.++.++..+.-.--.=+|.|
T Consensus 183 ~FEEHVL~Y~~~~aGLyLHGlN~N~p~F~T~p~~~V~~FA~ewGFk~~~~-~~~d~i~~vk~Fle~caeTGt~~GreiEG 261 (378)
T pfam08304 183 SFEEHILPYPKDKAGLYLHGLNYNTIEFKTYPMPKVSQFAEEWGFKKVDY-FTKNDIEELKKFLEECSETGTYNGQEVEG 261 (378)
T ss_pred CHHHHHCCCCHHHCCEEEECCCCCCCCEEECCHHHHHHHHHHHCCEEEEE-EEECCHHHHHHHHHHHHHCCCCCCEECCE
T ss_conf 17765347890104234301356877625278899999999838805558-87278999999998665328657863121
Q ss_pred EEEEECCHHCCCCCCCCCCCCCCEEEECCCC
Q ss_conf 3777311000111587656866312311456
Q gi|254781172|r 302 LVYKVDEFSLQKQLGERARSPRWMISHKFAE 332 (731)
Q Consensus 302 iVikvn~~~~q~~lG~ts~~PrwaiA~Kf~~ 332 (731)
.||+.... .. .--|=+-|||..
T Consensus 262 FVIRc~~~-------~~--g~d~FFKyKFeE 283 (378)
T pfam08304 262 FVIRCKMK-------SD--GDDFFFKYKFEE 283 (378)
T ss_pred EEEEEECC-------CC--CCCCEEEECCCC
T ss_conf 69987438-------88--876436762577
No 186
>PRK00076 recR recombination protein RecR; Reviewed
Probab=69.88 E-value=3.8 Score=20.30 Aligned_cols=16 Identities=25% Similarity=0.279 Sum_probs=9.3
Q ss_pred CCCCCCCEEEEECCCC
Q ss_conf 8821686699972588
Q gi|254781172|r 644 SSEIENKKLVFTGTLQ 659 (731)
Q Consensus 644 ~~~l~gk~vV~TGtl~ 659 (731)
++.+.|.-+|+-|.++
T Consensus 96 s~~y~G~YhVLgG~lS 111 (197)
T PRK00076 96 TGEYRGLYHVLGGLLS 111 (197)
T ss_pred CCCEEEEEEECCCCCC
T ss_conf 7945478358566248
No 187
>PRK05182 DNA-directed RNA polymerase subunit alpha; Provisional
Probab=69.77 E-value=3.7 Score=20.38 Aligned_cols=50 Identities=10% Similarity=0.206 Sum_probs=37.0
Q ss_pred HHHHHHHHHHHHCCCCCCEEEEEHHHHCCHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHH
Q ss_conf 5410355556530576540454101101067775310001000134210014568999987
Q gi|254781172|r 484 EGLGKQQLDFFFKSEDPAFSIRIPADIFTLQRRQQTSTTKIENILGFGDVSVTNLYDSINK 544 (731)
Q Consensus 484 ~GLG~k~Ie~L~e~~~~~g~I~~~~DLy~L~~~~~~~~~~l~~l~GfgeKsa~nL~~sIe~ 544 (731)
-.|+-+...-|=.++ |.++.||...+.. +|+++..||.||.+-+.+.++.
T Consensus 250 LeLSvRs~NcLk~a~-----I~tI~dLv~~se~------dLl~ikNfGkKSl~EI~~kL~~ 299 (306)
T PRK05182 250 LELSVRSYNCLKRAG-----INTIGDLVQRTEE------ELLKTPNLGKKSLEEIKEKLAE 299 (306)
T ss_pred HCCCHHHHHHHHHCC-----CCCHHHHHHCCHH------HHHHCCCCCCCCHHHHHHHHHH
T ss_conf 138688875587859-----9369998747999------9961899762039999999997
No 188
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=69.52 E-value=3.9 Score=20.20 Aligned_cols=60 Identities=18% Similarity=0.394 Sum_probs=34.7
Q ss_pred CCEEEEEECCCCHHHHHHHCCCCCCCCCCEEEEC--CCCCCCCCCCCCCCCCC---------CCCCCEEECCCC
Q ss_conf 7689998358702566541012357873047770--43265775010337865---------445210100354
Q gi|254781172|r 398 GDRVLVKRAGEVIPKVVDIIVNERHPDAQPFSFP--SFCPICQSRVVRDLNPK---------TGKLVAAHRCTG 460 (731)
Q Consensus 398 Gd~V~I~RaGdVIP~I~~Vi~~~r~~~~~~~~~P--~~CP~Cgs~l~~~~~~~---------~~~~~~~~rC~n 460 (731)
|-....+++.++.=++..++..... .+...| +.||.||++|+...-+. .......++|++
T Consensus 65 g~~~i~i~~~s~~~Ql~e~~~~~~l---~~~~~~e~~RCp~CN~~L~~vs~eev~~~Vp~~~~~~~~~f~~C~~ 135 (165)
T COG1656 65 GIKAILIRSDSIEEQLAEFLARLGL---KPRLFPEFSRCPECNGELEKVSREEVKEKVPEKVYRNYEEFYRCPK 135 (165)
T ss_pred CCCEEEEECCCHHHHHHHHHHHHCC---CHHCCCCCCCCCCCCCEECCCCHHHHHHCCCHHHHHCCCCEEECCC
T ss_conf 6732897179879999999998352---2001601032743497801076777752065244202001467799
No 189
>COG0122 AlkA 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=69.26 E-value=7.8 Score=17.91 Aligned_cols=23 Identities=17% Similarity=0.213 Sum_probs=19.3
Q ss_pred CCHHHHHCCCCCCHHHHHHHHHH
Q ss_conf 17787613888678999999999
Q gi|254781172|r 593 DDWLSLIRVPLVGDIIAQAIVEF 615 (731)
Q Consensus 593 ~~~e~L~~I~GiG~~~A~si~~f 615 (731)
.-++.|+.|+|||+.+|+.+.=|
T Consensus 195 ~a~e~L~~i~GIG~WTAe~~llf 217 (285)
T COG0122 195 EAIEELTALKGIGPWTAEMFLLF 217 (285)
T ss_pred HHHHHHHCCCCCCHHHHHHHHHH
T ss_conf 99999873788679999999998
No 190
>pfam03811 Ins_element1 Insertion element protein.
Probab=69.23 E-value=3.5 Score=20.58 Aligned_cols=65 Identities=23% Similarity=0.310 Sum_probs=36.4
Q ss_pred CCCCCCCC-C-CCCCCCCCCCCCCEEECCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCCCEEEEEHHH
Q ss_conf 43265775-0-103378654452101003543441144665533213012310354103555565305765404541011
Q gi|254781172|r 432 SFCPICQS-R-VVRDLNPKTGKLVAAHRCTGGLACSAQQLERLKHFVSRDAFNIEGLGKQQLDFFFKSEDPAFSIRIPAD 509 (731)
Q Consensus 432 ~~CP~Cgs-~-l~~~~~~~~~~~~~~~rC~n~~~Cpaq~~~~i~hF~SK~aldI~GLG~k~Ie~L~e~~~~~g~I~~~~D 509 (731)
-+||.|++ + +.+..-... ...-.+|. +|.-+++....|=+.+ .|+-+++++--++. + -|++++-
T Consensus 6 v~Cp~C~s~~~V~KnG~~~~--G~QRYrC~---~C~r~Fql~ytY~a~~-----p~vkeqiv~m~~nG---~-GiRdtaR 71 (88)
T pfam03811 6 IHCPRCSSTEGVYRHGQSTA--GHQRYRCR---HCRRTFQLTYTYEARQ-----PGTKEQIVDMAMNG---A-GCRYTAR 71 (88)
T ss_pred EECCCCCCCCCEEECCCCCC--CCCCEEEC---CCCCEEEEEECCCCCC-----CCHHHHHHHHHHCC---C-CHHHHHH
T ss_conf 47978889876771896899--98577727---7895566630114658-----14789999997679---8-5404478
Q ss_pred H
Q ss_conf 0
Q gi|254781172|r 510 I 510 (731)
Q Consensus 510 L 510 (731)
+
T Consensus 72 v 72 (88)
T pfam03811 72 T 72 (88)
T ss_pred H
T ss_conf 7
No 191
>pfam04551 GcpE GcpE protein. In a variety of organisms, including plants and several eubacteria, isoprenoids are synthesized by the mevalonate-independent 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway. Although different enzymes of this pathway have been described, the terminal biosynthetic steps of the MEP pathway have not been fully elucidated. GcpE gene of Escherichia coli is involved in this pathway.
Probab=68.43 E-value=5.2 Score=19.28 Aligned_cols=42 Identities=21% Similarity=0.404 Sum_probs=25.1
Q ss_pred CCCCCEEEEEECCCCHHHHH---HHCC--CCCCCCCCEEEECCCCCCCCCC
Q ss_conf 44076899983587025665---4101--2357873047770432657750
Q gi|254781172|r 395 IRVGDRVLVKRAGEVIPKVV---DIIV--NERHPDAQPFSFPSFCPICQSR 440 (731)
Q Consensus 395 I~iGd~V~I~RaGdVIP~I~---~Vi~--~~r~~~~~~~~~P~~CP~Cgs~ 440 (731)
=||||++.|+-++|-.-+|. ..+. ..|... .. --.||.||-.
T Consensus 219 ~GIGDTIRVSLt~dP~~EV~v~~~IL~sl~lR~~g---~~-iISCPtCGR~ 265 (345)
T pfam04551 219 EGIGDTIRVSLTEDPVEEVKVAFEILQSLGLRKRG---VE-IISCPTCGRT 265 (345)
T ss_pred CCCCCEEEEECCCCCHHHHHHHHHHHHHCCCCCCC---CE-EEECCCCCCC
T ss_conf 18865399967899547899999999972877578---64-8758874661
No 192
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha subunit, Gram-positive type; InterPro: IPR006308 These are the polypeptide chains of DNA polymerase III. Full-length homologs of this protein are restricted to the Gram-positive lineages, including the Mycoplasmas. This protein is designated alpha chain and given the gene symbol polC, but is not a full-length homolog of other polC genes. The N-terminal region of about 200 amino acids is rich in low-complexity sequence and poorly alignable. ; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication, 0005737 cytoplasm.
Probab=68.42 E-value=2 Score=22.39 Aligned_cols=29 Identities=24% Similarity=0.335 Sum_probs=14.2
Q ss_pred HHHHHHHHHHHHHHHCCCCCCCHHHHHHHH
Q ss_conf 999999999984331779820878999999
Q gi|254781172|r 23 SLEQEISYHDDCYYQYSKPIILDSEYDALK 52 (731)
Q Consensus 23 ~L~~~i~~~~~~Yy~~~~p~isD~eYD~L~ 52 (731)
.|=+.+....--||- ..|.|.=..++.-.
T Consensus 419 nLykLvS~s~~~Yfy-~~Pri~~s~L~~~~ 447 (1264)
T TIGR01405 419 NLYKLVSISLTKYFY-TRPRILRSLLKKYR 447 (1264)
T ss_pred HHHHHHHHHHHHHHC-CCCCCCHHHHHHHC
T ss_conf 899998799865314-68975178898643
No 193
>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=68.39 E-value=5.5 Score=19.10 Aligned_cols=12 Identities=17% Similarity=0.266 Sum_probs=5.0
Q ss_pred HHHHHHHCCCCC
Q ss_conf 689999759966
Q gi|254781172|r 257 MLQKMRCLGFPV 268 (731)
Q Consensus 257 ~l~~L~~~GF~v 268 (731)
....|++.|..|
T Consensus 219 q~~~L~~~GI~T 230 (457)
T TIGR03491 219 RYRLLQELGIHT 230 (457)
T ss_pred HHHHHHHCCCCC
T ss_conf 999999859987
No 194
>PRK08057 cobalt-precorrin-6x reductase; Reviewed
Probab=68.22 E-value=8.1 Score=17.76 Aligned_cols=50 Identities=18% Similarity=0.391 Sum_probs=36.7
Q ss_pred CCCEEEEECCCCCCCHHHHHHHHHHCCCEEEEEEECCEEEEEECCCC--C--CHHHHHHHCCCEEEC
Q ss_conf 68669997258899878999999982984998111632179977888--8--637989974991737
Q gi|254781172|r 648 ENKKLVFTGTLQKIQRHKAQEYVTQLGAVVSAILSRKTDIIIVGDNP--G--SKLEKAQQLGVKIMN 710 (731)
Q Consensus 648 ~gk~vV~TGtl~~~~R~e~~~~ie~~Ggkv~sSVSkkT~~LI~ge~~--g--SKl~KA~~LgI~Ii~ 710 (731)
....+.+.|- ||.+.-.++++..|. ++||.+++. | .|+.-|+++|||||-
T Consensus 165 ~~~iia~~gP---fs~e~e~al~~~~~i----------~~lVtK~SG~~g~~~Ki~AA~~lgi~vi~ 218 (241)
T PRK08057 165 RAEIIAARGP---FSLELERALLRQHRI----------DVVVTKNSGGAGTEAKLDAARELGIPVVM 218 (241)
T ss_pred HHCEEEECCC---CCHHHHHHHHHHHCC----------CEEEEECCCCHHHHHHHHHHHHCCCEEEE
T ss_conf 3208995599---999999999997099----------99999388865069999999984991999
No 195
>PRK09401 reverse gyrase; Reviewed
Probab=68.01 E-value=2.3 Score=22.05 Aligned_cols=45 Identities=24% Similarity=0.315 Sum_probs=27.9
Q ss_pred CCEEEEEECCCCHHHHHHHCCCCCCCCCCEEEECCCCCCCCCCCCC
Q ss_conf 7689998358702566541012357873047770432657750103
Q gi|254781172|r 398 GDRVLVKRAGEVIPKVVDIIVNERHPDAQPFSFPSFCPICQSRVVR 443 (731)
Q Consensus 398 Gd~V~I~RaGdVIP~I~~Vi~~~r~~~~~~~~~P~~CP~Cgs~l~~ 443 (731)
|-+=+...-|.+|| |...++..|.-..+=......||-||+..+.
T Consensus 659 g~~GV~~~~~~fiP-vY~~IkrC~~cg~qft~~~~~cP~Cgs~~i~ 703 (1176)
T PRK09401 659 GYYGVLVGNGKFVP-VYNSIKRCRDCGHQFTDESDRCPRCGSTNID 703 (1176)
T ss_pred CCEEEEEECCEEEE-EEHHHHHHHHCCCCCCCCCCCCCCCCCCCCC
T ss_conf 62269963780898-4166767753586012466668877888756
No 196
>KOG3123 consensus
Probab=67.97 E-value=4.6 Score=19.68 Aligned_cols=11 Identities=9% Similarity=0.326 Sum_probs=4.7
Q ss_pred HHHHHHHCCCC
Q ss_conf 68999975996
Q gi|254781172|r 257 MLQKMRCLGFP 267 (731)
Q Consensus 257 ~l~~L~~~GF~ 267 (731)
.+..|....|.
T Consensus 233 t~~~l~~~d~G 243 (272)
T KOG3123 233 TIKDLAEVDFG 243 (272)
T ss_pred EHHHHHHCCCC
T ss_conf 18767635247
No 197
>PTZ00035 Rad51; Provisional
Probab=67.70 E-value=4.7 Score=19.62 Aligned_cols=16 Identities=19% Similarity=0.281 Sum_probs=5.7
Q ss_pred CCCCCCCCCCHHHHHH
Q ss_conf 0001342100145689
Q gi|254781172|r 524 IENILGFGDVSVTNLY 539 (731)
Q Consensus 524 l~~l~GfgeKsa~nL~ 539 (731)
|..+.|++|..|+||+
T Consensus 70 L~~ikgise~k~~Ki~ 85 (350)
T PTZ00035 70 LCAIKGISEQKAEKLK 85 (350)
T ss_pred HHHCCCCCHHHHHHHH
T ss_conf 9773794699999999
No 198
>PRK03369 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=67.57 E-value=8.3 Score=17.67 Aligned_cols=15 Identities=13% Similarity=-0.039 Sum_probs=7.3
Q ss_pred CCEEEEECCHHCCCC
Q ss_conf 763777311000111
Q gi|254781172|r 300 DGLVYKVDEFSLQKQ 314 (731)
Q Consensus 300 DGiVikvn~~~~q~~ 314 (731)
+-.|+-.||...+..
T Consensus 217 ~~~v~n~DD~~~~~l 231 (487)
T PRK03369 217 RVAVAGLDDSRAAAL 231 (487)
T ss_pred CEEEEECCCHHHHHH
T ss_conf 879996876889999
No 199
>COG0052 RpsB Ribosomal protein S2 [Translation, ribosomal structure and biogenesis]
Probab=67.51 E-value=8.4 Score=17.66 Aligned_cols=32 Identities=25% Similarity=0.427 Sum_probs=17.9
Q ss_pred CHHHHHHHHH--HCCCEEEEEEECCE-----EEEEECCC
Q ss_conf 8789999999--82984998111632-----17997788
Q gi|254781172|r 662 QRHKAQEYVT--QLGAVVSAILSRKT-----DIIIVGDN 693 (731)
Q Consensus 662 ~R~e~~~~ie--~~Ggkv~sSVSkkT-----~~LI~ge~ 693 (731)
.|.|-....| +.|--|..=|-.++ ||.|=|.+
T Consensus 165 p~~e~iAv~EA~klgIPVvAlvDTn~dpd~VD~~IP~Nd 203 (252)
T COG0052 165 PRKEKIAVKEANKLGIPVVALVDTNCDPDGVDYVIPGND 203 (252)
T ss_pred CCHHHHHHHHHHHCCCCEEEEECCCCCCCCCCEEECCCC
T ss_conf 817689999999759998998418999765765522887
No 200
>PRK08938 DNA topoisomerase I; Validated
Probab=67.47 E-value=2.9 Score=21.20 Aligned_cols=20 Identities=25% Similarity=0.381 Sum_probs=11.4
Q ss_pred CCCCHHHHH-----HHHHHHHHCCC
Q ss_conf 231035410-----35555653057
Q gi|254781172|r 479 DAFNIEGLG-----KQQLDFFFKSE 498 (731)
Q Consensus 479 ~aldI~GLG-----~k~Ie~L~e~~ 498 (731)
++|.=.|+| ..+|+.|++.+
T Consensus 468 k~ME~~GIGrpsT~A~II~~L~~R~ 492 (692)
T PRK08938 468 KTLEENGIGRPSTYAPTLDTIQKRY 492 (692)
T ss_pred HHHHHCCCCCCCCHHHHHHHHHHCC
T ss_conf 9998579997165899999998568
No 201
>TIGR02770 nickel_nikD nickel import ATP-binding protein NikD; InterPro: IPR014138 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain . The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , . The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , . Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). This family represents the NikD subunit of a multisubunit nickel import ABC transporter complex. Nickel, once imported, may be used in urease and in certain classes of hydrogenase and superoxide dismutase. NikD and NikE are related families..
Probab=66.53 E-value=8.7 Score=17.52 Aligned_cols=75 Identities=25% Similarity=0.445 Sum_probs=41.1
Q ss_pred CCEEEEEEEEECCEEEEEEECCCCHHHHHHHHHHHHHCCCCCCCCCCCCCEEEEEEEEEEECHHHHHH--HHHHHHCCC-
Q ss_conf 58189999985998998886598655666999775310243223354455048999999852021234--556431485-
Q gi|254781172|r 134 IDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPTIPRVLSLNIPEIIEVRGEVYISKNDFLAL--NDEMIAVGR- 210 (731)
Q Consensus 134 iDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n~~~i~~iP~~l~~~~~~~ieiRGEv~m~~~~F~~l--N~~~~~~g~- 210 (731)
++|++++| +.|+- -|+==..| -|.=+|..+- |+.-.|+..++||||++.=.+...+ .+.+.-.|.
T Consensus 2 V~~~~L~l--k~G~~-~aLvG~SG-SGKS~tc~A~--------Lg~L~~~~~~~~G~i~l~G~~~~~~p~kemr~~Rg~~ 69 (239)
T TIGR02770 2 VQDVNLSL--KRGEV-LALVGESG-SGKSLTCLAI--------LGLLPPGLTQTSGEILLDGRPLLALPKKEMRSIRGRH 69 (239)
T ss_pred CCCCCCEE--ECCEE-EEEECCCC-CCHHHHHHHH--------HCCCCCCCEEEEEEEEECCCCCCCCCHHHHHHHHHHH
T ss_conf 41675203--32437-88874878-7589999998--------5035865223102667717231458736899886666
Q ss_pred --CCCCCHHHHH
Q ss_conf --4334234567
Q gi|254781172|r 211 --KPYANPRNAA 220 (731)
Q Consensus 211 --~~f~NpRN~a 220 (731)
-.+-|||++=
T Consensus 70 ~~~imQnPr~AF 81 (239)
T TIGR02770 70 IATIMQNPRTAF 81 (239)
T ss_pred HHHHCCCCCCCC
T ss_conf 301102850000
No 202
>pfam02371 Transposase_20 Transposase IS116/IS110/IS902 family. Transposases are needed for efficient transposition of the insertion sequence or transposon DNA. This family includes transposases for IS116, IS110 and IS902. This region is often found with pfam01548. The exact function of this region is uncertain. This family contains a HHH motif suggesting a DNA-binding function.
Probab=66.19 E-value=7.6 Score=18.00 Aligned_cols=39 Identities=18% Similarity=0.216 Sum_probs=27.8
Q ss_pred HHHCCCCCCHHHHHHHHHHHCCHHHHHHHHHHHHHCCCC
Q ss_conf 761388867899999999966979999999999733877
Q gi|254781172|r 597 SLIRVPLVGDIIAQAIVEFYQNPRNICAVEALLKEVSPS 635 (731)
Q Consensus 597 ~L~~I~GiG~~~A~si~~ff~~~~n~~~i~~L~~~~~~~ 635 (731)
-|+.|+|||+.+|..|+..+.+........++....+..
T Consensus 3 ~L~sipGiG~~~a~~l~aeigd~~rF~~~~~~~s~~Gl~ 41 (87)
T pfam02371 3 LLLSIPGIGPITAAALLAEIGDISRFKSARQLAAYAGLA 41 (87)
T ss_pred HHHCCCCCCHHHHHHHHHHHCCHHHCCCHHHHHHHCCCC
T ss_conf 342699952999999999929853278999999983999
No 203
>COG1241 MCM2 Predicted ATPase involved in replication control, Cdc46/Mcm family [DNA replication, recombination, and repair]
Probab=66.10 E-value=2.8 Score=21.35 Aligned_cols=19 Identities=11% Similarity=0.022 Sum_probs=9.0
Q ss_pred EECHHHHHHHHHHHCCCCC
Q ss_conf 7379999999988286568
Q gi|254781172|r 708 IMNEEQFLFLLQQYNTTLR 726 (731)
Q Consensus 708 Ii~e~ef~~ll~~~~~~~~ 726 (731)
-+++.+....|........
T Consensus 652 g~~~~~~e~~l~~l~~~g~ 670 (682)
T COG1241 652 GISEKEVEEALEKLKKKGD 670 (682)
T ss_pred CCCHHHHHHHHHHHHHCCC
T ss_conf 7888999999999975694
No 204
>pfam09151 DUF1936 Domain of unknown function (DUF1936). This domain is found in a set of hypothetical Archaeal proteins. Its exact function has not, as yet, been defined. It possesses a zinc ribbon fold.
Probab=65.82 E-value=3.4 Score=20.70 Aligned_cols=31 Identities=32% Similarity=0.785 Sum_probs=18.9
Q ss_pred CCCCCCCCCC-CCCCCCCCCCCEEECCCCCCCCHH
Q ss_conf 3265775010-337865445210100354344114
Q gi|254781172|r 433 FCPICQSRVV-RDLNPKTGKLVAAHRCTGGLACSA 466 (731)
Q Consensus 433 ~CP~Cgs~l~-~~~~~~~~~~~~~~rC~n~~~Cpa 466 (731)
.||-||-.+. ...+++ ++ ..+.||+|+ .|..
T Consensus 3 lcpkcgvgvlepvydek-ge-ikvfrcsnp-acdy 34 (36)
T pfam09151 3 LCPKCGVGVLEPVYDEK-GE-IKVFRCSNP-ACDY 34 (36)
T ss_pred CCCCCCCCCEEEECCCC-CC-EEEEECCCC-CCCC
T ss_conf 47745611003200577-73-889972797-6665
No 205
>COG0821 gcpE 1-hydroxy-2-methyl-2-(e)-butenyl 4-diphosphate synthase [Lipid metabolism]
Probab=65.23 E-value=6.2 Score=18.64 Aligned_cols=77 Identities=18% Similarity=0.295 Sum_probs=40.4
Q ss_pred CCCCCEEEEEECCCCHHHHH---HHCC--CCCCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCHHHHH
Q ss_conf 44076899983587025665---4101--235787304777043265775010337865445210100354344114466
Q gi|254781172|r 395 IRVGDRVLVKRAGEVIPKVV---DIIV--NERHPDAQPFSFPSFCPICQSRVVRDLNPKTGKLVAAHRCTGGLACSAQQL 469 (731)
Q Consensus 395 I~iGd~V~I~RaGdVIP~I~---~Vi~--~~r~~~~~~~~~P~~CP~Cgs~l~~~~~~~~~~~~~~~rC~n~~~Cpaq~~ 469 (731)
=||||++.|+-++|=.-+|. +.+. ..|+.. ..--.||.||-... +++ .--.|..
T Consensus 224 eGIGDTIRVSLt~~P~~EV~V~~eILqslglR~~~----v~~iaCP~CGR~~~------------dv~-----~~~~~~~ 282 (361)
T COG0821 224 EGIGDTIRVSLTADPVEEVKVAQEILQSLGLRSRG----VEVIACPTCGRTEF------------DVI-----QTLNEVE 282 (361)
T ss_pred HCCCCEEEEECCCCCHHHHHHHHHHHHHCCCCCCC----CEEEECCCCCCEEE------------HHH-----HHHHHHH
T ss_conf 25776599965888325579999999980866358----66998998776225------------699-----9999999
Q ss_pred HHHHHHHHCCCCCH-------HHHHHHHHHHH
Q ss_conf 55332130123103-------54103555565
Q gi|254781172|r 470 ERLKHFVSRDAFNI-------EGLGKQQLDFF 494 (731)
Q Consensus 470 ~~i~hF~SK~aldI-------~GLG~k~Ie~L 494 (731)
+++.|-- .-|+| .|.||.....+
T Consensus 283 ~~~~~~~--~pl~VAVMGCVVNGPGEak~Adi 312 (361)
T COG0821 283 QRLEHLK--TPLKVAVMGCVVNGPGEAKHADI 312 (361)
T ss_pred HHHHCCC--CCCEEEEEEEEECCCCCCCCCCE
T ss_conf 9864468--77349999757407850001652
No 206
>pfam01927 DUF82 Protein of unknown function DUF82. This prokaryotic protein family has no known function. The protein contains four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=64.95 E-value=5.8 Score=18.88 Aligned_cols=40 Identities=13% Similarity=-0.025 Sum_probs=23.9
Q ss_pred EECCCCHHHHHHHCCCCCCCCCCEEEECCCCCCCCCCCCCC
Q ss_conf 83587025665410123578730477704326577501033
Q gi|254781172|r 404 KRAGEVIPKVVDIIVNERHPDAQPFSFPSFCPICQSRVVRD 444 (731)
Q Consensus 404 ~RaGdVIP~I~~Vi~~~r~~~~~~~~~P~~CP~Cgs~l~~~ 444 (731)
.++.|+-=++.+|+..-.-.- ..-.+.+.||.||++++..
T Consensus 64 l~~~~~~~Ql~ev~~~~~l~~-~~~~~~sRC~~CN~~L~~v 103 (146)
T pfam01927 64 VRSLDPEEQLREVIERFGLKL-SLKPEFSRCLKCNGPLEPV 103 (146)
T ss_pred ECCCCHHHHHHHHHHHCCCCC-CCCCCCCCCCCCCCCCEEC
T ss_conf 789999999999999669974-3377778565679899581
No 207
>COG4468 GalT Galactose-1-phosphate uridyltransferase [Carbohydrate transport and metabolism]
Probab=64.89 E-value=7 Score=18.24 Aligned_cols=12 Identities=25% Similarity=0.202 Sum_probs=8.3
Q ss_pred HHCCCCCCCCEE
Q ss_conf 975996654148
Q gi|254781172|r 262 RCLGFPVNNGVR 273 (731)
Q Consensus 262 ~~~GF~v~~~~~ 273 (731)
..|||.-.||..
T Consensus 207 e~W~fQySPY~Y 218 (503)
T COG4468 207 EQWGFQYSPYVY 218 (503)
T ss_pred CEEEEEECCCEE
T ss_conf 355676166215
No 208
>PRK02472 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=64.71 E-value=9.4 Score=17.28 Aligned_cols=10 Identities=20% Similarity=0.152 Sum_probs=4.0
Q ss_pred HHHHHHHCCC
Q ss_conf 9999998298
Q gi|254781172|r 666 AQEYVTQLGA 675 (731)
Q Consensus 666 ~~~~ie~~Gg 675 (731)
.++++.++.|
T Consensus 440 F~~~V~~L~g 449 (450)
T PRK02472 440 FIDAVHELKG 449 (450)
T ss_pred HHHHHHHCCC
T ss_conf 9999997479
No 209
>PRK00366 ispG 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed
Probab=64.69 E-value=6.5 Score=18.50 Aligned_cols=42 Identities=21% Similarity=0.389 Sum_probs=24.2
Q ss_pred CCCCCEEEEEECCCCHHHHH---HHCC--CCCCCCCCEEEECCCCCCCCCC
Q ss_conf 44076899983587025665---4101--2357873047770432657750
Q gi|254781172|r 395 IRVGDRVLVKRAGEVIPKVV---DIIV--NERHPDAQPFSFPSFCPICQSR 440 (731)
Q Consensus 395 I~iGd~V~I~RaGdVIP~I~---~Vi~--~~r~~~~~~~~~P~~CP~Cgs~ 440 (731)
=||||++.|+-++|-.-+|. +.+. ..|... .. --.||.||-.
T Consensus 230 ~GIGDTIRVSLT~dPv~EV~va~~IL~slglR~~g---~~-iISCPtCGRt 276 (367)
T PRK00366 230 EGIGDTIRVSLTADPVEEVKVGQEILQSLGLRSRG---PN-VISCPTCGRT 276 (367)
T ss_pred CCCCCEEEEECCCCCHHHHHHHHHHHHHCCCCCCC---CE-EEECCCCCCC
T ss_conf 59964289856888177999999999972866368---51-7658875553
No 210
>KOG3084 consensus
Probab=64.65 E-value=3.2 Score=20.92 Aligned_cols=29 Identities=24% Similarity=0.592 Sum_probs=19.0
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCHH
Q ss_conf 043265775010337865445210100354344114
Q gi|254781172|r 431 PSFCPICQSRVVRDLNPKTGKLVAAHRCTGGLACSA 466 (731)
Q Consensus 431 P~~CP~Cgs~l~~~~~~~~~~~~~~~rC~n~~~Cpa 466 (731)
-.+||.||+++..++.... .-|.+. .||.
T Consensus 150 ykFCp~CG~~tkp~e~g~k------~~Cs~~-~C~~ 178 (345)
T KOG3084 150 YKFCPGCGSPTKPEEAGTK------LQCSDE-TCPS 178 (345)
T ss_pred HCCCCCCCCCCCCCCCCCC------CEEECC-CCCC
T ss_conf 3107566898643568853------230014-4884
No 211
>PRK08115 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=63.51 E-value=3.4 Score=20.67 Aligned_cols=22 Identities=18% Similarity=0.276 Sum_probs=12.0
Q ss_pred HHHHHHHHCCHHHHHHHHHHHHH
Q ss_conf 46667763010111168999999
Q gi|254781172|r 549 SLERFIFSLGIRHVGAEIARSLA 571 (731)
Q Consensus 549 ~L~r~L~ALGI~~vG~~~Ak~La 571 (731)
.|...|..||||+ |...|..++
T Consensus 553 GLAD~Li~LGi~Y-gSeEA~~la 574 (857)
T PRK08115 553 GLHDLLIYCEKKY-GSEEGNKLV 574 (857)
T ss_pred HHHHHHHHCCCCC-CCHHHHHHH
T ss_conf 0999999839986-999999999
No 212
>PRK09536 btuD corrinoid ABC transporter ATPase; Reviewed
Probab=62.74 E-value=9 Score=17.43 Aligned_cols=30 Identities=20% Similarity=0.367 Sum_probs=23.9
Q ss_pred CCEEEEECCCCHHHHHHHCCCCCCCCCCCCCCCCCEEEEEECCCCH
Q ss_conf 6400010148989997502345432224684407689998358702
Q gi|254781172|r 365 GALITNATLHNEDYIKGLDASGKVMRGGRDIRVGDRVLVKRAGEVI 410 (731)
Q Consensus 365 G~~V~ratlhN~~~I~~l~~~~~~~~~~~~I~iGd~V~I~RaGdVI 410 (731)
|.||= .++|+.+...++ -|+|.+.+.|.|+
T Consensus 188 G~TVI-~vtHDL~lA~~~---------------cDrVivl~~GrIv 217 (409)
T PRK09536 188 GKTVV-AAIHDLNLAARY---------------CDELVLLADGRVH 217 (409)
T ss_pred CCEEE-EEECCHHHHHHH---------------CCEEEEEECCEEE
T ss_conf 99999-995689999986---------------9999999899899
No 213
>PRK06196 oxidoreductase; Provisional
Probab=62.38 E-value=8.3 Score=17.67 Aligned_cols=14 Identities=14% Similarity=0.143 Sum_probs=6.3
Q ss_pred EECCCCHHHHHHHH
Q ss_conf 86598655666999
Q gi|254781172|r 152 ALRGDGHSGEDVSA 165 (731)
Q Consensus 152 ~TRGdG~~GeDVT~ 165 (731)
+|=|+.-+|--...
T Consensus 31 ITGa~sGIG~~tA~ 44 (316)
T PRK06196 31 VTGGYSGLGLETTR 44 (316)
T ss_pred ECCCCCHHHHHHHH
T ss_conf 91799679999999
No 214
>PRK12481 2-deoxy-D-gluconate 3-dehydrogenase; Provisional
Probab=62.33 E-value=10 Score=16.97 Aligned_cols=14 Identities=21% Similarity=0.266 Sum_probs=9.4
Q ss_pred CCCCCCCEEEEECC
Q ss_conf 88216866999725
Q gi|254781172|r 644 SSEIENKKLVFTGT 657 (731)
Q Consensus 644 ~~~l~gk~vV~TGt 657 (731)
++..+|.++++.|-
T Consensus 234 a~~iTG~~i~VDGG 247 (251)
T PRK12481 234 SDYVTGYTLAVDGG 247 (251)
T ss_pred HCCCCCCEEEECCC
T ss_conf 35904855897846
No 215
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=62.24 E-value=2.9 Score=21.25 Aligned_cols=14 Identities=50% Similarity=1.120 Sum_probs=10.6
Q ss_pred CCCCCCCCCCCCCC
Q ss_conf 04326577501033
Q gi|254781172|r 431 PSFCPICQSRVVRD 444 (731)
Q Consensus 431 P~~CP~Cgs~l~~~ 444 (731)
-+.||+||+++.+.
T Consensus 153 ~~~Cp~CG~~~~~~ 166 (177)
T COG1439 153 KDFCPICGSPLKRK 166 (177)
T ss_pred CCCCCCCCCCEEEE
T ss_conf 88077899911785
No 216
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=61.15 E-value=7.8 Score=17.90 Aligned_cols=17 Identities=24% Similarity=0.309 Sum_probs=8.5
Q ss_pred CCCCCCEEEEECCCCCC
Q ss_conf 82168669997258899
Q gi|254781172|r 645 SEIENKKLVFTGTLQKI 661 (731)
Q Consensus 645 ~~l~gk~vV~TGtl~~~ 661 (731)
+.+.|.-+|.-|.++-+
T Consensus 98 ~~f~G~YhVL~G~lspl 114 (198)
T COG0353 98 GEFRGLYHVLGGLLSPL 114 (198)
T ss_pred CCCCEEEEEECCCCCCC
T ss_conf 52572788845733734
No 217
>TIGR02707 butyr_kinase butyrate kinase; InterPro: IPR011245 This group represents bacterial butyrate kinase, an enzyme that facilitates the formation of butyryl-CoA by phosphorylating butyrate in the presence of ATP to form butyryl phosphate . The final steps in butyrate synthesis by anaerobic bacteria can occur via butyrate kinase and phosphotransbutyrylase or via butyryl-CoA:acetate CoA-transferase, the latter providing the dominant route for butyrate formation in human colonic bacteria .; GO: 0005524 ATP binding, 0047761 butyrate kinase activity, 0016310 phosphorylation, 0005737 cytoplasm.
Probab=61.03 E-value=4 Score=20.11 Aligned_cols=76 Identities=24% Similarity=0.309 Sum_probs=47.0
Q ss_pred HHHHHHHCCCCCCCCEEEEECCCCHHHHHHHHHHHHCCCCCCCCCEEEEECCHHCCCCC----CCCCCCCCCEEEECCCC
Q ss_conf 68999975996654148874032113455665531001123437637773110001115----87656866312311456
Q gi|254781172|r 257 MLQKMRCLGFPVNNGVRQANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSLQKQL----GERARSPRWMISHKFAE 332 (731)
Q Consensus 257 ~l~~L~~~GF~v~~~~~~~~~~~~~~~~~~~~~~~r~~l~y~iDGiVikvn~~~~q~~l----G~ts~~PrwaiA~Kf~~ 332 (731)
.+++|++.||++....-.+ -|--|==||.|=++-|||.=+++.. |.++.+==--||.+|++
T Consensus 52 i~~~L~e~Gi~~~~l~AvV---------------gRGGLLkPi~GGTY~Vn~~MleDLk~~~~GeHASNLGaIIA~~lA~ 116 (353)
T TIGR02707 52 ILEVLEEKGINISKLDAVV---------------GRGGLLKPIEGGTYLVNEKMLEDLKEGKRGEHASNLGAIIARELAD 116 (353)
T ss_pred HHHHHHHCCCCHHHEEEEE---------------ECCCCCCCCCCCEEEECHHHHHHHHHCCCCCCCCCHHHHHHHHHHH
T ss_conf 9999874088712431579---------------7277023338960477655688885105887843368999999876
Q ss_pred CEEEEEEEEEEEEECCCCEE-EEEEEEEEEEEC
Q ss_conf 21589987889940356225-899997433302
Q gi|254781172|r 333 KQASTRLLDIDIQIGRTGIL-TPVARLEPVNIG 364 (731)
Q Consensus 333 e~~~T~v~~I~wqvgRtG~i-tPva~~ePV~l~ 364 (731)
+ .= -|.=.+|||-++
T Consensus 117 ~-----------------~~diPafIVDPVVVD 132 (353)
T TIGR02707 117 E-----------------LNDIPAFIVDPVVVD 132 (353)
T ss_pred H-----------------CCCCCEEEECCCEEC
T ss_conf 5-----------------189435882683350
No 218
>PRK03806 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=61.02 E-value=11 Score=16.80 Aligned_cols=26 Identities=15% Similarity=0.378 Sum_probs=11.9
Q ss_pred CCEEEEECC---CCCCC----HH-HHHHHHHHCC
Q ss_conf 866999725---88998----78-9999999829
Q gi|254781172|r 649 NKKLVFTGT---LQKIQ----RH-KAQEYVTQLG 674 (731)
Q Consensus 649 gk~vV~TGt---l~~~~----R~-e~~~~ie~~G 674 (731)
|-+|+|+=. |..|+ |- ..+++++++|
T Consensus 405 gd~VLlSPacaSfD~f~nye~RG~~F~~lv~~Lg 438 (438)
T PRK03806 405 GDMVLLSPACASLDQFKNFEQRGDEFARLAKELG 438 (438)
T ss_pred CCEEEECCCCCCCCCCCCHHHHHHHHHHHHHHCC
T ss_conf 9989989745030142499999999999999629
No 219
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=60.98 E-value=3 Score=21.07 Aligned_cols=54 Identities=22% Similarity=0.396 Sum_probs=24.7
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCEEECCCC----CCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCC
Q ss_conf 43265775010337865445210100354----3441144665533213012310354103555565305
Q gi|254781172|r 432 SFCPICQSRVVRDLNPKTGKLVAAHRCTG----GLACSAQQLERLKHFVSRDAFNIEGLGKQQLDFFFKS 497 (731)
Q Consensus 432 ~~CP~Cgs~l~~~~~~~~~~~~~~~rC~n----~~~Cpaq~~~~i~hF~SK~aldI~GLG~k~Ie~L~e~ 497 (731)
-.||.|...+...... ....+++|-- +..||.=-...|. .-|.|-..|+.-+..
T Consensus 445 ~~Cp~Cd~~lt~H~~~---~~L~CH~Cg~~~~~p~~Cp~Cgs~~L~---------~~G~GterieeeL~~ 502 (730)
T COG1198 445 AECPNCDSPLTLHKAT---GQLRCHYCGYQEPIPQSCPECGSEHLR---------AVGPGTERIEEELKR 502 (730)
T ss_pred CCCCCCCCCEEEECCC---CEEEECCCCCCCCCCCCCCCCCCCEEE---------EECCCHHHHHHHHHH
T ss_conf 2489999512786479---806707799989988779899997369---------964619999999998
No 220
>pfam03786 UxuA D-mannonate dehydratase (UxuA). UxuA (this family) and UxuB are required for hexuronate degradation.
Probab=60.55 E-value=5.7 Score=18.97 Aligned_cols=81 Identities=17% Similarity=0.247 Sum_probs=40.6
Q ss_pred CCCCCCCHHHCCCHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCEEEEEEEEECCEEEEEEECCCCHHHHHHHHHHHHH
Q ss_conf 16642570215999999999999998612467776119999415818999998599899888659865566699977531
Q gi|254781172|r 91 HSIPTLSLEKIWNIEDLRKFITRIYRFWQKKDDNSIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAI 170 (731)
Q Consensus 91 H~~pMlSL~k~~~~~el~~w~~~~~~~~~~~~~~~~~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n~~~i 170 (731)
|..|- ..+++.++|.+--+.+... |+..+.+ |+--....+-+|.+..-+-|-.-..+|
T Consensus 34 h~~p~---GevW~~~~I~~~k~~ie~~------------------GL~~~vV-ESvPvhe~Ik~g~~~rd~~Ieny~~ti 91 (350)
T pfam03786 34 HDIPV---GEVWPKEEIMALKEIIEDA------------------GLTLSVI-ESVPVHEDIKLGTPTRDRYIENYKQTI 91 (350)
T ss_pred CCCCC---CCCCCHHHHHHHHHHHHHC------------------CCEEEEE-ECCCCHHHHHCCCCCHHHHHHHHHHHH
T ss_conf 68999---8948999999999999974------------------9969999-477866888749987899999999999
Q ss_pred CCCCCCCCCCCCCEEEEEEEEEEECHHHHH
Q ss_conf 024322335445504899999985202123
Q gi|254781172|r 171 PTIPRVLSLNIPEIIEVRGEVYISKNDFLA 200 (731)
Q Consensus 171 ~~iP~~l~~~~~~~ieiRGEv~m~~~~F~~ 200 (731)
+++-. .+ +.+=+==||+--+|-+
T Consensus 92 rNLa~-~G------I~vicYNFMPv~dW~R 114 (350)
T pfam03786 92 RNLAR-AG------IKVICYNFMPVFDWTR 114 (350)
T ss_pred HHHHH-CC------CCEEEEECCCCCCCCC
T ss_conf 99997-79------9889872455455114
No 221
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=60.43 E-value=3.7 Score=20.36 Aligned_cols=24 Identities=17% Similarity=0.713 Sum_probs=17.5
Q ss_pred EEECCCCCCCCCCCCCCCCCCCCCCCEEECCCCC
Q ss_conf 7770432657750103378654452101003543
Q gi|254781172|r 428 FSFPSFCPICQSRVVRDLNPKTGKLVAAHRCTGG 461 (731)
Q Consensus 428 ~~~P~~CP~Cgs~l~~~~~~~~~~~~~~~rC~n~ 461 (731)
+.+|-.||.||-++.. ..++|+|.
T Consensus 3 ~~~~~~cPvcg~~~iV----------TeL~c~~~ 26 (122)
T COG3877 3 YKVINRCPVCGRKLIV----------TELKCSNC 26 (122)
T ss_pred CCCCCCCCCCCCCCEE----------EEEECCCC
T ss_conf 7778899855632036----------78742888
No 222
>PRK08305 spoVFB dipicolinate synthase subunit B; Reviewed
Probab=60.09 E-value=11 Score=16.69 Aligned_cols=27 Identities=22% Similarity=0.288 Sum_probs=14.9
Q ss_pred CCCHHHHHHHHHHCCCHHHHHCCCEEEEEEECCCC
Q ss_conf 34234567777523455553011105664102454
Q gi|254781172|r 213 YANPRNAASGILRRLNPTDITRYLNFFVHGLGKTS 247 (731)
Q Consensus 213 f~NpRN~aaG~lr~~d~~~~~r~L~f~ay~~~~~~ 247 (731)
+.|++|... .++ .+++-|+.|+-..+.
T Consensus 135 ~~n~~Ni~~-Ll~-------~kniyfvPfgqd~~~ 161 (195)
T PRK08305 135 GLNAVNLGR-LLN-------TKNIYFVPFGQDDPE 161 (195)
T ss_pred HHCHHHHHH-HHH-------CCCEEEEECCCCCCC
T ss_conf 768999999-982-------697899956886734
No 223
>KOG4362 consensus
Probab=60.00 E-value=11 Score=16.68 Aligned_cols=62 Identities=24% Similarity=0.395 Sum_probs=49.1
Q ss_pred CCCCCCCEEEEECCCCCCCHHHHHHHHHHCCCEEE------EEEECCEEEEEECCCCC--C----HHHHHHHCC
Q ss_conf 88216866999725889987899999998298499------81116321799778888--6----379899749
Q gi|254781172|r 644 SSEIENKKLVFTGTLQKIQRHKAQEYVTQLGAVVS------AILSRKTDIIIVGDNPG--S----KLEKAQQLG 705 (731)
Q Consensus 644 ~~~l~gk~vV~TGtl~~~~R~e~~~~ie~~Ggkv~------sSVSkkT~~LI~ge~~g--S----Kl~KA~~Lg 705 (731)
...|.|+.|+|-|.|++...+++.+++...||.+. +|-+|+++..+..+.+. + |..+|..++
T Consensus 585 ~kLf~gl~~~~~g~fs~~p~~~l~~l~~~~gg~~l~~~~~~~~~~k~s~~~~~~~~~~~~~~~~~k~~~~ea~~ 658 (684)
T KOG4362 585 PKLFEGLKFYFVGDFSNPPKEQLQELVHLAGGTILQVPRVAYSDKKKSTIVVLSEKPVLDSILWQKVNDAEALA 658 (684)
T ss_pred CCHHCCCCCEEECCCCCCCHHHHHHHHHHCCCCEEECCCCCCCCCCCCCEEEEECCCCCCCHHHHHHCCHHHHH
T ss_conf 50114884136455344728998888764574265056765666533211575104688841555421288998
No 224
>pfam09862 DUF2089 Protein of unknown function(DUF2089). This domain, found in various hypothetical prokaryotic proteins, has no known function.
Probab=59.66 E-value=4.3 Score=19.86 Aligned_cols=26 Identities=23% Similarity=0.733 Sum_probs=16.3
Q ss_pred CCCCCCCCCCCCCCCCCCCCEEECCCCCCCCHHHHHHHH
Q ss_conf 265775010337865445210100354344114466553
Q gi|254781172|r 434 CPICQSRVVRDLNPKTGKLVAAHRCTGGLACSAQQLERL 472 (731)
Q Consensus 434 CP~Cgs~l~~~~~~~~~~~~~~~rC~n~~~Cpaq~~~~i 472 (731)
||+||+++.. .-++|++ |.--+.+.+
T Consensus 1 CPvCg~~l~V----------t~L~C~~---C~t~ieG~F 26 (113)
T pfam09862 1 CPVCGEELTV----------TRLECSK---CGTTIEGRF 26 (113)
T ss_pred CCCCCCCEEE----------EEEECCC---CCCEEEEEE
T ss_conf 9989981389----------9988489---986797365
No 225
>TIGR02644 Y_phosphoryl pyrimidine-nucleoside phosphorylase; InterPro: IPR000053 Two highly similar activities are represented in this group: thymidine phosphorylase (TP, gene deoA, 2.4.2.4 from EC) and pyrimidine-nucleoside phosphorylase (PyNP, gene pdp, 2.4.2.2 from EC). Both are dimeric enzymes that function in the salvage pathway to catalyse the reversible phosphorolysis of pyrimidine nucleosides to the free base and sugar moieties. In the case of thymidine phosphorylase, thymidine (and to a lesser extent, 2'-deoxyuridine) is lysed to produce thymine (or uracil) and 2'-deoxyribose-1-phosphate. Pyrimidine-nucleoside phosphorylase performs the analogous reaction on thymidine (to produce the same products) and uridine (to produce uracil and ribose-1-phosphate). PyNP is typically the only pyrimidine nucleoside phosphorylase encoded by Gram positive bacteria, while eukaryotes and proteobacteria encode two: TP, and the unrelated uridine phosphorylase. In humans, TP was originally characterised as platelet-derived endothelial cell growth factor and gliostatin . Structurally, the enzymes are homodimers, each composed of a rigid all alpha-helix lobe and a mixed alpha-helix/beta-sheet lobe, which are connected by a flexible hinge , . Prior to substrate binding, the lobes are separated by a large cleft. A functional active site and subsequent catalysis occurs upon closing of the cleft. The active site, composed of a phosphate binding site and a (deoxy)ribonucleotide binding site within the cleft region, is highly conserved between the two enzymes of this group. Active site residues (Escherichia coli DeoA numbering) include the phosphate binding Lys84 and Ser86 (close to a glycine-rich loop), Ser113, and Thr123, and the pyrimidine nucleoside-binding Arg171, Ser186, and Lys190. Sequence comparison between the active site residues for both enzymes reveals only one difference , which has been proposed to partially mediate substrate specificity. In TP, position 111 is a methionine, while the analogous position in PyNP is lysine. It should be noted that the uncharacterised archaeal members of this family differ in a number of respects from either of the characterised activities. The residue at position 108 is lysine, indicating the activity might be PyNP-like (though the determinants of substrate specificity have not been fully elucidated). Position 171 is glutamate (negative charge side chain) rather than arginine (positive charge side chain). In addition, a large loop that may "lock in" the substrates within the active site is much smaller than in the characterised members. It is not clear what effect these and other differences have on activity and specificity.; GO: 0006206 pyrimidine base metabolic process.
Probab=59.63 E-value=11 Score=16.63 Aligned_cols=44 Identities=14% Similarity=0.175 Sum_probs=23.7
Q ss_pred CCHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCEEEEEEEEECCEEEEEEECCCCHHHHHHHH
Q ss_conf 9999999999999986124677761199994158189999985998998886598655666999
Q gi|254781172|r 102 WNIEDLRKFITRIYRFWQKKDDNSIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSA 165 (731)
Q Consensus 102 ~~~~el~~w~~~~~~~~~~~~~~~~~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~ 165 (731)
-+.+|...|...+... +...+| ..+-|..+ -+=+|=| +|+-||-
T Consensus 49 M~~~Et~~LT~AM~~S-----G~~~Dl---s~~~g~~v---------DKHSTGG---VGDK~SL 92 (425)
T TIGR02644 49 MTDEETAYLTKAMIDS-----GEVLDL---SSLKGPKV---------DKHSTGG---VGDKVSL 92 (425)
T ss_pred CCHHHHHHHHHHHHHH-----CCEEEC---CCCCCCEE---------CCCCCCC---CCHHHHH
T ss_conf 9988999999999973-----867400---23788514---------0355788---3402467
No 226
>KOG2703 consensus
Probab=59.56 E-value=4.8 Score=19.50 Aligned_cols=58 Identities=14% Similarity=0.178 Sum_probs=31.2
Q ss_pred HHCCHHHHHHHHH-HHHHHHCCCHHHHHHHHHHHHHCCCCCHHHHHCCCCCCHHHHHHHHHHHC
Q ss_conf 6301011116899-99998829989999978977612511778761388867899999999966
Q gi|254781172|r 555 FSLGIRHVGAEIA-RSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVEFYQ 617 (731)
Q Consensus 555 ~ALGI~~vG~~~A-k~La~~f~si~~l~~~~~~~~~~~~~~~e~L~~I~GiG~~~A~si~~ff~ 617 (731)
++|.||.++-... -.|.-.|.+++.++..+........... -+...+-..+...+|+.
T Consensus 333 cs~~IPEl~lel~~~~LgGrfTTiEGLl~~~~e~l~~~~f~~-----~DS~~~~~~~~~~~F~~ 391 (460)
T KOG2703 333 CSLSIPELDLELGGGTLGGRFTTIEGLLTQIREQLDGRSFTF-----GDSMDEGQKARWQEFLA 391 (460)
T ss_pred CCEECCCCCEECCCCCCCCEEEEHHHHHHHHHHHHHCCCEEC-----CCCCCHHHHHHHHHHHH
T ss_conf 303444432000476245324537999999999972574002-----45678889999999999
No 227
>KOG2875 consensus
Probab=59.18 E-value=12 Score=16.58 Aligned_cols=43 Identities=23% Similarity=0.257 Sum_probs=26.4
Q ss_pred HHHHHHHHCCC---HHHHHHHHHHHHHCCCCCHHHHHCCCCCCHHHHHHHHH
Q ss_conf 99999988299---89999978977612511778761388867899999999
Q gi|254781172|r 566 IARSLAKYYLS---YQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVE 614 (731)
Q Consensus 566 ~Ak~La~~f~s---i~~l~~~~~~~~~~~~~~~e~L~~I~GiG~~~A~si~~ 614 (731)
+|+.|.+..+- +..+.+. .-++..+.|+.++|+|+|+|+.|-=
T Consensus 191 ta~~l~~~~g~~~wLqslr~~------~yeear~~L~~lpGVG~KVADCI~L 236 (323)
T KOG2875 191 TARALQEKQGGLAWLQSLRKS------SYEEAREALCSLPGVGPKVADCICL 236 (323)
T ss_pred HHHHHHHHCCCCHHHHHHHCC------CHHHHHHHHHCCCCCCCHHHHHHHH
T ss_conf 999999723500599988545------2899999985288876147562231
No 228
>PRK08174 DNA topoisomerase III; Validated
Probab=59.11 E-value=5.5 Score=19.08 Aligned_cols=21 Identities=0% Similarity=0.096 Sum_probs=13.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHH
Q ss_conf 999999999999999998433
Q gi|254781172|r 16 QARKELSSLEQEISYHDDCYY 36 (731)
Q Consensus 16 ~~~~~i~~L~~~i~~~~~~Yy 36 (731)
+.++++..|.+.+.+++..|.
T Consensus 78 ~~~~q~~~ik~l~k~ad~ii~ 98 (670)
T PRK08174 78 KTASQFKVVKRLLKQATELVI 98 (670)
T ss_pred CHHHHHHHHHHHHHCCCEEEE
T ss_conf 078999999999965999998
No 229
>pfam10391 DNA_pol_lambd_f Fingers domain of DNA polymerase lambda. 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. DNA_pol_lambd_f is 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.
Probab=58.94 E-value=3.5 Score=20.62 Aligned_cols=25 Identities=28% Similarity=0.488 Sum_probs=16.2
Q ss_pred CCHHHHHHHHHHHHHCCCCCCEEEEEHHHH
Q ss_conf 103541035555653057654045410110
Q gi|254781172|r 481 FNIEGLGKQQLDFFFKSEDPAFSIRIPADI 510 (731)
Q Consensus 481 ldI~GLG~k~Ie~L~e~~~~~g~I~~~~DL 510 (731)
++|=|+||++.+++++.| ++++.||
T Consensus 5 ~~I~GvGp~~A~~~~~~G-----~~ti~dL 29 (52)
T pfam10391 5 TNIWGVGPKTARKWYRQG-----IRTLEDL 29 (52)
T ss_pred HHCCCCCHHHHHHHHHHC-----CCCHHHH
T ss_conf 635440699999999947-----8889999
No 230
>PRK07141 DNA topoisomerase I; Validated
Probab=58.91 E-value=4.1 Score=20.07 Aligned_cols=21 Identities=5% Similarity=0.063 Sum_probs=14.2
Q ss_pred CCCCHHHHH-----HHHHHHHHCCCC
Q ss_conf 231035410-----355556530576
Q gi|254781172|r 479 DAFNIEGLG-----KQQLDFFFKSED 499 (731)
Q Consensus 479 ~aldI~GLG-----~k~Ie~L~e~~~ 499 (731)
++|+=.||| ..+|+.|++.+|
T Consensus 456 ~~Me~~gIGtpATrA~iIe~L~~R~Y 481 (622)
T PRK07141 456 EKLDDIKVGRPSTFASTVKILKDRLY 481 (622)
T ss_pred HHHHHCCCCCCCCHHHHHHHHHHCCC
T ss_conf 99874799852029999999975773
No 231
>PRK06139 short chain dehydrogenase; Provisional
Probab=58.87 E-value=7.9 Score=17.87 Aligned_cols=13 Identities=0% Similarity=-0.013 Sum_probs=5.7
Q ss_pred CHHHHHHHHHHHH
Q ss_conf 0145689999875
Q gi|254781172|r 533 VSVTNLYDSINKR 545 (731)
Q Consensus 533 Ksa~nL~~sIe~s 545 (731)
+-|+.|+.+.++-
T Consensus 216 ~vA~ai~~~~~~~ 228 (324)
T PRK06139 216 RVAKAMVRLADRP 228 (324)
T ss_pred HHHHHHHHHHHCC
T ss_conf 9999999998389
No 232
>TIGR01588 citE citrate lyase, beta subunit; InterPro: IPR006475 This group of sequences represent the beta subunit of the holoenzyme citrate lyase (4.1.3.6 from EC) composed of alpha (2.8.3.10 from EC), beta, and acyl carrier protein subunits in a stoichiometric relationship of 6:6:6. Citrate lyase is an enzyme which converts citrate to oxaloacetate. In bacteria, this reaction is involved in citrate fermentation. The beta subunit catalyzes the reaction (3S)-citryl-CoA = acetyl-CoA + oxaloacetate. The group contains an experimentally characterised member from Leuconostoc mesenteroides . The group contains sequences from a wide range of Gram-positive bacteria. For Gram-negative bacteria, it appears that only the sequences from gamma proteobacteria are present.; GO: 0008816 citryl-CoA lyase activity, 0006084 acetyl-CoA metabolic process, 0005737 cytoplasm, 0009346 citrate lyase complex.
Probab=58.47 E-value=7.9 Score=17.84 Aligned_cols=15 Identities=20% Similarity=0.235 Sum_probs=9.6
Q ss_pred HHHHHHHHHHHCCCC
Q ss_conf 410355556530576
Q gi|254781172|r 485 GLGKQQLDFFFKSED 499 (731)
Q Consensus 485 GLG~k~Ie~L~e~~~ 499 (731)
-||..=|+..+.+|.
T Consensus 72 pFG~~Dl~AvVkAgv 86 (288)
T TIGR01588 72 PFGLEDLKAVVKAGV 86 (288)
T ss_pred HHHHHHHHHHHHCCC
T ss_conf 545888998875388
No 233
>KOG2379 consensus
Probab=58.45 E-value=12 Score=16.49 Aligned_cols=29 Identities=14% Similarity=0.275 Sum_probs=14.6
Q ss_pred CCHHHHHHHHHHHHHHHCCCHHHHHHHHH
Q ss_conf 01011116899999988299899999789
Q gi|254781172|r 557 LGIRHVGAEIARSLAKYYLSYQNFAQEIN 585 (731)
Q Consensus 557 LGI~~vG~~~Ak~La~~f~si~~l~~~~~ 585 (731)
|-|++++...|-.|+.+|+++-.+..+.+
T Consensus 433 Mqvkg~S~erAiAI~d~YpTl~sLl~AY~ 461 (501)
T KOG2379 433 MQVKGMSLERAIAIADRYPTLRSLLSAYE 461 (501)
T ss_pred HHCCCCCHHHHHHHHHHCCCHHHHHHHHH
T ss_conf 84347548889999996568999999986
No 234
>TIGR01203 HGPRTase hypoxanthine phosphoribosyltransferase; InterPro: IPR005904 Phosphoribosyltransferases (PRT) are enzymes that catalyze the synthesis of beta-n-5'-monophosphates from phosphoribosylpyrophosphate (PRPP) and an enzyme specific amine. A number of PRT's are involved in the biosynthesis of purine, pyrimidine, and pyridine nucleotides, or in the salvage of purines and pyrimidines. Purine nucleotides are synthesized both via the de novo pathway and via the salvage pathway and are vital for cell functions and cell proliferation through DNA and RNA syntheses and ATP energy supply. This entry presents hypoxanthine phosphoribosyltransferase (2.4.2.8 from EC), which belongs to phosphoribosyltransferase family and is involved in purine salvage.; GO: 0004422 hypoxanthine phosphoribosyltransferase activity, 0006166 purine ribonucleoside salvage, 0005737 cytoplasm.
Probab=58.39 E-value=11 Score=16.61 Aligned_cols=20 Identities=25% Similarity=0.418 Sum_probs=17.5
Q ss_pred CCHHHHHHHHHHHHHHHHHH
Q ss_conf 89999999999999999999
Q gi|254781172|r 12 LSIEQARKELSSLEQEISYH 31 (731)
Q Consensus 12 ~s~~~~~~~i~~L~~~i~~~ 31 (731)
++.+++++|+++|+++|+.+
T Consensus 3 i~~~~i~~r~~eLa~~I~~~ 22 (183)
T TIGR01203 3 ISEEQIKARIAELAKQITED 22 (183)
T ss_pred CCHHHHHHHHHHHHHHHHHH
T ss_conf 67899999999999999987
No 235
>KOG0323 consensus
Probab=58.33 E-value=7.3 Score=18.10 Aligned_cols=81 Identities=26% Similarity=0.325 Sum_probs=59.7
Q ss_pred CCCCCCCEEEEECCCCCCC---HHHHHHHHHHCCCEEEEEEECCEEEEEECCCCC-CHHHHHHHCC-CEEECHHHHHHHH
Q ss_conf 8821686699972588998---789999999829849981116321799778888-6379899749-9173799999999
Q gi|254781172|r 644 SSEIENKKLVFTGTLQKIQ---RHKAQEYVTQLGAVVSAILSRKTDIIIVGDNPG-SKLEKAQQLG-VKIMNEEQFLFLL 718 (731)
Q Consensus 644 ~~~l~gk~vV~TGtl~~~~---R~e~~~~ie~~Ggkv~sSVSkkT~~LI~ge~~g-SKl~KA~~Lg-I~Ii~e~ef~~ll 718 (731)
...+.|..+||+|....+. +.++--.....|+.++-.++.+|..||+ .++| -|..+|...+ +.|....+++.-+
T Consensus 439 ~~v~~~~~~vfSg~~P~~~~~~~s~~~~~~~~~g~vs~~~~~~~~th~i~-~~~gt~k~~~a~~~~~~~Vv~~~wl~~~~ 517 (635)
T KOG0323 439 TKVLKGSQIVFSGLHPTGSTDESADILGVAQQLGAVSAPDVSDKTTHLIA-ANAGTKKVYKAVVSGSAKVVNAAWLWRSL 517 (635)
T ss_pred HHHHHCCCEEECCCCCCCCCCCHHHHHHHHHCCCCEECCCCCCHHHHHHH-HCCCCCEEECCCCCCCEEEECHHHHHHHH
T ss_conf 67763231010256667677001256664420353102566611355776-53585123312234540675134888878
Q ss_pred HHHCCCC
Q ss_conf 8828656
Q gi|254781172|r 719 QQYNTTL 725 (731)
Q Consensus 719 ~~~~~~~ 725 (731)
++.+.-.
T Consensus 518 e~w~~v~ 524 (635)
T KOG0323 518 EKWGKVE 524 (635)
T ss_pred HHHCCHH
T ss_conf 8752211
No 236
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=58.10 E-value=4 Score=20.11 Aligned_cols=35 Identities=9% Similarity=0.094 Sum_probs=21.2
Q ss_pred HCCCEEEEEEECCCCCCCCCCCHHHHHHHHHCCCCC
Q ss_conf 011105664102454332100003689999759966
Q gi|254781172|r 233 TRYLNFFVHGLGKTSEIFAKGQYEMLQKMRCLGFPV 268 (731)
Q Consensus 233 ~r~L~f~ay~~~~~~~~~~~~~~e~l~~L~~~GF~v 268 (731)
.+++.+-++.-. +......+-.+..++-++||++.
T Consensus 334 eKRVELh~HTkM-S~mDai~sv~~~vk~A~kwghka 368 (1444)
T COG2176 334 EKRVELHFHTKM-SQMDAITSVEELVKQAKKWGHKA 368 (1444)
T ss_pred CCEEEEEECCCH-HHHCCCCCHHHHHHHHHHCCCCE
T ss_conf 304899851532-44216678999999999759964
No 237
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family; 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=57.99 E-value=4.1 Score=20.08 Aligned_cols=15 Identities=20% Similarity=0.554 Sum_probs=11.2
Q ss_pred ECCCCCCCCCC-CCCC
Q ss_conf 70432657750-1033
Q gi|254781172|r 430 FPSFCPICQSR-VVRD 444 (731)
Q Consensus 430 ~P~~CP~Cgs~-l~~~ 444 (731)
..+.||+||++ +.+.
T Consensus 26 pl~~CP~C~~~~~~k~ 41 (43)
T TIGR02605 26 PLTTCPACGGPALRKQ 41 (43)
T ss_pred CCCCCCCCCCCCEEEE
T ss_conf 3447876787641241
No 238
>PRK10246 exonuclease subunit SbcC; Provisional
Probab=57.83 E-value=3.6 Score=20.46 Aligned_cols=13 Identities=31% Similarity=0.669 Sum_probs=9.0
Q ss_pred EECCCCCCCCCCC
Q ss_conf 7704326577501
Q gi|254781172|r 429 SFPSFCPICQSRV 441 (731)
Q Consensus 429 ~~P~~CP~Cgs~l 441 (731)
..-+-||+|||.-
T Consensus 501 ~~G~pCPVCGS~~ 513 (1047)
T PRK10246 501 QAGQPCPLCGSTS 513 (1047)
T ss_pred CCCCCCCCCCCCC
T ss_conf 7999899999978
No 239
>PRK02048 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Provisional
Probab=57.39 E-value=8.6 Score=17.55 Aligned_cols=63 Identities=19% Similarity=0.257 Sum_probs=29.4
Q ss_pred CCCCCCCEEEEECCCCCCCHHHHHHHHHHCCCEEEEEEECCEEEEEECCCCC--C--HHHHHHHCCCEEEC-HHHHHHHH
Q ss_conf 8821686699972588998789999999829849981116321799778888--6--37989974991737-99999999
Q gi|254781172|r 644 SSEIENKKLVFTGTLQKIQRHKAQEYVTQLGAVVSAILSRKTDIIIVGDNPG--S--KLEKAQQLGVKIMN-EEQFLFLL 718 (731)
Q Consensus 644 ~~~l~gk~vV~TGtl~~~~R~e~~~~ie~~Ggkv~sSVSkkT~~LI~ge~~g--S--Kl~KA~~LgI~Ii~-e~ef~~ll 718 (731)
.+.|.|.++-+-|-.-+-. -++. +-||=-||..+| + +-++.-+-|||-=. .+++++||
T Consensus 542 t~HLkGvkI~iMGCIVNGp----GEMA-------------DADfGYVG~~~gkI~LY~gk~~V~~nip~~~Avd~Li~LI 604 (613)
T PRK02048 542 TSHLKGLKIGIMGCIVNGP----GEMA-------------DADYGYVGAGRGKISLYKQKECVEKNIPEEEAVEKLIELI 604 (613)
T ss_pred HCCCCCCEEEEEEEEECCC----CCCC-------------CCCCCCCCCCCCEEEEECCCEEEECCCCHHHHHHHHHHHH
T ss_conf 3788787599983040287----4011-------------2666753788886888607564534898789999999999
Q ss_pred HHHCC
Q ss_conf 88286
Q gi|254781172|r 719 QQYNT 723 (731)
Q Consensus 719 ~~~~~ 723 (731)
++...
T Consensus 605 k~~gr 609 (613)
T PRK02048 605 KENGD 609 (613)
T ss_pred HHCCC
T ss_conf 96490
No 240
>KOG0477 consensus
Probab=56.32 E-value=6.9 Score=18.30 Aligned_cols=65 Identities=22% Similarity=0.322 Sum_probs=31.9
Q ss_pred CCCCCEEEEECCCCCCC---HHHHHHHHHHCCCEEE-----EEEECCEEEEEECCCC-C---CHHHHHH--HCCCEEEC
Q ss_conf 21686699972588998---7899999998298499-----8111632179977888-8---6379899--74991737
Q gi|254781172|r 646 EIENKKLVFTGTLQKIQ---RHKAQEYVTQLGAVVS-----AILSRKTDIIIVGDNP-G---SKLEKAQ--QLGVKIMN 710 (731)
Q Consensus 646 ~l~gk~vV~TGtl~~~~---R~e~~~~ie~~Ggkv~-----sSVSkkT~~LI~ge~~-g---SKl~KA~--~LgI~Ii~ 710 (731)
.|+.+-+|.---|.+|. |..+.+..|+.-..++ .|...-++++-+..-- | +-+.-|+ +|-=||++
T Consensus 543 VLADkGvClIDEFDKMndqDRtSIHEAMEQQSISISKAGIVtsLqArctvIAAanPigGRY~~s~tFaqNV~ltePIlS 621 (854)
T KOG0477 543 VLADKGVCLIDEFDKMNDQDRTSIHEAMEQQSISISKAGIVTSLQARCTVIAAANPIGGRYNPSLTFAQNVDLTEPILS 621 (854)
T ss_pred EECCCCEEEEEHHHHHCCCCCCHHHHHHHHCCHHHHHHHHHHHHHHHHHHHEECCCCCCCCCCCCCHHHCCCCCCCHHH
T ss_conf 9726853774121120401101599998751201446668998875544300027777756875114330554444121
No 241
>PRK06200 2,3-dihydroxy-2,3-dihydrophenylpropionate dehydrogenase; Provisional
Probab=56.09 E-value=12 Score=16.37 Aligned_cols=13 Identities=15% Similarity=0.194 Sum_probs=7.1
Q ss_pred CCCCCEEEEECCC
Q ss_conf 2168669997258
Q gi|254781172|r 646 EIENKKLVFTGTL 658 (731)
Q Consensus 646 ~l~gk~vV~TGtl 658 (731)
..+|.++++.|-+
T Consensus 245 ~iTG~~i~vDGG~ 257 (263)
T PRK06200 245 ALTGVVINADGGL 257 (263)
T ss_pred CEECCEEEECCCH
T ss_conf 8458678889362
No 242
>PRK07239 bifunctional uroporphyrinogen-III synthetase/response regulator domain protein; Validated
Probab=56.06 E-value=13 Score=16.21 Aligned_cols=163 Identities=15% Similarity=0.167 Sum_probs=71.1
Q ss_pred CCCCCHHHCCCHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCEEEEEEEEECCEEEEEEECCCCHHHHHHHHHHHHHCC
Q ss_conf 64257021599999999999999861246777611999941581899999859989988865986556669997753102
Q gi|254781172|r 93 IPTLSLEKIWNIEDLRKFITRIYRFWQKKDDNSIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPT 172 (731)
Q Consensus 93 ~pMlSL~k~~~~~el~~w~~~~~~~~~~~~~~~~~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n~~~i~~ 172 (731)
.|++..--..+..||..|.+++.. -..|=+ ..|-|-|..|= -+.+... +
T Consensus 39 aPalriVPl~DD~eL~~~t~~lia---------------~ppD~v-------------V~TTGiGfr~w--leaAe~~-G 87 (381)
T PRK07239 39 APALRIVPLADDDELRAATEALIA---------------APPDIV-------------VATTGIGFRGW--VEAADGW-G 87 (381)
T ss_pred CCCCCEECCCCCHHHHHHHHHHHC---------------CCCCEE-------------EEECHHHHHHH--HHHHHHC-C
T ss_conf 465330338885999999999854---------------899989-------------99236889999--9999971-7
Q ss_pred CCCCCCCC-CCCEEEEEEEEEEECHHHHHHHHHHHHCCCCC-CCCHHHHHHHHHHCCCHHHH-HCCCEEEEEEECCCCCC
Q ss_conf 43223354-45504899999985202123455643148543-34234567777523455553-01110566410245433
Q gi|254781172|r 173 IPRVLSLN-IPEIIEVRGEVYISKNDFLALNDEMIAVGRKP-YANPRNAASGILRRLNPTDI-TRYLNFFVHGLGKTSEI 249 (731)
Q Consensus 173 iP~~l~~~-~~~~ieiRGEv~m~~~~F~~lN~~~~~~g~~~-f~NpRN~aaG~lr~~d~~~~-~r~L~f~ay~~~~~~~~ 249 (731)
+-..|-.. -...+..||-= . .+. ..+.|... ++-+=+.-++.+..+....+ .+++..--||.....+.
T Consensus 88 l~d~Ll~aL~~ari~aRGPK----a----~gA-lRaaGL~e~wsp~ses~~Evl~~Ll~~gv~G~rIAVQlHGa~~~~eP 158 (381)
T PRK07239 88 LADELLEALSSARLVARGPK----A----TGA-LRAAGLREEWSPASESSAEVLEYLLEEGVAGKRIAVQLHGAADEWDP 158 (381)
T ss_pred CHHHHHHHHHCCEEEEECCC----H----HHH-HHHCCCCCCCCCCCCCHHHHHHHHHHCCCCCCEEEEEECCCCCCCCC
T ss_conf 77899999732807877764----6----878-98649986427999877999999971798888899981476666687
Q ss_pred CCCCCHHHHHHHHHCCCCC---CCCEEEE-ECCCCHHHHHHHHHHHHCCCCCCCCCEEEE
Q ss_conf 2100003689999759966---5414887-403211345566553100112343763777
Q gi|254781172|r 250 FAKGQYEMLQKMRCLGFPV---NNGVRQA-NTFHGIVSYYNEMKSIRSTLPYDIDGLVYK 305 (731)
Q Consensus 250 ~~~~~~e~l~~L~~~GF~v---~~~~~~~-~~~~~~~~~~~~~~~~r~~l~y~iDGiVik 305 (731)
.-++.+.|+.-|-.| .+|.+.. .+...+...++.+-. =++|-+.+.
T Consensus 159 ----~p~~~~~Lr~aGAeV~~V~vYRW~~p~d~~~l~~Lv~~i~~------g~vDAVtFT 208 (381)
T PRK07239 159 ----LPEFLEALRAAGAEVVPVPVYRWVPPPDGGPFDRLVDLIAT------RQLDAVTFT 208 (381)
T ss_pred ----CHHHHHHHHHCCCEEEEECCEECCCCCCCCHHHHHHHHHHH------CCCCEEEEC
T ss_conf ----88999999977986889565432699985479999999970------888889965
No 243
>PRK06556 vitamin B12-dependent ribonucleotide reductase; Validated
Probab=55.74 E-value=5.7 Score=18.94 Aligned_cols=87 Identities=9% Similarity=0.097 Sum_probs=49.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCHHHCCCCCCCCC-CCCCCCCCCCCCEEECCCC
Q ss_conf 999999999999999998433177982087899999999999989772031158999962-0036432357750451664
Q gi|254781172|r 16 QARKELSSLEQEISYHDDCYYQYSKPIILDSEYDALKRRCDAIAHAFPDLARSEDPNGPL-NKIGGEMNLSLFKVTHSIP 94 (731)
Q Consensus 16 ~~~~~i~~L~~~i~~~~~~Yy~~~~p~isD~eYD~L~~~L~~le~~~p~~~~~~~p~spt-~~Vg~~~~~~~~kv~H~~p 94 (731)
..|+-+..|+..+.+|-..+ -=--|+.+-...++||.-+- +.....||||. ..+|-. -.+.-|...
T Consensus 95 s~~q~~~r~~~~~~~~g~~~----gyf~~~~d~~~f~~e~~~~l-----~~q~~a~nsp~wfn~g~~----~~~Q~sACF 161 (957)
T PRK06556 95 SLRQLIDRVVKTYTAAGRED----GYFATEADAEIFEHELTWLL-----LHQKFSFNSPVWFNVGTS----SRQQVSACF 161 (957)
T ss_pred CHHHHHHHHHHHHHHHHHHC----CCCCCHHHHHHHHHHHHHHH-----HHHHCCCCCCEEEECCCC----CCCCCCEEE
T ss_conf 19999999999999987527----85278778999999999999-----975527999802667888----888741577
Q ss_pred CCCHHHCCCHHHHHHHHHHHHHH
Q ss_conf 25702159999999999999986
Q gi|254781172|r 95 TLSLEKIWNIEDLRKFITRIYRF 117 (731)
Q Consensus 95 MlSL~k~~~~~el~~w~~~~~~~ 117 (731)
.+|.+. +.+.|.+|+++-...
T Consensus 162 v~~v~D--~~~~I~d~~~~~a~i 182 (957)
T PRK06556 162 ILSVDD--SMESILDWYKEEGML 182 (957)
T ss_pred EECCCC--CHHHHHHHHHHHHHH
T ss_conf 723655--699999999997762
No 244
>PRK12496 hypothetical protein; Provisional
Probab=55.66 E-value=3.6 Score=20.47 Aligned_cols=21 Identities=29% Similarity=0.797 Sum_probs=16.5
Q ss_pred CCCCCCCCEEEEECCHHCCCCC
Q ss_conf 1123437637773110001115
Q gi|254781172|r 294 TLPYDIDGLVYKVDEFSLQKQL 315 (731)
Q Consensus 294 ~l~y~iDGiVikvn~~~~q~~l 315 (731)
.|.|+.+|+++. ||+..|+.+
T Consensus 87 ALA~el~~~l~T-DDy~~QNva 107 (166)
T PRK12496 87 ALAYELKGTLYT-DDYGIQNVA 107 (166)
T ss_pred HHHHHHCCEEEE-CCHHHHHHH
T ss_conf 999985998984-648889999
No 245
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=55.64 E-value=8.1 Score=17.75 Aligned_cols=68 Identities=24% Similarity=0.475 Sum_probs=36.0
Q ss_pred CCCCCCEEEEEECCCCHHHHHHHCCCCCCCCCCEEEECC-CCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCHHHHHHHH
Q ss_conf 844076899983587025665410123578730477704-3265775010337865445210100354344114466553
Q gi|254781172|r 394 DIRVGDRVLVKRAGEVIPKVVDIIVNERHPDAQPFSFPS-FCPICQSRVVRDLNPKTGKLVAAHRCTGGLACSAQQLERL 472 (731)
Q Consensus 394 ~I~iGd~V~I~RaGdVIP~I~~Vi~~~r~~~~~~~~~P~-~CP~Cgs~l~~~~~~~~~~~~~~~rC~n~~~Cpaq~~~~i 472 (731)
.+..||.|++ .|.|=|+.+.+-+-.-. .-.++..-+ .||.||.-+.-- +.. .+||. .|--+.-...
T Consensus 315 ~L~pGD~i~~--~G~~~~~~~n~ek~~v~-~l~~~~~~~p~Cp~Cg~~m~S~-----G~~--g~rC~---kCg~~~~~~~ 381 (421)
T COG1571 315 KLIPGDEITV--YGSVKPGTLNLEKFQVL-KLARYERVNPVCPRCGGRMKSA-----GRN--GFRCK---KCGTRARETL 381 (421)
T ss_pred HCCCCCEEEE--ECCCCCCCEEEEEEEEE-EEEEEEECCCCCCCCCCCHHHC-----CCC--CCCCC---CCCCCCCCCC
T ss_conf 5689998998--05745662368999999-8666677178897667713116-----789--85266---4266177553
Q ss_pred HH
Q ss_conf 32
Q gi|254781172|r 473 KH 474 (731)
Q Consensus 473 ~h 474 (731)
..
T Consensus 382 ~~ 383 (421)
T COG1571 382 IK 383 (421)
T ss_pred CC
T ss_conf 23
No 246
>TIGR01054 rgy reverse gyrase; InterPro: IPR005736 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. Reverse gyrase is a type IA topoisomerase that is unique among these enzymes in its requirement for ATP. Reverse gyrase is a hyperthermophile-specific enzyme that acts as a renaturase by positively supercoiling DNA, and by annealing complementary single-strand circles . Hyperthermophilic organisms must protect themselves against heat-induced degradation, and reverse gyrase acts to reduce the rate of double-strand DNA breakage, a function that does not require ATP hydrolysis and which is independent of its positive supercoiling abilities. Reverse gyrase achieves this by recognising nicked DNA and recruiting a protein coat to the site of damage . 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, 0006268 DNA unwinding during replication, 0005694 chromosome.
Probab=55.45 E-value=13 Score=16.14 Aligned_cols=232 Identities=21% Similarity=0.283 Sum_probs=102.6
Q ss_pred HHHHHHHHHHHHHHHHHHHCCCC---CCCHHHHHHHHHHHHHHHHHCCHHHCCCCCCCCCCCCCCCCCCC--CCEEECCC
Q ss_conf 99999999999999843317798---20878999999999999897720311589999620036432357--75045166
Q gi|254781172|r 19 KELSSLEQEISYHDDCYYQYSKP---IILDSEYDALKRRCDAIAHAFPDLARSEDPNGPLNKIGGEMNLS--LFKVTHSI 93 (731)
Q Consensus 19 ~~i~~L~~~i~~~~~~Yy~~~~p---~isD~eYD~L~~~L~~le~~~p~~~~~~~p~spt~~Vg~~~~~~--~~kv~H~~ 93 (731)
+-+..|.+++. +||-..+. -||+-....|.+++.+=-.+ ++--.... -+-+.|-.
T Consensus 599 ~~~~aL~kr~~----lyy~~~ei~fk~i~EVDL~~l~rEIDEdR~k----------------~r~~~~g~~~A~~~dLvK 658 (1843)
T TIGR01054 599 EAFEALKKRLK----LYYFTQEIEFKRIDEVDLEKLLREIDEDREK----------------VRRIVEGKVKAKVKDLVK 658 (1843)
T ss_pred HHHHHHHHHHH----HHHHHHCCCCCCCCCCCHHHHHHHHHHCCCC----------------CCEEEECCEEEEEECCCC
T ss_conf 89999998886----6665201355445600178887764101012----------------401220762664202424
Q ss_pred CCC----CHHHCCCHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEC-CEEEEEEEEE--CCE------------EEEEEEC
Q ss_conf 425----70215999999999999998612467776119999415-8189999985--998------------9988865
Q gi|254781172|r 94 PTL----SLEKIWNIEDLRKFITRIYRFWQKKDDNSIFFTLEPKI-DGTMITIRYE--KGK------------FVYAALR 154 (731)
Q Consensus 94 pMl----SL~k~~~~~el~~w~~~~~~~~~~~~~~~~~~~vepKi-DG~sisl~Y~--~G~------------L~~a~TR 154 (731)
|-| |=+||-+ |.+++++ |+. -|| +| +-+|| =|. +.-.+|=
T Consensus 659 t~L~vVESPnKART----------IA~FFGk---P~~-----R~iP~~---~~vYEv~~gDkilmim~~~G~V~~L~iTa 717 (1843)
T TIGR01054 659 TALLVVESPNKART----------IARFFGK---PSV-----RKIPGG---SVVYEVPVGDKILMIMAETGDVLVLVITA 717 (1843)
T ss_pred CEEEEEECCCCHHH----------HHHHCCC---CCC-----EECCCC---CEEEEEEECCEEEEEECCCCCEEEEEEEE
T ss_conf 13799827860445----------5343069---963-----551598---53899861682899851898378999984
Q ss_pred CCCHHHHHHHHHHHHHCCCCCCCCCC---C-CCE--E-EEE--EEEEEECHHHHH-HHHHHHHCCCCCCCCHHHHHHHHH
Q ss_conf 98655666999775310243223354---4-550--4-899--999985202123-455643148543342345677775
Q gi|254781172|r 155 GDGHSGEDVSACIRAIPTIPRVLSLN---I-PEI--I-EVR--GEVYISKNDFLA-LNDEMIAVGRKPYANPRNAASGIL 224 (731)
Q Consensus 155 GdG~~GeDVT~n~~~i~~iP~~l~~~---~-~~~--i-eiR--GEv~m~~~~F~~-lN~~~~~~g~~~f~NpRN~aaG~l 224 (731)
-=|+.=+=||.....+-|+-..-... + |-. | -+| ||=|...++.+. +.+...+.|...-.|.+|.+=| |
T Consensus 718 s~GHv~DL~t~~~~~f~GV~~~~~~g~~~Y~PvY~sIKrC~dcG~QfTd~~~leeli~e~cpkcgs~~~~d~~~~ve~-l 796 (1843)
T TIGR01054 718 SLGHVFDLVTDKVGGFYGVLVENGEGAEAYVPVYTSIKRCRDCGEQFTDEEDLEELIKELCPKCGSENIEDSKSIVEI-L 796 (1843)
T ss_pred ECCCHHHHCCCCCCCEEEEEEECCCCCCCCEEEECCCCEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCHHHHHHH-H
T ss_conf 110021103674463421153058896542004411011335887436715589999986025787555652678899-9
Q ss_pred HCCCHHHHHCCCEEEEEEECCCCCCCCCCCHHHH-----HHHHHCCCCCCCCEEEEECCCCHH--HHHHHHHHHH--CCC
Q ss_conf 2345555301110566410245433210000368-----999975996654148874032113--4556655310--011
Q gi|254781172|r 225 RRLNPTDITRYLNFFVHGLGKTSEIFAKGQYEML-----QKMRCLGFPVNNGVRQANTFHGIV--SYYNEMKSIR--STL 295 (731)
Q Consensus 225 r~~d~~~~~r~L~f~ay~~~~~~~~~~~~~~e~l-----~~L~~~GF~v~~~~~~~~~~~~~~--~~~~~~~~~r--~~l 295 (731)
|.+- ...+++.=+ ..|.|.-|.+ ..++ |-+|..++. .+++|- +..+.+++-| +.|
T Consensus 797 R~lA-----~EvD~v~ia------TDPDtEGEKIgwDl~~~~~----Py~pnv~R~-eFHEVT~rAi~eAl~s~rkGeel 860 (1843)
T TIGR01054 797 RELA-----SEVDEVFIA------TDPDTEGEKIGWDLALLLR----PYNPNVKRA-EFHEVTKRAILEALESPRKGEEL 860 (1843)
T ss_pred HHHH-----HHHCEEEEC------CCCCCCCCCHHHHHHHHHC----CCCCCEEEE-CCCCCCHHHHHHHHCCCCCCCCC
T ss_conf 8754-----442988872------5889875408999999808----877752462-14562379999986087657501
Q ss_pred CCC---CCCEEEE-ECC
Q ss_conf 234---3763777-311
Q gi|254781172|r 296 PYD---IDGLVYK-VDE 308 (731)
Q Consensus 296 ~y~---iDGiVik-vn~ 308 (731)
++| +++=||+ +-|
T Consensus 861 ~vd~NLVkAQvVRRI~D 877 (1843)
T TIGR01054 861 SVDENLVKAQVVRRIED 877 (1843)
T ss_pred CCCCCCCCEEEEEEEEE
T ss_conf 00023101158889875
No 247
>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated
Probab=54.75 E-value=6.2 Score=18.65 Aligned_cols=21 Identities=10% Similarity=0.129 Sum_probs=15.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHH
Q ss_conf 999999999999999998433
Q gi|254781172|r 16 QARKELSSLEQEISYHDDCYY 36 (731)
Q Consensus 16 ~~~~~i~~L~~~i~~~~~~Yy 36 (731)
..++.+.+|.+..++.+..|-
T Consensus 59 ~k~k~i~~Lkklak~ad~V~l 79 (864)
T PRK06319 59 DKQEVIRKICKLAKKCDVVYL 79 (864)
T ss_pred CHHHHHHHHHHHHHCCCEEEE
T ss_conf 768999999999846997998
No 248
>COG3743 Uncharacterized conserved protein [Function unknown]
Probab=54.72 E-value=5.7 Score=18.95 Aligned_cols=43 Identities=21% Similarity=0.159 Sum_probs=30.3
Q ss_pred CHHHHHHHHHHHHHCCCCCCEEEEEHHHHCCHHHHHHHHCCCCCCCCC
Q ss_conf 035410355556530576540454101101067775310001000134
Q gi|254781172|r 482 NIEGLGKQQLDFFFKSEDPAFSIRIPADIFTLQRRQQTSTTKIENILG 529 (731)
Q Consensus 482 dI~GLG~k~Ie~L~e~~~~~g~I~~~~DLy~L~~~~~~~~~~l~~l~G 529 (731)
.|.|+|++.-..|-+.| |.++++|=.++..+...+++++.++|
T Consensus 71 ~I~GIGPk~e~~Ln~~G-----I~tfaQIAAwt~~di~~id~~l~f~G 113 (133)
T COG3743 71 RISGIGPKLEKVLNELG-----IFTFAQIAAWTRADIAWIDDYLNFDG 113 (133)
T ss_pred HHCCCCHHHHHHHHHCC-----CCCHHHHHHCCHHHHHHHHHHCCCCC
T ss_conf 10043788998998747-----76399997448999999985448862
No 249
>TIGR00679 hpr-ser HPr(Ser) kinase/phosphatase; InterPro: IPR003755 HPr(Ser) kinase is the sensor in a multicomponent phosphorelay system that controls catabolite repression, sugar transport and carbon metabolism in Gram-positive bacteria. These are all phosphorylation-dependent carbon control mechanisms. This kinase in unusual in that it recognises the tertiary structure of its target protein, HPr, a phosphocarrier protein of the bacterial phosphotransferase system and a transcriptional cofactor controlling the phenomenon of catabolite repression .; GO: 0000155 two-component sensor activity, 0004672 protein kinase activity, 0005524 ATP binding, 0000160 two-component signal transduction system (phosphorelay), 0006109 regulation of carbohydrate metabolic process.
Probab=54.67 E-value=8.7 Score=17.53 Aligned_cols=61 Identities=18% Similarity=0.215 Sum_probs=39.5
Q ss_pred CCCCCCCCCCCCCEEECCCCCCCCHHH-HHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCCCEEEEEHHHH
Q ss_conf 103378654452101003543441144-6655332130123103541035555653057654045410110
Q gi|254781172|r 441 VVRDLNPKTGKLVAAHRCTGGLACSAQ-QLERLKHFVSRDAFNIEGLGKQQLDFFFKSEDPAFSIRIPADI 510 (731)
Q Consensus 441 l~~~~~~~~~~~~~~~rC~n~~~Cpaq-~~~~i~hF~SK~aldI~GLG~k~Ie~L~e~~~~~g~I~~~~DL 510 (731)
|+...+..-+++.+.++|.|+..=-.+ ..+.+.|| |.|.|||-=.|++||-. |-+++--.|
T Consensus 168 Li~rgH~LvaDD~vEI~~~~gn~L~GrGa~~~~~~~-----mEIRGLGIINv~~lyG~----~~~r~~~eI 229 (309)
T TIGR00679 168 LINRGHRLVADDAVEIYRLDGNRLVGRGAQELIKHF-----MEIRGLGIINVERLYGL----GIVRERKEI 229 (309)
T ss_pred HHHCCCCEEECCEEEEEEECCCEEECCHHHHHHHHC-----CEECCCHHHHHHHHHCC----CEEECCCEE
T ss_conf 975688077515368875258751140089888520-----21135407677566235----312014102
No 250
>cd01075 NAD_bind_Leu_Phe_Val_DH NAD(P) binding domain of leucine dehydrogenase, phenylalanine dehydrogenase, and valine dehydrogenase. Amino acid dehydrogenase (DH) is a widely distributed family of enzymes that catalyzes the oxidative deamination of an amino acid to its keto acid and ammonia with concomitant reduction of NADP+. For example, leucine DH catalyzes the reversible oxidative deamination of L-leucine and several other straight or branched chain amino acids to the corresponding 2-oxoacid derivative. Amino acid DH -like NAD(P)-binding domains are members of the Rossmann fold superfamily and include glutamate, leucine, and phenylalanine DHs, methylene tetrahydrofolate DH, methylene-tetrahydromethanopterin DH, methylene-tetrahydropholate DH/cyclohydrolase, Shikimate DH-like proteins, malate oxidoreductases, and glutamyl tRNA reductase. Amino acid DHs catalyze the deamination of amino acids to keto acids with NAD(P)+ as a cofactor. The NAD(P)-binding Rossmann fold superfamily inc
Probab=54.55 E-value=14 Score=16.03 Aligned_cols=27 Identities=26% Similarity=0.381 Sum_probs=14.8
Q ss_pred CCEEEEEEECCCCCCCCCCCHHHHHHHHHCCCCC
Q ss_conf 1105664102454332100003689999759966
Q gi|254781172|r 235 YLNFFVHGLGKTSEIFAKGQYEMLQKMRCLGFPV 268 (731)
Q Consensus 235 ~L~f~ay~~~~~~~~~~~~~~e~l~~L~~~GF~v 268 (731)
...+..-|++... +..-.+|.+.|-.+
T Consensus 28 gk~VaIqG~GnVG-------~~~A~~l~~~Gakv 54 (200)
T cd01075 28 GKTVAVQGLGKVG-------YKLAEHLLEEGAKL 54 (200)
T ss_pred CCEEEEECCCHHH-------HHHHHHHHHCCCEE
T ss_conf 9999998987999-------99999999679979
No 251
>PRK06599 DNA topoisomerase I; Validated
Probab=54.46 E-value=9.1 Score=17.37 Aligned_cols=36 Identities=14% Similarity=0.213 Sum_probs=22.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCCCC-----CCHHHHHHH
Q ss_conf 9999999999999999998433177982-----087899999
Q gi|254781172|r 15 EQARKELSSLEQEISYHDDCYYQYSKPI-----ILDSEYDAL 51 (731)
Q Consensus 15 ~~~~~~i~~L~~~i~~~~~~Yy~~~~p~-----isD~eYD~L 51 (731)
...++.+..|.+.++.++..|- ..+|- |+.+.|+.|
T Consensus 56 ~~~~k~i~~lk~l~k~ad~V~l-ATDpDREGEaIawhi~e~l 96 (776)
T PRK06599 56 DKAGKYVDAIVKDAKKAEAVYL-ATDPDREGESISWHVAEVI 96 (776)
T ss_pred CCHHHHHHHHHHHHHCCCEEEE-CCCCCCCHHHHHHHHHHHH
T ss_conf 7678899999999847998998-9899704369999999985
No 252
>PRK01390 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=54.37 E-value=14 Score=16.01 Aligned_cols=10 Identities=30% Similarity=0.265 Sum_probs=4.4
Q ss_pred CCEEEEECCH
Q ss_conf 7637773110
Q gi|254781172|r 300 DGLVYKVDEF 309 (731)
Q Consensus 300 DGiVikvn~~ 309 (731)
|-.|+-+||-
T Consensus 216 ~~~Vin~DD~ 225 (457)
T PRK01390 216 GTAVIGVDDA 225 (457)
T ss_pred CEEEEECCCH
T ss_conf 8699968888
No 253
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=54.37 E-value=6.5 Score=18.49 Aligned_cols=10 Identities=40% Similarity=1.251 Sum_probs=7.8
Q ss_pred CCCCCCCCCC
Q ss_conf 0432657750
Q gi|254781172|r 431 PSFCPICQSR 440 (731)
Q Consensus 431 P~~CP~Cgs~ 440 (731)
+..||+||+.
T Consensus 187 ~~~CPvCGs~ 196 (307)
T PRK03564 187 RQYCPVCGSM 196 (307)
T ss_pred CCCCCCCCCC
T ss_conf 8859988987
No 254
>KOG2906 consensus
Probab=53.94 E-value=4.9 Score=19.45 Aligned_cols=16 Identities=25% Similarity=0.760 Sum_probs=12.8
Q ss_pred CCCCCCCCCCCCCCCC
Q ss_conf 4326577501033786
Q gi|254781172|r 432 SFCPICQSRVVRDLNP 447 (731)
Q Consensus 432 ~~CP~Cgs~l~~~~~~ 447 (731)
.+||.||+-|+.+.+.
T Consensus 2 ~FCP~Cgn~Live~g~ 17 (105)
T KOG2906 2 LFCPTCGNMLIVESGE 17 (105)
T ss_pred CCCCCCCCEEEEECCC
T ss_conf 4468878889994287
No 255
>PRK05823 consensus
Probab=53.93 E-value=10 Score=17.06 Aligned_cols=20 Identities=15% Similarity=0.361 Sum_probs=11.9
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q ss_conf 99999999999999998433
Q gi|254781172|r 17 ARKELSSLEQEISYHDDCYY 36 (731)
Q Consensus 17 ~~~~i~~L~~~i~~~~~~Yy 36 (731)
.++.+..|.+.+..++..|-
T Consensus 72 k~~~ik~l~~~~k~ad~vii 91 (691)
T PRK05823 72 KKEIIKSIKDKASKANNIYL 91 (691)
T ss_pred HHHHHHHHHHHHHCCCEEEE
T ss_conf 99999999999847998998
No 256
>smart00350 MCM minichromosome maintenance proteins.
Probab=53.65 E-value=5.4 Score=19.10 Aligned_cols=15 Identities=33% Similarity=0.457 Sum_probs=6.1
Q ss_pred HHHHHHHHHHHHHHC
Q ss_conf 111168999999882
Q gi|254781172|r 560 RHVGAEIARSLAKYY 574 (731)
Q Consensus 560 ~~vG~~~Ak~La~~f 574 (731)
|-+-+...+.|.++|
T Consensus 436 P~ls~eA~~~i~~~Y 450 (509)
T smart00350 436 PKLSEEAAEKLVKAY 450 (509)
T ss_pred CCCCHHHHHHHHHHH
T ss_conf 978999999999999
No 257
>COG1458 Predicted DNA-binding protein containing PIN domain [General function prediction only]
Probab=53.47 E-value=14 Score=15.91 Aligned_cols=55 Identities=22% Similarity=0.326 Sum_probs=36.8
Q ss_pred CCCCCCCHHHHHHHHHHCCCEEEEEEECCEEEEEECCCCCCHHHHHHHCCCEEECHHHHHHHHHHHCC
Q ss_conf 25889987899999998298499811163217997788886379899749917379999999988286
Q gi|254781172|r 656 GTLQKIQRHKAQEYVTQLGAVVSAILSRKTDIIIVGDNPGSKLEKAQQLGVKIMNEEQFLFLLQQYNT 723 (731)
Q Consensus 656 Gtl~~~~R~e~~~~ie~~Ggkv~sSVSkkT~~LI~ge~~gSKl~KA~~LgI~Ii~e~ef~~ll~~~~~ 723 (731)
|.|..-.+=+.--+.+.+||-|++| ..| =.+=|++||++.++...|..||++|-.
T Consensus 157 GiLDSapDlDvLLLAkELdaavVss------------D~G-ir~WAe~LGlrfv~a~~Fp~ml~eylk 211 (221)
T COG1458 157 GILDSAPDLDVLLLAKELDAAVVSS------------DEG-IRTWAEKLGLRFVDAFKFPEMLEEYLK 211 (221)
T ss_pred CCCCCCCHHHHHHHHHHHCCEEEEC------------CHH-HHHHHHHHCCEEECHHHHHHHHHHHHH
T ss_conf 4446654068999999838637735------------366-999999819765677665999999999
No 258
>pfam00122 E1-E2_ATPase E1-E2 ATPase.
Probab=53.09 E-value=5.3 Score=19.20 Aligned_cols=24 Identities=33% Similarity=0.663 Sum_probs=18.7
Q ss_pred CCCCCCCEEEEEECCCCHHHHHHHCC
Q ss_conf 68440768999835870256654101
Q gi|254781172|r 393 RDIRVGDRVLVKRAGEVIPKVVDIIV 418 (731)
Q Consensus 393 ~~I~iGd~V~I~RaGdVIP~I~~Vi~ 418 (731)
.++.+||.|.| ++||.|| ...++.
T Consensus 50 ~~l~~GDiv~v-~~G~~IP-aDg~vi 73 (222)
T pfam00122 50 DELVVGDIVLL-KPGDRVP-ADGRII 73 (222)
T ss_pred HHCCCCCEEEE-CCCCEEE-CCCEEE
T ss_conf 99788999998-9999962-174575
No 259
>TIGR01647 ATPase-IIIA_H plasma-membrane proton-efflux P-type ATPase; InterPro: IPR006534 These sequences represent the plasma membrane proton efflux P-type ATPase found in plants, fungi, protozoa, slime molds and archaea. The best studied representative is from yeast . ; GO: 0016887 ATPase activity, 0015992 proton transport, 0016021 integral to membrane.
Probab=53.05 E-value=7.7 Score=17.94 Aligned_cols=16 Identities=31% Similarity=0.748 Sum_probs=5.4
Q ss_pred CCCCCEEEEEECCCCHH
Q ss_conf 44076899983587025
Q gi|254781172|r 395 IRVGDRVLVKRAGEVIP 411 (731)
Q Consensus 395 I~iGd~V~I~RaGdVIP 411 (731)
+=+||.|.+ |.|||||
T Consensus 117 LVPGDvv~l-~~GdivP 132 (835)
T TIGR01647 117 LVPGDVVRL-KLGDIVP 132 (835)
T ss_pred CCCCCEEEE-ECCCEEE
T ss_conf 797638987-2076401
No 260
>PRK06197 short chain dehydrogenase; Provisional
Probab=52.96 E-value=13 Score=16.17 Aligned_cols=14 Identities=14% Similarity=0.145 Sum_probs=6.0
Q ss_pred EECCCCHHHHHHHH
Q ss_conf 86598655666999
Q gi|254781172|r 152 ALRGDGHSGEDVSA 165 (731)
Q Consensus 152 ~TRGdG~~GeDVT~ 165 (731)
+|=|+.-+|-....
T Consensus 21 ITGa~sGIG~~~A~ 34 (306)
T PRK06197 21 VTGANTGLGYETAA 34 (306)
T ss_pred ECCCCCHHHHHHHH
T ss_conf 91689599999999
No 261
>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=52.88 E-value=4.7 Score=19.61 Aligned_cols=12 Identities=42% Similarity=0.952 Sum_probs=9.5
Q ss_pred ECCCCCCCCCCC
Q ss_conf 704326577501
Q gi|254781172|r 430 FPSFCPICQSRV 441 (731)
Q Consensus 430 ~P~~CP~Cgs~l 441 (731)
.|+.||.||.+-
T Consensus 17 aP~~CPvC~~~~ 28 (34)
T cd00729 17 APEKCPICGAPK 28 (34)
T ss_pred CCCCCCCCCCCH
T ss_conf 987586999967
No 262
>PRK10355 xylF D-xylose transporter subunit XylF; Provisional
Probab=52.52 E-value=12 Score=16.33 Aligned_cols=45 Identities=16% Similarity=0.135 Sum_probs=21.9
Q ss_pred HHHHHHHCCCCCCCCEEEEECCCCHHHHHHHHHHHHCCCCCCCCCEEEEECC
Q ss_conf 6899997599665414887403211345566553100112343763777311
Q gi|254781172|r 257 MLQKMRCLGFPVNNGVRQANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDE 308 (731)
Q Consensus 257 ~l~~L~~~GF~v~~~~~~~~~~~~~~~~~~~~~~~r~~l~y~iDGiVikvn~ 308 (731)
.-+..+++|..+. ..+.-.+.....+++ .+.+.-.+|+|||--.|
T Consensus 47 ~~~~Ake~G~~v~----v~dA~~D~~~Qi~qI---e~~I~qgvdaIiv~p~D 91 (330)
T PRK10355 47 FVKKAESLGAKVF----VQSANGNEETQMSQI---ENMINRGVDVLVIIPYN 91 (330)
T ss_pred HHHHHHHCCCEEE----EECCCCCHHHHHHHH---HHHHHCCCCEEEEECCC
T ss_conf 9999997599899----971899989999999---99998599999996998
No 263
>PRK06500 short chain dehydrogenase; Provisional
Probab=52.47 E-value=15 Score=15.80 Aligned_cols=15 Identities=20% Similarity=0.390 Sum_probs=9.0
Q ss_pred CCCCCCCEEEEECCC
Q ss_conf 882168669997258
Q gi|254781172|r 644 SSEIENKKLVFTGTL 658 (731)
Q Consensus 644 ~~~l~gk~vV~TGtl 658 (731)
++..+|.++++.|-+
T Consensus 232 as~iTG~~i~vDGG~ 246 (249)
T PRK06500 232 SAFIVGSEIIVDGGM 246 (249)
T ss_pred HCCCCCCEEEECCCC
T ss_conf 228148638889581
No 264
>PRK09001 DNA topoisomerase I; Validated
Probab=52.44 E-value=6.8 Score=18.34 Aligned_cols=17 Identities=29% Similarity=0.348 Sum_probs=8.2
Q ss_pred HHHHHHHHHHHHHHHHH
Q ss_conf 99999999999999843
Q gi|254781172|r 19 KELSSLEQEISYHDDCY 35 (731)
Q Consensus 19 ~~i~~L~~~i~~~~~~Y 35 (731)
+.+.+|.+..+.++.-|
T Consensus 96 kvv~~Lkklak~ad~V~ 112 (869)
T PRK09001 96 KVVSELKKLAEKADHIY 112 (869)
T ss_pred HHHHHHHHHHHCCCEEE
T ss_conf 99999999985699899
No 265
>PRK12825 fabG 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional
Probab=52.26 E-value=15 Score=15.77 Aligned_cols=16 Identities=13% Similarity=0.277 Sum_probs=9.7
Q ss_pred CCCCCCCEEEEECCCC
Q ss_conf 8821686699972588
Q gi|254781172|r 644 SSEIENKKLVFTGTLQ 659 (731)
Q Consensus 644 ~~~l~gk~vV~TGtl~ 659 (731)
++..+|.++++.|-+.
T Consensus 233 s~~itG~~i~vDGGl~ 248 (250)
T PRK12825 233 AGYITGQVIAVDGGMG 248 (250)
T ss_pred HCCCCCCEEEECCCCC
T ss_conf 2282488689896813
No 266
>COG4277 Predicted DNA-binding protein with the Helix-hairpin-helix motif [General function prediction only]
Probab=52.19 E-value=12 Score=16.44 Aligned_cols=87 Identities=21% Similarity=0.231 Sum_probs=47.4
Q ss_pred HHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHH--HHCCCHHHHHHHHHHHHHCCCCCHH
Q ss_conf 10001000134210014568999987522346667763010111168999999--8829989999978977612511778
Q gi|254781172|r 519 TSTTKIENILGFGDVSVTNLYDSINKRRNISLERFIFSLGIRHVGAEIARSLA--KYYLSYQNFAQEINNIIAHNNDDWL 596 (731)
Q Consensus 519 ~~~~~l~~l~GfgeKsa~nL~~sIe~sK~~~L~r~L~ALGI~~vG~~~Ak~La--~~f~si~~l~~~~~~~~~~~~~~~e 596 (731)
-+.+-|+..-||. +.-|+ .++.-.|+ +.+-.+++-.|- ..|+ ...+.++++
T Consensus 278 YQADwLlrfYgF~---~~Ei~----~~g~~~ld--------~~lDPK~~wAl~~~d~FP------------Vdvn~A~~~ 330 (404)
T COG4277 278 YQADWLLRFYGFS---ADEIL----ASGGDFLD--------PDLDPKTAWALKHMDRFP------------VDVNKAPYK 330 (404)
T ss_pred HHHHHHHHHHCCC---HHHHH----HCCCCCCC--------CCCCHHHHHHHHCCCCCC------------CCCCCCCHH
T ss_conf 7777899970888---78887----44897557--------887834577773355365------------133456777
Q ss_pred HHHCCCCCCHHHHHHHHHHHCCHHHHHHHHHHHHHCCC
Q ss_conf 76138886789999999996697999999999973387
Q gi|254781172|r 597 SLIRVPLVGDIIAQAIVEFYQNPRNICAVEALLKEVSP 634 (731)
Q Consensus 597 ~L~~I~GiG~~~A~si~~ff~~~~n~~~i~~L~~~~~~ 634 (731)
+|..++|||.++|..|+.-=. ...-.++.|.+.++.
T Consensus 331 ~llRVPGiG~ksa~rIv~~Rr--~~rl~~e~Lkk~Gvv 366 (404)
T COG4277 331 ELLRVPGIGVKSARRIVMTRR--RTRLTLEDLKKLGVV 366 (404)
T ss_pred HHCCCCCCCHHHHHHHHHHHH--HCCCCHHHHHHHCEE
T ss_conf 821168877378899988742--302679898653303
No 267
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=52.00 E-value=8.3 Score=17.70 Aligned_cols=19 Identities=16% Similarity=0.111 Sum_probs=10.8
Q ss_pred HHHHCCCCCCHHHHHHHHH
Q ss_conf 8761388867899999999
Q gi|254781172|r 596 LSLIRVPLVGDIIAQAIVE 614 (731)
Q Consensus 596 e~L~~I~GiG~~~A~si~~ 614 (731)
+.+-.|+|||+++|..++.
T Consensus 16 DnipGV~GIG~ktA~~ll~ 34 (36)
T smart00279 16 DNIPGVKGIGPKTALKLLR 34 (36)
T ss_pred CCCCCCCCCCHHHHHHHHH
T ss_conf 6889999747899999998
No 268
>TIGR02027 rpoA DNA-directed RNA polymerase, alpha subunit; InterPro: IPR011773 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 kD, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. 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 , .; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription DNA-dependent.
Probab=51.82 E-value=13 Score=16.10 Aligned_cols=56 Identities=14% Similarity=0.323 Sum_probs=40.6
Q ss_pred CCHHH--HHHHHHHHHHCCCCCCEEEEEHHHHCCHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHH
Q ss_conf 10354--10355556530576540454101101067775310001000134210014568999987522
Q gi|254781172|r 481 FNIEG--LGKQQLDFFFKSEDPAFSIRIPADIFTLQRRQQTSTTKIENILGFGDVSVTNLYDSINKRRN 547 (731)
Q Consensus 481 ldI~G--LG~k~Ie~L~e~~~~~g~I~~~~DLy~L~~~~~~~~~~l~~l~GfgeKsa~nL~~sIe~sK~ 547 (731)
|.|+. |+-....=|=.+| |.+++||-.++.. +|+++.-||.||.+=|.+.+++...
T Consensus 261 ~~IeeLdLSVRs~NCLk~~g-----I~t~geL~~~~e~------eLl~i~NfGkKSl~EI~ekL~~~lg 318 (324)
T TIGR02027 261 IKIEELDLSVRSYNCLKRAG-----IHTLGELVSKSEE------ELLKIKNFGKKSLDEIKEKLAEKLG 318 (324)
T ss_pred CCCHHHHHHHHHHHHHHHHC-----CHHHHHHHHHHHH------HHHCCCCCCHHHHHHHHHHHHHHCC
T ss_conf 78003245489886464603-----5417888860389------8841788573338999999887618
No 269
>pfam09538 FYDLN_acid Protein of unknown function (FYDLN_acid). Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=51.73 E-value=5.8 Score=18.88 Aligned_cols=11 Identities=45% Similarity=1.132 Sum_probs=5.1
Q ss_pred CCCCCCCCCCC
Q ss_conf 04326577501
Q gi|254781172|r 431 PSFCPICQSRV 441 (731)
Q Consensus 431 P~~CP~Cgs~l 441 (731)
|-.||+||...
T Consensus 26 p~~cp~cg~~~ 36 (104)
T pfam09538 26 PIVCPKCGEEV 36 (104)
T ss_pred CCCCCCCCCEE
T ss_conf 87189988874
No 270
>TIGR02354 thiF_fam2 thiamine biosynthesis protein ThiF; InterPro: IPR012729 Members of the HesA/MoeB/ThiF family of proteins (IPR000594 from INTERPRO) include a number of members encoded in the midst of thiamine biosynthetic operons. This mix of known and putative ThiF proteins shows a deep split in phylogenetic trees. The Escherichia coli ThiF and MoeB proteins are seemingly more closely related than the E. coli ThiF and Campylobacter (for example) ThiF. This entry represents the divergent clade of putative ThiF proteins as found in Campylobacter..
Probab=51.43 E-value=6.8 Score=18.36 Aligned_cols=121 Identities=16% Similarity=0.227 Sum_probs=56.6
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCHHHHHCCCCCCHHHHHH
Q ss_conf 00145689999875223466677630101111689999998829989999978977612511778761388867899999
Q gi|254781172|r 532 DVSVTNLYDSINKRRNISLERFIFSLGIRHVGAEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQA 611 (731)
Q Consensus 532 eKsa~nL~~sIe~sK~~~L~r~L~ALGI~~vG~~~Ak~La~~f~si~~l~~~~~~~~~~~~~~~e~L~~I~GiG~~~A~s 611 (731)
.|...++++.+++++- -++||| |+|...|=.||+..-....+-+ . +..+-++..++. -.|..+|...+++
T Consensus 9 ar~tpk~~~kL~~a~V-----AicGlG--GLGS~~AinLAR~GigkLiLvD-f-DvvepsNLnRQq-Y~~s~~G~~KteA 78 (200)
T TIGR02354 9 ARHTPKVYEKLKKASV-----AICGLG--GLGSNVAINLARAGIGKLILVD-F-DVVEPSNLNRQQ-YKVSDVGKKKTEA 78 (200)
T ss_pred HCCCHHHHHHHCCCCE-----EEEECC--CCHHHHHHHHHHHCCCCEEEEE-E-CEECCCCCCHHH-HHHHHCCCHHHHH
T ss_conf 4178268898505827-----897016--1168999999873022025664-0-432366561325-7876248621799
Q ss_pred HHHHHCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCHHHHHHHHHH
Q ss_conf 9999669799999999997338776543224688216866999725889987899999998
Q gi|254781172|r 612 IVEFYQNPRNICAVEALLKEVSPSIGRHEKNVSSEIENKKLVFTGTLQKIQRHKAQEYVTQ 672 (731)
Q Consensus 612 i~~ff~~~~n~~~i~~L~~~~~~~~~~~~~~~~~~l~gk~vV~TGtl~~~~R~e~~~~ie~ 672 (731)
|.|-++.-. -.-++ + .....-.+.+.++.|.+-=||+-- |...+++.++.+
T Consensus 79 lke~i~ein---Py~~i-e--~~d~ki~E~N~~~~fkdaDiv~EA----FDna~aKam~~n 129 (200)
T TIGR02354 79 LKENISEIN---PYVEI-E--IIDEKIDEENLDKLFKDADIVCEA----FDNAEAKAMLVN 129 (200)
T ss_pred HHHHHHHHC---CCCEE-E--EEECCCCHHHHHHHHHCCCEEEEC----CCCHHHHHHHHH
T ss_conf 998786508---84212-3--110212766798784067478871----699889999999
No 271
>TIGR00143 hypF [NiFe] hydrogenase maturation protein HypF; InterPro: IPR004421 The large subunit of [NiFe]-hydrogenase, as well as other nickel metalloenzymes, is synthesized as a precursor devoid of the metalloenzyme active site. This precursor then undergoes a complex post-translational maturation process that requires a number of accessory proteins , , . Members of the HypF family are accessory proteins involved in hydrogenase maturation. They contain the following domains: acylphosphatase, zinc fingers (2 repeats), a YrdC-like domain, and a C-terminal domain with a putative O-carbamoyltransferase motif. The presence of CO and CN- ligands of the active site iron atoms is essential for [NiFe]-hydrogenase enzyme activity . Both ligands have been suggested to originate from carbamoylphosphate , which is required for maturation of [NiFe]-hydrogenases . Escherichia coli HypF interacts with carbamoylphosphate as a substrate and releases inorganic phosphate . In addition, HypF also cleaves ATP into AMP and pyrophosphate in the presence of carbamoylphosphate. This, and the fact that HypF catalyzes a carbamoylphosphate-dependent pyrophosphate ATP exchange reaction, suggest that the protein catalyzes the activation of carbamoylphosphate . The mechanism of action of HypF, as well as of its individual domains, is not yet clear. Mutations in any of the three major signature motifs, the acylphosphatase, the zinc fingers, and the O-carbamoyltransferase motif, can block carbamoylphosphate phosphatase activity. This indicates an integrated cooperativity between these domains in the cleavage reaction . The N-terminal acylphosphatase (ACP) domain is thought to support the conversion of carbamoylphosphate into CO and CN- , . Biochemical results demonstrating its ACP activity are not available , . ACPs are small enzymes that specifically catalyze the hydrolysis of carboxylphosphate bonds in acylphosphates, including carbamoylphosphate . Zinc fingers have been implicated in bivalent cation binding or as part of a chaperone domain interacting with the large subunit precursor, but experimental studies on such a function are lacking thus far. The YrdC-like domain is present in protein families with regulatory functions (IPR012200 from INTERPRO, IPR010923 from INTERPRO) and has been implicated in RNA binding . It is not clear what function it may have in members of the HypF family. A C-terminal domain is distantly related to peptidase M22, but contains a conserved O-carbamoyltransferase motif required for the carbamoylphosphate phosphatase activity . The function of this domain is not clear. Nomenclature note: the following names are used as synonyms of HypF: HupY in Azotobacter chroococcum, HupN in Rhizobium leguminosarum, HydA in Escherichia coli. In other organisms, these names are used to designate various "hydrogenase cluster" proteins unrelated to the members of this family. ; GO: 0030528 transcription regulator activity.
Probab=51.07 E-value=4.4 Score=19.79 Aligned_cols=28 Identities=18% Similarity=0.375 Sum_probs=16.2
Q ss_pred CEEEEECCCCC--CCHHHHHHHHHHCCCEE
Q ss_conf 66999725889--98789999999829849
Q gi|254781172|r 650 KKLVFTGTLQK--IQRHKAQEYVTQLGAVV 677 (731)
Q Consensus 650 k~vV~TGtl~~--~~R~e~~~~ie~~Ggkv 677 (731)
++|++||-.-. +=+.++...+...|...
T Consensus 748 ~~i~~sGGV~~N~~l~~~~~~~~~~~gf~~ 777 (799)
T TIGR00143 748 EKIVISGGVFYNRLLLERVAKYLKKAGFEF 777 (799)
T ss_pred EEEEECCCHHHHHHHHHHHHHHHHHCCCCE
T ss_conf 699933843888999999999998579714
No 272
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=50.84 E-value=9.1 Score=17.39 Aligned_cols=48 Identities=19% Similarity=0.188 Sum_probs=35.9
Q ss_pred CCHHHHHHHHHHHHHHH-CCCHHHHHHHHHHHHHCCCCCHHHHHCCCCCCHHHHHHHHH
Q ss_conf 01011116899999988-29989999978977612511778761388867899999999
Q gi|254781172|r 557 LGIRHVGAEIARSLAKY-YLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVE 614 (731)
Q Consensus 557 LGI~~vG~~~Ak~La~~-f~si~~l~~~~~~~~~~~~~~~e~L~~I~GiG~~~A~si~~ 614 (731)
+.++++....+..|... |.+++.+. ..+.++|..++|+++..|..+..
T Consensus 377 ~~~~~~~~~~~~~l~~~g~~~~edl~----------~~~~del~~~~~~~~e~a~~li~ 425 (428)
T PRK09202 377 LNLEGLDPELAFKLAEKGVKTLEDLA----------ELAVDELIDIEGLDEEEAGELIM 425 (428)
T ss_pred HHCCCCCHHHHHHHHHCCCCCHHHHH----------CCCHHHHHHCCCCCHHHHHHHHH
T ss_conf 64569999999999986998799996----------57988896377989999999998
No 273
>PRK00141 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=50.80 E-value=15 Score=15.61 Aligned_cols=12 Identities=17% Similarity=0.003 Sum_probs=5.2
Q ss_pred CCEEEEECCHHC
Q ss_conf 763777311000
Q gi|254781172|r 300 DGLVYKVDEFSL 311 (731)
Q Consensus 300 DGiVikvn~~~~ 311 (731)
+..|+-.||-..
T Consensus 225 ~~~vi~~Dd~~~ 236 (476)
T PRK00141 225 PVAVIGADDPYV 236 (476)
T ss_pred CCEEEECCCHHH
T ss_conf 824997787899
No 274
>PRK08628 short chain dehydrogenase; Provisional
Probab=50.63 E-value=15 Score=15.59 Aligned_cols=16 Identities=19% Similarity=0.202 Sum_probs=8.6
Q ss_pred CCCCCCCEEEEECCCC
Q ss_conf 8821686699972588
Q gi|254781172|r 644 SSEIENKKLVFTGTLQ 659 (731)
Q Consensus 644 ~~~l~gk~vV~TGtl~ 659 (731)
++..+|..+.+-|-+-
T Consensus 236 s~~iTG~~i~VDGG~v 251 (258)
T PRK08628 236 ASHTTGQWLFVDGGYV 251 (258)
T ss_pred HCCCCCCEEEECCCEE
T ss_conf 3493388799739888
No 275
>COG2099 CobK Precorrin-6x reductase [Coenzyme metabolism]
Probab=50.30 E-value=16 Score=15.56 Aligned_cols=48 Identities=19% Similarity=0.512 Sum_probs=25.3
Q ss_pred CCEEEEECCCCCCCHHHHHHHHHHCCCEEEEEEECCEEEEEECCCC---CC--HHHHHHHCCCEEE
Q ss_conf 8669997258899878999999982984998111632179977888---86--3798997499173
Q gi|254781172|r 649 NKKLVFTGTLQKIQRHKAQEYVTQLGAVVSAILSRKTDIIIVGDNP---GS--KLEKAQQLGVKIM 709 (731)
Q Consensus 649 gk~vV~TGtl~~~~R~e~~~~ie~~Ggkv~sSVSkkT~~LI~ge~~---gS--Kl~KA~~LgI~Ii 709 (731)
...|.+-|- |+-+.=+.++++.+. ++||.+++. |+ |+.-|.+||||||
T Consensus 174 ~~Iia~~GP---fs~~~n~all~q~~i----------d~vItK~SG~~Gg~~~Ki~aA~eLgi~VI 226 (257)
T COG2099 174 ARIIAMRGP---FSEEDNKALLEQYRI----------DVVVTKNSGGAGGTYEKIEAARELGIPVI 226 (257)
T ss_pred HHEEEECCC---CCHHHHHHHHHHHCC----------CEEEECCCCCCCCCHHHHHHHHHCCCCEE
T ss_conf 668982388---675889999998488----------89998267766673898999998699389
No 276
>pfam11672 DUF3268 Protein of unknown function (DUF3268). This family of proteins has no known function.
Probab=50.28 E-value=6 Score=18.75 Aligned_cols=15 Identities=33% Similarity=0.691 Sum_probs=11.9
Q ss_pred ECCCCCCCCCCCCCC
Q ss_conf 704326577501033
Q gi|254781172|r 430 FPSFCPICQSRVVRD 444 (731)
Q Consensus 430 ~P~~CP~Cgs~l~~~ 444 (731)
.|..||.||...+..
T Consensus 1 ~p~~CpYCg~~~~l~ 15 (102)
T pfam11672 1 KPVRCPYCGGKVELR 15 (102)
T ss_pred CCCCCCCCCCEEEEE
T ss_conf 994079999955882
No 277
>TIGR01900 dapE-gram_pos succinyl-diaminopimelate desuccinylase; InterPro: IPR010174 This entry represents a clade of succinyl-diaminopimelate desuccinylases from actinobacteria (high-GC Gram-positives) and is based on the characterisation of the enzyme from Corynebacterium glutamicum . This enzyme is involved in the biosynthesis of lysine, and is related to the enzyme acetylornithine deacetylase and other amidases and peptidases. They are classified as non-peptidases homologs belonging to MEROPS peptidase family M20A.
Probab=50.23 E-value=9.7 Score=17.17 Aligned_cols=105 Identities=22% Similarity=0.385 Sum_probs=62.8
Q ss_pred ECCCCHHHHHHHCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCHHHHHHHHHHHHHCCCCCHH
Q ss_conf 35870256654101235787304777043265775010337865445210100354344114466553321301231035
Q gi|254781172|r 405 RAGEVIPKVVDIIVNERHPDAQPFSFPSFCPICQSRVVRDLNPKTGKLVAAHRCTGGLACSAQQLERLKHFVSRDAFNIE 484 (731)
Q Consensus 405 RaGdVIP~I~~Vi~~~r~~~~~~~~~P~~CP~Cgs~l~~~~~~~~~~~~~~~rC~n~~~Cpaq~~~~i~hF~SK~aldI~ 484 (731)
++.-|||....|-.+-|-+ |.. +.++. ..+..-. +. ..-.+.++|-+ .++..+
T Consensus 243 ~~~NVIPD~~~~~~NyRFA-------P~~----------~L~EA-----kalmmGa--da-GaelGn~EHV~--~~~~l~ 295 (373)
T TIGR01900 243 KATNVIPDLARVNLNYRFA-------PDK----------DLAEA-----KALMMGA--DA-GAELGNIEHVV--ETLVLD 295 (373)
T ss_pred CCCCCCCCCEEEEEEEECC-------CCC----------CHHHH-----HHHHHCC--CC-CCCCCCCCEEE--EEEEEC
T ss_conf 4244156512674212018-------872----------57889-----8886302--23-42115721467--401641
Q ss_pred HHHHHHHHHHHCCCCCCEEEEEHHHHCCHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHH-HHHHH-------HHH
Q ss_conf 4103555565305765404541011010677753100010001342100145689999875223-46667-------763
Q gi|254781172|r 485 GLGKQQLDFFFKSEDPAFSIRIPADIFTLQRRQQTSTTKIENILGFGDVSVTNLYDSINKRRNI-SLERF-------IFS 556 (731)
Q Consensus 485 GLG~k~Ie~L~e~~~~~g~I~~~~DLy~L~~~~~~~~~~l~~l~GfgeKsa~nL~~sIe~sK~~-~L~r~-------L~A 556 (731)
|-+- |+.=++. +.-..+||.+...++-|++.+.+.+.. ||.+| -.+
T Consensus 296 G~~G--ie~~~~D------------------------~~~~A~PGL~~~~~~~L~~~V~~~~~RdPlAKlGWTDV~RFS~ 349 (373)
T TIGR01900 296 GYDG--IEIEVKD------------------------EAGSALPGLNAQLASDLVDLVKRRKIRDPLAKLGWTDVARFSA 349 (373)
T ss_pred CCCC--EEEEEEC------------------------CCCCCCCCCCCHHHHHHHHHHHHCCCCCCHHHCCCHHHHHHHH
T ss_conf 7774--4799862------------------------8888788776356789999863114666222325303566653
Q ss_pred CCHHHH
Q ss_conf 010111
Q gi|254781172|r 557 LGIRHV 562 (731)
Q Consensus 557 LGI~~v 562 (731)
||||-+
T Consensus 350 lGIPA~ 355 (373)
T TIGR01900 350 LGIPAL 355 (373)
T ss_pred CCCCEE
T ss_conf 276602
No 278
>PRK03906 mannonate dehydratase; Provisional
Probab=50.04 E-value=8.9 Score=17.45 Aligned_cols=83 Identities=16% Similarity=0.219 Sum_probs=42.2
Q ss_pred EECCCCCCCHHHCCCHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCEEEEEEEEECCEEEEEEECCCCHHHHHHHHHHH
Q ss_conf 45166425702159999999999999986124677761199994158189999985998998886598655666999775
Q gi|254781172|r 89 VTHSIPTLSLEKIWNIEDLRKFITRIYRFWQKKDDNSIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIR 168 (731)
Q Consensus 89 v~H~~pMlSL~k~~~~~el~~w~~~~~~~~~~~~~~~~~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n~~ 168 (731)
-=|.+| -..+++.+||.+--+.|... |+..+.+ |.--....+-+|.|..-+-|-.-..
T Consensus 30 aLh~ip---~GevW~~eeI~~~k~~Ie~~------------------GL~w~VV-ESvPVhe~IK~g~~~~d~~Ienyk~ 87 (389)
T PRK03906 30 ALHHIP---NGEVWPVEEILKRKAEIEAA------------------GLEWSVV-ESVPVHEDIKTGTPNRDQYIENYKQ 87 (389)
T ss_pred ECCCCC---CCCCCCHHHHHHHHHHHHHC------------------CCCEEEE-ECCCCHHHHHCCCCCHHHHHHHHHH
T ss_conf 023689---98867999999999999974------------------9818998-4678568887499878999999999
Q ss_pred HHCCCCCCCCCCCCCEEEEEEEEEEECHHHHH
Q ss_conf 31024322335445504899999985202123
Q gi|254781172|r 169 AIPTIPRVLSLNIPEIIEVRGEVYISKNDFLA 200 (731)
Q Consensus 169 ~i~~iP~~l~~~~~~~ieiRGEv~m~~~~F~~ 200 (731)
+|+++-. .. +.+=+==|||--||-+
T Consensus 88 sirNLa~---~G----I~viCYNFMPv~DWtR 112 (389)
T PRK03906 88 TLRNLAA---AG----IKVVCYNFMPVFDWTR 112 (389)
T ss_pred HHHHHHH---CC----CCEEEEECCCCCCCCC
T ss_conf 9999997---69----9789650366465003
No 279
>TIGR01186 proV glycine betaine/L-proline transport ATP binding subunit; InterPro: IPR005892 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain . The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , . The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , . Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). This family comprises the glycine betaine/L-proline ATP binding subunit in bacteria and its equivalents in archaea. This transport system belong to the larger ATP-Binding Cassette (ABC) transporter superfamily. The characteristic feature of these transporters is the obligatory coupling of ATP hydrolysis to substrate translocation. Functionally, this transport system is involved in osmoregulation. Under conditions of stress, the organism recruits this transport system to accumulate glycine betaine and other solutes which offer osmo-protection. It has been demonstrated that glycine betaine uptake is accompanied by symport with sodium ions. The locus has been named variously as proU or opuA. A gene library from L. lactis functionally complements an Escherichia coli proU mutant. The complementing locus is similar to a opuA locus in Bacillus subtlis. This clarifies the differences in nomenclature.; GO: 0005524 ATP binding, 0015171 amino acid transmembrane transporter activity, 0006865 amino acid transport, 0016020 membrane.
Probab=49.85 E-value=7.5 Score=18.02 Aligned_cols=30 Identities=37% Similarity=0.673 Sum_probs=24.2
Q ss_pred CCEEEEECCCCHHHHHHHCCCCCCCCCCCCCCCCCEEEEEECCCCH
Q ss_conf 6400010148989997502345432224684407689998358702
Q gi|254781172|r 365 GALITNATLHNEDYIKGLDASGKVMRGGRDIRVGDRVLVKRAGEVI 410 (731)
Q Consensus 365 G~~V~ratlhN~~~I~~l~~~~~~~~~~~~I~iGd~V~I~RaGdVI 410 (731)
+-||=.+| |-.|+= |+|||+|.|-++|+|.
T Consensus 181 ~kTIvFit-HDlDEA---------------~rigDRIvilk~GeiV 210 (372)
T TIGR01186 181 QKTIVFIT-HDLDEA---------------LRIGDRIVILKAGEIV 210 (372)
T ss_pred CCEEEEEE-CCHHHH---------------HHHHHHHHHEECCCEE
T ss_conf 98089994-176788---------------7675132011068678
No 280
>pfam06054 CoiA Competence protein CoiA-like family. Many of the members of this family are described as transcription factors. CoiA falls within a competence-specific operon in Streptococcus. CoiA is an uncharacterized protein.
Probab=49.68 E-value=7 Score=18.25 Aligned_cols=18 Identities=17% Similarity=0.193 Sum_probs=12.4
Q ss_pred CCCCHHHHHHHHHCCCCC
Q ss_conf 100003689999759966
Q gi|254781172|r 251 AKGQYEMLQKMRCLGFPV 268 (731)
Q Consensus 251 ~~~~~e~l~~L~~~GF~v 268 (731)
.........+++..|++|
T Consensus 66 l~gK~~L~~~l~~~~~~v 83 (348)
T pfam06054 66 LAAKLLLYQWLKRQEFKV 83 (348)
T ss_pred HHHHHHHHHHHHHCCCCE
T ss_conf 999999999998579976
No 281
>pfam10941 DUF2620 Protein of unknown function DUF2620. This is a bacterial family of proteins with unknown function.
Probab=49.64 E-value=16 Score=15.48 Aligned_cols=72 Identities=22% Similarity=0.340 Sum_probs=37.4
Q ss_pred CEEEEECCCCCCCHHHHHHHHHHCCC-EEEEEEECC-----------EEEEEECCCCC--CHHHHHHHC-C------C--
Q ss_conf 66999725889987899999998298-499811163-----------21799778888--637989974-9------9--
Q gi|254781172|r 650 KKLVFTGTLQKIQRHKAQEYVTQLGA-VVSAILSRK-----------TDIIIVGDNPG--SKLEKAQQL-G------V-- 706 (731)
Q Consensus 650 k~vV~TGtl~~~~R~e~~~~ie~~Gg-kv~sSVSkk-----------T~~LI~ge~~g--SKl~KA~~L-g------I-- 706 (731)
|+||+.|- ..|+++++.|++.|+ ++.-.|..+ .||-+=-=++| .-|.=|--| | |
T Consensus 1 ~kivIgGq---l~K~~i~~~i~~~~~~~~ev~i~sDmdAAM~vK~G~aDYYiGACnTGgGgALamAIallG~~~C~Tvs~ 77 (117)
T pfam10941 1 KRIVIGGQ---LQKEEIAELIEETAGGAVEVTIKSDLDAAMAVKNGKADYYIGACNTGAGGALAMAIAILGKDKCATIAM 77 (117)
T ss_pred CEEEECCC---CCHHHHHHHHHHHCCCCEEEEECCHHHHHHHHHCCCCCEEEEECCCCCCHHHHHHHHHHCCCCEEEEEC
T ss_conf 91888472---259999999998689836999705099998876699676666447896199999999948463578556
Q ss_pred --EEECHHHHHHHHHHHCCC
Q ss_conf --173799999999882865
Q gi|254781172|r 707 --KIMNEEQFLFLLQQYNTT 724 (731)
Q Consensus 707 --~Ii~e~ef~~ll~~~~~~ 724 (731)
.+.+|++..+++++.+..
T Consensus 78 pg~~~~eeeI~~~v~~GKkA 97 (117)
T pfam10941 78 PGKPPKEEEIEKAVDEGKKA 97 (117)
T ss_pred CCCCCCHHHHHHHHHCCCCE
T ss_conf 99999999999999748804
No 282
>TIGR00789 flhB_rel FlhB domain protein; InterPro: IPR004683 This group describes a short protein (80-93 residues) homologous to the C-terminus of the flagellar biosynthetic protein FlhB. It is found so far only in species that also have FlhB. In a phylogenetic tree based on alignment of both this family and the homologous region of FlhB and its homologs, the members of this family form a monophyletic set..
Probab=49.51 E-value=13 Score=16.19 Aligned_cols=24 Identities=25% Similarity=0.445 Sum_probs=9.5
Q ss_pred HHHHHCCCEEECHHHHHHHHHHHC
Q ss_conf 989974991737999999998828
Q gi|254781172|r 699 EKAQQLGVKIMNEEQFLFLLQQYN 722 (731)
Q Consensus 699 ~KA~~LgI~Ii~e~ef~~ll~~~~ 722 (731)
+.|++.||||-..+.+.+.|.+-+
T Consensus 34 ~~AK~~gipi~ed~~L~~~L~~l~ 57 (84)
T TIGR00789 34 ELAKKHGIPIKEDEDLVDVLLKLD 57 (84)
T ss_pred HHHHHCCCCCCCCHHHHHHHHHCC
T ss_conf 999763899765828999874405
No 283
>TIGR02634 xylF D-xylose ABC transporter, substrate-binding protein; InterPro: IPR013456 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain . The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , . The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , . Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). This entry represents the D-xylose ABC transporter substrate-binding protein which is a periplasmic (when in Gram-negative bacteria) binding protein for D-xylose import by a high-affinity ATP-binding cassette (ABC) transporter..
Probab=49.46 E-value=16 Score=15.46 Aligned_cols=13 Identities=0% Similarity=0.066 Sum_probs=4.4
Q ss_pred CCCCHHHHHHHHH
Q ss_conf 2100145689999
Q gi|254781172|r 530 FGDVSVTNLYDSI 542 (731)
Q Consensus 530 fgeKsa~nL~~sI 542 (731)
|-...|.++++++
T Consensus 165 Wlp~~A~~~~E~~ 177 (307)
T TIGR02634 165 WLPENALKIMENA 177 (307)
T ss_pred CCHHHHHHHHHHH
T ss_conf 2568899999988
No 284
>TIGR00340 zpr1_rel zinc finger protein ZPR1 homolog; InterPro: IPR004470 Zinc finger (Znf) domains are relatively small protein motifs that bind one or more zinc atoms, and which usually contain multiple finger-like protrusions that make tandem contacts with their target molecule. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis, 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. (Note that in certain cases, some Znf domains have diverged such that they still maintain their core structure, but have lost their ability to bind zinc, using other means such as salt bridges or binding to other metals to stabilise the finger-like folds. These domains can show strong sequence identity to zinc-binding motifs, and may therefore be included in Znf entries). This entry represents ZPR1-type zinc finger domains. ZPR1 was shown experimentally to bind approximately two moles of zinc, and has two copies of a domain homologous to this protein, each containing a putative zinc finger of the form CXXCX(25)CXXC. ZPR1 binds the tyrosine kinase domain of epidermal growth factor receptor but is displaced by receptor activation and autophosphorylation after which it redistributes in part to the nucleus. The proteins described by this family by analogy may be suggested to play a role in signal transduction as proven for other Z-finger binding proteins. Deficiencies in ZPR1 may contribute to neurodegenerative disorders. ZPR1 appears to be down-regulated in patients with spinal muscular atrophy (SMA), a disease characterised by degeneration of the alpha-motor neurons in the spinal cord that can arise from mutations affecting the expression of Survival Motor Neurons (SMN) . ZPR1 interacts with complexes formed by SMN , and may act as a modifier that effects the severity of SMA. More information about these proteins can be found at Protein of the Month: Zinc Fingers .; GO: 0008270 zinc ion binding.
Probab=49.35 E-value=5.9 Score=18.85 Aligned_cols=37 Identities=14% Similarity=0.225 Sum_probs=20.2
Q ss_pred HHHHCCCCCCHHHHHHHH---HHHCCH---HHHHHHHHHHHHC
Q ss_conf 876138886789999999---996697---9999999999733
Q gi|254781172|r 596 LSLIRVPLVGDIIAQAIV---EFYQNP---RNICAVEALLKEV 632 (731)
Q Consensus 596 e~L~~I~GiG~~~A~si~---~ff~~~---~n~~~i~~L~~~~ 632 (731)
-.+++|+||=+...+.+. +|+.++ +....++.+++..
T Consensus 92 G~IsniEGvleR~~~~l~~~~~~~e~d~dEE~v~~~~~il~~I 134 (168)
T TIGR00340 92 GYISNIEGVLERVEEVLKTALDLEEEDRDEEKVKKVEEILKKI 134 (168)
T ss_pred CEEEHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHH
T ss_conf 0352146777889999988630013221047789999999875
No 285
>KOG0478 consensus
Probab=49.00 E-value=12 Score=16.47 Aligned_cols=44 Identities=20% Similarity=0.249 Sum_probs=22.3
Q ss_pred CCCCCC---HHHHHHHHHHC-----CCEEEEEEECCEEEEEECCCCCCHHHH
Q ss_conf 588998---78999999982-----984998111632179977888863798
Q gi|254781172|r 657 TLQKIQ---RHKAQEYVTQL-----GAVVSAILSRKTDIIIVGDNPGSKLEK 700 (731)
Q Consensus 657 tl~~~~---R~e~~~~ie~~-----Ggkv~sSVSkkT~~LI~ge~~gSKl~K 700 (731)
-|.+|+ |+-+.+..|+. -|=+-.|.+.-|+.|-+..-.+||+..
T Consensus 534 EFDKM~dStrSvLhEvMEQQTvSIAKAGII~sLNAR~SVLAaANP~~skynp 585 (804)
T KOG0478 534 EFDKMSDSTRSVLHEVMEQQTLSIAKAGIIASLNARCSVLAAANPIRSKYNP 585 (804)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHCCEEEECCCCCEEEEEECCCCCCCCC
T ss_conf 2333327788999999987631174302234216653034453543245799
No 286
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=48.49 E-value=5.9 Score=18.82 Aligned_cols=15 Identities=20% Similarity=0.603 Sum_probs=5.5
Q ss_pred EEEEEEC-CCEEEEEC
Q ss_conf 7433302-64000101
Q gi|254781172|r 358 LEPVNIG-GALITNAT 372 (731)
Q Consensus 358 ~ePV~l~-G~~V~rat 372 (731)
+.-++++ |-.|.+|.
T Consensus 90 ITSIE~~~gkRV~~A~ 105 (201)
T COG1326 90 ITSIELGGGKRVKSAK 105 (201)
T ss_pred EEEEEECCCCCCCCCC
T ss_conf 9998508875223021
No 287
>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed
Probab=48.29 E-value=13 Score=16.24 Aligned_cols=21 Identities=24% Similarity=0.243 Sum_probs=11.2
Q ss_pred EEEEEEEEEEECCCEEEEECC
Q ss_conf 899997433302640001014
Q gi|254781172|r 353 TPVARLEPVNIGGALITNATL 373 (731)
Q Consensus 353 tPva~~ePV~l~G~~V~ratl 373 (731)
+-...+.|-+|=|+|-.-..|
T Consensus 143 ~~~i~L~pFTLIGATTr~g~L 163 (328)
T PRK00080 143 SIRLDLPPFTLIGATTRAGLL 163 (328)
T ss_pred EEECCCCCEEEEECCCCCCCC
T ss_conf 455589983474013676657
No 288
>COG0474 MgtA Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=48.29 E-value=8.2 Score=17.73 Aligned_cols=48 Identities=19% Similarity=0.239 Sum_probs=25.3
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHCC
Q ss_conf 0001342100145689999875223466677630101111689999998829
Q gi|254781172|r 524 IENILGFGDVSVTNLYDSINKRRNISLERFIFSLGIRHVGAEIARSLAKYYL 575 (731)
Q Consensus 524 l~~l~GfgeKsa~nL~~sIe~sK~~~L~r~L~ALGI~~vG~~~Ak~La~~f~ 575 (731)
++.+-||-++-=+..-++|+..++....-.+ |-|=...||+.+++..+
T Consensus 538 ~lGl~g~~Dppr~~v~~aI~~l~~AGI~v~M----iTGD~~~TA~aIa~~~G 585 (917)
T COG0474 538 FLGLTGIEDPPREDVKEAIEELREAGIKVWM----ITGDHVETAIAIAKECG 585 (917)
T ss_pred EEEEEEECCCCCCCHHHHHHHHHHCCCCEEE----ECCCCHHHHHHHHHHHC
T ss_conf 0200121289971189999999988994799----87999899999999819
No 289
>PRK05876 short chain dehydrogenase; Provisional
Probab=48.20 E-value=17 Score=15.32 Aligned_cols=16 Identities=6% Similarity=0.320 Sum_probs=6.8
Q ss_pred CCHHHHHHHHHHHHHC
Q ss_conf 1035410355556530
Q gi|254781172|r 481 FNIEGLGKQQLDFFFK 496 (731)
Q Consensus 481 ldI~GLG~k~Ie~L~e 496 (731)
|..+-+++.+++.+-+
T Consensus 224 ~~~d~vA~~v~~~i~~ 239 (275)
T PRK05876 224 LGVDDIAQLTADAILA 239 (275)
T ss_pred CCHHHHHHHHHHHHHC
T ss_conf 9999999999999960
No 290
>COG3845 ABC-type uncharacterized transport systems, ATPase components [General function prediction only]
Probab=48.12 E-value=9.8 Score=17.13 Aligned_cols=43 Identities=35% Similarity=0.482 Sum_probs=30.1
Q ss_pred EEEEEEEEEEC------------CCEEEEECCCCHHHHHHHCCCCCCCCCCCCCCCCCEEEEEECCCCHHH
Q ss_conf 99997433302------------640001014898999750234543222468440768999835870256
Q gi|254781172|r 354 PVARLEPVNIG------------GALITNATLHNEDYIKGLDASGKVMRGGRDIRVGDRVLVKRAGEVIPK 412 (731)
Q Consensus 354 Pva~~ePV~l~------------G~~V~ratlhN~~~I~~l~~~~~~~~~~~~I~iGd~V~I~RaGdVIP~ 412 (731)
|+|++.|-+++ |.+|=..| |-.++|.++ -|+|+|.|.|.|+-.
T Consensus 167 PTaVLTP~E~~~lf~~l~~l~~~G~tIi~IT-HKL~Ev~~i---------------aDrvTVLR~Gkvvgt 221 (501)
T COG3845 167 PTAVLTPQEADELFEILRRLAAEGKTIIFIT-HKLKEVMAI---------------ADRVTVLRRGKVVGT 221 (501)
T ss_pred CCCCCCHHHHHHHHHHHHHHHHCCCEEEEEE-CCHHHHHHH---------------HCEEEEEECCEEEEE
T ss_conf 7535898999999999999997799799993-508999976---------------373699857748866
No 291
>pfam05876 Terminase_GpA Phage terminase large subunit (GpA). This family consists of several phage terminase large subunit proteins as well as related sequences from several bacterial species. The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, gpA, products of the Nu1 and A genes, respectively. Terminase is involved in the site-specific binding and cutting of the DNA in the initial stages of packaging. It is now known that gpA is actively involved in late stages of packaging, including DNA translocation, and that this enzyme contains separate functional domains for its early and late packaging activities.
Probab=48.06 E-value=15 Score=15.66 Aligned_cols=19 Identities=32% Similarity=0.342 Sum_probs=9.0
Q ss_pred HHHHHHHHHHHHHCCHHHC
Q ss_conf 9999999999897720311
Q gi|254781172|r 49 DALKRRCDAIAHAFPDLAR 67 (731)
Q Consensus 49 D~L~~~L~~le~~~p~~~~ 67 (731)
|....+|.-+=...|.+..
T Consensus 77 ~~s~~rl~Pmi~~sP~L~~ 95 (552)
T pfam05876 77 RFSKDRLDPMIRASPALRE 95 (552)
T ss_pred HHHHHHHHHHHHCCHHHHH
T ss_conf 9999989999861989997
No 292
>PRK00349 uvrA excinuclease ABC subunit A; Reviewed
Probab=47.71 E-value=17 Score=15.27 Aligned_cols=26 Identities=19% Similarity=0.220 Sum_probs=15.0
Q ss_pred EEEEECCCCHHHHHHHCCCCCCCCCCCCCCCCCEEEEE
Q ss_conf 00010148989997502345432224684407689998
Q gi|254781172|r 367 LITNATLHNEDYIKGLDASGKVMRGGRDIRVGDRVLVK 404 (731)
Q Consensus 367 ~V~ratlhN~~~I~~l~~~~~~~~~~~~I~iGd~V~I~ 404 (731)
+|+.|+.||.+.|. -+|-+|..+.|.
T Consensus 616 ~l~~a~~~NLk~v~------------v~iPlg~lt~Vt 641 (944)
T PRK00349 616 KLKGARENNLKNVD------------VEIPLGKFTCVT 641 (944)
T ss_pred EECCCCCCCCCCCC------------EEECCCCEEEEE
T ss_conf 62583020588764------------354389668996
No 293
>PRK05866 short chain dehydrogenase; Provisional
Probab=47.64 E-value=17 Score=15.29 Aligned_cols=13 Identities=8% Similarity=0.072 Sum_probs=7.7
Q ss_pred CCHHHHHHHHHHH
Q ss_conf 0014568999987
Q gi|254781172|r 532 DVSVTNLYDSINK 544 (731)
Q Consensus 532 eKsa~nL~~sIe~ 544 (731)
|.-|+.+++++++
T Consensus 245 e~~A~~iv~a~~~ 257 (290)
T PRK05866 245 DEAAEWMVTAART 257 (290)
T ss_pred HHHHHHHHHHHHC
T ss_conf 9999999999844
No 294
>PRK05582 DNA topoisomerase I; Validated
Probab=47.57 E-value=10 Score=16.96 Aligned_cols=22 Identities=9% Similarity=0.241 Sum_probs=14.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 9999999999999999998433
Q gi|254781172|r 15 EQARKELSSLEQEISYHDDCYY 36 (731)
Q Consensus 15 ~~~~~~i~~L~~~i~~~~~~Yy 36 (731)
...++.+..|.+.+.+++..|-
T Consensus 57 ~~~~k~i~~lk~l~k~ad~iii 78 (692)
T PRK05582 57 KDKKELVKKIKKLAKKADKIYL 78 (692)
T ss_pred CCHHHHHHHHHHHHHCCCEEEE
T ss_conf 6679999999999865998998
No 295
>PRK12823 benD 1,6-dihydroxycyclohexa-2,4-diene-1-carboxylate dehydrogenase; Provisional
Probab=47.32 E-value=17 Score=15.23 Aligned_cols=12 Identities=33% Similarity=0.279 Sum_probs=6.9
Q ss_pred CCCCCCEEEEEC
Q ss_conf 821686699972
Q gi|254781172|r 645 SEIENKKLVFTG 656 (731)
Q Consensus 645 ~~l~gk~vV~TG 656 (731)
+..+|.++.+.|
T Consensus 245 ~~iTG~~i~VDG 256 (260)
T PRK12823 245 SYITGSVLPVGG 256 (260)
T ss_pred CCCCCCEEEECC
T ss_conf 480478688685
No 296
>PRK09783 copper/silver efflux system membrane fusion protein CusB; Provisional
Probab=47.30 E-value=7.3 Score=18.12 Aligned_cols=95 Identities=16% Similarity=0.103 Sum_probs=47.4
Q ss_pred CCCCCCCCEEEEECCHHCCCCC-CC-----CCCCCCCEEEECCCCCEE-EEEEEEEE----EEECCC--CEEEEEEEEEE
Q ss_conf 1123437637773110001115-87-----656866312311456215-89987889----940356--22589999743
Q gi|254781172|r 294 TLPYDIDGLVYKVDEFSLQKQL-GE-----RARSPRWMISHKFAEKQA-STRLLDID----IQIGRT--GILTPVARLEP 360 (731)
Q Consensus 294 ~l~y~iDGiVikvn~~~~q~~l-G~-----ts~~PrwaiA~Kf~~e~~-~T~v~~I~----wqvgRt--G~itPva~~eP 360 (731)
.+-=++||+|...+-..-+-.- |. ..-+.-|..|-=|+.+.. ...-..+. -..|++ |++. .+.|
T Consensus 209 ti~AP~sGvV~~~~v~~G~~V~~G~~Lf~IaDLs~vWv~a~V~E~d~~~vk~Gq~v~v~~~a~Pg~~f~G~V~---~I~P 285 (407)
T PRK09783 209 TLKAPIDGVITAFDLRAGMNIAKDNVVAKIQGMDPVWVTAAIPESIAWLVKDASQFTLTVPARPDKTLTIRKW---TLLP 285 (407)
T ss_pred EEECCCCCEEEEEECCCCCEECCCCEEEEEECCCEEEEEEEECHHHHHHCCCCCEEEEEECCCCCCCEEEEEE---EEEC
T ss_conf 9976888079997447895667998069996477289999962786864568988999832689961258999---9804
Q ss_pred EE--ECCCEEEEECCCCHHHHHHHCCCCCCCCCCCCCCCCCEEEEEEC
Q ss_conf 33--02640001014898999750234543222468440768999835
Q gi|254781172|r 361 VN--IGGALITNATLHNEDYIKGLDASGKVMRGGRDIRVGDRVLVKRA 406 (731)
Q Consensus 361 V~--l~G~~V~ratlhN~~~I~~l~~~~~~~~~~~~I~iGd~V~I~Ra 406 (731)
.- -..+.--|+++-|.+. .+++|-.+.|.-.
T Consensus 286 ~vD~~TRT~~VRv~l~N~d~---------------~LkPGMfa~v~i~ 318 (407)
T PRK09783 286 GVDAATRTLQLRLEVDNADE---------------ALKPGMNAWLQLN 318 (407)
T ss_pred CCCCCCCEEEEEEEECCCCC---------------CCCCCCEEEEEEC
T ss_conf 55777754999999549987---------------3089988999982
No 297
>PRK13812 orotate phosphoribosyltransferase; Provisional
Probab=47.19 E-value=17 Score=15.21 Aligned_cols=62 Identities=24% Similarity=0.316 Sum_probs=42.7
Q ss_pred CCCEEEE------ECCCCCCCHHHHHHHHHHCCCEEEEEEECCEEEEEECCCCCCHHHHHHHCCCEEECHHHHHHHHHH
Q ss_conf 6866999------725889987899999998298499811163217997788886379899749917379999999988
Q gi|254781172|r 648 ENKKLVF------TGTLQKIQRHKAQEYVTQLGAVVSAILSRKTDIIIVGDNPGSKLEKAQQLGVKIMNEEQFLFLLQQ 720 (731)
Q Consensus 648 ~gk~vV~------TGtl~~~~R~e~~~~ie~~Ggkv~sSVSkkT~~LI~ge~~gSKl~KA~~LgI~Ii~e~ef~~ll~~ 720 (731)
.|+++++ || -|=.+..+.+++.|++|..-+. |+.-..|.+ +..++.||++.+--.+.++|++
T Consensus 106 ~g~rVlivEDViTTG----~S~~eai~~l~~~G~~V~~v~v------ivDR~eg~~-e~l~~~gv~~~sl~t~~dlla~ 173 (174)
T PRK13812 106 DGEEVVVLEDIATTG----QSAVDAVEALRDAGATVNRVLV------VVDREEGAR-ENLAEHDVEMEALVTASDLLAD 173 (174)
T ss_pred CCCEEEEEEEEECCC----CCHHHHHHHHHHCCCEEEEEEE------EEECCCCHH-HHHHHCCCEEEEEECHHHHHCC
T ss_conf 786699998644578----0199999999987997999999------997785658-9999779809997029997148
No 298
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=47.14 E-value=9.6 Score=17.20 Aligned_cols=28 Identities=25% Similarity=0.788 Sum_probs=18.5
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCHHH
Q ss_conf 0432657750103378654452101003543441144
Q gi|254781172|r 431 PSFCPICQSRVVRDLNPKTGKLVAAHRCTGGLACSAQ 467 (731)
Q Consensus 431 P~~CP~Cgs~l~~~~~~~~~~~~~~~rC~n~~~Cpaq 467 (731)
+-.||+|+.+.++.... ..|.|. .|-..
T Consensus 35 ~~~Cp~C~~~~VkR~a~------GIW~C~---kCg~~ 62 (89)
T COG1997 35 KHVCPFCGRTTVKRIAT------GIWKCR---KCGAK 62 (89)
T ss_pred CCCCCCCCCCCEEEECC------CEEECC---CCCCE
T ss_conf 77699789740455236------758717---88873
No 299
>PRK09138 DNA topoisomerase I; Validated
Probab=47.13 E-value=8.7 Score=17.52 Aligned_cols=35 Identities=29% Similarity=0.519 Sum_probs=21.1
Q ss_pred ECCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCHHH
Q ss_conf 70432657750103378654452101003543441144
Q gi|254781172|r 430 FPSFCPICQSRVVRDLNPKTGKLVAAHRCTGGLACSAQ 467 (731)
Q Consensus 430 ~P~~CP~Cgs~l~~~~~~~~~~~~~~~rC~n~~~Cpaq 467 (731)
-|..||.|++.-.. ...+.++..+-|.|--.|...
T Consensus 601 d~r~cp~c~~g~l~---l~~gk~G~figcsnypec~~t 635 (887)
T PRK09138 601 DPRICPTCGTGRLS---LKLGKFGAFVGCSNYPECRYT 635 (887)
T ss_pred CCCCCCCCCCCCEE---EECCCCCCCCCCCCCCCCCCC
T ss_conf 76336678887368---870576566656788644355
No 300
>pfam08745 UPF0278 UPF0278 family. Members of this family are uncharacterized proteins about 200 amino acids in length.
Probab=47.04 E-value=17 Score=15.20 Aligned_cols=52 Identities=25% Similarity=0.410 Sum_probs=34.7
Q ss_pred CCCCCCCHHHHH--HHHHHCCCEEEEEEECCEEEEEECCCCCCHHHHHHHCCCEEECHHHHHHHHHHHC
Q ss_conf 258899878999--9999829849981116321799778888637989974991737999999998828
Q gi|254781172|r 656 GTLQKIQRHKAQ--EYVTQLGAVVSAILSRKTDIIIVGDNPGSKLEKAQQLGVKIMNEEQFLFLLQQYN 722 (731)
Q Consensus 656 Gtl~~~~R~e~~--~~ie~~Ggkv~sSVSkkT~~LI~ge~~gSKl~KA~~LgI~Ii~e~ef~~ll~~~~ 722 (731)
|.|. |+.++. =+...++|.++++ ..| =.+=|+++||+.++...|..+|++|=
T Consensus 150 GiLD--S~eD~DvlLLA~ELda~vVt~------------D~G-i~kWA~~lGlr~i~~~~F~~~Lee~l 203 (206)
T pfam08745 150 GILD--SAEDLDVLLLAKELDAAVVAS------------DEG-IRKWAEKLGLRFVDASNFPEMLEEYL 203 (206)
T ss_pred CCCC--CHHHHHHHHHHHHHCCEEECC------------CHH-HHHHHHHCCCEEECHHHHHHHHHHHH
T ss_conf 6656--532378999999848757706------------264-99999980978878888689999999
No 301
>TIGR01701 Fdhalpha-like oxidoreductase alpha (molybdopterin) subunit; InterPro: IPR010046 This entry represents a well-defined clade of molybdopterin-dependent formate dehydrogenases, bacterial type , , , . It represents the alpha subunit, which contains a molybdopterin cofactor and generally associate with two other subunits which contain iron-sulphur clusters and cytochromes.; GO: 0008863 formate dehydrogenase activity, 0030151 molybdenum ion binding, 0051539 4 iron 4 sulfur cluster binding.
Probab=46.97 E-value=17 Score=15.19 Aligned_cols=81 Identities=17% Similarity=0.298 Sum_probs=40.2
Q ss_pred CCCEEEE---ECCC-CCCC-HHHHHHHHHHCCCEEEEEEE--CCEEEEEECCCC------CCHHHH-HHHCCCEEECHHH
Q ss_conf 6866999---7258-8998-78999999982984998111--632179977888------863798-9974991737999
Q gi|254781172|r 648 ENKKLVF---TGTL-QKIQ-RHKAQEYVTQLGAVVSAILS--RKTDIIIVGDNP------GSKLEK-AQQLGVKIMNEEQ 713 (731)
Q Consensus 648 ~gk~vV~---TGtl-~~~~-R~e~~~~ie~~Ggkv~sSVS--kkT~~LI~ge~~------gSKl~K-A~~LgI~Ii~e~e 713 (731)
.||.=+| =|.| +-+. +..+++-+++.-=.|.=+.- -+-++|++|+.+ | -.+. -+.-+-+..|-++
T Consensus 502 eG~~~~f~~~GGNF~~A~PD~a~~~~~L~~~~L~V~vatk~nLnrsH~l~~~~~~iLP~lg-R~E~d~~~~~~QavS~e~ 580 (824)
T TIGR01701 502 EGKVRAFICLGGNFLEAMPDTAAIEEALRQLDLRVHVATKFNLNRSHVLAKEEALILPVLG-RIEQDGQKTGKQAVSVED 580 (824)
T ss_pred CCEEEEEECCCHHHHHCCCCHHHHHHHHHHCCEEEEEEEECCCCCHHHHHCCEEEEECCCC-CCCCCCCCCCCCEEEECC
T ss_conf 6627544304326652088989999886424367898862256402433203135512566-301788888541476010
Q ss_pred HHHHHHHHCCCCCCCC
Q ss_conf 9999988286568756
Q gi|254781172|r 714 FLFLLQQYNTTLRIHD 729 (731)
Q Consensus 714 f~~ll~~~~~~~~~~~ 729 (731)
+.+|+-.....+.+..
T Consensus 581 s~~m~h~Srg~~~P~~ 596 (824)
T TIGR01701 581 SMRMVHESRGILKPRG 596 (824)
T ss_pred CEEHHHCCCCCCCCCC
T ss_conf 1000213765577711
No 302
>TIGR01525 ATPase-IB_hvy heavy metal translocating P-type ATPase; InterPro: IPR006416 This group encompasses the copper and cadmium-type heavy metal transporting P-type ATPases as well as those which cannot be assigned to one or other of the groups. ; GO: 0015662 ATPase activity coupled to transmembrane movement of ions phosphorylative mechanism, 0030001 metal ion transport, 0016021 integral to membrane.
Probab=46.95 E-value=11 Score=16.80 Aligned_cols=39 Identities=31% Similarity=0.555 Sum_probs=21.8
Q ss_pred HHHHHHHHHHC---CCEEEEEEECCEEEEEECCCCCCHHHHHHHCCCEE
Q ss_conf 78999999982---98499811163217997788886379899749917
Q gi|254781172|r 663 RHKAQEYVTQL---GAVVSAILSRKTDIIIVGDNPGSKLEKAQQLGVKI 708 (731)
Q Consensus 663 R~e~~~~ie~~---Ggkv~sSVSkkT~~LI~ge~~gSKl~KA~~LgI~I 708 (731)
|.|+++.|..+ ||. ..-+++.||+...=-.=|++|||++
T Consensus 452 R~~a~~~i~~Lk~~~g~-------~~~~mLTGD~~~~A~~~A~~lGI~~ 493 (639)
T TIGR01525 452 RPEAKEAIAALKRKGGI-------IEVVMLTGDNRAAAEAVAAELGIEI 493 (639)
T ss_pred CHHHHHHHHHHHHHCCC-------CEEEEECCCCHHHHHHHHHHHCCCC
T ss_conf 85479999999974387-------3477621888899999999829850
No 303
>pfam11382 DUF3186 Protein of unknown function (DUF3186). This bacterial family of proteins has no known function.
Probab=46.75 E-value=18 Score=15.16 Aligned_cols=14 Identities=7% Similarity=0.328 Sum_probs=7.8
Q ss_pred EEEECCEEEEEEEE
Q ss_conf 99415818999998
Q gi|254781172|r 130 LEPKIDGTMITIRY 143 (731)
Q Consensus 130 vepKiDG~sisl~Y 143 (731)
+.-++-|..+.++.
T Consensus 77 v~g~L~g~~Valv~ 90 (307)
T pfam11382 77 VAGRLTGKSVALVR 90 (307)
T ss_pred HHCCCCCCEEEEEE
T ss_conf 73754897599997
No 304
>PRK12278 50S ribosomal protein L21/unknown domain fusion protein; Provisional
Probab=46.59 E-value=8.4 Score=17.63 Aligned_cols=21 Identities=24% Similarity=0.311 Sum_probs=15.4
Q ss_pred CHHHHHCCCCCCHHHHHHHHH
Q ss_conf 778761388867899999999
Q gi|254781172|r 594 DWLSLIRVPLVGDIIAQAIVE 614 (731)
Q Consensus 594 ~~e~L~~I~GiG~~~A~si~~ 614 (731)
..++|..|.||||+.++.+.+
T Consensus 151 ~aDDLk~I~GIGP~~e~~Ln~ 171 (216)
T PRK12278 151 EADDLTKITGVGPALAKKLNE 171 (216)
T ss_pred CCCCCCEECCCCHHHHHHHHH
T ss_conf 996543602658899999998
No 305
>COG0773 MurC UDP-N-acetylmuramate-alanine ligase [Cell envelope biogenesis, outer membrane]
Probab=46.57 E-value=18 Score=15.15 Aligned_cols=67 Identities=21% Similarity=0.192 Sum_probs=38.0
Q ss_pred EEEEECCHHCCCCCCCCCCCCCCE--EEECCCCCEEEEEEEEEEEEECCCCEEEEEEEEEEEEECCCEEEEECCCCH
Q ss_conf 377731100011158765686631--231145621589987889940356225899997433302640001014898
Q gi|254781172|r 302 LVYKVDEFSLQKQLGERARSPRWM--ISHKFAEKQASTRLLDIDIQIGRTGILTPVARLEPVNIGGALITNATLHNE 376 (731)
Q Consensus 302 iVikvn~~~~q~~lG~ts~~Prwa--iA~Kf~~e~~~T~v~~I~wqvgRtG~itPva~~ePV~l~G~~V~ratlhN~ 376 (731)
+|+-.||-.+++.+... .|. +-|=|.++ +.....++.-+-+++ +--+.+.--.++..++.-.--||.
T Consensus 214 ~v~~~dd~~l~~l~~~~----~~~~v~tyG~~~~-ad~~a~ni~~~~~~~---~F~V~~~g~~~~~~~l~~pG~HNv 282 (459)
T COG0773 214 AVVCGDDPNLRELLSRG----CWSPVVTYGFDDE-ADWRAENIRQDGSGT---TFDVLFRGEELGEVKLPLPGRHNV 282 (459)
T ss_pred EEEECCCHHHHHHHHCC----CCCCEEEECCCCC-CCEEEEEEEEECCCC---EEEEEECCCEEEEEEECCCCHHHH
T ss_conf 99978888899987222----5873794247876-728999768706642---799998685567999726762268
No 306
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=46.57 E-value=7.6 Score=17.99 Aligned_cols=11 Identities=27% Similarity=0.718 Sum_probs=8.6
Q ss_pred CCCCCCCCCCC
Q ss_conf 43265775010
Q gi|254781172|r 432 SFCPICQSRVV 442 (731)
Q Consensus 432 ~~CP~Cgs~l~ 442 (731)
+.||.||+++.
T Consensus 50 t~CP~Cg~~~e 60 (115)
T COG1885 50 TSCPKCGEPFE 60 (115)
T ss_pred CCCCCCCCCCC
T ss_conf 55887799663
No 307
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=46.41 E-value=8.4 Score=17.67 Aligned_cols=45 Identities=24% Similarity=0.369 Sum_probs=27.1
Q ss_pred HCCCEEE-EEEECC--EEEEEECCC----------CC----CHHHHHHHCCCEEECHHHHHHH
Q ss_conf 8298499-811163--217997788----------88----6379899749917379999999
Q gi|254781172|r 672 QLGAVVS-AILSRK--TDIIIVGDN----------PG----SKLEKAQQLGVKIMNEEQFLFL 717 (731)
Q Consensus 672 ~~Ggkv~-sSVSkk--T~~LI~ge~----------~g----SKl~KA~~LgI~Ii~e~ef~~l 717 (731)
..|.++. -.|.+. +.|+|.|+. -| -.+-+|++-| |-.|.++|.+-
T Consensus 1345 ~rGi~~lppDinkS~a~~F~i~~~~Ir~pl~AIkgvG~~aa~~IveaR~eg-~F~S~eDf~~R 1406 (1436)
T PRK00448 1345 ERGFKFQKVDLYKSDATEFIIEGDTLIPPFNAIPGLGENVAKSIVEAREEG-EFLSKEDLRKR 1406 (1436)
T ss_pred HCCCEECCCCCCCCCCCCEEECCCEEEECHHHHCCCHHHHHHHHHHHHHCC-CCCCHHHHHHH
T ss_conf 779845388402457854077299077674664461199999999998079-98998999987
No 308
>PRK08413 consensus
Probab=46.36 E-value=11 Score=16.60 Aligned_cols=21 Identities=10% Similarity=0.143 Sum_probs=13.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHH
Q ss_conf 999999999999999998433
Q gi|254781172|r 16 QARKELSSLEQEISYHDDCYY 36 (731)
Q Consensus 16 ~~~~~i~~L~~~i~~~~~~Yy 36 (731)
..++.+..|.+.+++++..|-
T Consensus 59 ~~~k~~k~lk~l~k~ad~vil 79 (733)
T PRK08413 59 DHSAIVKEIKELAKKADTIYI 79 (733)
T ss_pred CHHHHHHHHHHHHHCCCEEEE
T ss_conf 689999999999856998998
No 309
>PRK01710 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=46.31 E-value=18 Score=15.12 Aligned_cols=15 Identities=7% Similarity=0.020 Sum_probs=5.7
Q ss_pred CCEEECHHHHHHHHH
Q ss_conf 991737999999998
Q gi|254781172|r 705 GVKIMNEEQFLFLLQ 719 (731)
Q Consensus 705 gI~Ii~e~ef~~ll~ 719 (731)
.+++...+.+.+.+.
T Consensus 403 ~~~~~~~~~l~~Av~ 417 (458)
T PRK01710 403 KIPIVIVNSLEEAVK 417 (458)
T ss_pred CCCEEHHHHHHHHHH
T ss_conf 865233735999999
No 310
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=46.30 E-value=8.6 Score=17.58 Aligned_cols=21 Identities=14% Similarity=0.524 Sum_probs=15.6
Q ss_pred CCCEEEECCCCCCCCCCCCCC
Q ss_conf 730477704326577501033
Q gi|254781172|r 424 DAQPFSFPSFCPICQSRVVRD 444 (731)
Q Consensus 424 ~~~~~~~P~~CP~Cgs~l~~~ 444 (731)
+-..+.+-+.||.||++++..
T Consensus 10 ~Cg~YTL~~~CP~CG~~t~~~ 30 (54)
T PRK13130 10 KCGRYTLKETCPECGGKTKNP 30 (54)
T ss_pred CCCCEECCCCCCCCCCCCCCC
T ss_conf 356430325286688726767
No 311
>TIGR00588 ogg 8-oxoguanine DNA-glycosylase (ogg); InterPro: IPR004577 All proteins in this family for which functions are known are 8-oxo-guanaine DNA glycosylases that function in base excision repair. The enzyme incises DNA at 8-oxoG residues, and excises 7,8-dihydro-8-oxoguanine from damaged DNA. It has beta-lyase activity that nicks DNA 3' to the lesion.; GO: 0008534 oxidized purine base lesion DNA N-glycosylase activity, 0006281 DNA repair, 0005634 nucleus.
Probab=45.96 E-value=11 Score=16.71 Aligned_cols=91 Identities=22% Similarity=0.300 Sum_probs=46.7
Q ss_pred HCCCCCCCCCCCCCHHHHHHHHHHHHH--HHHHHHHHHHCCH----HHHHHHHHHHHHHHCCCH-----HHHHHHHHHHH
Q ss_conf 000100013421001456899998752--2346667763010----111168999999882998-----99999789776
Q gi|254781172|r 520 STTKIENILGFGDVSVTNLYDSINKRR--NISLERFIFSLGI----RHVGAEIARSLAKYYLSY-----QNFAQEINNII 588 (731)
Q Consensus 520 ~~~~l~~l~GfgeKsa~nL~~sIe~sK--~~~L~r~L~ALGI----~~vG~~~Ak~La~~f~si-----~~l~~~~~~~~ 588 (731)
++..+..|-|..|-|-+.| .+.|..- +-++.. |-.||+ |+|-+ +||.|++.-... ...++.+.. .
T Consensus 191 ~FP~~~~LtgvaeGsledl-~~~E~nlPsdfsfn~-LR~lG~GYRA~Yi~~-tar~l~ee~~~~nitsdta~LQ~ic~-~ 266 (379)
T TIGR00588 191 GFPSLHALTGVAEGSLEDL-PEAEANLPSDFSFNH-LRKLGLGYRARYIRE-TARALLEEQGGRNITSDTAWLQQICK-D 266 (379)
T ss_pred CCCCHHHHHHHHHHHHHHH-HHHHHHCCCCCCHHH-HHHCCCCCCCHHHHH-HHHHHHHHCCCCCCHHHHHHHHHHCC-C
T ss_conf 7987566521210016679-998751564346265-752488754068999-99998841266420023579998606-6
Q ss_pred HCCCCCHHHHHCCCCCCHHHHHHHHH
Q ss_conf 12511778761388867899999999
Q gi|254781172|r 589 AHNNDDWLSLIRVPLVGDIIAQAIVE 614 (731)
Q Consensus 589 ~~~~~~~e~L~~I~GiG~~~A~si~~ 614 (731)
+.-++..+.|+..+|+|+|+|+.|.=
T Consensus 267 ~~Yedar~~L~~l~GVG~KVADCicL 292 (379)
T TIGR00588 267 ADYEDAREALLELPGVGPKVADCICL 292 (379)
T ss_pred CCHHHHHHHHHCCCCCCCHHHHHHHH
T ss_conf 88678999972169997048888886
No 312
>PRK08324 short chain dehydrogenase; Validated
Probab=45.83 E-value=18 Score=15.06 Aligned_cols=56 Identities=20% Similarity=0.224 Sum_probs=35.3
Q ss_pred CCCCHHHHHHHHHHHHHHHHHCCHHHCCCCCCCCCCCCC----CCCCCCCCEEECCCCCCCHHHCCCHHHHH
Q ss_conf 820878999999999999897720311589999620036----43235775045166425702159999999
Q gi|254781172|r 41 PIILDSEYDALKRRCDAIAHAFPDLARSEDPNGPLNKIG----GEMNLSLFKVTHSIPTLSLEKIWNIEDLR 108 (731)
Q Consensus 41 p~isD~eYD~L~~~L~~le~~~p~~~~~~~p~spt~~Vg----~~~~~~~~kv~H~~pMlSL~k~~~~~el~ 108 (731)
+.+|| |.|+..|+.. ..+|++|.-.|- +-....|--..|+-+.++|.|.-+-+++.
T Consensus 90 ~~~sd---~~Mv~~~~~~---------l~~~~~p~pSvEtlLHA~lP~k~VDHtHadailal~n~~~g~~~~ 149 (676)
T PRK08324 90 GVLSD---DEMVNYLRHC---------LFDPNAPAPSIETLLHAFLPFKHVDHTHPDAIIAIANQPDGEELT 149 (676)
T ss_pred CCCCH---HHHHHHHHHH---------HCCCCCCCCCHHHHHHHHCCCCCCCCCCCHHHHHHHCCCCHHHHH
T ss_conf 87888---9999999985---------079999998577887860671002446852999976599759999
No 313
>TIGR01523 ATPase-IID_K-Na potassium/sodium efflux P-type ATPase, fungal-type; InterPro: IPR006414 Initially described as a calcium efflux ATPase , more recent work has shown that the Schizosaccharomyces pombe CTA3 gene is in fact a potassium ion efflux pump . These sequences form the clade which represents the fungal P-type ATPases which are responsible for potassium and sodium efflux. The degree to which these pumps show preference for sodium or potassium varies. This group of ATPases has been classified by phylogentic analysis as type IID . ; GO: 0015662 ATPase activity coupled to transmembrane movement of ions phosphorylative mechanism, 0006812 cation transport, 0016021 integral to membrane.
Probab=45.77 E-value=12 Score=16.48 Aligned_cols=40 Identities=28% Similarity=0.337 Sum_probs=30.0
Q ss_pred CCCCCCCCCCCCEEEECCCCCEEEEEEEEEEEEECCCCEEEE
Q ss_conf 115876568663123114562158998788994035622589
Q gi|254781172|r 313 KQLGERARSPRWMISHKFAEKQASTRLLDIDIQIGRTGILTP 354 (731)
Q Consensus 313 ~~lG~ts~~PrwaiA~Kf~~e~~~T~v~~I~wqvgRtG~itP 354 (731)
=.+|...=.-|-.|-=|..+-||.--|.||==. |||.||-
T Consensus 329 M~~G~~~M~~R~VIVRKL~~LEALG~V~DICSD--KTGT~TQ 368 (1001)
T TIGR01523 329 MAVGAKVMVKRRVIVRKLDALEALGAVTDICSD--KTGTLTQ 368 (1001)
T ss_pred HHHCHHHHCCCCEEEEEHHHHHHHCCCCCCCCC--CCCCCCC
T ss_conf 872224322562157502555530475431358--7665333
No 314
>TIGR02194 GlrX_NrdH Glutaredoxin-like protein NrdH; InterPro: IPR011909 Glutaredoxins , , , also known as thioltransferases (disulphide reductases, are small proteins of approximately one hundred amino-acid residues which utilise glutathione and NADPH as cofactors. Oxidized glutathione is regenerated by glutathione reductase. Together these components compose the glutathione system . Glutaredoxin functions as an electron carrier in the glutathione-dependent synthesis of deoxyribonucleotides by the enzyme ribonucleotide reductase. Like thioredoxin, which functions in a similar way, glutaredoxin possesses an active centre disulphide bond . It exists in either a reduced or an oxidized form where the two cysteine residues are linked in an intramolecular disulphide bond. Glutaredoxin has been sequenced in a variety of species. On the basis of extensive sequence similarity, it has been proposed that Vaccinia virus protein O2L is most probably a glutaredoxin. Finally, it must be noted that Bacteriophage T4 thioredoxin seems also to be evolutionary related. In position 5 of the pattern T4 thioredoxin has Val instead of Pro. NrdH-redoxin is a representative of a class of small redox proteins that contain a conserved CXXC motif and are characterised by a glutaredoxin-like amino acid sequence and thioredoxin-like activity profile. Unlike other the glutaredoxins to which it is most closely related, NrdH aparrently does not interact with glutathione/glutathione reductase, but rather with thioredoxin reductase to catalyze the reduction of ribonucleotide reductase .; GO: 0006118 electron transport, 0045454 cell redox homeostasis.
Probab=45.76 E-value=13 Score=16.09 Aligned_cols=30 Identities=17% Similarity=0.118 Sum_probs=21.1
Q ss_pred EEEEECCCCCCCCCCCHHHHHHHHHCCCCCCCCEE
Q ss_conf 66410245433210000368999975996654148
Q gi|254781172|r 239 FVHGLGKTSEIFAKGQYEMLQKMRCLGFPVNNGVR 273 (731)
Q Consensus 239 ~ay~~~~~~~~~~~~~~e~l~~L~~~GF~v~~~~~ 273 (731)
++|+.++ +..|.|.+++|+++||.-.|-..
T Consensus 24 i~Fe~in-----id~~pea~d~vk~lGF~~~PVi~ 53 (72)
T TIGR02194 24 IAFEEIN-----IDEQPEAVDYVKALGFRQVPVIV 53 (72)
T ss_pred CCEEEEE-----CCCCHHHHHHHHHCCCEECCEEE
T ss_conf 9615763-----58884378999874863076267
No 315
>pfam04606 Ogr_Delta Ogr/Delta-like zinc finger. 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. This family also includes zinc fingers in recombinase proteins.
Probab=45.56 E-value=7.8 Score=17.91 Aligned_cols=37 Identities=22% Similarity=0.450 Sum_probs=18.8
Q ss_pred CCCCCCCCCCCCCCCCCCCCC--EEECCCCCCCCHHHHHH
Q ss_conf 326577501033786544521--01003543441144665
Q gi|254781172|r 433 FCPICQSRVVRDLNPKTGKLV--AAHRCTGGLACSAQQLE 470 (731)
Q Consensus 433 ~CP~Cgs~l~~~~~~~~~~~~--~~~rC~n~~~Cpaq~~~ 470 (731)
.||.||+.....-...-.... ...-|.|. .|-...+.
T Consensus 1 ~CP~Cg~~a~irts~~~s~~~~e~Y~qC~N~-~Cg~tfv~ 39 (47)
T pfam04606 1 RCPHCGAKARIRTSRRLSALVRELYYQCTNP-ECGHTFVT 39 (47)
T ss_pred CCCCCCCCEEEEEHHHCCHHHHEEEEECCCC-CCCCEEEE
T ss_conf 9598898389968356297553138880896-45968999
No 316
>PRK01216 DNA polymerase IV; Validated
Probab=45.53 E-value=11 Score=16.62 Aligned_cols=49 Identities=20% Similarity=0.311 Sum_probs=31.7
Q ss_pred CCCCHHHHHHHHHHHHHCCCCCCEEEEEHHHHCCHHHHHHHHCCCCCCCCCCCCCHHHHHHH
Q ss_conf 23103541035555653057654045410110106777531000100013421001456899
Q gi|254781172|r 479 DAFNIEGLGKQQLDFFFKSEDPAFSIRIPADIFTLQRRQQTSTTKIENILGFGDVSVTNLYD 540 (731)
Q Consensus 479 ~aldI~GLG~k~Ie~L~e~~~~~g~I~~~~DLy~L~~~~~~~~~~l~~l~GfgeKsa~nL~~ 540 (731)
..=+|-|+|+++-++|-+.| |.++.||+...... |.. -||++.+.-+++
T Consensus 179 pv~~i~GIG~~t~~~L~~~G-----I~ti~dL~~~~~~~------L~~--~fG~~~~~~l~~ 227 (351)
T PRK01216 179 DIDDVPGIGKVLSERLNELG-----INKLRDILSKSFNK------LKS--IIGEAKANYLYS 227 (351)
T ss_pred CCCEECCCCHHHHHHHHHCC-----CCCHHHHHHCCHHH------HHH--HHCHHHHHHHHH
T ss_conf 94385485799999999859-----96899975299999------999--977799999999
No 317
>TIGR00596 rad1 DNA repair protein (rad1); InterPro: IPR006167 All proteins in this family, for which functions are known, are components in a multiprotein endonuclease complex, usually made up of Rad1 and Rad10 homologues. This complex is used primarily for nucleotide excision repair but also for some aspects of recombinational repair in some species. Most Archaeal species also have homologues of these genes, but the function of the Archaeal proteins is not known, so are not included in this family.; GO: 0003676 nucleic acid binding, 0004519 endonuclease activity, 0006281 DNA repair.
Probab=45.35 E-value=18 Score=15.01 Aligned_cols=50 Identities=22% Similarity=0.274 Sum_probs=31.3
Q ss_pred CCHHHHHHHHHHHHHHH-CCCHHHHHHHHHHHHHCCCCCHHHHHCCCCCC-HHHHHHHHHHHCC
Q ss_conf 01011116899999988-29989999978977612511778761388867-8999999999669
Q gi|254781172|r 557 LGIRHVGAEIARSLAKY-YLSYQNFAQEINNIIAHNNDDWLSLIRVPLVG-DIIAQAIVEFYQN 618 (731)
Q Consensus 557 LGI~~vG~~~Ak~La~~-f~si~~l~~~~~~~~~~~~~~~e~L~~I~GiG-~~~A~si~~ff~~ 618 (731)
|++|||-.+..+-|..+ .+++.++... +..+|.++ || +..|..|++||+.
T Consensus 884 l~~PGV~~kN~rnl~~~G~k~~~el~~~----------S~~El~eL--~g~~e~a~~lY~Fl~~ 935 (939)
T TIGR00596 884 LKLPGVTKKNIRNLLKKGVKSIRELAKL----------SQEELEEL--IGDEEAAKRLYDFLRK 935 (939)
T ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHH----------HHHHHHHH--CCCHHHHHHHHHHHHH
T ss_conf 5789856023455554315559999998----------79999975--0797576689999876
No 318
>cd00513 Ribosomal_L32_L32e Ribosomal_L32_L32e: L32 is a protein from the large subunit that contains a surface-exposed globular domain and a finger-like projection that extends into the RNA core to stabilize the tertiary structure. L32 does not appear to play a role in forming the A (aminacyl), P (peptidyl) or E (exit) sites of the ribosome, but does interact with 23S rRNA, which has a "kink-turn" secondary structure motif. L32 is overexpressed in human prostate cancer and has been identified as a stably expressed housekeeping gene in macrophages of human chronic obstructive pulmonary disease (COPD) patients. In Schizosaccharomyces pombe, L32 has also been suggested to play a role as a transcriptional regulator in the nucleus. Found in archaea and eukaryotes, this protein is known as L32 in eukaryotes and L32e in archaea.
Probab=45.25 E-value=3.7 Score=20.43 Aligned_cols=36 Identities=14% Similarity=0.065 Sum_probs=18.4
Q ss_pred CCCCHHHHH-HHHHHHHHCCCCCCEEEEEHHHHCCHH
Q ss_conf 231035410-355556530576540454101101067
Q gi|254781172|r 479 DAFNIEGLG-KQQLDFFFKSEDPAFSIRIPADIFTLQ 514 (731)
Q Consensus 479 ~aldI~GLG-~k~Ie~L~e~~~~~g~I~~~~DLy~L~ 514 (731)
..|---|.| ++.+.-|.-.|+...+|.++.||-.|.
T Consensus 36 ~~~p~iGYgs~k~~Rgl~PsG~~~vlV~n~~dLe~l~ 72 (107)
T cd00513 36 PAMPKIGYGSPKKTRGLHPSGFKKVLVHNVKELEVLD 72 (107)
T ss_pred CCCCCCCCCCCHHHCCCCCCCCEEEEECCHHHHHHHC
T ss_conf 6787667787776657797888888866988988860
No 319
>COG0419 SbcC ATPase involved in DNA repair [DNA replication, recombination, and repair]
Probab=45.17 E-value=8.3 Score=17.67 Aligned_cols=14 Identities=21% Similarity=0.755 Sum_probs=9.7
Q ss_pred CCCCCCCCCCCCCC
Q ss_conf 04326577501033
Q gi|254781172|r 431 PSFCPICQSRVVRD 444 (731)
Q Consensus 431 P~~CP~Cgs~l~~~ 444 (731)
-..||+||.++-..
T Consensus 457 ~~~CPvCg~~l~~~ 470 (908)
T COG0419 457 GEKCPVCGQELPEE 470 (908)
T ss_pred CCCCCCCCCCCCCH
T ss_conf 99999888978607
No 320
>COG1312 UxuA D-mannonate dehydratase [Carbohydrate transport and metabolism]
Probab=45.08 E-value=14 Score=15.86 Aligned_cols=82 Identities=17% Similarity=0.242 Sum_probs=44.2
Q ss_pred ECCCCCCCHHHCCCHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCEEEEEEEEECCEEEEEEECCCCHHHHHHHHHHHH
Q ss_conf 51664257021599999999999999861246777611999941581899999859989988865986556669997753
Q gi|254781172|r 90 THSIPTLSLEKIWNIEDLRKFITRIYRFWQKKDDNSIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRA 169 (731)
Q Consensus 90 ~H~~pMlSL~k~~~~~el~~w~~~~~~~~~~~~~~~~~~~vepKiDG~sisl~Y~~G~L~~a~TRGdG~~GeDVT~n~~~ 169 (731)
-|..|- +.++..+++.+--+.+... |+..+.+ |.--..+.+-+|.+...+.|-.-..+
T Consensus 31 Lh~iP~---g~~W~~~~I~~~k~~ie~~------------------Gl~~~vv-ESvPvhedIK~g~~~rd~~Ieny~~t 88 (362)
T COG1312 31 LHHIPA---GEVWPVEEILKRKEEIESA------------------GLTWSVV-ESVPVHEDIKLGTPTRDRYIENYKQT 88 (362)
T ss_pred CCCCCC---CCCCCHHHHHHHHHHHHHC------------------CCEEEEE-CCCCHHHHHHHCCCCHHHHHHHHHHH
T ss_conf 777889---8857689999999999973------------------9669863-57788889871698478999999999
Q ss_pred HCCCCCCCCCCCCCEEEEEEEEEEECHHHHH
Q ss_conf 1024322335445504899999985202123
Q gi|254781172|r 170 IPTIPRVLSLNIPEIIEVRGEVYISKNDFLA 200 (731)
Q Consensus 170 i~~iP~~l~~~~~~~ieiRGEv~m~~~~F~~ 200 (731)
|+++-. .++ .+=.==||+--+|-+
T Consensus 89 irnLa~-~GI------~vvCYNfMpv~dWtR 112 (362)
T COG1312 89 IRNLAR-AGI------KVVCYNFMPVFDWTR 112 (362)
T ss_pred HHHHHH-CCC------CEEEECCCCCCCCCC
T ss_conf 999996-698------779851552137312
No 321
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE; 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. .
Probab=45.04 E-value=7.8 Score=17.90 Aligned_cols=80 Identities=23% Similarity=0.275 Sum_probs=36.3
Q ss_pred HHHHCCCCCCCCCCCCCEEEEEEEEEEECHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCHHHHHCCCEEEEEEECCC
Q ss_conf 75310243223354455048999999852021234556431485433423456777752345555301110566410245
Q gi|254781172|r 167 IRAIPTIPRVLSLNIPEIIEVRGEVYISKNDFLALNDEMIAVGRKPYANPRNAASGILRRLNPTDITRYLNFFVHGLGKT 246 (731)
Q Consensus 167 ~~~i~~iP~~l~~~~~~~ieiRGEv~m~~~~F~~lN~~~~~~g~~~f~NpRN~aaG~lr~~d~~~~~r~L~f~ay~~~~~ 246 (731)
.+|-..||-.|..+....+-=||| .|+.| +.| .+...==|++||.-|....-. |.....
T Consensus 15 ~~tad~iPp~L~p~l~~LfnrRae------Rl~~L-----Aeg-~plgdYLrf~Agi~r~Q~~ll---------~~~P~~ 73 (312)
T TIGR01562 15 KRTADKIPPLLKPRLKDLFNRRAE------RLEEL-----AEG-SPLGDYLRFVAGIARIQEELL---------SDLPAE 73 (312)
T ss_pred CCCCCCCCCCCCHHHHHHHHHHHH------HHHHH-----HCC-CCCHHHHHHHHHHHHHHHHHH---------HCCCCC
T ss_conf 763125886467126778878999------99998-----568-981058999999999999996---------347898
Q ss_pred CCCCCCCCHHHHHHHHHCCCCCCCC
Q ss_conf 4332100003689999759966541
Q gi|254781172|r 247 SEIFAKGQYEMLQKMRCLGFPVNNG 271 (731)
Q Consensus 247 ~~~~~~~~~e~l~~L~~~GF~v~~~ 271 (731)
. .-.-+.++.-+..|-|=..+
T Consensus 74 ~----pl~~~R~~~ara~g~PPld~ 94 (312)
T TIGR01562 74 E----PLDADRVKKARANGMPPLDI 94 (312)
T ss_pred C----CCCHHHHHHHHHCCCCCHHH
T ss_conf 8----88979999998618885237
No 322
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=44.90 E-value=11 Score=16.65 Aligned_cols=29 Identities=21% Similarity=0.639 Sum_probs=17.8
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCHHH
Q ss_conf 432657750103378654452101003543441144
Q gi|254781172|r 432 SFCPICQSRVVRDLNPKTGKLVAAHRCTGGLACSAQ 467 (731)
Q Consensus 432 ~~CP~Cgs~l~~~~~~~~~~~~~~~rC~n~~~Cpaq 467 (731)
.+||.||+-+....+... ..+.|. +|+..
T Consensus 1 kFCp~C~n~l~p~~~~~~----~~~~C~---~C~y~ 29 (52)
T smart00661 1 KFCPKCGNMLIPKEGKEK----RRFVCR---KCGYE 29 (52)
T ss_pred CCCCCCCCEEEEEECCCC----EEEECC---CCCCC
T ss_conf 978652888768536995----389748---99984
No 323
>pfam05559 DUF763 Protein of unknown function (DUF763). This family consists of several uncharacterized bacterial and archaeal proteins of unknown function.
Probab=44.67 E-value=19 Score=14.94 Aligned_cols=32 Identities=19% Similarity=0.241 Sum_probs=22.7
Q ss_pred HHHHHHHHHCCCCCHHHHHCCCCCCHHHHHHH
Q ss_conf 99789776125117787613888678999999
Q gi|254781172|r 581 AQEINNIIAHNNDDWLSLIRVPLVGDIIAQAI 612 (731)
Q Consensus 581 ~~~~~~~~~~~~~~~e~L~~I~GiG~~~A~si 612 (731)
........+..-.++++|..++|+|+.+..++
T Consensus 254 ~~~L~~a~e~~p~dfeeLLl~~GvGp~TlRAL 285 (319)
T pfam05559 254 WKVLRAAYERNPEDFEELLLLKGVGPSTLRAL 285 (319)
T ss_pred HHHHHHHHHCCCCCHHHHHHCCCCCHHHHHHH
T ss_conf 99999876268016999971479888999999
No 324
>PRK13809 orotate phosphoribosyltransferase; Provisional
Probab=44.61 E-value=19 Score=14.93 Aligned_cols=68 Identities=12% Similarity=0.096 Sum_probs=41.8
Q ss_pred CCCEEEE------ECCCCCCCHHHHHHHHHHCCCEEEEEEECCEEEEEECCCCCCHHHHHHHCCCEEECHHHHHHHHHHH
Q ss_conf 6866999------7258899878999999982984998111632179977888863798997499173799999999882
Q gi|254781172|r 648 ENKKLVF------TGTLQKIQRHKAQEYVTQLGAVVSAILSRKTDIIIVGDNPGSKLEKAQQLGVKIMNEEQFLFLLQQY 721 (731)
Q Consensus 648 ~gk~vV~------TGtl~~~~R~e~~~~ie~~Ggkv~sSVSkkT~~LI~ge~~gSKl~KA~~LgI~Ii~e~ef~~ll~~~ 721 (731)
.|+++|+ || -|=-++.+.+++.|+.|...+. ++--+..| .+.-++.||++.+--.+.+||+-.
T Consensus 117 ~G~kVvvIEDViTTG----gSil~ai~~lr~~G~~V~~v~v-----ivDReegg--~e~l~~~Gi~l~sl~t~~~ll~~l 185 (206)
T PRK13809 117 PGQTCLVINDMVSSG----KSIIETAVALEENGLVVREALV-----FLDRRKEA--CQPLGPQGIKVSSVFTVPTLIKAL 185 (206)
T ss_pred CCCEEEEEEEEECCC----HHHHHHHHHHHHCCCEEEEEEE-----EEECCCCH--HHHHHHCCCCEEEECCHHHHHHHH
T ss_conf 998899997334468----0099999999987996999999-----99265167--999997799189967799999999
Q ss_pred CCCCC
Q ss_conf 86568
Q gi|254781172|r 722 NTTLR 726 (731)
Q Consensus 722 ~~~~~ 726 (731)
-.+..
T Consensus 186 ~~~g~ 190 (206)
T PRK13809 186 IAYGK 190 (206)
T ss_pred HHCCC
T ss_conf 98499
No 325
>PRK12859 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional
Probab=44.58 E-value=19 Score=14.93 Aligned_cols=14 Identities=14% Similarity=0.110 Sum_probs=10.2
Q ss_pred CCCCCCCEEEEECC
Q ss_conf 88216866999725
Q gi|254781172|r 644 SSEIENKKLVFTGT 657 (731)
Q Consensus 644 ~~~l~gk~vV~TGt 657 (731)
++..+|.++.+.|-
T Consensus 241 a~~iTGq~i~VDGG 254 (257)
T PRK12859 241 AEWITGQVIHSEGG 254 (257)
T ss_pred HCCEECCEEEECCC
T ss_conf 25861875896879
No 326
>TIGR00375 TIGR00375 conserved hypothetical protein TIGR00375; InterPro: IPR005287 This family of conserved hypothetical proteins has no known function. .
Probab=44.41 E-value=19 Score=14.91 Aligned_cols=118 Identities=21% Similarity=0.328 Sum_probs=60.4
Q ss_pred ECCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHH-HHHHHHCCCCCCEEEEEHH
Q ss_conf 704326577501033786544521010035434411446655332130123103541035-5556530576540454101
Q gi|254781172|r 430 FPSFCPICQSRVVRDLNPKTGKLVAAHRCTGGLACSAQQLERLKHFVSRDAFNIEGLGKQ-QLDFFFKSEDPAFSIRIPA 508 (731)
Q Consensus 430 ~P~~CP~Cgs~l~~~~~~~~~~~~~~~rC~n~~~Cpaq~~~~i~hF~SK~aldI~GLG~k-~Ie~L~e~~~~~g~I~~~~ 508 (731)
.-|.|-.|+....-+...+ .+++|+ .|.+++.+-+.+= |.-|+.. -++.= .-.|.
T Consensus 246 h~TAC~~C~~~~~~E~a~~-----~~~~Cp---kCgg~ikKGV~~R-------~~ELSd~d~~e~p---------~~RPp 301 (384)
T TIGR00375 246 HLTACEKCYERYKSEDAKK-----ADAKCP---KCGGKIKKGVSDR-------VRELSDQDKLEHP---------KFRPP 301 (384)
T ss_pred HHHHHHHCCCCCCCCCHHH-----HHCCCC---CCCCEEECCHHHH-------HHHCCCCCCCCCC---------CCCCC
T ss_conf 7778875476466400255-----524697---9786055373567-------7633677867887---------56348
Q ss_pred HHCCHHHHHHHHCCCCCCCCCCCCCH--HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHCCCHHHHHHHHHH
Q ss_conf 10106777531000100013421001--4568999987522346667763010111168999999882998999997897
Q gi|254781172|r 509 DIFTLQRRQQTSTTKIENILGFGDVS--VTNLYDSINKRRNISLERFIFSLGIRHVGAEIARSLAKYYLSYQNFAQEINN 586 (731)
Q Consensus 509 DLy~L~~~~~~~~~~l~~l~GfgeKs--a~nL~~sIe~sK~~~L~r~L~ALGI~~vG~~~Ak~La~~f~si~~l~~~~~~ 586 (731)
-|+| + =|+.+.|++-++ .+|.+++| +++|+-++| ...+= |
T Consensus 302 -Yvhl-----i---PLae~ig~~~~kG~~TK~VQ~~-------wekl~k~fG-----tEi~V-L---------------- 343 (384)
T TIGR00375 302 -YVHL-----I---PLAEVIGLKIDKGVFTKAVQSL-------WEKLVKKFG-----TEIEV-L---------------- 343 (384)
T ss_pred -CEEE-----C---CCEEECCCCCCCCEEEHHHHHH-------HHHHHHHHC-----CHHHH-H----------------
T ss_conf -5020-----5---6300035345873130346778-------999864104-----15667-6----------------
Q ss_pred HHHCCCCCHHHHHCCCCCCHHHHHHHHHH
Q ss_conf 76125117787613888678999999999
Q gi|254781172|r 587 IIAHNNDDWLSLIRVPLVGDIIAQAIVEF 615 (731)
Q Consensus 587 ~~~~~~~~~e~L~~I~GiG~~~A~si~~f 615 (731)
-++..|+|..|.- |++|..|..|
T Consensus 344 ----~~A~~edla~~~p--PkvA~~i~~f 366 (384)
T TIGR00375 344 ----LEAALEDLAKVDP--PKVAALIEKF 366 (384)
T ss_pred ----HCCCHHHHHCCCC--CHHHHHHHHH
T ss_conf ----4278458733588--3588999986
No 327
>TIGR02339 thermosome_arch thermosome, various subunits, archaeal; InterPro: IPR012714 Thermosome is the name given to the archaeal rather than eukaryotic form of the group II chaperonin (counterpart to the group I chaperonin, GroEL/GroES, in bacteria), a toroidal, ATP-dependent molecular chaperone that assists in the folding or refolding of nascent or denatured proteins. Various homologous subunits, one to five per archaeal genome, may be designated alpha, beta, etc., but phylogenetic analysis does not show distinct alpha subunit and beta subunit lineages traceable to ancient paralogs.; GO: 0005524 ATP binding, 0051082 unfolded protein binding, 0006457 protein folding.
Probab=44.37 E-value=19 Score=14.90 Aligned_cols=22 Identities=9% Similarity=0.134 Sum_probs=12.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 4568999987522346667763
Q gi|254781172|r 535 VTNLYDSINKRRNISLERFIFS 556 (731)
Q Consensus 535 a~nL~~sIe~sK~~~L~r~L~A 556 (731)
.+.++++.|+|-+=.|+-+-.+
T Consensus 375 tehVVDE~ERsl~DAL~VV~~~ 396 (522)
T TIGR02339 375 TEHVVDELERSLQDALHVVASA 396 (522)
T ss_pred CCEEHHHHHHHHHHHHHHHHHH
T ss_conf 7501021346688899999998
No 328
>pfam01396 zf-C4_Topoisom Topoisomerase DNA binding C4 zinc finger.
Probab=44.33 E-value=13 Score=16.16 Aligned_cols=30 Identities=20% Similarity=0.388 Sum_probs=20.6
Q ss_pred CCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCHH
Q ss_conf 3265775010337865445210100354344114
Q gi|254781172|r 433 FCPICQSRVVRDLNPKTGKLVAAHRCTGGLACSA 466 (731)
Q Consensus 433 ~CP~Cgs~l~~~~~~~~~~~~~~~rC~n~~~Cpa 466 (731)
.||.||++++..... .+..+=|+|=-+|..
T Consensus 3 kCP~Cg~~l~~r~~r----~G~F~gCs~yP~C~~ 32 (39)
T pfam01396 3 KCPKCGGDLVLKRGK----FGKFVGCSNYPECKF 32 (39)
T ss_pred CCCCCCCEEEEEECC----CCEEEECCCCCCCCC
T ss_conf 377899981688368----770872899989888
No 329
>PRK07062 short chain dehydrogenase; Provisional
Probab=44.27 E-value=19 Score=14.89 Aligned_cols=15 Identities=20% Similarity=0.248 Sum_probs=10.8
Q ss_pred CCCCCCCEEEEECCC
Q ss_conf 882168669997258
Q gi|254781172|r 644 SSEIENKKLVFTGTL 658 (731)
Q Consensus 644 ~~~l~gk~vV~TGtl 658 (731)
++..+|.++++.|-+
T Consensus 247 s~~iTG~~i~VDGG~ 261 (265)
T PRK07062 247 SSYTTGSHIDVSGGF 261 (265)
T ss_pred HCCCCCCEEEECCCC
T ss_conf 257358427989780
No 330
>PRK05867 short chain dehydrogenase; Provisional
Probab=44.22 E-value=19 Score=14.89 Aligned_cols=14 Identities=29% Similarity=0.425 Sum_probs=7.9
Q ss_pred CCCCCCCEEEEECC
Q ss_conf 88216866999725
Q gi|254781172|r 644 SSEIENKKLVFTGT 657 (731)
Q Consensus 644 ~~~l~gk~vV~TGt 657 (731)
++..+|.++++.|-
T Consensus 236 s~~iTG~~i~VDGG 249 (253)
T PRK05867 236 SSYMTGSDIVIDGG 249 (253)
T ss_pred HCCCCCCEEEECCC
T ss_conf 14854871885889
No 331
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=43.99 E-value=8.7 Score=17.52 Aligned_cols=24 Identities=21% Similarity=0.392 Sum_probs=13.7
Q ss_pred CCCCCCCCCCCCCCCCCCCCCEEECCCC
Q ss_conf 3265775010337865445210100354
Q gi|254781172|r 433 FCPICQSRVVRDLNPKTGKLVAAHRCTG 460 (731)
Q Consensus 433 ~CP~Cgs~l~~~~~~~~~~~~~~~rC~n 460 (731)
.||.||+++++..-.. -..++|++
T Consensus 257 ~C~~Cg~~I~~~~~~g----R~t~~CP~ 280 (283)
T PRK13945 257 PCRKCGTPIERIKLAG----RSTHWCPN 280 (283)
T ss_pred CCCCCCCEEEEEEECC----CCCEECCC
T ss_conf 4899998888999999----75788921
No 332
>PRK06988 putative formyltransferase; Provisional
Probab=43.97 E-value=19 Score=14.86 Aligned_cols=15 Identities=20% Similarity=0.352 Sum_probs=7.0
Q ss_pred CCCEEECHHHHHHHH
Q ss_conf 499173799999999
Q gi|254781172|r 704 LGVKIMNEEQFLFLL 718 (731)
Q Consensus 704 LgI~Ii~e~ef~~ll 718 (731)
=|=+.|+-.+|.+=|
T Consensus 293 ~GKk~m~a~dFa~G~ 307 (313)
T PRK06988 293 GGETVVTPAQFAQFI 307 (313)
T ss_pred CCCCEECHHHHHHHC
T ss_conf 989751899996122
No 333
>PRK07677 short chain dehydrogenase; Provisional
Probab=43.96 E-value=19 Score=14.86 Aligned_cols=14 Identities=14% Similarity=0.287 Sum_probs=9.2
Q ss_pred CCCCCCCEEEEECC
Q ss_conf 88216866999725
Q gi|254781172|r 644 SSEIENKKLVFTGT 657 (731)
Q Consensus 644 ~~~l~gk~vV~TGt 657 (731)
.+..+|.++++.|-
T Consensus 233 asyiTG~~i~VDGG 246 (254)
T PRK07677 233 AAYINGTCITMDGG 246 (254)
T ss_pred HCCCCCCEEEECCC
T ss_conf 24824872886899
No 334
>PRK06701 short chain dehydrogenase; Provisional
Probab=43.86 E-value=19 Score=14.85 Aligned_cols=15 Identities=27% Similarity=0.384 Sum_probs=8.6
Q ss_pred EECCCCHHHHHHHHH
Q ss_conf 865986556669997
Q gi|254781172|r 152 ALRGDGHSGEDVSAC 166 (731)
Q Consensus 152 ~TRGdG~~GeDVT~n 166 (731)
+|=|.+-+|.-+...
T Consensus 50 VTGgs~GIG~aiA~~ 64 (289)
T PRK06701 50 ITGGDSGIGRAVAVA 64 (289)
T ss_pred EECCCCHHHHHHHHH
T ss_conf 968257999999999
No 335
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=43.79 E-value=13 Score=16.26 Aligned_cols=10 Identities=40% Similarity=0.903 Sum_probs=8.3
Q ss_pred CCCCCCCCCC
Q ss_conf 3265775010
Q gi|254781172|r 433 FCPICQSRVV 442 (731)
Q Consensus 433 ~CP~Cgs~l~ 442 (731)
-||.||+.-+
T Consensus 3 pCPFCG~~~~ 12 (53)
T TIGR03655 3 PCPFCGGADV 12 (53)
T ss_pred CCCCCCCCHH
T ss_conf 8887897531
No 336
>PRK04358 hypothetical protein; Provisional
Probab=43.58 E-value=19 Score=14.82 Aligned_cols=55 Identities=22% Similarity=0.376 Sum_probs=36.3
Q ss_pred CCCCCCCHHHHH--HHHHHCCCEEEEEEECCEEEEEECCCCCCHHHHHHHCCCEEECHHHHHHHHHHHCCCC
Q ss_conf 258899878999--9999829849981116321799778888637989974991737999999998828656
Q gi|254781172|r 656 GTLQKIQRHKAQ--EYVTQLGAVVSAILSRKTDIIIVGDNPGSKLEKAQQLGVKIMNEEQFLFLLQQYNTTL 725 (731)
Q Consensus 656 Gtl~~~~R~e~~--~~ie~~Ggkv~sSVSkkT~~LI~ge~~gSKl~KA~~LgI~Ii~e~ef~~ll~~~~~~~ 725 (731)
|.|. |+.++. =+...++|.|+++ ..| =.+=|+++||+.++...|..+|.+|-...
T Consensus 163 GiLD--S~eD~DvlLLA~ELda~vVt~------------D~G-I~kWAe~lGlr~i~a~~F~~~Lee~l~~~ 219 (223)
T PRK04358 163 GILD--SAEDLDVLLLAKELDAAVVSA------------DEG-IRKWAEKLGLRFVDARKFPEMLEEYLRHS 219 (223)
T ss_pred CCCC--CHHHHHHHHHHHHHCCEEECC------------CHH-HHHHHHHHCCEEECHHHHHHHHHHHHHHC
T ss_conf 6656--521378999999838757706------------264-99999980978778888689999999846
No 337
>PRK03922 hypothetical protein; Provisional
Probab=43.31 E-value=8.8 Score=17.48 Aligned_cols=11 Identities=27% Similarity=0.688 Sum_probs=8.7
Q ss_pred CCCCCCCCCCC
Q ss_conf 43265775010
Q gi|254781172|r 432 SFCPICQSRVV 442 (731)
Q Consensus 432 ~~CP~Cgs~l~ 442 (731)
+.||+||.++.
T Consensus 50 ~~cP~Cge~~~ 60 (113)
T PRK03922 50 TSCPKCGEPFD 60 (113)
T ss_pred CCCCCCCCCCC
T ss_conf 21887778667
No 338
>pfam08442 ATP-grasp_2 ATP-grasp domain.
Probab=43.27 E-value=20 Score=14.78 Aligned_cols=43 Identities=16% Similarity=0.115 Sum_probs=30.1
Q ss_pred CHHHHHHHHHCCCCCCCCEEEEECCCCHHHHHHHHHHHHCCCCCCCCCEEEEE
Q ss_conf 00368999975996654148874032113455665531001123437637773
Q gi|254781172|r 254 QYEMLQKMRCLGFPVNNGVRQANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKV 306 (731)
Q Consensus 254 ~~e~l~~L~~~GF~v~~~~~~~~~~~~~~~~~~~~~~~r~~l~y~iDGiVikv 306 (731)
.|+..+.|++.|.+|++ ...+.+.+++.+..+++ ..+-+|+|.
T Consensus 4 EyqaK~ll~~~gIpvp~-g~~~~~~~ea~~~~~~l---------~~~~~VvKa 46 (202)
T pfam08442 4 EYQAKEILAKYGVPVPR-GEVAFSPEEAEEIAKKL---------GGKVYVVKA 46 (202)
T ss_pred HHHHHHHHHHCCCCCCC-EEEECCHHHHHHHHHHH---------CCCEEEEEE
T ss_conf 88999999985998999-15969999999999980---------998699987
No 339
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=43.25 E-value=13 Score=16.18 Aligned_cols=112 Identities=24% Similarity=0.398 Sum_probs=54.3
Q ss_pred EECCCEEEEECCCCHHHHHHHCCCCCCCCCCCCCCC---CCEEEEEECCCCHHHHHHHC-----CCCC--CCC----CCE
Q ss_conf 302640001014898999750234543222468440---76899983587025665410-----1235--787----304
Q gi|254781172|r 362 NIGGALITNATLHNEDYIKGLDASGKVMRGGRDIRV---GDRVLVKRAGEVIPKVVDII-----VNER--HPD----AQP 427 (731)
Q Consensus 362 ~l~G~~V~ratlhN~~~I~~l~~~~~~~~~~~~I~i---Gd~V~I~RaGdVIP~I~~Vi-----~~~r--~~~----~~~ 427 (731)
..+|..|.|.|+---+|.+...+-.. . ....|.| |++|++. |.+.+-- .+.+ .++ .++
T Consensus 199 nfdgkRirrttGIPk~FLk~ve~p~e-~-~~a~imit~EG~yVv~q------pdvqsWe~Yq~r~~a~~~~~Dqv~k~~~ 270 (427)
T COG5222 199 NFDGKRIRRTTGIPKDFLKPVEGPNE-P-SNAAIMITPEGGYVVAQ------PDVQSWEKYQQRTKAVAEIPDQVYKMQP 270 (427)
T ss_pred CCCCEEEECCCCCCHHHCCCCCCCCC-C-CCCCEEECCCCCEEEEC------CCHHHHHHHHHHHHHHHHCCHHHHCCCC
T ss_conf 76630530368897776354557786-5-41235873788837855------3267799999887766408303310488
Q ss_pred EEECCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCHHHHHHHHHH--H----HHCCCCCHHHHHHHH
Q ss_conf 77704326577501033786544521010035434411446655332--1----301231035410355
Q gi|254781172|r 428 FSFPSFCPICQSRVVRDLNPKTGKLVAAHRCTGGLACSAQQLERLKH--F----VSRDAFNIEGLGKQQ 490 (731)
Q Consensus 428 ~~~P~~CP~Cgs~l~~~~~~~~~~~~~~~rC~n~~~Cpaq~~~~i~h--F----~SK~aldI~GLG~k~ 490 (731)
-.+|-.||.|+.-+..- .. --||+..-|.+-+...|.. | |+|+-+=++||-+-+
T Consensus 271 ~~i~LkCplc~~Llrnp-~k--------T~cC~~~fc~eci~~al~dsDf~CpnC~rkdvlld~l~pD~ 330 (427)
T COG5222 271 PNISLKCPLCHCLLRNP-MK--------TPCCGHTFCDECIGTALLDSDFKCPNCSRKDVLLDGLTPDI 330 (427)
T ss_pred CCCCCCCCCHHHHHHCC-CC--------CCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCHHHCCCCCH
T ss_conf 88631375210365385-45--------76566257999875555412654777654120020258217
No 340
>TIGR01652 ATPase-Plipid phospholipid-translocating P-type ATPase, flippase; InterPro: IPR006539 These sequences represent the P-type ATPase responsible for transporting phospholipids from one leaflet of bilayer membranes to the other . These ATPases are found only in eukaryotes. ; GO: 0000287 magnesium ion binding, 0004012 phospholipid-translocating ATPase activity, 0005524 ATP binding, 0015914 phospholipid transport, 0016021 integral to membrane.
Probab=43.16 E-value=9.9 Score=17.09 Aligned_cols=39 Identities=26% Similarity=0.457 Sum_probs=29.3
Q ss_pred CHHCCCCCCCCCCCCCCEEEECCCCCEEEEEEEEEEEEECCCCEEEEEE-EEEEEEECCCEEE
Q ss_conf 1000111587656866312311456215899878899403562258999-9743330264000
Q gi|254781172|r 308 EFSLQKQLGERARSPRWMISHKFAEKQASTRLLDIDIQIGRTGILTPVA-RLEPVNIGGALIT 369 (731)
Q Consensus 308 ~~~~q~~lG~ts~~PrwaiA~Kf~~e~~~T~v~~I~wqvgRtG~itPva-~~ePV~l~G~~V~ 369 (731)
...+-+.||. |=|=|.+ |||-||=-. +|.-..|+|++..
T Consensus 468 tsnl~EeLGQ--------veYifSD---------------KTGTLT~N~MeFkkcsI~Gv~Yg 507 (1249)
T TIGR01652 468 TSNLNEELGQ--------VEYIFSD---------------KTGTLTQNIMEFKKCSIAGVSYG 507 (1249)
T ss_pred ECCCCCCCCC--------EEEEEEC---------------CCCCCCCCCCEEEEEEECCEEEC
T ss_conf 3788520361--------4068754---------------73465545301488876556411
No 341
>PRK06128 oxidoreductase; Provisional
Probab=43.15 E-value=20 Score=14.77 Aligned_cols=15 Identities=13% Similarity=0.153 Sum_probs=8.4
Q ss_pred EECCCCHHHHHHHHH
Q ss_conf 865986556669997
Q gi|254781172|r 152 ALRGDGHSGEDVSAC 166 (731)
Q Consensus 152 ~TRGdG~~GeDVT~n 166 (731)
+|=|+.-+|.-|...
T Consensus 60 VTGgssGIG~AiA~~ 74 (300)
T PRK06128 60 ITGADSGIGRATAIA 74 (300)
T ss_pred EECCCCHHHHHHHHH
T ss_conf 917366999999999
No 342
>cd00528 MoaC MoaC family. Members of this family are involved in molybdenum cofactor (Moco) biosynthesis, an essential cofactor of a diverse group of redox enzymes. MoaC, a small hexameric protein, converts, together with MoaA, a guanosine derivative to the precursor Z by inserting the carbon-8 of the purine between the 2' and 3' ribose carbon atoms, which is the first of three phases of Moco biosynthesis.
Probab=43.13 E-value=20 Score=14.77 Aligned_cols=53 Identities=21% Similarity=0.364 Sum_probs=34.9
Q ss_pred EEEEEEEEECCCCEEEEEEEEEEEEECCCEEEEECCCCHHHHHHHCCCCCCCCCCCCCCCCCEEEEEECCC
Q ss_conf 98788994035622589999743330264000101489899975023454322246844076899983587
Q gi|254781172|r 338 RLLDIDIQIGRTGILTPVARLEPVNIGGALITNATLHNEDYIKGLDASGKVMRGGRDIRVGDRVLVKRAGE 408 (731)
Q Consensus 338 ~v~~I~wqvgRtG~itPva~~ePV~l~G~~V~ratlhN~~~I~~l~~~~~~~~~~~~I~iGd~V~I~RaGd 408 (731)
.+.--.=..||||. |-=-|-|++|.--|. +|.++-+ ++++.|++.-+++++|.
T Consensus 84 ~i~~~v~~~~kTGV-------EMEALtavsva~LTi--yDM~Kav---------dk~~~I~~i~L~~K~GG 136 (136)
T cd00528 84 RIRATVRTTGKTGV-------EMEALTAVSVAALTI--YDMCKAV---------DKDMVIENIRLLEKSGG 136 (136)
T ss_pred EEEEEEEECCCCCH-------HHHHHHHHHHHHHHH--HHHHHHC---------CCCCEEEEEEEEEECCC
T ss_conf 99999996689416-------886999999999999--9987631---------79978955799983188
No 343
>pfam04475 DUF555 Protein of unknown function (DUF555). Family of uncharacterized, hypothetical archaeal proteins.
Probab=43.07 E-value=8.9 Score=17.47 Aligned_cols=11 Identities=27% Similarity=0.824 Sum_probs=8.7
Q ss_pred CCCCCCCCCCC
Q ss_conf 43265775010
Q gi|254781172|r 432 SFCPICQSRVV 442 (731)
Q Consensus 432 ~~CP~Cgs~l~ 442 (731)
+.||+||.++.
T Consensus 48 ~~cP~Cge~~~ 58 (102)
T pfam04475 48 TACPKCGEELE 58 (102)
T ss_pred CCCCCCCCCCC
T ss_conf 10887678667
No 344
>TIGR00715 precor6x_red precorrin-6x reductase; InterPro: IPR003723 Cobalamin (vitamin B12) is a structurally complex cofactor, consisting of a modified tetrapyrrole with a centrally chelated cobalt. Cobalamin is usually found in one of two biologically active forms: methylcobalamin and adocobalamin. Most prokaryotes, as well as animals, have cobalamin-dependent enzymes, whereas plants and fungi do not appear to use it. In bacteria and archaea, these include methionine synthase, ribonucleotide reductase, glutamate and methylmalonyl-CoA mutases, ethanolamine ammonia lyase, and diol dehydratase . In mammals, cobalamin is obtained through the diet, and is required for methionine synthase and methylmalonyl-CoA mutase . There are at least two distinct cobalamin biosynthetic pathways in bacteria : Aerobic pathway that requires oxygen and in which cobalt is inserted late in the pathway ; found in Pseudomonas denitrificans and Rhodobacter capsulatus. Anaerobic pathway in which cobalt insertion is the first committed step towards cobalamin synthesis ; found in Salmonella typhimurium, Bacillus megaterium, and Propionibacterium freudenreichii shermanii. Either pathway can be divided into two parts: (1) corrin ring synthesis (differs in aerobic and anaerobic pathways) and (2) adenosylation of corrin ring, attachment of aminopropanol arm, and assembly of the nucleotide loop (common to both pathways) . There are about 30 enzymes involved in either pathway, where those involved in the aerobic pathway are prefixed Cob and those of the anaerobic pathway Cbi. Several of these enzymes are pathway-specific: CbiD, CbiG, and CbiK are specific to the anaerobic route of S. typhimurium, whereas CobE, CobF, CobG, CobN, CobS, CobT, and CobW are unique to the aerobic pathway of P. denitrificans. This entry represents CobK and CbiJ precorrin-6x reductase (1.3.1.54 from EC). In the aerobic pathway, CobK catalyses the reduction of the macrocycle of precorrin-6X to produce precorrin-6Y; while in the anaerobic pathway CbiJ catalyses the reduction of the macrocycle of cobalt-precorrin-6X into cobalt-precorrin-6Y , .; GO: 0016994 precorrin-6A reductase activity, 0009236 cobalamin biosynthetic process.
Probab=43.05 E-value=20 Score=14.76 Aligned_cols=43 Identities=19% Similarity=0.245 Sum_probs=20.1
Q ss_pred HHHHHHHHHHHHC---CCCCCCCCCCCCEEEEEEEEEEECHHHHHHHH
Q ss_conf 5666999775310---24322335445504899999985202123455
Q gi|254781172|r 159 SGEDVSACIRAIP---TIPRVLSLNIPEIIEVRGEVYISKNDFLALND 203 (731)
Q Consensus 159 ~GeDVT~n~~~i~---~iP~~l~~~~~~~ieiRGEv~m~~~~F~~lN~ 203 (731)
+-=.+|.|+..+- +|| .+...-|+.. +-|.-++.-+||+.+..
T Consensus 78 FA~~~t~~a~~vc~E~~~~-YvrfeRp~e~-~~~~~ii~V~d~~~a~~ 123 (260)
T TIGR00715 78 FAAQITKNALEVCKELGIP-YVRFERPEEL-VLGKNIIEVSDIEEAAR 123 (260)
T ss_pred HHHHHHHHHHHHHHHCCCE-EEEECCCCCC-CCCCCEEEECCHHHHHH
T ss_conf 5899999999999761981-7996088353-69986688567788877
No 345
>PRK07063 short chain dehydrogenase; Provisional
Probab=43.01 E-value=20 Score=14.76 Aligned_cols=15 Identities=13% Similarity=0.149 Sum_probs=10.9
Q ss_pred CCCCCCCEEEEECCC
Q ss_conf 882168669997258
Q gi|254781172|r 644 SSEIENKKLVFTGTL 658 (731)
Q Consensus 644 ~~~l~gk~vV~TGtl 658 (731)
++..+|.++++.|-+
T Consensus 239 as~iTG~~i~VDGG~ 253 (259)
T PRK07063 239 APFINATCITIDGGR 253 (259)
T ss_pred HCCCCCCEEEECCCH
T ss_conf 258248718988196
No 346
>TIGR01367 pyrE_Therm orotate phosphoribosyltransferase; InterPro: IPR006273 This group of sequences are a distinct clade of orotate phosphoribosyltransferases. Members include the experimentally determined example from Thermus aquaticus and additional examples from Caulobacter crescentus, Helicobacter pylori (Campylobacter pylori), Mesorhizobium loti, and related species. ; GO: 0004588 orotate phosphoribosyltransferase activity, 0019856 pyrimidine base biosynthetic process.
Probab=42.90 E-value=20 Score=14.74 Aligned_cols=27 Identities=30% Similarity=0.356 Sum_probs=22.6
Q ss_pred CCEEEE------ECCCCCCCHHHHHHHHHHCCCEEEE
Q ss_conf 866999------7258899878999999982984998
Q gi|254781172|r 649 NKKLVF------TGTLQKIQRHKAQEYVTQLGAVVSA 679 (731)
Q Consensus 649 gk~vV~------TGtl~~~~R~e~~~~ie~~Ggkv~s 679 (731)
|.+||+ || -|-.|..++||..||.|..
T Consensus 111 Gek~v~vEDvvTTG----GS~~e~~~~i~~~GG~vvg 143 (205)
T TIGR01367 111 GEKVVVVEDVVTTG----GSLLEAIKAIEELGGQVVG 143 (205)
T ss_pred CCEEEEEEEEECCC----HHHHHHHHHHHHCCCCEEE
T ss_conf 97799996211047----4489999999857982798
No 347
>PRK06194 hypothetical protein; Provisional
Probab=42.89 E-value=20 Score=14.74 Aligned_cols=20 Identities=20% Similarity=0.112 Sum_probs=7.7
Q ss_pred HHHHHCCCCCHHHHHHHHHHHH
Q ss_conf 3213012310354103555565
Q gi|254781172|r 473 KHFVSRDAFNIEGLGKQQLDFF 494 (731)
Q Consensus 473 ~hF~SK~aldI~GLG~k~Ie~L 494 (731)
.|-+||.+ +.||.+..-..|
T Consensus 160 ~Y~ASK~A--V~glT~sLa~EL 179 (301)
T PRK06194 160 VYNVSKHA--VVSLTETLYQDL 179 (301)
T ss_pred HHHHHHHH--HHHHHHHHHHHH
T ss_conf 78999999--999999999999
No 348
>TIGR02397 dnaX_nterm DNA polymerase III, subunits gamma and tau; InterPro: IPR012763 This entry represents the well-conserved first N-terminal domain of DnaX, approx. 365 aa. The full-length product of the dnaX gene in Escherichia coli encodes the DNA polymerase III tau subunit. A translational frameshift leads to early termination and a truncated protein subunit gamma, about 1/3 shorter than tau and present in roughly equal amounts. This frameshift mechanism is not necessarily universal for species with DNA polymerase III but appears conserved in the extreme thermophile Thermus thermophilis.; GO: 0003887 DNA-directed DNA polymerase activity, 0005524 ATP binding, 0006260 DNA replication, 0009360 DNA polymerase III complex.
Probab=42.83 E-value=16 Score=15.52 Aligned_cols=20 Identities=30% Similarity=0.557 Sum_probs=9.7
Q ss_pred HHHHHHHHHHHHHCCCCCHH
Q ss_conf 14466553321301231035
Q gi|254781172|r 465 SAQQLERLKHFVSRDAFNIE 484 (731)
Q Consensus 465 paq~~~~i~hF~SK~aldI~ 484 (731)
..+++++|.+=+.+..+++|
T Consensus 177 ~~~i~~~L~~I~~~E~I~~e 196 (363)
T TIGR02397 177 LEDIVERLKKILDKEGIKIE 196 (363)
T ss_pred HHHHHHHHHHHHHHHCCCCC
T ss_conf 89999999999987088317
No 349
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=42.74 E-value=9.7 Score=17.15 Aligned_cols=34 Identities=29% Similarity=0.508 Sum_probs=20.8
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHH
Q ss_conf 0432657750103378654452101003543441144665533213012310354103
Q gi|254781172|r 431 PSFCPICQSRVVRDLNPKTGKLVAAHRCTGGLACSAQQLERLKHFVSRDAFNIEGLGK 488 (731)
Q Consensus 431 P~~CP~Cgs~l~~~~~~~~~~~~~~~rC~n~~~Cpaq~~~~i~hF~SK~aldI~GLG~ 488 (731)
--.||-||.+++|-... .+--||||.|-+| .||+
T Consensus 7 ~v~CP~Cgkpv~w~~~s-----------------------~frPFCSkRCklI-DLg~ 40 (65)
T COG3024 7 TVPCPTCGKPVVWGEES-----------------------PFRPFCSKRCKLI-DLGE 40 (65)
T ss_pred CCCCCCCCCCCCCCCCC-----------------------CCCCCHHHHHHHC-CHHH
T ss_conf 15388778833346667-----------------------7676336766212-1536
No 350
>PRK08277 D-mannonate oxidoreductase; Provisional
Probab=42.66 E-value=20 Score=14.72 Aligned_cols=15 Identities=20% Similarity=0.186 Sum_probs=8.8
Q ss_pred CCCCCCEEEEECCCC
Q ss_conf 821686699972588
Q gi|254781172|r 645 SEIENKKLVFTGTLQ 659 (731)
Q Consensus 645 ~~l~gk~vV~TGtl~ 659 (731)
+..+|.++++.|-+.
T Consensus 259 ~yiTG~~i~VDGG~t 273 (278)
T PRK08277 259 SFVTGVVLPVDGGFS 273 (278)
T ss_pred CCCCCCEEEECCCHH
T ss_conf 773387288692545
No 351
>PRK06079 enoyl-(acyl carrier protein) reductase; Provisional
Probab=42.49 E-value=20 Score=14.70 Aligned_cols=12 Identities=0% Similarity=0.091 Sum_probs=5.0
Q ss_pred CCCCCCEEEEEC
Q ss_conf 821686699972
Q gi|254781172|r 645 SEIENKKLVFTG 656 (731)
Q Consensus 645 ~~l~gk~vV~TG 656 (731)
+..+|.++.+.|
T Consensus 236 ~~iTGq~i~VDG 247 (252)
T PRK06079 236 TGVTGDIIYVDK 247 (252)
T ss_pred CCCCCCEEEECC
T ss_conf 682597289794
No 352
>PRK07168 bifunctional uroporphyrinogen-III methyltransferase/uroporphyrinogen-III synthase; Reviewed
Probab=42.39 E-value=20 Score=14.69 Aligned_cols=130 Identities=13% Similarity=0.169 Sum_probs=68.8
Q ss_pred EEEEEEEEEEEECCCCEEEEEEEEEEEEECCCEEE-EECCCCHHHHHHHCCCCCCCCCCCCCCCCCEEEEEECCCCHHHH
Q ss_conf 58998788994035622589999743330264000-10148989997502345432224684407689998358702566
Q gi|254781172|r 335 ASTRLLDIDIQIGRTGILTPVARLEPVNIGGALIT-NATLHNEDYIKGLDASGKVMRGGRDIRVGDRVLVKRAGEVIPKV 413 (731)
Q Consensus 335 ~~T~v~~I~wqvgRtG~itPva~~ePV~l~G~~V~-ratlhN~~~I~~l~~~~~~~~~~~~I~iGd~V~I~RaGdVIP~I 413 (731)
.+++|.+|.=.+-+.|.-.|... +=|-.|+ |.+| .|.++.=--|-+|+|.|+-+---..
T Consensus 207 v~gTL~~Ia~~v~~~~i~~PAvI-----VVGeVV~lR~~L---------------~WfE~kPLfG~rVLVtRtreQA~~l 266 (474)
T PRK07168 207 VTGTLSTIVSIVKNENISNPSMT-----IVGDVVSLRNQI---------------AWKERKPLHGKKVLFTSATNKTSVM 266 (474)
T ss_pred EEEEHHHHHHHHHHCCCCCCEEE-----EECCCCCCCCCC---------------CCCCCCCCCCCEEEECCCHHHHHHH
T ss_conf 99999999999997378998299-----988400555536---------------7535688788679977866776999
Q ss_pred HHHCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCEEECC-CCCCCCHHHHHHHHHHHHH---CCCCCHHH----
Q ss_conf 541012357873047770432657750103378654452101003-5434411446655332130---12310354----
Q gi|254781172|r 414 VDIIVNERHPDAQPFSFPSFCPICQSRVVRDLNPKTGKLVAAHRC-TGGLACSAQQLERLKHFVS---RDAFNIEG---- 485 (731)
Q Consensus 414 ~~Vi~~~r~~~~~~~~~P~~CP~Cgs~l~~~~~~~~~~~~~~~rC-~n~~~Cpaq~~~~i~hF~S---K~aldI~G---- 485 (731)
..-+. .-.+.++++|+.-|.-.+++....... ..++-..++ .|+ ..+|+. +..+||..
T Consensus 267 s~~L~---~~GA~v~E~PtI~~~~~~~~~~~i~~l-~~ydwlvFTS~Ng----------V~~Ff~~L~~~g~D~R~L~~k 332 (474)
T PRK07168 267 KQKLQ---EAGAEIYQIPTFKKEEYTLTLEQINEI-FNVDRLVFCSAES----------VEILMQSCSKYKKDIRSLQAE 332 (474)
T ss_pred HHHHH---HCCCCEEEECCCCCCCCCHHHHHHHHH-CCCCEEEEECHHH----------HHHHHHHHHHCCCCHHHCCCE
T ss_conf 99999---769938994453168856379998753-3389899938789----------999999999739845760761
Q ss_pred ---HHHHHHHHHHCCC
Q ss_conf ---1035555653057
Q gi|254781172|r 486 ---LGKQQLDFFFKSE 498 (731)
Q Consensus 486 ---LG~k~Ie~L~e~~ 498 (731)
+|++|-+.|-+.|
T Consensus 333 iaaiG~aT~~~L~~~G 348 (474)
T PRK07168 333 LQHMNVATQEKLMQYG 348 (474)
T ss_pred EEEECHHHHHHHHHCC
T ss_conf 7887589999999769
No 353
>PRK12495 hypothetical protein; Provisional
Probab=42.35 E-value=11 Score=16.82 Aligned_cols=13 Identities=31% Similarity=0.749 Sum_probs=6.4
Q ss_pred CCCCCCCCCCCCC
Q ss_conf 4326577501033
Q gi|254781172|r 432 SFCPICQSRVVRD 444 (731)
Q Consensus 432 ~~CP~Cgs~l~~~ 444 (731)
.+|+-||+++.+.
T Consensus 43 ~HC~~CGdPIFR~ 55 (221)
T PRK12495 43 AHCDECGSPIFRH 55 (221)
T ss_pred CCCCCCCCHHHHC
T ss_conf 2002236723404
No 354
>PRK06550 fabG 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional
Probab=42.35 E-value=20 Score=14.68 Aligned_cols=15 Identities=7% Similarity=0.164 Sum_probs=10.6
Q ss_pred CCCCCCCEEEEECCC
Q ss_conf 882168669997258
Q gi|254781172|r 644 SSEIENKKLVFTGTL 658 (731)
Q Consensus 644 ~~~l~gk~vV~TGtl 658 (731)
++..+|.++.+.|-+
T Consensus 220 as~iTG~~i~VDGG~ 234 (237)
T PRK06550 220 ADYMQGTIVPIDGGW 234 (237)
T ss_pred HCCCCCCEEEECCCC
T ss_conf 338148628968273
No 355
>KOG4236 consensus
Probab=42.34 E-value=6.5 Score=18.51 Aligned_cols=86 Identities=13% Similarity=0.085 Sum_probs=35.3
Q ss_pred EEEEEEEEECCCCEEEEEEEEEEEEECCCEEEEECCCCHHHHHHHCCCCCCCCCCCCCCCCCEEEEEECCCCHH--HHHH
Q ss_conf 98788994035622589999743330264000101489899975023454322246844076899983587025--6654
Q gi|254781172|r 338 RLLDIDIQIGRTGILTPVARLEPVNIGGALITNATLHNEDYIKGLDASGKVMRGGRDIRVGDRVLVKRAGEVIP--KVVD 415 (731)
Q Consensus 338 ~v~~I~wqvgRtG~itPva~~ePV~l~G~~V~ratlhN~~~I~~l~~~~~~~~~~~~I~iGd~V~I~RaGdVIP--~I~~ 415 (731)
-|.-|.-+|+-|-+-+ ......|=.|-+.+-.|.. ..++|+..-|.|-.=---.-.|-=-.|| +|.+
T Consensus 395 PLmRvv~svkhtkRks-----st~~kEGWmvHyt~~d~lR------krHYWrldsk~itlfqn~s~~ryYkeIPLsEIl~ 463 (888)
T KOG4236 395 PLMRVVQSVKHTKRKS-----STKLKEGWMVHYTSKDNLR------KRHYWRLDSKCITLFQNESTNRYYKEIPLSEILS 463 (888)
T ss_pred CEEEECHHHCCCCCCC-----HHHHHCCEEEEEECHHHHH------HHHHHEECCCEEEEEECCCCCEEEEEECHHHHHE
T ss_conf 4165200212220001-----2422104389875336664------5454200366567653277743677502788312
Q ss_pred HCCCCCCCCCCEEEECCCCCCCC
Q ss_conf 10123578730477704326577
Q gi|254781172|r 416 IIVNERHPDAQPFSFPSFCPICQ 438 (731)
Q Consensus 416 Vi~~~r~~~~~~~~~P~~CP~Cg 438 (731)
|.... .....++.+-|.|-
T Consensus 464 v~~~~----~~~~vp~~~~phcF 482 (888)
T KOG4236 464 VSSNN----GFSLVPAGTNPHCF 482 (888)
T ss_pred EECCC----CCCCCCCCCCCCEE
T ss_conf 00368----85347899998338
No 356
>PRK08226 short chain dehydrogenase; Provisional
Probab=42.30 E-value=20 Score=14.68 Aligned_cols=15 Identities=27% Similarity=0.251 Sum_probs=10.8
Q ss_pred CCCCCCCEEEEECCC
Q ss_conf 882168669997258
Q gi|254781172|r 644 SSEIENKKLVFTGTL 658 (731)
Q Consensus 644 ~~~l~gk~vV~TGtl 658 (731)
++..+|.++.+.|-+
T Consensus 239 a~yiTG~~i~VDGG~ 253 (263)
T PRK08226 239 SSYLTGTQNVIDGGS 253 (263)
T ss_pred HCCCCCCEEEECCCC
T ss_conf 348048828858883
No 357
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=42.27 E-value=7.6 Score=17.97 Aligned_cols=14 Identities=36% Similarity=0.792 Sum_probs=8.5
Q ss_pred CCCCCCCCCCCCCC
Q ss_conf 04326577501033
Q gi|254781172|r 431 PSFCPICQSRVVRD 444 (731)
Q Consensus 431 P~~CP~Cgs~l~~~ 444 (731)
+-+||+||.-|.++
T Consensus 221 iv~CP~CgRILy~~ 234 (239)
T COG1579 221 IVFCPYCGRILYYD 234 (239)
T ss_pred CCCCCCCCHHHHHH
T ss_conf 75287611367775
No 358
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=42.10 E-value=11 Score=16.87 Aligned_cols=36 Identities=14% Similarity=0.093 Sum_probs=23.9
Q ss_pred HHHHHCCCCCCHHHHHHHHHHHCCHH-HHHHHHHHHH
Q ss_conf 78761388867899999999966979-9999999997
Q gi|254781172|r 595 WLSLIRVPLVGDIIAQAIVEFYQNPR-NICAVEALLK 630 (731)
Q Consensus 595 ~e~L~~I~GiG~~~A~si~~ff~~~~-n~~~i~~L~~ 630 (731)
.+.|..+|.++-+-=.|+.--|.+.. ..+.+.+|..
T Consensus 113 M~~Lk~lD~VAYvRFASVYr~F~dv~~F~e~i~~l~~ 149 (156)
T COG1327 113 MEELKKLDEVAYVRFASVYRSFKDVDDFEEEIEELTK 149 (156)
T ss_pred HHHHHHCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHH
T ss_conf 9999710502323466687032789999999999974
No 359
>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=42.04 E-value=11 Score=16.81 Aligned_cols=14 Identities=36% Similarity=0.617 Sum_probs=8.1
Q ss_pred ECCCCCCCCCCCCC
Q ss_conf 70432657750103
Q gi|254781172|r 430 FPSFCPICQSRVVR 443 (731)
Q Consensus 430 ~P~~CP~Cgs~l~~ 443 (731)
.|..||.||+.+.+
T Consensus 25 ~~~~CP~Cg~~~~r 38 (41)
T smart00834 25 PLATCPECGGDVRR 38 (41)
T ss_pred CCCCCCCCCCCCEE
T ss_conf 78858689992277
No 360
>TIGR01512 ATPase-IB2_Cd cadmium-translocating P-type ATPase; InterPro: IPR006404 These sequences describe the P-type ATPase primarily responsible for translocating cadmium ions (and other closely-related divalent heavy metals such as cobalt, mercury, lead and zinc) across biological membranes. These transporters are found in prokaryotes and plants. Experimentally characterised members include P37617 from SWISSPROT from Escherichia coli, Q10866 from SWISSPROT from Mycobacterium tuberculosis and Q59998 from SWISSPROT from Synechocystis PCC6803. The cadmium P-type ATPases have been characterised as Type IB based on a phylogenetic analysis which combines the copper-translocating ATPases with the cadmium-translocating species . This family and that describing the copper-ATPases (IPR006403 from INTERPRO) are well separated, and thus the copper-ATPases can be typed as IB1 and the cadmium-ATPases as IB2. ; GO: 0005524 ATP binding, 0016818 hydrolase activity acting on acid anhydrides in phosphorus-containing anhydrides, 0046872 metal ion binding, 0046873 metal ion transmembrane transporter activity, 0030001 metal ion transport, 0016020 membrane.
Probab=41.82 E-value=14 Score=16.01 Aligned_cols=54 Identities=19% Similarity=0.324 Sum_probs=29.6
Q ss_pred CCCCCCC--CCEEEEC-CCCCEEEEEEEEEEEEECCCCEEEEEEEEEEEEECCCEEEEECCCC
Q ss_conf 8765686--6312311-4562158998788994035622589999743330264000101489
Q gi|254781172|r 316 GERARSP--RWMISHK-FAEKQASTRLLDIDIQIGRTGILTPVARLEPVNIGGALITNATLHN 375 (731)
Q Consensus 316 G~ts~~P--rwaiA~K-f~~e~~~T~v~~I~wqvgRtG~itPva~~ePV~l~G~~V~ratlhN 375 (731)
...|.|| +==++|. +|.+=...++.+-.|-+|+..-+- .|.+++..+..-.++-
T Consensus 268 E~~S~HPlA~AIv~~~e~pG~G~~a~~~g~~v~~G~~~t~~------~v~~~~~~~G~i~l~D 324 (494)
T TIGR01512 268 EQQSSHPLARAIVAAEEVPGEGVKAVVDGEEVRIGNKRTLV------LVAVDGKLIGVILLSD 324 (494)
T ss_pred HHCCCCHHHHHHHHHHHCCCCCEEEEECCEEEEEECCCCEE------EEEECCEEEEEEEEEC
T ss_conf 31066868999997420477744899957799997376589------9998584999999733
No 361
>PRK10517 magnesium-transporting ATPase MgtA; Provisional
Probab=41.80 E-value=12 Score=16.53 Aligned_cols=15 Identities=20% Similarity=0.020 Sum_probs=8.2
Q ss_pred CCEEEEECCCCHHHH
Q ss_conf 640001014898999
Q gi|254781172|r 365 GALITNATLHNEDYI 379 (731)
Q Consensus 365 G~~V~ratlhN~~~I 379 (731)
|..|.=.|+-|..--
T Consensus 564 GI~V~MITGD~~~TA 578 (900)
T PRK10517 564 GITVKILTGDSELVA 578 (900)
T ss_pred CCEEEEECCCCHHHH
T ss_conf 993899899998999
No 362
>COG4213 XylF ABC-type xylose transport system, periplasmic component [Carbohydrate transport and metabolism]
Probab=41.79 E-value=13 Score=16.22 Aligned_cols=20 Identities=5% Similarity=0.258 Sum_probs=9.8
Q ss_pred HHHHHHHHHHHHHCCCCCHH
Q ss_conf 14466553321301231035
Q gi|254781172|r 465 SAQQLERLKHFVSRDAFNIE 484 (731)
Q Consensus 465 paq~~~~i~hF~SK~aldI~ 484 (731)
|++..+++..|.++..-+|+
T Consensus 200 ps~Aq~~men~lta~~~~vd 219 (341)
T COG4213 200 PSNAQQIMENLLTANYNDID 219 (341)
T ss_pred HHHHHHHHHHHHHCCCCCEE
T ss_conf 88999999988742367600
No 363
>PRK07758 hypothetical protein; Provisional
Probab=41.70 E-value=19 Score=14.96 Aligned_cols=24 Identities=21% Similarity=0.443 Sum_probs=18.7
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHH
Q ss_conf 010001342100145689999875
Q gi|254781172|r 522 TKIENILGFGDVSVTNLYDSINKR 545 (731)
Q Consensus 522 ~~l~~l~GfgeKsa~nL~~sIe~s 545 (731)
.+|+++-|||.++...|-+++++.
T Consensus 67 kELL~LHGmGP~ai~~L~~aLke~ 90 (95)
T PRK07758 67 KEILKLHGMGPASLPKLRKALEES 90 (95)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHC
T ss_conf 999998486888899999999983
No 364
>COG3791 Uncharacterized conserved protein [Function unknown]
Probab=41.56 E-value=10 Score=17.04 Aligned_cols=42 Identities=17% Similarity=0.242 Sum_probs=23.0
Q ss_pred CCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCHHHHHHHHHHHHH
Q ss_conf 326577501033786544521010035434411446655332130
Q gi|254781172|r 433 FCPICQSRVVRDLNPKTGKLVAAHRCTGGLACSAQQLERLKHFVS 477 (731)
Q Consensus 433 ~CP~Cgs~l~~~~~~~~~~~~~~~rC~n~~~Cpaq~~~~i~hF~S 477 (731)
+||.||++|-+.....+....+...|.++ |+...-.+..|++
T Consensus 71 FC~~CGs~l~~~~~~~~~~~~v~~~~ld~---p~~~~p~~~~~~~ 112 (133)
T COG3791 71 FCPTCGSPLFWRGPDEDPFVGVNAGALDD---PEFLPPQVQIFVG 112 (133)
T ss_pred ECCCCCCCCEEECCCCCCEEEEEEEEECC---CCCCCCCEEEEEE
T ss_conf 26668985163179987518898884258---5437973488860
No 365
>PRK13810 orotate phosphoribosyltransferase; Provisional
Probab=41.42 E-value=21 Score=14.58 Aligned_cols=60 Identities=23% Similarity=0.342 Sum_probs=40.5
Q ss_pred CCCEEEE------ECCCCCCCHHHHHHHHHHCCCEEEEEEECCEEEEEECCCCCCHHHHHHHCCCEEECHHHHHHHH
Q ss_conf 6866999------7258899878999999982984998111632179977888863798997499173799999999
Q gi|254781172|r 648 ENKKLVF------TGTLQKIQRHKAQEYVTQLGAVVSAILSRKTDIIIVGDNPGSKLEKAQQLGVKIMNEEQFLFLL 718 (731)
Q Consensus 648 ~gk~vV~------TGtl~~~~R~e~~~~ie~~Ggkv~sSVSkkT~~LI~ge~~gSKl~KA~~LgI~Ii~e~ef~~ll 718 (731)
.|.++++ || -|=-++.+.+++.|+.|..-+. |+.-..| ..+..++.||++++--.+.++|
T Consensus 121 ~g~rVlvVEDViTTG----gS~~eai~~l~~~G~~V~~v~~------ivDR~~g-~~e~l~~~gv~~~sl~t~~dll 186 (187)
T PRK13810 121 PEDRIVMLEDVTTSG----GSVRDAIEVVREAGAIVKYVIT------VVDREEG-ATENLKEADVELVPLVSASDLL 186 (187)
T ss_pred CCCEEEEEEEEECCC----CCHHHHHHHHHHCCCEEEEEEE------EEECCCC-HHHHHHHCCCCEEEECCHHHHH
T ss_conf 998899998543568----2399999999988997999999------9977847-6999997799099946198961
No 366
>PRK08217 fabG 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional
Probab=41.33 E-value=21 Score=14.57 Aligned_cols=11 Identities=18% Similarity=0.347 Sum_probs=4.6
Q ss_pred CCCCCEEEEEC
Q ss_conf 21686699972
Q gi|254781172|r 646 EIENKKLVFTG 656 (731)
Q Consensus 646 ~l~gk~vV~TG 656 (731)
.++|.++++.|
T Consensus 239 ~iTG~~i~VDG 249 (253)
T PRK08217 239 YVTGRVLEIDG 249 (253)
T ss_pred CCCCCEEEECC
T ss_conf 98899678696
No 367
>PRK06227 consensus
Probab=41.27 E-value=21 Score=14.57 Aligned_cols=15 Identities=20% Similarity=0.364 Sum_probs=9.7
Q ss_pred CCCCCCCEEEEECCC
Q ss_conf 882168669997258
Q gi|254781172|r 644 SSEIENKKLVFTGTL 658 (731)
Q Consensus 644 ~~~l~gk~vV~TGtl 658 (731)
++..+|.++++.|-+
T Consensus 234 as~iTG~~i~VDGG~ 248 (256)
T PRK06227 234 ASFITGVNFIVDGGM 248 (256)
T ss_pred HCCCCCCEEEECCCE
T ss_conf 249258638967891
No 368
>PRK05855 short chain dehydrogenase; Validated
Probab=41.27 E-value=21 Score=14.57 Aligned_cols=26 Identities=15% Similarity=0.213 Sum_probs=13.5
Q ss_pred HHHHCCCC---CHHHHHHHHHHHHHCCCC
Q ss_conf 21301231---035410355556530576
Q gi|254781172|r 474 HFVSRDAF---NIEGLGKQQLDFFFKSED 499 (731)
Q Consensus 474 hF~SK~al---dI~GLG~k~Ie~L~e~~~ 499 (731)
.|..|-++ --.|+|..+...|-+.|.
T Consensus 312 rFsGKvAvVTGA~sGIGrA~A~~fA~~GA 340 (582)
T PRK05855 312 RFGGKLVVVTGAGSGIGRATALAFAREGA 340 (582)
T ss_pred CCCCCEEEEECCCCHHHHHHHHHHHHCCC
T ss_conf 74995899958757899999999997799
No 369
>COG2100 Predicted Fe-S oxidoreductase [General function prediction only]
Probab=41.17 E-value=21 Score=14.56 Aligned_cols=15 Identities=33% Similarity=0.446 Sum_probs=6.0
Q ss_pred CCCCCHHHHHHHHHH
Q ss_conf 888678999999999
Q gi|254781172|r 601 VPLVGDIIAQAIVEF 615 (731)
Q Consensus 601 I~GiG~~~A~si~~f 615 (731)
++|+.+.-+..|++|
T Consensus 265 lPG~ND~E~~~iIe~ 279 (414)
T COG2100 265 LPGVNDDEMPKIIEW 279 (414)
T ss_pred CCCCCHHHHHHHHHH
T ss_conf 278681778999999
No 370
>PRK01103 formamidopyrimidine-DNA glycosylase; Validated
Probab=41.16 E-value=11 Score=16.72 Aligned_cols=24 Identities=13% Similarity=0.257 Sum_probs=13.8
Q ss_pred CCCCCCCCCCCCCCCCCCCCCEEECCCC
Q ss_conf 3265775010337865445210100354
Q gi|254781172|r 433 FCPICQSRVVRDLNPKTGKLVAAHRCTG 460 (731)
Q Consensus 433 ~CP~Cgs~l~~~~~~~~~~~~~~~rC~n 460 (731)
.||.||+++.+..-.. -..++|++
T Consensus 246 ~C~~Cg~~I~~~~~~g----R~t~~CP~ 269 (273)
T PRK01103 246 PCRRCGTPIEKIKQGG----RSTFFCPK 269 (273)
T ss_pred CCCCCCCEEEEEEECC----CCCEECCC
T ss_conf 4899999678999889----71199957
No 371
>PRK06171 sorbitol-6-phosphate 2-dehydrogenase; Provisional
Probab=41.16 E-value=21 Score=14.55 Aligned_cols=15 Identities=20% Similarity=0.109 Sum_probs=10.5
Q ss_pred CCCCCCCEEEEECCC
Q ss_conf 882168669997258
Q gi|254781172|r 644 SSEIENKKLVFTGTL 658 (731)
Q Consensus 644 ~~~l~gk~vV~TGtl 658 (731)
++..+|.++.+.|-+
T Consensus 249 as~iTG~~i~VDGG~ 263 (266)
T PRK06171 249 ASYITGVTTNIAGGK 263 (266)
T ss_pred HCCCCCCEEEECCCC
T ss_conf 258058628987882
No 372
>TIGR01082 murC UDP-N-acetylmuramate--alanine ligase; InterPro: IPR005758 The bacterial cell wall provides strength and rigidity to counteract internal osmotic pressure, and protection against the environment. The peptidoglycan layer gives the cell wall its strength, and helps maintain the overall shape of the cell. The basic peptidoglycan structure of both Gram-positive and Gram-negative bacteria is comprised of a sheet of glycan chains connected by short cross-linking polypeptides. Biosynthesis of peptidoglycan is a multi-step (11-12 steps) process comprising three main stages: (1) formation of UDP-N-acetylmuramic acid (UDPMurNAc) from N-acetylglucosamine (GlcNAc). (2) addition of a short polypeptide chain to the UDPMurNAc. (3) addition of a second GlcNAc to the disaccharide-pentapeptide building block and transport of this unit through the cytoplasmic membrane and incorporation into the growing peptidoglycan layer. Stage two involves four key Mur ligase enzymes: MurC (6.3.2.8 from EC) , MurD (6.3.2.9 from EC) , MurE (6.3.2.13 from EC) and MurF (6.3.2.10 from EC) . These four Mur ligases are responsible for the successive additions of L-alanine, D-glutamate, meso-diaminopimelate or L-lysine, and D-alanyl-D-alanine to UDP-N-acetylmuramic acid. All four Mur ligases are topologically similar to one another, even though they display low sequence identity. They are each composed of three domains: an N-terminal Rossmann-fold domain responsible for binding the UDPMurNAc substrate; a central domain (similar to ATP-binding domains of several ATPases and GTPases); and a C-terminal domain (similar to dihydrofolate reductase fold) that appears to be associated with binding the incoming amino acid. The conserved sequence motifs found in the four Mur enzymes also map to other members of the Mur ligase family, including folylpolyglutamate synthetase, cyanophycin synthetase and the capB enzyme from Bacillales . This entry represents UDP-N-acetylmuramate-alanine ligase (MurC). MurC is an essential, cytoplasmic peptidoglycan biosynthetic enzyme, catalyzes the ATP-dependent ligation of L-alanine (Ala) and UDP-N-acetylmuramic acid (UNAM) to form UDP-N-acetylmuramyl-L-alanine (UNAM-Ala). The enzyme is a nonribosomal peptide ligase which utilises ATP to form an amide bond between L-alanine and UNAM.1 Mechanistic studies on the Escherichia coli MurC enzyme using oxygen isotope analyses demonstrated that the enzyme-catalyzed reaction proceeds through an acyl phosphate UNAM intermediate prior to L-alanine addition.; GO: 0005524 ATP binding, 0008763 UDP-N-acetylmuramate-L-alanine ligase activity, 0008360 regulation of cell shape, 0009252 peptidoglycan biosynthetic process, 0009273 peptidoglycan-based cell wall biogenesis, 0051301 cell division, 0005737 cytoplasm.
Probab=41.11 E-value=21 Score=14.55 Aligned_cols=66 Identities=17% Similarity=0.197 Sum_probs=36.3
Q ss_pred ECCCCHHHHHHHHHHHHCCCCCCCCC-EEEEECCHHCCCCCCCCCC-CCCCEEEECCCCCEEEEEEEEEEEEE
Q ss_conf 40321134556655310011234376-3777311000111587656-86631231145621589987889940
Q gi|254781172|r 276 NTFHGIVSYYNEMKSIRSTLPYDIDG-LVYKVDEFSLQKQLGERAR-SPRWMISHKFAEKQASTRLLDIDIQI 346 (731)
Q Consensus 276 ~~~~~~~~~~~~~~~~r~~l~y~iDG-iVikvn~~~~q~~lG~ts~-~PrwaiA~Kf~~e~~~T~v~~I~wqv 346 (731)
++++.+...+.++. ..+| --| +|+-.||--+++..-.... -|+-.+-|-++.+.+.-++.++.-+-
T Consensus 198 ~~~E~~~~aF~~F~---~~l~--~~G~~v~c~DD~~~~~l~~~~~~~r~d~~~~y~~~~~~~~~~~~~~~~~~ 265 (491)
T TIGR01082 198 SSLERLKAAFEKFI---HNLP--FYGLAVICADDPVLRKLVPKATESRKDVVITYGGSGEDADIRAENIQQSG 265 (491)
T ss_pred CCHHHHHHHHHHHH---HHCC--CCCEEEEECCCHHHHHHHHHHHHCCCEEEEECCCCCCCCEEEEEEEEECC
T ss_conf 57899999999999---8278--88799998386547877635553387047866877764147788743226
No 373
>COG2216 KdpB High-affinity K+ transport system, ATPase chain B [Inorganic ion transport and metabolism]
Probab=40.88 E-value=19 Score=14.95 Aligned_cols=16 Identities=25% Similarity=0.393 Sum_probs=12.3
Q ss_pred HHHHHHHHHCCCHHHH
Q ss_conf 4567777523455553
Q gi|254781172|r 217 RNAASGILRRLNPTDI 232 (731)
Q Consensus 217 RN~aaG~lr~~d~~~~ 232 (731)
=+++-|+-|||-|.+.
T Consensus 201 I~LVEgA~R~KTPNEI 216 (681)
T COG2216 201 IALVEGAERQKTPNEI 216 (681)
T ss_pred HHHHHCHHCCCCHHHH
T ss_conf 9986352015891489
No 374
>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=40.72 E-value=10 Score=16.91 Aligned_cols=12 Identities=33% Similarity=0.924 Sum_probs=8.6
Q ss_pred ECCCCCCCCCCC
Q ss_conf 704326577501
Q gi|254781172|r 430 FPSFCPICQSRV 441 (731)
Q Consensus 430 ~P~~CP~Cgs~l 441 (731)
.|..||.||.+-
T Consensus 16 ~p~~CP~Cg~~k 27 (33)
T cd00350 16 APWVCPVCGAPK 27 (33)
T ss_pred CCCCCCCCCCCH
T ss_conf 987287889978
No 375
>PRK04690 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=40.63 E-value=21 Score=14.50 Aligned_cols=14 Identities=21% Similarity=0.254 Sum_probs=6.6
Q ss_pred CCCHHHHHCCCCCC
Q ss_conf 11778761388867
Q gi|254781172|r 592 NDDWLSLIRVPLVG 605 (731)
Q Consensus 592 ~~~~e~L~~I~GiG 605 (731)
..+...+..|||+|
T Consensus 453 ~~~~~~~~~~~~~~ 466 (468)
T PRK04690 453 GFDPAAISAIPGLG 466 (468)
T ss_pred CCCHHHHHHCCCCC
T ss_conf 80877785267757
No 376
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=40.62 E-value=13 Score=16.06 Aligned_cols=20 Identities=15% Similarity=0.532 Sum_probs=14.9
Q ss_pred CCEEEECCCCCCCCCCCCCC
Q ss_conf 30477704326577501033
Q gi|254781172|r 425 AQPFSFPSFCPICQSRVVRD 444 (731)
Q Consensus 425 ~~~~~~P~~CP~Cgs~l~~~ 444 (731)
-..+.+-+.||.||+.+..-
T Consensus 11 cg~YTLke~Cp~CG~~t~~~ 30 (59)
T COG2260 11 CGRYTLKEKCPVCGGDTKVP 30 (59)
T ss_pred CCCEEECCCCCCCCCCCCCC
T ss_conf 88146113377888745467
No 377
>PRK07231 fabG 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional
Probab=40.62 E-value=21 Score=14.49 Aligned_cols=14 Identities=29% Similarity=0.223 Sum_probs=9.0
Q ss_pred CCCCCCCEEEEECC
Q ss_conf 88216866999725
Q gi|254781172|r 644 SSEIENKKLVFTGT 657 (731)
Q Consensus 644 ~~~l~gk~vV~TGt 657 (731)
++.++|.++++.|-
T Consensus 234 s~~itG~~i~VDGG 247 (250)
T PRK07231 234 ASFITGVALEVDGG 247 (250)
T ss_pred HCCCCCCEEEECCC
T ss_conf 32946871884888
No 378
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=40.58 E-value=14 Score=16.01 Aligned_cols=34 Identities=12% Similarity=0.080 Sum_probs=20.7
Q ss_pred HHHHHCCCCCCHHHHHHHHHHHCCHH-HHHHHHHH
Q ss_conf 78761388867899999999966979-99999999
Q gi|254781172|r 595 WLSLIRVPLVGDIIAQAIVEFYQNPR-NICAVEAL 628 (731)
Q Consensus 595 ~e~L~~I~GiG~~~A~si~~ff~~~~-n~~~i~~L 628 (731)
.+.|..+|.++-+-=.|+..-|.+.. ..+.+++|
T Consensus 113 m~~Lk~lD~VAYvRFASVYr~F~d~~~F~~ei~~L 147 (149)
T PRK00464 113 MEELKKLDEVAYVRFASVYRSFKDVDDFEEEIEEL 147 (149)
T ss_pred HHHHHHCCCEEEHHHHHHHCCCCCHHHHHHHHHHH
T ss_conf 99886209310000245606779999999999997
No 379
>PRK07985 oxidoreductase; Provisional
Probab=40.42 E-value=22 Score=14.47 Aligned_cols=14 Identities=21% Similarity=0.330 Sum_probs=6.1
Q ss_pred ECCCCHHHHHHHHH
Q ss_conf 65986556669997
Q gi|254781172|r 153 LRGDGHSGEDVSAC 166 (731)
Q Consensus 153 TRGdG~~GeDVT~n 166 (731)
|=|.+-+|.-|...
T Consensus 55 TGas~GIG~aiA~~ 68 (294)
T PRK07985 55 TGGDSGIGRAAAIA 68 (294)
T ss_pred ECCCCHHHHHHHHH
T ss_conf 17266999999999
No 380
>TIGR02109 PQQ_syn_pqqE coenzyme PQQ biosynthesis protein E; InterPro: IPR011843 This entry describes coenzyme PQQ biosynthesis protein E, a gene required for the biosynthesis of pyrrolo-quinoline-quinone (coenzyme PQQ). PQQ is required for some glucose dehydrogenases and alcohol dehydrogenases.; GO: 0051539 4 iron 4 sulfur cluster binding, 0018189 pyrroloquinoline quinone biosynthetic process.
Probab=40.38 E-value=10 Score=16.97 Aligned_cols=74 Identities=12% Similarity=0.159 Sum_probs=36.2
Q ss_pred HHHHHHHHHHHCCCCCCEEEEEHHHHCCHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHH--HHHHHHHHHHHCCHHHH
Q ss_conf 4103555565305765404541011010677753100010001342100145689999875--22346667763010111
Q gi|254781172|r 485 GLGKQQLDFFFKSEDPAFSIRIPADIFTLQRRQQTSTTKIENILGFGDVSVTNLYDSINKR--RNISLERFIFSLGIRHV 562 (731)
Q Consensus 485 GLG~k~Ie~L~e~~~~~g~I~~~~DLy~L~~~~~~~~~~l~~l~GfgeKsa~nL~~sIe~s--K~~~L~r~L~ALGI~~v 562 (731)
||-+.-++.|.++|.+ ++ ++ .+-|--+-.+++| ...+++ ++....|.+.++|||++
T Consensus 92 GLt~~rl~~L~~aGLD-----Hv----------Ql------SfQ~vd~~~a~~i-aG~k~A~~~Kl~~A~~v~~~g~Plt 149 (363)
T TIGR02109 92 GLTEARLDALADAGLD-----HV----------QL------SFQGVDEALADRI-AGLKNAFEQKLAVARAVKAAGLPLT 149 (363)
T ss_pred HHHHHHHHHHHHCCCC-----EE----------EE------EEECCCHHHHHHH-CCHHHHHHHHHHHHHHHHHCCCCEE
T ss_conf 5679999999757985-----78----------87------6414787888641-2502589999999999996189817
Q ss_pred HHHHHHHHHHHCCCHHHHHHHHH
Q ss_conf 16899999988299899999789
Q gi|254781172|r 563 GAEIARSLAKYYLSYQNFAQEIN 585 (731)
Q Consensus 563 G~~~Ak~La~~f~si~~l~~~~~ 585 (731)
=- . .-|=.||+++-.-|+
T Consensus 150 LN----~-V~HR~Ni~~i~~~i~ 167 (363)
T TIGR02109 150 LN----F-VLHRHNIDQIPEIIE 167 (363)
T ss_pred EE----H-CCCCCHHHHHHHHHH
T ss_conf 60----2-002420213678999
No 381
>PRK06057 short chain dehydrogenase; Provisional
Probab=40.26 E-value=22 Score=14.46 Aligned_cols=15 Identities=20% Similarity=0.344 Sum_probs=10.2
Q ss_pred CCCCCCCEEEEECCC
Q ss_conf 882168669997258
Q gi|254781172|r 644 SSEIENKKLVFTGTL 658 (731)
Q Consensus 644 ~~~l~gk~vV~TGtl 658 (731)
++..+|.++.+.|-+
T Consensus 233 ss~iTG~~i~VDGG~ 247 (255)
T PRK06057 233 ASFITASTFLVDGGI 247 (255)
T ss_pred HCCCCCCEEEECCCH
T ss_conf 248268738869383
No 382
>PRK08220 2,3-dihydroxybenzoate-2,3-dehydrogenase; Validated
Probab=40.26 E-value=22 Score=14.45 Aligned_cols=14 Identities=29% Similarity=0.458 Sum_probs=8.9
Q ss_pred CCCCCCCEEEEECC
Q ss_conf 88216866999725
Q gi|254781172|r 644 SSEIENKKLVFTGT 657 (731)
Q Consensus 644 ~~~l~gk~vV~TGt 657 (731)
++..+|.++++.|-
T Consensus 235 s~~itGq~i~vDGG 248 (253)
T PRK08220 235 ASHITMQDIVVDGG 248 (253)
T ss_pred HCCCCCCEEEECCC
T ss_conf 33924832889937
No 383
>PRK08063 enoyl-(acyl carrier protein) reductase; Provisional
Probab=40.06 E-value=22 Score=14.43 Aligned_cols=14 Identities=14% Similarity=0.418 Sum_probs=8.7
Q ss_pred CCCCCCCEEEEECC
Q ss_conf 88216866999725
Q gi|254781172|r 644 SSEIENKKLVFTGT 657 (731)
Q Consensus 644 ~~~l~gk~vV~TGt 657 (731)
++..+|.++.+.|-
T Consensus 232 s~~iTG~~i~VDGG 245 (250)
T PRK08063 232 ADMIRGQTIIVDGG 245 (250)
T ss_pred HCCCCCCEEEECCC
T ss_conf 34822870885948
No 384
>PRK08993 2-deoxy-D-gluconate 3-dehydrogenase; Validated
Probab=40.01 E-value=22 Score=14.43 Aligned_cols=13 Identities=15% Similarity=0.248 Sum_probs=7.6
Q ss_pred CCCCCCEEEEECC
Q ss_conf 8216866999725
Q gi|254781172|r 645 SEIENKKLVFTGT 657 (731)
Q Consensus 645 ~~l~gk~vV~TGt 657 (731)
+..+|.++.+.|-
T Consensus 237 ~~iTG~~i~VDGG 249 (253)
T PRK08993 237 DYINGYTIAVDGG 249 (253)
T ss_pred CCCCCCEEEECCC
T ss_conf 2825853898957
No 385
>PRK05854 short chain dehydrogenase; Provisional
Probab=39.91 E-value=22 Score=14.42 Aligned_cols=14 Identities=7% Similarity=0.022 Sum_probs=5.9
Q ss_pred EECCCCHHHHHHHH
Q ss_conf 86598655666999
Q gi|254781172|r 152 ALRGDGHSGEDVSA 165 (731)
Q Consensus 152 ~TRGdG~~GeDVT~ 165 (731)
+|=|+.-+|.-...
T Consensus 19 ITGa~sGIG~~~a~ 32 (314)
T PRK05854 19 VTGASSGLGFGLAR 32 (314)
T ss_pred ECCCCCHHHHHHHH
T ss_conf 90688299999999
No 386
>PTZ00159 60S ribosomal protein L32; Provisional
Probab=39.84 E-value=8.1 Score=17.76 Aligned_cols=55 Identities=20% Similarity=0.315 Sum_probs=35.2
Q ss_pred EEECCCCCCCCHHHHHHHHHHHHHCCCCCHHHHH-HHHHHHHHCCCCCCEEEEEHHHHCCH
Q ss_conf 0100354344114466553321301231035410-35555653057654045410110106
Q gi|254781172|r 454 AAHRCTGGLACSAQQLERLKHFVSRDAFNIEGLG-KQQLDFFFKSEDPAFSIRIPADIFTL 513 (731)
Q Consensus 454 ~~~rC~n~~~Cpaq~~~~i~hF~SK~aldI~GLG-~k~Ie~L~e~~~~~g~I~~~~DLy~L 513 (731)
..||.+-+.++.-+ .+|-++..|---|.| ++-+.-|.-.|+...+|.++.||-.|
T Consensus 32 ~~WRkPrGidnkvR-----r~~kG~~~mp~iGYgs~k~tR~l~PsG~~~~lV~N~~eLe~L 87 (134)
T PTZ00159 32 PSWRKPRGIDNRVR-----RRFKGQRAMPKIGYGSDKKTRYLLPSGFKKFPISNVQDLEML 87 (134)
T ss_pred CCCCCCCCCCCCCC-----CCCCCCCCCCCCCCCCCHHHHCCCCCCCEEEEECCHHHHHHH
T ss_conf 56559888656511-----224775688766768667760558676878886788998998
No 387
>PRK10445 endonuclease VIII; Provisional
Probab=39.71 E-value=12 Score=16.54 Aligned_cols=24 Identities=17% Similarity=0.353 Sum_probs=13.0
Q ss_pred CCCCCCCCCCCCCCCCCCCCCEEECCCC
Q ss_conf 3265775010337865445210100354
Q gi|254781172|r 433 FCPICQSRVVRDLNPKTGKLVAAHRCTG 460 (731)
Q Consensus 433 ~CP~Cgs~l~~~~~~~~~~~~~~~rC~n 460 (731)
.||.||+++.+..-.. -...+|++
T Consensus 237 ~C~~Cg~~I~~~~~~g----Rst~~Cp~ 260 (263)
T PRK10445 237 ACERCGGIIEKTTLSS----RPFYWCPG 260 (263)
T ss_pred CCCCCCCEEEEEEECC----CCCEECCC
T ss_conf 3899997627999889----87887956
No 388
>pfam11290 DUF3090 Protein of unknown function (DUF3090). This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=39.45 E-value=19 Score=14.86 Aligned_cols=24 Identities=25% Similarity=0.704 Sum_probs=17.1
Q ss_pred HHHHHHCCCCCCCCCCEEEECCCCCCCCCCCCCC
Q ss_conf 5665410123578730477704326577501033
Q gi|254781172|r 411 PKVVDIIVNERHPDAQPFSFPSFCPICQSRVVRD 444 (731)
Q Consensus 411 P~I~~Vi~~~r~~~~~~~~~P~~CP~Cgs~l~~~ 444 (731)
=+-..||...|+. ||.||.++..+
T Consensus 144 ~ra~~VV~AGRp~----------Cp~Cg~Pidp~ 167 (171)
T pfam11290 144 KRARRVVAAGRPP----------CPLCGQPLDPD 167 (171)
T ss_pred HHHHHHHHCCCCC----------CCCCCCCCCCC
T ss_conf 9999999669999----------99889976999
No 389
>TIGR02187 GlrX_arch Glutaredoxin-like domain protein; InterPro: IPR011903 Glutaredoxins , , , also known as thioltransferases (disulphide reductases, are small proteins of approximately one hundred amino-acid residues which utilise glutathione and NADPH as cofactors. Oxidized glutathione is regenerated by glutathione reductase. Together these components compose the glutathione system . Glutaredoxin functions as an electron carrier in the glutathione-dependent synthesis of deoxyribonucleotides by the enzyme ribonucleotide reductase. Like thioredoxin, which functions in a similar way, glutaredoxin possesses an active centre disulphide bond . It exists in either a reduced or an oxidized form where the two cysteine residues are linked in an intramolecular disulphide bond. Glutaredoxin has been sequenced in a variety of species. On the basis of extensive sequence similarity, it has been proposed that Vaccinia virus protein O2L is most probably a glutaredoxin. Finally, it must be noted that Bacteriophage T4 thioredoxin seems also to be evolutionary related. In position 5 of the pattern T4 thioredoxin has Val instead of Pro. This entry of archaeal proteins contains a C-terminal domain with homology to bacterial and eukaryotic glutaredoxins, including a CPYC motif. There is an N-terminal domain which has even more distant homology to glutaredoxins. The name "glutaredoxin" may be inappropriate in the sense of working in tandem with glutathione and glutathione reductase which may not be present in the archaea. The overall domain structure appears to be related to bacterial alkylhydroperoxide reductases, but the homology may be distant enough that the function of this family is wholly different..
Probab=39.38 E-value=14 Score=16.02 Aligned_cols=14 Identities=21% Similarity=0.155 Sum_probs=6.2
Q ss_pred CCEEEEEECCCCHH
Q ss_conf 76899983587025
Q gi|254781172|r 398 GDRVLVKRAGEVIP 411 (731)
Q Consensus 398 Gd~V~I~RaGdVIP 411 (731)
-|.+.|++.+-=.+
T Consensus 121 edI~~vS~g~~~L~ 134 (237)
T TIGR02187 121 EDIVRVSEGESGLS 134 (237)
T ss_pred HHHHHHCCCCCCCC
T ss_conf 99985268999850
No 390
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=39.36 E-value=12 Score=16.49 Aligned_cols=18 Identities=22% Similarity=0.571 Sum_probs=11.4
Q ss_pred EECCCCCCCCC-CCCCCCC
Q ss_conf 77043265775-0103378
Q gi|254781172|r 429 SFPSFCPICQS-RVVRDLN 446 (731)
Q Consensus 429 ~~P~~CP~Cgs-~l~~~~~ 446 (731)
...+.||.||+ ++..++.
T Consensus 13 ~~~~~CP~Cgs~~~s~dW~ 31 (61)
T PRK08351 13 TTEDRCPVCGSRDLSEEWF 31 (61)
T ss_pred CCCCCCCCCCCCCCCCCCC
T ss_conf 6899589997986887734
No 391
>PRK07889 enoyl-(acyl carrier protein) reductase; Provisional
Probab=39.28 E-value=22 Score=14.35 Aligned_cols=13 Identities=8% Similarity=0.146 Sum_probs=7.4
Q ss_pred CCCCCCEEEEECC
Q ss_conf 8216866999725
Q gi|254781172|r 645 SEIENKKLVFTGT 657 (731)
Q Consensus 645 ~~l~gk~vV~TGt 657 (731)
+..+|.++.+.|-
T Consensus 238 ~~iTG~~l~VDGG 250 (256)
T PRK07889 238 PATTGEIIHVDGG 250 (256)
T ss_pred CCCCCCEEEECCC
T ss_conf 3716885887959
No 392
>PRK06172 short chain dehydrogenase; Provisional
Probab=39.20 E-value=22 Score=14.34 Aligned_cols=15 Identities=20% Similarity=0.220 Sum_probs=10.0
Q ss_pred CCCCCCCEEEEECCC
Q ss_conf 882168669997258
Q gi|254781172|r 644 SSEIENKKLVFTGTL 658 (731)
Q Consensus 644 ~~~l~gk~vV~TGtl 658 (731)
++..+|.++.+.|-+
T Consensus 236 a~~iTG~~i~VDGG~ 250 (253)
T PRK06172 236 ASFTTGHSLMVDGGA 250 (253)
T ss_pred HCCCCCCEEEECCCH
T ss_conf 268259828739241
No 393
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=39.12 E-value=10 Score=16.92 Aligned_cols=18 Identities=22% Similarity=0.674 Sum_probs=11.1
Q ss_pred EEECCC--CCCCCCC-CCCCC
Q ss_conf 777043--2657750-10337
Q gi|254781172|r 428 FSFPSF--CPICQSR-VVRDL 445 (731)
Q Consensus 428 ~~~P~~--CP~Cgs~-l~~~~ 445 (731)
+..++. ||.||++ +..++
T Consensus 13 l~~~d~e~CP~Cgs~~~te~W 33 (64)
T COG2093 13 LTPEDTEICPVCGSTDLTEEW 33 (64)
T ss_pred CCCCCCCCCCCCCCCCCCHHH
T ss_conf 378877408788994000101
No 394
>PRK06463 fabG 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional
Probab=38.99 E-value=23 Score=14.32 Aligned_cols=14 Identities=21% Similarity=0.280 Sum_probs=8.2
Q ss_pred CCCCCCCEEEEECC
Q ss_conf 88216866999725
Q gi|254781172|r 644 SSEIENKKLVFTGT 657 (731)
Q Consensus 644 ~~~l~gk~vV~TGt 657 (731)
.+..+|.++++-|-
T Consensus 232 a~~iTG~~i~VDGG 245 (254)
T PRK06463 232 ARYITGQVIVADGG 245 (254)
T ss_pred HCCCCCCEEEECCC
T ss_conf 24915865996399
No 395
>PRK07791 short chain dehydrogenase; Provisional
Probab=38.74 E-value=23 Score=14.29 Aligned_cols=14 Identities=21% Similarity=0.363 Sum_probs=9.0
Q ss_pred CCCCCCCEEEEECC
Q ss_conf 88216866999725
Q gi|254781172|r 644 SSEIENKKLVFTGT 657 (731)
Q Consensus 644 ~~~l~gk~vV~TGt 657 (731)
++..+|.++.+.|-
T Consensus 242 asyITGq~l~VDGG 255 (285)
T PRK07791 242 SRDVTGKVFEVEGG 255 (285)
T ss_pred CCCCCCCEEEECCC
T ss_conf 07877875997799
No 396
>PRK07109 short chain dehydrogenase; Provisional
Probab=38.68 E-value=23 Score=14.28 Aligned_cols=12 Identities=8% Similarity=0.130 Sum_probs=4.5
Q ss_pred ECCCCHHHHHHH
Q ss_conf 659865566699
Q gi|254781172|r 153 LRGDGHSGEDVS 164 (731)
Q Consensus 153 TRGdG~~GeDVT 164 (731)
|=+.+-+|..+.
T Consensus 14 TGASsGIGra~A 25 (338)
T PRK07109 14 TGASAGVGRATA 25 (338)
T ss_pred ECCCCHHHHHHH
T ss_conf 484349999999
No 397
>cd01701 Pol_zeta Pol_zeta, a member of the Y-family of DNA polymerases. Y-family polymerases can transverse normal replication-blocking DNA lesions, such as cyclobutane pyrimidine dimers resulting from UV damage, at higher error rate. The Y-family has no 3'-5' exonuclease activity. Pol zeta has also been named Rev1; this subfamily is mainly present in eukaryotes.
Probab=38.66 E-value=18 Score=15.06 Aligned_cols=16 Identities=13% Similarity=0.289 Sum_probs=7.2
Q ss_pred CHHHHHHHHHHHHHCC
Q ss_conf 0354103555565305
Q gi|254781172|r 482 NIEGLGKQQLDFFFKS 497 (731)
Q Consensus 482 dI~GLG~k~Ie~L~e~ 497 (731)
+|-|+|+++.++|-+.
T Consensus 228 ~i~GIG~~t~~kL~~~ 243 (405)
T cd01701 228 DLPGVGSSTKEKLKSL 243 (405)
T ss_pred CCCCCCHHHHHHHHHC
T ss_conf 1587178999999984
No 398
>PRK02406 DNA polymerase IV; Validated
Probab=38.60 E-value=18 Score=15.15 Aligned_cols=27 Identities=30% Similarity=0.365 Sum_probs=12.2
Q ss_pred CHHHHHHHHHHHHHCCCCCCEEEEEHHHHCCH
Q ss_conf 03541035555653057654045410110106
Q gi|254781172|r 482 NIEGLGKQQLDFFFKSEDPAFSIRIPADIFTL 513 (731)
Q Consensus 482 dI~GLG~k~Ie~L~e~~~~~g~I~~~~DLy~L 513 (731)
++-|+|+++.++|-+.| |.++.||..+
T Consensus 184 ~l~GIG~~~~~~L~~~G-----I~ti~DL~~~ 210 (355)
T PRK02406 184 KIPGVGKVTAEKLHALG-----IRTCADLQKW 210 (355)
T ss_pred CCCCCCHHHHHHHHHCC-----CCCHHHHHHC
T ss_conf 05885889999999829-----8179997609
No 399
>PRK05270 galactose-1-phosphate uridylyltransferase; Provisional
Probab=38.41 E-value=23 Score=14.25 Aligned_cols=12 Identities=17% Similarity=0.180 Sum_probs=7.7
Q ss_pred HHCCCCCCCCEE
Q ss_conf 975996654148
Q gi|254781172|r 262 RCLGFPVNNGVR 273 (731)
Q Consensus 262 ~~~GF~v~~~~~ 273 (731)
..|||.-.||..
T Consensus 205 e~W~fQYSPYaY 216 (496)
T PRK05270 205 ESWGFQYSPYAY 216 (496)
T ss_pred CEEEEEECCCCE
T ss_conf 701467454105
No 400
>PRK08936 glucose-1-dehydrogenase; Provisional
Probab=38.29 E-value=23 Score=14.24 Aligned_cols=15 Identities=20% Similarity=0.246 Sum_probs=8.3
Q ss_pred CCCCCCEEEEECCCC
Q ss_conf 821686699972588
Q gi|254781172|r 645 SEIENKKLVFTGTLQ 659 (731)
Q Consensus 645 ~~l~gk~vV~TGtl~ 659 (731)
+..+|.++.+.|-+.
T Consensus 237 syiTG~~i~VDGG~t 251 (261)
T PRK08936 237 SYVTGITLFADGGMT 251 (261)
T ss_pred CCCCCCEEEECCCCC
T ss_conf 683387388795810
No 401
>cd02173 ECT CTP:phosphoethanolamine cytidylyltransferase (ECT) catalyzes the conversion of phosphoethanolamine to CDP-ethanolamine as part of the CDP#ethanolamine biosynthesis pathway. ECT expression in hepatocytes is localized predominantly to areas of the cytoplasm that are rich in rough endoplasmic reticulum. Several ECT's, including yeast and human ECT, have large repetitive sequences located within their N- and C-termini.
Probab=38.24 E-value=23 Score=14.23 Aligned_cols=29 Identities=21% Similarity=0.194 Sum_probs=18.0
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 00013421001456899998752234666
Q gi|254781172|r 524 IENILGFGDVSVTNLYDSINKRRNISLER 552 (731)
Q Consensus 524 l~~l~GfgeKsa~nL~~sIe~sK~~~L~r 552 (731)
+..++...--|.+.|++-|-+++..-..|
T Consensus 119 ~~~~~~~~giSTt~II~RIl~~r~~y~~R 147 (152)
T cd02173 119 FKEIDSGSDLTTRDIVQRIIKNRLAYEAR 147 (152)
T ss_pred EEEECCCCCCCHHHHHHHHHHHHHHHHHH
T ss_conf 99958999967999999999829999998
No 402
>PRK06603 enoyl-(acyl carrier protein) reductase; Provisional
Probab=38.24 E-value=23 Score=14.23 Aligned_cols=15 Identities=7% Similarity=-0.042 Sum_probs=7.6
Q ss_pred CCCCCCCEEEEECCC
Q ss_conf 882168669997258
Q gi|254781172|r 644 SSEIENKKLVFTGTL 658 (731)
Q Consensus 644 ~~~l~gk~vV~TGtl 658 (731)
++..+|.++++-|-+
T Consensus 238 s~~iTG~~i~vDGG~ 252 (260)
T PRK06603 238 SKGVTGEIHYVDCGY 252 (260)
T ss_pred HCCCCCCEEEECCCC
T ss_conf 237258717889798
No 403
>PRK07825 short chain dehydrogenase; Provisional
Probab=38.06 E-value=23 Score=14.21 Aligned_cols=15 Identities=13% Similarity=0.186 Sum_probs=9.1
Q ss_pred CCHHHHHHHHHHHHH
Q ss_conf 001456899998752
Q gi|254781172|r 532 DVSVTNLYDSINKRR 546 (731)
Q Consensus 532 eKsa~nL~~sIe~sK 546 (731)
|.-|+.++++|++.+
T Consensus 203 e~vA~~iv~~i~~~~ 217 (273)
T PRK07825 203 EDVAAAIVALVAKPR 217 (273)
T ss_pred HHHHHHHHHHHHCCC
T ss_conf 999999999996899
No 404
>TIGR02869 spore_SleB spore cortex-lytic enzyme; InterPro: IPR014224 The entry represents the spore cortex-lytic enzyme SleB from Bacillus subtilis and other Gram-positive, endospore-forming bacterial species. SleB is stored in an inactive form in the spore and activated during germination..
Probab=37.95 E-value=17 Score=15.24 Aligned_cols=31 Identities=16% Similarity=0.508 Sum_probs=22.3
Q ss_pred HHHHHHHHHHHCCCCCHHHH-HHHHHHHHHCC
Q ss_conf 46655332130123103541-03555565305
Q gi|254781172|r 467 QQLERLKHFVSRDAFNIEGL-GKQQLDFFFKS 497 (731)
Q Consensus 467 q~~~~i~hF~SK~aldI~GL-G~k~Ie~L~e~ 497 (731)
+....+..|=+|.+|.+||| |++|..+|+++
T Consensus 40 ~Ty~AVr~FQ~knGL~VDGivG~~T~~aLv~A 71 (232)
T TIGR02869 40 KTYKAVRKFQSKNGLTVDGIVGPKTKAALVKA 71 (232)
T ss_pred HHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHH
T ss_conf 69999999888708855642075789999876
No 405
>PRK08562 rpl32e 50S ribosomal protein L32e; Validated
Probab=37.88 E-value=5.5 Score=19.04 Aligned_cols=26 Identities=8% Similarity=-0.007 Sum_probs=13.3
Q ss_pred HHHHHHHHCCCCCCEEEEEHHHHCCH
Q ss_conf 35555653057654045410110106
Q gi|254781172|r 488 KQQLDFFFKSEDPAFSIRIPADIFTL 513 (731)
Q Consensus 488 ~k~Ie~L~e~~~~~g~I~~~~DLy~L 513 (731)
++.+.-|.-.|+...+|.++.||-.|
T Consensus 67 ~k~~Rgl~PsG~~~vlV~n~~dLe~L 92 (127)
T PRK08562 67 PKAVRGLHPSGYEEVLVHNVKELEAL 92 (127)
T ss_pred CHHHCCCCCCCCEEEEECCHHHHHHH
T ss_conf 58766869776878886788998854
No 406
>pfam08394 Arc_trans_TRASH Archaeal TRASH domain. 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=37.65 E-value=16 Score=15.58 Aligned_cols=37 Identities=16% Similarity=0.284 Sum_probs=19.4
Q ss_pred CCCCCCCCCCCCCCCCCCCCEEECCCCCCCCHHHHHHHH
Q ss_conf 265775010337865445210100354344114466553
Q gi|254781172|r 434 CPICQSRVVRDLNPKTGKLVAAHRCTGGLACSAQQLERL 472 (731)
Q Consensus 434 CP~Cgs~l~~~~~~~~~~~~~~~rC~n~~~Cpaq~~~~i 472 (731)
|-.||.++.-+.-......-+-..|++ +|..++.+++
T Consensus 1 CDYCG~eI~g~Pi~~k~~nrvYy~CC~--tC~~~lkk~l 37 (37)
T pfam08394 1 CDYCGKEIKGEPITYKVKNRVYYVCCP--TCLSDLKKKL 37 (37)
T ss_pred CCCCCCCCCCCCEEEEECCEEEEEECH--HHHHHHHHHC
T ss_conf 985677505995799975779999876--8889988519
No 407
>TIGR00577 fpg formamidopyrimidine-DNA glycosylase; InterPro: IPR000191 Formamidopyrimidine-DNA glycosylase (3.2.2.23 from EC) (Fapy-DNA glycosylase) (gene fpg) is a bacterial enzyme involved in DNA repair and which excise oxidized purine bases to release 2,6-diamino-4-hydroxy-5N-methylformamido- pyrimidine (Fapy) and 7,8-dihydro-8-oxoguanine (8-OxoG) residues. In addition to its glycosylase activity, FPG can also nick DNA at apurinic/apyrimidinic sites (AP sites). FPG is a monomeric protein of about 32 Kd which binds and require zinc for its activity. The C-terminal region is the zinc binding site in the enzyme where four conserved and essential cysteines are located ..
Probab=36.90 E-value=16 Score=15.52 Aligned_cols=27 Identities=22% Similarity=0.545 Sum_probs=16.0
Q ss_pred CCCC-CCCCCCCCCCCC---CCCCCCEEECCCC
Q ss_conf 4326-577501033786---5445210100354
Q gi|254781172|r 432 SFCP-ICQSRVVRDLNP---KTGKLVAAHRCTG 460 (731)
Q Consensus 432 ~~CP-~Cgs~l~~~~~~---~~~~~~~~~rC~n 460 (731)
+.|| .||+++++..-. ++++ ..+||++
T Consensus 260 ~pC~a~CGt~I~k~~~~LYGkDgR--gthfCp~ 290 (292)
T TIGR00577 260 EPCRARCGTTIEKEKVGLYGKDGR--GTHFCPQ 290 (292)
T ss_pred CCCCCCCCCEEEEEEEECCCCCCC--CEECCCC
T ss_conf 834367884478876530151675--1012688
No 408
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=36.82 E-value=12 Score=16.31 Aligned_cols=12 Identities=42% Similarity=1.088 Sum_probs=8.8
Q ss_pred CCCCCCCCCCCC
Q ss_conf 043265775010
Q gi|254781172|r 431 PSFCPICQSRVV 442 (731)
Q Consensus 431 P~~CP~Cgs~l~ 442 (731)
-.+||+|||.-+
T Consensus 185 ~~~CPvCGS~Pv 196 (308)
T COG3058 185 RQYCPVCGSMPV 196 (308)
T ss_pred CCCCCCCCCCCC
T ss_conf 410777688774
No 409
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=36.75 E-value=13 Score=16.06 Aligned_cols=24 Identities=13% Similarity=0.195 Sum_probs=13.3
Q ss_pred CCCCCCCCCCCCCCCCCCCCCEEECCCC
Q ss_conf 3265775010337865445210100354
Q gi|254781172|r 433 FCPICQSRVVRDLNPKTGKLVAAHRCTG 460 (731)
Q Consensus 433 ~CP~Cgs~l~~~~~~~~~~~~~~~rC~n 460 (731)
-||.||+.+++..-.. -...+|++
T Consensus 247 pC~~CGt~I~k~~~~g----R~t~~CP~ 270 (273)
T COG0266 247 PCRRCGTPIEKIKLGG----RSTFYCPV 270 (273)
T ss_pred CCCCCCCEEEEEEECC----CCCEECCC
T ss_conf 8874588767999868----76776878
No 410
>PRK11827 hypothetical protein; Provisional
Probab=36.64 E-value=17 Score=15.35 Aligned_cols=15 Identities=20% Similarity=0.744 Sum_probs=12.0
Q ss_pred CCCCCCCCCCCCCCC
Q ss_conf 326577501033786
Q gi|254781172|r 433 FCPICQSRVVRDLNP 447 (731)
Q Consensus 433 ~CP~Cgs~l~~~~~~ 447 (731)
.||.|.++|.++...
T Consensus 10 vCP~ckg~L~yd~~~ 24 (60)
T PRK11827 10 ACPVCNGKLWYNQEK 24 (60)
T ss_pred ECCCCCCCCEECCCC
T ss_conf 577889903398768
No 411
>pfam01655 Ribosomal_L32e Ribosomal protein L32. This family includes ribosomal protein L32 from eukaryotes and archaebacteria.
Probab=36.62 E-value=5.3 Score=19.20 Aligned_cols=27 Identities=11% Similarity=-0.001 Sum_probs=16.0
Q ss_pred HHHHHHHHHCCCCCCEEEEEHHHHCCH
Q ss_conf 035555653057654045410110106
Q gi|254781172|r 487 GKQQLDFFFKSEDPAFSIRIPADIFTL 513 (731)
Q Consensus 487 G~k~Ie~L~e~~~~~g~I~~~~DLy~L 513 (731)
+++.+.-|.-.|+...+|.++.||-.|
T Consensus 47 s~k~~Rgl~PsG~~~vlV~n~~dLe~l 73 (110)
T pfam01655 47 SPKKVRGLHPSGFKEVLVHNVKDLELL 73 (110)
T ss_pred CCHHHCCCCCCCCEEEEECCHHHHHHH
T ss_conf 766664779888878886798998998
No 412
>PRK03754 DNA-directed RNA polymerase subunit P; Provisional
Probab=36.50 E-value=13 Score=16.09 Aligned_cols=13 Identities=31% Similarity=0.817 Sum_probs=8.9
Q ss_pred CCCCCCCCCCCCC
Q ss_conf 3265775010337
Q gi|254781172|r 433 FCPICQSRVVRDL 445 (731)
Q Consensus 433 ~CP~Cgs~l~~~~ 445 (731)
.||.||+++....
T Consensus 26 rcpycgskilykp 38 (49)
T PRK03754 26 RCPYCGSKILYKP 38 (49)
T ss_pred CCCCCCCEEEECC
T ss_conf 3777677545458
No 413
>PRK07060 short chain dehydrogenase; Provisional
Probab=36.45 E-value=25 Score=14.03 Aligned_cols=15 Identities=20% Similarity=0.251 Sum_probs=11.2
Q ss_pred CCCCCCCEEEEECCC
Q ss_conf 882168669997258
Q gi|254781172|r 644 SSEIENKKLVFTGTL 658 (731)
Q Consensus 644 ~~~l~gk~vV~TGtl 658 (731)
++..+|.++++-|-+
T Consensus 228 ss~iTG~~i~VDGG~ 242 (245)
T PRK07060 228 ASMVSGVSLPVDGGY 242 (245)
T ss_pred HCCCCCCEEEECCCH
T ss_conf 258148428869563
No 414
>PRK07792 fabG 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional
Probab=36.36 E-value=25 Score=14.02 Aligned_cols=14 Identities=7% Similarity=0.363 Sum_probs=7.3
Q ss_pred CCCCCCCEEEEECC
Q ss_conf 88216866999725
Q gi|254781172|r 644 SSEIENKKLVFTGT 657 (731)
Q Consensus 644 ~~~l~gk~vV~TGt 657 (731)
.+..+|++|++-|-
T Consensus 237 as~ITGq~l~VdGG 250 (303)
T PRK07792 237 AAGVNGQLFIVYGP 250 (303)
T ss_pred CCCCCCCEEEECCC
T ss_conf 06987987998699
No 415
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain; InterPro: IPR011723 Zinc finger (Znf) domains are relatively small protein motifs that bind one or more zinc atoms, and which usually contain multiple finger-like protrusions that make tandem contacts with their target molecule. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis, 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. (Note that in certain cases, some Znf domains have diverged such that they still maintain their core structure, but have lost their ability to bind zinc, using other means such as salt bridges or binding to other metals to stabilise the finger-like folds. These domains can show strong sequence identity to zinc-binding motifs, and may therefore be included in Znf entries). This entry represents a region, which contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterised gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility . More information about these proteins can be found at Protein of the Month: Zinc Fingers ..
Probab=36.30 E-value=19 Score=14.92 Aligned_cols=30 Identities=20% Similarity=0.279 Sum_probs=19.8
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCC-EEECCCC
Q ss_conf 04326577501033786544521-0100354
Q gi|254781172|r 431 PSFCPICQSRVVRDLNPKTGKLV-AAHRCTG 460 (731)
Q Consensus 431 P~~CP~Cgs~l~~~~~~~~~~~~-~~~rC~n 460 (731)
-..||.|.+......+....... +..||.+
T Consensus 2 ~~~CP~C~t~y~V~~~~~G~~g~kv~VrC~~ 32 (40)
T TIGR02098 2 RIQCPNCKTSYRVDDSQLGANGRKVKVRCGK 32 (40)
T ss_pred EEECCCCCCEEEEECCCCCCCCCEEEEEECC
T ss_conf 6568998506888433478789878888189
No 416
>pfam08645 PNK3P Polynucleotide kinase 3 phosphatase. Polynucleotide kinase 3 phosphatases play a role in the repair of single breaks in DNA induced by DNA-damaging agents such as gamma radiation and camptothecin.
Probab=36.23 E-value=25 Score=14.01 Aligned_cols=46 Identities=24% Similarity=0.390 Sum_probs=29.5
Q ss_pred HHHHHHHCCCEEEEEEECCEEEEEECCCCC----------CHHHHHHHCCCEEECHHHH
Q ss_conf 999999829849981116321799778888----------6379899749917379999
Q gi|254781172|r 666 AQEYVTQLGAVVSAILSRKTDIIIVGDNPG----------SKLEKAQQLGVKIMNEEQF 714 (731)
Q Consensus 666 ~~~~ie~~Ggkv~sSVSkkT~~LI~ge~~g----------SKl~KA~~LgI~Ii~e~ef 714 (731)
+..+++..-+ ..+|..+-+| .+||.|| |=++=|.-+||+..++|||
T Consensus 102 ~~~~~~~~~~--~~~iD~~~Sf-~vGDaagr~~~~~D~s~sD~~FA~N~gikF~tpee~ 157 (158)
T pfam08645 102 WDELLEDYND--GITIDLEKSF-YVGDAAGRPARKKDFSDSDRKFALNVGIKFKTPEEF 157 (158)
T ss_pred HHHHHHHCCC--CCCCCCCCEE-EEECCCCCCCCCCCCCHHHHHHHHHCCCEECCCHHC
T ss_conf 9999997256--7544653018-984366887777775403799999859816580202
No 417
>PRK03352 DNA polymerase IV; Validated
Probab=36.16 E-value=21 Score=14.64 Aligned_cols=27 Identities=19% Similarity=0.185 Sum_probs=13.3
Q ss_pred CHHHHHHHHHHHHHCCCCCCEEEEEHHHHCCH
Q ss_conf 03541035555653057654045410110106
Q gi|254781172|r 482 NIEGLGKQQLDFFFKSEDPAFSIRIPADIFTL 513 (731)
Q Consensus 482 dI~GLG~k~Ie~L~e~~~~~g~I~~~~DLy~L 513 (731)
+|-|+|+++-++|-..| |.++.||...
T Consensus 181 ~i~GIG~~~~~kL~~~G-----I~Ti~DL~~~ 207 (345)
T PRK03352 181 ALWGVGPKTAKKLAALG-----ITTVADLAAT 207 (345)
T ss_pred HCCCCCHHHHHHHHHCC-----CCCHHHHHCC
T ss_conf 12782899999999759-----9719998669
No 418
>cd01703 Pol_iota Pol iota is member of the DNA polymerase Y-family, and has also been called Rad30 homolog B. Unlike classic DNA polymerases,Y-family polymerases are induced by DNA damage. They can transverse normal replication-blocking DNA lesions. Unlike Pol eta, Pol iota is unable to replicate through a cis-syn T-T dimer. In human Pol iota, the base-pairing mode in the active site at the replicative end mat bee Hoogsteen instead of Watson-Click. Human Pol iota can incorporate the correct nucleotide opposite a purine much more efficiently than opposite a pyrimidine. Pol iota prefers to insert Guanosine instead of Adenosine opposite Thymidine.
Probab=36.14 E-value=21 Score=14.60 Aligned_cols=49 Identities=18% Similarity=0.242 Sum_probs=32.4
Q ss_pred CHHHHHHHHHHHHHCCCCCCEEEEEHHHHCCHHHHHHHHCCCCCCCCCCCCCHHHHHHHHH
Q ss_conf 0354103555565305765404541011010677753100010001342100145689999
Q gi|254781172|r 482 NIEGLGKQQLDFFFKSEDPAFSIRIPADIFTLQRRQQTSTTKIENILGFGDVSVTNLYDSI 542 (731)
Q Consensus 482 dI~GLG~k~Ie~L~e~~~~~g~I~~~~DLy~L~~~~~~~~~~l~~l~GfgeKsa~nL~~sI 542 (731)
+|-|+|.++.++|-+.| |.++.||....... .|. ..||+..+..|++-.
T Consensus 214 ki~GIG~kt~~~L~~~g-----i~ti~dl~~~~~~~-----~l~--~~fG~~~g~~l~~~a 262 (394)
T cd01703 214 KIPGIGYKTAKKLEDHG-----ISSVRDLQECSELL-----LLE--KGFGKGIAQRIWGLA 262 (394)
T ss_pred HHCCCCHHHHHHHHHCC-----CEEHHHHHCCCHHH-----HHH--HHHHHHHHHHHHHHH
T ss_conf 52781799999999838-----92679876588799-----999--987889999999995
No 419
>PRK02794 DNA polymerase IV; Provisional
Probab=35.84 E-value=22 Score=14.47 Aligned_cols=31 Identities=19% Similarity=0.111 Sum_probs=20.1
Q ss_pred CCHHHHHHHHHHHHHCCCCCCEEEEEHHHHCCHHHH
Q ss_conf 103541035555653057654045410110106777
Q gi|254781172|r 481 FNIEGLGKQQLDFFFKSEDPAFSIRIPADIFTLQRR 516 (731)
Q Consensus 481 ldI~GLG~k~Ie~L~e~~~~~g~I~~~~DLy~L~~~ 516 (731)
=+|-|+|+++-++|-..| |.++.||..++..
T Consensus 212 ~diwGIG~rt~~kL~~~G-----I~Ti~DL~~~~~~ 242 (417)
T PRK02794 212 GFIWGVGPATAARLAADG-----IRTIGDLQRADEA 242 (417)
T ss_pred HHHCCCCHHHHHHHHHCC-----CCCHHHHHCCCHH
T ss_conf 551684689999999849-----9099998659998
No 420
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=35.77 E-value=14 Score=15.83 Aligned_cols=11 Identities=36% Similarity=0.809 Sum_probs=9.1
Q ss_pred CCCCCCCCCCC
Q ss_conf 32657750103
Q gi|254781172|r 433 FCPICQSRVVR 443 (731)
Q Consensus 433 ~CP~Cgs~l~~ 443 (731)
+||.||.+.+.
T Consensus 24 tCp~Cghe~vs 34 (104)
T COG4888 24 TCPRCGHEKVS 34 (104)
T ss_pred ECCCCCCEEEE
T ss_conf 16855872355
No 421
>pfam06750 DiS_P_DiS Bacterial Peptidase A24 N-terminal domain. This family is found at the N-terminus of the pre-pilin peptidases (pfam01478). It's function has not been specifically determined; however some of the family have been characterized as bifunctional. and this domain may contain the N-methylation activity (EC:2.1.1.-). It consists of an intracellular region between a pair of transmembrane. This region contains an invariant proline and two almost fully conserved disulphide bridges - hence the name DiS-P-DiS. The cysteines have been shown to be essential to the overall function of the enzyme in, but their role was incorrectly ascribed.
Probab=35.75 E-value=13 Score=16.08 Aligned_cols=19 Identities=26% Similarity=0.349 Sum_probs=13.9
Q ss_pred EEECCCCCCCCCCCCCCCC
Q ss_conf 7770432657750103378
Q gi|254781172|r 428 FSFPSFCPICQSRVVRDLN 446 (731)
Q Consensus 428 ~~~P~~CP~Cgs~l~~~~~ 446 (731)
+..+++||.|+..+.+...
T Consensus 24 ~~prS~C~~C~~~L~~~~l 42 (86)
T pfam06750 24 VFPRSHCPHCGHKLRWYDN 42 (86)
T ss_pred CCCCCCCCCCCCCCHHHHH
T ss_conf 8999809356996754783
No 422
>KOG1247 consensus
Probab=35.74 E-value=9.5 Score=17.22 Aligned_cols=49 Identities=22% Similarity=0.265 Sum_probs=27.5
Q ss_pred EEEEEECHHHHH-HHHHHHHCC--CCCCCCHHHHHHHHHHC-CCHHHHHCCCE
Q ss_conf 999985202123-455643148--54334234567777523-45555301110
Q gi|254781172|r 189 GEVYISKNDFLA-LNDEMIAVG--RKPYANPRNAASGILRR-LNPTDITRYLN 237 (731)
Q Consensus 189 GEv~m~~~~F~~-lN~~~~~~g--~~~f~NpRN~aaG~lr~-~d~~~~~r~L~ 237 (731)
--+|++...|+. +-+-....+ ..==.|++|..--.||. +.|.-..|+|.
T Consensus 198 ~h~Fl~L~kl~~~lee~~~~~~~~~~WS~Na~~it~sWlk~gl~pRCiTRDLk 250 (567)
T KOG1247 198 QHLFLSLDKLEPRLEEWLRRTLVEGDWSQNAQNITRSWLKDGLKPRCITRDLK 250 (567)
T ss_pred EEEEEEHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCC
T ss_conf 27998757767899999973054577761167899999974666520002255
No 423
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=35.62 E-value=17 Score=15.29 Aligned_cols=13 Identities=23% Similarity=0.590 Sum_probs=7.3
Q ss_pred CCCCCCCCCCCCC
Q ss_conf 4326577501033
Q gi|254781172|r 432 SFCPICQSRVVRD 444 (731)
Q Consensus 432 ~~CP~Cgs~l~~~ 444 (731)
.+||.||+++...
T Consensus 101 rfC~~CG~~t~~~ 113 (257)
T PRK00241 101 RFCGYCGHPTHPS 113 (257)
T ss_pred CCCCCCCCCCCCC
T ss_conf 8456567366338
No 424
>PRK13638 cbiO cobalt transporter ATP-binding subunit; Provisional
Probab=35.58 E-value=23 Score=14.27 Aligned_cols=31 Identities=29% Similarity=0.491 Sum_probs=22.4
Q ss_pred CCEEEEECCCCHHHHHHHCCCCCCCCCCCCCCCCCEEEEEECCCCHH
Q ss_conf 64000101489899975023454322246844076899983587025
Q gi|254781172|r 365 GALITNATLHNEDYIKGLDASGKVMRGGRDIRVGDRVLVKRAGEVIP 411 (731)
Q Consensus 365 G~~V~ratlhN~~~I~~l~~~~~~~~~~~~I~iGd~V~I~RaGdVIP 411 (731)
|.||=- +-|+.+++.++ -|+|.|.+.|.||=
T Consensus 186 G~tiii-vsHdl~~v~~~---------------aDrv~vl~~G~iva 216 (271)
T PRK13638 186 GNHVII-SSHDIDLIYEI---------------SDAVYVLRQGQILT 216 (271)
T ss_pred CCEEEE-ECCCHHHHHHH---------------CCEEEEEECCEEEE
T ss_conf 999999-84888999996---------------99999998998999
No 425
>LOAD_Hrd consensus
Probab=35.37 E-value=26 Score=13.91 Aligned_cols=26 Identities=12% Similarity=0.026 Sum_probs=19.8
Q ss_pred CCCCHHHHHCCCCCCHHHHHHHHHHH
Q ss_conf 51177876138886789999999996
Q gi|254781172|r 591 NNDDWLSLIRVPLVGDIIAQAIVEFY 616 (731)
Q Consensus 591 ~~~~~e~L~~I~GiG~~~A~si~~ff 616 (731)
.-.+.++|..|+|||+...+.+-+.|
T Consensus 42 ~P~t~~eL~~I~Gig~~k~~~yG~~i 67 (77)
T LOAD_Hrd 42 LPTTVSELLAIDGVGEAKVEKYGDRI 67 (77)
T ss_pred CCCCHHHHCCCCCCCHHHHHHHHHHH
T ss_conf 89999998289996999999999999
No 426
>TIGR02311 HpaI 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase; InterPro: IPR012689 This entry represents the aldolase which performs the final step unique to the 4-hydroxyphenylacetic acid catabolism pathway in which 2,4-dihydroxyhept-2-ene-1,7-dioic acid is split into pyruvate and succinate-semialdehyde. The gene for enzyme is generally found adjacent to other genes for this pathway.; GO: 0018802 24-dihydroxyhept-2-ene-17-dioate aldolase activity, 0010124 phenylacetate catabolic process.
Probab=35.33 E-value=24 Score=14.17 Aligned_cols=68 Identities=24% Similarity=0.324 Sum_probs=37.0
Q ss_pred CCHHHHHHHHHHHHHHHCCCHHHHHHHHHH----------HHHCCCCCHHHHHCCCCCCHH------HHHHHHHHHCCHH
Q ss_conf 010111168999999882998999997897----------761251177876138886789------9999999966979
Q gi|254781172|r 557 LGIRHVGAEIARSLAKYYLSYQNFAQEINN----------IIAHNNDDWLSLIRVPLVGDI------IAQAIVEFYQNPR 620 (731)
Q Consensus 557 LGI~~vG~~~Ak~La~~f~si~~l~~~~~~----------~~~~~~~~~e~L~~I~GiG~~------~A~si~~ff~~~~ 620 (731)
-||||||.--|| +..|..+.+..+.-++ ..++ ...+++.++||+.-+ .|.|+ -|.-+|.
T Consensus 111 ~GiRGVGSALAR--ASrwNrIp~Ylq~AdeeiClLlQVEtr~al--~NL~~Ia~VeGVDGVFiGPADLaasm-GH~GnPs 185 (249)
T TIGR02311 111 KGIRGVGSALAR--ASRWNRIPDYLQQADEEICLLLQVETREAL--ENLEEIAAVEGVDGVFIGPADLAASM-GHLGNPS 185 (249)
T ss_pred CCCCCCHHHHHH--HHHCCCHHHHHCCHHHHEEHHHHHHHHHHH--HHHHHHHCCCCCCCEEECCHHHHHHC-CCCCCCC
T ss_conf 951340078776--322176125760521320232326579988--62157750178662475712443401-5688869
Q ss_pred HHHHHHHHH
Q ss_conf 999999999
Q gi|254781172|r 621 NICAVEALL 629 (731)
Q Consensus 621 n~~~i~~L~ 629 (731)
+-+..+...
T Consensus 186 HPEV~~AI~ 194 (249)
T TIGR02311 186 HPEVQDAID 194 (249)
T ss_pred CHHHHHHHH
T ss_conf 615899999
No 427
>PRK12367 short chain dehydrogenase; Provisional
Probab=35.30 E-value=26 Score=13.90 Aligned_cols=23 Identities=22% Similarity=0.341 Sum_probs=14.8
Q ss_pred CCEEEEEEECCCCHHHHHHHHHHH
Q ss_conf 998998886598655666999775
Q gi|254781172|r 145 KGKFVYAALRGDGHSGEDVSACIR 168 (731)
Q Consensus 145 ~G~L~~a~TRGdG~~GeDVT~n~~ 168 (731)
+|+= -|+|-..|..|.-.|...+
T Consensus 16 kgKt-IgITGAsGaLG~AL~k~f~ 38 (250)
T PRK12367 16 NGKR-IGITGASGALGKALTKLFR 38 (250)
T ss_pred CCCE-EEEECCCCHHHHHHHHHHH
T ss_conf 8987-9996787389999999999
No 428
>TIGR02390 RNA_pol_rpoA1 DNA-directed RNA polymerase subunit A'; InterPro: IPR012758 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 kD, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of the archaeal A' subunit of the DNA-directed RNA polymerase. The example from Methanococcus jannaschii contains an intein.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0008270 zinc ion binding, 0006350 transcription.
Probab=35.25 E-value=14 Score=15.89 Aligned_cols=63 Identities=14% Similarity=0.071 Sum_probs=32.5
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHCCHHHCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCHHHC---------CCHHHHHH
Q ss_conf 798208789999999999998977203115899996200364323577504516642570215---------99999999
Q gi|254781172|r 39 SKPIILDSEYDALKRRCDAIAHAFPDLARSEDPNGPLNKIGGEMNLSLFKVTHSIPTLSLEKI---------WNIEDLRK 109 (731)
Q Consensus 39 ~~p~isD~eYD~L~~~L~~le~~~p~~~~~~~p~spt~~Vg~~~~~~~~kv~H~~pMlSL~k~---------~~~~el~~ 109 (731)
..|..+...-+.|..++.....+.-. .| -....-.||+...|.-=.++. -+.+|+.+
T Consensus 124 ~~~a~~nfiq~~l~~~i~k~A~k~~~--------CP------hCg~~q~~ik~eKP~~f~e~~~~G~eeW~KLTP~eiRE 189 (901)
T TIGR02390 124 GSLALSNFIQETLIEKIVKEAAKRMK--------CP------HCGEEQKKIKFEKPTYFYEEDKEGKEEWVKLTPSEIRE 189 (901)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHCCC--------CC------CCCCCCCCEEEECCEEEEECCCCCCCCCEECCCHHHHH
T ss_conf 87467888888889999999861787--------98------88741243245277157755755551214428179999
Q ss_pred HHHHHH
Q ss_conf 999999
Q gi|254781172|r 110 FITRIY 115 (731)
Q Consensus 110 w~~~~~ 115 (731)
|.+||-
T Consensus 190 rLEkiP 195 (901)
T TIGR02390 190 RLEKIP 195 (901)
T ss_pred HHHCCC
T ss_conf 751687
No 429
>KOG4169 consensus
Probab=35.20 E-value=26 Score=13.89 Aligned_cols=17 Identities=24% Similarity=0.294 Sum_probs=11.5
Q ss_pred EEECCCCHHHHHHHHHH
Q ss_conf 88659865566699977
Q gi|254781172|r 151 AALRGDGHSGEDVSACI 167 (731)
Q Consensus 151 a~TRGdG~~GeDVT~n~ 167 (731)
.+|-|-|-+|-+.+..+
T Consensus 9 ~vtggagGIGl~~sk~L 25 (261)
T KOG4169 9 LVTGGAGGIGLATSKAL 25 (261)
T ss_pred EEECCCCHHHHHHHHHH
T ss_conf 99637863669999999
No 430
>PRK03918 chromosome segregation protein; Provisional
Probab=35.14 E-value=14 Score=15.93 Aligned_cols=12 Identities=25% Similarity=0.894 Sum_probs=9.0
Q ss_pred CCCCCCCCCCCC
Q ss_conf 432657750103
Q gi|254781172|r 432 SFCPICQSRVVR 443 (731)
Q Consensus 432 ~~CP~Cgs~l~~ 443 (731)
..||+||+++..
T Consensus 439 ~~CPvcg~~~~~ 450 (882)
T PRK03918 439 GKCPVCGRELTE 450 (882)
T ss_pred CCCCCCCCCCCC
T ss_conf 999989995761
No 431
>cd01403 Cyt_c_Oxidase_VIIb Cytochrome C oxidase chain VIIb. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. The VIIb subunit is found only in eukaryotes and its specific function remains unclear. A rare polymorphism of the CcO VIIb gene may be associated with the high risk of nasopharyngeal carcinoma in a Cantonese family.
Probab=35.09 E-value=22 Score=14.48 Aligned_cols=21 Identities=19% Similarity=0.248 Sum_probs=17.0
Q ss_pred EEEEEEEEEEEECCCCEEEEE
Q ss_conf 589987889940356225899
Q gi|254781172|r 335 ASTRLLDIDIQIGRTGILTPV 355 (731)
Q Consensus 335 ~~T~v~~I~wqvgRtG~itPv 355 (731)
...+-.+|+|+.|--|++||-
T Consensus 27 yv~TQ~gI~WnlSPVGrVtPk 47 (51)
T cd01403 27 YVMTQTGIEWNLSPVGRVTPK 47 (51)
T ss_pred HEEEEEEEEECCCCCCCCCCC
T ss_conf 203531123636654433640
No 432
>PTZ00180 60S ribosomal protein L2; Provisional
Probab=35.07 E-value=26 Score=13.88 Aligned_cols=87 Identities=17% Similarity=0.188 Sum_probs=46.9
Q ss_pred ECCCCCEEEEEEEEEEEEECCCCEEEEEEEEEEEEECCCEEEEECCCCHHHHHHHCCCCCCCCCCCCCCCCCEEEEEECC
Q ss_conf 11456215899878899403562258999974333026400010148989997502345432224684407689998358
Q gi|254781172|r 328 HKFAEKQASTRLLDIDIQIGRTGILTPVARLEPVNIGGALITNATLHNEDYIKGLDASGKVMRGGRDIRVGDRVLVKRAG 407 (731)
Q Consensus 328 ~Kf~~e~~~T~v~~I~wqvgRtG~itPva~~ePV~l~G~~V~ratlhN~~~I~~l~~~~~~~~~~~~I~iGd~V~I~RaG 407 (731)
||-...-...+|.+|+...+||..| |.++ +....++++++..-+. -.+|.+||.|.. |
T Consensus 34 f~r~~~~i~g~V~~IeyDPnRsA~I---Alv~----------y~dG~~~~~~k~yIlA------peGl~vGd~I~s---G 91 (260)
T PTZ00180 34 YAERHGYMRGVVKSIEHEAGRGAAL---ARVE----------FRHPYKFRRVKELMVA------PEGMFTGQSVFC---G 91 (260)
T ss_pred CCCCCCCCCEEEEEEEECCCCCCEE---EEEE----------ECCCCCCCCCEEEEEE------ECCCCCCCEEEE---C
T ss_conf 4333699778999989898998608---8999----------4377755662689980------389889998986---9
Q ss_pred CCHHHHHHHCCCCCCCCCCEEEECCCCCCCCCCCCC
Q ss_conf 702566541012357873047770432657750103
Q gi|254781172|r 408 EVIPKVVDIIVNERHPDAQPFSFPSFCPICQSRVVR 443 (731)
Q Consensus 408 dVIP~I~~Vi~~~r~~~~~~~~~P~~CP~Cgs~l~~ 443 (731)
+-.|--.+..... -.+|.=+..||=|+..
T Consensus 92 ~~a~i~~GN~lpL-------~~IP~Gt~IhNIE~~P 120 (260)
T PTZ00180 92 QKAPLAIGNVLPL-------GQITEGCIVCNVEAKP 120 (260)
T ss_pred CCCCCCCCCCCCH-------HHCCCCCEEEEEEECC
T ss_conf 8667777563546-------3389987788673038
No 433
>PRK12829 short chain dehydrogenase; Provisional
Probab=35.07 E-value=26 Score=13.88 Aligned_cols=16 Identities=13% Similarity=0.337 Sum_probs=11.6
Q ss_pred CCCCCCCEEEEECCCC
Q ss_conf 8821686699972588
Q gi|254781172|r 644 SSEIENKKLVFTGTLQ 659 (731)
Q Consensus 644 ~~~l~gk~vV~TGtl~ 659 (731)
++..+|.++.+.|-++
T Consensus 247 ss~iTG~~i~VDGGl~ 262 (264)
T PRK12829 247 ARYITGQAISVDGNVE 262 (264)
T ss_pred HCCCCCCEEEECCCCC
T ss_conf 4580587779787802
No 434
>pfam04423 Rad50_zn_hook Rad50 zinc hook motif. 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.
Probab=34.98 E-value=14 Score=15.97 Aligned_cols=10 Identities=30% Similarity=0.989 Sum_probs=7.6
Q ss_pred CCCCCCCCCC
Q ss_conf 3265775010
Q gi|254781172|r 433 FCPICQSRVV 442 (731)
Q Consensus 433 ~CP~Cgs~l~ 442 (731)
.||+||.++.
T Consensus 22 ~CPvC~r~l~ 31 (54)
T pfam04423 22 CCPVCGRPLD 31 (54)
T ss_pred CCCCCCCCCC
T ss_conf 7776699766
No 435
>COG1570 XseA Exonuclease VII, large subunit [DNA replication, recombination, and repair]
Probab=34.98 E-value=26 Score=13.87 Aligned_cols=16 Identities=38% Similarity=0.802 Sum_probs=9.3
Q ss_pred HHCCCHHHHHHHHHHH
Q ss_conf 2159999999999999
Q gi|254781172|r 99 EKIWNIEDLRKFITRI 114 (731)
Q Consensus 99 ~k~~~~~el~~w~~~~ 114 (731)
++.|+..||....++.
T Consensus 3 ~~~~sVSeln~~ik~l 18 (440)
T COG1570 3 EKILSVSELNDYIKRL 18 (440)
T ss_pred CCEECHHHHHHHHHHH
T ss_conf 8705199999999999
No 436
>PRK08416 7-alpha-hydroxysteroid dehydrogenase; Provisional
Probab=34.97 E-value=26 Score=13.86 Aligned_cols=13 Identities=15% Similarity=0.363 Sum_probs=7.0
Q ss_pred CCCCCCEEEEECC
Q ss_conf 8216866999725
Q gi|254781172|r 645 SEIENKKLVFTGT 657 (731)
Q Consensus 645 ~~l~gk~vV~TGt 657 (731)
+..+|.++++-|-
T Consensus 244 s~iTG~~i~VDGG 256 (260)
T PRK08416 244 SWLTGQTIIVDGG 256 (260)
T ss_pred CCCCCCEEEECCC
T ss_conf 6865983898977
No 437
>PRK09242 tropinone reductase; Provisional
Probab=34.53 E-value=26 Score=13.81 Aligned_cols=15 Identities=20% Similarity=0.308 Sum_probs=8.4
Q ss_pred CCCCCCCEEEEECCC
Q ss_conf 882168669997258
Q gi|254781172|r 644 SSEIENKKLVFTGTL 658 (731)
Q Consensus 644 ~~~l~gk~vV~TGtl 658 (731)
++..+|.++.+-|-+
T Consensus 239 s~~iTGq~i~VDGG~ 253 (258)
T PRK09242 239 ASYITGECIAVDGGF 253 (258)
T ss_pred HCCCCCCEEEECCCH
T ss_conf 247548538989073
No 438
>PRK01122 potassium-transporting ATPase subunit B; Provisional
Probab=34.53 E-value=17 Score=15.33 Aligned_cols=56 Identities=18% Similarity=0.327 Sum_probs=30.1
Q ss_pred CCCEEEEECCCCCCCHHHHHHHHHHCCCEE---EEEEECCE-EEEEECCCCCCHHHHHHHCCCEE
Q ss_conf 686699972588998789999999829849---98111632-17997788886379899749917
Q gi|254781172|r 648 ENKKLVFTGTLQKIQRHKAQEYVTQLGAVV---SAILSRKT-DIIIVGDNPGSKLEKAQQLGVKI 708 (731)
Q Consensus 648 ~gk~vV~TGtl~~~~R~e~~~~ie~~Ggkv---~sSVSkkT-~~LI~ge~~gSKl~KA~~LgI~I 708 (731)
.|+.+.|||- -=+|+-.+-.+.=|.. .+.|.|.. |.++..|+++ |+-.|-+-|=.|
T Consensus 511 ~G~vVAMtGD----GvNDAPALa~ADVGIAMgsGTdvAkEAADmVLLDdnf~-~iv~aV~~Gr~i 570 (684)
T PRK01122 511 EGRLVAMTGD----GTNDAPALAQADVGVAMNSGTQAAKEAGNMVDLDSNPT-KLIEVVEIGKQL 570 (684)
T ss_pred CCCEEEEECC----CCCHHHHHHHCCEEEEECCCCHHHHHHHCEEEECCCHH-HHHHHHHHHHHH
T ss_conf 8597999628----82158888409977873775689998608999459848-899999999999
No 439
>PRK13811 orotate phosphoribosyltransferase; Provisional
Probab=34.51 E-value=26 Score=13.81 Aligned_cols=63 Identities=21% Similarity=0.320 Sum_probs=40.3
Q ss_pred CCCCCCEEEE------ECCCCCCCHHHHHHHHHHCCCEEEEEEECCEEEEEECCCCCCHHHHHHHCCCEEECHHHHHHHH
Q ss_conf 8216866999------7258899878999999982984998111632179977888863798997499173799999999
Q gi|254781172|r 645 SEIENKKLVF------TGTLQKIQRHKAQEYVTQLGAVVSAILSRKTDIIIVGDNPGSKLEKAQQLGVKIMNEEQFLFLL 718 (731)
Q Consensus 645 ~~l~gk~vV~------TGtl~~~~R~e~~~~ie~~Ggkv~sSVSkkT~~LI~ge~~gSKl~KA~~LgI~Ii~e~ef~~ll 718 (731)
+.+.|++|++ || -|=.++.+.+++.|++|..-++ |+.-+.| .-+...+.||++.+--.+.++|
T Consensus 100 G~~~G~~VlvVEDViTTG----~S~~e~i~~l~~~G~~V~~v~~------ivDR~eg-~~e~l~~~Gv~~~sl~t~~dll 168 (170)
T PRK13811 100 GDVAGKRVLLVEDVTTSG----GSALYGIEQLRSAGAVVDDVVT------VVDREEG-AEELLAELDITLTPLVRVSELL 168 (170)
T ss_pred CCCCCCEEEEEEEEECCC----CCHHHHHHHHHHCCCEEEEEEE------EEECCCC-HHHHHHHCCCEEEEEEEHHHHH
T ss_conf 234899899999644578----1189999999988997999999------9977747-7999996699099953289942
No 440
>PRK12826 3-ketoacyl-(acyl-carrier-protein) reductase; Reviewed
Probab=34.49 E-value=26 Score=13.81 Aligned_cols=13 Identities=23% Similarity=0.279 Sum_probs=7.0
Q ss_pred CCCCCCEEEEECC
Q ss_conf 8216866999725
Q gi|254781172|r 645 SEIENKKLVFTGT 657 (731)
Q Consensus 645 ~~l~gk~vV~TGt 657 (731)
+..+|..+.+.|-
T Consensus 236 ~~itG~~i~vDGG 248 (253)
T PRK12826 236 RYITGQTLPVDGG 248 (253)
T ss_pred CCCCCCEEEECCC
T ss_conf 2956873887899
No 441
>pfam11376 DUF3179 Protein of unknown function (DUF3179). This family of proteins has no known function.
Probab=34.49 E-value=14 Score=15.96 Aligned_cols=11 Identities=18% Similarity=0.649 Sum_probs=5.2
Q ss_pred ECCEEEEEEEE
Q ss_conf 15818999998
Q gi|254781172|r 133 KIDGTMITIRY 143 (731)
Q Consensus 133 KiDG~sisl~Y 143 (731)
-++|..+.++|
T Consensus 54 ~igg~pv~vTy 64 (261)
T pfam11376 54 TLGGRPVAVTY 64 (261)
T ss_pred EECCEEEEEEE
T ss_conf 57898789986
No 442
>TIGR02487 NrdD anaerobic ribonucleoside-triphosphate reductase; InterPro: IPR012833 This entry is found in the oxygen-sensitive (anaerobic, class III) ribonucleotide reductase. The mechanism of the enzyme involves a glycine-centred radical , a C-terminal zinc binding site , and a set of conserved active site cysteines and asparagines . This enzyme requires an activating component, NrdG, a radical-SAM domain containing enzyme (IPR012837 from INTERPRO). Together the two form an alpha-2/beta-2 heterodimer.; GO: 0008998 ribonucleoside-triphosphate reductase activity, 0016491 oxidoreductase activity.
Probab=34.46 E-value=15 Score=15.70 Aligned_cols=86 Identities=13% Similarity=0.106 Sum_probs=41.1
Q ss_pred CCCCHHHHHHHHHHHHHCC-CCCCEEEEEHHHHCCHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHH-HHH-HHHHHHH
Q ss_conf 2310354103555565305-765404541011010677753100010001342100145689999875-223-4666776
Q gi|254781172|r 479 DAFNIEGLGKQQLDFFFKS-EDPAFSIRIPADIFTLQRRQQTSTTKIENILGFGDVSVTNLYDSINKR-RNI-SLERFIF 555 (731)
Q Consensus 479 ~aldI~GLG~k~Ie~L~e~-~~~~g~I~~~~DLy~L~~~~~~~~~~l~~l~GfgeKsa~nL~~sIe~s-K~~-~L~r~L~ 555 (731)
.++++-||-|.. ..|+.. + +..++. . -++.+ +-+.+-+++.-|... .+- .=..+.+
T Consensus 414 ~siGfiGl~E~~-~~l~G~e~----~~e~~~------r------rDWi~----a~~l~~~~~~~~~~~~~~~~~e~~~~~ 472 (655)
T TIGR02487 414 LSIGFIGLNEAL-VALTGKEH----LHEEEN------R------RDWIE----ARELAIKILEFIRDKVDELKKETGLNY 472 (655)
T ss_pred EEEEHHHHHHHH-HHHCCCCC----EEECCC------C------HHHHH----HHHHHHHHHHHHHHHHHHHHHHHCCCE
T ss_conf 874036789999-99719983----224775------2------46999----999999999999999999998619716
Q ss_pred HC-CHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCC-HHHHHC---CC-CCCHH
Q ss_conf 30-1011116899999988299899999789776125117-787613---88-86789
Q gi|254781172|r 556 SL-GIRHVGAEIARSLAKYYLSYQNFAQEINNIIAHNNDD-WLSLIR---VP-LVGDI 607 (731)
Q Consensus 556 AL-GI~~vG~~~Ak~La~~f~si~~l~~~~~~~~~~~~~~-~e~L~~---I~-GiG~~ 607 (731)
++ .-| +|++|-.+|+. + .++.-. |+ |++++
T Consensus 473 sv~~TP--AEsl~~Rfa~~--------------------Dl~~~fg~a~~i~kG~~d~ 508 (655)
T TIGR02487 473 SVYATP--AESLCGRFAKK--------------------DLREEFGEAAKIPKGVTDK 508 (655)
T ss_pred EEEECC--CHHHHHHHHHH--------------------HHHHHCCCCEEEECCCCCC
T ss_conf 899668--42078999998--------------------7676466410541033666
No 443
>COG1569 Predicted nucleic acid-binding protein, contains PIN domain [General function prediction only]
Probab=34.44 E-value=25 Score=14.04 Aligned_cols=38 Identities=24% Similarity=0.347 Sum_probs=24.5
Q ss_pred EECCEEEEEECCCCCCHHHHHHHC-CCEEECHHHHHHHHHH
Q ss_conf 116321799778888637989974-9917379999999988
Q gi|254781172|r 681 LSRKTDIIIVGDNPGSKLEKAQQL-GVKIMNEEQFLFLLQQ 720 (731)
Q Consensus 681 VSkkT~~LI~ge~~gSKl~KA~~L-gI~Ii~e~ef~~ll~~ 720 (731)
+++|-+|||.||... +.---+. -+.|++.+||+.....
T Consensus 101 ~~~kA~~lvTgD~dL--L~lr~~n~~~~Iltp~eF~~~~~~ 139 (142)
T COG1569 101 YESKADYLVTGDQDL--LVLRDENKRVEILTPQEFLEEVLK 139 (142)
T ss_pred HHCCCCEEEECCHHH--HEECCCCCCEEECCHHHHHHHHHH
T ss_conf 964688899726155--010366785797379999999997
No 444
>PRK06997 enoyl-(acyl carrier protein) reductase; Provisional
Probab=34.39 E-value=26 Score=13.80 Aligned_cols=15 Identities=7% Similarity=0.071 Sum_probs=9.3
Q ss_pred CCCCCCCEEEEECCC
Q ss_conf 882168669997258
Q gi|254781172|r 644 SSEIENKKLVFTGTL 658 (731)
Q Consensus 644 ~~~l~gk~vV~TGtl 658 (731)
.+..+|.++.+.|-+
T Consensus 237 as~iTGq~i~VDGG~ 251 (260)
T PRK06997 237 ASGVTGEITHVDSGF 251 (260)
T ss_pred HCCCCCCEEEECCCH
T ss_conf 337058726879785
No 445
>PRK08245 hypothetical protein; Validated
Probab=34.38 E-value=26 Score=13.80 Aligned_cols=21 Identities=24% Similarity=0.205 Sum_probs=16.4
Q ss_pred CCEEEEEEEEEEEEECCCEEE
Q ss_conf 622589999743330264000
Q gi|254781172|r 349 TGILTPVARLEPVNIGGALIT 369 (731)
Q Consensus 349 tG~itPva~~ePV~l~G~~V~ 369 (731)
.++..|++.=.||.++|++|.
T Consensus 149 ~~~~~~~~~n~pi~iggv~V~ 169 (239)
T PRK08245 149 LTGHTAVDINVPIGCGGVAVF 169 (239)
T ss_pred CCCCEEEEECCCEEECCEEEE
T ss_conf 876414662677897888982
No 446
>PRK12429 3-hydroxybutyrate dehydrogenase; Provisional
Probab=34.36 E-value=26 Score=13.80 Aligned_cols=14 Identities=14% Similarity=0.273 Sum_probs=8.8
Q ss_pred CCCCCCEEEEECCC
Q ss_conf 82168669997258
Q gi|254781172|r 645 SEIENKKLVFTGTL 658 (731)
Q Consensus 645 ~~l~gk~vV~TGtl 658 (731)
+.++|.++++.|-+
T Consensus 242 ~~itGq~i~VDGG~ 255 (258)
T PRK12429 242 KGVTGQAWVVDGGW 255 (258)
T ss_pred CCCCCCEEEECCCH
T ss_conf 49017638969463
No 447
>PRK11281 potassium efflux protein KefA; Provisional
Probab=34.19 E-value=18 Score=15.01 Aligned_cols=45 Identities=29% Similarity=0.426 Sum_probs=22.1
Q ss_pred CCCCHHHH----HHHHHHCCCEEEEEEECCEEEEE--ECCCCCCHHHHHHHCC
Q ss_conf 89987899----99999829849981116321799--7788886379899749
Q gi|254781172|r 659 QKIQRHKA----QEYVTQLGAVVSAILSRKTDIII--VGDNPGSKLEKAQQLG 705 (731)
Q Consensus 659 ~~~~R~e~----~~~ie~~Ggkv~sSVSkkT~~LI--~ge~~gSKl~KA~~Lg 705 (731)
..|.|+|+ ++.|... -+-=|.|-..+-+| +|-.-||-+++++++=
T Consensus 964 ~d~DrkEiivPNK~FiT~~--~iNWsLsd~itRv~i~vgvaygsD~~~v~~ll 1014 (1107)
T PRK11281 964 TDFDRKEVIVPNKAFVTER--LINWSLSDTVTRLVIKVGVAYGSDLEKVRKLL 1014 (1107)
T ss_pred ECCCCCEEECCCHHHHHHH--HHCEECCCCCEEEEEEECCCCCCCHHHHHHHH
T ss_conf 4477754734756567413--31001368605899981566688889999999
No 448
>COG1137 YhbG ABC-type (unclassified) transport system, ATPase component [General function prediction only]
Probab=34.14 E-value=17 Score=15.34 Aligned_cols=10 Identities=30% Similarity=0.119 Sum_probs=4.8
Q ss_pred CCCHHHHHHH
Q ss_conf 8678999999
Q gi|254781172|r 603 LVGDIIAQAI 612 (731)
Q Consensus 603 GiG~~~A~si 612 (731)
|+.|+....|
T Consensus 169 GVDPiaV~dI 178 (243)
T COG1137 169 GVDPIAVIDI 178 (243)
T ss_pred CCCCHHHHHH
T ss_conf 8994029999
No 449
>PRK07562 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=34.14 E-value=21 Score=14.58 Aligned_cols=94 Identities=16% Similarity=0.115 Sum_probs=48.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHH--HHHCCCCCCCHHHHHHHHHHHHHHHHHCCHHHCCCCCCCC-CCCCCCC--------C
Q ss_conf 999999999999999999984--3317798208789999999999998977203115899996-2003643--------2
Q gi|254781172|r 14 IEQARKELSSLEQEISYHDDC--YYQYSKPIILDSEYDALKRRCDAIAHAFPDLARSEDPNGP-LNKIGGE--------M 82 (731)
Q Consensus 14 ~~~~~~~i~~L~~~i~~~~~~--Yy~~~~p~isD~eYD~L~~~L~~le~~~p~~~~~~~p~sp-t~~Vg~~--------~ 82 (731)
...+|+-+..|+..+.+|-.. |+ -|+.+-.+.++||.-+-. .....|||| ...+|-. .
T Consensus 103 e~s~~q~~~r~~~~~~~wg~~~gyf------~~~~da~~f~~e~~~~l~-----~q~~a~nsp~wfn~gl~~~ygi~g~~ 171 (1177)
T PRK07562 103 ETSAKQVFDRLAGCWTYWGWKGGYF------DSEEDARAFYDELRYMLA-----TQMVAPNSPQWFNTGLHWAYGIDGPG 171 (1177)
T ss_pred CCCHHHHHHHHHHHHHHHHHHCCCC------CCHHHHHHHHHHHHHHHH-----HHHCCCCCCCEEECCCCHHCCCCCCC
T ss_conf 4409999999999999887637830------788899999999999999-----74527899832786740101666777
Q ss_pred ------CCCCC-------EEECCC----CCCCHHHCC-CHHHHHHHHHHHHHHH
Q ss_conf ------35775-------045166----425702159-9999999999999861
Q gi|254781172|r 83 ------NLSLF-------KVTHSI----PTLSLEKIW-NIEDLRKFITRIYRFW 118 (731)
Q Consensus 83 ------~~~~~-------kv~H~~----pMlSL~k~~-~~~el~~w~~~~~~~~ 118 (731)
..... --.|++ ..+|.+..- ++..+.+|+.+=.++.
T Consensus 172 ~g~~~~d~~~~~~~~~~~~y~~pq~~acfi~sv~d~l~~~~~i~~~~~~ea~~f 225 (1177)
T PRK07562 172 QGHFYVDPKTGKLTKSKSAYEHPQPHACFIQSVEDDLVNEGGIMDLWVREARLF 225 (1177)
T ss_pred CCCEEECCCCCCEECCCCCCCCCCCCEEEEEECCCCCCCCCCHHHHHHHHHHHE
T ss_conf 773322565572111576233777654678852333447540999999866543
No 450
>pfam00406 ADK Adenylate kinase.
Probab=33.90 E-value=26 Score=13.90 Aligned_cols=34 Identities=9% Similarity=0.088 Sum_probs=22.0
Q ss_pred EEECCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCHHHHHHHHHHHHH
Q ss_conf 77704326577501033786544521010035434411446655332130
Q gi|254781172|r 428 FSFPSFCPICQSRVVRDLNPKTGKLVAAHRCTGGLACSAQQLERLKHFVS 477 (731)
Q Consensus 428 ~~~P~~CP~Cgs~l~~~~~~~~~~~~~~~rC~n~~~Cpaq~~~~i~hF~S 477 (731)
...|..|++||+.++...+ +.++.+.+|+..|-.
T Consensus 139 p~~~~~~~~~~~~l~~R~D----------------D~~e~i~~Rl~~y~~ 172 (186)
T pfam00406 139 PKVPGKDDVTGEPLSQRSD----------------DNEETVKKRLETYHK 172 (186)
T ss_pred CCCCCCCCCCCCCCCCCCC----------------CCHHHHHHHHHHHHH
T ss_conf 5213645444223537899----------------999999999999999
No 451
>pfam01967 MoaC MoaC family. Members of this family are involved in molybdenum cofactor biosynthesis. However their molecular function is not known.
Probab=33.75 E-value=27 Score=13.72 Aligned_cols=52 Identities=19% Similarity=0.331 Sum_probs=34.2
Q ss_pred EEEEEEEECCCCEEEEEEEEEEEEECCCEEEEECCCCHHHHHHHCCCCCCCCCCCCCCCCCEEEEEECCC
Q ss_conf 8788994035622589999743330264000101489899975023454322246844076899983587
Q gi|254781172|r 339 LLDIDIQIGRTGILTPVARLEPVNIGGALITNATLHNEDYIKGLDASGKVMRGGRDIRVGDRVLVKRAGE 408 (731)
Q Consensus 339 v~~I~wqvgRtG~itPva~~ePV~l~G~~V~ratlhN~~~I~~l~~~~~~~~~~~~I~iGd~V~I~RaGd 408 (731)
+.--.=..||||. |-=-|-|++|.--|. +|.++-+ ++++.|++.-++.++|.
T Consensus 85 i~~~v~~~~kTGV-------EMEALtavsva~LTi--YDM~Kav---------dk~~~I~~i~L~~K~GG 136 (136)
T pfam01967 85 IQATVRTTGKTGV-------EMEALTAVSVAALTI--YDMCKAV---------DKDMVIEGIRLLEKSGG 136 (136)
T ss_pred EEEEEEECCCCCH-------HHHHHHHHHHHHHHH--HHHHHHC---------CCCCEEEEEEEEEECCC
T ss_conf 9999997079404-------250898999999999--9988611---------89979942699983088
No 452
>KOG2661 consensus
Probab=33.73 E-value=23 Score=14.23 Aligned_cols=16 Identities=19% Similarity=0.503 Sum_probs=8.9
Q ss_pred CCCEEEECCCCCCCCC
Q ss_conf 7304777043265775
Q gi|254781172|r 424 DAQPFSFPSFCPICQS 439 (731)
Q Consensus 424 ~~~~~~~P~~CP~Cgs 439 (731)
..+.|+|-..-|+|.+
T Consensus 256 gGKvfVFtgiLn~ck~ 271 (424)
T KOG2661 256 GGKVFVFTGILNSCKD 271 (424)
T ss_pred CCEEEEEECHHHCCCC
T ss_conf 9739999511010368
No 453
>PRK00724 formate dehydrogenase accessory protein; Reviewed
Probab=33.66 E-value=27 Score=13.71 Aligned_cols=52 Identities=17% Similarity=0.335 Sum_probs=41.3
Q ss_pred CCCCCEEEEECCCCCCCHHHHHHHHHHCCCEEEEEEECCEEEEEECCCCCCHHHHHHHCCCEEEC
Q ss_conf 21686699972588998789999999829849981116321799778888637989974991737
Q gi|254781172|r 646 EIENKKLVFTGTLQKIQRHKAQEYVTQLGAVVSAILSRKTDIIIVGDNPGSKLEKAQQLGVKIMN 710 (731)
Q Consensus 646 ~l~gk~vV~TGtl~~~~R~e~~~~ie~~Ggkv~sSVSkkT~~LI~ge~~gSKl~KA~~LgI~Ii~ 710 (731)
.++++.+++||-++ .|+..+.-..|.-+.-|+|.-|+. =++-|+++||.++.
T Consensus 196 ~~~~~~l~~SGR~s----~emV~Ka~~aGipvlvS~sapTsl---------AvelA~~~giTLig 247 (262)
T PRK00724 196 PLRDGALLVSGRAS----SEMVQKAAMAGIPILVAVSAPTSL---------AVELAEELGLTLVG 247 (262)
T ss_pred CCCCEEEEEECCCH----HHHHHHHHHCCCCEEEECCCCHHH---------HHHHHHHCCCEEEE
T ss_conf 86780999907663----999999998499899998632199---------99999981998999
No 454
>COG1717 RPL32 Ribosomal protein L32E [Translation, ribosomal structure and biogenesis]
Probab=33.59 E-value=21 Score=14.49 Aligned_cols=28 Identities=11% Similarity=0.012 Sum_probs=15.2
Q ss_pred HHHHHHHHCCCCCCEEEEEHHHHCCHHH
Q ss_conf 3555565305765404541011010677
Q gi|254781172|r 488 KQQLDFFFKSEDPAFSIRIPADIFTLQR 515 (731)
Q Consensus 488 ~k~Ie~L~e~~~~~g~I~~~~DLy~L~~ 515 (731)
|+-|.-|.-.|+..-+|.++.||=.|+.
T Consensus 68 Pk~vRglhPSG~~~VlV~Nv~dLe~ldp 95 (133)
T COG1717 68 PKAVRGLHPSGYEEVLVHNVKDLEKLDP 95 (133)
T ss_pred CHHHCCCCCCCCCEEEEECHHHHHHCCC
T ss_conf 2765256877660235516888742380
No 455
>TIGR01011 rpsB_bact ribosomal protein S2; InterPro: IPR005706 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 of 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 family describes the bacterial, mitochondrial and chloroplast forms of ribosomal protein S2.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015935 small ribosomal subunit.
Probab=33.46 E-value=22 Score=14.35 Aligned_cols=24 Identities=8% Similarity=0.158 Sum_probs=15.0
Q ss_pred CHHHHHHHHHHHHHHHHH--HHHHHH
Q ss_conf 014568999987522346--667763
Q gi|254781172|r 533 VSVTNLYDSINKRRNISL--ERFIFS 556 (731)
Q Consensus 533 Ksa~nL~~sIe~sK~~~L--~r~L~A 556 (731)
|-|+.++.+...+-..++ .|+|-|
T Consensus 74 kQA~~~i~~~A~r~g~~YVn~RWLGG 99 (227)
T TIGR01011 74 KQAKEIIKEEAERCGMFYVNQRWLGG 99 (227)
T ss_pred HHHHHHHHHHHHHCCCCEECCCCCCC
T ss_conf 89999999999874896211333464
No 456
>pfam05129 Elf1 Transcription elongation factor Elf1 like. This family of short proteins contains a putative zinc binding domain with four conserved cysteines. Elf1 has been identified as a transcription elongation factor in Saccharomyces cerevisiae.
Probab=33.44 E-value=10 Score=16.92 Aligned_cols=30 Identities=20% Similarity=0.528 Sum_probs=14.2
Q ss_pred ECC--CCCCCCCCCCCCCCCCCCCCCEEECCC
Q ss_conf 704--326577501033786544521010035
Q gi|254781172|r 430 FPS--FCPICQSRVVRDLNPKTGKLVAAHRCT 459 (731)
Q Consensus 430 ~P~--~CP~Cgs~l~~~~~~~~~~~~~~~rC~ 459 (731)
+|+ .||.||.+...............+.|.
T Consensus 14 L~~~F~CpfC~h~~sv~vkidk~~~~g~l~C~ 45 (74)
T pfam05129 14 LPTVFDCPFCNHKKSVSVKIDKKTGIAKLHCR 45 (74)
T ss_pred CCCEEECCCCCCCCEEEEEEECCCCEEEEEEE
T ss_conf 98567478679987599999814798999962
No 457
>PRK11033 zntA zinc/cadmium/mercury/lead-transporting ATPase; Provisional
Probab=33.24 E-value=19 Score=14.93 Aligned_cols=25 Identities=24% Similarity=0.456 Sum_probs=18.7
Q ss_pred CCCCCCCEEEEEECCCCHHHHHHHCCC
Q ss_conf 684407689998358702566541012
Q gi|254781172|r 393 RDIRVGDRVLVKRAGEVIPKVVDIIVN 419 (731)
Q Consensus 393 ~~I~iGd~V~I~RaGdVIP~I~~Vi~~ 419 (731)
.++.+||.|.| |+||.|| +.+++.+
T Consensus 256 ~~l~~GDiV~V-~~Ge~IP-aDG~vv~ 280 (739)
T PRK11033 256 NSLRPGDVIEV-APGGRLP-ADGKLLS 280 (739)
T ss_pred HHCCCCCEEEE-CCCCEEE-CCEEEEC
T ss_conf 99799999998-8999842-2279970
No 458
>TIGR01051 topA_bact DNA topoisomerase I; InterPro: IPR005733 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 describes topoisomerase I from bacteria, which is more closely related to archaeal than to eukaryotic topoisomerase I . Topoisomerase I is the major enzyme for relaxing negatively supercoiled DNA, and its presence is balanced by reverse gyrase, which can introduce negative supercoils. Prokaryotic topoisomerase I folds in an unusual way to give 4 distinct domains, enclosing a hole large enough to accommodate a double-stranded DNA segment. A tyrosine at the active site, which lies at the interface of 2 domains, is involved in transient breakage of a DNA strand, and the formation of a covalent protein-DNA intermediate through a 5-phosphotyrosine linkage. The structure reveals a plausible mechanism by which this and related enzymes could catalyse the passage of one DNA strand through a transient break in another strand . Topoisomerase I require Mg2+ as a cofactor for catalysis to take place. More information about this protein can be found at Protein of the Month: DNA Topoisomerase .; GO: 0003677 DNA binding, 0003917 DNA topoisomerase type I activity, 0006265 DNA topological change, 0006268 DNA unwinding during replication, 0005694 chromosome.
Probab=33.17 E-value=16 Score=15.47 Aligned_cols=18 Identities=17% Similarity=0.252 Sum_probs=9.8
Q ss_pred HHHHHHHHHHHHHHCCCH
Q ss_conf 111168999999882998
Q gi|254781172|r 560 RHVGAEIARSLAKYYLSY 577 (731)
Q Consensus 560 ~~vG~~~Ak~La~~f~si 577 (731)
--+|.....+|..||+.+
T Consensus 562 ~~~g~~V~~~Le~hF~~~ 579 (688)
T TIGR01051 562 TELGFAVTDLLEKHFGEL 579 (688)
T ss_pred HHHHHHHHHHHHHHCCCC
T ss_conf 277899999988642643
No 459
>PRK08589 short chain dehydrogenase; Validated
Probab=33.13 E-value=28 Score=13.65 Aligned_cols=18 Identities=22% Similarity=0.244 Sum_probs=11.6
Q ss_pred CCCCCCCEEEEECCCCCC
Q ss_conf 882168669997258899
Q gi|254781172|r 644 SSEIENKKLVFTGTLQKI 661 (731)
Q Consensus 644 ~~~l~gk~vV~TGtl~~~ 661 (731)
++..+|.++++-|-+.-|
T Consensus 238 asyiTG~~i~VDGG~~A~ 255 (272)
T PRK08589 238 SSFITGETIRIDGGVMAY 255 (272)
T ss_pred HCCCCCCEEEECCCHHHC
T ss_conf 178368548989085427
No 460
>pfam01215 COX5B Cytochrome c oxidase subunit Vb.
Probab=33.10 E-value=16 Score=15.52 Aligned_cols=10 Identities=50% Similarity=1.099 Sum_probs=5.5
Q ss_pred CCCCCCCCCC
Q ss_conf 0432657750
Q gi|254781172|r 431 PSFCPICQSR 440 (731)
Q Consensus 431 P~~CP~Cgs~ 440 (731)
|..||.||+-
T Consensus 81 p~RC~eCG~~ 90 (99)
T pfam01215 81 PTRCPECGSV 90 (99)
T ss_pred CCCCCCCCCE
T ss_conf 7307878878
No 461
>PRK07523 gluconate 5-dehydrogenase; Provisional
Probab=33.09 E-value=28 Score=13.65 Aligned_cols=15 Identities=27% Similarity=0.337 Sum_probs=10.2
Q ss_pred CCCCCCCEEEEECCC
Q ss_conf 882168669997258
Q gi|254781172|r 644 SSEIENKKLVFTGTL 658 (731)
Q Consensus 644 ~~~l~gk~vV~TGtl 658 (731)
++..+|.++++.|-+
T Consensus 233 s~~iTG~~i~VDGG~ 247 (251)
T PRK07523 233 SSFVNGHVLYVDGGI 247 (251)
T ss_pred HCCCCCCEEEECCCC
T ss_conf 248268748809381
No 462
>PRK13646 cbiO cobalt transporter ATP-binding subunit; Provisional
Probab=32.86 E-value=28 Score=13.64 Aligned_cols=31 Identities=19% Similarity=0.401 Sum_probs=24.3
Q ss_pred CCEEEEECCCCHHHHHHHCCCCCCCCCCCCCCCCCEEEEEECCCCHH
Q ss_conf 64000101489899975023454322246844076899983587025
Q gi|254781172|r 365 GALITNATLHNEDYIKGLDASGKVMRGGRDIRVGDRVLVKRAGEVIP 411 (731)
Q Consensus 365 G~~V~ratlhN~~~I~~l~~~~~~~~~~~~I~iGd~V~I~RaGdVIP 411 (731)
|.||=-+| |+.+++.++ -|+|.|-..|.||=
T Consensus 196 g~TiI~iT-Hdm~~v~~~---------------adrv~vm~~G~Iv~ 226 (286)
T PRK13646 196 NKAIILIS-HDMNEVARY---------------ADEVIVMKEGSIVS 226 (286)
T ss_pred CCEEEEEC-CCHHHHHHH---------------CCEEEEEECCEEEE
T ss_conf 98999991-389999996---------------99999998989999
No 463
>PRK00694 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated
Probab=32.86 E-value=13 Score=16.21 Aligned_cols=66 Identities=17% Similarity=0.249 Sum_probs=31.5
Q ss_pred CCCCCCCEEEEECCCCCCCHHHHHHHHHHCCCEEEEEEECCEEEEEECCCCC--C--HHHHHHHCCCEEEC-HHHHHHHH
Q ss_conf 8821686699972588998789999999829849981116321799778888--6--37989974991737-99999999
Q gi|254781172|r 644 SSEIENKKLVFTGTLQKIQRHKAQEYVTQLGAVVSAILSRKTDIIIVGDNPG--S--KLEKAQQLGVKIMN-EEQFLFLL 718 (731)
Q Consensus 644 ~~~l~gk~vV~TGtl~~~~R~e~~~~ie~~Ggkv~sSVSkkT~~LI~ge~~g--S--Kl~KA~~LgI~Ii~-e~ef~~ll 718 (731)
.+.|.|.++-+-|-.-+-. -++. +-||==||..+| | +=+.--+-|||-=. -+++++||
T Consensus 534 T~HLKGvKIgIMGCIVNGP----GEMA-------------DADfGYVGsGpGKIsLY~GKe~VkrNIPeeeAVD~LIeLI 596 (606)
T PRK00694 534 TQHLPGLKIAVMGCIVNGP----GEMA-------------DADFGFVGSKTGMIDLYVKHTCVKAHIPMEDAEEELVRLL 596 (606)
T ss_pred HCCCCCCEEEEEEEEECCC----CCCC-------------CCCCCCCCCCCCEEEEEECCEEEECCCCHHHHHHHHHHHH
T ss_conf 4788787489983040287----4011-------------3666754788886888607563424898789999999999
Q ss_pred HHHCCCCC
Q ss_conf 88286568
Q gi|254781172|r 719 QQYNTTLR 726 (731)
Q Consensus 719 ~~~~~~~~ 726 (731)
++...=.+
T Consensus 597 Ke~G~WvD 604 (606)
T PRK00694 597 KEHGVWKD 604 (606)
T ss_pred HHCCCCCC
T ss_conf 86587279
No 464
>PRK10671 copA copper exporting ATPase; Provisional
Probab=32.85 E-value=20 Score=14.74 Aligned_cols=24 Identities=25% Similarity=0.436 Sum_probs=18.2
Q ss_pred CCCCCCEEEEEECCCCHHHHHHHCCC
Q ss_conf 84407689998358702566541012
Q gi|254781172|r 394 DIRVGDRVLVKRAGEVIPKVVDIIVN 419 (731)
Q Consensus 394 ~I~iGd~V~I~RaGdVIP~I~~Vi~~ 419 (731)
+|.+||.|.| |+||.|| +.+++.+
T Consensus 340 ~l~~GDiv~V-~~Ge~IP-aDG~vv~ 363 (834)
T PRK10671 340 DVQPGMLLRL-TTGDRVP-VDGEITQ 363 (834)
T ss_pred HCCCCCEEEE-CCCCEEC-CCEEEEE
T ss_conf 9688999998-9999832-3369997
No 465
>PRK08690 enoyl-(acyl carrier protein) reductase; Provisional
Probab=32.48 E-value=28 Score=13.58 Aligned_cols=13 Identities=23% Similarity=0.207 Sum_probs=6.9
Q ss_pred CCCCCCEEEEECC
Q ss_conf 8216866999725
Q gi|254781172|r 645 SEIENKKLVFTGT 657 (731)
Q Consensus 645 ~~l~gk~vV~TGt 657 (731)
+..+|.++++-|-
T Consensus 239 s~iTG~~i~VDGG 251 (261)
T PRK08690 239 SGITGEITYVDGG 251 (261)
T ss_pred CCCCCCEEEECCC
T ss_conf 4705863997969
No 466
>pfam09889 DUF2116 Uncharacterized protein containing a Zn-ribbon (DUF2116). This domain, found in various hypothetical archaeal proteins, has no known function.
Probab=32.42 E-value=20 Score=14.79 Aligned_cols=30 Identities=17% Similarity=0.474 Sum_probs=19.0
Q ss_pred ECCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCHHHHHHH
Q ss_conf 704326577501033786544521010035434411446655
Q gi|254781172|r 430 FPSFCPICQSRVVRDLNPKTGKLVAAHRCTGGLACSAQQLER 471 (731)
Q Consensus 430 ~P~~CP~Cgs~l~~~~~~~~~~~~~~~rC~n~~~Cpaq~~~~ 471 (731)
+-.+||.||...--++ .+|+. .|.....++
T Consensus 2 pHkHC~vCG~~Ipp~e----------~fCS~--kC~~~~~~~ 31 (59)
T pfam09889 2 PHKHCIVCGTAIPPDE----------SFCSE--KCQEEYRKK 31 (59)
T ss_pred CCCCCCCCCCCCCCCC----------CCCCH--HHHHHHHHH
T ss_conf 9853565799789432----------23148--899999999
No 467
>TIGR01161 purK phosphoribosylaminoimidazole carboxylase, ATPase subunit; InterPro: IPR005875 Phosphoribosylaminoimidazole carboxylase is a fusion protein in plants and fungi, but consists of two non-interacting proteins in bacteria, PurK and PurE. This family represents PurK, N5-carboxyaminoimidazole ribonucleotide (N5_CAIR) synthetase, which catalyzes the conversion of 5-aminoimidazole ribonucleotide (AIR), ATP, and bicarbonate to N5-CAIR, ADP, and Pi. PurE converts N5-CAIR to CAIR. In the presence of high concentrations of bicarbonate, PurE is reported able to convert AIR to CAIR directly and without ATP. PurK belongs to the ATP grasp superfamily of C-N ligase enzymes. Each subunit of PurK is composed of three domains (A, B, and C). The B domain contains a flexible, glycine-rich loop (B loop, T123-G130) that is disordered in the sulphate-PurK structure and becomes ordered in the MgADP-PurK structure. MgADP is wedged between the B and C domains, as with all members of the ATP grasp superfamily. Other enzymes in this superfamily contain a conserved Omega loop proposed to interact with the B loop, define the specificity of their nonnucleotide substrate, and protect the acyl phosphate intermediate formed from this substrate. PurK contains a minimal Omega loop without conserved residues. In the reaction catalyzed by PurK, carboxyphosphate is the putative acyl phosphate intermediate. The sulphate of the sulphate ion-liganded PurK interacts electrostatically with Arg 242 and the backbone amide group of Asn 245, components of the J loop of the C domain. This sulphate may reveal the location of the carboxyphosphate binding site. Conserved residues within the C-terminus of the C domain define a pocket that is proposed to bind AIR in collaboration with an N-terminal strand loop helix motif in the A domain (P loop, G8-L1). The P loop is proposed to bind the phosphate of AIR on the basis of similar binding sites observed in PurN and PurE and proposed in PurD and PurT, four other enzymes in the purine pathway .; GO: 0004638 phosphoribosylaminoimidazole carboxylase activity, 0006189 'de novo' IMP biosynthetic process, 0009320 phosphoribosylaminoimidazole carboxylase complex.
Probab=32.39 E-value=28 Score=13.57 Aligned_cols=54 Identities=22% Similarity=0.220 Sum_probs=33.5
Q ss_pred CCCCHHHHHHHHHCCCCCCCCEEEE-ECCCCHHHHHHHHHHHHCCCCCCCCCEEEEECCHHCCCCCCCCCC
Q ss_conf 1000036899997599665414887-403211345566553100112343763777311000111587656
Q gi|254781172|r 251 AKGQYEMLQKMRCLGFPVNNGVRQA-NTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSLQKQLGERAR 320 (731)
Q Consensus 251 ~~~~~e~l~~L~~~GF~v~~~~~~~-~~~~~~~~~~~~~~~~r~~l~y~iDGiVikvn~~~~q~~lG~ts~ 320 (731)
..+.+..=++|+++|++|+++.... .+.+++... ...++|+. |+| ++++||.+|
T Consensus 100 ~~dk~~qK~~L~~~g~~vp~f~~~~~~~~~~~~~~-------~~~~g~p~---VlK------~~~gGYDGr 154 (386)
T TIGR01161 100 IQDKLTQKQFLQKLGLPVPPFVVIEIKDEEELDSA-------LQELGFPV---VLK------ARRGGYDGR 154 (386)
T ss_pred HHCHHHHHHHHHHCCCCCCCCCEEECCCHHHHHHH-------HHHCCCCE---EEE------EEECCCCCC
T ss_conf 83658999999966899884120223684257899-------98739847---998------420652773
No 468
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=32.37 E-value=14 Score=15.98 Aligned_cols=16 Identities=19% Similarity=0.453 Sum_probs=11.9
Q ss_pred EECCCCCCCCCCCCCC
Q ss_conf 7704326577501033
Q gi|254781172|r 429 SFPSFCPICQSRVVRD 444 (731)
Q Consensus 429 ~~P~~CP~Cgs~l~~~ 444 (731)
.+-.+||+||.....+
T Consensus 6 ~PH~HC~VCg~aIp~d 21 (64)
T COG4068 6 VPHRHCVVCGKAIPPD 21 (64)
T ss_pred CCCCCCCCCCCCCCCC
T ss_conf 8876566058868974
No 469
>KOG4450 consensus
Probab=32.28 E-value=23 Score=14.31 Aligned_cols=21 Identities=38% Similarity=0.605 Sum_probs=11.9
Q ss_pred CCCCCCCCCCCCE-EEEEEEEEEE
Q ss_conf 2432233544550-4899999985
Q gi|254781172|r 172 TIPRVLSLNIPEI-IEVRGEVYIS 194 (731)
Q Consensus 172 ~iP~~l~~~~~~~-ieiRGEv~m~ 194 (731)
+||--|.. |+. -.|+||+|--
T Consensus 54 nIPfLLnk--pGsG~~V~GElY~V 75 (168)
T KOG4450 54 NIPFLLNK--PGSGYHVEGELYEV 75 (168)
T ss_pred CCCEEECC--CCCCCEEEEEEEEE
T ss_conf 77258727--88763651479886
No 470
>PRK07041 short chain dehydrogenase; Provisional
Probab=32.09 E-value=29 Score=13.53 Aligned_cols=15 Identities=13% Similarity=0.220 Sum_probs=6.4
Q ss_pred EECCCCHHHHHHHHH
Q ss_conf 865986556669997
Q gi|254781172|r 152 ALRGDGHSGEDVSAC 166 (731)
Q Consensus 152 ~TRGdG~~GeDVT~n 166 (731)
+|=|.+-+|.-+...
T Consensus 12 ITGgs~GIG~aia~~ 26 (240)
T PRK07041 12 VVGGSSGIGLAAARA 26 (240)
T ss_pred EECCCCHHHHHHHHH
T ss_conf 957788899999999
No 471
>PRK06523 short chain dehydrogenase; Provisional
Probab=32.06 E-value=29 Score=13.53 Aligned_cols=15 Identities=20% Similarity=0.355 Sum_probs=11.1
Q ss_pred CCCCCCCCEEEEECC
Q ss_conf 688216866999725
Q gi|254781172|r 643 VSSEIENKKLVFTGT 657 (731)
Q Consensus 643 ~~~~l~gk~vV~TGt 657 (731)
.++..+|.++.+.|-
T Consensus 241 ~s~~iTG~~i~VDGG 255 (260)
T PRK06523 241 RAASITGTEYVIDGG 255 (260)
T ss_pred HHCCEECCEEEECCC
T ss_conf 426860855788788
No 472
>TIGR00705 SppA_67K signal peptide peptidase SppA, 67K type; InterPro: IPR004634 Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes . They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence . Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases . Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base . The geometric orientations of the catalytic residues are similar between families, despite different protein folds . The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) , . Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. This group of serine peptidases belong to MEROPS peptidase family S49 (protease IV family, clan S-). The predicted active site serine for members of this family occurs in a transmembrane domain. Signal peptides of secretory proteins seem to serve at least two important biological functions. First, they are required for protein targeting to and translocation across membranes, such as the eubacterial plasma membrane and the endoplasmic reticular membrane of eukaryotes. Second, in addition to their role as determinants for protein targeting and translocation, certain signal peptides have a signalling function. During or shortly after pre-protein translocation, the signal peptide is removed by signal peptidases. The integral membrane protein, SppA (protease IV), of Escherichia coli was shown experimentally to degrade signal peptides. The member of this family from Bacillus subtilis has only been shown to be required for efficient processing of pre-proteins under conditions of hyper-secretion . These enzymes have a molecular mass around 67 kDa and a duplication such that the N-terminal half shares extensive homology with the C-terminal half and was shown in E. coli to form homotetramers. E. coli SohB, which is most closely homologous to the C-terminal duplication of SppA, is predicted to perform a similar function of small peptide degradation, but in the periplasm. Many prokaryotes have a single SppA/SohB homolog that may perform the function of either or both. ; GO: 0009003 signal peptidase activity, 0006465 signal peptide processing, 0016021 integral to membrane.
Probab=31.99 E-value=29 Score=13.52 Aligned_cols=36 Identities=31% Similarity=0.484 Sum_probs=17.2
Q ss_pred EEEEEECCEEEEE-EECCCCHHHHHHHHHHHHHCCCC
Q ss_conf 9999859989988-86598655666999775310243
Q gi|254781172|r 139 ITIRYEKGKFVYA-ALRGDGHSGEDVSACIRAIPTIP 174 (731)
Q Consensus 139 isl~Y~~G~L~~a-~TRGdG~~GeDVT~n~~~i~~iP 174 (731)
|.++|-+|-.+.. -|.+||..|+.+.+.+|.++.=|
T Consensus 322 iaiv~~~G~I~~G~~t~~nG~ggD~~a~lLr~a~~D~ 358 (614)
T TIGR00705 322 IAIVYLEGSIVDGRDTEENGVGGDTVAALLRKARSDP 358 (614)
T ss_pred EEEEEEECCEECCCCCCCCCCHHHHHHHHHHHHCCCC
T ss_conf 6999700642357756678600367999999870799
No 473
>PRK08270 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=31.97 E-value=17 Score=15.19 Aligned_cols=10 Identities=50% Similarity=0.893 Sum_probs=3.8
Q ss_pred EEEEECCCEE
Q ss_conf 4333026400
Q gi|254781172|r 359 EPVNIGGALI 368 (731)
Q Consensus 359 ePV~l~G~~V 368 (731)
+|+-++|...
T Consensus 283 ~~~iigg~~~ 292 (681)
T PRK08270 283 QPVIIGGEEM 292 (681)
T ss_pred CCCEECCCCC
T ss_conf 3221177312
No 474
>PRK09072 short chain dehydrogenase; Provisional
Probab=31.88 E-value=29 Score=13.51 Aligned_cols=16 Identities=13% Similarity=0.297 Sum_probs=9.3
Q ss_pred CCHHHHHHHHHHHHHH
Q ss_conf 0014568999987522
Q gi|254781172|r 532 DVSVTNLYDSINKRRN 547 (731)
Q Consensus 532 eKsa~nL~~sIe~sK~ 547 (731)
+.-|+.++.+|++.|.
T Consensus 208 e~vA~~i~~~i~~~k~ 223 (262)
T PRK09072 208 EDVAAAVLQAIEQERA 223 (262)
T ss_pred HHHHHHHHHHHHCCCC
T ss_conf 9999999999946998
No 475
>pfam08996 zf-DNA_Pol DNA Polymerase alpha zinc finger. The DNA Polymerase alpha zinc finger domain adopts an alpha-helix-like structure, followed by three turns, all of which involve proline. The resulting motif is a helix-turn-helix motif, in contrast to other zinc finger domains, which show anti-parallel sheet and helix conformation. Zinc binding occurs due to the presence of four cysteine residues positioned to bind the metal centre in a tetrahedral coordination geometry. Function of this domain is uncertain: it has been proposed that the zinc finger motif may be an essential part of the DNA binding domain.
Probab=31.88 E-value=29 Score=13.51 Aligned_cols=25 Identities=24% Similarity=0.389 Sum_probs=15.1
Q ss_pred CCCCCCCEEEECCCCCCCCCCCCCCCC
Q ss_conf 357873047770432657750103378
Q gi|254781172|r 420 ERHPDAQPFSFPSFCPICQSRVVRDLN 446 (731)
Q Consensus 420 ~r~~~~~~~~~P~~CP~Cgs~l~~~~~ 446 (731)
.|-.+-.+|.+ .||.||++......
T Consensus 9 eRfr~c~~l~l--~Cp~C~~~~~f~gv 33 (186)
T pfam08996 9 ERFRDCARLKL--KCPSCGTEFPFPGI 33 (186)
T ss_pred HHHCCCCEEEE--ECCCCCCCEECCCE
T ss_conf 98667870597--89999984577886
No 476
>PRK06138 short chain dehydrogenase; Provisional
Probab=31.85 E-value=29 Score=13.50 Aligned_cols=31 Identities=26% Similarity=0.345 Sum_probs=0.0
Q ss_pred CCCCEEEEECCCCCCCHHHHHHHHHHCCCEEE
Q ss_conf 16866999725889987899999998298499
Q gi|254781172|r 647 IENKKLVFTGTLQKIQRHKAQEYVTQLGAVVS 678 (731)
Q Consensus 647 l~gk~vV~TGtl~~~~R~e~~~~ie~~Ggkv~ 678 (731)
|.||++++||.=.+.-|.-++.+. +.|++|.
T Consensus 3 L~gKvalVTGas~GIG~aia~~la-~~Ga~V~ 33 (252)
T PRK06138 3 LAGRVAIVTGAGSGIGRATAKLFA-REGARVV 33 (252)
T ss_pred CCCCEEEEECCCCHHHHHHHHHHH-HCCCEEE
T ss_conf 899889994746799999999999-8799899
No 477
>TIGR00463 gltX_arch glutamyl-tRNA synthetase; InterPro: IPR004526 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases . Glutamyl-tRNA synthetase (6.1.1.17 from EC) is a class Ic synthetase and shows several similarities with glutaminyl-tRNA synthetase concerning structure and catalytic properties. It is an alpha2 dimer. To date one crystal structure of a glutamyl-tRNA synthetase (Thermus thermophilus) has been solved. The molecule has the form of a bent cylinder and consists of four domains. The N-terminal half (domains 1 and 2) contains the 'Rossman fold' typical for class I synthetases and resembles the corresponding part of E. coli GlnRS, whereas the C-terminal half exhibits a GluRS-specific structure . ; GO: 0000166 nucleotide binding, 0004818 glutamate-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006424 glutamyl-tRNA aminoacylation, 0005737 cytoplasm.
Probab=31.83 E-value=29 Score=13.53 Aligned_cols=20 Identities=35% Similarity=0.698 Sum_probs=0.0
Q ss_pred EEEEEEEEEEECHHHHHHHH
Q ss_conf 04899999985202123455
Q gi|254781172|r 184 IIEVRGEVYISKNDFLALND 203 (731)
Q Consensus 184 ~ieiRGEv~m~~~~F~~lN~ 203 (731)
.|..+||||++++||+.+|.
T Consensus 454 ~l~~~~~iyv~kDd~~~~n~ 473 (600)
T TIGR00463 454 KLIYEGEIYVDKDDLEVLNE 473 (600)
T ss_pred EEEEEEEEEEECCCCCCCCC
T ss_conf 79860018870775100168
No 478
>TIGR02870 spore_II_D stage II sporulation protein D; InterPro: IPR014225 This entry contains the stage II sporulation protein D (SpoIID), which is a protein involved in the endospore formation program. SpoIID is one of the three genes (spoIID, spoIIM and spoIIP, , , ), under the control of sigma E, that have been shown to be essential for the engulfment of the forespore by the mother cell. Their products are involved in degradation of the septal peptidoglycan - mutations in spoIID, spoIIM or spoIIP block sporulation at morphological stage II, prior to the engulfment stage. These three genes are absolutely conserved (sometimes even duplicated) in all endospore formers .
Probab=31.68 E-value=15 Score=15.80 Aligned_cols=73 Identities=18% Similarity=0.254 Sum_probs=0.0
Q ss_pred CCCCCEEEECCCCCEEEEEE-------EEEEEEECCCC----EE---EEEEEEEEEEECCCEEEEECCCCHHHHHHHCCC
Q ss_conf 68663123114562158998-------78899403562----25---899997433302640001014898999750234
Q gi|254781172|r 320 RSPRWMISHKFAEKQASTRL-------LDIDIQIGRTG----IL---TPVARLEPVNIGGALITNATLHNEDYIKGLDAS 385 (731)
Q Consensus 320 ~~PrwaiA~Kf~~e~~~T~v-------~~I~wqvgRtG----~i---tPva~~ePV~l~G~~V~ratlhN~~~I~~l~~~ 385 (731)
|+||+.---+|+.++..-+| ....-.=++.| .| |+--+++-|.|+|.|++ .+.||..
T Consensus 227 hspky~~e~~~s~~~F~~klGl~~~~p~~~l~~~~~~G~~Pv~I~~RT~gGrV~~~~ig~~tl~------G~~~Re~--- 297 (358)
T TIGR02870 227 HSPKYKTETVMSIEEFVDKLGLKSSVPNLKLQNAASVGEKPVKILARTAGGRVKTIKIGGKTLK------GREIRER--- 297 (358)
T ss_pred CCCCCCCCEEECHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCEEEEEEECCEEEE------EEEHHHH---
T ss_conf 1666554137438999987505522575100012222789825886278971658898787886------0410256---
Q ss_pred CCCCCCCCCCCCCCE-EEEEECCCCH
Q ss_conf 543222468440768-9998358702
Q gi|254781172|r 386 GKVMRGGRDIRVGDR-VLVKRAGEVI 410 (731)
Q Consensus 386 ~~~~~~~~~I~iGd~-V~I~RaGdVI 410 (731)
||..++ -.+.+.+|=|
T Consensus 298 ---------lGLnStdF~~~~~~d~I 314 (358)
T TIGR02870 298 ---------LGLNSTDFTWKVQGDKI 314 (358)
T ss_pred ---------HCCCCCCEEEEEECCEE
T ss_conf ---------47874121899867879
No 479
>TIGR01966 RNasePH ribonuclease PH; InterPro: IPR002381 Prokaryotic ribonuclease PH (2.7.7.56 from EC) (RNase PH) is a phosphorolytic exoribonuclease that removes nucleotide residues following the -CCA terminus of tRNA and adds nucleotides to the ends of RNA molecules by using nucleoside diphosphates as substrates . There is a similar protein in Caenorhabditis elegans that belongs to this group. More information about these proteins can be found at Protein of the Month: RNA Exosomes .; GO: 0000049 tRNA binding, 0004549 tRNA-specific ribonuclease activity, 0008033 tRNA processing.
Probab=31.57 E-value=29 Score=13.47 Aligned_cols=22 Identities=23% Similarity=0.427 Sum_probs=0.0
Q ss_pred CCEEEEECCC-----------CCCCHHHHHHHH
Q ss_conf 8669997258-----------899878999999
Q gi|254781172|r 649 NKKLVFTGTL-----------QKIQRHKAQEYV 670 (731)
Q Consensus 649 gk~vV~TGtl-----------~~~~R~e~~~~i 670 (731)
.++||+||+. .-|||+|+-+++
T Consensus 186 D~NvVmT~~G~fvEvQGTaE~~pFsr~EL~~LL 218 (237)
T TIGR01966 186 DMNVVMTGSGGFVEVQGTAEEEPFSRDELNELL 218 (237)
T ss_pred CCEEEECCCCCEEEEEECCCCCCHHHHHHHHHH
T ss_conf 520588578765888705788970189999999
No 480
>PRK12828 short chain dehydrogenase; Provisional
Probab=31.57 E-value=29 Score=13.47 Aligned_cols=34 Identities=24% Similarity=0.403 Sum_probs=0.0
Q ss_pred CCCCCCCEEEEECCCCCCCHHHHHHHHHHCCCEEE
Q ss_conf 88216866999725889987899999998298499
Q gi|254781172|r 644 SSEIENKKLVFTGTLQKIQRHKAQEYVTQLGAVVS 678 (731)
Q Consensus 644 ~~~l~gk~vV~TGtl~~~~R~e~~~~ie~~Ggkv~ 678 (731)
+..|+||++++||.-.++-|.-++ .+-+.|++|.
T Consensus 2 ~~~L~gKvalITGas~GIG~aia~-~la~~Ga~V~ 35 (239)
T PRK12828 2 EHSLQGKVVAITGGFGGLGRATAA-WLAARGARVA 35 (239)
T ss_pred CCCCCCCEEEEECCCCHHHHHHHH-HHHHCCCEEE
T ss_conf 999698989994725489999999-9998799899
No 481
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=31.53 E-value=26 Score=13.84 Aligned_cols=22 Identities=23% Similarity=0.468 Sum_probs=0.0
Q ss_pred CCCCCCCCCCCCCCCCCCCCCEEECCCC
Q ss_conf 3265775010337865445210100354
Q gi|254781172|r 433 FCPICQSRVVRDLNPKTGKLVAAHRCTG 460 (731)
Q Consensus 433 ~CP~Cgs~l~~~~~~~~~~~~~~~rC~n 460 (731)
+||-||+++.....+ ....|++
T Consensus 113 FCg~CG~~~~~~~~g------~~~~C~~ 134 (279)
T COG2816 113 FCGRCGTKTYPREGG------WARVCPK 134 (279)
T ss_pred CCCCCCCCCCCCCCC------EEEECCC
T ss_conf 777789807435673------2455798
No 482
>pfam03129 HGTP_anticodon Anticodon binding domain. This domain is found in histidyl, glycyl, threonyl and prolyl tRNA synthetases it is probably the anticodon binding domain.
Probab=31.36 E-value=29 Score=13.45 Aligned_cols=43 Identities=21% Similarity=0.417 Sum_probs=0.0
Q ss_pred HHHHHHHHHCCCEEEEEEECCEEEEEECCCCCCHHHHHHHCCCE---EECHHHH
Q ss_conf 89999999829849981116321799778888637989974991---7379999
Q gi|254781172|r 664 HKAQEYVTQLGAVVSAILSRKTDIIIVGDNPGSKLEKAQQLGVK---IMNEEQF 714 (731)
Q Consensus 664 ~e~~~~ie~~Ggkv~sSVSkkT~~LI~ge~~gSKl~KA~~LgI~---Ii~e~ef 714 (731)
.++.+.+.+.| ++-..|+ -+.+.|.|+..|..+|+| |+.++|+
T Consensus 18 ~~i~~~Lr~~g------i~v~~d~--~~~~~~~k~~~a~~~g~p~~iiiG~~E~ 63 (93)
T pfam03129 18 QKLAEELREAG------IRVELDD--RNESLGKKFRDADLIGIPFRLVVGEKEL 63 (93)
T ss_pred HHHHHHHHHCC------CEEEEEC--CCCCHHHHHHHHHHHCCCEEEEECHHHH
T ss_conf 99999998789------9799988--9999789999898709990788977888
No 483
>PRK06720 hypothetical protein; Provisional
Probab=31.35 E-value=29 Score=13.44 Aligned_cols=31 Identities=29% Similarity=0.306 Sum_probs=0.0
Q ss_pred CCCCEEEEECCCCCCCHHHHHHHHHHCCCEEE
Q ss_conf 16866999725889987899999998298499
Q gi|254781172|r 647 IENKKLVFTGTLQKIQRHKAQEYVTQLGAVVS 678 (731)
Q Consensus 647 l~gk~vV~TGtl~~~~R~e~~~~ie~~Ggkv~ 678 (731)
|+||++++||.=.+.-|.-+. .+-+.|++|.
T Consensus 14 L~gKvalITGa~~GIG~a~A~-~la~~Ga~Vv 44 (169)
T PRK06720 14 LAGKVAIVTGGGIGIGRNTAL-LLAKQGAKVI 44 (169)
T ss_pred CCCCEEEEECCCCHHHHHHHH-HHHHCCCEEE
T ss_conf 299999998975489999999-9998699899
No 484
>PRK07890 short chain dehydrogenase; Provisional
Probab=31.33 E-value=29 Score=13.44 Aligned_cols=31 Identities=23% Similarity=0.234 Sum_probs=0.0
Q ss_pred CCCCEEEEECCCCCCCHHHHHHHHHHCCCEEE
Q ss_conf 16866999725889987899999998298499
Q gi|254781172|r 647 IENKKLVFTGTLQKIQRHKAQEYVTQLGAVVS 678 (731)
Q Consensus 647 l~gk~vV~TGtl~~~~R~e~~~~ie~~Ggkv~ 678 (731)
|+||++++||.=.+.-|.-++ .+-+.|++|.
T Consensus 3 L~gK~alVTG~s~GIG~aia~-~la~~Ga~V~ 33 (258)
T PRK07890 3 LKDKVVVVSGVGPGLGTTLAV-RAAREGADVV 33 (258)
T ss_pred CCCCEEEEECCCCHHHHHHHH-HHHHCCCEEE
T ss_conf 899889996856589999999-9998799899
No 485
>KOG2463 consensus
Probab=31.31 E-value=16 Score=15.42 Aligned_cols=10 Identities=40% Similarity=1.258 Sum_probs=0.0
Q ss_pred CCCCCCCCCC
Q ss_conf 4326577501
Q gi|254781172|r 432 SFCPICQSRV 441 (731)
Q Consensus 432 ~~CP~Cgs~l 441 (731)
.+||+||..+
T Consensus 258 ~FCp~CG~~T 267 (376)
T KOG2463 258 DFCPSCGHKT 267 (376)
T ss_pred HCCCCCCCCE
T ss_conf 0010049973
No 486
>pfam06676 DUF1178 Protein of unknown function (DUF1178). This family consists of several hypothetical bacterial proteins of around 150 residues in length. The function of this family is unknown.
Probab=31.28 E-value=18 Score=15.15 Aligned_cols=9 Identities=56% Similarity=1.339 Sum_probs=0.0
Q ss_pred CCCCCCCCC
Q ss_conf 265775010
Q gi|254781172|r 434 CPICQSRVV 442 (731)
Q Consensus 434 CP~Cgs~l~ 442 (731)
||.||+.-+
T Consensus 35 CP~Cgs~~V 43 (145)
T pfam06676 35 CPVCGSTEV 43 (145)
T ss_pred CCCCCCCEE
T ss_conf 999999836
No 487
>PRK12428 3-alpha-hydroxysteroid dehydrogenase; Provisional
Probab=31.22 E-value=29 Score=13.43 Aligned_cols=31 Identities=32% Similarity=0.422 Sum_probs=0.0
Q ss_pred CCCCEEEEECCCCCCCHHHHHHHHHHCCCEEE
Q ss_conf 16866999725889987899999998298499
Q gi|254781172|r 647 IENKKLVFTGTLQKIQRHKAQEYVTQLGAVVS 678 (731)
Q Consensus 647 l~gk~vV~TGtl~~~~R~e~~~~ie~~Ggkv~ 678 (731)
|+||++++||.=.++-|.-++ .+-+.|++|.
T Consensus 3 L~gK~alVTG~s~GIG~aia~-~la~~GA~V~ 33 (261)
T PRK12428 3 LDGKTIVVTGVASGIGAEVAR-LLRFLGARVI 33 (261)
T ss_pred CCCCEEEEECCCCHHHHHHHH-HHHHCCCEEE
T ss_conf 999889997857799999999-9998699999
No 488
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit; InterPro: IPR000438 Fatty acid synthesis involves a set of reactions, commencing with carboxylation of acetyl-CoA to malonyl-CoA. This is an irreversible reaction, catalysed by the acetyl-CoA carboxylase complex (6.4.1.2 from EC); a heterohexamer of biotin carboxyl carrier protein, biotin carboxylase and two non-identical carboxyl transferase subunits (alpha and beta) in a 2:2 association . The reaction involves two steps: Biotin carrier protein + ATP + HCO_3^- = Carboxybiotin carrier protein + ADP + P_i Carboxybiotin carrier protein + Acetyl-CoA = Malonyl-CoA + Biotin carrier protein In the first step, biotin carboxylase catalyses the carboxylation of the carrier protein to form an intermediate. Next, the transcarboxylase complex transfers the carboxyl group from the intermediate to acetyl-CoA forming malonyl-CoA.; GO: 0003989 acetyl-CoA carboxylase activity, 0006633 fatty acid biosynthetic process, 0009317 acetyl-CoA carboxylase complex.
Probab=31.15 E-value=20 Score=14.72 Aligned_cols=41 Identities=17% Similarity=0.391 Sum_probs=0.0
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCHHHHHHHHHHHH
Q ss_conf 432657750103378654452101003543441144665533213
Q gi|254781172|r 432 SFCPICQSRVVRDLNPKTGKLVAAHRCTGGLACSAQQLERLKHFV 476 (731)
Q Consensus 432 ~~CP~Cgs~l~~~~~~~~~~~~~~~rC~n~~~Cpaq~~~~i~hF~ 476 (731)
+.||.|+.-+ ...+....+.|...|.-.. +-...+||...+
T Consensus 34 tKCp~C~~~~--Y~keL~~n~~VC~~C~hH~--R~~A~eRi~~L~ 74 (292)
T TIGR00515 34 TKCPKCGQLL--YTKELQRNLSVCLKCDHHF--RMDARERIESLL 74 (292)
T ss_pred ECCCHHHHHH--HHHHHHCCCEECCCCCCCC--CCCHHHHHHHHC
T ss_conf 0144243443--4665303555742379877--468799998741
No 489
>PHA00439 exonuclease
Probab=31.07 E-value=23 Score=14.30 Aligned_cols=15 Identities=27% Similarity=0.450 Sum_probs=0.0
Q ss_pred CHHHHHHHHHHHHHH
Q ss_conf 101111689999998
Q gi|254781172|r 558 GIRHVGAEIARSLAK 572 (731)
Q Consensus 558 GI~~vG~~~Ak~La~ 572 (731)
|||+||.++|..|..
T Consensus 191 GvpGiG~ktA~klL~ 205 (288)
T PHA00439 191 GIPGWGPDTAEAFLN 205 (288)
T ss_pred CCCCCCHHHHHHHHC
T ss_conf 998848899999863
No 490
>PHA00732 hypothetical protein
Probab=31.03 E-value=27 Score=13.76 Aligned_cols=49 Identities=35% Similarity=0.579 Sum_probs=0.0
Q ss_pred CCCCCCCCCCCCCCCC--CCCCCEEECCCCCCCCHHHHHHHHHHHHHCCCCCHHHH
Q ss_conf 3265775010337865--44521010035434411446655332130123103541
Q gi|254781172|r 433 FCPICQSRVVRDLNPK--TGKLVAAHRCTGGLACSAQQLERLKHFVSRDAFNIEGL 486 (731)
Q Consensus 433 ~CP~Cgs~l~~~~~~~--~~~~~~~~rC~n~~~Cpaq~~~~i~hF~SK~aldI~GL 486 (731)
.||.||-..++--..+ .-..-+-..|+ -|.-.-..--.||.|+ -||+.|
T Consensus 3 kCPiCgF~tv~lFalKqH~R~~H~l~kCP---VC~~~y~~l~QHfy~~--~D~~HL 53 (79)
T PHA00732 3 RCPICGFTTVRLFALKQHTRKNHVLTKCP---VCNNSYRRLNQHFYSQ--YDIEHL 53 (79)
T ss_pred CCCCCCCEEEEEEHHHHHHHHHCCCCCCC---CCCHHHHHHHHHHHHH--CCCHHH
T ss_conf 68726857886412677776504652277---5047899999877643--420562
No 491
>COG1888 Uncharacterized protein conserved in archaea [Function unknown]
Probab=31.01 E-value=30 Score=13.40 Aligned_cols=29 Identities=24% Similarity=0.522 Sum_probs=0.0
Q ss_pred CCEEEEECCCCCCCHHHHHHHHHHCCCEEEE
Q ss_conf 8669997258899878999999982984998
Q gi|254781172|r 649 NKKLVFTGTLQKIQRHKAQEYVTQLGAVVSA 679 (731)
Q Consensus 649 gk~vV~TGtl~~~~R~e~~~~ie~~Ggkv~s 679 (731)
|.++.+-|+ +..=+++++.||+.||.+.|
T Consensus 50 ~~~itIeG~--~ldydei~~~iE~~Gg~IHS 78 (97)
T COG1888 50 NLKITIEGT--NLDYDEIEEVIEELGGAIHS 78 (97)
T ss_pred CEEEEEECC--CCCHHHHHHHHHHCCCEEEE
T ss_conf 358999737--78989999999972974565
No 492
>PRK07577 short chain dehydrogenase; Provisional
Probab=30.95 E-value=30 Score=13.40 Aligned_cols=31 Identities=16% Similarity=0.234 Sum_probs=0.0
Q ss_pred CCCCEEEEECCCCCCCHHHHHHHHHHCCCEEE
Q ss_conf 16866999725889987899999998298499
Q gi|254781172|r 647 IENKKLVFTGTLQKIQRHKAQEYVTQLGAVVS 678 (731)
Q Consensus 647 l~gk~vV~TGtl~~~~R~e~~~~ie~~Ggkv~ 678 (731)
|+||++++||.=.+.-|.=++.+.+. |++|.
T Consensus 1 L~~K~alITGas~GIG~aia~~la~~-G~~Vv 31 (234)
T PRK07577 1 MSSRTVLVTGATKGIGLALSLRLANL-GHQVI 31 (234)
T ss_pred CCCCEEEEECCCCHHHHHHHHHHHHC-CCEEE
T ss_conf 94198999377888999999999987-99999
No 493
>PRK06935 2-deoxy-D-gluconate 3-dehydrogenase; Provisional
Probab=30.92 E-value=30 Score=13.39 Aligned_cols=31 Identities=19% Similarity=0.216 Sum_probs=0.0
Q ss_pred CCCCEEEEECCCCCCCHHHHHHHHHHCCCEEE
Q ss_conf 16866999725889987899999998298499
Q gi|254781172|r 647 IENKKLVFTGTLQKIQRHKAQEYVTQLGAVVS 678 (731)
Q Consensus 647 l~gk~vV~TGtl~~~~R~e~~~~ie~~Ggkv~ 678 (731)
|+||++++||.=.+.-|.-++.+.+. |++|.
T Consensus 13 L~gKvalVTGas~GIG~aiA~~la~~-Ga~Vv 43 (258)
T PRK06935 13 LKGKVAIVTGGNTGLGQGYAVALAKA-GADII 43 (258)
T ss_pred CCCCEEEEECCCCHHHHHHHHHHHHC-CCEEE
T ss_conf 99998999485758999999999987-99999
No 494
>PRK10348 ribosome-associated heat shock protein Hsp15; Provisional
Probab=30.82 E-value=30 Score=13.38 Aligned_cols=28 Identities=7% Similarity=0.201 Sum_probs=0.0
Q ss_pred EEECCCEEEEECCCCHHHHHHHCCCCCCCCCCCCCCCCCEEEEEECCCC
Q ss_conf 3302640001014898999750234543222468440768999835870
Q gi|254781172|r 361 VNIGGALITNATLHNEDYIKGLDASGKVMRGGRDIRVGDRVLVKRAGEV 409 (731)
Q Consensus 361 V~l~G~~V~ratlhN~~~I~~l~~~~~~~~~~~~I~iGd~V~I~RaGdV 409 (731)
|.++|..++-+. .+++||.|.|.+.+.+
T Consensus 36 V~vnG~~~Kps~---------------------~V~~GD~l~i~~~~~~ 63 (133)
T PRK10348 36 VHYNGQRSKPSK---------------------IVELNATLTLRQGNDE 63 (133)
T ss_pred EEECCEECCCCC---------------------CCCCCCEEEEEECCEE
T ss_conf 898998868888---------------------7689999999869959
No 495
>PRK07776 consensus
Probab=30.74 E-value=30 Score=13.37 Aligned_cols=31 Identities=26% Similarity=0.314 Sum_probs=0.0
Q ss_pred CCCCEEEEECCCCCCCHHHHHHHHHHCCCEEE
Q ss_conf 16866999725889987899999998298499
Q gi|254781172|r 647 IENKKLVFTGTLQKIQRHKAQEYVTQLGAVVS 678 (731)
Q Consensus 647 l~gk~vV~TGtl~~~~R~e~~~~ie~~Ggkv~ 678 (731)
|+||++++||.-.+.-|.-++. +-+.|++|.
T Consensus 6 L~gKv~lITG~~~GIG~aiA~~-la~~Ga~V~ 36 (252)
T PRK07776 6 LTGRTAIVTGASRGIGLAIAQA-LAAAGANVV 36 (252)
T ss_pred CCCCEEEEECCCCHHHHHHHHH-HHHCCCEEE
T ss_conf 9999899947787999999999-998799899
No 496
>pfam09297 zf-NADH-PPase NADH pyrophosphatase zinc ribbon domain. This domain is found in between two duplicated NUDIX domains. It has a zinc ribbon structure.
Probab=30.73 E-value=26 Score=13.83 Aligned_cols=22 Identities=23% Similarity=0.418 Sum_probs=0.0
Q ss_pred CCCCCCCCCCCCCCCCCCCCCEEECCCC
Q ss_conf 3265775010337865445210100354
Q gi|254781172|r 433 FCPICQSRVVRDLNPKTGKLVAAHRCTG 460 (731)
Q Consensus 433 ~CP~Cgs~l~~~~~~~~~~~~~~~rC~n 460 (731)
+|+.||+++.....+ -..+|++
T Consensus 5 fC~~CG~~t~~~~~g------~~r~C~~ 26 (32)
T pfam09297 5 FCGRCGAPTEPAEGG------WARVCPS 26 (32)
T ss_pred CCCCCCCCCCCCCCC------CEEECCC
T ss_conf 424468847507785------1766887
No 497
>PRK12742 oxidoreductase; Provisional
Probab=30.72 E-value=30 Score=13.37 Aligned_cols=33 Identities=18% Similarity=0.162 Sum_probs=0.0
Q ss_pred CCCCCCEEEEECCCCCCCHHHHHHHHHHCCCEEE
Q ss_conf 8216866999725889987899999998298499
Q gi|254781172|r 645 SEIENKKLVFTGTLQKIQRHKAQEYVTQLGAVVS 678 (731)
Q Consensus 645 ~~l~gk~vV~TGtl~~~~R~e~~~~ie~~Ggkv~ 678 (731)
+.|+||++++||.=.+.-+.-++ .+-+.|++|.
T Consensus 2 ~~l~gK~alITGas~GIG~aia~-~la~~Ga~V~ 34 (237)
T PRK12742 2 GAFTGKSVLVLGGSRGIGAAIVR-RFVTDGANVV 34 (237)
T ss_pred CCCCCCEEEEECCCCHHHHHHHH-HHHHCCCEEE
T ss_conf 99899989992788799999999-9998799999
No 498
>pfam08605 Rad9_Rad53_bind Fungal Rad9-like Rad53-binding. In Saccharomyces cerevisiae the Rad9 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 Rad53 pfam00498 domains. This region is structurally composed of a pair of TUDOR domains.
Probab=30.70 E-value=13 Score=16.25 Aligned_cols=42 Identities=19% Similarity=0.181 Sum_probs=0.0
Q ss_pred CHHHHHHHCCCCCCCCCCCCCCCCCEEEEEECCCCHHHHHHHCCCCCCCCCCEEE
Q ss_conf 9899975023454322246844076899983587025665410123578730477
Q gi|254781172|r 375 NEDYIKGLDASGKVMRGGRDIRVGDRVLVKRAGEVIPKVVDIIVNERHPDAQPFS 429 (731)
Q Consensus 375 N~~~I~~l~~~~~~~~~~~~I~iGd~V~I~RaGdVIP~I~~Vi~~~r~~~~~~~~ 429 (731)
+.+.++.| ||||||.|.+. +--+|+|+.=+..+.+.+..++.
T Consensus 51 ~~~dv~~L-----------dLRIGD~Vkvd--~~k~~~iV~Gl~~~~s~~~~~i~ 92 (131)
T pfam08605 51 KNGDLYYL-----------DLRIGDAVKCD--MNKYTYIVTGLECLISADDKDIR 92 (131)
T ss_pred CCCCEEEE-----------EEECCCEEEEC--CCCCCEEEEEEEECCCCCCCCEE
T ss_conf 52513478-----------65118999879--99867899986762788898438
No 499
>pfam02680 DUF211 Uncharacterized ArCR, COG1888.
Probab=30.67 E-value=30 Score=13.36 Aligned_cols=61 Identities=21% Similarity=0.345 Sum_probs=0.0
Q ss_pred CCHHHHHHHHHHHH-HCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCHHHHHHHHHHCCCEEEE
Q ss_conf 69799999999997-3387765432246882168669997258899878999999982984998
Q gi|254781172|r 617 QNPRNICAVEALLK-EVSPSIGRHEKNVSSEIENKKLVFTGTLQKIQRHKAQEYVTQLGAVVSA 679 (731)
Q Consensus 617 ~~~~n~~~i~~L~~-~~~~~~~~~~~~~~~~l~gk~vV~TGtl~~~~R~e~~~~ie~~Ggkv~s 679 (731)
+.|...++...|.+ .+.....-.-......-.|.++++-|. +..=+++++.||.+||.+.|
T Consensus 15 ~~p~i~d~A~~l~~~~gv~gVni~v~EvD~~t~~~kitIEG~--~id~d~i~~~IE~~Gg~IHS 76 (91)
T pfam02680 15 HEPSIVDLARELAELEGVDGVNITVTEIDVETENIKVTIEGS--DIDFDEIKEAIEELGGVIHS 76 (91)
T ss_pred CCCCHHHHHHHHHHCCCCCEEEEEEEEEECCCEEEEEEEEEC--CCCHHHHHHHHHHCCCEEEE
T ss_conf 999799999999727796549999999613650689999947--87979999999975983774
No 500
>TIGR02389 RNA_pol_rpoA2 DNA-directed RNA polymerase, subunit A''; InterPro: IPR012757 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 kD, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of the archaeal A'' subunit of the DNA-directed RNA polymerase. The example from Methanococcus jannaschii contains an intein.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006350 transcription.
Probab=30.61 E-value=24 Score=14.14 Aligned_cols=78 Identities=22% Similarity=0.243 Sum_probs=0.0
Q ss_pred CCHHHHHHHHHHHCCHHHHHHHHHHHHHCC------------CCCCCCCCCCCCCCCCCEEEEECCCCC---CCHHHHHH
Q ss_conf 678999999999669799999999997338------------776543224688216866999725889---98789999
Q gi|254781172|r 604 VGDIIAQAIVEFYQNPRNICAVEALLKEVS------------PSIGRHEKNVSSEIENKKLVFTGTLQK---IQRHKAQE 668 (731)
Q Consensus 604 iG~~~A~si~~ff~~~~n~~~i~~L~~~~~------------~~~~~~~~~~~~~l~gk~vV~TGtl~~---~~R~e~~~ 668 (731)
+|-++||||-+ |--+-.+..|--+|. +.+-...+..+.|+ |++=++.-+.+ |.|+-+++
T Consensus 48 vGiVAAQSiGE----PGTQMTmRTFHYAGv~ElnVTlGLPRLIEIVDArk~PSTP~--MtIYL~~ey~~dyaydrE~a~~ 121 (397)
T TIGR02389 48 VGIVAAQSIGE----PGTQMTMRTFHYAGVAELNVTLGLPRLIEIVDARKTPSTPL--MTIYLEDEYEKDYAYDREKAEE 121 (397)
T ss_pred CEEEEEEEECC----CHHHHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCE--EEEEECCCCCCCCCCCHHHHHH
T ss_conf 10388442188----45478777665776678876447840145450666789863--7996278863224566789999
Q ss_pred HHHHCCCEEEEEEECCEEE
Q ss_conf 9998298499811163217
Q gi|254781172|r 669 YVTQLGAVVSAILSRKTDI 687 (731)
Q Consensus 669 ~ie~~Ggkv~sSVSkkT~~ 687 (731)
...+...+--++|.++++.
T Consensus 122 va~kie~t~l~~v~~~i~~ 140 (397)
T TIGR02389 122 VAKKIEATKLEDVAKDISI 140 (397)
T ss_pred HHHHHHHCCHHHHHCEEEE
T ss_conf 9987520333252241248
Done!