Query 001089
Match_columns 1159
No_of_seqs 406 out of 2327
Neff 6.7
Searched_HMMs 46136
Date Thu Mar 28 15:31:37 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/001089.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/001089hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0966 ATP-dependent DNA liga 100.0 5E-150 1E-154 1309.8 61.8 852 3-909 1-881 (881)
2 PLN03113 DNA ligase 1; Provisi 100.0 4E-100 8E-105 932.3 56.4 553 5-604 127-731 (744)
3 PRK01109 ATP-dependent DNA lig 100.0 3.8E-97 8E-102 903.6 54.2 544 7-604 1-583 (590)
4 KOG0967 ATP-dependent DNA liga 100.0 6.3E-95 1.4E-99 831.3 36.4 551 5-603 97-704 (714)
5 TIGR00574 dnl1 DNA ligase I, A 100.0 1.1E-89 2.5E-94 829.0 50.6 494 62-600 1-513 (514)
6 PRK09247 ATP-dependent DNA lig 100.0 1.4E-88 2.9E-93 818.7 51.7 522 9-602 1-537 (539)
7 PRK03180 ligB ATP-dependent DN 100.0 4.3E-88 9.3E-93 808.2 50.9 493 7-600 1-506 (508)
8 PHA02587 30 DNA ligase; Provis 100.0 9.9E-61 2.1E-65 570.7 42.3 445 13-597 3-484 (488)
9 COG1793 CDC9 ATP-dependent DNA 100.0 2.1E-59 4.5E-64 550.8 32.4 421 100-600 18-443 (444)
10 TIGR02779 NHEJ_ligase_lig DNA 100.0 1E-54 2.2E-59 491.6 33.2 288 243-591 10-297 (298)
11 PRK09632 ATP-dependent DNA lig 100.0 2.7E-54 5.8E-59 528.2 32.9 307 218-591 455-761 (764)
12 PRK08224 ligC ATP-dependent DN 100.0 3.6E-52 7.9E-57 477.0 33.2 314 217-591 2-330 (350)
13 PRK05972 ligD ATP-dependent DN 100.0 2.4E-51 5.1E-56 506.4 32.5 304 222-591 232-536 (860)
14 PRK09633 ligD ATP-dependent DN 100.0 3.6E-50 7.9E-55 486.7 32.1 309 224-600 1-317 (610)
15 PRK07636 ligB ATP-dependent DN 100.0 1.5E-45 3.4E-50 411.2 30.2 272 224-582 3-274 (275)
16 cd07900 Adenylation_DNA_ligase 100.0 1.9E-44 4E-49 390.5 22.7 213 216-445 2-219 (219)
17 TIGR02776 NHEJ_ligase_prk DNA 100.0 9.9E-43 2.2E-47 417.8 25.9 257 271-591 1-258 (552)
18 cd07903 Adenylation_DNA_ligase 100.0 1.4E-41 3E-46 370.8 21.7 214 215-446 3-224 (225)
19 cd07902 Adenylation_DNA_ligase 100.0 6.6E-41 1.4E-45 361.8 22.0 206 216-445 6-213 (213)
20 cd07901 Adenylation_DNA_ligase 100.0 1.4E-40 3E-45 358.1 22.4 204 220-444 1-207 (207)
21 PRK09125 DNA ligase; Provision 100.0 3.2E-40 7E-45 369.1 25.5 254 224-585 28-282 (282)
22 PHA00454 ATP-dependent DNA lig 100.0 3.3E-39 7.1E-44 367.5 29.8 284 225-583 7-314 (315)
23 cd07897 Adenylation_DNA_ligase 100.0 3.4E-39 7.4E-44 347.0 20.9 201 222-445 3-206 (207)
24 cd08039 Adenylation_DNA_ligase 100.0 7.5E-39 1.6E-43 348.9 22.1 200 234-445 11-235 (235)
25 cd07898 Adenylation_DNA_ligase 100.0 9.2E-39 2E-43 342.6 22.2 199 224-444 1-201 (201)
26 PF01068 DNA_ligase_A_M: ATP d 100.0 5E-37 1.1E-41 329.1 20.1 199 226-442 1-202 (202)
27 cd07905 Adenylation_DNA_ligase 100.0 5.8E-37 1.3E-41 326.7 19.9 190 224-444 1-193 (194)
28 cd07906 Adenylation_DNA_ligase 100.0 2.5E-36 5.4E-41 321.0 18.1 189 224-443 1-189 (190)
29 cd07967 OBF_DNA_ligase_III The 100.0 7.9E-32 1.7E-36 270.0 14.8 137 449-595 2-139 (139)
30 cd07896 Adenylation_kDNA_ligas 100.0 1.3E-30 2.8E-35 273.4 15.4 173 224-443 1-174 (174)
31 cd06846 Adenylation_DNA_ligase 100.0 1.5E-28 3.3E-33 259.6 17.6 178 225-443 1-182 (182)
32 PF04675 DNA_ligase_A_N: DNA l 100.0 4.5E-29 9.7E-34 262.4 13.2 169 7-187 1-177 (177)
33 cd07968 OBF_DNA_ligase_IV The 99.9 1.4E-27 3E-32 241.1 14.5 139 449-593 1-140 (140)
34 cd07969 OBF_DNA_ligase_I The O 99.9 2.5E-26 5.5E-31 232.4 15.7 134 449-601 1-143 (144)
35 cd07972 OBF_DNA_ligase_Arch_Li 99.9 5.5E-25 1.2E-29 217.1 14.2 121 450-597 1-121 (122)
36 KOG4437 ATP-dependent DNA liga 99.9 2E-24 4.3E-29 232.2 19.3 318 7-345 155-482 (482)
37 cd07895 Adenylation_mRNA_cappi 99.9 3.6E-25 7.8E-30 240.0 13.2 172 240-443 36-215 (215)
38 cd07893 OBF_DNA_ligase The Oli 99.9 1E-23 2.2E-28 209.9 14.7 122 450-590 1-129 (129)
39 cd07971 OBF_DNA_ligase_LigD Th 99.8 1.3E-18 2.8E-23 170.2 13.9 114 451-590 2-115 (115)
40 PF04679 DNA_ligase_A_C: ATP d 99.7 1.2E-17 2.6E-22 158.5 11.7 97 466-585 1-97 (97)
41 cd08040 OBF_DNA_ligase_family 99.7 3E-17 6.6E-22 158.8 13.5 108 450-582 1-108 (108)
42 cd07894 Adenylation_RNA_ligase 99.6 1.8E-15 3.8E-20 173.4 14.8 162 245-445 48-218 (342)
43 cd07970 OBF_DNA_ligase_LigC Th 99.6 5.7E-15 1.2E-19 145.6 13.4 120 450-591 1-121 (122)
44 PF00533 BRCT: BRCA1 C Terminu 99.1 1.1E-10 2.3E-15 105.4 8.0 74 653-727 2-78 (78)
45 PF01331 mRNA_cap_enzyme: mRNA 99.1 3.1E-11 6.8E-16 128.9 0.8 173 241-442 12-192 (192)
46 smart00292 BRCT breast cancer 99.0 2E-09 4.2E-14 96.2 8.2 76 655-730 1-80 (80)
47 KOG1929 Nucleotide excision re 98.9 9.4E-09 2E-13 127.6 14.0 183 654-913 7-191 (811)
48 cd08041 OBF_kDNA_ligase_like T 98.9 5E-09 1.1E-13 95.3 8.4 76 451-582 2-77 (77)
49 KOG3524 Predicted guanine nucl 98.9 4.5E-09 9.8E-14 124.3 8.7 183 652-913 114-296 (850)
50 COG5226 CEG1 mRNA capping enzy 98.9 4.8E-09 1E-13 113.8 7.9 183 242-458 59-257 (404)
51 cd00027 BRCT Breast Cancer Sup 98.8 1.7E-08 3.7E-13 88.0 7.7 70 659-728 1-72 (72)
52 PF00533 BRCT: BRCA1 C Terminu 98.7 4.6E-08 1E-12 88.1 7.5 75 800-897 3-78 (78)
53 KOG3226 DNA repair protein [Re 98.6 2.1E-08 4.5E-13 111.1 4.4 94 649-744 310-404 (508)
54 COG1423 ATP-dependent DNA liga 98.5 1.5E-06 3.2E-11 97.0 15.1 151 241-430 84-239 (382)
55 smart00292 BRCT breast cancer 98.5 3.2E-07 6.9E-12 81.8 7.6 76 802-900 2-80 (80)
56 TIGR01209 RNA ligase, Pab1020 98.5 1.8E-06 4E-11 99.2 15.3 151 241-428 75-229 (374)
57 PF12738 PTCB-BRCT: twin BRCT 98.4 2.2E-07 4.8E-12 81.0 4.8 62 660-722 1-63 (63)
58 PRK07956 ligA NAD-dependent DN 98.4 6.8E-05 1.5E-09 94.0 25.9 74 656-729 590-664 (665)
59 cd00027 BRCT Breast Cancer Sup 98.2 3E-06 6.6E-11 73.7 7.5 71 805-898 1-72 (72)
60 KOG3548 DNA damage checkpoint 98.1 4.9E-06 1.1E-10 101.8 8.1 88 654-744 923-1038(1176)
61 PF11411 DNA_ligase_IV: DNA li 98.1 1.9E-06 4.1E-11 65.1 2.6 35 746-780 1-35 (36)
62 KOG1929 Nucleotide excision re 98.1 8E-06 1.7E-10 102.1 9.2 179 653-858 100-285 (811)
63 cd09232 Snurportin-1_C C-termi 98.1 3.6E-05 7.9E-10 81.7 12.8 176 225-444 5-186 (186)
64 KOG2481 Protein required for n 97.9 6.1E-06 1.3E-10 95.9 4.3 79 654-738 325-413 (570)
65 COG0272 Lig NAD-dependent DNA 97.8 0.0017 3.7E-08 79.6 22.9 73 655-727 593-666 (667)
66 PF14743 DNA_ligase_OB_2: DNA 97.8 1.5E-05 3.3E-10 70.1 3.9 37 462-509 2-38 (66)
67 COG5163 NOP7 Protein required 97.7 2.9E-05 6.3E-10 87.3 3.9 79 654-738 348-437 (591)
68 PLN03122 Poly [ADP-ribose] pol 97.6 0.00015 3.2E-09 91.7 8.6 87 653-741 186-278 (815)
69 smart00532 LIGANc Ligase N fam 97.5 0.0011 2.4E-08 79.5 14.5 195 246-471 104-332 (441)
70 KOG2481 Protein required for n 97.5 8.4E-05 1.8E-09 86.7 4.9 83 799-912 324-417 (570)
71 cd00114 LIGANc NAD+ dependent 97.4 0.0019 4.2E-08 74.0 14.2 167 246-438 102-299 (307)
72 PF12738 PTCB-BRCT: twin BRCT 97.3 0.00045 9.7E-09 60.2 5.7 62 806-892 1-63 (63)
73 PRK08097 ligB NAD-dependent DN 97.2 0.0047 1E-07 75.8 14.8 209 224-471 95-329 (562)
74 KOG3226 DNA repair protein [Re 97.2 0.00068 1.5E-08 76.1 6.7 90 800-914 315-405 (508)
75 TIGR00575 dnlj DNA ligase, NAD 97.2 0.0033 7.2E-08 79.1 13.4 225 246-509 97-355 (652)
76 PF01653 DNA_ligase_aden: NAD- 97.1 0.00019 4.1E-09 82.5 1.2 155 246-430 108-294 (315)
77 PRK14351 ligA NAD-dependent DN 96.9 0.011 2.3E-07 74.8 15.1 223 245-508 132-388 (689)
78 PLN03123 poly [ADP-ribose] pol 96.8 0.0022 4.7E-08 83.1 7.8 86 652-738 389-478 (981)
79 COG5163 NOP7 Protein required 96.7 0.0015 3.3E-08 73.9 4.5 83 800-913 348-442 (591)
80 PRK01109 ATP-dependent DNA lig 96.6 0.0098 2.1E-07 74.4 10.9 97 4-114 112-211 (590)
81 PRK14350 ligA NAD-dependent DN 96.6 0.027 5.9E-07 70.9 14.6 225 246-508 111-363 (669)
82 PLN03122 Poly [ADP-ribose] pol 96.2 0.01 2.2E-07 75.6 8.3 95 799-913 186-280 (815)
83 KOG4362 Transcriptional regula 96.2 0.016 3.4E-07 71.5 9.2 195 654-902 472-680 (684)
84 TIGR02307 RNA_lig_RNL2 RNA lig 96.1 0.06 1.3E-06 61.8 12.7 106 242-366 22-145 (325)
85 PRK14350 ligA NAD-dependent DN 95.6 0.025 5.4E-07 71.2 7.9 74 654-727 591-665 (669)
86 PLN03123 poly [ADP-ribose] pol 95.6 0.023 4.9E-07 74.0 7.5 90 800-911 391-481 (981)
87 PF09414 RNA_ligase: RNA ligas 95.5 0.025 5.3E-07 60.2 6.4 106 246-366 2-129 (186)
88 KOG2093 Translesion DNA polyme 95.4 0.021 4.6E-07 71.0 5.9 199 650-910 41-244 (1016)
89 PRK14351 ligA NAD-dependent DN 95.2 0.043 9.3E-07 69.5 8.2 76 654-729 607-684 (689)
90 PRK06063 DNA polymerase III su 94.9 0.059 1.3E-06 62.3 7.7 74 653-727 229-305 (313)
91 PRK06195 DNA polymerase III su 94.9 0.054 1.2E-06 62.5 7.2 75 653-727 217-306 (309)
92 TIGR00575 dnlj DNA ligase, NAD 94.6 0.066 1.4E-06 67.7 7.4 68 654-721 582-650 (652)
93 COG5275 BRCT domain type II [G 94.3 0.14 2.9E-06 54.4 7.7 81 648-728 148-230 (276)
94 KOG2043 Signaling protein SWIF 94.1 0.14 2.9E-06 66.3 8.7 127 674-849 671-799 (896)
95 PHA02142 putative RNA ligase 92.7 1.3 2.9E-05 51.8 13.0 103 242-366 166-298 (366)
96 KOG2043 Signaling protein SWIF 90.7 0.2 4.3E-06 64.9 3.9 71 830-913 671-741 (896)
97 TIGR02306 RNA_lig_DRB0094 RNA 89.4 3.2 6.9E-05 48.5 11.9 154 244-444 158-336 (341)
98 KOG3132 m3G-cap-specific nucle 89.0 1.9 4.2E-05 46.8 8.9 172 226-440 101-277 (325)
99 PRK09247 ATP-dependent DNA lig 86.7 0.99 2.1E-05 56.2 6.0 82 127-208 2-91 (539)
100 KOG3548 DNA damage checkpoint 86.3 0.97 2.1E-05 57.2 5.4 39 883-921 1008-1046(1176)
101 KOG0966 ATP-dependent DNA liga 85.0 1.5 3.2E-05 55.0 6.2 88 800-908 631-719 (881)
102 PRK03180 ligB ATP-dependent DN 84.1 5.8 0.00012 49.1 10.8 93 6-114 72-167 (508)
103 KOG4362 Transcriptional regula 80.5 2.1 4.5E-05 53.6 5.1 82 653-734 584-682 (684)
104 PF04675 DNA_ligase_A_N: DNA l 80.3 1.9 4.2E-05 45.3 4.2 84 126-209 3-100 (177)
105 PLN03113 DNA ligase 1; Provisi 73.8 6.4 0.00014 50.7 6.9 86 122-207 127-229 (744)
106 KOG2386 mRNA capping enzyme, g 72.8 2.3 4.9E-05 50.2 2.4 92 245-365 285-383 (393)
107 TIGR00574 dnl1 DNA ligase I, A 67.3 18 0.0004 44.9 8.8 94 5-114 53-149 (514)
108 PRK06195 DNA polymerase III su 62.7 27 0.00059 40.4 8.6 48 801-858 219-267 (309)
109 COG4566 TtrR Response regulato 54.3 44 0.00096 35.9 7.4 81 101-181 84-174 (202)
110 KOG3524 Predicted guanine nucl 52.6 8.9 0.00019 47.7 2.4 75 654-730 208-283 (850)
111 PF02178 AT_hook: AT hook moti 52.4 6.1 0.00013 23.9 0.5 12 970-981 1-12 (13)
112 KOG0323 TFIIF-interacting CTD 51.8 7.7 0.00017 48.7 1.7 83 655-737 440-527 (635)
113 PRK07956 ligA NAD-dependent DN 48.4 34 0.00073 43.9 6.7 224 246-508 109-366 (665)
114 PRK06063 DNA polymerase III su 44.8 61 0.0013 37.7 7.6 50 800-860 230-280 (313)
115 KOG0323 TFIIF-interacting CTD 43.0 25 0.00054 44.3 4.2 95 800-914 439-534 (635)
116 PF09511 RNA_lig_T4_1: RNA lig 40.5 2.3E+02 0.0051 31.0 11.0 32 246-277 46-78 (221)
117 PF14538 Raptor_N: Raptor N-te 37.9 65 0.0014 33.5 5.7 40 298-345 106-145 (154)
118 COG0272 Lig NAD-dependent DNA 33.6 76 0.0017 40.2 6.3 195 245-470 109-336 (667)
119 KOG2093 Translesion DNA polyme 31.6 48 0.001 42.8 4.1 89 799-914 44-134 (1016)
120 COG5275 BRCT domain type II [G 27.4 2E+02 0.0043 31.4 7.2 53 799-861 153-206 (276)
121 cd00950 DHDPS Dihydrodipicolin 25.7 1.4E+02 0.0031 33.8 6.5 67 342-425 36-104 (284)
122 smart00384 AT_hook DNA binding 24.0 43 0.00093 24.2 1.1 13 970-982 1-13 (26)
123 PF00701 DHDPS: Dihydrodipicol 23.7 1.7E+02 0.0036 33.4 6.5 65 344-425 39-105 (289)
124 cd00408 DHDPS-like Dihydrodipi 22.9 1.8E+02 0.0039 32.9 6.6 65 344-425 35-101 (281)
125 PRK03170 dihydrodipicolinate s 21.9 1.8E+02 0.004 33.2 6.4 58 351-425 48-105 (292)
126 cd00952 CHBPH_aldolase Trans-o 21.8 1.9E+02 0.0041 33.5 6.5 65 344-425 46-112 (309)
127 TIGR02313 HpaI-NOT-DapA 2,4-di 21.8 1.9E+02 0.0041 33.3 6.4 65 344-425 38-104 (294)
128 TIGR00683 nanA N-acetylneurami 21.5 1.9E+02 0.0042 33.1 6.5 66 342-424 37-104 (290)
129 PF15101 DUF4557: Domain of un 20.6 2.3E+02 0.0051 30.7 6.2 70 674-746 14-92 (212)
No 1
>KOG0966 consensus ATP-dependent DNA ligase IV [Replication, recombination and repair]
Probab=100.00 E-value=4.6e-150 Score=1309.76 Aligned_cols=852 Identities=41% Similarity=0.685 Sum_probs=706.1
Q ss_pred CCCCCcHHHHHHHHHHHHhhCChHHHHHHHHHHHhhcCCC----chHHHHHHHhCCCCCCCccccCCCHHHHHHHHHHHh
Q 001089 3 KTEETEVIVLVSLFNWIQKTKPAAKKRSKFRKFLDTYCDS----VDYFSALRLILPSLDRERGSYGLKESVLANCLIDAL 78 (1159)
Q Consensus 3 ~~~~~~F~~l~~lle~i~~~~~~~~K~~~l~~~l~~~~~~----~d~~p~lrLllP~~d~~r~~ygike~~L~k~~~~~l 78 (1159)
||+++.|+.+|++|+.|+.+.....|++++++++.+|+.+ +|+||++||++|++||+|+.||||+..|+++|+++|
T Consensus 1 ~~~~~~F~~~~~~f~~i~~t~~~~~k~~~~~k~~~s~~~~~e~~sd~y~~lRL~lp~lDReR~~Yglket~La~l~i~~l 80 (881)
T KOG0966|consen 1 MASPQNFSEVVDFFNKIRRTSNVKSKQAKFRKNFESWCRPCEVGSDMYVALRLILPDLDRERGSYGLKETVLARLYIRAL 80 (881)
T ss_pred CCCccccchHHHHHHHHHHhhhhHhHHHHHhhccccccccccCCcchhhhhhhcccchhhcccccCchHHHHHHHHHHHh
Confidence 7899999999999999999999999999999999999876 999999999999999999999999999999999999
Q ss_pred CCCcChHHHHHHhhhhcCCCCCCCCCHHHHHHHHhhhccCCC-CCCCCHHHHHHHHHHHHhhhhHHHHH-HHHHHHHHhC
Q 001089 79 GMSKDSADAVRLINWRKGGAAPNAGNFPMVAAEVLQRRQGMI-SGGLTIKELNDLLDRLASSENRAEKI-SVLSTLIKKT 156 (1159)
Q Consensus 79 gl~~~s~~~~~L~~wk~~~~~~~~GD~~~~a~~vl~~r~~~~-~~~LTi~eVn~~Ld~LA~~~~~~~k~-~il~~ll~~~ 156 (1159)
++|++|.||++|.+|+.++.++ |||+.++++++++|+... ++.|||.|||++||.||+......+. ..|..++++|
T Consensus 81 ~lprds~Da~rL~nwr~~~~~~--Gdfs~i~~~vl~~R~~~~~s~alTi~evN~lLD~LA~~~~~~~~~~~~l~~lv~~~ 158 (881)
T KOG0966|consen 81 HLPRDSADAVRLKNWRASTGAR--GDFSLILYEVLQRRCENPSSGALTIKEVNDLLDSLASGPSEDGKKFKKLSQLVEQC 158 (881)
T ss_pred cCCCCcHHHHHHHhhccCCCcC--ccHHHHHHHHHHHHhcCCCCCceeHHHHHHHHHHHcCCchhhhhhhHHHHHHHHhC
Confidence 9999999999999999987755 999999999999998654 45599999999999999887655443 7899999999
Q ss_pred CHHHHHHHHHHHHhhhccCCcccccccccCccHHHHhhhcCCHHHHHHHHhhhhccccccC--cccCCccccccccccCC
Q 001089 157 NAQEMKWIIMIILKDLKLGISEKSIFHEFHPDAEDLFNVTCDLKLVCEKLKDRNQRHKRQD--IEVGKAVRPQLAMRIGD 234 (1159)
Q Consensus 157 s~~E~k~l~RiIlkdLriGi~e~til~~~hpda~~~~~~~~dL~~V~~~L~~~~~~~~~~~--i~~g~p~~PMLA~~~~~ 234 (1159)
||.|+|||+|||||++++|+++++||.+|||||+++|++|+||+.||+.|.||+.+++..+ |++|..|+||||++...
T Consensus 159 S~~ElkWliriiLK~lklG~se~~Il~vfHPdA~dl~~vtsDLk~Vc~~L~Dp~~~l~~~~~~i~lfsa~~PqLa~~~~~ 238 (881)
T KOG0966|consen 159 SPLELKWLIRIILKNLKLGASEKKILSVFHPDAQDLYNVTSDLKAVCKKLYDPSVGLKELDEDIELFSAFRPQLAQKQKL 238 (881)
T ss_pred CHHHHHHHHHHHHHhhhcCCccchhhhhcCccHHHHHHHhhhHHHHHHHhcCCccCccccccceeehhhcCHHHHhhhcc
Confidence 9999999999999999999999999999999999999999999999999999999998877 99999999999999877
Q ss_pred hH-HHHHhcCCCcEEEEEecceEEEEEEEeCCEEEEEecCCCCcCcc-----hhh-HHHHHHHhc--ccCceeecceEEE
Q 001089 235 AH-AAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEY-----GHA-MSKIIEQNV--LVDRCILDGEMLV 305 (1159)
Q Consensus 235 ~~-~~~~k~~~~~~~vE~K~DGeR~qih~~g~~v~~fSR~g~d~t~~-----~p~-l~~~l~~~~--~~~~~ILDGElv~ 305 (1159)
.. +++++|++.+|++|+|+||||+|+|++|+.++||||||.|||.. ..+ +...+...+ .+..||||||||+
T Consensus 239 ~~~~~~e~m~~~~f~lEtK~DGERiQlHk~g~~~~yfSRNg~dyT~~yg~s~~~g~lt~~i~~~f~~~v~~cILDGEMm~ 318 (881)
T KOG0966|consen 239 GDWAIIEKMGGQDFYLETKFDGERIQLHKDGGEYKYFSRNGNDYTYEYGASYAHGTLTQRIHGAFNKEVESCILDGEMMT 318 (881)
T ss_pred chHHHHHHhcCCceEEEeeccCceEEEEecCCEEEEEecCCcchhhhcCcccccccccHHHHhhhhhcchheEecceEEE
Confidence 66 68999999999999999999999999999999999999999932 122 223333222 2789999999999
Q ss_pred EeCCCCcccccccHHHHHHHhhcCCCCCCCeEEEEEeeeecCCccccCCCHHHHHHHHHHhhccCCCcceeeccCCCCCc
Q 001089 306 WDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNS 385 (1159)
Q Consensus 306 ~d~~~~~~~pFg~lq~i~~~~r~~~~~~~~~~~~vFDiL~lnG~~l~~~pl~eRr~~L~~~i~~~~~~~~i~~p~~~~~~ 385 (1159)
||+.+.+++|||+++++...... +.+.++||+|||+||+||++|.+.||.+|+++|..++.+.+++++++
T Consensus 319 wD~~~~~f~~~G~~~dik~~~~~--~~~~qp~yvvfDLLylNgksL~~~~l~qR~e~L~~v~~p~~~~iei~-------- 388 (881)
T KOG0966|consen 319 WDTKTKRFCPFGSNSDIKELSSR--DGSQQPCYVVFDLLYLNGKSLFGAPLHQRLEILKKVIVPKSGRIEIV-------- 388 (881)
T ss_pred eecchhhhccCCchhhHHHhhcc--ccCCCceEEEeeeeeecCcccCCccHHHHHHHHHhcccCCCCeeEEe--------
Confidence 99999999999999988766542 45689999999999999999999999999999999999999998765
Q ss_pred cccCCCCCccceecCCHHHHHHHHHHHHHcCCceEEEecCCCCCcCCCCCCCeEEEcccccc-cCCcccEEEEEEEeCCC
Q 001089 386 HVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIR-AGSDLDVLIIGGYYGSG 464 (1159)
Q Consensus 386 ~v~~~~~~~~~~~~~~~~ei~~~~~~ai~~g~EGlVlK~~ds~Y~pGkRs~~WlKiKpey~~-~g~~lDlvVIG~~~G~G 464 (1159)
+...+++.++|+++|++||++|.||||+|.++|.|.||.|+++|+|+||+|+. +|+++|++|||||||.|
T Consensus 389 ---------~~~~~~~~edi~~~f~~ai~~~~EGIVlK~~~S~Y~pg~R~~gW~K~KPeYlkg~g~dLD~lIiGgy~G~g 459 (881)
T KOG0966|consen 389 ---------RSEVGSTKEDIEQFFEEAIDNGEEGIVLKKPDSSYVPGQRSNGWIKLKPEYLKGFGEDLDLLIIGGYYGRG 459 (881)
T ss_pred ---------ehhhcccHHHHHHHHHHHHhcCCCceEEeccCcccCccccCCCcEeecHHHHhhcCccccEEEEecccCCC
Confidence 24568899999999999999999999999999999999999999999999999 58999999999999999
Q ss_pred CCCCccceEEEEEecCCCCCCCCceEEEEEEecCCCCHHHHHHHHHhhcccccccCCCCCCCCCcccccCCCCCCCcEEE
Q 001089 465 RRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDVWI 544 (1159)
Q Consensus 465 rr~g~~gsfllg~~d~~~~~~~~~~f~~v~kVgtG~sdeel~~l~~~l~~~~~~~~~~~~~pP~~~~~~~~~~~~Pdvwi 544 (1159)
+++|.+.+|+||+.++..++.+|.+|.++|+||+|+|++|+..+.++|++||.+ .....+|++++..+ ...||+||
T Consensus 460 ~rgg~~~~fl~a~~ek~~p~~~p~~f~sfcrvg~g~s~~e~~~v~~klr~~w~~-~~~~apP~s~l~~t---k~~Pd~wI 535 (881)
T KOG0966|consen 460 DRGGKVLSFLCALAEKAPPNSRPEKFCSFCRVGNGISQKERDTVREKLRGHWKP-TSLEAPPESFLFGT---KKIPDVWI 535 (881)
T ss_pred CCCCeeeeeeehhcccCCCCCccceeeEeeEecCCccHHHHHHHHHhhhhhccc-ccccCCCHHHHhcc---cCCCceeE
Confidence 999999999999998877777899999999999999999999999999999987 24444344444433 34799999
Q ss_pred eCCcceEEEEEEeeeeeeecccccCCceeeCceeeeeecCCCccCcCCHHHHHHHHHccCCCcccccccCCCCCCCCccc
Q 001089 545 ESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDKPWHDCLDVQSFVELVHSSNGTTQKGKEYGGLQDDKPKQF 624 (1159)
Q Consensus 545 ~~P~~s~Vlev~a~i~~i~s~~~~~g~tLRFPR~~riR~DK~~~d~~t~~el~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 624 (1159)
+ |..|+|++|++ .+++.+..|.++|||||||+.+||+||+|+||+|+++|.++...+. ++.+.+. ++++
T Consensus 536 ~-P~~SiIlqika-a~i~~s~~f~tn~tLrfPr~ekvR~DK~W~ec~tl~~l~~l~~~~~-------~d~~~~~-kk~~- 604 (881)
T KOG0966|consen 536 D-PDNSIILQIKA-AEIVPSSNFVTNYTLRFPRIEKVRLDKPWHECLTLNELGDLVNVSK-------SDVEDKE-KKKR- 604 (881)
T ss_pred C-CCCceEEEeeh-heeeecccccccceeecceeeeeecCCcHHHHhhHHHHHHHhcccc-------CCcchhh-hhcc-
Confidence 9 99999999995 3456899999999999999999999999999999999999985311 1111111 1111
Q ss_pred ccccccccccccccCCccccCccccccCCCCcccCeEEEEEcCC-CCCChHHHHHHHHHcCCEEEecCCCCceEEEE-ec
Q 001089 625 RSSRKGEKKNVSIVPSHFLQTDVSDIKGETSIFSDMVFYFVNVP-PAYSLDSLHKMVVENGGTFSMNLNNSVTHCVA-AD 702 (1159)
Q Consensus 625 ~~~~~~~~~~~~~~~~~~~~~~~s~~~~~s~lF~G~~F~vv~~~-~~~~k~eLe~lI~~~GG~iv~n~~~~~Th~Ia-~~ 702 (1159)
.+.+++++.+. .-+...+..+.+.+.|++|.|+.|||+++. ...++.+|+++|++|||++++|++++.|+||+ ++
T Consensus 605 ~t~~~~k~~~~---~i~~~~~~~~~~~~~s~if~gl~f~Vlsgt~~~~tk~~le~~ivenGG~iv~nv~p~~~~ci~~a~ 681 (881)
T KOG0966|consen 605 DTLKVRKRTRK---AIHDSAPNRSKVAKISNIFDGLEFCVLSGTSETHTKAKLEEIIVENGGKIVQNVGPSDTLCIATAG 681 (881)
T ss_pred cchhhhhhhhh---hhcccccchhcccchhhhhcCeeEEEecCCcccccHHHHHHHHHHcCCEEEEcCCCCCcceEEecc
Confidence 11111111111 123344566677889999999999999876 45679999999999999999999988999996 33
Q ss_pred C--CChhhHhHhcCCCeeecchHHHHHhcCccCCCCcccccccChhhhhhhhhcccccCCCcccCCChhHHHHHhhccCC
Q 001089 703 N--KGLKYEAAKRRGDVIHYSWVLDCCSQKKLLQLQPKYYLHLSDSSKKKLQEEVDEFSDLYFWDLDLADIKQLLSNVDR 780 (1159)
Q Consensus 703 ~--~~~k~~~a~~~~~VV~p~WV~dCi~~~~lLp~~p~~~l~~s~~t~~~~~~~~D~~GDSy~~~~~~~~L~~ll~~~~~ 780 (1159)
. .+.++.++.+..+||+|+||+||++..+++||.|++++++++.+++.++..+|+|||||++|++.+.|+.+++.+..
T Consensus 682 ~et~~vk~~~~~~~cdVl~p~Wlldcc~~~~l~p~~P~~~fh~~e~~~~~~a~~~D~~gdSy~~di~l~~l~~~ls~~k~ 761 (881)
T KOG0966|consen 682 KETTRVKAQAIKRSCDVLKPAWLLDCCKKQRLLPWLPRDLFHATEKGREKLAKEVDCLGDSYENDIDLEQLKKVLSGIKK 761 (881)
T ss_pred ccchHHHHHHHhccCceeeHHHHHHHHhhhhccccccHHHHhhCchHHHHHHHHHhhhcchhhhhccHHHHHHHHhhhhh
Confidence 3 33455555565599999999999999999999999999999999999999999999999999999999999998887
Q ss_pred CCCcchhHHHhhhcCCCCCCCcCCCeEEEEcCCCCCCCCchHHHHHHHHHHHHHHHHhcCCEEEccCC-------CceEE
Q 001089 781 SEDPKTIDYYKKKYCPQDKWSCFHGCCIYFYHSTEPLSPDWEVLLGLALRRLKLEISFHGGKVCNNLA-------NATHV 853 (1159)
Q Consensus 781 s~~~~~i~~l~~~~~~~~~~~lF~gc~~yl~~~~~~~~~d~~~i~~~~~~~l~~~I~~~GG~v~~~ls-------~vTHV 853 (1159)
+.+...........++...+.+|.-|..+|+......+.+ .......+..+||.+.+.-. .+||+
T Consensus 762 S~ds~~~~~~~~~~~~e~r~~~~~~~~~~f~~~~~~~~se--------~~~~~l~~k~~g~~i~~~~~~~~~~~~~~t~~ 833 (881)
T KOG0966|consen 762 SQDSLPPMGASEKDSLERRFSLFLSSLRMFYVLRRKLSSE--------EVIIELKLKNFGGRITDAQSECNNIGAKYTHC 833 (881)
T ss_pred cccccCchhhhhhhcHHHhhccccccceeeecccccccHH--------HHHHHHHHHHhcceeeeccchhhhcccceeee
Confidence 6654322211111112222333333333333333222222 23445567888999887643 36999
Q ss_pred EEeccCCcccchhhHHHHHHHHhhhhccCCccEEecccHHHHHHHcCCccCCCCCC
Q 001089 854 VVLSVLGYDVNFNSLTESFTAREKHLLWNKKLHVVRSQWLEDCLAKEQKSEEYEYS 909 (1159)
Q Consensus 854 IV~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~IVs~~WL~~ci~~g~~v~E~~Y~ 909 (1159)
|+...+ ......+.. .......++ +||.+.||.+|+.+++++||++|.
T Consensus 834 v~~~i~-----~~h~~~~~~--~~~~lt~~r-kv~~~~wv~~s~~~~~~~~e~~~~ 881 (881)
T KOG0966|consen 834 VLRCID-----EDHEKIKEQ--KKASLTIKR-KVVAPSWVDHSINENCLLPEEDFP 881 (881)
T ss_pred eeeecc-----hHHHHHHHH--HHHHhcccc-cccCHHHHHHhhcccccCccccCC
Confidence 987322 111111111 111122234 999999999999999999999984
No 2
>PLN03113 DNA ligase 1; Provisional
Probab=100.00 E-value=3.7e-100 Score=932.26 Aligned_cols=553 Identities=23% Similarity=0.415 Sum_probs=472.9
Q ss_pred CCCcHHHHHHHHHHHHhhCChHHHHHHHHHHHhhc--CCCchHHHHHHHhCCCC--CCCccccCCCHHHHHHHHHHHhCC
Q 001089 5 EETEVIVLVSLFNWIQKTKPAAKKRSKFRKFLDTY--CDSVDYFSALRLILPSL--DRERGSYGLKESVLANCLIDALGM 80 (1159)
Q Consensus 5 ~~~~F~~l~~lle~i~~~~~~~~K~~~l~~~l~~~--~~~~d~~p~lrLllP~~--d~~r~~ygike~~L~k~~~~~lgl 80 (1159)
.+|+|+.||.+|++|+.++++.+|+.+|.+||... ..++|++|+++|++..+ +.++.+|||+++.|+++|++++|+
T Consensus 127 ~~~~f~~l~~~~~~Ie~tt~rlek~~~L~~~~r~~~~~~p~dl~~~vyL~~~~l~P~~e~~elgige~~L~kai~e~~g~ 206 (744)
T PLN03113 127 ERVPFLFVALAFDLISNETGRIVITDIVCNMLRTVMATTPEDLVAVVYLLANRIAPAHEGVELGIGEATIIKALAEAFGR 206 (744)
T ss_pred CCccHHHHHHHHHHHHhccCHHHHHHHHHHHHHHhccCChHHHHHHHHHHhCCCCccccCcccCcCHHHHHHHHHHHHCc
Confidence 56999999999999999999999999999999986 35789999999954333 234679999999999999999999
Q ss_pred CcChHHHHHHhhhhcCCCCCCCCCHHHHHHHHhhhccC-CCCCCCCHHHHHHHHHHHHhhhh---HHHHHHHHHHHHHhC
Q 001089 81 SKDSADAVRLINWRKGGAAPNAGNFPMVAAEVLQRRQG-MISGGLTIKELNDLLDRLASSEN---RAEKISVLSTLIKKT 156 (1159)
Q Consensus 81 ~~~s~~~~~L~~wk~~~~~~~~GD~~~~a~~vl~~r~~-~~~~~LTi~eVn~~Ld~LA~~~~---~~~k~~il~~ll~~~ 156 (1159)
+...... .| ...||||+||+.+.+.+.. ..+.+|||.+|++.|.+||..+| +.+|..+|..||..+
T Consensus 207 ~~~~ik~----~y------~~~GDlG~vA~~~~~~q~~~~~~~~LTi~~V~~~L~~IA~~~G~~sq~~K~~~i~~Ll~~~ 276 (744)
T PLN03113 207 TEKQVKK----QY------KELGDLGLVAKASRSSQSMMRKPEPLTVVKVFNTFQQIAKESGKDSQEKKKNRIKALLVAA 276 (744)
T ss_pred CHHHHHH----HH------HHhCCHHHHHHhhhcccccccCCCCCCHHHHHHHHHHHHhhhCccCHHHHHHHHHHHHHhC
Confidence 9754321 34 4579999999977654442 23578999999999999998876 567889999999999
Q ss_pred CHHHHHHHHHHHHhhhccCCcccccccccCccH------------------------HHHhhhcCCHHHHHHHHhhhh-c
Q 001089 157 NAQEMKWIIMIILKDLKLGISEKSIFHEFHPDA------------------------EDLFNVTCDLKLVCEKLKDRN-Q 211 (1159)
Q Consensus 157 s~~E~k~l~RiIlkdLriGi~e~til~~~hpda------------------------~~~~~~~~dL~~V~~~L~~~~-~ 211 (1159)
++.|++||+|+|+++||||+++++|+.++|+.+ .++|+.++|++.|+..|.... .
T Consensus 277 ~~~E~k~liR~l~g~LRIGv~e~tVl~ALa~a~~~~~~~~~~~~~~~~~l~~~~~~v~~a~~~~p~~~~i~~~ll~~g~~ 356 (744)
T PLN03113 277 TDCEPLYLIRLLQTKLRIGLAGQTLLAALGQAAVYNEEHSTPPPNIQSPLEEAAKIVKQVYSVLPVYDKIVPALLSGGVW 356 (744)
T ss_pred CHHHHHHHHHHHhccccccccHHHHHHHHHHHhcccccccccccccchhhHHHHHHHHHHhccCCCHHHHHHHHHhCCcc
Confidence 999999999999999999999999999887643 357888899988888776533 2
Q ss_pred cc-cccCcccCCccccccccccCChHHHHHhcCCCcEEEEEecceEEEEEEE-eCCEEEEEecCCCCcCcchhhHHHHHH
Q 001089 212 RH-KRQDIEVGKAVRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHK-NGSEIHYFSRSFLDHSEYGHAMSKIIE 289 (1159)
Q Consensus 212 ~~-~~~~i~~g~p~~PMLA~~~~~~~~~~~k~~~~~~~vE~K~DGeR~qih~-~g~~v~~fSR~g~d~t~~~p~l~~~l~ 289 (1159)
.+ ....|++|+||+||||++...+.+++++|.+..|++|+||||+|+|||+ .++.|++|||||+++|..||++...+.
T Consensus 357 ~l~~~~~i~~g~Pi~PMLA~~~~~~~eil~~~~g~~~~~E~KyDGeR~QiH~~~~g~v~lfSRn~ed~T~~fPel~~~~~ 436 (744)
T PLN03113 357 NLPKTCSFTPGVPVGPMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHFLEDGSVEIYSRNAERNTGKYPDVVVAIS 436 (744)
T ss_pred cccccccccCCCCCCCccCCCCCChHHHhhccCCCCEEEEEeeccceEEEEEecCCEEEEEeCCCCcccccchhHHHHHH
Confidence 23 5677999999999999999999889999988899999999999999998 478999999999999999999988765
Q ss_pred Hhcc--cCceeecceEEEEeCCCCcccccccHHHHHHHhhcCC---CCCCCeEEEEEeeeecCCccccCCCHHHHHHHHH
Q 001089 290 QNVL--VDRCILDGEMLVWDTSLNRFAEFGSNQEIAKAARDGL---SSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQ 364 (1159)
Q Consensus 290 ~~~~--~~~~ILDGElv~~d~~~~~~~pFg~lq~i~~~~r~~~---~~~~~~~~~vFDiL~lnG~~l~~~pl~eRr~~L~ 364 (1159)
.... +.+||||||+|+||..+++++||+.+|.. .++.. +...++||++|||||+||++|++.||.+||++|+
T Consensus 437 ~~~~~~~~~~ILDGEiVa~d~~~~~~lpFq~Lq~R---~rk~~~~~~~~~pv~~~aFDlLylnG~~L~~~PL~eRR~~L~ 513 (744)
T PLN03113 437 RLKKPSVKSFILDCELVAYDREKKKILPFQILSTR---ARKNVVMSDIKVDVCIFAFDMLYLNGQPLIQEQLKIRREHLY 513 (744)
T ss_pred HhccccCCCEEEEeEEEEEECCCCCcCCHHHHHhh---hccccchhccccceEEEEEeccccCccChhcCCHHHHHHHHH
Confidence 4321 57899999999999888889999887753 22221 2247899999999999999999999999999999
Q ss_pred HhhccCCCcceeeccCCCCCccccCCCCCccceecCCHHHHHHHHHHHHHcCCceEEEecC--CCCCcCCCCCCCeEEEc
Q 001089 365 KVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDL--GSKWEPGDRSGKWLKLK 442 (1159)
Q Consensus 365 ~~i~~~~~~~~i~~p~~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~ai~~g~EGlVlK~~--ds~Y~pGkRs~~WlKiK 442 (1159)
+++.+.+++++++. ...+.+.++++++|++++++|+||||+|++ +|+|.||+|+.+|+|+|
T Consensus 514 ~~~~~~~~~i~~~~-----------------~~~~~~~ee~~~~~~~ai~~g~EGlmvK~l~~dS~Y~pGkRs~~WlKlK 576 (744)
T PLN03113 514 ESFEEDPGFFQFAT-----------------AITSNDLEEIQKFLDAAVDASCEGLIIKTLNKDATYEPSKRSNNWLKLK 576 (744)
T ss_pred HHhccCCCcEEEee-----------------eeccCCHHHHHHHHHHHHHcCCceEEEeccCCCCCccCCCCCCCeEEEe
Confidence 99988777765431 234578999999999999999999999986 89999999999999999
Q ss_pred cccccc-CCcccEEEEEEEeCCCCCCCccceEEEEEecCCCCCCCCceEEEEEEecCCCCHHHHHHHHHhhcccccccCC
Q 001089 443 PEYIRA-GSDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEY 521 (1159)
Q Consensus 443 pey~~~-g~~lDlvVIG~~~G~Grr~g~~gsfllg~~d~~~~~~~~~~f~~v~kVgtG~sdeel~~l~~~l~~~~~~~~~ 521 (1159)
++|+++ ++++||||||||||+|+|+|.+|+||||||++++ +.|++||+||||||++++++|.+.|++++..
T Consensus 577 ~dy~~~~~dtlDlVvIGa~~G~GkR~g~~g~fLla~yd~~~-----~~~~~v~KvgTGfsd~~l~~l~~~L~~~~~~--- 648 (744)
T PLN03113 577 KDYMESIGDSLDLVPIAAFHGRGKRTGVYGAFLLACYDSNK-----EEFQSICKIGTGFSEAVLEERSASLRSQVIP--- 648 (744)
T ss_pred chhhccccccccEEEEEEEeCCCCcCCccceEEEEEEcCCC-----CEEEEeeEECCCCCHHHHHHHHHHHHHhccc---
Confidence 999984 7899999999999999999999999999998653 3899999999999999999999999988864
Q ss_pred CCCCCCCcccccCCCCCCCcEEEeCCcceEEEEEEeeeeeeeccccc---------CCceeeCceeeeeecCCCccCcCC
Q 001089 522 PKRAPPSFYQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFS---------APYSLRFPRIDRVRYDKPWHDCLD 592 (1159)
Q Consensus 522 ~~~~pP~~~~~~~~~~~~Pdvwi~~P~~s~Vlev~a~i~~i~s~~~~---------~g~tLRFPR~~riR~DK~~~d~~t 592 (1159)
.||.|+... ...+||+||+ |. +|+||++... ..|+.|+ .|++||||||+|||+||+|+||+|
T Consensus 649 ---~~~~~~~~~--~~~~pdvwve-P~--~V~EV~~aei-t~Sp~h~a~~g~~~~~~G~sLRFPRf~riR~DK~~~datt 719 (744)
T PLN03113 649 ---TPKSYYRYG--DSIKPDVWFE-PT--EVWEVKAADL-TISPVHRAAVGIVDPDKGISLRFPRLVRVREDKSPEQATS 719 (744)
T ss_pred ---CCCcccccC--CCCCCcEEEC-Cc--eEEEEEeeee-ccCcccccccccccCCCCeEEECCEEEEEECCCChHHCCC
Confidence 145565443 2468999998 85 7999996432 3688887 489999999999999999999999
Q ss_pred HHHHHHHHHccC
Q 001089 593 VQSFVELVHSSN 604 (1159)
Q Consensus 593 ~~el~~l~~~~~ 604 (1159)
++++.+||+++.
T Consensus 720 ~~~l~~ly~~Q~ 731 (744)
T PLN03113 720 SEQVADMYNAQK 731 (744)
T ss_pred HHHHHHHHHHHH
Confidence 999999997543
No 3
>PRK01109 ATP-dependent DNA ligase; Provisional
Probab=100.00 E-value=3.8e-97 Score=903.59 Aligned_cols=544 Identities=27% Similarity=0.473 Sum_probs=472.9
Q ss_pred CcHHHHHHHHHHHHhhCChHHHHHHHHHHHhhcCCCc----hHHHHHHHhCCCCCCCccccCCCHHHHHHHHHHHhCCCc
Q 001089 7 TEVIVLVSLFNWIQKTKPAAKKRSKFRKFLDTYCDSV----DYFSALRLILPSLDRERGSYGLKESVLANCLIDALGMSK 82 (1159)
Q Consensus 7 ~~F~~l~~lle~i~~~~~~~~K~~~l~~~l~~~~~~~----d~~p~lrLllP~~d~~r~~ygike~~L~k~~~~~lgl~~ 82 (1159)
|+|+.||++|++|+.++++++|+.+|.+||.... ++ .+|+++++++|..+. ++|||+++.|+++|++++|++.
T Consensus 1 m~f~~l~~~~~~i~~t~~r~~k~~~l~~~~~~~~-~~~~~~~~~l~~~~~~p~~~~--~~~gi~~~~l~k~i~~~~g~~~ 77 (590)
T PRK01109 1 MEFSELAEYFERLEKTTSRTQLTKLLADLLKKTP-PEIIDKVVYLIQGKLWPDWLG--LELGVGEKLLIKAISMATGISE 77 (590)
T ss_pred CcHHHHHHHHHHHHhhhchHHHHHHHHHHHHhCC-HHhhhhhHHHHhCCcCccccC--cccCcCHHHHHHHHHHHHCcCH
Confidence 7899999999999999999999999999999874 33 356777777888874 6999999999999999999998
Q ss_pred ChHHHHHHhhhhcCCCCCCCCCHHHHHHHHhhhccCC------CCCCCCHHHHHHHHHHHHhhh---hHHHHHHHHHHHH
Q 001089 83 DSADAVRLINWRKGGAAPNAGNFPMVAAEVLQRRQGM------ISGGLTIKELNDLLDRLASSE---NRAEKISVLSTLI 153 (1159)
Q Consensus 83 ~s~~~~~L~~wk~~~~~~~~GD~~~~a~~vl~~r~~~------~~~~LTi~eVn~~Ld~LA~~~---~~~~k~~il~~ll 153 (1159)
+..+. .| ...||||.+|+.++++++.. .+++||+.+|++.|++||..+ ++.+|..+|..||
T Consensus 78 ~~~~~----~~------~~~GDlg~~a~~~~~~~~~~~~~~~~~~~~lti~eV~~~L~~Ia~~sg~~s~~~k~~iL~~Ll 147 (590)
T PRK01109 78 KEVEN----LY------KKTGDLGEVARRLKSKKKQKSLLAFFSKEPLTVKEVYDTLVKIALATGEGSQDLKIKLLAGLL 147 (590)
T ss_pred HHHHH----HH------HhcCCHHHHHHHHHhhcccccccccCCCCCcCHHHHHHHHHHHHhhhCCCcHHHHHHHHHHHH
Confidence 76543 23 45799999999999876532 357899999999999999887 3678899999999
Q ss_pred HhCCHHHHHHHHHHHHhhhccCCccccccc----ccC-----ccHHHHhhhcCCHHHHHHHHhhhh-ccccccCcccCCc
Q 001089 154 KKTNAQEMKWIIMIILKDLKLGISEKSIFH----EFH-----PDAEDLFNVTCDLKLVCEKLKDRN-QRHKRQDIEVGKA 223 (1159)
Q Consensus 154 ~~~s~~E~k~l~RiIlkdLriGi~e~til~----~~h-----pda~~~~~~~~dL~~V~~~L~~~~-~~~~~~~i~~g~p 223 (1159)
.++++.|++||+|+|+++||+|+++++|++ +|| ++++++|+.++||+.||+.|..+. ..+....+++|.|
T Consensus 148 ~~~~~~E~k~iirli~g~lriGv~e~~il~ALa~A~~~~~~~~~ve~~y~~~~Dlg~va~~l~~~g~~~~~~~~i~~~~P 227 (590)
T PRK01109 148 KDASPLEAKYIARFVEGRLRLGVGDATILDALAIAFGGAVARELVERAYNLRADLGYIAKILAEGGIEALKKVKPQVGIP 227 (590)
T ss_pred HhCCHHHHHHHHHHHhhhhhcCccHHHHHHHHHHHHhcccchHHHHHHHHhCCCHHHHHHHHHhcchhhhccCcccCCCC
Confidence 999999999999999999999999999997 344 788999999999999999998764 3456778999999
Q ss_pred cccccccccCChHHHHHhcCCCcEEEEEecceEEEEEEEeCCEEEEEecCCCCcCcchhhHHHHHHHhcccCceeecceE
Q 001089 224 VRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDGEM 303 (1159)
Q Consensus 224 ~~PMLA~~~~~~~~~~~k~~~~~~~vE~K~DGeR~qih~~g~~v~~fSR~g~d~t~~~p~l~~~l~~~~~~~~~ILDGEl 303 (1159)
|+||||++++.+++++++++ ..|++|+||||+|||+|++|+.|++|||||+|+|..+|++.+.+..++...+|||||||
T Consensus 228 v~PmLA~~~~~~~~~~~~~~-~~~~~E~K~DG~R~qih~~~~~v~l~SR~~~d~T~~~pel~~~~~~~~~~~~~ILDGEl 306 (590)
T PRK01109 228 IRPMLAERLSSPKEILKKMG-GEALVEYKYDGERAQIHKKGDKVKIFSRRLENITHQYPDVVEYAKEAIKAEEAIVEGEI 306 (590)
T ss_pred CCcccCCccCCHHHHHHHcC-CCeEEEecCCceEEEEEEcCCEEEEEeCCchhhccccchHHHHHHHhcCccceEEeeeE
Confidence 99999999998888899885 46999999999999999999999999999999999999999887666667899999999
Q ss_pred EEEeCCCCcccccccHHHHHHHhhcC-C---CCCCCeEEEEEeeeecCCccccCCCHHHHHHHHHHhhccCCCcceeecc
Q 001089 304 LVWDTSLNRFAEFGSNQEIAKAARDG-L---SSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVP 379 (1159)
Q Consensus 304 v~~d~~~~~~~pFg~lq~i~~~~r~~-~---~~~~~~~~~vFDiL~lnG~~l~~~pl~eRr~~L~~~i~~~~~~~~i~~p 379 (1159)
|+||+.+++++||+.++.. .+.. . ....++||++|||||+||++|++.||.+||++|++++.+.+. +.+.
T Consensus 307 v~~d~~~g~~~~F~~l~~R---~r~~~~~~~~~~~p~~~~vFDiL~l~g~~l~~~pl~eRr~~L~~~~~~~~~-~~~~-- 380 (590)
T PRK01109 307 VAVDPETGEMRPFQELMHR---KRKYDIEEAIKEYPVNVFLFDLLYVDGEDLTDKPLPERRKKLEEIVKENDK-VKLA-- 380 (590)
T ss_pred EEEECCCCcccChHHHhhc---ccccchhhhcccCceEEEEEEEEEECCcchhhCcHHHHHHHHHHhcCCCCc-eEEe--
Confidence 9999777888999877654 1211 1 124689999999999999999999999999999999987543 4332
Q ss_pred CCCCCccccCCCCCccceecCCHHHHHHHHHHHHHcCCceEEEecC--CCCCcCCCCCCCeEEEccccccc-CCcccEEE
Q 001089 380 DHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDL--GSKWEPGDRSGKWLKLKPEYIRA-GSDLDVLI 456 (1159)
Q Consensus 380 ~~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~ai~~g~EGlVlK~~--ds~Y~pGkRs~~WlKiKpey~~~-g~~lDlvV 456 (1159)
....+++.+++.++|++++++|+||||+|++ +|+|.||+|+.+|+|+|++|++. ++++||||
T Consensus 381 ---------------~~~~~~~~~~~~~~~~~a~~~g~EGiv~K~~~~ds~Y~~g~Rs~~WlK~K~dy~~~~~~~~Dlvv 445 (590)
T PRK01109 381 ---------------ERIITDDVEELEKFFHRAIEEGCEGLMAKSLGKDSIYQAGARGWLWIKYKRDYQSEMADTVDLVV 445 (590)
T ss_pred ---------------eeEecCCHHHHHHHHHHHHHcCCceEEEecCCCCCCcCCCCCCccHHHhhHHhhcccCCceeEEE
Confidence 1345678999999999999999999999999 99999999999999999999984 78999999
Q ss_pred EEEEeCCCCCCCccceEEEEEecCCCCCCCCceEEEEEEecCCCCHHHHHHHHHhhcccccccCCCCCCCCCcccccCCC
Q 001089 457 IGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNS 536 (1159)
Q Consensus 457 IG~~~G~Grr~g~~gsfllg~~d~~~~~~~~~~f~~v~kVgtG~sdeel~~l~~~l~~~~~~~~~~~~~pP~~~~~~~~~ 536 (1159)
||++||+|+|+|.+|+||||+|++++ +.|++||+||||||++++++|.+.|.+++... .|| ++ ..
T Consensus 446 iG~~~g~Gkr~~~~g~~ll~~~d~~~-----~~~~~v~kvgtG~sd~~~~~l~~~l~~~~~~~-----~~~-~~----~~ 510 (590)
T PRK01109 446 VGAFYGRGRRGGKYGSLLMAAYDPKT-----DTFETVCKVGSGFTDEDLDELPKMLKPYKIDH-----KHP-RV----VS 510 (590)
T ss_pred EEeEeCCCccCCccccEEEEEEcCCC-----CeEEEEEEECCCCCHHHHHHHHHHhhhhcccC-----CCc-cc----cc
Confidence 99999999999999999999998643 38999999999999999999999999988641 133 22 13
Q ss_pred CCCCcEEEeCCcceEEEEEEeeeeeeeccccc---------CCceeeCceeeeeecCCCccCcCCHHHHHHHHHccC
Q 001089 537 KERPDVWIESPEKSIILSITSDIRTIRSEVFS---------APYSLRFPRIDRVRYDKPWHDCLDVQSFVELVHSSN 604 (1159)
Q Consensus 537 ~~~Pdvwi~~P~~s~Vlev~a~i~~i~s~~~~---------~g~tLRFPR~~riR~DK~~~d~~t~~el~~l~~~~~ 604 (1159)
..+||+||+ | ++|+||+++.. ..|+.|+ .|++||||||++||+||+|+||+|++++.+||+++.
T Consensus 511 ~~~pdvwv~-P--~~V~eV~~~~i-t~S~~~~~~~~~~~~~~g~~LRfPr~~~~R~DK~~~d~~t~~~~~~ly~~q~ 583 (590)
T PRK01109 511 KMEPDVWVE-P--KLVAEIIGAEI-TLSPLHTCCLGVVEKGAGLAIRFPRFIRWRDDKSPEDATTTEEILEMYKRQK 583 (590)
T ss_pred ccCCcEEEe-c--cEEEEEEeeec-ccCcceecccccccCCCceeEEcCeeeEeeCCCChhhCcCHHHHHHHHHHhh
Confidence 568999999 7 49999997543 3578888 689999999999999999999999999999997543
No 4
>KOG0967 consensus ATP-dependent DNA ligase I [Replication, recombination and repair]
Probab=100.00 E-value=6.3e-95 Score=831.27 Aligned_cols=551 Identities=27% Similarity=0.501 Sum_probs=477.2
Q ss_pred CCCcHHHHHHHHHHHHhhCChHHHHHHHHHHHhhcC--CCchHHHHHHHhCCCC--CCCccccCCCHHHHHHHHHHHhCC
Q 001089 5 EETEVIVLVSLFNWIQKTKPAAKKRSKFRKFLDTYC--DSVDYFSALRLILPSL--DRERGSYGLKESVLANCLIDALGM 80 (1159)
Q Consensus 5 ~~~~F~~l~~lle~i~~~~~~~~K~~~l~~~l~~~~--~~~d~~p~lrLllP~~--d~~r~~ygike~~L~k~~~~~lgl 80 (1159)
+.+||.+||..|+.|+.+++|.+.+.+|.+||.+.. +|+|+.|+++|.+..+ |.++.++||+|.+|.|+|++++|.
T Consensus 97 ~~~py~~~a~tF~kIe~~s~Rl~i~~il~n~f~~v~~~sP~dLlp~vYLsiN~l~P~yeGlELGvGes~l~KAi~EatGr 176 (714)
T KOG0967|consen 97 SKVPYLELARTFEKIEETSGRLEIIDILSNFLRSVLATSPDDLLPTVYLSINKLAPDYEGLELGVGESLLMKAIAEATGR 176 (714)
T ss_pred CcCcHHHHHHHHHHHHhhccceeHHHHHHHHHHHHHhcCchhhhhHHHHhhhccCccccCccccccHHHHHHHHHHHhCc
Confidence 469999999999999999999999999999999864 5899999999998887 667889999999999999999999
Q ss_pred CcChHHHHHHhhhhcCCCCCCCCCHHHHHHHHhhhccC-CCCCCCCHHHHHHHHHHHHhhhh---HHHHHHHHHHHHHhC
Q 001089 81 SKDSADAVRLINWRKGGAAPNAGNFPMVAAEVLQRRQG-MISGGLTIKELNDLLDRLASSEN---RAEKISVLSTLIKKT 156 (1159)
Q Consensus 81 ~~~s~~~~~L~~wk~~~~~~~~GD~~~~a~~vl~~r~~-~~~~~LTi~eVn~~Ld~LA~~~~---~~~k~~il~~ll~~~ 156 (1159)
+...+ |+ .| ...||+|.||+........ ..+.+|||.+|+..|.+||..+| +.+|..++..||..|
T Consensus 177 t~~~v---k~-~~------~~~GDLG~VA~~sR~sQ~~m~~P~pLtV~~VF~~Lr~IAk~sG~~S~~kK~~lik~Llvac 246 (714)
T KOG0967|consen 177 TLSHV---KN-QY------NKLGDLGLVAQGSRSSQRMMFKPKPLTVRDVFSTLRKIAKESGKGSQNKKKDLIKALLVAC 246 (714)
T ss_pred cHHHH---HH-HH------HhcCcHHHHHhhcccccccccCCCCccHHHHHHHHHHHHHhhCcchhHHHHHHHHHHHHhc
Confidence 97543 33 23 5689999999876443222 35779999999999999999887 678899999999999
Q ss_pred CHHHHHHHHHHHHhhhccCCccccccccc------C----------cc------------HHHHhhhcCCHHHHHHHHhh
Q 001089 157 NAQEMKWIIMIILKDLKLGISEKSIFHEF------H----------PD------------AEDLFNVTCDLKLVCEKLKD 208 (1159)
Q Consensus 157 s~~E~k~l~RiIlkdLriGi~e~til~~~------h----------pd------------a~~~~~~~~dL~~V~~~L~~ 208 (1159)
++.|+|||+|.|.++||||++++|||.++ + ++ +.++|..++|+..|+..|..
T Consensus 247 ~~~E~kyLiRsL~gkLRiGlaeqTvL~AL~~A~~~~~~~~~~~~~~~d~~kd~le~~~~ivk~afcq~P~ydiivp~lL~ 326 (714)
T KOG0967|consen 247 RGIEAKYLIRSLEGKLRIGLAEQTVLAALGQAFVLNDNNDEEKSKKPDSLKDPLEEAAQIVKQAFCQLPDYDIIVPALLE 326 (714)
T ss_pred ccccHHHHHHHHHhhhhhhhhHHHHHHHHHHHHhccCchhhhccCCcchhhhhhHHHHHHHHHHHhcCCchhhhHHHHHH
Confidence 99999999999999999999999999654 1 22 24579999999999988765
Q ss_pred hh--ccccccCcccCCccccccccccCChHHHHHhcCCCcEEEEEecceEEEEEEE-eCCEEEEEecCCCCcCcchhhHH
Q 001089 209 RN--QRHKRQDIEVGKAVRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHK-NGSEIHYFSRSFLDHSEYGHAMS 285 (1159)
Q Consensus 209 ~~--~~~~~~~i~~g~p~~PMLA~~~~~~~~~~~k~~~~~~~vE~K~DGeR~qih~-~g~~v~~fSR~g~d~t~~~p~l~ 285 (1159)
.. ...+.+.+.||.|++||||++.+.+.+++++|++..|.+|+||||+|+|||+ .+|.|.+||||+++.|..+|++.
T Consensus 327 ~Gie~L~e~c~l~PGIPlKPMLAkpTK~i~evl~rf~~~~FTCEyKYDGeRAQIH~~edG~v~IfSRN~E~~T~kYPDi~ 406 (714)
T KOG0967|consen 327 HGIENLPETCKLTPGIPLKPMLAKPTKGIQEVLERFQDKAFTCEYKYDGERAQIHKLEDGTVEIFSRNSENNTGKYPDII 406 (714)
T ss_pred hhhhhccccCccCCCCCCcchhcCcchhHHHHHHHhhCceeEEEeecCceeeeeEEccCCcEEEEecccccccccCccHH
Confidence 43 2346688999999999999999999999999999999999999999999997 57899999999999999999998
Q ss_pred HHHHHhc--ccCceeecceEEEEeCCCCcccccccHHHHHHHhhcCCC---CCCCeEEEEEeeeecCCccccCCCHHHHH
Q 001089 286 KIIEQNV--LVDRCILDGEMLVWDTSLNRFAEFGSNQEIAKAARDGLS---SDRQLCYFAFDVLYVGDTSVIHQSLKERH 360 (1159)
Q Consensus 286 ~~l~~~~--~~~~~ILDGElv~~d~~~~~~~pFg~lq~i~~~~r~~~~---~~~~~~~~vFDiL~lnG~~l~~~pl~eRr 360 (1159)
..+.... .+.++|||||+|+||...++++||+-+ ..+.|+..+ ....+|+++||+||+||++|++.||.+||
T Consensus 407 ~~~~~~~kp~v~sFIlD~EvVA~Dr~~~~IlpFQvL---STRkRk~v~v~dikV~Vcvf~FDily~ng~~Li~~pL~eRR 483 (714)
T KOG0967|consen 407 EVISKLKKPSVKSFILDCEVVAWDREKGKILPFQVL---STRKRKNVDVNDIKVKVCVFVFDILYLNGESLIQEPLRERR 483 (714)
T ss_pred HHHHHhhCCccceeEEeeeEEEEeccCCccCchhhh---hhhhccccchhhceEEEEEEEEeeeeeCChhhhhhhHHHHH
Confidence 7765433 257999999999999998999999544 444444432 34689999999999999999999999999
Q ss_pred HHHHHhhccCCCcceeeccCCCCCccccCCCCCccceecCCHHHHHHHHHHHHHcCCceEEEecC--CCCCcCCCCCCCe
Q 001089 361 ELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDL--GSKWEPGDRSGKW 438 (1159)
Q Consensus 361 ~~L~~~i~~~~~~~~i~~p~~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~ai~~g~EGlVlK~~--ds~Y~pGkRs~~W 438 (1159)
++|.+.+..++|.++++. ...+.+.++|++||++++..++||+|+|.+ ++.|+|.+|+.+|
T Consensus 484 ~~l~e~f~e~~g~f~fat-----------------~~~tn~~~eiq~Fl~~sv~~~cEGlMvKtLd~~atYep~kRs~~W 546 (714)
T KOG0967|consen 484 ELLHESFKEIPGEFQFAT-----------------SLDTNDIDEIQEFLEESVQNSCEGLMVKTLDTNATYEPSKRSNNW 546 (714)
T ss_pred HHHHhhcccCCCceeEee-----------------eeccCCHHHHHHHHHHhhccCcceeEEEeeccccccCchhhccch
Confidence 999999999999887652 234689999999999999999999999977 5789999999999
Q ss_pred EEEccccccc-CCcccEEEEEEEeCCCCCCCccceEEEEEecCCCCCCCCceEEEEEEecCCCCHHHHHHHHHhhccccc
Q 001089 439 LKLKPEYIRA-GSDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFR 517 (1159)
Q Consensus 439 lKiKpey~~~-g~~lDlvVIG~~~G~Grr~g~~gsfllg~~d~~~~~~~~~~f~~v~kVgtG~sdeel~~l~~~l~~~~~ 517 (1159)
+|+|++|+++ |+++||||||||||.|||.|++|+||+|||+++. ..|+++||+||||||+++.++...|.....
T Consensus 547 lKlKkDYldgvgdslDLv~iga~~G~GrrtG~yg~fLlacyn~dt-----eefqsiCKigtGFsD~~l~e~~~~l~~~~~ 621 (714)
T KOG0967|consen 547 LKLKKDYLDGVGDSLDLVVIGAYYGRGRRTGWYGGFLLACYNPDT-----EEFQSICKIGTGFSDEFLQELHESLSSTVI 621 (714)
T ss_pred hhhhhhhhcccccceeeeeeeeeeccccccccccceeEEeecCch-----HHHHHHHhhcCCCCHHHHHHHHHHhhhccc
Confidence 9999999996 8999999999999999999999999999999875 389999999999999999999998875543
Q ss_pred ccCCCCCCCCCcccccCCCCCCCcEEEeCCcceEEEEEE-eeeeeeeccccc---------CCceeeCceeeeeecCCCc
Q 001089 518 KYEYPKRAPPSFYQVTNNSKERPDVWIESPEKSIILSIT-SDIRTIRSEVFS---------APYSLRFPRIDRVRYDKPW 587 (1159)
Q Consensus 518 ~~~~~~~~pP~~~~~~~~~~~~Pdvwi~~P~~s~Vlev~-a~i~~i~s~~~~---------~g~tLRFPR~~riR~DK~~ 587 (1159)
. .|+.+|.+. ...+||+|++ |. .||||+ |++. -|+.|. .|.+||||||.|+|+||.+
T Consensus 622 ~------~~~~~y~~d--~s~kPd~wf~-p~--~VwEvk~Adlt--~SPiy~Aa~Glv~~dkGISlRFPRfiRiR~DK~p 688 (714)
T KOG0967|consen 622 D------SPKPYYRFD--ESLKPDVWFE-PT--EVWEVKAADLT--LSPIYKAALGLVDPDKGISLRFPRFIRIRDDKNP 688 (714)
T ss_pred c------CcHhhcccC--ccCCCccccC-HH--HHHHHhhcccc--ccchhHhhhcCcCCCCceeEecceeeEeeccCCh
Confidence 2 255677664 4567999998 76 689998 5553 366665 3789999999999999999
Q ss_pred cCcCCHHHHHHHHHcc
Q 001089 588 HDCLDVQSFVELVHSS 603 (1159)
Q Consensus 588 ~d~~t~~el~~l~~~~ 603 (1159)
+||+|-+++.+||+.+
T Consensus 689 eeAtts~qiaemY~~Q 704 (714)
T KOG0967|consen 689 EEATTSSQIAEMYQAQ 704 (714)
T ss_pred hhcccHHHHHHHHHHH
Confidence 9999999999999765
No 5
>TIGR00574 dnl1 DNA ligase I, ATP-dependent (dnl1). All proteins in this family with known functions are ATP-dependent DNA ligases. Functions include DNA repair, DNA replication, and DNA recombination (or any process requiring ligation of two single-stranded DNA sections). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=100.00 E-value=1.1e-89 Score=829.03 Aligned_cols=494 Identities=34% Similarity=0.608 Sum_probs=428.0
Q ss_pred ccCCCHHHHHHHHHHHhCCCcChHHHHHHhhhhcCCCCCCCCCHHHHHHHHhhhcc--CCCCCCCCHHHHHHHHHHHHhh
Q 001089 62 SYGLKESVLANCLIDALGMSKDSADAVRLINWRKGGAAPNAGNFPMVAAEVLQRRQ--GMISGGLTIKELNDLLDRLASS 139 (1159)
Q Consensus 62 ~ygike~~L~k~~~~~lgl~~~s~~~~~L~~wk~~~~~~~~GD~~~~a~~vl~~r~--~~~~~~LTi~eVn~~Ld~LA~~ 139 (1159)
+||||+++|+++|++++|+++++.++..+ ..||+|.+++.++.... ...+.+|||.+||+.|++||+.
T Consensus 1 ~~gi~~~~l~k~~~~~~~~~~~~~~~~~~----------~~gd~g~~~~~~~~~~~~~~~~~~~lti~eV~~~L~~ia~~ 70 (514)
T TIGR00574 1 EYGIGEKLLIKAISKALGIPKDEIEEKVK----------EDGDLGEVIEGLFSKQKQTSFFSAPLTVKEVYETLKNIAET 70 (514)
T ss_pred CCCCcHHHHHHHHHHHHCcCHHHHHHHHH----------hcCCHHHHHHHHhccccccccCCCCcCHHHHHHHHHHHHHh
Confidence 49999999999999999999988877443 35899999998886553 2346789999999999999988
Q ss_pred hh---HHHHHHHHHHHHHhCCHHHHHHHHHHHHhhhccCCcccccccccCccH-------HHHhhhcCCHHHHHHHHhhh
Q 001089 140 EN---RAEKISVLSTLIKKTNAQEMKWIIMIILKDLKLGISEKSIFHEFHPDA-------EDLFNVTCDLKLVCEKLKDR 209 (1159)
Q Consensus 140 ~~---~~~k~~il~~ll~~~s~~E~k~l~RiIlkdLriGi~e~til~~~hpda-------~~~~~~~~dL~~V~~~L~~~ 209 (1159)
++ +.+|..+|..|+.+|+|.|++||+|||+++||+|+++++|+.++|+++ +++|++|+||+.||+.|.++
T Consensus 71 ~g~~s~~~k~~~l~~ll~~~~~~e~k~l~r~i~~~lriG~~~~~il~al~~~~~~~~~~~~~~~~~~~dl~~v~~~l~~~ 150 (514)
T TIGR00574 71 SGEGSQDKKIKLLKSLLKRASPLEAKYLIRTILGDLRIGIAEKTILDALAKAFLLSHPDVERAFNLTNDLGKVAKILLEP 150 (514)
T ss_pred hCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHhhhcccCccHHHHHHHHHHHhccchHHHHHHHHhCCCHHHHHHHHHhc
Confidence 75 578889999999999999999999999999999999999999998877 99999999999999999876
Q ss_pred hccc--cccCcccCCccccccccccCChHHHHHhcCCCcEEEEEecceEEEEEEEeCCEEEEEecCCCCcCcchhhH-HH
Q 001089 210 NQRH--KRQDIEVGKAVRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAM-SK 286 (1159)
Q Consensus 210 ~~~~--~~~~i~~g~p~~PMLA~~~~~~~~~~~k~~~~~~~vE~K~DGeR~qih~~g~~v~~fSR~g~d~t~~~p~l-~~ 286 (1159)
.... ....+++|.||+||||+++..+++++.++.+ +|++|+||||+|||+|+++++|++|||||+++|..+|++ .+
T Consensus 151 ~~~~~~~~~~i~~~~p~~PMLA~~~~~~~~~~~~~~~-~~~~E~K~DG~R~qih~~~~~v~l~SR~g~~~t~~~pei~~~ 229 (514)
T TIGR00574 151 GLRGLDKDLSIQLGIPFKPMLAERAKSIEEALKKKGN-KFYVEYKYDGERVQIHKDGDKFKIFSRRLENYTYAYPEIFTE 229 (514)
T ss_pred ChhhhcccceeecCCcCccccCCccCCHHHHHHHhCC-ceEEEEeecceEEEEEEcCCEEEEEcCCCcccccccchhHHH
Confidence 5422 3467999999999999999988888888754 899999999999999999999999999999999989998 76
Q ss_pred HHHHhcc-cCceeecceEEEEeCCCCcccccccHHHHHHHhh-cCCCCCCCeEEEEEeeeecCCccccCCCHHHHHHHHH
Q 001089 287 IIEQNVL-VDRCILDGEMLVWDTSLNRFAEFGSNQEIAKAAR-DGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQ 364 (1159)
Q Consensus 287 ~l~~~~~-~~~~ILDGElv~~d~~~~~~~pFg~lq~i~~~~r-~~~~~~~~~~~~vFDiL~lnG~~l~~~pl~eRr~~L~ 364 (1159)
.+...+. ..+||||||||+||+.+++++||+.++...+... .......+++|++|||||+||++++++||.+|+++|+
T Consensus 230 ~~~~~~~~~~~~ILDGElv~~d~~~g~~~~F~~l~~r~~~~~~~~~~~~~~~~~~vFDiL~l~g~~l~~~pl~eRr~~L~ 309 (514)
T TIGR00574 230 FIKEAFPGIKSCILDGEMVAIDPETGKILPFQTLLRRKRRYDIDSMEKKVPVCLFVFDILYLNGESLIDEPLIERREILE 309 (514)
T ss_pred HHHHhcCccceeeecceEEEEEcCCCCCcCcHhHHhhhhhccccccccccceEEEEEEEEEECCcchhcCcHHHHHHHHH
Confidence 6655444 3689999999999987788999988876533210 1112346899999999999999999999999999999
Q ss_pred HhhccCCCcceeeccCCCCCccccCCCCCccceecCCHHHHHHHHHHHHHcCCceEEEecCCCCCcCCCCCCCeEEEccc
Q 001089 365 KVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPE 444 (1159)
Q Consensus 365 ~~i~~~~~~~~i~~p~~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~ai~~g~EGlVlK~~ds~Y~pGkRs~~WlKiKpe 444 (1159)
+++.+.++++.++. ...+++.+++.++|++++++|+||||+|+++|+|.||+|+..|+|+|++
T Consensus 310 ~~~~~~~~~i~~~~-----------------~~~~~~~e~~~~~~~~~~~~g~EGlv~K~~ds~Y~~G~Rs~~WlK~K~~ 372 (514)
T TIGR00574 310 SILKPIPNRIEIAE-----------------MKITSNVEELEKFLNEAISEGCEGLMLKDLKSIYEPGKRGWLWLKFKPE 372 (514)
T ss_pred HhccCCCCcEEEEE-----------------EEecCCHHHHHHHHHHHHHcCCceEEEecCCCcccCCCCCCcceeCchh
Confidence 99988877765431 3456789999999999999999999999999999999999999999999
Q ss_pred cccc-CCcccEEEEEEEeCCCCCCCccceEEEEEecCCCCCCCCceEEEEEEecCCCCHHHHHHHHHhhcccccccCCCC
Q 001089 445 YIRA-GSDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPK 523 (1159)
Q Consensus 445 y~~~-g~~lDlvVIG~~~G~Grr~g~~gsfllg~~d~~~~~~~~~~f~~v~kVgtG~sdeel~~l~~~l~~~~~~~~~~~ 523 (1159)
|+++ ++++|++|||+++|+|+++|.+|+|+||+++++. +.|++||+||||||++++++|.+.+.++|.... +.
T Consensus 373 y~~~~~~~~D~vvig~~~g~gk~~g~~~~~l~g~~d~~~-----~~~~~v~kvgsG~sd~~l~~l~~~l~~~~~~~~-~~ 446 (514)
T TIGR00574 373 YLEGMGDTLDLVVIGAYYGKGKRTGMYGSFLLACYDPES-----EEFKTITKVGTGFTDADLQELGKKLPPLWIDPP-GS 446 (514)
T ss_pred hcccccCceeEEEEeeEecCCccCCceeEEEEEEEcCCC-----CeEEEEEEECCCCCHHHHHHHHHhccCcEecCC-CC
Confidence 9984 6899999999999999999999999999997653 389999999999999999999999999987521 11
Q ss_pred CCCCCcccccCCCCCCCcEEEeCCcceEEEEEEeeeeeeecccccC-CceeeCceeeeeecCCCccCcCCHHHHHHHH
Q 001089 524 RAPPSFYQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSA-PYSLRFPRIDRVRYDKPWHDCLDVQSFVELV 600 (1159)
Q Consensus 524 ~~pP~~~~~~~~~~~~Pdvwi~~P~~s~Vlev~a~i~~i~s~~~~~-g~tLRFPR~~riR~DK~~~d~~t~~el~~l~ 600 (1159)
.+|.+ ....|++|+. |. +|+||+++.. ..|+.|++ |++||||||++||+||+|+||+|++++.+||
T Consensus 447 -~~~~~------~~~~~~~w~~-p~--~V~eV~~~e~-t~s~~~~~~g~~LRfPr~~~~R~DK~~~d~~~~~~~~~ly 513 (514)
T TIGR00574 447 -RVPSI------LSDEPDIWFD-PA--IVWEVTGAEI-TRSPTYKANGISLRFPRFSRIRDDKGPEDATTIEEIKELY 513 (514)
T ss_pred -CCccc------ccCCCeEEec-CC--eEEEEEhhhe-eecCcccccceEEEcceEEEEcCCCChHHCCCHHHHHHHh
Confidence 12222 1357999998 74 8999997543 47899999 9999999999999999999999999999998
No 6
>PRK09247 ATP-dependent DNA ligase; Validated
Probab=100.00 E-value=1.4e-88 Score=818.68 Aligned_cols=522 Identities=20% Similarity=0.255 Sum_probs=440.6
Q ss_pred HHHHHHHHHHHHhhCChHHHHHHHHHHHhhcCCCchHHHHHHHhCCCCCCCccccCCCHHHHHHHHHHHhCCCcChHHHH
Q 001089 9 VIVLVSLFNWIQKTKPAAKKRSKFRKFLDTYCDSVDYFSALRLILPSLDRERGSYGLKESVLANCLIDALGMSKDSADAV 88 (1159)
Q Consensus 9 F~~l~~lle~i~~~~~~~~K~~~l~~~l~~~~~~~d~~p~lrLllP~~d~~r~~ygike~~L~k~~~~~lgl~~~s~~~~ 88 (1159)
+++||++|++|+.++++++|+++|.+||.++ +++++.++++|+++... .|||+++.|+++|++++|++....+.
T Consensus 1 ~~~fa~~~~~i~~t~~~~ek~~~l~~~~~~~-~~~d~~~~~~ll~g~~~----~~~i~~~~l~k~~~~~~g~~~~~~~~- 74 (539)
T PRK09247 1 MKAFAELLDRLDLTTSTNAKLALLADYFRSA-PDPDRAWALALLTGGLP----RRLVKTRLLRELAAERADLPPWLFEE- 74 (539)
T ss_pred ChHHHHHHHHHHhccCHHHHHHHHHHHHHhC-CHHHHHHHHHHhcCCcc----cCCCCHHHHHHHHHHHHCcCHHHHHH-
Confidence 4789999999999999999999999999998 46789999999999886 48999999999999999999765442
Q ss_pred HHhhhhcCCCCCCCCCHHHHHHHHhhhccCCC---CCCCCHHHHHHHHHHHHhhhhHHHHHHHHHHHHHhCCHHHHHHHH
Q 001089 89 RLINWRKGGAAPNAGNFPMVAAEVLQRRQGMI---SGGLTIKELNDLLDRLASSENRAEKISVLSTLIKKTNAQEMKWII 165 (1159)
Q Consensus 89 ~L~~wk~~~~~~~~GD~~~~a~~vl~~r~~~~---~~~LTi~eVn~~Ld~LA~~~~~~~k~~il~~ll~~~s~~E~k~l~ 165 (1159)
.| ...||+|++|+.+++.++... +..+||.+|.+.|..+|.. +|...|..||.+++|.|++||+
T Consensus 75 ---~~------~~~GDlg~~~~~~~~~~~~~~~~~~~~~tv~~v~~~l~~~~~~----~k~~~l~~ll~~~~~~e~~~i~ 141 (539)
T PRK09247 75 ---SY------DYVGDLAETIALLLPAPSDEASDLPLAPWLEEVLLPLRGLGRE----ELRAALADLWDRLDEDGRFALN 141 (539)
T ss_pred ---HH------HhcCCHHHHHHHhcccccccccCCCccccHHHHHHHHHhhhHH----HHHHHHHHHHHhCCHHHHHHHH
Confidence 22 457999999999987665321 2569999999988888743 4778899999999999999999
Q ss_pred HHHHhhhccCCcccccccccC----c---cHHHHhhh--cCCHHHHHHHHhhhhccccccCcccCCccccccccccCChH
Q 001089 166 MIILKDLKLGISEKSIFHEFH----P---DAEDLFNV--TCDLKLVCEKLKDRNQRHKRQDIEVGKAVRPQLAMRIGDAH 236 (1159)
Q Consensus 166 RiIlkdLriGi~e~til~~~h----p---da~~~~~~--~~dL~~V~~~L~~~~~~~~~~~i~~g~p~~PMLA~~~~~~~ 236 (1159)
|+|+++||||+++++|+.+++ . .++++|+. ++|++.+++.+... .....+++|.|++||||+++.+..
T Consensus 142 rli~g~lRiG~~~~~v~~ala~a~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~P~~pMLA~~~~~~~ 218 (539)
T PRK09247 142 KLITGGFRVGVSARLVTRALAELGGVDEARIAQRLMGLWPPYADLFAWLIGPE---EDPLPADPGQPYPFFLAHPLEDED 218 (539)
T ss_pred HHhhCccccchhHHHHHHHHHHHhCCCHHHHHHHHhCCCCCcHHHHHHHhhCC---ccccCCCCCCcCCCeeCCcCCCch
Confidence 999999999999999998663 2 23456666 78888888777542 256679999999999999998765
Q ss_pred HHHHhcCCCcEEEEEecceEEEEEEEeCCEEEEEecCCCCcCcchhhHHHHHHHhcccCceeecceEEEEeCCCCccccc
Q 001089 237 AAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDGEMLVWDTSLNRFAEF 316 (1159)
Q Consensus 237 ~~~~k~~~~~~~vE~K~DGeR~qih~~g~~v~~fSR~g~d~t~~~p~l~~~l~~~~~~~~~ILDGElv~~d~~~~~~~pF 316 (1159)
+.. +...+|++|+||||+|||+|+.++.+++|||||+++|..||++.+.+. .+ +.+||||||||+||+.++.+.||
T Consensus 219 ~~~--~~~~~~~~E~K~DG~R~qih~~~~~v~lfSR~g~d~t~~fPei~~~~~-~l-~~~~ILDGElv~~~~~~~~~~~F 294 (539)
T PRK09247 219 LTL--GDPADWQAEWKWDGIRVQLVRRGGEVRLWSRGEELITERFPELAEAAE-AL-PDGTVLDGELLVWRPEDGRPQPF 294 (539)
T ss_pred hhh--cCCCcEEEEEeEcceEEEEEEeCCEEEEEeCCCccchhhhHHHHHHHH-hC-CCCEEEEeEEEEEECCCCCcCCH
Confidence 433 334589999999999999999999999999999999999999988763 44 46799999999999766788999
Q ss_pred ccHHHHHHHhhc--CCCCCCCeEEEEEeeeecCCccccCCCHHHHHHHHHHhhccCCC-cceeeccCCCCCccccCCCCC
Q 001089 317 GSNQEIAKAARD--GLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKG-RLETLVPDHGLNSHVRPQGEP 393 (1159)
Q Consensus 317 g~lq~i~~~~r~--~~~~~~~~~~~vFDiL~lnG~~l~~~pl~eRr~~L~~~i~~~~~-~~~i~~p~~~~~~~v~~~~~~ 393 (1159)
+.+|....+... ....+.++||++|||||+||++|++.||.+||++|++++.+.++ ++.++
T Consensus 295 ~~l~~R~~rk~~~~~~~~~~pv~~~vFDiL~l~g~~l~~~Pl~eRr~~L~~~~~~~~~~~i~~~---------------- 358 (539)
T PRK09247 295 ADLQQRIGRKTVGKKLLADYPAFLRAYDLLEDGGEDLRALPLAERRARLEALIARLPDPRLDLS---------------- 358 (539)
T ss_pred HHHHHHhcccccchhhhhcCCeEEEEEEeeeeCCcchhhCCHHHHHHHHHHHhcccCCCeEEec----------------
Confidence 888765432111 01124689999999999999999999999999999999987643 44332
Q ss_pred ccceecCCHHHHHHHHHHHHHcCCceEEEecCCCCCcCCCCCCCeEEEcccccccCCcccEEEEEEEeCCCCCCCccceE
Q 001089 394 CWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLIIGGYYGSGRRGGEVAQF 473 (1159)
Q Consensus 394 ~~~~~~~~~~ei~~~~~~ai~~g~EGlVlK~~ds~Y~pGkRs~~WlKiKpey~~~g~~lDlvVIG~~~G~Grr~g~~gsf 473 (1159)
....+.+.+++.++|++++++|+||||+|+++|+|.||+|++.|+|+|++| .++|+|||||++|+|+|+|.+|+|
T Consensus 359 -~~~~~~~~~e~~~~~~~a~~~g~EGlm~K~~~s~Y~~Grr~~~WlK~K~~~----~t~DlVvig~~~G~Gkr~g~~~~~ 433 (539)
T PRK09247 359 -PLVPFSDWDELAALRAAARERGVEGLMLKRRDSPYLVGRKKGPWWKWKRDP----LTIDAVLMYAQRGHGRRASLYTDY 433 (539)
T ss_pred -CceecCCHHHHHHHHHHHHHCCCceEEEecCCCCcCCCCCcchhhcccCCC----CcEEEEEEEeecCCCCcCCccccE
Confidence 134467899999999999999999999999999999999999999999998 489999999999999999999999
Q ss_pred EEEEecCCCCCCCCceEEEEEEecCCCCHHHHHHHHHhhcccccccCCCCCCCCCcccccCCCCCCCcEEEeCCcceEEE
Q 001089 474 LVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDVWIESPEKSIIL 553 (1159)
Q Consensus 474 llg~~d~~~~~~~~~~f~~v~kVgtG~sdeel~~l~~~l~~~~~~~~~~~~~pP~~~~~~~~~~~~Pdvwi~~P~~s~Vl 553 (1159)
+|||++++.+ .+.|++||+||||||++++++|.+.++++... ...|++||+ |. +|+
T Consensus 434 lla~~~~~~~---~~~~~~v~kvgsGftd~~l~~l~~~l~~~~~~------------------~~~~~~~v~-P~--~V~ 489 (539)
T PRK09247 434 TFGVWDGPEG---GRQLVPFAKAYSGLTDEEIKQLDRWVRKNTVE------------------RFGPVRSVR-PE--LVF 489 (539)
T ss_pred EEEEEcCCCC---ceeEEEEEEECCCCCHHHHHHHHHHHhhcccc------------------cCCCceEec-Cc--eEE
Confidence 9999976531 13699999999999999999999877653211 125899998 75 899
Q ss_pred EEEeeeeeeecccccCCceeeCceeeeeecCCCccCcCCHHHHHHHHHc
Q 001089 554 SITSDIRTIRSEVFSAPYSLRFPRIDRVRYDKPWHDCLDVQSFVELVHS 602 (1159)
Q Consensus 554 ev~a~i~~i~s~~~~~g~tLRFPR~~riR~DK~~~d~~t~~el~~l~~~ 602 (1159)
||+++. +..|+.|++|++||||||.++|+||+|+||+|++++.+||+.
T Consensus 490 EV~~~e-it~S~~~~~G~~LRfPr~~~~R~DK~~~ea~t~~~l~~l~~~ 537 (539)
T PRK09247 490 EIAFEG-IQRSKRHKSGIAVRFPRILRWRWDKPAREADTLETLQALLDA 537 (539)
T ss_pred EEEece-eeecCCcCCCcEEEcceEEEEeCCCChHHCcCHHHHHHHHhc
Confidence 999753 247899999999999999999999999999999999999963
No 7
>PRK03180 ligB ATP-dependent DNA ligase; Reviewed
Probab=100.00 E-value=4.3e-88 Score=808.20 Aligned_cols=493 Identities=21% Similarity=0.346 Sum_probs=424.9
Q ss_pred CcHHHHHHHHHHHHhhCChHHHHHHHHHHHhhcCCCchHHHHHHHhCCCCCCCccccCCCHHHHHHHHHHHhCCCcChHH
Q 001089 7 TEVIVLVSLFNWIQKTKPAAKKRSKFRKFLDTYCDSVDYFSALRLILPSLDRERGSYGLKESVLANCLIDALGMSKDSAD 86 (1159)
Q Consensus 7 ~~F~~l~~lle~i~~~~~~~~K~~~l~~~l~~~~~~~d~~p~lrLllP~~d~~r~~ygike~~L~k~~~~~lgl~~~s~~ 86 (1159)
|+|++||++|++|+.|+++++|+++|++||.+. .++++.++++|+...+. .+..|++++.+.++++.
T Consensus 1 m~f~~~~~~~~~l~~tt~r~~k~~~l~~~~~~~-~~~d~~~~~~~~~g~~~--~~~l~~~~~~v~~~~~~---------- 67 (508)
T PRK03180 1 MLLADVAATSAAVAATSSRLAKVARLAELLRRA-DPAEVAIVVAWLSGELR--QRRIGVGWATLRSLPAP---------- 67 (508)
T ss_pred CcHHHHHHHHHHHHhccCHHHHHHHHHHHHHhC-CHHHHHHHHHHhcCCCC--CCccCccHHHHHhcccc----------
Confidence 789999999999999999999999999999988 46899999999999996 35889997666655211
Q ss_pred HHHHhhhhcCCCCCCCCCHHHHHHHHhhhccCCCCCCCCHHHHHHHHHHHHhhhh---HHHHHHHHHHHHHhCCHHHHHH
Q 001089 87 AVRLINWRKGGAAPNAGNFPMVAAEVLQRRQGMISGGLTIKELNDLLDRLASSEN---RAEKISVLSTLIKKTNAQEMKW 163 (1159)
Q Consensus 87 ~~~L~~wk~~~~~~~~GD~~~~a~~vl~~r~~~~~~~LTi~eVn~~Ld~LA~~~~---~~~k~~il~~ll~~~s~~E~k~ 163 (1159)
...++|||.+||+.|++||..+| +..|..+|..||.+|++.|++|
T Consensus 68 --------------------------------~~~~~ltl~~V~~~l~~ia~~~g~~s~~~k~~~l~~ll~~~~~~E~~~ 115 (508)
T PRK03180 68 --------------------------------AAEPTLTVADVDAALSEIAAVAGAGSQARRAALLAALFAAATEDEQRF 115 (508)
T ss_pred --------------------------------cCCCCCcHHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHhCCHHHHHH
Confidence 01257999999999999998765 5788999999999999999999
Q ss_pred HHHHHHhhhccCCcccccccccC-------ccHHHHhhhcCCHHHHHHHHh-hhhccccccCcccCCccccccccccCCh
Q 001089 164 IIMIILKDLKLGISEKSIFHEFH-------PDAEDLFNVTCDLKLVCEKLK-DRNQRHKRQDIEVGKAVRPQLAMRIGDA 235 (1159)
Q Consensus 164 l~RiIlkdLriGi~e~til~~~h-------pda~~~~~~~~dL~~V~~~L~-~~~~~~~~~~i~~g~p~~PMLA~~~~~~ 235 (1159)
|+|||+++||||+++++|+.+++ ++++++|++|+||+.||+.+. ++...+....|++|.||+||||++...+
T Consensus 116 l~r~i~~~lRiGv~~~~v~~Ala~a~~~~~~~v~~a~~~~~dl~~v~~~~l~~~~~~~~~~~i~~~~P~~PMLA~~~~~~ 195 (508)
T PRK03180 116 LRRLLTGELRQGALDGVMADAVARAAGVPAAAVRRAAMLAGDLPAVAAAALTGGAAALARFRLEVGRPVRPMLAQTATSV 195 (508)
T ss_pred HHHHHhCCCcccccHHHHHHHHHHHhCCCHHHHHHHHHHcCCHHHHHHHHHhcCccccccCCCCCCCCCCCccCCcCCCh
Confidence 99999999999999999998773 567889999999999999655 4445567778999999999999999888
Q ss_pred HHHHHhcCCCcEEEEEecceEEEEEEEeCCEEEEEecCCCCcCcchhhHHHHHHHhcccCceeecceEEEEeCCCCcccc
Q 001089 236 HAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDGEMLVWDTSLNRFAE 315 (1159)
Q Consensus 236 ~~~~~k~~~~~~~vE~K~DGeR~qih~~g~~v~~fSR~g~d~t~~~p~l~~~l~~~~~~~~~ILDGElv~~d~~~~~~~p 315 (1159)
++++++++ .+|++|+||||+|||+|++++++++|||||+++|..+|++.+.+. .+..++||||||||+||+ .++++|
T Consensus 196 ~~~~~~~~-~~~~~E~K~DG~R~qih~~~~~v~l~SR~~~d~T~~fPei~~~~~-~~~~~~~ILDGElv~~d~-~g~~~~ 272 (508)
T PRK03180 196 AEALARLG-GPAAVEAKLDGARVQVHRDGDDVRVYTRTLDDITARLPEVVEAVR-ALPVRSLVLDGEAIALRP-DGRPRP 272 (508)
T ss_pred HHHHHHhC-CCeEEEEEEceeEEEEEEECCEEEEEeCCCCcchhhhHHHHHHHH-hCCCcceeecceEEEECC-CCCcCC
Confidence 88888884 579999999999999999999999999999999999999988653 355678999999999997 467889
Q ss_pred cccHHHHHHHhhc--CCCCCCCeEEEEEeeeecCCccccCCCHHHHHHHHHHhhccCCCcceeeccCCCCCccccCCCCC
Q 001089 316 FGSNQEIAKAARD--GLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEP 393 (1159)
Q Consensus 316 Fg~lq~i~~~~r~--~~~~~~~~~~~vFDiL~lnG~~l~~~pl~eRr~~L~~~i~~~~~~~~i~~p~~~~~~~v~~~~~~ 393 (1159)
|+.++...++... ......+++|++|||||+||++|+++||.+||++|++++.+. .. .|
T Consensus 273 F~~l~~R~~~k~~~~~~~~~~pv~~~~FDlL~l~G~dl~~~pl~eRr~~L~~~~~~~-~~----~~-------------- 333 (508)
T PRK03180 273 FQVTASRFGRRVDVAAARATQPLSPFFFDALHLDGRDLLDAPLSERLAALDALVPAA-HR----VP-------------- 333 (508)
T ss_pred HHHHHHHhccccchhhhcccCceEEEEEeehhcCCcchhcCCHHHHHHHHHHhhccc-cc----cc--------------
Confidence 9776654322110 011246899999999999999999999999999999998642 11 01
Q ss_pred ccceecCCHHHHHHHHHHHHHcCCceEEEecCCCCCcCCCCCCCeEEEcccccccCCcccEEEEEEEeCCCCCCCccceE
Q 001089 394 CWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLIIGGYYGSGRRGGEVAQF 473 (1159)
Q Consensus 394 ~~~~~~~~~~ei~~~~~~ai~~g~EGlVlK~~ds~Y~pGkRs~~WlKiKpey~~~g~~lDlvVIG~~~G~Grr~g~~gsf 473 (1159)
.....+.+++.++|++++++|+||||+|+++|+|.||+|+.+|+|+|+. +++|+||||+++|+|+|+|.+|+|
T Consensus 334 --~~~~~~~~~~~~~~~~a~~~g~EGlm~K~~ds~Y~~GrR~~~WlK~K~~-----~t~D~VviG~~~G~Gkr~g~~~~~ 406 (508)
T PRK03180 334 --RLVTADPAAAAAFLAAALAAGHEGVMVKSLDAPYAAGRRGAGWLKVKPV-----HTLDLVVLAAEWGSGRRTGKLSNL 406 (508)
T ss_pred --ceecCCHHHHHHHHHHHHHcCCceEEEeCCCCCcCCCCCCCCcEEEcCC-----CceEEEEEeeecCCCCCCCCccce
Confidence 2335678999999999999999999999999999999999999999996 499999999999999999999999
Q ss_pred EEEEecCCCCCCCCceEEEEEEecCCCCHHHHHHHHHhhcccccccCCCCCCCCCcccccCCCCCCCcEEEeCCcceEEE
Q 001089 474 LVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDVWIESPEKSIIL 553 (1159)
Q Consensus 474 llg~~d~~~~~~~~~~f~~v~kVgtG~sdeel~~l~~~l~~~~~~~~~~~~~pP~~~~~~~~~~~~Pdvwi~~P~~s~Vl 553 (1159)
+||+||+++ +.|++||+||||||++++++|.+.+.++... ...|++||+ |. +|+
T Consensus 407 llg~~d~~~-----~~l~~vgkv~sG~td~~l~~l~~~l~~~~~~------------------~~~~~vwv~-P~--~V~ 460 (508)
T PRK03180 407 HLGARDPAT-----GGFVMLGKTFKGMTDAMLAWQTERFLELAVG------------------RDGWTVYVR-PE--LVV 460 (508)
T ss_pred EEEEEeCCC-----CeEEEecCccCCCCHHHHHHHHHHHHhhccC------------------CCCCCEEee-CC--EEE
Confidence 999997543 3899999999999999999999888765321 235899999 76 899
Q ss_pred EEEeeeeeeecccccCCceeeCceeeeeecCCCccCcCCHHHHHHHH
Q 001089 554 SITSDIRTIRSEVFSAPYSLRFPRIDRVRYDKPWHDCLDVQSFVELV 600 (1159)
Q Consensus 554 ev~a~i~~i~s~~~~~g~tLRFPR~~riR~DK~~~d~~t~~el~~l~ 600 (1159)
||+++.. ..|+.|++|++||||||++||+||+|+||+|++++.+||
T Consensus 461 EV~~~~i-t~S~~~~~G~~LRfPr~~r~R~DK~~~ea~tl~~~~~l~ 506 (508)
T PRK03180 461 EIAFDGV-QRSTRYPGGVALRFARVLRYRPDKTPAEADTIDTVRALL 506 (508)
T ss_pred EEEeeEe-eeCCcccCCeEEECCeeeEeeCCCChHHCcCHHHHHHHh
Confidence 9997542 478899999999999999999999999999999999998
No 8
>PHA02587 30 DNA ligase; Provisional
Probab=100.00 E-value=9.9e-61 Score=570.68 Aligned_cols=445 Identities=20% Similarity=0.286 Sum_probs=334.0
Q ss_pred HHHHHHHHhhCChHHHHHHHHHHHhhcCCCchHHHHHHHhCCCCCCCccccCCCHHHHHHHHHHHhCCCcChHHHHHHhh
Q 001089 13 VSLFNWIQKTKPAAKKRSKFRKFLDTYCDSVDYFSALRLILPSLDRERGSYGLKESVLANCLIDALGMSKDSADAVRLIN 92 (1159)
Q Consensus 13 ~~lle~i~~~~~~~~K~~~l~~~l~~~~~~~d~~p~lrLllP~~d~~r~~ygike~~L~k~~~~~lgl~~~s~~~~~L~~ 92 (1159)
-+++++|+++.++++|.+||.+... ++.+--+++|.+...- .|||+.
T Consensus 3 ~~il~~~~~~~~~~~k~~il~~~~~----n~~l~~~~~~~~~~~~----~~~~~~------------------------- 49 (488)
T PHA02587 3 LDILNELASTDSTKEKEAILKENKD----NELLKEVFRLTYNKQI----NFGIKK------------------------- 49 (488)
T ss_pred HHHHHHHHhccCcchHHHHHHhccc----ChHHHHHHHHHhCcce----eEeeeE-------------------------
Confidence 4789999999999999998887633 3556677788776653 567442
Q ss_pred hhcCCCCCCCCCHHHHHHHHhhhccCCCCCCCCHHH-HHHHHHHHHhhhh-HHHHHHHHHHHHHhCCHHHHHHHHHHHHh
Q 001089 93 WRKGGAAPNAGNFPMVAAEVLQRRQGMISGGLTIKE-LNDLLDRLASSEN-RAEKISVLSTLIKKTNAQEMKWIIMIILK 170 (1159)
Q Consensus 93 wk~~~~~~~~GD~~~~a~~vl~~r~~~~~~~LTi~e-Vn~~Ld~LA~~~~-~~~k~~il~~ll~~~s~~E~k~l~RiIlk 170 (1159)
|.+++.. ....+.+++.+ +..++.+||...- ....+..|..++.+|++.|++||+|||++
T Consensus 50 ~~~~~~~------------------~~~~~~~~~~~~~~~~~~~l~~r~~~~~~~~~~l~~ll~~~~~~e~~~l~rli~~ 111 (488)
T PHA02587 50 WPKPGHV------------------EGSDGMLSLEDLLDFLEFDLATRKLTGNAAIEELAQILSSMNEDDAEVLRRVLMR 111 (488)
T ss_pred cCCCccc------------------cCCCCceeHHHHHHHHHHHHHHhhcchhHHHHHHHHHHHhCCHHHHHHHHHHHhc
Confidence 2111110 00124466666 4555667887653 56678899999999999999999999999
Q ss_pred hhccCCcccccccccCccHHHHhhhcCCHHHHHHHHhhhhccccccCcccCCcccc-ccccccCChHHHHHhcCCCcEEE
Q 001089 171 DLKLGISEKSIFHEFHPDAEDLFNVTCDLKLVCEKLKDRNQRHKRQDIEVGKAVRP-QLAMRIGDAHAAWRKLHGKEVVI 249 (1159)
Q Consensus 171 dLriGi~e~til~~~hpda~~~~~~~~dL~~V~~~L~~~~~~~~~~~i~~g~p~~P-MLA~~~~~~~~~~~k~~~~~~~v 249 (1159)
+||||+++++|+++||+ +.|++| |||++... ++++++-+.+|++
T Consensus 112 ~lriGvs~~~i~~~~~~---------------------------------~~P~~p~mLA~~~~~--~~~~~~~~~~~~~ 156 (488)
T PHA02587 112 DLECGASEKIANKVWKG---------------------------------LIPEQPQMLASSFSE--KLIKKNIKFPAYA 156 (488)
T ss_pred ccCCCccHHHHHHHhcC---------------------------------CccCCCCccCCCCCH--HHHHhhccCcEEE
Confidence 99999999999988864 578887 99998543 4566632448999
Q ss_pred EEecceEEEEEEEeCCEEEEEecCCCCcCcchhhHHHHHHHhcc-----cCceeecceEEEEeCCCCccccccc------
Q 001089 250 ECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVL-----VDRCILDGEMLVWDTSLNRFAEFGS------ 318 (1159)
Q Consensus 250 E~K~DGeR~qih~~g~~v~~fSR~g~d~t~~~p~l~~~l~~~~~-----~~~~ILDGElv~~d~~~~~~~pFg~------ 318 (1159)
|+||||+|||+|+.++++++|||+|++++. +|++...+..... +.+||||||+|+|+..++ .||+.
T Consensus 157 E~K~DG~R~q~h~~~~~v~l~SR~g~~~~~-~p~i~~~l~~~~~~~~~~~~~~VLDGElv~~~~~~~--~~~~~~f~~~~ 233 (488)
T PHA02587 157 QLKADGARCFADIDADGIEIRSRNGNEYLG-LDLLKEELKKMTAEARQRPGGVVIDGELVYVEVETK--KPNGLSFLFDD 233 (488)
T ss_pred EEccCceEEEEEEeCCEEEEEecCCccccC-ChhHHHHHHHHhhhhcccCCcEEEEeEEEEEecccC--CCccchhhccc
Confidence 999999999999999999999999999986 4887776543221 478999999999987554 34431
Q ss_pred -----H-HHHHHHhh-cCC-----------CCCCCeEEEEEeeeecC---CccccCCCHHHHHHHHHHhhcc-CCCccee
Q 001089 319 -----N-QEIAKAAR-DGL-----------SSDRQLCYFAFDVLYVG---DTSVIHQSLKERHELLQKVVKP-SKGRLET 376 (1159)
Q Consensus 319 -----l-q~i~~~~r-~~~-----------~~~~~~~~~vFDiL~ln---G~~l~~~pl~eRr~~L~~~i~~-~~~~~~i 376 (1159)
. |.++.+.+ .++ ....+++|++||||+++ |..+++.||.+||++|++++.. ..+++.+
T Consensus 234 ~~~~~f~q~l~~R~~~~~i~~~~l~~~~~~~~~~pv~~~vFDiL~ld~y~~~~~~~~pl~eRr~~L~~l~~~~~~~~i~l 313 (488)
T PHA02587 234 SKAKEFVGVVADRATGNGIVNKSLKGTISKEEAQEIVFQVWDIVPLEVYYGKEKSDMPYDDRFSKLAQMFEDCGYDRVEL 313 (488)
T ss_pred ccccchhhhhhhhhhccchhhhhhccccchhhccceEEEEEEeechhhccCCccccCCHHHHHHHHHHHHhhcCCCcEEE
Confidence 0 22222211 110 12368999999999653 4447889999999999999963 2334433
Q ss_pred eccCCCCCccccCCCCCccceecCCHHHHHHHHHHHHHcCCceEEEecCCCCCcCCCCCCCeEEEcccccccCCcccEEE
Q 001089 377 LVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLI 456 (1159)
Q Consensus 377 ~~p~~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~ai~~g~EGlVlK~~ds~Y~pGkRs~~WlKiKpey~~~g~~lDlvV 456 (1159)
+ ....+++.+++.++|+++++.|+||||+|+++|+|.+| |+.+|+|+|+.+ ++|++|
T Consensus 314 ~-----------------~~~~~~~~ee~~~~~~~a~~~G~EGimlK~~ds~Y~~G-Rs~~WlKiK~~~-----~~dlvV 370 (488)
T PHA02587 314 I-----------------ENQVVNNLEEAKEIYKRYVDQGLEGIILKNTDGLWEDG-RSKDQIKFKEVI-----DIDLEI 370 (488)
T ss_pred E-----------------eeEEcCCHHHHHHHHHHHHhCCCCeEEEECCCCCCCCC-CCCCcEEecCCC-----ceEEEE
Confidence 2 12346789999999999999999999999999999998 888999999974 899999
Q ss_pred EEEEeCCCCCCCccceEEEEEecCCCCCCCCceEEEEEEecCCCCHHHHHHHHHhhcccccccCCCCCCCCCcccccCCC
Q 001089 457 IGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNS 536 (1159)
Q Consensus 457 IG~~~G~Grr~g~~gsfllg~~d~~~~~~~~~~f~~v~kVgtG~sdeel~~l~~~l~~~~~~~~~~~~~pP~~~~~~~~~ 536 (1159)
||+|+|. +++|.+|+|+|++++ + . .+|+||||||++++++|...+. . +| +... ..
T Consensus 371 vG~~~~~-k~~~~~gs~ll~~~~--g------~--~~~~vgsGftd~~~~~l~~~~~--~---------~p-~~~~--~~ 425 (488)
T PHA02587 371 VGVYEHK-KDPNKVGGFTLESAC--G------K--ITVNTGSGLTDTTHRKKDGKKV--V---------IP-LSER--HE 425 (488)
T ss_pred EeEEeCC-CCCCceeEEEEEecC--C------c--EEEEECCCCChHHhhhhccccc--e---------ec-cccc--ch
Confidence 9999965 577889999997653 1 2 4799999999999999866543 1 11 1011 12
Q ss_pred CCCCcEEEeCCc-ceEEEEEEeeeeeeecccccCCceeeCceeeeeecCCCccCcCCHHHHH
Q 001089 537 KERPDVWIESPE-KSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDKPWHDCLDVQSFV 597 (1159)
Q Consensus 537 ~~~Pdvwi~~P~-~s~Vlev~a~i~~i~s~~~~~g~tLRFPR~~riR~DK~~~d~~t~~el~ 597 (1159)
..++.+|.+++. ...|+||+++.. ..|+.|++|++||||||+|||+||+ +|+|++++.
T Consensus 426 ~~r~~~~~~~~~~~~~V~EV~~~~i-t~S~~~~~g~sLRfPrf~r~R~DK~--~Adt~~~v~ 484 (488)
T PHA02587 426 LDREELMANKGKYIGKIAECECNGL-QRSKGRKDKVSLFLPIIKRIRIDKT--EANTLEDVF 484 (488)
T ss_pred hcchhhhhCcccccceEEEEEeceE-EeCCCCCCCeeEEccceeEEeCCCC--cccCHHHHh
Confidence 345677876321 247999997543 4788999999999999999999999 999999986
No 9
>COG1793 CDC9 ATP-dependent DNA ligase [DNA replication, recombination, and repair]
Probab=100.00 E-value=2.1e-59 Score=550.76 Aligned_cols=421 Identities=27% Similarity=0.410 Sum_probs=347.9
Q ss_pred CCCCCHHHHHHHHhhhccCCCCCCCCHHHHHHHHHHHHhhhhHHHHHHHHHHHHHhCCHHHHHHHHHHHHhhhccCCccc
Q 001089 100 PNAGNFPMVAAEVLQRRQGMISGGLTIKELNDLLDRLASSENRAEKISVLSTLIKKTNAQEMKWIIMIILKDLKLGISEK 179 (1159)
Q Consensus 100 ~~~GD~~~~a~~vl~~r~~~~~~~LTi~eVn~~Ld~LA~~~~~~~k~~il~~ll~~~s~~E~k~l~RiIlkdLriGi~e~ 179 (1159)
...||+|..+..+.. +.+|+..|..++...| .. .++..|+..++ +|++++
T Consensus 18 ~~~Gdlg~~~~~~~~-----------v~~v~~~~~~~~~~~g-~~--~~~~~L~~~~~----------------~gv~~~ 67 (444)
T COG1793 18 IPQGDLGEGAVLLWD-----------VEGVYLTLSKVAERTG-QE--RLLWLLLDEAD----------------IGVSEG 67 (444)
T ss_pred cccCccchhheeeee-----------cccchhhHHHHHhhcC-ch--hHHHHHHHhcc----------------cchhhH
Confidence 568999998766543 8899999999998888 22 78888888887 999999
Q ss_pred ccccccCccHHHHhhhcCCHHHHHHHHhhh-hccccccCcccCCccccccccccCChHHHHHhcCCCcEEEEEecceEEE
Q 001089 180 SIFHEFHPDAEDLFNVTCDLKLVCEKLKDR-NQRHKRQDIEVGKAVRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRI 258 (1159)
Q Consensus 180 til~~~hpda~~~~~~~~dL~~V~~~L~~~-~~~~~~~~i~~g~p~~PMLA~~~~~~~~~~~k~~~~~~~vE~K~DGeR~ 258 (1159)
+++.++..-.+..|+.++|++.++..+... ..++....+.+|.|++||||.......+...+..+ .|++|+||||+|+
T Consensus 68 ~~~~ala~~~~~~~~~~~d~g~~a~~~~~~~~~~~~~~~~~~~~p~~~~la~~~~~~~~~~~~~~~-~w~~E~K~DG~R~ 146 (444)
T COG1793 68 TVLDALAEAVERAYLWHNDLGALAKILLTLGAEALDKATLLPGRPLPPMLAPMLASLEEALPRDGG-DWAYEEKFDGYRV 146 (444)
T ss_pred HHHHHHHHHhhhhhccCCCchhhhhhhhhcccccccccccccCCccchhhccccccccccCCCCCC-CEEEEEeeceEEE
Confidence 999877665888899999999988877543 23445566789999999999998876655555433 5999999999999
Q ss_pred EEEEeCCEEEEEecCCCCcCcchhhHHHHHHHhcccCceeecceEEEEeCCCCcccccccHHHHHHHhhc--CCCCCCCe
Q 001089 259 QIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDGEMLVWDTSLNRFAEFGSNQEIAKAARD--GLSSDRQL 336 (1159)
Q Consensus 259 qih~~g~~v~~fSR~g~d~t~~~p~l~~~l~~~~~~~~~ILDGElv~~d~~~~~~~pFg~lq~i~~~~r~--~~~~~~~~ 336 (1159)
|+|+.++.|++|||+|.|+|..+|++...+...+..+++|||||+|++|+. ...||+.+|...++... ......++
T Consensus 147 q~h~~~~~vrl~SR~g~d~T~~fP~~~~~~~~~l~~~~~iiDGE~V~~~~~--~~~~F~~Lq~r~~~k~~v~~~~~~~~~ 224 (444)
T COG1793 147 QIHIDGGKVRLYSRNGEDWTGRFPDILEAAAEALPADDFILDGEIVVLDEE--GRLDFQALQQRLRRKYDVAKLRRETPL 224 (444)
T ss_pred EEEEcCCEEEEEeCCCccchhhChHHHHHHHhcCCCCceEEeeeEEEECCC--CCCCHHHHHHHhhhccchhhhccCCce
Confidence 999999999999999999999999766666666777899999999999975 46899888876543211 12345689
Q ss_pred EEEEEeeeecCCccccCCCHHHHHHHHHHhhccCCCcceeeccCCCCCccccCCCCCccceecCCHHHHHHHHHHHHHcC
Q 001089 337 CYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENR 416 (1159)
Q Consensus 337 ~~~vFDiL~lnG~~l~~~pl~eRr~~L~~~i~~~~~~~~i~~p~~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~ai~~g 416 (1159)
+|++|||||+||.+|.++||.+||++|++++... +.+.+. ..+..++.+++..+|+.+++.|
T Consensus 225 ~~~aFDlL~~dG~dL~~~pl~eRr~~Le~lv~~~-~~~~~~-----------------~~i~~~~~~~~~~~~~~a~~~g 286 (444)
T COG1793 225 VLFAFDLLYLDGEDLRGLPLEERRALLEELVKSS-DKIEIA-----------------ERIPFSDAEEGEAFLEAAIELG 286 (444)
T ss_pred EEEEEEEEeECCcccccCchHHHHHHHHHHhccc-cccccc-----------------cceeccChhhHHHHHHHHHhcC
Confidence 9999999999999999999999999999999874 222111 0223378899999999999999
Q ss_pred CceEEEecCCCCCcCCCCCCCeEEEcccccccCCcccEEEEEEEeCCCCCCCccceEEEEEecCCCCCCCCceEEEEEEe
Q 001089 417 DEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRV 496 (1159)
Q Consensus 417 ~EGlVlK~~ds~Y~pGkRs~~WlKiKpey~~~g~~lDlvVIG~~~G~Grr~g~~gsfllg~~d~~~~~~~~~~f~~v~kV 496 (1159)
+||||+|+++|+|++|+|+..|+|+|++ +++|++|+|+++|.|+++ .+|+|+||+|++++ +.|.++|+|
T Consensus 287 ~EGvv~K~~ds~Y~~g~R~~~W~K~K~~-----~~~d~vv~G~~~g~Gkr~-~~~slll~~~~~~~-----~~~~~v~kV 355 (444)
T COG1793 287 LEGVVAKRPDSPYRAGGRSNKWLKVKRD-----ETLDLVVVGAEYGKGKRS-LYGSLLLGVYDGDG-----GGLLYVGKV 355 (444)
T ss_pred ceEEEEeCCCCCcCCCCCCCcceEeccC-----CcccEEEEEEEecCCccc-ccceEEEEEEcCCC-----ceEEEEecc
Confidence 9999999999999999999999999998 489999999999999999 89999999998764 379999999
Q ss_pred cCCCCHHHHHHHHHhhcccccccCCCCCCCCCcccccCCCCCCCcEEEeCCcceEEEEEEeeeeeeecccccC--Cceee
Q 001089 497 GTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSA--PYSLR 574 (1159)
Q Consensus 497 gtG~sdeel~~l~~~l~~~~~~~~~~~~~pP~~~~~~~~~~~~Pdvwi~~P~~s~Vlev~a~i~~i~s~~~~~--g~tLR 574 (1159)
||||+++++++|.++|++++... . .|. .+..|+.+|. +|+||.+... ..+..|.. |++||
T Consensus 356 gtGf~~~~l~~l~~~l~~~~~~~----~-~~~----------~~~~~~~~p~--~V~EV~~~~~-t~~~~~r~~~~~~lR 417 (444)
T COG1793 356 GTGFSDAELEELTERLEPLIVSR----F-NGK----------VPGKVVPPPG--LVAEVRFAEI-TKSGRLRHASGLGLR 417 (444)
T ss_pred cCCCCHHHHHHHHHHHHHhccCc----C-CCc----------cCceeecCCc--EEEEEEEeec-ccCCceecccCcccC
Confidence 99999999999999999988641 0 110 1111554454 8999987543 25677766 89999
Q ss_pred CceeeeeecCCCccCcCCHHHHHHHH
Q 001089 575 FPRIDRVRYDKPWHDCLDVQSFVELV 600 (1159)
Q Consensus 575 FPR~~riR~DK~~~d~~t~~el~~l~ 600 (1159)
|||+.++|.||.+.+++|++++.+|+
T Consensus 418 fpr~~rvr~dk~~~~a~t~~~~~~~~ 443 (444)
T COG1793 418 FPRFVRVRDDKLPEDADTIEEIEALY 443 (444)
T ss_pred cCcccccccccCcccccccccchhhc
Confidence 99999999999999999999998876
No 10
>TIGR02779 NHEJ_ligase_lig DNA polymerase LigD, ligase domain. DNA repair of double-stranded breaks by non-homologous end joining (NHEJ) is accomplished by a two-protein system that is present in a minority of prokaryotes. One component is the Ku protein (see TIGR02772), which binds DNA ends. The other is a DNA ligase, a protein that is a multidomain polypeptide in most of those bacteria that have NHEJ, a permuted polypeptide in Mycobacterium tuberculosis and a few other species, and the product of tandem genes in some other bacteria. This model represents the ligase domain.
Probab=100.00 E-value=1e-54 Score=491.59 Aligned_cols=288 Identities=28% Similarity=0.419 Sum_probs=241.3
Q ss_pred CCCcEEEEEecceEEEEEEEeCCEEEEEecCCCCcCcchhhHHHHHHHhcccCceeecceEEEEeCCCCcccccccHHHH
Q 001089 243 HGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDGEMLVWDTSLNRFAEFGSNQEI 322 (1159)
Q Consensus 243 ~~~~~~vE~K~DGeR~qih~~g~~v~~fSR~g~d~t~~~p~l~~~l~~~~~~~~~ILDGElv~~d~~~~~~~pFg~lq~i 322 (1159)
.+.+|++|+||||+|||+|++++.|++|||||+++|..+|.+...+ ..+...+||||||||+||.. ++ .+|+.+|..
T Consensus 10 ~~~~~~~E~K~DG~R~~~~~~~~~v~l~SR~g~~~t~~~p~l~~~~-~~~~~~~~iLDGElv~~d~~-g~-~~F~~l~~r 86 (298)
T TIGR02779 10 TGDDWRYEVKYDGYRCLARIEGGKVRLISRNGHDWTEKFPILAAAL-AALPILPAVLDGEIVVLDES-GR-SDFSALQNR 86 (298)
T ss_pred CCCCEEEEEEEceEEEEEEEeCCEEEEEeCCCCchHhHhHHHHHHH-HhCCCCcEEEEeEEEEECCC-CC-CCHHHHHhh
Confidence 4678999999999999999999999999999999999889887764 44556799999999999974 33 589777754
Q ss_pred HHHhhcCCCCCCCeEEEEEeeeecCCccccCCCHHHHHHHHHHhhccCCCcceeeccCCCCCccccCCCCCccceecCCH
Q 001089 323 AKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNV 402 (1159)
Q Consensus 323 ~~~~r~~~~~~~~~~~~vFDiL~lnG~~l~~~pl~eRr~~L~~~i~~~~~~~~i~~p~~~~~~~v~~~~~~~~~~~~~~~ 402 (1159)
... ....+++|++|||||+||++++++||.+|+++|++++.+.++++.+.. . ..++.
T Consensus 87 ~~~-----~~~~~~~~~vFDiL~l~g~~l~~~pl~eRr~~L~~l~~~~~~~~~~~~-----------------~-~~~~~ 143 (298)
T TIGR02779 87 LRA-----GRDRPATYYAFDLLYLDGEDLRDLPLSERKKLLEELLKAIKGPLAPDR-----------------Y-SVHFE 143 (298)
T ss_pred hhc-----CCCCceEEEEEeeeeECceehhcCCHHHHHHHHHHHhcccCCCceeEe-----------------c-ccCch
Confidence 332 123789999999999999999999999999999999987654432210 0 24567
Q ss_pred HHHHHHHHHHHHcCCceEEEecCCCCCcCCCCCCCeEEEcccccccCCcccEEEEEEEeCCCCCCCccceEEEEEecCCC
Q 001089 403 DEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLIIGGYYGSGRRGGEVAQFLVALAERPA 482 (1159)
Q Consensus 403 ~ei~~~~~~ai~~g~EGlVlK~~ds~Y~pGkRs~~WlKiKpey~~~g~~lDlvVIG~~~G~Grr~g~~gsfllg~~d~~~ 482 (1159)
+++.++|++++++|+||||+|+++|+|.||+ +..|+|+|+.+ +.|++|+|+++|.|++ |.+|+|+||++++.
T Consensus 144 ~~~~~~~~~~~~~g~EGiv~K~~ds~Y~~Gr-s~~WlK~K~~~-----~~d~vV~G~~~g~g~~-~~~gslll~~~~~~- 215 (298)
T TIGR02779 144 GDGQALLEAACRLGLEGVVAKRRDSPYRSGR-SADWLKLKCRR-----RQEFVIGGYTPPNGSR-SGFGALLLGVYEGG- 215 (298)
T ss_pred hHHHHHHHHHHHcCCceEEEeCCCCCCCCCC-CCCcEEEccCC-----CCEEEEEEEECCCCCC-CccceEEEEEECCC-
Confidence 8999999999999999999999999999995 99999999986 8999998888899988 77999999999642
Q ss_pred CCCCCceEEEEEEecCCCCHHHHHHHHHhhcccccccCCCCCCCCCcccccCCCCCCCcEEEeCCcceEEEEEEeeeeee
Q 001089 483 PDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDVWIESPEKSIILSITSDIRTI 562 (1159)
Q Consensus 483 ~~~~~~~f~~v~kVgtG~sdeel~~l~~~l~~~~~~~~~~~~~pP~~~~~~~~~~~~Pdvwi~~P~~s~Vlev~a~i~~i 562 (1159)
.|.++|+||||||++++++|.+.|.+++... . +|. .....|++||+ |. +|+||++..
T Consensus 216 ------~l~~vg~vgsG~s~~~~~~l~~~l~~~~~~~----~-~~~------~~~~~~~~wv~-P~--lV~eV~~~~--- 272 (298)
T TIGR02779 216 ------GLRYVGRVGTGFSEAELATIKERLKPLESKP----D-KPG------AREKRGVHWVK-PE--LVAEVEFAG--- 272 (298)
T ss_pred ------eEEEEeEecCCCCHHHHHHHHHHHHhhccCc----C-CCC------cccCCCCEEeC-Ce--EEEEEEecc---
Confidence 6899999999999999999999999988652 1 221 12346899998 75 899997632
Q ss_pred ecccccCCceeeCceeeeeecCCCccCcC
Q 001089 563 RSEVFSAPYSLRFPRIDRVRYDKPWHDCL 591 (1159)
Q Consensus 563 ~s~~~~~g~tLRFPR~~riR~DK~~~d~~ 591 (1159)
++.|++||||||+++|+||+|+||+
T Consensus 273 ----~t~~~~lR~P~~~~~R~Dk~~~~~~ 297 (298)
T TIGR02779 273 ----WTRDGRLRQASFVGLREDKPASEVT 297 (298)
T ss_pred ----cCCCCeEeccEEEeeeCCCCHHHcc
Confidence 3457899999999999999999996
No 11
>PRK09632 ATP-dependent DNA ligase; Reviewed
Probab=100.00 E-value=2.7e-54 Score=528.17 Aligned_cols=307 Identities=26% Similarity=0.396 Sum_probs=254.4
Q ss_pred cccCCccccccccccCChHHHHHhcCCCcEEEEEecceEEEEEEEeCCEEEEEecCCCCcCcchhhHHHHHHHhcccCce
Q 001089 218 IEVGKAVRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRC 297 (1159)
Q Consensus 218 i~~g~p~~PMLA~~~~~~~~~~~k~~~~~~~vE~K~DGeR~qih~~g~~v~~fSR~g~d~t~~~p~l~~~l~~~~~~~~~ 297 (1159)
..++.+|+||||+..... .+.+..|++|+||||+|||+|++++.|++|||||+++|..||++... ...+...+|
T Consensus 455 ~~~~~~v~PMLA~~~~~~-----~~~~~~w~~E~K~DG~R~~~~~~~g~vrL~SRnG~d~T~~fPel~~~-~~~l~~~~~ 528 (764)
T PRK09632 455 AEEADDLAPMLATAGTVA-----GLKASQWAFEGKWDGYRLLAEADHGALRLRSRSGRDVTAEYPELAAL-AEDLADHHV 528 (764)
T ss_pred CCCCCCCcCccCCcCCCC-----CCCCCCEEEEEEECceeEEEEEeCCEEEEEeCCCCCccccchhHHHH-HhhCCCcce
Confidence 578899999999976432 13567899999999999999999999999999999999999998875 355656799
Q ss_pred eecceEEEEeCCCCcccccccHHHHHHHhhcCCCCCCCeEEEEEeeeecCCccccCCCHHHHHHHHHHhhccCCCcceee
Q 001089 298 ILDGEMLVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETL 377 (1159)
Q Consensus 298 ILDGElv~~d~~~~~~~pFg~lq~i~~~~r~~~~~~~~~~~~vFDiL~lnG~~l~~~pl~eRr~~L~~~i~~~~~~~~i~ 377 (1159)
|||||||+||..+ + .+|+.+|... ...+++|++|||||+||++|+++||.+||++|++++... +.+.+
T Consensus 529 ILDGEiVvld~~G-~-~~F~~Lq~r~--------~~~~v~y~vFDLL~lnG~dL~~~Pl~eRR~~L~~l~~~~-~~i~~- 596 (764)
T PRK09632 529 VLDGEIVALDDSG-V-PSFGLLQNRG--------RDTRVEFWAFDLLYLDGRSLLRKPYRDRRKLLEALAPSG-GSLTV- 596 (764)
T ss_pred eeeeEEEEeCCCC-C-CCHHHHhhhh--------hcCCeEEEEEeeeccCCcccccCCHHHHHHHHHHhhCCC-CcEEe-
Confidence 9999999999753 3 5898877541 236799999999999999999999999999999998632 23321
Q ss_pred ccCCCCCccccCCCCCccceecCCHHHHHHHHHHHHHcCCceEEEecCCCCCcCCCCCCCeEEEcccccccCCcccEEEE
Q 001089 378 VPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLII 457 (1159)
Q Consensus 378 ~p~~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~ai~~g~EGlVlK~~ds~Y~pGkRs~~WlKiKpey~~~g~~lDlvVI 457 (1159)
+ .....++.++|+.++++|.||||+|+++|+|++|+|+.+|+|+|+.| +.|+||+
T Consensus 597 -s-------------------~~~~~~~~~~l~~a~~~GlEGIVaKr~dS~Y~pGrRs~~WlKiK~~~-----~~e~VI~ 651 (764)
T PRK09632 597 -P-------------------PLLPGDGAEALAYSRELGWEGVVAKRRDSTYQPGRRSSSWIKDKHWR-----TQEVVIG 651 (764)
T ss_pred -c-------------------ceecccHHHHHHHHHHcCCcEEEEeCCCCCCCCCCcCCCeEEEecCC-----ceEEEEE
Confidence 1 01123578899999999999999999999999999999999999987 7999999
Q ss_pred EEEeCCCCCCCccceEEEEEecCCCCCCCCceEEEEEEecCCCCHHHHHHHHHhhcccccccCCCCCCCCCcccccCCCC
Q 001089 458 GGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSK 537 (1159)
Q Consensus 458 G~~~G~Grr~g~~gsfllg~~d~~~~~~~~~~f~~v~kVgtG~sdeel~~l~~~l~~~~~~~~~~~~~pP~~~~~~~~~~ 537 (1159)
|+++|.|+++|.+|+||||+++++ .|.++|+||||||++++++|.++|.++.+. .|| |........
T Consensus 652 G~~~g~G~r~g~~gsLLlGv~d~~-------~L~yvGkVGTGftd~~l~~L~~~L~~l~~~------~~P-f~~~~~~~~ 717 (764)
T PRK09632 652 GWRPGEGGRSSGIGSLLLGIPDPG-------GLRYVGRVGTGFTERELASLKETLAPLHRD------TSP-FDADLPAAD 717 (764)
T ss_pred EEEcCCCCcCCceeeEEEEEEcCC-------eeEEEEEEeCCCCHHHHHHHHHHHHhhccC------CCC-ccccccccc
Confidence 988999999999999999999753 589999999999999999999999987653 123 321111124
Q ss_pred CCCcEEEeCCcceEEEEEEeeeeeeecccccCCceeeCceeeeeecCCCccCcC
Q 001089 538 ERPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDKPWHDCL 591 (1159)
Q Consensus 538 ~~Pdvwi~~P~~s~Vlev~a~i~~i~s~~~~~g~tLRFPR~~riR~DK~~~d~~ 591 (1159)
.+|++||+ |. +|+||++. .++.+++||||+|+++|.||++.||+
T Consensus 718 ~~~~~WV~-P~--LV~EV~f~-------e~T~~g~LR~P~f~glR~DK~p~dv~ 761 (764)
T PRK09632 718 AKGATWVR-PE--LVGEVRYS-------EWTPDGRLRQPSWRGLRPDKKPGDVV 761 (764)
T ss_pred CCCcEEEe-cc--EEEEEEEe-------eccCCCceecceEEEeeCCCCHHHcc
Confidence 57899999 86 89999753 24567899999999999999999986
No 12
>PRK08224 ligC ATP-dependent DNA ligase; Reviewed
Probab=100.00 E-value=3.6e-52 Score=476.98 Aligned_cols=314 Identities=23% Similarity=0.364 Sum_probs=249.3
Q ss_pred CcccCCccccccccccCChHHHHHhcCCCcEEEEEecceEEEEEEEeCCEEEEEecCCCCcCcchhhHHHHHHHhcccCc
Q 001089 217 DIEVGKAVRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDR 296 (1159)
Q Consensus 217 ~i~~g~p~~PMLA~~~~~~~~~~~k~~~~~~~vE~K~DGeR~qih~~g~~v~~fSR~g~d~t~~~p~l~~~l~~~~~~~~ 296 (1159)
++.+|.|++||||.....++ .+.+|++|+||||+|||+|+++++|++|||||+++|..||+|.+.+.. +.+.+
T Consensus 2 ~~~~~~~i~PMLA~~~~~~~------~~~~w~~E~K~DG~R~~~~~~~~~v~l~SRng~d~t~~fPel~~~~~~-~~~~~ 74 (350)
T PRK08224 2 DLPVMPPVEPMLAKSVDAIP------PGDGWSYEPKWDGFRCLVFRDGDEVELGSRNGKPLTRYFPELVAALRA-ELPER 74 (350)
T ss_pred CCCCCCCcCCccCCccCCCC------CCCcEEEEEeECeeEEEEEEECCEEEEEeCCCCCchhhhHHHHHHHHh-hCCCC
Confidence 56789999999999876542 345799999999999999999999999999999999999999887643 44679
Q ss_pred eeecceEEEEeCCCCcccccccHHHHHHHhhc---CCCCCCCeEEEEEeeeecCCccccCCCHHHHHHHHHHhhccCCCc
Q 001089 297 CILDGEMLVWDTSLNRFAEFGSNQEIAKAARD---GLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGR 373 (1159)
Q Consensus 297 ~ILDGElv~~d~~~~~~~pFg~lq~i~~~~r~---~~~~~~~~~~~vFDiL~lnG~~l~~~pl~eRr~~L~~~i~~~~~~ 373 (1159)
||||||||+++.. + .+|+.+|........ ......+++|++|||||+||++|+++||.+|+++|++++...+ .
T Consensus 75 ~vLDGEiVv~~~~-~--~~F~~Lq~r~~~~~~~~~~~~~~~pv~~~vFDlL~l~G~dl~~~Pl~eRr~~L~~l~~~~~-~ 150 (350)
T PRK08224 75 CVLDGEIVVARDG-G--LDFEALQQRIHPAASRVRKLAEETPASFVAFDLLALGDRDLTGRPFAERRAALEAAAAGSG-P 150 (350)
T ss_pred EEEeeEEEEeCCC-C--CCHHHHHhhhhccccchhhhhhcCCEEEEEEeeeeECCcChhhCCHHHHHHHHHHhcCCCC-c
Confidence 9999999999843 2 799888765432110 0112468999999999999999999999999999999986432 3
Q ss_pred ceeeccCCCCCccccCCCCCccceecCCHHHHHHHHHHHHHcCCceEEEecCCCCCcCCCCCCCeEEEcccccccCCccc
Q 001089 374 LETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLD 453 (1159)
Q Consensus 374 ~~i~~p~~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~ai~~g~EGlVlK~~ds~Y~pGkRs~~WlKiKpey~~~g~~lD 453 (1159)
+.+. + ...+.++++++|++++++|+||||+|+.+|+|.+|+|+ |+|+|+.+ ++|
T Consensus 151 i~~~-----------~--------~~~~~~~~~~~~~~a~~~G~EGIV~Kr~dS~Y~~Grr~--WlKiK~~~-----~~d 204 (350)
T PRK08224 151 VHLT-----------P--------ATTDPATARRWFEEFEGAGLDGVIAKPLDGPYQPGKRA--MFKVKHER-----TAD 204 (350)
T ss_pred EEEe-----------c--------ccCCHHHHHHHHHHHHhCCCcEEEEeCCCCCcCCCCcC--EEEEccCC-----cEE
Confidence 3221 0 12456799999999999999999999999999999887 99999974 899
Q ss_pred EEEEEEEeCCCCCCCccceEEEEEecCCCCCCCCceEEEEEEecCCCCHHHHHHHHHhhcccccccCCCCCCCC----Cc
Q 001089 454 VLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPP----SF 529 (1159)
Q Consensus 454 lvVIG~~~G~Grr~g~~gsfllg~~d~~~~~~~~~~f~~v~kVgtG~sdeel~~l~~~l~~~~~~~~~~~~~pP----~~ 529 (1159)
++|+|+++|.|+ |.+|+|+||+|++++ ++.++|+|| |||++++++|.+.|+++++... .+| .|
T Consensus 205 ~vI~G~~~g~~~--~~~gslllg~~d~~g------~l~~vG~v~-Gf~~~~~~~L~~~l~~l~~~~~----~~p~~~~pf 271 (350)
T PRK08224 205 CVVAGYRYHKSG--PVVGSLLLGLYDDDG------QLHHVGVTS-AFPMARRRELTAELEPLRTPFG----DHPWNWAAF 271 (350)
T ss_pred EEEEEEEcCCCC--CccccEEEEEECCCC------cEEEEEEEC-CCCHHHHHHHHHHHHhhhcCCC----CCccccCcc
Confidence 999999988875 789999999997543 789999986 9999999999999998876411 012 12
Q ss_pred ccccC-----CCCCCCcEE--EeCCcceEEEEEEeeeeeeecccccCCceeeCc-eeeeeecCCCccCcC
Q 001089 530 YQVTN-----NSKERPDVW--IESPEKSIILSITSDIRTIRSEVFSAPYSLRFP-RIDRVRYDKPWHDCL 591 (1159)
Q Consensus 530 ~~~~~-----~~~~~Pdvw--i~~P~~s~Vlev~a~i~~i~s~~~~~g~tLRFP-R~~riR~DK~~~d~~ 591 (1159)
..... ....+..+| ++ |. +|+||++. .++ +..||+| +|+++|.||++.||+
T Consensus 272 ~~~~~~~~~~~~~~~~~~w~~v~-P~--lv~eV~~~-------~~t-~~~lR~p~~f~g~r~Dk~p~~v~ 330 (350)
T PRK08224 272 TGRAPGGPSRWSAGKDLSWVPLR-PE--RVVEVRYD-------HME-GGRFRHTAQFLRWRPDRDPRSCT 330 (350)
T ss_pred cccCCCccccccccCCcEEEeee-EE--EEEEEecC-------ccc-CCeecCCCeeEEEcCCCChHHCC
Confidence 11000 011235689 88 75 78888652 344 4499998 999999999999997
No 13
>PRK05972 ligD ATP-dependent DNA ligase; Reviewed
Probab=100.00 E-value=2.4e-51 Score=506.38 Aligned_cols=304 Identities=26% Similarity=0.400 Sum_probs=245.6
Q ss_pred CccccccccccCChHHHHHhcCCCcEEEEEecceEEEEEEEeCCEEEEEecCCCCcCcchhhHHHHHHHhcccCceeecc
Q 001089 222 KAVRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDG 301 (1159)
Q Consensus 222 ~p~~PMLA~~~~~~~~~~~k~~~~~~~vE~K~DGeR~qih~~g~~v~~fSR~g~d~t~~~p~l~~~l~~~~~~~~~ILDG 301 (1159)
..|+||||..+..++ .+..|++|+||||+|||+|++++.+++|||||+++|..||+|.+.+. .+...+|||||
T Consensus 232 ~~i~PMLAt~~~~~p------~g~~W~~E~K~DG~R~~a~~~gg~vrL~SRnG~d~T~~fPel~~~~~-~l~~~~~ILDG 304 (860)
T PRK05972 232 DFLAPQLATLVDRPP------SGDGWIYEIKFDGYRILARIEGGEVRLFTRNGLDWTAKLPALAKAAA-ALGLPDAWLDG 304 (860)
T ss_pred cccCcccCccCCCCC------CcCceEEEeeeCcEEEEEEEECCEEEEEeCCCCccccccHHHHHHHH-hcCCCceeEeE
Confidence 458999999887654 35689999999999999999999999999999999999999988764 45568999999
Q ss_pred eEEEEeCCCCcccccccHHHHHHHhhcCCCCCCCeEEEEEeeeecCCccccCCCHHHHHHHHHHhhccCCC-cceeeccC
Q 001089 302 EMLVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKG-RLETLVPD 380 (1159)
Q Consensus 302 Elv~~d~~~~~~~pFg~lq~i~~~~r~~~~~~~~~~~~vFDiL~lnG~~l~~~pl~eRr~~L~~~i~~~~~-~~~i~~p~ 380 (1159)
|||+||.. ++ .+|+.+|...... ...+++|++|||||+||++|+++||.+|+++|++++.+..+ ++.+.
T Consensus 305 EIVvld~~-G~-~~F~~Lq~r~~~~-----~~~~v~f~vFDLL~l~G~dL~~~PL~eRr~~L~~ll~~~~~~~i~~s--- 374 (860)
T PRK05972 305 EIVVLDED-GV-PDFQALQNAFDEG-----RTEDLVYFAFDLPFLGGEDLRELPLEERRARLRALLEAARSDRIRFS--- 374 (860)
T ss_pred EEEEECCC-CC-CCHHHHHHHhhcc-----CCCceEEEEEeccccCCcccccCCHHHHHHHHHHHhhhcCCCcEEEe---
Confidence 99999975 33 5898887644321 23579999999999999999999999999999999976532 22221
Q ss_pred CCCCccccCCCCCccceecCCHHHHHHHHHHHHHcCCceEEEecCCCCCcCCCCCCCeEEEcccccccCCcccEEEEEEE
Q 001089 381 HGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLIIGGY 460 (1159)
Q Consensus 381 ~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~ai~~g~EGlVlK~~ds~Y~pGkRs~~WlKiKpey~~~g~~lDlvVIG~~ 460 (1159)
.+...+..++|+.+++.|+||||+|+.+|+|.+| |+.+|+|+|+.+ +.|+||+|.+
T Consensus 375 ------------------~~~~~~g~~ll~~a~~~GlEGIVaKr~dS~Y~~G-Rs~~WlKiK~~~-----~~E~VIgGy~ 430 (860)
T PRK05972 375 ------------------EHFDAGGDAVLASACRLGLEGVIGKRADSPYVSG-RSEDWIKLKCRA-----RQEFVIGGYT 430 (860)
T ss_pred ------------------ceecchHHHHHHHHHHcCCceEEEeCCCCCCCCC-CCCCcEEEecCC-----CceEEEEEEe
Confidence 1122457889999999999999999999999987 899999999975 5677665555
Q ss_pred eCCCCCCCccceEEEEEecCCCCCCCCceEEEEEEecCCCCHHHHHHHHHhhcccccccCCCCCCCCCcccccCCCCCCC
Q 001089 461 YGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERP 540 (1159)
Q Consensus 461 ~G~Grr~g~~gsfllg~~d~~~~~~~~~~f~~v~kVgtG~sdeel~~l~~~l~~~~~~~~~~~~~pP~~~~~~~~~~~~P 540 (1159)
.|.|+++| +|+||||++++. +|+++|+||||||++++++|.++|.++.+. .+| |..........+
T Consensus 431 ~~~Gkr~g-~gSLLlGvyd~~-------~L~yvGkVGTGfsd~~l~~L~~~L~~l~~~------~~P-f~~~~~~~~~~~ 495 (860)
T PRK05972 431 DPKGSRSG-FGSLLLGVHDDD-------HLRYAGRVGTGFGAATLKTLLPRLKALATD------KSP-FAGKPAPRKARG 495 (860)
T ss_pred CCCCcccc-ceeEEEEEecCC-------EEEEEEEECCCCCHHHHHHHHHHHHhhccC------CCC-ccccCccccCCC
Confidence 56788887 999999999753 799999999999999999999999987653 133 321111122345
Q ss_pred cEEEeCCcceEEEEEEeeeeeeecccccCCceeeCceeeeeecCCCccCcC
Q 001089 541 DVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDKPWHDCL 591 (1159)
Q Consensus 541 dvwi~~P~~s~Vlev~a~i~~i~s~~~~~g~tLRFPR~~riR~DK~~~d~~ 591 (1159)
++||+ |+ +|+||++.. ++.+..||||+|+++|.||+++||+
T Consensus 496 ~~WV~-P~--LV~EV~f~e-------~T~~g~LR~P~F~glR~DK~p~ev~ 536 (860)
T PRK05972 496 VHWVK-PE--LVAEVEFAG-------WTRDGIVRQAVFKGLREDKPAREVV 536 (860)
T ss_pred CEEEc-cC--EEEEEEEee-------ccCCCCCccceEEEeecCCChHHhC
Confidence 79998 86 899998632 3445689999999999999999997
No 14
>PRK09633 ligD ATP-dependent DNA ligase; Reviewed
Probab=100.00 E-value=3.6e-50 Score=486.74 Aligned_cols=309 Identities=22% Similarity=0.275 Sum_probs=241.2
Q ss_pred cccccccccCChHHHHHhcCCCcEEEEEecceEEEEEEEeCCEEEEEecCCCCcCcchhhHHHHHHHhcc----cCceee
Q 001089 224 VRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVL----VDRCIL 299 (1159)
Q Consensus 224 ~~PMLA~~~~~~~~~~~k~~~~~~~vE~K~DGeR~qih~~g~~v~~fSR~g~d~t~~~p~l~~~l~~~~~----~~~~IL 299 (1159)
++||||.....++ .+..|++|+||||+|||+|++++.|++|||||+++|..||++.+.+..... ..+|||
T Consensus 1 ~~PMLa~~~~~~p------~g~~w~~E~K~DG~R~~~h~~~~~V~L~SRng~d~T~~fPel~~~~~~~~~~~~~~~~~IL 74 (610)
T PRK09633 1 MKPMQPTLTTSIP------IGDEWRYEVKYDGFRCLLIIDETGITLISRNGRELTNTFPEIIEFCESNFEHLKEELPLTL 74 (610)
T ss_pred CCCCcCCcCCCCC------CCCcEEEEEeEcceEEEEEEECCEEEEEeCCCCcchhhhhHHHHHHHhhhhccccCCceee
Confidence 4799998877653 467899999999999999999999999999999999999998876533211 137999
Q ss_pred cceEEEEeCCCCcccccccHHHHHHHhhcC----CCCCCCeEEEEEeeeecCCccccCCCHHHHHHHHHHhhccCCCcce
Q 001089 300 DGEMLVWDTSLNRFAEFGSNQEIAKAARDG----LSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLE 375 (1159)
Q Consensus 300 DGElv~~d~~~~~~~pFg~lq~i~~~~r~~----~~~~~~~~~~vFDiL~lnG~~l~~~pl~eRr~~L~~~i~~~~~~~~ 375 (1159)
|||||+||..+. .+|+.+|......+.. .....+++|++|||||+||++|++.||.+||++|++++.+......
T Consensus 75 DGEiVvld~~g~--~~F~~Lq~R~~~~~~~~i~~~~~~~pv~~~vFDlL~lnG~dL~~~PL~eRr~~L~~ll~~~~~~~~ 152 (610)
T PRK09633 75 DGELVCLVNPYR--SDFEHVQQRGRLKNTEVIAKSANARPCQLLAFDLLELKGESLTSLPYLERKKQLDKLMKAAKLPAS 152 (610)
T ss_pred eeEEEEecCCCC--CCHHHHHhhhhccccchhhhhhcccceEEEEEeecccCCcccccCCHHHHHHHHHHHhhhcccccc
Confidence 999999986432 5898777653221111 1123678999999999999999999999999999999975431100
Q ss_pred eeccCCCCCccccCCCCCccceecCCHHHHHHHHHHHHHcCCceEEEecCCCCCcCCCCCCCeEEEcccccccCCcccEE
Q 001089 376 TLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVL 455 (1159)
Q Consensus 376 i~~p~~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~ai~~g~EGlVlK~~ds~Y~pGkRs~~WlKiKpey~~~g~~lDlv 455 (1159)
+. +.+.+. ...+.+.++++++|+.+++.|+||||+|+.+|+|.+|+|+.+|+|+|+.+ +.|++
T Consensus 153 ---~~--------~~~~~~-i~~~~~~~~~~~l~~~a~~~g~EGIV~Kr~dS~Y~~G~Rs~~WlKiK~~~-----~~d~v 215 (610)
T PRK09633 153 ---PD--------PYAKAR-IQYIPSTTDFDALWEAVKRYDGEGIVAKKKTSKWLENKRSKDWLKIKNWR-----YVHVI 215 (610)
T ss_pred ---cc--------cccccc-eEEcCCHHHHHHHHHHHHHcCCceEEEeCCCCCCCCCCCCCCeEEEeccC-----CceeE
Confidence 00 000000 11234577999999999999999999999999999999999999999964 78998
Q ss_pred EEEEEeCCCCCCCccceEEEEEecCCCCCCCCceEEEEEEecCCCCHHHHHHHHHhhcccccccCCCCCCCCCcccccCC
Q 001089 456 IIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNN 535 (1159)
Q Consensus 456 VIG~~~G~Grr~g~~gsfllg~~d~~~~~~~~~~f~~v~kVgtG~sdeel~~l~~~l~~~~~~~~~~~~~pP~~~~~~~~ 535 (1159)
|+|+..|. |.|++|+++. ++|.++|+||||||++++++|.+.|.++.+.
T Consensus 216 I~G~~~~~-------g~~llgv~~~-------g~l~~vGkvgtGft~~~~~~L~~~l~~l~~~----------------- 264 (610)
T PRK09633 216 VTGYDPSN-------GYFTGSVYKD-------GQLTEVGSVKHGMEDEERQTLRAIFKQNGTK----------------- 264 (610)
T ss_pred EEEEecCC-------ceEEEEEecC-------CeEEEEEEecCCCCHHHHHHHHHHHHHhccC-----------------
Confidence 87765433 3688898843 2799999999999999999999999876432
Q ss_pred CCCCCcEEEeCCcceEEEEEEeeeeeeecccccCCceeeCceeeeeecCCCccCcCCHHHHHHHH
Q 001089 536 SKERPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDKPWHDCLDVQSFVELV 600 (1159)
Q Consensus 536 ~~~~Pdvwi~~P~~s~Vlev~a~i~~i~s~~~~~g~tLRFPR~~riR~DK~~~d~~t~~el~~l~ 600 (1159)
...+.+|++ |. +|+||++.. + +|+.||||+|+++|.||+++||++.++..+++
T Consensus 265 -~~~~~~wV~-P~--LV~EV~~~e-------~-t~g~LR~P~f~glR~DK~~~ev~~~~~~~~~~ 317 (610)
T PRK09633 265 -TKSGEYTLE-PS--ICVTVACIT-------F-DGGTLREPSFVSFLFDMDPTECTYQQLQRQLA 317 (610)
T ss_pred -CCCCcEEEe-ee--EEEEEEEee-------c-CCCeEEeeEEeEEEcCCChHHcchhhhhhhhc
Confidence 123578998 76 899997632 2 27899999999999999999999887766544
No 15
>PRK07636 ligB ATP-dependent DNA ligase; Reviewed
Probab=100.00 E-value=1.5e-45 Score=411.17 Aligned_cols=272 Identities=24% Similarity=0.334 Sum_probs=214.3
Q ss_pred cccccccccCChHHHHHhcCCCcEEEEEecceEEEEEEEeCCEEEEEecCCCCcCcchhhHHHHHHHhcccCceeecceE
Q 001089 224 VRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDGEM 303 (1159)
Q Consensus 224 ~~PMLA~~~~~~~~~~~k~~~~~~~vE~K~DGeR~qih~~g~~v~~fSR~g~d~t~~~p~l~~~l~~~~~~~~~ILDGEl 303 (1159)
++||||.....+ +.+.+|++|+||||+|||+|+.++.+++|||||+++|..+|++.... ...+|||||||
T Consensus 3 ~~PmLa~~~~~~------~~~~~~~~E~K~DG~R~~~~~~~~~v~l~SR~g~~~t~~fPe~~~~~----~~~~~vLDGEl 72 (275)
T PRK07636 3 ISPMLLESAKEP------FNSENYITEPKFDGIRLIASKNNGLIRLYTRHNNEVTAKFPELLNLD----IPDGTVLDGEL 72 (275)
T ss_pred cCCccCCcCCCC------CCCCcEEEEEEEceeEEEEEEeCCEEEEEeCCCCCchhhhhhHHhhh----cCCCEEEEeEE
Confidence 789999887643 34668999999999999999999999999999999999899877642 24679999999
Q ss_pred EEEeCCCCcccccccHHHHHHHhhcCCCCCCCeEEEEEeeeecCCccccCCCHHHHHHHHHHhhccCCCcceeeccCCCC
Q 001089 304 LVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGL 383 (1159)
Q Consensus 304 v~~d~~~~~~~pFg~lq~i~~~~r~~~~~~~~~~~~vFDiL~lnG~~l~~~pl~eRr~~L~~~i~~~~~~~~i~~p~~~~ 383 (1159)
|+||.. ++ .+|+.+|...... ......+++|++|||||+||++|+++||.+|+++|++++.+.+ .+.++
T Consensus 73 v~~d~~-g~-~~F~~l~~r~~~~--~~~~~~~~~~~vFDlL~~~g~~l~~~pl~eRr~~L~~~~~~~~-~~~~~------ 141 (275)
T PRK07636 73 IVLGST-GA-PDFEAVMERFQSK--KSTKIHPVVFCVFDVLYINGVSLTALPLSERKEILASLLLPHP-NVKII------ 141 (275)
T ss_pred EEECCC-CC-CCHHHHHHHhccc--cccccCceEEEEEEeEEECceehhhCCHHHHHHHHHHhcCCCC-CEEEc------
Confidence 999974 33 4898777543321 1122468999999999999999999999999999999986543 22211
Q ss_pred CccccCCCCCccceecCCHHHHHHHHHHHHHcCCceEEEecCCCCCcCCCCCCCeEEEcccccccCCcccEEEEEEEeCC
Q 001089 384 NSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLIIGGYYGS 463 (1159)
Q Consensus 384 ~~~v~~~~~~~~~~~~~~~~ei~~~~~~ai~~g~EGlVlK~~ds~Y~pGkRs~~WlKiKpey~~~g~~lDlvVIG~~~G~ 463 (1159)
....+++.++|+.++++|.||||+|+++|+|.+|+|+.+|+|+|+. ++.|++|+|+..
T Consensus 142 ---------------~~~~~~~~~~~~~~~~~g~EGiV~K~~ds~Y~~g~Rs~~WlKiK~~-----~~~e~vV~G~~~-- 199 (275)
T PRK07636 142 ---------------EGIEGHGTAYFELVEERELEGIVIKKANSPYEINKRSDNWLKVINY-----QYTDVLITGYRK-- 199 (275)
T ss_pred ---------------ccccccHHHHHHHHHHcCCcEEEEeCCCCCCCCCCCCCCeEEEecC-----CeEEEEEEEEec--
Confidence 1123467889999999999999999999999999999999999974 579988777532
Q ss_pred CCCCCccceEEEEEecCCCCCCCCceEEEEEEecCCCCHHHHHHHHHhhcccccccCCCCCCCCCcccccCCCCCCCcEE
Q 001089 464 GRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDVW 543 (1159)
Q Consensus 464 Grr~g~~gsfllg~~d~~~~~~~~~~f~~v~kVgtG~sdeel~~l~~~l~~~~~~~~~~~~~pP~~~~~~~~~~~~Pdvw 543 (1159)
+.+|.+ ||+++ + . ++|+||| |+++++++|.+.|.++... ..++.+|
T Consensus 200 ----~~~g~l-lg~~~--g------~--~~G~vgt-~~~~~~~~l~~~l~~~~~~------------------~~~~~~w 245 (275)
T PRK07636 200 ----EEFGLL-LSYLD--G------R--SAGIMEF-MPYDARKKFYKRAKRLVVG------------------EDKKFVY 245 (275)
T ss_pred ----CCCcEE-EEecC--C------e--EEEEECC-CCHHHHHHHHHHhhhhccC------------------ccCCCEE
Confidence 225655 78774 1 3 6899999 9999999999888754321 2356899
Q ss_pred EeCCcceEEEEEEeeeeeeecccccCCceeeCceeeeee
Q 001089 544 IESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVR 582 (1159)
Q Consensus 544 i~~P~~s~Vlev~a~i~~i~s~~~~~g~tLRFPR~~riR 582 (1159)
+. |. +|.||++.. ++.+..||||+|+++|
T Consensus 246 v~-P~--lv~eV~~~e-------~t~~g~lR~p~f~g~r 274 (275)
T PRK07636 246 IE-PI--IGCRVKHRF-------KTKNGMLRIPSFVEWR 274 (275)
T ss_pred eC-Cc--EEEEEEEEE-------ecCCCCEEccEEEEEe
Confidence 98 75 788887522 3344459999999998
No 16
>cd07900 Adenylation_DNA_ligase_I_Euk Adenylation domain of eukaryotic DNA Ligase I. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. Some organisms express a variety of different ligases which appear to be targeted to specific functions. There are three classes of ATP-dependent DNA ligases in eukaryotic cells (I, III and IV). DNA ligase I is required for the ligation of Okazaki fragments during lagging-strand DNA synthesis and for base excision repair (BER). DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains. The adenylation and C-terminal oligonucleotide/oligo
Probab=100.00 E-value=1.9e-44 Score=390.47 Aligned_cols=213 Identities=30% Similarity=0.547 Sum_probs=184.4
Q ss_pred cCcccCCccccccccccCChHHHHHhcCCCcEEEEEecceEEEEEEEeC-CEEEEEecCCCCcCcchhhHHHHHHHhc--
Q 001089 216 QDIEVGKAVRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNG-SEIHYFSRSFLDHSEYGHAMSKIIEQNV-- 292 (1159)
Q Consensus 216 ~~i~~g~p~~PMLA~~~~~~~~~~~k~~~~~~~vE~K~DGeR~qih~~g-~~v~~fSR~g~d~t~~~p~l~~~l~~~~-- 292 (1159)
..|++|.||+||||++..+++++++++.+.+|++|+||||+|||+|+.+ +.|++|||||+++|..+|++...+...+
T Consensus 2 ~~~~~~~pi~PMLA~~~~~~~~~~~~~~~~~~~~E~K~DG~R~~~h~~~~~~v~l~SR~g~~~t~~~pel~~~~~~~~~~ 81 (219)
T cd07900 2 CKLTPGIPVKPMLAKPTKGVSEVLDRFEDKEFTCEYKYDGERAQIHLLEDGKVKIFSRNLENNTEKYPDIVAVLPKSLKP 81 (219)
T ss_pred ceeecCCccccccCCccCCHHHHHHHhCCCeEEEEEeecceEEEEEEcCCCeEEEECCCCccccchhhHHHHHHHHHhcc
Confidence 4688999999999999888888888898889999999999999999986 8999999999999999999988776543
Q ss_pred ccCceeecceEEEEeCCCCcccccccHHHHHHHhhcCCCCCCCeEEEEEeeeecCCccccCCCHHHHHHHHHHhhccCCC
Q 001089 293 LVDRCILDGEMLVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKG 372 (1159)
Q Consensus 293 ~~~~~ILDGElv~~d~~~~~~~pFg~lq~i~~~~r~~~~~~~~~~~~vFDiL~lnG~~l~~~pl~eRr~~L~~~i~~~~~ 372 (1159)
...+||||||||+||..++++.||+.++...+..........+++|++|||||+||++|+++||.+|+++|++++.+.++
T Consensus 82 ~~~~~iLDGElv~~~~~~g~~~~F~~l~~r~~~~~~~~~~~~~~~~~vFDiL~l~g~~l~~~pl~eRr~~L~~~~~~~~~ 161 (219)
T cd07900 82 SVKSFILDSEIVAYDRETGKILPFQVLSTRKRKDVDANDIKVQVCVFAFDLLYLNGESLLKKPLRERRELLHSLFKEVPG 161 (219)
T ss_pred cCccEEEeeEEEEEEcCCCCCcChHHHhhhcccccccccCcccEEEEEEEEEEECCchhhcCCHHHHHHHHHHhcCCCCC
Confidence 36799999999999987777889988876432111111224789999999999999999999999999999999987776
Q ss_pred cceeeccCCCCCccccCCCCCccceecCCHHHHHHHHHHHHHcCCceEEEecCC--CCCcCCCCCCCeEEEcccc
Q 001089 373 RLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLG--SKWEPGDRSGKWLKLKPEY 445 (1159)
Q Consensus 373 ~~~i~~p~~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~ai~~g~EGlVlK~~d--s~Y~pGkRs~~WlKiKpey 445 (1159)
++.++. ...+++.+++.++|++++++|.||||+|+++ |+|.||+|+++|+|+|++|
T Consensus 162 ~~~~~~-----------------~~~~~~~~~~~~~~~~~~~~g~EGiv~K~~~~~s~Y~~g~Rs~~W~K~K~dY 219 (219)
T cd07900 162 RFQFAT-----------------SKDSEDTEEIQEFLEEAVKNNCEGLMVKTLDSDATYEPSKRSHNWLKLKKDY 219 (219)
T ss_pred eEEEEE-----------------EEecCCHHHHHHHHHHHHHcCCceEEEecCCCCCccCCCCcCCCceEeCCCC
Confidence 665431 3456789999999999999999999999999 9999999999999999998
No 17
>TIGR02776 NHEJ_ligase_prk DNA ligase D. Members of this protein family are DNA ligases involved in the repair of DNA double-stranded breaks by non-homologous end joining (NHEJ). The system of the bacterial Ku protein (TIGR02772) plus this DNA ligase is seen in about 20 % of bacterial genomes to date and at least one archaeon (Archeoglobus fulgidus). This model describes a central and a C-terminal domain. These two domains may be permuted, as in genus Mycobacterium, or divided into tandem ORFs, and therefore not be identified by this model. An additional N-terminal 3'-phosphoesterase (PE) domain present in some but not all examples of this ligase is not included in the seed alignment for this model; This alignment models only the central ATP-dependent ligase domain and the C-terminal polymerase domain. Most examples of genes for this ligase are adjacent to the gene for Ku.
Probab=100.00 E-value=9.9e-43 Score=417.80 Aligned_cols=257 Identities=25% Similarity=0.397 Sum_probs=204.7
Q ss_pred ecCCCCcCcchhhHHHHHHHhcccCceeecceEEEEeCCCCcccccccHHHHHHHhhcCCCCCCCeEEEEEeeeecCCcc
Q 001089 271 SRSFLDHSEYGHAMSKIIEQNVLVDRCILDGEMLVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTS 350 (1159)
Q Consensus 271 SR~g~d~t~~~p~l~~~l~~~~~~~~~ILDGElv~~d~~~~~~~pFg~lq~i~~~~r~~~~~~~~~~~~vFDiL~lnG~~ 350 (1159)
||||+++|..||+|.+.+. .+...+||||||||+||.. ++ .+|+.+|.+.... ...+++|++|||||+||++
T Consensus 1 SRng~d~T~~fPel~~~~~-~l~~~~~ILDGElVvld~~-G~-~~F~~Lq~~~~~~-----~~~pv~~~vFDlL~l~G~d 72 (552)
T TIGR02776 1 TRNGHDWTKRFPEIVKALA-LLKLLPAWIDGEIVVLDER-GR-ADFAALQNALSAG-----ASRPLTYYAFDLLFLSGED 72 (552)
T ss_pred CCCcCcchhhhHHHHHHHh-hCCCCCEEEEEEEEEECCC-CC-CCHHHHHHHHHhc-----ccCceEEEEEeccccCCcc
Confidence 8999999999999998864 4566899999999999974 43 5798888754321 2368999999999999999
Q ss_pred ccCCCHHHHHHHHHHhhccCCCc-ceeeccCCCCCccccCCCCCccceecCCHHHHHHHHHHHHHcCCceEEEecCCCCC
Q 001089 351 VIHQSLKERHELLQKVVKPSKGR-LETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKW 429 (1159)
Q Consensus 351 l~~~pl~eRr~~L~~~i~~~~~~-~~i~~p~~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~ai~~g~EGlVlK~~ds~Y 429 (1159)
|+++||.+||++|++++.+..+. +.+. .. ..++..++|++++++|+||||+|+++|+|
T Consensus 73 L~~~Pl~eRr~~L~~ll~~~~~~~i~~~-----------------~~----~~~~~~~~~~~a~~~G~EGIV~K~~dS~Y 131 (552)
T TIGR02776 73 LRDLPLEERKKRLKQLLKAQDEPAIRYS-----------------DH----FESDGDALLESACRLGLEGVVSKRLDSPY 131 (552)
T ss_pred cccCCHHHHHHHHHHHhhhcCCCcEEEe-----------------ee----ecccHHHHHHHHHHCCCceEEEeCCCCCC
Confidence 99999999999999999765322 2211 01 12344599999999999999999999999
Q ss_pred cCCCCCCCeEEEcccccccCCcccEEEEEEEeCCCCCCCccceEEEEEecCCCCCCCCceEEEEEEecCCCCHHHHHHHH
Q 001089 430 EPGDRSGKWLKLKPEYIRAGSDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVV 509 (1159)
Q Consensus 430 ~pGkRs~~WlKiKpey~~~g~~lDlvVIG~~~G~Grr~g~~gsfllg~~d~~~~~~~~~~f~~v~kVgtG~sdeel~~l~ 509 (1159)
.+| |+.+|+|+|+.| +.|++|+| |++.+ |.+|+||||+++. ++|+++|+||||||++++++|.
T Consensus 132 ~~G-Rs~~WlKlK~~~-----~~e~vI~G-y~~~~---r~~gslLlg~~d~-------g~l~~vgkVgsGfsd~~~~~L~ 194 (552)
T TIGR02776 132 RSG-RSKDWLKLKCRR-----RQEFVITG-YTPPN---RRFGALLVGVYEG-------GQLVYAGKVGTGFGADTLKTLL 194 (552)
T ss_pred CCC-CCcchhcccccc-----cceEEEEE-EecCC---CceeeEEEEEecC-------CeEEEEEEEcCCCCHHHHHHHH
Confidence 999 999999999986 66765555 55444 2399999999962 2799999999999999999999
Q ss_pred HhhcccccccCCCCCCCCCcccccCCCCCCCcEEEeCCcceEEEEEEeeeeeeecccccCCceeeCceeeeeecCCCccC
Q 001089 510 TKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDKPWHD 589 (1159)
Q Consensus 510 ~~l~~~~~~~~~~~~~pP~~~~~~~~~~~~Pdvwi~~P~~s~Vlev~a~i~~i~s~~~~~g~tLRFPR~~riR~DK~~~d 589 (1159)
+.|+++++.. +| |.. .......|++||+ |. +|+||++.. ++.|++||||||+++|.||+|+|
T Consensus 195 ~~l~~~~~~~------~P-f~~-~~~~~~~~~~Wv~-P~--lV~EV~~~e-------~T~~g~LR~Prf~~~R~DK~~~e 256 (552)
T TIGR02776 195 ARLKALGAKA------SP-FSG-PAGAKTRGVHWVR-PS--LVAEVEYAG-------ITRDGILREASFKGLREDKPAEE 256 (552)
T ss_pred HHHHhhcccC------CC-ccC-CccccCCCcEEEc-cC--EEEEEEeee-------ccCCCeeEccEEEEEeCCCCHHH
Confidence 9999987641 12 211 1112346799999 75 899998632 34588999999999999999999
Q ss_pred cC
Q 001089 590 CL 591 (1159)
Q Consensus 590 ~~ 591 (1159)
|+
T Consensus 257 ~t 258 (552)
T TIGR02776 257 VT 258 (552)
T ss_pred cc
Confidence 96
No 18
>cd07903 Adenylation_DNA_ligase_IV Adenylation domain of DNA Ligase IV. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. There are three classes of ATP-dependent DNA ligase in eukaryotic cells (I, III and IV). DNA ligase IV is required for DNA non-homologous end joining pathways, including recombination of the V(D)J immunoglobulin gene segments in cells of the mammalian immune system. DNA ligase IV is stabilized by forming a complex with XRCC4, a nuclear phosphoprotein, which is phosphorylated by DNA-dependent protein kinase. DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more di
Probab=100.00 E-value=1.4e-41 Score=370.75 Aligned_cols=214 Identities=43% Similarity=0.708 Sum_probs=181.6
Q ss_pred ccCcccCCccccccccccCChHHHHHhcCCCcEEEEEecceEEEEEEEeCCEEEEEecCCCCcCcchhhHHHHH------
Q 001089 215 RQDIEVGKAVRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKII------ 288 (1159)
Q Consensus 215 ~~~i~~g~p~~PMLA~~~~~~~~~~~k~~~~~~~vE~K~DGeR~qih~~g~~v~~fSR~g~d~t~~~p~l~~~l------ 288 (1159)
..++++|.||+||||+++.....++..+.+.+|++|+||||+|||+|++++.+++|||+|+++|..+|.+....
T Consensus 3 ~~~~~~~~p~~PmLa~~~~~~~~~~~~~~~~~~~~E~K~DG~R~~i~~~~~~v~l~SR~g~~~t~~~p~~~~~~~~~~~l 82 (225)
T cd07903 3 DLSIELFSPFRPMLAERLNIGYVEIKLLKGKPFYIETKLDGERIQLHKDGNEFKYFSRNGNDYTYLYGASLTPGSLTPYI 82 (225)
T ss_pred CceeecCCcCccccCCCCCCHHHHHHhhcCCeEEEEEeeCceEEEEEecCCEEEEEeCCCccccccccccccccccchhh
Confidence 35689999999999999987666556777889999999999999999999999999999999999888776532
Q ss_pred H--HhcccCceeecceEEEEeCCCCcccccccHHHHHHHhhcCCCCCCCeEEEEEeeeecCCccccCCCHHHHHHHHHHh
Q 001089 289 E--QNVLVDRCILDGEMLVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKV 366 (1159)
Q Consensus 289 ~--~~~~~~~~ILDGElv~~d~~~~~~~pFg~lq~i~~~~r~~~~~~~~~~~~vFDiL~lnG~~l~~~pl~eRr~~L~~~ 366 (1159)
. ......+||||||||+||..++.+.+|+.++....... ......+++|+|||||++||.+++++||.+|+++|.++
T Consensus 83 ~~~~~~~~~~~iLDGElv~~~~~~~~~~~f~~l~~~~~~~~-~~~~~~~~~~~vFDiL~~~g~~l~~~pl~eR~~~L~~~ 161 (225)
T cd07903 83 HLAFNPKVKSCILDGEMVVWDKETKRFLPFGTLKDVAKLRE-VEDSDLQPCFVVFDILYLNGKSLTNLPLHERKKLLEKI 161 (225)
T ss_pred hhhccccCcEEEeceEEEEEEcCcCeeccchHHHHHHhhcc-cccCCccEEEEEEEEEEECCeecccCcHHHHHHHHHHh
Confidence 1 11235789999999999987778899998876543211 01234679999999999999999999999999999999
Q ss_pred hccCCCcceeeccCCCCCccccCCCCCccceecCCHHHHHHHHHHHHHcCCceEEEecCCCCCcCCCCCCCeEEEccccc
Q 001089 367 VKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYI 446 (1159)
Q Consensus 367 i~~~~~~~~i~~p~~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~ai~~g~EGlVlK~~ds~Y~pGkRs~~WlKiKpey~ 446 (1159)
+.+.++++.++. ...+++.+++.++|++++++|+||||+|+++|+|++|+|+.+|+|+||+|+
T Consensus 162 ~~~~~~~i~~~~-----------------~~~~~~~~~~~~~~~~~~~~g~EGlv~K~~~s~Y~~g~Rs~~wlK~K~~Y~ 224 (225)
T cd07903 162 ITPIPGRLEVVK-----------------RTEASTKEEIEEALNEAIDNREEGIVVKDLDSKYKPGKRGGGWIKIKPEYL 224 (225)
T ss_pred cCCCCCeEEEEE-----------------EEeCCCHHHHHHHHHHHHHcCCceEEEecCCCCCccCCcCCCcEEechhhc
Confidence 988776665431 344678899999999999999999999999999999999999999999996
No 19
>cd07902 Adenylation_DNA_ligase_III Adenylation domain of DNA Ligase III. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three-step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. There are three classes of ATP-dependent DNA ligases in eukaryotic cells (I, III and IV). DNA ligase III is not found in lower eukaryotes and is present both in the nucleus and mitochondria. It has several isoforms; two splice forms, III-alpha and III-beta, differ in their carboxy-terminal sequences. DNA ligase III-beta is believed to play a role in homologous recombination during meiotic prophase. DNA ligase III-alpha interacts with X-ray Cross Complementing factor 1 (XRCC1) and functions in single nuc
Probab=100.00 E-value=6.6e-41 Score=361.80 Aligned_cols=206 Identities=30% Similarity=0.480 Sum_probs=174.5
Q ss_pred cCcccCCccccccccccCChHHHHHhcCCCcEEEEEecceEEEEEEEeCCEEEEEecCCCCcCc-chhhHHHHHHHhcc-
Q 001089 216 QDIEVGKAVRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSE-YGHAMSKIIEQNVL- 293 (1159)
Q Consensus 216 ~~i~~g~p~~PMLA~~~~~~~~~~~k~~~~~~~vE~K~DGeR~qih~~g~~v~~fSR~g~d~t~-~~p~l~~~l~~~~~- 293 (1159)
.+|++|.||+||||++...++++++++. ..|++|+||||+|||+|++++.+++|||||+++|. .+|++.+.+.+.+.
T Consensus 6 ~~~~~~~p~~PmLA~~~~~~~~~i~~~~-~~~~~E~K~DG~R~~i~~~~~~v~l~SR~g~~~t~~~~~~~~~~~~~~~~~ 84 (213)
T cd07902 6 VRASLMTPVKPMLAEACKSVEDAMKKCP-NGMYAEIKYDGERVQVHKQGDNFKFFSRSLKPVLPHKVAHFKDYIPKAFPH 84 (213)
T ss_pred EEeEcCCcccCccCCcCCCHHHHHHhcC-CceEEEeccCCEEEEEEEcCCEEEEEcCCCcccccchhHHHHHHHHHhccc
Confidence 4588999999999999888776666652 46999999999999999999999999999999995 57777776655554
Q ss_pred cCceeecceEEEEeCCCCcccccccHHHHHHHhhcCCCCCCCeEEEEEeeeecCCccccCCCHHHHHHHHHHhhccCCCc
Q 001089 294 VDRCILDGEMLVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGR 373 (1159)
Q Consensus 294 ~~~~ILDGElv~~d~~~~~~~pFg~lq~i~~~~r~~~~~~~~~~~~vFDiL~lnG~~l~~~pl~eRr~~L~~~i~~~~~~ 373 (1159)
..+||||||||+||..++++++|+.++...+. .....+++|++||||++||.+++++||.+|+++|++++.+.+++
T Consensus 85 ~~~~iLDGEiv~~d~~~g~~~~F~~l~~~~~~----~~~~~~v~~~vFDiL~l~g~~l~~~pl~eR~~~L~~~~~~~~~~ 160 (213)
T cd07902 85 GHSMILDSEVLLVDTKTGKPLPFGTLGIHKKS----AFKDANVCLFVFDCLYYNGESLMDKPLRERRKILEDNMVEIPNR 160 (213)
T ss_pred ccceeeeeEEEEEECCCCcccccchhhhhhcc----ccccCceEEEEEEEeeeCCcchhcCcHHHHHHHHHHhccCCCCe
Confidence 67899999999999877888899887643221 11335799999999999999999999999999999999877655
Q ss_pred ceeeccCCCCCccccCCCCCccceecCCHHHHHHHHHHHHHcCCceEEEecCCCCCcCCCCCCCeEEEcccc
Q 001089 374 LETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEY 445 (1159)
Q Consensus 374 ~~i~~p~~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~ai~~g~EGlVlK~~ds~Y~pGkRs~~WlKiKpey 445 (1159)
+.+. ....+.+.+++.++|++++++|.||||+|+++|+|.+|+| +|+|+|+||
T Consensus 161 ~~~~-----------------~~~~~~~~~~l~~~~~~~~~~g~EGvV~K~~~s~Y~~G~r--~W~K~K~dY 213 (213)
T cd07902 161 IMLS-----------------EMKFVKKADDLSAMIARVIKEGLEGLVLKDLKSVYEPGKR--HWLKVKKDY 213 (213)
T ss_pred EEEE-----------------EEEEcCCHHHHHHHHHHHHHCCCCeEEEeCCCCCccCCCC--CceEeCCCC
Confidence 4332 1234678899999999999999999999999999999988 699999998
No 20
>cd07901 Adenylation_DNA_ligase_Arch_LigB Adenylation domain of archaeal and bacterial LigB-like DNA ligases. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. Bacterial DNA ligases are divided into two broad classes: NAD-dependent and ATP-dependent. All bacterial species have a NAD-dependent DNA ligase (LigA). Some bacterial genomes contain multiple genes for DNA ligases that are predicted to use ATP as their cofactor, including Mycobacterium tuberculosis LigB, LigC, and LigD. This group is composed of archaeal DNA ligases and bacterial proteins similar to Mycobacterium tuberculosis LigB. Members of this group contain adeny
Probab=100.00 E-value=1.4e-40 Score=358.08 Aligned_cols=204 Identities=32% Similarity=0.564 Sum_probs=172.6
Q ss_pred cCCccccccccccCChHHHHHhcCCCcEEEEEecceEEEEEEEeCCEEEEEecCCCCcCcchhhHHHHHHHhcccCceee
Q 001089 220 VGKAVRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCIL 299 (1159)
Q Consensus 220 ~g~p~~PMLA~~~~~~~~~~~k~~~~~~~vE~K~DGeR~qih~~g~~v~~fSR~g~d~t~~~p~l~~~l~~~~~~~~~IL 299 (1159)
||.||+||||+....+++++++. +.+|++|+||||+|||+|++++.+++|||+|+++|..+|++...+.......+|||
T Consensus 1 ~~~p~~PmLA~~~~~~~~~~~~~-~~~~~~E~K~DG~R~~~~~~~~~v~~~SR~~~~~t~~~pel~~~~~~~~~~~~~iL 79 (207)
T cd07901 1 VGRPVRPMLAQRAPSVEEALIKE-GGEAAVEYKYDGIRVQIHKDGDEVRIFSRRLEDITNALPEVVEAVRELVKAEDAIL 79 (207)
T ss_pred CCCCCccccCCCCCCHHHHHHhc-CCcEEEEEeEcceeEEEEEeCCEEEEEeCCCccccchhhHHHHHHHhcCCCCCEEE
Confidence 68999999999998887766665 56899999999999999999999999999999999999999887754432378999
Q ss_pred cceEEEEeCCCCcccccccHHHHHHHhhcCC---CCCCCeEEEEEeeeecCCccccCCCHHHHHHHHHHhhccCCCccee
Q 001089 300 DGEMLVWDTSLNRFAEFGSNQEIAKAARDGL---SSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLET 376 (1159)
Q Consensus 300 DGElv~~d~~~~~~~pFg~lq~i~~~~r~~~---~~~~~~~~~vFDiL~lnG~~l~~~pl~eRr~~L~~~i~~~~~~~~i 376 (1159)
|||||+||+ .+++.+|+.++....+.. .. ....+++|+||||||+||++++++||.+|+++|.+++.+. +++.+
T Consensus 80 DGElv~~~~-~g~~~~F~~l~~r~~~~~-~~~~~~~~~~~~~~vFDil~~~g~~l~~~pl~eR~~~L~~~~~~~-~~i~~ 156 (207)
T cd07901 80 DGEAVAYDP-DGRPLPFQETLRRFRRKY-DVEEAAEEIPLTLFLFDILYLDGEDLLDLPLSERRKILEEIVPET-EAILL 156 (207)
T ss_pred eCEEEEECC-CCCccCHHHHHHHhcccc-chhhhhccCcEEEEEEEEEEECCcchhcCCHHHHHHHHHHhcCcC-CcEEE
Confidence 999999997 577789988876543211 11 1135799999999999999999999999999999999875 34433
Q ss_pred eccCCCCCccccCCCCCccceecCCHHHHHHHHHHHHHcCCceEEEecCCCCCcCCCCCCCeEEEccc
Q 001089 377 LVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPE 444 (1159)
Q Consensus 377 ~~p~~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~ai~~g~EGlVlK~~ds~Y~pGkRs~~WlKiKpe 444 (1159)
+ ....+.+.+++.++|++++++|.||||+|+++|+|.+|+|+.+|+|+|||
T Consensus 157 ~-----------------~~~~~~~~~~~~~~~~~~~~~g~EGiv~K~~~s~Y~~g~Rs~~wlK~K~~ 207 (207)
T cd07901 157 A-----------------PRIVTDDPEEAEEFFEEALEAGHEGVMVKSLDSPYQAGRRGKNWLKVKPD 207 (207)
T ss_pred E-----------------EEEecCCHHHHHHHHHHHHHcCCceEEEeCCCCCcCCCCCCCCeEEecCC
Confidence 2 13346788999999999999999999999999999999999999999996
No 21
>PRK09125 DNA ligase; Provisional
Probab=100.00 E-value=3.2e-40 Score=369.12 Aligned_cols=254 Identities=23% Similarity=0.357 Sum_probs=194.5
Q ss_pred cccccccccCChHHHHHhcCCCcEEEEEecceEEEEEEEeCCEEEEEecCCCCcCcchhhHHHHHHHhcccCceeecceE
Q 001089 224 VRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDGEM 303 (1159)
Q Consensus 224 ~~PMLA~~~~~~~~~~~k~~~~~~~vE~K~DGeR~qih~~g~~v~~fSR~g~d~t~~~p~l~~~l~~~~~~~~~ILDGEl 303 (1159)
+.||||...... +.+.+|++|+||||+|||+ + .+++|||+|++++. |.. +...+ .++|||||+
T Consensus 28 ~~~~LA~~~~~~------~~~~~~~~E~K~DG~R~~~--~--~v~l~SR~g~~it~--p~~---~~~~~--~~~vLDGEl 90 (282)
T PRK09125 28 PDLQLATVYDKG------QDISGYLVSEKLDGVRAYW--D--GKQLLTRQGNPIAA--PAW---FTAGF--PPFPLDGEL 90 (282)
T ss_pred CCceechhcccC------CChhhEEEEeeeeeEeEEE--C--CeEEEcCCCCcCCC--chh---HHhcC--CCccEeEEE
Confidence 689999887431 2346899999999999975 2 48999999999997 432 22223 389999999
Q ss_pred EEEeCCCCcccccccHHHHHHHhhcCCCCCCCeEEEEEeeeecCCccccCCCHHHHHHHHHHhhccCC-CcceeeccCCC
Q 001089 304 LVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSK-GRLETLVPDHG 382 (1159)
Q Consensus 304 v~~d~~~~~~~pFg~lq~i~~~~r~~~~~~~~~~~~vFDiL~lnG~~l~~~pl~eRr~~L~~~i~~~~-~~~~i~~p~~~ 382 (1159)
|+++ .+|+.++...++.........+++|++||||++|| ||.+|+++|++++.+.+ +.+.++
T Consensus 91 v~~~------~~F~~l~~r~~~k~~~~~~~~~v~~~vFDll~~~g------pl~eRr~~L~~li~~~~~~~i~~~----- 153 (282)
T PRK09125 91 WAGR------GQFEAISSIVRDKTPDDAAWRKVRFMVFDLPDAPG------DFEERLAVLKKLLAKLPSPYIKII----- 153 (282)
T ss_pred EeCC------CCHHHHHHHHccCCcchhhhcccEEEEEEcCCCCC------CHHHHHHHHHHHHhhCCCCcEEEE-----
Confidence 9864 36877766543321111112579999999999986 99999999999997653 233221
Q ss_pred CCccccCCCCCccceecCCHHHHHHHHHHHHHcCCceEEEecCCCCCcCCCCCCCeEEEcccccccCCcccEEEEEEEeC
Q 001089 383 LNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLIIGGYYG 462 (1159)
Q Consensus 383 ~~~~v~~~~~~~~~~~~~~~~ei~~~~~~ai~~g~EGlVlK~~ds~Y~pGkRs~~WlKiKpey~~~g~~lDlvVIG~~~G 462 (1159)
..+.+++.++++++|++++++|+||||+|+++|+|++| |+.+|+|+|++| +.|++|||+++|
T Consensus 154 ------------~~~~~~~~~~~~~~~~~~~~~G~EGiV~K~~ds~Y~~G-Rs~~wlKiK~~~-----~~d~vIvG~~~g 215 (282)
T PRK09125 154 ------------EQIRVRSEAALQQFLDQIVAAGGEGLMLHRPDAPYEAG-RSDDLLKLKPYY-----DAEATVIGHLPG 215 (282)
T ss_pred ------------eEEEcCCHHHHHHHHHHHHHcCCCEEEEeCCCCCCcCC-CCCCcEEEEecC-----CCcEEEEEEEcC
Confidence 13456789999999999999999999999999999999 899999999987 789999999999
Q ss_pred CCCCCCccceEEEEEecCCCCCCCCceEEEEEEecCCCCHHHHHHHHHhhcccccccCCCCCCCCCcccccCCCCCCCcE
Q 001089 463 SGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDV 542 (1159)
Q Consensus 463 ~Grr~g~~gsfllg~~d~~~~~~~~~~f~~v~kVgtG~sdeel~~l~~~l~~~~~~~~~~~~~pP~~~~~~~~~~~~Pdv 542 (1159)
.|+++|.+|+|+|+..++. .| +||||||+++++. +|.+
T Consensus 216 ~Gk~~g~~gsllv~~~~g~-------~~----~VgsG~t~~~r~~------------------~~~~------------- 253 (282)
T PRK09125 216 KGKFAGMLGALLVETPDGR-------EF----KIGSGFSDAEREN------------------PPKI------------- 253 (282)
T ss_pred CCcccCceeeEEEEeCCCC-------EE----EeCCCCCHHHhcC------------------CCCC-------------
Confidence 9999999999999964321 33 7899999998641 1211
Q ss_pred EEeCCcceEEEEEEeeeeeeecccccCCceeeCceeeeeecCC
Q 001089 543 WIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDK 585 (1159)
Q Consensus 543 wi~~P~~s~Vlev~a~i~~i~s~~~~~g~tLRFPR~~riR~DK 585 (1159)
..+++|++ ..++....||||+|++||+|.
T Consensus 254 -------g~~~~V~y-------~e~t~~g~lR~P~f~g~R~D~ 282 (282)
T PRK09125 254 -------GSIITYKY-------RGLTKNGLPRFASFLRVREDE 282 (282)
T ss_pred -------CCEEEEEe-------cccCCCCcccCCEEEEEecCC
Confidence 12556654 224466789999999999983
No 22
>PHA00454 ATP-dependent DNA ligase
Probab=100.00 E-value=3.3e-39 Score=367.55 Aligned_cols=284 Identities=21% Similarity=0.310 Sum_probs=210.3
Q ss_pred ccccccccCC--hHHHHHhcCCCcEEEEEecceEEEEEEEeCC-EEEEEecCCCCcCcchhhHH-------HHHHH--hc
Q 001089 225 RPQLAMRIGD--AHAAWRKLHGKEVVIECKFDGDRIQIHKNGS-EIHYFSRSFLDHSEYGHAMS-------KIIEQ--NV 292 (1159)
Q Consensus 225 ~PMLA~~~~~--~~~~~~k~~~~~~~vE~K~DGeR~qih~~g~-~v~~fSR~g~d~t~~~p~l~-------~~l~~--~~ 292 (1159)
+|++|...+. +.+++.+++ .|++|+||||+|||+|++++ .+++|||||+++++.. ++. +.+.. +.
T Consensus 7 ~~~~~~~~~~~~i~~~~~~~g--~~~~E~K~DG~R~~~~~~~~~~v~l~SR~g~~~p~l~-~~~~~~~~~~~~~~~~~~~ 83 (315)
T PHA00454 7 NPFRAVDFNESAIEKALEKAG--YLIADVKYDGVRGNIVVDNTADHGWLSREGKTIPALE-HLNGFDRRWAKLLNDDRCI 83 (315)
T ss_pred CccccccCCHHHHHHHHHhCC--cEEEEEccceEEEEEEEcCCCeEEEEeCCCCcccchh-hhhhhhhhhhhhhhhhhhc
Confidence 6889988776 777888873 89999999999999999876 4999999999876531 111 11110 12
Q ss_pred ccCceeecceEEEEeCCCCcccccccHHHHHHHhhc--CCCCCCCeEEEEEeeeecC----Cccc---cCCCHHHHHHHH
Q 001089 293 LVDRCILDGEMLVWDTSLNRFAEFGSNQEIAKAARD--GLSSDRQLCYFAFDVLYVG----DTSV---IHQSLKERHELL 363 (1159)
Q Consensus 293 ~~~~~ILDGElv~~d~~~~~~~pFg~lq~i~~~~r~--~~~~~~~~~~~vFDiL~ln----G~~l---~~~pl~eRr~~L 363 (1159)
.++++|||||+|+.+ .+|..++.++++... ......+++|+|||||++| |+++ ..+||.+|+++|
T Consensus 84 l~~~~vLDGElv~~~------~~f~~~~~~l~~k~~~~~~~~~~~v~~~vFDll~l~~~~~g~~l~~l~~~pl~~Rr~~L 157 (315)
T PHA00454 84 FPDGFMLDGELMVKG------VDFNTGSGLLRRKWKVLFELHLKKLHVVVYDVTPLDVLESGEDYDVMSLLMYEHVRAMV 157 (315)
T ss_pred CCCCeEEEEEEEecC------CCHHHHHHHhccCccchhhhccCceEEEEEEeeEeccccCCccccccccccHHHHHHHH
Confidence 246899999999964 467665555432210 1122468999999999999 6665 789999999999
Q ss_pred HHhhccCCC-cceeeccCCCCCccccCCCCCccceecCCHHHHHHHHHHHHHcCCceEEEecCCCCCcCCCCCCCeEEEc
Q 001089 364 QKVVKPSKG-RLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLK 442 (1159)
Q Consensus 364 ~~~i~~~~~-~~~i~~p~~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~ai~~g~EGlVlK~~ds~Y~pGkRs~~WlKiK 442 (1159)
+.++...+. .+.++ ..+.+.+.+++.++|+++++.|.||||+|+++|+|++|+|+. |+|+|
T Consensus 158 ~~l~~~~~~~~~~~~-----------------~~~~~~~~~~~~~~~~~~~~~g~EGiv~K~~ds~Y~~Grr~~-~~K~K 219 (315)
T PHA00454 158 PLLMEYFPEIDWFLS-----------------ESYEVYDMESLQELYEKKRAEGHEGLVVKDPSLIYRRGKKSG-WWKMK 219 (315)
T ss_pred HHHHhhCCCcceEee-----------------ceEEcCCHHHHHHHHHHHHhCCCceEEEeCCCCCCCCCCccC-cEEEc
Confidence 999865442 12111 134567899999999999999999999999999999998875 88999
Q ss_pred ccccccCCcccEEEEEEEeCCCC--CCCccceEEEEEecCCCCCCCCceEEEEEEecCCCCHHHHHHHHHhhcccccccC
Q 001089 443 PEYIRAGSDLDVLIIGGYYGSGR--RGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYE 520 (1159)
Q Consensus 443 pey~~~g~~lDlvVIG~~~G~Gr--r~g~~gsfllg~~d~~~~~~~~~~f~~v~kVgtG~sdeel~~l~~~l~~~~~~~~ 520 (1159)
+.+ ++|++|+|+++|.|. ..|.+++|+|++. ++ .+.. |||||++++++|...+.++-..
T Consensus 220 ~~~-----~~d~vIvG~~~g~g~~~~~g~~~~~~~~~~--~g------~l~~----gtGfs~~~~~~l~~~l~~~~~~-- 280 (315)
T PHA00454 220 PEC-----EADGTIVGVVWGTPGLANEGKVIGFRVLLE--DG------RVVN----ATGISRALMEEFTANVKEHGED-- 280 (315)
T ss_pred ccC-----ceeEEEEEEEECCCCccCCceEEEEEEEeC--CC------cEEE----ccCCCHHHHHHHHHHHHhhccC--
Confidence 985 899999999999864 3467777777652 22 4432 8999999999999998875221
Q ss_pred CCCCCCCCcccccCCCCCCCcEEEeCCcceEEEEEEeeeeeeecccccCCceeeCceeeeeec
Q 001089 521 YPKRAPPSFYQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRY 583 (1159)
Q Consensus 521 ~~~~~pP~~~~~~~~~~~~Pdvwi~~P~~s~Vlev~a~i~~i~s~~~~~g~tLRFPR~~riR~ 583 (1159)
...+ |....|+||++. .++.+..||||+|+++|+
T Consensus 281 --~~~~--------------------p~~~~v~eV~y~-------e~T~~g~lR~P~F~g~Rd 314 (315)
T PHA00454 281 --YEAM--------------------PYNGRACQVSYM-------ERTPDGSLRHPSFDRFRD 314 (315)
T ss_pred --cccc--------------------CCCCeEEEEEEE-------EcCCCCcccCceeeeeec
Confidence 0001 222257788652 255678999999999995
No 23
>cd07897 Adenylation_DNA_ligase_Bac1 Adenylation domain of putative bacterial ATP-dependent DNA ligases. Bacterial DNA ligases are divided into two broad classes: NAD-dependent and ATP-dependent. All bacterial species have a NAD-dependent DNA ligase (LigA). Some bacterial genomes contain multiple genes for DNA ligases that are predicted to use ATP as their cofactor, including Mycobacterium tuberculosis LigB, LigC, and LigD. This group is composed of predicted bacterial ATP-dependent DNA ligases. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three-step reaction mechanism. The adenylation and C-terminal oligonucleotide/oligosaccharide binding (OB)-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family, including this group. The adenylation domain binds ATP and contains many of the active site residues.
Probab=100.00 E-value=3.4e-39 Score=347.00 Aligned_cols=201 Identities=24% Similarity=0.306 Sum_probs=167.4
Q ss_pred CccccccccccCChHHHHHhcCCCcEEEEEecceEEEEEEEeCCEEEEEecCCCCcCcchhhHHHHHHHhcccCceeecc
Q 001089 222 KAVRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDG 301 (1159)
Q Consensus 222 ~p~~PMLA~~~~~~~~~~~k~~~~~~~vE~K~DGeR~qih~~g~~v~~fSR~g~d~t~~~p~l~~~l~~~~~~~~~ILDG 301 (1159)
.|++||||+++....+.+ .....|++|+||||+|||+|+.++.+++|||||+++|..+|++...+. .+ +.+|||||
T Consensus 3 ~~~~pmLA~~~~~~~~~~--~~~~~~~~E~K~DG~R~~~~~~~~~v~l~SR~g~~~t~~~p~l~~~~~-~l-~~~~iLDG 78 (207)
T cd07897 3 RPYPFMLAHPLEDDPEDL--GDPSDWQAEWKWDGIRGQLIRRGGEVFLWSRGEELITGSFPELLAAAE-AL-PDGTVLDG 78 (207)
T ss_pred CCCCceeCCcCCCchhhh--cCcccEEEEEeEceEEEEEEEcCCEEEEEeCCCCcccccchHHHHHHH-hC-CCCeEEEe
Confidence 689999999998776543 345689999999999999999999999999999999999999887653 33 46899999
Q ss_pred eEEEEeCCCCcccccccHHHHHHHhhcC--CCCCCCeEEEEEeeeecCCccccCCCHHHHHHHHHHhhccCC-Ccceeec
Q 001089 302 EMLVWDTSLNRFAEFGSNQEIAKAARDG--LSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSK-GRLETLV 378 (1159)
Q Consensus 302 Elv~~d~~~~~~~pFg~lq~i~~~~r~~--~~~~~~~~~~vFDiL~lnG~~l~~~pl~eRr~~L~~~i~~~~-~~~~i~~ 378 (1159)
|||+||. +...+|+.++....+.... .....+++|++|||||+||.++++.||.+|+++|++++.+.+ +++.+.
T Consensus 79 Elv~~~~--~~~~~F~~l~~r~~~~~~~~~~~~~~~~~~~vFDil~l~g~~l~~~pl~eRr~~L~~l~~~~~~~~i~~~- 155 (207)
T cd07897 79 ELLVWRD--GRPLPFNDLQQRLGRKTVGKKLLAEAPAAFRAYDLLELNGEDLRALPLRERRARLEALLARLPPPRLDLS- 155 (207)
T ss_pred EEEEecC--CCccCHHHHHHHhcccccchhhHhhCCeEEEEEeeeeECceEhhhCCHHHHHHHHHHhhhhcCCCceeec-
Confidence 9999986 4568998887654322110 112457999999999999999999999999999999997763 333321
Q ss_pred cCCCCCccccCCCCCccceecCCHHHHHHHHHHHHHcCCceEEEecCCCCCcCCCCCCCeEEEcccc
Q 001089 379 PDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEY 445 (1159)
Q Consensus 379 p~~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~ai~~g~EGlVlK~~ds~Y~pGkRs~~WlKiKpey 445 (1159)
....+++.+++.++|++++++|+||||+|+++|+|.+|+|+++|+|+|++-
T Consensus 156 ----------------~~~~~~~~~~~~~~~~~~~~~g~EGiv~K~~~s~Y~~Grr~~~W~K~K~d~ 206 (207)
T cd07897 156 ----------------PLIAFADWEELAALRAQSRERGAEGLMLKRRDSPYLVGRKKGDWWKWKIDP 206 (207)
T ss_pred ----------------ceEecCCHHHHHHHHHHHHHcCCeEEEEeCCCCCcCCCCcCCCeeEeCCCC
Confidence 134567899999999999999999999999999999999999999999973
No 24
>cd08039 Adenylation_DNA_ligase_Fungal Adenylation domain of uncharacterized fungal ATP-dependent DNA ligase-like proteins. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. This group is composed of uncharacterized fungal proteins with similarity to ATP-dependent DNA ligases. ATP dependent DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains including a DNA-binding domain, an adenylation (nucleotidyltransferase (NTase)) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The adenylation domain binds ATP and contains many of the active-site res
Probab=100.00 E-value=7.5e-39 Score=348.87 Aligned_cols=200 Identities=26% Similarity=0.408 Sum_probs=163.0
Q ss_pred ChHHHHHhcCCCcEEEEEecceEEEEEEEe----CCEEEEEecCCCCcCcchhhHHHHHHHhc--------ccCceeecc
Q 001089 234 DAHAAWRKLHGKEVVIECKFDGDRIQIHKN----GSEIHYFSRSFLDHSEYGHAMSKIIEQNV--------LVDRCILDG 301 (1159)
Q Consensus 234 ~~~~~~~k~~~~~~~vE~K~DGeR~qih~~----g~~v~~fSR~g~d~t~~~p~l~~~l~~~~--------~~~~~ILDG 301 (1159)
++..+++.+.+..|++|+||||+|||+|+. ++.|++|||||+++|..+|++.+.+...+ .+++|||||
T Consensus 11 ~~~~~~~~~~~~~~~~E~K~DG~R~qih~~~~~~~~~v~lfSR~~~d~T~~~pel~~~~~~~~~~~~~~~~~~~~~ILDG 90 (235)
T cd08039 11 SIKHCCKMIGSRRMWVETKYDGEYCQIHIDLSKDSSPIRIFSKSGKDSTADRAGVHSIIRKALRIGKPGCKFSKNCILEG 90 (235)
T ss_pred CHHHHHHHhCCCcEEEEEeecceEEEEEEecccCCCEEEEEeCCCCcccccchhHHHHHHHHhhccccccCCCccEEEEe
Confidence 456678888889999999999999999997 88999999999999999999887664432 257899999
Q ss_pred eEEEEeCCCCcccccccHHHHHHHhhc--------CCCCCCCeEEEEEeeeecCCccccCCCHHHHHHHHHHhhccCCCc
Q 001089 302 EMLVWDTSLNRFAEFGSNQEIAKAARD--------GLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGR 373 (1159)
Q Consensus 302 Elv~~d~~~~~~~pFg~lq~i~~~~r~--------~~~~~~~~~~~vFDiL~lnG~~l~~~pl~eRr~~L~~~i~~~~~~ 373 (1159)
|||+||..++++.||+.+|....+... ......++||++|||||+||++|++.||.+||++|++++.+.+++
T Consensus 91 EiVv~d~~~g~~~~F~~L~~~~~~~~~~~~~~~~~~~~~~~~v~~~vFDlL~lnG~~l~~~pl~eRr~~L~~l~~~~~~~ 170 (235)
T cd08039 91 EMVVWSDRQGKIDPFHKIRKHVERSGSFIGTDNDSPPHEYEHLMIVFFDVLLLDDESLLSKPYSERRDLLESLVHVIPGY 170 (235)
T ss_pred EEEEEECCCCccCCHHHHHhhcccccchhccccccccccccceEEEEEEEEEECChhhhcCCHHHHHHHHHHhcccCCCc
Confidence 999999877888999988765332110 011235799999999999999999999999999999999888776
Q ss_pred ceeeccCCCCCccccCCCCCccceecCCHHHHHHHHHHHHHcCCceEEEecCCCCCcCCCC-----CCCeEEEcccc
Q 001089 374 LETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDR-----SGKWLKLKPEY 445 (1159)
Q Consensus 374 ~~i~~p~~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~ai~~g~EGlVlK~~ds~Y~pGkR-----s~~WlKiKpey 445 (1159)
++++... .+. .....+.++++++|++++++|+||||+|+++|+|.||++ +..|+|+||||
T Consensus 171 ~~~~~~~-----~i~-------~~~~~~~~~l~~~~~~a~~~g~EGIv~K~~~S~Y~pgr~~~~~r~~~WlKlK~dY 235 (235)
T cd08039 171 AGLSERF-----PID-------FSRSSGYERLRQIFARAIAERWEGLVLKGDEEPYFDLFLEQGSFSGCWIKLKKDY 235 (235)
T ss_pred EEEEEEE-----eec-------ccCCCCHHHHHHHHHHHHHcCCceEEEecCCCCcccCcccccccCCCeEEeCCCC
Confidence 6543210 000 011346789999999999999999999999999999753 58999999998
No 25
>cd07898 Adenylation_DNA_ligase Adenylation domain of ATP-dependent DNA Ligases. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. Some organisms express a variety of different ligases which appear to be targeted to specific functions. ATP-dependent DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains including a DNA-binding domain, an adenylation (nucleotidyltransferase (NTase)) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The adenylation domain binds ATP and contains many of the active-site residues. The adenylation and C-terminal OB-f
Probab=100.00 E-value=9.2e-39 Score=342.57 Aligned_cols=199 Identities=33% Similarity=0.510 Sum_probs=167.7
Q ss_pred cccccccccCChHHHHHhcCCCcEEEEEecceEEEEEEEeCCEEEEEecCCCCcCcchhhHHHHHHHhcccCceeecceE
Q 001089 224 VRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDGEM 303 (1159)
Q Consensus 224 ~~PMLA~~~~~~~~~~~k~~~~~~~vE~K~DGeR~qih~~g~~v~~fSR~g~d~t~~~p~l~~~l~~~~~~~~~ILDGEl 303 (1159)
|+||||++++.+.++ .++.+.+|++|+||||+|||+|+++++|++|||+|+++|..+|.+...+.. .+.+|||||||
T Consensus 1 i~pmLa~~~~~~~~~-~~~~~~~~~~E~K~DG~R~~~~~~~~~v~l~SR~g~~~t~~~p~i~~~~~~--~~~~~vLDGEl 77 (201)
T cd07898 1 IKPMLAHPEESAEAA-KAKKPAAAWVEDKYDGIRAQVHKDGGRVEIFSRSLEDITDQFPELAAAAKA--LPHEFILDGEI 77 (201)
T ss_pred CCCeecCcCCChHHH-HhhCCCeEEEEEeeceEEEEEEEeCCEEEEEcCCChhchhhhhhHHHHHHh--CCCCEEEEEEE
Confidence 689999999887654 556788999999999999999999999999999999999988988876542 35799999999
Q ss_pred EEEeCCCCcccccccHHHHHHHhhcC--CCCCCCeEEEEEeeeecCCccccCCCHHHHHHHHHHhhccCCCcceeeccCC
Q 001089 304 LVWDTSLNRFAEFGSNQEIAKAARDG--LSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDH 381 (1159)
Q Consensus 304 v~~d~~~~~~~pFg~lq~i~~~~r~~--~~~~~~~~~~vFDiL~lnG~~l~~~pl~eRr~~L~~~i~~~~~~~~i~~p~~ 381 (1159)
|+||... ..||..++....+.... ...+.+++|+|||||++||++++++||.||+++|++++.+.++++.++
T Consensus 78 v~~~~~~--~~~f~~~~~~~~~~~~~~~~~~~~~~~~~vFDil~~~g~~l~~~p~~eR~~~L~~~~~~~~~~i~~~---- 151 (201)
T cd07898 78 LAWDDNR--GLPFSELFKRLGRKFRDKFLDEDVPVVLMAFDLLYLNGESLLDRPLRERRQLLEELFVEIPGRIRIA---- 151 (201)
T ss_pred EEEeCCC--CCcHHHHHHHhcccccchhhhccCcEEEEEEeEEeECCcchhhCCHHHHHHHHHHhhcCCCCcEEEe----
Confidence 9998643 36898777654332111 123467999999999999999999999999999999998876665442
Q ss_pred CCCccccCCCCCccceecCCHHHHHHHHHHHHHcCCceEEEecCCCCCcCCCCCCCeEEEccc
Q 001089 382 GLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPE 444 (1159)
Q Consensus 382 ~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~ai~~g~EGlVlK~~ds~Y~pGkRs~~WlKiKpe 444 (1159)
....+++.+++.++|++++++|.||||+|+++|+|.+|+|+.+|+|+|||
T Consensus 152 -------------~~~~~~~~~~~~~~~~~~~~~g~EGim~K~~~s~Y~~g~Rs~~wlK~K~~ 201 (201)
T cd07898 152 -------------PALPVESAEELEAAFARARARGNEGLMLKDPDSPYEPGRRGLAWLKLKKE 201 (201)
T ss_pred -------------eeEEcCCHHHHHHHHHHHHHcCCceEEEeCCCCCcCCCCcCCCcEEeCCC
Confidence 12346788899999999999999999999999999999999999999996
No 26
>PF01068 DNA_ligase_A_M: ATP dependent DNA ligase domain; InterPro: IPR012310 DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA fragments by catalysing the formation of an internucleotide ester bond between phosphate and deoxyribose. It is active during DNA replication, DNA repair and DNA recombination. There are two forms of DNA ligase, one requires ATP (6.5.1.1 from EC), the other NAD (6.5.1.2 from EC), the latter being restricted to eubacteria. Eukaryotic, archaebacterial, viral and some eubacterial DNA ligases are ATP-dependent. The first step in the ligation reaction is the formation of a covalent enzyme-AMP complex. The co-factor ATP is cleaved to pyrophosphate and AMP, with the AMP being covalently joined to a highly conserved lysine residue in the active site of the ligase. The activated AMP residue is then transferred to the 5'phosphate of the nick, before the nick is sealed by phosphodiester-bond formation and AMP elimination [,]. Vertebrate cells encode three well-characterised DNA ligases (DNA ligases I, III and IV), all of which are related in structure and sequence. With the exception of the atypically small PBCV-1 viral enzyme, two regions of primary sequence are common to all members of the family. The catalytic region comprises six conserved sequence motifs (I, III, IIIa, IV, V-VI), motif I includes the lysine residue that is adenylated in the first step of the ligation reaction. The function of the second, less well-conserved region is unknown. When folded, each protein comprises of two distinct sub-domains: a large amino-terminal sub-domain ('domain 1') and a smaller carboxy-terminal sub-domain ('domain 2'). The ATP-binding site of the enzyme lies in the cleft between the two sub-domains. Domain 1 consists of two antiparallel beta sheets flanked by alpha helices, whereas domain 2 consists of a five-stranded beta barrel and a single alpha helix, which form the oligonucleotide-binding fold [, ]. This domain belongs to a more diverse superfamily, including catalytic domain of the mRNA capping enzyme (IPR001339 from INTERPRO) and NAD-dependent DNA ligase (IPR001679 from INTERPRO) []. ; GO: 0003910 DNA ligase (ATP) activity, 0005524 ATP binding, 0006281 DNA repair, 0006310 DNA recombination; PDB: 3RR5_A 1X9N_A 2CFM_A 3QWU_B 3GDE_A 2Q2U_C 2Q2T_A 1FVI_A 1P8L_A 2VUG_A ....
Probab=100.00 E-value=5e-37 Score=329.07 Aligned_cols=199 Identities=31% Similarity=0.525 Sum_probs=167.3
Q ss_pred cccccccCChHHHHHhcCCCcEEEEEecceEEEEEEEeCCEEEEEecCCCCcCcchhhHHHHHHHhccc--CceeecceE
Q 001089 226 PQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLV--DRCILDGEM 303 (1159)
Q Consensus 226 PMLA~~~~~~~~~~~k~~~~~~~vE~K~DGeR~qih~~g~~v~~fSR~g~d~t~~~p~l~~~l~~~~~~--~~~ILDGEl 303 (1159)
||||+++..++.+++++ +.+|++|+||||+|||+|+.++.+++|||+|++++..+|.+...+...+.. .+|||||||
T Consensus 1 PmLA~~~~~~~~~~~~~-~~~~~~e~K~DG~R~~i~~~~~~v~~~SR~g~~~~~~~~~l~~~l~~~~~~~~~~~vLDGEl 79 (202)
T PF01068_consen 1 PMLAQPFDSIEKALKKF-GGPWYVEPKYDGVRCQIHKDGGGVRLFSRNGKDITSQFPELAEALRELLFPDGPDFVLDGEL 79 (202)
T ss_dssp -EEEEEESSHHHHHHHT-TSCEEEEEEESSEEEEEEEETTEEEEEETTSSB-GGGHHHHHHHHHHHBCTSCTEEEEEEEE
T ss_pred CcCCccccCHHHHHHhc-CCCeEEEEeEeeEEeeeeeccccceeecccccchhhHHHHHHHHHHHHhcCCCCceEEEEEE
Confidence 99999999888889888 678999999999999999999999999999999999889988877665443 479999999
Q ss_pred EEEeCCCCcccccccHHHHHHHhhcCCC-CCCCeEEEEEeeeecCCccccCCCHHHHHHHHHHhhccCCCcceeeccCCC
Q 001089 304 LVWDTSLNRFAEFGSNQEIAKAARDGLS-SDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHG 382 (1159)
Q Consensus 304 v~~d~~~~~~~pFg~lq~i~~~~r~~~~-~~~~~~~~vFDiL~lnG~~l~~~pl~eRr~~L~~~i~~~~~~~~i~~p~~~ 382 (1159)
|+||+.++.+.||+.++....+...... ...+++|+|||||++||.++++.||.+|+++|++++.+..+.+.++
T Consensus 80 v~~d~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~vFDil~l~~~~l~~~p~~eR~~~L~~~~~~~~~~i~~~----- 154 (202)
T PF01068_consen 80 VVLDPNTGSPLPFQELSGRLNRRSKKIPEQSEPLQFVVFDILYLDGKDLLDLPYEERRELLEELLEPPPPRIRIV----- 154 (202)
T ss_dssp EEBETTTSSBCCHHHHHHHHBHSSSCHHHHHSCEEEEEEEEEEETTEECTTSCHHHHHHHHHHHBG-BTSSEEEE-----
T ss_pred EEEecCCCcchhHHHHhhhhhhhcccchhccCcEEEEEEEEEEeCCeEeeeccHHHHHHHHHHhhccCCCceeEe-----
Confidence 9999988889999777665422111000 1368999999999999999999999999999999996555555432
Q ss_pred CCccccCCCCCccceecCCHHHHHHHHHHHHHcCCceEEEecCCCCCcCCCCCCCeEEEc
Q 001089 383 LNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLK 442 (1159)
Q Consensus 383 ~~~~v~~~~~~~~~~~~~~~~ei~~~~~~ai~~g~EGlVlK~~ds~Y~pGkRs~~WlKiK 442 (1159)
....+.+.++++++|++++++|+||+|+|+++|+|++|+|+.+|+|+|
T Consensus 155 ------------~~~~~~~~~~~~~~~~~~~~~g~EG~v~K~~~~~Y~~Gkrs~~w~K~K 202 (202)
T PF01068_consen 155 ------------ESYVVNSKEELEELFEEAIDQGFEGLVLKDPDSPYEPGKRSSGWLKVK 202 (202)
T ss_dssp ------------EEEEESSHHHHHHHHHHHHHTTSSEEEEEETTSSC-TTEEEEEEEEEE
T ss_pred ------------eeecCCCHHHHHHHHHHHHHcCCceEEEECCCCccCCCCcCCCcEEEC
Confidence 245678999999999999999999999999999999999999999998
No 27
>cd07905 Adenylation_DNA_ligase_LigC Adenylation domain of Mycobacterium tuberculosis LigC-like ATP-dependent DNA ligases. Bacterial DNA ligases are divided into two broad classes: NAD-dependent and ATP-dependent. All bacterial species have a NAD-dependent DNA ligase (LigA). Some bacterial genomes contain multiple genes for DNA ligases that are predicted to use ATP as their cofactor, including Mycobacterium tuberculosis LigB, LigC, and LigD. This group is composed of ATP-dependent DNA ligases similar to Mycobacterium tuberculosis LigC. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. Members of this group contain adenylation and C-terminal oligonucleotide/oligosaccharide binding (OB)-fold domains, comprising a catalytic core unit that is
Probab=100.00 E-value=5.8e-37 Score=326.68 Aligned_cols=190 Identities=27% Similarity=0.410 Sum_probs=157.3
Q ss_pred cccccccccCChHHHHHhcCCCcEEEEEecceEEEEEEEeCCEEEEEecCCCCcCcchhhHHHHHHHhcccCceeecceE
Q 001089 224 VRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDGEM 303 (1159)
Q Consensus 224 ~~PMLA~~~~~~~~~~~k~~~~~~~vE~K~DGeR~qih~~g~~v~~fSR~g~d~t~~~p~l~~~l~~~~~~~~~ILDGEl 303 (1159)
|+||||..+..+++ +.+|++|+||||+|||+|++++.+++|||||+++|..+|++.+.+... .+.+|||||||
T Consensus 1 i~PmLa~~~~~~~~------~~~~~~E~K~DG~R~~~~~~~~~v~l~SR~g~~~t~~~p~~~~~~~~~-~~~~~iLDGEl 73 (194)
T cd07905 1 VEPMLARAVDALPE------PGGWQYEPKWDGFRCLAFRDGDEVRLQSRSGKPLTRYFPELVAAARAL-LPPGCVLDGEL 73 (194)
T ss_pred CCceeCCccCCCCC------CCceEEEeeeceEEEEEEEeCCEEEEEeCCCCchhhhhHHHHHHHHhh-CCCCEEEEeEE
Confidence 58999998876532 568999999999999999999999999999999999999998876543 45789999999
Q ss_pred EEEeCCCCcccccccHHHHHHHhhcC---CCCCCCeEEEEEeeeecCCccccCCCHHHHHHHHHHhhccCCCcceeeccC
Q 001089 304 LVWDTSLNRFAEFGSNQEIAKAARDG---LSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPD 380 (1159)
Q Consensus 304 v~~d~~~~~~~pFg~lq~i~~~~r~~---~~~~~~~~~~vFDiL~lnG~~l~~~pl~eRr~~L~~~i~~~~~~~~i~~p~ 380 (1159)
|+||+. . .+|+.+|......... .....+++|++|||||+||.++++.||.+|+++|++++.+..+++.++ |
T Consensus 74 v~~~~~--~-~~F~~l~~r~~~~~~~~~~~~~~~~~~~~vFDiL~l~g~~l~~~pl~eRr~~L~~~~~~~~~~i~~~-~- 148 (194)
T cd07905 74 VVWRGG--R-LDFDALQQRIHPAASRVRRLAEETPASFVAFDLLALGGRDLRGRPLRERRAALEALLAGWGPPLHLS-P- 148 (194)
T ss_pred EEEcCC--C-CCHHHHHHHhcccccchhhhhccCCEEEEEEeeeeeCCcccccCCHHHHHHHHHHHhcccCCCeEEC-C-
Confidence 999863 2 4998887654321111 123467999999999999999999999999999999998764454432 1
Q ss_pred CCCCccccCCCCCccceecCCHHHHHHHHHHHHHcCCceEEEecCCCCCcCCCCCCCeEEEccc
Q 001089 381 HGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPE 444 (1159)
Q Consensus 381 ~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~ai~~g~EGlVlK~~ds~Y~pGkRs~~WlKiKpe 444 (1159)
...+.+++.++|++++++|+||||+|+++|+|.+|+| +|+|+|+.
T Consensus 149 -----------------~~~~~~~~~~~~~~~~~~g~EGiv~K~~~s~Y~~Gr~--~WlK~K~~ 193 (194)
T cd07905 149 -----------------ATTDRAEAREWLEEFEGAGLEGVVAKRLDGPYRPGER--AMLKVKHR 193 (194)
T ss_pred -----------------ccCCHHHHHHHHHHHHHCCCceEEEeCCCCCcCCCCC--cEEEEecc
Confidence 1346789999999999999999999999999999974 89999984
No 28
>cd07906 Adenylation_DNA_ligase_LigD_LigC Adenylation domain of Mycobacterium tuberculosis LigD and LigC-like ATP-dependent DNA ligases. Bacterial DNA ligases are divided into two broad classes: NAD-dependent and ATP-dependent. All bacterial species have a NAD-dependent DNA ligase (LigA). Some bacterial genomes contain multiple genes for DNA ligases that are predicted to use ATP as their cofactor, including Mycobacterium tuberculosis LigB, LigC, and LigD. This group is composed of ATP-dependent DNA ligases similar to Mycobacterium tuberculosis LigC. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. Members of this group contain adenylation and C-terminal oligonucleotide/oligosaccharide binding (OB)-fold domains, comprising a catalytic cor
Probab=100.00 E-value=2.5e-36 Score=320.97 Aligned_cols=189 Identities=29% Similarity=0.456 Sum_probs=155.9
Q ss_pred cccccccccCChHHHHHhcCCCcEEEEEecceEEEEEEEeCCEEEEEecCCCCcCcchhhHHHHHHHhcccCceeecceE
Q 001089 224 VRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDGEM 303 (1159)
Q Consensus 224 ~~PMLA~~~~~~~~~~~k~~~~~~~vE~K~DGeR~qih~~g~~v~~fSR~g~d~t~~~p~l~~~l~~~~~~~~~ILDGEl 303 (1159)
++||||+++..+. .+.+|++|+||||+|||+|+.++.+++|||+|+++|..+|++...+.+ +...+|||||||
T Consensus 1 i~pmLa~~~~~~~------~~~~~~~e~K~DG~R~~i~~~~~~v~~~SR~g~~~t~~~p~l~~~~~~-~~~~~~iLDGEl 73 (190)
T cd07906 1 IEPMLATLVDEPP------DGEDWLYEIKWDGYRALARVDGGRVRLYSRNGLDWTARFPELAEALAA-LPVRDAVLDGEI 73 (190)
T ss_pred CCCeECCcCCCCC------CCCCeEEEEeEceEEEEEEEECCEEEEEcCCCCcchhhhHHHHHHHHh-cCCCCEEEEeEE
Confidence 5899999988652 356899999999999999999999999999999999988998877643 346899999999
Q ss_pred EEEeCCCCcccccccHHHHHHHhhcCCCCCCCeEEEEEeeeecCCccccCCCHHHHHHHHHHhhccCCCcceeeccCCCC
Q 001089 304 LVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGL 383 (1159)
Q Consensus 304 v~~d~~~~~~~pFg~lq~i~~~~r~~~~~~~~~~~~vFDiL~lnG~~l~~~pl~eRr~~L~~~i~~~~~~~~i~~p~~~~ 383 (1159)
|+||..+. .+|+.++....+.. ......+++|+|||||++||.+++++||.||+++|++++.+..+++.++.
T Consensus 74 v~~~~~~~--~~F~~l~~~~~~~~-~~~~~~~~~~~vFDil~~~~~~~~~~p~~eR~~~L~~~~~~~~~~i~~~~----- 145 (190)
T cd07906 74 VVLDEGGR--PDFQALQNRLRLRR-RLARTVPVVYYAFDLLYLDGEDLRGLPLLERKELLEELLPAGSPRLRVSE----- 145 (190)
T ss_pred EEECCCCC--CCHHHHHHhhcccc-hhcccCceEEEEEeeeeeCCcchhhCCHHHHHHHHHHHhccCCCcEEECc-----
Confidence 99997532 58877665433211 12244689999999999999999999999999999999987755554321
Q ss_pred CccccCCCCCccceecCCHHHHHHHHHHHHHcCCceEEEecCCCCCcCCCCCCCeEEEcc
Q 001089 384 NSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKP 443 (1159)
Q Consensus 384 ~~~v~~~~~~~~~~~~~~~~ei~~~~~~ai~~g~EGlVlK~~ds~Y~pGkRs~~WlKiKp 443 (1159)
... .+.+++|++++++|.||||+|+++|+|++|+|+.+|+|+|+
T Consensus 146 ------------~~~----~~~~~~~~~~~~~g~EGiv~K~~~s~Y~~g~rs~~wlK~K~ 189 (190)
T cd07906 146 ------------HFE----GGGAALFAAACELGLEGIVAKRADSPYRSGRRSRDWLKIKC 189 (190)
T ss_pred ------------eEc----CCHHHHHHHHHHcCCcEEEEecCCCCcCCCCCCCccEEEec
Confidence 111 12378999999999999999999999999999999999996
No 29
>cd07967 OBF_DNA_ligase_III The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase III is a DNA-binding module that is part 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 proph
Probab=99.97 E-value=7.9e-32 Score=270.03 Aligned_cols=137 Identities=26% Similarity=0.522 Sum_probs=118.2
Q ss_pred CCcccEEEEEEEeCCCCCCCccceEEEEEecCCCCCCCCceEEEEEEecCCCCHHHHHHHHHhhcccccccCCCCCCCCC
Q 001089 449 GSDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPS 528 (1159)
Q Consensus 449 g~~lDlvVIG~~~G~Grr~g~~gsfllg~~d~~~~~~~~~~f~~v~kVgtG~sdeel~~l~~~l~~~~~~~~~~~~~pP~ 528 (1159)
++++||||||||+|.|+++|.+|+||||++++++ +.|++||+||||||++++++|.++|+++++.. +...||.
T Consensus 2 ~dtlDlVViG~~~g~G~r~~~~gslLlg~~d~~~-----~~l~~vgkVGTGfs~~~l~~l~~~L~~l~~~~--~~~~~p~ 74 (139)
T cd07967 2 ADTADLVVLGAYYGTGSKGGMMSVFLMGCYDPNS-----KKWCTVTKCGNGHDDATLARLQKELKMVKISK--DPSKVPS 74 (139)
T ss_pred CceEeEEEEEEEECCCCCCCccceEEEEEEeCCC-----CEEEEEeEECCCCCHHHHHHHHHHhhhhcccc--CCcCCCc
Confidence 4789999999999999999999999999998653 38999999999999999999999999999763 2334677
Q ss_pred cccccCCCCCCCcEEEeCCcceEEEEEEeeeeeeeccccc-CCceeeCceeeeeecCCCccCcCCHHH
Q 001089 529 FYQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFS-APYSLRFPRIDRVRYDKPWHDCLDVQS 595 (1159)
Q Consensus 529 ~~~~~~~~~~~Pdvwi~~P~~s~Vlev~a~i~~i~s~~~~-~g~tLRFPR~~riR~DK~~~d~~t~~e 595 (1159)
|+.+. ...+||+||.+|++|+|+||+++.. ..|+.|. +|+|||||||++||+||+|+||+|++|
T Consensus 75 ~~~~~--~~~~Pdv~~~~P~~s~V~EV~~aei-t~S~~~~a~G~tLRFPr~~~iR~DK~~~d~~t~~~ 139 (139)
T cd07967 75 WLKCN--KSLVPDFIVKDPKKAPVWEITGAEF-SKSEAHTADGISIRFPRVTRIRDDKDWKTATSLPE 139 (139)
T ss_pred eEeec--CCCCCCEEEeCCCccEEEEEEeeeE-EecCcccccCEEEEccEEEEEeCCCCHHHCccccC
Confidence 77653 3579999997799999999996543 3577777 699999999999999999999999875
No 30
>cd07896 Adenylation_kDNA_ligase_like Adenylation domain of kDNA ligases and similar proteins. The mitochondrial DNA of parasitic protozoans is highly unusual. It is termed the kinetoplast DNA (kDNA) and consists of circular DNA molecules (maxicircles) and several thousand smaller circular molecules (minicircles). This group is composed of kDNA ligase, Chlorella virus DNA ligase, and similar proteins. kDNA ligase and Chlorella virus DNA ligase are the smallest known ATP-dependent ligases. They are involved in DNA replication or repair. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. They have a highly modular architecture consisting of a unique arrangement of two or more discrete domains. The adenylation and the C-terminal oligonucleotide/oligosaccharide binding (OB)-fold domains comprise a catalytic core unit that is common to most me
Probab=99.97 E-value=1.3e-30 Score=273.41 Aligned_cols=173 Identities=20% Similarity=0.309 Sum_probs=136.1
Q ss_pred cccccccccCChHHHHHhcCCCcEEEEEecceEEEEEEEeCCEEEEEecCCCCcCcchhhHHHHHHHhcccCceeecceE
Q 001089 224 VRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDGEM 303 (1159)
Q Consensus 224 ~~PMLA~~~~~~~~~~~k~~~~~~~vE~K~DGeR~qih~~g~~v~~fSR~g~d~t~~~p~l~~~l~~~~~~~~~ILDGEl 303 (1159)
|+||||.++....+ +.+|++|+||||+|||+|. + ++|||+|+++|.. + .+...+ ..+||||||
T Consensus 1 ~~pmla~~~~~~~~------~~~~~~e~K~DG~R~~~~~--~--~~~SR~g~~~t~~-~----~~~~~l--~~~ilDGEl 63 (174)
T cd07896 1 PELLLAKTYDEGED------ISGYLVSEKLDGVRAYWDG--K--QLLSRSGKPIAAP-A----WFTAGL--PPFPLDGEL 63 (174)
T ss_pred CccccccccccCCC------hHHeeechhhceEEEEEec--c--EEEecCCcCCCCC-H----HHHhhC--CCCccCceE
Confidence 58999998876532 4579999999999999973 2 9999999999974 2 222333 349999999
Q ss_pred EEEeCCCCcccccccHHHHHHHhhcCCCCCCCeEEEEEeeeecCCccccCCCHHHHHHHHHHhhccCC-CcceeeccCCC
Q 001089 304 LVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSK-GRLETLVPDHG 382 (1159)
Q Consensus 304 v~~d~~~~~~~pFg~lq~i~~~~r~~~~~~~~~~~~vFDiL~lnG~~l~~~pl~eRr~~L~~~i~~~~-~~~~i~~p~~~ 382 (1159)
|+|++ ||+.++...+..........+++|++||||+ ++.||.+|+++|+.++.+.+ +.+.++
T Consensus 64 v~~~~------~f~~l~~~~~~~~~~~~~~~~~~f~vFDil~------~~~p~~eR~~~L~~~i~~~~~~~~~~~----- 126 (174)
T cd07896 64 WIGRG------QFEQTSSIVRSKKPDDEDWRKVKFMVFDLPS------AKGPFEERLERLKNLLEKIPNPHIKIV----- 126 (174)
T ss_pred EcCCC------CHHHHHHHHhcCCCChhhcccceEEEEeCCC------CCCCHHHHHHHHHHHHHhCCCCcEEEE-----
Confidence 99863 8877776554322111124689999999999 67899999999999998752 333332
Q ss_pred CCccccCCCCCccceecCCHHHHHHHHHHHHHcCCceEEEecCCCCCcCCCCCCCeEEEcc
Q 001089 383 LNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKP 443 (1159)
Q Consensus 383 ~~~~v~~~~~~~~~~~~~~~~ei~~~~~~ai~~g~EGlVlK~~ds~Y~pGkRs~~WlKiKp 443 (1159)
..+.+.+.+++.+++++++++|+||||+|+++|+|.+| |+.+|+|+||
T Consensus 127 ------------~~~~~~~~~~i~~~~~~~~~~g~EGlv~K~~ds~Y~~g-R~~~wlK~Kp 174 (174)
T cd07896 127 ------------PQIPVKSNEALDQYLDEVVAAGGEGLMLRRPDAPYETG-RSDNLLKLKP 174 (174)
T ss_pred ------------eeeeeCCHHHHHHHHHHHHhcCCCeEEEecCCCcccCC-cCCCceeeCC
Confidence 13456788999999999999999999999999999988 7899999997
No 31
>cd06846 Adenylation_DNA_ligase_like Adenylation domain of proteins similar to ATP-dependent polynucleotide ligases. ATP-dependent polynucleotide ligases catalyze the phosphodiester bond formation of nicked nucleic acid substrates using ATP as a cofactor in a three step reaction mechanism. This family includes ATP-dependent DNA and RNA ligases. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent DNA ligases have a highly modular architecture, consisting of a unique arrangement of two or more discrete domains, including a DNA-binding domain, an adenylation or nucleotidyltransferase (NTase) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The adenylation domain binds ATP and contains many active site residues. Together with the C-terminal OB-fold domain, it comprises a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The catalytic core contains six conserved seq
Probab=99.96 E-value=1.5e-28 Score=259.61 Aligned_cols=178 Identities=22% Similarity=0.316 Sum_probs=139.5
Q ss_pred ccccccccCChHHHHHhcCCCcEEEEEecceEEEEEEEeCCEEEEEecCCCCcCcchhhHHHHHHHhcccCceeecceEE
Q 001089 225 RPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDGEML 304 (1159)
Q Consensus 225 ~PMLA~~~~~~~~~~~k~~~~~~~vE~K~DGeR~qih~~g~~v~~fSR~g~d~t~~~p~l~~~l~~~~~~~~~ILDGElv 304 (1159)
.||||........ ..+.+.+|++|+||||+|||+|+.++.+++|||+|+++|..++.+..... .....++|||||||
T Consensus 1 ~~~~~~~~~~~~~--~~~~~~~~~~e~K~DG~R~~~~~~~~~v~~~sR~g~~~~~~~~~~~~~~~-~~~~~~~ilDGElv 77 (182)
T cd06846 1 PQLLNPILEEALS--EYDEQDEYYVQEKYDGKRALIVALNGGVFAISRTGLEVPLPSILIPGREL-LTLKPGFILDGELV 77 (182)
T ss_pred CCccchhhhHHHh--hccccCcEEEEEccCceEEEEEEcCCeEEEEeCCCCEEecccccccchHH-hccCCCeeEEEEEE
Confidence 3788887765432 24557789999999999999999999999999999999987776543111 11357899999999
Q ss_pred EEeCCCCcccccccHHHHHHHhhcCCCCCCCeEEEEEeeeecCCccccCCCHHHHHHHHHHhhccCCC--cceeeccCCC
Q 001089 305 VWDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKG--RLETLVPDHG 382 (1159)
Q Consensus 305 ~~d~~~~~~~pFg~lq~i~~~~r~~~~~~~~~~~~vFDiL~lnG~~l~~~pl~eRr~~L~~~i~~~~~--~~~i~~p~~~ 382 (1159)
+|+... ...+++|++||||++||.+++++||.+|+++|++++...++ .+.+...
T Consensus 78 ~~~~~~---------------------~~~~~~~~~FDil~~~~~~~~~~p~~eR~~~L~~~v~~~~~~~~~~i~~~--- 133 (182)
T cd06846 78 VENREV---------------------ANPKPTYYAFDVVPLSGVGLRDLPYSDRFAYLKSLLKEFEGLDPVKLVPL--- 133 (182)
T ss_pred eccCCC---------------------ccceeEEEEEEEEEECCCccccCCHHHHHHHHHHHhhhhccCCceeEEEe---
Confidence 987521 12478999999999999999999999999999999987642 2222100
Q ss_pred CCccccCCCCCccceecCCHHHHHHHHHHHHHcCCceEEEecCCCCC--cCCCCCCCeEEEcc
Q 001089 383 LNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKW--EPGDRSGKWLKLKP 443 (1159)
Q Consensus 383 ~~~~v~~~~~~~~~~~~~~~~ei~~~~~~ai~~g~EGlVlK~~ds~Y--~pGkRs~~WlKiKp 443 (1159)
..... ..+++.+++++++++|.||||+|+++|+| .+| |+..|+|+||
T Consensus 134 ------------~~~~~-~~~~~~~~~~~~~~~g~EGvi~K~~~s~Y~~~~g-r~~~wlK~Kp 182 (182)
T cd06846 134 ------------ENAPS-YDETLDDLLEKLKKKGKEGLVFKHPDAPYKGRPG-SSGNQLKLKP 182 (182)
T ss_pred ------------ecccc-cchHHHHHHHHhhhcCCceEEEEcCCCCccccCC-CCCceEeecC
Confidence 01111 23348999999999999999999999999 888 8999999998
No 32
>PF04675 DNA_ligase_A_N: DNA ligase N terminus; InterPro: IPR012308 DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA fragments by catalysing the formation of an internucleotide ester bond between phosphate and deoxyribose. It is active during DNA replication, DNA repair and DNA recombination. There are two forms of DNA ligase, one requires ATP (6.5.1.1 from EC), the other NAD (6.5.1.2 from EC), the latter being restricted to eubacteria. Eukaryotic, archaebacterial, viral and some eubacterial DNA ligases are ATP-dependent. The first step in the ligation reaction is the formation of a covalent enzyme-AMP complex. The co-factor ATP is cleaved to pyrophosphate and AMP, with the AMP being covalently joined to a highly conserved lysine residue in the active site of the ligase. The activated AMP residue is then transferred to the 5'phosphate of the nick, before the nick is sealed by phosphodiester-bond formation and AMP elimination [,]. Vertebrate cells encode three well-characterised DNA ligases (DNA ligases I, III and IV), all of which are related in structure and sequence. With the exception of the atypically small PBCV-1 viral enzyme, two regions of primary sequence are common to all members of the family. The catalytic region comprises six conserved sequence motifs (I, III, IIIa, IV, V-VI), motif I includes the lysine residue that is adenylated in the first step of the ligation reaction. The function of the second, less well-conserved region is unknown. When folded, each protein comprises of two distinct sub-domains: a large amino-terminal sub-domain ('domain 1') and a smaller carboxy-terminal sub-domain ('domain 2'). The ATP-binding site of the enzyme lies in the cleft between the two sub-domains. Domain 1 consists of two antiparallel beta sheets flanked by alpha helices, whereas domain 2 consists of a five-stranded beta barrel and a single alpha helix, which form the oligonucleotide-binding fold [, ]. This region is found in many but not all ATP-dependent DNA ligase enzymes (6.5.1.1 from EC). It is thought to be involved in DNA binding and in catalysis. In human DNA ligase I (P18858 from SWISSPROT), and in Saccharomyces cerevisiae (Baker's yeast) (P04819 from SWISSPROT), this region was necessary for catalysis, and separated from the amino terminus by targeting elements. In Vaccinia virus (P16272 from SWISSPROT) this region was not essential for catalysis, but deletion decreases the affinity for nicked DNA and decreased the rate of strand joining at a step subsequent to enzyme-adenylate formation []. ; GO: 0003677 DNA binding, 0003910 DNA ligase (ATP) activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 2CFM_A 3RR5_A 2HIX_A 2HIV_A 3L2P_A 1X9N_A 4EQ5_A 3GDE_A.
Probab=99.96 E-value=4.5e-29 Score=262.43 Aligned_cols=169 Identities=36% Similarity=0.656 Sum_probs=136.8
Q ss_pred CcHHHHHHHHHHHHhhCChHHHHHHHHHHHhhcCCC---chHHHHHHHhCCCCCCCccccCCCHHHHHHHHHHHhCCCcC
Q 001089 7 TEVIVLVSLFNWIQKTKPAAKKRSKFRKFLDTYCDS---VDYFSALRLILPSLDRERGSYGLKESVLANCLIDALGMSKD 83 (1159)
Q Consensus 7 ~~F~~l~~lle~i~~~~~~~~K~~~l~~~l~~~~~~---~d~~p~lrLllP~~d~~r~~ygike~~L~k~~~~~lgl~~~ 83 (1159)
|+|+.||++|++|++++++.+|+++|++||..+... .++|+++|+++|+.| +| +|||+++.|++++++++|++++
T Consensus 1 m~F~~l~~l~~~l~~~~~~~~k~~~l~~~~~~~~~~~~~~~~~~~~~~l~P~~d-~r-~~~i~~~~L~k~~~~~~~~~~~ 78 (177)
T PF04675_consen 1 MPFSDLCELFEKLESTSSRLEKIAILSNFFRSWREEDLGPDLYLLLRLLFPEYD-GR-EYGIGEKLLAKAIAEALGLPEK 78 (177)
T ss_dssp GBHHHHHHHHHHHHT---HHHHHHHHHHHHHTSHCCGHHCHHHHHHTHSSTTTC-S----S--HHHHHHHHHHHHTS-HH
T ss_pred CcHHHHHHHHHHHHhccCHHHHHHHHHHHHHHcccchhhhHHHHHhcccccchh-hh-HhccchhHHHHHHHHHHcCCHH
Confidence 799999999999999999999999999999999653 689999999999999 55 9999999999999999999998
Q ss_pred hHHHHHHhhhhcCCCCCCCCCHHHHHHHHhhhccCC--CCCCCCHHHHHHHHHHHHhhh---hHHHHHHHHHHHHHhCCH
Q 001089 84 SADAVRLINWRKGGAAPNAGNFPMVAAEVLQRRQGM--ISGGLTIKELNDLLDRLASSE---NRAEKISVLSTLIKKTNA 158 (1159)
Q Consensus 84 s~~~~~L~~wk~~~~~~~~GD~~~~a~~vl~~r~~~--~~~~LTi~eVn~~Ld~LA~~~---~~~~k~~il~~ll~~~s~ 158 (1159)
+.++ .|+ ..||||.+|+++++++... .+.+|||.+||+.|++||..+ ++..|..+|..|+.+|+|
T Consensus 79 ~~~~----~~~------~~GD~g~~~~~~~~~~~~~~~~~~~lTi~~V~~~L~~la~~~g~~s~~~k~~~l~~ll~~~s~ 148 (177)
T PF04675_consen 79 SIDE----SYK------KVGDLGEVAEEVLQKRKSETSKPSPLTISEVNETLDELAAASGKGSQDEKIDILKELLRRCSP 148 (177)
T ss_dssp HHHH----HHH------HHS-HHHHHHHHHHHHTTTS--SS--BHHHHHHHHHHHHH--STTHHHHHHHHHHHHHTTS-H
T ss_pred HHHH----HHH------hcCcHHHHHHHHHhhccccccCCCCCCHHHHHHHHHHHHHhhCccchHHHHHHHHHHHHhCCH
Confidence 7765 453 3799999999999887743 358999999999999999987 478889999999999999
Q ss_pred HHHHHHHHHHHhhhccCCcccccccccCc
Q 001089 159 QEMKWIIMIILKDLKLGISEKSIFHEFHP 187 (1159)
Q Consensus 159 ~E~k~l~RiIlkdLriGi~e~til~~~hp 187 (1159)
.|++||+|||+|+||||+++++|+.+|||
T Consensus 149 ~E~k~i~Riil~~lriG~~~~~il~ala~ 177 (177)
T PF04675_consen 149 EEAKWIVRIILKDLRIGVSEKTILDALAP 177 (177)
T ss_dssp HHHHHHHHHHTT--SSS--HHHHHHHHHH
T ss_pred HHHHHHHHHHhCCCeeCccHHHHHHHhCc
Confidence 99999999999999999999999999997
No 33
>cd07968 OBF_DNA_ligase_IV The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase IV is a DNA-binding module that is part 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 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 pro
Probab=99.95 E-value=1.4e-27 Score=241.10 Aligned_cols=139 Identities=53% Similarity=1.053 Sum_probs=114.4
Q ss_pred CCcccEEEEEEEeCCCCCCCccceEEEEEecCCCC-CCCCceEEEEEEecCCCCHHHHHHHHHhhcccccccCCCCCCCC
Q 001089 449 GSDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAP-DTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPP 527 (1159)
Q Consensus 449 g~~lDlvVIG~~~G~Grr~g~~gsfllg~~d~~~~-~~~~~~f~~v~kVgtG~sdeel~~l~~~l~~~~~~~~~~~~~pP 527 (1159)
++++||||||||+|.|+++|.+|+||||+++.++. ...+.+|++||+||||||++++++|.++|+++|.. ++...||
T Consensus 1 ~~~lDlvViG~~~g~g~~~~~~~slllG~~~~~~~~~~~~~~l~~vgkVgtGfs~~~~~~L~~~l~~~~~~--~~~~~~P 78 (140)
T cd07968 1 GEDLDLLIIGGYYGEGRRGGKVSSFLCGVAEDDDPESDKPSVFYSFCKVGSGFSDEELDEIRRKLKPHWKP--FDKKAPP 78 (140)
T ss_pred CCcEeEEEEccEeCCCCcCCccccEEEEEEcCCCCCCCCCCEEEEEEEEccCCCHHHHHHHHHHhcCcEEE--cCcCCCC
Confidence 47899999999999999999999999999975431 11234899999999999999999999999999876 3333355
Q ss_pred CcccccCCCCCCCcEEEeCCcceEEEEEEeeeeeeecccccCCceeeCceeeeeecCCCccCcCCH
Q 001089 528 SFYQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDKPWHDCLDV 593 (1159)
Q Consensus 528 ~~~~~~~~~~~~Pdvwi~~P~~s~Vlev~a~i~~i~s~~~~~g~tLRFPR~~riR~DK~~~d~~t~ 593 (1159)
.+ .......+|++||+ |..|+|+||++... ..+..|.+|++||||||+++|+||+|+||+|+
T Consensus 79 ~~--~~~~~~~~~~~Wv~-P~~slV~EV~~~e~-t~s~~~~~g~~LR~Pr~~~~R~DK~~~e~~t~ 140 (140)
T cd07968 79 SS--LLKFGKEKPDVWIE-PKDSVVLEVKAAEI-VPSDSYKTGYTLRFPRCEKIRYDKDWHDCLTL 140 (140)
T ss_pred cc--cccccccCCcEEEe-cCCCEEEEEEeeeE-eecCcccCCcEEEcceEeEEECCCCHHHccCC
Confidence 43 11234568999998 88899999997533 36788899999999999999999999999984
No 34
>cd07969 OBF_DNA_ligase_I The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase I is a DNA-binding module that is part 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). This group is composed of eukaryotic DNA ligase I, Sulfolobus solfataricus DNA ligase and similar proteins. DNA ligase I is required for the ligation of Okazaki fragments during lagging-strand DNA synthesis and for base excision repair (BER). ATP dependent DNA ligases have a highly modular architecture consist
Probab=99.94 E-value=2.5e-26 Score=232.44 Aligned_cols=134 Identities=37% Similarity=0.585 Sum_probs=114.4
Q ss_pred CCcccEEEEEEEeCCCCCCCccceEEEEEecCCCCCCCCceEEEEEEecCCCCHHHHHHHHHhhcccccccCCCCCCCCC
Q 001089 449 GSDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPS 528 (1159)
Q Consensus 449 g~~lDlvVIG~~~G~Grr~g~~gsfllg~~d~~~~~~~~~~f~~v~kVgtG~sdeel~~l~~~l~~~~~~~~~~~~~pP~ 528 (1159)
++++||||||+++|+|++.|.+|+||||++++++ ++|.+||+||||||++++++|.++|.++++.. ||.
T Consensus 1 ~~t~D~vViG~~~g~g~~~~~~~slllG~~~~~~-----~~l~~vgkvgtGft~~~~~~L~~~l~~~~~~~------~p~ 69 (144)
T cd07969 1 GDTLDLVPIGAYYGKGKRTGVYGAFLLACYDPET-----EEFQTVCKIGTGFSDEFLEELYESLKEHVIPK------KPY 69 (144)
T ss_pred CCceeEEEEEEEECCCCCCCCcceEEEEEEeCCC-----CEEEEEeEEccCCCHHHHHHHHHHhhhhcccc------CCc
Confidence 4789999999999999998999999999997653 38999999999999999999999999998751 232
Q ss_pred cccccCCCCCCCcEEEeCCcceEEEEEEeeeeeeecccccC---------CceeeCceeeeeecCCCccCcCCHHHHHHH
Q 001089 529 FYQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSA---------PYSLRFPRIDRVRYDKPWHDCLDVQSFVEL 599 (1159)
Q Consensus 529 ~~~~~~~~~~~Pdvwi~~P~~s~Vlev~a~i~~i~s~~~~~---------g~tLRFPR~~riR~DK~~~d~~t~~el~~l 599 (1159)
+.. ...+|++||+ |. +|+||+++.. ..|+.|++ |++||||||+++|+||+|+||+++++|.+|
T Consensus 70 ~~~----~~~~~~vWv~-P~--lV~EV~~~e~-t~s~~~~~~~~~~~~~~g~~LRfPr~~~~R~Dk~~~~~~~~~~l~~l 141 (144)
T cd07969 70 RVD----SSLEPDVWFE-PK--EVWEVKAADL-TLSPVHTAAIGLVDEEKGISLRFPRFIRVRDDKKPEDATTSEQIAEM 141 (144)
T ss_pred ccc----ccCCCcEEEe-ee--EEEEEEEeEe-ecCcceeccccccccCCceEEEeeEEEEeeCCCChHHCCCHHHHHHH
Confidence 211 1258999999 74 8999997543 35778876 889999999999999999999999999999
Q ss_pred HH
Q 001089 600 VH 601 (1159)
Q Consensus 600 ~~ 601 (1159)
++
T Consensus 142 ~~ 143 (144)
T cd07969 142 YK 143 (144)
T ss_pred Hh
Confidence 85
No 35
>cd07972 OBF_DNA_ligase_Arch_LigB The Oligonucleotide/oligosaccharide binding (OB)-fold domain of archaeal and bacterial ATP-dependent DNA ligases is a DNA-binding module that is part 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 Pyrococcus furiosus DN
Probab=99.92 E-value=5.5e-25 Score=217.08 Aligned_cols=121 Identities=31% Similarity=0.575 Sum_probs=106.4
Q ss_pred CcccEEEEEEEeCCCCCCCccceEEEEEecCCCCCCCCceEEEEEEecCCCCHHHHHHHHHhhcccccccCCCCCCCCCc
Q 001089 450 SDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSF 529 (1159)
Q Consensus 450 ~~lDlvVIG~~~G~Grr~g~~gsfllg~~d~~~~~~~~~~f~~v~kVgtG~sdeel~~l~~~l~~~~~~~~~~~~~pP~~ 529 (1159)
+++|+||+|+++|.|+++|.+|+||||+|++++ +.|++||+||||||++++++|.++|+++++.
T Consensus 1 ~t~d~vi~G~~~~~g~~~~~~~slllg~~d~~~-----g~l~~vg~vgtG~~~~~~~~l~~~l~~~~~~----------- 64 (122)
T cd07972 1 ETLDLVVIGAEWGEGRRAGLLGSYTLAVRDEET-----GELVPVGKVATGLTDEELEELTERLRELIIE----------- 64 (122)
T ss_pred CceeEEEEeeEeCCCCcCCCcccEEEEEEcCCC-----CeEEEEEEEccCCCHHHHHHHHHHhhhhhcc-----------
Confidence 479999999999999999999999999997652 3899999999999999999999999887653
Q ss_pred ccccCCCCCCCcEEEeCCcceEEEEEEeeeeeeecccccCCceeeCceeeeeecCCCccCcCCHHHHH
Q 001089 530 YQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDKPWHDCLDVQSFV 597 (1159)
Q Consensus 530 ~~~~~~~~~~Pdvwi~~P~~s~Vlev~a~i~~i~s~~~~~g~tLRFPR~~riR~DK~~~d~~t~~el~ 597 (1159)
..+|++||+ |. +|+||++.. ...|+.|++|++||||||+++|+||+|+||+|++||.
T Consensus 65 -------~~~~~~wv~-P~--lV~eV~~~e-~t~s~~~~~g~~LR~Prf~~~R~Dk~~~~~~t~~~~~ 121 (122)
T cd07972 65 -------KFGPVVSVK-PE--LVFEVAFEE-IQRSPRYKSGYALRFPRIVRIRDDKDPDEADTLERVE 121 (122)
T ss_pred -------ccCCcEEEe-ce--EEEEEEeeE-EEecCccccCceEEccEEeEEeCCCChHHCcCHHHHh
Confidence 125789998 75 899999643 3468889999999999999999999999999999985
No 36
>KOG4437 consensus ATP-dependent DNA ligase III [Replication, recombination and repair]
Probab=99.92 E-value=2e-24 Score=232.23 Aligned_cols=318 Identities=24% Similarity=0.344 Sum_probs=247.4
Q ss_pred CcHHHHHHHHHHHHhhCChHHHHHHHHHHHhhcCCCchHHHHHHHhCCCCCCCccccCCCHHHHHHHHHHHhCCCcChHH
Q 001089 7 TEVIVLVSLFNWIQKTKPAAKKRSKFRKFLDTYCDSVDYFSALRLILPSLDRERGSYGLKESVLANCLIDALGMSKDSAD 86 (1159)
Q Consensus 7 ~~F~~l~~lle~i~~~~~~~~K~~~l~~~l~~~~~~~d~~p~lrLllP~~d~~r~~ygike~~L~k~~~~~lgl~~~s~~ 86 (1159)
-+|.+|..+|.-|+..+....|.+.|..+|.+---..|+|.+|++|+-+-|. |.|+|.++.|+++++++|.+..++.
T Consensus 155 N~F~ef~kiCS~L~~~p~~~~Kt~VI~~LL~kdNFDGDL~LWL~FLIRESD~--R~YNl~DkKLI~lfsKiLn~~~~~~- 231 (482)
T KOG4437|consen 155 NLFREFRKLCSMLADNPSYNTKTQVIQDLLRKDNFDGDLYLWLKFLIRESDK--RVYNLNDKKLIKLFSKILNCNPDDM- 231 (482)
T ss_pred hHHHHHHHHHHHHHhCcCccchhHHHHHHHhccCCCcchhhhhhhhhccccc--ccccccHHHHHHHHHHHHccChHHH-
Confidence 3578888888888888888899999999997533358999999999999986 6999999999999999999986532
Q ss_pred HHHHhhhhcCCCCCCCCCHHHHHHHHhhhccCCCCCCCCHHHHHHHHHHHHhhhhHHHHHHHHHHHHHhCCHHHHHHHHH
Q 001089 87 AVRLINWRKGGAAPNAGNFPMVAAEVLQRRQGMISGGLTIKELNDLLDRLASSENRAEKISVLSTLIKKTNAQEMKWIIM 166 (1159)
Q Consensus 87 ~~~L~~wk~~~~~~~~GD~~~~a~~vl~~r~~~~~~~LTi~eVn~~Ld~LA~~~~~~~k~~il~~ll~~~s~~E~k~l~R 166 (1159)
+..|-.. ..+.+..+...-.+......+-+||++|+++|.+|+..+..++.+..|+.+..+|++.|++.|+|
T Consensus 232 ---~~~Y~~~-----S~~~~i~i~~~~~K~~~~~K~~~siQ~~D~~L~rLSKi~~~D~~~~~L~~~A~R~~~~~L~~iIR 303 (482)
T KOG4437|consen 232 ---ARDYEQG-----SVSETIRVFFEQSKSFPPAKSLLTIQEVDEFLLRLSKLTKEDEQQQALQDIASRCTANDLKCIIR 303 (482)
T ss_pred ---HHHHHhc-----cchhhhhhhHhhccCCCCcccceeHHHHHHHHHHHhcccchHHHHHHHHHHHHhcccchHHHHHH
Confidence 2334322 23555544444444445567899999999999999999998888999999999999999999999
Q ss_pred HHHhhhccCCcccccccccCccHHHHhhhcCCHHHHHHHHhhhhccc-------cccC--cccCCccccccccccCChHH
Q 001089 167 IILKDLKLGISEKSIFHEFHPDAEDLFNVTCDLKLVCEKLKDRNQRH-------KRQD--IEVGKAVRPQLAMRIGDAHA 237 (1159)
Q Consensus 167 iIlkdLriGi~e~til~~~hpda~~~~~~~~dL~~V~~~L~~~~~~~-------~~~~--i~~g~p~~PMLA~~~~~~~~ 237 (1159)
+|-++|++..+.+.||.++||.|+++|.. +.|..|.+......+.. .... -....|+.|||+...++++-
T Consensus 304 LIr~~L~~~s~A~~iL~~~~P~A~E~F~S-~~L~~ViEr~~~N~~~~~~~~~~~~~~s~~s~~~s~~Q~~~~~~~~~VE~ 382 (482)
T KOG4437|consen 304 LIKHDLKMNSGAKHVLDALDPNAYEAFKS-RNLQDVVERVLHNAQEVEKEPGQRRALSVQASLMTPVQPMLAEACKSVEY 382 (482)
T ss_pred HHHHHhccCCChhHHHhccCCCcHHHHHh-cCHHHHHHHHHHhHHHHhhCccccccccchhhhcCCcChhhhhhhhhHHH
Confidence 99999999999999999999999999964 45777777654321100 1111 22457899999999888876
Q ss_pred HHHhcCCCcEEEEEecceEEEEEEEeCCEEEEEecCCCCcCcchhhHHHHHHHhc-ccCceeecceEEEEeCCCCccccc
Q 001089 238 AWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNV-LVDRCILDGEMLVWDTSLNRFAEF 316 (1159)
Q Consensus 238 ~~~k~~~~~~~vE~K~DGeR~qih~~g~~v~~fSR~g~d~t~~~p~l~~~l~~~~-~~~~~ILDGElv~~d~~~~~~~pF 316 (1159)
+.++..| +..-|.||||+|.|+|.+|+.|.+|||--....++. +.+-+.+ ...+.|+|||....+..+++++||
T Consensus 383 s~~~~~~-~~~S~~~~D~E~~~~~~~~D~~S~~S~~~~~~s~FK----~~~P~~~~~G~~~~~~~~~~~I~~K~~~P~~~ 457 (482)
T KOG4437|consen 383 AMKKCPN-GMFSEIKYDGERVQVHKNGDHFSYFSRLPHKVAHFK----DYIPQAFPGGHSMILDSEVLLIDNKTGKPLPF 457 (482)
T ss_pred HhccCCC-CccccccCCCceeeccCCCcchhhhccChHhhhhhh----hcCchhcCCCccccccccccceecccCCCCCc
Confidence 6666654 577999999999999999999999999765544321 1111222 357899999999999999999999
Q ss_pred ccHHHHHHHhhcCCCCCCCeEEEEEeeee
Q 001089 317 GSNQEIAKAARDGLSSDRQLCYFAFDVLY 345 (1159)
Q Consensus 317 g~lq~i~~~~r~~~~~~~~~~~~vFDiL~ 345 (1159)
+++.--.++.+. +..+|..+||++|
T Consensus 458 ~~~~~~~K~~~~----~~~~~~~~~~~~~ 482 (482)
T KOG4437|consen 458 GTLGVHKKAAFQ----DANVCLFVFDCIY 482 (482)
T ss_pred hhcchhhHHHhc----CcchheeecccCC
Confidence 987655454442 4568999999875
No 37
>cd07895 Adenylation_mRNA_capping Adenylation domain of GTP-dependent mRNA capping enzymes. RNA capping enzymes transfer GMP from GTP to the 5'-diphosphate end of nascent mRNAs to form a G(5')ppp(5')RNA cap structure. The RNA cap is found only in eukarya. RNA capping is chemically analogous to the first two steps of polynucleotide ligation. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation of nicked nucleic acid substrates using the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. Structural studies reveal a shared structure for DNA ligases and capping enzymes, with a common catalytic core composed of an adenylation or nucleotidyltransferase domain and a C-terminal OB-fold domain containing conserved sequence motifs. The adenylation domain binds ATP and contains many active site residues.
Probab=99.92 E-value=3.6e-25 Score=240.02 Aligned_cols=172 Identities=22% Similarity=0.285 Sum_probs=129.0
Q ss_pred HhcCCCcEEEEEecceEEEEEEEeC-CEEEEEecCCCCcCcchhhHHHHHHHhcccCceeecceEEEEeCCCCccccccc
Q 001089 240 RKLHGKEVVIECKFDGDRIQIHKNG-SEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDGEMLVWDTSLNRFAEFGS 318 (1159)
Q Consensus 240 ~k~~~~~~~vE~K~DGeR~qih~~g-~~v~~fSR~g~d~t~~~p~l~~~l~~~~~~~~~ILDGElv~~d~~~~~~~pFg~ 318 (1159)
..+...+|++|+||||+|+|+|+.+ +.+.+|||+++.++..+|.+............+|||||||+++...
T Consensus 36 ~~~~~~~y~ve~K~DG~R~~l~~~~~~~v~l~sR~~~~~~~~~~~~~~~~~~~~~~~~~ilDGElv~~~~~~-------- 107 (215)
T cd07895 36 ELLKQNDYFVCEKSDGVRYLLLITGRGEVYLIDRKNDVFKVPGLFFPRRKNLEPHHQGTLLDGELVIDKVPG-------- 107 (215)
T ss_pred HHHhhCCeEEEEeEcCeEEEEEEecCCcEEEEeCCCCeEEeccccCCCcccccccccCeeeEEEEEEEcCCC--------
Confidence 3455678999999999999999998 9999999999998876665432111112357899999999987531
Q ss_pred HHHHHHHhhcCCCCCCCeEEEEEeeeecCCccccCCCHHHHHHHHHHhhccCCCcce----eeccCCCCCccccCCCCCc
Q 001089 319 NQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLE----TLVPDHGLNSHVRPQGEPC 394 (1159)
Q Consensus 319 lq~i~~~~r~~~~~~~~~~~~vFDiL~lnG~~l~~~pl~eRr~~L~~~i~~~~~~~~----i~~p~~~~~~~v~~~~~~~ 394 (1159)
..+++|+|||||++||+++.+.||.+|+++|++++........ ...+ ...+.|+
T Consensus 108 --------------~~~~~~~vFDiL~~~g~~l~~~pl~~R~~~L~~~i~~~~~~~~~~~~~~~~--~~~~~i~------ 165 (215)
T cd07895 108 --------------KKRPRYLIFDILAFNGQSVTEKPLSERLKYIKKEVIEPRNELLKKGPIDKA--KEPFSVR------ 165 (215)
T ss_pred --------------ceEEEEEEEEEEEECCcCccCCCHHHHHHHHHHhchhHHHHhhhcChhhcC--CCCeEEE------
Confidence 2468999999999999999999999999999999855321100 0000 0001111
Q ss_pred cceecCCHHHHHHHHHHH---HHcCCceEEEecCCCCCcCCCCCCCeEEEcc
Q 001089 395 WSLVAHNVDEVEKFFKET---IENRDEGIVLKDLGSKWEPGDRSGKWLKLKP 443 (1159)
Q Consensus 395 ~~~~~~~~~ei~~~~~~a---i~~g~EGlVlK~~ds~Y~pGkRs~~WlKiKp 443 (1159)
.......+++..+|+.+ +..|.||||+|+.+++|.+| |+..|+|+||
T Consensus 166 -~k~~~~~~~~~~~~~~~~~~~~~~~EGlIfk~~~~~Y~~G-r~~~~lKwKp 215 (215)
T cd07895 166 -LKDFFPLYKIEKLFEKIIPKLPHENDGLIFTPNDEPYVPG-TDKNLLKWKP 215 (215)
T ss_pred -ecceEeHHhHHHHHHhccccCCCCCCCEEEccCCCCccCc-cCCcceeeCC
Confidence 00122356788888888 59999999999999999999 9999999997
No 38
>cd07893 OBF_DNA_ligase The Oligonucleotide/oligosaccharide binding (OB)-fold domain is a DNA-binding module that is part of the catalytic core unit of ATP dependent DNA ligases. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP dependent 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 and C-terminal OB-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The catalytic core unit contains six conserved sequence motifs (I, III, IIIa, IV, V and V
Probab=99.91 E-value=1e-23 Score=209.88 Aligned_cols=122 Identities=42% Similarity=0.787 Sum_probs=103.5
Q ss_pred CcccEEEEEEEeCCCCCCCccceEEEEEecCCCCCCCCceEEEEEEecCCCCHHHHHHHHHhhcccccccCCCCCCCCCc
Q 001089 450 SDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSF 529 (1159)
Q Consensus 450 ~~lDlvVIG~~~G~Grr~g~~gsfllg~~d~~~~~~~~~~f~~v~kVgtG~sdeel~~l~~~l~~~~~~~~~~~~~pP~~ 529 (1159)
+++||||+|+++|.|+++|.+|+||||++++++ +.|+++|+||||||++++++|.++|.+++... .|| +
T Consensus 1 d~~D~VI~G~~~~~g~~~~~~~slLlg~~d~~~-----~~l~~vgkvgtGfs~~~~~~l~~~l~~~~~~~-----~p~-~ 69 (129)
T cd07893 1 DTLDLVIVGAYYGKGRRGGGIGAFLCAVYDPER-----DEFQTICKVGSGFTDEELEELRELLKELKTPE-----KPP-R 69 (129)
T ss_pred CcEEEEEEeeEcCCCCcCCCcceEEEEEEcCCC-----CEEEEEeEECCCCCHHHHHHHHHHhhcccccC-----CCC-c
Confidence 479999999999999999999999999997543 38999999999999999999999999988641 133 2
Q ss_pred ccccCCCCCCCcEEEeCCcceEEEEEEeeeeeeecccccC-------CceeeCceeeeeecCCCccCc
Q 001089 530 YQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSA-------PYSLRFPRIDRVRYDKPWHDC 590 (1159)
Q Consensus 530 ~~~~~~~~~~Pdvwi~~P~~s~Vlev~a~i~~i~s~~~~~-------g~tLRFPR~~riR~DK~~~d~ 590 (1159)
. ....+|++||+ | ++|+||+++.. ..|+.|++ |++||||||+++|+||+|+||
T Consensus 70 ~----~~~~~~~~wv~-P--~lV~EV~~~e~-t~s~~~~~~~~~~~~g~~LRfPr~~~~R~Dk~~~e~ 129 (129)
T cd07893 70 V----NSIEKPDFWVE-P--KVVVEVLADEI-TRSPMHTAGRGEEEEGYALRFPRFVRIRDDKGPEDA 129 (129)
T ss_pred c----cccCCCcEEEe-e--eEEEEEEeeee-eeCcccccccccCCCceEEECCEEEEEeCCCChhhC
Confidence 1 23568999999 7 59999996533 35788888 899999999999999999997
No 39
>cd07971 OBF_DNA_ligase_LigD The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase LigD is a DNA-binding module that is part 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 Mycobacterium tuberculosis LigD and similar ba
Probab=99.78 E-value=1.3e-18 Score=170.23 Aligned_cols=114 Identities=26% Similarity=0.423 Sum_probs=90.4
Q ss_pred cccEEEEEEEeCCCCCCCccceEEEEEecCCCCCCCCceEEEEEEecCCCCHHHHHHHHHhhcccccccCCCCCCCCCcc
Q 001089 451 DLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFY 530 (1159)
Q Consensus 451 ~lDlvVIG~~~G~Grr~g~~gsfllg~~d~~~~~~~~~~f~~v~kVgtG~sdeel~~l~~~l~~~~~~~~~~~~~pP~~~ 530 (1159)
+.|++|+|++.+.| +.|.+|+||||++++. .|+++|+||||||++++++|.+.|.+++.. .||...
T Consensus 2 ~~~~vI~G~~~~~g-~~~~~gslllg~~~~~-------~l~~vG~vgtG~s~~~~~~l~~~l~~~~~~------~~p~~~ 67 (115)
T cd07971 2 RQEFVIGGYTPPKG-SRGGFGSLLLGVYDGG-------RLVYVGRVGTGFSAATLRELRERLAPLERK------TSPFAD 67 (115)
T ss_pred CceEEEEEEECCCC-CCCcccEEEEEEEcCC-------EEEEeeeEcCCCCHHHHHHHHHHhhcccCC------CCCCcc
Confidence 46887777766777 7788999999999754 799999999999999999999999988753 133211
Q ss_pred cccCCCCCCCcEEEeCCcceEEEEEEeeeeeeecccccCCceeeCceeeeeecCCCccCc
Q 001089 531 QVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDKPWHDC 590 (1159)
Q Consensus 531 ~~~~~~~~~Pdvwi~~P~~s~Vlev~a~i~~i~s~~~~~g~tLRFPR~~riR~DK~~~d~ 590 (1159)
. ......|++||+ |. +|+||++.. ++.+++||||+|+++|+||+|++|
T Consensus 68 ~--~~~~~~~~~wv~-P~--lv~eV~~~~-------~t~~~~LR~P~f~~~R~Dk~~~~~ 115 (115)
T cd07971 68 P--PPADARGAVWVK-PE--LVAEVEFAE-------WTPDGRLRHPVFKGLREDKPAAEV 115 (115)
T ss_pred c--ccccCCCCEEec-CC--EEEEEEEEE-------ecCCCcEECCeeeEeeCCCCcccC
Confidence 1 113457899998 75 899998642 235679999999999999999987
No 40
>PF04679 DNA_ligase_A_C: ATP dependent DNA ligase C terminal region ; InterPro: IPR012309 DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA fragments by catalysing the formation of an internucleotide ester bond between phosphate and deoxyribose. It is active during DNA replication, DNA repair and DNA recombination. There are two forms of DNA ligase, one requires ATP (6.5.1.1 from EC), the other NAD (6.5.1.2 from EC), the latter being restricted to eubacteria. Eukaryotic, archaebacterial, viral and some eubacterial DNA ligases are ATP-dependent. The first step in the ligation reaction is the formation of a covalent enzyme-AMP complex. The co-factor ATP is cleaved to pyrophosphate and AMP, with the AMP being covalently joined to a highly conserved lysine residue in the active site of the ligase. The activated AMP residue is then transferred to the 5'phosphate of the nick, before the nick is sealed by phosphodiester-bond formation and AMP elimination [,]. Vertebrate cells encode three well-characterised DNA ligases (DNA ligases I, III and IV), all of which are related in structure and sequence. With the exception of the atypically small PBCV-1 viral enzyme, two regions of primary sequence are common to all members of the family. The catalytic region comprises six conserved sequence motifs (I, III, IIIa, IV, V-VI), motif I includes the lysine residue that is adenylated in the first step of the ligation reaction. The function of the second, less well-conserved region is unknown. When folded, each protein comprises of two distinct sub-domains: a large amino-terminal sub-domain ('domain 1') and a smaller carboxy-terminal sub-domain ('domain 2'). The ATP-binding site of the enzyme lies in the cleft between the two sub-domains. Domain 1 consists of two antiparallel beta sheets flanked by alpha helices, whereas domain 2 consists of a five-stranded beta barrel and a single alpha helix, which form the oligonucleotide-binding fold [, ]. This region is found in many but not all ATP-dependent DNA ligase enzymes (6.5.1.1 from EC). It is thought to constitute part of the catalytic core of ATP dependent DNA ligase []. ; GO: 0003910 DNA ligase (ATP) activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 3RR5_A 2CFM_A 1X9N_A 1VS0_B 3GDE_A 2HIX_A 2HIV_A 3L2P_A 4EQ5_A.
Probab=99.74 E-value=1.2e-17 Score=158.50 Aligned_cols=97 Identities=42% Similarity=0.746 Sum_probs=73.3
Q ss_pred CCCccceEEEEEecCCCCCCCCceEEEEEEecCCCCHHHHHHHHHhhcccccccCCCCCCCCCcccccCCCCCCCcEEEe
Q 001089 466 RGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDVWIE 545 (1159)
Q Consensus 466 r~g~~gsfllg~~d~~~~~~~~~~f~~v~kVgtG~sdeel~~l~~~l~~~~~~~~~~~~~pP~~~~~~~~~~~~Pdvwi~ 545 (1159)
|+|.+|+||||+++++. +.|.+||+||||||++++++|.++|.+++... ||...... ...+|++||+
T Consensus 1 R~g~~~slllg~~d~~~-----~~l~~vg~vgtG~~~~~~~~l~~~l~~~~~~~------~p~~~~~~--~~~~~~~wv~ 67 (97)
T PF04679_consen 1 RGGGIGSLLLGVYDPDS-----GRLVYVGKVGTGFSDEELRELRERLEPLWIKK------PPFDVKPP--SRERPDVWVE 67 (97)
T ss_dssp GTTSEEEEEEEEEETTT-----TEEEEEEEE-SS--HHHHHHHHHHHGGGEEEE------ETTTCCEC--CSCTTEEEE-
T ss_pred CCCccceEEEEEEcCCC-----CcEEEEEEECCCCCHHHHHHHHHHhhCccccC------CCCccccc--cCccCcEEeC
Confidence 56889999999999762 38999999999999999999999999998652 33222221 2268999998
Q ss_pred CCcceEEEEEEeeeeeeecccccCCceeeCceeeeeecCC
Q 001089 546 SPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDK 585 (1159)
Q Consensus 546 ~P~~s~Vlev~a~i~~i~s~~~~~g~tLRFPR~~riR~DK 585 (1159)
|. +|+||++...+ .+ | +||||||++||+||
T Consensus 68 -P~--~V~eV~~~e~t-~~-----G-~lR~P~~~~~R~DK 97 (97)
T PF04679_consen 68 -PE--LVVEVKFAEIT-PS-----G-SLRFPRFKRIREDK 97 (97)
T ss_dssp -ST---EEEEEESEEE-EE-----S-EEESEEEEEEETTS
T ss_pred -CC--EEEEEEEEEEc-CC-----C-eEECCEEeEEeCCC
Confidence 87 59999975432 22 7 99999999999998
No 41
>cd08040 OBF_DNA_ligase_family The Oligonucleotide/oligosaccharide binding (OB)-fold domain is a DNA-binding module that is part of the catalytic core unit of ATP dependent DNA ligases. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP dependent 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 and C-terminal OB-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The catalytic core unit contains six conserved sequence motifs (I, III, IIIa, IV,
Probab=99.73 E-value=3e-17 Score=158.81 Aligned_cols=108 Identities=22% Similarity=0.332 Sum_probs=87.3
Q ss_pred CcccEEEEEEEeCCCCCCCccceEEEEEecCCCCCCCCceEEEEEEecCCCCHHHHHHHHHhhcccccccCCCCCCCCCc
Q 001089 450 SDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSF 529 (1159)
Q Consensus 450 ~~lDlvVIG~~~G~Grr~g~~gsfllg~~d~~~~~~~~~~f~~v~kVgtG~sdeel~~l~~~l~~~~~~~~~~~~~pP~~ 529 (1159)
+++|+||+|+++|.|+++|.+|+||||+++++ .+.++|+||||||++++++|.+.|+++.... . |+.+
T Consensus 1 ~~~d~vV~G~~~~~g~~~~~~gslllg~~~~~-------~~~~vg~vgtGf~~~~~~~l~~~l~~~~~~~----~-~~~~ 68 (108)
T cd08040 1 KTAEAVIIGMRAGFGNRSDVMGSLLLGYYGED-------GLQAVFSVGTGFSADERRDLWQNLEPLVTSF----D-DHPV 68 (108)
T ss_pred CceeEEEEEeEeCCCCCCCceEEEEEEEECCC-------ceEEEEEEcCCCCHHHHHHHHHhcchhccCC----C-CCcc
Confidence 47899999999999999999999999999754 4779999999999999999999999887641 1 2211
Q ss_pred ccccCCCCCCCcEEEeCCcceEEEEEEeeeeeeecccccCCceeeCceeeeee
Q 001089 530 YQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVR 582 (1159)
Q Consensus 530 ~~~~~~~~~~Pdvwi~~P~~s~Vlev~a~i~~i~s~~~~~g~tLRFPR~~riR 582 (1159)
. .....+|++|++ |. +|+||++.. ++.+.+||||||+++|
T Consensus 69 ~---~~~~~~~~vwv~-P~--lv~eV~~~~-------~t~~~~lR~P~f~~~R 108 (108)
T cd08040 69 W---NVGKDLSFVPLY-PG--KVVEVKYFE-------MGSKDCLRFPVFIGIR 108 (108)
T ss_pred c---ccccCCCCEEee-ce--EEEEEEeEE-------eeCCCeEECCeEEEeC
Confidence 1 123457999999 74 899998642 3458999999999997
No 42
>cd07894 Adenylation_RNA_ligase Adenylation domain of RNA circularization proteins. RNA circularization proteins are capable of circularizing RNA molecules in an ATP-dependent reaction. RNA circularization may protect RNA from exonuclease activity. This model comprises the adenylation domain, the minimal catalytic unit that is common to all members of the ATP-dependent DNA ligase family, and the carboxy-terminal extension of RNA circularization protein that serves as a dimerization module. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation of nicked nucleic acid substrates using the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. The adenylation domain binds ATP and contains many active site residues.
Probab=99.63 E-value=1.8e-15 Score=173.42 Aligned_cols=162 Identities=20% Similarity=0.269 Sum_probs=118.3
Q ss_pred CcEEEEEecceEEEEEEEeCCEEEEEecCCCCc---CcchhhHHHH-HHHhcccCceeecceEEEEeCCCCcccccccHH
Q 001089 245 KEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDH---SEYGHAMSKI-IEQNVLVDRCILDGEMLVWDTSLNRFAEFGSNQ 320 (1159)
Q Consensus 245 ~~~~vE~K~DGeR~qih~~g~~v~~fSR~g~d~---t~~~p~l~~~-l~~~~~~~~~ILDGElv~~d~~~~~~~pFg~lq 320 (1159)
.+|++|+||||.|+++|+.++++..|||+|... |+.+|.+... +.. ...++|||||+++.+. ||. +
T Consensus 48 ~~~~vEEKlDG~nvri~~~~G~v~a~TR~G~i~e~~T~~~~eiv~~~~~~--~~p~~iLdGElvg~~~------p~v--~ 117 (342)
T cd07894 48 GPVAVEEKMNGYNVRIVRIGGKVLAFTRGGFICPFTTDRLRDLIDPEFFD--DHPDLVLCGEVVGPEN------PYV--P 117 (342)
T ss_pred CCEEEEEeECCcEEEEEEECCEEEEEeCCCccCccchhhHhhhchHHhhc--cCCCEEEEEEEEecCC------ccc--c
Confidence 589999999999999999999999999998644 6666766321 111 1357999999998652 221 0
Q ss_pred HHHHHhhcCCCCCCCeEEEEEeeeecCCccccCCCHHHHHHHHHHhhccCCCcceeeccCCCCCccccCCCCCccceecC
Q 001089 321 EIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAH 400 (1159)
Q Consensus 321 ~i~~~~r~~~~~~~~~~~~vFDiL~lnG~~l~~~pl~eRr~~L~~~i~~~~~~~~i~~p~~~~~~~v~~~~~~~~~~~~~ 400 (1159)
.......++.|++|||++.|+ ...+|+.+|+++|+++--+... ++ ......
T Consensus 118 -------~~~~~~~~v~F~vFDI~~~~~--~~~lp~~eR~~lLe~lg~~~v~---~~-----------------~~~~~~ 168 (342)
T cd07894 118 -------GSYPEVEDVGFFVFDIRKKNT--GRPLPVEERRELLEKYGLPTVR---LF-----------------GEFTAD 168 (342)
T ss_pred -------ccCccccccEEEEEeeEEcCC--CCCCCHHHHHHHHHhcCCCCcc---eE-----------------EEEecC
Confidence 001112478999999999885 5678999999999987322211 10 023345
Q ss_pred CHHHHHHHHHHHHHcCCceEEEecCCC-----CCcCCCCCCCeEEEcccc
Q 001089 401 NVDEVEKFFKETIENRDEGIVLKDLGS-----KWEPGDRSGKWLKLKPEY 445 (1159)
Q Consensus 401 ~~~ei~~~~~~ai~~g~EGlVlK~~ds-----~Y~pGkRs~~WlKiKpey 445 (1159)
+.+++.++|+.+.++|.||||+|++++ .|.-...+-.+|++--.|
T Consensus 169 d~~~l~~~l~~~~~~G~EGVVlK~~~~~~~~~Ky~t~~~~~~di~~~~~~ 218 (342)
T cd07894 169 EIEELKEIIRELDKEGREGVVLKDPDMRVPPLKYTTSYSNCSDIRYAFRY 218 (342)
T ss_pred CHHHHHHHHHHHHHCCCceEEEeccccccCcceeecCCCCcHHHHHHhhh
Confidence 689999999999999999999999999 677655555666666655
No 43
>cd07970 OBF_DNA_ligase_LigC The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase LigC is a DNA-binding module that is part 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 Mycobacterium tuberculosis LigC and similar ba
Probab=99.61 E-value=5.7e-15 Score=145.61 Aligned_cols=120 Identities=22% Similarity=0.261 Sum_probs=86.4
Q ss_pred CcccEEEEEEEeCCCCCCCccceEEEEEecCCCCCCCCceEEEEEEecCCCCHHHHHHHHHhhcccccccCCCCCCCCCc
Q 001089 450 SDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSF 529 (1159)
Q Consensus 450 ~~lDlvVIG~~~G~Grr~g~~gsfllg~~d~~~~~~~~~~f~~v~kVgtG~sdeel~~l~~~l~~~~~~~~~~~~~pP~~ 529 (1159)
++.|+||+|+.++. +.+|++|||+|++++ +|.++|+| ||||++++++|.+.|+++.....++ ..++.|
T Consensus 1 ~~~e~vI~G~~~~~----~~~gsLlLg~~~~~g------~l~yvG~v-tGf~~~~~~~L~~~l~~l~~~~p~~-~~~~~~ 68 (122)
T cd07970 1 RTADCVVGGVRGHK----DRPGSLLLGLYDDGG------RLRHVGRT-SPLAAAERRELAELLEPARAGHPWT-GRAPGF 68 (122)
T ss_pred CcEeEEEEEEECCC----CCccEEEEEEECCCC------CEEEEEEE-CCCCHHHHHHHHHHHHHhhcCCCCc-cccccc
Confidence 36788777766655 459999999996542 69999999 9999999999999999876431111 111212
Q ss_pred ccccCCCCCCCcEEEeCCcceEEEEEEeeeeeeecccccCCceeeCc-eeeeeecCCCccCcC
Q 001089 530 YQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFP-RIDRVRYDKPWHDCL 591 (1159)
Q Consensus 530 ~~~~~~~~~~Pdvwi~~P~~s~Vlev~a~i~~i~s~~~~~g~tLRFP-R~~riR~DK~~~d~~ 591 (1159)
..........+.+|++ |. +|+||++.. ++.+..|||| +|+++|+||++.||+
T Consensus 69 ~~~~~~~~~~~~~wv~-P~--lV~eV~~~e-------~t~~G~LRhP~~f~glR~Dk~~~~v~ 121 (122)
T cd07970 69 PSRWGTRKSLEWVPVR-PE--LVVEVSADT-------AEGGGRFRHPLRFLRWRPDKSPEDCT 121 (122)
T ss_pred ccccCcccCCCeEEee-cc--EEEEEEeeE-------EecCCceeCCceeEEEcCCCCHHHCc
Confidence 1111112345789999 75 899997632 3345599999 899999999999986
No 44
>PF00533 BRCT: BRCA1 C Terminus (BRCT) domain; InterPro: IPR001357 The BRCT domain (after the C_terminal domain of a breast cancer susceptibility protein) is found predominantly in proteins involved in cell cycle checkpoint functions responsive to DNA damage [], for example as found in the breast cancer DNA-repair protein BRCA1. The domain is an approximately 100 amino acid tandem repeat, which appears to act as a phospho-protein binding domain []. A chitin biosynthesis protein from yeast also seems to belong to this group. ; GO: 0005622 intracellular; PDB: 3L46_A 3AL3_A 3AL2_A 1WF6_A 3II6_X 2NTE_B 3FA2_A 2R1Z_A 2COK_A 2K7F_A ....
Probab=99.14 E-value=1.1e-10 Score=105.37 Aligned_cols=74 Identities=24% Similarity=0.501 Sum_probs=66.2
Q ss_pred CCCcccCeEEEEEcCCCCCChHHHHHHHHHcCCEEEecCCCCceEEEEecC--CChhhHhHhcCC-CeeecchHHHHH
Q 001089 653 ETSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADN--KGLKYEAAKRRG-DVIHYSWVLDCC 727 (1159)
Q Consensus 653 ~s~lF~G~~F~vv~~~~~~~k~eLe~lI~~~GG~iv~n~~~~~Th~Ia~~~--~~~k~~~a~~~~-~VV~p~WV~dCi 727 (1159)
.+.+|+|+.||+ ++.....+++|+++|+.|||++....+..+||+|+... .+.++..+...+ +||+++||.|||
T Consensus 2 ~~~~F~g~~f~i-~~~~~~~~~~l~~~i~~~GG~v~~~~~~~~thvI~~~~~~~~~k~~~~~~~~i~iV~~~Wi~~ci 78 (78)
T PF00533_consen 2 KPKIFEGCTFCI-SGFDSDEREELEQLIKKHGGTVSNSFSKKTTHVIVGNPNKRTKKYKAAIANGIPIVSPDWIEDCI 78 (78)
T ss_dssp STTTTTTEEEEE-SSTSSSHHHHHHHHHHHTTEEEESSSSTTSSEEEESSSHCCCHHHHHHHHTTSEEEETHHHHHHH
T ss_pred CCCCCCCEEEEE-ccCCCCCHHHHHHHHHHcCCEEEeecccCcEEEEeCCCCCccHHHHHHHHCCCeEecHHHHHHhC
Confidence 357999999999 66667889999999999999999999888999998776 677888888887 999999999997
No 45
>PF01331 mRNA_cap_enzyme: mRNA capping enzyme, catalytic domain; InterPro: IPR001339 The mRNA capping enzyme in yeasts is composed of two separate chains, alpha a mRNA guanyltransferase and beta an RNA 5'-triphosphate. X-ray crystallography reveals a large conformational change during guanyl transfer by mRNA capping enzymes []. Binding of the enzyme to nucleotides is specific to the GMP moiety of GTP. The viral mRNA capping enzyme is a monomer that transfers a GMP cap onto the end of mRNA that terminates with a 5'-diphosphate tail.; GO: 0004484 mRNA guanylyltransferase activity, 0006370 mRNA capping, 0006397 mRNA processing; PDB: 3RTX_A 3KYH_D 3S24_G 1CKN_B 1CKO_A 1CKM_B 1P16_B.
Probab=99.06 E-value=3.1e-11 Score=128.91 Aligned_cols=173 Identities=18% Similarity=0.260 Sum_probs=104.5
Q ss_pred hcCCCcEEEEEecceEEEEEEEeCCEEEEEecCCCCcCc---chhhHHHHHHHhcccCceeecceEEEEeCCCCcccccc
Q 001089 241 KLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSE---YGHAMSKIIEQNVLVDRCILDGEMLVWDTSLNRFAEFG 317 (1159)
Q Consensus 241 k~~~~~~~vE~K~DGeR~qih~~g~~v~~fSR~g~d~t~---~~p~l~~~l~~~~~~~~~ILDGElv~~d~~~~~~~pFg 317 (1159)
.+...+|+|.+|-||.|+.+.+.++++.++.|+..-+.- .+|.-.+.. ..-.....+||||||. |...
T Consensus 12 ~l~~~~Y~V~eKaDG~Ryll~i~~~~~ylidr~~~~~~v~~~~~p~~~~~~-~~~~~~~TLLDGElV~-d~~~------- 82 (192)
T PF01331_consen 12 LLQQKDYFVCEKADGTRYLLLITDNGVYLIDRKNNVFKVDNLHFPSKKDSS-DGRHHQDTLLDGELVL-DKDP------- 82 (192)
T ss_dssp HHHHS-EEEEEEESSEEEEEEEEEEEEEEEETTS-EEEESSST-ECTTC---TTCEGCSEEEEEEEEE-EECT-------
T ss_pred HHhhCCcEEEECCCCcEEEEEEecceEEEEeCCCcEEEecCcccccccccc-cccccCCEEEEEEEEc-ccCC-------
Confidence 344468999999999999999988899999999765431 222211000 0112468999999987 3211
Q ss_pred cHHHHHHHhhcCCCCCCCeEEEEEeeeecCCccccCCCHHHHHHHHHHhhccCCCcceeecc----CCCCCccccCCCCC
Q 001089 318 SNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVP----DHGLNSHVRPQGEP 393 (1159)
Q Consensus 318 ~lq~i~~~~r~~~~~~~~~~~~vFDiL~lnG~~l~~~pl~eRr~~L~~~i~~~~~~~~i~~p----~~~~~~~v~~~~~~ 393 (1159)
....+.|++||+|++||.++++.|+.+|...|.+.+........ +.+ ....++.++.-
T Consensus 83 --------------~~~~~~flifD~l~~~G~~v~~~~~~~Rl~~l~~~i~~p~~~~~-~~~~~~~~~~~pf~i~~K--- 144 (192)
T PF01331_consen 83 --------------GEKKPRFLIFDILAINGQNVTDKPLDERLAYLQEEIIEPRKNAE-LKSGIIKKKKEPFSIRIK--- 144 (192)
T ss_dssp --------------TCEEEEEEEEEEEEETTEEGCCSBHHHHHHHHHHHTHHHHHHHH-CHTTSCTCTTSSSEEEE----
T ss_pred --------------CCCceEEEEEeeehhCCcEeccCCHHHHHHHHHHHHHHHHHhhc-cccccccccccceeeecc---
Confidence 12458899999999999999999999999999765432111100 000 00001111100
Q ss_pred ccceecCCHHH-HHHHHHHHHHcCCceEEEecCCCCCcCCCCCCCeEEEc
Q 001089 394 CWSLVAHNVDE-VEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLK 442 (1159)
Q Consensus 394 ~~~~~~~~~~e-i~~~~~~ai~~g~EGlVlK~~ds~Y~pGkRs~~WlKiK 442 (1159)
........+. +...+..-+.....|||+-..+.+|.+| +...++|||
T Consensus 145 -~~~~~~~~~~~~~~~~~~~l~h~~DGLIFtp~~~pY~~G-t~~~llKWK 192 (192)
T PF01331_consen 145 -DFFPIYQIEKLLFEEFIPKLPHETDGLIFTPVNTPYVPG-TCPNLLKWK 192 (192)
T ss_dssp ---EEGGGHHHHCHHCCCCCTTSTEEEEEEEESSSB--SE-EEEEEEEE-
T ss_pred -ccHHHHhhHHHHHHHhhccCCCCCCEEEEecCCCCccCC-CCCccEeeC
Confidence 0111222233 2222223356788999999999999999 667999998
No 46
>smart00292 BRCT breast cancer carboxy-terminal domain.
Probab=98.96 E-value=2e-09 Score=96.23 Aligned_cols=76 Identities=24% Similarity=0.430 Sum_probs=63.2
Q ss_pred CcccCeEEEEEcCCCCCChHHHHHHHHHcCCEEEecCCC-CceEEEEecCCChh--hHhHhcCC-CeeecchHHHHHhcC
Q 001089 655 SIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNN-SVTHCVAADNKGLK--YEAAKRRG-DVIHYSWVLDCCSQK 730 (1159)
Q Consensus 655 ~lF~G~~F~vv~~~~~~~k~eLe~lI~~~GG~iv~n~~~-~~Th~Ia~~~~~~k--~~~a~~~~-~VV~p~WV~dCi~~~ 730 (1159)
.+|+|+.||+.+......+++|.++|..+||+++..+.. .+||+|+.+....+ +..+...+ +||+++||.||++.+
T Consensus 1 ~~f~g~~~~~~g~~~~~~~~~l~~~i~~~Gg~~~~~~~~~~~thvi~~~~~~~~~~~~~~~~~~~~iV~~~Wi~~~~~~~ 80 (80)
T smart00292 1 KLFKGKVFVITGKFDKNERDELKELIEALGGKVTSSLSSKTTTHVIVGSPEGGKLELLLAIALGIPIVTEDWLLDCLKAG 80 (80)
T ss_pred CccCCeEEEEeCCCCCccHHHHHHHHHHcCCEEecccCccceeEEEEcCCCCccHHHHHHHHcCCCCccHHHHHHHHHCc
Confidence 489999999986355678999999999999999999886 79999998765544 45555555 999999999999864
No 47
>KOG1929 consensus Nucleotide excision repair factor NEF2, RAD4/CUT5 component [Replication, recombination and repair]
Probab=98.90 E-value=9.4e-09 Score=127.62 Aligned_cols=183 Identities=21% Similarity=0.297 Sum_probs=137.8
Q ss_pred CCcccCeEEEEEcCCCCCChHHHHHHHHHcCCEEEecCCCCceEEEEecCCChhhHhHhcCC-CeeecchHHHHHhcCcc
Q 001089 654 TSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADNKGLKYEAAKRRG-DVIHYSWVLDCCSQKKL 732 (1159)
Q Consensus 654 s~lF~G~~F~vv~~~~~~~k~eLe~lI~~~GG~iv~n~~~~~Th~Ia~~~~~~k~~~a~~~~-~VV~p~WV~dCi~~~~l 732 (1159)
+..|+|+.||-.. .....+++|.+.+..+||.++...+.++||+|+.....-+|.++.+.+ +|++++||...+....+
T Consensus 7 ~~~~~~v~~~~t~-i~p~~~~~l~~~~~~~Gg~~~~~~t~~~thli~~~~~s~~~~~a~~~~~~~~~~~wi~~~~d~~~~ 85 (811)
T KOG1929|consen 7 SKPMSGVTFSPTG-INPIKREELSKKFIKLGGIDFKDFTPSVTHLIVGSVTSSKYAAAHRFDIKVLDSSWIDYIYDLWLL 85 (811)
T ss_pred CcccCCceeccCc-CCHHHHHHHHHHHHhcCceeeeccCCcCceeecccccccchhhhhcCCCceecchHHHHHHHHhhh
Confidence 4578899999643 345678999999999999999999999999998877777886666656 99999999988876654
Q ss_pred CCCCcccccccChhhhhhhhhcccccCCCcccCCChhHHHHHhhccCCCCCcchhHHHhhhcCCCCCCCcCCCeEEEEcC
Q 001089 733 LQLQPKYYLHLSDSSKKKLQEEVDEFSDLYFWDLDLADIKQLLSNVDRSEDPKTIDYYKKKYCPQDKWSCFHGCCIYFYH 812 (1159)
Q Consensus 733 Lp~~p~~~l~~s~~t~~~~~~~~D~~GDSy~~~~~~~~L~~ll~~~~~s~~~~~i~~l~~~~~~~~~~~lF~gc~~yl~~ 812 (1159)
. .- .+. .|...| .....+|.||.||+.+
T Consensus 86 -~-~e--~~~------------~~~l~~------------------------------------~~~~p~~~~~~Vc~tg 113 (811)
T KOG1929|consen 86 -N-KE--IRL------------LDPLRD------------------------------------TMKCPGFFGLKVCLTG 113 (811)
T ss_pred -h-cc--Ccc------------Cccchh------------------------------------hhcCCcccceEEEecc
Confidence 2 10 000 000000 1234579999999999
Q ss_pred CCCCCCCchHHHHHHHHHHHHHHHHhcCCEEEccCC-CceEEEEeccCCcccchhhHHHHHHHHhhhhccCCccEEeccc
Q 001089 813 STEPLSPDWEVLLGLALRRLKLEISFHGGKVCNNLA-NATHVVVLSVLGYDVNFNSLTESFTAREKHLLWNKKLHVVRSQ 891 (1159)
Q Consensus 813 ~~~~~~~d~~~i~~~~~~~l~~~I~~~GG~v~~~ls-~vTHVIV~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~IVs~~ 891 (1159)
+.. .++..++.+|..+||+....|+ +++||++...... .+|+ ..+ .+..+||+.+
T Consensus 114 l~~-----------~eK~ei~~~v~k~gg~~~~~L~s~v~~~~~~~~~~~-~kYe---~al---------~wn~~v~~~~ 169 (811)
T KOG1929|consen 114 LSG-----------DEKSEIKILVPKHGGTLHRSLSSDVNSLKILPEVKT-EKYE---QAL---------KWNIPVVSDD 169 (811)
T ss_pred cch-----------HHHHHHHHHhhhcccEEehhhhhhhheeeeccccch-HHHH---HHH---------hhCCccccHH
Confidence 863 2467889999999999999998 5677776644321 2233 222 4678999999
Q ss_pred HHHHHHHcCCccCCCCCCCCCC
Q 001089 892 WLEDCLAKEQKSEEYEYSLKPT 913 (1159)
Q Consensus 892 WL~~ci~~g~~v~E~~Y~v~~~ 913 (1159)
|+++|+..+..++...|.+.+.
T Consensus 170 w~~~s~~~~~~~~~~~~e~~~~ 191 (811)
T KOG1929|consen 170 WLFDSIEKTAVLETKPYEGAPV 191 (811)
T ss_pred HHhhhhcccccccccccccccc
Confidence 9999999999999999999985
No 48
>cd08041 OBF_kDNA_ligase_like The Oligonucleotide/oligosaccharide binding (OB)-fold domain of kDNA ligase-like ATP-dependent DNA ligases is a DNA-binding module that is part 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. 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-de
Probab=98.89 E-value=5e-09 Score=95.25 Aligned_cols=76 Identities=25% Similarity=0.387 Sum_probs=60.0
Q ss_pred cccEEEEEEEeCCCCCCCccceEEEEEecCCCCCCCCceEEEEEEecCCCCHHHHHHHHHhhcccccccCCCCCCCCCcc
Q 001089 451 DLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFY 530 (1159)
Q Consensus 451 ~lDlvVIG~~~G~Grr~g~~gsfllg~~d~~~~~~~~~~f~~v~kVgtG~sdeel~~l~~~l~~~~~~~~~~~~~pP~~~ 530 (1159)
+.|++|+|.++|.|++.|.+|+|+|+.++.. .++||||||+++++++. | +
T Consensus 2 ~~e~vIvG~~~g~g~~~~~~g~llv~~~~g~-----------~~~vgtG~t~~~r~~~~-----------------~-~- 51 (77)
T cd08041 2 DAEARVVGYEEGKGKYEGMLGALVVETKDGI-----------RFKIGSGFSDEQRRNPP-----------------P-I- 51 (77)
T ss_pred ceeEEEEEEEcCCCccCCcEEEEEEEecCCC-----------EEEEcCCCCHHHHhcCC-----------------C-C-
Confidence 6899999999999999999999999987521 45899999999988542 1 0
Q ss_pred cccCCCCCCCcEEEeCCcceEEEEEEeeeeeeecccccCCceeeCceeeeee
Q 001089 531 QVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVR 582 (1159)
Q Consensus 531 ~~~~~~~~~Pdvwi~~P~~s~Vlev~a~i~~i~s~~~~~g~tLRFPR~~riR 582 (1159)
..|+||++- .+++...||||+|+++|
T Consensus 52 -------------------g~v~~V~y~-------e~t~~g~lR~P~f~g~R 77 (77)
T cd08041 52 -------------------GSIITYKYQ-------GLTKNGLPRFPVFLRVR 77 (77)
T ss_pred -------------------CCEEEEEEE-------ecCCCCcccCCEEEecC
Confidence 036677652 24567899999999997
No 49
>KOG3524 consensus Predicted guanine nucleotide exchange factor (PEBBLE) [Signal transduction mechanisms]
Probab=98.86 E-value=4.5e-09 Score=124.32 Aligned_cols=183 Identities=19% Similarity=0.214 Sum_probs=133.3
Q ss_pred CCCCcccCeEEEEEcCCCCCChHHHHHHHHHcCCEEEecCCCCceEEEEecCCChhhHhHhcCCCeeecchHHHHHhcCc
Q 001089 652 GETSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADNKGLKYEAAKRRGDVIHYSWVLDCCSQKK 731 (1159)
Q Consensus 652 ~~s~lF~G~~F~vv~~~~~~~k~eLe~lI~~~GG~iv~n~~~~~Th~Ia~~~~~~k~~~a~~~~~VV~p~WV~dCi~~~~ 731 (1159)
.-...|.|+..|+.+.- ...++|-.+|+.+||.|..+.+..+||.|+....+-++..+.-..++++|.||+.||+...
T Consensus 114 ly~~~m~~vvlcfTg~r--kk~e~lv~lvh~mgg~irkd~nsktthli~n~s~gek~~~a~t~~~~~rp~wv~~aw~~rn 191 (850)
T KOG3524|consen 114 LYCELMKDVVMCFTGER--KKKEELVDLVHYMGGSIRKDTNSKTTHLIANKVEGEKQSIALVGVPTMRPDWVTEAWKHRN 191 (850)
T ss_pred ccchhhcCceeeeeccc--hhhHHHHHHHHHhcceeEeeeccCceEEEeecccceEEEEEeeccceechHhhhhhhcCcc
Confidence 34568999999986442 2345899999999999999888789999998887877777655569999999999997553
Q ss_pred cCCCCcccccccChhhhhhhhhcccccCCCcccCCChhHHHHHhhccCCCCCcchhHHHhhhcCCCCCCCcCCCeEEEEc
Q 001089 732 LLQLQPKYYLHLSDSSKKKLQEEVDEFSDLYFWDLDLADIKQLLSNVDRSEDPKTIDYYKKKYCPQDKWSCFHGCCIYFY 811 (1159)
Q Consensus 732 lLp~~p~~~l~~s~~t~~~~~~~~D~~GDSy~~~~~~~~L~~ll~~~~~s~~~~~i~~l~~~~~~~~~~~lF~gc~~yl~ 811 (1159)
-+- +....+.|-|-| ...-|.||.|+|.
T Consensus 192 ~~y----------------fda~~~~f~d~h------------------------------------rl~~feg~~~~f~ 219 (850)
T KOG3524|consen 192 DSY----------------FDAMEPCFVDKH------------------------------------RLGVFEGLSLFFH 219 (850)
T ss_pred hhh----------------hhhhccchhhhh------------------------------------ccccccCCeEeec
Confidence 111 000111122212 2345999999999
Q ss_pred CCCCCCCCchHHHHHHHHHHHHHHHHhcCCEEEccCCCceEEEEeccCCcccchhhHHHHHHHHhhhhccCCccEEeccc
Q 001089 812 HSTEPLSPDWEVLLGLALRRLKLEISFHGGKVCNNLANATHVVVLSVLGYDVNFNSLTESFTAREKHLLWNKKLHVVRSQ 891 (1159)
Q Consensus 812 ~~~~~~~~d~~~i~~~~~~~l~~~I~~~GG~v~~~ls~vTHVIV~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~IVs~~ 891 (1159)
||.. .+.+.|-+.....||.+......||||||.+.......+ ..+..-++|..+
T Consensus 220 gF~~-----------ee~~~m~~sle~~gg~~a~~d~~cthvvv~e~~~~~~p~--------------~~s~~~~~vk~e 274 (850)
T KOG3524|consen 220 GFKQ-----------EEIDDMLRSLENTGGKLAPSDTLCTHVVVNEDNDEVEPL--------------AVSSNQVHVKKE 274 (850)
T ss_pred CCcH-----------HHHHHHHHHHHhcCCcccCCCCCceeEeecCCccccccc--------------cccccceeeccc
Confidence 9963 234677888999999999966679999998643111111 113456899999
Q ss_pred HHHHHHHcCCccCCCCCCCCCC
Q 001089 892 WLEDCLAKEQKSEEYEYSLKPT 913 (1159)
Q Consensus 892 WL~~ci~~g~~v~E~~Y~v~~~ 913 (1159)
|.|-+|..|...-|++|...--
T Consensus 275 wfw~siq~g~~a~e~~yl~~~~ 296 (850)
T KOG3524|consen 275 WFWVSIQRGCCAIEDNYLLPTG 296 (850)
T ss_pred ceEEEEecchhccccceecccc
Confidence 9999999999999999976544
No 50
>COG5226 CEG1 mRNA capping enzyme, guanylyltransferase (alpha) subunit [RNA processing and modification]
Probab=98.85 E-value=4.8e-09 Score=113.76 Aligned_cols=183 Identities=20% Similarity=0.302 Sum_probs=118.8
Q ss_pred cCCCcEEEEEecceEEEEEEEeC------CEEEEEecCCCCcC---cchhhHHHHHHHhcccCceeecceEEEEeCCCCc
Q 001089 242 LHGKEVVIECKFDGDRIQIHKNG------SEIHYFSRSFLDHS---EYGHAMSKIIEQNVLVDRCILDGEMLVWDTSLNR 312 (1159)
Q Consensus 242 ~~~~~~~vE~K~DGeR~qih~~g------~~v~~fSR~g~d~t---~~~p~l~~~l~~~~~~~~~ILDGElv~~d~~~~~ 312 (1159)
+...+|++.+|-||.||++.+.. -...+|.|..+-|. ..+|.+...........+..||||+|. |
T Consensus 59 Ll~~dy~VCEKsDGvR~Ll~vte~p~tg~~~~y~~DR~nnfY~v~~~f~p~~~~~k~ge~l~~dtlldgelV~-d----- 132 (404)
T COG5226 59 LLNNDYLVCEKSDGVRALLLVTEEPVTGAFRGYFYDRRNNFYEVHTSFPPCSTVLKDGEVLLEDTLLDGELVF-D----- 132 (404)
T ss_pred HHhCCeEEEEccCCeEEEEEEEecccCCCcceEEEeccCceEEeccccCCcccccccCcEEeccceecceEEE-E-----
Confidence 44578999999999999988742 25789999887653 233322211111223467799999986 3
Q ss_pred ccccccHHHHHHHhhcCCCCCCCeEEEEEeeeecCCccccCCCHHHHHHHHHHhhccCCCcceeeccCC--CCCccccCC
Q 001089 313 FAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDH--GLNSHVRPQ 390 (1159)
Q Consensus 313 ~~pFg~lq~i~~~~r~~~~~~~~~~~~vFDiL~lnG~~l~~~pl~eRr~~L~~~i~~~~~~~~i~~p~~--~~~~~v~~~ 390 (1159)
..|.+.+++ +.|.+||+|-++|.-+..++.++|...|.+-+...-.+.....+.. ..++|
T Consensus 133 ~~p~~k~~q--------------lryl~fdcLa~~g~~~~~~~~s~Rl~~l~Ke~~kp~~~~r~s~~~~~~~fpf~---- 194 (404)
T COG5226 133 CLPYEKVPQ--------------LRYLLFDCLAYAGMFVERMEKSERLKTLQKEDEKPRERKRVSIEIDSGSFPFH---- 194 (404)
T ss_pred eccccchHH--------------HHHHHHHHhhhcceeEeecchhhHHHHhhhhhcccHhhhhheeecccccccee----
Confidence 356655443 4578999999999999999999999999876543211111111111 00111
Q ss_pred CCCccceecCCH---HHHHHHHHHH--HHcCCceEEEecCCCCCcCCCCCCCeEEEcccccccCCcccEEEEE
Q 001089 391 GEPCWSLVAHNV---DEVEKFFKET--IENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLIIG 458 (1159)
Q Consensus 391 ~~~~~~~~~~~~---~ei~~~~~~a--i~~g~EGlVlK~~ds~Y~pGkRs~~WlKiKpey~~~g~~lDlvVIG 458 (1159)
+..... -.+-++|+.. +.+|..|||+-..+.+|..|++ +..+|+||.-+ .++|+..|-
T Consensus 195 ------~s~K~M~~syg~~ki~k~ip~L~HgnDGLIFTp~~~PY~~Gkd-~~lLKWKP~~~---NTiDF~lvl 257 (404)
T COG5226 195 ------FSVKQMLKSYGFWKIYKKIPELKHGNDGLIFTPADEPYSVGKD-GALLKWKPASL---NTIDFRLVL 257 (404)
T ss_pred ------eeHHHHHhhhhHHHHHhhcccccCCCCceEeccCCCCcccCcc-ceeeecCcccc---Cceeeeeee
Confidence 111111 1233444222 4689999999999999999965 68999999753 478876654
No 51
>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=98.78 E-value=1.7e-08 Score=88.03 Aligned_cols=70 Identities=23% Similarity=0.492 Sum_probs=58.7
Q ss_pred CeEEEEEcCCCCCChHHHHHHHHHcCCEEEecCCCCceEEEEecCCChh-hHhHhcCC-CeeecchHHHHHh
Q 001089 659 DMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADNKGLK-YEAAKRRG-DVIHYSWVLDCCS 728 (1159)
Q Consensus 659 G~~F~vv~~~~~~~k~eLe~lI~~~GG~iv~n~~~~~Th~Ia~~~~~~k-~~~a~~~~-~VV~p~WV~dCi~ 728 (1159)
|+.||+.+......+++|+++|.++||+++..+...+||+|+......+ +..+...+ +||+++||.||++
T Consensus 1 ~~~~~i~g~~~~~~~~~l~~~i~~~Gg~v~~~~~~~~thvI~~~~~~~~~~~~~~~~~~~iV~~~Wi~~~~~ 72 (72)
T cd00027 1 GLTFVITGDLPSEERDELKELIEKLGGKVTSSVSKKTTHVIVGSDAGPKKLLKAIKLGIPIVTPEWLLDCLK 72 (72)
T ss_pred CCEEEEEecCCCcCHHHHHHHHHHcCCEEeccccCCceEEEECCCCCchHHHHHHHcCCeEecHHHHHHHhC
Confidence 6789987655467899999999999999999888789999998765554 66666666 9999999999984
No 52
>PF00533 BRCT: BRCA1 C Terminus (BRCT) domain; InterPro: IPR001357 The BRCT domain (after the C_terminal domain of a breast cancer susceptibility protein) is found predominantly in proteins involved in cell cycle checkpoint functions responsive to DNA damage [], for example as found in the breast cancer DNA-repair protein BRCA1. The domain is an approximately 100 amino acid tandem repeat, which appears to act as a phospho-protein binding domain []. A chitin biosynthesis protein from yeast also seems to belong to this group. ; GO: 0005622 intracellular; PDB: 3L46_A 3AL3_A 3AL2_A 1WF6_A 3II6_X 2NTE_B 3FA2_A 2R1Z_A 2COK_A 2K7F_A ....
Probab=98.68 E-value=4.6e-08 Score=88.10 Aligned_cols=75 Identities=25% Similarity=0.439 Sum_probs=55.0
Q ss_pred CCcCCCeEEEEcCCCCCCCCchHHHHHHHHHHHHHHHHhcCCEEEccCC-CceEEEEeccCCcccchhhHHHHHHHHhhh
Q 001089 800 WSCFHGCCIYFYHSTEPLSPDWEVLLGLALRRLKLEISFHGGKVCNNLA-NATHVVVLSVLGYDVNFNSLTESFTAREKH 878 (1159)
Q Consensus 800 ~~lF~gc~~yl~~~~~~~~~d~~~i~~~~~~~l~~~I~~~GG~v~~~ls-~vTHVIV~~~~~~~~~~~~l~~~l~~~~~~ 878 (1159)
..+|+||.|||.++.. . ..+.+..+|+.+||++++.++ .+||||+....... .+ ....
T Consensus 3 ~~~F~g~~f~i~~~~~---~--------~~~~l~~~i~~~GG~v~~~~~~~~thvI~~~~~~~~--~k-~~~~------- 61 (78)
T PF00533_consen 3 PKIFEGCTFCISGFDS---D--------EREELEQLIKKHGGTVSNSFSKKTTHVIVGNPNKRT--KK-YKAA------- 61 (78)
T ss_dssp TTTTTTEEEEESSTSS---S--------HHHHHHHHHHHTTEEEESSSSTTSSEEEESSSHCCC--HH-HHHH-------
T ss_pred CCCCCCEEEEEccCCC---C--------CHHHHHHHHHHcCCEEEeecccCcEEEEeCCCCCcc--HH-HHHH-------
Confidence 4689999999955432 1 256789999999999999998 59999998641111 11 1111
Q ss_pred hccCCccEEecccHHHHHH
Q 001089 879 LLWNKKLHVVRSQWLEDCL 897 (1159)
Q Consensus 879 ~~~~~~~~IVs~~WL~~ci 897 (1159)
....+.||+++||.+||
T Consensus 62 --~~~~i~iV~~~Wi~~ci 78 (78)
T PF00533_consen 62 --IANGIPIVSPDWIEDCI 78 (78)
T ss_dssp --HHTTSEEEETHHHHHHH
T ss_pred --HHCCCeEecHHHHHHhC
Confidence 13568999999999997
No 53
>KOG3226 consensus DNA repair protein [Replication, recombination and repair]
Probab=98.63 E-value=2.1e-08 Score=111.08 Aligned_cols=94 Identities=21% Similarity=0.435 Sum_probs=84.1
Q ss_pred cccCCCCcccCeEEEEEcCCCCCChHHHHHHHHHcCCEEEecCCCCceEEEEecCCChhhHhHhcCC-CeeecchHHHHH
Q 001089 649 DIKGETSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADNKGLKYEAAKRRG-DVIHYSWVLDCC 727 (1159)
Q Consensus 649 ~~~~~s~lF~G~~F~vv~~~~~~~k~eLe~lI~~~GG~iv~n~~~~~Th~Ia~~~~~~k~~~a~~~~-~VV~p~WV~dCi 727 (1159)
+-..-+.|++|++|++ +|..+..+.+|+......|++|-.+++..+||+||+.++|+||++....| .||+-+||.+|.
T Consensus 310 ~t~el~klL~GVV~Vl-SGfqNP~Rs~LRskAl~LGAkY~pDW~~gsThLICAF~NTPKy~QV~g~Gg~IV~keWI~~Cy 388 (508)
T KOG3226|consen 310 NTTELSKLLEGVVFVL-SGFQNPERSTLRSKALTLGAKYQPDWNAGSTHLICAFPNTPKYRQVEGNGGTIVSKEWITECY 388 (508)
T ss_pred CchhHHHhhhceEEEE-ecccCchHHHHHHHHHhhcccccCCcCCCceeEEEecCCCcchhhcccCCceEeeHHHHHHHH
Confidence 4446689999999886 56778899999999999999999999988999999999999999998887 999999999999
Q ss_pred hcCccCCCCcccccccC
Q 001089 728 SQKKLLQLQPKYYLHLS 744 (1159)
Q Consensus 728 ~~~~lLp~~p~~~l~~s 744 (1159)
+++++|||+ +|++++.
T Consensus 389 ~~kk~lp~r-rYlm~~~ 404 (508)
T KOG3226|consen 389 AQKKLLPIR-RYLMHAG 404 (508)
T ss_pred HHHhhccHH-HHHhcCC
Confidence 999999999 4566654
No 54
>COG1423 ATP-dependent DNA ligase, homolog of eukaryotic ligase III [DNA replication, recombination, and repair]
Probab=98.52 E-value=1.5e-06 Score=96.98 Aligned_cols=151 Identities=22% Similarity=0.302 Sum_probs=104.2
Q ss_pred hcCCCcEEEEEecceEEEEEEEeCCEEEEEecCCCCc--C-cchhhHHHH-HHHhcccCceeecceEEEEeCCCCccccc
Q 001089 241 KLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDH--S-EYGHAMSKI-IEQNVLVDRCILDGEMLVWDTSLNRFAEF 316 (1159)
Q Consensus 241 k~~~~~~~vE~K~DGeR~qih~~g~~v~~fSR~g~d~--t-~~~p~l~~~-l~~~~~~~~~ILDGElv~~d~~~~~~~pF 316 (1159)
.|+...+++|+|+||..+-|.+-+|.+.-.||+|.-. | +..+.+.+. +... ..+.+|.|||+.-+. -+.|-
T Consensus 84 ~F~~~~v~VEEKmnGYNVRV~k~~g~vyAiTRgG~ICPfTT~r~~~l~~~eff~d--~p~lvlcgEmvG~en---PYv~~ 158 (382)
T COG1423 84 HFGRGKVVVEEKMNGYNVRVVKLGGEVYAITRGGLICPFTTERLRDLIDLEFFDD--YPDLVLCGEMVGPEN---PYVPG 158 (382)
T ss_pred hcCCCcEEEEEeccCceEEEEEECCEEEEEecCceecCchhHHHHhhcchhhHhh--CCCcEEEEEeccCCC---CCCCC
Confidence 4556789999999999999999999999999999754 3 233333221 1121 368899999998542 12220
Q ss_pred ccHHHHHHHhhcCCCCCCCeEEEEEeeeecCCccccCCCHHHHHHHHHHhhccCCCcceeeccCCCCCccccCCCCCccc
Q 001089 317 GSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWS 396 (1159)
Q Consensus 317 g~lq~i~~~~r~~~~~~~~~~~~vFDiL~lnG~~l~~~pl~eRr~~L~~~i~~~~~~~~i~~p~~~~~~~v~~~~~~~~~ 396 (1159)
.......+.|++|||--.|.. ..+|..||++++++.--+ +++++ | .
T Consensus 159 ------------~~y~~e~v~fFvFDire~~tg--r~Lp~eer~~l~ekYgl~---~V~~f-------------g----~ 204 (382)
T COG1423 159 ------------PYYEKEDVGFFVFDIREKNTG--RPLPVEERLELAEKYGLP---HVEIF-------------G----E 204 (382)
T ss_pred ------------CCCccCCceEEEEEEEecCCC--CCCCHHHHHHHHHHcCCC---ceEEe-------------e----e
Confidence 111235688999999987642 246999999999886322 12221 1 1
Q ss_pred eecCCH-HHHHHHHHHHHHcCCceEEEecCCCCCc
Q 001089 397 LVAHNV-DEVEKFFKETIENRDEGIVLKDLGSKWE 430 (1159)
Q Consensus 397 ~~~~~~-~ei~~~~~~ai~~g~EGlVlK~~ds~Y~ 430 (1159)
+..++. ++|.+..++.-.+|.||+|+|+++..=.
T Consensus 205 ~~~~e~~eei~eIve~L~keGREGVV~Kdpdm~~~ 239 (382)
T COG1423 205 FPADEAGEEIYEIVERLNKEGREGVVMKDPDMRVP 239 (382)
T ss_pred echhHhHHHHHHHHHHHhhcCCcceEecCcccccC
Confidence 223344 7888999999999999999999876543
No 55
>smart00292 BRCT breast cancer carboxy-terminal domain.
Probab=98.50 E-value=3.2e-07 Score=81.81 Aligned_cols=76 Identities=30% Similarity=0.389 Sum_probs=57.0
Q ss_pred cCCCeEEEEcC-CCCCCCCchHHHHHHHHHHHHHHHHhcCCEEEccCC--CceEEEEeccCCcccchhhHHHHHHHHhhh
Q 001089 802 CFHGCCIYFYH-STEPLSPDWEVLLGLALRRLKLEISFHGGKVCNNLA--NATHVVVLSVLGYDVNFNSLTESFTAREKH 878 (1159)
Q Consensus 802 lF~gc~~yl~~-~~~~~~~d~~~i~~~~~~~l~~~I~~~GG~v~~~ls--~vTHVIV~~~~~~~~~~~~l~~~l~~~~~~ 878 (1159)
+|+||+||+.+ ... . ....+.+.+..+||+++..++ ++||||+.+.... ... ++..
T Consensus 2 ~f~g~~~~~~g~~~~---~--------~~~~l~~~i~~~Gg~~~~~~~~~~~thvi~~~~~~~--~~~-~~~~------- 60 (80)
T smart00292 2 LFKGKVFVITGKFDK---N--------ERDELKELIEALGGKVTSSLSSKTTTHVIVGSPEGG--KLE-LLLA------- 60 (80)
T ss_pred ccCCeEEEEeCCCCC---c--------cHHHHHHHHHHcCCEEecccCccceeEEEEcCCCCc--cHH-HHHH-------
Confidence 69999999998 321 2 256889999999999999998 7999999865421 111 1211
Q ss_pred hccCCccEEecccHHHHHHHcC
Q 001089 879 LLWNKKLHVVRSQWLEDCLAKE 900 (1159)
Q Consensus 879 ~~~~~~~~IVs~~WL~~ci~~g 900 (1159)
....++||+++||.+|++++
T Consensus 61 --~~~~~~iV~~~Wi~~~~~~~ 80 (80)
T smart00292 61 --IALGIPIVTEDWLLDCLKAG 80 (80)
T ss_pred --HHcCCCCccHHHHHHHHHCc
Confidence 13567999999999999864
No 56
>TIGR01209 RNA ligase, Pab1020 family. Members of this family are found, so far, in a single copy per genome and largely in thermophiles, of which only Aquifex aeolicus is bacterial rather than archaeal. PSI-BLAST converges after a single iteration to the whole of this family and reveals no convincing similarity to any other protein. The member protein Pab1020 has been characterized as an RNA ligase with circularization activity.
Probab=98.49 E-value=1.8e-06 Score=99.23 Aligned_cols=151 Identities=23% Similarity=0.313 Sum_probs=96.1
Q ss_pred hcCCCcEEEEEecceEEEEEEEeCCEEEEEecCCCCcCcchhhHHHHHHHhccc--CceeecceEEEEeCCCCccccccc
Q 001089 241 KLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLV--DRCILDGEMLVWDTSLNRFAEFGS 318 (1159)
Q Consensus 241 k~~~~~~~vE~K~DGeR~qih~~g~~v~~fSR~g~d~t~~~p~l~~~l~~~~~~--~~~ILDGElv~~d~~~~~~~pFg~ 318 (1159)
.|.+..+++|+|+||..+-|..-+|++..+||.|.-.+-...-+.+.+...++. ++.+|.|||+.-+. |+.
T Consensus 75 ~f~~~~v~vEEKlDG~Nvri~~~~g~l~a~tRGgyicp~tt~r~~~~~~~~~~~d~p~l~LcGE~iGpen------pY~- 147 (374)
T TIGR01209 75 HFKDPEVVVEEKMNGYNVRIVKYGGNVYALTRGGFICPFTTERLPDLIDLEFFDDNPDLVLCGEMAGPEN------PYT- 147 (374)
T ss_pred hcCCCcEEEEEeecCceEEEEeECCEEEEEccCcccCCCcHHHHHHHhhHHhhccCCCeEEEEEEcCCCC------CCc-
Confidence 355656999999999999998888999999999986532111122222222333 78999999987332 220
Q ss_pred HHHHHHHhhcCCC-CCCCeEEEEEeeeecCCccccCCCHHHHHHHHHHhhccCCCcceeeccCCCCCccccCCCCCccce
Q 001089 319 NQEIAKAARDGLS-SDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSL 397 (1159)
Q Consensus 319 lq~i~~~~r~~~~-~~~~~~~~vFDiL~lnG~~l~~~pl~eRr~~L~~~i~~~~~~~~i~~p~~~~~~~v~~~~~~~~~~ 397 (1159)
+..+. ...+..|++|||.- ...-.-+|..+|+++++..=-+.. .++ . .+
T Consensus 148 --------~hs~~y~~l~~~FfvFDI~d--~~t~~~L~~~er~~l~e~yglp~V---pvl--------g---------~~ 197 (374)
T TIGR01209 148 --------PEYYPEVKEDLGFFLFDIRE--GKTNRSLPVEERLELAEKYGLPHV---EIL--------G---------VY 197 (374)
T ss_pred --------ccCccccCCCceEEEEEEEE--CCCCccCCHHHHHHHHHHCCCCcc---cee--------e---------EE
Confidence 01111 22467899999973 333456799999999987622210 000 0 11
Q ss_pred ecCCH-HHHHHHHHHHHHcCCceEEEecCCCC
Q 001089 398 VAHNV-DEVEKFFKETIENRDEGIVLKDLGSK 428 (1159)
Q Consensus 398 ~~~~~-~ei~~~~~~ai~~g~EGlVlK~~ds~ 428 (1159)
...+. +++.+.++..-++|.||||+|+++..
T Consensus 198 ~~~~~~~~~~eii~~L~~~gREGVVlK~~~~~ 229 (374)
T TIGR01209 198 TADEAVEEIYEIIERLNKEGREGVVMKDPEMR 229 (374)
T ss_pred cHHHHHHHHHHHHHHhhhcCcceEEEcCcccc
Confidence 11222 25666777777899999999998654
No 57
>PF12738 PTCB-BRCT: twin BRCT domain; PDB: 3PA6_A 3KTF_C 2WT8_C 3EF1_A 3EF0_A.
Probab=98.44 E-value=2.2e-07 Score=80.99 Aligned_cols=62 Identities=29% Similarity=0.545 Sum_probs=50.2
Q ss_pred eEEEEEcCCCCCChHHHHHHHHHcCCEEEecCCCCceEEEEecCCChhhHhHhcCC-Ceeecch
Q 001089 660 MVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADNKGLKYEAAKRRG-DVIHYSW 722 (1159)
Q Consensus 660 ~~F~vv~~~~~~~k~eLe~lI~~~GG~iv~n~~~~~Th~Ia~~~~~~k~~~a~~~~-~VV~p~W 722 (1159)
+.||+.+.. ..+++.|.++|..+||++..+++..+||+|+....+.||+.|.+++ +||+|+|
T Consensus 1 ~~i~~sg~~-~~~~~~l~~~i~~~Gg~~~~~lt~~~THLI~~~~~~~K~~~A~~~gi~vV~~~W 63 (63)
T PF12738_consen 1 VVICFSGFS-GKERSQLRKLIEALGGKYSKDLTKKTTHLICSSPEGKKYRKAKEWGIPVVSPDW 63 (63)
T ss_dssp -EEEEEEB--TTTCCHHHHHHHCTT-EEESSSSTT-SEEEEES--HHHHHHHHHCTSEEEEHHH
T ss_pred CEEEECCCC-HHHHHHHHHHHHHCCCEEeccccCCceEEEEeCCCcHHHHHHHHCCCcEECCCC
Confidence 357775443 4558999999999999999999989999999888999999999998 9999999
No 58
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=98.36 E-value=6.8e-05 Score=94.00 Aligned_cols=74 Identities=16% Similarity=0.163 Sum_probs=65.3
Q ss_pred cccCeEEEEEcCCCCCChHHHHHHHHHcCCEEEecCCCCceEEEEecCCChhhHhHhcCC-CeeecchHHHHHhc
Q 001089 656 IFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADNKGLKYEAAKRRG-DVIHYSWVLDCCSQ 729 (1159)
Q Consensus 656 lF~G~~F~vv~~~~~~~k~eLe~lI~~~GG~iv~n~~~~~Th~Ia~~~~~~k~~~a~~~~-~VV~p~WV~dCi~~ 729 (1159)
.|.|+.|||++.....+|++++++|.++||+++.+++..++++|+++..+-|...|...+ +|++-+-+++.+++
T Consensus 590 ~~~g~~~v~TG~l~~~~R~e~~~~i~~~G~~v~~sVs~kt~~lv~G~~~gsK~~kA~~lgI~ii~E~~f~~~l~~ 664 (665)
T PRK07956 590 DLAGKTVVLTGTLEQLSRDEAKEKLEALGAKVSGSVSKKTDLVVAGEAAGSKLAKAQELGIEVLDEEEFLRLLGE 664 (665)
T ss_pred CccccEEEEeCCCCCCCHHHHHHHHHHcCCEEeCcccCCCCEEEECCCCChHHHHHHHcCCeEEcHHHHHHHHhc
Confidence 499999999876666799999999999999999999988888998877778898888888 99999998888765
No 59
>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=98.24 E-value=3e-06 Score=73.69 Aligned_cols=71 Identities=31% Similarity=0.431 Sum_probs=52.9
Q ss_pred CeEEEEcCCCCCCCCchHHHHHHHHHHHHHHHHhcCCEEEccCC-CceEEEEeccCCcccchhhHHHHHHHHhhhhccCC
Q 001089 805 GCCIYFYHSTEPLSPDWEVLLGLALRRLKLEISFHGGKVCNNLA-NATHVVVLSVLGYDVNFNSLTESFTAREKHLLWNK 883 (1159)
Q Consensus 805 gc~~yl~~~~~~~~~d~~~i~~~~~~~l~~~I~~~GG~v~~~ls-~vTHVIV~~~~~~~~~~~~l~~~l~~~~~~~~~~~ 883 (1159)
||.|||.++.. ..+ ...+...|..+||++.+.++ .+||||+.+..... .++.. ...
T Consensus 1 ~~~~~i~g~~~--~~~--------~~~l~~~i~~~Gg~v~~~~~~~~thvI~~~~~~~~----~~~~~---------~~~ 57 (72)
T cd00027 1 GLTFVITGDLP--SEE--------RDELKELIEKLGGKVTSSVSKKTTHVIVGSDAGPK----KLLKA---------IKL 57 (72)
T ss_pred CCEEEEEecCC--CcC--------HHHHHHHHHHcCCEEeccccCCceEEEECCCCCch----HHHHH---------HHc
Confidence 68999999752 122 46889999999999999998 79999998654211 01111 135
Q ss_pred ccEEecccHHHHHHH
Q 001089 884 KLHVVRSQWLEDCLA 898 (1159)
Q Consensus 884 ~~~IVs~~WL~~ci~ 898 (1159)
.++||+++||.+|++
T Consensus 58 ~~~iV~~~Wi~~~~~ 72 (72)
T cd00027 58 GIPIVTPEWLLDCLK 72 (72)
T ss_pred CCeEecHHHHHHHhC
Confidence 689999999999984
No 60
>KOG3548 consensus DNA damage checkpoint protein RHP9/CRB2/53BP1 [Replication, recombination and repair]
Probab=98.12 E-value=4.9e-06 Score=101.79 Aligned_cols=88 Identities=23% Similarity=0.348 Sum_probs=61.6
Q ss_pred CCcccCeEEEEEcCCCCCChHHHHHHHHHcCCEEEe----c-CC-------------------CCc-eEEEEecC--CCh
Q 001089 654 TSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSM----N-LN-------------------NSV-THCVAADN--KGL 706 (1159)
Q Consensus 654 s~lF~G~~F~vv~~~~~~~k~eLe~lI~~~GG~iv~----n-~~-------------------~~~-Th~Ia~~~--~~~ 706 (1159)
.+||.||.|.+.+.. .+.+....-+..|||.+.. + ++ .++ --|+++++ .+.
T Consensus 923 kniFd~cvF~lTsa~--~sd~~~r~s~e~~gg~vle~gl~~~Fn~p~~g~~~~lr~Ln~~q~~ks~~qalLIsdth~Rt~ 1000 (1176)
T KOG3548|consen 923 KNIFDGCVFMLTSAN--RSDSASRPSMEKHGGLVLEKGLMNLFNTPFKGGGIVLRQLNSFQERKSNYQALLISDTHYRTH 1000 (1176)
T ss_pred cchhcceeEEEeccc--cchhhhhhhhhccCChhhhccccccccccccCCcchHHhhhHHhhhccccceeEeehhhhHHH
Confidence 489999999987543 2345555566668888742 1 11 012 22455654 467
Q ss_pred hhHhHhcCC-CeeecchHHHHHhcCccCCCCcccccccC
Q 001089 707 KYEAAKRRG-DVIHYSWVLDCCSQKKLLQLQPKYYLHLS 744 (1159)
Q Consensus 707 k~~~a~~~~-~VV~p~WV~dCi~~~~lLp~~p~~~l~~s 744 (1159)
||-.+...| |||++.||.+|+++++++++.+| +|.+.
T Consensus 1001 KYLeaLA~giPcVh~~fI~aC~e~nr~Vdy~~Y-LLpsG 1038 (1176)
T KOG3548|consen 1001 KYLEALARGIPCVHNTFIQACGEQNRCVDYTDY-LLPSG 1038 (1176)
T ss_pred HHHHHHHcCCCcccHHHHHHHHhccccccchhh-cccCc
Confidence 888777777 99999999999999999999875 66543
No 61
>PF11411 DNA_ligase_IV: DNA ligase IV; InterPro: IPR021536 DNA ligase IV along with Xrcc4 functions in DNA non-homologous end joining. This process is required to mend double-strand breaks. Upon ligase binding to an Xrcc4 dimer, the helical tails unwind leading to a flat interaction surface []. ; GO: 0003910 DNA ligase (ATP) activity; PDB: 3II6_Y 2E2W_A 1IK9_C.
Probab=98.10 E-value=1.9e-06 Score=65.10 Aligned_cols=35 Identities=26% Similarity=0.495 Sum_probs=26.4
Q ss_pred hhhhhhhhcccccCCCcccCCChhHHHHHhhccCC
Q 001089 746 SSKKKLQEEVDEFSDLYFWDLDLADIKQLLSNVDR 780 (1159)
Q Consensus 746 ~t~~~~~~~~D~~GDSy~~~~~~~~L~~ll~~~~~ 780 (1159)
+|+++++++||+|||||+.++++++|+.++++|..
T Consensus 1 sTk~~fa~eyD~yGDSY~~Dtd~~~Lk~vF~~i~~ 35 (36)
T PF11411_consen 1 STKEHFAKEYDCYGDSYTVDTDEDQLKEVFNRIKK 35 (36)
T ss_dssp HHHHHHHHHB-TTS-BSSS---HHHHHHHHHCS--
T ss_pred CHHHHHHHHhccccccccccCCHHHHHHHHHHhcc
Confidence 47899999999999999999999999999998864
No 62
>KOG1929 consensus Nucleotide excision repair factor NEF2, RAD4/CUT5 component [Replication, recombination and repair]
Probab=98.08 E-value=8e-06 Score=102.11 Aligned_cols=179 Identities=14% Similarity=0.132 Sum_probs=119.2
Q ss_pred CCCcccCeEEEEEcCCCCCChHHHHHHHHHcCCEEEecCCCCceEEEEecC-CChhhHhHhcCC-CeeecchHHHHHhcC
Q 001089 653 ETSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADN-KGLKYEAAKRRG-DVIHYSWVLDCCSQK 730 (1159)
Q Consensus 653 ~s~lF~G~~F~vv~~~~~~~k~eLe~lI~~~GG~iv~n~~~~~Th~Ia~~~-~~~k~~~a~~~~-~VV~p~WV~dCi~~~ 730 (1159)
.+..|.|+.+|+.+ .....|.++..+|..|||++...+...++++++... .+-||++|+++. +||+.+|+++|++++
T Consensus 100 ~~p~~~~~~Vc~tg-l~~~eK~ei~~~v~k~gg~~~~~L~s~v~~~~~~~~~~~~kYe~al~wn~~v~~~~w~~~s~~~~ 178 (811)
T KOG1929|consen 100 KCPGFFGLKVCLTG-LSGDEKSEIKILVPKHGGTLHRSLSSDVNSLKILPEVKTEKYEQALKWNIPVVSDDWLFDSIEKT 178 (811)
T ss_pred cCCcccceEEEecc-cchHHHHHHHHHhhhcccEEehhhhhhhheeeeccccchHHHHHHHhhCCccccHHHHhhhhccc
Confidence 35689999999754 445689999999999999999888877878776554 348999999997 999999999999999
Q ss_pred ccCCCCcccccccChhhhhhh-h---hcccccCCCcccCCChhHHHHHhhccCCCCCcchhHHHhhhcCCCCCCCcCCCe
Q 001089 731 KLLQLQPKYYLHLSDSSKKKL-Q---EEVDEFSDLYFWDLDLADIKQLLSNVDRSEDPKTIDYYKKKYCPQDKWSCFHGC 806 (1159)
Q Consensus 731 ~lLp~~p~~~l~~s~~t~~~~-~---~~~D~~GDSy~~~~~~~~L~~ll~~~~~s~~~~~i~~l~~~~~~~~~~~lF~gc 806 (1159)
.+++..|+..-.... ..... . --.---||+|+...+...- .+..++ .+..+ ..+..+..+|
T Consensus 179 ~~~~~~~~e~~~~~~-~is~~~~~~~~~~~~~~~s~t~~~~~~~~-~~~~n~-------~~~p~------~a~~~~~~~c 243 (811)
T KOG1929|consen 179 AVLETKPYEGAPVAE-AISGPIGSTLPKEILDGDSRTANDTWSTS-KVVTNI-------KVLPF------QAKIGNLDDC 243 (811)
T ss_pred ccccccccccccccc-eeccCCccccccccccccchhhhccccch-hccccc-------ccchh------hhhccccccc
Confidence 999988864433110 00000 0 0000123333221111000 000000 00000 0122378999
Q ss_pred EEEEcCCCCCCCCchHHHHHHHHHHHHHHHHhcCCEEEccCC-CceEEEEecc
Q 001089 807 CIYFYHSTEPLSPDWEVLLGLALRRLKLEISFHGGKVCNNLA-NATHVVVLSV 858 (1159)
Q Consensus 807 ~~yl~~~~~~~~~d~~~i~~~~~~~l~~~I~~~GG~v~~~ls-~vTHVIV~~~ 858 (1159)
.+|++++.. . .++.+.+.++.+||..+++.. .++|+++.+.
T Consensus 244 ~v~~s~~~~-~----------~~s~l~r~~~~g~~~~~~e~~e~~st~l~~~~ 285 (811)
T KOG1929|consen 244 LVETSGTTS-R----------NRSALSRLSNNGGSLRFLERLEETSTSLLGDF 285 (811)
T ss_pred eeeecCCcc-c----------chhHhHHhhhcccceeecccCccccchhhccc
Confidence 999999874 1 256889999999999999876 6999999763
No 63
>cd09232 Snurportin-1_C C-terminal m3G cap-binding domain of nuclear import adaptor snurportin-1. Snurportin-1 (SPN1 or SNUPN) is a nuclear import adaptor for m3G-capped spliceosomal U small nucleoproteins (snRNPs), which are assembled in the cytoplasm. After capping and assembly, the U snRNPs are transported into the nucleus by SPN1 and importin beta; SPN1 is then returned to the cytoplasm by exportin 1 (CRM1), which also transports the non-capped U snRNPs. The U snRNPs are essential elements of the spliceosome, which catalyzes the excision of introns and the ligation of exons to form a mature mRNA. SPN1 contains two domains, an N-terminal importin beta-binding (IBB) domain and a C-terminal m3G cap-binding domain.
Probab=98.08 E-value=3.6e-05 Score=81.65 Aligned_cols=176 Identities=15% Similarity=0.102 Sum_probs=118.5
Q ss_pred ccccccccCChHHHHHhcCCCcEEEEEecceEEEEEEEeCCEEEEEecCCCCcCc---chhhHHHHHHHhcccCceeecc
Q 001089 225 RPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSE---YGHAMSKIIEQNVLVDRCILDG 301 (1159)
Q Consensus 225 ~PMLA~~~~~~~~~~~k~~~~~~~vE~K~DGeR~qih~~g~~v~~fSR~g~d~t~---~~p~l~~~l~~~~~~~~~ILDG 301 (1159)
..||++-...+++- + ..+|++=+===|-||+|....|.+.+++|+|.-+.. .+|+=. ..+ -+||
T Consensus 5 ~lml~Ewm~~~p~~---l-~~~w~~~~~P~G~R~lvv~~~g~t~~~~r~g~~~~~f~s~lP~g~--------~~~-~~~g 71 (186)
T cd09232 5 QLMLSEWMVEVPDD---L-SEEWLVVPCPVGKRCLVVASKGKTVARSKNGRTLHRFSSALPGGS--------RKT-SNSG 71 (186)
T ss_pred ceechhhcccCCCc---c-CcceEEEECcCceEEEEEEeCCEEEEEeCCCCEEEecccCCCCCC--------cCC-CCCC
Confidence 35666655444332 1 356888888889999999999999999999987532 223200 001 4566
Q ss_pred eEEEEeCCCCcccccccHHHHHHHhhcCCCCCCCeEEEEEeeeecCCccccCCCHHHHHHHHHHhhccCCCcceeeccCC
Q 001089 302 EMLVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDH 381 (1159)
Q Consensus 302 Elv~~d~~~~~~~pFg~lq~i~~~~r~~~~~~~~~~~~vFDiL~lnG~~l~~~pl~eRr~~L~~~i~~~~~~~~i~~p~~ 381 (1159)
|+|. |..-+ .....|+|+|||..||.++.+.+...|...|++-+.+.+..-. ...
T Consensus 72 ~tIL-Dci~~---------------------~~~~~yyVlDii~w~g~~l~d~~~~~Rf~wl~skl~E~~~~~~---~~~ 126 (186)
T cd09232 72 YTIL-DCIYN---------------------EDDRTYYVLDVLCWNGHPLYDCETEFRFFWLRSKLEELPELDE---PSE 126 (186)
T ss_pred CEEE-EEecC---------------------CCCCEEEEEEEeeeCCcccccCCcchhHHHHHhhCCCcccccc---ccc
Confidence 6653 32100 1135799999999999999999999999999988876542110 000
Q ss_pred CCCccccCCCCCccceecCCHHHHHHHHHHHH---HcCCceEEEecCCCCCcCCCCCCCeEEEccc
Q 001089 382 GLNSHVRPQGEPCWSLVAHNVDEVEKFFKETI---ENRDEGIVLKDLGSKWEPGDRSGKWLKLKPE 444 (1159)
Q Consensus 382 ~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~ai---~~g~EGlVlK~~ds~Y~pGkRs~~WlKiKpe 444 (1159)
.-.+.+++. ....+ +.+.+.+.|...+ ..-..||++-..++.|.+| +++.|+|+||.
T Consensus 127 ~~~~~f~~~----p~~~~-~~~~l~~~~~~~~~~~~~e~DGLlFyhk~~~Y~~G-~tPlvl~wKp~ 186 (186)
T cd09232 127 KNPFRFVPL----PYFPC-TKESLQSAYSGPLNDDPYELDGLLFYHKESHYTPG-STPLVLWLKDY 186 (186)
T ss_pred cCCceEEec----CcccC-cHHHHHHHHhcccccCCCCCceEEEEeCCCcccCc-CCCcEEEecCC
Confidence 001111111 12223 3377888888888 8889999999999999998 78999999983
No 64
>KOG2481 consensus Protein required for normal rRNA processing [RNA processing and modification]
Probab=97.95 E-value=6.1e-06 Score=95.93 Aligned_cols=79 Identities=23% Similarity=0.376 Sum_probs=59.1
Q ss_pred CCcccCeEEEEEcCCCCCChHHHHHHHHHcCCEEEecCC----------CCceEEEEecCCChhhHhHhcCCCeeecchH
Q 001089 654 TSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLN----------NSVTHCVAADNKGLKYEAAKRRGDVIHYSWV 723 (1159)
Q Consensus 654 s~lF~G~~F~vv~~~~~~~k~eLe~lI~~~GG~iv~n~~----------~~~Th~Ia~~~~~~k~~~a~~~~~VV~p~WV 723 (1159)
-.||+|+.||+-.. ..++.|+-+|..+||.++..+. ..+||-|+ +..+..-. .-....|.||||
T Consensus 325 kslF~glkFfl~re---VPresL~fiI~s~GG~V~wd~~~~g~~~~~~d~~ITH~Iv-DrP~~~~~--v~gR~YvQPQWv 398 (570)
T KOG2481|consen 325 KSLFSGLKFFLNRE---VPRESLEFIIRSFGGKVSWDPLGIGATYDESDERITHQIV-DRPGQQTS--VIGRTYVQPQWV 398 (570)
T ss_pred HHHhhcceeeeecc---CchHHHHHHHHHcCCceecCccCCCCcccccccceeeeee-cccCccce--eeeeeeecchhh
Confidence 46999999998543 4589999999999999998851 23588875 33232211 111288999999
Q ss_pred HHHHhcCccCCCCcc
Q 001089 724 LDCCSQKKLLQLQPK 738 (1159)
Q Consensus 724 ~dCi~~~~lLp~~p~ 738 (1159)
+||++++.++|.+-|
T Consensus 399 fDsvNar~llpt~~Y 413 (570)
T KOG2481|consen 399 FDSVNARLLLPTEKY 413 (570)
T ss_pred hhhccchhhccHhhh
Confidence 999999999998854
No 65
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=97.85 E-value=0.0017 Score=79.61 Aligned_cols=73 Identities=21% Similarity=0.228 Sum_probs=65.0
Q ss_pred CcccCeEEEEEcCCCCCChHHHHHHHHHcCCEEEecCCCCceEEEEecCCChhhHhHhcCC-CeeecchHHHHH
Q 001089 655 SIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADNKGLKYEAAKRRG-DVIHYSWVLDCC 727 (1159)
Q Consensus 655 ~lF~G~~F~vv~~~~~~~k~eLe~lI~~~GG~iv~n~~~~~Th~Ia~~~~~~k~~~a~~~~-~VV~p~WV~dCi 727 (1159)
..|.|+.|++.+.-+..+|.+...+|...||++....+..++++|+++.-|-|+..|...+ .|+.-+++..-+
T Consensus 593 ~~l~gkt~V~TGtL~~~sR~eak~~le~lGakv~~SVSkktD~vvaG~~aGSKl~kA~eLgv~i~~E~~~~~ll 666 (667)
T COG0272 593 SPLAGKTFVLTGTLEGMSRDEAKALLEALGAKVSGSVSKKTDYVVAGENAGSKLAKAQELGVKIIDEEEFLALL 666 (667)
T ss_pred cccCCCEEEEeccCCCCCHHHHHHHHHHcCCEEeceecccccEEEEcCCCChHHHHHHHcCCeEecHHHHHHhh
Confidence 7899999999877778999999999999999999999877788888888888999999988 999988877643
No 66
>PF14743 DNA_ligase_OB_2: DNA ligase OB-like domain; PDB: 2Q2U_D 2Q2T_A 1FVI_A 1P8L_A.
Probab=97.83 E-value=1.5e-05 Score=70.07 Aligned_cols=37 Identities=22% Similarity=0.449 Sum_probs=24.4
Q ss_pred CCCCCCCccceEEEEEecCCCCCCCCceEEEEEEecCCCCHHHHHHHH
Q 001089 462 GSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVV 509 (1159)
Q Consensus 462 G~Grr~g~~gsfllg~~d~~~~~~~~~~f~~v~kVgtG~sdeel~~l~ 509 (1159)
|.|+..|++|+|+|...+. ..++|||||||++++++.
T Consensus 2 G~Gk~~g~~Galv~~~~~G-----------~~f~iGsG~td~~R~~~~ 38 (66)
T PF14743_consen 2 GKGKFKGMLGALVCETEDG-----------VEFKIGSGFTDEEREEPP 38 (66)
T ss_dssp ---EEEEEEEEEEEEE-TT-----------EEEEE-SS--HHHHHHHH
T ss_pred CccccCCCEEEEEEEeCCC-----------CEEEECCCCCHHHHhcCC
Confidence 7889999999999987431 356899999999998764
No 67
>COG5163 NOP7 Protein required for biogenesis of the 60S ribosomal subunit [Translation, ribosomal structure and biogenesis]
Probab=97.68 E-value=2.9e-05 Score=87.28 Aligned_cols=79 Identities=25% Similarity=0.374 Sum_probs=57.9
Q ss_pred CCcccCeEEEEEcCCCCCChHHHHHHHHHcCCEEEecCC-----------CCceEEEEecCCChhhHhHhcCCCeeecch
Q 001089 654 TSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLN-----------NSVTHCVAADNKGLKYEAAKRRGDVIHYSW 722 (1159)
Q Consensus 654 s~lF~G~~F~vv~~~~~~~k~eLe~lI~~~GG~iv~n~~-----------~~~Th~Ia~~~~~~k~~~a~~~~~VV~p~W 722 (1159)
..||+|+.|||... .....|+-+|.++||.++..+- ..+||-|+ +...++ +-......|+|+|
T Consensus 348 ~slFS~f~Fyisre---Vp~dsLefiilscGG~V~~~p~~~~i~~~~~vD~~vth~i~-drp~~~--~kvegrtYiQPQw 421 (591)
T COG5163 348 KSLFSGFKFYISRE---VPGDSLEFIILSCGGSVVGSPCEADIHVSEKVDEKVTHQIV-DRPVMK--NKVEGRTYIQPQW 421 (591)
T ss_pred hhhhhceEEEEecc---ccchHHHHHHHHcCCcccCchhhccCCchhhccchhhhhhc-cchhhh--hhhcceeeechHH
Confidence 46999999999754 3467899999999999987652 23688775 332222 1111227899999
Q ss_pred HHHHHhcCccCCCCcc
Q 001089 723 VLDCCSQKKLLQLQPK 738 (1159)
Q Consensus 723 V~dCi~~~~lLp~~p~ 738 (1159)
|+|||++|.+.+.+.|
T Consensus 422 ~fDsiNkG~l~~~~~Y 437 (591)
T COG5163 422 LFDSINKGKLACVENY 437 (591)
T ss_pred HHhhhccccchhhhhc
Confidence 9999999999987743
No 68
>PLN03122 Poly [ADP-ribose] polymerase; Provisional
Probab=97.58 E-value=0.00015 Score=91.73 Aligned_cols=87 Identities=21% Similarity=0.323 Sum_probs=73.3
Q ss_pred CCCcccCeEEEEEcCCCCCChHHHHHHHHHcCCEEEecCCCCceEEEEecCC----C-hhhHhHhcCC-CeeecchHHHH
Q 001089 653 ETSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADNK----G-LKYEAAKRRG-DVIHYSWVLDC 726 (1159)
Q Consensus 653 ~s~lF~G~~F~vv~~~~~~~k~eLe~lI~~~GG~iv~n~~~~~Th~Ia~~~~----~-~k~~~a~~~~-~VV~p~WV~dC 726 (1159)
....|.|+.|+|++.... ++.++.++|..+||+++...+ .+||||++... + -|++.|...+ +||+.+||.+|
T Consensus 186 ~~kpL~G~~fviTGtl~~-sr~elK~~Ie~~GGkvsssVs-~~T~lIvt~~ev~k~gsSKlkkAk~lgIpIVsEd~L~d~ 263 (815)
T PLN03122 186 PGKPFSGMMISLSGRLSR-THQYWKKDIEKHGGKVANSVE-GVTCLVVSPAERERGGSSKIAEAMERGIPVVREAWLIDS 263 (815)
T ss_pred cCCCcCCcEEEEeCCCCC-CHHHHHHHHHHcCCEEccccc-cceEEEEcCccccccCccHHHHHHHcCCcCccHHHHHHH
Confidence 445799999999865543 899999999999999998884 58899987643 2 5788888887 99999999999
Q ss_pred HhcCccCCCCccccc
Q 001089 727 CSQKKLLQLQPKYYL 741 (1159)
Q Consensus 727 i~~~~lLp~~p~~~l 741 (1159)
++.+..+++.++++.
T Consensus 264 i~~~k~~~~~~y~l~ 278 (815)
T PLN03122 264 IEKQEAQPLEAYDVV 278 (815)
T ss_pred HhcCCcccchhhhhc
Confidence 999999999887654
No 69
>smart00532 LIGANc Ligase N family.
Probab=97.52 E-value=0.0011 Score=79.47 Aligned_cols=195 Identities=18% Similarity=0.291 Sum_probs=116.4
Q ss_pred cEEEEEecceEEEEEEEeCCE-EEEEec----CCCCcCcchhhH---HHHHHHhcccCceeecceEEEEeCCCCc-----
Q 001089 246 EVVIECKFDGDRIQIHKNGSE-IHYFSR----SFLDHSEYGHAM---SKIIEQNVLVDRCILDGEMLVWDTSLNR----- 312 (1159)
Q Consensus 246 ~~~vE~K~DGeR~qih~~g~~-v~~fSR----~g~d~t~~~p~l---~~~l~~~~~~~~~ILDGElv~~d~~~~~----- 312 (1159)
.|++|+|+||.-+.+.+.+|. ++..|| .|+|+|+....+ -..|. .-.+..+.+-||++.-...-.+
T Consensus 104 ~~~~epKiDGlsisL~Ye~G~l~~a~TRGDG~~GeDVT~nv~~i~~iP~~i~-~~~p~~leiRGEv~~~~~~F~~ln~~~ 182 (441)
T smart00532 104 AYVVEPKIDGLSVSLLYENGKLVQAATRGDGTVGEDVTQNVKTIRSIPLRLS-GDVPERLEVRGEVFMPKEDFLALNEEL 182 (441)
T ss_pred eEEEEEecccEEEEEEEECCEEEEEEecCCCCcceehhhhhhhhcCcChhhc-ccCCCeEEEEceEEEEHHHHHHHHHHH
Confidence 589999999999999887765 889999 688998633222 11121 0013458899999873211000
Q ss_pred ----ccccccHHHHH-HHhhc---CCCCCCCeEEEEEeeeecCCccccCCCHHHHHHHHHHhhccCCCcceeeccCCCCC
Q 001089 313 ----FAEFGSNQEIA-KAARD---GLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLN 384 (1159)
Q Consensus 313 ----~~pFg~lq~i~-~~~r~---~~~~~~~~~~~vFDiL~lnG~~l~~~pl~eRr~~L~~~i~~~~~~~~i~~p~~~~~ 384 (1159)
-.+|..-+..+ ...+. .....+++.|++|++...++... .....++.+.|..+-=+.. +
T Consensus 183 ~~~g~~~faNpRN~aAG~lr~ld~~~~~~r~L~~~~y~~~~~~~~~~-~~t~~e~l~~L~~~GF~v~-------~----- 249 (441)
T smart00532 183 EEEGEKPFANPRNAAAGSLRQLDPRITAKRKLRAFFYGLGTGEELFL-PKTQSEALKWLKELGFPVS-------P----- 249 (441)
T ss_pred HhcCCCcccChHHHHHHHHHhcCchhhhhccceEEEEEcccCCCCCC-ccCHHHHHHHHHHCCCCCC-------C-----
Confidence 01232222211 11111 11123579999999864443211 2467888888887521110 0
Q ss_pred ccccCCCCCccceecCCHHHHHHHHHHHHHc------CCceEEEecCCCCCcC--C--CCCCCe---EEEcccccccCCc
Q 001089 385 SHVRPQGEPCWSLVAHNVDEVEKFFKETIEN------RDEGIVLKDLGSKWEP--G--DRSGKW---LKLKPEYIRAGSD 451 (1159)
Q Consensus 385 ~~v~~~~~~~~~~~~~~~~ei~~~~~~ai~~------g~EGlVlK~~ds~Y~p--G--kRs~~W---lKiKpey~~~g~~ 451 (1159)
....+.+.+++..+++...+. .-.|||+|--+-.+.. | .+.+.| +|+.++ .
T Consensus 250 ----------~~~~~~~~~ei~~~~~~~~~~r~~l~y~iDGiViKvn~~~~~~~lG~ts~~PrwaiA~Kf~~~------~ 313 (441)
T smart00532 250 ----------HTRLCKNADEVIEYYEEWEEKRAELPYEIDGVVVKVDDLALQRELGFTSKAPRWAIAYKFPAE------E 313 (441)
T ss_pred ----------CeEeeCCHHHHHHHHHHHHHhcccCCCCcCcEEEEecCHHHHHHhCccCCCCCeeEEECCCCc------e
Confidence 123456788999999877653 5689999987766554 3 245667 566564 4
Q ss_pred ccEEEEEEEeCCCCCCCccc
Q 001089 452 LDVLIIGGYYGSGRRGGEVA 471 (1159)
Q Consensus 452 lDlvVIG~~~G~Grr~g~~g 471 (1159)
..-.|.+-.|-.|| .|.+.
T Consensus 314 ~~T~l~~I~~qVGR-TG~iT 332 (441)
T smart00532 314 AETKLLDIIVQVGR-TGKIT 332 (441)
T ss_pred eEEEEEEEEEecCC-Cceee
Confidence 55577787887775 44443
No 70
>KOG2481 consensus Protein required for normal rRNA processing [RNA processing and modification]
Probab=97.52 E-value=8.4e-05 Score=86.73 Aligned_cols=83 Identities=20% Similarity=0.203 Sum_probs=64.2
Q ss_pred CCCcCCCeEEEEcCCCCCCCCchHHHHHHHHHHHHHHHHhcCCEEEccC---------C--CceEEEEeccCCcccchhh
Q 001089 799 KWSCFHGCCIYFYHSTEPLSPDWEVLLGLALRRLKLEISFHGGKVCNNL---------A--NATHVVVLSVLGYDVNFNS 867 (1159)
Q Consensus 799 ~~~lF~gc~~yl~~~~~~~~~d~~~i~~~~~~~l~~~I~~~GG~v~~~l---------s--~vTHVIV~~~~~~~~~~~~ 867 (1159)
...||+||+|||....+ .+-|..+|+.+||.|+.+. + .+||=||+.+. ....+
T Consensus 324 ~kslF~glkFfl~reVP-------------resL~fiI~s~GG~V~wd~~~~g~~~~~~d~~ITH~IvDrP~-~~~~v-- 387 (570)
T KOG2481|consen 324 HKSLFSGLKFFLNREVP-------------RESLEFIIRSFGGKVSWDPLGIGATYDESDERITHQIVDRPG-QQTSV-- 387 (570)
T ss_pred HHHHhhcceeeeeccCc-------------hHHHHHHHHHcCCceecCccCCCCcccccccceeeeeecccC-cccee--
Confidence 34689999999998654 4578889999999999883 1 26999997653 11111
Q ss_pred HHHHHHHHhhhhccCCccEEecccHHHHHHHcCCccCCCCCCCCC
Q 001089 868 LTESFTAREKHLLWNKKLHVVRSQWLEDCLAKEQKSEEYEYSLKP 912 (1159)
Q Consensus 868 l~~~l~~~~~~~~~~~~~~IVs~~WL~~ci~~g~~v~E~~Y~v~~ 912 (1159)
-.-..|.|.||.+|+.++.++|.+.|.+..
T Consensus 388 ---------------~gR~YvQPQWvfDsvNar~llpt~~Y~~G~ 417 (570)
T KOG2481|consen 388 ---------------IGRTYVQPQWVFDSVNARLLLPTEKYFPGK 417 (570)
T ss_pred ---------------eeeeeecchhhhhhccchhhccHhhhCCCc
Confidence 123679999999999999999999997654
No 71
>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=97.42 E-value=0.0019 Score=74.03 Aligned_cols=167 Identities=17% Similarity=0.256 Sum_probs=98.9
Q ss_pred cEEEEEecceEEEEEEEeCCE-EEEEec----CCCCcCcchhhH---HHHHHHhcccCceeecceEEEEeCCCCc-----
Q 001089 246 EVVIECKFDGDRIQIHKNGSE-IHYFSR----SFLDHSEYGHAM---SKIIEQNVLVDRCILDGEMLVWDTSLNR----- 312 (1159)
Q Consensus 246 ~~~vE~K~DGeR~qih~~g~~-v~~fSR----~g~d~t~~~p~l---~~~l~~~~~~~~~ILDGElv~~d~~~~~----- 312 (1159)
.|++|+|+||.-+.+.+.+|. ++..|| .|+|+|+-...+ -..|. . .+..+.+=||++.-...-.+
T Consensus 102 ~~~vepKiDGlsisL~Y~~G~L~~a~TRGdG~~GeDVT~nv~~I~~IP~~i~-~-~~~~levRGEv~m~~~~F~~~n~~~ 179 (307)
T cd00114 102 AYVVEPKIDGLSISLRYENGVLVQAATRGDGTTGEDVTENVRTIRSIPLTLA-G-APETLEVRGEVFMPKADFEALNKER 179 (307)
T ss_pred cEEEEEeccceEEEEEEECCEEEEEEecCCCcchhhHHhhHhhhcccChhhc-C-CCCeEEEEEEEEEEHHHHHHHHHHH
Confidence 699999999999998887664 788999 588888633221 11221 1 14468899999874211000
Q ss_pred ----ccccccHHHHH-HHhhc---CCCCCCCeEEEEEeeeecCCccccCCCHHHHHHHHHHhhccCCCcceeeccCCCCC
Q 001089 313 ----FAEFGSNQEIA-KAARD---GLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLN 384 (1159)
Q Consensus 313 ----~~pFg~lq~i~-~~~r~---~~~~~~~~~~~vFDiL~lnG~~l~~~pl~eRr~~L~~~i~~~~~~~~i~~p~~~~~ 384 (1159)
-.+|..-+..+ ...|. .....+++.|++|++...++.. -....++.+.|..+-=++..
T Consensus 180 ~~~~~~~faNpRNaaAGsLr~ld~~~~~~r~L~f~~y~~~~~~~~~--~~t~~e~l~~L~~~GF~v~~------------ 245 (307)
T cd00114 180 EERGEKPFANPRNAAAGSLRQLDPKITAKRPLRFFIYGLGEAEGLG--PKTQSEALAFLKEWGFPVSP------------ 245 (307)
T ss_pred HHcCCCCccChHHHHHHHHHhcCcchhhcCcceEEEEecccccCCC--CCCHHHHHHHHHHCCCCCCC------------
Confidence 01232212111 11111 1112468999999997544311 24778888888875211110
Q ss_pred ccccCCCCCccceecCCHHHHHHHHHHHHHc------CCceEEEecCCCCCc----CCCCCCCe
Q 001089 385 SHVRPQGEPCWSLVAHNVDEVEKFFKETIEN------RDEGIVLKDLGSKWE----PGDRSGKW 438 (1159)
Q Consensus 385 ~~v~~~~~~~~~~~~~~~~ei~~~~~~ai~~------g~EGlVlK~~ds~Y~----pGkRs~~W 438 (1159)
....+.+.+++.++++..... .-.|||+|--+-.+. ...+.+.|
T Consensus 246 ----------~~~~~~~~~ev~~~~~~~~~~R~~l~y~iDGiViKvn~~~~~~~lG~tsk~PrW 299 (307)
T cd00114 246 ----------ETRLCKNIEEVLAFYDEIEAKRDSLPYEIDGVVVKVDDLALQRELGFTSKAPRW 299 (307)
T ss_pred ----------CeEEeCCHHHHHHHHHHHHHhhhcCCCCCCcEEEEEeCHHHHHHhCccCCCCCc
Confidence 123456789999998887443 567999997665443 23344666
No 72
>PF12738 PTCB-BRCT: twin BRCT domain; PDB: 3PA6_A 3KTF_C 2WT8_C 3EF1_A 3EF0_A.
Probab=97.30 E-value=0.00045 Score=60.15 Aligned_cols=62 Identities=24% Similarity=0.384 Sum_probs=41.7
Q ss_pred eEEEEcCCCCCCCCchHHHHHHHHHHHHHHHHhcCCEEEccCC-CceEEEEeccCCcccchhhHHHHHHHHhhhhccCCc
Q 001089 806 CCIYFYHSTEPLSPDWEVLLGLALRRLKLEISFHGGKVCNNLA-NATHVVVLSVLGYDVNFNSLTESFTAREKHLLWNKK 884 (1159)
Q Consensus 806 c~~yl~~~~~~~~~d~~~i~~~~~~~l~~~I~~~GG~v~~~ls-~vTHVIV~~~~~~~~~~~~l~~~l~~~~~~~~~~~~ 884 (1159)
|+||+.++.+. + +..+..++..+||++..+++ ++||+|+....+. .++ ... ...
T Consensus 1 ~~i~~sg~~~~---~--------~~~l~~~i~~~Gg~~~~~lt~~~THLI~~~~~~~--K~~---~A~---------~~g 55 (63)
T PF12738_consen 1 VVICFSGFSGK---E--------RSQLRKLIEALGGKYSKDLTKKTTHLICSSPEGK--KYR---KAK---------EWG 55 (63)
T ss_dssp -EEEEEEB-TT---T--------CCHHHHHHHCTT-EEESSSSTT-SEEEEES--HH--HHH---HHH---------HCT
T ss_pred CEEEECCCCHH---H--------HHHHHHHHHHCCCEEeccccCCceEEEEeCCCcH--HHH---HHH---------HCC
Confidence 57999998752 2 34788999999999999998 5999999764421 122 111 244
Q ss_pred cEEecccH
Q 001089 885 LHVVRSQW 892 (1159)
Q Consensus 885 ~~IVs~~W 892 (1159)
++||+++|
T Consensus 56 i~vV~~~W 63 (63)
T PF12738_consen 56 IPVVSPDW 63 (63)
T ss_dssp SEEEEHHH
T ss_pred CcEECCCC
Confidence 89999999
No 73
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=97.19 E-value=0.0047 Score=75.76 Aligned_cols=209 Identities=15% Similarity=0.200 Sum_probs=119.1
Q ss_pred cccccccc-cCChHHH---HHhcCCCcEEEEEecceEEEEEEEeCCE-EEEEec----CCCCcCcchh---hHHHHHHHh
Q 001089 224 VRPQLAMR-IGDAHAA---WRKLHGKEVVIECKFDGDRIQIHKNGSE-IHYFSR----SFLDHSEYGH---AMSKIIEQN 291 (1159)
Q Consensus 224 ~~PMLA~~-~~~~~~~---~~k~~~~~~~vE~K~DGeR~qih~~g~~-v~~fSR----~g~d~t~~~p---~l~~~l~~~ 291 (1159)
-.|||.-. +.+.++. +++. ..|++|+|+||.-+.+.+.+|. ++..|| -|+|+|+..- ++-..+. .
T Consensus 95 ~~PMlSL~k~~s~eel~~w~~~~--~~~~vepKiDGlsisL~Ye~G~Lv~a~TRGDG~~GEDVT~nv~~I~~IP~~l~-~ 171 (562)
T PRK08097 95 PVAHTGVKKLADKQALARWMAGR--SDLWVQPKVDGVAVTLVYRDGKLVQAISRGNGLKGEDWTAKARLIPAIPQQLP-G 171 (562)
T ss_pred CCCcccccccCCHHHHHHHHhhc--cceEEEEecccEEEEEEEECCEEEEEEecCCCccchhHHhhHhhhcccchhhc-C
Confidence 35898653 2233332 2222 2699999999999999887664 688999 5788886321 2211221 1
Q ss_pred cccCceeecceEEEEeCCCCcc-----cccccHHHHHHHhhcCCCCCCCeEEEEEeeeecCCccccCCCHHHHHHHHHHh
Q 001089 292 VLVDRCILDGEMLVWDTSLNRF-----AEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKV 366 (1159)
Q Consensus 292 ~~~~~~ILDGElv~~d~~~~~~-----~pFg~lq~i~~~~r~~~~~~~~~~~~vFDiL~lnG~~l~~~pl~eRr~~L~~~ 366 (1159)
.+..+.+-||++.-...-.+. -|.......+++..... ..+++.|++|++. +| .....++.+.|..+
T Consensus 172 -~~~~levRGEv~m~~~~F~~~~~g~aNPRN~AAGsLr~~d~~~-~~r~L~~f~y~~~--~~----~~t~~e~l~~L~~~ 243 (562)
T PRK08097 172 -ALANLVLQGELFLRREGHIQQQMGGINARAKVAGLMMRKDPSP-TLNQIGVFVWAWP--DG----PASMPERLAQLATA 243 (562)
T ss_pred -CCCeEEEEEEEEEeHHHHHHHhcCcCCchHHHhHHHhhcCcHh-hhccceEEEEECC--CC----CCCHHHHHHHHHHC
Confidence 133588899998742210000 01100011111110011 1467999999983 44 24677888888765
Q ss_pred hccCCCcceeeccCCCCCccccCCCCCccceecCCHHHHHHHHHHHHH----cCCceEEEecCCCCCcCC--CCCCCe--
Q 001089 367 VKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIE----NRDEGIVLKDLGSKWEPG--DRSGKW-- 438 (1159)
Q Consensus 367 i~~~~~~~~i~~p~~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~ai~----~g~EGlVlK~~ds~Y~pG--kRs~~W-- 438 (1159)
-=+... .....+.+.+++.++++.... -.-.|||+|--+-.|..| .+.+.|
T Consensus 244 GF~v~~---------------------~~~~~~~~~~~i~~~~~~~~r~~l~y~iDGiViKvn~~~~~~~~ts~~PrWAi 302 (562)
T PRK08097 244 GFPLTQ---------------------RYTHPVKNAEEVARWRERWYRAPLPFVTDGVVVRQAKEPPGRYWQPGQGEWAV 302 (562)
T ss_pred CCCcCc---------------------cceEeeCCHHHHHHHHHHHhhccCCCCCCcEEEEecCHHHHhhccCCCCCceE
Confidence 211110 012235678888887776542 367899999777666543 356677
Q ss_pred -EEEcccccccCCcccEEEEEEEeCCCCCCCccc
Q 001089 439 -LKLKPEYIRAGSDLDVLIIGGYYGSGRRGGEVA 471 (1159)
Q Consensus 439 -lKiKpey~~~g~~lDlvVIG~~~G~Grr~g~~g 471 (1159)
+|+-++ ...-.|.+-.|..|| .|.+.
T Consensus 303 AyKf~~~------~~~T~l~~I~~qVGR-TG~iT 329 (562)
T PRK08097 303 AWKYPPV------QQVAEVRAVQFAVGR-TGKIT 329 (562)
T ss_pred EEcCCCc------EEEEEEEEEEEecCC-Cceee
Confidence 455554 455677888887775 44443
No 74
>KOG3226 consensus DNA repair protein [Replication, recombination and repair]
Probab=97.17 E-value=0.00068 Score=76.10 Aligned_cols=90 Identities=13% Similarity=0.248 Sum_probs=70.1
Q ss_pred CCcCCCeEEEEcCCCCCCCCchHHHHHHHHHHHHHHHHhcCCEEEccCC-CceEEEEeccCCcccchhhHHHHHHHHhhh
Q 001089 800 WSCFHGCCIYFYHSTEPLSPDWEVLLGLALRRLKLEISFHGGKVCNNLA-NATHVVVLSVLGYDVNFNSLTESFTAREKH 878 (1159)
Q Consensus 800 ~~lF~gc~~yl~~~~~~~~~d~~~i~~~~~~~l~~~I~~~GG~v~~~ls-~vTHVIV~~~~~~~~~~~~l~~~l~~~~~~ 878 (1159)
..|+.|.+|-|+||.. ++ +..|+.....+|+++..+-+ +|||+|+.-++ ...|..+.
T Consensus 315 ~klL~GVV~VlSGfqN---P~--------Rs~LRskAl~LGAkY~pDW~~gsThLICAF~N--TPKy~QV~--------- 372 (508)
T KOG3226|consen 315 SKLLEGVVFVLSGFQN---PE--------RSTLRSKALTLGAKYQPDWNAGSTHLICAFPN--TPKYRQVE--------- 372 (508)
T ss_pred HHhhhceEEEEecccC---ch--------HHHHHHHHHhhcccccCCcCCCceeEEEecCC--Ccchhhcc---------
Confidence 3579999999999964 34 34677788899999999987 79999998654 23343211
Q ss_pred hccCCccEEecccHHHHHHHcCCccCCCCCCCCCCC
Q 001089 879 LLWNKKLHVVRSQWLEDCLAKEQKSEEYEYSLKPTG 914 (1159)
Q Consensus 879 ~~~~~~~~IVs~~WL~~ci~~g~~v~E~~Y~v~~~~ 914 (1159)
...-+||+-+||++|.+..++||-+.|++.-..
T Consensus 373 ---g~Gg~IV~keWI~~Cy~~kk~lp~rrYlm~~~~ 405 (508)
T KOG3226|consen 373 ---GNGGTIVSKEWITECYAQKKLLPIRRYLMHAGK 405 (508)
T ss_pred ---cCCceEeeHHHHHHHHHHHhhccHHHHHhcCCC
Confidence 123389999999999999999999999877664
No 75
>TIGR00575 dnlj DNA ligase, NAD-dependent. The member of this family from Treponema pallidum differs in having three rather than just one copy of the BRCT (BRCA1 C Terminus) domain (pfam00533) at the C-terminus. It is included in the seed.
Probab=97.15 E-value=0.0033 Score=79.07 Aligned_cols=225 Identities=18% Similarity=0.250 Sum_probs=127.1
Q ss_pred cEEEEEecceEEEEEEEeCCE-EEEEec----CCCCcCcchhh---HHHHHHHhcccCceeecceEEEEeCCCCc-----
Q 001089 246 EVVIECKFDGDRIQIHKNGSE-IHYFSR----SFLDHSEYGHA---MSKIIEQNVLVDRCILDGEMLVWDTSLNR----- 312 (1159)
Q Consensus 246 ~~~vE~K~DGeR~qih~~g~~-v~~fSR----~g~d~t~~~p~---l~~~l~~~~~~~~~ILDGElv~~d~~~~~----- 312 (1159)
.|++|+|+||.-+.+.+.+|. ++..|| .|+|+|+-... +-..+.....+..+.+-||++.-...-.+
T Consensus 97 ~~~~epKiDGlaisL~Ye~G~L~~a~TRGDG~~GeDvT~nv~~I~~iP~~i~~~~~p~~levRGEv~m~~~~F~~~N~~~ 176 (652)
T TIGR00575 97 EYVVEPKIDGLSVSLTYENGVLVRALTRGDGTVGEDVTANVRTIRSIPLRLAGDNPPERLEVRGEVFMPKEDFEALNEER 176 (652)
T ss_pred eEEEEEeccceEEEEEEECCEEEEEEecCCCccchhHhhhhhhhcccchhhcCCCCCceEEEEEEEEEEHHHHHHHHHHH
Confidence 599999999999999987665 788999 58888863221 11112100013458899999873211000
Q ss_pred ----ccccccHHHHH-HHhhc---CCCCCCCeEEEEEeeeecCCccccCCCHHHHHHHHHHhhccCCCcceeeccCCCCC
Q 001089 313 ----FAEFGSNQEIA-KAARD---GLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLN 384 (1159)
Q Consensus 313 ----~~pFg~lq~i~-~~~r~---~~~~~~~~~~~vFDiL~lnG~~l~~~pl~eRr~~L~~~i~~~~~~~~i~~p~~~~~ 384 (1159)
-.+|..-+..+ ...|. .....+++.|++|++....+ .......++.+.|..+-=+...
T Consensus 177 ~~~g~~~faNpRN~aAGslr~ld~~~~~~r~L~~~~y~~~~~~~--~~~~t~~e~l~~L~~~GF~v~~------------ 242 (652)
T TIGR00575 177 REQGEKPFANPRNAAAGSLRQLDPRITAKRKLRFFAYGLGEGLE--LPDATQYEALAWLKKWGFPVSP------------ 242 (652)
T ss_pred HHcCCCCCCCcHHHHHHHHHcCCchhhhcCccEEEEEeccccCC--CCCCCHHHHHHHHHHCCCCCCC------------
Confidence 01232222211 11111 11124689999999853221 1124778888888775211110
Q ss_pred ccccCCCCCccceecCCHHHHHHHHHHHHH------cCCceEEEecCCCCCcC----CCCCCCe---EEEcccccccCCc
Q 001089 385 SHVRPQGEPCWSLVAHNVDEVEKFFKETIE------NRDEGIVLKDLGSKWEP----GDRSGKW---LKLKPEYIRAGSD 451 (1159)
Q Consensus 385 ~~v~~~~~~~~~~~~~~~~ei~~~~~~ai~------~g~EGlVlK~~ds~Y~p----GkRs~~W---lKiKpey~~~g~~ 451 (1159)
....+.+.+++.++++++.+ -.-.|||+|--+-.+.. ..+.+.| +|+.++ .
T Consensus 243 ----------~~~~~~~~~ei~~~~~~~~~~R~~l~y~iDGiViKvn~~~~~~~lG~t~~~PrwaiA~Kf~~~------~ 306 (652)
T TIGR00575 243 ----------HIRLCDSIEEVLEYYREIEEKRDSLPYEIDGVVVKVDDLALQDELGFTSKAPRWAIAYKFPAE------E 306 (652)
T ss_pred ----------CeEeeCCHHHHHHHHHHHHHhhhcCCCCCCcEEEEecCHHHHHHhCccCCCCCceEEEcCCCc------e
Confidence 12245678999998887744 35689999976655431 2345667 566654 4
Q ss_pred ccEEEEEEEeCCCCCCCccceEEEEEecCCCCCCCCceEEEEEEecCCCCHHHHHHHH
Q 001089 452 LDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVV 509 (1159)
Q Consensus 452 lDlvVIG~~~G~Grr~g~~gsfllg~~d~~~~~~~~~~f~~v~kVgtG~sdeel~~l~ 509 (1159)
..-.|.+-.|-.|| .|.+.-. |..++-.- .+. +|.++ |..+.++++.+.
T Consensus 307 ~~T~l~~I~~qVGR-TG~iTPv--A~lePV~l---~G~--~VsrA-tLhN~~~i~~~~ 355 (652)
T TIGR00575 307 AQTKLLDVVVQVGR-TGAITPV--AKLEPVFV---AGT--TVSRA-TLHNEDEIEELD 355 (652)
T ss_pred eeEEEEEEEEecCC-CceeeeE--EEEeeEEE---CCE--EEEEe-ecCCHHHHHHcC
Confidence 56678888887775 4445332 22222100 011 34443 777777776543
No 76
>PF01653 DNA_ligase_aden: NAD-dependent DNA ligase adenylation domain; InterPro: IPR013839 DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA fragments by catalyzing the formation of an internucleotide ester bond between phosphate and deoxyribose. It is active during DNA replication, DNA repair and DNA recombination. There are two forms of DNA ligase: one requires ATP (6.5.1.1 from EC), the other NAD (6.5.1.2 from EC). This entry represents the N-terminal adenylation domain of NAD-dependent DNA ligases. These are proteins of about 75 to 85 Kd whose sequence is well conserved [, ]. They also show similarity to yicF, an Escherichia coli hypothetical protein of 63 Kd. Despite a complete lack of detectable sequence similarity, the fold of the central core of this adenyaltion domain shares homology with the equivalent region of ATP-dependent DNA ligases [, ].; GO: 0003911 DNA ligase (NAD+) activity; PDB: 1ZAU_A 3SGI_A 1B04_A 3JSL_A 3JSN_A 1DGS_A 1V9P_A 3PN1_A 3BAC_A 3UQ8_A ....
Probab=97.06 E-value=0.00019 Score=82.46 Aligned_cols=155 Identities=21% Similarity=0.302 Sum_probs=90.7
Q ss_pred cEEEEEecceEEEEEEEeCCE-EEEEecC----CCCcCcchhhHHHHHHHhcc--cCceeecceEEEEeCCCCccccccc
Q 001089 246 EVVIECKFDGDRIQIHKNGSE-IHYFSRS----FLDHSEYGHAMSKIIEQNVL--VDRCILDGEMLVWDTSLNRFAEFGS 318 (1159)
Q Consensus 246 ~~~vE~K~DGeR~qih~~g~~-v~~fSR~----g~d~t~~~p~l~~~l~~~~~--~~~~ILDGElv~~d~~~~~~~pFg~ 318 (1159)
.|++|+|+||.-|.+++.+|. ++..||. |+|+|+....+.. +-..+. +..+.+=||++.-. ..|..
T Consensus 108 ~~~~e~KiDGlsi~L~Y~~G~L~~a~TRGdG~~GeDvT~n~~~i~~-iP~~i~~~p~~~eVRGEv~m~~------~~F~~ 180 (315)
T PF01653_consen 108 EFVVEPKIDGLSISLIYENGKLVRAATRGDGEVGEDVTHNVRTIKS-IPLRIPEKPGRLEVRGEVYMSK------SDFEK 180 (315)
T ss_dssp EEEEEEEESSEEEEEEEETTEEEEEEEETTSSEEEB-HHHHCTSTT-S-SB-SSSSSEEEEEEEEE--H------HHHHH
T ss_pred ceeEeeccceeEEEEEEeCCEEEEEEEcCCCccchhHHHHHHHHhc-CchhhccCCcceEEEEEEEEeh------hhHHH
Confidence 499999999999999988776 6889994 6778753221111 001111 35778889998621 12322
Q ss_pred HH---------------HHHH-HhhcC---CCCCCCeEEEEEeeeecCCccccCCCHHHHHHHHHHhhccCCCcceeecc
Q 001089 319 NQ---------------EIAK-AARDG---LSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVP 379 (1159)
Q Consensus 319 lq---------------~i~~-~~r~~---~~~~~~~~~~vFDiL~lnG~~l~~~pl~eRr~~L~~~i~~~~~~~~i~~p 379 (1159)
+. ..+. ..+.. ....+++.|++|++.+.+| ...-....++.+.|..+-=++..
T Consensus 181 ln~~~~~~~~~~faNpRN~aAGsLr~~d~~~~~~r~L~f~~y~~~~~~~-~~~~~t~~e~l~~L~~~GF~v~~------- 252 (315)
T PF01653_consen 181 LNEEREEEGEKPFANPRNAAAGSLRQKDPSITAERKLSFFAYGIGEPEG-DLGFNTQSERLQFLKEWGFPVNP------- 252 (315)
T ss_dssp HHHHHHHTTS---SSHHHHHHHHHTSSSHHHHHTS--EEEEEEEEEETT-STT-SBHHHHHHHHHHTT--B-T-------
T ss_pred HHHHHHHhccchhhhhhHHHHHhhhhccchhhhcCeeEEEEEEeccccc-ccChHHHHHHHHHHHHcCCCCCc-------
Confidence 22 1111 11110 0123579999999999887 33345778888888875211110
Q ss_pred CCCCCccccCCCCCccceecCCHHHHHHHHHHHHHc------CCceEEEecCCCCCc
Q 001089 380 DHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIEN------RDEGIVLKDLGSKWE 430 (1159)
Q Consensus 380 ~~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~ai~~------g~EGlVlK~~ds~Y~ 430 (1159)
....+.+.+++..+++...+. .-.|||+|--+-.+.
T Consensus 253 ---------------~~~~~~~~~~v~~~~~~~~~~R~~l~y~iDGiVikvn~~~~~ 294 (315)
T PF01653_consen 253 ---------------YIRFCKSIEEVEEYIEEWEERREELPYPIDGIVIKVNDLALQ 294 (315)
T ss_dssp ---------------TEEEESSHHHHHHHHHHHHHHGCCSSS-EEEEEEEESBHHHH
T ss_pred ---------------ceEecCCHHHHHHHHHHHHhhhhccccccCcEEEEecCHHHH
Confidence 123456889999999887763 457999997554443
No 77
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=96.94 E-value=0.011 Score=74.75 Aligned_cols=223 Identities=18% Similarity=0.199 Sum_probs=125.7
Q ss_pred CcEEEEEecceEEEEEEEeCC-EEEEEec----CCCCcCcchhhH---HHHHHHhcccCceeecceEEEEeCCCCc----
Q 001089 245 KEVVIECKFDGDRIQIHKNGS-EIHYFSR----SFLDHSEYGHAM---SKIIEQNVLVDRCILDGEMLVWDTSLNR---- 312 (1159)
Q Consensus 245 ~~~~vE~K~DGeR~qih~~g~-~v~~fSR----~g~d~t~~~p~l---~~~l~~~~~~~~~ILDGElv~~d~~~~~---- 312 (1159)
..|++|+|+||.-+-+.+.+| =++..|| .|+|+|+-...+ -..+. ...+..+.+=||++.-...-.+
T Consensus 132 ~~~~~epKiDGlaisL~Ye~G~L~~a~TRGDG~~GeDVT~nv~~I~~IP~~l~-~~~p~~levRGEv~m~~~~F~~lN~~ 210 (689)
T PRK14351 132 VEYVCEPKFDGLSVEVVYEDGEYQRAATRGDGREGDDVTANVRTIRSVPQKLR-GDYPDFLAVRGEVYMPKDAFQAYNRE 210 (689)
T ss_pred ceEEEEEecccEEEEEEEECCEEEEEEecCCCCcceeHhhhhhhhcccchhhc-ccCCCeEEEEEEEEEEHHHHHHHHHH
Confidence 469999999999999888765 4788999 588998642222 11121 1113457788999874211000
Q ss_pred -----ccccccHHHHH-HHhhcC---CCCCCCeEEEEEeeeecCCccccCCCHHHHHHHHHHhhccCCCcceeeccCCCC
Q 001089 313 -----FAEFGSNQEIA-KAARDG---LSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGL 383 (1159)
Q Consensus 313 -----~~pFg~lq~i~-~~~r~~---~~~~~~~~~~vFDiL~lnG~~l~~~pl~eRr~~L~~~i~~~~~~~~i~~p~~~~ 383 (1159)
-.+|..-+..+ ...|.. ....+++.|++|++...++. .....++.+.|..+-=+...
T Consensus 211 ~~~~g~~~faNpRN~aAGslR~ldp~~~~~r~L~f~~y~~~~~~~~---~~t~~e~l~~L~~~GF~v~~----------- 276 (689)
T PRK14351 211 RIERGEEPFANPRNAAAGTLRQLDPSVVAERPLDIFFFDVLDASEL---FDSHWEELERFPEWGLRVTD----------- 276 (689)
T ss_pred HHHcCCCCcCCHHHHHhhHhhccChHHHhcCCceEEEEecccCCCC---CCCHHHHHHHHHHCCCCcCC-----------
Confidence 01232212111 111110 11236799999998755541 24677888888765211110
Q ss_pred CccccCCCCCccceecCCHHHHHHHHHHHHH------cCCceEEEecCCCCCc----CCCCCCCe---EEEcccccccCC
Q 001089 384 NSHVRPQGEPCWSLVAHNVDEVEKFFKETIE------NRDEGIVLKDLGSKWE----PGDRSGKW---LKLKPEYIRAGS 450 (1159)
Q Consensus 384 ~~~v~~~~~~~~~~~~~~~~ei~~~~~~ai~------~g~EGlVlK~~ds~Y~----pGkRs~~W---lKiKpey~~~g~ 450 (1159)
....+.+.+++.++++...+ -.-.|||+|--+-.+. ...+.+.| +|+.++
T Consensus 277 -----------~~~~~~~~~~~~~~~~~~~~~R~~l~y~iDGiViKvn~~~~q~~lG~ts~~PrWaiA~Kf~~~------ 339 (689)
T PRK14351 277 -----------RTERVDDIDDAIAYRDRLLAARDDLNYEIDGVVIKVDDRDAREELGATARAPRWAFAYKFPAR------ 339 (689)
T ss_pred -----------ceEeeCCHHHHHHHHHHHHHhhhcCCCCCceEEEEeCCHHHHHHhCccCCCCCceEEEcCCCc------
Confidence 01235678888888876653 3457999997665442 12356677 466654
Q ss_pred cccEEEEEEEeCCCCCCCccceEEEEEecCCCCCCCCceEEEEEEecCCCCHHHHHHH
Q 001089 451 DLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAV 508 (1159)
Q Consensus 451 ~lDlvVIG~~~G~Grr~g~~gsfllg~~d~~~~~~~~~~f~~v~kVgtG~sdeel~~l 508 (1159)
...-.|.+-.|-.|| .|.+.-. |..++-.- .+ .+|.++ |..+.++++.+
T Consensus 340 ~~~T~l~~I~~qVGR-TG~iTPV--A~lePV~l---~G--~tVsra-tLhN~~~i~~~ 388 (689)
T PRK14351 340 AEETTIRDIVVQVGR-TGRLTPV--ALLDPVDV---GG--VTVSRA-SLHNPAEIEEL 388 (689)
T ss_pred eeEEEEEEEEEecCC-CceeeeE--EEEEeEEE---CC--EEEEEe-ccCCHHHHHHc
Confidence 455677788887775 4444332 22222100 01 134444 66777776654
No 78
>PLN03123 poly [ADP-ribose] polymerase; Provisional
Probab=96.81 E-value=0.0022 Score=83.14 Aligned_cols=86 Identities=17% Similarity=0.361 Sum_probs=70.7
Q ss_pred CCCCcccCeEEEEEcCCCCCChHHHHHHHHHcCCEEEecCCCCceEEEEec---CCChhhHhHhcCC-CeeecchHHHHH
Q 001089 652 GETSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAAD---NKGLKYEAAKRRG-DVIHYSWVLDCC 727 (1159)
Q Consensus 652 ~~s~lF~G~~F~vv~~~~~~~k~eLe~lI~~~GG~iv~n~~~~~Th~Ia~~---~~~~k~~~a~~~~-~VV~p~WV~dCi 727 (1159)
+....|.|+.|++++.. ...+.++.++|..|||+++......+||+|+.. +.+.+++.|...+ +||+.+||.||+
T Consensus 389 ~~~~~l~~~~i~i~G~~-~~~~~~~k~~Ie~~GG~~s~~v~~~~t~l~tt~e~~k~~~kv~qAk~~~ipIVsedwL~ds~ 467 (981)
T PLN03123 389 SESEFLGDLKVSIVGAS-KEKVTEWKAKIEEAGGVFHATVKKDTNCLVVCGELDDEDAEMRKARRMKIPIVREDYLVDCF 467 (981)
T ss_pred ccCCCcCCeEEEEecCC-CCcHHHHHHHHHhcCCEEeeeccCCceEEEccHHhhhcchHHHHHHhcCCCcccHHHHHHHH
Confidence 56789999999998654 455689999999999999998887789887653 2455788887777 999999999999
Q ss_pred hcCccCCCCcc
Q 001089 728 SQKKLLQLQPK 738 (1159)
Q Consensus 728 ~~~~lLp~~p~ 738 (1159)
..+..+|...+
T Consensus 468 ~~~~~~p~~~y 478 (981)
T PLN03123 468 KKKKKLPFDKY 478 (981)
T ss_pred hccccCcchhh
Confidence 99988877654
No 79
>COG5163 NOP7 Protein required for biogenesis of the 60S ribosomal subunit [Translation, ribosomal structure and biogenesis]
Probab=96.70 E-value=0.0015 Score=73.86 Aligned_cols=83 Identities=22% Similarity=0.294 Sum_probs=62.2
Q ss_pred CCcCCCeEEEEcCCCCCCCCchHHHHHHHHHHHHHHHHhcCCEEEccCC------------CceEEEEeccCCcccchhh
Q 001089 800 WSCFHGCCIYFYHSTEPLSPDWEVLLGLALRRLKLEISFHGGKVCNNLA------------NATHVVVLSVLGYDVNFNS 867 (1159)
Q Consensus 800 ~~lF~gc~~yl~~~~~~~~~d~~~i~~~~~~~l~~~I~~~GG~v~~~ls------------~vTHVIV~~~~~~~~~~~~ 867 (1159)
.+||+|++||++...+ ...|..+|..+||.|..+.. .+||-||+.+.
T Consensus 348 ~slFS~f~FyisreVp-------------~dsLefiilscGG~V~~~p~~~~i~~~~~vD~~vth~i~drp~-------- 406 (591)
T COG5163 348 KSLFSGFKFYISREVP-------------GDSLEFIILSCGGSVVGSPCEADIHVSEKVDEKVTHQIVDRPV-------- 406 (591)
T ss_pred hhhhhceEEEEecccc-------------chHHHHHHHHcCCcccCchhhccCCchhhccchhhhhhccchh--------
Confidence 4689999999998654 24678899999999976531 27888886532
Q ss_pred HHHHHHHHhhhhccCCccEEecccHHHHHHHcCCccCCCCCCCCCC
Q 001089 868 LTESFTAREKHLLWNKKLHVVRSQWLEDCLAKEQKSEEYEYSLKPT 913 (1159)
Q Consensus 868 l~~~l~~~~~~~~~~~~~~IVs~~WL~~ci~~g~~v~E~~Y~v~~~ 913 (1159)
+.+.. -....|.|.||.+||..|.+++.+.|.+...
T Consensus 407 ~~~kv----------egrtYiQPQw~fDsiNkG~l~~~~~Y~~G~~ 442 (591)
T COG5163 407 MKNKV----------EGRTYIQPQWLFDSINKGKLACVENYCVGKR 442 (591)
T ss_pred hhhhh----------cceeeechHHHHhhhccccchhhhhcccccc
Confidence 11111 2336799999999999999999999987643
No 80
>PRK01109 ATP-dependent DNA ligase; Provisional
Probab=96.57 E-value=0.0098 Score=74.41 Aligned_cols=97 Identities=14% Similarity=0.112 Sum_probs=79.3
Q ss_pred CCCCcHHHHHHHHHHHHhhC---ChHHHHHHHHHHHhhcCCCchHHHHHHHhCCCCCCCccccCCCHHHHHHHHHHHhCC
Q 001089 4 TEETEVIVLVSLFNWIQKTK---PAAKKRSKFRKFLDTYCDSVDYFSALRLILPSLDRERGSYGLKESVLANCLIDALGM 80 (1159)
Q Consensus 4 ~~~~~F~~l~~lle~i~~~~---~~~~K~~~l~~~l~~~~~~~d~~p~lrLllP~~d~~r~~ygike~~L~k~~~~~lgl 80 (1159)
.++++|.+++++|++|++++ ++.+|..+|.++|.+. .+.+...++||++..+. .|++++++.++|+.++|.
T Consensus 112 ~~~lti~eV~~~L~~Ia~~sg~~s~~~k~~iL~~Ll~~~-~~~E~k~iirli~g~lr-----iGv~e~~il~ALa~A~~~ 185 (590)
T PRK01109 112 KEPLTVKEVYDTLVKIALATGEGSQDLKIKLLAGLLKDA-SPLEAKYIARFVEGRLR-----LGVGDATILDALAIAFGG 185 (590)
T ss_pred CCCcCHHHHHHHHHHHHhhhCCCcHHHHHHHHHHHHHhC-CHHHHHHHHHHHhhhhh-----cCccHHHHHHHHHHHHhc
Confidence 46799999999999999997 7789999999999987 56889999999999983 699999999999999982
Q ss_pred CcChHHHHHHhhhhcCCCCCCCCCHHHHHHHHhh
Q 001089 81 SKDSADAVRLINWRKGGAAPNAGNFPMVAAEVLQ 114 (1159)
Q Consensus 81 ~~~s~~~~~L~~wk~~~~~~~~GD~~~~a~~vl~ 114 (1159)
.....+..++.+ ..||++.+|..+..
T Consensus 186 ~~~~~~ve~~y~--------~~~Dlg~va~~l~~ 211 (590)
T PRK01109 186 AVARELVERAYN--------LRADLGYIAKILAE 211 (590)
T ss_pred ccchHHHHHHHH--------hCCCHHHHHHHHHh
Confidence 222334444433 47999999887653
No 81
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=96.55 E-value=0.027 Score=70.93 Aligned_cols=225 Identities=16% Similarity=0.159 Sum_probs=121.7
Q ss_pred cEEEEEecceEEEEEEEeCCE-EEEEec----CCCCcCcchhhHHHHHHHhcc-cCceeecceEEEEeCCCC-----ccc
Q 001089 246 EVVIECKFDGDRIQIHKNGSE-IHYFSR----SFLDHSEYGHAMSKIIEQNVL-VDRCILDGEMLVWDTSLN-----RFA 314 (1159)
Q Consensus 246 ~~~vE~K~DGeR~qih~~g~~-v~~fSR----~g~d~t~~~p~l~~~l~~~~~-~~~~ILDGElv~~d~~~~-----~~~ 314 (1159)
.|++|+|+||.-+.+.+.+|. ++..|| .|+|+|+-.-.+.. +-..+. ...+.+-||++.-...-. .-.
T Consensus 111 ~~~~epKiDGlaisL~YenG~L~~a~TRGDG~~GEDVT~n~~~I~~-IP~~l~~~~~levRGEv~m~~~~F~~lN~~~~~ 189 (669)
T PRK14350 111 GISVEPKIDGCSIVLYYKDGILEKALTRGDGRFGNDVTENVRTIRN-VPLFIDEKVELVLRGEIYITKENFLKINKTLEK 189 (669)
T ss_pred eEEEEEecccEEEEEEEECCEEEEEEecCCCCcchhHhhhhhhhcc-cchhcCCCceEEEEEEEEeeHHHHHHHHHhhhc
Confidence 599999999999998887664 678999 58888863211111 101111 245788899987321100 002
Q ss_pred ccccHHHHH-HHhhc---CCCCCCCeEEEEEeeeecCCccccCCCHHHHHHHHHHhhccCCCcceeeccCCCCCccccCC
Q 001089 315 EFGSNQEIA-KAARD---GLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQ 390 (1159)
Q Consensus 315 pFg~lq~i~-~~~r~---~~~~~~~~~~~vFDiL~lnG~~l~~~pl~eRr~~L~~~i~~~~~~~~i~~p~~~~~~~v~~~ 390 (1159)
+|..-+..+ ...|. .....+++.|++|++...++. ..+..++.+.|.++-=+......+
T Consensus 190 ~faNpRNaaAGsLr~~d~~~~a~r~L~f~~y~~~~~~~~---~~t~~e~l~~L~~~GF~v~~~~~~-------------- 252 (669)
T PRK14350 190 PYTNARNLASGILRRIDSREVANFPLDIFVYDILYSSLE---LKTNHDAFDKLKKFGFKVNPFCRF-------------- 252 (669)
T ss_pred cCCChhHHHHHHHHccCchhhhcCceEEEEEEcccCCCC---CCCHHHHHHHHHHCCCCCCcceEE--------------
Confidence 332222211 11111 111246899999998532221 236778888887752121110000
Q ss_pred CCCccceecCCHHHHHHHHHHHHH------cCCceEEEecCCCCCcC--C--CCCCCe---EEEcccccccCCcccEEEE
Q 001089 391 GEPCWSLVAHNVDEVEKFFKETIE------NRDEGIVLKDLGSKWEP--G--DRSGKW---LKLKPEYIRAGSDLDVLII 457 (1159)
Q Consensus 391 ~~~~~~~~~~~~~ei~~~~~~ai~------~g~EGlVlK~~ds~Y~p--G--kRs~~W---lKiKpey~~~g~~lDlvVI 457 (1159)
.....+.+++..+++++.. -.-.|||+|--+-.+.. | .+.+.| +|+.++ ...-.|.
T Consensus 253 -----~~~~~~~~e~~~~~~~~~~~R~~l~y~iDGiViKvn~~~~q~~lG~ts~~PrWaiA~Kf~~~------~~~T~l~ 321 (669)
T PRK14350 253 -----FDGKNSIEEILNYVKDIEKKRNSFEYEIDGVVLKVSDFALREILGYTSHHPKWSMAYKFESL------SGFSKVN 321 (669)
T ss_pred -----EcCCCcHHHHHHHHHHHHHHHhcCCCCCCcEEEEecCHHHHHhcCCcCCCCCceEEEcCCCc------eeEEEEE
Confidence 0001247788887776533 34589999975543332 2 245677 566664 4556777
Q ss_pred EEEeCCCCCCCccceEEEEEecCCCCCCCCceEEEEEEecCCCCHHHHHHH
Q 001089 458 GGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAV 508 (1159)
Q Consensus 458 G~~~G~Grr~g~~gsfllg~~d~~~~~~~~~~f~~v~kVgtG~sdeel~~l 508 (1159)
+-.|-.|| .|.+.-. |..++-.- .+ .+|.++ |..+.++++++
T Consensus 322 ~I~~qVGR-TG~iTPV--A~l~PV~l---~G--~tVsrA-TLhN~~~I~~~ 363 (669)
T PRK14350 322 DIVVQVGR-SGKITPV--ANIEKVFV---AG--AFITNA-SLHNQDYIDSI 363 (669)
T ss_pred EEEEecCC-ceeeeEE--EEEEeEEE---CC--EEEEEe-ccCCHHHHHHc
Confidence 88887775 4444322 22222100 01 234443 67777777654
No 82
>PLN03122 Poly [ADP-ribose] polymerase; Provisional
Probab=96.24 E-value=0.01 Score=75.64 Aligned_cols=95 Identities=24% Similarity=0.327 Sum_probs=69.4
Q ss_pred CCCcCCCeEEEEcCCCCCCCCchHHHHHHHHHHHHHHHHhcCCEEEccCCCceEEEEeccCCcccchhhHHHHHHHHhhh
Q 001089 799 KWSCFHGCCIYFYHSTEPLSPDWEVLLGLALRRLKLEISFHGGKVCNNLANATHVVVLSVLGYDVNFNSLTESFTAREKH 878 (1159)
Q Consensus 799 ~~~lF~gc~~yl~~~~~~~~~d~~~i~~~~~~~l~~~I~~~GG~v~~~ls~vTHVIV~~~~~~~~~~~~l~~~l~~~~~~ 878 (1159)
+...|.|++|.|.|... . ....++.+|..+||++++.++.+||+|+....-....-..++++.
T Consensus 186 ~~kpL~G~~fviTGtl~---~--------sr~elK~~Ie~~GGkvsssVs~~T~lIvt~~ev~k~gsSKlkkAk------ 248 (815)
T PLN03122 186 PGKPFSGMMISLSGRLS---R--------THQYWKKDIEKHGGKVANSVEGVTCLVVSPAERERGGSSKIAEAM------ 248 (815)
T ss_pred cCCCcCCcEEEEeCCCC---C--------CHHHHHHHHHHcCCEEccccccceEEEEcCccccccCccHHHHHH------
Confidence 34469999999999642 1 145789999999999999998899999875320000001122211
Q ss_pred hccCCccEEecccHHHHHHHcCCccCCCCCCCCCC
Q 001089 879 LLWNKKLHVVRSQWLEDCLAKEQKSEEYEYSLKPT 913 (1159)
Q Consensus 879 ~~~~~~~~IVs~~WL~~ci~~g~~v~E~~Y~v~~~ 913 (1159)
...++||+.+||.+|++.+..+++..|.+..+
T Consensus 249 ---~lgIpIVsEd~L~d~i~~~k~~~~~~y~l~~~ 280 (815)
T PLN03122 249 ---ERGIPVVREAWLIDSIEKQEAQPLEAYDVVSD 280 (815)
T ss_pred ---HcCCcCccHHHHHHHHhcCCcccchhhhhccc
Confidence 24689999999999999999999999988533
No 83
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=96.19 E-value=0.016 Score=71.52 Aligned_cols=195 Identities=22% Similarity=0.249 Sum_probs=115.4
Q ss_pred CCcccCeEEEEEcCCCCCChHHHHHHHHHcCCEEEecCCCCceEEEEecC------CChhhHhHhcCC-CeeecchHHHH
Q 001089 654 TSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADN------KGLKYEAAKRRG-DVIHYSWVLDC 726 (1159)
Q Consensus 654 s~lF~G~~F~vv~~~~~~~k~eLe~lI~~~GG~iv~n~~~~~Th~Ia~~~------~~~k~~~a~~~~-~VV~p~WV~dC 726 (1159)
+.=|.--.-.++++....+++-|++.++. ++..++...+||+|+..- .|.+|.-.+-.| =|+++.|+..|
T Consensus 472 ~~~~~kk~~~~~s~l~p~ek~~v~~~a~~---t~~k~~~~~~thvi~~~~~~g~c~rTlk~~~gil~gkwi~~~~w~~~s 548 (684)
T KOG4362|consen 472 THRFKKKLVLLVSGLTPSEKQLVEKFAVD---TISKFWIEPVTHVIASTDLEGACLRTLKVLMGILRGKWILSYDWVLAS 548 (684)
T ss_pred ccCcccceeeeeccCCcchHHHHHHHHHH---HHhhccCCCceeeeeecccccchhhhHHHHHHhhcCceeeeHHHHHHH
Confidence 33344444445566655667888888877 777777778999998532 455666556666 89999999999
Q ss_pred HhcCccCCCCcccccccChhhhhhhhhcccccCCCcccCCChhHHHHHhhccCCCCCcchhHHHhhhcCCCCCCCcCCCe
Q 001089 727 CSQKKLLQLQPKYYLHLSDSSKKKLQEEVDEFSDLYFWDLDLADIKQLLSNVDRSEDPKTIDYYKKKYCPQDKWSCFHGC 806 (1159)
Q Consensus 727 i~~~~lLp~~p~~~l~~s~~t~~~~~~~~D~~GDSy~~~~~~~~L~~ll~~~~~s~~~~~i~~l~~~~~~~~~~~lF~gc 806 (1159)
+..+.+++.+|+.+-..+...++.. + ... + -.......||.|.
T Consensus 549 ~k~~~~~~eepfEl~~d~~~~~~~~----------~-----~~~-------------------~---~a~s~~~kLf~gl 591 (684)
T KOG4362|consen 549 LKLRKWVSEEPFELQIDVPGAREGP----------K-----EKR-------------------L---RAESYKPKLFEGL 591 (684)
T ss_pred HHhcCCCCCCCeeEeecccCcccCc----------c-----ccc-------------------c---cccccCcchhcCC
Confidence 9999999999865432211111100 0 000 0 0011245789999
Q ss_pred EEEEcCCCCCCCCchHHHHHHHHHHHHHHHHhcCCEEEccCC------CceEEEEecc-CCcccchhhHHHHHHHHhhhh
Q 001089 807 CIYFYHSTEPLSPDWEVLLGLALRRLKLEISFHGGKVCNNLA------NATHVVVLSV-LGYDVNFNSLTESFTAREKHL 879 (1159)
Q Consensus 807 ~~yl~~~~~~~~~d~~~i~~~~~~~l~~~I~~~GG~v~~~ls------~vTHVIV~~~-~~~~~~~~~l~~~l~~~~~~~ 879 (1159)
-|||.+--. +.. .+.|..++-.-||++..--+ .++-|++.+. +........-...+ . .+
T Consensus 592 ~~~~~g~fs--~~p--------~~~l~~l~~~~gg~~l~~~~~~~~~~k~s~~~~~~~~~~~~~~~~~k~~~~-e---a~ 657 (684)
T KOG4362|consen 592 KFYFVGDFS--NPP--------KEQLQELVHLAGGTILQVPRVAYSDKKKSTIVVLSEKPVLDSILWQKVNDA-E---AL 657 (684)
T ss_pred cceeecccc--cCc--------HHHHHHHHhhcCcceeeccCcccccccccceeEeecccCCCchhhhhhccH-H---HH
Confidence 999998432 222 35788899999999865432 3555555432 11111110000000 0 01
Q ss_pred ccCCccEEecccHHHHHHHcCCc
Q 001089 880 LWNKKLHVVRSQWLEDCLAKEQK 902 (1159)
Q Consensus 880 ~~~~~~~IVs~~WL~~ci~~g~~ 902 (1159)
....+...|+..||.++|.-.+.
T Consensus 658 ~~s~~a~~~~~~wvl~s~a~~~~ 680 (684)
T KOG4362|consen 658 ALSQRARAVSSSWVLDSIAGYQI 680 (684)
T ss_pred HHhcCCCccchhhhhcchhceee
Confidence 12245688999999999875443
No 84
>TIGR02307 RNA_lig_RNL2 RNA ligase, Rnl2 family. Members of this family ligate (seal breaks in) RNA. Members so far include phage proteins that can counteract a host defense of cleavage of specific tRNA molecules, trypanosome ligases involved in RNA editing, but no prokaryotic host proteins.
Probab=96.09 E-value=0.06 Score=61.80 Aligned_cols=106 Identities=17% Similarity=0.093 Sum_probs=63.7
Q ss_pred cCCCcEEEEEecceEEEEEEEeCC-EEEEEecCCCCcC-cch-------hhHHHHHH---Hhc------ccCceeecceE
Q 001089 242 LHGKEVVIECKFDGDRIQIHKNGS-EIHYFSRSFLDHS-EYG-------HAMSKIIE---QNV------LVDRCILDGEM 303 (1159)
Q Consensus 242 ~~~~~~~vE~K~DGeR~qih~~g~-~v~~fSR~g~d~t-~~~-------p~l~~~l~---~~~------~~~~~ILDGEl 303 (1159)
+.+..|.+.+|.||..+-+.++++ .+++.||++.-.. +.| +.+...+. ..+ ...++++=||+
T Consensus 22 l~~~ewvatEKlhGaNfsi~~~~~~~i~~akR~~~l~~~e~f~G~~~i~~~l~~~~~~l~~~l~~~~~~~~~~v~IyGEl 101 (325)
T TIGR02307 22 LGLTEWVAREKIHGTNFSIIIERDFKVTCAKRTGIILPNEDFFGYHILIKNYTASVKAIQDILETKAIIVVVSVQVFGEL 101 (325)
T ss_pred cCCceEEEEEEecCcceEEEEeCCceEEEeecccccCcccccccHHHHHHHHHHHHHHHHHHHhhhcccccceEEEEEEe
Confidence 445689999999999998888877 8999999965332 111 21211111 111 23678899999
Q ss_pred EEEeCCCCcccccccHHHHHHHhhcCCCCCCCeEEEEEeeeecCCccccCCCHHHHHHHHHHh
Q 001089 304 LVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKV 366 (1159)
Q Consensus 304 v~~d~~~~~~~pFg~lq~i~~~~r~~~~~~~~~~~~vFDiL~lnG~~l~~~pl~eRr~~L~~~ 366 (1159)
+.|.-..+. . +. ...|++|||.+....+..=+++.+-.+.....
T Consensus 102 ~G~~~q~~~------~----------Y~---~~~fyaFdI~~~~~~~~~~L~~d~~~e~~~~~ 145 (325)
T TIGR02307 102 AGPGYQKPV------V----------YS---DKDFYAFDIKYTETSDDVTLVDDYMMESFCNV 145 (325)
T ss_pred ecCcccCcc------c----------cc---cccEEEEEEEEeccCcceEecHHHHHHHHHHc
Confidence 886421110 0 11 35799999955312123345666666655543
No 85
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=95.62 E-value=0.025 Score=71.21 Aligned_cols=74 Identities=16% Similarity=0.249 Sum_probs=64.7
Q ss_pred CCcccCeEEEEEcCCCCCChHHHHHHHHHcCCEEEecCCCCceEEEEecCCChhhHhHhcCC-CeeecchHHHHH
Q 001089 654 TSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADNKGLKYEAAKRRG-DVIHYSWVLDCC 727 (1159)
Q Consensus 654 s~lF~G~~F~vv~~~~~~~k~eLe~lI~~~GG~iv~n~~~~~Th~Ia~~~~~~k~~~a~~~~-~VV~p~WV~dCi 727 (1159)
...|.|..|||++.....+|++++++|.++||++....+..++++|++...+-|...|...| +|++.+.+.+-+
T Consensus 591 ~~~l~gktfV~TG~l~~~~R~e~~~lie~~Ggkv~ssVSkktd~LV~G~~aGsKl~KA~~LGI~Ii~e~~f~~~l 665 (669)
T PRK14350 591 NSFLFGKKFCITGSFNGYSRSVLIDKLTKKGAIFNTCVTKYLDFLLVGEKAGLKLKKANNLGIKIMSLFDIKSYV 665 (669)
T ss_pred CCccCCcEEEEecccCCCCHHHHHHHHHHcCCEEeccccCCCcEEEECCCCCchHHHHHHcCCEEecHHHHHHHh
Confidence 34799999999876667899999999999999999999988889998877788999998888 999988887744
No 86
>PLN03123 poly [ADP-ribose] polymerase; Provisional
Probab=95.57 E-value=0.023 Score=74.01 Aligned_cols=90 Identities=19% Similarity=0.285 Sum_probs=65.5
Q ss_pred CCcCCCeEEEEcCCCCCCCCchHHHHHHHHHHHHHHHHhcCCEEEccCC-CceEEEEeccCCcccchhhHHHHHHHHhhh
Q 001089 800 WSCFHGCCIYFYHSTEPLSPDWEVLLGLALRRLKLEISFHGGKVCNNLA-NATHVVVLSVLGYDVNFNSLTESFTAREKH 878 (1159)
Q Consensus 800 ~~lF~gc~~yl~~~~~~~~~d~~~i~~~~~~~l~~~I~~~GG~v~~~ls-~vTHVIV~~~~~~~~~~~~l~~~l~~~~~~ 878 (1159)
...|.|+.|.+.|... .. ...++..|..+||+++..++ .|||||+.... ...-..+..+
T Consensus 391 ~~~l~~~~i~i~G~~~---~~--------~~~~k~~Ie~~GG~~s~~v~~~~t~l~tt~e~------~k~~~kv~qA--- 450 (981)
T PLN03123 391 SEFLGDLKVSIVGASK---EK--------VTEWKAKIEEAGGVFHATVKKDTNCLVVCGEL------DDEDAEMRKA--- 450 (981)
T ss_pred CCCcCCeEEEEecCCC---Cc--------HHHHHHHHHhcCCEEeeeccCCceEEEccHHh------hhcchHHHHH---
Confidence 4569999999999542 11 24678899999999999998 59998876421 1111111111
Q ss_pred hccCCccEEecccHHHHHHHcCCccCCCCCCCC
Q 001089 879 LLWNKKLHVVRSQWLEDCLAKEQKSEEYEYSLK 911 (1159)
Q Consensus 879 ~~~~~~~~IVs~~WL~~ci~~g~~v~E~~Y~v~ 911 (1159)
....++||+.+||.+|+..+.++|+..|.+.
T Consensus 451 --k~~~ipIVsedwL~ds~~~~~~~p~~~y~~~ 481 (981)
T PLN03123 451 --RRMKIPIVREDYLVDCFKKKKKLPFDKYKLE 481 (981)
T ss_pred --HhcCCCcccHHHHHHHHhccccCcchhhhhc
Confidence 1235899999999999999999999999664
No 87
>PF09414 RNA_ligase: RNA ligase; InterPro: IPR021122 This entry represents the RNA ligase domain. RNA ligase enzyme repairs RNA strand breaks in nicked DNA:RNA and RNA:RNA but not in DNA:DNA duplexes []. Members of this RNA ligase family include: RNA editing ligase 1 (REL1) , which is essential for RNA editing and may be active in U-deletion editing [, , ]. RNA editing ligase 2 (REL2), which may be active in U-insertion editing []. RnlB RNA ligase 2 (or Rnl2), second RNA ligase of Enterobacteria phage T4 (Bacteriophage T4); unlike RNA ligase 1, RnlB prefers doule stranded substrates [, ]. ; PDB: 2HVS_B 2HVR_A 1S68_A 2HVQ_A 1XDN_A.
Probab=95.51 E-value=0.025 Score=60.20 Aligned_cols=106 Identities=22% Similarity=0.315 Sum_probs=60.6
Q ss_pred cEEEEEecceEEEEEEEe-CCEEEEEecCCCC-----cCcc------hhhH----HHHHHHh-----cccCceeecceEE
Q 001089 246 EVVIECKFDGDRIQIHKN-GSEIHYFSRSFLD-----HSEY------GHAM----SKIIEQN-----VLVDRCILDGEML 304 (1159)
Q Consensus 246 ~~~vE~K~DGeR~qih~~-g~~v~~fSR~g~d-----~t~~------~p~l----~~~l~~~-----~~~~~~ILDGElv 304 (1159)
+|.+.+|+||.-+.+... ++.+++.+|++.- +... +... ....... ....++++=||++
T Consensus 2 e~vvtEKldGtn~~i~~~~~~~~~~~~R~~~l~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~GE~~ 81 (186)
T PF09414_consen 2 EVVVTEKLDGTNFSIYFDNDGRVRFQSRSHILDPNEDFFGYQSGDNRYWAQARWLFELLKLAELASELLPENIIIYGELV 81 (186)
T ss_dssp EEEEEEE-SSEEEEEEEEECTCEEEEETTEE--TT---TTCHHHHHHCHHHHHHHHHHHHHHCCEC----SEEEEEEEEE
T ss_pred eEEEEEEeCCccEEEEEeCCCceeEeccccccCccccccccccchHHHHHHHHHHHhhhhhhhhcccccceEEEEEEEee
Confidence 689999999999998885 4459999999822 1111 0111 1111111 2356889999999
Q ss_pred EEeCCCCcccccccHHHHHHHhhcCCCCCCCeEEEEEeeeecCCc-cccCCCHHHHHHHHHHh
Q 001089 305 VWDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDT-SVIHQSLKERHELLQKV 366 (1159)
Q Consensus 305 ~~d~~~~~~~pFg~lq~i~~~~r~~~~~~~~~~~~vFDiL~lnG~-~l~~~pl~eRr~~L~~~ 366 (1159)
.|-+. +... .. . ...+..|++|||...+.. ...=++..+.+.+++.+
T Consensus 82 G~~~~---Iq~~-~~---------~--~~~~~~F~~Fdi~~~~~~~~~~~l~~~~~~~~~~~~ 129 (186)
T PF09414_consen 82 GAKPS---IQKN-RY---------Q--LDPPKDFYVFDIYDIDEQGEIRYLSWDEVREFAEEL 129 (186)
T ss_dssp CEECT---TCSS----------------ECCCEEEEEEEEEEETCCGEEE-HHHHHHHHHCCC
T ss_pred eeccc---cccc-cc---------c--cCCCceEEEEEEEEcCCCCeeEECCHHHHHHHHHHC
Confidence 86532 1000 00 0 012578999999988532 22345777777777654
No 88
>KOG2093 consensus Translesion DNA polymerase - REV1 deoxycytidyl transferase [Replication, recombination and repair]
Probab=95.37 E-value=0.021 Score=70.98 Aligned_cols=199 Identities=15% Similarity=0.157 Sum_probs=118.7
Q ss_pred ccCCCCcccCeEEEEEcCCCCCChHHHHHHHHHcCCEEE-ecCCCCceEEEEecCCChhhHhHhcCC-CeeecchHHHHH
Q 001089 650 IKGETSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFS-MNLNNSVTHCVAADNKGLKYEAAKRRG-DVIHYSWVLDCC 727 (1159)
Q Consensus 650 ~~~~s~lF~G~~F~vv~~~~~~~k~eLe~lI~~~GG~iv-~n~~~~~Th~Ia~~~~~~k~~~a~~~~-~VV~p~WV~dCi 727 (1159)
-...++.|+|..||+ ++....+..++.+.-.-|||.+. ......++|+|+.+-...+++.+ .. ..++++|+.+|+
T Consensus 41 ~~t~~s~fs~is~~~-ngs~~e~~nelk~~~~~~t~~~~~~~~rs~T~~ii~~~l~a~~vk~~--~~~~~~~~e~iie~~ 117 (1016)
T KOG2093|consen 41 AATGSSSFSGISISV-NGSTDESANELKLQNMFHTGASAASYERSGTENIIAQGLPADLVKGF--TIPKHISIEWIIECC 117 (1016)
T ss_pred CcCCcceeeeeeecc-CCccccchHHHhhhhhhcccccccccccccceeeecccchHHHhccc--cchhhhcHHHHHHHH
Confidence 346788999999996 67667788899999999999986 44445578898766443333332 22 789999999999
Q ss_pred hcCccCCCCcccccccChhhhhhhhhcccccCCCcccCCChhHHHHHhhccCCCCCcchhHHHhhhcCCCCCCCcCCCeE
Q 001089 728 SQKKLLQLQPKYYLHLSDSSKKKLQEEVDEFSDLYFWDLDLADIKQLLSNVDRSEDPKTIDYYKKKYCPQDKWSCFHGCC 807 (1159)
Q Consensus 728 ~~~~lLp~~p~~~l~~s~~t~~~~~~~~D~~GDSy~~~~~~~~L~~ll~~~~~s~~~~~i~~l~~~~~~~~~~~lF~gc~ 807 (1159)
+.+.++.+.|++........+..+.-..++ +- .+ +-....+.-+|.+|+
T Consensus 118 ~~~~~~~~~~~~~~t~~~h~q~~~~~~~~~----~~------------------~D---------~q~~~~~~ki~~~n~ 166 (1016)
T KOG2093|consen 118 ENGMDVGYYPYQLYTGQSHEQAQLAFPVTS----FP------------------KD---------QQISSQSSKIFKNNV 166 (1016)
T ss_pred hccCccccccceeeccchhcccccCCCccc----CC------------------cc---------ccccccchhccccce
Confidence 999999999876554332222221111110 00 00 000112456899999
Q ss_pred EEEcCCCCCCCCchHHHHHHHHHHHHHHHHhcCCEEEccCC--C-ceEEEEeccCCcccchhhHHHHHHHHhhhhccCCc
Q 001089 808 IYFYHSTEPLSPDWEVLLGLALRRLKLEISFHGGKVCNNLA--N-ATHVVVLSVLGYDVNFNSLTESFTAREKHLLWNKK 884 (1159)
Q Consensus 808 ~yl~~~~~~~~~d~~~i~~~~~~~l~~~I~~~GG~v~~~ls--~-vTHVIV~~~~~~~~~~~~l~~~l~~~~~~~~~~~~ 884 (1159)
||+-|+....+-| + + --....+++...+..+ + ++|.+.... +++ .+-..
T Consensus 167 ikinG~~E~~~~d------l--e--pp~gv~~d~~~~~~~~~rd~v~~~l~~~~---------l~n---------~~f~n 218 (1016)
T KOG2093|consen 167 IKINGYNEPESLD------L--E--PPSGVLHDKAEDDSTSARDHVDHELAGNL---------LLN---------KRFVN 218 (1016)
T ss_pred eeecCCCCccccc------c--C--CCcccccchhhhhhhhHHHHHHHHhcccc---------ccc---------cccce
Confidence 9999987422101 0 0 0011112333322222 2 455554321 000 00134
Q ss_pred cEEecccHHHHHHHcCCccCCCCCCC
Q 001089 885 LHVVRSQWLEDCLAKEQKSEEYEYSL 910 (1159)
Q Consensus 885 ~~IVs~~WL~~ci~~g~~v~E~~Y~v 910 (1159)
...++|.|+.+.+..-....-..|.-
T Consensus 219 ~~~~sP~~~~~k~~~a~~~~~~~~Ss 244 (1016)
T KOG2093|consen 219 IENTSPDWIVDKELTAHTGTGQNYSS 244 (1016)
T ss_pred eeecCchhhhhhhhhhccCCcccccc
Confidence 57799999999998877777777773
No 89
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=95.24 E-value=0.043 Score=69.46 Aligned_cols=76 Identities=14% Similarity=0.252 Sum_probs=66.5
Q ss_pred CCcccCeEEEEEcCCCCCChHHHHHHHHHcCCEEEecCCCCceEEEEecCCC-hhhHhHhcCC-CeeecchHHHHHhc
Q 001089 654 TSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADNKG-LKYEAAKRRG-DVIHYSWVLDCCSQ 729 (1159)
Q Consensus 654 s~lF~G~~F~vv~~~~~~~k~eLe~lI~~~GG~iv~n~~~~~Th~Ia~~~~~-~k~~~a~~~~-~VV~p~WV~dCi~~ 729 (1159)
...|.|..|||++.....+|++++++|.++||++..+.+..++++|+++..+ -|.+.|...+ +|++-+-+++-++.
T Consensus 607 ~~~l~g~~~v~TG~l~~~~R~~~~~~i~~~Gg~v~~sVs~kt~~Lv~G~~~g~sKl~kA~~lgi~ii~E~~f~~ll~~ 684 (689)
T PRK14351 607 GDALDGLTFVFTGSLSGYTRSEAQELVEAHGGNATGSVSGNTDYLVVGENPGQSKRDDAEANDVPTLDEEEFEELLAE 684 (689)
T ss_pred CCCCCCcEEEEccCCCCCCHHHHHHHHHHcCCEEcCCcCCCccEEEEcCCCChhHHHHHHHCCCeEecHHHHHHHHHh
Confidence 4579999999987666789999999999999999999998889999887777 5888888888 99999988887765
No 90
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=94.95 E-value=0.059 Score=62.28 Aligned_cols=74 Identities=15% Similarity=0.146 Sum_probs=62.1
Q ss_pred CCCcccCeEEEEEcCCCCCChHHHHHHHHHcCCEEEecCCCCceEEEEecCCC--hhhHhHhcCC-CeeecchHHHHH
Q 001089 653 ETSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADNKG--LKYEAAKRRG-DVIHYSWVLDCC 727 (1159)
Q Consensus 653 ~s~lF~G~~F~vv~~~~~~~k~eLe~lI~~~GG~iv~n~~~~~Th~Ia~~~~~--~k~~~a~~~~-~VV~p~WV~dCi 727 (1159)
...+|.|+.|+|.+... .+|++++++|.++||++..+.+..++++|+++..+ -|.+.|.+.+ +||+.+=+++-+
T Consensus 229 ~~~l~~g~~~v~TG~l~-~~R~e~~~~~~~~G~~v~~sVs~~t~~lv~g~~~~~ssK~~kA~~~gi~ii~e~~f~~ll 305 (313)
T PRK06063 229 GRPLVQGMRVALSAEVS-RTHEELVERILHAGLAYSDSVDRDTSLVVCNDPAPEQGKGYHARQLGVPVLDEAAFLELL 305 (313)
T ss_pred CCcccCCCEEEEecCCC-CCHHHHHHHHHHcCCEecCccccCccEEEECCCCCcccHHHHHHHcCCccccHHHHHHHH
Confidence 35789999999986554 79999999999999999999998889999887655 5888888777 999887776655
No 91
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=94.89 E-value=0.054 Score=62.51 Aligned_cols=75 Identities=19% Similarity=0.197 Sum_probs=57.2
Q ss_pred CCCcccCeEEEEEcCCCCCChHHHHHHHHHcCCEEEecCCCCceEEEEecC---------CChhhHhHhcC-----C-Ce
Q 001089 653 ETSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADN---------KGLKYEAAKRR-----G-DV 717 (1159)
Q Consensus 653 ~s~lF~G~~F~vv~~~~~~~k~eLe~lI~~~GG~iv~n~~~~~Th~Ia~~~---------~~~k~~~a~~~-----~-~V 717 (1159)
....|.|+.||+.+.....+|.+++++|.++||++..+.+..++++|+++. .+-|++.|... + +|
T Consensus 217 ~~~~l~g~~~vfTG~l~~~~R~~~~~~~~~~Gg~v~~sVs~~t~~lV~G~~~~~~~~~~~~~~K~~kA~~l~~~g~~i~i 296 (309)
T PRK06195 217 GFTAFKEEVVVFTGGLASMTRDEAMILVRRLGGTVGSSVTKKTTYLVTNTKDIEDLNREEMSNKLKKAIDLKKKGQNIKF 296 (309)
T ss_pred CCccccCCEEEEccccCCCCHHHHHHHHHHhCCEecCCcccCceEEEECCCcchhhcccCcChHHHHHHHHHhCCCCcEE
Confidence 346799999999876667899999999999999999999888888888742 34466666543 3 78
Q ss_pred eecchHHHHH
Q 001089 718 IHYSWVLDCC 727 (1159)
Q Consensus 718 V~p~WV~dCi 727 (1159)
++-+=+++-+
T Consensus 297 i~E~~f~~l~ 306 (309)
T PRK06195 297 LNEEEFLQKC 306 (309)
T ss_pred ecHHHHHHHH
Confidence 7765444443
No 92
>TIGR00575 dnlj DNA ligase, NAD-dependent. The member of this family from Treponema pallidum differs in having three rather than just one copy of the BRCT (BRCA1 C Terminus) domain (pfam00533) at the C-terminus. It is included in the seed.
Probab=94.61 E-value=0.066 Score=67.67 Aligned_cols=68 Identities=18% Similarity=0.286 Sum_probs=58.5
Q ss_pred CCcccCeEEEEEcCCCCCChHHHHHHHHHcCCEEEecCCCCceEEEEecCCChhhHhHhcCC-Ceeecc
Q 001089 654 TSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADNKGLKYEAAKRRG-DVIHYS 721 (1159)
Q Consensus 654 s~lF~G~~F~vv~~~~~~~k~eLe~lI~~~GG~iv~n~~~~~Th~Ia~~~~~~k~~~a~~~~-~VV~p~ 721 (1159)
...|.|..|||++.....+|++++++|.++||+++.+.+..++++|+++..+-|+..|...+ +|++-+
T Consensus 582 ~~~l~gk~~v~TG~l~~~~R~~~~~~i~~~G~~v~~sVs~kt~~lv~G~~~gsKl~kA~~lgi~ii~E~ 650 (652)
T TIGR00575 582 GSPLAGKTFVLTGTLSQMSRDEAKELLENLGGKVASSVSKKTDYVIAGEKAGSKLAKAQELGIPIINEE 650 (652)
T ss_pred CCCccCcEEEEeccCCCCCHHHHHHHHHHcCCEEeCCcCCCccEEEECCCCChHHHHHHHcCCcEechh
Confidence 35799999999876667899999999999999999999988889998877777998888877 888654
No 93
>COG5275 BRCT domain type II [General function prediction only]
Probab=94.34 E-value=0.14 Score=54.44 Aligned_cols=81 Identities=25% Similarity=0.215 Sum_probs=67.0
Q ss_pred ccccCCCCcccCeEEEEEcCCCCCChHHHHHHHHHcCCEEEecCCCCceEEEEecCCCh-hhHhHhcCC-CeeecchHHH
Q 001089 648 SDIKGETSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADNKGL-KYEAAKRRG-DVIHYSWVLD 725 (1159)
Q Consensus 648 s~~~~~s~lF~G~~F~vv~~~~~~~k~eLe~lI~~~GG~iv~n~~~~~Th~Ia~~~~~~-k~~~a~~~~-~VV~p~WV~d 725 (1159)
|-..+..+++.|+.|+|.+.-...+|.+-+.+|..+||++...+...++++|+++.-++ |...++..+ ++|.-+=++.
T Consensus 148 S~peg~~~cL~G~~fVfTG~l~TlsR~~a~~lvk~yGgrvT~~pSskTtflvlGdnaGP~K~ekiKqlkIkaidEegf~~ 227 (276)
T COG5275 148 SVPEGERECLKGKVFVFTGDLKTLSRDDAKTLVKVYGGRVTAVPSSKTTFLVLGDNAGPSKMEKIKQLKIKAIDEEGFDS 227 (276)
T ss_pred CCCCCCcccccccEEEEecccccccchhHHHHHHHhCCeeecccccceeEEEecCCCChHHHHHHHHhCCccccHHHHHH
Confidence 34457889999999999877667899999999999999999999877899999887776 577777776 8888777766
Q ss_pred HHh
Q 001089 726 CCS 728 (1159)
Q Consensus 726 Ci~ 728 (1159)
.|.
T Consensus 228 LI~ 230 (276)
T COG5275 228 LIK 230 (276)
T ss_pred HHh
Confidence 663
No 94
>KOG2043 consensus Signaling protein SWIFT and related BRCT domain proteins [Transcription; Signal transduction mechanisms; Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]
Probab=94.11 E-value=0.14 Score=66.32 Aligned_cols=127 Identities=19% Similarity=0.283 Sum_probs=85.0
Q ss_pred HHHHHHHHHcCCEEEecCCCCceEEEEec-CCChhhHhHhcCC-CeeecchHHHHHhcCccCCCCcccccccChhhhhhh
Q 001089 674 DSLHKMVVENGGTFSMNLNNSVTHCVAAD-NKGLKYEAAKRRG-DVIHYSWVLDCCSQKKLLQLQPKYYLHLSDSSKKKL 751 (1159)
Q Consensus 674 ~eLe~lI~~~GG~iv~n~~~~~Th~Ia~~-~~~~k~~~a~~~~-~VV~p~WV~dCi~~~~lLp~~p~~~l~~s~~t~~~~ 751 (1159)
.-+...++-.||.+..+.. ..||+|+.. ..|.++-.++..| +||+++||.+|+..|..++..|| +++.....++ +
T Consensus 671 ~~~k~~~k~lg~s~~ss~~-e~Th~i~~rirRT~k~Leai~~G~~ivT~~wL~s~~k~g~~~dek~y-il~D~ekEk~-~ 747 (896)
T KOG2043|consen 671 KNYKLAKKFLGGSVASSDS-EATHFIADRIRRTLKFLEAISSGKPLVTPQWLVSSLKSGEKLDEKPY-ILHDEEKEKE-F 747 (896)
T ss_pred hhhhhHHhhccceeecccc-cceeeeehhhhccHHHHhhhccCCcccchHHHHHHhhccccccCccc-cccCHHHHhc-c
Confidence 4577888888988887776 479998743 3567777777787 99999999999999999999875 4432211100 0
Q ss_pred hhcccccCCCcccCCChhHHHHHhhccCCCCCcchhHHHhhhcCCCCCCCcCCCeEEEEcCCCCCCCCchHHHHHHHHHH
Q 001089 752 QEEVDEFSDLYFWDLDLADIKQLLSNVDRSEDPKTIDYYKKKYCPQDKWSCFHGCCIYFYHSTEPLSPDWEVLLGLALRR 831 (1159)
Q Consensus 752 ~~~~D~~GDSy~~~~~~~~L~~ll~~~~~s~~~~~i~~l~~~~~~~~~~~lF~gc~~yl~~~~~~~~~d~~~i~~~~~~~ 831 (1159)
| | . +...+.+ .....+|.|..||+..+.... ...
T Consensus 748 -------g--f------~-l~ssl~R-------------------Ar~~plL~g~~v~vtp~v~p~-----------~~~ 781 (896)
T KOG2043|consen 748 -------G--F------R-LKSSLLR-------------------ARADPLLEGINVHVTPSVTPS-----------PKT 781 (896)
T ss_pred -------C--c------c-hhhHHHH-------------------hhcchhhcCceEEeccccccC-----------cch
Confidence 0 0 0 0000000 011257899999998754311 245
Q ss_pred HHHHHHhcCCEEEccCCC
Q 001089 832 LKLEISFHGGKVCNNLAN 849 (1159)
Q Consensus 832 l~~~I~~~GG~v~~~ls~ 849 (1159)
+-.+|...||.++..+..
T Consensus 782 v~eiie~~ggnvv~~~p~ 799 (896)
T KOG2043|consen 782 VVEIIEISGGNVVSDSPK 799 (896)
T ss_pred hHHHHhhcCcceecccCc
Confidence 677999999999998763
No 95
>PHA02142 putative RNA ligase
Probab=92.67 E-value=1.3 Score=51.75 Aligned_cols=103 Identities=15% Similarity=0.187 Sum_probs=64.4
Q ss_pred cCCCcEEEEEecceEEEEEEEe---------------------CCEEEEEecCCCC-cC--c-ch-----hhHHHHHHHh
Q 001089 242 LHGKEVVIECKFDGDRIQIHKN---------------------GSEIHYFSRSFLD-HS--E-YG-----HAMSKIIEQN 291 (1159)
Q Consensus 242 ~~~~~~~vE~K~DGeR~qih~~---------------------g~~v~~fSR~g~d-~t--~-~~-----p~l~~~l~~~ 291 (1159)
..+..|.+-+|+||.-|.+.+. .+.+...|||..- +. . +. ..+.+.+.+
T Consensus 166 ~~~~~f~~TeKLDGsS~tvy~~~~~~~~~~~~~~~~~~~~~~~~~~~gv~srn~~l~~~~~~~~W~~a~~~~i~~~l~~- 244 (366)
T PHA02142 166 YADVKFAKSLKLDGSSITMAWVTDPDLFLDLGTEDEPYAHDYDDAQFIVASRNQVLRYNADSKWWKGVENYQIVDRLKE- 244 (366)
T ss_pred hcCceEEEEEEecceeEEEEEecCCcccccccccccccccccCCCceeEeeccccccccCCchHHHHHHHcCcHHHHHh-
Confidence 4467799999999999988732 4577888998752 11 1 11 112222221
Q ss_pred cccCceeecceEEEEeCCCCcccccccHHHHHHHhhcCCCCCCCeEEEEEeeeecCCccccCCCHHHHHHHHHHh
Q 001089 292 VLVDRCILDGEMLVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKV 366 (1159)
Q Consensus 292 ~~~~~~ILDGElv~~d~~~~~~~pFg~lq~i~~~~r~~~~~~~~~~~~vFDiL~lnG~~l~~~pl~eRr~~L~~~ 366 (1159)
+ ..++.+=||++.-.-.++. ..-....|++|||-.+++.. =+++.+++++++++
T Consensus 245 ~-~~~iaIqGEl~Gp~IQ~N~------------------~~~~~~~F~vF~v~~i~~~~--yl~~~e~~~~~~~~ 298 (366)
T PHA02142 245 L-GMSVAIQGELMGPGIQKNR------------------ENFDKYRIFAFRAWFIDEQR--FATDEEFQDLCRTL 298 (366)
T ss_pred h-CCcEEEEEEEecccccCcc------------------ccCCCCceEEEEEEEeccce--eCCHHHHHHHHHHc
Confidence 1 3578899999872211110 00112469999997777664 46889999988875
No 96
>KOG2043 consensus Signaling protein SWIFT and related BRCT domain proteins [Transcription; Signal transduction mechanisms; Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]
Probab=90.73 E-value=0.2 Score=64.88 Aligned_cols=71 Identities=27% Similarity=0.403 Sum_probs=53.8
Q ss_pred HHHHHHHHhcCCEEEccCCCceEEEEeccCCcccchhhHHHHHHHHhhhhccCCccEEecccHHHHHHHcCCccCCCCCC
Q 001089 830 RRLKLEISFHGGKVCNNLANATHVVVLSVLGYDVNFNSLTESFTAREKHLLWNKKLHVVRSQWLEDCLAKEQKSEEYEYS 909 (1159)
Q Consensus 830 ~~l~~~I~~~GG~v~~~ls~vTHVIV~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~IVs~~WL~~ci~~g~~v~E~~Y~ 909 (1159)
..+++.+++.||.+.....++||+|+..-- +. .. +..++ ....-||++.||.+|++.|..++|..|.
T Consensus 671 ~~~k~~~k~lg~s~~ss~~e~Th~i~~rir-RT--~k-----~Leai-----~~G~~ivT~~wL~s~~k~g~~~dek~yi 737 (896)
T KOG2043|consen 671 KNYKLAKKFLGGSVASSDSEATHFIADRIR-RT--LK-----FLEAI-----SSGKPLVTPQWLVSSLKSGEKLDEKPYI 737 (896)
T ss_pred hhhhhHHhhccceeecccccceeeeehhhh-cc--HH-----HHhhh-----ccCCcccchHHHHHHhhccccccCcccc
Confidence 357889999999999999999999997321 11 11 11111 2345899999999999999999999998
Q ss_pred CCCC
Q 001089 910 LKPT 913 (1159)
Q Consensus 910 v~~~ 913 (1159)
+.-.
T Consensus 738 l~D~ 741 (896)
T KOG2043|consen 738 LHDE 741 (896)
T ss_pred ccCH
Confidence 7654
No 97
>TIGR02306 RNA_lig_DRB0094 RNA ligase, DRB0094 family. The member of this family from Deinococcus radiodurans, a species that withstands and recovers from extensive radiation or dessication damage, is an apparent RNA ligase. It repairs RNA stand breaks in nicked DNA:RNA and RNA:RNA but not DNA:DNA duplexes. It has adenylyltransferase activity associated with the C-terminal domain. Related proteins also in this family are found in Streptomyces avermitilis MA-4680 and in bacteriophage 44RR2.8t. The phage example is unsurprising since one mechanism of host cell defense against phage is cleavage and inactivation of certain tRNA molecules. A fungal sequence from Neurospora crassa scores between trusted and noise cutofffs and may be similar in function.
Probab=89.37 E-value=3.2 Score=48.53 Aligned_cols=154 Identities=18% Similarity=0.231 Sum_probs=82.4
Q ss_pred CCcEEEEEecceEEEEEEEeCC--EEE-----EEecCCCCc---Cc-c-----hhhHHHHHHHhcccCceeecceEEEEe
Q 001089 244 GKEVVIECKFDGDRIQIHKNGS--EIH-----YFSRSFLDH---SE-Y-----GHAMSKIIEQNVLVDRCILDGEMLVWD 307 (1159)
Q Consensus 244 ~~~~~vE~K~DGeR~qih~~g~--~v~-----~fSR~g~d~---t~-~-----~p~l~~~l~~~~~~~~~ILDGElv~~d 307 (1159)
+..|.+-+|+||--|.+.+..+ .+. +-|||..-. .. | ...|.+.+.+.....++.+=||++.-.
T Consensus 158 ~~~~~~TeKldGss~tv~~~~~~~~~~~~~~Gvcsr~~~l~~~~~~~~W~~a~~~~i~~~l~~~~~~~~vaiqGEl~G~g 237 (341)
T TIGR02306 158 GEKVAKTEKLHGTSITVAWVTDEERFLVLSKGVASRNLVLRENADNKYWKAVENYQIVDRAKAAELRMSVAIFGEVMGPG 237 (341)
T ss_pred CceEEEEEEecceeEEEEEecCCcccccccceeecCCcccccCCCchhHHHHHhcChHHHHhhcccCceEEEEEEEeCcc
Confidence 5789999999999998876432 222 346886521 11 1 122333443222345678889998722
Q ss_pred CCCCcccccccHHHHHHHhhcCCCCCCCeEEEEEeeeecCCccccCCCHHHHHHHHHHhhccCCCcceeeccCCCCCccc
Q 001089 308 TSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHV 387 (1159)
Q Consensus 308 ~~~~~~~pFg~lq~i~~~~r~~~~~~~~~~~~vFDiL~lnG~~l~~~pl~eRr~~L~~~i~~~~~~~~i~~p~~~~~~~v 387 (1159)
-.++ .. + .+.+-.|++|++ +.+|.. .=+++.++.+++.++..|. +.
T Consensus 238 IQ~n---~Y------------g--~~~~~~~f~F~v-~~~~~~-ryld~~~~~~~~~~~~VPv------L~--------- 283 (341)
T TIGR02306 238 IQKN---RY------------G--FDKYRTVFAFRA-FFDGEQ-RFLTDEDFQDLCLTLIVPQ------LY--------- 283 (341)
T ss_pred ccCC---cC------------C--CCCCceEEEEEE-EEcCcc-eecCHHHHHHHHHhcccce------EE---------
Confidence 1111 00 1 111222777877 555443 2358899998887752221 10
Q ss_pred cCCCCCccceecCCHHHHHHHHHHHHHc---------CCceEEEecCCCCCcCCCCCCCeEEEccc
Q 001089 388 RPQGEPCWSLVAHNVDEVEKFFKETIEN---------RDEGIVLKDLGSKWEPGDRSGKWLKLKPE 444 (1159)
Q Consensus 388 ~~~~~~~~~~~~~~~~ei~~~~~~ai~~---------g~EGlVlK~~ds~Y~pGkRs~~WlKiKpe 444 (1159)
..+.++ ...++.++.. =.||+|+|.....+.... +.-|+|.|..
T Consensus 284 -----------~g~~de-~~~~~~~ig~a~~~~~~~~irEGvViKp~~~~~~~~G-~r~~fK~is~ 336 (341)
T TIGR02306 284 -----------EGPFDE-FTVVKDMLGAETVSGIGLHIREGVVYKSVELRFAVDG-RMVHFKAISN 336 (341)
T ss_pred -----------EechhH-hhhhhhhhcccccCccccceeceEEEeeccccccCCC-ceEEEEEcCH
Confidence 011111 1222222221 289999999877664322 2359999873
No 98
>KOG3132 consensus m3G-cap-specific nuclear import receptor (Snurportin1) [RNA processing and modification]
Probab=89.00 E-value=1.9 Score=46.79 Aligned_cols=172 Identities=13% Similarity=0.129 Sum_probs=111.0
Q ss_pred cccccccCChHHHHHhcCCCcEEEEEecceEEEEEEEeCCEEEEEecCCCCcCcchhhHHHH-HHHhcc-cCceeecceE
Q 001089 226 PQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKI-IEQNVL-VDRCILDGEM 303 (1159)
Q Consensus 226 PMLA~~~~~~~~~~~k~~~~~~~vE~K~DGeR~qih~~g~~v~~fSR~g~d~t~~~p~l~~~-l~~~~~-~~~~ILDGEl 303 (1159)
-||..-+-++++. + +.+|++=.-==|-||+|.-..|...-|.|+|..... ||..... -.++-. ..=.|||+
T Consensus 101 lMLsEWliDvP~~---L-sqdW~vv~~PvGKR~lvVaSrG~Tvay~k~G~~v~r-F~S~LPGGnrr~~~a~~ytILDC-- 173 (325)
T KOG3132|consen 101 LMLSEWLIDVPDN---L-SQDWYVVARPVGKRCLVVASRGTTVAYVKNGSTVHR-FPSALPGGNRRKGPANSYTILDC-- 173 (325)
T ss_pred hhhHHHhccCccc---c-CcceEEEEeecCceEEEEecCCceEEEecCCeeEee-ccccCCCCCcCCCCcccceeeee--
Confidence 4666554444332 2 467999888899999998888888899999987642 2221100 001001 11236664
Q ss_pred EEEeCCCCcccccccHHHHHHHhhcCCCCCCCeEEEEEeeeecCCccccCCCHHHHHHHHHHhhccCCCcceeeccCCCC
Q 001089 304 LVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGL 383 (1159)
Q Consensus 304 v~~d~~~~~~~pFg~lq~i~~~~r~~~~~~~~~~~~vFDiL~lnG~~l~~~pl~eRr~~L~~~i~~~~~~~~i~~p~~~~ 383 (1159)
+|+. ..-.|+|.|++..+|.++.+-|+.-|.-.|++-+.+.++- ..|...-
T Consensus 174 -Iy~e-------------------------snQTYYVlD~~cWrgh~~yec~~dFRffwl~SKL~E~~~l---~~~t~~~ 224 (325)
T KOG3132|consen 174 -IYHE-------------------------SNQTYYVLDMVCWRGHSLYECTSDFRFFWLQSKLAETGAL---DPPTVYH 224 (325)
T ss_pred -eecc-------------------------cCceEEEEEEEeecCcccccCchHHHHHHHhhhccccccC---CCCCcCc
Confidence 2221 1235999999999999999999999999999887665431 0010000
Q ss_pred --CccccCCCCCccceecCCHHHHHHHHHHHHHcCCceEEEecCCCCCcCCCC-CCCeEE
Q 001089 384 --NSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDR-SGKWLK 440 (1159)
Q Consensus 384 --~~~v~~~~~~~~~~~~~~~~ei~~~~~~ai~~g~EGlVlK~~ds~Y~pGkR-s~~WlK 440 (1159)
.+.+.| .+ .-+.+.+.+++.-.+.-...||.+-.-.-.|.||.- =-+|+|
T Consensus 225 ~f~Fs~vp------~~-pC~q~~l~~~~~~~~pf~~DGLLFYhks~~yqpgqsplvgwlk 277 (325)
T KOG3132|consen 225 KFRFSVVP------FY-PCDQSGLHSAYTGSLPFVRDGLLFYHKSVVYQPGQSPLVGWLK 277 (325)
T ss_pred cceecccC------CC-CCCHHHHHHHHcCCCceeeeeEEEeecceeeCCCCCccccccc
Confidence 011111 11 236788888888888888999999999999999964 247864
No 99
>PRK09247 ATP-dependent DNA ligase; Validated
Probab=86.71 E-value=0.99 Score=56.15 Aligned_cols=82 Identities=17% Similarity=0.257 Sum_probs=69.2
Q ss_pred HHHHHHHHHHHhhhhHHHHHHHHHHHHHhCCHHHHHHHHHHHHhhhc-cCCcccccccccC----c---cHHHHhhhcCC
Q 001089 127 KELNDLLDRLASSENRAEKISVLSTLIKKTNAQEMKWIIMIILKDLK-LGISEKSIFHEFH----P---DAEDLFNVTCD 198 (1159)
Q Consensus 127 ~eVn~~Ld~LA~~~~~~~k~~il~~ll~~~s~~E~k~l~RiIlkdLr-iGi~e~til~~~h----p---da~~~~~~~~d 198 (1159)
.+.-+++++|+..+++.+|..+|..+|..+++.+.-|.++++++.+. .|++++.+.+++. . ...+.|.-..|
T Consensus 2 ~~fa~~~~~i~~t~~~~ek~~~l~~~~~~~~~~d~~~~~~ll~g~~~~~~i~~~~l~k~~~~~~g~~~~~~~~~~~~~GD 81 (539)
T PRK09247 2 KAFAELLDRLDLTTSTNAKLALLADYFRSAPDPDRAWALALLTGGLPRRLVKTRLLRELAAERADLPPWLFEESYDYVGD 81 (539)
T ss_pred hHHHHHHHHHHhccCHHHHHHHHHHHHHhCCHHHHHHHHHHhcCCcccCCCCHHHHHHHHHHHHCcCHHHHHHHHHhcCC
Confidence 35567788999999999999999999999999999999999999885 8999999887652 1 24566888899
Q ss_pred HHHHHHHHhh
Q 001089 199 LKLVCEKLKD 208 (1159)
Q Consensus 199 L~~V~~~L~~ 208 (1159)
|+.||..+..
T Consensus 82 lg~~~~~~~~ 91 (539)
T PRK09247 82 LAETIALLLP 91 (539)
T ss_pred HHHHHHHhcc
Confidence 9999988853
No 100
>KOG3548 consensus DNA damage checkpoint protein RHP9/CRB2/53BP1 [Replication, recombination and repair]
Probab=86.27 E-value=0.97 Score=57.22 Aligned_cols=39 Identities=10% Similarity=0.175 Sum_probs=31.4
Q ss_pred CccEEecccHHHHHHHcCCccCCCCCCCCCCCCCccccc
Q 001089 883 KKLHVVRSQWLEDCLAKEQKSEEYEYSLKPTGMQESYLE 921 (1159)
Q Consensus 883 ~~~~IVs~~WL~~ci~~g~~v~E~~Y~v~~~~~~e~~~~ 921 (1159)
..+.+|...||-+|++++++|+-.+|+++.-......++
T Consensus 1008 ~giPcVh~~fI~aC~e~nr~Vdy~~YLLpsGyS~rlds~ 1046 (1176)
T KOG3548|consen 1008 RGIPCVHNTFIQACGEQNRCVDYTDYLLPSGYSIRLDSQ 1046 (1176)
T ss_pred cCCCcccHHHHHHHHhccccccchhhcccCccccccccc
Confidence 567899999999999999999999998876653333333
No 101
>KOG0966 consensus ATP-dependent DNA ligase IV [Replication, recombination and repair]
Probab=85.04 E-value=1.5 Score=55.04 Aligned_cols=88 Identities=18% Similarity=0.280 Sum_probs=60.7
Q ss_pred CCcCCCeEEEEcCCCCCCCCchHHHHHHHHHHHHHHHHhcCCEEEccCC-CceEEEEeccCCcccchhhHHHHHHHHhhh
Q 001089 800 WSCFHGCCIYFYHSTEPLSPDWEVLLGLALRRLKLEISFHGGKVCNNLA-NATHVVVLSVLGYDVNFNSLTESFTAREKH 878 (1159)
Q Consensus 800 ~~lF~gc~~yl~~~~~~~~~d~~~i~~~~~~~l~~~I~~~GG~v~~~ls-~vTHVIV~~~~~~~~~~~~l~~~l~~~~~~ 878 (1159)
..+|.|..||+...... .+ .+..++..|.-+||+++.++. +.||.|...+... .... .+.+
T Consensus 631 s~if~gl~f~Vlsgt~~--~~-------tk~~le~~ivenGG~iv~nv~p~~~~ci~~a~~et-~~vk--~~~~------ 692 (881)
T KOG0966|consen 631 SNIFDGLEFCVLSGTSE--TH-------TKAKLEEIIVENGGKIVQNVGPSDTLCIATAGKET-TRVK--AQAI------ 692 (881)
T ss_pred hhhhcCeeEEEecCCcc--cc-------cHHHHHHHHHHcCCEEEEcCCCCCcceEEeccccc-hHHH--HHHH------
Confidence 45899999999875531 11 246889999999999999886 5889887432211 1111 1111
Q ss_pred hccCCccEEecccHHHHHHHcCCccCCCCC
Q 001089 879 LLWNKKLHVVRSQWLEDCLAKEQKSEEYEY 908 (1159)
Q Consensus 879 ~~~~~~~~IVs~~WL~~ci~~g~~v~E~~Y 908 (1159)
.....||.+.||.+|....++++-.++
T Consensus 693 ---~~~cdVl~p~Wlldcc~~~~l~p~~P~ 719 (881)
T KOG0966|consen 693 ---KRSCDVLKPAWLLDCCKKQRLLPWLPR 719 (881)
T ss_pred ---hccCceeeHHHHHHHHhhhhccccccH
Confidence 136789999999999999997775443
No 102
>PRK03180 ligB ATP-dependent DNA ligase; Reviewed
Probab=84.10 E-value=5.8 Score=49.14 Aligned_cols=93 Identities=22% Similarity=0.245 Sum_probs=72.9
Q ss_pred CCcHHHHHHHHHHHHhhC---ChHHHHHHHHHHHhhcCCCchHHHHHHHhCCCCCCCccccCCCHHHHHHHHHHHhCCCc
Q 001089 6 ETEVIVLVSLFNWIQKTK---PAAKKRSKFRKFLDTYCDSVDYFSALRLILPSLDRERGSYGLKESVLANCLIDALGMSK 82 (1159)
Q Consensus 6 ~~~F~~l~~lle~i~~~~---~~~~K~~~l~~~l~~~~~~~d~~p~lrLllP~~d~~r~~ygike~~L~k~~~~~lgl~~ 82 (1159)
+.+..++-+.|++|...+ +..+|..+|..++.+. .+.+...++|+|+..+. .|+++.++..+++.+++++.
T Consensus 72 ~ltl~~V~~~l~~ia~~~g~~s~~~k~~~l~~ll~~~-~~~E~~~l~r~i~~~lR-----iGv~~~~v~~Ala~a~~~~~ 145 (508)
T PRK03180 72 TLTVADVDAALSEIAAVAGAGSQARRAALLAALFAAA-TEDEQRFLRRLLTGELR-----QGALDGVMADAVARAAGVPA 145 (508)
T ss_pred CCcHHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHhC-CHHHHHHHHHHHhCCCc-----ccccHHHHHHHHHHHhCCCH
Confidence 466777777888888775 4478889999999987 57889999999999983 69999999999999998864
Q ss_pred ChHHHHHHhhhhcCCCCCCCCCHHHHHHHHhh
Q 001089 83 DSADAVRLINWRKGGAAPNAGNFPMVAAEVLQ 114 (1159)
Q Consensus 83 ~s~~~~~L~~wk~~~~~~~~GD~~~~a~~vl~ 114 (1159)
.+..+..+| .||++.++...+.
T Consensus 146 --~~v~~a~~~--------~~dl~~v~~~~l~ 167 (508)
T PRK03180 146 --AAVRRAAML--------AGDLPAVAAAALT 167 (508)
T ss_pred --HHHHHHHHH--------cCCHHHHHHHHHh
Confidence 333344333 6899988876553
No 103
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=80.46 E-value=2.1 Score=53.55 Aligned_cols=82 Identities=23% Similarity=0.322 Sum_probs=54.7
Q ss_pred CCCcccCeEEEEEcCCCCCChHHHHHHHHHcCCEEEecCC-----CCceEEE-EecCC------Ch---hhHhHhcC-C-
Q 001089 653 ETSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLN-----NSVTHCV-AADNK------GL---KYEAAKRR-G- 715 (1159)
Q Consensus 653 ~s~lF~G~~F~vv~~~~~~~k~eLe~lI~~~GG~iv~n~~-----~~~Th~I-a~~~~------~~---k~~~a~~~-~- 715 (1159)
.-.||.|+.||+++......+++|.++|...||++.+-.+ ...+-++ ..... .. +..++... +
T Consensus 584 ~~kLf~gl~~~~~g~fs~~p~~~l~~l~~~~gg~~l~~~~~~~~~~k~s~~~~~~~~~~~~~~~~~k~~~~ea~~~s~~a 663 (684)
T KOG4362|consen 584 KPKLFEGLKFYFVGDFSNPPKEQLQELVHLAGGTILQVPRVAYSDKKKSTIVVLSEKPVLDSILWQKVNDAEALALSQRA 663 (684)
T ss_pred CcchhcCCcceeecccccCcHHHHHHHHhhcCcceeeccCcccccccccceeEeecccCCCchhhhhhccHHHHHHhcCC
Confidence 3469999999998877778899999999999999976432 1122122 11110 01 12333332 4
Q ss_pred CeeecchHHHHHhcCccCC
Q 001089 716 DVIHYSWVLDCCSQKKLLQ 734 (1159)
Q Consensus 716 ~VV~p~WV~dCi~~~~lLp 734 (1159)
.+|+-.||+|+|+--.+++
T Consensus 664 ~~~~~~wvl~s~a~~~~~~ 682 (684)
T KOG4362|consen 664 RAVSSSWVLDSIAGYQILV 682 (684)
T ss_pred Cccchhhhhcchhceeeee
Confidence 9999999999997655544
No 104
>PF04675 DNA_ligase_A_N: DNA ligase N terminus; InterPro: IPR012308 DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA fragments by catalysing the formation of an internucleotide ester bond between phosphate and deoxyribose. It is active during DNA replication, DNA repair and DNA recombination. There are two forms of DNA ligase, one requires ATP (6.5.1.1 from EC), the other NAD (6.5.1.2 from EC), the latter being restricted to eubacteria. Eukaryotic, archaebacterial, viral and some eubacterial DNA ligases are ATP-dependent. The first step in the ligation reaction is the formation of a covalent enzyme-AMP complex. The co-factor ATP is cleaved to pyrophosphate and AMP, with the AMP being covalently joined to a highly conserved lysine residue in the active site of the ligase. The activated AMP residue is then transferred to the 5'phosphate of the nick, before the nick is sealed by phosphodiester-bond formation and AMP elimination [,]. Vertebrate cells encode three well-characterised DNA ligases (DNA ligases I, III and IV), all of which are related in structure and sequence. With the exception of the atypically small PBCV-1 viral enzyme, two regions of primary sequence are common to all members of the family. The catalytic region comprises six conserved sequence motifs (I, III, IIIa, IV, V-VI), motif I includes the lysine residue that is adenylated in the first step of the ligation reaction. The function of the second, less well-conserved region is unknown. When folded, each protein comprises of two distinct sub-domains: a large amino-terminal sub-domain ('domain 1') and a smaller carboxy-terminal sub-domain ('domain 2'). The ATP-binding site of the enzyme lies in the cleft between the two sub-domains. Domain 1 consists of two antiparallel beta sheets flanked by alpha helices, whereas domain 2 consists of a five-stranded beta barrel and a single alpha helix, which form the oligonucleotide-binding fold [, ]. This region is found in many but not all ATP-dependent DNA ligase enzymes (6.5.1.1 from EC). It is thought to be involved in DNA binding and in catalysis. In human DNA ligase I (P18858 from SWISSPROT), and in Saccharomyces cerevisiae (Baker's yeast) (P04819 from SWISSPROT), this region was necessary for catalysis, and separated from the amino terminus by targeting elements. In Vaccinia virus (P16272 from SWISSPROT) this region was not essential for catalysis, but deletion decreases the affinity for nicked DNA and decreased the rate of strand joining at a step subsequent to enzyme-adenylate formation []. ; GO: 0003677 DNA binding, 0003910 DNA ligase (ATP) activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 2CFM_A 3RR5_A 2HIX_A 2HIV_A 3L2P_A 1X9N_A 4EQ5_A 3GDE_A.
Probab=80.25 E-value=1.9 Score=45.35 Aligned_cols=84 Identities=24% Similarity=0.423 Sum_probs=60.2
Q ss_pred HHHHHHHHHHHHhhhhHHHHHHHHHHHHHhCCHHHHHHHHHHHHhhh-------ccCCccccccccc----Cc---cHHH
Q 001089 126 IKELNDLLDRLASSENRAEKISVLSTLIKKTNAQEMKWIIMIILKDL-------KLGISEKSIFHEF----HP---DAED 191 (1159)
Q Consensus 126 i~eVn~~Ld~LA~~~~~~~k~~il~~ll~~~s~~E~k~l~RiIlkdL-------riGi~e~til~~~----hp---da~~ 191 (1159)
..++-++|++|+..+++.+|..+|+.+|....+.+.-|.+.++++-+ ..|++++++.+++ +- ...+
T Consensus 3 F~~l~~l~~~l~~~~~~~~k~~~l~~~~~~~~~~~~~~~~~~~~~~l~P~~d~r~~~i~~~~L~k~~~~~~~~~~~~~~~ 82 (177)
T PF04675_consen 3 FSDLCELFEKLESTSSRLEKIAILSNFFRSWREEDLGPDLYLLLRLLFPEYDGREYGIGEKLLAKAIAEALGLPEKSIDE 82 (177)
T ss_dssp HHHHHHHHHHHHT---HHHHHHHHHHHHHTSHCCGHHCHHHHHHTHSSTTTCS---S--HHHHHHHHHHHHTS-HHHHHH
T ss_pred HHHHHHHHHHHHhccCHHHHHHHHHHHHHHcccchhhhHHHHHhcccccchhhhHhccchhHHHHHHHHHHcCCHHHHHH
Confidence 45677889999998889999999999999988777888888888844 6899999988654 42 2445
Q ss_pred HhhhcCCHHHHHHHHhhh
Q 001089 192 LFNVTCDLKLVCEKLKDR 209 (1159)
Q Consensus 192 ~~~~~~dL~~V~~~L~~~ 209 (1159)
.|....|++.|+..+...
T Consensus 83 ~~~~~GD~g~~~~~~~~~ 100 (177)
T PF04675_consen 83 SYKKVGDLGEVAEEVLQK 100 (177)
T ss_dssp HHHHHS-HHHHHHHHHHH
T ss_pred HHHhcCcHHHHHHHHHhh
Confidence 677899999999988653
No 105
>PLN03113 DNA ligase 1; Provisional
Probab=73.78 E-value=6.4 Score=50.67 Aligned_cols=86 Identities=13% Similarity=0.293 Sum_probs=72.2
Q ss_pred CCCCHHHHHHHHHHHHhhhhHHHHHHHHHHHHHhC---CHHHHHHHHHHHHhhhc-------cCCcccccccccC----c
Q 001089 122 GGLTIKELNDLLDRLASSENRAEKISVLSTLIKKT---NAQEMKWIIMIILKDLK-------LGISEKSIFHEFH----P 187 (1159)
Q Consensus 122 ~~LTi~eVn~~Ld~LA~~~~~~~k~~il~~ll~~~---s~~E~k~l~RiIlkdLr-------iGi~e~til~~~h----p 187 (1159)
.++.-.++-+.|++|...+++.++..+|.++|... +|.+.-|.+.++++.+- +||+++.|.+++. .
T Consensus 127 ~~~~f~~l~~~~~~Ie~tt~rlek~~~L~~~~r~~~~~~p~dl~~~vyL~~~~l~P~~e~~elgige~~L~kai~e~~g~ 206 (744)
T PLN03113 127 ERVPFLFVALAFDLISNETGRIVITDIVCNMLRTVMATTPEDLVAVVYLLANRIAPAHEGVELGIGEATIIKALAEAFGR 206 (744)
T ss_pred CCccHHHHHHHHHHHHhccCHHHHHHHHHHHHHHhccCChHHHHHHHHHHhCCCCccccCcccCcCHHHHHHHHHHHHCc
Confidence 45778889999999999999999999999999985 99999999999988764 6999999987663 1
Q ss_pred ---cHHHHhhhcCCHHHHHHHHh
Q 001089 188 ---DAEDLFNVTCDLKLVCEKLK 207 (1159)
Q Consensus 188 ---da~~~~~~~~dL~~V~~~L~ 207 (1159)
.....|....||+.|+..+.
T Consensus 207 ~~~~ik~~y~~~GDlG~vA~~~~ 229 (744)
T PLN03113 207 TEKQVKKQYKELGDLGLVAKASR 229 (744)
T ss_pred CHHHHHHHHHHhCCHHHHHHhhh
Confidence 24556788899999998664
No 106
>KOG2386 consensus mRNA capping enzyme, guanylyltransferase (alpha) subunit [RNA processing and modification]
Probab=72.83 E-value=2.3 Score=50.22 Aligned_cols=92 Identities=20% Similarity=0.319 Sum_probs=61.3
Q ss_pred CcEEEEEecceEEEEEEEeCCE-EEEEecCCCCcCc---chh---hHHHHHHHhcccCceeecceEEEEeCCCCcccccc
Q 001089 245 KEVVIECKFDGDRIQIHKNGSE-IHYFSRSFLDHSE---YGH---AMSKIIEQNVLVDRCILDGEMLVWDTSLNRFAEFG 317 (1159)
Q Consensus 245 ~~~~vE~K~DGeR~qih~~g~~-v~~fSR~g~d~t~---~~p---~l~~~l~~~~~~~~~ILDGElv~~d~~~~~~~pFg 317 (1159)
..|.+.+|.||.|..+-.+++. +..|-|.-.-+-. +++ .... .....++||||+. |..+.
T Consensus 285 ~~y~~~We~dg~~~~~L~~~~~~~~~~dR~~~~~~~~~~~~~~~~~~~~------~~~~tl~dge~~l-D~l~~------ 351 (393)
T KOG2386|consen 285 EYYEASWEADGTRYMMLIDGDGEYYDFDRWRFVKGRENLRKIREDSDTK------VLHQTLLDGEMIL-DRLKE------ 351 (393)
T ss_pred hhhhhhhcccCcEEEEEecCCceeEechhhhHHHhhhhhhcccccccch------hhhhhhcccceec-ccccc------
Confidence 3567999999999988887654 5555544221110 000 1111 1245799999998 64321
Q ss_pred cHHHHHHHhhcCCCCCCCeEEEEEeeeecCCccccCCCHHHHHHHHHH
Q 001089 318 SNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQK 365 (1159)
Q Consensus 318 ~lq~i~~~~r~~~~~~~~~~~~vFDiL~lnG~~l~~~pl~eRr~~L~~ 365 (1159)
...+.|.+||++-+|++.+...|+. |.+.+.+
T Consensus 352 ---------------~~~~r~l~Yd~~r~n~~~v~~~~f~-r~~~~~~ 383 (393)
T KOG2386|consen 352 ---------------EAIPRYLIYDMVRFNSQKVEKRPFS-RWQIIEK 383 (393)
T ss_pred ---------------ccchhheeeeeeeccCcccccCcch-HHHHHHH
Confidence 0134589999999999999999999 8887754
No 107
>TIGR00574 dnl1 DNA ligase I, ATP-dependent (dnl1). All proteins in this family with known functions are ATP-dependent DNA ligases. Functions include DNA repair, DNA replication, and DNA recombination (or any process requiring ligation of two single-stranded DNA sections). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=67.28 E-value=18 Score=44.87 Aligned_cols=94 Identities=21% Similarity=0.256 Sum_probs=72.2
Q ss_pred CCCcHHHHHHHHHHHHhhC---ChHHHHHHHHHHHhhcCCCchHHHHHHHhCCCCCCCccccCCCHHHHHHHHHHHhCCC
Q 001089 5 EETEVIVLVSLFNWIQKTK---PAAKKRSKFRKFLDTYCDSVDYFSALRLILPSLDRERGSYGLKESVLANCLIDALGMS 81 (1159)
Q Consensus 5 ~~~~F~~l~~lle~i~~~~---~~~~K~~~l~~~l~~~~~~~d~~p~lrLllP~~d~~r~~ygike~~L~k~~~~~lgl~ 81 (1159)
.+++-.++-+.|++|.+.+ +..+|..+|..++.+. .+.+...++|+|+-++. .|++++++..+|+.+++++
T Consensus 53 ~~lti~eV~~~L~~ia~~~g~~s~~~k~~~l~~ll~~~-~~~e~k~l~r~i~~~lr-----iG~~~~~il~al~~~~~~~ 126 (514)
T TIGR00574 53 APLTVKEVYETLKNIAETSGEGSQDKKIKLLKSLLKRA-SPLEAKYLIRTILGDLR-----IGIAEKTILDALAKAFLLS 126 (514)
T ss_pred CCcCHHHHHHHHHHHHHhhCCCcHHHHHHHHHHHHHhC-CHHHHHHHHHHHhhhcc-----cCccHHHHHHHHHHHhccc
Confidence 3466778888888887775 3568889999999876 57888999999999883 5999999999999999876
Q ss_pred cChHHHHHHhhhhcCCCCCCCCCHHHHHHHHhh
Q 001089 82 KDSADAVRLINWRKGGAAPNAGNFPMVAAEVLQ 114 (1159)
Q Consensus 82 ~~s~~~~~L~~wk~~~~~~~~GD~~~~a~~vl~ 114 (1159)
.. +..++ | ....|++.++..++.
T Consensus 127 ~~--~~~~~--~------~~~~dl~~v~~~l~~ 149 (514)
T TIGR00574 127 HP--DVERA--F------NLTNDLGKVAKILLE 149 (514)
T ss_pred hH--HHHHH--H------HhCCCHHHHHHHHHh
Confidence 43 22222 2 346789988877653
No 108
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=62.68 E-value=27 Score=40.40 Aligned_cols=48 Identities=15% Similarity=0.211 Sum_probs=38.5
Q ss_pred CcCCCeEEEEcCCCCCCCCchHHHHHHHHHHHHHHHHhcCCEEEccCC-CceEEEEecc
Q 001089 801 SCFHGCCIYFYHSTEPLSPDWEVLLGLALRRLKLEISFHGGKVCNNLA-NATHVVVLSV 858 (1159)
Q Consensus 801 ~lF~gc~~yl~~~~~~~~~d~~~i~~~~~~~l~~~I~~~GG~v~~~ls-~vTHVIV~~~ 858 (1159)
..|.|-+|+|.|..... .+..+..+|..+||++.+..+ +++++|+++.
T Consensus 219 ~~l~g~~~vfTG~l~~~----------~R~~~~~~~~~~Gg~v~~sVs~~t~~lV~G~~ 267 (309)
T PRK06195 219 TAFKEEVVVFTGGLASM----------TRDEAMILVRRLGGTVGSSVTKKTTYLVTNTK 267 (309)
T ss_pred ccccCCEEEEccccCCC----------CHHHHHHHHHHhCCEecCCcccCceEEEECCC
Confidence 46999999999964211 256788899999999999998 5889998853
No 109
>COG4566 TtrR Response regulator [Signal transduction mechanisms]
Probab=54.26 E-value=44 Score=35.88 Aligned_cols=81 Identities=19% Similarity=0.345 Sum_probs=52.9
Q ss_pred CCCCHHHHHHHHhhhccCCCCCCCCHHHHHHHHH----HHHhhhhHHHHHHHHHHHHHhCCHHHHHHHHHHHHhhhc---
Q 001089 101 NAGNFPMVAAEVLQRRQGMISGGLTIKELNDLLD----RLASSENRAEKISVLSTLIKKTNAQEMKWIIMIILKDLK--- 173 (1159)
Q Consensus 101 ~~GD~~~~a~~vl~~r~~~~~~~LTi~eVn~~Ld----~LA~~~~~~~k~~il~~ll~~~s~~E~k~l~RiIlkdLr--- 173 (1159)
-.||.+.+++.+...--..-..+..-.++.+.+. ..+..........-+..+|..+||.|...|-+++.+-+.
T Consensus 84 GhgDIpmaV~AmK~GAvDFLeKP~~~q~Lldav~~Al~~~~~~~~~~~~~~~~~~~l~tLT~RERqVl~~vV~G~~NKqI 163 (202)
T COG4566 84 GHGDIPMAVQAMKAGAVDFLEKPFSEQDLLDAVERALARDASRRAEADRQAAIRARLATLTPRERQVLDLVVRGLMNKQI 163 (202)
T ss_pred CCCChHHHHHHHHcchhhHHhCCCchHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhcCHHHHHHHHHHHcCcccHHH
Confidence 3589998876653221112234555555444443 333333344455678899999999999999999977653
Q ss_pred ---cCCccccc
Q 001089 174 ---LGISEKSI 181 (1159)
Q Consensus 174 ---iGi~e~ti 181 (1159)
+|+|+.||
T Consensus 164 A~dLgiS~rTV 174 (202)
T COG4566 164 AFDLGISERTV 174 (202)
T ss_pred HHHcCCchhhH
Confidence 79999987
No 110
>KOG3524 consensus Predicted guanine nucleotide exchange factor (PEBBLE) [Signal transduction mechanisms]
Probab=52.62 E-value=8.9 Score=47.71 Aligned_cols=75 Identities=13% Similarity=0.269 Sum_probs=52.8
Q ss_pred CCcccCeEEEEEcCCCCCChHHHHHHHHHcCCEEEecCCCCceEEEEecCCChhhHhHhcCC-CeeecchHHHHHhcC
Q 001089 654 TSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADNKGLKYEAAKRRG-DVIHYSWVLDCCSQK 730 (1159)
Q Consensus 654 s~lF~G~~F~vv~~~~~~~k~eLe~lI~~~GG~iv~n~~~~~Th~Ia~~~~~~k~~~a~~~~-~VV~p~WV~dCi~~~ 730 (1159)
-..|.|+.||+.+ ......+.+.....+.||..-.. ...+||+|+.+-...-.-.+.... ++|.-.|..-+|..|
T Consensus 208 l~~feg~~~~f~g-F~~ee~~~m~~sle~~gg~~a~~-d~~cthvvv~e~~~~~~p~~~s~~~~~vk~ewfw~siq~g 283 (850)
T KOG3524|consen 208 LGVFEGLSLFFHG-FKQEEIDDMLRSLENTGGKLAPS-DTLCTHVVVNEDNDEVEPLAVSSNQVHVKKEWFWVSIQRG 283 (850)
T ss_pred cccccCCeEeecC-CcHHHHHHHHHHHHhcCCcccCC-CCCceeEeecCCccccccccccccceeecccceEEEEecc
Confidence 3589999999864 44566788888889999999773 346899998654322111122233 899999988777766
No 111
>PF02178 AT_hook: AT hook motif; InterPro: IPR017956 AT hooks are DNA-binding motifs with a preference for A/T rich regions. These motifs are found in a variety of proteins, including the high mobility group (HMG) proteins [], in DNA-binding proteins from plants [] and in hBRG1 protein, a central ATPase of the human switching/sucrose non-fermenting (SWI/SNF) remodeling complex []. High mobility group (HMG) proteins are a family of relatively low molecular weight non-histone components in chromatin []. HMG-I and HMG-Y (HMGA) are proteins of about 100 amino acid residues which are produced by the alternative splicing of a single gene. HMG-I/Y proteins bind preferentially to the minor groove of AT-rich regions in double-stranded DNA in a non-sequence specific manner [, ]. It is suggested that these proteins could function in nucleosome phasing and in the 3' end processing of mRNA transcripts. They are also involved in the transcription regulation of genes containing, or in close proximity to, AT-rich regions. ; GO: 0003677 DNA binding; PDB: 2EZE_A 2EZD_A 2EZF_A 2EZG_A.
Probab=52.37 E-value=6.1 Score=23.92 Aligned_cols=12 Identities=58% Similarity=0.947 Sum_probs=3.8
Q ss_pred ccccCCCCCCCc
Q 001089 970 KRKRGRPAGGSA 981 (1159)
Q Consensus 970 ~~~~~~~~~~~~ 981 (1159)
+++||||+....
T Consensus 1 ~r~RGRP~k~~~ 12 (13)
T PF02178_consen 1 KRKRGRPRKNAK 12 (13)
T ss_dssp S--SS--TT---
T ss_pred CCcCCCCccccC
Confidence 478899987543
No 112
>KOG0323 consensus TFIIF-interacting CTD phosphatases, including NLI-interacting factor [Transcription]
Probab=51.79 E-value=7.7 Score=48.69 Aligned_cols=83 Identities=13% Similarity=0.191 Sum_probs=55.3
Q ss_pred CcccCeEEEEEcCC---CCCChHHHHHHHHHcCCEEEecCCCCceEEEEecCCChhhHhHhcCC--CeeecchHHHHHhc
Q 001089 655 SIFSDMVFYFVNVP---PAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADNKGLKYEAAKRRG--DVIHYSWVLDCCSQ 729 (1159)
Q Consensus 655 ~lF~G~~F~vv~~~---~~~~k~eLe~lI~~~GG~iv~n~~~~~Th~Ia~~~~~~k~~~a~~~~--~VV~p~WV~dCi~~ 729 (1159)
..+.|+.+.+.+.. ......++-.+....|...+.+....+||+|+....+.+...+...+ .||.+.|+..|+++
T Consensus 440 ~v~~~~~~vfSg~~P~~~~~~~s~~~~~~~~~g~vs~~~~~~~~th~i~~~~gt~k~~~a~~~~~~~Vv~~~wl~~~~e~ 519 (635)
T KOG0323|consen 440 KVLKGSQIVFSGLHPTGSTDESADILGVAQQLGAVSAPDVSDKTTHLIAANAGTKKVYKAVVSGSAKVVNAAWLWRSLEK 519 (635)
T ss_pred HHhhccceeecccccCcCCcchhhhhhhhhcccceecccccchhhhHHhhccCcceeeccccccceeEechhHHHHHHHH
Confidence 44555555543321 12223555556667887777777777899998887777666655554 89999999999998
Q ss_pred CccCCCCc
Q 001089 730 KKLLQLQP 737 (1159)
Q Consensus 730 ~~lLp~~p 737 (1159)
...+.-.+
T Consensus 520 w~~v~ek~ 527 (635)
T KOG0323|consen 520 WGKVEEKL 527 (635)
T ss_pred hcchhccc
Confidence 66554443
No 113
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=48.37 E-value=34 Score=43.92 Aligned_cols=224 Identities=20% Similarity=0.274 Sum_probs=127.0
Q ss_pred cEEEEEecceEEEEEEEeCCE-EEEEec----CCCCcCcch---hhHHHHHHHhcccCceeecceEEEEeCCCCc-----
Q 001089 246 EVVIECKFDGDRIQIHKNGSE-IHYFSR----SFLDHSEYG---HAMSKIIEQNVLVDRCILDGEMLVWDTSLNR----- 312 (1159)
Q Consensus 246 ~~~vE~K~DGeR~qih~~g~~-v~~fSR----~g~d~t~~~---p~l~~~l~~~~~~~~~ILDGElv~~d~~~~~----- 312 (1159)
.|++|+|+||.-+.+.+.+|. ++..|| .|+|+|+-. +++-..|... .+..+.+-||++.-...-.+
T Consensus 109 ~~~~epKiDGlsisL~Y~~G~L~~a~TRGDG~~GeDvT~n~~~I~~IP~~l~~~-~p~~levRGEv~m~~~~F~~lN~~~ 187 (665)
T PRK07956 109 TYLCELKIDGLAVSLLYENGVLVRAATRGDGTTGEDITANVRTIRSIPLRLHGN-EPERLEVRGEVFMPKADFEALNEER 187 (665)
T ss_pred ceEEEEecccEEEEEEEECCEEEEEEecCCCccchhHhhhhhhhccCChhhccc-CCCeEEEEEEEEEEHHHHHHHHHHH
Confidence 599999999999998887664 688999 588998632 2222222101 13458899999874221000
Q ss_pred ----ccccccHHHHH-HHhhc---CCCCCCCeEEEEEeeeecCCccccCCCHHHHHHHHHHhhccCCCcceeeccCCCCC
Q 001089 313 ----FAEFGSNQEIA-KAARD---GLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLN 384 (1159)
Q Consensus 313 ----~~pFg~lq~i~-~~~r~---~~~~~~~~~~~vFDiL~lnG~~l~~~pl~eRr~~L~~~i~~~~~~~~i~~p~~~~~ 384 (1159)
-.+|..-+..+ ...|. .....+++.|++|++...++ ........++.+.|.++-=++..
T Consensus 188 ~~~g~~~faNpRNaaAGslr~ld~~~~~~r~L~f~~y~~~~~~~-~~~~~t~~e~l~~L~~~GF~v~~------------ 254 (665)
T PRK07956 188 REEGEKPFANPRNAAAGSLRQLDPKITAKRPLSFFAYGVGEVEG-GELPDSQSEALEFLKAWGFPVNP------------ 254 (665)
T ss_pred HhcCCCcccChHHHHhhhhhccChHHHhcCCCEEEEEecccccC-CCCCCCHHHHHHHHHHCCCCcCC------------
Confidence 01232212111 01111 11124689999999864432 11134778888888875211110
Q ss_pred ccccCCCCCccceecCCHHHHHHHHHHHHH------cCCceEEEecCCCCCcC--C--CCCCCe---EEEcccccccCCc
Q 001089 385 SHVRPQGEPCWSLVAHNVDEVEKFFKETIE------NRDEGIVLKDLGSKWEP--G--DRSGKW---LKLKPEYIRAGSD 451 (1159)
Q Consensus 385 ~~v~~~~~~~~~~~~~~~~ei~~~~~~ai~------~g~EGlVlK~~ds~Y~p--G--kRs~~W---lKiKpey~~~g~~ 451 (1159)
....+.+.+++.++++.+.+ -.-.|||+|--+-.|.. | .+.+.| +|+.++ .
T Consensus 255 ----------~~~~~~~~~ei~~~~~~~~~~R~~l~y~iDGiViKvn~~~~~~~lG~t~~~PrWaiA~Kf~~~------~ 318 (665)
T PRK07956 255 ----------YRKLCTSIEEVLAFYEEIEEERHDLPYDIDGVVIKVDDLALQEELGFTAKAPRWAIAYKFPAE------E 318 (665)
T ss_pred ----------ceEeeCCHHHHHHHHHHHHHhhccCCCCCCcEEEEecCHHHHHhcCccCCCCCceeEecCCCc------e
Confidence 12345678999999887764 35679999976644431 2 345667 566664 4
Q ss_pred ccEEEEEEEeCCCCCCCccceEEEEEecCCCCCCCCceEEEEEEecCCCCHHHHHHH
Q 001089 452 LDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAV 508 (1159)
Q Consensus 452 lDlvVIG~~~G~Grr~g~~gsfllg~~d~~~~~~~~~~f~~v~kVgtG~sdeel~~l 508 (1159)
..-.|.+-.|..|| .|.+.-. |..++-.- .+. +|.++ |..+.++++.+
T Consensus 319 ~~T~l~~I~~qVGR-TG~iTPV--A~l~PV~l---~G~--tVsrA-tLhN~~~i~~~ 366 (665)
T PRK07956 319 ATTKLLDIEVQVGR-TGAVTPV--ARLEPVEV---AGV--TVSRA-TLHNADEIERK 366 (665)
T ss_pred eEEEEEEEEEecCC-CceeeeE--EEEEeEEE---CCE--EEEEe-ecCCHHHHHHc
Confidence 55677888887775 4444332 22222100 011 34443 67777777654
No 114
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=44.85 E-value=61 Score=37.66 Aligned_cols=50 Identities=12% Similarity=0.063 Sum_probs=40.4
Q ss_pred CCcCCCeEEEEcCCCCCCCCchHHHHHHHHHHHHHHHHhcCCEEEccCC-CceEEEEeccCC
Q 001089 800 WSCFHGCCIYFYHSTEPLSPDWEVLLGLALRRLKLEISFHGGKVCNNLA-NATHVVVLSVLG 860 (1159)
Q Consensus 800 ~~lF~gc~~yl~~~~~~~~~d~~~i~~~~~~~l~~~I~~~GG~v~~~ls-~vTHVIV~~~~~ 860 (1159)
..||.|-+|.|.|.-. .+ ++.++..|..+||++.+..+ +++++|+++..+
T Consensus 230 ~~l~~g~~~v~TG~l~---~~--------R~e~~~~~~~~G~~v~~sVs~~t~~lv~g~~~~ 280 (313)
T PRK06063 230 RPLVQGMRVALSAEVS---RT--------HEELVERILHAGLAYSDSVDRDTSLVVCNDPAP 280 (313)
T ss_pred CcccCCCEEEEecCCC---CC--------HHHHHHHHHHcCCEecCccccCccEEEECCCCC
Confidence 3578999999999642 12 46888999999999999998 589999987543
No 115
>KOG0323 consensus TFIIF-interacting CTD phosphatases, including NLI-interacting factor [Transcription]
Probab=42.97 E-value=25 Score=44.32 Aligned_cols=95 Identities=19% Similarity=0.148 Sum_probs=63.4
Q ss_pred CCcCCCeEEEEcCCCCCCCCchHHHHHHHHHHHHHHHHhcCCEEEccCC-CceEEEEeccCCcccchhhHHHHHHHHhhh
Q 001089 800 WSCFHGCCIYFYHSTEPLSPDWEVLLGLALRRLKLEISFHGGKVCNNLA-NATHVVVLSVLGYDVNFNSLTESFTAREKH 878 (1159)
Q Consensus 800 ~~lF~gc~~yl~~~~~~~~~d~~~i~~~~~~~l~~~I~~~GG~v~~~ls-~vTHVIV~~~~~~~~~~~~l~~~l~~~~~~ 878 (1159)
..-++||.+-|++.-+....+.. ...-.....+|...+.+.+ .+||+|........ .++ .
T Consensus 439 ~~v~~~~~~vfSg~~P~~~~~~~-------s~~~~~~~~~g~vs~~~~~~~~th~i~~~~gt~k-~~~---a-------- 499 (635)
T KOG0323|consen 439 TKVLKGSQIVFSGLHPTGSTDES-------ADILGVAQQLGAVSAPDVSDKTTHLIAANAGTKK-VYK---A-------- 499 (635)
T ss_pred hHHhhccceeecccccCcCCcch-------hhhhhhhhcccceecccccchhhhHHhhccCcce-eec---c--------
Confidence 34588999999986552222111 1222345677888887887 59999987543111 111 1
Q ss_pred hccCCccEEecccHHHHHHHcCCccCCCCCCCCCCC
Q 001089 879 LLWNKKLHVVRSQWLEDCLAKEQKSEEYEYSLKPTG 914 (1159)
Q Consensus 879 ~~~~~~~~IVs~~WL~~ci~~g~~v~E~~Y~v~~~~ 914 (1159)
......+||.+.||+.|+..=..+.|-.|......
T Consensus 500 -~~~~~~~Vv~~~wl~~~~e~w~~v~ek~~~l~~~~ 534 (635)
T KOG0323|consen 500 -VVSGSAKVVNAAWLWRSLEKWGKVEEKLEPLDDDQ 534 (635)
T ss_pred -ccccceeEechhHHHHHHHHhcchhcccccccccc
Confidence 11234899999999999999999999999877766
No 116
>PF09511 RNA_lig_T4_1: RNA ligase; InterPro: IPR019039 Members of this family include T4 phage proteins with ATP-dependent RNA ligase activity. Host defence to phage may include cleavage and inactivation of specific tRNA molecules; members of this family act to reverse this RNA damage. The enzyme is adenylated, transiently, on a Lys residue in a motif KXDGSL. This family also includes fungal tRNA ligases that have adenylyltransferase activity []. tRNA ligases are enzymes required for the splicing of precursor tRNA molecules containing introns. Please see the following relevant references: [, ]. ; PDB: 2C5U_B.
Probab=40.45 E-value=2.3e+02 Score=31.01 Aligned_cols=32 Identities=25% Similarity=0.158 Sum_probs=23.3
Q ss_pred cEEEEEecceEEE-EEEEeCCEEEEEecCCCCc
Q 001089 246 EVVIECKFDGDRI-QIHKNGSEIHYFSRSFLDH 277 (1159)
Q Consensus 246 ~~~vE~K~DGeR~-qih~~g~~v~~fSR~g~d~ 277 (1159)
++.+-.|+||.=+ .....+|.+.+-|+++-.-
T Consensus 46 p~~v~~K~dGsli~~~~~~~g~~~~~SK~s~~s 78 (221)
T PF09511_consen 46 PVEVYEKEDGSLIFIPYLDDGELIVASKGSFDS 78 (221)
T ss_dssp EEEEEEE--SEEE-EEEEETTEEEEEETTBSSS
T ss_pred cEEEEEecCcEEEEEeeecCCeEEEEecCcccc
Confidence 7999999999444 3345788999999998643
No 117
>PF14538 Raptor_N: Raptor N-terminal CASPase like domain
Probab=37.86 E-value=65 Score=33.55 Aligned_cols=40 Identities=13% Similarity=0.293 Sum_probs=24.5
Q ss_pred eecceEEEEeCCCCcccccccHHHHHHHhhcCCCCCCCeEEEEEeeee
Q 001089 298 ILDGEMLVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLY 345 (1159)
Q Consensus 298 ILDGElv~~d~~~~~~~pFg~lq~i~~~~r~~~~~~~~~~~~vFDiL~ 345 (1159)
+-+||++++|+....+.|.. +.++.... ..++++|||+=.
T Consensus 106 t~~GeIw~f~~~~tqyip~s-i~dL~~~l-------g~Psi~V~DC~~ 145 (154)
T PF14538_consen 106 TENGEIWVFNKNYTQYIPLS-IYDLQSWL-------GSPSIYVFDCSN 145 (154)
T ss_pred CCCCeEEEEcCCCCcceEEE-HHHHHHhc-------CCCEEEEEECCc
Confidence 45788888887766666652 33333322 246788899754
No 118
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=33.57 E-value=76 Score=40.24 Aligned_cols=195 Identities=21% Similarity=0.290 Sum_probs=116.0
Q ss_pred CcEEEEEecceEEEEEEEeCC-EEEEEecC----CCCcCcchhhHHHHHHHhc--ccCceeecceEEEEeCCC---C---
Q 001089 245 KEVVIECKFDGDRIQIHKNGS-EIHYFSRS----FLDHSEYGHAMSKIIEQNV--LVDRCILDGEMLVWDTSL---N--- 311 (1159)
Q Consensus 245 ~~~~vE~K~DGeR~qih~~g~-~v~~fSR~----g~d~t~~~p~l~~~l~~~~--~~~~~ILDGElv~~d~~~---~--- 311 (1159)
..|++|+|+||.-+-+.+.+| =++--||. |+|+|.-...|... -..+ .+...-+=||++.--..- +
T Consensus 109 ~~y~~EpKiDGlsisL~YenG~Lv~aaTRGdG~~GEDiT~NvrtI~~I-P~~l~~~p~~lEVRGEvfm~k~~F~~lN~~~ 187 (667)
T COG0272 109 VEYVVEPKIDGLAISLVYENGKLVRAATRGDGTTGEDITANVRTIRSI-PLKLPGAPAVLEVRGEVFMPKEDFEALNEER 187 (667)
T ss_pred cceEEEeecceEEEEEEEECCEEEEeeccCCCccccchhhhhhhHhhh-hhhccCCCceEEEEeEEEEeHHHHHHHHHHH
Confidence 479999999999998888766 47788885 78898644433322 1112 256678889987631100 0
Q ss_pred ---cccccccHHHHHH-Hhh---cCCCCCCCeEEEEEeeeecCCccccCCCHHHHHHHHHHhhccCCCcceeeccCCCCC
Q 001089 312 ---RFAEFGSNQEIAK-AAR---DGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLN 384 (1159)
Q Consensus 312 ---~~~pFg~lq~i~~-~~r---~~~~~~~~~~~~vFDiL~lnG~~l~~~pl~eRr~~L~~~i~~~~~~~~i~~p~~~~~ 384 (1159)
--.+|..-+..+. ..| ......+++.+++|.+-+..+. ..-.+..++.+.|..+-=+...
T Consensus 188 ~~~g~~~faNpRNaAAGsLRqlD~~ita~R~L~~f~y~~~~~~~~-~~~~t~~e~l~~L~~~GF~v~~------------ 254 (667)
T COG0272 188 EEEGEKPFANPRNAAAGSLRQLDPKITAKRKLGFFIYAVGDGEEG-LLADTQSERLAFLKAWGFPVNP------------ 254 (667)
T ss_pred HHhCCCCcCChhhhhhhhhhccCHHHHhcCCceEEEEeCCccCCC-CCccCHHHHHHHHHHcCCCCCc------------
Confidence 0012211111100 001 0112346899999999876654 5567888999999876322110
Q ss_pred ccccCCCCCccceecCCHHHHHHHHHHHHHcC------CceEEEecCCCCCcC--C--CCCCCe---EEEcccccccCCc
Q 001089 385 SHVRPQGEPCWSLVAHNVDEVEKFFKETIENR------DEGIVLKDLGSKWEP--G--DRSGKW---LKLKPEYIRAGSD 451 (1159)
Q Consensus 385 ~~v~~~~~~~~~~~~~~~~ei~~~~~~ai~~g------~EGlVlK~~ds~Y~p--G--kRs~~W---lKiKpey~~~g~~ 451 (1159)
....+.+.+++.++++.+...+ -.|+|+|--+-.... | .|.+.| +|+.++-
T Consensus 255 ----------~~~~~~~~~ev~~~~~~~~~~R~~L~y~IDGvViKvn~l~~q~~lG~tsk~PrWAiAyKFpa~e------ 318 (667)
T COG0272 255 ----------YTRLCKNADEVLAFYEEWEKKRASLPYDIDGVVIKVNDLALQRELGFTSKAPRWAIAYKFPAEE------ 318 (667)
T ss_pred ----------HhhhcCCHHHHHHHHHHHHhhcccCCCccceEEEEeccHHHHHHhCCccCCCceeeeecCCchh------
Confidence 1234778999999999987743 579999965432211 2 356788 6887762
Q ss_pred ccEEEEEEEeCCCCCCCcc
Q 001089 452 LDVLIIGGYYGSGRRGGEV 470 (1159)
Q Consensus 452 lDlvVIG~~~G~Grr~g~~ 470 (1159)
.--.+.+-.+..|| .|.+
T Consensus 319 ~~T~l~dI~~qVGR-TG~i 336 (667)
T COG0272 319 AVTKLLDIEVQVGR-TGAI 336 (667)
T ss_pred eeeEEEEEEEecCC-ceee
Confidence 22244555555554 4444
No 119
>KOG2093 consensus Translesion DNA polymerase - REV1 deoxycytidyl transferase [Replication, recombination and repair]
Probab=31.58 E-value=48 Score=42.76 Aligned_cols=89 Identities=20% Similarity=0.290 Sum_probs=64.7
Q ss_pred CCCcCCCeEEEEcCCCCCCCCchHHHHHHHHHHHHHHHHhcCCEEEc-cCC-CceEEEEeccCCcccchhhHHHHHHHHh
Q 001089 799 KWSCFHGCCIYFYHSTEPLSPDWEVLLGLALRRLKLEISFHGGKVCN-NLA-NATHVVVLSVLGYDVNFNSLTESFTARE 876 (1159)
Q Consensus 799 ~~~lF~gc~~yl~~~~~~~~~d~~~i~~~~~~~l~~~I~~~GG~v~~-~ls-~vTHVIV~~~~~~~~~~~~l~~~l~~~~ 876 (1159)
....|++..+|..+... +. ...+++.-.++||.... ... ..||||....+ .++-.
T Consensus 44 ~~s~fs~is~~~ngs~~---e~--------~nelk~~~~~~t~~~~~~~~rs~T~~ii~~~l~------a~~vk------ 100 (1016)
T KOG2093|consen 44 GSSSFSGISISVNGSTD---ES--------ANELKLQNMFHTGASAASYERSGTENIIAQGLP------ADLVK------ 100 (1016)
T ss_pred CcceeeeeeeccCCccc---cc--------hHHHhhhhhhcccccccccccccceeeecccch------HHHhc------
Confidence 56789999999999763 22 24677788899999874 343 58999986533 11111
Q ss_pred hhhccCCccEEecccHHHHHHHcCCccCCCCCCCCCCC
Q 001089 877 KHLLWNKKLHVVRSQWLEDCLAKEQKSEEYEYSLKPTG 914 (1159)
Q Consensus 877 ~~~~~~~~~~IVs~~WL~~ci~~g~~v~E~~Y~v~~~~ 914 (1159)
.-..+...+++|+.+|++.+..+.--+|......
T Consensus 101 ----~~~~~~~~~~e~iie~~~~~~~~~~~~~~~~t~~ 134 (1016)
T KOG2093|consen 101 ----GFTIPKHISIEWIIECCENGMDVGYYPYQLYTGQ 134 (1016)
T ss_pred ----cccchhhhcHHHHHHHHhccCccccccceeeccc
Confidence 1245678999999999999999998888766555
No 120
>COG5275 BRCT domain type II [General function prediction only]
Probab=27.36 E-value=2e+02 Score=31.42 Aligned_cols=53 Identities=21% Similarity=0.286 Sum_probs=39.9
Q ss_pred CCCcCCCeEEEEcCCCCCCCCchHHHHHHHHHHHHHHHHhcCCEEEccCC-CceEEEEeccCCc
Q 001089 799 KWSCFHGCCIYFYHSTEPLSPDWEVLLGLALRRLKLEISFHGGKVCNNLA-NATHVVVLSVLGY 861 (1159)
Q Consensus 799 ~~~lF~gc~~yl~~~~~~~~~d~~~i~~~~~~~l~~~I~~~GG~v~~~ls-~vTHVIV~~~~~~ 861 (1159)
....+.|.+|-|-|....+ .++.-..++..|||.|+-.++ ..|+||.++..++
T Consensus 153 ~~~cL~G~~fVfTG~l~Tl----------sR~~a~~lvk~yGgrvT~~pSskTtflvlGdnaGP 206 (276)
T COG5275 153 ERECLKGKVFVFTGDLKTL----------SRDDAKTLVKVYGGRVTAVPSSKTTFLVLGDNAGP 206 (276)
T ss_pred CcccccccEEEEecccccc----------cchhHHHHHHHhCCeeecccccceeEEEecCCCCh
Confidence 3456889999999865422 244567789999999999998 4888888876554
No 121
>cd00950 DHDPS Dihydrodipicolinate synthase (DHDPS) is a key enzyme in lysine biosynthesis. It catalyzes the aldol condensation of L-aspartate-beta- semialdehyde and pyruvate to dihydropicolinic acid via a Schiff base formation between pyruvate and a lysine residue. The functional enzyme is a homotetramer consisting of a dimer of dimers. DHDPS is member of dihydrodipicolinate synthase family that comprises several pyruvate-dependent class I aldolases that use the same catalytic step to catalyze different reactions in different pathways.
Probab=25.68 E-value=1.4e+02 Score=33.82 Aligned_cols=67 Identities=19% Similarity=0.217 Sum_probs=50.3
Q ss_pred eeeecCCc--cccCCCHHHHHHHHHHhhccCCCcceeeccCCCCCccccCCCCCccceecCCHHHHHHHHHHHHHcCCce
Q 001089 342 DVLYVGDT--SVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEG 419 (1159)
Q Consensus 342 DiL~lnG~--~l~~~pl~eRr~~L~~~i~~~~~~~~i~~p~~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~ai~~g~EG 419 (1159)
|-++++|. ....++..||+++++.+.....+++.++. .....+.++..++.+.+.+.|..|
T Consensus 36 ~gl~v~GstGE~~~lt~~Er~~l~~~~~~~~~~~~~vi~-----------------gv~~~~~~~~~~~a~~a~~~G~d~ 98 (284)
T cd00950 36 DGLVVCGTTGESPTLSDEEHEAVIEAVVEAVNGRVPVIA-----------------GTGSNNTAEAIELTKRAEKAGADA 98 (284)
T ss_pred CEEEECCCCcchhhCCHHHHHHHHHHHHHHhCCCCcEEe-----------------ccCCccHHHHHHHHHHHHHcCCCE
Confidence 44555553 23578999999999999887777665432 123457788999999999999999
Q ss_pred EEEecC
Q 001089 420 IVLKDL 425 (1159)
Q Consensus 420 lVlK~~ 425 (1159)
+|+=.+
T Consensus 99 v~~~~P 104 (284)
T cd00950 99 ALVVTP 104 (284)
T ss_pred EEEccc
Confidence 999865
No 122
>smart00384 AT_hook DNA binding domain with preference for A/T rich regions. Small DNA-binding motif first described in the high mobility group non-histone chromosomal protein HMG-I(Y).
Probab=24.02 E-value=43 Score=24.22 Aligned_cols=13 Identities=54% Similarity=0.871 Sum_probs=8.9
Q ss_pred ccccCCCCCCCcc
Q 001089 970 KRKRGRPAGGSAK 982 (1159)
Q Consensus 970 ~~~~~~~~~~~~~ 982 (1159)
+|+||||+.....
T Consensus 1 kRkRGRPrK~~~~ 13 (26)
T smart00384 1 KRKRGRPRKAPKD 13 (26)
T ss_pred CCCCCCCCCCCCc
Confidence 4788888765543
No 123
>PF00701 DHDPS: Dihydrodipicolinate synthetase family; InterPro: IPR002220 Dihydropicolinate synthase (DHDPS) is the key enzyme in lysine biosynthesis via the diaminopimelate pathway of prokaryotes, some phycomycetes and higher plants. The enzyme catalyses the condensation of L-aspartate-beta- semialdehyde and pyruvate to dihydropicolinic acid via a ping-pong mechanism in which pyruvate binds to the enzyme by forming a Schiff-base with a lysine residue []. Three other proteins are structurally related to DHDPS and probably also act via a similar catalytic mechanism. These are Escherichia coli N-acetylneuraminate lyase (4.1.3.3 from EC) (gene nanA), which catalyzes the condensation of N-acetyl-D-mannosamine and pyruvate to form N-acetylneuraminate; Rhizobium meliloti (Sinorhizobium meliloti) protein mosA [], which is involved in the biosynthesis of the rhizopine 3-o-methyl-scyllo-inosamine; and E. coli hypothetical protein yjhH. The sequences of DHDPS from different sources are well-conserved. The structure takes the form of a homotetramer, in which 2 monomers are related by an approximate 2-fold symmetry []. Each monomer comprises 2 domains: an 8-fold alpha-/beta-barrel, and a C-terminal alpha-helical domain. The fold resembles that of N-acetylneuraminate lyase. The active site lysine is located in the barrel domain, and has access via 2 channels on the C-terminal side of the barrel.; GO: 0016829 lyase activity, 0008152 metabolic process; PDB: 3B4U_B 3S8H_A 3QZE_B 1XXX_F 3L21_F 3IRD_A 3A5F_B 3G0S_B 3DAQ_C 3UQN_A ....
Probab=23.68 E-value=1.7e+02 Score=33.39 Aligned_cols=65 Identities=20% Similarity=0.311 Sum_probs=48.3
Q ss_pred eecCCc--cccCCCHHHHHHHHHHhhccCCCcceeeccCCCCCccccCCCCCccceecCCHHHHHHHHHHHHHcCCceEE
Q 001089 344 LYVGDT--SVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIV 421 (1159)
Q Consensus 344 L~lnG~--~l~~~pl~eRr~~L~~~i~~~~~~~~i~~p~~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~ai~~g~EGlV 421 (1159)
+++.|. ....++.+||+++++.++....+++.++. .+.+.+.++..++.+.+.+.|-.|+|
T Consensus 39 l~~~GstGE~~~Lt~~Er~~l~~~~~~~~~~~~~vi~-----------------gv~~~st~~~i~~a~~a~~~Gad~v~ 101 (289)
T PF00701_consen 39 LVVLGSTGEFYSLTDEERKELLEIVVEAAAGRVPVIA-----------------GVGANSTEEAIELARHAQDAGADAVL 101 (289)
T ss_dssp EEESSTTTTGGGS-HHHHHHHHHHHHHHHTTSSEEEE-----------------EEESSSHHHHHHHHHHHHHTT-SEEE
T ss_pred EEECCCCcccccCCHHHHHHHHHHHHHHccCceEEEe-----------------cCcchhHHHHHHHHHHHhhcCceEEE
Confidence 444442 24578999999999998887777765442 33456889999999999999999999
Q ss_pred EecC
Q 001089 422 LKDL 425 (1159)
Q Consensus 422 lK~~ 425 (1159)
+=.+
T Consensus 102 v~~P 105 (289)
T PF00701_consen 102 VIPP 105 (289)
T ss_dssp EEES
T ss_pred Eecc
Confidence 9765
No 124
>cd00408 DHDPS-like Dihydrodipicolinate synthase family. A member of the class I aldolases, which use an active-site lysine which stablilzes a reaction intermediate via Schiff base formation, and have TIM beta/alpha barrel fold. The dihydrodipicolinate synthase family comprises several pyruvate-dependent class I aldolases that use the same catalytic step to catalyze different reactions in different pathways and includes such proteins as N-acetylneuraminate lyase, MosA protein, 5-keto-4-deoxy-glucarate dehydratase, trans-o-hydroxybenzylidenepyruvate hydratase-aldolase, trans-2'-carboxybenzalpyruvate hydratase-aldolase, and 2-keto-3-deoxy- gluconate aldolase. The family is also referred to as the N-acetylneuraminate lyase (NAL) family.
Probab=22.92 E-value=1.8e+02 Score=32.85 Aligned_cols=65 Identities=22% Similarity=0.305 Sum_probs=47.7
Q ss_pred eecCCc--cccCCCHHHHHHHHHHhhccCCCcceeeccCCCCCccccCCCCCccceecCCHHHHHHHHHHHHHcCCceEE
Q 001089 344 LYVGDT--SVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIV 421 (1159)
Q Consensus 344 L~lnG~--~l~~~pl~eRr~~L~~~i~~~~~~~~i~~p~~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~ai~~g~EGlV 421 (1159)
++++|. ....++.+||+++++.+.....+++.++. .....+..+..++.+.+.+.|-.|+|
T Consensus 35 i~~~GstGE~~~ls~~Er~~l~~~~~~~~~~~~~vi~-----------------gv~~~~~~~~i~~a~~a~~~Gad~v~ 97 (281)
T cd00408 35 LVVLGTTGEAPTLTDEERKEVIEAVVEAVAGRVPVIA-----------------GVGANSTREAIELARHAEEAGADGVL 97 (281)
T ss_pred EEECCCCcccccCCHHHHHHHHHHHHHHhCCCCeEEE-----------------ecCCccHHHHHHHHHHHHHcCCCEEE
Confidence 445543 23567999999999999887766665442 12345678888999999999999999
Q ss_pred EecC
Q 001089 422 LKDL 425 (1159)
Q Consensus 422 lK~~ 425 (1159)
+=.+
T Consensus 98 v~pP 101 (281)
T cd00408 98 VVPP 101 (281)
T ss_pred ECCC
Confidence 9543
No 125
>PRK03170 dihydrodipicolinate synthase; Provisional
Probab=21.90 E-value=1.8e+02 Score=33.17 Aligned_cols=58 Identities=17% Similarity=0.235 Sum_probs=45.5
Q ss_pred ccCCCHHHHHHHHHHhhccCCCcceeeccCCCCCccccCCCCCccceecCCHHHHHHHHHHHHHcCCceEEEecC
Q 001089 351 VIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDL 425 (1159)
Q Consensus 351 l~~~pl~eRr~~L~~~i~~~~~~~~i~~p~~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~ai~~g~EGlVlK~~ 425 (1159)
...++.+||+++++.++....+++.++. .....+.++..++.+.+.+.|..|+|+=.+
T Consensus 48 ~~~ls~~Er~~~~~~~~~~~~~~~~vi~-----------------gv~~~~~~~~i~~a~~a~~~G~d~v~~~pP 105 (292)
T PRK03170 48 SPTLTHEEHEELIRAVVEAVNGRVPVIA-----------------GTGSNSTAEAIELTKFAEKAGADGALVVTP 105 (292)
T ss_pred cccCCHHHHHHHHHHHHHHhCCCCcEEe-----------------ecCCchHHHHHHHHHHHHHcCCCEEEECCC
Confidence 3578999999999999887777765432 122456788899999999999999999654
No 126
>cd00952 CHBPH_aldolase Trans-o-hydroxybenzylidenepyruvate hydratase-aldolase (HBPHA) and trans-2'-carboxybenzalpyruvate hydratase-aldolase (CBPHA). HBPHA catalyzes HBP to salicyaldehyde and pyruvate. This reaction is part of the degradative pathways for naphthalene and naphthalenesulfonates by bacteria. CBPHA is homologous to HBPHA and catalyzes the cleavage of CBP to 2-carboxylbenzaldehyde and pyruvate during the degradation of phenanthrene. They are member of the DHDPS family of Schiff-base-dependent class I aldolases.
Probab=21.85 E-value=1.9e+02 Score=33.53 Aligned_cols=65 Identities=15% Similarity=0.238 Sum_probs=49.6
Q ss_pred eecCCc--cccCCCHHHHHHHHHHhhccCCCcceeeccCCCCCccccCCCCCccceecCCHHHHHHHHHHHHHcCCceEE
Q 001089 344 LYVGDT--SVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIV 421 (1159)
Q Consensus 344 L~lnG~--~l~~~pl~eRr~~L~~~i~~~~~~~~i~~p~~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~ai~~g~EGlV 421 (1159)
|+++|. ....++.+||+++++.++....+++.++. ...+.+.++..++.+.+.+.|-.|+|
T Consensus 46 i~v~GstGE~~~Lt~eEr~~v~~~~~~~~~grvpvi~-----------------Gv~~~~t~~ai~~a~~A~~~Gad~vl 108 (309)
T cd00952 46 ILTMGTFGECATLTWEEKQAFVATVVETVAGRVPVFV-----------------GATTLNTRDTIARTRALLDLGADGTM 108 (309)
T ss_pred EEECcccccchhCCHHHHHHHHHHHHHHhCCCCCEEE-----------------EeccCCHHHHHHHHHHHHHhCCCEEE
Confidence 444543 24578999999999999887777765432 22345788999999999999999999
Q ss_pred EecC
Q 001089 422 LKDL 425 (1159)
Q Consensus 422 lK~~ 425 (1159)
+=.+
T Consensus 109 v~~P 112 (309)
T cd00952 109 LGRP 112 (309)
T ss_pred ECCC
Confidence 9765
No 127
>TIGR02313 HpaI-NOT-DapA 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase. This model represents a subset of the DapA (dihydrodipicolinate synthase) family which has apparently evolved a separate function. The product of DapA, dihydrodipicolinate, results from the non-enzymatic cyclization and dehydration of 6-amino-2,4-dihydroxyhept-2-ene-1,7-dioic acid, which is different from the substrate of this reaction only in the presence of the amino group. In the absence of this amino group, and running the reaction in the opposite direction, the reaction corresponds to the HpaI aldolase component of the 4-hydroxyphenylacetic acid catabolism pathway (see TIGR02311). At present, this variant of DapA is found only in Oceanobacillus iheyensis HTE831 and Thermus thermophilus HB27. In both of these cases, one or more other DapA genes can be found and the one identified by this model is part of an operon for 4-hydroxyphenylacetic acid catabolism.
Probab=21.83 E-value=1.9e+02 Score=33.29 Aligned_cols=65 Identities=22% Similarity=0.202 Sum_probs=48.4
Q ss_pred eecCCc--cccCCCHHHHHHHHHHhhccCCCcceeeccCCCCCccccCCCCCccceecCCHHHHHHHHHHHHHcCCceEE
Q 001089 344 LYVGDT--SVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIV 421 (1159)
Q Consensus 344 L~lnG~--~l~~~pl~eRr~~L~~~i~~~~~~~~i~~p~~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~ai~~g~EGlV 421 (1159)
++++|. ....++..||+++++.++....+++.++. .....+..+..++-+.+.+.|..|+|
T Consensus 38 i~v~GstGE~~~Ls~~Er~~l~~~~~~~~~g~~pvi~-----------------gv~~~~t~~ai~~a~~A~~~Gad~v~ 100 (294)
T TIGR02313 38 ISVGGTSGEPGSLTLEERKQAIENAIDQIAGRIPFAP-----------------GTGALNHDETLELTKFAEEAGADAAM 100 (294)
T ss_pred EEECccCcccccCCHHHHHHHHHHHHHHhCCCCcEEE-----------------ECCcchHHHHHHHHHHHHHcCCCEEE
Confidence 444442 24568999999999999887777765442 12345678888889999999999999
Q ss_pred EecC
Q 001089 422 LKDL 425 (1159)
Q Consensus 422 lK~~ 425 (1159)
+=.+
T Consensus 101 v~pP 104 (294)
T TIGR02313 101 VIVP 104 (294)
T ss_pred EcCc
Confidence 9764
No 128
>TIGR00683 nanA N-acetylneuraminate lyase. N-acetylneuraminate lyase is also known as N-acetylneuraminic acid aldolase, sialic acid aldolase, or sialate lyase. It is an intracellular enzyme. The structure of this homotetrameric enzyme related to dihydrodipicolinate synthase is known. In Clostridium tertium, the enzyme appears to be in an operon with a secreted sialidase that releases sialic acid from host sialoglycoconjugates. In several E. coli strains, however, this enzyme is responsible for N-acetyl-D-neuraminic acid synthesis for capsule production by condensing N-acetyl-D-mannosamine and pyruvate.
Probab=21.51 E-value=1.9e+02 Score=33.08 Aligned_cols=66 Identities=20% Similarity=0.239 Sum_probs=48.4
Q ss_pred eeeecCCc--cccCCCHHHHHHHHHHhhccCCCcceeeccCCCCCccccCCCCCccceecCCHHHHHHHHHHHHHcCCce
Q 001089 342 DVLYVGDT--SVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEG 419 (1159)
Q Consensus 342 DiL~lnG~--~l~~~pl~eRr~~L~~~i~~~~~~~~i~~p~~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~ai~~g~EG 419 (1159)
|-|+++|. ....++.+||.++++.++....+++.++. .+...+.++..++.+.+.+.|-.|
T Consensus 37 ~gi~~~GstGE~~~Lt~eEr~~~~~~~~~~~~~~~pvi~-----------------gv~~~~t~~~i~la~~a~~~Gad~ 99 (290)
T TIGR00683 37 DGLYVGGSTGENFMLSTEEKKEIFRIAKDEAKDQIALIA-----------------QVGSVNLKEAVELGKYATELGYDC 99 (290)
T ss_pred CEEEECCcccccccCCHHHHHHHHHHHHHHhCCCCcEEE-----------------ecCCCCHHHHHHHHHHHHHhCCCE
Confidence 34555553 13467999999999999887777765432 122456788899999999999999
Q ss_pred EEEec
Q 001089 420 IVLKD 424 (1159)
Q Consensus 420 lVlK~ 424 (1159)
+|+=.
T Consensus 100 v~v~~ 104 (290)
T TIGR00683 100 LSAVT 104 (290)
T ss_pred EEEeC
Confidence 99954
No 129
>PF15101 DUF4557: Domain of unknown function (DUF4557)
Probab=20.62 E-value=2.3e+02 Score=30.66 Aligned_cols=70 Identities=20% Similarity=0.335 Sum_probs=45.1
Q ss_pred HHHHHHHHHcCCEEEecCCCCceEEEEecC---CChh-hH--hHhcCC-CeeecchHHHHHhcCc--cCCCCcccccccC
Q 001089 674 DSLHKMVVENGGTFSMNLNNSVTHCVAADN---KGLK-YE--AAKRRG-DVIHYSWVLDCCSQKK--LLQLQPKYYLHLS 744 (1159)
Q Consensus 674 ~eLe~lI~~~GG~iv~n~~~~~Th~Ia~~~---~~~k-~~--~a~~~~-~VV~p~WV~dCi~~~~--lLp~~p~~~l~~s 744 (1159)
.++.++=+.+||+++. +. ...++-..+. .|.. |. .++... .|.++.||..|.+... -+++. .|+|++.
T Consensus 14 ~~~~~~Wv~~GG~isd-~~-~AdFLFS~DAshpDT~~iy~S~dY~~d~aTVFha~yl~a~~na~s~~sV~LG-hyVL~~P 90 (212)
T PF15101_consen 14 QDLRQFWVKEGGTISD-WD-AADFLFSCDASHPDTARIYQSLDYIEDRATVFHASYLSAVANAESKNSVALG-HYVLNTP 90 (212)
T ss_pred hHHHHHHHhcCCccCC-hh-hcceeeecCCCCcchHhhhhhhhhhhcCeeeeeHHHHHHHhhhhhcCCcccc-ceEecCC
Confidence 6888999999999987 33 2456665443 2322 22 233444 8999999999998653 34444 4566566
Q ss_pred hh
Q 001089 745 DS 746 (1159)
Q Consensus 745 ~~ 746 (1159)
++
T Consensus 91 P~ 92 (212)
T PF15101_consen 91 PE 92 (212)
T ss_pred HH
Confidence 65
Done!