Query 002803
Match_columns 879
No_of_seqs 399 out of 2059
Neff 7.2
Searched_HMMs 46136
Date Fri Mar 29 07:25:55 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/002803.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/002803hhsearch_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 4E-158 8E-163 1334.1 59.9 807 3-857 1-836 (881)
2 PLN03113 DNA ligase 1; Provisi 100.0 1E-102 2E-107 923.7 54.6 550 5-603 127-730 (744)
3 PRK01109 ATP-dependent DNA lig 100.0 2E-100 5E-105 901.6 53.2 544 7-603 1-582 (590)
4 KOG0967 ATP-dependent DNA liga 100.0 9.4E-97 2E-101 819.0 36.8 551 5-603 97-704 (714)
5 TIGR00574 dnl1 DNA ligase I, A 100.0 3.3E-93 7.2E-98 831.5 50.6 494 62-600 1-513 (514)
6 PRK09247 ATP-dependent DNA lig 100.0 1.8E-90 3.8E-95 807.5 50.2 522 9-602 1-537 (539)
7 PRK03180 ligB ATP-dependent DN 100.0 3.1E-90 6.8E-95 799.2 49.3 494 7-601 1-507 (508)
8 PHA02587 30 DNA ligase; Provis 100.0 8.6E-63 1.9E-67 568.8 41.5 445 13-597 3-484 (488)
9 COG1793 CDC9 ATP-dependent DNA 100.0 2.6E-60 5.6E-65 539.6 31.8 421 100-600 18-443 (444)
10 TIGR02779 NHEJ_ligase_lig DNA 100.0 2.8E-56 6.1E-61 487.2 33.1 288 243-591 10-297 (298)
11 PRK09632 ATP-dependent DNA lig 100.0 2.2E-55 4.9E-60 520.0 32.1 307 218-591 455-761 (764)
12 PRK08224 ligC ATP-dependent DN 100.0 5.6E-53 1.2E-57 467.1 33.9 314 217-591 2-330 (350)
13 PRK05972 ligD ATP-dependent DN 100.0 4.7E-52 1E-56 495.9 32.2 304 222-591 232-536 (860)
14 PRK09633 ligD ATP-dependent DN 100.0 1E-50 2.2E-55 475.3 32.1 310 224-601 1-318 (610)
15 PRK07636 ligB ATP-dependent DN 100.0 1.7E-46 3.7E-51 404.4 30.2 272 224-582 3-274 (275)
16 cd07900 Adenylation_DNA_ligase 100.0 7.6E-46 1.7E-50 387.3 22.4 213 216-445 2-219 (219)
17 TIGR02776 NHEJ_ligase_prk DNA 100.0 9.8E-44 2.1E-48 412.2 25.3 257 271-591 1-258 (552)
18 cd07903 Adenylation_DNA_ligase 100.0 3.5E-43 7.6E-48 370.2 21.8 214 215-446 3-224 (225)
19 cd07902 Adenylation_DNA_ligase 100.0 5.1E-42 1.1E-46 357.6 21.5 206 216-445 6-213 (213)
20 cd07901 Adenylation_DNA_ligase 100.0 1E-41 2.2E-46 354.2 22.1 204 220-444 1-207 (207)
21 PRK09125 DNA ligase; Provision 100.0 2E-41 4.4E-46 365.6 23.5 254 224-585 28-282 (282)
22 PHA00454 ATP-dependent DNA lig 100.0 3.8E-40 8.2E-45 362.4 29.0 284 225-583 7-314 (315)
23 cd07898 Adenylation_DNA_ligase 100.0 2.4E-40 5.3E-45 342.6 21.9 199 224-444 1-201 (201)
24 cd08039 Adenylation_DNA_ligase 100.0 4E-40 8.7E-45 346.2 22.1 201 233-445 10-235 (235)
25 cd07897 Adenylation_DNA_ligase 100.0 2.7E-40 5.9E-45 343.1 20.5 200 222-444 3-205 (207)
26 PF01068 DNA_ligase_A_M: ATP d 100.0 2.6E-38 5.7E-43 327.6 20.2 199 226-442 1-202 (202)
27 cd07905 Adenylation_DNA_ligase 100.0 4E-38 8.7E-43 323.9 19.8 190 224-444 1-193 (194)
28 cd07906 Adenylation_DNA_ligase 100.0 1.7E-37 3.7E-42 318.5 18.4 189 224-443 1-189 (190)
29 cd07967 OBF_DNA_ligase_III The 100.0 1E-33 2.2E-38 273.1 15.2 137 449-595 2-139 (139)
30 cd07896 Adenylation_kDNA_ligas 100.0 8.4E-32 1.8E-36 272.6 14.0 173 224-443 1-174 (174)
31 PF04675 DNA_ligase_A_N: DNA l 100.0 9E-31 1.9E-35 265.8 13.1 169 7-187 1-177 (177)
32 cd06846 Adenylation_DNA_ligase 100.0 9.9E-30 2.1E-34 259.3 17.8 177 226-443 2-182 (182)
33 cd07968 OBF_DNA_ligase_IV The 100.0 3.2E-29 7E-34 243.7 14.6 139 449-593 1-140 (140)
34 cd07969 OBF_DNA_ligase_I The O 100.0 1.2E-27 2.6E-32 233.2 15.9 134 449-601 1-143 (144)
35 KOG4437 ATP-dependent DNA liga 99.9 8.2E-26 1.8E-30 234.6 18.8 317 8-345 156-482 (482)
36 cd07895 Adenylation_mRNA_cappi 99.9 2.3E-26 5E-31 240.7 14.8 175 239-443 35-215 (215)
37 cd07972 OBF_DNA_ligase_Arch_Li 99.9 4E-26 8.7E-31 216.8 14.2 121 450-597 1-121 (122)
38 cd07893 OBF_DNA_ligase The Oli 99.9 3.4E-25 7.3E-30 212.4 15.2 122 450-590 1-129 (129)
39 cd07971 OBF_DNA_ligase_LigD Th 99.8 2.9E-19 6.3E-24 168.3 13.7 114 451-590 2-115 (115)
40 PF04679 DNA_ligase_A_C: ATP d 99.8 2.1E-18 4.5E-23 157.5 11.4 97 466-585 1-97 (97)
41 cd08040 OBF_DNA_ligase_family 99.8 3.8E-18 8.3E-23 158.9 13.2 108 450-582 1-108 (108)
42 cd07894 Adenylation_RNA_ligase 99.7 2.4E-16 5.1E-21 174.2 14.8 163 245-445 48-218 (342)
43 cd07970 OBF_DNA_ligase_LigC Th 99.6 5.7E-15 1.2E-19 140.1 13.0 120 450-591 1-121 (122)
44 PF01331 mRNA_cap_enzyme: mRNA 99.3 6.2E-13 1.3E-17 136.9 1.2 174 240-442 11-192 (192)
45 PF00533 BRCT: BRCA1 C Terminu 99.2 1.9E-11 4.1E-16 106.2 7.0 74 653-727 2-78 (78)
46 COG5226 CEG1 mRNA capping enzy 99.1 1E-10 2.2E-15 122.0 8.0 184 241-458 58-257 (404)
47 smart00292 BRCT breast cancer 99.0 5.6E-10 1.2E-14 96.2 7.8 76 655-730 1-80 (80)
48 KOG3226 DNA repair protein [Re 99.0 3.5E-10 7.5E-15 120.5 4.5 95 648-744 309-404 (508)
49 cd08041 OBF_kDNA_ligase_like T 98.9 2.4E-09 5.1E-14 93.5 8.0 76 451-582 2-77 (77)
50 cd00027 BRCT Breast Cancer Sup 98.9 6.6E-09 1.4E-13 87.4 7.4 70 659-728 1-72 (72)
51 COG1423 ATP-dependent DNA liga 98.8 6.8E-08 1.5E-12 103.5 14.7 151 240-429 83-238 (382)
52 PF11411 DNA_ligase_IV: DNA li 98.8 5.1E-09 1.1E-13 75.1 3.2 35 746-780 1-35 (36)
53 TIGR01209 RNA ligase, Pab1020 98.7 1.5E-07 3.3E-12 104.0 15.0 151 241-428 75-229 (374)
54 PF12738 PTCB-BRCT: twin BRCT 98.5 1.1E-07 2.4E-12 79.6 3.9 61 661-722 2-63 (63)
55 KOG2481 Protein required for n 98.5 9E-08 2E-12 106.8 4.4 79 653-737 324-412 (570)
56 PRK07956 ligA NAD-dependent DN 98.4 3E-05 6.4E-10 93.8 23.7 224 246-509 109-367 (665)
57 cd09232 Snurportin-1_C C-termi 98.4 2.6E-06 5.5E-11 86.9 11.1 176 225-444 5-186 (186)
58 COG5163 NOP7 Protein required 98.2 6.2E-07 1.3E-11 96.8 3.5 79 653-737 347-436 (591)
59 KOG1929 Nucleotide excision re 98.2 3.3E-06 7.2E-11 101.8 8.0 194 653-874 100-300 (811)
60 PF14743 DNA_ligase_OB_2: DNA 98.0 6E-06 1.3E-10 69.5 3.7 36 462-508 2-37 (66)
61 COG0272 Lig NAD-dependent DNA 97.7 0.0053 1.1E-07 72.8 23.8 195 245-471 109-337 (667)
62 smart00532 LIGANc Ligase N fam 97.7 0.00048 1E-08 79.4 14.5 223 246-508 104-361 (441)
63 PLN03122 Poly [ADP-ribose] pol 97.7 7.1E-05 1.5E-09 91.3 7.9 87 653-741 186-278 (815)
64 cd00114 LIGANc NAD+ dependent 97.6 0.00052 1.1E-08 75.7 12.6 167 246-438 102-299 (307)
65 PRK08097 ligB NAD-dependent DN 97.5 0.0013 2.7E-08 77.8 15.1 211 224-471 95-329 (562)
66 TIGR00575 dnlj DNA ligase, NAD 97.5 0.0012 2.5E-08 80.2 15.2 224 246-509 97-355 (652)
67 PF01653 DNA_ligase_aden: NAD- 97.4 0.00013 2.8E-09 80.8 4.4 160 246-429 108-293 (315)
68 PRK14351 ligA NAD-dependent DN 97.4 0.0022 4.8E-08 77.9 14.7 223 245-509 132-389 (689)
69 KOG3524 Predicted guanine nucl 97.1 0.0023 4.9E-08 74.7 10.1 144 653-862 115-258 (850)
70 PLN03123 poly [ADP-ribose] pol 97.0 0.0011 2.4E-08 82.8 7.3 86 652-738 389-478 (981)
71 PRK14350 ligA NAD-dependent DN 96.9 0.011 2.3E-07 71.8 14.5 223 246-509 111-364 (669)
72 PF00533 BRCT: BRCA1 C Terminu 96.7 0.0048 1E-07 53.1 6.7 49 800-859 3-51 (78)
73 TIGR02307 RNA_lig_RNL2 RNA lig 96.7 0.023 5E-07 62.6 13.3 106 242-366 22-145 (325)
74 PRK01109 ATP-dependent DNA lig 96.6 0.0087 1.9E-07 72.2 10.4 97 4-114 112-211 (590)
75 PF09414 RNA_ligase: RNA ligas 96.4 0.0059 1.3E-07 62.5 6.4 106 246-366 2-129 (186)
76 KOG3548 DNA damage checkpoint 96.2 0.0037 8.1E-08 74.9 4.2 92 654-748 923-1042(1176)
77 KOG1929 Nucleotide excision re 95.8 0.037 8E-07 67.7 9.9 143 654-861 7-151 (811)
78 smart00292 BRCT breast cancer 95.5 0.025 5.5E-07 47.9 5.2 51 802-862 2-53 (80)
79 KOG2093 Translesion DNA polyme 95.4 0.011 2.3E-07 71.0 3.2 101 650-752 41-142 (1016)
80 PHA02142 putative RNA ligase 95.0 0.36 7.8E-06 54.2 13.6 104 242-367 166-299 (366)
81 PRK14351 ligA NAD-dependent DN 94.7 0.066 1.4E-06 65.4 7.5 76 654-729 607-684 (689)
82 PRK14350 ligA NAD-dependent DN 94.6 0.069 1.5E-06 64.9 7.4 74 654-727 591-665 (669)
83 PRK06063 DNA polymerase III su 94.6 0.077 1.7E-06 59.0 7.1 73 654-727 230-305 (313)
84 cd00027 BRCT Breast Cancer Sup 94.0 0.11 2.4E-06 42.8 5.3 48 805-862 1-48 (72)
85 PRK06195 DNA polymerase III su 93.9 0.11 2.4E-06 57.7 6.6 49 654-702 218-266 (309)
86 TIGR00575 dnlj DNA ligase, NAD 93.5 0.14 3.1E-06 62.4 7.1 67 654-720 582-649 (652)
87 TIGR02306 RNA_lig_DRB0094 RNA 93.0 0.72 1.6E-05 51.7 11.1 104 244-366 158-277 (341)
88 KOG4362 Transcriptional regula 92.4 0.49 1.1E-05 56.7 9.1 131 664-844 482-619 (684)
89 COG5275 BRCT domain type II [G 92.2 0.46 9.9E-06 48.6 7.4 80 648-727 148-229 (276)
90 KOG3132 m3G-cap-specific nucle 90.8 1.6 3.5E-05 45.6 9.7 173 225-440 100-277 (325)
91 KOG2386 mRNA capping enzyme, g 87.8 0.31 6.8E-06 55.0 2.3 97 245-367 285-385 (393)
92 KOG2043 Signaling protein SWIF 87.6 0.5 1.1E-05 59.1 4.1 69 675-745 672-742 (896)
93 PRK09247 ATP-dependent DNA lig 87.0 0.93 2E-05 54.3 5.8 82 127-208 2-91 (539)
94 KOG4362 Transcriptional regula 85.3 1.1 2.4E-05 53.9 5.1 81 653-733 584-681 (684)
95 PF04675 DNA_ligase_A_N: DNA l 82.3 1.2 2.7E-05 44.9 3.5 85 125-209 2-100 (177)
96 PRK03180 ligB ATP-dependent DN 80.0 10 0.00022 45.2 10.6 93 6-114 72-167 (508)
97 PF12738 PTCB-BRCT: twin BRCT 74.6 2 4.4E-05 35.5 1.9 42 806-858 1-42 (63)
98 PLN03113 DNA ligase 1; Provisi 72.9 7.1 0.00015 48.4 6.7 86 122-207 127-229 (744)
99 KOG2481 Protein required for n 72.7 3.1 6.8E-05 48.0 3.3 45 801-858 326-380 (570)
100 KOG0966 ATP-dependent DNA liga 72.1 4.2 9.1E-05 49.4 4.4 86 7-115 125-211 (881)
101 KOG0323 TFIIF-interacting CTD 62.6 3.8 8.2E-05 49.4 1.5 83 654-737 439-527 (635)
102 TIGR00574 dnl1 DNA ligase I, A 61.0 26 0.00057 41.8 8.2 94 5-114 53-149 (514)
103 COG4566 TtrR Response regulato 60.9 27 0.00059 35.8 6.9 82 101-182 84-175 (202)
104 KOG3524 Predicted guanine nucl 51.2 12 0.00026 45.0 3.0 74 654-730 208-283 (850)
105 PF09511 RNA_lig_T4_1: RNA lig 47.0 1.9E+02 0.0041 30.4 11.1 32 246-277 46-78 (221)
106 PF15101 DUF4557: Domain of un 45.1 41 0.00088 34.6 5.3 80 674-756 14-103 (212)
107 COG5163 NOP7 Protein required 35.7 21 0.00046 40.1 1.8 45 800-857 348-403 (591)
108 cd00950 DHDPS Dihydrodipicolin 30.4 1.1E+02 0.0024 33.3 6.5 67 342-425 36-104 (284)
109 KOG2872 Uroporphyrinogen decar 27.2 55 0.0012 35.7 3.1 107 670-776 227-351 (359)
110 cd00408 DHDPS-like Dihydrodipi 26.8 1.5E+02 0.0032 32.2 6.6 66 343-425 34-101 (281)
111 TIGR02313 HpaI-NOT-DapA 2,4-di 25.3 1.6E+02 0.0034 32.5 6.5 59 351-426 47-105 (294)
112 PRK03170 dihydrodipicolinate s 25.0 1.5E+02 0.0034 32.3 6.4 67 343-426 38-106 (292)
113 TIGR00683 nanA N-acetylneurami 24.0 1.8E+02 0.0039 32.0 6.6 67 342-425 37-105 (290)
114 PLN02417 dihydrodipicolinate s 23.2 1.8E+02 0.004 31.7 6.5 57 352-425 49-105 (280)
115 cd00952 CHBPH_aldolase Trans-o 23.0 1.8E+02 0.0039 32.3 6.5 65 344-425 46-112 (309)
116 TIGR00674 dapA dihydrodipicoli 22.7 1.8E+02 0.004 31.7 6.4 58 352-426 46-103 (285)
117 cd00954 NAL N-Acetylneuraminic 22.6 2.1E+02 0.0046 31.3 6.8 68 342-426 37-106 (288)
118 KOG3673 FtsJ-like RNA methyltr 22.5 72 0.0016 37.6 3.1 39 332-370 654-692 (845)
119 TIGR03544 DivI1A_domain DivIVA 22.3 1.6E+02 0.0034 21.4 3.8 29 110-138 4-32 (34)
120 PRK04147 N-acetylneuraminate l 21.9 2.1E+02 0.0045 31.4 6.6 57 352-425 52-108 (293)
121 KOG2386 mRNA capping enzyme, g 21.7 4.4E+02 0.0094 30.4 9.0 174 236-445 51-242 (393)
122 PF02969 TAF: TATA box binding 21.5 1.1E+02 0.0025 25.9 3.4 56 69-134 7-66 (66)
123 PF00701 DHDPS: Dihydrodipicol 21.2 1.6E+02 0.0035 32.1 5.6 65 344-425 39-105 (289)
124 cd00951 KDGDH 5-dehydro-4-deox 21.0 2.2E+02 0.0047 31.3 6.5 64 343-424 37-102 (289)
No 1
>KOG0966 consensus ATP-dependent DNA ligase IV [Replication, recombination and repair]
Probab=100.00 E-value=3.8e-158 Score=1334.08 Aligned_cols=807 Identities=42% Similarity=0.700 Sum_probs=678.6
Q ss_pred CCCCCcHHHHHHHHHHHHhcCChhHHHHHHHHHHhhcCCC----ChHhhhHhhcCCCCCcCccccCCCHHHHHHHHHHHh
Q 002803 3 KTEETEVIVLVSLFNWIQKTKPAAKKRSKFRKFLDTYCDS----VDYFSALRLILPSLDRERGSYGLKESVLANCLIDAL 78 (879)
Q Consensus 3 ~~~~~~F~~l~~~~e~i~~~~~~~~k~~~l~~~~~~~~~~----~~~~p~lrLllP~~d~~r~~yglke~~L~k~~~~~~ 78 (879)
||+++.|+.+|++|+.|+.+.....|++++++++++|+.+ +|+||+|||+||++||+|+.|||||..||++|+++|
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 CCCcChHHHHHHhhhhcCCCCCCCCCHHHHHHHHHhhhcCCC-CCCCCHHHHHHHHHHHHhccChHHHH-HHHHHHHHhC
Q 002803 79 GMSKDSADAVRLINWRKGGAAPNAGNFPMVAAEVLQRRQGMI-SGGLTIKELNDLLDRLASSENRAEKI-SVLSTLIKKT 156 (879)
Q Consensus 79 ~~~~~s~~~~~L~~wk~~~~~~~~gD~~~~~~~v~~~r~~~~-~~~lTi~eVn~~Ld~La~~~~~~~k~-~~l~~ll~~~ 156 (879)
++|++|.||.+|.||+.++..+ |||+.++++++++|+..+ ++.+||.|||++||.||+......+. ..|..|+++|
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 9999999999999999987655 999999999999998654 45699999999999999988765554 7899999999
Q ss_pred CHHHHHHHHHHHhhhhccCCcccccccccCcCHHHHHhhcCCHHHHHHHHhhhhhccccCC--cccCCcccccceeeccC
Q 002803 157 NAQEMKWIIMIILKDLKLGISEKSIFHEFHPDAEDLFNVTCDLKLVCEKLKDRNQRHKRQD--IEVGKAVRPQLAMRIGD 234 (879)
Q Consensus 157 s~~E~k~l~RiIlk~lriG~~e~til~~~hpda~~~~~~~~dL~~V~~~L~~~~~~~~~~~--i~~~~~~~PmLA~~~~~ 234 (879)
||.|+|||+|||||++++|++|++||.+|||||+++|++|+||+.||+.|+||+.+++..+ |++|.+|+||||++...
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 9999999999999999999999999999999999999999999999999999999998887 99999999999999876
Q ss_pred hH-HHHHHhCCCceEEEEecceEEEEEEEeCCEEEEEecCCCCCCC-chh----hhHHHHHhhcc---ccceeeeceEEE
Q 002803 235 AH-AAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSE-YGH----AMSKIIEQNVL---VDRCILDGEMLV 305 (879)
Q Consensus 235 ~~-~~~~~~~~~~~~iE~K~DGeR~qih~~g~~v~~~SR~g~~~t~-~~~----~l~~~~~~~~~---~~~~ILDGEmv~ 305 (879)
.. +++++|++++||+|+|+||||+|+|++|+.++||||||.|||. |+. +......++++ +..||||||||+
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 65 6899999999999999999999999999999999999999993 322 21222223333 789999999999
Q ss_pred eeCCCCccccccchHHHHHHhhcCCCCCCceEEEEEEEEEeCCccccCCCHHHHHHHHHhhcCCCCCcceecccCCCCCc
Q 002803 306 WDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNS 385 (879)
Q Consensus 306 ~d~~~~~~~pF~~l~~~~~~~~~~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~v~~~~~~~~i~~p~~~~~~ 385 (879)
||+.+.++.|||+++++..+... +.+.++||+|||+||+||++|.+.||.+|+++|+.++.|.+++++++
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 99999999999999988766532 45678999999999999999999999999999999999999998775
Q ss_pred cccCCCCCccccccCCHHHHHHHHHHHHHcCCceEEEecCCCCCcCCCCCCCeEEEcccccc-CCCcceEEEEEEEeCCC
Q 002803 386 HVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIR-AGSDLDVLIIGGYYGSG 464 (879)
Q Consensus 386 ~v~~~~~~~~~~~~~~~~ei~~~~~~~i~~g~EGlV~K~~~s~Y~~g~Rs~~WlKvKp~y~~-~g~~lDlvVIG~~~G~G 464 (879)
++..+++.++|+++|++||++|.||||+|.++|.|.||.|+++|+|+||+|+. +|+++|++|||||||.|
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 69999999999999999
Q ss_pred CCCCCcceEEEEEecCCCCCCCCceEEEEEEecCCCCHHHHHHHHHhhccccccccCCCCCCCcceeecCCCCCCCcEEE
Q 002803 465 RRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDVWI 544 (879)
Q Consensus 465 rr~g~~~sfl~g~~~~~~~~~~~~~~~~~~kVgtG~s~~~~~~l~~~l~~~~~~~~~~~~~pp~~~~~~~~~~~~Pdvwi 544 (879)
+++|++.+|+||+.++..++.+|.+|.++|+||+|+|++|+..+.+++++||.+ +++..+|++++.. +..+||+||
T Consensus 460 ~rgg~~~~fl~a~~ek~~p~~~p~~f~sfcrvg~g~s~~e~~~v~~klr~~w~~-~~~~apP~s~l~~---tk~~Pd~wI 535 (881)
T KOG0966|consen 460 DRGGKVLSFLCALAEKAPPNSRPEKFCSFCRVGNGISQKERDTVREKLRGHWKP-TSLEAPPESFLFG---TKKIPDVWI 535 (881)
T ss_pred CCCCeeeeeeehhcccCCCCCccceeeEeeEecCCccHHHHHHHHHhhhhhccc-ccccCCCHHHHhc---ccCCCceeE
Confidence 999999999999998877777899999999999999999999999999999987 3455434444443 334799999
Q ss_pred eCCCceEEEEEeeeceecccCccCCCeeeeccEEEEEecCCCccCCCCHHHHHHHHHccCCCcccccccCCCCCCCCccc
Q 002803 545 ESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDKPWHDCLDVQSFVELVHSSNGTTQKGKEYGGLQDDKPKQF 624 (879)
Q Consensus 545 ~~P~~s~V~ev~a~~~~~~s~~~~~g~tLRfPR~~riR~DK~~~~~~t~~e~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 624 (879)
+ |+.|+|++|++. +++++..|.++|||||||+.++|+||+|+||+|++||.++...+. ++.+.+. ++++
T Consensus 536 ~-P~~SiIlqikaa-~i~~s~~f~tn~tLrfPr~ekvR~DK~W~ec~tl~~l~~l~~~~~-------~d~~~~~-kk~~- 604 (881)
T KOG0966|consen 536 D-PDNSIILQIKAA-EIVPSSNFVTNYTLRFPRIEKVRLDKPWHECLTLNELGDLVNVSK-------SDVEDKE-KKKR- 604 (881)
T ss_pred C-CCCceEEEeehh-eeeecccccccceeecceeeeeecCCcHHHHhhHHHHHHHhcccc-------CCcchhh-hhcc-
Confidence 9 999999999953 456899999999999999999999999999999999999986321 1111111 1111
Q ss_pred ccccccccccccccCCccccCcccccCCCCCcccCeEEEEEcCC-CCCCHHHHHHHHHHcCCEEeeccCCCeeEEEE-ec
Q 002803 625 RSSRKGEKKNVSIVPSHFLQTDVSDIKGETSIFSDMVFYFVNVP-PAYSLDSLHKMVVENGGTFSMNLNNSVTHCVA-AD 702 (879)
Q Consensus 625 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~iF~g~~F~vl~~~-~~~~k~eLe~lI~~~GG~~v~n~~~~~T~~I~-~~ 702 (879)
.+.+++++.+.. -+......+.+.+.+++|.|++|||+++. ..++|++||++|++|||+++||++++.|+||+ |+
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 DTLKVRKRTRKA---IHDSAPNRSKVAKISNIFDGLEFCVLSGTSETHTKAKLEEIIVENGGKIVQNVGPSDTLCIATAG 681 (881)
T ss_pred cchhhhhhhhhh---hcccccchhcccchhhhhcCeeEEEecCCcccccHHHHHHHHHHcCCEEEEcCCCCCcceEEecc
Confidence 111111111111 12334455677788999999999999876 56779999999999999999999988999996 44
Q ss_pred CC--chhhhhhccCCCeeeechHHHhhhcCcccCCCccccccCChhhHhHhhhhhccCCCcccccCCHHHHHHHHhhcCC
Q 002803 703 NK--GLKYEAAKRRGDVIHYSWVLDCCSQKKLLQLQPKYYLHLSDSSKKKLQEEVDEFSDLYFWDLDLADIKQLLSNVDR 780 (879)
Q Consensus 703 ~~--~~k~~~~~~~~~IV~p~Wl~dCi~~~~llp~~p~~~l~~s~~~~~~~~~~~D~ygDSy~~~~~~~~l~~ll~~~~~ 780 (879)
.. ++|.+.+.+.+|||||+||+||++..+++||.|++|||+++.+++.+++++|+|||||+.|++.++|+.+++.+..
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 43 3455556665699999999999999999999999999999999999999999999999999999999999999987
Q ss_pred CCChhhHHHHHhhcCCCCCCCC-CCCcEEEEcCCCCCCCChhHHHHHHHHHHHHHHhhhcCceeccCCC------CCeeE
Q 002803 781 SEDPKTIDYYKKKYCPQDKWSC-FHGCCIYFYHSTEPLSPDWEVLLGLALRRLKLEISFHGVSLPERNI------FYGTR 853 (879)
Q Consensus 781 ~~~~~~~~~l~~~~~~~~~~~l-F~~~~vy~~~~~~~~~~~~~~~~~~~l~~~~~~i~~~GG~v~~~~~------~~vTH 853 (879)
++++...+...+.......+.+ |..|++ |+......+. ........++-.||.+++... ..+||
T Consensus 762 S~ds~~~~~~~~~~~~e~r~~~~~~~~~~-f~~~~~~~~s--------e~~~~~l~~k~~g~~i~~~~~~~~~~~~~~t~ 832 (881)
T KOG0966|consen 762 SQDSLPPMGASEKDSLERRFSLFLSSLRM-FYVLRRKLSS--------EEVIIELKLKNFGGRITDAQSECNNIGAKYTH 832 (881)
T ss_pred cccccCchhhhhhhcHHHhhcccccccee-eecccccccH--------HHHHHHHHHHHhcceeeeccchhhhcccceee
Confidence 7765322111111111111222 333333 3332222222 222344456778888885433 24799
Q ss_pred EEEc
Q 002803 854 SCML 857 (879)
Q Consensus 854 VVv~ 857 (879)
+|+.
T Consensus 833 ~v~~ 836 (881)
T KOG0966|consen 833 CVLR 836 (881)
T ss_pred eeee
Confidence 9986
No 2
>PLN03113 DNA ligase 1; Provisional
Probab=100.00 E-value=1e-102 Score=923.72 Aligned_cols=550 Identities=24% Similarity=0.421 Sum_probs=472.3
Q ss_pred CCCcHHHHHHHHHHHHhcCChhHHHHHHHHHHhhc--CCCChHhhhHhh----cCCCCCcCccccCCCHHHHHHHHHHHh
Q 002803 5 EETEVIVLVSLFNWIQKTKPAAKKRSKFRKFLDTY--CDSVDYFSALRL----ILPSLDRERGSYGLKESVLANCLIDAL 78 (879)
Q Consensus 5 ~~~~F~~l~~~~e~i~~~~~~~~k~~~l~~~~~~~--~~~~~~~p~lrL----llP~~d~~r~~yglke~~L~k~~~~~~ 78 (879)
.+|||..||++|++|+.++++.+|+++|.+||... .+++|++|+++| ++|.. ++.+|||+++.|+|+|++++
T Consensus 127 ~~~~f~~l~~~~~~Ie~tt~rlek~~~L~~~~r~~~~~~p~dl~~~vyL~~~~l~P~~--e~~elgige~~L~kai~e~~ 204 (744)
T PLN03113 127 ERVPFLFVALAFDLISNETGRIVITDIVCNMLRTVMATTPEDLVAVVYLLANRIAPAH--EGVELGIGEATIIKALAEAF 204 (744)
T ss_pred CCccHHHHHHHHHHHHhccCHHHHHHHHHHHHHHhccCChHHHHHHHHHHhCCCCccc--cCcccCcCHHHHHHHHHHHH
Confidence 57999999999999999999999999999999986 367899999999 56665 46799999999999999999
Q ss_pred CCCcChHHHHHHhhhhcCCCCCCCCCHHHHHHHHHhhhcC-CCCCCCCHHHHHHHHHHHHhccC---hHHHHHHHHHHHH
Q 002803 79 GMSKDSADAVRLINWRKGGAAPNAGNFPMVAAEVLQRRQG-MISGGLTIKELNDLLDRLASSEN---RAEKISVLSTLIK 154 (879)
Q Consensus 79 ~~~~~s~~~~~L~~wk~~~~~~~~gD~~~~~~~v~~~r~~-~~~~~lTi~eVn~~Ld~La~~~~---~~~k~~~l~~ll~ 154 (879)
|++...... .| ...||+|++|+.+.+.++. ..+.+|||.+|++.|++||..+| +++|..+|..|+.
T Consensus 205 g~~~~~ik~----~y------~~~GDlG~vA~~~~~~q~~~~~~~~LTi~~V~~~L~~IA~~~G~~sq~~K~~~i~~Ll~ 274 (744)
T PLN03113 205 GRTEKQVKK----QY------KELGDLGLVAKASRSSQSMMRKPEPLTVVKVFNTFQQIAKESGKDSQEKKKNRIKALLV 274 (744)
T ss_pred CcCHHHHHH----HH------HHhCCHHHHHHhhhcccccccCCCCCCHHHHHHHHHHHHhhhCccCHHHHHHHHHHHHH
Confidence 998654321 33 3579999999977655543 34678999999999999999876 5678889999999
Q ss_pred hCCHHHHHHHHHHHhhhhccCCcccccccccCcCH------------------------HHHHhhcCCHHHHHHHHhhhh
Q 002803 155 KTNAQEMKWIIMIILKDLKLGISEKSIFHEFHPDA------------------------EDLFNVTCDLKLVCEKLKDRN 210 (879)
Q Consensus 155 ~~s~~E~k~l~RiIlk~lriG~~e~til~~~hpda------------------------~~~~~~~~dL~~V~~~L~~~~ 210 (879)
.+++.|++||+|+|+++||||++++||+.++|+.+ .++|+.++|++.|+..|....
T Consensus 275 ~~~~~E~k~liR~l~g~LRIGv~e~tVl~ALa~a~~~~~~~~~~~~~~~~~l~~~~~~v~~a~~~~p~~~~i~~~ll~~g 354 (744)
T PLN03113 275 AATDCEPLYLIRLLQTKLRIGLAGQTLLAALGQAAVYNEEHSTPPPNIQSPLEEAAKIVKQVYSVLPVYDKIVPALLSGG 354 (744)
T ss_pred hCCHHHHHHHHHHHhccccccccHHHHHHHHHHHhcccccccccccccchhhHHHHHHHHHHhccCCCHHHHHHHHHhCC
Confidence 99999999999999999999999999999887654 256888889888887776543
Q ss_pred -hcc-ccCCcccCCcccccceeeccChHHHHHHhCCCceEEEEecceEEEEEEE-eCCEEEEEecCCCCCCCchhhhHHH
Q 002803 211 -QRH-KRQDIEVGKAVRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHK-NGSEIHYFSRSFLDHSEYGHAMSKI 287 (879)
Q Consensus 211 -~~~-~~~~i~~~~~~~PmLA~~~~~~~~~~~~~~~~~~~iE~K~DGeR~qih~-~g~~v~~~SR~g~~~t~~~~~l~~~ 287 (879)
..+ ....+++|.||+||||++..++++++++|.+.+|++|+||||+|+|+|+ .++.+++|||||+++|..+|++.+.
T Consensus 355 ~~~l~~~~~i~~g~Pi~PMLA~~~~~~~eil~~~~g~~~~~E~KyDGeR~QiH~~~~g~v~lfSRn~ed~T~~fPel~~~ 434 (744)
T PLN03113 355 VWNLPKTCSFTPGVPVGPMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHFLEDGSVEIYSRNAERNTGKYPDVVVA 434 (744)
T ss_pred cccccccccccCCCCCCCccCCCCCChHHHhhccCCCCEEEEEeeccceEEEEEecCCEEEEEeCCCCcccccchhHHHH
Confidence 233 5667999999999999999998899999988899999999999999998 4789999999999999999999886
Q ss_pred HHhhc--cccceeeeceEEEeeCCCCccccccchHHHHHHhhcCC---CCCCceEEEEEEEEEeCCccccCCCHHHHHHH
Q 002803 288 IEQNV--LVDRCILDGEMLVWDTSLNRFAEFGSNQEIAKAARDGL---SSDRQLCYFAFDVLYVGDTSVIHQSLKERHEL 362 (879)
Q Consensus 288 ~~~~~--~~~~~ILDGEmv~~d~~~~~~~pF~~l~~~~~~~~~~~---~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~ 362 (879)
+.... .+++||||||+|+||+.+++++||+.+|.. .++.. +...++||++|||||+||++|++.||.+||++
T Consensus 435 ~~~~~~~~~~~~ILDGEiVa~d~~~~~~lpFq~Lq~R---~rk~~~~~~~~~pv~~~aFDlLylnG~~L~~~PL~eRR~~ 511 (744)
T PLN03113 435 ISRLKKPSVKSFILDCELVAYDREKKKILPFQILSTR---ARKNVVMSDIKVDVCIFAFDMLYLNGQPLIQEQLKIRREH 511 (744)
T ss_pred HHHhccccCCCEEEEeEEEEEECCCCCcCCHHHHHhh---hccccchhccccceEEEEEeccccCccChhcCCHHHHHHH
Confidence 54322 157899999999999988889999887754 22221 12478999999999999999999999999999
Q ss_pred HHhhcCCCCCcceecccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHcCCceEEEecC--CCCCcCCCCCCCeEE
Q 002803 363 LQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDL--GSKWEPGDRSGKWLK 440 (879)
Q Consensus 363 L~~~v~~~~~~~~i~~p~~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~~i~~g~EGlV~K~~--~s~Y~~g~Rs~~WlK 440 (879)
|++++.+.+++++++. .....+.++++++|++++++|+||||+|++ +|+|+||+|+.+|+|
T Consensus 512 L~~~~~~~~~~i~~~~-----------------~~~~~~~ee~~~~~~~ai~~g~EGlmvK~l~~dS~Y~pGkRs~~WlK 574 (744)
T PLN03113 512 LYESFEEDPGFFQFAT-----------------AITSNDLEEIQKFLDAAVDASCEGLIIKTLNKDATYEPSKRSNNWLK 574 (744)
T ss_pred HHHHhccCCCcEEEee-----------------eeccCCHHHHHHHHHHHHHcCCceEEEeccCCCCCccCCCCCCCeEE
Confidence 9999988777665431 234578999999999999999999999986 899999999999999
Q ss_pred EccccccC-CCcceEEEEEEEeCCCCCCCCcceEEEEEecCCCCCCCCceEEEEEEecCCCCHHHHHHHHHhhccccccc
Q 002803 441 LKPEYIRA-GSDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKY 519 (879)
Q Consensus 441 vKp~y~~~-g~~lDlvVIG~~~G~Grr~g~~~sfl~g~~~~~~~~~~~~~~~~~~kVgtG~s~~~~~~l~~~l~~~~~~~ 519 (879)
+|++|+++ ++++|+||||||||+|+|+|.+|+||||+|++++ +.|+++|+||||||+++++++.+.|++++..
T Consensus 575 lK~dy~~~~~dtlDlVvIGa~~G~GkR~g~~g~fLla~yd~~~-----~~~~~v~KvgTGfsd~~l~~l~~~L~~~~~~- 648 (744)
T PLN03113 575 LKKDYMESIGDSLDLVPIAAFHGRGKRTGVYGAFLLACYDSNK-----EEFQSICKIGTGFSEAVLEERSASLRSQVIP- 648 (744)
T ss_pred EechhhccccccccEEEEEEEeCCCCcCCccceEEEEEEcCCC-----CEEEEeeEECCCCCHHHHHHHHHHHHHhccc-
Confidence 99999984 8999999999999999999999999999998653 3899999999999999999999999988754
Q ss_pred cCCCCCCCcceeecCCCCCCCcEEEeCCCceEEEEEeeeceecccCccC---------CCeeeeccEEEEEecCCCccCC
Q 002803 520 EYPKRAPPSFYQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFS---------APYSLRFPRIDRVRYDKPWHDC 590 (879)
Q Consensus 520 ~~~~~~pp~~~~~~~~~~~~Pdvwi~~P~~s~V~ev~a~~~~~~s~~~~---------~g~tLRfPR~~riR~DK~~~~~ 590 (879)
.||+|+... ...+||+||+ | .+|+||+++.. ..|+.|+ .|++||||||.|||+||+|+||
T Consensus 649 -----~~~~~~~~~--~~~~pdvwve-P--~~V~EV~~aei-t~Sp~h~a~~g~~~~~~G~sLRFPRf~riR~DK~~~da 717 (744)
T PLN03113 649 -----TPKSYYRYG--DSIKPDVWFE-P--TEVWEVKAADL-TISPVHRAAVGIVDPDKGISLRFPRLVRVREDKSPEQA 717 (744)
T ss_pred -----CCCcccccC--CCCCCcEEEC-C--ceEEEEEeeee-ccCcccccccccccCCCCeEEECCEEEEEECCCChHHC
Confidence 245555442 3468999999 7 47999986432 3688887 4899999999999999999999
Q ss_pred CCHHHHHHHHHcc
Q 002803 591 LDVQSFVELVHSS 603 (879)
Q Consensus 591 ~t~~e~~~l~~~~ 603 (879)
+|++++.+||+++
T Consensus 718 tt~~~l~~ly~~Q 730 (744)
T PLN03113 718 TSSEQVADMYNAQ 730 (744)
T ss_pred CCHHHHHHHHHHH
Confidence 9999999999744
No 3
>PRK01109 ATP-dependent DNA ligase; Provisional
Probab=100.00 E-value=2.1e-100 Score=901.58 Aligned_cols=544 Identities=28% Similarity=0.487 Sum_probs=473.1
Q ss_pred CcHHHHHHHHHHHHhcCChhHHHHHHHHHHhhcCCC---ChHhhhHhhcCCCCCcCccccCCCHHHHHHHHHHHhCCCcC
Q 002803 7 TEVIVLVSLFNWIQKTKPAAKKRSKFRKFLDTYCDS---VDYFSALRLILPSLDRERGSYGLKESVLANCLIDALGMSKD 83 (879)
Q Consensus 7 ~~F~~l~~~~e~i~~~~~~~~k~~~l~~~~~~~~~~---~~~~p~lrLllP~~d~~r~~yglke~~L~k~~~~~~~~~~~ 83 (879)
|+|+.||++|++|++++++.+|+++|.+||.....+ ..+|+++++++|..+. .+|||+++.|+++|++++|++.+
T Consensus 1 m~f~~l~~~~~~i~~t~~r~~k~~~l~~~~~~~~~~~~~~~~~l~~~~~~p~~~~--~~~gi~~~~l~k~i~~~~g~~~~ 78 (590)
T PRK01109 1 MEFSELAEYFERLEKTTSRTQLTKLLADLLKKTPPEIIDKVVYLIQGKLWPDWLG--LELGVGEKLLIKAISMATGISEK 78 (590)
T ss_pred CcHHHHHHHHHHHHhhhchHHHHHHHHHHHHhCCHHhhhhhHHHHhCCcCccccC--cccCcCHHHHHHHHHHHHCcCHH
Confidence 789999999999999999999999999999987321 3467777788898874 59999999999999999999987
Q ss_pred hHHHHHHhhhhcCCCCCCCCCHHHHHHHHHhhhcCC------CCCCCCHHHHHHHHHHHHhccC---hHHHHHHHHHHHH
Q 002803 84 SADAVRLINWRKGGAAPNAGNFPMVAAEVLQRRQGM------ISGGLTIKELNDLLDRLASSEN---RAEKISVLSTLIK 154 (879)
Q Consensus 84 s~~~~~L~~wk~~~~~~~~gD~~~~~~~v~~~r~~~------~~~~lTi~eVn~~Ld~La~~~~---~~~k~~~l~~ll~ 154 (879)
..+. + | ...||||.+|+.++++++.. .+++||+.+|++.|++||..+| +.+|..+|..||.
T Consensus 79 ~~~~--~--~------~~~GDlg~~a~~~~~~~~~~~~~~~~~~~~lti~eV~~~L~~Ia~~sg~~s~~~k~~iL~~Ll~ 148 (590)
T PRK01109 79 EVEN--L--Y------KKTGDLGEVARRLKSKKKQKSLLAFFSKEPLTVKEVYDTLVKIALATGEGSQDLKIKLLAGLLK 148 (590)
T ss_pred HHHH--H--H------HhcCCHHHHHHHHHhhcccccccccCCCCCcCHHHHHHHHHHHHhhhCCCcHHHHHHHHHHHHH
Confidence 6553 1 3 34799999999999876532 3578999999999999999874 6788999999999
Q ss_pred hCCHHHHHHHHHHHhhhhccCCccccccc----cc-----CcCHHHHHhhcCCHHHHHHHHhhhh-hccccCCcccCCcc
Q 002803 155 KTNAQEMKWIIMIILKDLKLGISEKSIFH----EF-----HPDAEDLFNVTCDLKLVCEKLKDRN-QRHKRQDIEVGKAV 224 (879)
Q Consensus 155 ~~s~~E~k~l~RiIlk~lriG~~e~til~----~~-----hpda~~~~~~~~dL~~V~~~L~~~~-~~~~~~~i~~~~~~ 224 (879)
++++.|++||+|+|+++|++|+++++|++ ++ |++++++|+.++||+.||+.|..+. ..+....+++|.||
T Consensus 149 ~~~~~E~k~iirli~g~lriGv~e~~il~ALa~A~~~~~~~~~ve~~y~~~~Dlg~va~~l~~~g~~~~~~~~i~~~~Pv 228 (590)
T PRK01109 149 DASPLEAKYIARFVEGRLRLGVGDATILDALAIAFGGAVARELVERAYNLRADLGYIAKILAEGGIEALKKVKPQVGIPI 228 (590)
T ss_pred hCCHHHHHHHHHHHhhhhhcCccHHHHHHHHHHHHhcccchHHHHHHHHhCCCHHHHHHHHHhcchhhhccCcccCCCCC
Confidence 99999999999999999999999999997 34 4888999999999999999998764 35667789999999
Q ss_pred cccceeeccChHHHHHHhCCCceEEEEecceEEEEEEEeCCEEEEEecCCCCCCCchhhhHHHHHhhccccceeeeceEE
Q 002803 225 RPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDGEML 304 (879)
Q Consensus 225 ~PmLA~~~~~~~~~~~~~~~~~~~iE~K~DGeR~qih~~g~~v~~~SR~g~~~t~~~~~l~~~~~~~~~~~~~ILDGEmv 304 (879)
+||||++.+.++++++++.+ +|++|+||||+|||+|++|+.+++|||||+|+|..+|++.+.+...+.+++||||||||
T Consensus 229 ~PmLA~~~~~~~~~~~~~~~-~~~~E~K~DG~R~qih~~~~~v~l~SR~~~d~T~~~pel~~~~~~~~~~~~~ILDGElv 307 (590)
T PRK01109 229 RPMLAERLSSPKEILKKMGG-EALVEYKYDGERAQIHKKGDKVKIFSRRLENITHQYPDVVEYAKEAIKAEEAIVEGEIV 307 (590)
T ss_pred CcccCCccCCHHHHHHHcCC-CeEEEecCCceEEEEEEcCCEEEEEeCCchhhccccchHHHHHHHhcCccceEEeeeEE
Confidence 99999999888888888854 69999999999999999999999999999999999999998776555568999999999
Q ss_pred EeeCCCCccccccchHHHHHHhhcC-C---CCCCceEEEEEEEEEeCCccccCCCHHHHHHHHHhhcCCCCCcceecccC
Q 002803 305 VWDTSLNRFAEFGSNQEIAKAARDG-L---SSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPD 380 (879)
Q Consensus 305 ~~d~~~~~~~pF~~l~~~~~~~~~~-~---~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~v~~~~~~~~i~~p~ 380 (879)
+||+.+++++||+.++.. .++. . ....++||++|||||+||+++++.||.+||++|++++.+.+ ++.+.
T Consensus 308 ~~d~~~g~~~~F~~l~~R---~r~~~~~~~~~~~p~~~~vFDiL~l~g~~l~~~pl~eRr~~L~~~~~~~~-~~~~~--- 380 (590)
T PRK01109 308 AVDPETGEMRPFQELMHR---KRKYDIEEAIKEYPVNVFLFDLLYVDGEDLTDKPLPERRKKLEEIVKEND-KVKLA--- 380 (590)
T ss_pred EEECCCCcccChHHHhhc---ccccchhhhcccCceEEEEEEEEEECCcchhhCcHHHHHHHHHHhcCCCC-ceEEe---
Confidence 999877888999877653 1111 1 12468999999999999999999999999999999998754 34332
Q ss_pred CCCCccccCCCCCccccccCCHHHHHHHHHHHHHcCCceEEEecC--CCCCcCCCCCCCeEEEcccccc-CCCcceEEEE
Q 002803 381 HGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDL--GSKWEPGDRSGKWLKLKPEYIR-AGSDLDVLII 457 (879)
Q Consensus 381 ~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~~i~~g~EGlV~K~~--~s~Y~~g~Rs~~WlKvKp~y~~-~g~~lDlvVI 457 (879)
....+++.++++++|++++++|+||||+|++ +|+|.||+|+.+|+|+|++|++ .++++|+|||
T Consensus 381 --------------~~~~~~~~~~~~~~~~~a~~~g~EGiv~K~~~~ds~Y~~g~Rs~~WlK~K~dy~~~~~~~~Dlvvi 446 (590)
T PRK01109 381 --------------ERIITDDVEELEKFFHRAIEEGCEGLMAKSLGKDSIYQAGARGWLWIKYKRDYQSEMADTVDLVVV 446 (590)
T ss_pred --------------eeEecCCHHHHHHHHHHHHHcCCceEEEecCCCCCCcCCCCCCccHHHhhHHhhcccCCceeEEEE
Confidence 1345678999999999999999999999999 9999999999999999999998 4789999999
Q ss_pred EEEeCCCCCCCCcceEEEEEecCCCCCCCCceEEEEEEecCCCCHHHHHHHHHhhccccccccCCCCCCCcceeecCCCC
Q 002803 458 GGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSK 537 (879)
Q Consensus 458 G~~~G~Grr~g~~~sfl~g~~~~~~~~~~~~~~~~~~kVgtG~s~~~~~~l~~~l~~~~~~~~~~~~~pp~~~~~~~~~~ 537 (879)
|++||+|+|+|.+|+||||+|++++ +.|+++|+||||||++++++|.+.+.++|.. . .|| +. ...
T Consensus 447 G~~~g~Gkr~~~~g~~ll~~~d~~~-----~~~~~v~kvgtG~sd~~~~~l~~~l~~~~~~----~-~~~-~~----~~~ 511 (590)
T PRK01109 447 GAFYGRGRRGGKYGSLLMAAYDPKT-----DTFETVCKVGSGFTDEDLDELPKMLKPYKID----H-KHP-RV----VSK 511 (590)
T ss_pred EeEeCCCccCCccccEEEEEEcCCC-----CeEEEEEEECCCCCHHHHHHHHHHhhhhccc----C-CCc-cc----ccc
Confidence 9999999999999999999998653 3899999999999999999999999999864 1 233 22 135
Q ss_pred CCCcEEEeCCCceEEEEEeeeceecccCccC---------CCeeeeccEEEEEecCCCccCCCCHHHHHHHHHcc
Q 002803 538 ERPDVWIESPEKSIILSITSDIRTIRSEVFS---------APYSLRFPRIDRVRYDKPWHDCLDVQSFVELVHSS 603 (879)
Q Consensus 538 ~~Pdvwi~~P~~s~V~ev~a~~~~~~s~~~~---------~g~tLRfPR~~riR~DK~~~~~~t~~e~~~l~~~~ 603 (879)
.+||+||+ | ++|+||+++..+ .|+.|+ .|++||||||+++|+||+|+||+|++++.+||+++
T Consensus 512 ~~pdvwv~-P--~~V~eV~~~~it-~S~~~~~~~~~~~~~~g~~LRfPr~~~~R~DK~~~d~~t~~~~~~ly~~q 582 (590)
T PRK01109 512 MEPDVWVE-P--KLVAEIIGAEIT-LSPLHTCCLGVVEKGAGLAIRFPRFIRWRDDKSPEDATTTEEILEMYKRQ 582 (590)
T ss_pred cCCcEEEe-c--cEEEEEEeeecc-cCcceecccccccCCCceeEEcCeeeEeeCCCChhhCcCHHHHHHHHHHh
Confidence 68999999 7 799999965333 578887 69999999999999999999999999999999743
No 4
>KOG0967 consensus ATP-dependent DNA ligase I [Replication, recombination and repair]
Probab=100.00 E-value=9.4e-97 Score=819.01 Aligned_cols=551 Identities=27% Similarity=0.498 Sum_probs=476.5
Q ss_pred CCCcHHHHHHHHHHHHhcCChhHHHHHHHHHHhhcC--CCChHhhhHhhcCCCC--CcCccccCCCHHHHHHHHHHHhCC
Q 002803 5 EETEVIVLVSLFNWIQKTKPAAKKRSKFRKFLDTYC--DSVDYFSALRLILPSL--DRERGSYGLKESVLANCLIDALGM 80 (879)
Q Consensus 5 ~~~~F~~l~~~~e~i~~~~~~~~k~~~l~~~~~~~~--~~~~~~p~lrLllP~~--d~~r~~yglke~~L~k~~~~~~~~ 80 (879)
+.+||.+||.+|++|+++++|.+...++.+||.+.. +|+|+.|++.|.++.+ |.++.++|++|++|.|++++++|.
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 569999999999999999999999999999998774 5899999999987777 677889999999999999999999
Q ss_pred CcChHHHHHHhhhhcCCCCCCCCCHHHHHHHHHhhhc-CCCCCCCCHHHHHHHHHHHHhccC---hHHHHHHHHHHHHhC
Q 002803 81 SKDSADAVRLINWRKGGAAPNAGNFPMVAAEVLQRRQ-GMISGGLTIKELNDLLDRLASSEN---RAEKISVLSTLIKKT 156 (879)
Q Consensus 81 ~~~s~~~~~L~~wk~~~~~~~~gD~~~~~~~v~~~r~-~~~~~~lTi~eVn~~Ld~La~~~~---~~~k~~~l~~ll~~~ 156 (879)
+..... +. | ...||+|.||+....... +..|.+|||.+|+..|.+||..+| +.+|..++..||..|
T Consensus 177 t~~~vk---~~-~------~~~GDLG~VA~~sR~sQ~~m~~P~pLtV~~VF~~Lr~IAk~sG~~S~~kK~~lik~Llvac 246 (714)
T KOG0967|consen 177 TLSHVK---NQ-Y------NKLGDLGLVAQGSRSSQRMMFKPKPLTVRDVFSTLRKIAKESGKGSQNKKKDLIKALLVAC 246 (714)
T ss_pred cHHHHH---HH-H------HhcCcHHHHHhhcccccccccCCCCccHHHHHHHHHHHHHhhCcchhHHHHHHHHHHHHhc
Confidence 975443 22 2 458999999988754433 346789999999999999999987 568889999999999
Q ss_pred CHHHHHHHHHHHhhhhccCCccccccccc------C----------cC------------HHHHHhhcCCHHHHHHHHhh
Q 002803 157 NAQEMKWIIMIILKDLKLGISEKSIFHEF------H----------PD------------AEDLFNVTCDLKLVCEKLKD 208 (879)
Q Consensus 157 s~~E~k~l~RiIlk~lriG~~e~til~~~------h----------pd------------a~~~~~~~~dL~~V~~~L~~ 208 (879)
++.|+|||+|.|.++||||+.++|||.++ + || ..++|+.++|+..|...|-.
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 99999999999999999999999998643 1 22 23579999999999988876
Q ss_pred hhh--ccccCCcccCCcccccceeeccChHHHHHHhCCCceEEEEecceEEEEEEE-eCCEEEEEecCCCCCCCchhhhH
Q 002803 209 RNQ--RHKRQDIEVGKAVRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHK-NGSEIHYFSRSFLDHSEYGHAMS 285 (879)
Q Consensus 209 ~~~--~~~~~~i~~~~~~~PmLA~~~~~~~~~~~~~~~~~~~iE~K~DGeR~qih~-~g~~v~~~SR~g~~~t~~~~~l~ 285 (879)
... ..+.+.+.||.|++||||++.+.+.++++++.+..|.+|+||||+|+|||+ .+|.|.+||||+++.|..+|++.
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 532 245678999999999999999999999999999999999999999999997 57899999999999999999998
Q ss_pred HHHHhhc--cccceeeeceEEEeeCCCCccccccchHHHHHHhhcCCC---CCCceEEEEEEEEEeCCccccCCCHHHHH
Q 002803 286 KIIEQNV--LVDRCILDGEMLVWDTSLNRFAEFGSNQEIAKAARDGLS---SDRQLCYFAFDVLYVGDTSVIHQSLKERH 360 (879)
Q Consensus 286 ~~~~~~~--~~~~~ILDGEmv~~d~~~~~~~pF~~l~~~~~~~~~~~~---~~~~~~~~vFDiL~lng~~l~~~pl~eRr 360 (879)
..+.... .+.++|||||+|+||...++++||+.+ ..+.|+..+ ....+|.++||+||+||++|.+.||.+||
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 7664332 258999999999999998999999544 344444432 34589999999999999999999999999
Q ss_pred HHHHhhcCCCCCcceecccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHcCCceEEEecC--CCCCcCCCCCCCe
Q 002803 361 ELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDL--GSKWEPGDRSGKW 438 (879)
Q Consensus 361 ~~L~~~v~~~~~~~~i~~p~~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~~i~~g~EGlV~K~~--~s~Y~~g~Rs~~W 438 (879)
++|.+.+..++|+++++. ...+.+.++|+++|++++.+++||+|+|.+ ++.|+|.+||.+|
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 999999999999876642 234678999999999999999999999976 5789999999999
Q ss_pred EEEccccccC-CCcceEEEEEEEeCCCCCCCCcceEEEEEecCCCCCCCCceEEEEEEecCCCCHHHHHHHHHhhccccc
Q 002803 439 LKLKPEYIRA-GSDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFR 517 (879)
Q Consensus 439 lKvKp~y~~~-g~~lDlvVIG~~~G~Grr~g~~~sfl~g~~~~~~~~~~~~~~~~~~kVgtG~s~~~~~~l~~~l~~~~~ 517 (879)
+|+|.+|+++ |+++|||+||+|||.|||.|++|+||+|||+++. ++|.++||+||||||+++.++...+.....
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 489999999999999999999988865432
Q ss_pred cccCCCCCCCcceeecCCCCCCCcEEEeCCCceEEEEEe-eeceecccCccC---------CCeeeeccEEEEEecCCCc
Q 002803 518 KYEYPKRAPPSFYQVTNNSKERPDVWIESPEKSIILSIT-SDIRTIRSEVFS---------APYSLRFPRIDRVRYDKPW 587 (879)
Q Consensus 518 ~~~~~~~~pp~~~~~~~~~~~~Pdvwi~~P~~s~V~ev~-a~~~~~~s~~~~---------~g~tLRfPR~~riR~DK~~ 587 (879)
..|+.+|.+. ...+||+|++ |. .||||+ |++ + -|+.|. .|.|||||||.|+|+||.+
T Consensus 622 ------~~~~~~y~~d--~s~kPd~wf~-p~--~VwEvk~Adl-t-~SPiy~Aa~Glv~~dkGISlRFPRfiRiR~DK~p 688 (714)
T KOG0967|consen 622 ------DSPKPYYRFD--ESLKPDVWFE-PT--EVWEVKAADL-T-LSPIYKAALGLVDPDKGISLRFPRFIRIRDDKNP 688 (714)
T ss_pred ------cCcHhhcccC--ccCCCccccC-HH--HHHHHhhccc-c-ccchhHhhhcCcCCCCceeEecceeeEeeccCCh
Confidence 2356677764 4568999999 74 689998 554 3 366664 4889999999999999999
Q ss_pred cCCCCHHHHHHHHHcc
Q 002803 588 HDCLDVQSFVELVHSS 603 (879)
Q Consensus 588 ~~~~t~~e~~~l~~~~ 603 (879)
+||+|-+++.+||+++
T Consensus 689 eeAtts~qiaemY~~Q 704 (714)
T KOG0967|consen 689 EEATTSSQIAEMYQAQ 704 (714)
T ss_pred hhcccHHHHHHHHHHH
Confidence 9999999999999755
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=3.3e-93 Score=831.53 Aligned_cols=494 Identities=34% Similarity=0.608 Sum_probs=428.5
Q ss_pred ccCCCHHHHHHHHHHHhCCCcChHHHHHHhhhhcCCCCCCCCCHHHHHHHHHhhhc--CCCCCCCCHHHHHHHHHHHHhc
Q 002803 62 SYGLKESVLANCLIDALGMSKDSADAVRLINWRKGGAAPNAGNFPMVAAEVLQRRQ--GMISGGLTIKELNDLLDRLASS 139 (879)
Q Consensus 62 ~yglke~~L~k~~~~~~~~~~~s~~~~~L~~wk~~~~~~~~gD~~~~~~~v~~~r~--~~~~~~lTi~eVn~~Ld~La~~ 139 (879)
+|||||++|+|++++++|+++++.++..+ ..||+|.+++.++++.. ...+++|||.|||+.|++||+.
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 49999999999999999999998887543 35899999998887654 2346899999999999999988
Q ss_pred cC---hHHHHHHHHHHHHhCCHHHHHHHHHHHhhhhccCCcccccccccCcCH-------HHHHhhcCCHHHHHHHHhhh
Q 002803 140 EN---RAEKISVLSTLIKKTNAQEMKWIIMIILKDLKLGISEKSIFHEFHPDA-------EDLFNVTCDLKLVCEKLKDR 209 (879)
Q Consensus 140 ~~---~~~k~~~l~~ll~~~s~~E~k~l~RiIlk~lriG~~e~til~~~hpda-------~~~~~~~~dL~~V~~~L~~~ 209 (879)
++ +.+|..+|..|+.+|+|.|++||+|+|+++||+|+++++|+.++|+++ +++|++|+||+.||+.|.++
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 568889999999999999999999999999999999999999998887 99999999999999999987
Q ss_pred hhcc--ccCCcccCCcccccceeeccChHHHHHHhCCCceEEEEecceEEEEEEEeCCEEEEEecCCCCCCCchhhh-HH
Q 002803 210 NQRH--KRQDIEVGKAVRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAM-SK 286 (879)
Q Consensus 210 ~~~~--~~~~i~~~~~~~PmLA~~~~~~~~~~~~~~~~~~~iE~K~DGeR~qih~~g~~v~~~SR~g~~~t~~~~~l-~~ 286 (879)
..+. ....+++|.||+||||+++..++++++++.+ +|++|+||||+|||+|++|+++++|||||+++|..+|++ .+
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 6432 3467999999999999999988888888754 899999999999999999999999999999999988998 66
Q ss_pred HHHhhcc-ccceeeeceEEEeeCCCCccccccchHHHHHHhh-cCCCCCCceEEEEEEEEEeCCccccCCCHHHHHHHHH
Q 002803 287 IIEQNVL-VDRCILDGEMLVWDTSLNRFAEFGSNQEIAKAAR-DGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQ 364 (879)
Q Consensus 287 ~~~~~~~-~~~~ILDGEmv~~d~~~~~~~pF~~l~~~~~~~~-~~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~ 364 (879)
.+...+. ..+||||||||+||+.+++++||+.++...+... .....+.+++|++|||||+||+++++.||.+|+++|+
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 5544343 3589999999999988788899988876533210 1112346899999999999999999999999999999
Q ss_pred hhcCCCCCcceecccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHcCCceEEEecCCCCCcCCCCCCCeEEEccc
Q 002803 365 KVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPE 444 (879)
Q Consensus 365 ~~v~~~~~~~~i~~p~~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~~i~~g~EGlV~K~~~s~Y~~g~Rs~~WlKvKp~ 444 (879)
+++.+.+++++++. ...+++.+++.++|++++++|+||||+|+++|+|+||+|+.+|+|+||+
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 99988777665431 3456789999999999999999999999999999999999999999999
Q ss_pred ccc-CCCcceEEEEEEEeCCCCCCCCcceEEEEEecCCCCCCCCceEEEEEEecCCCCHHHHHHHHHhhccccccccCCC
Q 002803 445 YIR-AGSDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPK 523 (879)
Q Consensus 445 y~~-~g~~lDlvVIG~~~G~Grr~g~~~sfl~g~~~~~~~~~~~~~~~~~~kVgtG~s~~~~~~l~~~l~~~~~~~~~~~ 523 (879)
|++ .++++|++|||++||+|+++|.+|+|+||+++++. ++|+++|+||||||++++++|.+++.++|.... +.
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 999 47899999999999999999999999999997653 389999999999999999999999999987521 11
Q ss_pred CCCCcceeecCCCCCCCcEEEeCCCceEEEEEeeeceecccCccCC-CeeeeccEEEEEecCCCccCCCCHHHHHHHH
Q 002803 524 RAPPSFYQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSA-PYSLRFPRIDRVRYDKPWHDCLDVQSFVELV 600 (879)
Q Consensus 524 ~~pp~~~~~~~~~~~~Pdvwi~~P~~s~V~ev~a~~~~~~s~~~~~-g~tLRfPR~~riR~DK~~~~~~t~~e~~~l~ 600 (879)
.+|.+ ....|++|++ | ++|+||+++.. ..|+.|++ |++||||||.++|+||+|+||+|++++.+||
T Consensus 447 -~~~~~------~~~~~~~w~~-p--~~V~eV~~~e~-t~s~~~~~~g~~LRfPr~~~~R~DK~~~d~~~~~~~~~ly 513 (514)
T TIGR00574 447 -RVPSI------LSDEPDIWFD-P--AIVWEVTGAEI-TRSPTYKANGISLRFPRFSRIRDDKGPEDATTIEEIKELY 513 (514)
T ss_pred -CCccc------ccCCCeEEec-C--CeEEEEEhhhe-eecCcccccceEEEcceEEEEcCCCChHHCCCHHHHHHHh
Confidence 12222 1357999998 7 68999996433 36899999 9999999999999999999999999999998
No 6
>PRK09247 ATP-dependent DNA ligase; Validated
Probab=100.00 E-value=1.8e-90 Score=807.48 Aligned_cols=522 Identities=20% Similarity=0.253 Sum_probs=438.7
Q ss_pred HHHHHHHHHHHHhcCChhHHHHHHHHHHhhcCCCChHhhhHhhcCCCCCcCccccCCCHHHHHHHHHHHhCCCcChHHHH
Q 002803 9 VIVLVSLFNWIQKTKPAAKKRSKFRKFLDTYCDSVDYFSALRLILPSLDRERGSYGLKESVLANCLIDALGMSKDSADAV 88 (879)
Q Consensus 9 F~~l~~~~e~i~~~~~~~~k~~~l~~~~~~~~~~~~~~p~lrLllP~~d~~r~~yglke~~L~k~~~~~~~~~~~s~~~~ 88 (879)
+++||++|++|++++++.+|+++|.+||.++ +++++.++++|++|... .|||+++.|.+++++++|++....+.
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 3689999999999999999999999999998 56789999999999886 48999999999999999999765542
Q ss_pred HHhhhhcCCCCCCCCCHHHHHHHHHhhhcCCC---CCCCCHHHHHHHHHHHHhccChHHHHHHHHHHHHhCCHHHHHHHH
Q 002803 89 RLINWRKGGAAPNAGNFPMVAAEVLQRRQGMI---SGGLTIKELNDLLDRLASSENRAEKISVLSTLIKKTNAQEMKWII 165 (879)
Q Consensus 89 ~L~~wk~~~~~~~~gD~~~~~~~v~~~r~~~~---~~~lTi~eVn~~Ld~La~~~~~~~k~~~l~~ll~~~s~~E~k~l~ 165 (879)
. +...||+|++|+.+++.++... +.++||.+|.+.|..+|.. +|...|..|+.+++|.|++||+
T Consensus 75 ---~------~~~~GDlg~~~~~~~~~~~~~~~~~~~~~tv~~v~~~l~~~~~~----~k~~~l~~ll~~~~~~e~~~i~ 141 (539)
T PRK09247 75 ---S------YDYVGDLAETIALLLPAPSDEASDLPLAPWLEEVLLPLRGLGRE----ELRAALADLWDRLDEDGRFALN 141 (539)
T ss_pred ---H------HHhcCCHHHHHHHhcccccccccCCCccccHHHHHHHHHhhhHH----HHHHHHHHHHHhCCHHHHHHHH
Confidence 1 2457999999999987765321 3579999999988888754 4778899999999999999999
Q ss_pred HHHhhhhccCCccccccccc----CcC---HHHHHhh--cCCHHHHHHHHhhhhhccccCCcccCCcccccceeeccChH
Q 002803 166 MIILKDLKLGISEKSIFHEF----HPD---AEDLFNV--TCDLKLVCEKLKDRNQRHKRQDIEVGKAVRPQLAMRIGDAH 236 (879)
Q Consensus 166 RiIlk~lriG~~e~til~~~----hpd---a~~~~~~--~~dL~~V~~~L~~~~~~~~~~~i~~~~~~~PmLA~~~~~~~ 236 (879)
|+|+++||||+++++|+.++ +.+ .++.|+. ++|++.+++.+.... ....+++|.|++||||++..+..
T Consensus 142 rli~g~lRiG~~~~~v~~ala~a~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~P~~pMLA~~~~~~~ 218 (539)
T PRK09247 142 KLITGGFRVGVSARLVTRALAELGGVDEARIAQRLMGLWPPYADLFAWLIGPEE---DPLPADPGQPYPFFLAHPLEDED 218 (539)
T ss_pred HHhhCccccchhHHHHHHHHHHHhCCCHHHHHHHHhCCCCCcHHHHHHHhhCCc---cccCCCCCCcCCCeeCCcCCCch
Confidence 99999999999999999865 322 3455665 788888887766522 56678999999999999988764
Q ss_pred HHHHHhCCCceEEEEecceEEEEEEEeCCEEEEEecCCCCCCCchhhhHHHHHhhccccceeeeceEEEeeCCCCccccc
Q 002803 237 AAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDGEMLVWDTSLNRFAEF 316 (879)
Q Consensus 237 ~~~~~~~~~~~~iE~K~DGeR~qih~~g~~v~~~SR~g~~~t~~~~~l~~~~~~~~~~~~~ILDGEmv~~d~~~~~~~pF 316 (879)
+. .+...+|++|+||||+|||+|++|+.+++|||||+++|..+|++.+.+. .+ +.+||||||||+||+.++.+.||
T Consensus 219 ~~--~~~~~~~~~E~K~DG~R~qih~~~~~v~lfSR~g~d~t~~fPei~~~~~-~l-~~~~ILDGElv~~~~~~~~~~~F 294 (539)
T PRK09247 219 LT--LGDPADWQAEWKWDGIRVQLVRRGGEVRLWSRGEELITERFPELAEAAE-AL-PDGTVLDGELLVWRPEDGRPQPF 294 (539)
T ss_pred hh--hcCCCcEEEEEeEcceEEEEEEeCCEEEEEeCCCccchhhhHHHHHHHH-hC-CCCEEEEeEEEEEECCCCCcCCH
Confidence 43 2334589999999999999999999999999999999999999988653 33 56899999999999866788999
Q ss_pred cchHHHHHHhhc--CCCCCCceEEEEEEEEEeCCccccCCCHHHHHHHHHhhcCCCCC-cceecccCCCCCccccCCCCC
Q 002803 317 GSNQEIAKAARD--GLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKG-RLETLVPDHGLNSHVRPQGEP 393 (879)
Q Consensus 317 ~~l~~~~~~~~~--~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~v~~~~~-~~~i~~p~~~~~~~v~~~~~~ 393 (879)
+.++...++... ....+.++||++|||||+||+++++.||.+|+++|++++.+.++ ++.++.
T Consensus 295 ~~l~~R~~rk~~~~~~~~~~pv~~~vFDiL~l~g~~l~~~Pl~eRr~~L~~~~~~~~~~~i~~~~--------------- 359 (539)
T PRK09247 295 ADLQQRIGRKTVGKKLLADYPAFLRAYDLLEDGGEDLRALPLAERRARLEALIARLPDPRLDLSP--------------- 359 (539)
T ss_pred HHHHHHhcccccchhhhhcCCeEEEEEEeeeeCCcchhhCCHHHHHHHHHHHhcccCCCeEEecC---------------
Confidence 888764332110 01124689999999999999999999999999999999987643 444321
Q ss_pred ccccccCCHHHHHHHHHHHHHcCCceEEEecCCCCCcCCCCCCCeEEEccccccCCCcceEEEEEEEeCCCCCCCCcceE
Q 002803 394 CWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLIIGGYYGSGRRGGEVAQF 473 (879)
Q Consensus 394 ~~~~~~~~~~ei~~~~~~~i~~g~EGlV~K~~~s~Y~~g~Rs~~WlKvKp~y~~~g~~lDlvVIG~~~G~Grr~g~~~sf 473 (879)
...+.+.+++.++|++++++|+||||+|+++|+|.||+|+..|+|+|++| .++|+||||+++|+|+|+|.+|+|
T Consensus 360 --~~~~~~~~e~~~~~~~a~~~g~EGlm~K~~~s~Y~~Grr~~~WlK~K~~~----~t~DlVvig~~~G~Gkr~g~~~~~ 433 (539)
T PRK09247 360 --LVPFSDWDELAALRAAARERGVEGLMLKRRDSPYLVGRKKGPWWKWKRDP----LTIDAVLMYAQRGHGRRASLYTDY 433 (539)
T ss_pred --ceecCCHHHHHHHHHHHHHCCCceEEEecCCCCcCCCCCcchhhcccCCC----CcEEEEEEEeecCCCCcCCccccE
Confidence 34467889999999999999999999999999999999999999999997 489999999999999999999999
Q ss_pred EEEEecCCCCCCCCceEEEEEEecCCCCHHHHHHHHHhhccccccccCCCCCCCcceeecCCCCCCCcEEEeCCCceEEE
Q 002803 474 LVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDVWIESPEKSIIL 553 (879)
Q Consensus 474 l~g~~~~~~~~~~~~~~~~~~kVgtG~s~~~~~~l~~~l~~~~~~~~~~~~~pp~~~~~~~~~~~~Pdvwi~~P~~s~V~ 553 (879)
+||+++++.+ ...|++||+||||||++++++|.+.+.++.. ....|++|++ | .+|+
T Consensus 434 lla~~~~~~~---~~~~~~v~kvgsGftd~~l~~l~~~l~~~~~------------------~~~~~~~~v~-P--~~V~ 489 (539)
T PRK09247 434 TFGVWDGPEG---GRQLVPFAKAYSGLTDEEIKQLDRWVRKNTV------------------ERFGPVRSVR-P--ELVF 489 (539)
T ss_pred EEEEEcCCCC---ceeEEEEEEECCCCCHHHHHHHHHHHhhccc------------------ccCCCceEec-C--ceEE
Confidence 9999976531 1369999999999999999999887765321 1125899999 7 5899
Q ss_pred EEeeeceecccCccCCCeeeeccEEEEEecCCCccCCCCHHHHHHHHHc
Q 002803 554 SITSDIRTIRSEVFSAPYSLRFPRIDRVRYDKPWHDCLDVQSFVELVHS 602 (879)
Q Consensus 554 ev~a~~~~~~s~~~~~g~tLRfPR~~riR~DK~~~~~~t~~e~~~l~~~ 602 (879)
||+++. ...|+.|++|++||||||.++|+||+|+||+|++++.+||+.
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 999643 237899999999999999999999999999999999999963
No 7
>PRK03180 ligB ATP-dependent DNA ligase; Reviewed
Probab=100.00 E-value=3.1e-90 Score=799.19 Aligned_cols=494 Identities=21% Similarity=0.347 Sum_probs=423.8
Q ss_pred CcHHHHHHHHHHHHhcCChhHHHHHHHHHHhhcCCCChHhhhHhhcCCCCCcCccccCCCHHHHHHHHHHHhCCCcChHH
Q 002803 7 TEVIVLVSLFNWIQKTKPAAKKRSKFRKFLDTYCDSVDYFSALRLILPSLDRERGSYGLKESVLANCLIDALGMSKDSAD 86 (879)
Q Consensus 7 ~~F~~l~~~~e~i~~~~~~~~k~~~l~~~~~~~~~~~~~~p~lrLllP~~d~~r~~yglke~~L~k~~~~~~~~~~~s~~ 86 (879)
|+|+.||++|++|+.|+++++|+++|.+||.+. .++|+.++++|+..... .+..|++++.+.++++.
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 689999999999999999999999999999988 56899999999999886 35799998666665211
Q ss_pred HHHHhhhhcCCCCCCCCCHHHHHHHHHhhhcCCCCCCCCHHHHHHHHHHHHhccC---hHHHHHHHHHHHHhCCHHHHHH
Q 002803 87 AVRLINWRKGGAAPNAGNFPMVAAEVLQRRQGMISGGLTIKELNDLLDRLASSEN---RAEKISVLSTLIKKTNAQEMKW 163 (879)
Q Consensus 87 ~~~L~~wk~~~~~~~~gD~~~~~~~v~~~r~~~~~~~lTi~eVn~~Ld~La~~~~---~~~k~~~l~~ll~~~s~~E~k~ 163 (879)
..+++|||.+||+.|++||..+| +.+|..+|..++.+|+|.|++|
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 01257999999999999999875 4788899999999999999999
Q ss_pred HHHHHhhhhccCCccccccccc-------CcCHHHHHhhcCCHHHHHHHHh-hhhhccccCCcccCCcccccceeeccCh
Q 002803 164 IIMIILKDLKLGISEKSIFHEF-------HPDAEDLFNVTCDLKLVCEKLK-DRNQRHKRQDIEVGKAVRPQLAMRIGDA 235 (879)
Q Consensus 164 l~RiIlk~lriG~~e~til~~~-------hpda~~~~~~~~dL~~V~~~L~-~~~~~~~~~~i~~~~~~~PmLA~~~~~~ 235 (879)
|+|+|+++||||+++++|+.++ +++++++|++|+||+.||+.+. ++...+....|++|.||+||||++..++
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 9999999999999999999877 3567889999999999999655 4555667778999999999999999888
Q ss_pred HHHHHHhCCCceEEEEecceEEEEEEEeCCEEEEEecCCCCCCCchhhhHHHHHhhccccceeeeceEEEeeCCCCcccc
Q 002803 236 HAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDGEMLVWDTSLNRFAE 315 (879)
Q Consensus 236 ~~~~~~~~~~~~~iE~K~DGeR~qih~~g~~v~~~SR~g~~~t~~~~~l~~~~~~~~~~~~~ILDGEmv~~d~~~~~~~p 315 (879)
++++++++ .+|++|+||||+|||+|++|+++++|||||+++|..+|++.+.+. .+..++||||||||+||+. +++.|
T Consensus 196 ~~~~~~~~-~~~~~E~K~DG~R~qih~~~~~v~l~SR~~~d~T~~fPei~~~~~-~~~~~~~ILDGElv~~d~~-g~~~~ 272 (508)
T PRK03180 196 AEALARLG-GPAAVEAKLDGARVQVHRDGDDVRVYTRTLDDITARLPEVVEAVR-ALPVRSLVLDGEAIALRPD-GRPRP 272 (508)
T ss_pred HHHHHHhC-CCeEEEEEEceeEEEEEEECCEEEEEeCCCCcchhhhHHHHHHHH-hCCCcceeecceEEEECCC-CCcCC
Confidence 88888875 579999999999999999999999999999999999999987653 3445789999999999974 67889
Q ss_pred ccchHHHHHHhhc--CCCCCCceEEEEEEEEEeCCccccCCCHHHHHHHHHhhcCCCCCcceecccCCCCCccccCCCCC
Q 002803 316 FGSNQEIAKAARD--GLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEP 393 (879)
Q Consensus 316 F~~l~~~~~~~~~--~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~v~~~~~~~~i~~p~~~~~~~v~~~~~~ 393 (879)
|+.++....+... ......+++|++|||||+||+++++.||.+||++|++++.+. ..+ |
T Consensus 273 F~~l~~R~~~k~~~~~~~~~~pv~~~~FDlL~l~G~dl~~~pl~eRr~~L~~~~~~~-~~~----~-------------- 333 (508)
T PRK03180 273 FQVTASRFGRRVDVAAARATQPLSPFFFDALHLDGRDLLDAPLSERLAALDALVPAA-HRV----P-------------- 333 (508)
T ss_pred HHHHHHHhccccchhhhcccCceEEEEEeehhcCCcchhcCCHHHHHHHHHHhhccc-ccc----c--------------
Confidence 9776643322100 011246899999999999999999999999999999998742 111 1
Q ss_pred ccccccCCHHHHHHHHHHHHHcCCceEEEecCCCCCcCCCCCCCeEEEccccccCCCcceEEEEEEEeCCCCCCCCcceE
Q 002803 394 CWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLIIGGYYGSGRRGGEVAQF 473 (879)
Q Consensus 394 ~~~~~~~~~~ei~~~~~~~i~~g~EGlV~K~~~s~Y~~g~Rs~~WlKvKp~y~~~g~~lDlvVIG~~~G~Grr~g~~~sf 473 (879)
.....+.++++++|++++++|+||||+|+++|+|.||+|+.+|+|+|+. +++|+||||+++|+|+|+|.+|+|
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 2235678999999999999999999999999999999999999999996 499999999999999999999999
Q ss_pred EEEEecCCCCCCCCceEEEEEEecCCCCHHHHHHHHHhhccccccccCCCCCCCcceeecCCCCCCCcEEEeCCCceEEE
Q 002803 474 LVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDVWIESPEKSIIL 553 (879)
Q Consensus 474 l~g~~~~~~~~~~~~~~~~~~kVgtG~s~~~~~~l~~~l~~~~~~~~~~~~~pp~~~~~~~~~~~~Pdvwi~~P~~s~V~ 553 (879)
+||++++++ +.|++||+||||||+++++++.+.+.++-.. ...|++||+ |. +|+
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 3899999999999999999999887755211 136899999 74 799
Q ss_pred EEeeeceecccCccCCCeeeeccEEEEEecCCCccCCCCHHHHHHHHH
Q 002803 554 SITSDIRTIRSEVFSAPYSLRFPRIDRVRYDKPWHDCLDVQSFVELVH 601 (879)
Q Consensus 554 ev~a~~~~~~s~~~~~g~tLRfPR~~riR~DK~~~~~~t~~e~~~l~~ 601 (879)
||+++.. ..|+.|++|++||||||++||+||+|+||+|++++.+||.
T Consensus 461 EV~~~~i-t~S~~~~~G~~LRfPr~~r~R~DK~~~ea~tl~~~~~l~~ 507 (508)
T PRK03180 461 EIAFDGV-QRSTRYPGGVALRFARVLRYRPDKTPAEADTIDTVRALLP 507 (508)
T ss_pred EEEeeEe-eeCCcccCCeEEECCeeeEeeCCCChHHCcCHHHHHHHhc
Confidence 9986432 3688999999999999999999999999999999999983
No 8
>PHA02587 30 DNA ligase; Provisional
Probab=100.00 E-value=8.6e-63 Score=568.77 Aligned_cols=445 Identities=20% Similarity=0.283 Sum_probs=334.4
Q ss_pred HHHHHHHHhcCChhHHHHHHHHHHhhcCCCChHhhhHhhcCCCCCcCccccCCCHHHHHHHHHHHhCCCcChHHHHHHhh
Q 002803 13 VSLFNWIQKTKPAAKKRSKFRKFLDTYCDSVDYFSALRLILPSLDRERGSYGLKESVLANCLIDALGMSKDSADAVRLIN 92 (879)
Q Consensus 13 ~~~~e~i~~~~~~~~k~~~l~~~~~~~~~~~~~~p~lrLllP~~d~~r~~yglke~~L~k~~~~~~~~~~~s~~~~~L~~ 92 (879)
-+++++|+++.++++|.+||.+..+ .+.+--+++|.+...- .|||+.
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 4689999999999999999887643 3456777788776553 577543
Q ss_pred hhcCCCCCCCCCHHHHHHHHHhhhcCCCCCCCCHHH-HHHHHHHHHhccC-hHHHHHHHHHHHHhCCHHHHHHHHHHHhh
Q 002803 93 WRKGGAAPNAGNFPMVAAEVLQRRQGMISGGLTIKE-LNDLLDRLASSEN-RAEKISVLSTLIKKTNAQEMKWIIMIILK 170 (879)
Q Consensus 93 wk~~~~~~~~gD~~~~~~~v~~~r~~~~~~~lTi~e-Vn~~Ld~La~~~~-~~~k~~~l~~ll~~~s~~E~k~l~RiIlk 170 (879)
|.+++.. ....+.+++.+ +..+..+||...- .+.++..|..++.+|+|.|++||+|+|++
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 01134567777 5556667887654 56778899999999999999999999999
Q ss_pred hhccCCcccccccccCcCHHHHHhhcCCHHHHHHHHhhhhhccccCCcccCCcccc-cceeeccChHHHHHHhCCCceEE
Q 002803 171 DLKLGISEKSIFHEFHPDAEDLFNVTCDLKLVCEKLKDRNQRHKRQDIEVGKAVRP-QLAMRIGDAHAAWRKLHGKEVVI 249 (879)
Q Consensus 171 ~lriG~~e~til~~~hpda~~~~~~~~dL~~V~~~L~~~~~~~~~~~i~~~~~~~P-mLA~~~~~~~~~~~~~~~~~~~i 249 (879)
+||||+++++|+++||+ +.|++| |||++... ++++++.+.+|++
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 99999999999998864 578888 99998543 4566633448999
Q ss_pred EEecceEEEEEEEeCCEEEEEecCCCCCCCchhhhHHHHHhhcc-----ccceeeeceEEEeeCCCCccccccc------
Q 002803 250 ECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVL-----VDRCILDGEMLVWDTSLNRFAEFGS------ 318 (879)
Q Consensus 250 E~K~DGeR~qih~~g~~v~~~SR~g~~~t~~~~~l~~~~~~~~~-----~~~~ILDGEmv~~d~~~~~~~pF~~------ 318 (879)
|+||||+|||+|++++++++|||||++++. +|++.+.+..... +.++|||||+|+||+.++ .||+.
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 5777765533211 478999999999987655 34432
Q ss_pred -----h-HHHHHHhh-cCC-----------CCCCceEEEEEEEEEeC---CccccCCCHHHHHHHHHhhcCC-CCCccee
Q 002803 319 -----N-QEIAKAAR-DGL-----------SSDRQLCYFAFDVLYVG---DTSVIHQSLKERHELLQKVVKP-SKGRLET 376 (879)
Q Consensus 319 -----l-~~~~~~~~-~~~-----------~~~~~~~~~vFDiL~ln---g~~l~~~pl~eRr~~L~~~v~~-~~~~~~i 376 (879)
. |.+..+.+ .+. ....+++|++||||+++ |..+++.||.+|+++|++++.. ..+++.+
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 12222211 010 12368999999999653 4447789999999999999963 2334433
Q ss_pred cccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHcCCceEEEecCCCCCcCCCCCCCeEEEccccccCCCcceEEE
Q 002803 377 LVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLI 456 (879)
Q Consensus 377 ~~p~~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~~i~~g~EGlV~K~~~s~Y~~g~Rs~~WlKvKp~y~~~g~~lDlvV 456 (879)
+. ...+++.+++.++|++++++|.||||+|+++|+|++| |+.+|+|+|+.+ ++|++|
T Consensus 314 ~~-----------------~~~~~~~ee~~~~~~~a~~~G~EGimlK~~ds~Y~~G-Rs~~WlKiK~~~-----~~dlvV 370 (488)
T PHA02587 314 IE-----------------NQVVNNLEEAKEIYKRYVDQGLEGIILKNTDGLWEDG-RSKDQIKFKEVI-----DIDLEI 370 (488)
T ss_pred Ee-----------------eEEcCCHHHHHHHHHHHHhCCCCeEEEECCCCCCCCC-CCCCcEEecCCC-----ceEEEE
Confidence 21 2346789999999999999999999999999999998 888999999974 899999
Q ss_pred EEEEeCCCCCCCCcceEEEEEecCCCCCCCCceEEEEEEecCCCCHHHHHHHHHhhccccccccCCCCCCCcceeecCCC
Q 002803 457 IGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNS 536 (879)
Q Consensus 457 IG~~~G~Grr~g~~~sfl~g~~~~~~~~~~~~~~~~~~kVgtG~s~~~~~~l~~~l~~~~~~~~~~~~~pp~~~~~~~~~ 536 (879)
||+++|. +++|.+|+|+|++++ + . .+|+||||||++++++|..... . +| +-.. ..
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 567889999997642 1 2 4799999999999998865432 0 11 1001 12
Q ss_pred CCCCcEEEeCC-CceEEEEEeeeceecccCccCCCeeeeccEEEEEecCCCccCCCCHHHHH
Q 002803 537 KERPDVWIESP-EKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDKPWHDCLDVQSFV 597 (879)
Q Consensus 537 ~~~Pdvwi~~P-~~s~V~ev~a~~~~~~s~~~~~g~tLRfPR~~riR~DK~~~~~~t~~e~~ 597 (879)
..++.+|.+++ ....|+||+++.. ..|+.|++|++||||||.++|+||+ +|+|++++.
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 24567787632 1247999986543 3788999999999999999999999 999999985
No 9
>COG1793 CDC9 ATP-dependent DNA ligase [DNA replication, recombination, and repair]
Probab=100.00 E-value=2.6e-60 Score=539.56 Aligned_cols=421 Identities=27% Similarity=0.413 Sum_probs=345.6
Q ss_pred CCCCCHHHHHHHHHhhhcCCCCCCCCHHHHHHHHHHHHhccChHHHHHHHHHHHHhCCHHHHHHHHHHHhhhhccCCccc
Q 002803 100 PNAGNFPMVAAEVLQRRQGMISGGLTIKELNDLLDRLASSENRAEKISVLSTLIKKTNAQEMKWIIMIILKDLKLGISEK 179 (879)
Q Consensus 100 ~~~gD~~~~~~~v~~~r~~~~~~~lTi~eVn~~Ld~La~~~~~~~k~~~l~~ll~~~s~~E~k~l~RiIlk~lriG~~e~ 179 (879)
...||+|..+..+.. +.+|...|..++...+ .+ .++..|+..++ +|++++
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 568999987766533 8999999999999988 22 77888888888 999999
Q ss_pred ccccccCcCHHHHHhhcCCHHHHHHHHhhh-hhccccCCcccCCcccccceeeccChHHHHHHhCCCceEEEEecceEEE
Q 002803 180 SIFHEFHPDAEDLFNVTCDLKLVCEKLKDR-NQRHKRQDIEVGKAVRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRI 258 (879)
Q Consensus 180 til~~~hpda~~~~~~~~dL~~V~~~L~~~-~~~~~~~~i~~~~~~~PmLA~~~~~~~~~~~~~~~~~~~iE~K~DGeR~ 258 (879)
+++.+...-.+..|+.++|++.++..+... ..++....+.+|.|+.||||.......+...+..+ .|++|+||||+|+
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 999876555778899999999988877643 23445566789999999999998877655555443 5999999999999
Q ss_pred EEEEeCCEEEEEecCCCCCCCchhhhHHHHHhhccccceeeeceEEEeeCCCCccccccchHHHHHHhhc--CCCCCCce
Q 002803 259 QIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDGEMLVWDTSLNRFAEFGSNQEIAKAARD--GLSSDRQL 336 (879)
Q Consensus 259 qih~~g~~v~~~SR~g~~~t~~~~~l~~~~~~~~~~~~~ILDGEmv~~d~~~~~~~pF~~l~~~~~~~~~--~~~~~~~~ 336 (879)
|+|+.++.+++|||+|.|+|..+|++.+.+...+..+++|||||+|++|+. ...||+.+|...++... ......++
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 999999999999999999999999766665566667899999999999976 46899888765533211 12245689
Q ss_pred EEEEEEEEEeCCccccCCCHHHHHHHHHhhcCCCCCcceecccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHcC
Q 002803 337 CYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENR 416 (879)
Q Consensus 337 ~~~vFDiL~lng~~l~~~pl~eRr~~L~~~v~~~~~~~~i~~p~~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~~i~~g 416 (879)
+|++||+||+||++|.++||.+||+.|++++.+. +.+.+.. ....++.++++.+|+.+++.|
T Consensus 225 ~~~aFDlL~~dG~dL~~~pl~eRr~~Le~lv~~~-~~~~~~~-----------------~i~~~~~~~~~~~~~~a~~~g 286 (444)
T COG1793 225 VLFAFDLLYLDGEDLRGLPLEERRALLEELVKSS-DKIEIAE-----------------RIPFSDAEEGEAFLEAAIELG 286 (444)
T ss_pred EEEEEEEEeECCcccccCchHHHHHHHHHHhccc-ccccccc-----------------ceeccChhhHHHHHHHHHhcC
Confidence 9999999999999999999999999999999874 2222110 122378899999999999999
Q ss_pred CceEEEecCCCCCcCCCCCCCeEEEccccccCCCcceEEEEEEEeCCCCCCCCcceEEEEEecCCCCCCCCceEEEEEEe
Q 002803 417 DEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRV 496 (879)
Q Consensus 417 ~EGlV~K~~~s~Y~~g~Rs~~WlKvKp~y~~~g~~lDlvVIG~~~G~Grr~g~~~sfl~g~~~~~~~~~~~~~~~~~~kV 496 (879)
.||||+|+++|+|++|+|+..|+|+|++ +++||+|+|+++|.|+++ .+|+|+||++++.+ +.|.++|+|
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 499999999999999999 89999999998764 379999999
Q ss_pred cCCCCHHHHHHHHHhhccccccccCCCCCCCcceeecCCCCCCCcEEEeCCCceEEEEEeeeceecccCccCC--Ceeee
Q 002803 497 GTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSA--PYSLR 574 (879)
Q Consensus 497 gtG~s~~~~~~l~~~l~~~~~~~~~~~~~pp~~~~~~~~~~~~Pdvwi~~P~~s~V~ev~a~~~~~~s~~~~~--g~tLR 574 (879)
||||+++++++|.++|++++... . +|. .+.-|..+| ++|+||+++.. ..++.|.. |.+||
T Consensus 356 gtGf~~~~l~~l~~~l~~~~~~~----~-~~~----------~~~~~~~~p--~~V~EV~~~~~-t~~~~~r~~~~~~lR 417 (444)
T COG1793 356 GTGFSDAELEELTERLEPLIVSR----F-NGK----------VPGKVVPPP--GLVAEVRFAEI-TKSGRLRHASGLGLR 417 (444)
T ss_pred cCCCCHHHHHHHHHHHHHhccCc----C-CCc----------cCceeecCC--cEEEEEEEeec-ccCCceecccCcccC
Confidence 99999999999999999987641 1 111 111154435 68999986433 25777766 89999
Q ss_pred ccEEEEEecCCCccCCCCHHHHHHHH
Q 002803 575 FPRIDRVRYDKPWHDCLDVQSFVELV 600 (879)
Q Consensus 575 fPR~~riR~DK~~~~~~t~~e~~~l~ 600 (879)
|||+.++|.||.+.+++|++++.+|+
T Consensus 418 fpr~~rvr~dk~~~~a~t~~~~~~~~ 443 (444)
T COG1793 418 FPRFVRVRDDKLPEDADTIEEIEALY 443 (444)
T ss_pred cCcccccccccCcccccccccchhhc
Confidence 99999999999999999999998775
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=2.8e-56 Score=487.15 Aligned_cols=288 Identities=28% Similarity=0.416 Sum_probs=240.7
Q ss_pred CCCceEEEEecceEEEEEEEeCCEEEEEecCCCCCCCchhhhHHHHHhhccccceeeeceEEEeeCCCCccccccchHHH
Q 002803 243 HGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDGEMLVWDTSLNRFAEFGSNQEI 322 (879)
Q Consensus 243 ~~~~~~iE~K~DGeR~qih~~g~~v~~~SR~g~~~t~~~~~l~~~~~~~~~~~~~ILDGEmv~~d~~~~~~~pF~~l~~~ 322 (879)
.+.+|++|+||||+|||+|++++.+++|||||+++|..+|++...+ ..+...+||||||||+||.. ++ .+|+.+|..
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 4678999999999999999999999999999999998889887653 34446799999999999974 33 589777754
Q ss_pred HHHhhcCCCCCCceEEEEEEEEEeCCccccCCCHHHHHHHHHhhcCCCCCcceecccCCCCCccccCCCCCccccccCCH
Q 002803 323 AKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNV 402 (879)
Q Consensus 323 ~~~~~~~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~v~~~~~~~~i~~p~~~~~~~v~~~~~~~~~~~~~~~ 402 (879)
... ....+++|++||||++||++++++||.+|+++|++++.+.+++..+.. . ..++.
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 HHHHHHHHHHHHcCCceEEEecCCCCCcCCCCCCCeEEEccccccCCCcceEEEEEEEeCCCCCCCCcceEEEEEecCCC
Q 002803 403 DEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLIIGGYYGSGRRGGEVAQFLVALAERPA 482 (879)
Q Consensus 403 ~ei~~~~~~~i~~g~EGlV~K~~~s~Y~~g~Rs~~WlKvKp~y~~~g~~lDlvVIG~~~G~Grr~g~~~sfl~g~~~~~~ 482 (879)
+++.++|++++++|.||||+|+++|+|+||+ +.+|+|+|+.+ +.|++|+|+++|.|++ |.+|+|+||++++.
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 89999999986 8999999988999988 77999999998642
Q ss_pred CCCCCceEEEEEEecCCCCHHHHHHHHHhhccccccccCCCCCCCcceeecCCCCCCCcEEEeCCCceEEEEEeeeceec
Q 002803 483 PDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDVWIESPEKSIILSITSDIRTI 562 (879)
Q Consensus 483 ~~~~~~~~~~~~kVgtG~s~~~~~~l~~~l~~~~~~~~~~~~~pp~~~~~~~~~~~~Pdvwi~~P~~s~V~ev~a~~~~~ 562 (879)
.|.++|+||||||++++++|.+++.+++... . ||. .....|++|++ | .+|+||++.
T Consensus 216 ------~l~~vg~vgsG~s~~~~~~l~~~l~~~~~~~----~-~~~------~~~~~~~~wv~-P--~lV~eV~~~---- 271 (298)
T TIGR02779 216 ------GLRYVGRVGTGFSEAELATIKERLKPLESKP----D-KPG------AREKRGVHWVK-P--ELVAEVEFA---- 271 (298)
T ss_pred ------eEEEEeEecCCCCHHHHHHHHHHHHhhccCc----C-CCC------cccCCCCEEeC-C--eEEEEEEec----
Confidence 6889999999999999999999999988652 1 221 12346889999 7 589999762
Q ss_pred ccCccCCCeeeeccEEEEEecCCCccCCC
Q 002803 563 RSEVFSAPYSLRFPRIDRVRYDKPWHDCL 591 (879)
Q Consensus 563 ~s~~~~~g~tLRfPR~~riR~DK~~~~~~ 591 (879)
.++.|.+||||||+++|+||+|+||+
T Consensus 272 ---~~t~~~~lR~P~~~~~R~Dk~~~~~~ 297 (298)
T TIGR02779 272 ---GWTRDGRLRQASFVGLREDKPASEVT 297 (298)
T ss_pred ---ccCCCCeEeccEEEeeeCCCCHHHcc
Confidence 23457899999999999999999996
No 11
>PRK09632 ATP-dependent DNA ligase; Reviewed
Probab=100.00 E-value=2.2e-55 Score=520.03 Aligned_cols=307 Identities=25% Similarity=0.383 Sum_probs=253.3
Q ss_pred cccCCcccccceeeccChHHHHHHhCCCceEEEEecceEEEEEEEeCCEEEEEecCCCCCCCchhhhHHHHHhhccccce
Q 002803 218 IEVGKAVRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRC 297 (879)
Q Consensus 218 i~~~~~~~PmLA~~~~~~~~~~~~~~~~~~~iE~K~DGeR~qih~~g~~v~~~SR~g~~~t~~~~~l~~~~~~~~~~~~~ 297 (879)
..++.+|+||||+..... .+.+..|++|+||||+|||+|++++.+++|||||+++|..+|++.+. ...+...+|
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 578899999999976422 13567899999999999999999999999999999999999998774 445556799
Q ss_pred eeeceEEEeeCCCCccccccchHHHHHHhhcCCCCCCceEEEEEEEEEeCCccccCCCHHHHHHHHHhhcCCCCCcceec
Q 002803 298 ILDGEMLVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETL 377 (879)
Q Consensus 298 ILDGEmv~~d~~~~~~~pF~~l~~~~~~~~~~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~v~~~~~~~~i~ 377 (879)
|||||||+||+.+ + .+|+.+|... ...+++|++|||||+||++|+++||.+|+++|++++.+ .+++.+.
T Consensus 529 ILDGEiVvld~~G-~-~~F~~Lq~r~--------~~~~v~y~vFDLL~lnG~dL~~~Pl~eRR~~L~~l~~~-~~~i~~s 597 (764)
T PRK09632 529 VLDGEIVALDDSG-V-PSFGLLQNRG--------RDTRVEFWAFDLLYLDGRSLLRKPYRDRRKLLEALAPS-GGSLTVP 597 (764)
T ss_pred eeeeEEEEeCCCC-C-CCHHHHhhhh--------hcCCeEEEEEeeeccCCcccccCCHHHHHHHHHHhhCC-CCcEEec
Confidence 9999999999753 3 5898877541 23579999999999999999999999999999999863 2233221
Q ss_pred ccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHcCCceEEEecCCCCCcCCCCCCCeEEEccccccCCCcceEEEE
Q 002803 378 VPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLII 457 (879)
Q Consensus 378 ~p~~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~~i~~g~EGlV~K~~~s~Y~~g~Rs~~WlKvKp~y~~~g~~lDlvVI 457 (879)
.....+++++|+.++++|.||||+|+++|+|++|+||.+|+|+|+.| +.|++|+
T Consensus 598 ---------------------~~~~~~~~~~l~~a~~~GlEGIVaKr~dS~Y~pGrRs~~WlKiK~~~-----~~e~VI~ 651 (764)
T PRK09632 598 ---------------------PLLPGDGAEALAYSRELGWEGVVAKRRDSTYQPGRRSSSWIKDKHWR-----TQEVVIG 651 (764)
T ss_pred ---------------------ceecccHHHHHHHHHHcCCcEEEEeCCCCCCCCCCcCCCeEEEecCC-----ceEEEEE
Confidence 11123578899999999999999999999999999999999999997 8999999
Q ss_pred EEEeCCCCCCCCcceEEEEEecCCCCCCCCceEEEEEEecCCCCHHHHHHHHHhhccccccccCCCCCCCcceeecCCCC
Q 002803 458 GGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSK 537 (879)
Q Consensus 458 G~~~G~Grr~g~~~sfl~g~~~~~~~~~~~~~~~~~~kVgtG~s~~~~~~l~~~l~~~~~~~~~~~~~pp~~~~~~~~~~ 537 (879)
|+++|+|+++|.+|+||||+++.+ .+.++|+||||||++++++|.++|.++.+. .|| |........
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 989999999999999999999642 588999999999999999999999987643 122 211111134
Q ss_pred CCCcEEEeCCCceEEEEEeeeceecccCccCCCeeeeccEEEEEecCCCccCCC
Q 002803 538 ERPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDKPWHDCL 591 (879)
Q Consensus 538 ~~Pdvwi~~P~~s~V~ev~a~~~~~~s~~~~~g~tLRfPR~~riR~DK~~~~~~ 591 (879)
.+|++||+ |. +|+||++. .++.+++||||||+++|.||++.||.
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 74 79999752 24467799999999999999999985
No 12
>PRK08224 ligC ATP-dependent DNA ligase; Reviewed
Probab=100.00 E-value=5.6e-53 Score=467.15 Aligned_cols=314 Identities=22% Similarity=0.354 Sum_probs=248.0
Q ss_pred CcccCCcccccceeeccChHHHHHHhCCCceEEEEecceEEEEEEEeCCEEEEEecCCCCCCCchhhhHHHHHhhccccc
Q 002803 217 DIEVGKAVRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDR 296 (879)
Q Consensus 217 ~i~~~~~~~PmLA~~~~~~~~~~~~~~~~~~~iE~K~DGeR~qih~~g~~v~~~SR~g~~~t~~~~~l~~~~~~~~~~~~ 296 (879)
+..+|.|++||||.....++ .+.+|++|+||||+|||+|++|+++++|||||+++|..||++.+.+. .+.+.+
T Consensus 2 ~~~~~~~i~PMLA~~~~~~~------~~~~w~~E~K~DG~R~~~~~~~~~v~l~SRng~d~t~~fPel~~~~~-~~~~~~ 74 (350)
T PRK08224 2 DLPVMPPVEPMLAKSVDAIP------PGDGWSYEPKWDGFRCLVFRDGDEVELGSRNGKPLTRYFPELVAALR-AELPER 74 (350)
T ss_pred CCCCCCCcCCccCCccCCCC------CCCcEEEEEeECeeEEEEEEECCEEEEEeCCCCCchhhhHHHHHHHH-hhCCCC
Confidence 46789999999999876442 34579999999999999999999999999999999999999988654 345679
Q ss_pred eeeeceEEEeeCCCCccccccchHHHHHHhhc---CCCCCCceEEEEEEEEEeCCccccCCCHHHHHHHHHhhcCCCCCc
Q 002803 297 CILDGEMLVWDTSLNRFAEFGSNQEIAKAARD---GLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGR 373 (879)
Q Consensus 297 ~ILDGEmv~~d~~~~~~~pF~~l~~~~~~~~~---~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~v~~~~~~ 373 (879)
||||||||+++.. . .+|+.+|........ ......+++|++|||||+||+++++.||.+|+++|++++.+. +.
T Consensus 75 ~vLDGEiVv~~~~--~-~~F~~Lq~r~~~~~~~~~~~~~~~pv~~~vFDlL~l~G~dl~~~Pl~eRr~~L~~l~~~~-~~ 150 (350)
T PRK08224 75 CVLDGEIVVARDG--G-LDFEALQQRIHPAASRVRKLAEETPASFVAFDLLALGDRDLTGRPFAERRAALEAAAAGS-GP 150 (350)
T ss_pred EEEeeEEEEeCCC--C-CCHHHHHhhhhccccchhhhhhcCCEEEEEEeeeeECCcChhhCCHHHHHHHHHHhcCCC-Cc
Confidence 9999999999853 2 799888765321110 011246899999999999999999999999999999998643 23
Q ss_pred ceecccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHcCCceEEEecCCCCCcCCCCCCCeEEEccccccCCCcce
Q 002803 374 LETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLD 453 (879)
Q Consensus 374 ~~i~~p~~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~~i~~g~EGlV~K~~~s~Y~~g~Rs~~WlKvKp~y~~~g~~lD 453 (879)
+.+. ....+.++++++|++++++|.||||+|+++|+|++|+|+ |+|+|+.+ +.|
T Consensus 151 i~~~-------------------~~~~~~~~~~~~~~~a~~~G~EGIV~Kr~dS~Y~~Grr~--WlKiK~~~-----~~d 204 (350)
T PRK08224 151 VHLT-------------------PATTDPATARRWFEEFEGAGLDGVIAKPLDGPYQPGKRA--MFKVKHER-----TAD 204 (350)
T ss_pred EEEe-------------------cccCCHHHHHHHHHHHHhCCCcEEEEeCCCCCcCCCCcC--EEEEccCC-----cEE
Confidence 3221 113456799999999999999999999999999999886 99999985 999
Q ss_pred EEEEEEEeCCCCCCCCcceEEEEEecCCCCCCCCceEEEEEEecCCCCHHHHHHHHHhhccccccccCCCCCCC----cc
Q 002803 454 VLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPP----SF 529 (879)
Q Consensus 454 lvVIG~~~G~Grr~g~~~sfl~g~~~~~~~~~~~~~~~~~~kVgtG~s~~~~~~l~~~l~~~~~~~~~~~~~pp----~~ 529 (879)
++|+|+++|+|+ |.+|+|+||++++++ ++.++|+|| |||++++++|.+++.+++... + .+| +|
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-AFPMARRRELTAELEPLRTPF--G--DHPWNWAAF 271 (350)
T ss_pred EEEEEEEcCCCC--CccccEEEEEECCCC------cEEEEEEEC-CCCHHHHHHHHHHHHhhhcCC--C--CCccccCcc
Confidence 999999998875 789999999997542 688999985 999999999999999887541 1 011 12
Q ss_pred eeecC-----CCCCCCcEE--EeCCCceEEEEEeeeceecccCccCCCeeeecc-EEEEEecCCCccCCC
Q 002803 530 YQVTN-----NSKERPDVW--IESPEKSIILSITSDIRTIRSEVFSAPYSLRFP-RIDRVRYDKPWHDCL 591 (879)
Q Consensus 530 ~~~~~-----~~~~~Pdvw--i~~P~~s~V~ev~a~~~~~~s~~~~~g~tLRfP-R~~riR~DK~~~~~~ 591 (879)
..... ....+..+| ++ | .+|+||++ ..++ +..||+| +|+++|.||++.||+
T Consensus 272 ~~~~~~~~~~~~~~~~~~w~~v~-P--~lv~eV~~-------~~~t-~~~lR~p~~f~g~r~Dk~p~~v~ 330 (350)
T PRK08224 272 TGRAPGGPSRWSAGKDLSWVPLR-P--ERVVEVRY-------DHME-GGRFRHTAQFLRWRPDRDPRSCT 330 (350)
T ss_pred cccCCCccccccccCCcEEEeee-E--EEEEEEec-------Cccc-CCeecCCCeeEEEcCCCChHHCC
Confidence 11000 011235689 98 7 47888864 2344 3489998 999999999999997
No 13
>PRK05972 ligD ATP-dependent DNA ligase; Reviewed
Probab=100.00 E-value=4.7e-52 Score=495.94 Aligned_cols=304 Identities=26% Similarity=0.396 Sum_probs=244.5
Q ss_pred CcccccceeeccChHHHHHHhCCCceEEEEecceEEEEEEEeCCEEEEEecCCCCCCCchhhhHHHHHhhccccceeeec
Q 002803 222 KAVRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDG 301 (879)
Q Consensus 222 ~~~~PmLA~~~~~~~~~~~~~~~~~~~iE~K~DGeR~qih~~g~~v~~~SR~g~~~t~~~~~l~~~~~~~~~~~~~ILDG 301 (879)
..++||||..+..++ .+..|++|.||||+|||+|++++++++|||||+++|..+|++.+.+. .+..++|||||
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 458999999877653 34689999999999999999999999999999999999999988753 45567999999
Q ss_pred eEEEeeCCCCccccccchHHHHHHhhcCCCCCCceEEEEEEEEEeCCccccCCCHHHHHHHHHhhcCCCCC-cceecccC
Q 002803 302 EMLVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKG-RLETLVPD 380 (879)
Q Consensus 302 Emv~~d~~~~~~~pF~~l~~~~~~~~~~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~v~~~~~-~~~i~~p~ 380 (879)
|+|+||..+ + .+|+.+|...+. ....+++|++|||||+||++|+++||.+|+++|++++.+.++ ++.+.
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 EIVVLDEDG-V-PDFQALQNAFDE-----GRTEDLVYFAFDLPFLGGEDLRELPLEERRARLRALLEAARSDRIRFS--- 374 (860)
T ss_pred EEEEECCCC-C-CCHHHHHHHhhc-----cCCCceEEEEEeccccCCcccccCCHHHHHHHHHHHhhhcCCCcEEEe---
Confidence 999999753 3 589888764432 123579999999999999999999999999999999976532 23221
Q ss_pred CCCCccccCCCCCccccccCCHHHHHHHHHHHHHcCCceEEEecCCCCCcCCCCCCCeEEEccccccCCCcceEEEEEEE
Q 002803 381 HGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLIIGGY 460 (879)
Q Consensus 381 ~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~~i~~g~EGlV~K~~~s~Y~~g~Rs~~WlKvKp~y~~~g~~lDlvVIG~~ 460 (879)
.+...+.+++|+.++++|.||||+|+++|+|++| |+.+|+|+|+.+ +.|++|+|.+
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 899999999986 5677766666
Q ss_pred eCCCCCCCCcceEEEEEecCCCCCCCCceEEEEEEecCCCCHHHHHHHHHhhccccccccCCCCCCCcceeecCCCCCCC
Q 002803 461 YGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERP 540 (879)
Q Consensus 461 ~G~Grr~g~~~sfl~g~~~~~~~~~~~~~~~~~~kVgtG~s~~~~~~l~~~l~~~~~~~~~~~~~pp~~~~~~~~~~~~P 540 (879)
.|.|+++| +|+||||++++. +|+++|+||||||++++++|.++|.++.+. .+| |..........+
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 67888887 999999999742 799999999999999999999999987653 123 211111112245
Q ss_pred cEEEeCCCceEEEEEeeeceecccCccCCCeeeeccEEEEEecCCCccCCC
Q 002803 541 DVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDKPWHDCL 591 (879)
Q Consensus 541 dvwi~~P~~s~V~ev~a~~~~~~s~~~~~g~tLRfPR~~riR~DK~~~~~~ 591 (879)
.+||+ |. +|+||++. .++.+..||||+|+++|.||+++||.
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--LVAEVEFA-------GWTRDGIVRQAVFKGLREDKPAREVV 536 (860)
T ss_pred CEEEc-cC--EEEEEEEe-------eccCCCCCccceEEEeecCCChHHhC
Confidence 79999 74 79999753 23344589999999999999999986
No 14
>PRK09633 ligD ATP-dependent DNA ligase; Reviewed
Probab=100.00 E-value=1e-50 Score=475.29 Aligned_cols=310 Identities=22% Similarity=0.261 Sum_probs=241.6
Q ss_pred ccccceeeccChHHHHHHhCCCceEEEEecceEEEEEEEeCCEEEEEecCCCCCCCchhhhHHHHHhhcc----ccceee
Q 002803 224 VRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVL----VDRCIL 299 (879)
Q Consensus 224 ~~PmLA~~~~~~~~~~~~~~~~~~~iE~K~DGeR~qih~~g~~v~~~SR~g~~~t~~~~~l~~~~~~~~~----~~~~IL 299 (879)
++||||.....++ .+.+|++|+||||+|||+|++|+.+++|||||+++|..||++.+.+..... ..+|||
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 4799998876543 467899999999999999999999999999999999999998876532111 137999
Q ss_pred eceEEEeeCCCCccccccchHHHHHHhhcC----CCCCCceEEEEEEEEEeCCccccCCCHHHHHHHHHhhcCCCCCcce
Q 002803 300 DGEMLVWDTSLNRFAEFGSNQEIAKAARDG----LSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLE 375 (879)
Q Consensus 300 DGEmv~~d~~~~~~~pF~~l~~~~~~~~~~----~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~v~~~~~~~~ 375 (879)
|||||+||..+. .+|+.+|......+.. .....+++|++|||||+||+++++.||.+|+++|++++.+.....+
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 999999986532 5898777653221111 0123678999999999999999999999999999999975431100
Q ss_pred ecccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHcCCceEEEecCCCCCcCCCCCCCeEEEccccccCCCcceEE
Q 002803 376 TLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVL 455 (879)
Q Consensus 376 i~~p~~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~~i~~g~EGlV~K~~~s~Y~~g~Rs~~WlKvKp~y~~~g~~lDlv 455 (879)
+. .... +. ...+.+.++++++|++++++|.||||+|+++|+|++|+||.+|+|+|+.+ +.|++
T Consensus 153 ---~~---~~~~-----~~-i~~~~~~~~~~~l~~~a~~~g~EGIV~Kr~dS~Y~~G~Rs~~WlKiK~~~-----~~d~v 215 (610)
T PRK09633 153 ---PD---PYAK-----AR-IQYIPSTTDFDALWEAVKRYDGEGIVAKKKTSKWLENKRSKDWLKIKNWR-----YVHVI 215 (610)
T ss_pred ---cc---cccc-----cc-eEEcCCHHHHHHHHHHHHHcCCceEEEeCCCCCCCCCCCCCCeEEEeccC-----CceeE
Confidence 00 0000 00 11234577999999999999999999999999999999999999999964 89998
Q ss_pred EEEEEeCCCCCCCCcceEEEEEecCCCCCCCCceEEEEEEecCCCCHHHHHHHHHhhccccccccCCCCCCCcceeecCC
Q 002803 456 IIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNN 535 (879)
Q Consensus 456 VIG~~~G~Grr~g~~~sfl~g~~~~~~~~~~~~~~~~~~kVgtG~s~~~~~~l~~~l~~~~~~~~~~~~~pp~~~~~~~~ 535 (879)
|+|+..|. |.|++|+++. +++.++|+||||||++++++|.++|.++.+.
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 88865443 3678898842 2799999999999999999999999876432
Q ss_pred CCCCCcEEEeCCCceEEEEEeeeceecccCccCCCeeeeccEEEEEecCCCccCCCCHHHHHHHHH
Q 002803 536 SKERPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDKPWHDCLDVQSFVELVH 601 (879)
Q Consensus 536 ~~~~Pdvwi~~P~~s~V~ev~a~~~~~~s~~~~~g~tLRfPR~~riR~DK~~~~~~t~~e~~~l~~ 601 (879)
...+.+|++ | .+|+||++.. + +|+.||||+|+++|.||+++||++.++..+++.
T Consensus 265 -~~~~~~wV~-P--~LV~EV~~~e-------~-t~g~LR~P~f~glR~DK~~~ev~~~~~~~~~~~ 318 (610)
T PRK09633 265 -TKSGEYTLE-P--SICVTVACIT-------F-DGGTLREPSFVSFLFDMDPTECTYQQLQRQLAP 318 (610)
T ss_pred -CCCCcEEEe-e--eEEEEEEEee-------c-CCCeEEeeEEeEEEcCCChHHcchhhhhhhhcc
Confidence 123578999 7 4799997532 2 278899999999999999999999888777664
No 15
>PRK07636 ligB ATP-dependent DNA ligase; Reviewed
Probab=100.00 E-value=1.7e-46 Score=404.40 Aligned_cols=272 Identities=24% Similarity=0.334 Sum_probs=213.9
Q ss_pred ccccceeeccChHHHHHHhCCCceEEEEecceEEEEEEEeCCEEEEEecCCCCCCCchhhhHHHHHhhccccceeeeceE
Q 002803 224 VRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDGEM 303 (879)
Q Consensus 224 ~~PmLA~~~~~~~~~~~~~~~~~~~iE~K~DGeR~qih~~g~~v~~~SR~g~~~t~~~~~l~~~~~~~~~~~~~ILDGEm 303 (879)
++||||.....+ +.+.+|++|+||||+|||+|++++.+++|||||+++|..+|++.+.. .+++|||||||
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 34668999999999999999999999999999999999889887642 34679999999
Q ss_pred EEeeCCCCccccccchHHHHHHhhcCCCCCCceEEEEEEEEEeCCccccCCCHHHHHHHHHhhcCCCCCcceecccCCCC
Q 002803 304 LVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGL 383 (879)
Q Consensus 304 v~~d~~~~~~~pF~~l~~~~~~~~~~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~v~~~~~~~~i~~p~~~~ 383 (879)
|+||.. ++ .+|+.++...... ......+++|+|||||++||++++++||.+|+++|++++.+.+ ++.++
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 999975 33 4898776543221 1122468999999999999999999999999999999987543 22211
Q ss_pred CccccCCCCCccccccCCHHHHHHHHHHHHHcCCceEEEecCCCCCcCCCCCCCeEEEccccccCCCcceEEEEEEEeCC
Q 002803 384 NSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLIIGGYYGS 463 (879)
Q Consensus 384 ~~~v~~~~~~~~~~~~~~~~ei~~~~~~~i~~g~EGlV~K~~~s~Y~~g~Rs~~WlKvKp~y~~~g~~lDlvVIG~~~G~ 463 (879)
....++++++|+.++++|.||||+|+++|+|.+|+||.+|+|+|+. ++.|++|+|+..
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 1123567889999999999999999999999999999999999974 589998877532
Q ss_pred CCCCCCcceEEEEEecCCCCCCCCceEEEEEEecCCCCHHHHHHHHHhhccccccccCCCCCCCcceeecCCCCCCCcEE
Q 002803 464 GRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDVW 543 (879)
Q Consensus 464 Grr~g~~~sfl~g~~~~~~~~~~~~~~~~~~kVgtG~s~~~~~~l~~~l~~~~~~~~~~~~~pp~~~~~~~~~~~~Pdvw 543 (879)
+.+|++ +|+++ + + ++|+||| |+++++.+|.+.+.+.... ..++.+|
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 78764 1 3 5899999 9999999999888755321 2356899
Q ss_pred EeCCCceEEEEEeeeceecccCccCCCeeeeccEEEEEe
Q 002803 544 IESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVR 582 (879)
Q Consensus 544 i~~P~~s~V~ev~a~~~~~~s~~~~~g~tLRfPR~~riR 582 (879)
++ | .+|.||++. .++.+..||||+|+++|
T Consensus 246 v~-P--~lv~eV~~~-------e~t~~g~lR~p~f~g~r 274 (275)
T PRK07636 246 IE-P--IIGCRVKHR-------FKTKNGMLRIPSFVEWR 274 (275)
T ss_pred eC-C--cEEEEEEEE-------EecCCCCEEccEEEEEe
Confidence 98 7 478888752 23334459999999998
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=7.6e-46 Score=387.31 Aligned_cols=213 Identities=30% Similarity=0.547 Sum_probs=183.7
Q ss_pred CCcccCCcccccceeeccChHHHHHHhCCCceEEEEecceEEEEEEEeC-CEEEEEecCCCCCCCchhhhHHHHHhhc--
Q 002803 216 QDIEVGKAVRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNG-SEIHYFSRSFLDHSEYGHAMSKIIEQNV-- 292 (879)
Q Consensus 216 ~~i~~~~~~~PmLA~~~~~~~~~~~~~~~~~~~iE~K~DGeR~qih~~g-~~v~~~SR~g~~~t~~~~~l~~~~~~~~-- 292 (879)
..|++|.||+||||++..+++++++.+.+.+|++|+||||+|||+|+.+ +.+++|||||+++|..+|++.+.+...+
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 4588999999999999888888888898889999999999999999986 8999999999999999999988765433
Q ss_pred cccceeeeceEEEeeCCCCccccccchHHHHHHhhcCCCCCCceEEEEEEEEEeCCccccCCCHHHHHHHHHhhcCCCCC
Q 002803 293 LVDRCILDGEMLVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKG 372 (879)
Q Consensus 293 ~~~~~ILDGEmv~~d~~~~~~~pF~~l~~~~~~~~~~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~v~~~~~ 372 (879)
..++||||||||+||..++++.||+.++...+..........+++|++|||||+||++++++||.+|+++|++++.+.++
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 36799999999999987777889988876432111111234789999999999999999999999999999999987776
Q ss_pred cceecccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHcCCceEEEecCC--CCCcCCCCCCCeEEEcccc
Q 002803 373 RLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLG--SKWEPGDRSGKWLKLKPEY 445 (879)
Q Consensus 373 ~~~i~~p~~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~~i~~g~EGlV~K~~~--s~Y~~g~Rs~~WlKvKp~y 445 (879)
+++++. ...+++.++++++|++++++|.||||+|+++ |+|.||+|+.+|+|+||+|
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=9.8e-44 Score=412.17 Aligned_cols=257 Identities=26% Similarity=0.394 Sum_probs=203.7
Q ss_pred ecCCCCCCCchhhhHHHHHhhccccceeeeceEEEeeCCCCccccccchHHHHHHhhcCCCCCCceEEEEEEEEEeCCcc
Q 002803 271 SRSFLDHSEYGHAMSKIIEQNVLVDRCILDGEMLVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTS 350 (879)
Q Consensus 271 SR~g~~~t~~~~~l~~~~~~~~~~~~~ILDGEmv~~d~~~~~~~pF~~l~~~~~~~~~~~~~~~~~~~~vFDiL~lng~~ 350 (879)
||||+++|..||++.+.+. .+...+||||||+|+||+. ++ .+|+.+|.+.+. ....+++|++|||||+||++
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-ADFAALQNALSA-----GASRPLTYYAFDLLFLSGED 72 (552)
T ss_pred CCCcCcchhhhHHHHHHHh-hCCCCCEEEEEEEEEECCC-CC-CCHHHHHHHHHh-----cccCceEEEEEeccccCCcc
Confidence 8999999999999988754 4556799999999999974 33 579888875432 13468999999999999999
Q ss_pred ccCCCHHHHHHHHHhhcCCCCCc-ceecccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHcCCceEEEecCCCCC
Q 002803 351 VIHQSLKERHELLQKVVKPSKGR-LETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKW 429 (879)
Q Consensus 351 l~~~pl~eRr~~L~~~v~~~~~~-~~i~~p~~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~~i~~g~EGlV~K~~~s~Y 429 (879)
++++||.+|+++|++++.+.... +.+. .+ ..++.+++|++++++|.||||+|+++|+|
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 12344589999999999999999999999
Q ss_pred cCCCCCCCeEEEccccccCCCcceEEEEEEEeCCCCCCCCcceEEEEEecCCCCCCCCceEEEEEEecCCCCHHHHHHHH
Q 002803 430 EPGDRSGKWLKLKPEYIRAGSDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVV 509 (879)
Q Consensus 430 ~~g~Rs~~WlKvKp~y~~~g~~lDlvVIG~~~G~Grr~g~~~sfl~g~~~~~~~~~~~~~~~~~~kVgtG~s~~~~~~l~ 509 (879)
++| ||.+|+|+|+.| +.|++|+| |++.+ |.+|+||||+++. ++|.++|+||||||++++++|.
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 67776555 54443 2399999999962 2789999999999999999999
Q ss_pred HhhccccccccCCCCCCCcceeecCCCCCCCcEEEeCCCceEEEEEeeeceecccCccCCCeeeeccEEEEEecCCCccC
Q 002803 510 TKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDKPWHD 589 (879)
Q Consensus 510 ~~l~~~~~~~~~~~~~pp~~~~~~~~~~~~Pdvwi~~P~~s~V~ev~a~~~~~~s~~~~~g~tLRfPR~~riR~DK~~~~ 589 (879)
++|+++++.. +|+. . .......|++|++ | .+|+||++. .++.|++||||||+++|.||+|+|
T Consensus 195 ~~l~~~~~~~-----~Pf~--~-~~~~~~~~~~Wv~-P--~lV~EV~~~-------e~T~~g~LR~Prf~~~R~DK~~~e 256 (552)
T TIGR02776 195 ARLKALGAKA-----SPFS--G-PAGAKTRGVHWVR-P--SLVAEVEYA-------GITRDGILREASFKGLREDKPAEE 256 (552)
T ss_pred HHHHhhcccC-----CCcc--C-CccccCCCcEEEc-c--CEEEEEEee-------eccCCCeeEccEEEEEeCCCCHHH
Confidence 9999987641 1111 1 1112346899999 7 489999863 234578999999999999999999
Q ss_pred CC
Q 002803 590 CL 591 (879)
Q Consensus 590 ~~ 591 (879)
|+
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=3.5e-43 Score=370.18 Aligned_cols=214 Identities=43% Similarity=0.711 Sum_probs=181.8
Q ss_pred cCCcccCCcccccceeeccChHHHHHHhCCCceEEEEecceEEEEEEEeCCEEEEEecCCCCCCCchhhhHHHH------
Q 002803 215 RQDIEVGKAVRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKII------ 288 (879)
Q Consensus 215 ~~~i~~~~~~~PmLA~~~~~~~~~~~~~~~~~~~iE~K~DGeR~qih~~g~~v~~~SR~g~~~t~~~~~l~~~~------ 288 (879)
..++++|.||+||||++.......+..+.+.+|++|+||||+|||+|++++.+++|||+|+++|..+|++.+..
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--hhccccceeeeceEEEeeCCCCccccccchHHHHHHhhcCCCCCCceEEEEEEEEEeCCccccCCCHHHHHHHHHhh
Q 002803 289 E--QNVLVDRCILDGEMLVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKV 366 (879)
Q Consensus 289 ~--~~~~~~~~ILDGEmv~~d~~~~~~~pF~~l~~~~~~~~~~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~ 366 (879)
. ......+||||||||+||+.++.+.||+.+++..... .......+++|+|||||++||++++++||.+|+++|+++
T Consensus 83 ~~~~~~~~~~~iLDGElv~~~~~~~~~~~f~~l~~~~~~~-~~~~~~~~~~~~vFDiL~~~g~~l~~~pl~eR~~~L~~~ 161 (225)
T cd07903 83 HLAFNPKVKSCILDGEMVVWDKETKRFLPFGTLKDVAKLR-EVEDSDLQPCFVVFDILYLNGKSLTNLPLHERKKLLEKI 161 (225)
T ss_pred hhhccccCcEEEeceEEEEEEcCcCeeccchHHHHHHhhc-ccccCCccEEEEEEEEEEECCeecccCcHHHHHHHHHHh
Confidence 0 1123679999999999998878889999987654321 111234679999999999999999999999999999999
Q ss_pred cCCCCCcceecccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHcCCceEEEecCCCCCcCCCCCCCeEEEccccc
Q 002803 367 VKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYI 446 (879)
Q Consensus 367 v~~~~~~~~i~~p~~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~~i~~g~EGlV~K~~~s~Y~~g~Rs~~WlKvKp~y~ 446 (879)
+.+.++++.++. ...+++.+++.++|++++++|.||||+|+++|+|++|+|+.+|+|+||+|+
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 988766665431 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=5.1e-42 Score=357.59 Aligned_cols=206 Identities=30% Similarity=0.485 Sum_probs=173.4
Q ss_pred CCcccCCcccccceeeccChHHHHHHhCCCceEEEEecceEEEEEEEeCCEEEEEecCCCCCCC-chhhhHHHHHhhcc-
Q 002803 216 QDIEVGKAVRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSE-YGHAMSKIIEQNVL- 293 (879)
Q Consensus 216 ~~i~~~~~~~PmLA~~~~~~~~~~~~~~~~~~~iE~K~DGeR~qih~~g~~v~~~SR~g~~~t~-~~~~l~~~~~~~~~- 293 (879)
.++++|.||+||||++....+++++++. .+|++|+||||+|||+|++|+.+++|||||+++|. .+|++.+.+.+.+.
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 4588999999999999887776666653 46999999999999999999999999999999995 56777765554443
Q ss_pred ccceeeeceEEEeeCCCCccccccchHHHHHHhhcCCCCCCceEEEEEEEEEeCCccccCCCHHHHHHHHHhhcCCCCCc
Q 002803 294 VDRCILDGEMLVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGR 373 (879)
Q Consensus 294 ~~~~ILDGEmv~~d~~~~~~~pF~~l~~~~~~~~~~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~v~~~~~~ 373 (879)
..+||||||||+||..++++++|+.++...+ .. ....+++|++||||++||.++++.||.+|+++|++++.+.+++
T Consensus 85 ~~~~iLDGEiv~~d~~~g~~~~F~~l~~~~~---~~-~~~~~v~~~vFDiL~l~g~~l~~~pl~eR~~~L~~~~~~~~~~ 160 (213)
T cd07902 85 GHSMILDSEVLLVDTKTGKPLPFGTLGIHKK---SA-FKDANVCLFVFDCLYYNGESLMDKPLRERRKILEDNMVEIPNR 160 (213)
T ss_pred ccceeeeeEEEEEECCCCcccccchhhhhhc---cc-cccCceEEEEEEEeeeCCcchhcCcHHHHHHHHHHhccCCCCe
Confidence 6799999999999987788889988764322 11 1235799999999999999999999999999999999876655
Q ss_pred ceecccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHcCCceEEEecCCCCCcCCCCCCCeEEEcccc
Q 002803 374 LETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEY 445 (879)
Q Consensus 374 ~~i~~p~~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~~i~~g~EGlV~K~~~s~Y~~g~Rs~~WlKvKp~y 445 (879)
+.+.. ...+.+.+++.++|++++++|.||||+|+++|+|.+|+| +|+|+||||
T Consensus 161 ~~~~~-----------------~~~~~~~~~l~~~~~~~~~~g~EGvV~K~~~s~Y~~G~r--~W~K~K~dY 213 (213)
T cd07902 161 IMLSE-----------------MKFVKKADDLSAMIARVIKEGLEGLVLKDLKSVYEPGKR--HWLKVKKDY 213 (213)
T ss_pred EEEEE-----------------EEEcCCHHHHHHHHHHHHHCCCCeEEEeCCCCCccCCCC--CceEeCCCC
Confidence 44321 234578899999999999999999999999999999987 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=1e-41 Score=354.21 Aligned_cols=204 Identities=32% Similarity=0.567 Sum_probs=171.4
Q ss_pred cCCcccccceeeccChHHHHHHhCCCceEEEEecceEEEEEEEeCCEEEEEecCCCCCCCchhhhHHHHHhhccccceee
Q 002803 220 VGKAVRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCIL 299 (879)
Q Consensus 220 ~~~~~~PmLA~~~~~~~~~~~~~~~~~~~iE~K~DGeR~qih~~g~~v~~~SR~g~~~t~~~~~l~~~~~~~~~~~~~IL 299 (879)
||.||+||||+....+++++++. +.+|++|+||||+|||+|++++.+++|||||+++|..+|++.+.+......++|||
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 68999999999988877766554 56899999999999999999999999999999999999999887644322379999
Q ss_pred eceEEEeeCCCCccccccchHHHHHHhhcCC---CCCCceEEEEEEEEEeCCccccCCCHHHHHHHHHhhcCCCCCccee
Q 002803 300 DGEMLVWDTSLNRFAEFGSNQEIAKAARDGL---SSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLET 376 (879)
Q Consensus 300 DGEmv~~d~~~~~~~pF~~l~~~~~~~~~~~---~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~v~~~~~~~~i 376 (879)
|||||+||+ .+++.+|+.++...++. ... ....+++|+|||||++||++++++||.+|+++|++++.+. +++.+
T Consensus 80 DGElv~~~~-~g~~~~F~~l~~r~~~~-~~~~~~~~~~~~~~~vFDil~~~g~~l~~~pl~eR~~~L~~~~~~~-~~i~~ 156 (207)
T cd07901 80 DGEAVAYDP-DGRPLPFQETLRRFRRK-YDVEEAAEEIPLTLFLFDILYLDGEDLLDLPLSERRKILEEIVPET-EAILL 156 (207)
T ss_pred eCEEEEECC-CCCccCHHHHHHHhccc-cchhhhhccCcEEEEEEEEEEECCcchhcCCHHHHHHHHHHhcCcC-CcEEE
Confidence 999999997 56778998877653221 111 1135799999999999999999999999999999999875 34433
Q ss_pred cccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHcCCceEEEecCCCCCcCCCCCCCeEEEccc
Q 002803 377 LVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPE 444 (879)
Q Consensus 377 ~~p~~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~~i~~g~EGlV~K~~~s~Y~~g~Rs~~WlKvKp~ 444 (879)
+. ...+++.+++.++|++++++|.||||+|+++|+|.+|+|+.+|+|+|||
T Consensus 157 ~~-----------------~~~~~~~~~~~~~~~~~~~~g~EGiv~K~~~s~Y~~g~Rs~~wlK~K~~ 207 (207)
T cd07901 157 AP-----------------RIVTDDPEEAEEFFEEALEAGHEGVMVKSLDSPYQAGRRGKNWLKVKPD 207 (207)
T ss_pred EE-----------------EEecCCHHHHHHHHHHHHHcCCceEEEeCCCCCcCCCCCCCCeEEecCC
Confidence 21 3346788999999999999999999999999999999999999999996
No 21
>PRK09125 DNA ligase; Provisional
Probab=100.00 E-value=2e-41 Score=365.64 Aligned_cols=254 Identities=24% Similarity=0.367 Sum_probs=193.3
Q ss_pred ccccceeeccChHHHHHHhCCCceEEEEecceEEEEEEEeCCEEEEEecCCCCCCCchhhhHHHHHhhccccceeeeceE
Q 002803 224 VRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDGEM 303 (879)
Q Consensus 224 ~~PmLA~~~~~~~~~~~~~~~~~~~iE~K~DGeR~qih~~g~~v~~~SR~g~~~t~~~~~l~~~~~~~~~~~~~ILDGEm 303 (879)
+.||||...... +.+.+|++|+||||+|||+ + .+++|||+|+++|. |.. +...+ +++|||||+
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 2346899999999999985 2 48999999999987 432 12222 489999999
Q ss_pred EEeeCCCCccccccchHHHHHHhhcCCCCCCceEEEEEEEEEeCCccccCCCHHHHHHHHHhhcCCCC-CcceecccCCC
Q 002803 304 LVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSK-GRLETLVPDHG 382 (879)
Q Consensus 304 v~~d~~~~~~~pF~~l~~~~~~~~~~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~v~~~~-~~~~i~~p~~~ 382 (879)
|+++ .+|+.++...++.........+++|++||+|++|| ||.+|+++|++++.+.+ +.++++
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 36866665433211111112579999999999986 99999999999997652 233221
Q ss_pred CCccccCCCCCccccccCCHHHHHHHHHHHHHcCCceEEEecCCCCCcCCCCCCCeEEEccccccCCCcceEEEEEEEeC
Q 002803 383 LNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLIIGGYYG 462 (879)
Q Consensus 383 ~~~~v~~~~~~~~~~~~~~~~ei~~~~~~~i~~g~EGlV~K~~~s~Y~~g~Rs~~WlKvKp~y~~~g~~lDlvVIG~~~G 462 (879)
....+++.++++++|++++++|.||||+|+++|+|++| |+.+|+|+|+++ +.|++|||+++|
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 889999999999
Q ss_pred CCCCCCCcceEEEEEecCCCCCCCCceEEEEEEecCCCCHHHHHHHHHhhccccccccCCCCCCCcceeecCCCCCCCcE
Q 002803 463 SGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDV 542 (879)
Q Consensus 463 ~Grr~g~~~sfl~g~~~~~~~~~~~~~~~~~~kVgtG~s~~~~~~l~~~l~~~~~~~~~~~~~pp~~~~~~~~~~~~Pdv 542 (879)
.|+++|.+|+|+|+..+ + ..| +||||||+++++. ||.+
T Consensus 216 ~Gk~~g~~gsllv~~~~--g-----~~~----~VgsG~t~~~r~~------------------~~~~------------- 253 (282)
T PRK09125 216 KGKFAGMLGALLVETPD--G-----REF----KIGSGFSDAEREN------------------PPKI------------- 253 (282)
T ss_pred CCcccCceeeEEEEeCC--C-----CEE----EeCCCCCHHHhcC------------------CCCC-------------
Confidence 99999999999999543 2 123 7999999998641 1211
Q ss_pred EEeCCCceEEEEEeeeceecccCccCCCeeeeccEEEEEecCC
Q 002803 543 WIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDK 585 (879)
Q Consensus 543 wi~~P~~s~V~ev~a~~~~~~s~~~~~g~tLRfPR~~riR~DK 585 (879)
..+++|++ ..++....||||+|+++|+|.
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 12556754 233456779999999999983
No 22
>PHA00454 ATP-dependent DNA ligase
Probab=100.00 E-value=3.8e-40 Score=362.40 Aligned_cols=284 Identities=20% Similarity=0.289 Sum_probs=208.2
Q ss_pred cccceeeccC--hHHHHHHhCCCceEEEEecceEEEEEEEeCC-EEEEEecCCCCCCCchhhhH------HHHHh---hc
Q 002803 225 RPQLAMRIGD--AHAAWRKLHGKEVVIECKFDGDRIQIHKNGS-EIHYFSRSFLDHSEYGHAMS------KIIEQ---NV 292 (879)
Q Consensus 225 ~PmLA~~~~~--~~~~~~~~~~~~~~iE~K~DGeR~qih~~g~-~v~~~SR~g~~~t~~~~~l~------~~~~~---~~ 292 (879)
+|++|..... +.+++.+++ .|++|.||||+|||+|++++ .+++|||||++|++.. ++. ..+.. +.
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 6888888765 777888763 89999999999999999876 4999999999887521 111 11111 12
Q ss_pred cccceeeeceEEEeeCCCCccccccchHHHHHHhhc--CCCCCCceEEEEEEEEEeC----Cccc---cCCCHHHHHHHH
Q 002803 293 LVDRCILDGEMLVWDTSLNRFAEFGSNQEIAKAARD--GLSSDRQLCYFAFDVLYVG----DTSV---IHQSLKERHELL 363 (879)
Q Consensus 293 ~~~~~ILDGEmv~~d~~~~~~~pF~~l~~~~~~~~~--~~~~~~~~~~~vFDiL~ln----g~~l---~~~pl~eRr~~L 363 (879)
.++++|||||+|+.+ .||..++...++... ......++.|+|||+|++| |+++ ...||.+|+++|
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 346899999999965 467555544332110 0112468999999999999 5554 689999999999
Q ss_pred HhhcCCCCC-cceecccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHcCCceEEEecCCCCCcCCCCCCCeEEEc
Q 002803 364 QKVVKPSKG-RLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLK 442 (879)
Q Consensus 364 ~~~v~~~~~-~~~i~~p~~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~~i~~g~EGlV~K~~~s~Y~~g~Rs~~WlKvK 442 (879)
+.++.+.+. .+.++ ....+.+.+++.++|++++++|.||||+|+++|+|++|+|+. |+|+|
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 998865442 12211 134567899999999999999999999999999999998874 88999
Q ss_pred cccccCCCcceEEEEEEEeCCCCC--CCCcceEEEEEecCCCCCCCCceEEEEEEecCCCCHHHHHHHHHhhcccccccc
Q 002803 443 PEYIRAGSDLDVLIIGGYYGSGRR--GGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYE 520 (879)
Q Consensus 443 p~y~~~g~~lDlvVIG~~~G~Grr--~g~~~sfl~g~~~~~~~~~~~~~~~~~~kVgtG~s~~~~~~l~~~l~~~~~~~~ 520 (879)
+.+ ++|++|+|+++|.|++ .|.+++|+|.+ +++ .+. .|||||++++++|.+++.++-+.
T Consensus 220 ~~~-----~~d~vIvG~~~g~g~~~~~g~~~~~~~~~--~~g------~l~----~gtGfs~~~~~~l~~~l~~~~~~-- 280 (315)
T PHA00454 220 PEC-----EADGTIVGVVWGTPGLANEGKVIGFRVLL--EDG------RVV----NATGISRALMEEFTANVKEHGED-- 280 (315)
T ss_pred ccC-----ceeEEEEEEEECCCCccCCceEEEEEEEe--CCC------cEE----EccCCCHHHHHHHHHHHHhhccC--
Confidence 985 9999999999998642 36677777754 221 443 28999999999999998875221
Q ss_pred CCCCCCCcceeecCCCCCCCcEEEeCCCceEEEEEeeeceecccCccCCCeeeeccEEEEEec
Q 002803 521 YPKRAPPSFYQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRY 583 (879)
Q Consensus 521 ~~~~~pp~~~~~~~~~~~~Pdvwi~~P~~s~V~ev~a~~~~~~s~~~~~g~tLRfPR~~riR~ 583 (879)
...| |....|+||++. .++.+.+||||+|+++|+
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 1001 222347788652 355677999999999996
No 23
>cd07898 Adenylation_DNA_ligase Adenylation domain of ATP-dependent DNA Ligases. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. Some organisms express a variety of different ligases which appear to be targeted to specific functions. ATP-dependent DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains including a DNA-binding domain, an adenylation (nucleotidyltransferase (NTase)) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The adenylation domain binds ATP and contains many of the active-site residues. The adenylation and C-terminal OB-f
Probab=100.00 E-value=2.4e-40 Score=342.55 Aligned_cols=199 Identities=33% Similarity=0.525 Sum_probs=167.4
Q ss_pred ccccceeeccChHHHHHHhCCCceEEEEecceEEEEEEEeCCEEEEEecCCCCCCCchhhhHHHHHhhccccceeeeceE
Q 002803 224 VRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDGEM 303 (879)
Q Consensus 224 ~~PmLA~~~~~~~~~~~~~~~~~~~iE~K~DGeR~qih~~g~~v~~~SR~g~~~t~~~~~l~~~~~~~~~~~~~ILDGEm 303 (879)
|+||||+++..++++ .++.+.+|++|+||||+|||+|++++++++|||+|+++|..+|++.+.+.. .+++|||||||
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 566788999999999999999999999999999999999988988776542 35899999999
Q ss_pred EEeeCCCCccccccchHHHHHHhhcC--CCCCCceEEEEEEEEEeCCccccCCCHHHHHHHHHhhcCCCCCcceecccCC
Q 002803 304 LVWDTSLNRFAEFGSNQEIAKAARDG--LSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDH 381 (879)
Q Consensus 304 v~~d~~~~~~~pF~~l~~~~~~~~~~--~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~v~~~~~~~~i~~p~~ 381 (879)
|+||..+. .||..++....+.... .....+++|+|||||++||++++++||.+|+++|++++.+.++++.++.
T Consensus 78 v~~~~~~~--~~f~~~~~~~~~~~~~~~~~~~~~~~~~vFDil~~~g~~l~~~p~~eR~~~L~~~~~~~~~~i~~~~--- 152 (201)
T cd07898 78 LAWDDNRG--LPFSELFKRLGRKFRDKFLDEDVPVVLMAFDLLYLNGESLLDRPLRERRQLLEELFVEIPGRIRIAP--- 152 (201)
T ss_pred EEEeCCCC--CcHHHHHHHhcccccchhhhccCcEEEEEEeEEeECCcchhhCCHHHHHHHHHHhhcCCCCcEEEee---
Confidence 99986432 5898776544322111 1234679999999999999999999999999999999988766665421
Q ss_pred CCCccccCCCCCccccccCCHHHHHHHHHHHHHcCCceEEEecCCCCCcCCCCCCCeEEEccc
Q 002803 382 GLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPE 444 (879)
Q Consensus 382 ~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~~i~~g~EGlV~K~~~s~Y~~g~Rs~~WlKvKp~ 444 (879)
...+++.+++.++|++++++|.||||+|+++|+|++|+|+.+|+|+|||
T Consensus 153 --------------~~~~~~~~~~~~~~~~~~~~g~EGim~K~~~s~Y~~g~Rs~~wlK~K~~ 201 (201)
T cd07898 153 --------------ALPVESAEELEAAFARARARGNEGLMLKDPDSPYEPGRRGLAWLKLKKE 201 (201)
T ss_pred --------------eEEcCCHHHHHHHHHHHHHcCCceEEEeCCCCCcCCCCcCCCcEEeCCC
Confidence 2346788899999999999999999999999999999999999999996
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=4e-40 Score=346.18 Aligned_cols=201 Identities=26% Similarity=0.404 Sum_probs=163.2
Q ss_pred cChHHHHHHhCCCceEEEEecceEEEEEEEe----CCEEEEEecCCCCCCCchhhhHHHHHhhc--------cccceeee
Q 002803 233 GDAHAAWRKLHGKEVVIECKFDGDRIQIHKN----GSEIHYFSRSFLDHSEYGHAMSKIIEQNV--------LVDRCILD 300 (879)
Q Consensus 233 ~~~~~~~~~~~~~~~~iE~K~DGeR~qih~~----g~~v~~~SR~g~~~t~~~~~l~~~~~~~~--------~~~~~ILD 300 (879)
.+++.+++.+.+..|++|+||||+|||+|+. |+.|++|||||+++|..+|++.+.+...+ .+++||||
T Consensus 10 ~~~~~~~~~~~~~~~~~E~K~DG~R~qih~~~~~~~~~v~lfSR~~~d~T~~~pel~~~~~~~~~~~~~~~~~~~~~ILD 89 (235)
T cd08039 10 RSIKHCCKMIGSRRMWVETKYDGEYCQIHIDLSKDSSPIRIFSKSGKDSTADRAGVHSIIRKALRIGKPGCKFSKNCILE 89 (235)
T ss_pred cCHHHHHHHhCCCcEEEEEeecceEEEEEEecccCCCEEEEEeCCCCcccccchhHHHHHHHHhhccccccCCCccEEEE
Confidence 3467788888999999999999999999997 88999999999999999999877654332 25789999
Q ss_pred ceEEEeeCCCCccccccchHHHHHHhhc--------CCCCCCceEEEEEEEEEeCCccccCCCHHHHHHHHHhhcCCCCC
Q 002803 301 GEMLVWDTSLNRFAEFGSNQEIAKAARD--------GLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKG 372 (879)
Q Consensus 301 GEmv~~d~~~~~~~pF~~l~~~~~~~~~--------~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~v~~~~~ 372 (879)
||||+||+.++++.||+.+|....+... ......++||++|||||+||+++++.||.+|+++|++++.+.++
T Consensus 90 GEiVv~d~~~g~~~~F~~L~~~~~~~~~~~~~~~~~~~~~~~~v~~~vFDlL~lnG~~l~~~pl~eRr~~L~~l~~~~~~ 169 (235)
T cd08039 90 GEMVVWSDRQGKIDPFHKIRKHVERSGSFIGTDNDSPPHEYEHLMIVFFDVLLLDDESLLSKPYSERRDLLESLVHVIPG 169 (235)
T ss_pred eEEEEEECCCCccCCHHHHHhhcccccchhccccccccccccceEEEEEEEEEECChhhhcCCHHHHHHHHHHhcccCCC
Confidence 9999999887888999988765321110 01123579999999999999999999999999999999988877
Q ss_pred cceecccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHcCCceEEEecCCCCCcCCCC-----CCCeEEEcccc
Q 002803 373 RLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDR-----SGKWLKLKPEY 445 (879)
Q Consensus 373 ~~~i~~p~~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~~i~~g~EGlV~K~~~s~Y~~g~R-----s~~WlKvKp~y 445 (879)
+++++... .+. .....+.++++++|++++++|+||||+|+++|+|.||++ +.+|+|+||||
T Consensus 170 ~~~~~~~~-----~i~-------~~~~~~~~~l~~~~~~a~~~g~EGIv~K~~~S~Y~pgr~~~~~r~~~WlKlK~dY 235 (235)
T cd08039 170 YAGLSERF-----PID-------FSRSSGYERLRQIFARAIAERWEGLVLKGDEEPYFDLFLEQGSFSGCWIKLKKDY 235 (235)
T ss_pred cEEEEEEE-----eec-------ccCCCCHHHHHHHHHHHHHcCCceEEEecCCCCcccCcccccccCCCeEEeCCCC
Confidence 66553210 110 111346789999999999999999999999999999743 58999999998
No 25
>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=2.7e-40 Score=343.12 Aligned_cols=200 Identities=25% Similarity=0.316 Sum_probs=166.2
Q ss_pred CcccccceeeccChHHHHHHhCCCceEEEEecceEEEEEEEeCCEEEEEecCCCCCCCchhhhHHHHHhhccccceeeec
Q 002803 222 KAVRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDG 301 (879)
Q Consensus 222 ~~~~PmLA~~~~~~~~~~~~~~~~~~~iE~K~DGeR~qih~~g~~v~~~SR~g~~~t~~~~~l~~~~~~~~~~~~~ILDG 301 (879)
.|+.||||+++....+.+ .....|++|+||||+|||+|++++.+++|||||+++|..+|++.+.+. . ++.+|||||
T Consensus 3 ~~~~pmLA~~~~~~~~~~--~~~~~~~~E~K~DG~R~~~~~~~~~v~l~SR~g~~~t~~~p~l~~~~~-~-l~~~~iLDG 78 (207)
T cd07897 3 RPYPFMLAHPLEDDPEDL--GDPSDWQAEWKWDGIRGQLIRRGGEVFLWSRGEELITGSFPELLAAAE-A-LPDGTVLDG 78 (207)
T ss_pred CCCCceeCCcCCCchhhh--cCcccEEEEEeEceEEEEEEEcCCEEEEEeCCCCcccccchHHHHHHH-h-CCCCeEEEe
Confidence 689999999998766543 345689999999999999999999999999999999998999887643 2 356899999
Q ss_pred eEEEeeCCCCccccccchHHHHHHhhcC--CCCCCceEEEEEEEEEeCCccccCCCHHHHHHHHHhhcCCCC-Ccceecc
Q 002803 302 EMLVWDTSLNRFAEFGSNQEIAKAARDG--LSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSK-GRLETLV 378 (879)
Q Consensus 302 Emv~~d~~~~~~~pF~~l~~~~~~~~~~--~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~v~~~~-~~~~i~~ 378 (879)
|||+||. +...||+.++....+.... .....+++|++|||||+||+++++.||.+|+++|++++.+.+ .++.+.
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 4568998887653321110 112457999999999999999999999999999999998763 344321
Q ss_pred cCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHcCCceEEEecCCCCCcCCCCCCCeEEEccc
Q 002803 379 PDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPE 444 (879)
Q Consensus 379 p~~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~~i~~g~EGlV~K~~~s~Y~~g~Rs~~WlKvKp~ 444 (879)
....+++.+++.++|++++++|.||||+|+++|+|++|+|+++|+|+|++
T Consensus 156 ----------------~~~~~~~~~~~~~~~~~~~~~g~EGiv~K~~~s~Y~~Grr~~~W~K~K~d 205 (207)
T cd07897 156 ----------------PLIAFADWEELAALRAQSRERGAEGLMLKRRDSPYLVGRKKGDWWKWKID 205 (207)
T ss_pred ----------------ceEecCCHHHHHHHHHHHHHcCCeEEEEeCCCCCcCCCCcCCCeeEeCCC
Confidence 13456789999999999999999999999999999999999999999997
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=2.6e-38 Score=327.62 Aligned_cols=199 Identities=31% Similarity=0.529 Sum_probs=166.1
Q ss_pred ccceeeccChHHHHHHhCCCceEEEEecceEEEEEEEeCCEEEEEecCCCCCCCchhhhHHHHHhhccc--cceeeeceE
Q 002803 226 PQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLV--DRCILDGEM 303 (879)
Q Consensus 226 PmLA~~~~~~~~~~~~~~~~~~~iE~K~DGeR~qih~~g~~v~~~SR~g~~~t~~~~~l~~~~~~~~~~--~~~ILDGEm 303 (879)
||||++...++++++++ +.+|++|+||||+|||+|+.++.+++|||+|+++|..+|++...+...+.. .+|||||||
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 678999999999999999999999999999999999888888776554433 479999999
Q ss_pred EEeeCCCCccccccchHHHHHHhhcCCC-CCCceEEEEEEEEEeCCccccCCCHHHHHHHHHhhcCCCCCcceecccCCC
Q 002803 304 LVWDTSLNRFAEFGSNQEIAKAARDGLS-SDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHG 382 (879)
Q Consensus 304 v~~d~~~~~~~pF~~l~~~~~~~~~~~~-~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~v~~~~~~~~i~~p~~~ 382 (879)
|+||+.++.+.||+.++....+...... ...+++|+|||||++||.++++.||.+|+++|++++.+...++.++.
T Consensus 80 v~~d~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~vFDil~l~~~~l~~~p~~eR~~~L~~~~~~~~~~i~~~~---- 155 (202)
T PF01068_consen 80 VVLDPNTGSPLPFQELSGRLNRRSKKIPEQSEPLQFVVFDILYLDGKDLLDLPYEERRELLEELLEPPPPRIRIVE---- 155 (202)
T ss_dssp EEBETTTSSBCCHHHHHHHHBHSSSCHHHHHSCEEEEEEEEEEETTEECTTSCHHHHHHHHHHHBG-BTSSEEEEE----
T ss_pred EEEecCCCcchhHHHHhhhhhhhcccchhccCcEEEEEEEEEEeCCeEeeeccHHHHHHHHHHhhccCCCceeEee----
Confidence 9999998889999776654421110000 13689999999999999999999999999999999965555554331
Q ss_pred CCccccCCCCCccccccCCHHHHHHHHHHHHHcCCceEEEecCCCCCcCCCCCCCeEEEc
Q 002803 383 LNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLK 442 (879)
Q Consensus 383 ~~~~v~~~~~~~~~~~~~~~~ei~~~~~~~i~~g~EGlV~K~~~s~Y~~g~Rs~~WlKvK 442 (879)
+..+++.+++++++++++++|.||+|+|+++|+|++|+|+.+|+|+|
T Consensus 156 -------------~~~~~~~~~~~~~~~~~~~~g~EG~v~K~~~~~Y~~Gkrs~~w~K~K 202 (202)
T PF01068_consen 156 -------------SYVVNSKEELEELFEEAIDQGFEGLVLKDPDSPYEPGKRSSGWLKVK 202 (202)
T ss_dssp -------------EEEESSHHHHHHHHHHHHHTTSSEEEEEETTSSC-TTEEEEEEEEEE
T ss_pred -------------eecCCCHHHHHHHHHHHHHcCCceEEEECCCCccCCCCcCCCcEEEC
Confidence 45578899999999999999999999999999999999999999998
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=4e-38 Score=323.89 Aligned_cols=190 Identities=26% Similarity=0.390 Sum_probs=156.9
Q ss_pred ccccceeeccChHHHHHHhCCCceEEEEecceEEEEEEEeCCEEEEEecCCCCCCCchhhhHHHHHhhccccceeeeceE
Q 002803 224 VRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDGEM 303 (879)
Q Consensus 224 ~~PmLA~~~~~~~~~~~~~~~~~~~iE~K~DGeR~qih~~g~~v~~~SR~g~~~t~~~~~l~~~~~~~~~~~~~ILDGEm 303 (879)
++||||+....++ .+.+|++|+||||+|||+|++|+.+++|||||+++|..+|++.+.+.. ..+.+|||||||
T Consensus 1 i~PmLa~~~~~~~------~~~~~~~E~K~DG~R~~~~~~~~~v~l~SR~g~~~t~~~p~~~~~~~~-~~~~~~iLDGEl 73 (194)
T cd07905 1 VEPMLARAVDALP------EPGGWQYEPKWDGFRCLAFRDGDEVRLQSRSGKPLTRYFPELVAAARA-LLPPGCVLDGEL 73 (194)
T ss_pred CCceeCCccCCCC------CCCceEEEeeeceEEEEEEEeCCEEEEEeCCCCchhhhhHHHHHHHHh-hCCCCEEEEeEE
Confidence 5899999987653 256899999999999999999999999999999999999999887643 346799999999
Q ss_pred EEeeCCCCccccccchHHHHHHhhcC---CCCCCceEEEEEEEEEeCCccccCCCHHHHHHHHHhhcCCCCCcceecccC
Q 002803 304 LVWDTSLNRFAEFGSNQEIAKAARDG---LSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPD 380 (879)
Q Consensus 304 v~~d~~~~~~~pF~~l~~~~~~~~~~---~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~v~~~~~~~~i~~p~ 380 (879)
|+||+.+ .||+.++......... .....+++|+|||||++||+++++.||.+|+++|++++.+...+++++.
T Consensus 74 v~~~~~~---~~F~~l~~r~~~~~~~~~~~~~~~~~~~~vFDiL~l~g~~l~~~pl~eRr~~L~~~~~~~~~~i~~~~-- 148 (194)
T cd07905 74 VVWRGGR---LDFDALQQRIHPAASRVRRLAEETPASFVAFDLLALGGRDLRGRPLRERRAALEALLAGWGPPLHLSP-- 148 (194)
T ss_pred EEEcCCC---CCHHHHHHHhcccccchhhhhccCCEEEEEEeeeeeCCcccccCCHHHHHHHHHHHhcccCCCeEECC--
Confidence 9998642 4998887654221111 1234689999999999999999999999999999999987655544321
Q ss_pred CCCCccccCCCCCccccccCCHHHHHHHHHHHHHcCCceEEEecCCCCCcCCCCCCCeEEEccc
Q 002803 381 HGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPE 444 (879)
Q Consensus 381 ~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~~i~~g~EGlV~K~~~s~Y~~g~Rs~~WlKvKp~ 444 (879)
...+.+++.++|++++++|.||||+|+++|+|++|+| +|+|+|+.
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 1346789999999999999999999999999999964 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=1.7e-37 Score=318.51 Aligned_cols=189 Identities=29% Similarity=0.456 Sum_probs=155.5
Q ss_pred ccccceeeccChHHHHHHhCCCceEEEEecceEEEEEEEeCCEEEEEecCCCCCCCchhhhHHHHHhhccccceeeeceE
Q 002803 224 VRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDGEM 303 (879)
Q Consensus 224 ~~PmLA~~~~~~~~~~~~~~~~~~~iE~K~DGeR~qih~~g~~v~~~SR~g~~~t~~~~~l~~~~~~~~~~~~~ILDGEm 303 (879)
++||||+++.... .+.+|++|+||||+|||+|++|+.+++|||+|+++|..+|++...+.+ +...++||||||
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 5899999987652 356899999999999999999999999999999999988988776543 346899999999
Q ss_pred EEeeCCCCccccccchHHHHHHhhcCCCCCCceEEEEEEEEEeCCccccCCCHHHHHHHHHhhcCCCCCcceecccCCCC
Q 002803 304 LVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGL 383 (879)
Q Consensus 304 v~~d~~~~~~~pF~~l~~~~~~~~~~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~v~~~~~~~~i~~p~~~~ 383 (879)
|+||..+. .+|+.++....+.. ......+++|+|||||++||+++.++||.+|+++|++++.+..+++.++.
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 99997542 58877665433211 12244689999999999999999999999999999999988755554321
Q ss_pred CccccCCCCCccccccCCHHHHHHHHHHHHHcCCceEEEecCCCCCcCCCCCCCeEEEcc
Q 002803 384 NSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKP 443 (879)
Q Consensus 384 ~~~v~~~~~~~~~~~~~~~~ei~~~~~~~i~~g~EGlV~K~~~s~Y~~g~Rs~~WlKvKp 443 (879)
+.. .+.+++|++++++|.||||+|+++|+|++|+|+.+|+|+|+
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 23378999999999999999999999999999999999996
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=100.00 E-value=1e-33 Score=273.08 Aligned_cols=137 Identities=26% Similarity=0.530 Sum_probs=118.8
Q ss_pred CCcceEEEEEEEeCCCCCCCCcceEEEEEecCCCCCCCCceEEEEEEecCCCCHHHHHHHHHhhccccccccCCCCCCCc
Q 002803 449 GSDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPS 528 (879)
Q Consensus 449 g~~lDlvVIG~~~G~Grr~g~~~sfl~g~~~~~~~~~~~~~~~~~~kVgtG~s~~~~~~l~~~l~~~~~~~~~~~~~pp~ 528 (879)
+|++||||||+|+|+|+++|.+|+||||++++++ ++|.++|+||||||++++++|.++|+++|+.. +...||.
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 5799999999999999999999999999998653 38999999999999999999999999999763 3335677
Q ss_pred ceeecCCCCCCCcEEEeCCCceEEEEEeeeceecccCccC-CCeeeeccEEEEEecCCCccCCCCHHH
Q 002803 529 FYQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFS-APYSLRFPRIDRVRYDKPWHDCLDVQS 595 (879)
Q Consensus 529 ~~~~~~~~~~~Pdvwi~~P~~s~V~ev~a~~~~~~s~~~~-~g~tLRfPR~~riR~DK~~~~~~t~~e 595 (879)
|+.+. ..++||+||.+|++|+|+||+++..+ .|+.|. +|+|||||||++||+||+|+||+|++|
T Consensus 75 ~~~~~--~~~~Pdv~~~~P~~s~V~EV~~aeit-~S~~~~a~G~tLRFPr~~~iR~DK~~~d~~t~~~ 139 (139)
T cd07967 75 WLKCN--KSLVPDFIVKDPKKAPVWEITGAEFS-KSEAHTADGISIRFPRVTRIRDDKDWKTATSLPE 139 (139)
T ss_pred eEeec--CCCCCCEEEeCCCccEEEEEEeeeEE-ecCcccccCEEEEccEEEEEeCCCCHHHCccccC
Confidence 87763 46799999977999999999964433 577777 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=8.4e-32 Score=272.57 Aligned_cols=173 Identities=20% Similarity=0.314 Sum_probs=135.3
Q ss_pred ccccceeeccChHHHHHHhCCCceEEEEecceEEEEEEEeCCEEEEEecCCCCCCCchhhhHHHHHhhccccceeeeceE
Q 002803 224 VRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDGEM 303 (879)
Q Consensus 224 ~~PmLA~~~~~~~~~~~~~~~~~~~iE~K~DGeR~qih~~g~~v~~~SR~g~~~t~~~~~l~~~~~~~~~~~~~ILDGEm 303 (879)
|+||||.+.....+ +.+|++|+||||+|||+|. + ++|||+|+++|.. +. +...+ .++||||||
T Consensus 1 ~~pmla~~~~~~~~------~~~~~~e~K~DG~R~~~~~--~--~~~SR~g~~~t~~-~~----~~~~l--~~~ilDGEl 63 (174)
T cd07896 1 PELLLAKTYDEGED------ISGYLVSEKLDGVRAYWDG--K--QLLSRSGKPIAAP-AW----FTAGL--PPFPLDGEL 63 (174)
T ss_pred CccccccccccCCC------hHHeeechhhceEEEEEec--c--EEEecCCcCCCCC-HH----HHhhC--CCCccCceE
Confidence 68999999875432 4589999999999999973 2 8999999999974 22 22222 349999999
Q ss_pred EEeeCCCCccccccchHHHHHHhhcCCCCCCceEEEEEEEEEeCCccccCCCHHHHHHHHHhhcCCC-CCcceecccCCC
Q 002803 304 LVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPS-KGRLETLVPDHG 382 (879)
Q Consensus 304 v~~d~~~~~~~pF~~l~~~~~~~~~~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~v~~~-~~~~~i~~p~~~ 382 (879)
|+|++ ||+.++...+..........+++|++||||+ ++.||.+|+++|+.++.+. .+.+.++.
T Consensus 64 v~~~~------~f~~l~~~~~~~~~~~~~~~~~~f~vFDil~------~~~p~~eR~~~L~~~i~~~~~~~~~~~~---- 127 (174)
T cd07896 64 WIGRG------QFEQTSSIVRSKKPDDEDWRKVKFMVFDLPS------AKGPFEERLERLKNLLEKIPNPHIKIVP---- 127 (174)
T ss_pred EcCCC------CHHHHHHHHhcCCCChhhcccceEEEEeCCC------CCCCHHHHHHHHHHHHHhCCCCcEEEEe----
Confidence 99864 8877665543321111124689999999999 6789999999999999765 23343321
Q ss_pred CCccccCCCCCccccccCCHHHHHHHHHHHHHcCCceEEEecCCCCCcCCCCCCCeEEEcc
Q 002803 383 LNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKP 443 (879)
Q Consensus 383 ~~~~v~~~~~~~~~~~~~~~~ei~~~~~~~i~~g~EGlV~K~~~s~Y~~g~Rs~~WlKvKp 443 (879)
...+.+.+++.+++++++++|+||+|+|+++|+|++| |+.+|+|+||
T Consensus 128 -------------~~~~~~~~~i~~~~~~~~~~g~EGlv~K~~ds~Y~~g-R~~~wlK~Kp 174 (174)
T cd07896 128 -------------QIPVKSNEALDQYLDEVVAAGGEGLMLRRPDAPYETG-RSDNLLKLKP 174 (174)
T ss_pred -------------eeeeCCHHHHHHHHHHHHhcCCCeEEEecCCCcccCC-cCCCceeeCC
Confidence 3456788999999999999999999999999999988 8899999998
No 31
>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=99.97 E-value=9e-31 Score=265.79 Aligned_cols=169 Identities=37% Similarity=0.660 Sum_probs=137.2
Q ss_pred CcHHHHHHHHHHHHhcCChhHHHHHHHHHHhhcCCC---ChHhhhHhhcCCCCCcCccccCCCHHHHHHHHHHHhCCCcC
Q 002803 7 TEVIVLVSLFNWIQKTKPAAKKRSKFRKFLDTYCDS---VDYFSALRLILPSLDRERGSYGLKESVLANCLIDALGMSKD 83 (879)
Q Consensus 7 ~~F~~l~~~~e~i~~~~~~~~k~~~l~~~~~~~~~~---~~~~p~lrLllP~~d~~r~~yglke~~L~k~~~~~~~~~~~ 83 (879)
|+|+.||++|++|++++++.+|+++|++||..|... .++||++|+++|+.| +| +|||+++.|++++++++|++++
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 799999999999999999999999999999999754 689999999999999 55 9999999999999999999998
Q ss_pred hHHHHHHhhhhcCCCCCCCCCHHHHHHHHHhhhcCC--CCCCCCHHHHHHHHHHHHhccC---hHHHHHHHHHHHHhCCH
Q 002803 84 SADAVRLINWRKGGAAPNAGNFPMVAAEVLQRRQGM--ISGGLTIKELNDLLDRLASSEN---RAEKISVLSTLIKKTNA 158 (879)
Q Consensus 84 s~~~~~L~~wk~~~~~~~~gD~~~~~~~v~~~r~~~--~~~~lTi~eVn~~Ld~La~~~~---~~~k~~~l~~ll~~~s~ 158 (879)
+.++ .|++ .||||.++++++++++.. .++++||.|||+.||+||..+| +..|..+|..++++|||
T Consensus 79 ~~~~----~~~~------~GD~g~~~~~~~~~~~~~~~~~~~lTi~~V~~~L~~la~~~g~~s~~~k~~~l~~ll~~~s~ 148 (177)
T PF04675_consen 79 SIDE----SYKK------VGDLGEVAEEVLQKRKSETSKPSPLTISEVNETLDELAAASGKGSQDEKIDILKELLRRCSP 148 (177)
T ss_dssp HHHH----HHHH------HS-HHHHHHHHHHHHTTTS--SS--BHHHHHHHHHHHHH--STTHHHHHHHHHHHHHTTS-H
T ss_pred HHHH----HHHh------cCcHHHHHHHHHhhccccccCCCCCCHHHHHHHHHHHHHhhCccchHHHHHHHHHHHHhCCH
Confidence 7776 4433 799999999999888743 3689999999999999999874 67889999999999999
Q ss_pred HHHHHHHHHHhhhhccCCcccccccccCc
Q 002803 159 QEMKWIIMIILKDLKLGISEKSIFHEFHP 187 (879)
Q Consensus 159 ~E~k~l~RiIlk~lriG~~e~til~~~hp 187 (879)
.|++||+|||+|+||||+++++|+++|||
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 32
>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=99.97 E-value=9.9e-30 Score=259.33 Aligned_cols=177 Identities=23% Similarity=0.333 Sum_probs=138.8
Q ss_pred ccceeeccChHHHHHHhCCCceEEEEecceEEEEEEEeCCEEEEEecCCCCCCCchhhhHHHHHhhccccceeeeceEEE
Q 002803 226 PQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDGEMLV 305 (879)
Q Consensus 226 PmLA~~~~~~~~~~~~~~~~~~~iE~K~DGeR~qih~~g~~v~~~SR~g~~~t~~~~~l~~~~~~~~~~~~~ILDGEmv~ 305 (879)
||||........ ..+.+.+|++|+|+||+|||+|+.++.+++|||+|+++|..++.+..... .....++|||||||+
T Consensus 2 ~~~~~~~~~~~~--~~~~~~~~~~e~K~DG~R~~~~~~~~~v~~~sR~g~~~~~~~~~~~~~~~-~~~~~~~ilDGElv~ 78 (182)
T cd06846 2 QLLNPILEEALS--EYDEQDEYYVQEKYDGKRALIVALNGGVFAISRTGLEVPLPSILIPGREL-LTLKPGFILDGELVV 78 (182)
T ss_pred CccchhhhHHHh--hccccCcEEEEEccCceEEEEEEcCCeEEEEeCCCCEEecccccccchHH-hccCCCeeEEEEEEe
Confidence 788887654422 24567889999999999999999999999999999999987776543111 123578999999999
Q ss_pred eeCCCCccccccchHHHHHHhhcCCCCCCceEEEEEEEEEeCCccccCCCHHHHHHHHHhhcCCCCC--cceecccCCCC
Q 002803 306 WDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKG--RLETLVPDHGL 383 (879)
Q Consensus 306 ~d~~~~~~~pF~~l~~~~~~~~~~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~v~~~~~--~~~i~~p~~~~ 383 (879)
|+... ...+++|++||||++||.+++++||.+|+++|++++.+.+. ++.+..
T Consensus 79 ~~~~~---------------------~~~~~~~~~FDil~~~~~~~~~~p~~eR~~~L~~~v~~~~~~~~~~i~~----- 132 (182)
T cd06846 79 ENREV---------------------ANPKPTYYAFDVVPLSGVGLRDLPYSDRFAYLKSLLKEFEGLDPVKLVP----- 132 (182)
T ss_pred ccCCC---------------------ccceeEEEEEEEEEECCCccccCCHHHHHHHHHHHhhhhccCCceeEEE-----
Confidence 87531 12468999999999999999999999999999999987542 222211
Q ss_pred CccccCCCCCccccccCCHHHHHHHHHHHHHcCCceEEEecCCCCC--cCCCCCCCeEEEcc
Q 002803 384 NSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKW--EPGDRSGKWLKLKP 443 (879)
Q Consensus 384 ~~~v~~~~~~~~~~~~~~~~ei~~~~~~~i~~g~EGlV~K~~~s~Y--~~g~Rs~~WlKvKp 443 (879)
+. ... ...+++.+++++++++|.||||+|+++|+| .+| |+..|+|+||
T Consensus 133 ---~~-------~~~-~~~~~~~~~~~~~~~~g~EGvi~K~~~s~Y~~~~g-r~~~wlK~Kp 182 (182)
T cd06846 133 ---LE-------NAP-SYDETLDDLLEKLKKKGKEGLVFKHPDAPYKGRPG-SSGNQLKLKP 182 (182)
T ss_pred ---ee-------ccc-ccchHHHHHHHHhhhcCCceEEEEcCCCCccccCC-CCCceEeecC
Confidence 00 111 123348999999999999999999999999 888 8999999998
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=99.96 E-value=3.2e-29 Score=243.67 Aligned_cols=139 Identities=53% Similarity=1.053 Sum_probs=114.8
Q ss_pred CCcceEEEEEEEeCCCCCCCCcceEEEEEecCCCC-CCCCceEEEEEEecCCCCHHHHHHHHHhhccccccccCCCCCCC
Q 002803 449 GSDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAP-DTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPP 527 (879)
Q Consensus 449 g~~lDlvVIG~~~G~Grr~g~~~sfl~g~~~~~~~-~~~~~~~~~~~kVgtG~s~~~~~~l~~~l~~~~~~~~~~~~~pp 527 (879)
+|++||||||||+|+|+++|.+++||||+++.++. ...+.+|+++|+||||||++++++|.++|+++|.. ++...||
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 47999999999999999999999999999976431 11234899999999999999999999999999876 2333355
Q ss_pred cceeecCCCCCCCcEEEeCCCceEEEEEeeeceecccCccCCCeeeeccEEEEEecCCCccCCCCH
Q 002803 528 SFYQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDKPWHDCLDV 593 (879)
Q Consensus 528 ~~~~~~~~~~~~Pdvwi~~P~~s~V~ev~a~~~~~~s~~~~~g~tLRfPR~~riR~DK~~~~~~t~ 593 (879)
.+ .......+|++||+ |.+|+|+||++... ..|+.|.+|++||||||+++|+||+|+||+|+
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 88899999996433 36888999999999999999999999999984
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=99.95 E-value=1.2e-27 Score=233.18 Aligned_cols=134 Identities=37% Similarity=0.590 Sum_probs=114.4
Q ss_pred CCcceEEEEEEEeCCCCCCCCcceEEEEEecCCCCCCCCceEEEEEEecCCCCHHHHHHHHHhhccccccccCCCCCCCc
Q 002803 449 GSDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPS 528 (879)
Q Consensus 449 g~~lDlvVIG~~~G~Grr~g~~~sfl~g~~~~~~~~~~~~~~~~~~kVgtG~s~~~~~~l~~~l~~~~~~~~~~~~~pp~ 528 (879)
+|++|++|||+++|+|++.|.+|+||||++++++ ++|.++|+||||||++++++|.++|.++|... +||.
T Consensus 1 ~~t~D~vViG~~~g~g~~~~~~~slllG~~~~~~-----~~l~~vgkvgtGft~~~~~~L~~~l~~~~~~~-----~p~~ 70 (144)
T cd07969 1 GDTLDLVPIGAYYGKGKRTGVYGAFLLACYDPET-----EEFQTVCKIGTGFSDEFLEELYESLKEHVIPK-----KPYR 70 (144)
T ss_pred CCceeEEEEEEEECCCCCCCCcceEEEEEEeCCC-----CEEEEEeEEccCCCHHHHHHHHHHhhhhcccc-----CCcc
Confidence 4799999999999999998999999999997653 38999999999999999999999999998641 2332
Q ss_pred ceeecCCCCCCCcEEEeCCCceEEEEEeeeceecccCccCC---------CeeeeccEEEEEecCCCccCCCCHHHHHHH
Q 002803 529 FYQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSA---------PYSLRFPRIDRVRYDKPWHDCLDVQSFVEL 599 (879)
Q Consensus 529 ~~~~~~~~~~~Pdvwi~~P~~s~V~ev~a~~~~~~s~~~~~---------g~tLRfPR~~riR~DK~~~~~~t~~e~~~l 599 (879)
+ . ...+|++||+ | .+|+||+++.. ..|+.|++ |++||||||+++|+||+|+||+++++|.+|
T Consensus 71 ~-~----~~~~~~vWv~-P--~lV~EV~~~e~-t~s~~~~~~~~~~~~~~g~~LRfPr~~~~R~Dk~~~~~~~~~~l~~l 141 (144)
T cd07969 71 V-D----SSLEPDVWFE-P--KEVWEVKAADL-TLSPVHTAAIGLVDEEKGISLRFPRFIRVRDDKKPEDATTSEQIAEM 141 (144)
T ss_pred c-c----ccCCCcEEEe-e--eEEEEEEEeEe-ecCcceeccccccccCCceEEEeeEEEEeeCCCChHHCCCHHHHHHH
Confidence 2 1 1258999999 7 58999996433 36788875 899999999999999999999999999999
Q ss_pred HH
Q 002803 600 VH 601 (879)
Q Consensus 600 ~~ 601 (879)
++
T Consensus 142 ~~ 143 (144)
T cd07969 142 YK 143 (144)
T ss_pred Hh
Confidence 85
No 35
>KOG4437 consensus ATP-dependent DNA ligase III [Replication, recombination and repair]
Probab=99.94 E-value=8.2e-26 Score=234.62 Aligned_cols=317 Identities=24% Similarity=0.338 Sum_probs=249.2
Q ss_pred cHHHHHHHHHHHHhcCChhHHHHHHHHHHhhcCCCChHhhhHhhcCCCCCcCccccCCCHHHHHHHHHHHhCCCcChHHH
Q 002803 8 EVIVLVSLFNWIQKTKPAAKKRSKFRKFLDTYCDSVDYFSALRLILPSLDRERGSYGLKESVLANCLIDALGMSKDSADA 87 (879)
Q Consensus 8 ~F~~l~~~~e~i~~~~~~~~k~~~l~~~~~~~~~~~~~~p~lrLllP~~d~~r~~yglke~~L~k~~~~~~~~~~~s~~~ 87 (879)
+|..|..+|.-|+..+....|+++|..++.+=--+.|+|..|++|+-+.|. |.|+|.++.|+++++++|.+...+.
T Consensus 156 ~F~ef~kiCS~L~~~p~~~~Kt~VI~~LL~kdNFDGDL~LWL~FLIRESD~--R~YNl~DkKLI~lfsKiLn~~~~~~-- 231 (482)
T KOG4437|consen 156 LFREFRKLCSMLADNPSYNTKTQVIQDLLRKDNFDGDLYLWLKFLIRESDK--RVYNLNDKKLIKLFSKILNCNPDDM-- 231 (482)
T ss_pred HHHHHHHHHHHHHhCcCccchhHHHHHHHhccCCCcchhhhhhhhhccccc--ccccccHHHHHHHHHHHHccChHHH--
Confidence 577888888888888888899999999997432358999999999999885 5999999999999999999986532
Q ss_pred HHHhhhhcCCCCCCCCCHHHHHHHHHhhhcCCCCCCCCHHHHHHHHHHHHhccChHHHHHHHHHHHHhCCHHHHHHHHHH
Q 002803 88 VRLINWRKGGAAPNAGNFPMVAAEVLQRRQGMISGGLTIKELNDLLDRLASSENRAEKISVLSTLIKKTNAQEMKWIIMI 167 (879)
Q Consensus 88 ~~L~~wk~~~~~~~~gD~~~~~~~v~~~r~~~~~~~lTi~eVn~~Ld~La~~~~~~~k~~~l~~ll~~~s~~E~k~l~Ri 167 (879)
+..|-. ...+.+..+...-.+...+.++-+||++|++.|.+|+..+..+++...|+....+|++.|++.|||+
T Consensus 232 --~~~Y~~-----~S~~~~i~i~~~~~K~~~~~K~~~siQ~~D~~L~rLSKi~~~D~~~~~L~~~A~R~~~~~L~~iIRL 304 (482)
T KOG4437|consen 232 --ARDYEQ-----GSVSETIRVFFEQSKSFPPAKSLLTIQEVDEFLLRLSKLTKEDEQQQALQDIASRCTANDLKCIIRL 304 (482)
T ss_pred --HHHHHh-----ccchhhhhhhHhhccCCCCcccceeHHHHHHHHHHHhcccchHHHHHHHHHHHHhcccchHHHHHHH
Confidence 223322 2345666565555555556789999999999999999999999999999999999999999999999
Q ss_pred HhhhhccCCcccccccccCcCHHHHHhhcCCHHHHHHHHhhhhhcc---------ccCCcccCCcccccceeeccChHHH
Q 002803 168 ILKDLKLGISEKSIFHEFHPDAEDLFNVTCDLKLVCEKLKDRNQRH---------KRQDIEVGKAVRPQLAMRIGDAHAA 238 (879)
Q Consensus 168 Ilk~lriG~~e~til~~~hpda~~~~~~~~dL~~V~~~L~~~~~~~---------~~~~i~~~~~~~PmLA~~~~~~~~~ 238 (879)
|-++|+...+.+.||++.||.|+++|. ++.|..|.+......... .......+.|++||||...++++-+
T Consensus 305 Ir~~L~~~s~A~~iL~~~~P~A~E~F~-S~~L~~ViEr~~~N~~~~~~~~~~~~~~s~~s~~~s~~Q~~~~~~~~~VE~s 383 (482)
T KOG4437|consen 305 IKHDLKMNSGAKHVLDALDPNAYEAFK-SRNLQDVVERVLHNAQEVEKEPGQRRALSVQASLMTPVQPMLAEACKSVEYA 383 (482)
T ss_pred HHHHhccCCChhHHHhccCCCcHHHHH-hcCHHHHHHHHHHhHHHHhhCccccccccchhhhcCCcChhhhhhhhhHHHH
Confidence 999999999999999999999999996 456777777654321111 1112346789999999998887766
Q ss_pred HHHhCCCceEEEEecceEEEEEEEeCCEEEEEecCCCCCCCchhhhHHHHHhhc-cccceeeeceEEEeeCCCCcccccc
Q 002803 239 WRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNV-LVDRCILDGEMLVWDTSLNRFAEFG 317 (879)
Q Consensus 239 ~~~~~~~~~~iE~K~DGeR~qih~~g~~v~~~SR~g~~~t~~~~~l~~~~~~~~-~~~~~ILDGEmv~~d~~~~~~~pF~ 317 (879)
.++..| ...-|.||||||.|+|.+|+.+.+|||--+...++ .+.+.+.+ ...+.++|||....+..+++++||+
T Consensus 384 ~~~~~~-~~~S~~~~D~E~~~~~~~~D~~S~~S~~~~~~s~F----K~~~P~~~~~G~~~~~~~~~~~I~~K~~~P~~~~ 458 (482)
T KOG4437|consen 384 MKKCPN-GMFSEIKYDGERVQVHKNGDHFSYFSRLPHKVAHF----KDYIPQAFPGGHSMILDSEVLLIDNKTGKPLPFG 458 (482)
T ss_pred hccCCC-CccccccCCCceeeccCCCcchhhhccChHhhhhh----hhcCchhcCCCccccccccccceecccCCCCCch
Confidence 666554 56789999999999999999999999966544332 11111222 2568999999999999999999999
Q ss_pred chHHHHHHhhcCCCCCCceEEEEEEEEE
Q 002803 318 SNQEIAKAARDGLSSDRQLCYFAFDVLY 345 (879)
Q Consensus 318 ~l~~~~~~~~~~~~~~~~~~~~vFDiL~ 345 (879)
++....+..+. +...|..+||+.|
T Consensus 459 ~~~~~~K~~~~----~~~~~~~~~~~~~ 482 (482)
T KOG4437|consen 459 TLGVHKKAAFQ----DANVCLFVFDCIY 482 (482)
T ss_pred hcchhhHHHhc----CcchheeecccCC
Confidence 88765555432 3567899999865
No 36
>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=99.94 E-value=2.3e-26 Score=240.66 Aligned_cols=175 Identities=21% Similarity=0.297 Sum_probs=130.4
Q ss_pred HHHhCCCceEEEEecceEEEEEEEeC-CEEEEEecCCCCCCCchhhhHHHHHhhccccceeeeceEEEeeCCCCcccccc
Q 002803 239 WRKLHGKEVVIECKFDGDRIQIHKNG-SEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDGEMLVWDTSLNRFAEFG 317 (879)
Q Consensus 239 ~~~~~~~~~~iE~K~DGeR~qih~~g-~~v~~~SR~g~~~t~~~~~l~~~~~~~~~~~~~ILDGEmv~~d~~~~~~~pF~ 317 (879)
+..+...+|++|+|+||+|+|+|+.+ +.+.++||+++.++..+|.+.+.........++|||||||+++...
T Consensus 35 ~~~~~~~~y~ve~K~DG~R~~l~~~~~~~v~l~sR~~~~~~~~~~~~~~~~~~~~~~~~~ilDGElv~~~~~~------- 107 (215)
T cd07895 35 LELLKQNDYFVCEKSDGVRYLLLITGRGEVYLIDRKNDVFKVPGLFFPRRKNLEPHHQGTLLDGELVIDKVPG------- 107 (215)
T ss_pred HHHHhhCCeEEEEeEcCeEEEEEEecCCcEEEEeCCCCeEEeccccCCCcccccccccCeeeEEEEEEEcCCC-------
Confidence 34456678999999999999999998 9999999999998876666532111112357899999999987531
Q ss_pred chHHHHHHhhcCCCCCCceEEEEEEEEEeCCccccCCCHHHHHHHHHhhcCCCCCc-cee-cccCCCCCccccCCCCCcc
Q 002803 318 SNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGR-LET-LVPDHGLNSHVRPQGEPCW 395 (879)
Q Consensus 318 ~l~~~~~~~~~~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~v~~~~~~-~~i-~~p~~~~~~~v~~~~~~~~ 395 (879)
..+++|+|||||++||+++.+.||.+|+++|++++...... +.. ..........|+.
T Consensus 108 ---------------~~~~~~~vFDiL~~~g~~l~~~pl~~R~~~L~~~i~~~~~~~~~~~~~~~~~~~~~i~~------ 166 (215)
T cd07895 108 ---------------KKRPRYLIFDILAFNGQSVTEKPLSERLKYIKKEVIEPRNELLKKGPIDKAKEPFSVRL------ 166 (215)
T ss_pred ---------------ceEEEEEEEEEEEECCcCccCCCHHHHHHHHHHhchhHHHHhhhcChhhcCCCCeEEEe------
Confidence 24689999999999999999999999999999998653211 000 0000000111110
Q ss_pred ccccCCHHHHHHHHHHH---HHcCCceEEEecCCCCCcCCCCCCCeEEEcc
Q 002803 396 SLVAHNVDEVEKFFKET---IENRDEGIVLKDLGSKWEPGDRSGKWLKLKP 443 (879)
Q Consensus 396 ~~~~~~~~ei~~~~~~~---i~~g~EGlV~K~~~s~Y~~g~Rs~~WlKvKp 443 (879)
......++++.+++.+ +.+|.||||+|+.+++|.+| |+.+|+|+||
T Consensus 167 -k~~~~~~~~~~~~~~~~~~~~~~~EGlIfk~~~~~Y~~G-r~~~~lKwKp 215 (215)
T cd07895 167 -KDFFPLYKIEKLFEKIIPKLPHENDGLIFTPNDEPYVPG-TDKNLLKWKP 215 (215)
T ss_pred -cceEeHHhHHHHHHhccccCCCCCCCEEEccCCCCccCc-cCCcceeeCC
Confidence 1122456888888888 59999999999999999999 9999999998
No 37
>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=99.94 E-value=4e-26 Score=216.85 Aligned_cols=121 Identities=30% Similarity=0.566 Sum_probs=106.2
Q ss_pred CcceEEEEEEEeCCCCCCCCcceEEEEEecCCCCCCCCceEEEEEEecCCCCHHHHHHHHHhhccccccccCCCCCCCcc
Q 002803 450 SDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSF 529 (879)
Q Consensus 450 ~~lDlvVIG~~~G~Grr~g~~~sfl~g~~~~~~~~~~~~~~~~~~kVgtG~s~~~~~~l~~~l~~~~~~~~~~~~~pp~~ 529 (879)
|++|+||+|+++|.|+++|.+|+||||++++++ +.|+++|+||+|||++++++|.++|++++..
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 3899999999999999999999999887643
Q ss_pred eeecCCCCCCCcEEEeCCCceEEEEEeeeceecccCccCCCeeeeccEEEEEecCCCccCCCCHHHHH
Q 002803 530 YQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDKPWHDCLDVQSFV 597 (879)
Q Consensus 530 ~~~~~~~~~~Pdvwi~~P~~s~V~ev~a~~~~~~s~~~~~g~tLRfPR~~riR~DK~~~~~~t~~e~~ 597 (879)
..+|++||+ | ++|+||++.. ...|+.|++|++||||||+++|+||+|+||+|++||.
T Consensus 65 -------~~~~~~wv~-P--~lV~eV~~~e-~t~s~~~~~g~~LR~Prf~~~R~Dk~~~~~~t~~~~~ 121 (122)
T cd07972 65 -------KFGPVVSVK-P--ELVFEVAFEE-IQRSPRYKSGYALRFPRIVRIRDDKDPDEADTLERVE 121 (122)
T ss_pred -------ccCCcEEEe-c--eEEEEEEeeE-EEecCccccCceEEccEEeEEeCCCChHHCcCHHHHh
Confidence 125789999 7 4899999643 2368889999999999999999999999999999985
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=99.93 E-value=3.4e-25 Score=212.38 Aligned_cols=122 Identities=42% Similarity=0.787 Sum_probs=103.7
Q ss_pred CcceEEEEEEEeCCCCCCCCcceEEEEEecCCCCCCCCceEEEEEEecCCCCHHHHHHHHHhhccccccccCCCCCCCcc
Q 002803 450 SDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSF 529 (879)
Q Consensus 450 ~~lDlvVIG~~~G~Grr~g~~~sfl~g~~~~~~~~~~~~~~~~~~kVgtG~s~~~~~~l~~~l~~~~~~~~~~~~~pp~~ 529 (879)
|++|+||+|+++|.|+++|.+|+||||++++++ ++|+++|+||||||++++++|.++|.++|... .|| +
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 589999999999999999999999999997543 38999999999999999999999999998641 233 2
Q ss_pred eeecCCCCCCCcEEEeCCCceEEEEEeeeceecccCccCC-------CeeeeccEEEEEecCCCccCC
Q 002803 530 YQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSA-------PYSLRFPRIDRVRYDKPWHDC 590 (879)
Q Consensus 530 ~~~~~~~~~~Pdvwi~~P~~s~V~ev~a~~~~~~s~~~~~-------g~tLRfPR~~riR~DK~~~~~ 590 (879)
. ....+|++||+ | ++|+||+++.. ..|+.|++ |++||||||+++|+||+|+||
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 79999996432 35788888 999999999999999999997
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=99.81 E-value=2.9e-19 Score=168.30 Aligned_cols=114 Identities=25% Similarity=0.413 Sum_probs=90.0
Q ss_pred cceEEEEEEEeCCCCCCCCcceEEEEEecCCCCCCCCceEEEEEEecCCCCHHHHHHHHHhhccccccccCCCCCCCcce
Q 002803 451 DLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFY 530 (879)
Q Consensus 451 ~lDlvVIG~~~G~Grr~g~~~sfl~g~~~~~~~~~~~~~~~~~~kVgtG~s~~~~~~l~~~l~~~~~~~~~~~~~pp~~~ 530 (879)
+.|++|+|++.+.| +.|.+|+||||++++. .|+++|+||||||++++++|.++|++++.. .||...
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 56888777777777 7788999999998753 789999999999999999999999988643 123211
Q ss_pred eecCCCCCCCcEEEeCCCceEEEEEeeeceecccCccCCCeeeeccEEEEEecCCCccCC
Q 002803 531 QVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDKPWHDC 590 (879)
Q Consensus 531 ~~~~~~~~~Pdvwi~~P~~s~V~ev~a~~~~~~s~~~~~g~tLRfPR~~riR~DK~~~~~ 590 (879)
. ......|++|++ | .+|+||++.. ++.+.+||||+|+++|+||+|++|
T Consensus 68 ~--~~~~~~~~~wv~-P--~lv~eV~~~~-------~t~~~~LR~P~f~~~R~Dk~~~~~ 115 (115)
T cd07971 68 P--PPADARGAVWVK-P--ELVAEVEFAE-------WTPDGRLRHPVFKGLREDKPAAEV 115 (115)
T ss_pred c--ccccCCCCEEec-C--CEEEEEEEEE-------ecCCCcEECCeeeEeeCCCCcccC
Confidence 1 113457899999 7 4899998632 234669999999999999999987
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=99.77 E-value=2.1e-18 Score=157.54 Aligned_cols=97 Identities=42% Similarity=0.730 Sum_probs=73.0
Q ss_pred CCCCcceEEEEEecCCCCCCCCceEEEEEEecCCCCHHHHHHHHHhhccccccccCCCCCCCcceeecCCCCCCCcEEEe
Q 002803 466 RGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDVWIE 545 (879)
Q Consensus 466 r~g~~~sfl~g~~~~~~~~~~~~~~~~~~kVgtG~s~~~~~~l~~~l~~~~~~~~~~~~~pp~~~~~~~~~~~~Pdvwi~ 545 (879)
|+|.+|+||||+++++. ++|.++|+||||||++++++|.++|.++|... ||...... ...+|++||+
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 23222221 2268999998
Q ss_pred CCCceEEEEEeeeceecccCccCCCeeeeccEEEEEecCC
Q 002803 546 SPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDK 585 (879)
Q Consensus 546 ~P~~s~V~ev~a~~~~~~s~~~~~g~tLRfPR~~riR~DK 585 (879)
|.. |+||+++..+ .+ | +||||||+++|+||
T Consensus 68 -P~~--V~eV~~~e~t-~~-----G-~lR~P~~~~~R~DK 97 (97)
T PF04679_consen 68 -PEL--VVEVKFAEIT-PS-----G-SLRFPRFKRIREDK 97 (97)
T ss_dssp -ST---EEEEEESEEE-EE-----S-EEESEEEEEEETTS
T ss_pred -CCE--EEEEEEEEEc-CC-----C-eEECCEEeEEeCCC
Confidence 864 9999874322 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=99.77 E-value=3.8e-18 Score=158.89 Aligned_cols=108 Identities=22% Similarity=0.310 Sum_probs=87.0
Q ss_pred CcceEEEEEEEeCCCCCCCCcceEEEEEecCCCCCCCCceEEEEEEecCCCCHHHHHHHHHhhccccccccCCCCCCCcc
Q 002803 450 SDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSF 529 (879)
Q Consensus 450 ~~lDlvVIG~~~G~Grr~g~~~sfl~g~~~~~~~~~~~~~~~~~~kVgtG~s~~~~~~l~~~l~~~~~~~~~~~~~pp~~ 529 (879)
+++|++|+|+++|.|+++|.+|+||||+++++ .+.++|+||||||++++++|.+++++++.. .. |+.+
T Consensus 1 ~~~d~vV~G~~~~~g~~~~~~gslllg~~~~~-------~~~~vg~vgtGf~~~~~~~l~~~l~~~~~~----~~-~~~~ 68 (108)
T cd08040 1 KTAEAVIIGMRAGFGNRSDVMGSLLLGYYGED-------GLQAVFSVGTGFSADERRDLWQNLEPLVTS----FD-DHPV 68 (108)
T ss_pred CceeEEEEEeEeCCCCCCCceEEEEEEEECCC-------ceEEEEEEcCCCCHHHHHHHHHhcchhccC----CC-CCcc
Confidence 47899999999999999999999999998753 367999999999999999999999988754 21 2222
Q ss_pred eeecCCCCCCCcEEEeCCCceEEEEEeeeceecccCccCCCeeeeccEEEEEe
Q 002803 530 YQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVR 582 (879)
Q Consensus 530 ~~~~~~~~~~Pdvwi~~P~~s~V~ev~a~~~~~~s~~~~~g~tLRfPR~~riR 582 (879)
. .....+|++|++ | ++|+||++.. ++.+.+||||||+++|
T Consensus 69 ~---~~~~~~~~vwv~-P--~lv~eV~~~~-------~t~~~~lR~P~f~~~R 108 (108)
T cd08040 69 W---NVGKDLSFVPLY-P--GKVVEVKYFE-------MGSKDCLRFPVFIGIR 108 (108)
T ss_pred c---ccccCCCCEEee-c--eEEEEEEeEE-------eeCCCeEECCeEEEeC
Confidence 1 123457999999 7 5899998632 3358999999999997
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=99.68 E-value=2.4e-16 Score=174.15 Aligned_cols=163 Identities=20% Similarity=0.252 Sum_probs=118.6
Q ss_pred CceEEEEecceEEEEEEEeCCEEEEEecCCCCC---CCchhhhHHHHHhhccccceeeeceEEEeeCCCCccccccchHH
Q 002803 245 KEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDH---SEYGHAMSKIIEQNVLVDRCILDGEMLVWDTSLNRFAEFGSNQE 321 (879)
Q Consensus 245 ~~~~iE~K~DGeR~qih~~g~~v~~~SR~g~~~---t~~~~~l~~~~~~~~~~~~~ILDGEmv~~d~~~~~~~pF~~l~~ 321 (879)
.+|++|+|+||.|+++|+.++++..|||+|... |+..|.+...-.. ...++++||||+++.+. ||- +
T Consensus 48 ~~~~vEEKlDG~nvri~~~~G~v~a~TR~G~i~e~~T~~~~eiv~~~~~-~~~p~~iLdGElvg~~~------p~v--~- 117 (342)
T cd07894 48 GPVAVEEKMNGYNVRIVRIGGKVLAFTRGGFICPFTTDRLRDLIDPEFF-DDHPDLVLCGEVVGPEN------PYV--P- 117 (342)
T ss_pred CCEEEEEeECCcEEEEEEECCEEEEEeCCCccCccchhhHhhhchHHhh-ccCCCEEEEEEEEecCC------ccc--c-
Confidence 589999999999999999999999999998644 5666766321110 11367999999998652 220 0
Q ss_pred HHHHhhcCCCCCCceEEEEEEEEEeCCccccCCCHHHHHHHHHhhcCCCCCcceecccCCCCCccccCCCCCccccccCC
Q 002803 322 IAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHN 401 (879)
Q Consensus 322 ~~~~~~~~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~v~~~~~~~~i~~p~~~~~~~v~~~~~~~~~~~~~~ 401 (879)
.......++.|++|||++.|+ ...+|+.+|+++|+++..+....+. .....+
T Consensus 118 ------~~~~~~~~v~F~vFDI~~~~~--~~~lp~~eR~~lLe~lg~~~v~~~~--------------------~~~~~d 169 (342)
T cd07894 118 ------GSYPEVEDVGFFVFDIRKKNT--GRPLPVEERRELLEKYGLPTVRLFG--------------------EFTADE 169 (342)
T ss_pred ------ccCccccccEEEEEeeEEcCC--CCCCCHHHHHHHHHhcCCCCcceEE--------------------EEecCC
Confidence 001112578999999999885 5579999999999997433211110 223456
Q ss_pred HHHHHHHHHHHHHcCCceEEEecCCC-----CCcCCCCCCCeEEEcccc
Q 002803 402 VDEVEKFFKETIENRDEGIVLKDLGS-----KWEPGDRSGKWLKLKPEY 445 (879)
Q Consensus 402 ~~ei~~~~~~~i~~g~EGlV~K~~~s-----~Y~~g~Rs~~WlKvKp~y 445 (879)
.+++.++++.+.++|.||||+|++++ .|.....+-+++++.-.|
T Consensus 170 ~~~l~~~l~~~~~~G~EGVVlK~~~~~~~~~Ky~t~~~~~~di~~~~~~ 218 (342)
T cd07894 170 IEELKEIIRELDKEGREGVVLKDPDMRVPPLKYTTSYSNCSDIRYAFRY 218 (342)
T ss_pred HHHHHHHHHHHHHCCCceEEEeccccccCcceeecCCCCcHHHHHHhhh
Confidence 89999999999999999999999998 677665556666666655
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=140.09 Aligned_cols=120 Identities=22% Similarity=0.263 Sum_probs=85.8
Q ss_pred CcceEEEEEEEeCCCCCCCCcceEEEEEecCCCCCCCCceEEEEEEecCCCCHHHHHHHHHhhccccccccCCCCCCCcc
Q 002803 450 SDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSF 529 (879)
Q Consensus 450 ~~lDlvVIG~~~G~Grr~g~~~sfl~g~~~~~~~~~~~~~~~~~~kVgtG~s~~~~~~l~~~l~~~~~~~~~~~~~pp~~ 529 (879)
++.|++|+|+.++. +.+||+|||++++++ .|.++|+| ||||++++++|.++|+++-....++ ..++.+
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 46898888877665 459999999996532 78999999 8999999999999998875431111 111212
Q ss_pred eeecCCCCCCCcEEEeCCCceEEEEEeeeceecccCccCCCeeeecc-EEEEEecCCCccCCC
Q 002803 530 YQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFP-RIDRVRYDKPWHDCL 591 (879)
Q Consensus 530 ~~~~~~~~~~Pdvwi~~P~~s~V~ev~a~~~~~~s~~~~~g~tLRfP-R~~riR~DK~~~~~~ 591 (879)
..........+.+|++ |. +|+||++. .++.+..|||| +|+++|+||++.||.
T Consensus 69 ~~~~~~~~~~~~~wv~-P~--lV~eV~~~-------e~t~~G~LRhP~~f~glR~Dk~~~~v~ 121 (122)
T cd07970 69 PSRWGTRKSLEWVPVR-PE--LVVEVSAD-------TAEGGGRFRHPLRFLRWRPDKSPEDCT 121 (122)
T ss_pred ccccCcccCCCeEEee-cc--EEEEEEee-------EEecCCceeCCceeEEEcCCCCHHHCc
Confidence 1111112245789999 74 78899753 23334589999 899999999999986
No 44
>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=99.29 E-value=6.2e-13 Score=136.90 Aligned_cols=174 Identities=18% Similarity=0.270 Sum_probs=106.6
Q ss_pred HHhCCCceEEEEecceEEEEEEEeCCEEEEEecCCCCCCC---chhhhHHHHHhhccccceeeeceEEEeeCCCCccccc
Q 002803 240 RKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSE---YGHAMSKIIEQNVLVDRCILDGEMLVWDTSLNRFAEF 316 (879)
Q Consensus 240 ~~~~~~~~~iE~K~DGeR~qih~~g~~v~~~SR~g~~~t~---~~~~l~~~~~~~~~~~~~ILDGEmv~~d~~~~~~~pF 316 (879)
..+...+|+|.+|-||.|+++...++.+.++.|+..-+-- .+|.-.+.. ..-...+.+||||||. |...
T Consensus 11 ~~l~~~~Y~V~eKaDG~Ryll~i~~~~~ylidr~~~~~~v~~~~~p~~~~~~-~~~~~~~TLLDGElV~-d~~~------ 82 (192)
T PF01331_consen 11 QLLQQKDYFVCEKADGTRYLLLITDNGVYLIDRKNNVFKVDNLHFPSKKDSS-DGRHHQDTLLDGELVL-DKDP------ 82 (192)
T ss_dssp HHHHHS-EEEEEEESSEEEEEEEEEEEEEEEETTS-EEEESSST-ECTTC---TTCEGCSEEEEEEEEE-EECT------
T ss_pred HHHhhCCcEEEECCCCcEEEEEEecceEEEEeCCCcEEEecCcccccccccc-cccccCCEEEEEEEEc-ccCC------
Confidence 3444568999999999999999988899999998765431 223211100 0123568999999987 3211
Q ss_pred cchHHHHHHhhcCCCCCCceEEEEEEEEEeCCccccCCCHHHHHHHHHhhcCCCCCcceeccc----CCCCCccccCCCC
Q 002803 317 GSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVP----DHGLNSHVRPQGE 392 (879)
Q Consensus 317 ~~l~~~~~~~~~~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~v~~~~~~~~i~~p----~~~~~~~v~~~~~ 392 (879)
....++|++||+|++||+++++.|+.+|...|++.+........ +.+ ....++.++..
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 12457899999999999999999999999999775432111100 000 00011122110
Q ss_pred CccccccCCHHH-HHHHHHHHHHcCCceEEEecCCCCCcCCCCCCCeEEEc
Q 002803 393 PCWSLVAHNVDE-VEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLK 442 (879)
Q Consensus 393 ~~~~~~~~~~~e-i~~~~~~~i~~g~EGlV~K~~~s~Y~~g~Rs~~WlKvK 442 (879)
. .......+. +...+..-+.+...|||+-..+.+|.+| +..+++|||
T Consensus 145 ~--~~~~~~~~~~~~~~~~~~l~h~~DGLIFtp~~~pY~~G-t~~~llKWK 192 (192)
T PF01331_consen 145 D--FFPIYQIEKLLFEEFIPKLPHETDGLIFTPVNTPYVPG-TCPNLLKWK 192 (192)
T ss_dssp ----EEGGGHHHHCHHCCCCCTTSTEEEEEEEESSSB--SE-EEEEEEEE-
T ss_pred c--cHHHHhhHHHHHHHhhccCCCCCCEEEEecCCCCccCC-CCCccEeeC
Confidence 0 111122222 1222333456889999999999999999 678999998
No 45
>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=99.22 E-value=1.9e-11 Score=106.23 Aligned_cols=74 Identities=24% Similarity=0.501 Sum_probs=66.7
Q ss_pred CCCcccCeEEEEEcCCCCCCHHHHHHHHHHcCCEEeeccCCCeeEEEEecC--CchhhhhhccCC-CeeeechHHHhh
Q 002803 653 ETSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADN--KGLKYEAAKRRG-DVIHYSWVLDCC 727 (879)
Q Consensus 653 ~s~iF~g~~F~vl~~~~~~~k~eLe~lI~~~GG~~v~n~~~~~T~~I~~~~--~~~k~~~~~~~~-~IV~p~Wl~dCi 727 (879)
++++|+|+.||+ ++....++++|+++|++|||++....++.+||+|+... .+.|+..+...+ .||+|+||.|||
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 367999999998 77788999999999999999999998888999998765 778888888888 999999999997
No 46
>COG5226 CEG1 mRNA capping enzyme, guanylyltransferase (alpha) subunit [RNA processing and modification]
Probab=99.13 E-value=1e-10 Score=122.01 Aligned_cols=184 Identities=21% Similarity=0.305 Sum_probs=121.2
Q ss_pred HhCCCceEEEEecceEEEEEEEe-----C-CEEEEEecCCCCCC---CchhhhHHHHHhhccccceeeeceEEEeeCCCC
Q 002803 241 KLHGKEVVIECKFDGDRIQIHKN-----G-SEIHYFSRSFLDHS---EYGHAMSKIIEQNVLVDRCILDGEMLVWDTSLN 311 (879)
Q Consensus 241 ~~~~~~~~iE~K~DGeR~qih~~-----g-~~v~~~SR~g~~~t---~~~~~l~~~~~~~~~~~~~ILDGEmv~~d~~~~ 311 (879)
.+....|++.+|-||.||++.+. | -+..+|.|..+-|. ..+|.+...........+..||||+|. |
T Consensus 58 ~Ll~~dy~VCEKsDGvR~Ll~vte~p~tg~~~~y~~DR~nnfY~v~~~f~p~~~~~k~ge~l~~dtlldgelV~-d---- 132 (404)
T COG5226 58 LLLNNDYLVCEKSDGVRALLLVTEEPVTGAFRGYFYDRRNNFYEVHTSFPPCSTVLKDGEVLLEDTLLDGELVF-D---- 132 (404)
T ss_pred HHHhCCeEEEEccCCeEEEEEEEecccCCCcceEEEeccCceEEeccccCCcccccccCcEEeccceecceEEE-E----
Confidence 34567899999999999998874 2 25789999887653 233433221111223567899999987 3
Q ss_pred ccccccchHHHHHHhhcCCCCCCceEEEEEEEEEeCCccccCCCHHHHHHHHHhhcCCCCCcceecccC--CCCCccccC
Q 002803 312 RFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPD--HGLNSHVRP 389 (879)
Q Consensus 312 ~~~pF~~l~~~~~~~~~~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~v~~~~~~~~i~~p~--~~~~~~v~~ 389 (879)
..|.+.++ ++.|.+||+|.++|.-+..++.++|.+.|.+-+...-.+.....+. +..++|+
T Consensus 133 -~~p~~k~~--------------qlryl~fdcLa~~g~~~~~~~~s~Rl~~l~Ke~~kp~~~~r~s~~~~~~~fpf~~-- 195 (404)
T COG5226 133 -CLPYEKVP--------------QLRYLLFDCLAYAGMFVERMEKSERLKTLQKEDEKPRERKRVSIEIDSGSFPFHF-- 195 (404)
T ss_pred -eccccchH--------------HHHHHHHHHhhhcceeEeecchhhHHHHhhhhhcccHhhhhheeeccccccceee--
Confidence 35665444 3458999999999999999999999999987664322121111111 1111121
Q ss_pred CCCCccccccCCH---HHHHHHHHHH--HHcCCceEEEecCCCCCcCCCCCCCeEEEccccccCCCcceEEEEE
Q 002803 390 QGEPCWSLVAHNV---DEVEKFFKET--IENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLIIG 458 (879)
Q Consensus 390 ~~~~~~~~~~~~~---~ei~~~~~~~--i~~g~EGlV~K~~~s~Y~~g~Rs~~WlKvKp~y~~~g~~lDlvVIG 458 (879)
..... -.+-++++.. +.+|..|||+-..+.||..|++ +..+||||.-+ .++|+..|-
T Consensus 196 --------s~K~M~~syg~~ki~k~ip~L~HgnDGLIFTp~~~PY~~Gkd-~~lLKWKP~~~---NTiDF~lvl 257 (404)
T COG5226 196 --------SVKQMLKSYGFWKIYKKIPELKHGNDGLIFTPADEPYSVGKD-GALLKWKPASL---NTIDFRLVL 257 (404)
T ss_pred --------eHHHHHhhhhHHHHHhhcccccCCCCceEeccCCCCcccCcc-ceeeecCcccc---Cceeeeeee
Confidence 11111 1233444322 4689999999999999999965 58999999864 478886654
No 47
>smart00292 BRCT breast cancer carboxy-terminal domain.
Probab=99.04 E-value=5.6e-10 Score=96.22 Aligned_cols=76 Identities=24% Similarity=0.430 Sum_probs=62.8
Q ss_pred CcccCeEEEEEcCCCCCCHHHHHHHHHHcCCEEeeccCC-CeeEEEEecCCchh--hhhhccCC-CeeeechHHHhhhcC
Q 002803 655 SIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNN-SVTHCVAADNKGLK--YEAAKRRG-DVIHYSWVLDCCSQK 730 (879)
Q Consensus 655 ~iF~g~~F~vl~~~~~~~k~eLe~lI~~~GG~~v~n~~~-~~T~~I~~~~~~~k--~~~~~~~~-~IV~p~Wl~dCi~~~ 730 (879)
.+|+|+.||+........+++|+++|.++||+++.++.. .+||+|+.+....+ +..+...+ +||+++||.||++.+
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 479999999865467889999999999999999999886 79999987665544 35555555 899999999999764
No 48
>KOG3226 consensus DNA repair protein [Replication, recombination and repair]
Probab=98.97 E-value=3.5e-10 Score=120.47 Aligned_cols=95 Identities=22% Similarity=0.442 Sum_probs=87.4
Q ss_pred cccCCCCCcccCeEEEEEcCCCCCCHHHHHHHHHHcCCEEeeccCCCeeEEEEecCCchhhhhhccCC-CeeeechHHHh
Q 002803 648 SDIKGETSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADNKGLKYEAAKRRG-DVIHYSWVLDC 726 (879)
Q Consensus 648 ~~~~~~s~iF~g~~F~vl~~~~~~~k~eLe~lI~~~GG~~v~n~~~~~T~~I~~~~~~~k~~~~~~~~-~IV~p~Wl~dC 726 (879)
++...-++|++|++| |++|..++.+.+|.......|.+|-.+++..+||+|+|.++|.||+.....| .||+-+||.+|
T Consensus 309 s~t~el~klL~GVV~-VlSGfqNP~Rs~LRskAl~LGAkY~pDW~~gsThLICAF~NTPKy~QV~g~Gg~IV~keWI~~C 387 (508)
T KOG3226|consen 309 SNTTELSKLLEGVVF-VLSGFQNPERSTLRSKALTLGAKYQPDWNAGSTHLICAFPNTPKYRQVEGNGGTIVSKEWITEC 387 (508)
T ss_pred CCchhHHHhhhceEE-EEecccCchHHHHHHHHHhhcccccCCcCCCceeEEEecCCCcchhhcccCCceEeeHHHHHHH
Confidence 344566899999998 6799999999999999999999999999988999999999999999998887 99999999999
Q ss_pred hhcCcccCCCccccccCC
Q 002803 727 CSQKKLLQLQPKYYLHLS 744 (879)
Q Consensus 727 i~~~~llp~~p~~~l~~s 744 (879)
.+++++|||+ +|++++.
T Consensus 388 y~~kk~lp~r-rYlm~~~ 404 (508)
T KOG3226|consen 388 YAQKKLLPIR-RYLMHAG 404 (508)
T ss_pred HHHHhhccHH-HHHhcCC
Confidence 9999999999 7888875
No 49
>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=98.95 E-value=2.4e-09 Score=93.48 Aligned_cols=76 Identities=26% Similarity=0.405 Sum_probs=59.7
Q ss_pred cceEEEEEEEeCCCCCCCCcceEEEEEecCCCCCCCCceEEEEEEecCCCCHHHHHHHHHhhccccccccCCCCCCCcce
Q 002803 451 DLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFY 530 (879)
Q Consensus 451 ~lDlvVIG~~~G~Grr~g~~~sfl~g~~~~~~~~~~~~~~~~~~kVgtG~s~~~~~~l~~~l~~~~~~~~~~~~~pp~~~ 530 (879)
+.|++|+|.++|.|++.|.+|+|+|+.++. . .++||||||+++++++. |
T Consensus 2 ~~e~vIvG~~~g~g~~~~~~g~llv~~~~g--------~---~~~vgtG~t~~~r~~~~-----------------~--- 50 (77)
T cd08041 2 DAEARVVGYEEGKGKYEGMLGALVVETKDG--------I---RFKIGSGFSDEQRRNPP-----------------P--- 50 (77)
T ss_pred ceeEEEEEEEcCCCccCCcEEEEEEEecCC--------C---EEEEcCCCCHHHHhcCC-----------------C---
Confidence 689999999999999999999999998752 1 45899999999988642 1
Q ss_pred eecCCCCCCCcEEEeCCCceEEEEEeeeceecccCccCCCeeeeccEEEEEe
Q 002803 531 QVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVR 582 (879)
Q Consensus 531 ~~~~~~~~~Pdvwi~~P~~s~V~ev~a~~~~~~s~~~~~g~tLRfPR~~riR 582 (879)
| ..|+||++ ..++...+||||+|+++|
T Consensus 51 -------------~-----g~v~~V~y-------~e~t~~g~lR~P~f~g~R 77 (77)
T cd08041 51 -------------I-----GSIITYKY-------QGLTKNGLPRFPVFLRVR 77 (77)
T ss_pred -------------C-----CCEEEEEE-------EecCCCCcccCCEEEecC
Confidence 0 12677765 234457889999999987
No 50
>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=98.85 E-value=6.6e-09 Score=87.42 Aligned_cols=70 Identities=23% Similarity=0.492 Sum_probs=57.6
Q ss_pred CeEEEEEcCCCCCCHHHHHHHHHHcCCEEeeccCCCeeEEEEecCCchh-hhhhccCC-CeeeechHHHhhh
Q 002803 659 DMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADNKGLK-YEAAKRRG-DVIHYSWVLDCCS 728 (879)
Q Consensus 659 g~~F~vl~~~~~~~k~eLe~lI~~~GG~~v~n~~~~~T~~I~~~~~~~k-~~~~~~~~-~IV~p~Wl~dCi~ 728 (879)
|+.||+.+.....++.+|+++|.++||+++......+||+|+......+ +..+...+ .||+++||.||+.
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 6789875544478999999999999999999988789999987665544 55666666 8999999999984
No 51
>COG1423 ATP-dependent DNA ligase, homolog of eukaryotic ligase III [DNA replication, recombination, and repair]
Probab=98.81 E-value=6.8e-08 Score=103.48 Aligned_cols=151 Identities=23% Similarity=0.324 Sum_probs=105.7
Q ss_pred HHhCCCceEEEEecceEEEEEEEeCCEEEEEecCCCC--CC-CchhhhHH-HHHhhccccceeeeceEEEeeCCCCcccc
Q 002803 240 RKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLD--HS-EYGHAMSK-IIEQNVLVDRCILDGEMLVWDTSLNRFAE 315 (879)
Q Consensus 240 ~~~~~~~~~iE~K~DGeR~qih~~g~~v~~~SR~g~~--~t-~~~~~l~~-~~~~~~~~~~~ILDGEmv~~d~~~~~~~p 315 (879)
+.|....+++|+|+||..+.|.+-+|.+.-.||.|.- || +..+.+.+ .+... .++.+|-|||+.-+. -++|
T Consensus 83 ~~F~~~~v~VEEKmnGYNVRV~k~~g~vyAiTRgG~ICPfTT~r~~~l~~~eff~d--~p~lvlcgEmvG~en---PYv~ 157 (382)
T COG1423 83 KHFGRGKVVVEEKMNGYNVRVVKLGGEVYAITRGGLICPFTTERLRDLIDLEFFDD--YPDLVLCGEMVGPEN---PYVP 157 (382)
T ss_pred hhcCCCcEEEEEeccCceEEEEEECCEEEEEecCceecCchhHHHHhhcchhhHhh--CCCcEEEEEeccCCC---CCCC
Confidence 3455678999999999999999999999999999984 44 23344332 12222 378999999998542 1222
Q ss_pred ccchHHHHHHhhcCCCCCCceEEEEEEEEEeCCccccCCCHHHHHHHHHhhcCCCCCcceecccCCCCCccccCCCCCcc
Q 002803 316 FGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCW 395 (879)
Q Consensus 316 F~~l~~~~~~~~~~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~v~~~~~~~~i~~p~~~~~~~v~~~~~~~~ 395 (879)
+ .......+.|++||+--.|.. ..+|..+|++++++.--+. ++++ |
T Consensus 158 -~-----------~~y~~e~v~fFvFDire~~tg--r~Lp~eer~~l~ekYgl~~---V~~f-------------g---- 203 (382)
T COG1423 158 -G-----------PYYEKEDVGFFVFDIREKNTG--RPLPVEERLELAEKYGLPH---VEIF-------------G---- 203 (382)
T ss_pred -C-----------CCCccCCceEEEEEEEecCCC--CCCCHHHHHHHHHHcCCCc---eEEe-------------e----
Confidence 0 112235688999999987742 2579999999999864321 2221 1
Q ss_pred ccccCCH-HHHHHHHHHHHHcCCceEEEecCCCCC
Q 002803 396 SLVAHNV-DEVEKFFKETIENRDEGIVLKDLGSKW 429 (879)
Q Consensus 396 ~~~~~~~-~ei~~~~~~~i~~g~EGlV~K~~~s~Y 429 (879)
.+..++. ++|.++.++.=.+|.||+|+|+|+..=
T Consensus 204 ~~~~~e~~eei~eIve~L~keGREGVV~Kdpdm~~ 238 (382)
T COG1423 204 EFPADEAGEEIYEIVERLNKEGREGVVMKDPDMRV 238 (382)
T ss_pred eechhHhHHHHHHHHHHHhhcCCcceEecCccccc
Confidence 1223344 788899999999999999999987654
No 52
>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=98.77 E-value=5.1e-09 Score=75.07 Aligned_cols=35 Identities=26% Similarity=0.495 Sum_probs=26.9
Q ss_pred hhHhHhhhhhccCCCcccccCCHHHHHHHHhhcCC
Q 002803 746 SSKKKLQEEVDEFSDLYFWDLDLADIKQLLSNVDR 780 (879)
Q Consensus 746 ~~~~~~~~~~D~ygDSy~~~~~~~~l~~ll~~~~~ 780 (879)
+|+++++++||+|||||+.|+|+++|+++|++|.+
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 58899999999999999999999999999999974
No 53
>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=98.73 E-value=1.5e-07 Score=104.04 Aligned_cols=151 Identities=23% Similarity=0.306 Sum_probs=96.6
Q ss_pred HhCCCceEEEEecceEEEEEEEeCCEEEEEecCCCCCCCchhhhHHHHHhhccc--cceeeeceEEEeeCCCCccccccc
Q 002803 241 KLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLV--DRCILDGEMLVWDTSLNRFAEFGS 318 (879)
Q Consensus 241 ~~~~~~~~iE~K~DGeR~qih~~g~~v~~~SR~g~~~t~~~~~l~~~~~~~~~~--~~~ILDGEmv~~d~~~~~~~pF~~ 318 (879)
.+.++.+++|+|+||..+-|..-+|++..+||.|.-.+--..-+.+.+...++. ++.+|.|||+.-+. |+.
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 356666999999999999998888999999999976531111122222222333 78999999997432 210
Q ss_pred hHHHHHHhhcCC-CCCCceEEEEEEEEEeCCccccCCCHHHHHHHHHhhcCCCCCcceecccCCCCCccccCCCCCcccc
Q 002803 319 NQEIAKAARDGL-SSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSL 397 (879)
Q Consensus 319 l~~~~~~~~~~~-~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~v~~~~~~~~i~~p~~~~~~~v~~~~~~~~~~ 397 (879)
+... ....+..|++|||.- ...-.-+|..+|++++++.--+....+ . ..
T Consensus 148 --------~hs~~y~~l~~~FfvFDI~d--~~t~~~L~~~er~~l~e~yglp~Vpvl-----------g---------~~ 197 (374)
T TIGR01209 148 --------PEYYPEVKEDLGFFLFDIRE--GKTNRSLPVEERLELAEKYGLPHVEIL-----------G---------VY 197 (374)
T ss_pred --------ccCccccCCCceEEEEEEEE--CCCCccCCHHHHHHHHHHCCCCcccee-----------e---------EE
Confidence 0011 122467899999973 333456899999999988632211000 0 01
Q ss_pred ccCC-HHHHHHHHHHHHHcCCceEEEecCCCC
Q 002803 398 VAHN-VDEVEKFFKETIENRDEGIVLKDLGSK 428 (879)
Q Consensus 398 ~~~~-~~ei~~~~~~~i~~g~EGlV~K~~~s~ 428 (879)
.... .+++.++++..=++|.||||+|+++..
T Consensus 198 ~~~~~~~~~~eii~~L~~~gREGVVlK~~~~~ 229 (374)
T TIGR01209 198 TADEAVEEIYEIIERLNKEGREGVVMKDPEMR 229 (374)
T ss_pred cHHHHHHHHHHHHHHhhhcCcceEEEcCcccc
Confidence 1122 236667777777899999999998655
No 54
>PF12738 PTCB-BRCT: twin BRCT domain; PDB: 3PA6_A 3KTF_C 2WT8_C 3EF1_A 3EF0_A.
Probab=98.48 E-value=1.1e-07 Score=79.58 Aligned_cols=61 Identities=30% Similarity=0.514 Sum_probs=50.4
Q ss_pred EEEEEcCCCCCCHHHHHHHHHHcCCEEeeccCCCeeEEEEecCCchhhhhhccCC-Ceeeech
Q 002803 661 VFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADNKGLKYEAAKRRG-DVIHYSW 722 (879)
Q Consensus 661 ~F~vl~~~~~~~k~eLe~lI~~~GG~~v~n~~~~~T~~I~~~~~~~k~~~~~~~~-~IV~p~W 722 (879)
.+|+ +|.....+++|.++|..+||++..+.+..+||+|+....+.|++.+.+++ +||+|+|
T Consensus 2 ~i~~-sg~~~~~~~~l~~~i~~~Gg~~~~~lt~~~THLI~~~~~~~K~~~A~~~gi~vV~~~W 63 (63)
T PF12738_consen 2 VICF-SGFSGKERSQLRKLIEALGGKYSKDLTKKTTHLICSSPEGKKYRKAKEWGIPVVSPDW 63 (63)
T ss_dssp EEEE-EEB-TTTCCHHHHHHHCTT-EEESSSSTT-SEEEEES--HHHHHHHHHCTSEEEEHHH
T ss_pred EEEE-CCCCHHHHHHHHHHHHHCCCEEeccccCCceEEEEeCCCcHHHHHHHHCCCcEECCCC
Confidence 5665 55566669999999999999999999889999999888999999999999 9999999
No 55
>KOG2481 consensus Protein required for normal rRNA processing [RNA processing and modification]
Probab=98.48 E-value=9e-08 Score=106.80 Aligned_cols=79 Identities=24% Similarity=0.451 Sum_probs=61.9
Q ss_pred CCCcccCeEEEEEcCCCCCCHHHHHHHHHHcCCEEeecc----------CCCeeEEEEecCCchhhhhhccCCCeeeech
Q 002803 653 ETSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNL----------NNSVTHCVAADNKGLKYEAAKRRGDVIHYSW 722 (879)
Q Consensus 653 ~s~iF~g~~F~vl~~~~~~~k~eLe~lI~~~GG~~v~n~----------~~~~T~~I~~~~~~~k~~~~~~~~~IV~p~W 722 (879)
...+|+|+.||+ | ...+++-|+-+|.++||.|++.+ +...||-|+ ++.+.+ ........|+|||
T Consensus 324 ~kslF~glkFfl-~--reVPresL~fiI~s~GG~V~wd~~~~g~~~~~~d~~ITH~Iv-DrP~~~--~~v~gR~YvQPQW 397 (570)
T KOG2481|consen 324 HKSLFSGLKFFL-N--REVPRESLEFIIRSFGGKVSWDPLGIGATYDESDERITHQIV-DRPGQQ--TSVIGRTYVQPQW 397 (570)
T ss_pred HHHHhhcceeee-e--ccCchHHHHHHHHHcCCceecCccCCCCcccccccceeeeee-cccCcc--ceeeeeeeecchh
Confidence 357999999987 4 46788999999999999999986 124688885 665543 2222337899999
Q ss_pred HHHhhhcCcccCCCc
Q 002803 723 VLDCCSQKKLLQLQP 737 (879)
Q Consensus 723 l~dCi~~~~llp~~p 737 (879)
|+||++++.++|.+.
T Consensus 398 vfDsvNar~llpt~~ 412 (570)
T KOG2481|consen 398 VFDSVNARLLLPTEK 412 (570)
T ss_pred hhhhccchhhccHhh
Confidence 999999999999884
No 56
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=98.41 E-value=3e-05 Score=93.78 Aligned_cols=224 Identities=20% Similarity=0.258 Sum_probs=130.9
Q ss_pred ceEEEEecceEEEEEEEeCCE-EEEEec----CCCCCCCc---hhhhHHHHHhhccccceeeeceEEEeeCCCCc-----
Q 002803 246 EVVIECKFDGDRIQIHKNGSE-IHYFSR----SFLDHSEY---GHAMSKIIEQNVLVDRCILDGEMLVWDTSLNR----- 312 (879)
Q Consensus 246 ~~~iE~K~DGeR~qih~~g~~-v~~~SR----~g~~~t~~---~~~l~~~~~~~~~~~~~ILDGEmv~~d~~~~~----- 312 (879)
.|++|+|+||.-+.+.+.+|. ++..|| .|+|+|+- .+++-..+.. ..+..+.+-||++.-...-.+
T Consensus 109 ~~~~epKiDGlsisL~Y~~G~L~~a~TRGDG~~GeDvT~n~~~I~~IP~~l~~-~~p~~levRGEv~m~~~~F~~lN~~~ 187 (665)
T PRK07956 109 TYLCELKIDGLAVSLLYENGVLVRAATRGDGTTGEDITANVRTIRSIPLRLHG-NEPERLEVRGEVFMPKADFEALNEER 187 (665)
T ss_pred ceEEEEecccEEEEEEEECCEEEEEEecCCCccchhHhhhhhhhccCChhhcc-cCCCeEEEEEEEEEEHHHHHHHHHHH
Confidence 599999999999999887665 688999 58888862 2222222211 114468899999974321000
Q ss_pred ----cccccchHHHH-HHhhcC---CCCCCceEEEEEEEEEeCCccccCCCHHHHHHHHHhhcCCCCCcceecccCCCCC
Q 002803 313 ----FAEFGSNQEIA-KAARDG---LSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLN 384 (879)
Q Consensus 313 ----~~pF~~l~~~~-~~~~~~---~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~v~~~~~~~~i~~p~~~~~ 384 (879)
-.+|..-++.+ ...|.. ....+++.|++|++...++ ........++.+.|.++-=++..
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 02343323221 111111 1124689999999964431 11134778888888875322211
Q ss_pred ccccCCCCCccccccCCHHHHHHHHHHHHHc------CCceEEEecCCCCCc--CC--CCCCCe---EEEccccccCCCc
Q 002803 385 SHVRPQGEPCWSLVAHNVDEVEKFFKETIEN------RDEGIVLKDLGSKWE--PG--DRSGKW---LKLKPEYIRAGSD 451 (879)
Q Consensus 385 ~~v~~~~~~~~~~~~~~~~ei~~~~~~~i~~------g~EGlV~K~~~s~Y~--~g--~Rs~~W---lKvKp~y~~~g~~ 451 (879)
....+.+.+++.++++++.+. .-.|+|+|--+-.|. .| .+.+.| +|+.++ .
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 123356789999998877643 557999997663332 12 345677 566665 5
Q ss_pred ceEEEEEEEeCCCCCCCCcceEEEEEecCCC-CCCCCceEEEEEEecCCCCHHHHHHHH
Q 002803 452 LDVLIIGGYYGSGRRGGEVAQFLVALAERPA-PDTYPRRFISFCRVGTGLSDEELDAVV 509 (879)
Q Consensus 452 lDlvVIG~~~G~Grr~g~~~sfl~g~~~~~~-~~~~~~~~~~~~kVgtG~s~~~~~~l~ 509 (879)
..-.|.+..|..|| .|.+.-. |..++-. + +. ++.++ |..+.++.+++.
T Consensus 319 ~~T~l~~I~~qVGR-TG~iTPV--A~l~PV~l~----G~--tVsrA-tLhN~~~i~~~~ 367 (665)
T PRK07956 319 ATTKLLDIEVQVGR-TGAVTPV--ARLEPVEVA----GV--TVSRA-TLHNADEIERKD 367 (665)
T ss_pred eEEEEEEEEEecCC-CceeeeE--EEEEeEEEC----CE--EEEEe-ecCCHHHHHHcC
Confidence 66788888888886 4555432 2222210 0 11 23333 677777777654
No 57
>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=98.36 E-value=2.6e-06 Score=86.86 Aligned_cols=176 Identities=14% Similarity=0.120 Sum_probs=119.0
Q ss_pred cccceeeccChHHHHHHhCCCceEEEEecceEEEEEEEeCCEEEEEecCCCCCCC---chhhhHHHHHhhccccceeeec
Q 002803 225 RPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSE---YGHAMSKIIEQNVLVDRCILDG 301 (879)
Q Consensus 225 ~PmLA~~~~~~~~~~~~~~~~~~~iE~K~DGeR~qih~~g~~v~~~SR~g~~~t~---~~~~l~~~~~~~~~~~~~ILDG 301 (879)
+.||++-+..+++-+ ..+|++=+===|-||+|....|.+.+++|+|.-+.. .+|+-.. .+ -+||
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 QLMLSEWMVEVPDDL----SEEWLVVPCPVGKRCLVVASKGKTVARSKNGRTLHRFSSALPGGSR--------KT-SNSG 71 (186)
T ss_pred ceechhhcccCCCcc----CcceEEEECcCceEEEEEEeCCEEEEEeCCCCEEEecccCCCCCCc--------CC-CCCC
Confidence 456666554443211 357888888889999999999999999999986532 2332111 01 3566
Q ss_pred eEEEeeCCCCccccccchHHHHHHhhcCCCCCCceEEEEEEEEEeCCccccCCCHHHHHHHHHhhcCCCCCcceecccCC
Q 002803 302 EMLVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDH 381 (879)
Q Consensus 302 Emv~~d~~~~~~~pF~~l~~~~~~~~~~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~v~~~~~~~~i~~p~~ 381 (879)
|+|. |- +.. +....|+|+|||..||.++.+.+...|...|++-+.+....-. ...
T Consensus 72 ~tIL-Dc----i~~-----------------~~~~~yyVlDii~w~g~~l~d~~~~~Rf~wl~skl~E~~~~~~---~~~ 126 (186)
T cd09232 72 YTIL-DC----IYN-----------------EDDRTYYVLDVLCWNGHPLYDCETEFRFFWLRSKLEELPELDE---PSE 126 (186)
T ss_pred CEEE-EE----ecC-----------------CCCCEEEEEEEeeeCCcccccCCcchhHHHHHhhCCCcccccc---ccc
Confidence 6653 31 100 1124799999999999999999999999999998876432110 000
Q ss_pred CCCccccCCCCCccccccCCHHHHHHHHHHHH---HcCCceEEEecCCCCCcCCCCCCCeEEEccc
Q 002803 382 GLNSHVRPQGEPCWSLVAHNVDEVEKFFKETI---ENRDEGIVLKDLGSKWEPGDRSGKWLKLKPE 444 (879)
Q Consensus 382 ~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~~i---~~g~EGlV~K~~~s~Y~~g~Rs~~WlKvKp~ 444 (879)
.-++.+++. | ...++ .+.+++.|...+ ..-..||++-..++.|.+| +++.|+|+||.
T Consensus 127 ~~~~~f~~~--p--~~~~~-~~~l~~~~~~~~~~~~~e~DGLlFyhk~~~Y~~G-~tPlvl~wKp~ 186 (186)
T cd09232 127 KNPFRFVPL--P--YFPCT-KESLQSAYSGPLNDDPYELDGLLFYHKESHYTPG-STPLVLWLKDY 186 (186)
T ss_pred cCCceEEec--C--cccCc-HHHHHHHHhcccccCCCCCceEEEEeCCCcccCc-CCCcEEEecCC
Confidence 011122211 1 22233 377888888888 8899999999999999999 78999999983
No 58
>COG5163 NOP7 Protein required for biogenesis of the 60S ribosomal subunit [Translation, ribosomal structure and biogenesis]
Probab=98.24 E-value=6.2e-07 Score=96.82 Aligned_cols=79 Identities=25% Similarity=0.381 Sum_probs=60.3
Q ss_pred CCCcccCeEEEEEcCCCCCCHHHHHHHHHHcCCEEeeccC-----------CCeeEEEEecCCchhhhhhccCCCeeeec
Q 002803 653 ETSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLN-----------NSVTHCVAADNKGLKYEAAKRRGDVIHYS 721 (879)
Q Consensus 653 ~s~iF~g~~F~vl~~~~~~~k~eLe~lI~~~GG~~v~n~~-----------~~~T~~I~~~~~~~k~~~~~~~~~IV~p~ 721 (879)
...+|+|+.|||-+ ..+...|+.+|.++||.++..|. ..+||-|+ ++..+|-+ ......|+||
T Consensus 347 ~~slFS~f~Fyisr---eVp~dsLefiilscGG~V~~~p~~~~i~~~~~vD~~vth~i~-drp~~~~k--vegrtYiQPQ 420 (591)
T COG5163 347 LKSLFSGFKFYISR---EVPGDSLEFIILSCGGSVVGSPCEADIHVSEKVDEKVTHQIV-DRPVMKNK--VEGRTYIQPQ 420 (591)
T ss_pred hhhhhhceEEEEec---cccchHHHHHHHHcCCcccCchhhccCCchhhccchhhhhhc-cchhhhhh--hcceeeechH
Confidence 36799999999853 45667899999999999998762 23788884 66555322 1222699999
Q ss_pred hHHHhhhcCcccCCCc
Q 002803 722 WVLDCCSQKKLLQLQP 737 (879)
Q Consensus 722 Wl~dCi~~~~llp~~p 737 (879)
||+|||++|.+.+.+.
T Consensus 421 w~fDsiNkG~l~~~~~ 436 (591)
T COG5163 421 WLFDSINKGKLACVEN 436 (591)
T ss_pred HHHhhhccccchhhhh
Confidence 9999999999888774
No 59
>KOG1929 consensus Nucleotide excision repair factor NEF2, RAD4/CUT5 component [Replication, recombination and repair]
Probab=98.17 E-value=3.3e-06 Score=101.82 Aligned_cols=194 Identities=15% Similarity=0.138 Sum_probs=129.5
Q ss_pred CCCcccCeEEEEEcCCCCCCHHHHHHHHHHcCCEEeeccCCCeeEEEEecC-CchhhhhhccCC-CeeeechHHHhhhcC
Q 002803 653 ETSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADN-KGLKYEAAKRRG-DVIHYSWVLDCCSQK 730 (879)
Q Consensus 653 ~s~iF~g~~F~vl~~~~~~~k~eLe~lI~~~GG~~v~n~~~~~T~~I~~~~-~~~k~~~~~~~~-~IV~p~Wl~dCi~~~ 730 (879)
.+..|.|+.+|. +|.....|.++..+|..|||++.......++++++..- .+-||+++++|. +|++.+|++||++++
T Consensus 100 ~~p~~~~~~Vc~-tgl~~~eK~ei~~~v~k~gg~~~~~L~s~v~~~~~~~~~~~~kYe~al~wn~~v~~~~w~~~s~~~~ 178 (811)
T KOG1929|consen 100 KCPGFFGLKVCL-TGLSGDEKSEIKILVPKHGGTLHRSLSSDVNSLKILPEVKTEKYEQALKWNIPVVSDDWLFDSIEKT 178 (811)
T ss_pred cCCcccceEEEe-cccchHHHHHHHHHhhhcccEEehhhhhhhheeeeccccchHHHHHHHhhCCccccHHHHhhhhccc
Confidence 366899999996 67677789999999999999999887766666665433 348999999998 999999999999999
Q ss_pred cccCCCccccccCChhhH-----hHhhhhhccCCCcccccCCHHHHHHHHhhcCCCCChhhHHHHHhhcCCCCCCCCCCC
Q 002803 731 KLLQLQPKYYLHLSDSSK-----KKLQEEVDEFSDLYFWDLDLADIKQLLSNVDRSEDPKTIDYYKKKYCPQDKWSCFHG 805 (879)
Q Consensus 731 ~llp~~p~~~l~~s~~~~-----~~~~~~~D~ygDSy~~~~~~~~l~~ll~~~~~~~~~~~~~~l~~~~~~~~~~~lF~~ 805 (879)
.+++..|+..-....+.- ....+.-+ ||+|+..-+... ..+..++ ....+ ..+..+-.+
T Consensus 179 ~~~~~~~~e~~~~~~~is~~~~~~~~~~~~~--~~s~t~~~~~~~-~~~~~n~---~~~p~----------~a~~~~~~~ 242 (811)
T KOG1929|consen 179 AVLETKPYEGAPVAEAISGPIGSTLPKEILD--GDSRTANDTWST-SKVVTNI---KVLPF----------QAKIGNLDD 242 (811)
T ss_pred ccccccccccccccceeccCCcccccccccc--ccchhhhccccc-hhccccc---ccchh----------hhhcccccc
Confidence 999988754333111000 00111111 444422111100 0000010 00000 112235689
Q ss_pred cEEEEcCCCCCCCChhHHHHHHHHHHHHHHhhhcCceeccCCCCCeeEEEEccCCCCchhHHhhhcccc
Q 002803 806 CCIYFYHSTEPLSPDWEVLLGLALRRLKLEISFHGVSLPERNIFYGTRSCMLLDPSGWKIAWRRSKSRK 874 (879)
Q Consensus 806 ~~vy~~~~~~~~~~~~~~~~~~~l~~~~~~i~~~GG~v~~~~~~~vTHVVv~~d~~~~~~~~~~~~~~~ 874 (879)
|.+|..++.. ...+.+.+.++-+||.-++...+.++|+++.....++.+.|-+.-.+.
T Consensus 243 c~v~~s~~~~-----------~~~s~l~r~~~~g~~~~~~e~~e~~st~l~~~~~~~~~q~~d~~g~~~ 300 (811)
T KOG1929|consen 243 CLVETSGTTS-----------RNRSALSRLSNNGGSLRFLERLEETSTSLLGDFDPNLEQLWDDNGLKQ 300 (811)
T ss_pred ceeeecCCcc-----------cchhHhHHhhhcccceeecccCccccchhhcccchHHHhhhhhccCcc
Confidence 9999998752 345678888999999998566789999999888888888887765443
No 60
>PF14743 DNA_ligase_OB_2: DNA ligase OB-like domain; PDB: 2Q2U_D 2Q2T_A 1FVI_A 1P8L_A.
Probab=97.98 E-value=6e-06 Score=69.54 Aligned_cols=36 Identities=22% Similarity=0.492 Sum_probs=23.6
Q ss_pred CCCCCCCCcceEEEEEecCCCCCCCCceEEEEEEecCCCCHHHHHHH
Q 002803 462 GSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAV 508 (879)
Q Consensus 462 G~Grr~g~~~sfl~g~~~~~~~~~~~~~~~~~~kVgtG~s~~~~~~l 508 (879)
|.|+..|++|+++|-..+ + ..++||||||+++++++
T Consensus 2 G~Gk~~g~~Galv~~~~~--G---------~~f~iGsG~td~~R~~~ 37 (66)
T PF14743_consen 2 GKGKFKGMLGALVCETED--G---------VEFKIGSGFTDEEREEP 37 (66)
T ss_dssp ---EEEEEEEEEEEEE-T--T---------EEEEE-SS--HHHHHHH
T ss_pred CccccCCCEEEEEEEeCC--C---------CEEEECCCCCHHHHhcC
Confidence 788889999999997633 1 35689999999999875
No 61
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=97.74 E-value=0.0053 Score=72.77 Aligned_cols=195 Identities=21% Similarity=0.285 Sum_probs=118.6
Q ss_pred CceEEEEecceEEEEEEEeCCE-EEEEecC----CCCCCCchhhhHHHHHhhc--cccceeeeceEEEeeCC--------
Q 002803 245 KEVVIECKFDGDRIQIHKNGSE-IHYFSRS----FLDHSEYGHAMSKIIEQNV--LVDRCILDGEMLVWDTS-------- 309 (879)
Q Consensus 245 ~~~~iE~K~DGeR~qih~~g~~-v~~~SR~----g~~~t~~~~~l~~~~~~~~--~~~~~ILDGEmv~~d~~-------- 309 (879)
..|++|+|+||.-+-+.+.+|. ++--||. |+|+|.-...+.. +...+ .+..+-+=||++.--..
T Consensus 109 ~~y~~EpKiDGlsisL~YenG~Lv~aaTRGdG~~GEDiT~NvrtI~~-IP~~l~~~p~~lEVRGEvfm~k~~F~~lN~~~ 187 (667)
T COG0272 109 VEYVVEPKIDGLAISLVYENGKLVRAATRGDGTTGEDITANVRTIRS-IPLKLPGAPAVLEVRGEVFMPKEDFEALNEER 187 (667)
T ss_pred cceEEEeecceEEEEEEEECCEEEEeeccCCCccccchhhhhhhHhh-hhhhccCCCceEEEEeEEEEeHHHHHHHHHHH
Confidence 4799999999999998887664 7788886 7888864333332 11112 25677889999873110
Q ss_pred --CCccccccchHHHH-HHhhc---CCCCCCceEEEEEEEEEeCCccccCCCHHHHHHHHHhhcCCCCCcceecccCCCC
Q 002803 310 --LNRFAEFGSNQEIA-KAARD---GLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGL 383 (879)
Q Consensus 310 --~~~~~pF~~l~~~~-~~~~~---~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~v~~~~~~~~i~~p~~~~ 383 (879)
.+ -.||..-++.+ ...|. .....+++.+++|.+-...+. ..-.+..++.+.|..+-=++..
T Consensus 188 ~~~g-~~~faNpRNaAAGsLRqlD~~ita~R~L~~f~y~~~~~~~~-~~~~t~~e~l~~L~~~GF~v~~----------- 254 (667)
T COG0272 188 EEEG-EKPFANPRNAAAGSLRQLDPKITAKRKLGFFIYAVGDGEEG-LLADTQSERLAFLKAWGFPVNP----------- 254 (667)
T ss_pred HHhC-CCCcCChhhhhhhhhhccCHHHHhcCCceEEEEeCCccCCC-CCccCHHHHHHHHHHcCCCCCc-----------
Confidence 00 02232222211 11111 011246899999999866554 5556788999999886433221
Q ss_pred CccccCCCCCccccccCCHHHHHHHHHHHHHcC------CceEEEecCCCCCc--CC--CCCCCe---EEEccccccCCC
Q 002803 384 NSHVRPQGEPCWSLVAHNVDEVEKFFKETIENR------DEGIVLKDLGSKWE--PG--DRSGKW---LKLKPEYIRAGS 450 (879)
Q Consensus 384 ~~~v~~~~~~~~~~~~~~~~ei~~~~~~~i~~g------~EGlV~K~~~s~Y~--~g--~Rs~~W---lKvKp~y~~~g~ 450 (879)
....+.+.+++.++++.+...+ -.|+|+|--+-... .| .|++.| +|..|+-
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 1235789999999999887743 47999996442211 12 357788 6888863
Q ss_pred cceEEEEEEEeCCCCCCCCcc
Q 002803 451 DLDVLIIGGYYGSGRRGGEVA 471 (879)
Q Consensus 451 ~lDlvVIG~~~G~Grr~g~~~ 471 (879)
.--.+.+..+..|| .|.+.
T Consensus 319 -~~T~l~dI~~qVGR-TG~iT 337 (667)
T COG0272 319 -AVTKLLDIEVQVGR-TGAIT 337 (667)
T ss_pred -eeeEEEEEEEecCC-ceeee
Confidence 33345555666664 44443
No 62
>smart00532 LIGANc Ligase N family.
Probab=97.70 E-value=0.00048 Score=79.44 Aligned_cols=223 Identities=18% Similarity=0.254 Sum_probs=131.5
Q ss_pred ceEEEEecceEEEEEEEeCCE-EEEEec----CCCCCCCch---hhhHHHHHhhccccceeeeceEEEeeCCCCc-----
Q 002803 246 EVVIECKFDGDRIQIHKNGSE-IHYFSR----SFLDHSEYG---HAMSKIIEQNVLVDRCILDGEMLVWDTSLNR----- 312 (879)
Q Consensus 246 ~~~iE~K~DGeR~qih~~g~~-v~~~SR----~g~~~t~~~---~~l~~~~~~~~~~~~~ILDGEmv~~d~~~~~----- 312 (879)
.|++|+|+||.-+.+.+.+|. ++..|| .|+|+|+.. +++-..+. .-.+..+.+-||++.-...-.+
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 699999999999999987765 889999 688998632 22222221 1013468899999974321000
Q ss_pred ----cccccchHHHH-HHhhcC---CCCCCceEEEEEEEEEeCCccccCCCHHHHHHHHHhhcCCCCCcceecccCCCCC
Q 002803 313 ----FAEFGSNQEIA-KAARDG---LSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLN 384 (879)
Q Consensus 313 ----~~pF~~l~~~~-~~~~~~---~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~v~~~~~~~~i~~p~~~~~ 384 (879)
-.+|..-++.+ ...+.. ....+++.|++|++...++.. ...+..++.+.|..+-=++..
T Consensus 183 ~~~g~~~faNpRN~aAG~lr~ld~~~~~~r~L~~~~y~~~~~~~~~-~~~t~~e~l~~L~~~GF~v~~------------ 249 (441)
T smart00532 183 EEEGEKPFANPRNAAAGSLRQLDPRITAKRKLRAFFYGLGTGEELF-LPKTQSEALKWLKELGFPVSP------------ 249 (441)
T ss_pred HhcCCCcccChHHHHHHHHHhcCchhhhhccceEEEEEcccCCCCC-CccCHHHHHHHHHHCCCCCCC------------
Confidence 02343333321 111111 112358999999986443321 124678888888875222111
Q ss_pred ccccCCCCCccccccCCHHHHHHHHHHHHHc------CCceEEEecCCCCCcC--C--CCCCCe---EEEccccccCCCc
Q 002803 385 SHVRPQGEPCWSLVAHNVDEVEKFFKETIEN------RDEGIVLKDLGSKWEP--G--DRSGKW---LKLKPEYIRAGSD 451 (879)
Q Consensus 385 ~~v~~~~~~~~~~~~~~~~ei~~~~~~~i~~------g~EGlV~K~~~s~Y~~--g--~Rs~~W---lKvKp~y~~~g~~ 451 (879)
....+.+.++++.+++...+. .-.|||+|--+-.+.. | .+++.| +|..++ .
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 123456788999988877653 5689999987665544 3 345677 566665 5
Q ss_pred ceEEEEEEEeCCCCCCCCcceEEEEEecCCC-CCCCCceEEEEEEecCCCCHHHHHHH
Q 002803 452 LDVLIIGGYYGSGRRGGEVAQFLVALAERPA-PDTYPRRFISFCRVGTGLSDEELDAV 508 (879)
Q Consensus 452 lDlvVIG~~~G~Grr~g~~~sfl~g~~~~~~-~~~~~~~~~~~~kVgtG~s~~~~~~l 508 (879)
..-.|.+..|..|| .|.+.-. |..++-. + + .++.++ |..+.+..+++
T Consensus 314 ~~T~l~~I~~qVGR-TG~iTPv--A~lePV~l~----G--~tVsrA-TLhN~~~i~~~ 361 (441)
T smart00532 314 AETKLLDIIVQVGR-TGKITPV--AELEPVFLA----G--STVSRA-TLHNEDEIEEK 361 (441)
T ss_pred eEEEEEEEEEecCC-CceeeEE--EEEEeEEEC----C--EEEEec-ccCCHHHHHHc
Confidence 66678888888886 4555432 3222211 1 1 134443 77777777654
No 63
>PLN03122 Poly [ADP-ribose] polymerase; Provisional
Probab=97.70 E-value=7.1e-05 Score=91.26 Aligned_cols=87 Identities=21% Similarity=0.318 Sum_probs=72.2
Q ss_pred CCCcccCeEEEEEcCCCCCCHHHHHHHHHHcCCEEeeccCCCeeEEEEecCC----c-hhhhhhccCC-CeeeechHHHh
Q 002803 653 ETSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADNK----G-LKYEAAKRRG-DVIHYSWVLDC 726 (879)
Q Consensus 653 ~s~iF~g~~F~vl~~~~~~~k~eLe~lI~~~GG~~v~n~~~~~T~~I~~~~~----~-~k~~~~~~~~-~IV~p~Wl~dC 726 (879)
....|.|+.|++ .|.-..++++++++|.++||+++.... .+||||+++.. + -|++.+.+.+ +||+.+||+||
T Consensus 186 ~~kpL~G~~fvi-TGtl~~sr~elK~~Ie~~GGkvsssVs-~~T~lIvt~~ev~k~gsSKlkkAk~lgIpIVsEd~L~d~ 263 (815)
T PLN03122 186 PGKPFSGMMISL-SGRLSRTHQYWKKDIEKHGGKVANSVE-GVTCLVVSPAERERGGSSKIAEAMERGIPVVREAWLIDS 263 (815)
T ss_pred cCCCcCCcEEEE-eCCCCCCHHHHHHHHHHcCCEEccccc-cceEEEEcCccccccCccHHHHHHHcCCcCccHHHHHHH
Confidence 355699999987 454444899999999999999999884 58899987643 2 6888888888 99999999999
Q ss_pred hhcCcccCCCccccc
Q 002803 727 CSQKKLLQLQPKYYL 741 (879)
Q Consensus 727 i~~~~llp~~p~~~l 741 (879)
++.+..+|+.++++.
T Consensus 264 i~~~k~~~~~~y~l~ 278 (815)
T PLN03122 264 IEKQEAQPLEAYDVV 278 (815)
T ss_pred HhcCCcccchhhhhc
Confidence 999999999987654
No 64
>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=97.61 E-value=0.00052 Score=75.66 Aligned_cols=167 Identities=17% Similarity=0.251 Sum_probs=100.5
Q ss_pred ceEEEEecceEEEEEEEeCCE-EEEEec----CCCCCCCchh---hhHHHHHhhccccceeeeceEEEeeCCCCc-----
Q 002803 246 EVVIECKFDGDRIQIHKNGSE-IHYFSR----SFLDHSEYGH---AMSKIIEQNVLVDRCILDGEMLVWDTSLNR----- 312 (879)
Q Consensus 246 ~~~iE~K~DGeR~qih~~g~~-v~~~SR----~g~~~t~~~~---~l~~~~~~~~~~~~~ILDGEmv~~d~~~~~----- 312 (879)
.|++|+|+||.-+.+.+.+|. ++..|| .|+|+|+-.. ++-..|. . .+..+.+-||++.-...-.+
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 699999999999999887665 789999 5788886322 2222221 1 24568899999974211000
Q ss_pred ----cccccchHHHH-HHhhcC---CCCCCceEEEEEEEEEeCCccccCCCHHHHHHHHHhhcCCCCCcceecccCCCCC
Q 002803 313 ----FAEFGSNQEIA-KAARDG---LSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLN 384 (879)
Q Consensus 313 ----~~pF~~l~~~~-~~~~~~---~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~v~~~~~~~~i~~p~~~~~ 384 (879)
-.+|..-++.+ ...+.. ....+++.|++|++...++.. .....++.+.|+++-=++..
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 01343323321 111211 112468999999996544211 34778888888875322211
Q ss_pred ccccCCCCCccccccCCHHHHHHHHHHHHHc------CCceEEEecCCCCCc----CCCCCCCe
Q 002803 385 SHVRPQGEPCWSLVAHNVDEVEKFFKETIEN------RDEGIVLKDLGSKWE----PGDRSGKW 438 (879)
Q Consensus 385 ~~v~~~~~~~~~~~~~~~~ei~~~~~~~i~~------g~EGlV~K~~~s~Y~----~g~Rs~~W 438 (879)
....+.+.+++.+++++.... .-.|||+|--+-.+. ...+++.|
T Consensus 246 ----------~~~~~~~~~ev~~~~~~~~~~R~~l~y~iDGiViKvn~~~~~~~lG~tsk~PrW 299 (307)
T cd00114 246 ----------ETRLCKNIEEVLAFYDEIEAKRDSLPYEIDGVVVKVDDLALQRELGFTSKAPRW 299 (307)
T ss_pred ----------CeEEeCCHHHHHHHHHHHHHhhhcCCCCCCcEEEEEeCHHHHHHhCccCCCCCc
Confidence 123456789999998877543 567999997655443 23345666
No 65
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=97.54 E-value=0.0013 Score=77.76 Aligned_cols=211 Identities=16% Similarity=0.192 Sum_probs=122.0
Q ss_pred ccccceee-ccChHHHHHHhC--CCceEEEEecceEEEEEEEeCCE-EEEEec----CCCCCCCc---hhhhHHHHHhhc
Q 002803 224 VRPQLAMR-IGDAHAAWRKLH--GKEVVIECKFDGDRIQIHKNGSE-IHYFSR----SFLDHSEY---GHAMSKIIEQNV 292 (879)
Q Consensus 224 ~~PmLA~~-~~~~~~~~~~~~--~~~~~iE~K~DGeR~qih~~g~~-v~~~SR----~g~~~t~~---~~~l~~~~~~~~ 292 (879)
-.|||.-. +.+.++. .++. -..|++|+|+||.-+.+.+.+|. ++..|| .|+|+|+- .+++-..+. .
T Consensus 95 ~~PMlSL~k~~s~eel-~~w~~~~~~~~vepKiDGlsisL~Ye~G~Lv~a~TRGDG~~GEDVT~nv~~I~~IP~~l~-~- 171 (562)
T PRK08097 95 PVAHTGVKKLADKQAL-ARWMAGRSDLWVQPKVDGVAVTLVYRDGKLVQAISRGNGLKGEDWTAKARLIPAIPQQLP-G- 171 (562)
T ss_pred CCCcccccccCCHHHH-HHHHhhccceEEEEecccEEEEEEEECCEEEEEEecCCCccchhHHhhHhhhcccchhhc-C-
Confidence 35898543 2233332 2221 12699999999999999887665 688999 57788852 222222221 1
Q ss_pred cccceeeeceEEEeeCCCCcc-ccccchHHH-HHHhhc--CCCCCCceEEEEEEEEEeCCccccCCCHHHHHHHHHhhcC
Q 002803 293 LVDRCILDGEMLVWDTSLNRF-AEFGSNQEI-AKAARD--GLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVK 368 (879)
Q Consensus 293 ~~~~~ILDGEmv~~d~~~~~~-~pF~~l~~~-~~~~~~--~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~v~ 368 (879)
.+..+.+-||++.-...-.+. ..|..-++. +...|. .....+++.|++|++. +| .....++.+.|+.+-=
T Consensus 172 ~~~~levRGEv~m~~~~F~~~~~g~aNPRN~AAGsLr~~d~~~~~r~L~~f~y~~~--~~----~~t~~e~l~~L~~~GF 245 (562)
T PRK08097 172 ALANLVLQGELFLRREGHIQQQMGGINARAKVAGLMMRKDPSPTLNQIGVFVWAWP--DG----PASMPERLAQLATAGF 245 (562)
T ss_pred CCCeEEEEEEEEEeHHHHHHHhcCcCCchHHHhHHHhhcCcHhhhccceEEEEECC--CC----CCCHHHHHHHHHHCCC
Confidence 133688999998743210000 001111111 111111 1011467999999983 44 2467888888887542
Q ss_pred CCCCcceecccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHH----cCCceEEEecCCCCCcCC--CCCCCe---E
Q 002803 369 PSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIE----NRDEGIVLKDLGSKWEPG--DRSGKW---L 439 (879)
Q Consensus 369 ~~~~~~~i~~p~~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~~i~----~g~EGlV~K~~~s~Y~~g--~Rs~~W---l 439 (879)
++... ....+.+.+++..+++.... -.-.|+|+|--+-.|..| .+.+.| +
T Consensus 246 ~v~~~---------------------~~~~~~~~~~i~~~~~~~~r~~l~y~iDGiViKvn~~~~~~~~ts~~PrWAiAy 304 (562)
T PRK08097 246 PLTQR---------------------YTHPVKNAEEVARWRERWYRAPLPFVTDGVVVRQAKEPPGRYWQPGQGEWAVAW 304 (562)
T ss_pred CcCcc---------------------ceEeeCCHHHHHHHHHHHhhccCCCCCCcEEEEecCHHHHhhccCCCCCceEEE
Confidence 22110 12235678888887776543 256899999766555543 356677 5
Q ss_pred EEccccccCCCcceEEEEEEEeCCCCCCCCcc
Q 002803 440 KLKPEYIRAGSDLDVLIIGGYYGSGRRGGEVA 471 (879)
Q Consensus 440 KvKp~y~~~g~~lDlvVIG~~~G~Grr~g~~~ 471 (879)
|+.++ ...-.+.+..|..|| .|.+.
T Consensus 305 Kf~~~------~~~T~l~~I~~qVGR-TG~iT 329 (562)
T PRK08097 305 KYPPV------QQVAEVRAVQFAVGR-TGKIT 329 (562)
T ss_pred cCCCc------EEEEEEEEEEEecCC-Cceee
Confidence 66554 566678888888886 45554
No 66
>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=97.54 E-value=0.0012 Score=80.15 Aligned_cols=224 Identities=18% Similarity=0.244 Sum_probs=130.8
Q ss_pred ceEEEEecceEEEEEEEeCCE-EEEEec----CCCCCCCch---hhhHHHHHhhccccceeeeceEEEeeCCCCc-----
Q 002803 246 EVVIECKFDGDRIQIHKNGSE-IHYFSR----SFLDHSEYG---HAMSKIIEQNVLVDRCILDGEMLVWDTSLNR----- 312 (879)
Q Consensus 246 ~~~iE~K~DGeR~qih~~g~~-v~~~SR----~g~~~t~~~---~~l~~~~~~~~~~~~~ILDGEmv~~d~~~~~----- 312 (879)
.|++|+|+||.-+.+.+.+|+ ++..|| .|+|+|+-. +.+-..+.....+..+.+-||++.-...-.+
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 789999 588888622 2222222100014468899999974211000
Q ss_pred ----cccccchHHHH-HHhhcC---CCCCCceEEEEEEEEEeCCccccCCCHHHHHHHHHhhcCCCCCcceecccCCCCC
Q 002803 313 ----FAEFGSNQEIA-KAARDG---LSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLN 384 (879)
Q Consensus 313 ----~~pF~~l~~~~-~~~~~~---~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~v~~~~~~~~i~~p~~~~~ 384 (879)
-.+|..-++.+ ...|.. ....+++.|++|++...+ .....+..++.+.|..+-=++..
T Consensus 177 ~~~g~~~faNpRN~aAGslr~ld~~~~~~r~L~~~~y~~~~~~--~~~~~t~~e~l~~L~~~GF~v~~------------ 242 (652)
T TIGR00575 177 REQGEKPFANPRNAAAGSLRQLDPRITAKRKLRFFAYGLGEGL--ELPDATQYEALAWLKKWGFPVSP------------ 242 (652)
T ss_pred HHcCCCCCCCcHHHHHHHHHcCCchhhhcCccEEEEEeccccC--CCCCCCHHHHHHHHHHCCCCCCC------------
Confidence 01343333321 122211 112468999999985322 21124778888888875322211
Q ss_pred ccccCCCCCccccccCCHHHHHHHHHHHHHc------CCceEEEecCCCCCc----CCCCCCCe---EEEccccccCCCc
Q 002803 385 SHVRPQGEPCWSLVAHNVDEVEKFFKETIEN------RDEGIVLKDLGSKWE----PGDRSGKW---LKLKPEYIRAGSD 451 (879)
Q Consensus 385 ~~v~~~~~~~~~~~~~~~~ei~~~~~~~i~~------g~EGlV~K~~~s~Y~----~g~Rs~~W---lKvKp~y~~~g~~ 451 (879)
....+.+.+++.++++++.+. .-.|+|+|--+-.+. ...+++.| +|+.++ .
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 122356789999988877543 568999997654443 12356677 566665 5
Q ss_pred ceEEEEEEEeCCCCCCCCcceEEEEEecCCC-CCCCCceEEEEEEecCCCCHHHHHHHH
Q 002803 452 LDVLIIGGYYGSGRRGGEVAQFLVALAERPA-PDTYPRRFISFCRVGTGLSDEELDAVV 509 (879)
Q Consensus 452 lDlvVIG~~~G~Grr~g~~~sfl~g~~~~~~-~~~~~~~~~~~~kVgtG~s~~~~~~l~ 509 (879)
..-.|.+..|..|| .|.+.-. |..++-. + +. ++.++ |..+.++.+++.
T Consensus 307 ~~T~l~~I~~qVGR-TG~iTPv--A~lePV~l~----G~--~VsrA-tLhN~~~i~~~~ 355 (652)
T TIGR00575 307 AQTKLLDVVVQVGR-TGAITPV--AKLEPVFVA----GT--TVSRA-TLHNEDEIEELD 355 (652)
T ss_pred eeEEEEEEEEecCC-CceeeeE--EEEeeEEEC----CE--EEEEe-ecCCHHHHHHcC
Confidence 66688888898886 4555432 3222211 1 11 34443 778887776643
No 67
>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=97.41 E-value=0.00013 Score=80.79 Aligned_cols=160 Identities=21% Similarity=0.286 Sum_probs=90.3
Q ss_pred ceEEEEecceEEEEEEEeCCE-EEEEecC----CCCCCCchhhhHHHHHhhcc--ccceeeeceEEEeeCCCCc------
Q 002803 246 EVVIECKFDGDRIQIHKNGSE-IHYFSRS----FLDHSEYGHAMSKIIEQNVL--VDRCILDGEMLVWDTSLNR------ 312 (879)
Q Consensus 246 ~~~iE~K~DGeR~qih~~g~~-v~~~SR~----g~~~t~~~~~l~~~~~~~~~--~~~~ILDGEmv~~d~~~~~------ 312 (879)
.|++|+|+||.-+.+++.+|. ++..||. |+|+|+....+.. +-..+. +..+.+=||++.-...-.+
T Consensus 108 ~~~~e~KiDGlsi~L~Y~~G~L~~a~TRGdG~~GeDvT~n~~~i~~-iP~~i~~~p~~~eVRGEv~m~~~~F~~ln~~~~ 186 (315)
T PF01653_consen 108 EFVVEPKIDGLSISLIYENGKLVRAATRGDGEVGEDVTHNVRTIKS-IPLRIPEKPGRLEVRGEVYMSKSDFEKLNEERE 186 (315)
T ss_dssp EEEEEEEESSEEEEEEEETTEEEEEEEETTSSEEEB-HHHHCTSTT-S-SB-SSSSSEEEEEEEEE--HHHHHHHHHHHH
T ss_pred ceeEeeccceeEEEEEEeCCEEEEEEEcCCCccchhHHHHHHHHhc-CchhhccCCcceEEEEEEEEehhhHHHHHHHHH
Confidence 599999999999999998776 6899994 6777752211111 011111 3678888999863210000
Q ss_pred ---cccccchHHHHH-HhhcC---CCCCCceEEEEEEEEEeCCccccCCCHHHHHHHHHhhcCCCCCcceecccCCCCCc
Q 002803 313 ---FAEFGSNQEIAK-AARDG---LSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNS 385 (879)
Q Consensus 313 ---~~pF~~l~~~~~-~~~~~---~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~v~~~~~~~~i~~p~~~~~~ 385 (879)
-.+|..-++.+. ..+.. ....+++.|++|++.+.+| ...-.+..++.+.|.++-=++...
T Consensus 187 ~~~~~~faNpRN~aAGsLr~~d~~~~~~r~L~f~~y~~~~~~~-~~~~~t~~e~l~~L~~~GF~v~~~------------ 253 (315)
T PF01653_consen 187 EEGEKPFANPRNAAAGSLRQKDPSITAERKLSFFAYGIGEPEG-DLGFNTQSERLQFLKEWGFPVNPY------------ 253 (315)
T ss_dssp HTTS---SSHHHHHHHHHTSSSHHHHHTS--EEEEEEEEEETT-STT-SBHHHHHHHHHHTT--B-TT------------
T ss_pred HhccchhhhhhHHHHHhhhhccchhhhcCeeEEEEEEeccccc-ccChHHHHHHHHHHHHcCCCCCcc------------
Confidence 012322222211 11111 0123689999999999987 333446788888888753222111
Q ss_pred cccCCCCCccccccCCHHHHHHHHHHHHHc------CCceEEEecCCCCC
Q 002803 386 HVRPQGEPCWSLVAHNVDEVEKFFKETIEN------RDEGIVLKDLGSKW 429 (879)
Q Consensus 386 ~v~~~~~~~~~~~~~~~~ei~~~~~~~i~~------g~EGlV~K~~~s~Y 429 (879)
...+.+.+++..+++...+. .-.|||+|--+-.+
T Consensus 254 ----------~~~~~~~~~v~~~~~~~~~~R~~l~y~iDGiVikvn~~~~ 293 (315)
T PF01653_consen 254 ----------IRFCKSIEEVEEYIEEWEERREELPYPIDGIVIKVNDLAL 293 (315)
T ss_dssp ----------EEEESSHHHHHHHHHHHHHHGCCSSS-EEEEEEEESBHHH
T ss_pred ----------eEecCCHHHHHHHHHHHHhhhhccccccCcEEEEecCHHH
Confidence 23456889999999887764 44699999655443
No 68
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=97.37 E-value=0.0022 Score=77.91 Aligned_cols=223 Identities=19% Similarity=0.214 Sum_probs=130.0
Q ss_pred CceEEEEecceEEEEEEEeCCE-EEEEec----CCCCCCCchh---hhHHHHHhhccccceeeeceEEEeeCCCCc----
Q 002803 245 KEVVIECKFDGDRIQIHKNGSE-IHYFSR----SFLDHSEYGH---AMSKIIEQNVLVDRCILDGEMLVWDTSLNR---- 312 (879)
Q Consensus 245 ~~~~iE~K~DGeR~qih~~g~~-v~~~SR----~g~~~t~~~~---~l~~~~~~~~~~~~~ILDGEmv~~d~~~~~---- 312 (879)
..|++|+|+||.=+-+.+.+|+ ++..|| .|+|+|+-.. ++-..+. ...+..+.+=||++.-...-.+
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 4699999999999998887664 788999 6888886322 2222221 1123457888999874321000
Q ss_pred -----cccccchHHHH-HHhhcC---CCCCCceEEEEEEEEEeCCccccCCCHHHHHHHHHhhcCCCCCcceecccCCCC
Q 002803 313 -----FAEFGSNQEIA-KAARDG---LSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGL 383 (879)
Q Consensus 313 -----~~pF~~l~~~~-~~~~~~---~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~v~~~~~~~~i~~p~~~~ 383 (879)
-.+|..-++.+ ...|.. ....+++.|++|++...++. .....++.+.|..+-=++...
T Consensus 211 ~~~~g~~~faNpRN~aAGslR~ldp~~~~~r~L~f~~y~~~~~~~~---~~t~~e~l~~L~~~GF~v~~~---------- 277 (689)
T PRK14351 211 RIERGEEPFANPRNAAAGTLRQLDPSVVAERPLDIFFFDVLDASEL---FDSHWEELERFPEWGLRVTDR---------- 277 (689)
T ss_pred HHHcCCCCcCCHHHHHhhHhhccChHHHhcCCceEEEEecccCCCC---CCCHHHHHHHHHHCCCCcCCc----------
Confidence 02343323221 111211 01236899999999654431 246788888888753222211
Q ss_pred CccccCCCCCccccccCCHHHHHHHHHHHHHc------CCceEEEecCCCCCc----CCCCCCCe---EEEccccccCCC
Q 002803 384 NSHVRPQGEPCWSLVAHNVDEVEKFFKETIEN------RDEGIVLKDLGSKWE----PGDRSGKW---LKLKPEYIRAGS 450 (879)
Q Consensus 384 ~~~v~~~~~~~~~~~~~~~~ei~~~~~~~i~~------g~EGlV~K~~~s~Y~----~g~Rs~~W---lKvKp~y~~~g~ 450 (879)
...+.+.+++..++++..+. .-.|||+|--+-.+. ...+++.| +|+.++
T Consensus 278 ------------~~~~~~~~~~~~~~~~~~~~R~~l~y~iDGiViKvn~~~~q~~lG~ts~~PrWaiA~Kf~~~------ 339 (689)
T PRK14351 278 ------------TERVDDIDDAIAYRDRLLAARDDLNYEIDGVVIKVDDRDAREELGATARAPRWAFAYKFPAR------ 339 (689)
T ss_pred ------------eEeeCCHHHHHHHHHHHHHhhhcCCCCCceEEEEeCCHHHHHHhCccCCCCCceEEEcCCCc------
Confidence 22356788888888766533 457999997665442 12356777 466654
Q ss_pred cceEEEEEEEeCCCCCCCCcceEEEEEecCCC-CCCCCceEEEEEEecCCCCHHHHHHHH
Q 002803 451 DLDVLIIGGYYGSGRRGGEVAQFLVALAERPA-PDTYPRRFISFCRVGTGLSDEELDAVV 509 (879)
Q Consensus 451 ~lDlvVIG~~~G~Grr~g~~~sfl~g~~~~~~-~~~~~~~~~~~~kVgtG~s~~~~~~l~ 509 (879)
...-.|.+..|..|| .|.+.- +|..++-. + +. ++.++ |..+.++.+++.
T Consensus 340 ~~~T~l~~I~~qVGR-TG~iTP--VA~lePV~l~----G~--tVsra-tLhN~~~i~~~d 389 (689)
T PRK14351 340 AEETTIRDIVVQVGR-TGRLTP--VALLDPVDVG----GV--TVSRA-SLHNPAEIEELG 389 (689)
T ss_pred eeEEEEEEEEEecCC-Cceeee--EEEEEeEEEC----CE--EEEEe-ccCCHHHHHHcC
Confidence 566678888888886 455543 23222211 1 11 34444 677777776643
No 69
>KOG3524 consensus Predicted guanine nucleotide exchange factor (PEBBLE) [Signal transduction mechanisms]
Probab=97.09 E-value=0.0023 Score=74.67 Aligned_cols=144 Identities=17% Similarity=0.210 Sum_probs=94.9
Q ss_pred CCCcccCeEEEEEcCCCCCCHHHHHHHHHHcCCEEeeccCCCeeEEEEecCCchhhhhhccCCCeeeechHHHhhhcCcc
Q 002803 653 ETSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADNKGLKYEAAKRRGDVIHYSWVLDCCSQKKL 732 (879)
Q Consensus 653 ~s~iF~g~~F~vl~~~~~~~k~eLe~lI~~~GG~~v~n~~~~~T~~I~~~~~~~k~~~~~~~~~IV~p~Wl~dCi~~~~l 732 (879)
-+..|+++.-|.. | ....+.+|-.+|...||-|.-..+..+||.|+....+-|+..+.-.-++++|.||..|++...
T Consensus 115 y~~~m~~vvlcfT-g-~rkk~e~lv~lvh~mgg~irkd~nsktthli~n~s~gek~~~a~t~~~~~rp~wv~~aw~~rn- 191 (850)
T KOG3524|consen 115 YCELMKDVVMCFT-G-ERKKKEELVDLVHYMGGSIRKDTNSKTTHLIANKVEGEKQSIALVGVPTMRPDWVTEAWKHRN- 191 (850)
T ss_pred cchhhcCceeeee-c-cchhhHHHHHHHHHhcceeEeeeccCceEEEeecccceEEEEEeeccceechHhhhhhhcCcc-
Confidence 3668899988874 3 234455999999999999988877678999975544544444333348999999999986321
Q ss_pred cCCCccccccCChhhHhHhhhhhccCCCcccccCCHHHHHHHHhhcCCCCChhhHHHHHhhcCCCCCCCCCCCcEEEEcC
Q 002803 733 LQLQPKYYLHLSDSSKKKLQEEVDEFSDLYFWDLDLADIKQLLSNVDRSEDPKTIDYYKKKYCPQDKWSCFHGCCIYFYH 812 (879)
Q Consensus 733 lp~~p~~~l~~s~~~~~~~~~~~D~ygDSy~~~~~~~~l~~ll~~~~~~~~~~~~~~l~~~~~~~~~~~lF~~~~vy~~~ 812 (879)
.. .+....+.|-|-| ..--|.||.++|++
T Consensus 192 ------~~---------yfda~~~~f~d~h------------------------------------rl~~feg~~~~f~g 220 (850)
T KOG3524|consen 192 ------DS---------YFDAMEPCFVDKH------------------------------------RLGVFEGLSLFFHG 220 (850)
T ss_pred ------hh---------hhhhhccchhhhh------------------------------------ccccccCCeEeecC
Confidence 10 0111111111111 12348999999999
Q ss_pred CCCCCCChhHHHHHHHHHHHHHHhhhcCceeccCCCCCeeEEEEccCCCC
Q 002803 813 STEPLSPDWEVLLGLALRRLKLEISFHGVSLPERNIFYGTRSCMLLDPSG 862 (879)
Q Consensus 813 ~~~~~~~~~~~~~~~~l~~~~~~i~~~GG~v~~~~~~~vTHVVv~~d~~~ 862 (879)
+.+- .-+-+-.-..--||+.. ..+..||||||.++-..
T Consensus 221 F~~e-----------e~~~m~~sle~~gg~~a-~~d~~cthvvv~e~~~~ 258 (850)
T KOG3524|consen 221 FKQE-----------EIDDMLRSLENTGGKLA-PSDTLCTHVVVNEDNDE 258 (850)
T ss_pred CcHH-----------HHHHHHHHHHhcCCccc-CCCCCceeEeecCCccc
Confidence 8621 22234455678899999 47788999999775443
No 70
>PLN03123 poly [ADP-ribose] polymerase; Provisional
Probab=97.01 E-value=0.0011 Score=82.76 Aligned_cols=86 Identities=17% Similarity=0.347 Sum_probs=69.4
Q ss_pred CCCCcccCeEEEEEcCCCCCCHHHHHHHHHHcCCEEeeccCCCeeEEEEec---CCchhhhhhccCC-CeeeechHHHhh
Q 002803 652 GETSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAAD---NKGLKYEAAKRRG-DVIHYSWVLDCC 727 (879)
Q Consensus 652 ~~s~iF~g~~F~vl~~~~~~~k~eLe~lI~~~GG~~v~n~~~~~T~~I~~~---~~~~k~~~~~~~~-~IV~p~Wl~dCi 727 (879)
+....|.|+.|+++ |....++.++.++|..|||+++......+||+|+.. +.+.|++.+.+.+ +||+.+||.||+
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 SESEFLGDLKVSIV-GASKEKVTEWKAKIEEAGGVFHATVKKDTNCLVVCGELDDEDAEMRKARRMKIPIVREDYLVDCF 467 (981)
T ss_pred ccCCCcCCeEEEEe-cCCCCcHHHHHHHHHhcCCEEeeeccCCceEEEccHHhhhcchHHHHHHhcCCCcccHHHHHHHH
Confidence 56788999999875 444566799999999999999998877778776532 3455677777777 999999999999
Q ss_pred hcCcccCCCcc
Q 002803 728 SQKKLLQLQPK 738 (879)
Q Consensus 728 ~~~~llp~~p~ 738 (879)
..+..+|...+
T Consensus 468 ~~~~~~p~~~y 478 (981)
T PLN03123 468 KKKKKLPFDKY 478 (981)
T ss_pred hccccCcchhh
Confidence 99888887754
No 71
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=96.94 E-value=0.011 Score=71.82 Aligned_cols=223 Identities=17% Similarity=0.163 Sum_probs=125.8
Q ss_pred ceEEEEecceEEEEEEEeCCE-EEEEec----CCCCCCCch---hhhHHHHHhhccccceeeeceEEEeeCCCC-----c
Q 002803 246 EVVIECKFDGDRIQIHKNGSE-IHYFSR----SFLDHSEYG---HAMSKIIEQNVLVDRCILDGEMLVWDTSLN-----R 312 (879)
Q Consensus 246 ~~~iE~K~DGeR~qih~~g~~-v~~~SR----~g~~~t~~~---~~l~~~~~~~~~~~~~ILDGEmv~~d~~~~-----~ 312 (879)
.|++|+|+||.-+.+.+.+|. ++..|| .|+|+|+-. +++-..+. ....+.+-||++.-...-. .
T Consensus 111 ~~~~epKiDGlaisL~YenG~L~~a~TRGDG~~GEDVT~n~~~I~~IP~~l~---~~~~levRGEv~m~~~~F~~lN~~~ 187 (669)
T PRK14350 111 GISVEPKIDGCSIVLYYKDGILEKALTRGDGRFGNDVTENVRTIRNVPLFID---EKVELVLRGEIYITKENFLKINKTL 187 (669)
T ss_pred eEEEEEecccEEEEEEEECCEEEEEEecCCCCcchhHhhhhhhhcccchhcC---CCceEEEEEEEEeeHHHHHHHHHhh
Confidence 599999999999999887665 788999 588888622 22221111 1245788999987321100 0
Q ss_pred cccccchHHHH-HHhhcC---CCCCCceEEEEEEEEEeCCccccCCCHHHHHHHHHhhcCCCCCcceecccCCCCCcccc
Q 002803 313 FAEFGSNQEIA-KAARDG---LSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVR 388 (879)
Q Consensus 313 ~~pF~~l~~~~-~~~~~~---~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~v~~~~~~~~i~~p~~~~~~~v~ 388 (879)
-.+|..-++.+ ...|.. ....+++.|++|++..-++ ...+..++.+.|.++-=++.....+
T Consensus 188 ~~~faNpRNaaAGsLr~~d~~~~a~r~L~f~~y~~~~~~~---~~~t~~e~l~~L~~~GF~v~~~~~~------------ 252 (669)
T PRK14350 188 EKPYTNARNLASGILRRIDSREVANFPLDIFVYDILYSSL---ELKTNHDAFDKLKKFGFKVNPFCRF------------ 252 (669)
T ss_pred hccCCChhHHHHHHHHccCchhhhcCceEEEEEEcccCCC---CCCCHHHHHHHHHHCCCCCCcceEE------------
Confidence 12343333321 111211 1124589999999853222 1236788888888753222211000
Q ss_pred CCCCCccccccCCHHHHHHHHHHHHHc------CCceEEEecCCCCCcC--C--CCCCCe---EEEccccccCCCcceEE
Q 002803 389 PQGEPCWSLVAHNVDEVEKFFKETIEN------RDEGIVLKDLGSKWEP--G--DRSGKW---LKLKPEYIRAGSDLDVL 455 (879)
Q Consensus 389 ~~~~~~~~~~~~~~~ei~~~~~~~i~~------g~EGlV~K~~~s~Y~~--g--~Rs~~W---lKvKp~y~~~g~~lDlv 455 (879)
.....+.+++..+++++... .-.|||+|--+-.+.. | .+++.| +|+.++ ...-.
T Consensus 253 -------~~~~~~~~e~~~~~~~~~~~R~~l~y~iDGiViKvn~~~~q~~lG~ts~~PrWaiA~Kf~~~------~~~T~ 319 (669)
T PRK14350 253 -------FDGKNSIEEILNYVKDIEKKRNSFEYEIDGVVLKVSDFALREILGYTSHHPKWSMAYKFESL------SGFSK 319 (669)
T ss_pred -------EcCCCcHHHHHHHHHHHHHHHhcCCCCCCcEEEEecCHHHHHhcCCcCCCCCceEEEcCCCc------eeEEE
Confidence 00113477888877765433 4589999965543321 2 346777 577665 56667
Q ss_pred EEEEEeCCCCCCCCcceEEEEEecCCC-CCCCCceEEEEEEecCCCCHHHHHHHH
Q 002803 456 IIGGYYGSGRRGGEVAQFLVALAERPA-PDTYPRRFISFCRVGTGLSDEELDAVV 509 (879)
Q Consensus 456 VIG~~~G~Grr~g~~~sfl~g~~~~~~-~~~~~~~~~~~~kVgtG~s~~~~~~l~ 509 (879)
|.+..|..|| .|.+.- +|..++-. + + .++.++ |..+.++.+++.
T Consensus 320 l~~I~~qVGR-TG~iTP--VA~l~PV~l~----G--~tVsrA-TLhN~~~I~~~d 364 (669)
T PRK14350 320 VNDIVVQVGR-SGKITP--VANIEKVFVA----G--AFITNA-SLHNQDYIDSIG 364 (669)
T ss_pred EEEEEEecCC-ceeeeE--EEEEEeEEEC----C--EEEEEe-ccCCHHHHHHcC
Confidence 8888888886 455543 22222211 1 1 234444 777777776643
No 72
>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=96.69 E-value=0.0048 Score=53.08 Aligned_cols=49 Identities=18% Similarity=0.068 Sum_probs=37.3
Q ss_pred CCCCCCcEEEEcCCCCCCCChhHHHHHHHHHHHHHHhhhcCceeccCCCCCeeEEEEccC
Q 002803 800 WSCFHGCCIYFYHSTEPLSPDWEVLLGLALRRLKLEISFHGVSLPERNIFYGTRSCMLLD 859 (879)
Q Consensus 800 ~~lF~~~~vy~~~~~~~~~~~~~~~~~~~l~~~~~~i~~~GG~v~~~~~~~vTHVVv~~d 859 (879)
..+|+||+||+.... . ...+.+...|+.+||+++......+||||+...
T Consensus 3 ~~~F~g~~f~i~~~~---~--------~~~~~l~~~i~~~GG~v~~~~~~~~thvI~~~~ 51 (78)
T PF00533_consen 3 PKIFEGCTFCISGFD---S--------DEREELEQLIKKHGGTVSNSFSKKTTHVIVGNP 51 (78)
T ss_dssp TTTTTTEEEEESSTS---S--------SHHHHHHHHHHHTTEEEESSSSTTSSEEEESSS
T ss_pred CCCCCCEEEEEccCC---C--------CCHHHHHHHHHHcCCEEEeecccCcEEEEeCCC
Confidence 468999999993332 1 134466889999999998555678999999765
No 73
>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=96.68 E-value=0.023 Score=62.60 Aligned_cols=106 Identities=17% Similarity=0.118 Sum_probs=64.1
Q ss_pred hCCCceEEEEecceEEEEEEEeCC-EEEEEecCCCCCC-----Cc---hhhhHHHHH---hh------ccccceeeeceE
Q 002803 242 LHGKEVVIECKFDGDRIQIHKNGS-EIHYFSRSFLDHS-----EY---GHAMSKIIE---QN------VLVDRCILDGEM 303 (879)
Q Consensus 242 ~~~~~~~iE~K~DGeR~qih~~g~-~v~~~SR~g~~~t-----~~---~~~l~~~~~---~~------~~~~~~ILDGEm 303 (879)
+.+.+|.+.+|+||...-+.++++ .+++.||++.-.. .+ .+.+...+. .. ....++++=||+
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 445689999999999999988877 8999999965322 11 122211111 11 124678899999
Q ss_pred EEeeCCCCccccccchHHHHHHhhcCCCCCCceEEEEEEEEEeCCccccCCCHHHHHHHHHhh
Q 002803 304 LVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKV 366 (879)
Q Consensus 304 v~~d~~~~~~~pF~~l~~~~~~~~~~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~ 366 (879)
+.|.-..+. . +. ...|++|||.........-+++.+-.+.....
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 986421110 0 11 35799999955322123445666666655543
No 74
>PRK01109 ATP-dependent DNA ligase; Provisional
Probab=96.60 E-value=0.0087 Score=72.19 Aligned_cols=97 Identities=14% Similarity=0.112 Sum_probs=79.6
Q ss_pred CCCCcHHHHHHHHHHHHhcC---ChhHHHHHHHHHHhhcCCCChHhhhHhhcCCCCCcCccccCCCHHHHHHHHHHHhCC
Q 002803 4 TEETEVIVLVSLFNWIQKTK---PAAKKRSKFRKFLDTYCDSVDYFSALRLILPSLDRERGSYGLKESVLANCLIDALGM 80 (879)
Q Consensus 4 ~~~~~F~~l~~~~e~i~~~~---~~~~k~~~l~~~~~~~~~~~~~~p~lrLllP~~d~~r~~yglke~~L~k~~~~~~~~ 80 (879)
.++++|.+++++|++|++++ ++.+|..+|.++|.+. ++.+...++||++-.+- .|++++++.++|+.+++.
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 56889999999999882 899999999999999983
Q ss_pred CcChHHHHHHhhhhcCCCCCCCCCHHHHHHHHHh
Q 002803 81 SKDSADAVRLINWRKGGAAPNAGNFPMVAAEVLQ 114 (879)
Q Consensus 81 ~~~s~~~~~L~~wk~~~~~~~~gD~~~~~~~v~~ 114 (879)
.....+..++.+ ..||++.+|..+..
T Consensus 186 ~~~~~~ve~~y~--------~~~Dlg~va~~l~~ 211 (590)
T PRK01109 186 AVARELVERAYN--------LRADLGYIAKILAE 211 (590)
T ss_pred ccchHHHHHHHH--------hCCCHHHHHHHHHh
Confidence 223334444443 47999999887654
No 75
>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=96.42 E-value=0.0059 Score=62.46 Aligned_cols=106 Identities=22% Similarity=0.333 Sum_probs=61.6
Q ss_pred ceEEEEecceEEEEEEEe-CCEEEEEecCCC-----CCCCc-------hhhhH--HHHHh-h-----ccccceeeeceEE
Q 002803 246 EVVIECKFDGDRIQIHKN-GSEIHYFSRSFL-----DHSEY-------GHAMS--KIIEQ-N-----VLVDRCILDGEML 304 (879)
Q Consensus 246 ~~~iE~K~DGeR~qih~~-g~~v~~~SR~g~-----~~t~~-------~~~l~--~~~~~-~-----~~~~~~ILDGEmv 304 (879)
+|.+++|+||.-+.+.+. ++.+++.+|++. ++-.. ...+. ..+.. . ....++++=||++
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 445999999982 22111 11110 01111 1 2356889999999
Q ss_pred EeeCCCCccccccchHHHHHHhhcCCCCCCceEEEEEEEEEeCCc-cccCCCHHHHHHHHHhh
Q 002803 305 VWDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDT-SVIHQSLKERHELLQKV 366 (879)
Q Consensus 305 ~~d~~~~~~~pF~~l~~~~~~~~~~~~~~~~~~~~vFDiL~lng~-~l~~~pl~eRr~~L~~~ 366 (879)
.|-+.-.. ... + ...+..|++|||...+.. ...-++..+.+.+++.+
T Consensus 82 G~~~~Iq~----~~~---------~--~~~~~~F~~Fdi~~~~~~~~~~~l~~~~~~~~~~~~ 129 (186)
T PF09414_consen 82 GAKPSIQK----NRY---------Q--LDPPKDFYVFDIYDIDEQGEIRYLSWDEVREFAEEL 129 (186)
T ss_dssp CEECTTCS----S---------------ECCCEEEEEEEEEEETCCGEEE-HHHHHHHHHCCC
T ss_pred eecccccc----ccc---------c--cCCCceEEEEEEEEcCCCCeeEECCHHHHHHHHHHC
Confidence 87642110 000 0 012578999999988542 22445777788777764
No 76
>KOG3548 consensus DNA damage checkpoint protein RHP9/CRB2/53BP1 [Replication, recombination and repair]
Probab=96.24 E-value=0.0037 Score=74.91 Aligned_cols=92 Identities=24% Similarity=0.354 Sum_probs=63.9
Q ss_pred CCcccCeEEEEEcCCCCCCHHHHHHHHHHcCCEEeec-cCC-----------------------Ce-eEEEEecC--Cch
Q 002803 654 TSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMN-LNN-----------------------SV-THCVAADN--KGL 706 (879)
Q Consensus 654 s~iF~g~~F~vl~~~~~~~k~eLe~lI~~~GG~~v~n-~~~-----------------------~~-T~~I~~~~--~~~ 706 (879)
.+||.||.|.. .+. ..+.+.+..-+..|||.+... ..+ ++ --|++++. ++.
T Consensus 923 kniFd~cvF~l-Tsa-~~sd~~~r~s~e~~gg~vle~gl~~~Fn~p~~g~~~~lr~Ln~~q~~ks~~qalLIsdth~Rt~ 1000 (1176)
T KOG3548|consen 923 KNIFDGCVFML-TSA-NRSDSASRPSMEKHGGLVLEKGLMNLFNTPFKGGGIVLRQLNSFQERKSNYQALLISDTHYRTH 1000 (1176)
T ss_pred cchhcceeEEE-ecc-ccchhhhhhhhhccCChhhhccccccccccccCCcchHHhhhHHhhhccccceeEeehhhhHHH
Confidence 37999999965 442 344555666666699887532 110 11 12444554 678
Q ss_pred hhhhhccCC-CeeeechHHHhhhcCcccCCCccccccCChhhH
Q 002803 707 KYEAAKRRG-DVIHYSWVLDCCSQKKLLQLQPKYYLHLSDSSK 748 (879)
Q Consensus 707 k~~~~~~~~-~IV~p~Wl~dCi~~~~llp~~p~~~l~~s~~~~ 748 (879)
||-.+...| +|||+.||.+|+++++++|+.+ |+|.+..+.+
T Consensus 1001 KYLeaLA~giPcVh~~fI~aC~e~nr~Vdy~~-YLLpsGyS~r 1042 (1176)
T KOG3548|consen 1001 KYLEALARGIPCVHNTFIQACGEQNRCVDYTD-YLLPSGYSIR 1042 (1176)
T ss_pred HHHHHHHcCCCcccHHHHHHHHhccccccchh-hcccCccccc
Confidence 888888888 9999999999999999999997 6777654433
No 77
>KOG1929 consensus Nucleotide excision repair factor NEF2, RAD4/CUT5 component [Replication, recombination and repair]
Probab=95.77 E-value=0.037 Score=67.70 Aligned_cols=143 Identities=21% Similarity=0.224 Sum_probs=99.9
Q ss_pred CCcccCeEEEEEcCCCCCCHHHHHHHHHHcCCEEeeccCCCeeEEEEecCCchhhhhhccCC-CeeeechHHHhhhcCcc
Q 002803 654 TSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADNKGLKYEAAKRRG-DVIHYSWVLDCCSQKKL 732 (879)
Q Consensus 654 s~iF~g~~F~vl~~~~~~~k~eLe~lI~~~GG~~v~n~~~~~T~~I~~~~~~~k~~~~~~~~-~IV~p~Wl~dCi~~~~l 732 (879)
+.-|+|+.||- ++.....+.+|.+.+...||.+.+..+.++||+|+..-..-|+.++.+.+ +|++++|+..-..++.+
T Consensus 7 ~~~~~~v~~~~-t~i~p~~~~~l~~~~~~~Gg~~~~~~t~~~thli~~~~~s~~~~~a~~~~~~~~~~~wi~~~~d~~~~ 85 (811)
T KOG1929|consen 7 SKPMSGVTFSP-TGINPIKREELSKKFIKLGGIDFKDFTPSVTHLIVGSVTSSKYAAAHRFDIKVLDSSWIDYIYDLWLL 85 (811)
T ss_pred CcccCCceecc-CcCCHHHHHHHHHHHHhcCceeeeccCCcCceeecccccccchhhhhcCCCceecchHHHHHHHHhhh
Confidence 45788999985 55567788999999999999999999999999997665566675555555 89999999886654432
Q ss_pred cCCCccccccCChhhHhHhhhhhccCCCcccccCCHHHHHHHHhhcCCCCChhhHHHHHhhcCCCCCCCCCCCcEEEEcC
Q 002803 733 LQLQPKYYLHLSDSSKKKLQEEVDEFSDLYFWDLDLADIKQLLSNVDRSEDPKTIDYYKKKYCPQDKWSCFHGCCIYFYH 812 (879)
Q Consensus 733 lp~~p~~~l~~s~~~~~~~~~~~D~ygDSy~~~~~~~~l~~ll~~~~~~~~~~~~~~l~~~~~~~~~~~lF~~~~vy~~~ 812 (879)
- +. .+ ..|. +. .....-.|.+|.|++.+
T Consensus 86 -~-~e---------~~-----~~~~--------------------------------l~----~~~~~p~~~~~~Vc~tg 113 (811)
T KOG1929|consen 86 -N-KE---------IR-----LLDP--------------------------------LR----DTMKCPGFFGLKVCLTG 113 (811)
T ss_pred -h-cc---------Cc-----cCcc--------------------------------ch----hhhcCCcccceEEEecc
Confidence 1 10 00 0010 00 00112357899999988
Q ss_pred CCCCCCChhHHHHHHHHHHHHHHhhhcCceeccCCC-CCeeEEEEccCCC
Q 002803 813 STEPLSPDWEVLLGLALRRLKLEISFHGVSLPERNI-FYGTRSCMLLDPS 861 (879)
Q Consensus 813 ~~~~~~~~~~~~~~~~l~~~~~~i~~~GG~v~~~~~-~~vTHVVv~~d~~ 861 (879)
+. +.....++.+|.-+||+.. ..+ ..++||++..-..
T Consensus 114 l~-----------~~eK~ei~~~v~k~gg~~~-~~L~s~v~~~~~~~~~~ 151 (811)
T KOG1929|consen 114 LS-----------GDEKSEIKILVPKHGGTLH-RSLSSDVNSLKILPEVK 151 (811)
T ss_pred cc-----------hHHHHHHHHHhhhcccEEe-hhhhhhhheeeeccccc
Confidence 75 2356678889999999999 555 5678887766443
No 78
>smart00292 BRCT breast cancer carboxy-terminal domain.
Probab=95.48 E-value=0.025 Score=47.93 Aligned_cols=51 Identities=16% Similarity=-0.019 Sum_probs=37.5
Q ss_pred CCCCcEEEEcCCCCCCCChhHHHHHHHHHHHHHHhhhcCceeccCCCC-CeeEEEEccCCCC
Q 002803 802 CFHGCCIYFYHSTEPLSPDWEVLLGLALRRLKLEISFHGVSLPERNIF-YGTRSCMLLDPSG 862 (879)
Q Consensus 802 lF~~~~vy~~~~~~~~~~~~~~~~~~~l~~~~~~i~~~GG~v~~~~~~-~vTHVVv~~d~~~ 862 (879)
+|+||+||+.+.. . ....+.+...+..+||++...... ++||||+......
T Consensus 2 ~f~g~~~~~~g~~-~---------~~~~~~l~~~i~~~Gg~~~~~~~~~~~thvi~~~~~~~ 53 (80)
T smart00292 2 LFKGKVFVITGKF-D---------KNERDELKELIEALGGKVTSSLSSKTTTHVIVGSPEGG 53 (80)
T ss_pred ccCCeEEEEeCCC-C---------CccHHHHHHHHHHcCCEEecccCccceeEEEEcCCCCc
Confidence 6999999998721 1 124457788999999999933334 8999999765543
No 79
>KOG2093 consensus Translesion DNA polymerase - REV1 deoxycytidyl transferase [Replication, recombination and repair]
Probab=95.39 E-value=0.011 Score=71.03 Aligned_cols=101 Identities=14% Similarity=0.155 Sum_probs=76.7
Q ss_pred cCCCCCcccCeEEEEEcCCCCCCHHHHHHHHHHcCCEEe-eccCCCeeEEEEecCCchhhhhhccCCCeeeechHHHhhh
Q 002803 650 IKGETSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFS-MNLNNSVTHCVAADNKGLKYEAAKRRGDVIHYSWVLDCCS 728 (879)
Q Consensus 650 ~~~~s~iF~g~~F~vl~~~~~~~k~eLe~lI~~~GG~~v-~n~~~~~T~~I~~~~~~~k~~~~~~~~~IV~p~Wl~dCi~ 728 (879)
-...++.|+|..||+ +|....+..+|.+.-.-|||.+. .+....++++|+.+....+++.. +.-+.++++|+.+|++
T Consensus 41 ~~t~~s~fs~is~~~-ngs~~e~~nelk~~~~~~t~~~~~~~~rs~T~~ii~~~l~a~~vk~~-~~~~~~~~e~iie~~~ 118 (1016)
T KOG2093|consen 41 AATGSSSFSGISISV-NGSTDESANELKLQNMFHTGASAASYERSGTENIIAQGLPADLVKGF-TIPKHISIEWIIECCE 118 (1016)
T ss_pred CcCCcceeeeeeecc-CCccccchHHHhhhhhhcccccccccccccceeeecccchHHHhccc-cchhhhcHHHHHHHHh
Confidence 345688999999997 89889999999999999999997 44434567888655444444433 1127899999999999
Q ss_pred cCcccCCCccccccCChhhHhHhh
Q 002803 729 QKKLLQLQPKYYLHLSDSSKKKLQ 752 (879)
Q Consensus 729 ~~~llp~~p~~~l~~s~~~~~~~~ 752 (879)
++.++.+.|+++.......+...+
T Consensus 119 ~~~~~~~~~~~~~t~~~h~q~~~~ 142 (1016)
T KOG2093|consen 119 NGMDVGYYPYQLYTGQSHEQAQLA 142 (1016)
T ss_pred ccCccccccceeeccchhcccccC
Confidence 999999999887766554444443
No 80
>PHA02142 putative RNA ligase
Probab=95.00 E-value=0.36 Score=54.23 Aligned_cols=104 Identities=15% Similarity=0.202 Sum_probs=65.1
Q ss_pred hCCCceEEEEecceEEEEEEEe---------------------CCEEEEEecCCC-CCCC---chh-----hhHHHHHhh
Q 002803 242 LHGKEVVIECKFDGDRIQIHKN---------------------GSEIHYFSRSFL-DHSE---YGH-----AMSKIIEQN 291 (879)
Q Consensus 242 ~~~~~~~iE~K~DGeR~qih~~---------------------g~~v~~~SR~g~-~~t~---~~~-----~l~~~~~~~ 291 (879)
..+..|.+.+|+||.-|.+.+. .+.+..-|||.. ++.. +.. .+.+.+.+
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 4467899999999999988732 456778889875 2221 111 12222211
Q ss_pred ccccceeeeceEEEeeCCCCccccccchHHHHHHhhcCCCCCCceEEEEEEEEEeCCccccCCCHHHHHHHHHhhc
Q 002803 292 VLVDRCILDGEMLVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVV 367 (879)
Q Consensus 292 ~~~~~~ILDGEmv~~d~~~~~~~pF~~l~~~~~~~~~~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~v 367 (879)
...++.+=||++.-.-.++. ..-....|++|||-.++++. -+++.++.++++++=
T Consensus 245 -~~~~iaIqGEl~Gp~IQ~N~------------------~~~~~~~F~vF~v~~i~~~~--yl~~~e~~~~~~~~g 299 (366)
T PHA02142 245 -LGMSVAIQGELMGPGIQKNR------------------ENFDKYRIFAFRAWFIDEQR--FATDEEFQDLCRTLG 299 (366)
T ss_pred -hCCcEEEEEEEecccccCcc------------------ccCCCCceEEEEEEEeccce--eCCHHHHHHHHHHcC
Confidence 13578899999872211110 01112469999998777664 568899999888753
No 81
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=94.71 E-value=0.066 Score=65.36 Aligned_cols=76 Identities=14% Similarity=0.252 Sum_probs=63.4
Q ss_pred CCcccCeEEEEEcCCCCCCHHHHHHHHHHcCCEEeeccCCCeeEEEEecCCc-hhhhhhccCC-CeeeechHHHhhhc
Q 002803 654 TSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADNKG-LKYEAAKRRG-DVIHYSWVLDCCSQ 729 (879)
Q Consensus 654 s~iF~g~~F~vl~~~~~~~k~eLe~lI~~~GG~~v~n~~~~~T~~I~~~~~~-~k~~~~~~~~-~IV~p~Wl~dCi~~ 729 (879)
...|.|..||+...-...++++++++|.++||++..+++..++++|+++..+ -|.+.+.+.| .||.-+-+++-+++
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 4579999999854445679999999999999999999988788888877667 5888888888 99998888886653
No 82
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=94.64 E-value=0.069 Score=64.93 Aligned_cols=74 Identities=16% Similarity=0.249 Sum_probs=61.0
Q ss_pred CCcccCeEEEEEcCCCCCCHHHHHHHHHHcCCEEeeccCCCeeEEEEecCCchhhhhhccCC-CeeeechHHHhh
Q 002803 654 TSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADNKGLKYEAAKRRG-DVIHYSWVLDCC 727 (879)
Q Consensus 654 s~iF~g~~F~vl~~~~~~~k~eLe~lI~~~GG~~v~n~~~~~T~~I~~~~~~~k~~~~~~~~-~IV~p~Wl~dCi 727 (879)
...|.|..||+...-...++++++++|.++||+++..++..++++|++...+-|...+.+-| .|+.-+.+++-+
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 34699999987544467899999999999999999999877778888766778888888878 899888777643
No 83
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=94.56 E-value=0.077 Score=59.00 Aligned_cols=73 Identities=15% Similarity=0.172 Sum_probs=58.8
Q ss_pred CCcccCeEEEEEcCCCCCCHHHHHHHHHHcCCEEeeccCCCeeEEEEecCCc--hhhhhhccCC-CeeeechHHHhh
Q 002803 654 TSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADNKG--LKYEAAKRRG-DVIHYSWVLDCC 727 (879)
Q Consensus 654 s~iF~g~~F~vl~~~~~~~k~eLe~lI~~~GG~~v~n~~~~~T~~I~~~~~~--~k~~~~~~~~-~IV~p~Wl~dCi 727 (879)
..+|.|..|++ .|.-..++++++++|.++||++..+++..++++|+++..+ -|.+.+.+-| .||.-+=+++-+
T Consensus 230 ~~l~~g~~~v~-TG~l~~~R~e~~~~~~~~G~~v~~sVs~~t~~lv~g~~~~~ssK~~kA~~~gi~ii~e~~f~~ll 305 (313)
T PRK06063 230 RPLVQGMRVAL-SAEVSRTHEELVERILHAGLAYSDSVDRDTSLVVCNDPAPEQGKGYHARQLGVPVLDEAAFLELL 305 (313)
T ss_pred CcccCCCEEEE-ecCCCCCHHHHHHHHHHcCCEecCccccCccEEEECCCCCcccHHHHHHHcCCccccHHHHHHHH
Confidence 57899999976 5554579999999999999999999988788888876655 5888777777 888776665544
No 84
>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=93.95 E-value=0.11 Score=42.78 Aligned_cols=48 Identities=15% Similarity=-0.055 Sum_probs=35.1
Q ss_pred CcEEEEcCCCCCCCChhHHHHHHHHHHHHHHhhhcCceeccCCCCCeeEEEEccCCCC
Q 002803 805 GCCIYFYHSTEPLSPDWEVLLGLALRRLKLEISFHGVSLPERNIFYGTRSCMLLDPSG 862 (879)
Q Consensus 805 ~~~vy~~~~~~~~~~~~~~~~~~~l~~~~~~i~~~GG~v~~~~~~~vTHVVv~~d~~~ 862 (879)
||.||+.+.... .....+...++.+||++.+.....+||+|+......
T Consensus 1 ~~~~~i~g~~~~----------~~~~~l~~~i~~~Gg~v~~~~~~~~thvI~~~~~~~ 48 (72)
T cd00027 1 GLTFVITGDLPS----------EERDELKELIEKLGGKVTSSVSKKTTHVIVGSDAGP 48 (72)
T ss_pred CCEEEEEecCCC----------cCHHHHHHHHHHcCCEEeccccCCceEEEECCCCCc
Confidence 688999886411 134567889999999999444458999999775553
No 85
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=93.89 E-value=0.11 Score=57.68 Aligned_cols=49 Identities=20% Similarity=0.235 Sum_probs=41.1
Q ss_pred CCcccCeEEEEEcCCCCCCHHHHHHHHHHcCCEEeeccCCCeeEEEEec
Q 002803 654 TSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAAD 702 (879)
Q Consensus 654 s~iF~g~~F~vl~~~~~~~k~eLe~lI~~~GG~~v~n~~~~~T~~I~~~ 702 (879)
...|.|..||+...-...++.+++++|+++||++..+++..++++|+++
T Consensus 218 ~~~l~g~~~vfTG~l~~~~R~~~~~~~~~~Gg~v~~sVs~~t~~lV~G~ 266 (309)
T PRK06195 218 FTAFKEEVVVFTGGLASMTRDEAMILVRRLGGTVGSSVTKKTTYLVTNT 266 (309)
T ss_pred CccccCCEEEEccccCCCCHHHHHHHHHHhCCEecCCcccCceEEEECC
Confidence 4579999998754445789999999999999999999987777788753
No 86
>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=93.53 E-value=0.14 Score=62.38 Aligned_cols=67 Identities=18% Similarity=0.289 Sum_probs=54.5
Q ss_pred CCcccCeEEEEEcCCCCCCHHHHHHHHHHcCCEEeeccCCCeeEEEEecCCchhhhhhccCC-Ceeee
Q 002803 654 TSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADNKGLKYEAAKRRG-DVIHY 720 (879)
Q Consensus 654 s~iF~g~~F~vl~~~~~~~k~eLe~lI~~~GG~~v~n~~~~~T~~I~~~~~~~k~~~~~~~~-~IV~p 720 (879)
...|.|..||+...-...++++++++|.++||+++.+++..++++|+++..+-|.+.+.+-| .|+.-
T Consensus 582 ~~~l~gk~~v~TG~l~~~~R~~~~~~i~~~G~~v~~sVs~kt~~lv~G~~~gsKl~kA~~lgi~ii~E 649 (652)
T TIGR00575 582 GSPLAGKTFVLTGTLSQMSRDEAKELLENLGGKVASSVSKKTDYVIAGEKAGSKLAKAQELGIPIINE 649 (652)
T ss_pred CCCccCcEEEEeccCCCCCHHHHHHHHHHcCCEEeCCcCCCccEEEECCCCChHHHHHHHcCCcEech
Confidence 34699999987543456899999999999999999999877778888776677888887777 77654
No 87
>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=93.03 E-value=0.72 Score=51.66 Aligned_cols=104 Identities=16% Similarity=0.163 Sum_probs=58.3
Q ss_pred CCceEEEEecceEEEEEEEeCC--EEE-----EEecCCCCCC---C-ch-----hhhHHHHHhhccccceeeeceEEEee
Q 002803 244 GKEVVIECKFDGDRIQIHKNGS--EIH-----YFSRSFLDHS---E-YG-----HAMSKIIEQNVLVDRCILDGEMLVWD 307 (879)
Q Consensus 244 ~~~~~iE~K~DGeR~qih~~g~--~v~-----~~SR~g~~~t---~-~~-----~~l~~~~~~~~~~~~~ILDGEmv~~d 307 (879)
+..|.+-+|+||.-|.+.+..+ .+. +-|||..-.. . |. ..+.+.+.+.....++.+=||++.-.
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 5789999999999998876322 222 3468765211 1 11 12333333222345778889998722
Q ss_pred CCCCccccccchHHHHHHhhcCCCCCCceEEEEEEEEEeCCccccCCCHHHHHHHHHhh
Q 002803 308 TSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKV 366 (879)
Q Consensus 308 ~~~~~~~pF~~l~~~~~~~~~~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~ 366 (879)
-.++ . +..+.+-.|++|++ +..|.. .=+++.++.++++++
T Consensus 238 IQ~n---~--------------Yg~~~~~~~f~F~v-~~~~~~-ryld~~~~~~~~~~~ 277 (341)
T TIGR02306 238 IQKN---R--------------YGFDKYRTVFAFRA-FFDGEQ-RFLTDEDFQDLCLTL 277 (341)
T ss_pred ccCC---c--------------CCCCCCceEEEEEE-EEcCcc-eecCHHHHHHHHHhc
Confidence 1111 0 11111212778888 555443 345889999988875
No 88
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=92.38 E-value=0.49 Score=56.70 Aligned_cols=131 Identities=22% Similarity=0.247 Sum_probs=89.7
Q ss_pred EEcCCCCCCHHHHHHHHHHcCCEEeeccCCCeeEEEEe------cCCchhhhhhccCC-CeeeechHHHhhhcCcccCCC
Q 002803 664 FVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAA------DNKGLKYEAAKRRG-DVIHYSWVLDCCSQKKLLQLQ 736 (879)
Q Consensus 664 vl~~~~~~~k~eLe~lI~~~GG~~v~n~~~~~T~~I~~------~~~~~k~~~~~~~~-~IV~p~Wl~dCi~~~~llp~~ 736 (879)
+.++-+.-.++-+++..+. ++..+++.++||+|+. ..+|.|+.--+-+| =|++..|++.|+..+.++|-+
T Consensus 482 ~~s~l~p~ek~~v~~~a~~---t~~k~~~~~~thvi~~~~~~g~c~rTlk~~~gil~gkwi~~~~w~~~s~k~~~~~~ee 558 (684)
T KOG4362|consen 482 LVSGLTPSEKQLVEKFAVD---TISKFWIEPVTHVIASTDLEGACLRTLKVLMGILRGKWILSYDWVLASLKLRKWVSEE 558 (684)
T ss_pred eeccCCcchHHHHHHHHHH---HHhhccCCCceeeeeecccccchhhhHHHHHHhhcCceeeeHHHHHHHHHhcCCCCCC
Confidence 4466566667778888877 8888888889999973 24677888777788 699999999999999999999
Q ss_pred ccccccCChhhHhHhhhhhccCCCcccccCCHHHHHHHHhhcCCCCChhhHHHHHhhcCCCCCCCCCCCcEEEEcCCCCC
Q 002803 737 PKYYLHLSDSSKKKLQEEVDEFSDLYFWDLDLADIKQLLSNVDRSEDPKTIDYYKKKYCPQDKWSCFHGCCIYFYHSTEP 816 (879)
Q Consensus 737 p~~~l~~s~~~~~~~~~~~D~ygDSy~~~~~~~~l~~ll~~~~~~~~~~~~~~l~~~~~~~~~~~lF~~~~vy~~~~~~~ 816 (879)
|..+-.-+...++.... .- ........-||.|.-|||.+...
T Consensus 559 pfEl~~d~~~~~~~~~~-------------------------------~~------~~a~s~~~kLf~gl~~~~~g~fs- 600 (684)
T KOG4362|consen 559 PFELQIDVPGAREGPKE-------------------------------KR------LRAESYKPKLFEGLKFYFVGDFS- 600 (684)
T ss_pred CeeEeecccCcccCccc-------------------------------cc------ccccccCcchhcCCcceeecccc-
Confidence 96544333322221100 00 00011235689999999998532
Q ss_pred CCChhHHHHHHHHHHHHHHhhhcCceec
Q 002803 817 LSPDWEVLLGLALRRLKLEISFHGVSLP 844 (879)
Q Consensus 817 ~~~~~~~~~~~~l~~~~~~i~~~GG~v~ 844 (879)
+.. -+.+...+...||.+-
T Consensus 601 -~~p--------~~~l~~l~~~~gg~~l 619 (684)
T KOG4362|consen 601 -NPP--------KEQLQELVHLAGGTIL 619 (684)
T ss_pred -cCc--------HHHHHHHHhhcCccee
Confidence 222 2356778899999885
No 89
>COG5275 BRCT domain type II [General function prediction only]
Probab=92.22 E-value=0.46 Score=48.59 Aligned_cols=80 Identities=25% Similarity=0.218 Sum_probs=59.9
Q ss_pred cccCCCCCcccCeEEEEEcCCCCCCHHHHHHHHHHcCCEEeeccCCCeeEEEEecCCch-hhhhhccCC-CeeeechHHH
Q 002803 648 SDIKGETSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADNKGL-KYEAAKRRG-DVIHYSWVLD 725 (879)
Q Consensus 648 ~~~~~~s~iF~g~~F~vl~~~~~~~k~eLe~lI~~~GG~~v~n~~~~~T~~I~~~~~~~-k~~~~~~~~-~IV~p~Wl~d 725 (879)
|..+++.+++.|..|.+...-...++.+-+.+|+.+||++..-|....+++|+++..++ |++.++..+ ++|.-+=++.
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 33456789999999966444456899999999999999999999877788888877655 566665555 6666655554
Q ss_pred hh
Q 002803 726 CC 727 (879)
Q Consensus 726 Ci 727 (879)
-|
T Consensus 228 LI 229 (276)
T COG5275 228 LI 229 (276)
T ss_pred HH
Confidence 44
No 90
>KOG3132 consensus m3G-cap-specific nuclear import receptor (Snurportin1) [RNA processing and modification]
Probab=90.82 E-value=1.6 Score=45.55 Aligned_cols=173 Identities=13% Similarity=0.146 Sum_probs=110.9
Q ss_pred cccceeeccChHHHHHHhCCCceEEEEecceEEEEEEEeCCEEEEEecCCCCCCCchhhhHHH-HHhhc-cccceeeece
Q 002803 225 RPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKI-IEQNV-LVDRCILDGE 302 (879)
Q Consensus 225 ~PmLA~~~~~~~~~~~~~~~~~~~iE~K~DGeR~qih~~g~~v~~~SR~g~~~t~~~~~l~~~-~~~~~-~~~~~ILDGE 302 (879)
+-||.+-+-++++. + +.+|++=.-==|-||.|.-..|...-|.|+|..... ||..... -.++. ...-.|||+
T Consensus 100 qlMLsEWliDvP~~---L-sqdW~vv~~PvGKR~lvVaSrG~Tvay~k~G~~v~r-F~S~LPGGnrr~~~a~~ytILDC- 173 (325)
T KOG3132|consen 100 QLMLSEWLIDVPDN---L-SQDWYVVARPVGKRCLVVASRGTTVAYVKNGSTVHR-FPSALPGGNRRKGPANSYTILDC- 173 (325)
T ss_pred HhhhHHHhccCccc---c-CcceEEEEeecCceEEEEecCCceEEEecCCeeEee-ccccCCCCCcCCCCcccceeeee-
Confidence 34665554444332 2 467999888899999998877888899999976542 2221100 00111 122357776
Q ss_pred EEEeeCCCCccccccchHHHHHHhhcCCCCCCceEEEEEEEEEeCCccccCCCHHHHHHHHHhhcCCCCCcceecccCCC
Q 002803 303 MLVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHG 382 (879)
Q Consensus 303 mv~~d~~~~~~~pF~~l~~~~~~~~~~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~v~~~~~~~~i~~p~~~ 382 (879)
+|+. ..-.|+|.|++..+|.++.+.|+.-|.-.|.+-+.+.++- ..|..+
T Consensus 174 --Iy~e-------------------------snQTYYVlD~~cWrgh~~yec~~dFRffwl~SKL~E~~~l---~~~t~~ 223 (325)
T KOG3132|consen 174 --IYHE-------------------------SNQTYYVLDMVCWRGHSLYECTSDFRFFWLQSKLAETGAL---DPPTVY 223 (325)
T ss_pred --eecc-------------------------cCceEEEEEEEeecCcccccCchHHHHHHHhhhccccccC---CCCCcC
Confidence 2322 1125999999999999999999999999999877654321 111100
Q ss_pred --CCccccCCCCCccccccCCHHHHHHHHHHHHHcCCceEEEecCCCCCcCCCCC-CCeEE
Q 002803 383 --LNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRS-GKWLK 440 (879)
Q Consensus 383 --~~~~v~~~~~~~~~~~~~~~~ei~~~~~~~i~~g~EGlV~K~~~s~Y~~g~Rs-~~WlK 440 (879)
..+.+.| .+ .-+.+.+.+++.-.+.-...||.+-.-.-.|.||... -+|+|
T Consensus 224 ~~f~Fs~vp------~~-pC~q~~l~~~~~~~~pf~~DGLLFYhks~~yqpgqsplvgwlk 277 (325)
T KOG3132|consen 224 HKFRFSVVP------FY-PCDQSGLHSAYTGSLPFVRDGLLFYHKSVVYQPGQSPLVGWLK 277 (325)
T ss_pred ccceecccC------CC-CCCHHHHHHHHcCCCceeeeeEEEeecceeeCCCCCccccccc
Confidence 0111111 12 2367778888877777888999999989999999642 37865
No 91
>KOG2386 consensus mRNA capping enzyme, guanylyltransferase (alpha) subunit [RNA processing and modification]
Probab=87.81 E-value=0.31 Score=54.99 Aligned_cols=97 Identities=19% Similarity=0.283 Sum_probs=63.4
Q ss_pred CceEEEEecceEEEEEEEeCCE-EEEEecCCCCCCC---chhhhHHHHHhhccccceeeeceEEEeeCCCCccccccchH
Q 002803 245 KEVVIECKFDGDRIQIHKNGSE-IHYFSRSFLDHSE---YGHAMSKIIEQNVLVDRCILDGEMLVWDTSLNRFAEFGSNQ 320 (879)
Q Consensus 245 ~~~~iE~K~DGeR~qih~~g~~-v~~~SR~g~~~t~---~~~~l~~~~~~~~~~~~~ILDGEmv~~d~~~~~~~pF~~l~ 320 (879)
..|.+++|.||.|..+-.+++. +..+-|.-..+-. +++.-.. ........++||||+. |..+..
T Consensus 285 ~~y~~~We~dg~~~~~L~~~~~~~~~~dR~~~~~~~~~~~~~~~~~---~~~~~~~tl~dge~~l-D~l~~~-------- 352 (393)
T KOG2386|consen 285 EYYEASWEADGTRYMMLIDGDGEYYDFDRWRFVKGRENLRKIREDS---DTKVLHQTLLDGEMIL-DRLKEE-------- 352 (393)
T ss_pred hhhhhhhcccCcEEEEEecCCceeEechhhhHHHhhhhhhcccccc---cchhhhhhhcccceec-cccccc--------
Confidence 4577999999999998887754 5555554322110 1110000 0001346789999998 643211
Q ss_pred HHHHHhhcCCCCCCceEEEEEEEEEeCCccccCCCHHHHHHHHHhhc
Q 002803 321 EIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVV 367 (879)
Q Consensus 321 ~~~~~~~~~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~v 367 (879)
..+.|.++|++-+|++.+...|+. |.+.+++-+
T Consensus 353 -------------~~~r~l~Yd~~r~n~~~v~~~~f~-r~~~~~~ev 385 (393)
T KOG2386|consen 353 -------------AIPRYLIYDMVRFNSQKVEKRPFS-RWQIIEKEV 385 (393)
T ss_pred -------------cchhheeeeeeeccCcccccCcch-HHHHHHHHh
Confidence 134699999999999999999999 998776533
No 92
>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=87.64 E-value=0.5 Score=59.06 Aligned_cols=69 Identities=22% Similarity=0.346 Sum_probs=55.9
Q ss_pred HHHHHHHHcCCEEeeccCCCeeEEEEe-cCCchhhhhhccCC-CeeeechHHHhhhcCcccCCCccccccCCh
Q 002803 675 SLHKMVVENGGTFSMNLNNSVTHCVAA-DNKGLKYEAAKRRG-DVIHYSWVLDCCSQKKLLQLQPKYYLHLSD 745 (879)
Q Consensus 675 eLe~lI~~~GG~~v~n~~~~~T~~I~~-~~~~~k~~~~~~~~-~IV~p~Wl~dCi~~~~llp~~p~~~l~~s~ 745 (879)
-+...++..||.+..+.. ..||.|+. .++|.|.-.++..| .||.++||.+|+..|..++..| |+++-.+
T Consensus 672 ~~k~~~k~lg~s~~ss~~-e~Th~i~~rirRT~k~Leai~~G~~ivT~~wL~s~~k~g~~~dek~-yil~D~e 742 (896)
T KOG2043|consen 672 NYKLAKKFLGGSVASSDS-EATHFIADRIRRTLKFLEAISSGKPLVTPQWLVSSLKSGEKLDEKP-YILHDEE 742 (896)
T ss_pred hhhhHHhhccceeecccc-cceeeeehhhhccHHHHhhhccCCcccchHHHHHHhhccccccCcc-ccccCHH
Confidence 477888888999988876 47998863 23788888888888 8999999999999999999997 5666543
No 93
>PRK09247 ATP-dependent DNA ligase; Validated
Probab=87.05 E-value=0.93 Score=54.29 Aligned_cols=82 Identities=17% Similarity=0.261 Sum_probs=69.2
Q ss_pred HHHHHHHHHHHhccChHHHHHHHHHHHHhCCHHHHHHHHHHHhhhhc-cCCccccccccc----Cc---CHHHHHhhcCC
Q 002803 127 KELNDLLDRLASSENRAEKISVLSTLIKKTNAQEMKWIIMIILKDLK-LGISEKSIFHEF----HP---DAEDLFNVTCD 198 (879)
Q Consensus 127 ~eVn~~Ld~La~~~~~~~k~~~l~~ll~~~s~~E~k~l~RiIlk~lr-iG~~e~til~~~----hp---da~~~~~~~~d 198 (879)
.+.-+++++|+..+++.+|..+|..+|...++.+.-|.+++++..+. .|++++.+.+++ .. ...+.|.-..|
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 35667889999999999999999999999999999999999999885 899999988765 22 23456788899
Q ss_pred HHHHHHHHhh
Q 002803 199 LKLVCEKLKD 208 (879)
Q Consensus 199 L~~V~~~L~~ 208 (879)
|+.||..+..
T Consensus 82 lg~~~~~~~~ 91 (539)
T PRK09247 82 LAETIALLLP 91 (539)
T ss_pred HHHHHHHhcc
Confidence 9999988764
No 94
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=85.27 E-value=1.1 Score=53.87 Aligned_cols=81 Identities=27% Similarity=0.361 Sum_probs=54.9
Q ss_pred CCCcccCeEEEEEcCCCCCCHHHHHHHHHHcCCEEeeccCC------CeeEEEEecCCch------h---hhhhccC-C-
Q 002803 653 ETSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNN------SVTHCVAADNKGL------K---YEAAKRR-G- 715 (879)
Q Consensus 653 ~s~iF~g~~F~vl~~~~~~~k~eLe~lI~~~GG~~v~n~~~------~~T~~I~~~~~~~------k---~~~~~~~-~- 715 (879)
+..||+|+.||++......++++|..+|...||++.+-+.. ..|..+....... | ..++... +
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 35799999999988888999999999999999999876431 1222322221111 1 2223222 2
Q ss_pred CeeeechHHHhhhcCccc
Q 002803 716 DVIHYSWVLDCCSQKKLL 733 (879)
Q Consensus 716 ~IV~p~Wl~dCi~~~~ll 733 (879)
..|.-.||+|+|+--.+.
T Consensus 664 ~~~~~~wvl~s~a~~~~~ 681 (684)
T KOG4362|consen 664 RAVSSSWVLDSIAGYQIL 681 (684)
T ss_pred Cccchhhhhcchhceeee
Confidence 799999999999744443
No 95
>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=82.28 E-value=1.2 Score=44.94 Aligned_cols=85 Identities=24% Similarity=0.413 Sum_probs=60.8
Q ss_pred CHHHHHHHHHHHHhccChHHHHHHHHHHHHhCCHHHHHHHHHHHhhhh-------ccCCccccccccc----CcC---HH
Q 002803 125 TIKELNDLLDRLASSENRAEKISVLSTLIKKTNAQEMKWIIMIILKDL-------KLGISEKSIFHEF----HPD---AE 190 (879)
Q Consensus 125 Ti~eVn~~Ld~La~~~~~~~k~~~l~~ll~~~s~~E~k~l~RiIlk~l-------riG~~e~til~~~----hpd---a~ 190 (879)
.-.++-++|++|+..+++.+|..+|+.+|....+.+.-|.+..+++-+ ..|++++++.+++ +-+ ..
T Consensus 2 ~F~~l~~l~~~l~~~~~~~~k~~~l~~~~~~~~~~~~~~~~~~~~~~l~P~~d~r~~~i~~~~L~k~~~~~~~~~~~~~~ 81 (177)
T PF04675_consen 2 PFSDLCELFEKLESTSSRLEKIAILSNFFRSWREEDLGPDLYLLLRLLFPEYDGREYGIGEKLLAKAIAEALGLPEKSID 81 (177)
T ss_dssp BHHHHHHHHHHHHT---HHHHHHHHHHHHHTSHCCGHHCHHHHHHTHSSTTTCS---S--HHHHHHHHHHHHTS-HHHHH
T ss_pred cHHHHHHHHHHHHhccCHHHHHHHHHHHHHHcccchhhhHHHHHhcccccchhhhHhccchhHHHHHHHHHHcCCHHHHH
Confidence 345677889999999999999999999999988777888888888844 6899999987654 422 34
Q ss_pred HHHhhcCCHHHHHHHHhhh
Q 002803 191 DLFNVTCDLKLVCEKLKDR 209 (879)
Q Consensus 191 ~~~~~~~dL~~V~~~L~~~ 209 (879)
+.|.-..|++.|+..+...
T Consensus 82 ~~~~~~GD~g~~~~~~~~~ 100 (177)
T PF04675_consen 82 ESYKKVGDLGEVAEEVLQK 100 (177)
T ss_dssp HHHHHHS-HHHHHHHHHHH
T ss_pred HHHHhcCcHHHHHHHHHhh
Confidence 5677889999999988754
No 96
>PRK03180 ligB ATP-dependent DNA ligase; Reviewed
Probab=80.01 E-value=10 Score=45.16 Aligned_cols=93 Identities=20% Similarity=0.236 Sum_probs=72.3
Q ss_pred CCcHHHHHHHHHHHHhcC---ChhHHHHHHHHHHhhcCCCChHhhhHhhcCCCCCcCccccCCCHHHHHHHHHHHhCCCc
Q 002803 6 ETEVIVLVSLFNWIQKTK---PAAKKRSKFRKFLDTYCDSVDYFSALRLILPSLDRERGSYGLKESVLANCLIDALGMSK 82 (879)
Q Consensus 6 ~~~F~~l~~~~e~i~~~~---~~~~k~~~l~~~~~~~~~~~~~~p~lrLllP~~d~~r~~yglke~~L~k~~~~~~~~~~ 82 (879)
+.+-.++-+.|++|...+ +..+|..+|..++.+. ++.+..-++|+|+-.+ ..|+++.++..+++++++++.
T Consensus 72 ~ltl~~V~~~l~~ia~~~g~~s~~~k~~~l~~ll~~~-~~~E~~~l~r~i~~~l-----RiGv~~~~v~~Ala~a~~~~~ 145 (508)
T PRK03180 72 TLTVADVDAALSEIAAVAGAGSQARRAALLAALFAAA-TEDEQRFLRRLLTGEL-----RQGALDGVMADAVARAAGVPA 145 (508)
T ss_pred CCcHHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHhC-CHHHHHHHHHHHhCCC-----cccccHHHHHHHHHHHhCCCH
Confidence 456677777899988875 4478889999999986 5678888999999987 389999999999999998764
Q ss_pred ChHHHHHHhhhhcCCCCCCCCCHHHHHHHHHh
Q 002803 83 DSADAVRLINWRKGGAAPNAGNFPMVAAEVLQ 114 (879)
Q Consensus 83 ~s~~~~~L~~wk~~~~~~~~gD~~~~~~~v~~ 114 (879)
. +..+..+| .||++.++...+.
T Consensus 146 ~--~v~~a~~~--------~~dl~~v~~~~l~ 167 (508)
T PRK03180 146 A--AVRRAAML--------AGDLPAVAAAALT 167 (508)
T ss_pred H--HHHHHHHH--------cCCHHHHHHHHHh
Confidence 3 33343333 6899988876553
No 97
>PF12738 PTCB-BRCT: twin BRCT domain; PDB: 3PA6_A 3KTF_C 2WT8_C 3EF1_A 3EF0_A.
Probab=74.56 E-value=2 Score=35.45 Aligned_cols=42 Identities=14% Similarity=-0.039 Sum_probs=27.1
Q ss_pred cEEEEcCCCCCCCChhHHHHHHHHHHHHHHhhhcCceeccCCCCCeeEEEEcc
Q 002803 806 CCIYFYHSTEPLSPDWEVLLGLALRRLKLEISFHGVSLPERNIFYGTRSCMLL 858 (879)
Q Consensus 806 ~~vy~~~~~~~~~~~~~~~~~~~l~~~~~~i~~~GG~v~~~~~~~vTHVVv~~ 858 (879)
|+|++.++... ..+.+...++.+||+++.+....+||+|...
T Consensus 1 ~~i~~sg~~~~-----------~~~~l~~~i~~~Gg~~~~~lt~~~THLI~~~ 42 (63)
T PF12738_consen 1 VVICFSGFSGK-----------ERSQLRKLIEALGGKYSKDLTKKTTHLICSS 42 (63)
T ss_dssp -EEEEEEB-TT-----------TCCHHHHHHHCTT-EEESSSSTT-SEEEEES
T ss_pred CEEEECCCCHH-----------HHHHHHHHHHHCCCEEeccccCCceEEEEeC
Confidence 46677766532 1236778899999999944557899999844
No 98
>PLN03113 DNA ligase 1; Provisional
Probab=72.89 E-value=7.1 Score=48.42 Aligned_cols=86 Identities=13% Similarity=0.291 Sum_probs=72.2
Q ss_pred CCCCHHHHHHHHHHHHhccChHHHHHHHHHHHHhC---CHHHHHHHHHHHhhhhc-------cCCccccccccc----Cc
Q 002803 122 GGLTIKELNDLLDRLASSENRAEKISVLSTLIKKT---NAQEMKWIIMIILKDLK-------LGISEKSIFHEF----HP 187 (879)
Q Consensus 122 ~~lTi~eVn~~Ld~La~~~~~~~k~~~l~~ll~~~---s~~E~k~l~RiIlk~lr-------iG~~e~til~~~----hp 187 (879)
.++.-.++-+.+++|...+++.++..+|..+|... +|.+.-|.+.++.+.+- +|++++.+.+++ ..
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 46788999999999999999999999999999984 99999999999887764 699999988765 22
Q ss_pred ---CHHHHHhhcCCHHHHHHHHh
Q 002803 188 ---DAEDLFNVTCDLKLVCEKLK 207 (879)
Q Consensus 188 ---da~~~~~~~~dL~~V~~~L~ 207 (879)
.....|.-..||+.|+..+.
T Consensus 207 ~~~~ik~~y~~~GDlG~vA~~~~ 229 (744)
T PLN03113 207 TEKQVKKQYKELGDLGLVAKASR 229 (744)
T ss_pred CHHHHHHHHHHhCCHHHHHHhhh
Confidence 23456778899999998665
No 99
>KOG2481 consensus Protein required for normal rRNA processing [RNA processing and modification]
Probab=72.66 E-value=3.1 Score=48.01 Aligned_cols=45 Identities=16% Similarity=0.037 Sum_probs=33.4
Q ss_pred CCCCCcEEEEcCCCCCCCChhHHHHHHHHHHHHHHhhhcCceeccCC----------CCCeeEEEEcc
Q 002803 801 SCFHGCCIYFYHSTEPLSPDWEVLLGLALRRLKLEISFHGVSLPERN----------IFYGTRSCMLL 858 (879)
Q Consensus 801 ~lF~~~~vy~~~~~~~~~~~~~~~~~~~l~~~~~~i~~~GG~v~~~~----------~~~vTHVVv~~ 858 (879)
.||.||+||+.... .-+-|...|+++||.|+-+. +..+||=||+.
T Consensus 326 slF~glkFfl~reV-------------PresL~fiI~s~GG~V~wd~~~~g~~~~~~d~~ITH~IvDr 380 (570)
T KOG2481|consen 326 SLFSGLKFFLNREV-------------PRESLEFIIRSFGGKVSWDPLGIGATYDESDERITHQIVDR 380 (570)
T ss_pred HHhhcceeeeeccC-------------chHHHHHHHHHcCCceecCccCCCCcccccccceeeeeecc
Confidence 68999999998743 12357788999999998431 13489988854
No 100
>KOG0966 consensus ATP-dependent DNA ligase IV [Replication, recombination and repair]
Probab=72.10 E-value=4.2 Score=49.39 Aligned_cols=86 Identities=16% Similarity=0.289 Sum_probs=58.2
Q ss_pred CcHHHHHHHHHHHHhcCChhHHH-HHHHHHHhhcCCCChHhhhHhhcCCCCCcCccccCCCHHHHHHHHHHHhCCCcChH
Q 002803 7 TEVIVLVSLFNWIQKTKPAAKKR-SKFRKFLDTYCDSVDYFSALRLILPSLDRERGSYGLKESVLANCLIDALGMSKDSA 85 (879)
Q Consensus 7 ~~F~~l~~~~e~i~~~~~~~~k~-~~l~~~~~~~~~~~~~~p~lrLllP~~d~~r~~yglke~~L~k~~~~~~~~~~~s~ 85 (879)
+.-.++=++|+.|.+......+. ..|..|+.+. ++.++--++|+||-.+ .||+.|+.|-..+ .+
T Consensus 125 lTi~evN~lLD~LA~~~~~~~~~~~~l~~lv~~~-S~~ElkWliriiLK~l-----klG~se~~Il~vf---------HP 189 (881)
T KOG0966|consen 125 LTIKEVNDLLDSLASGPSEDGKKFKKLSQLVEQC-SPLELKWLIRIILKNL-----KLGASEKKILSVF---------HP 189 (881)
T ss_pred eeHHHHHHHHHHHcCCchhhhhhhHHHHHHHHhC-CHHHHHHHHHHHHHhh-----hcCCccchhhhhc---------Cc
Confidence 55667888888888887766554 6778888765 5566777778777654 4888887765543 23
Q ss_pred HHHHHhhhhcCCCCCCCCCHHHHHHHHHhh
Q 002803 86 DAVRLINWRKGGAAPNAGNFPMVAAEVLQR 115 (879)
Q Consensus 86 ~~~~L~~wk~~~~~~~~gD~~~~~~~v~~~ 115 (879)
||..|.+ .+.|+..||......
T Consensus 190 dA~dl~~--------vtsDLk~Vc~~L~Dp 211 (881)
T KOG0966|consen 190 DAQDLYN--------VTSDLKAVCKKLYDP 211 (881)
T ss_pred cHHHHHH--------HhhhHHHHHHHhcCC
Confidence 5555543 367888887776543
No 101
>KOG0323 consensus TFIIF-interacting CTD phosphatases, including NLI-interacting factor [Transcription]
Probab=62.62 E-value=3.8 Score=49.37 Aligned_cols=83 Identities=16% Similarity=0.222 Sum_probs=56.7
Q ss_pred CCcccCeEEEEEcC--C--CCCCHHHHHHHHHHcCCEEeeccCCCeeEEEEecCCchhhhhhccCC--CeeeechHHHhh
Q 002803 654 TSIFSDMVFYFVNV--P--PAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADNKGLKYEAAKRRG--DVIHYSWVLDCC 727 (879)
Q Consensus 654 s~iF~g~~F~vl~~--~--~~~~k~eLe~lI~~~GG~~v~n~~~~~T~~I~~~~~~~k~~~~~~~~--~IV~p~Wl~dCi 727 (879)
+.+++|+.+.+ +| | ......++-......|-..+.+....+||+|++...+.|+..+...+ .||.++|+..|+
T Consensus 439 ~~v~~~~~~vf-Sg~~P~~~~~~~s~~~~~~~~~g~vs~~~~~~~~th~i~~~~gt~k~~~a~~~~~~~Vv~~~wl~~~~ 517 (635)
T KOG0323|consen 439 TKVLKGSQIVF-SGLHPTGSTDESADILGVAQQLGAVSAPDVSDKTTHLIAANAGTKKVYKAVVSGSAKVVNAAWLWRSL 517 (635)
T ss_pred hHHhhccceee-cccccCcCCcchhhhhhhhhcccceecccccchhhhHHhhccCcceeeccccccceeEechhHHHHHH
Confidence 44555555532 32 1 22233666677778887777676667899998877787777766665 899999999999
Q ss_pred hcCcccCCCc
Q 002803 728 SQKKLLQLQP 737 (879)
Q Consensus 728 ~~~~llp~~p 737 (879)
+++.-++-.+
T Consensus 518 e~w~~v~ek~ 527 (635)
T KOG0323|consen 518 EKWGKVEEKL 527 (635)
T ss_pred HHhcchhccc
Confidence 9875444443
No 102
>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=60.97 E-value=26 Score=41.84 Aligned_cols=94 Identities=21% Similarity=0.247 Sum_probs=71.6
Q ss_pred CCCcHHHHHHHHHHHHhcC---ChhHHHHHHHHHHhhcCCCChHhhhHhhcCCCCCcCccccCCCHHHHHHHHHHHhCCC
Q 002803 5 EETEVIVLVSLFNWIQKTK---PAAKKRSKFRKFLDTYCDSVDYFSALRLILPSLDRERGSYGLKESVLANCLIDALGMS 81 (879)
Q Consensus 5 ~~~~F~~l~~~~e~i~~~~---~~~~k~~~l~~~~~~~~~~~~~~p~lrLllP~~d~~r~~yglke~~L~k~~~~~~~~~ 81 (879)
.+..-.++-++|++|.+.+ +..+|..+|..++.+. ++.+..-++|+|+-++ ..|++++++..+++.+++++
T Consensus 53 ~~lti~eV~~~L~~ia~~~g~~s~~~k~~~l~~ll~~~-~~~e~k~l~r~i~~~l-----riG~~~~~il~al~~~~~~~ 126 (514)
T TIGR00574 53 APLTVKEVYETLKNIAETSGEGSQDKKIKLLKSLLKRA-SPLEAKYLIRTILGDL-----RIGIAEKTILDALAKAFLLS 126 (514)
T ss_pred CCcCHHHHHHHHHHHHHhhCCCcHHHHHHHHHHHHHhC-CHHHHHHHHHHHhhhc-----ccCccHHHHHHHHHHHhccc
Confidence 3456677888888888775 3568888999999875 5688888999999887 38999999999999998876
Q ss_pred cChHHHHHHhhhhcCCCCCCCCCHHHHHHHHHh
Q 002803 82 KDSADAVRLINWRKGGAAPNAGNFPMVAAEVLQ 114 (879)
Q Consensus 82 ~~s~~~~~L~~wk~~~~~~~~gD~~~~~~~v~~ 114 (879)
.. +..++. ....|++.+|.++..
T Consensus 127 ~~--~~~~~~--------~~~~dl~~v~~~l~~ 149 (514)
T TIGR00574 127 HP--DVERAF--------NLTNDLGKVAKILLE 149 (514)
T ss_pred hH--HHHHHH--------HhCCCHHHHHHHHHh
Confidence 43 222322 346789988887753
No 103
>COG4566 TtrR Response regulator [Signal transduction mechanisms]
Probab=60.86 E-value=27 Score=35.81 Aligned_cols=82 Identities=18% Similarity=0.325 Sum_probs=54.8
Q ss_pred CCCCHHHHHHHHHhhhcCCCCCCCCHHHHHHHHHH----HHhccChHHHHHHHHHHHHhCCHHHHHHHHHHHhhhhc---
Q 002803 101 NAGNFPMVAAEVLQRRQGMISGGLTIKELNDLLDR----LASSENRAEKISVLSTLIKKTNAQEMKWIIMIILKDLK--- 173 (879)
Q Consensus 101 ~~gD~~~~~~~v~~~r~~~~~~~lTi~eVn~~Ld~----La~~~~~~~k~~~l~~ll~~~s~~E~k~l~RiIlk~lr--- 173 (879)
-.||.+..++.+...--..-..|.+-+++-+.+.+ .+..........-+...|..+||.|...|-+++.+-+.
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 36899987766533222223456666665555444 33333344455678889999999999999999987663
Q ss_pred ---cCCcccccc
Q 002803 174 ---LGISEKSIF 182 (879)
Q Consensus 174 ---iG~~e~til 182 (879)
+|+|+.|+-
T Consensus 164 A~dLgiS~rTVe 175 (202)
T COG4566 164 AFDLGISERTVE 175 (202)
T ss_pred HHHcCCchhhHH
Confidence 799999873
No 104
>KOG3524 consensus Predicted guanine nucleotide exchange factor (PEBBLE) [Signal transduction mechanisms]
Probab=51.22 E-value=12 Score=44.97 Aligned_cols=74 Identities=14% Similarity=0.270 Sum_probs=53.1
Q ss_pred CCcccCeEEEEEcCCCCCCHHHHHHHHHHcCCEEeeccCCCeeEEEEecCCchhhhhhccC--CCeeeechHHHhhhcC
Q 002803 654 TSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADNKGLKYEAAKRR--GDVIHYSWVLDCCSQK 730 (879)
Q Consensus 654 s~iF~g~~F~vl~~~~~~~k~eLe~lI~~~GG~~v~n~~~~~T~~I~~~~~~~k~~~~~~~--~~IV~p~Wl~dCi~~~ 730 (879)
-..|+|+.||+ .|......+.+.....+.||++-. -+..+||+++.+. +.+..-+-.+ -++|.-.|.-=.|..|
T Consensus 208 l~~feg~~~~f-~gF~~ee~~~m~~sle~~gg~~a~-~d~~cthvvv~e~-~~~~~p~~~s~~~~~vk~ewfw~siq~g 283 (850)
T KOG3524|consen 208 LGVFEGLSLFF-HGFKQEEIDDMLRSLENTGGKLAP-SDTLCTHVVVNED-NDEVEPLAVSSNQVHVKKEWFWVSIQRG 283 (850)
T ss_pred cccccCCeEee-cCCcHHHHHHHHHHHHhcCCcccC-CCCCceeEeecCC-ccccccccccccceeecccceEEEEecc
Confidence 45799999997 566777788899999999999988 3446999997543 3333332222 2788888887666554
No 105
>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=47.04 E-value=1.9e+02 Score=30.39 Aligned_cols=32 Identities=25% Similarity=0.158 Sum_probs=23.0
Q ss_pred ceEEEEecceEEE-EEEEeCCEEEEEecCCCCC
Q 002803 246 EVVIECKFDGDRI-QIHKNGSEIHYFSRSFLDH 277 (879)
Q Consensus 246 ~~~iE~K~DGeR~-qih~~g~~v~~~SR~g~~~ 277 (879)
++.+-.|+||.=+ .....+|.+.+-|+.+..-
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 106
>PF15101 DUF4557: Domain of unknown function (DUF4557)
Probab=45.10 E-value=41 Score=34.64 Aligned_cols=80 Identities=18% Similarity=0.282 Sum_probs=52.0
Q ss_pred HHHHHHHHHcCCEEeeccCCCeeEEEEecCCchhhhh------hccCC-CeeeechHHHhhhcCc--ccCCCccccccCC
Q 002803 674 DSLHKMVVENGGTFSMNLNNSVTHCVAADNKGLKYEA------AKRRG-DVIHYSWVLDCCSQKK--LLQLQPKYYLHLS 744 (879)
Q Consensus 674 ~eLe~lI~~~GG~~v~n~~~~~T~~I~~~~~~~k~~~------~~~~~-~IV~p~Wl~dCi~~~~--llp~~p~~~l~~s 744 (879)
.+|.++=+++||+++. +. ..-++..+|........ .++.+ .|.|+.||..|.+... -+++. .|+|++.
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 3688899999999987 43 24566665543332222 23444 7999999999997653 45554 6777777
Q ss_pred hh-hHhHhhhhhc
Q 002803 745 DS-SKKKLQEEVD 756 (879)
Q Consensus 745 ~~-~~~~~~~~~D 756 (879)
|+ +.+++..-.+
T Consensus 91 P~~lq~eirrkig 103 (212)
T PF15101_consen 91 PECLQKEIRRKIG 103 (212)
T ss_pred HHHHHHHHHHHhc
Confidence 77 4444544343
No 107
>COG5163 NOP7 Protein required for biogenesis of the 60S ribosomal subunit [Translation, ribosomal structure and biogenesis]
Probab=35.67 E-value=21 Score=40.08 Aligned_cols=45 Identities=20% Similarity=0.030 Sum_probs=31.9
Q ss_pred CCCCCCcEEEEcCCCCCCCChhHHHHHHHHHHHHHHhhhcCceeccCC-----------CCCeeEEEEc
Q 002803 800 WSCFHGCCIYFYHSTEPLSPDWEVLLGLALRRLKLEISFHGVSLPERN-----------IFYGTRSCML 857 (879)
Q Consensus 800 ~~lF~~~~vy~~~~~~~~~~~~~~~~~~~l~~~~~~i~~~GG~v~~~~-----------~~~vTHVVv~ 857 (879)
-+||+|.+||+...- ..+.|...|..+||.|.-+. ++.|||-||.
T Consensus 348 ~slFS~f~FyisreV-------------p~dsLefiilscGG~V~~~p~~~~i~~~~~vD~~vth~i~d 403 (591)
T COG5163 348 KSLFSGFKFYISREV-------------PGDSLEFIILSCGGSVVGSPCEADIHVSEKVDEKVTHQIVD 403 (591)
T ss_pred hhhhhceEEEEeccc-------------cchHHHHHHHHcCCcccCchhhccCCchhhccchhhhhhcc
Confidence 468999999998742 12356788999999997431 1238888874
No 108
>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=30.37 E-value=1.1e+02 Score=33.27 Aligned_cols=67 Identities=19% Similarity=0.217 Sum_probs=50.6
Q ss_pred EEEEeCCc--cccCCCHHHHHHHHHhhcCCCCCcceecccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHcCCce
Q 002803 342 DVLYVGDT--SVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEG 419 (879)
Q Consensus 342 DiL~lng~--~l~~~pl~eRr~~L~~~v~~~~~~~~i~~p~~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~~i~~g~EG 419 (879)
|-++++|. ....++..||+++++.+.....+++.++. .....+.++..++.+.+.+.|-.|
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 44555652 23578999999999999887776654431 223457889999999999999999
Q ss_pred EEEecC
Q 002803 420 IVLKDL 425 (879)
Q Consensus 420 lV~K~~ 425 (879)
+|+=.|
T Consensus 99 v~~~~P 104 (284)
T cd00950 99 ALVVTP 104 (284)
T ss_pred EEEccc
Confidence 999876
No 109
>KOG2872 consensus Uroporphyrinogen decarboxylase [Coenzyme transport and metabolism]
Probab=27.17 E-value=55 Score=35.68 Aligned_cols=107 Identities=16% Similarity=0.256 Sum_probs=65.5
Q ss_pred CCCHHHHHHHHHHcCCEEeeccCCCeeEEEEecCCchhhhhhccCC-CeeeechHHHhhhcCccc--------CCCcccc
Q 002803 670 AYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADNKGLKYEAAKRRG-DVIHYSWVLDCCSQKKLL--------QLQPKYY 740 (879)
Q Consensus 670 ~~~k~eLe~lI~~~GG~~v~n~~~~~T~~I~~~~~~~k~~~~~~~~-~IV~p~Wl~dCi~~~~ll--------p~~p~~~ 740 (879)
+.+...|++++.+---+.-.--...+..++-+...+.-...+...| |||..+|-.|-.+..+++ .+.|.+|
T Consensus 227 e~s~PYl~~I~~~Vk~rl~~~~~~~vPmi~fakG~g~~Le~l~~tG~DVvgLDWTvdp~ear~~~g~~VtlQGNlDP~~l 306 (359)
T KOG2872|consen 227 EFSLPYLRQIAEAVKKRLPELGLAPVPMILFAKGSGGALEELAQTGYDVVGLDWTVDPAEARRRVGNRVTLQGNLDPGVL 306 (359)
T ss_pred HhhhHHHHHHHHHHHHhhhhhcCCCCceEEEEcCcchHHHHHHhcCCcEEeecccccHHHHHHhhCCceEEecCCChHHh
Confidence 3444556666555332222111123344454555566677788888 999999999855432211 3557889
Q ss_pred ccCChhhHhHhhhhhccCCCc-cc--------ccCCHHHHHHHHh
Q 002803 741 LHLSDSSKKKLQEEVDEFSDL-YF--------WDLDLADIKQLLS 776 (879)
Q Consensus 741 l~~s~~~~~~~~~~~D~ygDS-y~--------~~~~~~~l~~ll~ 776 (879)
+.+.+...+...+-+++||-| |. -.++++.+...++
T Consensus 307 y~s~e~it~~v~~mv~~fG~~ryI~NLGHGi~p~tp~e~v~~f~E 351 (359)
T KOG2872|consen 307 YGSKEEITQLVKQMVKDFGKSRYIANLGHGITPGTPPEHVAHFVE 351 (359)
T ss_pred cCCHHHHHHHHHHHHHHhCccceEEecCCCCCCCCCHHHHHHHHH
Confidence 999888888888889999966 32 2334555555544
No 110
>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=26.83 E-value=1.5e+02 Score=32.25 Aligned_cols=66 Identities=21% Similarity=0.283 Sum_probs=48.4
Q ss_pred EEEeCCc--cccCCCHHHHHHHHHhhcCCCCCcceecccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHcCCceE
Q 002803 343 VLYVGDT--SVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGI 420 (879)
Q Consensus 343 iL~lng~--~l~~~pl~eRr~~L~~~v~~~~~~~~i~~p~~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~~i~~g~EGl 420 (879)
-++++|. ....++.+||+++++.++....+++.++. .....+.++..++.+.+.+.|-.|+
T Consensus 34 gi~~~GstGE~~~ls~~Er~~l~~~~~~~~~~~~~vi~-----------------gv~~~~~~~~i~~a~~a~~~Gad~v 96 (281)
T cd00408 34 GLVVLGTTGEAPTLTDEERKEVIEAVVEAVAGRVPVIA-----------------GVGANSTREAIELARHAEEAGADGV 96 (281)
T ss_pred EEEECCCCcccccCCHHHHHHHHHHHHHHhCCCCeEEE-----------------ecCCccHHHHHHHHHHHHHcCCCEE
Confidence 3455552 23567899999999999887666654432 2234577888999999999999999
Q ss_pred EEecC
Q 002803 421 VLKDL 425 (879)
Q Consensus 421 V~K~~ 425 (879)
|+=.|
T Consensus 97 ~v~pP 101 (281)
T cd00408 97 LVVPP 101 (281)
T ss_pred EECCC
Confidence 99654
No 111
>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=25.31 E-value=1.6e+02 Score=32.53 Aligned_cols=59 Identities=19% Similarity=0.123 Sum_probs=46.1
Q ss_pred ccCCCHHHHHHHHHhhcCCCCCcceecccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHcCCceEEEecCC
Q 002803 351 VIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLG 426 (879)
Q Consensus 351 l~~~pl~eRr~~L~~~v~~~~~~~~i~~p~~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~~i~~g~EGlV~K~~~ 426 (879)
...++..||.++++.++....+++.++. .....+.++..++-+.+.+.|-.|+|+=.|-
T Consensus 47 ~~~Ls~~Er~~l~~~~~~~~~g~~pvi~-----------------gv~~~~t~~ai~~a~~A~~~Gad~v~v~pP~ 105 (294)
T TIGR02313 47 PGSLTLEERKQAIENAIDQIAGRIPFAP-----------------GTGALNHDETLELTKFAEEAGADAAMVIVPY 105 (294)
T ss_pred cccCCHHHHHHHHHHHHHHhCCCCcEEE-----------------ECCcchHHHHHHHHHHHHHcCCCEEEEcCcc
Confidence 3578999999999999887777764431 2234577888888999999999999998653
No 112
>PRK03170 dihydrodipicolinate synthase; Provisional
Probab=25.01 E-value=1.5e+02 Score=32.35 Aligned_cols=67 Identities=19% Similarity=0.196 Sum_probs=49.2
Q ss_pred EEEeCCc--cccCCCHHHHHHHHHhhcCCCCCcceecccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHcCCceE
Q 002803 343 VLYVGDT--SVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGI 420 (879)
Q Consensus 343 iL~lng~--~l~~~pl~eRr~~L~~~v~~~~~~~~i~~p~~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~~i~~g~EGl 420 (879)
-++++|. ....++.+||+++++.++....+++.++. .....+.++..++.+.+.+.|-.|+
T Consensus 38 gi~~~Gs~GE~~~ls~~Er~~~~~~~~~~~~~~~~vi~-----------------gv~~~~~~~~i~~a~~a~~~G~d~v 100 (292)
T PRK03170 38 GLVVVGTTGESPTLTHEEHEELIRAVVEAVNGRVPVIA-----------------GTGSNSTAEAIELTKFAEKAGADGA 100 (292)
T ss_pred EEEECCcCCccccCCHHHHHHHHHHHHHHhCCCCcEEe-----------------ecCCchHHHHHHHHHHHHHcCCCEE
Confidence 3444542 23578999999999999887777654431 2234577888999999999999999
Q ss_pred EEecCC
Q 002803 421 VLKDLG 426 (879)
Q Consensus 421 V~K~~~ 426 (879)
|+=.|.
T Consensus 101 ~~~pP~ 106 (292)
T PRK03170 101 LVVTPY 106 (292)
T ss_pred EECCCc
Confidence 997653
No 113
>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=23.99 E-value=1.8e+02 Score=31.98 Aligned_cols=67 Identities=19% Similarity=0.224 Sum_probs=48.9
Q ss_pred EEEEeCCc--cccCCCHHHHHHHHHhhcCCCCCcceecccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHcCCce
Q 002803 342 DVLYVGDT--SVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEG 419 (879)
Q Consensus 342 DiL~lng~--~l~~~pl~eRr~~L~~~v~~~~~~~~i~~p~~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~~i~~g~EG 419 (879)
|-++++|. ....++.+||.++++.++....+++.++. .....+.++..++.+.+.+.|-.|
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 44556652 12467999999999999887777654431 223457788899999999999999
Q ss_pred EEEecC
Q 002803 420 IVLKDL 425 (879)
Q Consensus 420 lV~K~~ 425 (879)
+|+=.|
T Consensus 100 v~v~~P 105 (290)
T TIGR00683 100 LSAVTP 105 (290)
T ss_pred EEEeCC
Confidence 999543
No 114
>PLN02417 dihydrodipicolinate synthase
Probab=23.20 E-value=1.8e+02 Score=31.69 Aligned_cols=57 Identities=11% Similarity=0.028 Sum_probs=45.4
Q ss_pred cCCCHHHHHHHHHhhcCCCCCcceecccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHcCCceEEEecC
Q 002803 352 IHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDL 425 (879)
Q Consensus 352 ~~~pl~eRr~~L~~~v~~~~~~~~i~~p~~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~~i~~g~EGlV~K~~ 425 (879)
..++..||+++++.++....+++.++. .....+..+..++.+.+.+.|-.|+|+-.|
T Consensus 49 ~~ls~~Er~~~~~~~~~~~~~~~pvi~-----------------gv~~~~t~~~i~~a~~a~~~Gadav~~~~P 105 (280)
T PLN02417 49 QLMSWDEHIMLIGHTVNCFGGKIKVIG-----------------NTGSNSTREAIHATEQGFAVGMHAALHINP 105 (280)
T ss_pred hhCCHHHHHHHHHHHHHHhCCCCcEEE-----------------ECCCccHHHHHHHHHHHHHcCCCEEEEcCC
Confidence 467899999999998887777654431 233457889999999999999999999776
No 115
>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=23.01 E-value=1.8e+02 Score=32.27 Aligned_cols=65 Identities=15% Similarity=0.238 Sum_probs=49.6
Q ss_pred EEeCCc--cccCCCHHHHHHHHHhhcCCCCCcceecccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHcCCceEE
Q 002803 344 LYVGDT--SVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIV 421 (879)
Q Consensus 344 L~lng~--~l~~~pl~eRr~~L~~~v~~~~~~~~i~~p~~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~~i~~g~EGlV 421 (879)
++++|. ....++.+||+++++.++....+++-++. .....+.++..++.+.+.+.|-.|+|
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 344542 24578999999999999887777754431 23345788999999999999999999
Q ss_pred EecC
Q 002803 422 LKDL 425 (879)
Q Consensus 422 ~K~~ 425 (879)
+=.|
T Consensus 109 v~~P 112 (309)
T cd00952 109 LGRP 112 (309)
T ss_pred ECCC
Confidence 9876
No 116
>TIGR00674 dapA dihydrodipicolinate synthase. Dihydrodipicolinate synthase is a homotetrameric enzyme of lysine biosynthesis. E. coli has several paralogs closely related to dihydrodipicoline synthase (DapA), as well as the more distant N-acetylneuraminate lyase. In Pyrococcus horikoshii, the bidirectional best hit with E. coli is to an uncharacterized paralog of DapA, not DapA itself, and it is omitted from the seed. The putative members from the Chlamydias (pathogens with a parasitic metabolism) are easily the most divergent members of the multiple alignment.
Probab=22.68 E-value=1.8e+02 Score=31.67 Aligned_cols=58 Identities=16% Similarity=0.174 Sum_probs=45.9
Q ss_pred cCCCHHHHHHHHHhhcCCCCCcceecccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHcCCceEEEecCC
Q 002803 352 IHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLG 426 (879)
Q Consensus 352 ~~~pl~eRr~~L~~~v~~~~~~~~i~~p~~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~~i~~g~EGlV~K~~~ 426 (879)
..++..||+++++.++....+++.++. ...+.+.++..++-+.+.+.|-.|+|+=.|.
T Consensus 46 ~~Ls~~Er~~~~~~~~~~~~~~~~vi~-----------------gv~~~s~~~~i~~a~~a~~~Gad~v~v~pP~ 103 (285)
T TIGR00674 46 PTLSHEEHKKVIEFVVDLVNGRVPVIA-----------------GTGSNATEEAISLTKFAEDVGADGFLVVTPY 103 (285)
T ss_pred ccCCHHHHHHHHHHHHHHhCCCCeEEE-----------------eCCCccHHHHHHHHHHHHHcCCCEEEEcCCc
Confidence 578999999999998887777654431 2334578889999999999999999997654
No 117
>cd00954 NAL N-Acetylneuraminic acid aldolase, also called N-acetylneuraminate lyase (NAL), which catalyses the reversible aldol reaction of N-acetyl-D-mannosamine and pyruvate to give N-acetyl-D-neuraminic acid (D-sialic acid). It has a widespread application as biocatalyst for the synthesis of sialic acid and its derivatives. This enzyme has been shown to be quite specific for pyruvate as the donor, but flexible to a variety of D- and, to some extent, L-hexoses and pentoses as acceptor substrates. NAL is member of dihydrodipicolinate synthase family that comprises several pyruvate-dependent class I aldolases.
Probab=22.63 E-value=2.1e+02 Score=31.29 Aligned_cols=68 Identities=22% Similarity=0.268 Sum_probs=50.0
Q ss_pred EEEEeCCc--cccCCCHHHHHHHHHhhcCCCCCcceecccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHcCCce
Q 002803 342 DVLYVGDT--SVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEG 419 (879)
Q Consensus 342 DiL~lng~--~l~~~pl~eRr~~L~~~v~~~~~~~~i~~p~~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~~i~~g~EG 419 (879)
|-+.++|. ....++.+||.++++..+....+++.++. .....+.++..++.+.+.+.|-.|
T Consensus 37 ~gi~~~GstGE~~~Lt~~Er~~~~~~~~~~~~~~~~via-----------------gv~~~~~~~ai~~a~~a~~~Gad~ 99 (288)
T cd00954 37 DGLYVNGSTGEGFLLSVEERKQIAEIVAEAAKGKVTLIA-----------------HVGSLNLKESQELAKHAEELGYDA 99 (288)
T ss_pred CEEEECcCCcCcccCCHHHHHHHHHHHHHHhCCCCeEEe-----------------ccCCCCHHHHHHHHHHHHHcCCCE
Confidence 44555552 23577899999999998877666654431 223457889999999999999999
Q ss_pred EEEecCC
Q 002803 420 IVLKDLG 426 (879)
Q Consensus 420 lV~K~~~ 426 (879)
+|+=.|-
T Consensus 100 v~~~~P~ 106 (288)
T cd00954 100 ISAITPF 106 (288)
T ss_pred EEEeCCC
Confidence 9987653
No 118
>KOG3673 consensus FtsJ-like RNA methyltransferase [RNA processing and modification]
Probab=22.51 E-value=72 Score=37.58 Aligned_cols=39 Identities=18% Similarity=0.128 Sum_probs=33.8
Q ss_pred CCCceEEEEEEEEEeCCccccCCCHHHHHHHHHhhcCCC
Q 002803 332 SDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPS 370 (879)
Q Consensus 332 ~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~v~~~ 370 (879)
...+..+++.|.+.|+|.++.++||.||.++-++.+..+
T Consensus 654 ~~~~~avhIiD~~vL~G~Dvr~~py~eR~~~aeKFv~al 692 (845)
T KOG3673|consen 654 SSEPQAVHIIDAAVLFGDDVRNLPYEERMKAAEKFVAAL 692 (845)
T ss_pred cccchheeeeeeeeecCchhhcccHHHHHHHHHHHHHHh
Confidence 345667999999999999999999999999999987643
No 119
>TIGR03544 DivI1A_domain DivIVA domain. This model describes a domain found in Bacillus subtilis cell division initiation protein DivIVA, and homologs, toward the N-terminus. It is also found as a repeated domain in certain other proteins, including family TIGR03543.
Probab=22.29 E-value=1.6e+02 Score=21.39 Aligned_cols=29 Identities=24% Similarity=0.394 Sum_probs=20.2
Q ss_pred HHHHhhhcCCCCCCCCHHHHHHHHHHHHh
Q 002803 110 AEVLQRRQGMISGGLTIKELNDLLDRLAS 138 (879)
Q Consensus 110 ~~v~~~r~~~~~~~lTi~eVn~~Ld~La~ 138 (879)
.+|...+...........||+++|+++|.
T Consensus 4 ~dIr~~~F~~~~rGY~~~eVD~fLd~v~~ 32 (34)
T TIGR03544 4 EDIRNKRFKKKLRGYDAAEVDAFLDRVAD 32 (34)
T ss_pred HHHhhCcCCCCCCCCCHHHHHHHHHHHHH
Confidence 34444443333467899999999999985
No 120
>PRK04147 N-acetylneuraminate lyase; Provisional
Probab=21.88 E-value=2.1e+02 Score=31.43 Aligned_cols=57 Identities=19% Similarity=0.247 Sum_probs=45.5
Q ss_pred cCCCHHHHHHHHHhhcCCCCCcceecccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHcCCceEEEecC
Q 002803 352 IHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDL 425 (879)
Q Consensus 352 ~~~pl~eRr~~L~~~v~~~~~~~~i~~p~~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~~i~~g~EGlV~K~~ 425 (879)
..++..||.++++.++....+++.++. ...+.+.++..++.+.+.+.|-.|+|+=.|
T Consensus 52 ~~Ls~eEr~~~~~~~~~~~~~~~~via-----------------gvg~~~t~~ai~~a~~a~~~Gad~v~v~~P 108 (293)
T PRK04147 52 FLLSTEEKKQVLEIVAEEAKGKVKLIA-----------------QVGSVNTAEAQELAKYATELGYDAISAVTP 108 (293)
T ss_pred ccCCHHHHHHHHHHHHHHhCCCCCEEe-----------------cCCCCCHHHHHHHHHHHHHcCCCEEEEeCC
Confidence 467899999999999987777754432 223457889999999999999999999764
No 121
>KOG2386 consensus mRNA capping enzyme, guanylyltransferase (alpha) subunit [RNA processing and modification]
Probab=21.65 E-value=4.4e+02 Score=30.40 Aligned_cols=174 Identities=16% Similarity=0.192 Sum_probs=89.8
Q ss_pred HHHHHHhCCCceEEEEecceEEEEEEEe-----CCEEEEEecCCC--CCC---CchhhhHHHHHhhccccceeeeceEEE
Q 002803 236 HAAWRKLHGKEVVIECKFDGDRIQIHKN-----GSEIHYFSRSFL--DHS---EYGHAMSKIIEQNVLVDRCILDGEMLV 305 (879)
Q Consensus 236 ~~~~~~~~~~~~~iE~K~DGeR~qih~~-----g~~v~~~SR~g~--~~t---~~~~~l~~~~~~~~~~~~~ILDGEmv~ 305 (879)
.+.+..+....+.+.+|.||.|++..+. +..+.|.=++-. ... .+...+...+ +. +..++-+|||+|.
T Consensus 51 ~dl~~~l~~~~~~vgl~iDltnt~ryy~~~~~~~~g~~Y~K~~c~g~~~vp~~~~v~~fv~~v-~~-f~~~~~~~~~LI~ 128 (393)
T KOG2386|consen 51 KDLFELLKEHNYKVGLKIDLTNTLRYYDKPELEERGVKYLKRNCPGRGVVPRTELVDKFVKLV-KG-FVDDTKLDDELIG 128 (393)
T ss_pred HHHHHHHHhcCceEEEEEeccceeeeeccccccccceeEEEeccCCcccCCCccchHHHHHHH-HH-HHhcccCCCCEEE
Confidence 3455666667899999999999998883 234555555432 211 1111222222 11 2567789999998
Q ss_pred eeCCCCccccccchHHHHHHhhcCCCCCCceEEEEEEEEEeCCccccCCCHHHHHHHHHhhcCCCCC---cceecccCCC
Q 002803 306 WDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKG---RLETLVPDHG 382 (879)
Q Consensus 306 ~d~~~~~~~pF~~l~~~~~~~~~~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~v~~~~~---~~~i~~p~~~ 382 (879)
.. .|-|. .+.-|.+|+.|.-++. +...++.+.++..-.+.-- .+.-+.+..
T Consensus 129 vh------cthG~---------------NrtgyLI~~yL~~~~~----~s~~~aik~f~~~r~~gi~k~dyi~~L~~~~- 182 (393)
T KOG2386|consen 129 VH------CTHGL---------------NRTGYLICAYLADVGG----YSSSEAIKRFADARPPGIEKQDYIDALYSRY- 182 (393)
T ss_pred Ee------CCCcc---------------cccceeeeeeeeeccC----ccHHHHHHHHHHhCCCccCchHHHHHHhhcc-
Confidence 54 22221 1245999999987763 4445555555443322100 000000000
Q ss_pred CCccccCCCCCcccccc---CCHHHHHHHHHHHHH-cCCceEEEecCCCCCc-CCCCCCCeEEEcccc
Q 002803 383 LNSHVRPQGEPCWSLVA---HNVDEVEKFFKETIE-NRDEGIVLKDLGSKWE-PGDRSGKWLKLKPEY 445 (879)
Q Consensus 383 ~~~~v~~~~~~~~~~~~---~~~~ei~~~~~~~i~-~g~EGlV~K~~~s~Y~-~g~Rs~~WlKvKp~y 445 (879)
..+.| +...+ .+-............ ++..|++.-...-+|. .| +....+|+||+-
T Consensus 183 --~~~~p-----~~vs~p~~~~~~~~~~~~~~~~~~~~~Dg~i~t~~~~pg~~~g-~~~~~~k~k~~~ 242 (393)
T KOG2386|consen 183 --HDIFP-----FKVSCPSMPDWKRSIKLKKPVHKLHGNDGLIFTPAEIPGSKNG-KQEALLKWKPFS 242 (393)
T ss_pred --ccccc-----ccccCCCCcchhhhhhhccccccccccCCCcCCcccCcccccc-chhhhhcCCchh
Confidence 00000 00011 011111111221111 7888999888888894 45 446889999974
No 122
>PF02969 TAF: TATA box binding protein associated factor (TAF); InterPro: IPR004823 The TATA box binding protein associated factor (TAF) is part of the transcription initiation factor TFIID multimeric protein complex. TFIID plays a central role in mediating promoter responses to various activators and repressors. It binds tightly to TAFII-250 and directly interacts with TAFII-40. TFIID is composed of TATA binding protein (TBP)and a number of TBP-associated factors (TAFS). TAF proteins adopt a histone-like fold.; GO: 0006352 transcription initiation, DNA-dependent, 0005634 nucleus; PDB: 1TAF_B.
Probab=21.49 E-value=1.1e+02 Score=25.87 Aligned_cols=56 Identities=21% Similarity=0.283 Sum_probs=29.0
Q ss_pred HHHHHHHHHhCCCcChHHHHHHhhhhcCCCCCCCCCHHHHHHHHHhhh----cCCCCCCCCHHHHHHHHH
Q 002803 69 VLANCLIDALGMSKDSADAVRLINWRKGGAAPNAGNFPMVAAEVLQRR----QGMISGGLTIKELNDLLD 134 (879)
Q Consensus 69 ~L~k~~~~~~~~~~~s~~~~~L~~wk~~~~~~~~gD~~~~~~~v~~~r----~~~~~~~lTi~eVn~~Ld 134 (879)
.-+|.+++.+|++.=+.++.+.+ +-|.--.+.++++.- .......||.+|||..|.
T Consensus 7 esvk~iAes~Gi~~l~de~a~~L----------a~dveyrlreiiq~a~kfm~hskR~~Lt~~Di~~ALr 66 (66)
T PF02969_consen 7 ESVKDIAESLGISNLSDEAAKAL----------AEDVEYRLREIIQEALKFMRHSKRTKLTTDDINSALR 66 (66)
T ss_dssp HHHHHHHHHTT---B-HHHHHHH----------HHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHH-
T ss_pred HHHHHHHHHcCCCCCCHHHHHHH----------HHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhC
Confidence 35788999999977666655544 123333334444321 112346799999999873
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=21.19 E-value=1.6e+02 Score=32.11 Aligned_cols=65 Identities=20% Similarity=0.311 Sum_probs=47.9
Q ss_pred EEeCCc--cccCCCHHHHHHHHHhhcCCCCCcceecccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHcCCceEE
Q 002803 344 LYVGDT--SVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIV 421 (879)
Q Consensus 344 L~lng~--~l~~~pl~eRr~~L~~~v~~~~~~~~i~~p~~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~~i~~g~EGlV 421 (879)
+++.|. ....++.+||+++++.++...++++.++. ...+.+.++..++.+.+.+.|-.|+|
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 444542 24578999999999998877666654432 34456889999999999999999999
Q ss_pred EecC
Q 002803 422 LKDL 425 (879)
Q Consensus 422 ~K~~ 425 (879)
+=.|
T Consensus 102 v~~P 105 (289)
T PF00701_consen 102 VIPP 105 (289)
T ss_dssp EEES
T ss_pred Eecc
Confidence 9776
No 124
>cd00951 KDGDH 5-dehydro-4-deoxyglucarate dehydratase, also called 5-keto-4-deoxy-glucarate dehydratase (KDGDH), which is member of dihydrodipicolinate synthase (DHDPS) family that comprises several pyruvate-dependent class I aldolases. The enzyme is involved in glucarate metabolism, and its mechanism presumbly involves a Schiff-base intermediate similar to members of DHDPS family. While in the case of Pseudomonas sp. 5-dehydro-4-deoxy-D-glucarate is degraded by KDGDH to 2,5-dioxopentanoate, in certain species of Enterobacteriaceae it is degraded instead to pyruvate and glycerate.
Probab=20.99 E-value=2.2e+02 Score=31.27 Aligned_cols=64 Identities=14% Similarity=0.242 Sum_probs=46.6
Q ss_pred EEEeCCc--cccCCCHHHHHHHHHhhcCCCCCcceecccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHcCCceE
Q 002803 343 VLYVGDT--SVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGI 420 (879)
Q Consensus 343 iL~lng~--~l~~~pl~eRr~~L~~~v~~~~~~~~i~~p~~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~~i~~g~EGl 420 (879)
-++++|. ....++.+||.++++.++....+++.++. .... +..+..++.+.+.+.|..|+
T Consensus 37 gi~v~GstGE~~~Ls~eEr~~l~~~~~~~~~~~~pvi~-----------------gv~~-~t~~~i~~a~~a~~~Gad~v 98 (289)
T cd00951 37 ALFAAGGTGEFFSLTPDEYAQVVRAAVEETAGRVPVLA-----------------GAGY-GTATAIAYAQAAEKAGADGI 98 (289)
T ss_pred EEEECcCCcCcccCCHHHHHHHHHHHHHHhCCCCCEEE-----------------ecCC-CHHHHHHHHHHHHHhCCCEE
Confidence 3445542 23578999999999999887777654431 1223 67788889999999999999
Q ss_pred EEec
Q 002803 421 VLKD 424 (879)
Q Consensus 421 V~K~ 424 (879)
|+=.
T Consensus 99 ~~~p 102 (289)
T cd00951 99 LLLP 102 (289)
T ss_pred EECC
Confidence 9954
Done!