Query 005331
Match_columns 702
No_of_seqs 373 out of 1859
Neff 7.3
Searched_HMMs 46136
Date Thu Mar 28 21:47:42 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/005331.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/005331hhsearch_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 1E-138 2E-143 1147.0 54.0 659 3-700 1-678 (881)
2 PLN03113 DNA ligase 1; Provisi 100.0 2E-106 5E-111 928.4 54.4 550 5-603 127-730 (744)
3 PRK01109 ATP-dependent DNA lig 100.0 5E-104 1E-108 905.7 52.6 543 7-603 1-582 (590)
4 KOG0967 ATP-dependent DNA liga 100.0 2.4E-99 5E-104 819.1 36.2 551 5-603 97-704 (714)
5 TIGR00574 dnl1 DNA ligase I, A 100.0 3.4E-96 7E-101 831.5 50.3 494 62-600 1-513 (514)
6 PRK09247 ATP-dependent DNA lig 100.0 6.3E-94 1.4E-98 812.4 50.3 522 9-602 1-537 (539)
7 PRK03180 ligB ATP-dependent DN 100.0 1E-93 2.2E-98 804.5 49.1 493 7-600 1-506 (508)
8 PHA02587 30 DNA ligase; Provis 100.0 5E-65 1.1E-69 570.4 41.2 447 13-597 3-484 (488)
9 COG1793 CDC9 ATP-dependent DNA 100.0 1.3E-63 2.8E-68 550.5 31.4 421 100-600 18-443 (444)
10 TIGR02779 NHEJ_ligase_lig DNA 100.0 2.1E-59 4.6E-64 496.8 33.3 288 243-591 10-297 (298)
11 PRK09632 ATP-dependent DNA lig 100.0 3.4E-59 7.3E-64 537.4 32.5 307 218-591 455-761 (764)
12 PRK08224 ligC ATP-dependent DN 100.0 2.8E-57 6E-62 487.2 34.2 314 217-591 2-330 (350)
13 PRK05972 ligD ATP-dependent DN 100.0 7.2E-56 1.6E-60 514.2 32.4 305 222-592 232-537 (860)
14 PRK09633 ligD ATP-dependent DN 100.0 1.4E-54 2.9E-59 493.6 32.1 310 224-601 1-318 (610)
15 PRK07636 ligB ATP-dependent DN 100.0 1.9E-50 4.2E-55 422.5 30.3 273 223-582 2-274 (275)
16 cd07900 Adenylation_DNA_ligase 100.0 5.1E-48 1.1E-52 392.0 22.4 213 216-445 2-219 (219)
17 TIGR02776 NHEJ_ligase_prk DNA 100.0 1.7E-46 3.6E-51 423.0 25.4 258 271-592 1-259 (552)
18 cd07903 Adenylation_DNA_ligase 100.0 5.1E-45 1.1E-49 372.7 21.6 214 215-446 3-224 (225)
19 cd07902 Adenylation_DNA_ligase 100.0 4.9E-44 1.1E-48 361.9 21.5 206 216-445 6-213 (213)
20 PRK09125 DNA ligase; Provision 100.0 8.1E-44 1.8E-48 373.3 23.6 254 224-585 28-282 (282)
21 cd07901 Adenylation_DNA_ligase 100.0 6.6E-44 1.4E-48 359.7 22.1 205 220-444 1-207 (207)
22 PHA00454 ATP-dependent DNA lig 100.0 9.4E-43 2E-47 371.9 28.8 284 225-583 7-314 (315)
23 cd07898 Adenylation_DNA_ligase 100.0 2.7E-42 6E-47 346.5 21.9 199 224-444 1-201 (201)
24 cd07897 Adenylation_DNA_ligase 100.0 1.8E-42 3.9E-47 348.9 20.4 201 222-445 3-206 (207)
25 cd08039 Adenylation_DNA_ligase 100.0 3.3E-42 7E-47 351.7 21.9 200 234-445 11-235 (235)
26 cd07905 Adenylation_DNA_ligase 100.0 2.3E-40 5.1E-45 330.5 19.8 190 224-444 1-193 (194)
27 PF01068 DNA_ligase_A_M: ATP d 100.0 3.4E-40 7.4E-45 331.3 18.1 199 226-442 1-202 (202)
28 cd07906 Adenylation_DNA_ligase 100.0 2.1E-39 4.6E-44 322.7 19.0 189 224-443 1-189 (190)
29 cd07967 OBF_DNA_ligase_III The 100.0 1.4E-33 3E-38 264.7 14.9 137 449-595 2-139 (139)
30 cd07896 Adenylation_kDNA_ligas 100.0 3.6E-33 7.9E-38 274.1 13.8 173 224-443 1-174 (174)
31 cd06846 Adenylation_DNA_ligase 100.0 2.9E-31 6.2E-36 262.5 17.8 177 226-443 2-182 (182)
32 PF04675 DNA_ligase_A_N: DNA l 100.0 7.4E-32 1.6E-36 265.5 13.1 169 7-187 1-177 (177)
33 cd07968 OBF_DNA_ligase_IV The 100.0 1.3E-29 2.8E-34 239.4 14.5 139 449-593 1-140 (140)
34 cd07969 OBF_DNA_ligase_I The O 100.0 2.8E-28 6.1E-33 230.9 15.9 134 449-601 1-143 (144)
35 cd07895 Adenylation_mRNA_cappi 99.9 1.2E-27 2.5E-32 243.0 14.5 174 240-443 36-215 (215)
36 KOG4437 ATP-dependent DNA liga 99.9 1.6E-26 3.5E-31 234.2 18.6 318 7-345 155-482 (482)
37 cd07972 OBF_DNA_ligase_Arch_Li 99.9 7.4E-27 1.6E-31 215.6 14.3 121 450-597 1-121 (122)
38 cd07893 OBF_DNA_ligase The Oli 99.9 8.1E-26 1.8E-30 210.5 14.9 122 450-590 1-129 (129)
39 cd07971 OBF_DNA_ligase_LigD Th 99.8 1.9E-20 4.1E-25 171.2 13.5 114 451-590 2-115 (115)
40 cd08040 OBF_DNA_ligase_family 99.8 6.3E-19 1.4E-23 159.4 13.8 108 450-582 1-108 (108)
41 PF04679 DNA_ligase_A_C: ATP d 99.8 3.1E-19 6.7E-24 158.2 11.1 97 466-585 1-97 (97)
42 cd07894 Adenylation_RNA_ligase 99.7 1.8E-17 4E-22 177.7 14.6 163 245-445 48-218 (342)
43 cd07970 OBF_DNA_ligase_LigC Th 99.7 6E-17 1.3E-21 149.2 13.2 120 450-591 1-121 (122)
44 PF01331 mRNA_cap_enzyme: mRNA 99.3 5.2E-13 1.1E-17 133.3 0.6 173 242-442 13-192 (192)
45 COG5226 CEG1 mRNA capping enzy 99.1 1.1E-10 2.3E-15 118.9 8.0 183 242-458 59-257 (404)
46 cd08041 OBF_kDNA_ligase_like T 99.1 2.5E-10 5.3E-15 96.8 8.2 76 451-582 2-77 (77)
47 COG1423 ATP-dependent DNA liga 98.9 3.6E-08 7.8E-13 102.9 14.8 150 241-429 84-238 (382)
48 TIGR01209 RNA ligase, Pab1020 98.8 5.9E-08 1.3E-12 104.3 15.1 148 241-428 75-229 (374)
49 cd09232 Snurportin-1_C C-termi 98.5 8E-07 1.7E-11 87.9 10.6 176 225-444 5-186 (186)
50 PF14743 DNA_ligase_OB_2: DNA 98.2 1.5E-06 3.2E-11 71.1 4.3 65 462-582 2-66 (66)
51 smart00532 LIGANc Ligase N fam 97.9 0.00033 7.2E-09 78.4 16.5 223 246-508 104-361 (441)
52 PF00533 BRCT: BRCA1 C Terminu 97.8 3.2E-05 6.9E-10 64.8 4.6 48 653-701 2-49 (78)
53 cd00114 LIGANc NAD+ dependent 97.8 0.00042 9.2E-09 74.1 14.1 167 246-438 102-299 (307)
54 PRK08097 ligB NAD-dependent DN 97.7 0.00056 1.2E-08 78.3 14.9 211 224-471 95-329 (562)
55 TIGR00575 dnlj DNA ligase, NAD 97.7 0.0008 1.7E-08 79.1 16.0 195 246-471 97-325 (652)
56 PRK07956 ligA NAD-dependent DN 97.6 0.0012 2.5E-08 77.8 16.5 195 246-471 109-337 (665)
57 smart00292 BRCT breast cancer 97.6 0.00014 3.1E-09 60.2 6.3 48 655-702 1-49 (80)
58 PRK14351 ligA NAD-dependent DN 97.6 0.00098 2.1E-08 78.5 15.4 193 245-471 132-359 (689)
59 PF01653 DNA_ligase_aden: NAD- 97.5 3.5E-05 7.5E-10 82.7 0.7 169 246-438 108-306 (315)
60 cd00027 BRCT Breast Cancer Sup 97.0 0.0015 3.3E-08 52.6 6.0 44 659-702 1-44 (72)
61 PRK14350 ligA NAD-dependent DN 97.0 0.0084 1.8E-07 70.5 13.9 196 246-471 111-334 (669)
62 TIGR02307 RNA_lig_RNL2 RNA lig 97.0 0.012 2.5E-07 63.0 13.4 106 242-366 22-145 (325)
63 PF09414 RNA_ligase: RNA ligas 96.9 0.0018 4E-08 64.1 6.8 106 246-366 2-129 (186)
64 PRK01109 ATP-dependent DNA lig 96.9 0.0038 8.2E-08 73.0 10.3 97 4-114 112-211 (590)
65 COG0272 Lig NAD-dependent DNA 95.9 0.2 4.3E-06 58.2 15.5 176 245-444 109-317 (667)
66 PHA02142 putative RNA ligase 95.7 0.19 4.1E-06 54.8 14.0 104 242-367 166-299 (366)
67 TIGR02306 RNA_lig_DRB0094 RNA 94.4 0.53 1.2E-05 51.1 12.9 104 244-366 158-277 (341)
68 KOG3132 m3G-cap-specific nucle 94.2 0.35 7.5E-06 49.0 9.9 173 225-440 100-277 (325)
69 PRK09247 ATP-dependent DNA lig 89.4 0.55 1.2E-05 54.5 5.8 82 127-208 2-91 (539)
70 PF12738 PTCB-BRCT: twin BRCT 89.2 0.41 8.9E-06 38.4 3.3 30 672-701 12-41 (63)
71 PRK06195 DNA polymerase III su 86.5 1.1 2.4E-05 48.2 5.5 49 653-701 217-265 (309)
72 KOG2386 mRNA capping enzyme, g 86.3 0.42 9.1E-06 52.4 2.2 98 245-368 285-387 (393)
73 PF04675 DNA_ligase_A_N: DNA l 85.0 0.81 1.8E-05 44.8 3.3 85 125-209 2-100 (177)
74 COG5275 BRCT domain type II [G 84.5 2 4.3E-05 43.0 5.6 54 649-702 149-202 (276)
75 PRK03180 ligB ATP-dependent DN 83.9 6.5 0.00014 45.4 10.5 93 6-114 72-167 (508)
76 PLN03122 Poly [ADP-ribose] pol 78.2 3.8 8.3E-05 49.5 6.2 47 653-701 186-232 (815)
77 PLN03113 DNA ligase 1; Provisi 76.5 5 0.00011 48.2 6.5 86 122-207 127-229 (744)
78 PRK06063 DNA polymerase III su 76.1 4.5 9.6E-05 43.7 5.5 47 654-701 230-276 (313)
79 KOG4362 Transcriptional regula 74.9 2.6 5.6E-05 49.4 3.4 40 654-693 585-624 (684)
80 PRK14351 ligA NAD-dependent DN 74.8 4.6 0.0001 48.2 5.6 48 654-701 607-654 (689)
81 TIGR00575 dnlj DNA ligase, NAD 73.0 6 0.00013 47.0 6.0 48 654-701 582-629 (652)
82 PRK14350 ligA NAD-dependent DN 69.3 8 0.00017 46.0 5.9 48 654-701 591-638 (669)
83 PRK07956 ligA NAD-dependent DN 67.0 8.5 0.00019 45.9 5.6 46 656-701 590-635 (665)
84 COG4566 TtrR Response regulato 66.2 22 0.00047 35.4 7.2 81 102-182 85-175 (202)
85 TIGR00574 dnl1 DNA ligase I, A 64.1 22 0.00048 41.1 8.1 93 5-113 53-148 (514)
86 PLN03123 poly [ADP-ribose] pol 50.1 29 0.00063 43.2 6.2 48 652-700 389-436 (981)
87 PF09511 RNA_lig_T4_1: RNA lig 47.8 2.1E+02 0.0044 29.1 11.2 31 246-276 46-77 (221)
88 COG5163 NOP7 Protein required 38.7 22 0.00049 38.8 2.5 37 652-691 346-382 (591)
89 cd00950 DHDPS Dihydrodipicolin 36.6 78 0.0017 33.3 6.3 67 342-425 36-104 (284)
90 COG0272 Lig NAD-dependent DNA 33.2 79 0.0017 37.4 6.0 46 655-700 593-638 (667)
91 cd00408 DHDPS-like Dihydrodipi 31.7 1.1E+02 0.0023 32.2 6.4 65 344-425 35-101 (281)
92 KOG2481 Protein required for n 31.7 46 0.001 37.8 3.6 37 652-691 323-359 (570)
93 PRK03170 dihydrodipicolinate s 31.4 1E+02 0.0023 32.6 6.3 65 344-425 39-105 (292)
94 TIGR03544 DivI1A_domain DivIVA 31.1 92 0.002 21.8 3.9 28 111-138 5-32 (34)
95 TIGR00683 nanA N-acetylneurami 30.9 1.1E+02 0.0024 32.5 6.4 66 342-424 37-104 (290)
96 TIGR02313 HpaI-NOT-DapA 2,4-di 30.1 1.1E+02 0.0025 32.5 6.3 65 344-425 38-104 (294)
97 PF14909 SPATA6: Spermatogenes 29.8 1.4E+02 0.0031 28.3 6.0 59 539-602 11-71 (140)
98 TIGR00674 dapA dihydrodipicoli 27.8 1.3E+02 0.0028 31.8 6.2 58 352-426 46-103 (285)
99 cd00952 CHBPH_aldolase Trans-o 27.8 1.3E+02 0.0028 32.3 6.3 65 344-425 46-112 (309)
100 PF00701 DHDPS: Dihydrodipicol 27.1 1.1E+02 0.0024 32.3 5.5 65 344-425 39-105 (289)
101 PRK02289 4-oxalocrotonate taut 26.3 1.3E+02 0.0028 23.7 4.5 25 493-517 5-29 (60)
102 PLN02417 dihydrodipicolinate s 25.8 1.5E+02 0.0033 31.2 6.3 58 351-425 48-105 (280)
103 PRK04147 N-acetylneuraminate l 25.7 1.6E+02 0.0034 31.3 6.4 57 352-425 52-108 (293)
104 KOG3673 FtsJ-like RNA methyltr 24.8 72 0.0016 36.6 3.6 38 332-369 654-691 (845)
105 cd00954 NAL N-Acetylneuraminic 24.8 1.7E+02 0.0038 30.9 6.5 67 342-425 37-105 (288)
106 cd00951 KDGDH 5-dehydro-4-deox 24.5 1.7E+02 0.0037 31.0 6.3 63 344-424 38-102 (289)
107 KOG2386 mRNA capping enzyme, g 22.5 3.7E+02 0.0079 30.1 8.4 175 236-445 51-242 (393)
108 PF11459 DUF2893: Protein of u 22.0 2.4E+02 0.0051 23.5 5.2 45 121-170 15-59 (69)
109 COG0329 DapA Dihydrodipicolina 21.2 2E+02 0.0044 30.8 6.1 64 344-424 42-107 (299)
110 PF02969 TAF: TATA box binding 21.1 1E+02 0.0023 25.3 3.0 56 69-134 7-66 (66)
No 1
>KOG0966 consensus ATP-dependent DNA ligase IV [Replication, recombination and repair]
Probab=100.00 E-value=1.1e-138 Score=1146.96 Aligned_cols=659 Identities=45% Similarity=0.751 Sum_probs=576.0
Q ss_pred CCCCCcHHHHHHHHHHHHhcCChhHHHHHHHHHhhhcCCC----chHhhhHhhcCCCCCCCccccCCCHHHHHHHHHHHh
Q 005331 3 KTEETEVIVLVSLFNWIQKTKPAAKKRSKFRKFLDTYCDS----VDYFSALRLILPSLDRERGSYGLKESVLANCLIDAL 78 (702)
Q Consensus 3 ~~~~~~F~~l~~~~e~i~~~~~~~~k~~~l~~~l~~~~~~----~~~~~~lrLllp~~d~~r~~ygike~~L~k~~~~~~ 78 (702)
||+++.|+.+|++|+.|+.+.....|.+++++++++|+.+ +|+||++||++|++||+|+.|||||..||++|+++|
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 7899999999999999999999999999999999999865 999999999999999999999999999999999999
Q ss_pred CCCcChHHHHHHhhhhcCCCCCCCCCHHHHHHHHhhhccCCC-CCCCCHHHHHHHHHHHHhhhchHhHH-HHHHHHHHhC
Q 005331 79 GMSKDSADAVRLINWRKGGAAPNAGNFPMVAAEVLQRRQGMI-SGGLTIKELNDLLDRLASSENRAEKI-SVLSTLIKKT 156 (702)
Q Consensus 79 ~l~~~s~~~~~L~~wk~~~~~~~~gD~~~~~~~v~~~r~~~~-~~~lTi~eVn~~Ld~La~~~~~~~k~-~~l~~ll~~~ 156 (702)
++|++|.||.+|.||+.++..+ |||+.++++++++|+... ++.|||.|||++||.||.......+. ..|..++++|
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 9999999999999999887765 999999999999998654 44599999999999999887765554 8999999999
Q ss_pred CHHHHHHHHHHHhhhhccCccccccccccCcCHHHHHhhhCCHHHHHHHHhhhhcccccCC--cccCCccccccccccCC
Q 005331 157 NAQEMKWIIMIILKDLKLGISEKSIFHEFHPDAEDLFNVTCDLKLVCEKLKDRNQRHKRQD--IEVGKAVRPQLAMRIGD 234 (702)
Q Consensus 157 t~~E~k~l~RiIlk~lriG~~e~~il~~~hpda~~~~~~~~dL~~V~~~L~~~~~~~~~~~--i~~~~~~~PmLA~~~~~ 234 (702)
||.|+|||+|||||++++|++|++||.+|||||+++||+|+||+.||+.|.||+.+++..+ |++|..|+||||++...
T Consensus 159 S~~ElkWliriiLK~lklG~se~~Il~vfHPdA~dl~~vtsDLk~Vc~~L~Dp~~~l~~~~~~i~lfsa~~PqLa~~~~~ 238 (881)
T KOG0966|consen 159 SPLELKWLIRIILKNLKLGASEKKILSVFHPDAQDLYNVTSDLKAVCKKLYDPSVGLKELDEDIELFSAFRPQLAQKQKL 238 (881)
T ss_pred CHHHHHHHHHHHHHhhhcCCccchhhhhcCccHHHHHHHhhhHHHHHHHhcCCccCccccccceeehhhcCHHHHhhhcc
Confidence 9999999999999999999999999999999999999999999999999999999998877 99999999999999876
Q ss_pred hH-HHHHHcCCCceEEEEecceEEEEEEEeCCEEEEEeCCCCCCCcch-h----h-HHHHHHhhc--cccceeeeceEEE
Q 005331 235 AH-AAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYG-H----A-MSKIIEQNV--LVDRCILDGEMLV 305 (702)
Q Consensus 235 ~~-~~~~~~~~~~~~~E~K~DG~R~qvh~~g~~v~~~SR~g~d~t~~~-p----~-l~~~~~~~~--~~~~~ILDGE~v~ 305 (702)
.. +++++|+++.|++|+|+||||+|+|++|+.++||||||.|||..| . + +...+...+ ....||||||||+
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 688999999999999999999999999999999999999999422 1 1 222222222 2789999999999
Q ss_pred eeCCCCccccccchHHHHHHhhcCCCCCCceEEEEEEEeeeCCccccCCCHHHHHHHHHhhccCCCCcccccccCCCCCc
Q 005331 306 WDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNS 385 (702)
Q Consensus 306 ~d~~~~~~~~F~~lq~~~~~~r~~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~~~~~~~~p~~~~~~ 385 (702)
||+.+.+++|||+++++...... +.+.++||+|||+||+||++|.+.||..|++.|+.++.+.+++++++.
T Consensus 319 wD~~~~~f~~~G~~~dik~~~~~--~~~~qp~yvvfDLLylNgksL~~~~l~qR~e~L~~v~~p~~~~iei~~------- 389 (881)
T KOG0966|consen 319 WDTKTKRFCPFGSNSDIKELSSR--DGSQQPCYVVFDLLYLNGKSLFGAPLHQRLEILKKVIVPKSGRIEIVR------- 389 (881)
T ss_pred eecchhhhccCCchhhHHHhhcc--ccCCCceEEEeeeeeecCcccCCccHHHHHHHHHhcccCCCCeeEEee-------
Confidence 99999999999999988765542 456789999999999999999999999999999999999999987652
Q ss_pred cccCCCCCccccccCCHHHHHHHHHHHHHCCCceEEEecCCCCcccCCCCCCeEEEcccccc-CCCcceEEEEEEEecCC
Q 005331 386 HVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIR-AGSDLDVLIIGGYYGSG 464 (702)
Q Consensus 386 ~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EGlV~K~~ds~Y~~G~Rs~~WlKvK~~y~~-~g~~~DlvVIG~~~G~G 464 (702)
...+++.++++++|++|+++|.||||+|+++|.|.||.|+++|+|+||+|+. +|+++|++|||||||+|
T Consensus 390 ----------~~~~~~~edi~~~f~~ai~~~~EGIVlK~~~S~Y~pg~R~~gW~K~KPeYlkg~g~dLD~lIiGgy~G~g 459 (881)
T KOG0966|consen 390 ----------SEVGSTKEDIEQFFEEAIDNGEEGIVLKKPDSSYVPGQRSNGWIKLKPEYLKGFGEDLDLLIIGGYYGRG 459 (881)
T ss_pred ----------hhhcccHHHHHHHHHHHHhcCCCceEEeccCcccCccccCCCcEeecHHHHhhcCccccEEEEecccCCC
Confidence 4567899999999999999999999999999999999999999999999999 59999999999999999
Q ss_pred CCCCccceEEEEEecCCCCCCCCcceEEEEEecCCCCHHHHHHHHHhhccccccccCCCCCCCCcccccCCCCCCCcEEE
Q 005331 465 RRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDVWI 544 (702)
Q Consensus 465 ~r~g~~gs~llg~~d~~~~~~~~~~~~~v~kVgtG~s~~~~~~l~~~l~~~~~~~~~~~~~pp~~~~~~~~~~~~pdvwi 544 (702)
+|+|++.+|+||+.++..++.+|.+|.++|+||+|+|++|+..+.++++++|.+ ..+..+|++++.. +...||+||
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 2344333334433 234799999
Q ss_pred eCCCceEEEEEeeeceeecccccCCCceeeccEEEEEecCCCccCCCCHHHHHHHHHccCCCcccccccCCCCCCCcccc
Q 005331 545 ESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDKPWHDCLDVQSFVELVHSSNGTTQKGKEYGGLQDDKPKQF 624 (702)
Q Consensus 545 ~~P~~s~v~ev~a~~~~~~s~~~~~g~tLRfPr~~riR~DK~~~d~~t~~el~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 624 (702)
+ |..|+|++|++. +++.+..|.+++||||||+.++|.||+|+||+|+++|.++...+. ++.+.+ .++++.
T Consensus 536 ~-P~~SiIlqikaa-~i~~s~~f~tn~tLrfPr~ekvR~DK~W~ec~tl~~l~~l~~~~~-------~d~~~~-~kk~~~ 605 (881)
T KOG0966|consen 536 D-PDNSIILQIKAA-EIVPSSNFVTNYTLRFPRIEKVRLDKPWHECLTLNELGDLVNVSK-------SDVEDK-EKKKRD 605 (881)
T ss_pred C-CCCceEEEeehh-eeeecccccccceeecceeeeeecCCcHHHHhhHHHHHHHhcccc-------CCcchh-hhhccc
Confidence 9 999999999953 446889999999999999999999999999999999999985311 111111 111111
Q ss_pred ccccccccccccccCCccccCCccCccccccccCCcEEEEEeCC-CCCCHHHHHHHHHHcCCEEEEecCCCeeEEEe
Q 005331 625 RSSRKGEKKNVSIVPSHFLQTDVSDIKGETSIFSDMVFYFVNVP-PAYSLDSLHKMVVENGGTFSMNLNNSVTHCVA 700 (702)
Q Consensus 625 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~f~g~~f~v~~~~-~~~~k~~l~~~i~~~gG~~~~n~~~~~~~~i~ 700 (702)
..+++++.+ ..-+......+.+.+.|++|+|++|||+++. .++||++||++|++|||+||||+++++|+||+
T Consensus 606 -t~~~~k~~~---~~i~~~~~~~~~~~~~s~if~gl~f~Vlsgt~~~~tk~~le~~ivenGG~iv~nv~p~~~~ci~ 678 (881)
T KOG0966|consen 606 -TLKVRKRTR---KAIHDSAPNRSKVAKISNIFDGLEFCVLSGTSETHTKAKLEEIIVENGGKIVQNVGPSDTLCIA 678 (881)
T ss_pred -chhhhhhhh---hhhcccccchhcccchhhhhcCeeEEEecCCcccccHHHHHHHHHHcCCEEEEcCCCCCcceEE
Confidence 111111111 1223445566788899999999999999986 57889999999999999999999998999996
No 2
>PLN03113 DNA ligase 1; Provisional
Probab=100.00 E-value=2.4e-106 Score=928.36 Aligned_cols=550 Identities=24% Similarity=0.420 Sum_probs=471.9
Q ss_pred CCCcHHHHHHHHHHHHhcCChhHHHHHHHHHhhhc--CCCchHhhhHhh----cCCCCCCCccccCCCHHHHHHHHHHHh
Q 005331 5 EETEVIVLVSLFNWIQKTKPAAKKRSKFRKFLDTY--CDSVDYFSALRL----ILPSLDRERGSYGLKESVLANCLIDAL 78 (702)
Q Consensus 5 ~~~~F~~l~~~~e~i~~~~~~~~k~~~l~~~l~~~--~~~~~~~~~lrL----llp~~d~~r~~ygike~~L~k~~~~~~ 78 (702)
.+|||..||++|++|++|+++.+|+.+|.+||... .+++|++++++| ++|.. ++.+|||+++.|+++|++++
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 56999999999999999999999999999999985 367899999999 56665 46799999999999999999
Q ss_pred CCCcChHHHHHHhhhhcCCCCCCCCCHHHHHHHHhhhccC-CCCCCCCHHHHHHHHHHHHhhhc---hHhHHHHHHHHHH
Q 005331 79 GMSKDSADAVRLINWRKGGAAPNAGNFPMVAAEVLQRRQG-MISGGLTIKELNDLLDRLASSEN---RAEKISVLSTLIK 154 (702)
Q Consensus 79 ~l~~~s~~~~~L~~wk~~~~~~~~gD~~~~~~~v~~~r~~-~~~~~lTi~eVn~~Ld~La~~~~---~~~k~~~l~~ll~ 154 (702)
|++...... .| ...||||++|+.+.++++. ..+.+|||.+|++.|++||..+| ++.|..+|..|+.
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 998664331 34 3579999999987665543 23578999999999999999876 4577889999999
Q ss_pred hCCHHHHHHHHHHHhhhhccCccccccccccCcCH------------------------HHHHhhhCCHHHHHHHHhhhh
Q 005331 155 KTNAQEMKWIIMIILKDLKLGISEKSIFHEFHPDA------------------------EDLFNVTCDLKLVCEKLKDRN 210 (702)
Q Consensus 155 ~~t~~E~k~l~RiIlk~lriG~~e~~il~~~hpda------------------------~~~~~~~~dL~~V~~~L~~~~ 210 (702)
.+++.|++||+|+|+++||||+++++|+.++|+.+ .++|+.++|++.|+..|....
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 99999999999999999999999999999887643 357888999998888776533
Q ss_pred -ccc-ccCCcccCCccccccccccCChHHHHHHcCCCceEEEEecceEEEEEEE-eCCEEEEEeCCCCCCCcchhhHHHH
Q 005331 211 -QRH-KRQDIEVGKAVRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHK-NGSEIHYFSRSFLDHSEYGHAMSKI 287 (702)
Q Consensus 211 -~~~-~~~~i~~~~~~~PmLA~~~~~~~~~~~~~~~~~~~~E~K~DG~R~qvh~-~g~~v~~~SR~g~d~t~~~p~l~~~ 287 (702)
..+ ....+++|.||+||||++.++++++++++.+.+|++|+||||+|+|+|+ .+++|++|||||+|+|..||++.+.
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 333 5677999999999999999988889999988899999999999999998 5789999999999999999999886
Q ss_pred HHhhc--cccceeeeceEEEeeCCCCccccccchHHHHHHhhcCC---CCCCceEEEEEEEeeeCCccccCCCHHHHHHH
Q 005331 288 IEQNV--LVDRCILDGEMLVWDTSLNRFAEFGSNQEIAKAARDGL---SSDRQLCYFAFDVLYVGDTSVIHQSLKERHEL 362 (702)
Q Consensus 288 ~~~~~--~~~~~ILDGE~v~~d~~~~~~~~F~~lq~~~~~~r~~~---~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~ 362 (702)
+.... .+.+||||||+|+||+.+++++||+.||... +... +...++||+||||||+||++|++.||.+||++
T Consensus 435 ~~~~~~~~~~~~ILDGEiVa~d~~~~~~lpFq~Lq~R~---rk~~~~~~~~~pv~~~aFDlLylnG~~L~~~PL~eRR~~ 511 (744)
T PLN03113 435 ISRLKKPSVKSFILDCELVAYDREKKKILPFQILSTRA---RKNVVMSDIKVDVCIFAFDMLYLNGQPLIQEQLKIRREH 511 (744)
T ss_pred HHHhccccCCCEEEEeEEEEEECCCCCcCCHHHHHhhh---ccccchhccccceEEEEEeccccCccChhcCCHHHHHHH
Confidence 64422 1578999999999999888899998887642 2221 22478999999999999999999999999999
Q ss_pred HHhhccCCCCcccccccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHCCCceEEEecC--CCCcccCCCCCCeEE
Q 005331 363 LQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDL--GSKWEPGDRSGKWLK 440 (702)
Q Consensus 363 L~~~~~~~~~~~~~~~p~~~~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EGlV~K~~--ds~Y~~G~Rs~~WlK 440 (702)
|++++.+.+++++++. .....+.++++++|++++++|+||||+|++ +|+|.||+|+.+|+|
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-CCcceEEEEEEEecCCCCCCccceEEEEEecCCCCCCCCcceEEEEEecCCCCHHHHHHHHHhhccccccc
Q 005331 441 LKPEYIRA-GSDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKY 519 (702)
Q Consensus 441 vK~~y~~~-g~~~DlvVIG~~~G~G~r~g~~gs~llg~~d~~~~~~~~~~~~~v~kVgtG~s~~~~~~l~~~l~~~~~~~ 519 (702)
+|++|+++ ++++|+||||||+|+|+|+|.+|+||||+||+++ +.|++|||||||||++++++|.+.|++++..
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 7999999999999999999999999999998653 4899999999999999999999999988754
Q ss_pred cCCCCCCCCcccccCCCCCCCcEEEeCCCceEEEEEeeeceeecccccC---------CCceeeccEEEEEecCCCccCC
Q 005331 520 EYPKRAPPSFYQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFS---------APYSLRFPRIDRVRYDKPWHDC 590 (702)
Q Consensus 520 ~~~~~~pp~~~~~~~~~~~~pdvwi~~P~~s~v~ev~a~~~~~~s~~~~---------~g~tLRfPr~~riR~DK~~~d~ 590 (702)
.||+|+... ...+||+||+ |. .|+||+++.. ..|+.|+ .|++||||||+|+|+||+|+||
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-PT--EVWEVKAADL-TISPVHRAAVGIVDPDKGISLRFPRLVRVREDKSPEQA 717 (744)
T ss_pred -----CCCcccccC--CCCCCcEEEC-Cc--eEEEEEeeee-ccCcccccccccccCCCCeEEECCEEEEEECCCChHHC
Confidence 244455432 2457999999 84 6999985432 3577786 4899999999999999999999
Q ss_pred CCHHHHHHHHHcc
Q 005331 591 LDVQSFVELVHSS 603 (702)
Q Consensus 591 ~t~~el~~l~~~~ 603 (702)
+|++++.+||+.+
T Consensus 718 tt~~~l~~ly~~Q 730 (744)
T PLN03113 718 TSSEQVADMYNAQ 730 (744)
T ss_pred CCHHHHHHHHHHH
Confidence 9999999999743
No 3
>PRK01109 ATP-dependent DNA ligase; Provisional
Probab=100.00 E-value=4.7e-104 Score=905.65 Aligned_cols=543 Identities=27% Similarity=0.478 Sum_probs=472.4
Q ss_pred CcHHHHHHHHHHHHhcCChhHHHHHHHHHhhhcCCCc----hHhhhHhhcCCCCCCCccccCCCHHHHHHHHHHHhCCCc
Q 005331 7 TEVIVLVSLFNWIQKTKPAAKKRSKFRKFLDTYCDSV----DYFSALRLILPSLDRERGSYGLKESVLANCLIDALGMSK 82 (702)
Q Consensus 7 ~~F~~l~~~~e~i~~~~~~~~k~~~l~~~l~~~~~~~----~~~~~lrLllp~~d~~r~~ygike~~L~k~~~~~~~l~~ 82 (702)
|+|+.||++|++|++|+++.+|+.+|.+||.+.. ++ .+|+++++++|..+. .+|||+++.|+++|++++|++.
T Consensus 1 m~f~~l~~~~~~i~~t~~r~~k~~~l~~~~~~~~-~~~~~~~~~l~~~~~~p~~~~--~~~gi~~~~l~k~i~~~~g~~~ 77 (590)
T PRK01109 1 MEFSELAEYFERLEKTTSRTQLTKLLADLLKKTP-PEIIDKVVYLIQGKLWPDWLG--LELGVGEKLLIKAISMATGISE 77 (590)
T ss_pred CcHHHHHHHHHHHHhhhchHHHHHHHHHHHHhCC-HHhhhhhHHHHhCCcCccccC--cccCcCHHHHHHHHHHHHCcCH
Confidence 7899999999999999999999999999999873 33 467777778899875 5899999999999999999998
Q ss_pred ChHHHHHHhhhhcCCCCCCCCCHHHHHHHHhhhccCC------CCCCCCHHHHHHHHHHHHhhhc---hHhHHHHHHHHH
Q 005331 83 DSADAVRLINWRKGGAAPNAGNFPMVAAEVLQRRQGM------ISGGLTIKELNDLLDRLASSEN---RAEKISVLSTLI 153 (702)
Q Consensus 83 ~s~~~~~L~~wk~~~~~~~~gD~~~~~~~v~~~r~~~------~~~~lTi~eVn~~Ld~La~~~~---~~~k~~~l~~ll 153 (702)
+..+. .| ...||||++|+.++++++.. .+++||+.+|++.|++||..+| +.+|..+|..||
T Consensus 78 ~~~~~----~~------~~~GDlg~~a~~~~~~~~~~~~~~~~~~~~lti~eV~~~L~~Ia~~sg~~s~~~k~~iL~~Ll 147 (590)
T PRK01109 78 KEVEN----LY------KKTGDLGEVARRLKSKKKQKSLLAFFSKEPLTVKEVYDTLVKIALATGEGSQDLKIKLLAGLL 147 (590)
T ss_pred HHHHH----HH------HhcCCHHHHHHHHHhhcccccccccCCCCCcCHHHHHHHHHHHHhhhCCCcHHHHHHHHHHHH
Confidence 76653 23 35799999999999877532 3578999999999999999874 578899999999
Q ss_pred HhCCHHHHHHHHHHHhhhhccCcccccccc----cc-----CcCHHHHHhhhCCHHHHHHHHhhhh-cccccCCcccCCc
Q 005331 154 KKTNAQEMKWIIMIILKDLKLGISEKSIFH----EF-----HPDAEDLFNVTCDLKLVCEKLKDRN-QRHKRQDIEVGKA 223 (702)
Q Consensus 154 ~~~t~~E~k~l~RiIlk~lriG~~e~~il~----~~-----hpda~~~~~~~~dL~~V~~~L~~~~-~~~~~~~i~~~~~ 223 (702)
.++++.|++||+|+|+++|++|+++++|++ ++ |++++++|+.|+||+.||+.|.++. ..+....+++|.|
T Consensus 148 ~~~~~~E~k~iirli~g~lriGv~e~~il~ALa~A~~~~~~~~~ve~~y~~~~Dlg~va~~l~~~g~~~~~~~~i~~~~P 227 (590)
T PRK01109 148 KDASPLEAKYIARFVEGRLRLGVGDATILDALAIAFGGAVARELVERAYNLRADLGYIAKILAEGGIEALKKVKPQVGIP 227 (590)
T ss_pred HhCCHHHHHHHHHHHhhhhhcCccHHHHHHHHHHHHhcccchHHHHHHHHhCCCHHHHHHHHHhcchhhhccCcccCCCC
Confidence 999999999999999999999999999997 34 4889999999999999999998764 3566778999999
Q ss_pred cccccccccCChHHHHHHcCCCceEEEEecceEEEEEEEeCCEEEEEeCCCCCCCcchhhHHHHHHhhccccceeeeceE
Q 005331 224 VRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDGEM 303 (702)
Q Consensus 224 ~~PmLA~~~~~~~~~~~~~~~~~~~~E~K~DG~R~qvh~~g~~v~~~SR~g~d~t~~~p~l~~~~~~~~~~~~~ILDGE~ 303 (702)
|+||||++.+.++++++++++ +|++|+||||+|||+|++|++|++|||||+|+|..||++.+.+...+...+|||||||
T Consensus 228 v~PmLA~~~~~~~~~~~~~~~-~~~~E~K~DG~R~qih~~~~~v~l~SR~~~d~T~~~pel~~~~~~~~~~~~~ILDGEl 306 (590)
T PRK01109 228 IRPMLAERLSSPKEILKKMGG-EALVEYKYDGERAQIHKKGDKVKIFSRRLENITHQYPDVVEYAKEAIKAEEAIVEGEI 306 (590)
T ss_pred CCcccCCccCCHHHHHHHcCC-CeEEEecCCceEEEEEEcCCEEEEEeCCchhhccccchHHHHHHHhcCccceEEeeeE
Confidence 999999999988888888864 6999999999999999999999999999999999999999887655556899999999
Q ss_pred EEeeCCCCccccccchHHHHHHhhcC----CCCCCceEEEEEEEeeeCCccccCCCHHHHHHHHHhhccCCCCccccccc
Q 005331 304 LVWDTSLNRFAEFGSNQEIAKAARDG----LSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVP 379 (702)
Q Consensus 304 v~~d~~~~~~~~F~~lq~~~~~~r~~----~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~~~~~~~~p 379 (702)
|+||+.+++++||+.+|.. + +.. .....|+||+||||||+||++|++.||.+||++|++++.+.+. +.+.
T Consensus 307 v~~d~~~g~~~~F~~l~~R-~--r~~~~~~~~~~~p~~~~vFDiL~l~g~~l~~~pl~eRr~~L~~~~~~~~~-~~~~-- 380 (590)
T PRK01109 307 VAVDPETGEMRPFQELMHR-K--RKYDIEEAIKEYPVNVFLFDLLYVDGEDLTDKPLPERRKKLEEIVKENDK-VKLA-- 380 (590)
T ss_pred EEEECCCCcccChHHHhhc-c--cccchhhhcccCceEEEEEEEEEECCcchhhCcHHHHHHHHHHhcCCCCc-eEEe--
Confidence 9999777888999887754 1 111 1134689999999999999999999999999999999987542 4322
Q ss_pred CCCCCccccCCCCCccccccCCHHHHHHHHHHHHHCCCceEEEecC--CCCcccCCCCCCeEEEccccccC-CCcceEEE
Q 005331 380 DHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDL--GSKWEPGDRSGKWLKLKPEYIRA-GSDLDVLI 456 (702)
Q Consensus 380 ~~~~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EGlV~K~~--ds~Y~~G~Rs~~WlKvK~~y~~~-g~~~DlvV 456 (702)
....+++.++++++|++++++|+||||+|++ +|+|.||+|+.+|+|+|++|+++ ++++|+||
T Consensus 381 ---------------~~~~~~~~~~~~~~~~~a~~~g~EGiv~K~~~~ds~Y~~g~Rs~~WlK~K~dy~~~~~~~~Dlvv 445 (590)
T PRK01109 381 ---------------ERIITDDVEELEKFFHRAIEEGCEGLMAKSLGKDSIYQAGARGWLWIKYKRDYQSEMADTVDLVV 445 (590)
T ss_pred ---------------eeEecCCHHHHHHHHHHHHHcCCceEEEecCCCCCCcCCCCCCccHHHhhHHhhcccCCceeEEE
Confidence 1234678899999999999999999999999 99999999999999999999984 78999999
Q ss_pred EEEEecCCCCCCccceEEEEEecCCCCCCCCcceEEEEEecCCCCHHHHHHHHHhhccccccccCCCCCCCCcccccCCC
Q 005331 457 IGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNS 536 (702)
Q Consensus 457 IG~~~G~G~r~g~~gs~llg~~d~~~~~~~~~~~~~v~kVgtG~s~~~~~~l~~~l~~~~~~~~~~~~~pp~~~~~~~~~ 536 (702)
||+|+|+|+|+|.+|+|+||+||+++ +.|+++|+||||||++++++|.+.+.+++... .|| +. ..
T Consensus 446 iG~~~g~Gkr~~~~g~~ll~~~d~~~-----~~~~~v~kvgtG~sd~~~~~l~~~l~~~~~~~-----~~~-~~----~~ 510 (590)
T PRK01109 446 VGAFYGRGRRGGKYGSLLMAAYDPKT-----DTFETVCKVGSGFTDEDLDELPKMLKPYKIDH-----KHP-RV----VS 510 (590)
T ss_pred EEeEeCCCccCCccccEEEEEEcCCC-----CeEEEEEEECCCCCHHHHHHHHHHhhhhcccC-----CCc-cc----cc
Confidence 99999999999999999999998653 38999999999999999999999999988641 133 22 13
Q ss_pred CCCCcEEEeCCCceEEEEEeeeceeecccccC---------CCceeeccEEEEEecCCCccCCCCHHHHHHHHHcc
Q 005331 537 KERPDVWIESPEKSIILSITSDIRTIRSEVFS---------APYSLRFPRIDRVRYDKPWHDCLDVQSFVELVHSS 603 (702)
Q Consensus 537 ~~~pdvwi~~P~~s~v~ev~a~~~~~~s~~~~---------~g~tLRfPr~~riR~DK~~~d~~t~~el~~l~~~~ 603 (702)
..+||+||+ | ++|+||+++.. ..|+.|+ .|++||||||+++|+||+|+||+|++++.+||+++
T Consensus 511 ~~~pdvwv~-P--~~V~eV~~~~i-t~S~~~~~~~~~~~~~~g~~LRfPr~~~~R~DK~~~d~~t~~~~~~ly~~q 582 (590)
T PRK01109 511 KMEPDVWVE-P--KLVAEIIGAEI-TLSPLHTCCLGVVEKGAGLAIRFPRFIRWRDDKSPEDATTTEEILEMYKRQ 582 (590)
T ss_pred ccCCcEEEe-c--cEEEEEEeeec-ccCcceecccccccCCCceeEEcCeeeEeeCCCChhhCcCHHHHHHHHHHh
Confidence 468999999 7 68999986532 3577777 68899999999999999999999999999999743
No 4
>KOG0967 consensus ATP-dependent DNA ligase I [Replication, recombination and repair]
Probab=100.00 E-value=2.4e-99 Score=819.12 Aligned_cols=551 Identities=27% Similarity=0.498 Sum_probs=475.6
Q ss_pred CCCcHHHHHHHHHHHHhcCChhHHHHHHHHHhhhcC--CCchHhhhHhhcCCCC--CCCccccCCCHHHHHHHHHHHhCC
Q 005331 5 EETEVIVLVSLFNWIQKTKPAAKKRSKFRKFLDTYC--DSVDYFSALRLILPSL--DRERGSYGLKESVLANCLIDALGM 80 (702)
Q Consensus 5 ~~~~F~~l~~~~e~i~~~~~~~~k~~~l~~~l~~~~--~~~~~~~~lrLllp~~--d~~r~~ygike~~L~k~~~~~~~l 80 (702)
+.+||.+||..|++|+++++|.+...++.+||.+.. .|+|+.|+++|.+..+ |.++.++||+|..|.|+|++++|.
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 469999999999999999999999999999998854 6899999999987777 667899999999999999999999
Q ss_pred CcChHHHHHHhhhhcCCCCCCCCCHHHHHHHHhhhccC-CCCCCCCHHHHHHHHHHHHhhhc---hHhHHHHHHHHHHhC
Q 005331 81 SKDSADAVRLINWRKGGAAPNAGNFPMVAAEVLQRRQG-MISGGLTIKELNDLLDRLASSEN---RAEKISVLSTLIKKT 156 (702)
Q Consensus 81 ~~~s~~~~~L~~wk~~~~~~~~gD~~~~~~~v~~~r~~-~~~~~lTi~eVn~~Ld~La~~~~---~~~k~~~l~~ll~~~ 156 (702)
+..... + .| ...||+|.||+...+.... ..+.+|||.+|++.|.+||..+| +..|..++..||..|
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---N-QY------NKLGDLGLVAQGSRSSQRMMFKPKPLTVRDVFSTLRKIAKESGKGSQNKKKDLIKALLVAC 246 (714)
T ss_pred cHHHHH---H-HH------HhcCcHHHHHhhcccccccccCCCCccHHHHHHHHHHHHHhhCcchhHHHHHHHHHHHHhc
Confidence 976433 2 23 4589999999987554433 35789999999999999999887 567889999999999
Q ss_pred CHHHHHHHHHHHhhhhccCcccccccccc------C----------cC------------HHHHHhhhCCHHHHHHHHhh
Q 005331 157 NAQEMKWIIMIILKDLKLGISEKSIFHEF------H----------PD------------AEDLFNVTCDLKLVCEKLKD 208 (702)
Q Consensus 157 t~~E~k~l~RiIlk~lriG~~e~~il~~~------h----------pd------------a~~~~~~~~dL~~V~~~L~~ 208 (702)
++.|+|||+|.|.++||||+.++|||.++ + +| ..++|+.++|+..++..|.+
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 24579999999999988866
Q ss_pred hhc--ccccCCcccCCccccccccccCChHHHHHHcCCCceEEEEecceEEEEEEE-eCCEEEEEeCCCCCCCcchhhHH
Q 005331 209 RNQ--RHKRQDIEVGKAVRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHK-NGSEIHYFSRSFLDHSEYGHAMS 285 (702)
Q Consensus 209 ~~~--~~~~~~i~~~~~~~PmLA~~~~~~~~~~~~~~~~~~~~E~K~DG~R~qvh~-~g~~v~~~SR~g~d~t~~~p~l~ 285 (702)
... ..+.+.+.||.|++||||++.+.+.++++++.+..|.+|+||||+|+|||. .+|.|.+||||+++.|..||++.
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 432 245678999999999999999999999999999999999999999999996 57899999999999999999998
Q ss_pred HHHHhhc--cccceeeeceEEEeeCCCCccccccchHHHHHHhhcCC---CCCCceEEEEEEEeeeCCccccCCCHHHHH
Q 005331 286 KIIEQNV--LVDRCILDGEMLVWDTSLNRFAEFGSNQEIAKAARDGL---SSDRQLCYFAFDVLYVGDTSVIHQSLKERH 360 (702)
Q Consensus 286 ~~~~~~~--~~~~~ILDGE~v~~d~~~~~~~~F~~lq~~~~~~r~~~---~~~~~~~~~vFDiL~lng~~l~~~pl~eRr 360 (702)
..+.... .+.++|||||+|+||...++++||+-|. .+.|+.. +....+|+++||+||+||++|++.||.+||
T Consensus 407 ~~~~~~~kp~v~sFIlD~EvVA~Dr~~~~IlpFQvLS---TRkRk~v~v~dikV~Vcvf~FDily~ng~~Li~~pL~eRR 483 (714)
T KOG0967|consen 407 EVISKLKKPSVKSFILDCEVVAWDREKGKILPFQVLS---TRKRKNVDVNDIKVKVCVFVFDILYLNGESLIQEPLRERR 483 (714)
T ss_pred HHHHHhhCCccceeEEeeeEEEEeccCCccCchhhhh---hhhccccchhhceEEEEEEEEeeeeeCChhhhhhhHHHHH
Confidence 7664332 2578999999999999988999995443 3444333 234689999999999999999999999999
Q ss_pred HHHHhhccCCCCcccccccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHCCCceEEEecC--CCCcccCCCCCCe
Q 005331 361 ELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDL--GSKWEPGDRSGKW 438 (702)
Q Consensus 361 ~~L~~~~~~~~~~~~~~~p~~~~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EGlV~K~~--ds~Y~~G~Rs~~W 438 (702)
++|.+.+..++|.++++. ...+.+.++++++|++++.+++||+|+|-+ ++.|+|.+||.+|
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 999999999999887642 234689999999999999999999999976 4789999999999
Q ss_pred EEEccccccC-CCcceEEEEEEEecCCCCCCccceEEEEEecCCCCCCCCcceEEEEEecCCCCHHHHHHHHHhhccccc
Q 005331 439 LKLKPEYIRA-GSDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFR 517 (702)
Q Consensus 439 lKvK~~y~~~-g~~~DlvVIG~~~G~G~r~g~~gs~llg~~d~~~~~~~~~~~~~v~kVgtG~s~~~~~~l~~~l~~~~~ 517 (702)
+|+|.+|+++ |+++||||||+|+|.|+|.|++|+||+|||+++. ..|.++||+||||||+++.++.+.|.....
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 489999999999999999999998866533
Q ss_pred cccCCCCCCCCcccccCCCCCCCcEEEeCCCceEEEEEe-eeceeecccccC---------CCceeeccEEEEEecCCCc
Q 005331 518 KYEYPKRAPPSFYQVTNNSKERPDVWIESPEKSIILSIT-SDIRTIRSEVFS---------APYSLRFPRIDRVRYDKPW 587 (702)
Q Consensus 518 ~~~~~~~~pp~~~~~~~~~~~~pdvwi~~P~~s~v~ev~-a~~~~~~s~~~~---------~g~tLRfPr~~riR~DK~~ 587 (702)
. .|+++|.+. ...+||+|++ |. .||||+ |++. -|+.|. .|.+||||||.|+|+||.+
T Consensus 622 ~------~~~~~y~~d--~s~kPd~wf~-p~--~VwEvk~Adlt--~SPiy~Aa~Glv~~dkGISlRFPRfiRiR~DK~p 688 (714)
T KOG0967|consen 622 D------SPKPYYRFD--ESLKPDVWFE-PT--EVWEVKAADLT--LSPIYKAALGLVDPDKGISLRFPRFIRIRDDKNP 688 (714)
T ss_pred c------CcHhhcccC--ccCCCccccC-HH--HHHHHhhcccc--ccchhHhhhcCcCCCCceeEecceeeEeeccCCh
Confidence 2 355677664 4567999999 75 589998 5653 245553 4899999999999999999
Q ss_pred cCCCCHHHHHHHHHcc
Q 005331 588 HDCLDVQSFVELVHSS 603 (702)
Q Consensus 588 ~d~~t~~el~~l~~~~ 603 (702)
+||+|.+++.+||+.+
T Consensus 689 eeAtts~qiaemY~~Q 704 (714)
T KOG0967|consen 689 EEATTSSQIAEMYQAQ 704 (714)
T ss_pred hhcccHHHHHHHHHHH
Confidence 9999999999999754
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=3.4e-96 Score=831.50 Aligned_cols=494 Identities=34% Similarity=0.610 Sum_probs=428.1
Q ss_pred ccCCCHHHHHHHHHHHhCCCcChHHHHHHhhhhcCCCCCCCCCHHHHHHHHhhhcc--CCCCCCCCHHHHHHHHHHHHhh
Q 005331 62 SYGLKESVLANCLIDALGMSKDSADAVRLINWRKGGAAPNAGNFPMVAAEVLQRRQ--GMISGGLTIKELNDLLDRLASS 139 (702)
Q Consensus 62 ~ygike~~L~k~~~~~~~l~~~s~~~~~L~~wk~~~~~~~~gD~~~~~~~v~~~r~--~~~~~~lTi~eVn~~Ld~La~~ 139 (702)
+|||||++|+|++++++|+++++.++..+ ..||+|.+++.++++.. ...+++|||.|||+.|++||+.
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 35899999999887653 2346899999999999999988
Q ss_pred hc---hHhHHHHHHHHHHhCCHHHHHHHHHHHhhhhccCccccccccccCcCH-------HHHHhhhCCHHHHHHHHhhh
Q 005331 140 EN---RAEKISVLSTLIKKTNAQEMKWIIMIILKDLKLGISEKSIFHEFHPDA-------EDLFNVTCDLKLVCEKLKDR 209 (702)
Q Consensus 140 ~~---~~~k~~~l~~ll~~~t~~E~k~l~RiIlk~lriG~~e~~il~~~hpda-------~~~~~~~~dL~~V~~~L~~~ 209 (702)
++ +.+|..+|..|+.+|+|.|++||+|+|+++||||+++++|+.++|+++ +++|++|+||+.||+.|.++
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 99999999999999999976
Q ss_pred hccc--ccCCcccCCccccccccccCChHHHHHHcCCCceEEEEecceEEEEEEEeCCEEEEEeCCCCCCCcchhhH-HH
Q 005331 210 NQRH--KRQDIEVGKAVRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAM-SK 286 (702)
Q Consensus 210 ~~~~--~~~~i~~~~~~~PmLA~~~~~~~~~~~~~~~~~~~~E~K~DG~R~qvh~~g~~v~~~SR~g~d~t~~~p~l-~~ 286 (702)
..+. ....+++|.||+||||++++.++++++++.+ +|++|+||||+|||+|++|++|++|||||+++|..+|++ .+
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 5432 3467999999999999999988888888754 899999999999999999999999999999999999998 66
Q ss_pred HHHhhcc-ccceeeeceEEEeeCCCCccccccchHHHHHHhh-cCCCCCCceEEEEEEEeeeCCccccCCCHHHHHHHHH
Q 005331 287 IIEQNVL-VDRCILDGEMLVWDTSLNRFAEFGSNQEIAKAAR-DGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQ 364 (702)
Q Consensus 287 ~~~~~~~-~~~~ILDGE~v~~d~~~~~~~~F~~lq~~~~~~r-~~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~ 364 (702)
.+...+. ..+||||||||+||+.+++++||+.++...+... .....+.+++|++|||||+||+++++.||.+|+++|+
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 3589999999999987788899988876543210 1112346899999999999999999999999999999
Q ss_pred hhccCCCCcccccccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHCCCceEEEecCCCCcccCCCCCCeEEEccc
Q 005331 365 KVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPE 444 (702)
Q Consensus 365 ~~~~~~~~~~~~~~p~~~~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EGlV~K~~ds~Y~~G~Rs~~WlKvK~~ 444 (702)
+++.+.++++.++. ...+++.+++.++|++++++|+||||+|+++|+|.||+|+.+|+|+|++
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 99988777665432 3446789999999999999999999999999999999999999999999
Q ss_pred cccC-CCcceEEEEEEEecCCCCCCccceEEEEEecCCCCCCCCcceEEEEEecCCCCHHHHHHHHHhhccccccccCCC
Q 005331 445 YIRA-GSDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPK 523 (702)
Q Consensus 445 y~~~-g~~~DlvVIG~~~G~G~r~g~~gs~llg~~d~~~~~~~~~~~~~v~kVgtG~s~~~~~~l~~~l~~~~~~~~~~~ 523 (702)
|+++ ++++|++|||+++|+|+++|.+|+|+||++|++. ++|+++|+||||||++++++|.+++.++|.... +.
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 9994 7899999999999999999999999999998653 389999999999999999999999999987521 11
Q ss_pred CCCCCcccccCCCCCCCcEEEeCCCceEEEEEeeeceeecccccCC-CceeeccEEEEEecCCCccCCCCHHHHHHHH
Q 005331 524 RAPPSFYQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSA-PYSLRFPRIDRVRYDKPWHDCLDVQSFVELV 600 (702)
Q Consensus 524 ~~pp~~~~~~~~~~~~pdvwi~~P~~s~v~ev~a~~~~~~s~~~~~-g~tLRfPr~~riR~DK~~~d~~t~~el~~l~ 600 (702)
.+|.+ ....|++|++ | ++|+||+++. +..|+.|++ |++||||||.++|+||+|+||+|++|+.+||
T Consensus 447 -~~~~~------~~~~~~~w~~-p--~~V~eV~~~e-~t~s~~~~~~g~~LRfPr~~~~R~DK~~~d~~~~~~~~~ly 513 (514)
T TIGR00574 447 -RVPSI------LSDEPDIWFD-P--AIVWEVTGAE-ITRSPTYKANGISLRFPRFSRIRDDKGPEDATTIEEIKELY 513 (514)
T ss_pred -CCccc------ccCCCeEEec-C--CeEEEEEhhh-eeecCcccccceEEEcceEEEEcCCCChHHCCCHHHHHHHh
Confidence 12222 1357899999 7 5799999654 246888999 9999999999999999999999999999998
No 6
>PRK09247 ATP-dependent DNA ligase; Validated
Probab=100.00 E-value=6.3e-94 Score=812.41 Aligned_cols=522 Identities=20% Similarity=0.258 Sum_probs=439.8
Q ss_pred HHHHHHHHHHHHhcCChhHHHHHHHHHhhhcCCCchHhhhHhhcCCCCCCCccccCCCHHHHHHHHHHHhCCCcChHHHH
Q 005331 9 VIVLVSLFNWIQKTKPAAKKRSKFRKFLDTYCDSVDYFSALRLILPSLDRERGSYGLKESVLANCLIDALGMSKDSADAV 88 (702)
Q Consensus 9 F~~l~~~~e~i~~~~~~~~k~~~l~~~l~~~~~~~~~~~~lrLllp~~d~~r~~ygike~~L~k~~~~~~~l~~~s~~~~ 88 (702)
+++||++|++|++|+++.+|+.+|.+||.++ +++++.++++|+++... .|||+++.|.+++++++|++....+.
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 HHhhhhcCCCCCCCCCHHHHHHHHhhhccCCC---CCCCCHHHHHHHHHHHHhhhchHhHHHHHHHHHHhCCHHHHHHHH
Q 005331 89 RLINWRKGGAAPNAGNFPMVAAEVLQRRQGMI---SGGLTIKELNDLLDRLASSENRAEKISVLSTLIKKTNAQEMKWII 165 (702)
Q Consensus 89 ~L~~wk~~~~~~~~gD~~~~~~~v~~~r~~~~---~~~lTi~eVn~~Ld~La~~~~~~~k~~~l~~ll~~~t~~E~k~l~ 165 (702)
.| ...||+|++|+.+++.++... +.++||.+|.+.|..+|.. +|...|..|+.+++|.|++||+
T Consensus 75 ---~~------~~~GDlg~~~~~~~~~~~~~~~~~~~~~tv~~v~~~l~~~~~~----~k~~~l~~ll~~~~~~e~~~i~ 141 (539)
T PRK09247 75 ---SY------DYVGDLAETIALLLPAPSDEASDLPLAPWLEEVLLPLRGLGRE----ELRAALADLWDRLDEDGRFALN 141 (539)
T ss_pred ---HH------HhcCCHHHHHHHhcccccccccCCCccccHHHHHHHHHhhhHH----HHHHHHHHHHHhCCHHHHHHHH
Confidence 22 457999999999987765321 3579999999999888754 4778899999999999999999
Q ss_pred HHHhhhhccCccccccccccC----cC---HHHHHhh--hCCHHHHHHHHhhhhcccccCCcccCCccccccccccCChH
Q 005331 166 MIILKDLKLGISEKSIFHEFH----PD---AEDLFNV--TCDLKLVCEKLKDRNQRHKRQDIEVGKAVRPQLAMRIGDAH 236 (702)
Q Consensus 166 RiIlk~lriG~~e~~il~~~h----pd---a~~~~~~--~~dL~~V~~~L~~~~~~~~~~~i~~~~~~~PmLA~~~~~~~ 236 (702)
|+|+++||||+++++|+.+++ .+ .++.|+. ++|++.+++.+..+. ....+++|.|++||||++..+..
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 999999999999999998653 22 3456666 788888888776532 56678999999999999998764
Q ss_pred HHHHHcCCCceEEEEecceEEEEEEEeCCEEEEEeCCCCCCCcchhhHHHHHHhhccccceeeeceEEEeeCCCCccccc
Q 005331 237 AAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDGEMLVWDTSLNRFAEF 316 (702)
Q Consensus 237 ~~~~~~~~~~~~~E~K~DG~R~qvh~~g~~v~~~SR~g~d~t~~~p~l~~~~~~~~~~~~~ILDGE~v~~d~~~~~~~~F 316 (702)
+. .+...+|++|+||||+|||+|++++++++|||||+++|..||++.+.+. .+ +.+||||||+|+||+.++.+.||
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 46799999999999766788999
Q ss_pred cchHHHHHHhhc--CCCCCCceEEEEEEEeeeCCccccCCCHHHHHHHHHhhccCCCC-cccccccCCCCCccccCCCCC
Q 005331 317 GSNQEIAKAARD--GLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKG-RLETLVPDHGLNSHVRPQGEP 393 (702)
Q Consensus 317 ~~lq~~~~~~r~--~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~~-~~~~~~p~~~~~~~v~~~~~~ 393 (702)
+.+|....+... ....+.|++|+||||||+||+++++.||.+||++|++++.+.++ ++.++.
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 888765432110 11124689999999999999999999999999999999987643 444321
Q ss_pred ccccccCCHHHHHHHHHHHHHCCCceEEEecCCCCcccCCCCCCeEEEccccccCCCcceEEEEEEEecCCCCCCccceE
Q 005331 394 CWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLIIGGYYGSGRRGGEVAQF 473 (702)
Q Consensus 394 ~~~~~~~~~~~i~~~~~~ai~~g~EGlV~K~~ds~Y~~G~Rs~~WlKvK~~y~~~g~~~DlvVIG~~~G~G~r~g~~gs~ 473 (702)
...+.+.+++.++|++++++|+||||+|+++|+|.||+|++.|+|+|++| .++|+|||||++|+|+|+|.+|+|
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 23457889999999999999999999999999999999999999999998 489999999999999999999999
Q ss_pred EEEEecCCCCCCCCcceEEEEEecCCCCHHHHHHHHHhhccccccccCCCCCCCCcccccCCCCCCCcEEEeCCCceEEE
Q 005331 474 LVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDVWIESPEKSIIL 553 (702)
Q Consensus 474 llg~~d~~~~~~~~~~~~~v~kVgtG~s~~~~~~l~~~l~~~~~~~~~~~~~pp~~~~~~~~~~~~pdvwi~~P~~s~v~ 553 (702)
+||+++++.+ ...|++|||||||||++++++|.+.+.++... ...|++|++ | .+|+
T Consensus 434 lla~~~~~~~---~~~~~~v~kvgsGftd~~l~~l~~~l~~~~~~------------------~~~~~~~v~-P--~~V~ 489 (539)
T PRK09247 434 TFGVWDGPEG---GRQLVPFAKAYSGLTDEEIKQLDRWVRKNTVE------------------RFGPVRSVR-P--ELVF 489 (539)
T ss_pred EEEEEcCCCC---ceeEEEEEEECCCCCHHHHHHHHHHHhhcccc------------------cCCCceEec-C--ceEE
Confidence 9999986531 13699999999999999999999877653211 124899999 7 4799
Q ss_pred EEeeeceeecccccCCCceeeccEEEEEecCCCccCCCCHHHHHHHHHc
Q 005331 554 SITSDIRTIRSEVFSAPYSLRFPRIDRVRYDKPWHDCLDVQSFVELVHS 602 (702)
Q Consensus 554 ev~a~~~~~~s~~~~~g~tLRfPr~~riR~DK~~~d~~t~~el~~l~~~ 602 (702)
||+++. +..|+.|++|++||||||.++|+||+|+||+|++++.+||+.
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 999653 246888999999999999999999999999999999999964
No 7
>PRK03180 ligB ATP-dependent DNA ligase; Reviewed
Probab=100.00 E-value=1e-93 Score=804.51 Aligned_cols=493 Identities=21% Similarity=0.350 Sum_probs=424.5
Q ss_pred CcHHHHHHHHHHHHhcCChhHHHHHHHHHhhhcCCCchHhhhHhhcCCCCCCCccccCCCHHHHHHHHHHHhCCCcChHH
Q 005331 7 TEVIVLVSLFNWIQKTKPAAKKRSKFRKFLDTYCDSVDYFSALRLILPSLDRERGSYGLKESVLANCLIDALGMSKDSAD 86 (702)
Q Consensus 7 ~~F~~l~~~~e~i~~~~~~~~k~~~l~~~l~~~~~~~~~~~~lrLllp~~d~~r~~ygike~~L~k~~~~~~~l~~~s~~ 86 (702)
|+|.+||++|++|++|+++++|+++|++||.+. .++++.++++|+...+. .+..|++++.+.++++.
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 789999999999999999999999999999987 56899999999998886 35799998666655321
Q ss_pred HHHHhhhhcCCCCCCCCCHHHHHHHHhhhccCCCCCCCCHHHHHHHHHHHHhhhc---hHhHHHHHHHHHHhCCHHHHHH
Q 005331 87 AVRLINWRKGGAAPNAGNFPMVAAEVLQRRQGMISGGLTIKELNDLLDRLASSEN---RAEKISVLSTLIKKTNAQEMKW 163 (702)
Q Consensus 87 ~~~L~~wk~~~~~~~~gD~~~~~~~v~~~r~~~~~~~lTi~eVn~~Ld~La~~~~---~~~k~~~l~~ll~~~t~~E~k~ 163 (702)
..+++|||.+||+.|++||..++ +.+|..+|..++.+|+|.|++|
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 01257999999999999998865 4788899999999999999999
Q ss_pred HHHHHhhhhccCcccccccccc-------CcCHHHHHhhhCCHHHHHHHHh-hhhcccccCCcccCCccccccccccCCh
Q 005331 164 IIMIILKDLKLGISEKSIFHEF-------HPDAEDLFNVTCDLKLVCEKLK-DRNQRHKRQDIEVGKAVRPQLAMRIGDA 235 (702)
Q Consensus 164 l~RiIlk~lriG~~e~~il~~~-------hpda~~~~~~~~dL~~V~~~L~-~~~~~~~~~~i~~~~~~~PmLA~~~~~~ 235 (702)
|+|+|+++||||+++++|+.++ +++++++|++|+||+.||+.+. ++...+....+++|.||+||||++..++
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 3567899999999999999655 4555667778999999999999999888
Q ss_pred HHHHHHcCCCceEEEEecceEEEEEEEeCCEEEEEeCCCCCCCcchhhHHHHHHhhccccceeeeceEEEeeCCCCcccc
Q 005331 236 HAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDGEMLVWDTSLNRFAE 315 (702)
Q Consensus 236 ~~~~~~~~~~~~~~E~K~DG~R~qvh~~g~~v~~~SR~g~d~t~~~p~l~~~~~~~~~~~~~ILDGE~v~~d~~~~~~~~ 315 (702)
++++++++ .+|++|+||||+|||+|++++++++|||||+|+|..||++.+.+. .+..++||||||||+||+. +++.|
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 579999999999999999999999999999999999999988653 3455789999999999974 67889
Q ss_pred ccchHHHHHHhhc--CCCCCCceEEEEEEEeeeCCccccCCCHHHHHHHHHhhccCCCCcccccccCCCCCccccCCCCC
Q 005331 316 FGSNQEIAKAARD--GLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEP 393 (702)
Q Consensus 316 F~~lq~~~~~~r~--~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~~~~~~~~p~~~~~~~v~~~~~~ 393 (702)
|+.++....+... ......|++|++|||||+||+++++.||.+||++|++++.+. ..+ |
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 9777654322110 011246899999999999999999999999999999998642 110 1
Q ss_pred ccccccCCHHHHHHHHHHHHHCCCceEEEecCCCCcccCCCCCCeEEEccccccCCCcceEEEEEEEecCCCCCCccceE
Q 005331 394 CWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLIIGGYYGSGRRGGEVAQF 473 (702)
Q Consensus 394 ~~~~~~~~~~~i~~~~~~ai~~g~EGlV~K~~ds~Y~~G~Rs~~WlKvK~~y~~~g~~~DlvVIG~~~G~G~r~g~~gs~ 473 (702)
.....+.++++++|++++++|+||||+|+++|+|.||+|+.+|+|+|+. +++|+||||+++|+|+|+|.+|+|
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 1234678999999999999999999999999999999999999999996 499999999999999999999999
Q ss_pred EEEEecCCCCCCCCcceEEEEEecCCCCHHHHHHHHHhhccccccccCCCCCCCCcccccCCCCCCCcEEEeCCCceEEE
Q 005331 474 LVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDVWIESPEKSIIL 553 (702)
Q Consensus 474 llg~~d~~~~~~~~~~~~~v~kVgtG~s~~~~~~l~~~l~~~~~~~~~~~~~pp~~~~~~~~~~~~pdvwi~~P~~s~v~ 553 (702)
+||+||+++ +.|++||+||||||++++++|.+.+.++... ...|++||+ |. +|+
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 999998643 3899999999999999999999888765321 135899999 75 699
Q ss_pred EEeeeceeecccccCCCceeeccEEEEEecCCCccCCCCHHHHHHHH
Q 005331 554 SITSDIRTIRSEVFSAPYSLRFPRIDRVRYDKPWHDCLDVQSFVELV 600 (702)
Q Consensus 554 ev~a~~~~~~s~~~~~g~tLRfPr~~riR~DK~~~d~~t~~el~~l~ 600 (702)
||+++. ...|+.|++|++||||||+|+|+||+|+||+|++++.+||
T Consensus 461 EV~~~~-it~S~~~~~G~~LRfPr~~r~R~DK~~~ea~tl~~~~~l~ 506 (508)
T PRK03180 461 EIAFDG-VQRSTRYPGGVALRFARVLRYRPDKTPAEADTIDTVRALL 506 (508)
T ss_pred EEEeeE-eeeCCcccCCeEEECCeeeEeeCCCChHHCcCHHHHHHHh
Confidence 998654 2468889999999999999999999999999999999998
No 8
>PHA02587 30 DNA ligase; Provisional
Probab=100.00 E-value=5e-65 Score=570.42 Aligned_cols=447 Identities=20% Similarity=0.279 Sum_probs=334.4
Q ss_pred HHHHHHHHhcCChhHHHHHHHHHhhhcCCCchHhhhHhhcCCCCCCCccccCCCHHHHHHHHHHHhCCCcChHHHHHHhh
Q 005331 13 VSLFNWIQKTKPAAKKRSKFRKFLDTYCDSVDYFSALRLILPSLDRERGSYGLKESVLANCLIDALGMSKDSADAVRLIN 92 (702)
Q Consensus 13 ~~~~e~i~~~~~~~~k~~~l~~~l~~~~~~~~~~~~lrLllp~~d~~r~~ygike~~L~k~~~~~~~l~~~s~~~~~L~~ 92 (702)
-+++++|++|.++++|.+||.+..+ .+.+--+++|.+...- .|||+.
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 4789999999999999999887744 3567777888766553 577442
Q ss_pred hhcCCCCCCCCCHHHHHHHHhhhccCCCCCCCCHHH-HHHHHHHHHhhhc-hHhHHHHHHHHHHhCCHHHHHHHHHHHhh
Q 005331 93 WRKGGAAPNAGNFPMVAAEVLQRRQGMISGGLTIKE-LNDLLDRLASSEN-RAEKISVLSTLIKKTNAQEMKWIIMIILK 170 (702)
Q Consensus 93 wk~~~~~~~~gD~~~~~~~v~~~r~~~~~~~lTi~e-Vn~~Ld~La~~~~-~~~k~~~l~~ll~~~t~~E~k~l~RiIlk 170 (702)
|.+++.. ....+.+++.+ +..+..+||+..- ...++..|..++.+|+|.|++||+|+|++
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 2111000 01134567777 5556667887654 56778899999999999999999999999
Q ss_pred hhccCccccccccccCcCHHHHHhhhCCHHHHHHHHhhhhcccccCCcccCCcccc-ccccccCChHHHHHHcCCCceEE
Q 005331 171 DLKLGISEKSIFHEFHPDAEDLFNVTCDLKLVCEKLKDRNQRHKRQDIEVGKAVRP-QLAMRIGDAHAAWRKLHGKEVVI 249 (702)
Q Consensus 171 ~lriG~~e~~il~~~hpda~~~~~~~~dL~~V~~~L~~~~~~~~~~~i~~~~~~~P-mLA~~~~~~~~~~~~~~~~~~~~ 249 (702)
+||||+++++|+++||+ +.|++| |||++.+. ++++++-+.+|++
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 99999999999988863 568888 99998543 4566633448999
Q ss_pred EEecceEEEEEEEeCCEEEEEeCCCCCCCcchhhHHHHHHhhcc-----ccceeeeceEEEeeCCCCccccc--------
Q 005331 250 ECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVL-----VDRCILDGEMLVWDTSLNRFAEF-------- 316 (702)
Q Consensus 250 E~K~DG~R~qvh~~g~~v~~~SR~g~d~t~~~p~l~~~~~~~~~-----~~~~ILDGE~v~~d~~~~~~~~F-------- 316 (702)
|+||||+|||+|++++++++|||||++++. +|++.+.+..... +.++|||||+|+||+.++.+.+|
T Consensus 157 E~K~DG~R~q~h~~~~~v~l~SR~g~~~~~-~p~i~~~l~~~~~~~~~~~~~~VLDGElv~~~~~~~~~~~~~f~~~~~~ 235 (488)
T PHA02587 157 QLKADGARCFADIDADGIEIRSRNGNEYLG-LDLLKEELKKMTAEARQRPGGVVIDGELVYVEVETKKPNGLSFLFDDSK 235 (488)
T ss_pred EEccCceEEEEEEeCCEEEEEecCCccccC-ChhHHHHHHHHhhhhcccCCcEEEEeEEEEEecccCCCccchhhccccc
Confidence 999999999999999999999999999975 6887766543221 37899999999998765533333
Q ss_pred -----cchHHHHH------Hh-hcC--CCCCCceEEEEEEEeeeC---CccccCCCHHHHHHHHHhhccC-CCCcccccc
Q 005331 317 -----GSNQEIAK------AA-RDG--LSSDRQLCYFAFDVLYVG---DTSVIHQSLKERHELLQKVVKP-SKGRLETLV 378 (702)
Q Consensus 317 -----~~lq~~~~------~~-r~~--~~~~~~~~~~vFDiL~ln---g~~l~~~pl~eRr~~L~~~~~~-~~~~~~~~~ 378 (702)
+.++.... .. +.. .....+++|+|||||++| |..+++.||.+||++|++++.. ..+++.++.
T Consensus 236 ~~~f~q~l~~R~~~~~i~~~~l~~~~~~~~~~pv~~~vFDiL~ld~y~~~~~~~~pl~eRr~~L~~l~~~~~~~~i~l~~ 315 (488)
T PHA02587 236 AKEFVGVVADRATGNGIVNKSLKGTISKEEAQEIVFQVWDIVPLEVYYGKEKSDMPYDDRFSKLAQMFEDCGYDRVELIE 315 (488)
T ss_pred ccchhhhhhhhhhccchhhhhhccccchhhccceEEEEEEeechhhccCCccccCCHHHHHHHHHHHHhhcCCCcEEEEe
Confidence 22332211 00 000 022468999999999653 4457889999999999999963 233443221
Q ss_pred cCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHCCCceEEEecCCCCcccCCCCCCeEEEccccccCCCcceEEEEE
Q 005331 379 PDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLIIG 458 (702)
Q Consensus 379 p~~~~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EGlV~K~~ds~Y~~G~Rs~~WlKvK~~y~~~g~~~DlvVIG 458 (702)
...+++.+++.++|+++++.|+||||+|+++|+|++| |+.+|+|+|+.+ ++|++|||
T Consensus 316 -----------------~~~~~~~ee~~~~~~~a~~~G~EGimlK~~ds~Y~~G-Rs~~WlKiK~~~-----~~dlvVvG 372 (488)
T PHA02587 316 -----------------NQVVNNLEEAKEIYKRYVDQGLEGIILKNTDGLWEDG-RSKDQIKFKEVI-----DIDLEIVG 372 (488)
T ss_pred -----------------eEEcCCHHHHHHHHHHHHhCCCCeEEEECCCCCCCCC-CCCCcEEecCCC-----ceEEEEEe
Confidence 2345788999999999999999999999999999998 888999999974 89999999
Q ss_pred EEecCCCCCCccceEEEEEecCCCCCCCCcceEEEEEecCCCCHHHHHHHHHhhccccccccCCCCCCCCcccccCCCCC
Q 005331 459 GYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKE 538 (702)
Q Consensus 459 ~~~G~G~r~g~~gs~llg~~d~~~~~~~~~~~~~v~kVgtG~s~~~~~~l~~~l~~~~~~~~~~~~~pp~~~~~~~~~~~ 538 (702)
+|+|. +++|.+|+|+|++++ + . .+|+||||||++++++|...+. . +| +... ....
T Consensus 373 ~~~~~-k~~~~~gs~ll~~~~--g------~--~~~~vgsGftd~~~~~l~~~~~----~-------~p-~~~~--~~~~ 427 (488)
T PHA02587 373 VYEHK-KDPNKVGGFTLESAC--G------K--ITVNTGSGLTDTTHRKKDGKKV----V-------IP-LSER--HELD 427 (488)
T ss_pred EEeCC-CCCCceeEEEEEecC--C------c--EEEEECCCCChHHhhhhccccc----e-------ec-cccc--chhc
Confidence 99865 567889999997653 1 2 4799999999999999865532 1 11 1111 0123
Q ss_pred CCcEEEeCCC-ceEEEEEeeeceeecccccCCCceeeccEEEEEecCCCccCCCCHHHHH
Q 005331 539 RPDVWIESPE-KSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDKPWHDCLDVQSFV 597 (702)
Q Consensus 539 ~pdvwi~~P~-~s~v~ev~a~~~~~~s~~~~~g~tLRfPr~~riR~DK~~~d~~t~~el~ 597 (702)
++.+|.+++. ...|+||+++.. ..|+.|++|++||||||+|+|+||+ +|+|++++.
T Consensus 428 r~~~~~~~~~~~~~V~EV~~~~i-t~S~~~~~g~sLRfPrf~r~R~DK~--~Adt~~~v~ 484 (488)
T PHA02587 428 REELMANKGKYIGKIAECECNGL-QRSKGRKDKVSLFLPIIKRIRIDKT--EANTLEDVF 484 (488)
T ss_pred chhhhhCcccccceEEEEEeceE-EeCCCCCCCeeEEccceeEEeCCCC--cccCHHHHh
Confidence 5678876321 247999987543 4688899999999999999999999 999999875
No 9
>COG1793 CDC9 ATP-dependent DNA ligase [DNA replication, recombination, and repair]
Probab=100.00 E-value=1.3e-63 Score=550.54 Aligned_cols=421 Identities=27% Similarity=0.413 Sum_probs=345.5
Q ss_pred CCCCCHHHHHHHHhhhccCCCCCCCCHHHHHHHHHHHHhhhchHhHHHHHHHHHHhCCHHHHHHHHHHHhhhhccCcccc
Q 005331 100 PNAGNFPMVAAEVLQRRQGMISGGLTIKELNDLLDRLASSENRAEKISVLSTLIKKTNAQEMKWIIMIILKDLKLGISEK 179 (702)
Q Consensus 100 ~~~gD~~~~~~~v~~~r~~~~~~~lTi~eVn~~Ld~La~~~~~~~k~~~l~~ll~~~t~~E~k~l~RiIlk~lriG~~e~ 179 (702)
...||+|..+..+.. +.+|...|..++...+ .. .++..|+..++ +|++++
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 567999988766543 8999999999999888 22 78888888888 999999
Q ss_pred ccccccCcCHHHHHhhhCCHHHHHHHHhhh-hcccccCCcccCCccccccccccCChHHHHHHcCCCceEEEEecceEEE
Q 005331 180 SIFHEFHPDAEDLFNVTCDLKLVCEKLKDR-NQRHKRQDIEVGKAVRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRI 258 (702)
Q Consensus 180 ~il~~~hpda~~~~~~~~dL~~V~~~L~~~-~~~~~~~~i~~~~~~~PmLA~~~~~~~~~~~~~~~~~~~~E~K~DG~R~ 258 (702)
+++.+...-.+..|+.++|++.++..+... ..++....+.+|.|+.||||.......+...+..+ .|++|+||||+|+
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 999877555788899999999988877643 33445566789999999999998776555444433 5999999999999
Q ss_pred EEEEeCCEEEEEeCCCCCCCcchhhHHHHHHhhccccceeeeceEEEeeCCCCccccccchHHHHHHhhc--CCCCCCce
Q 005331 259 QIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDGEMLVWDTSLNRFAEFGSNQEIAKAARD--GLSSDRQL 336 (702)
Q Consensus 259 qvh~~g~~v~~~SR~g~d~t~~~p~l~~~~~~~~~~~~~ILDGE~v~~d~~~~~~~~F~~lq~~~~~~r~--~~~~~~~~ 336 (702)
|+|++++.|++|||||.|+|.+||++...+...+..+++|||||+|++|+. ...||+.+|...++..+ ......++
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 999999999999999999999999766655556667899999999999975 45899888876543211 12345789
Q ss_pred EEEEEEEeeeCCccccCCCHHHHHHHHHhhccCCCCcccccccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHCC
Q 005331 337 CYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENR 416 (702)
Q Consensus 337 ~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~~~~~~~~p~~~~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g 416 (702)
+|++||+||+||++|+++||.+||+.|++++... +.+.+.. ....++.++++.+|+.+++.|
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 2222111 122378899999999999999
Q ss_pred CceEEEecCCCCcccCCCCCCeEEEccccccCCCcceEEEEEEEecCCCCCCccceEEEEEecCCCCCCCCcceEEEEEe
Q 005331 417 DEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRV 496 (702)
Q Consensus 417 ~EGlV~K~~ds~Y~~G~Rs~~WlKvK~~y~~~g~~~DlvVIG~~~G~G~r~g~~gs~llg~~d~~~~~~~~~~~~~v~kV 496 (702)
+||||+|+++|+|++|+|+..|+|+|++ +++|+||+|+++|.|+++ .+|+|+||+|++++ +.|+++|+|
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 cCCCCHHHHHHHHHhhccccccccCCCCCCCCcccccCCCCCCCcEEEeCCCceEEEEEeeeceeecccccCC--Cceee
Q 005331 497 GTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSA--PYSLR 574 (702)
Q Consensus 497 gtG~s~~~~~~l~~~l~~~~~~~~~~~~~pp~~~~~~~~~~~~pdvwi~~P~~s~v~ev~a~~~~~~s~~~~~--g~tLR 574 (702)
||||+++++++|.++|++++... .+++ .+..|..+| ++|+||.+... ..+..|.. |.+||
T Consensus 356 gtGf~~~~l~~l~~~l~~~~~~~----~~~~-----------~~~~~~~~p--~~V~EV~~~~~-t~~~~~r~~~~~~lR 417 (444)
T COG1793 356 GTGFSDAELEELTERLEPLIVSR----FNGK-----------VPGKVVPPP--GLVAEVRFAEI-TKSGRLRHASGLGLR 417 (444)
T ss_pred cCCCCHHHHHHHHHHHHHhccCc----CCCc-----------cCceeecCC--cEEEEEEEeec-ccCCceecccCcccC
Confidence 99999999999999999987651 1111 111155446 57999986432 24666665 89999
Q ss_pred ccEEEEEecCCCccCCCCHHHHHHHH
Q 005331 575 FPRIDRVRYDKPWHDCLDVQSFVELV 600 (702)
Q Consensus 575 fPr~~riR~DK~~~d~~t~~el~~l~ 600 (702)
|||+.++|.||.+.+++|+++..+++
T Consensus 418 fpr~~rvr~dk~~~~a~t~~~~~~~~ 443 (444)
T COG1793 418 FPRFVRVRDDKLPEDADTIEEIEALY 443 (444)
T ss_pred cCcccccccccCcccccccccchhhc
Confidence 99999999999999999999988775
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=2.1e-59 Score=496.78 Aligned_cols=288 Identities=28% Similarity=0.416 Sum_probs=240.9
Q ss_pred CCCceEEEEecceEEEEEEEeCCEEEEEeCCCCCCCcchhhHHHHHHhhccccceeeeceEEEeeCCCCccccccchHHH
Q 005331 243 HGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDGEMLVWDTSLNRFAEFGSNQEI 322 (702)
Q Consensus 243 ~~~~~~~E~K~DG~R~qvh~~g~~v~~~SR~g~d~t~~~p~l~~~~~~~~~~~~~ILDGE~v~~d~~~~~~~~F~~lq~~ 322 (702)
.+.+|++|+||||+|||+|+++++|++|||||+++|..||++.+.+ ..+...+||||||||+||.. ++ .+|+.+|.+
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 5678999999999999999999999999999999999889988754 34456799999999999974 33 589777765
Q ss_pred HHHhhcCCCCCCceEEEEEEEeeeCCccccCCCHHHHHHHHHhhccCCCCcccccccCCCCCccccCCCCCccccccCCH
Q 005331 323 AKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNV 402 (702)
Q Consensus 323 ~~~~r~~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~~~~~~~~p~~~~~~~v~~~~~~~~~~~~~~~ 402 (702)
... ....+++|++||||++||++++++||.+|+++|++++.+.++.+.+.. . ..++.
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 432 224789999999999999999999999999999999977554332110 0 24567
Q ss_pred HHHHHHHHHHHHCCCceEEEecCCCCcccCCCCCCeEEEccccccCCCcceEEEEEEEecCCCCCCccceEEEEEecCCC
Q 005331 403 DEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLIIGGYYGSGRRGGEVAQFLVALAERPA 482 (702)
Q Consensus 403 ~~i~~~~~~ai~~g~EGlV~K~~ds~Y~~G~Rs~~WlKvK~~y~~~g~~~DlvVIG~~~G~G~r~g~~gs~llg~~d~~~ 482 (702)
+++.++|++++++|+||||+|+++|+|+||+ +.+|+|+|+.+ +.|++|+|++.|.|++ |.+|+|+||++++.
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 99999999985 8899888888899988 78999999999642
Q ss_pred CCCCCcceEEEEEecCCCCHHHHHHHHHhhccccccccCCCCCCCCcccccCCCCCCCcEEEeCCCceEEEEEeeeceee
Q 005331 483 PDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDVWIESPEKSIILSITSDIRTI 562 (702)
Q Consensus 483 ~~~~~~~~~~v~kVgtG~s~~~~~~l~~~l~~~~~~~~~~~~~pp~~~~~~~~~~~~pdvwi~~P~~s~v~ev~a~~~~~ 562 (702)
.|.++|+||||||++++++|.++|.+++... .+|. .....|++|++ | .+|+||++.
T Consensus 216 ------~l~~vg~vgsG~s~~~~~~l~~~l~~~~~~~-----~~~~------~~~~~~~~wv~-P--~lV~eV~~~---- 271 (298)
T TIGR02779 216 ------GLRYVGRVGTGFSEAELATIKERLKPLESKP-----DKPG------AREKRGVHWVK-P--ELVAEVEFA---- 271 (298)
T ss_pred ------eEEEEeEecCCCCHHHHHHHHHHHHhhccCc-----CCCC------cccCCCCEEeC-C--eEEEEEEec----
Confidence 6899999999999999999999999987652 1221 12346889999 7 478899752
Q ss_pred cccccCCCceeeccEEEEEecCCCccCCC
Q 005331 563 RSEVFSAPYSLRFPRIDRVRYDKPWHDCL 591 (702)
Q Consensus 563 ~s~~~~~g~tLRfPr~~riR~DK~~~d~~ 591 (702)
.++.|++||||||+++|+||+|+||+
T Consensus 272 ---~~t~~~~lR~P~~~~~R~Dk~~~~~~ 297 (298)
T TIGR02779 272 ---GWTRDGRLRQASFVGLREDKPASEVT 297 (298)
T ss_pred ---ccCCCCeEeccEEEeeeCCCCHHHcc
Confidence 35568899999999999999999996
No 11
>PRK09632 ATP-dependent DNA ligase; Reviewed
Probab=100.00 E-value=3.4e-59 Score=537.42 Aligned_cols=307 Identities=25% Similarity=0.384 Sum_probs=254.5
Q ss_pred cccCCccccccccccCChHHHHHHcCCCceEEEEecceEEEEEEEeCCEEEEEeCCCCCCCcchhhHHHHHHhhccccce
Q 005331 218 IEVGKAVRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRC 297 (702)
Q Consensus 218 i~~~~~~~PmLA~~~~~~~~~~~~~~~~~~~~E~K~DG~R~qvh~~g~~v~~~SR~g~d~t~~~p~l~~~~~~~~~~~~~ 297 (702)
..++.+|+||||+..... .+.+.+|++|+||||+|||+|++++.+++|||||+|+|..||++.+. ...+...+|
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 568899999999976532 14567899999999999999999999999999999999999999874 345556799
Q ss_pred eeeceEEEeeCCCCccccccchHHHHHHhhcCCCCCCceEEEEEEEeeeCCccccCCCHHHHHHHHHhhccCCCCccccc
Q 005331 298 ILDGEMLVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETL 377 (702)
Q Consensus 298 ILDGE~v~~d~~~~~~~~F~~lq~~~~~~r~~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~~~~~~~ 377 (702)
|||||||+||+.+ + .+|+.+|... ...+++|+||||||+||++|+++||.+||++|++++.+ .+.+.+
T Consensus 529 ILDGEiVvld~~G-~-~~F~~Lq~r~--------~~~~v~y~vFDLL~lnG~dL~~~Pl~eRR~~L~~l~~~-~~~i~~- 596 (764)
T PRK09632 529 VLDGEIVALDDSG-V-PSFGLLQNRG--------RDTRVEFWAFDLLYLDGRSLLRKPYRDRRKLLEALAPS-GGSLTV- 596 (764)
T ss_pred eeeeEEEEeCCCC-C-CCHHHHhhhh--------hcCCeEEEEEeeeccCCcccccCCHHHHHHHHHHhhCC-CCcEEe-
Confidence 9999999999753 3 5898887641 23679999999999999999999999999999999863 223321
Q ss_pred ccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHCCCceEEEecCCCCcccCCCCCCeEEEccccccCCCcceEEEE
Q 005331 378 VPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLII 457 (702)
Q Consensus 378 ~p~~~~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EGlV~K~~ds~Y~~G~Rs~~WlKvK~~y~~~g~~~DlvVI 457 (702)
......+++++|+.++++|.||||+|+.+|+|++|+||.+|+|+|+.| +.|+||+
T Consensus 597 --------------------s~~~~~~~~~~l~~a~~~GlEGIVaKr~dS~Y~pGrRs~~WlKiK~~~-----~~e~VI~ 651 (764)
T PRK09632 597 --------------------PPLLPGDGAEALAYSRELGWEGVVAKRRDSTYQPGRRSSSWIKDKHWR-----TQEVVIG 651 (764)
T ss_pred --------------------cceecccHHHHHHHHHHcCCcEEEEeCCCCCCCCCCcCCCeEEEecCC-----ceEEEEE
Confidence 111223578899999999999999999999999999999999999986 7899888
Q ss_pred EEEecCCCCCCccceEEEEEecCCCCCCCCcceEEEEEecCCCCHHHHHHHHHhhccccccccCCCCCCCCcccccCCCC
Q 005331 458 GGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSK 537 (702)
Q Consensus 458 G~~~G~G~r~g~~gs~llg~~d~~~~~~~~~~~~~v~kVgtG~s~~~~~~l~~~l~~~~~~~~~~~~~pp~~~~~~~~~~ 537 (702)
|+++|+|+++|.+|+||||+++++ .|+++|+||||||++++++|.++|.++.+. .|| |........
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 888899999999999999999753 589999999999999999999999987654 122 321111224
Q ss_pred CCCcEEEeCCCceEEEEEeeeceeecccccCCCceeeccEEEEEecCCCccCCC
Q 005331 538 ERPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDKPWHDCL 591 (702)
Q Consensus 538 ~~pdvwi~~P~~s~v~ev~a~~~~~~s~~~~~g~tLRfPr~~riR~DK~~~d~~ 591 (702)
.+|++||+ |. +|+||++. .|+.+++||||+|+++|+||+++||+
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 85 68888652 36678899999999999999999986
No 12
>PRK08224 ligC ATP-dependent DNA ligase; Reviewed
Probab=100.00 E-value=2.8e-57 Score=487.19 Aligned_cols=314 Identities=22% Similarity=0.362 Sum_probs=249.4
Q ss_pred CcccCCccccccccccCChHHHHHHcCCCceEEEEecceEEEEEEEeCCEEEEEeCCCCCCCcchhhHHHHHHhhccccc
Q 005331 217 DIEVGKAVRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDR 296 (702)
Q Consensus 217 ~i~~~~~~~PmLA~~~~~~~~~~~~~~~~~~~~E~K~DG~R~qvh~~g~~v~~~SR~g~d~t~~~p~l~~~~~~~~~~~~ 296 (702)
+..+|.|++||||.....++ .+.+|++|+||||+|||+|++++++++|||||+++|..||++.+.+.. +.+.+
T Consensus 2 ~~~~~~~i~PMLA~~~~~~~------~~~~w~~E~K~DG~R~~~~~~~~~v~l~SRng~d~t~~fPel~~~~~~-~~~~~ 74 (350)
T PRK08224 2 DLPVMPPVEPMLAKSVDAIP------PGDGWSYEPKWDGFRCLVFRDGDEVELGSRNGKPLTRYFPELVAALRA-ELPER 74 (350)
T ss_pred CCCCCCCcCCccCCccCCCC------CCCcEEEEEeECeeEEEEEEECCEEEEEeCCCCCchhhhHHHHHHHHh-hCCCC
Confidence 46789999999999876542 345799999999999999999999999999999999999999887643 44679
Q ss_pred eeeeceEEEeeCCCCccccccchHHHHHHhhc---CCCCCCceEEEEEEEeeeCCccccCCCHHHHHHHHHhhccCCCCc
Q 005331 297 CILDGEMLVWDTSLNRFAEFGSNQEIAKAARD---GLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGR 373 (702)
Q Consensus 297 ~ILDGE~v~~d~~~~~~~~F~~lq~~~~~~r~---~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~~~ 373 (702)
||||||||++|.. . .+|+.+|........ ......+++|++|||||+||++|+++||.+|+++|++++... +.
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 799888865421110 112346899999999999999999999999999999998643 22
Q ss_pred ccccccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHCCCceEEEecCCCCcccCCCCCCeEEEccccccCCCcce
Q 005331 374 LETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLD 453 (702)
Q Consensus 374 ~~~~~p~~~~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EGlV~K~~ds~Y~~G~Rs~~WlKvK~~y~~~g~~~D 453 (702)
+.+. ....+.++++++|++++++|+||||+|+.+|+|.+|+|+ |+|+|+.+ +.|
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 3211 012456789999999999999999999999999999887 99999974 899
Q ss_pred EEEEEEEecCCCCCCccceEEEEEecCCCCCCCCcceEEEEEecCCCCHHHHHHHHHhhccccccccCCCCCCC----Cc
Q 005331 454 VLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPP----SF 529 (702)
Q Consensus 454 lvVIG~~~G~G~r~g~~gs~llg~~d~~~~~~~~~~~~~v~kVgtG~s~~~~~~l~~~l~~~~~~~~~~~~~pp----~~ 529 (702)
++|+|+++|+|+ |.+|+|+||+|++++ +++++|+|| |||++++++|.++|.+++.... .+| +|
T Consensus 205 ~vI~G~~~g~~~--~~~gslllg~~d~~g------~l~~vG~v~-Gf~~~~~~~L~~~l~~l~~~~~----~~p~~~~pf 271 (350)
T PRK08224 205 CVVAGYRYHKSG--PVVGSLLLGLYDDDG------QLHHVGVTS-AFPMARRRELTAELEPLRTPFG----DHPWNWAAF 271 (350)
T ss_pred EEEEEEEcCCCC--CccccEEEEEECCCC------cEEEEEEEC-CCCHHHHHHHHHHHHhhhcCCC----CCccccCcc
Confidence 999998888875 789999999997543 789999985 9999999999999998875411 012 22
Q ss_pred ccccCC-----CCCCCcEE--EeCCCceEEEEEeeeceeecccccCCCceeecc-EEEEEecCCCccCCC
Q 005331 530 YQVTNN-----SKERPDVW--IESPEKSIILSITSDIRTIRSEVFSAPYSLRFP-RIDRVRYDKPWHDCL 591 (702)
Q Consensus 530 ~~~~~~-----~~~~pdvw--i~~P~~s~v~ev~a~~~~~~s~~~~~g~tLRfP-r~~riR~DK~~~d~~ 591 (702)
...... ...+..+| ++ |. +|+||++ ..|+ +..|||| +|+++|.||+++||+
T Consensus 272 ~~~~~~~~~~~~~~~~~~w~~v~-P~--lv~eV~~-------~~~t-~~~lR~p~~f~g~r~Dk~p~~v~ 330 (350)
T PRK08224 272 TGRAPGGPSRWSAGKDLSWVPLR-PE--RVVEVRY-------DHME-GGRFRHTAQFLRWRPDRDPRSCT 330 (350)
T ss_pred cccCCCccccccccCCcEEEeee-EE--EEEEEec-------Cccc-CCeecCCCeeEEEcCCCChHHCC
Confidence 111000 11235789 98 74 5778854 3466 4599998 999999999999997
No 13
>PRK05972 ligD ATP-dependent DNA ligase; Reviewed
Probab=100.00 E-value=7.2e-56 Score=514.22 Aligned_cols=305 Identities=26% Similarity=0.396 Sum_probs=245.7
Q ss_pred CccccccccccCChHHHHHHcCCCceEEEEecceEEEEEEEeCCEEEEEeCCCCCCCcchhhHHHHHHhhccccceeeec
Q 005331 222 KAVRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDG 301 (702)
Q Consensus 222 ~~~~PmLA~~~~~~~~~~~~~~~~~~~~E~K~DG~R~qvh~~g~~v~~~SR~g~d~t~~~p~l~~~~~~~~~~~~~ILDG 301 (702)
..++||||..+..++ .+.+|++|+||||+|||+|++++++++|||||+|+|..||+|.+.+. .+..++|||||
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 458999999887653 35689999999999999999999999999999999999999988754 35567999999
Q ss_pred eEEEeeCCCCccccccchHHHHHHhhcCCCCCCceEEEEEEEeeeCCccccCCCHHHHHHHHHhhccCCCC-cccccccC
Q 005331 302 EMLVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKG-RLETLVPD 380 (702)
Q Consensus 302 E~v~~d~~~~~~~~F~~lq~~~~~~r~~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~~-~~~~~~p~ 380 (702)
|+|+||..+ + .+|+.+|..... ....+++|++|||||+||++|+++||.+|+++|++++.+.++ ++.+
T Consensus 305 EIVvld~~G-~-~~F~~Lq~r~~~-----~~~~~v~f~vFDLL~l~G~dL~~~PL~eRr~~L~~ll~~~~~~~i~~---- 373 (860)
T PRK05972 305 EIVVLDEDG-V-PDFQALQNAFDE-----GRTEDLVYFAFDLPFLGGEDLRELPLEERRARLRALLEAARSDRIRF---- 373 (860)
T ss_pred EEEEECCCC-C-CCHHHHHHHhhc-----cCCCceEEEEEeccccCCcccccCCHHHHHHHHHHHhhhcCCCcEEE----
Confidence 999999753 3 589888765432 123689999999999999999999999999999999976432 2221
Q ss_pred CCCCccccCCCCCccccccCCHHHHHHHHHHHHHCCCceEEEecCCCCcccCCCCCCeEEEccccccCCCcceEEEEEEE
Q 005331 381 HGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLIIGGY 460 (702)
Q Consensus 381 ~~~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EGlV~K~~ds~Y~~G~Rs~~WlKvK~~y~~~g~~~DlvVIG~~ 460 (702)
+.+...+++++|+.++++|+||||+|+.+|+|++| |+.+|+|+|+.+ +.|+||+|.+
T Consensus 374 -----------------s~~~~~~g~~ll~~a~~~GlEGIVaKr~dS~Y~~G-Rs~~WlKiK~~~-----~~E~VIgGy~ 430 (860)
T PRK05972 374 -----------------SEHFDAGGDAVLASACRLGLEGVIGKRADSPYVSG-RSEDWIKLKCRA-----RQEFVIGGYT 430 (860)
T ss_pred -----------------eceecchHHHHHHHHHHcCCceEEEeCCCCCCCCC-CCCCcEEEecCC-----CceEEEEEEe
Confidence 11223467899999999999999999999999997 899999999985 5566554444
Q ss_pred ecCCCCCCccceEEEEEecCCCCCCCCcceEEEEEecCCCCHHHHHHHHHhhccccccccCCCCCCCCcccccCCCCCCC
Q 005331 461 YGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERP 540 (702)
Q Consensus 461 ~G~G~r~g~~gs~llg~~d~~~~~~~~~~~~~v~kVgtG~s~~~~~~l~~~l~~~~~~~~~~~~~pp~~~~~~~~~~~~p 540 (702)
.|.|+++| +|+||||++++. +|+++|+||||||++++++|.++|.++.+. .+| |..........+
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 46788877 999999999753 799999999999999999999999987654 133 322111122345
Q ss_pred cEEEeCCCceEEEEEeeeceeecccccCCCceeeccEEEEEecCCCccCCCC
Q 005331 541 DVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDKPWHDCLD 592 (702)
Q Consensus 541 dvwi~~P~~s~v~ev~a~~~~~~s~~~~~g~tLRfPr~~riR~DK~~~d~~t 592 (702)
++||+ |+ +|+||++. .|+.++.||||+|+++|+||+++||+-
T Consensus 496 ~~WV~-P~--LV~EV~f~-------e~T~~g~LR~P~F~glR~DK~p~ev~~ 537 (860)
T PRK05972 496 VHWVK-PE--LVAEVEFA-------GWTRDGIVRQAVFKGLREDKPAREVVA 537 (860)
T ss_pred CEEEc-cC--EEEEEEEe-------eccCCCCCccceEEEeecCCChHHhCh
Confidence 79999 85 68898752 356667999999999999999999973
No 14
>PRK09633 ligD ATP-dependent DNA ligase; Reviewed
Probab=100.00 E-value=1.4e-54 Score=493.60 Aligned_cols=310 Identities=22% Similarity=0.272 Sum_probs=242.0
Q ss_pred cccccccccCChHHHHHHcCCCceEEEEecceEEEEEEEeCCEEEEEeCCCCCCCcchhhHHHHHHhhcc----ccceee
Q 005331 224 VRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVL----VDRCIL 299 (702)
Q Consensus 224 ~~PmLA~~~~~~~~~~~~~~~~~~~~E~K~DG~R~qvh~~g~~v~~~SR~g~d~t~~~p~l~~~~~~~~~----~~~~IL 299 (702)
++||||.....++ .+.+|++|+||||+|||+|++++.|++|||||+|+|..||++.+.+..... ..+|||
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 5799998877653 467899999999999999999999999999999999999999876532111 137999
Q ss_pred eceEEEeeCCCCccccccchHHHHHHhhcC----CCCCCceEEEEEEEeeeCCccccCCCHHHHHHHHHhhccCCCCccc
Q 005331 300 DGEMLVWDTSLNRFAEFGSNQEIAKAARDG----LSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLE 375 (702)
Q Consensus 300 DGE~v~~d~~~~~~~~F~~lq~~~~~~r~~----~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~~~~~ 375 (702)
|||||+||..+. .+|+.+|......+.. .....+++|+||||||+||++|++.||.+||++|++++.+.....+
T Consensus 75 DGEiVvld~~g~--~~F~~Lq~R~~~~~~~~i~~~~~~~pv~~~vFDlL~lnG~dL~~~PL~eRr~~L~~ll~~~~~~~~ 152 (610)
T PRK09633 75 DGELVCLVNPYR--SDFEHVQQRGRLKNTEVIAKSANARPCQLLAFDLLELKGESLTSLPYLERKKQLDKLMKAAKLPAS 152 (610)
T ss_pred eeEEEEecCCCC--CCHHHHHhhhhccccchhhhhhcccceEEEEEeecccCCcccccCCHHHHHHHHHHHhhhcccccc
Confidence 999999986432 5898777653221110 1224688999999999999999999999999999999975431000
Q ss_pred ccccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHCCCceEEEecCCCCcccCCCCCCeEEEccccccCCCcceEE
Q 005331 376 TLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVL 455 (702)
Q Consensus 376 ~~~p~~~~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EGlV~K~~ds~Y~~G~Rs~~WlKvK~~y~~~g~~~Dlv 455 (702)
+ + +...+.+. .+.+.++++++|++++++|+||||+|+.+|+|.+|+||.+|+|+|+.+ +.|++
T Consensus 153 ---~------~--~~~~~~i~-~~~~~~~~~~l~~~a~~~g~EGIV~Kr~dS~Y~~G~Rs~~WlKiK~~~-----~~d~v 215 (610)
T PRK09633 153 ---P------D--PYAKARIQ-YIPSTTDFDALWEAVKRYDGEGIVAKKKTSKWLENKRSKDWLKIKNWR-----YVHVI 215 (610)
T ss_pred ---c------c--cccccceE-EcCCHHHHHHHHHHHHHcCCceEEEeCCCCCCCCCCCCCCeEEEeccC-----CceeE
Confidence 0 0 00000112 234567999999999999999999999999999999999999999963 78987
Q ss_pred EEEEEecCCCCCCccceEEEEEecCCCCCCCCcceEEEEEecCCCCHHHHHHHHHhhccccccccCCCCCCCCcccccCC
Q 005331 456 IIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNN 535 (702)
Q Consensus 456 VIG~~~G~G~r~g~~gs~llg~~d~~~~~~~~~~~~~v~kVgtG~s~~~~~~l~~~l~~~~~~~~~~~~~pp~~~~~~~~ 535 (702)
|+|...|. |+|++|+++. ++|+++|+||||||++++++|.++|.++.+.
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 77754432 3688999843 3799999999999999999999999876432
Q ss_pred CCCCCcEEEeCCCceEEEEEeeeceeecccccCCCceeeccEEEEEecCCCccCCCCHHHHHHHHH
Q 005331 536 SKERPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDKPWHDCLDVQSFVELVH 601 (702)
Q Consensus 536 ~~~~pdvwi~~P~~s~v~ev~a~~~~~~s~~~~~g~tLRfPr~~riR~DK~~~d~~t~~el~~l~~ 601 (702)
...+.+|++ |. +|+||++. .|+ |++||||+|+++|+||+++||++.++..+++.
T Consensus 265 -~~~~~~wV~-P~--LV~EV~~~-------e~t-~g~LR~P~f~glR~DK~~~ev~~~~~~~~~~~ 318 (610)
T PRK09633 265 -TKSGEYTLE-PS--ICVTVACI-------TFD-GGTLREPSFVSFLFDMDPTECTYQQLQRQLAP 318 (610)
T ss_pred -CCCCcEEEe-ee--EEEEEEEe-------ecC-CCeEEeeEEeEEEcCCChHHcchhhhhhhhcc
Confidence 123579999 84 68888753 233 78999999999999999999999888777664
No 15
>PRK07636 ligB ATP-dependent DNA ligase; Reviewed
Probab=100.00 E-value=1.9e-50 Score=422.49 Aligned_cols=273 Identities=23% Similarity=0.330 Sum_probs=216.0
Q ss_pred ccccccccccCChHHHHHHcCCCceEEEEecceEEEEEEEeCCEEEEEeCCCCCCCcchhhHHHHHHhhccccceeeece
Q 005331 223 AVRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDGE 302 (702)
Q Consensus 223 ~~~PmLA~~~~~~~~~~~~~~~~~~~~E~K~DG~R~qvh~~g~~v~~~SR~g~d~t~~~p~l~~~~~~~~~~~~~ILDGE 302 (702)
.++||||.....+ +.+.+|++|+||||+|||+|++++++++|||||+++|..||++.+.. ...+||||||
T Consensus 2 ~~~PmLa~~~~~~------~~~~~~~~E~K~DG~R~~~~~~~~~v~l~SR~g~~~t~~fPe~~~~~----~~~~~vLDGE 71 (275)
T PRK07636 2 FISPMLLESAKEP------FNSENYITEPKFDGIRLIASKNNGLIRLYTRHNNEVTAKFPELLNLD----IPDGTVLDGE 71 (275)
T ss_pred CcCCccCCcCCCC------CCCCcEEEEEEEceeEEEEEEeCCEEEEEeCCCCCchhhhhhHHhhh----cCCCEEEEeE
Confidence 3799999887643 45678999999999999999999999999999999999999987642 2467999999
Q ss_pred EEEeeCCCCccccccchHHHHHHhhcCCCCCCceEEEEEEEeeeCCccccCCCHHHHHHHHHhhccCCCCcccccccCCC
Q 005331 303 MLVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHG 382 (702)
Q Consensus 303 ~v~~d~~~~~~~~F~~lq~~~~~~r~~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~~~~~~~~p~~~ 382 (702)
||+||.. ++ .+|+.+|...... ......+++|+|||||++||++++++||.+|+++|++++.+.+ .+.+
T Consensus 72 lv~~d~~-g~-~~F~~l~~r~~~~--~~~~~~~~~~~vFDlL~~~g~~l~~~pl~eRr~~L~~~~~~~~-~~~~------ 140 (275)
T PRK07636 72 LIVLGST-GA-PDFEAVMERFQSK--KSTKIHPVVFCVFDVLYINGVSLTALPLSERKEILASLLLPHP-NVKI------ 140 (275)
T ss_pred EEEECCC-CC-CCHHHHHHHhccc--cccccCceEEEEEEeEEECceehhhCCHHHHHHHHHHhcCCCC-CEEE------
Confidence 9999974 33 5898777644321 1122478999999999999999999999999999999986543 2211
Q ss_pred CCccccCCCCCccccccCCHHHHHHHHHHHHHCCCceEEEecCCCCcccCCCCCCeEEEccccccCCCcceEEEEEEEec
Q 005331 383 LNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLIIGGYYG 462 (702)
Q Consensus 383 ~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EGlV~K~~ds~Y~~G~Rs~~WlKvK~~y~~~g~~~DlvVIG~~~G 462 (702)
.....++++++|++++++|.||||+|+++|+|.+|+||.+|+|+|+. ++.|++|+|+..
T Consensus 141 ---------------~~~~~~~~~~~~~~~~~~g~EGiV~K~~ds~Y~~g~Rs~~WlKiK~~-----~~~e~vV~G~~~- 199 (275)
T PRK07636 141 ---------------IEGIEGHGTAYFELVEERELEGIVIKKANSPYEINKRSDNWLKVINY-----QYTDVLITGYRK- 199 (275)
T ss_pred ---------------cccccccHHHHHHHHHHcCCcEEEEeCCCCCCCCCCCCCCeEEEecC-----CeEEEEEEEEec-
Confidence 11223567889999999999999999999999999999999999975 588987666432
Q ss_pred CCCCCCccceEEEEEecCCCCCCCCcceEEEEEecCCCCHHHHHHHHHhhccccccccCCCCCCCCcccccCCCCCCCcE
Q 005331 463 SGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDV 542 (702)
Q Consensus 463 ~G~r~g~~gs~llg~~d~~~~~~~~~~~~~v~kVgtG~s~~~~~~l~~~l~~~~~~~~~~~~~pp~~~~~~~~~~~~pdv 542 (702)
+.+|++ +|+++ + . ++|+||| |+++++++|.+.+.+.... ..++.+
T Consensus 200 -----~~~g~l-lg~~~--g------~--~~G~vgt-~~~~~~~~l~~~l~~~~~~------------------~~~~~~ 244 (275)
T PRK07636 200 -----EEFGLL-LSYLD--G------R--SAGIMEF-MPYDARKKFYKRAKRLVVG------------------EDKKFV 244 (275)
T ss_pred -----CCCcEE-EEecC--C------e--EEEEECC-CCHHHHHHHHHHhhhhccC------------------ccCCCE
Confidence 225655 78774 1 2 6899999 9999999999888765321 235689
Q ss_pred EEeCCCceEEEEEeeeceeecccccCCCceeeccEEEEEe
Q 005331 543 WIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVR 582 (702)
Q Consensus 543 wi~~P~~s~v~ev~a~~~~~~s~~~~~g~tLRfPr~~riR 582 (702)
|++ |. +|.||++. .||.++.||||+|+++|
T Consensus 245 wv~-P~--lv~eV~~~-------e~t~~g~lR~p~f~g~r 274 (275)
T PRK07636 245 YIE-PI--IGCRVKHR-------FKTKNGMLRIPSFVEWR 274 (275)
T ss_pred EeC-Cc--EEEEEEEE-------EecCCCCEEccEEEEEe
Confidence 998 74 57777542 35666779999999998
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=5.1e-48 Score=392.01 Aligned_cols=213 Identities=30% Similarity=0.547 Sum_probs=183.9
Q ss_pred CCcccCCccccccccccCChHHHHHHcCCCceEEEEecceEEEEEEEeC-CEEEEEeCCCCCCCcchhhHHHHHHhhc--
Q 005331 216 QDIEVGKAVRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNG-SEIHYFSRSFLDHSEYGHAMSKIIEQNV-- 292 (702)
Q Consensus 216 ~~i~~~~~~~PmLA~~~~~~~~~~~~~~~~~~~~E~K~DG~R~qvh~~g-~~v~~~SR~g~d~t~~~p~l~~~~~~~~-- 292 (702)
..|++|.||+||||++..+++++++++.+.+|++|+||||+|||+|+.+ +.|++|||||+++|..||++.+.+...+
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 3588999999999999888888888898889999999999999999986 8999999999999999999988765443
Q ss_pred cccceeeeceEEEeeCCCCccccccchHHHHHHhhcCCCCCCceEEEEEEEeeeCCccccCCCHHHHHHHHHhhccCCCC
Q 005331 293 LVDRCILDGEMLVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKG 372 (702)
Q Consensus 293 ~~~~~ILDGE~v~~d~~~~~~~~F~~lq~~~~~~r~~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~~ 372 (702)
...+||||||||+||..++++.||+.+|...+..........+++|++|||||+||++|+++||.+|+++|++++.+.++
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 36789999999999987677889988876532211111234789999999999999999999999999999999987766
Q ss_pred cccccccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHCCCceEEEecCC--CCcccCCCCCCeEEEcccc
Q 005331 373 RLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLG--SKWEPGDRSGKWLKLKPEY 445 (702)
Q Consensus 373 ~~~~~~p~~~~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EGlV~K~~d--s~Y~~G~Rs~~WlKvK~~y 445 (702)
+++++. ...+++.++++++|++++++|.||||+|+++ |+|.||+||++|+|+|++|
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 2356789999999999999999999999999 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=1.7e-46 Score=423.03 Aligned_cols=258 Identities=26% Similarity=0.407 Sum_probs=205.3
Q ss_pred eCCCCCCCcchhhHHHHHHhhccccceeeeceEEEeeCCCCccccccchHHHHHHhhcCCCCCCceEEEEEEEeeeCCcc
Q 005331 271 SRSFLDHSEYGHAMSKIIEQNVLVDRCILDGEMLVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTS 350 (702)
Q Consensus 271 SR~g~d~t~~~p~l~~~~~~~~~~~~~ILDGE~v~~d~~~~~~~~F~~lq~~~~~~r~~~~~~~~~~~~vFDiL~lng~~ 350 (702)
||||+|+|..||+|.+.+. .+...+||||||+|+||.. ++ .+|+.+|.+.+. ....+++|++|||||+||++
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 8999999999999998764 4556799999999999974 33 579888875432 13468999999999999999
Q ss_pred ccCCCHHHHHHHHHhhccCCCCc-ccccccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHCCCceEEEecCCCCc
Q 005331 351 VIHQSLKERHELLQKVVKPSKGR-LETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKW 429 (702)
Q Consensus 351 l~~~pl~eRr~~L~~~~~~~~~~-~~~~~p~~~~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EGlV~K~~ds~Y 429 (702)
|+++||.+|+++|++++.+.... +.+ ..+..++..++|++++++|+||||+|+++|+|
T Consensus 73 L~~~Pl~eRr~~L~~ll~~~~~~~i~~---------------------~~~~~~~~~~~~~~a~~~G~EGIV~K~~dS~Y 131 (552)
T TIGR02776 73 LRDLPLEERKKRLKQLLKAQDEPAIRY---------------------SDHFESDGDALLESACRLGLEGVVSKRLDSPY 131 (552)
T ss_pred cccCCHHHHHHHHHHHhhhcCCCcEEE---------------------eeeecccHHHHHHHHHHCCCceEEEeCCCCCC
Confidence 99999999999999999764321 211 11122345599999999999999999999999
Q ss_pred ccCCCCCCeEEEccccccCCCcceEEEEEEEecCCCCCCccceEEEEEecCCCCCCCCcceEEEEEecCCCCHHHHHHHH
Q 005331 430 EPGDRSGKWLKLKPEYIRAGSDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVV 509 (702)
Q Consensus 430 ~~G~Rs~~WlKvK~~y~~~g~~~DlvVIG~~~G~G~r~g~~gs~llg~~d~~~~~~~~~~~~~v~kVgtG~s~~~~~~l~ 509 (702)
++| ||.+|+|+|+.| +.|++ ||||++.+ +.+|+|+||+++. ++|+++|+||||||++++++|.
T Consensus 132 ~~G-Rs~~WlKlK~~~-----~~e~v-I~Gy~~~~---r~~gslLlg~~d~-------g~l~~vgkVgsGfsd~~~~~L~ 194 (552)
T TIGR02776 132 RSG-RSKDWLKLKCRR-----RQEFV-ITGYTPPN---RRFGALLVGVYEG-------GQLVYAGKVGTGFGADTLKTLL 194 (552)
T ss_pred CCC-CCcchhcccccc-----cceEE-EEEEecCC---CceeeEEEEEecC-------CeEEEEEEEcCCCCHHHHHHHH
Confidence 999 999999999986 56765 55565444 2399999999972 3799999999999999999999
Q ss_pred HhhccccccccCCCCCCCCcccccCCCCCCCcEEEeCCCceEEEEEeeeceeecccccCCCceeeccEEEEEecCCCccC
Q 005331 510 TKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDKPWHD 589 (702)
Q Consensus 510 ~~l~~~~~~~~~~~~~pp~~~~~~~~~~~~pdvwi~~P~~s~v~ev~a~~~~~~s~~~~~g~tLRfPr~~riR~DK~~~d 589 (702)
++|++++... +| |.. .......|++|++ |. +|+||++. .++.|++||||||+++|+||+|+|
T Consensus 195 ~~l~~~~~~~------~P-f~~-~~~~~~~~~~Wv~-P~--lV~EV~~~-------e~T~~g~LR~Prf~~~R~DK~~~e 256 (552)
T TIGR02776 195 ARLKALGAKA------SP-FSG-PAGAKTRGVHWVR-PS--LVAEVEYA-------GITRDGILREASFKGLREDKPAEE 256 (552)
T ss_pred HHHHhhcccC------CC-ccC-CccccCCCcEEEc-cC--EEEEEEee-------eccCCCeeEccEEEEEeCCCCHHH
Confidence 9999987641 12 211 1112346799999 84 68999753 356788999999999999999999
Q ss_pred CCC
Q 005331 590 CLD 592 (702)
Q Consensus 590 ~~t 592 (702)
|+.
T Consensus 257 ~t~ 259 (552)
T TIGR02776 257 VTL 259 (552)
T ss_pred cch
Confidence 964
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=5.1e-45 Score=372.70 Aligned_cols=214 Identities=43% Similarity=0.707 Sum_probs=181.7
Q ss_pred cCCcccCCccccccccccCChHHHHHHcCCCceEEEEecceEEEEEEEeCCEEEEEeCCCCCCCcchhhHHHHH------
Q 005331 215 RQDIEVGKAVRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKII------ 288 (702)
Q Consensus 215 ~~~i~~~~~~~PmLA~~~~~~~~~~~~~~~~~~~~E~K~DG~R~qvh~~g~~v~~~SR~g~d~t~~~p~l~~~~------ 288 (702)
..++++|.||+||||++.+.....+..+.+.+|++|+||||+|||+|++++++++|||||+++|..+|++.+..
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 35689999999999999987666556777889999999999999999999999999999999999899876532
Q ss_pred --HhhccccceeeeceEEEeeCCCCccccccchHHHHHHhhcCCCCCCceEEEEEEEeeeCCccccCCCHHHHHHHHHhh
Q 005331 289 --EQNVLVDRCILDGEMLVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKV 366 (702)
Q Consensus 289 --~~~~~~~~~ILDGE~v~~d~~~~~~~~F~~lq~~~~~~r~~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~ 366 (702)
.......+||||||||+||..++.+.+|+.+++...... ......+++|+|||||++||++++++||.+|+++|+++
T Consensus 83 ~~~~~~~~~~~iLDGElv~~~~~~~~~~~f~~l~~~~~~~~-~~~~~~~~~~~vFDiL~~~g~~l~~~pl~eR~~~L~~~ 161 (225)
T cd07903 83 HLAFNPKVKSCILDGEMVVWDKETKRFLPFGTLKDVAKLRE-VEDSDLQPCFVVFDILYLNGKSLTNLPLHERKKLLEKI 161 (225)
T ss_pred hhhccccCcEEEeceEEEEEEcCcCeeccchHHHHHHhhcc-cccCCccEEEEEEEEEEECCeecccCcHHHHHHHHHHh
Confidence 011235789999999999987778899999876543211 11234689999999999999999999999999999999
Q ss_pred ccCCCCcccccccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHCCCceEEEecCCCCcccCCCCCCeEEEccccc
Q 005331 367 VKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYI 446 (702)
Q Consensus 367 ~~~~~~~~~~~~p~~~~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EGlV~K~~ds~Y~~G~Rs~~WlKvK~~y~ 446 (702)
+.+.++++.++. ...+++.+++.++|++++++|.||||+|+++|+|++|+|+.+|+|+||+|+
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 988766665432 234567899999999999999999999999999999999999999999996
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=4.9e-44 Score=361.92 Aligned_cols=206 Identities=30% Similarity=0.484 Sum_probs=173.8
Q ss_pred CCcccCCccccccccccCChHHHHHHcCCCceEEEEecceEEEEEEEeCCEEEEEeCCCCCCCc-chhhHHHHHHhhcc-
Q 005331 216 QDIEVGKAVRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSE-YGHAMSKIIEQNVL- 293 (702)
Q Consensus 216 ~~i~~~~~~~PmLA~~~~~~~~~~~~~~~~~~~~E~K~DG~R~qvh~~g~~v~~~SR~g~d~t~-~~p~l~~~~~~~~~- 293 (702)
..+++|.||+||||++.+..+++++++. .+|++|+||||+|||+|++++++++|||||+++|. .+|++.+.+.+.+.
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 57887776555443
Q ss_pred ccceeeeceEEEeeCCCCccccccchHHHHHHhhcCCCCCCceEEEEEEEeeeCCccccCCCHHHHHHHHHhhccCCCCc
Q 005331 294 VDRCILDGEMLVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGR 373 (702)
Q Consensus 294 ~~~~ILDGE~v~~d~~~~~~~~F~~lq~~~~~~r~~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~~~ 373 (702)
..+||||||||+||..++++++|+.++...+. .....+++|+|||||++||.++++.||.+|+++|++++.+.+++
T Consensus 85 ~~~~iLDGEiv~~d~~~g~~~~F~~l~~~~~~----~~~~~~v~~~vFDiL~l~g~~l~~~pl~eR~~~L~~~~~~~~~~ 160 (213)
T cd07902 85 GHSMILDSEVLLVDTKTGKPLPFGTLGIHKKS----AFKDANVCLFVFDCLYYNGESLMDKPLRERRKILEDNMVEIPNR 160 (213)
T ss_pred ccceeeeeEEEEEECCCCcccccchhhhhhcc----ccccCceEEEEEEEeeeCCcchhcCcHHHHHHHHHHhccCCCCe
Confidence 67899999999999877888899888753221 12345799999999999999999999999999999999876655
Q ss_pred ccccccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHCCCceEEEecCCCCcccCCCCCCeEEEcccc
Q 005331 374 LETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEY 445 (702)
Q Consensus 374 ~~~~~p~~~~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EGlV~K~~ds~Y~~G~Rs~~WlKvK~~y 445 (702)
+.+.. ...+.+.+++.++|++++++|.||||+|+++|+|.+|+| +|+|+|+||
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 43321 234567899999999999999999999999999999988 699999998
No 20
>PRK09125 DNA ligase; Provisional
Probab=100.00 E-value=8.1e-44 Score=373.28 Aligned_cols=254 Identities=24% Similarity=0.362 Sum_probs=194.6
Q ss_pred cccccccccCChHHHHHHcCCCceEEEEecceEEEEEEEeCCEEEEEeCCCCCCCcchhhHHHHHHhhccccceeeeceE
Q 005331 224 VRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDGEM 303 (702)
Q Consensus 224 ~~PmLA~~~~~~~~~~~~~~~~~~~~E~K~DG~R~qvh~~g~~v~~~SR~g~d~t~~~p~l~~~~~~~~~~~~~ILDGE~ 303 (702)
..||||...... +.+.+|++|+||||+|||+ + .+++|||+|+++|. |+.. ...+ +++|||||+
T Consensus 28 ~~~~LA~~~~~~------~~~~~~~~E~K~DG~R~~~--~--~v~l~SR~g~~it~--p~~~---~~~~--~~~vLDGEl 90 (282)
T PRK09125 28 PDLQLATVYDKG------QDISGYLVSEKLDGVRAYW--D--GKQLLTRQGNPIAA--PAWF---TAGF--PPFPLDGEL 90 (282)
T ss_pred CCceechhcccC------CChhhEEEEeeeeeEeEEE--C--CeEEEcCCCCcCCC--chhH---HhcC--CCccEeEEE
Confidence 689999887532 3346899999999999975 2 48999999999987 4422 2222 489999999
Q ss_pred EEeeCCCCccccccchHHHHHHhhcCCCCCCceEEEEEEEeeeCCccccCCCHHHHHHHHHhhccCCC-CcccccccCCC
Q 005331 304 LVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSK-GRLETLVPDHG 382 (702)
Q Consensus 304 v~~d~~~~~~~~F~~lq~~~~~~r~~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~-~~~~~~~p~~~ 382 (702)
|+++ .+|+.++.+.++.........+++|++||+|++|| ||.+|+++|++++.+.+ +.++++
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 9854 36877766543221111112589999999999986 99999999999997652 233221
Q ss_pred CCccccCCCCCccccccCCHHHHHHHHHHHHHCCCceEEEecCCCCcccCCCCCCeEEEccccccCCCcceEEEEEEEec
Q 005331 383 LNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLIIGGYYG 462 (702)
Q Consensus 383 ~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EGlV~K~~ds~Y~~G~Rs~~WlKvK~~y~~~g~~~DlvVIG~~~G 462 (702)
....+++.++++++|++++++|+||||+|+++|+|++| |+.+|+|+|+.+ +.|++|||+++|
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 13446789999999999999999999999999999999 899999999986 789999999999
Q ss_pred CCCCCCccceEEEEEecCCCCCCCCcceEEEEEecCCCCHHHHHHHHHhhccccccccCCCCCCCCcccccCCCCCCCcE
Q 005331 463 SGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDV 542 (702)
Q Consensus 463 ~G~r~g~~gs~llg~~d~~~~~~~~~~~~~v~kVgtG~s~~~~~~l~~~l~~~~~~~~~~~~~pp~~~~~~~~~~~~pdv 542 (702)
+|+++|++|+|+|+.++ + ..| +||||||+++++. +|.+
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 99999999999999643 2 123 7999999998641 2211
Q ss_pred EEeCCCceEEEEEeeeceeecccccCCCceeeccEEEEEecCC
Q 005331 543 WIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDK 585 (702)
Q Consensus 543 wi~~P~~s~v~ev~a~~~~~~s~~~~~g~tLRfPr~~riR~DK 585 (702)
..+++|++ ..++..+.||||+|+++|+|.
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 12556643 345677889999999999983
No 21
>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=6.6e-44 Score=359.74 Aligned_cols=205 Identities=33% Similarity=0.568 Sum_probs=171.6
Q ss_pred cCCccccccccccCChHHHHHHcCCCceEEEEecceEEEEEEEeCCEEEEEeCCCCCCCcchhhHHHHHHhhccccceee
Q 005331 220 VGKAVRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCIL 299 (702)
Q Consensus 220 ~~~~~~PmLA~~~~~~~~~~~~~~~~~~~~E~K~DG~R~qvh~~g~~v~~~SR~g~d~t~~~p~l~~~~~~~~~~~~~IL 299 (702)
||.||+||||+..+.+++++++. +.+|++|+||||+|||+|++++.+++|||||+|+|..+|++.+.+.......+|||
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 68999999999998877766554 56899999999999999999999999999999999999999887654322378999
Q ss_pred eceEEEeeCCCCccccccchHHHHHHhhc--CCCCCCceEEEEEEEeeeCCccccCCCHHHHHHHHHhhccCCCCccccc
Q 005331 300 DGEMLVWDTSLNRFAEFGSNQEIAKAARD--GLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETL 377 (702)
Q Consensus 300 DGE~v~~d~~~~~~~~F~~lq~~~~~~r~--~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~~~~~~~ 377 (702)
|||||+||+ .+.+.+|+.+|....+... ......+++|+|||||++||++++++||.+|+++|++++.+. +++.++
T Consensus 80 DGElv~~~~-~g~~~~F~~l~~r~~~~~~~~~~~~~~~~~~~vFDil~~~g~~l~~~pl~eR~~~L~~~~~~~-~~i~~~ 157 (207)
T cd07901 80 DGEAVAYDP-DGRPLPFQETLRRFRRKYDVEEAAEEIPLTLFLFDILYLDGEDLLDLPLSERRKILEEIVPET-EAILLA 157 (207)
T ss_pred eCEEEEECC-CCCccCHHHHHHHhccccchhhhhccCcEEEEEEEEEEECCcchhcCCHHHHHHHHHHhcCcC-CcEEEE
Confidence 999999997 5677899888775432110 001235799999999999999999999999999999999865 344332
Q ss_pred ccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHCCCceEEEecCCCCcccCCCCCCeEEEccc
Q 005331 378 VPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPE 444 (702)
Q Consensus 378 ~p~~~~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EGlV~K~~ds~Y~~G~Rs~~WlKvK~~ 444 (702)
. ...+++.+++.++|++++++|.||||+|+++|+|.+|+|+.+|+|+||+
T Consensus 158 ~-----------------~~~~~~~~~~~~~~~~~~~~g~EGiv~K~~~s~Y~~g~Rs~~wlK~K~~ 207 (207)
T cd07901 158 P-----------------RIVTDDPEEAEEFFEEALEAGHEGVMVKSLDSPYQAGRRGKNWLKVKPD 207 (207)
T ss_pred E-----------------EEecCCHHHHHHHHHHHHHcCCceEEEeCCCCCcCCCCCCCCeEEecCC
Confidence 1 2345788999999999999999999999999999999999999999996
No 22
>PHA00454 ATP-dependent DNA ligase
Probab=100.00 E-value=9.4e-43 Score=371.85 Aligned_cols=284 Identities=20% Similarity=0.294 Sum_probs=208.4
Q ss_pred ccccccccCC--hHHHHHHcCCCceEEEEecceEEEEEEEeCC-EEEEEeCCCCCCCcchhhHH------HHHHh---hc
Q 005331 225 RPQLAMRIGD--AHAAWRKLHGKEVVIECKFDGDRIQIHKNGS-EIHYFSRSFLDHSEYGHAMS------KIIEQ---NV 292 (702)
Q Consensus 225 ~PmLA~~~~~--~~~~~~~~~~~~~~~E~K~DG~R~qvh~~g~-~v~~~SR~g~d~t~~~p~l~------~~~~~---~~ 292 (702)
+|++|...+. +.+++.+++ .|++|+||||+|||+|++++ .+++|||||+++++.. ++. ..+.. +.
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 5788888765 777888763 89999999999999999876 4999999999876421 111 00111 11
Q ss_pred cccceeeeceEEEeeCCCCccccccchHHHHHHhhc--CCCCCCceEEEEEEEeeeC----Cccc---cCCCHHHHHHHH
Q 005331 293 LVDRCILDGEMLVWDTSLNRFAEFGSNQEIAKAARD--GLSSDRQLCYFAFDVLYVG----DTSV---IHQSLKERHELL 363 (702)
Q Consensus 293 ~~~~~ILDGE~v~~d~~~~~~~~F~~lq~~~~~~r~--~~~~~~~~~~~vFDiL~ln----g~~l---~~~pl~eRr~~L 363 (702)
.++++|||||+|+.+ .+|..++.+.++... ......++.|+|||+|++| |+++ ..+||.+|+++|
T Consensus 84 l~~~~vLDGElv~~~------~~f~~~~~~l~~k~~~~~~~~~~~v~~~vFDll~l~~~~~g~~l~~l~~~pl~~Rr~~L 157 (315)
T PHA00454 84 FPDGFMLDGELMVKG------VDFNTGSGLLRRKWKVLFELHLKKLHVVVYDVTPLDVLESGEDYDVMSLLMYEHVRAMV 157 (315)
T ss_pred CCCCeEEEEEEEecC------CCHHHHHHHhccCccchhhhccCceEEEEEEeeEeccccCCccccccccccHHHHHHHH
Confidence 246899999999964 467655554432110 1123468999999999999 6665 789999999999
Q ss_pred HhhccCCCC-cccccccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHCCCceEEEecCCCCcccCCCCCCeEEEc
Q 005331 364 QKVVKPSKG-RLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLK 442 (702)
Q Consensus 364 ~~~~~~~~~-~~~~~~p~~~~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EGlV~K~~ds~Y~~G~Rs~~WlKvK 442 (702)
++++...+. .+.++ ..+.+.+.+++.++|++++++|.||||+|+++|+|++|+|+. |+|+|
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 12111 134567889999999999999999999999999999998875 88999
Q ss_pred cccccCCCcceEEEEEEEecCCCC--CCccceEEEEEecCCCCCCCCcceEEEEEecCCCCHHHHHHHHHhhcccccccc
Q 005331 443 PEYIRAGSDLDVLIIGGYYGSGRR--GGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYE 520 (702)
Q Consensus 443 ~~y~~~g~~~DlvVIG~~~G~G~r--~g~~gs~llg~~d~~~~~~~~~~~~~v~kVgtG~s~~~~~~l~~~l~~~~~~~~ 520 (702)
+.+ ++|++|+|+++|.|++ .|.+++|+|.+ +++ .+.+ |||||++++++|.+++.++...
T Consensus 220 ~~~-----~~d~vIvG~~~g~g~~~~~g~~~~~~~~~--~~g------~l~~----gtGfs~~~~~~l~~~l~~~~~~-- 280 (315)
T PHA00454 220 PEC-----EADGTIVGVVWGTPGLANEGKVIGFRVLL--EDG------RVVN----ATGISRALMEEFTANVKEHGED-- 280 (315)
T ss_pred ccC-----ceeEEEEEEEECCCCccCCceEEEEEEEe--CCC------cEEE----ccCCCHHHHHHHHHHHHhhccC--
Confidence 984 8999999999998643 36677777754 222 4443 8999999999999998875221
Q ss_pred CCCCCCCCcccccCCCCCCCcEEEeCCCceEEEEEeeeceeecccccCCCceeeccEEEEEec
Q 005331 521 YPKRAPPSFYQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRY 583 (702)
Q Consensus 521 ~~~~~pp~~~~~~~~~~~~pdvwi~~P~~s~v~ev~a~~~~~~s~~~~~g~tLRfPr~~riR~ 583 (702)
...| |....|+||++ ..||.+++||||+|+++|+
T Consensus 281 --~~~~--------------------p~~~~v~eV~y-------~e~T~~g~lR~P~F~g~Rd 314 (315)
T PHA00454 281 --YEAM--------------------PYNGRACQVSY-------MERTPDGSLRHPSFDRFRD 314 (315)
T ss_pred --cccc--------------------CCCCeEEEEEE-------EEcCCCCcccCceeeeeec
Confidence 0001 22234677754 2467788999999999985
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=2.7e-42 Score=346.53 Aligned_cols=199 Identities=33% Similarity=0.516 Sum_probs=167.6
Q ss_pred cccccccccCChHHHHHHcCCCceEEEEecceEEEEEEEeCCEEEEEeCCCCCCCcchhhHHHHHHhhccccceeeeceE
Q 005331 224 VRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDGEM 303 (702)
Q Consensus 224 ~~PmLA~~~~~~~~~~~~~~~~~~~~E~K~DG~R~qvh~~g~~v~~~SR~g~d~t~~~p~l~~~~~~~~~~~~~ILDGE~ 303 (702)
|+||||++++.++++ ..+.+.+|++|+||||+|||+|++++++++|||+|+++|..+|++.+.+.. .+++|||||||
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 556778999999999999999999999999999999999999998876542 35799999999
Q ss_pred EEeeCCCCccccccchHHHHHHhhcC--CCCCCceEEEEEEEeeeCCccccCCCHHHHHHHHHhhccCCCCcccccccCC
Q 005331 304 LVWDTSLNRFAEFGSNQEIAKAARDG--LSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDH 381 (702)
Q Consensus 304 v~~d~~~~~~~~F~~lq~~~~~~r~~--~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~~~~~~~~p~~ 381 (702)
|+||... ..||..++....+.... .....+++|+|||||++||++++++||.||+++|++++.+.++++.++.
T Consensus 78 v~~~~~~--~~~f~~~~~~~~~~~~~~~~~~~~~~~~~vFDil~~~g~~l~~~p~~eR~~~L~~~~~~~~~~i~~~~--- 152 (201)
T cd07898 78 LAWDDNR--GLPFSELFKRLGRKFRDKFLDEDVPVVLMAFDLLYLNGESLLDRPLRERRQLLEELFVEIPGRIRIAP--- 152 (201)
T ss_pred EEEeCCC--CCcHHHHHHHhcccccchhhhccCcEEEEEEeEEeECCcchhhCCHHHHHHHHHHhhcCCCCcEEEee---
Confidence 9998643 26888777654322111 1234679999999999999999999999999999999988766664421
Q ss_pred CCCccccCCCCCccccccCCHHHHHHHHHHHHHCCCceEEEecCCCCcccCCCCCCeEEEccc
Q 005331 382 GLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPE 444 (702)
Q Consensus 382 ~~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EGlV~K~~ds~Y~~G~Rs~~WlKvK~~ 444 (702)
...+++.+++.++|++++++|.||||+|+++|+|.+|+||.+|+|+|||
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 2345778899999999999999999999999999999999999999996
No 24
>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=1.8e-42 Score=348.95 Aligned_cols=201 Identities=24% Similarity=0.297 Sum_probs=166.9
Q ss_pred CccccccccccCChHHHHHHcCCCceEEEEecceEEEEEEEeCCEEEEEeCCCCCCCcchhhHHHHHHhhccccceeeec
Q 005331 222 KAVRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDG 301 (702)
Q Consensus 222 ~~~~PmLA~~~~~~~~~~~~~~~~~~~~E~K~DG~R~qvh~~g~~v~~~SR~g~d~t~~~p~l~~~~~~~~~~~~~ILDG 301 (702)
.|+.||||++++..++.+ .....|++|+||||+|||+|++++.+++|||||+++|..||++.+.+. . .+.+|||||
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 589999999998765543 345689999999999999999999999999999999999999987653 2 346899999
Q ss_pred eEEEeeCCCCccccccchHHHHHHhhc--CCCCCCceEEEEEEEeeeCCccccCCCHHHHHHHHHhhccCCC-Ccccccc
Q 005331 302 EMLVWDTSLNRFAEFGSNQEIAKAARD--GLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSK-GRLETLV 378 (702)
Q Consensus 302 E~v~~d~~~~~~~~F~~lq~~~~~~r~--~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~-~~~~~~~ 378 (702)
|||+||. +...||+.++....+... ....+.+++|+||||||+||+++++.||.+|+++|++++.+.+ +++.+.
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 456899888765432111 0112467999999999999999999999999999999997763 333321
Q ss_pred cCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHCCCceEEEecCCCCcccCCCCCCeEEEcccc
Q 005331 379 PDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEY 445 (702)
Q Consensus 379 p~~~~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EGlV~K~~ds~Y~~G~Rs~~WlKvK~~y 445 (702)
....+++.+++.++|++++++|+||||+|+++|+|.+|+|+++|+|+|++-
T Consensus 156 ----------------~~~~~~~~~~~~~~~~~~~~~g~EGiv~K~~~s~Y~~Grr~~~W~K~K~d~ 206 (207)
T cd07897 156 ----------------PLIAFADWEELAALRAQSRERGAEGLMLKRRDSPYLVGRKKGDWWKWKIDP 206 (207)
T ss_pred ----------------ceEecCCHHHHHHHHHHHHHcCCeEEEEeCCCCCcCCCCcCCCeeEeCCCC
Confidence 123467889999999999999999999999999999999999999999973
No 25
>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=3.3e-42 Score=351.74 Aligned_cols=200 Identities=26% Similarity=0.408 Sum_probs=162.5
Q ss_pred ChHHHHHHcCCCceEEEEecceEEEEEEEe----CCEEEEEeCCCCCCCcchhhHHHHHHhhc--------cccceeeec
Q 005331 234 DAHAAWRKLHGKEVVIECKFDGDRIQIHKN----GSEIHYFSRSFLDHSEYGHAMSKIIEQNV--------LVDRCILDG 301 (702)
Q Consensus 234 ~~~~~~~~~~~~~~~~E~K~DG~R~qvh~~----g~~v~~~SR~g~d~t~~~p~l~~~~~~~~--------~~~~~ILDG 301 (702)
++..+++.+.+..|++|+||||+|||+|++ ++.|++|||||+|+|..||++.+.+...+ .+++|||||
T Consensus 11 ~~~~~~~~~~~~~~~~E~K~DG~R~qih~~~~~~~~~v~lfSR~~~d~T~~~pel~~~~~~~~~~~~~~~~~~~~~ILDG 90 (235)
T cd08039 11 SIKHCCKMIGSRRMWVETKYDGEYCQIHIDLSKDSSPIRIFSKSGKDSTADRAGVHSIIRKALRIGKPGCKFSKNCILEG 90 (235)
T ss_pred CHHHHHHHhCCCcEEEEEeecceEEEEEEecccCCCEEEEEeCCCCcccccchhHHHHHHHHhhccccccCCCccEEEEe
Confidence 466677888889999999999999999997 88999999999999999999887654332 257899999
Q ss_pred eEEEeeCCCCccccccchHHHHHHhhc--------CCCCCCceEEEEEEEeeeCCccccCCCHHHHHHHHHhhccCCCCc
Q 005331 302 EMLVWDTSLNRFAEFGSNQEIAKAARD--------GLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGR 373 (702)
Q Consensus 302 E~v~~d~~~~~~~~F~~lq~~~~~~r~--------~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~~~ 373 (702)
|||+||+.++++.||+.+|....+... ......++||+||||||+||+++++.||.+|+++|++++.+.+++
T Consensus 91 EiVv~d~~~g~~~~F~~L~~~~~~~~~~~~~~~~~~~~~~~~v~~~vFDlL~lnG~~l~~~pl~eRr~~L~~l~~~~~~~ 170 (235)
T cd08039 91 EMVVWSDRQGKIDPFHKIRKHVERSGSFIGTDNDSPPHEYEHLMIVFFDVLLLDDESLLSKPYSERRDLLESLVHVIPGY 170 (235)
T ss_pred EEEEEECCCCccCCHHHHHhhcccccchhccccccccccccceEEEEEEEEEECChhhhcCCHHHHHHHHHHhcccCCCc
Confidence 999999877888999988765431110 011236799999999999999999999999999999999887776
Q ss_pred ccccccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHCCCceEEEecCCCCcccCCC-----CCCeEEEcccc
Q 005331 374 LETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDR-----SGKWLKLKPEY 445 (702)
Q Consensus 374 ~~~~~p~~~~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EGlV~K~~ds~Y~~G~R-----s~~WlKvK~~y 445 (702)
++++... .+. .....+.++++++|++++++|+||||+|+++|+|.||++ +.+|+|+||||
T Consensus 171 ~~~~~~~-----~i~-------~~~~~~~~~l~~~~~~a~~~g~EGIv~K~~~S~Y~pgr~~~~~r~~~WlKlK~dY 235 (235)
T cd08039 171 AGLSERF-----PID-------FSRSSGYERLRQIFARAIAERWEGLVLKGDEEPYFDLFLEQGSFSGCWIKLKKDY 235 (235)
T ss_pred EEEEEEE-----eec-------ccCCCCHHHHHHHHHHHHHcCCceEEEecCCCCcccCcccccccCCCeEEeCCCC
Confidence 6543210 000 011246789999999999999999999999999999753 57999999998
No 26
>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=2.3e-40 Score=330.50 Aligned_cols=190 Identities=26% Similarity=0.390 Sum_probs=157.2
Q ss_pred cccccccccCChHHHHHHcCCCceEEEEecceEEEEEEEeCCEEEEEeCCCCCCCcchhhHHHHHHhhccccceeeeceE
Q 005331 224 VRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDGEM 303 (702)
Q Consensus 224 ~~PmLA~~~~~~~~~~~~~~~~~~~~E~K~DG~R~qvh~~g~~v~~~SR~g~d~t~~~p~l~~~~~~~~~~~~~ILDGE~ 303 (702)
|+||||+....++ .+.+|++|+||||+|||+|++++.+++|||||+++|..||++.+++.. ..+.+|||||||
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 6899999887653 256899999999999999999999999999999999999999887654 245789999999
Q ss_pred EEeeCCCCccccccchHHHHHHhhcC---CCCCCceEEEEEEEeeeCCccccCCCHHHHHHHHHhhccCCCCcccccccC
Q 005331 304 LVWDTSLNRFAEFGSNQEIAKAARDG---LSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPD 380 (702)
Q Consensus 304 v~~d~~~~~~~~F~~lq~~~~~~r~~---~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~~~~~~~~p~ 380 (702)
|+||+.+ .+|+.+|......... .....+++|+|||||++||+++++.||.+|+++|++++.+..++++++.
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 4998888754321110 1234689999999999999999999999999999999987644443321
Q ss_pred CCCCccccCCCCCccccccCCHHHHHHHHHHHHHCCCceEEEecCCCCcccCCCCCCeEEEccc
Q 005331 381 HGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPE 444 (702)
Q Consensus 381 ~~~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EGlV~K~~ds~Y~~G~Rs~~WlKvK~~ 444 (702)
...+.+++.++|++++++|+||||+|+++|+|.+|+| +|+|+|+.
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 1246778999999999999999999999999999974 89999984
No 27
>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=3.4e-40 Score=331.33 Aligned_cols=199 Identities=31% Similarity=0.529 Sum_probs=166.3
Q ss_pred cccccccCChHHHHHHcCCCceEEEEecceEEEEEEEeCCEEEEEeCCCCCCCcchhhHHHHHHhhccc--cceeeeceE
Q 005331 226 PQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLV--DRCILDGEM 303 (702)
Q Consensus 226 PmLA~~~~~~~~~~~~~~~~~~~~E~K~DG~R~qvh~~g~~v~~~SR~g~d~t~~~p~l~~~~~~~~~~--~~~ILDGE~ 303 (702)
||||++.+.++.+++++ +.+|++|+||||+|||+|+.++.+++|||+|+++|..+|++...+...+.. .+||||||+
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 99999999888888888 678999999999999999999999999999999999899988777654433 479999999
Q ss_pred EEeeCCCCccccccchHHHHHHhhcCC-CCCCceEEEEEEEeeeCCccccCCCHHHHHHHHHhhccCCCCcccccccCCC
Q 005331 304 LVWDTSLNRFAEFGSNQEIAKAARDGL-SSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHG 382 (702)
Q Consensus 304 v~~d~~~~~~~~F~~lq~~~~~~r~~~-~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~~~~~~~~p~~~ 382 (702)
|+||+.++.+.||+.++....+..... ....+++|+|||+|++||.++++.||.+|+++|++++.+..+.+.++.
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 999999888899977766542111000 014689999999999999999999999999999999965555554331
Q ss_pred CCccccCCCCCccccccCCHHHHHHHHHHHHHCCCceEEEecCCCCcccCCCCCCeEEEc
Q 005331 383 LNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLK 442 (702)
Q Consensus 383 ~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EGlV~K~~ds~Y~~G~Rs~~WlKvK 442 (702)
...+++.++++++|++++++|+||+|+|+++|+|++|+|+.+|+|+|
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 34567899999999999999999999999999999999999999998
No 28
>cd07906 Adenylation_DNA_ligase_LigD_LigC Adenylation domain of Mycobacterium tuberculosis LigD and LigC-like ATP-dependent DNA ligases. Bacterial DNA ligases are divided into two broad classes: NAD-dependent and ATP-dependent. All bacterial species have a NAD-dependent DNA ligase (LigA). Some bacterial genomes contain multiple genes for DNA ligases that are predicted to use ATP as their cofactor, including Mycobacterium tuberculosis LigB, LigC, and LigD. This group is composed of ATP-dependent DNA ligases similar to Mycobacterium tuberculosis LigC. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. Members of this group contain adenylation and C-terminal oligonucleotide/oligosaccharide binding (OB)-fold domains, comprising a catalytic cor
Probab=100.00 E-value=2.1e-39 Score=322.73 Aligned_cols=189 Identities=29% Similarity=0.456 Sum_probs=156.0
Q ss_pred cccccccccCChHHHHHHcCCCceEEEEecceEEEEEEEeCCEEEEEeCCCCCCCcchhhHHHHHHhhccccceeeeceE
Q 005331 224 VRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDGEM 303 (702)
Q Consensus 224 ~~PmLA~~~~~~~~~~~~~~~~~~~~E~K~DG~R~qvh~~g~~v~~~SR~g~d~t~~~p~l~~~~~~~~~~~~~ILDGE~ 303 (702)
++||||++++... .+.+|++|+||||+|||+|++++.+++|||+|+++|..+|++...+.+ +...++||||||
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 6899999988652 356899999999999999999999999999999999999998876543 346899999999
Q ss_pred EEeeCCCCccccccchHHHHHHhhcCCCCCCceEEEEEEEeeeCCccccCCCHHHHHHHHHhhccCCCCcccccccCCCC
Q 005331 304 LVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGL 383 (702)
Q Consensus 304 v~~d~~~~~~~~F~~lq~~~~~~r~~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~~~~~~~~p~~~~ 383 (702)
|+||.... .+|+.++....+.. ......+++|+|||||++||++++++||.||+++|++++.+..+++.++.
T Consensus 74 v~~~~~~~--~~F~~l~~~~~~~~-~~~~~~~~~~~vFDil~~~~~~~~~~p~~eR~~~L~~~~~~~~~~i~~~~----- 145 (190)
T cd07906 74 VVLDEGGR--PDFQALQNRLRLRR-RLARTVPVVYYAFDLLYLDGEDLRGLPLLERKELLEELLPAGSPRLRVSE----- 145 (190)
T ss_pred EEECCCCC--CCHHHHHHhhcccc-hhcccCceEEEEEeeeeeCCcchhhCCHHHHHHHHHHHhccCCCcEEECc-----
Confidence 99997532 68877766443211 12345789999999999999999999999999999999987655544321
Q ss_pred CccccCCCCCccccccCCHHHHHHHHHHHHHCCCceEEEecCCCCcccCCCCCCeEEEcc
Q 005331 384 NSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKP 443 (702)
Q Consensus 384 ~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EGlV~K~~ds~Y~~G~Rs~~WlKvK~ 443 (702)
.. ..+.+++|++++++|.||||+|+++|+|++|+|+.+|+|+|+
T Consensus 146 ------------~~----~~~~~~~~~~~~~~g~EGiv~K~~~s~Y~~g~rs~~wlK~K~ 189 (190)
T cd07906 146 ------------HF----EGGGAALFAAACELGLEGIVAKRADSPYRSGRRSRDWLKIKC 189 (190)
T ss_pred ------------eE----cCCHHHHHHHHHHcCCcEEEEecCCCCcCCCCCCCccEEEec
Confidence 11 123378999999999999999999999999999999999997
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=1.4e-33 Score=264.67 Aligned_cols=137 Identities=26% Similarity=0.530 Sum_probs=117.5
Q ss_pred CCcceEEEEEEEecCCCCCCccceEEEEEecCCCCCCCCcceEEEEEecCCCCHHHHHHHHHhhccccccccCCCCCCCC
Q 005331 449 GSDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPS 528 (702)
Q Consensus 449 g~~~DlvVIG~~~G~G~r~g~~gs~llg~~d~~~~~~~~~~~~~v~kVgtG~s~~~~~~l~~~l~~~~~~~~~~~~~pp~ 528 (702)
++++||||||||+|+|+++|.+|+||||++++++ ++|+++||||||||++++++|.++|+++++.. +...||.
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 4799999999999999999999999999998653 48999999999999999999999999998762 2334666
Q ss_pred cccccCCCCCCCcEEEeCCCceEEEEEeeeceeecccccC-CCceeeccEEEEEecCCCccCCCCHHH
Q 005331 529 FYQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFS-APYSLRFPRIDRVRYDKPWHDCLDVQS 595 (702)
Q Consensus 529 ~~~~~~~~~~~pdvwi~~P~~s~v~ev~a~~~~~~s~~~~-~g~tLRfPr~~riR~DK~~~d~~t~~e 595 (702)
|+... ...+||+||.+|+.|+|+||+++..+ .|+.|. +|+|||||||+++|+||+|+||+|++|
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 76642 35789999977999999999964433 567776 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=100.00 E-value=3.6e-33 Score=274.13 Aligned_cols=173 Identities=20% Similarity=0.312 Sum_probs=135.3
Q ss_pred cccccccccCChHHHHHHcCCCceEEEEecceEEEEEEEeCCEEEEEeCCCCCCCcchhhHHHHHHhhccccceeeeceE
Q 005331 224 VRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDGEM 303 (702)
Q Consensus 224 ~~PmLA~~~~~~~~~~~~~~~~~~~~E~K~DG~R~qvh~~g~~v~~~SR~g~d~t~~~p~l~~~~~~~~~~~~~ILDGE~ 303 (702)
|+||||.+.....+ +.+|++|+||||+|||+|. + ++|||+|+++|.. +. +...+ .++|||||+
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 58999998875422 4589999999999999973 2 8999999999974 22 22222 349999999
Q ss_pred EEeeCCCCccccccchHHHHHHhhcCCCCCCceEEEEEEEeeeCCccccCCCHHHHHHHHHhhccCCC-CcccccccCCC
Q 005331 304 LVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSK-GRLETLVPDHG 382 (702)
Q Consensus 304 v~~d~~~~~~~~F~~lq~~~~~~r~~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~-~~~~~~~p~~~ 382 (702)
|++++ ||+.++.+.+..........+++|++||||+ ++.||.+|+++|++++.+.+ +.+.++.
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 99763 8877776554322111134689999999998 67899999999999997652 3333221
Q ss_pred CCccccCCCCCccccccCCHHHHHHHHHHHHHCCCceEEEecCCCCcccCCCCCCeEEEcc
Q 005331 383 LNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKP 443 (702)
Q Consensus 383 ~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EGlV~K~~ds~Y~~G~Rs~~WlKvK~ 443 (702)
...+.+.+++.+++++++++|+||||+|+++|+|.+| |+.+|+|+||
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 7889999997
No 31
>cd06846 Adenylation_DNA_ligase_like Adenylation domain of proteins similar to ATP-dependent polynucleotide ligases. ATP-dependent polynucleotide ligases catalyze the phosphodiester bond formation of nicked nucleic acid substrates using ATP as a cofactor in a three step reaction mechanism. This family includes ATP-dependent DNA and RNA ligases. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent DNA ligases have a highly modular architecture, consisting of a unique arrangement of two or more discrete domains, including a DNA-binding domain, an adenylation or nucleotidyltransferase (NTase) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The adenylation domain binds ATP and contains many active site residues. Together with the C-terminal OB-fold domain, it comprises a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The catalytic core contains six conserved seq
Probab=99.97 E-value=2.9e-31 Score=262.55 Aligned_cols=177 Identities=23% Similarity=0.332 Sum_probs=139.1
Q ss_pred cccccccCChHHHHHHcCCCceEEEEecceEEEEEEEeCCEEEEEeCCCCCCCcchhhHHHHHHhhccccceeeeceEEE
Q 005331 226 PQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDGEMLV 305 (702)
Q Consensus 226 PmLA~~~~~~~~~~~~~~~~~~~~E~K~DG~R~qvh~~g~~v~~~SR~g~d~t~~~p~l~~~~~~~~~~~~~ILDGE~v~ 305 (702)
||||........ ..+.+.+|++|+||||+|||+|++++.+++|||+|+++|..+|.+..... .....++|||||||+
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 788887665422 24567789999999999999999999999999999999988777643111 123578999999999
Q ss_pred eeCCCCccccccchHHHHHHhhcCCCCCCceEEEEEEEeeeCCccccCCCHHHHHHHHHhhccCCCC--cccccccCCCC
Q 005331 306 WDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKG--RLETLVPDHGL 383 (702)
Q Consensus 306 ~d~~~~~~~~F~~lq~~~~~~r~~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~~--~~~~~~p~~~~ 383 (702)
++... ...+++|++||+|++||.+++++||.+|+++|++++.+.++ .+.+..
T Consensus 79 ~~~~~---------------------~~~~~~~~~FDil~~~~~~~~~~p~~eR~~~L~~~v~~~~~~~~~~i~~----- 132 (182)
T cd06846 79 ENREV---------------------ANPKPTYYAFDVVPLSGVGLRDLPYSDRFAYLKSLLKEFEGLDPVKLVP----- 132 (182)
T ss_pred ccCCC---------------------ccceeEEEEEEEEEECCCccccCCHHHHHHHHHHHhhhhccCCceeEEE-----
Confidence 87521 12578999999999999999999999999999999987542 122110
Q ss_pred CccccCCCCCccccccCCHHHHHHHHHHHHHCCCceEEEecCCCCc--ccCCCCCCeEEEcc
Q 005331 384 NSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKW--EPGDRSGKWLKLKP 443 (702)
Q Consensus 384 ~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EGlV~K~~ds~Y--~~G~Rs~~WlKvK~ 443 (702)
+ .......+++.+++++++++|.||||+|+++|+| .+| |+..|+|+||
T Consensus 133 ---~--------~~~~~~~~~~~~~~~~~~~~g~EGvi~K~~~s~Y~~~~g-r~~~wlK~Kp 182 (182)
T cd06846 133 ---L--------ENAPSYDETLDDLLEKLKKKGKEGLVFKHPDAPYKGRPG-SSGNQLKLKP 182 (182)
T ss_pred ---e--------ecccccchHHHHHHHHhhhcCCceEEEEcCCCCccccCC-CCCceEeecC
Confidence 0 0111123338999999999999999999999999 888 8999999998
No 32
>PF04675 DNA_ligase_A_N: DNA ligase N terminus; InterPro: IPR012308 DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA fragments by catalysing the formation of an internucleotide ester bond between phosphate and deoxyribose. It is active during DNA replication, DNA repair and DNA recombination. There are two forms of DNA ligase, one requires ATP (6.5.1.1 from EC), the other NAD (6.5.1.2 from EC), the latter being restricted to eubacteria. Eukaryotic, archaebacterial, viral and some eubacterial DNA ligases are ATP-dependent. The first step in the ligation reaction is the formation of a covalent enzyme-AMP complex. The co-factor ATP is cleaved to pyrophosphate and AMP, with the AMP being covalently joined to a highly conserved lysine residue in the active site of the ligase. The activated AMP residue is then transferred to the 5'phosphate of the nick, before the nick is sealed by phosphodiester-bond formation and AMP elimination [,]. Vertebrate cells encode three well-characterised DNA ligases (DNA ligases I, III and IV), all of which are related in structure and sequence. With the exception of the atypically small PBCV-1 viral enzyme, two regions of primary sequence are common to all members of the family. The catalytic region comprises six conserved sequence motifs (I, III, IIIa, IV, V-VI), motif I includes the lysine residue that is adenylated in the first step of the ligation reaction. The function of the second, less well-conserved region is unknown. When folded, each protein comprises of two distinct sub-domains: a large amino-terminal sub-domain ('domain 1') and a smaller carboxy-terminal sub-domain ('domain 2'). The ATP-binding site of the enzyme lies in the cleft between the two sub-domains. Domain 1 consists of two antiparallel beta sheets flanked by alpha helices, whereas domain 2 consists of a five-stranded beta barrel and a single alpha helix, which form the oligonucleotide-binding fold [, ]. This region is found in many but not all ATP-dependent DNA ligase enzymes (6.5.1.1 from EC). It is thought to be involved in DNA binding and in catalysis. In human DNA ligase I (P18858 from SWISSPROT), and in Saccharomyces cerevisiae (Baker's yeast) (P04819 from SWISSPROT), this region was necessary for catalysis, and separated from the amino terminus by targeting elements. In Vaccinia virus (P16272 from SWISSPROT) this region was not essential for catalysis, but deletion decreases the affinity for nicked DNA and decreased the rate of strand joining at a step subsequent to enzyme-adenylate formation []. ; GO: 0003677 DNA binding, 0003910 DNA ligase (ATP) activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 2CFM_A 3RR5_A 2HIX_A 2HIV_A 3L2P_A 1X9N_A 4EQ5_A 3GDE_A.
Probab=99.97 E-value=7.4e-32 Score=265.54 Aligned_cols=169 Identities=36% Similarity=0.656 Sum_probs=137.3
Q ss_pred CcHHHHHHHHHHHHhcCChhHHHHHHHHHhhhcCCC---chHhhhHhhcCCCCCCCccccCCCHHHHHHHHHHHhCCCcC
Q 005331 7 TEVIVLVSLFNWIQKTKPAAKKRSKFRKFLDTYCDS---VDYFSALRLILPSLDRERGSYGLKESVLANCLIDALGMSKD 83 (702)
Q Consensus 7 ~~F~~l~~~~e~i~~~~~~~~k~~~l~~~l~~~~~~---~~~~~~lrLllp~~d~~r~~ygike~~L~k~~~~~~~l~~~ 83 (702)
|+|+.||++|++|++++++.+|+++|++||..|... .++|+++++++|+.| +| +|||+++.|++++++++|++++
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 799999999999999999999999999999998754 689999999999999 55 9999999999999999999998
Q ss_pred hHHHHHHhhhhcCCCCCCCCCHHHHHHHHhhhccCC--CCCCCCHHHHHHHHHHHHhhh---chHhHHHHHHHHHHhCCH
Q 005331 84 SADAVRLINWRKGGAAPNAGNFPMVAAEVLQRRQGM--ISGGLTIKELNDLLDRLASSE---NRAEKISVLSTLIKKTNA 158 (702)
Q Consensus 84 s~~~~~L~~wk~~~~~~~~gD~~~~~~~v~~~r~~~--~~~~lTi~eVn~~Ld~La~~~---~~~~k~~~l~~ll~~~t~ 158 (702)
+.++ .|+ ..||||.++++++++++.. .+++|||.|||+.||+||..+ ++..|..+|..++++|||
T Consensus 79 ~~~~----~~~------~~GD~g~~~~~~~~~~~~~~~~~~~lTi~~V~~~L~~la~~~g~~s~~~k~~~l~~ll~~~s~ 148 (177)
T PF04675_consen 79 SIDE----SYK------KVGDLGEVAEEVLQKRKSETSKPSPLTISEVNETLDELAAASGKGSQDEKIDILKELLRRCSP 148 (177)
T ss_dssp HHHH----HHH------HHS-HHHHHHHHHHHHTTTS--SS--BHHHHHHHHHHHHH--STTHHHHHHHHHHHHHTTS-H
T ss_pred HHHH----HHH------hcCcHHHHHHHHHhhccccccCCCCCCHHHHHHHHHHHHHhhCccchHHHHHHHHHHHHhCCH
Confidence 7775 454 3799999999999888743 358999999999999999987 478889999999999999
Q ss_pred HHHHHHHHHHhhhhccCccccccccccCc
Q 005331 159 QEMKWIIMIILKDLKLGISEKSIFHEFHP 187 (702)
Q Consensus 159 ~E~k~l~RiIlk~lriG~~e~~il~~~hp 187 (702)
.|++||+|||+|+||||+++++|+++|||
T Consensus 149 ~E~k~i~Riil~~lriG~~~~~il~ala~ 177 (177)
T PF04675_consen 149 EEAKWIVRIILKDLRIGVSEKTILDALAP 177 (177)
T ss_dssp HHHHHHHHHHTT--SSS--HHHHHHHHHH
T ss_pred HHHHHHHHHHhCCCeeCccHHHHHHHhCc
Confidence 99999999999999999999999999997
No 33
>cd07968 OBF_DNA_ligase_IV The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase IV is a DNA-binding module that is part of the catalytic core unit. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriohages, eukarya, archaea and bacteria. There are three classes of ATP-dependent DNA ligases in eukaryotic cells (I, III and IV). DNA ligase IV is required for DNA non-homologous end joining pathways, including recombination of the V(D)J immunoglobulin gene segments in cells of the mammalian immune system. DNA ligase IV is stabilized by forming a complex with XRCC4, a nuclear phosphoprotein, which is phosphorylated by DNA-dependent pro
Probab=99.96 E-value=1.3e-29 Score=239.39 Aligned_cols=139 Identities=53% Similarity=1.058 Sum_probs=113.8
Q ss_pred CCcceEEEEEEEecCCCCCCccceEEEEEecCCCC-CCCCcceEEEEEecCCCCHHHHHHHHHhhccccccccCCCCCCC
Q 005331 449 GSDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAP-DTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPP 527 (702)
Q Consensus 449 g~~~DlvVIG~~~G~G~r~g~~gs~llg~~d~~~~-~~~~~~~~~v~kVgtG~s~~~~~~l~~~l~~~~~~~~~~~~~pp 527 (702)
++++||||||||+|+|+++|.+|+||||+++.++. ...+.+|++||+||||||++++++|.++|.++|.. .+...||
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 11223899999999999999999999999999876 3333355
Q ss_pred CcccccCCCCCCCcEEEeCCCceEEEEEeeeceeecccccCCCceeeccEEEEEecCCCccCCCCH
Q 005331 528 SFYQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDKPWHDCLDV 593 (702)
Q Consensus 528 ~~~~~~~~~~~~pdvwi~~P~~s~v~ev~a~~~~~~s~~~~~g~tLRfPr~~riR~DK~~~d~~t~ 593 (702)
.+ .......+|++||+ |+.|+|+||++.. +..+..|++|++||||||+++|+||+|+||+|+
T Consensus 79 ~~--~~~~~~~~~~~Wv~-P~~slV~EV~~~e-~t~s~~~~~g~~LR~Pr~~~~R~DK~~~e~~t~ 140 (140)
T cd07968 79 SS--LLKFGKEKPDVWIE-PKDSVVLEVKAAE-IVPSDSYKTGYTLRFPRCEKIRYDKDWHDCLTL 140 (140)
T ss_pred cc--cccccccCCcEEEe-cCCCEEEEEEeee-EeecCcccCCcEEEcceEeEEECCCCHHHccCC
Confidence 33 11234568999998 8889999999653 246778889999999999999999999999984
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=99.96 E-value=2.8e-28 Score=230.86 Aligned_cols=134 Identities=37% Similarity=0.590 Sum_probs=113.5
Q ss_pred CCcceEEEEEEEecCCCCCCccceEEEEEecCCCCCCCCcceEEEEEecCCCCHHHHHHHHHhhccccccccCCCCCCCC
Q 005331 449 GSDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPS 528 (702)
Q Consensus 449 g~~~DlvVIG~~~G~G~r~g~~gs~llg~~d~~~~~~~~~~~~~v~kVgtG~s~~~~~~l~~~l~~~~~~~~~~~~~pp~ 528 (702)
++++|+||||+++|+|++.+.+|+||||++++++ ++|++||+||||||++++++|.++|.+++... .||.
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 4789999999999999998999999999997653 38999999999999999999999999998651 1332
Q ss_pred cccccCCCCCCCcEEEeCCCceEEEEEeeeceeecccccCC---------CceeeccEEEEEecCCCccCCCCHHHHHHH
Q 005331 529 FYQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSA---------PYSLRFPRIDRVRYDKPWHDCLDVQSFVEL 599 (702)
Q Consensus 529 ~~~~~~~~~~~pdvwi~~P~~s~v~ev~a~~~~~~s~~~~~---------g~tLRfPr~~riR~DK~~~d~~t~~el~~l 599 (702)
+ . ...+|++||+ | .+|+||+++.. ..|+.|++ |++||||||+++|+||+|+||+++++|.+|
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 1257999999 7 47999986532 35777775 889999999999999999999999999999
Q ss_pred HH
Q 005331 600 VH 601 (702)
Q Consensus 600 ~~ 601 (702)
++
T Consensus 142 ~~ 143 (144)
T cd07969 142 YK 143 (144)
T ss_pred Hh
Confidence 85
No 35
>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=99.95 E-value=1.2e-27 Score=242.99 Aligned_cols=174 Identities=21% Similarity=0.300 Sum_probs=130.0
Q ss_pred HHcCCCceEEEEecceEEEEEEEeC-CEEEEEeCCCCCCCcchhhHHHHHHhhccccceeeeceEEEeeCCCCccccccc
Q 005331 240 RKLHGKEVVIECKFDGDRIQIHKNG-SEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDGEMLVWDTSLNRFAEFGS 318 (702)
Q Consensus 240 ~~~~~~~~~~E~K~DG~R~qvh~~g-~~v~~~SR~g~d~t~~~p~l~~~~~~~~~~~~~ILDGE~v~~d~~~~~~~~F~~ 318 (702)
..+...+|++|+|+||+|+|+|+.+ +.+.++||+++.++..+|.+.+.........++|||||+|+++...
T Consensus 36 ~~~~~~~y~ve~K~DG~R~~l~~~~~~~v~l~sR~~~~~~~~~~~~~~~~~~~~~~~~~ilDGElv~~~~~~-------- 107 (215)
T cd07895 36 ELLKQNDYFVCEKSDGVRYLLLITGRGEVYLIDRKNDVFKVPGLFFPRRKNLEPHHQGTLLDGELVIDKVPG-------- 107 (215)
T ss_pred HHHhhCCeEEEEeEcCeEEEEEEecCCcEEEEeCCCCeEEeccccCCCcccccccccCeeeEEEEEEEcCCC--------
Confidence 3455678999999999999999999 9999999999998877776543111112357899999999987431
Q ss_pred hHHHHHHhhcCCCCCCceEEEEEEEeeeCCccccCCCHHHHHHHHHhhccCCCCc-ccc-cccCCCCCccccCCCCCccc
Q 005331 319 NQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGR-LET-LVPDHGLNSHVRPQGEPCWS 396 (702)
Q Consensus 319 lq~~~~~~r~~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~~~-~~~-~~p~~~~~~~v~~~~~~~~~ 396 (702)
..+++|+|||||++||+++++.||.+|+++|++++...... +.. .......++.++.
T Consensus 108 --------------~~~~~~~vFDiL~~~g~~l~~~pl~~R~~~L~~~i~~~~~~~~~~~~~~~~~~~~~i~~------- 166 (215)
T cd07895 108 --------------KKRPRYLIFDILAFNGQSVTEKPLSERLKYIKKEVIEPRNELLKKGPIDKAKEPFSVRL------- 166 (215)
T ss_pred --------------ceEEEEEEEEEEEECCcCccCCCHHHHHHHHHHhchhHHHHhhhcChhhcCCCCeEEEe-------
Confidence 24689999999999999999999999999999998543211 000 0000000111110
Q ss_pred cccCCHHHHHHHHHHH---HHCCCceEEEecCCCCcccCCCCCCeEEEcc
Q 005331 397 LVAHNVDEVEKFFKET---IENRDEGIVLKDLGSKWEPGDRSGKWLKLKP 443 (702)
Q Consensus 397 ~~~~~~~~i~~~~~~a---i~~g~EGlV~K~~ds~Y~~G~Rs~~WlKvK~ 443 (702)
......+++.++++.+ +.+|.||||+|+.+++|.+| |+.+|+|+||
T Consensus 167 k~~~~~~~~~~~~~~~~~~~~~~~EGlIfk~~~~~Y~~G-r~~~~lKwKp 215 (215)
T cd07895 167 KDFFPLYKIEKLFEKIIPKLPHENDGLIFTPNDEPYVPG-TDKNLLKWKP 215 (215)
T ss_pred cceEeHHhHHHHHHhccccCCCCCCCEEEccCCCCccCc-cCCcceeeCC
Confidence 0112356788888888 59999999999999999999 9999999997
No 36
>KOG4437 consensus ATP-dependent DNA ligase III [Replication, recombination and repair]
Probab=99.94 E-value=1.6e-26 Score=234.24 Aligned_cols=318 Identities=24% Similarity=0.344 Sum_probs=249.3
Q ss_pred CcHHHHHHHHHHHHhcCChhHHHHHHHHHhhhcCCCchHhhhHhhcCCCCCCCccccCCCHHHHHHHHHHHhCCCcChHH
Q 005331 7 TEVIVLVSLFNWIQKTKPAAKKRSKFRKFLDTYCDSVDYFSALRLILPSLDRERGSYGLKESVLANCLIDALGMSKDSAD 86 (702)
Q Consensus 7 ~~F~~l~~~~e~i~~~~~~~~k~~~l~~~l~~~~~~~~~~~~lrLllp~~d~~r~~ygike~~L~k~~~~~~~l~~~s~~ 86 (702)
-+|.+|..+|.-|+..+....|++.|+.+|.+-.-+.|+|.+|++++-+-|. |.|+|.++.|+++++++|.+...+.-
T Consensus 155 N~F~ef~kiCS~L~~~p~~~~Kt~VI~~LL~kdNFDGDL~LWL~FLIRESD~--R~YNl~DkKLI~lfsKiLn~~~~~~~ 232 (482)
T KOG4437|consen 155 NLFREFRKLCSMLADNPSYNTKTQVIQDLLRKDNFDGDLYLWLKFLIRESDK--RVYNLNDKKLIKLFSKILNCNPDDMA 232 (482)
T ss_pred hHHHHHHHHHHHHHhCcCccchhHHHHHHHhccCCCcchhhhhhhhhccccc--ccccccHHHHHHHHHHHHccChHHHH
Confidence 4588888888888888888899999999997522257999999999999986 58999999999999999999865432
Q ss_pred HHHHhhhhcCCCCCCCCCHHHHHHHHhhhccCCCCCCCCHHHHHHHHHHHHhhhchHhHHHHHHHHHHhCCHHHHHHHHH
Q 005331 87 AVRLINWRKGGAAPNAGNFPMVAAEVLQRRQGMISGGLTIKELNDLLDRLASSENRAEKISVLSTLIKKTNAQEMKWIIM 166 (702)
Q Consensus 87 ~~~L~~wk~~~~~~~~gD~~~~~~~v~~~r~~~~~~~lTi~eVn~~Ld~La~~~~~~~k~~~l~~ll~~~t~~E~k~l~R 166 (702)
..|-. ...+.+..+...-.+..++.++-+||++|++.|.+|+..+..+++...|+.+..+|++.|++.|+|
T Consensus 233 ----~~Y~~-----~S~~~~i~i~~~~~K~~~~~K~~~siQ~~D~~L~rLSKi~~~D~~~~~L~~~A~R~~~~~L~~iIR 303 (482)
T KOG4437|consen 233 ----RDYEQ-----GSVSETIRVFFEQSKSFPPAKSLLTIQEVDEFLLRLSKLTKEDEQQQALQDIASRCTANDLKCIIR 303 (482)
T ss_pred ----HHHHh-----ccchhhhhhhHhhccCCCCcccceeHHHHHHHHHHHhcccchHHHHHHHHHHHHhcccchHHHHHH
Confidence 23321 234566666655555556678899999999999999999999999999999999999999999999
Q ss_pred HHhhhhccCccccccccccCcCHHHHHhhhCCHHHHHHHHhhhh--------cc-cccCCcccCCccccccccccCChHH
Q 005331 167 IILKDLKLGISEKSIFHEFHPDAEDLFNVTCDLKLVCEKLKDRN--------QR-HKRQDIEVGKAVRPQLAMRIGDAHA 237 (702)
Q Consensus 167 iIlk~lriG~~e~~il~~~hpda~~~~~~~~dL~~V~~~L~~~~--------~~-~~~~~i~~~~~~~PmLA~~~~~~~~ 237 (702)
+|-++|+...+.+.||++.||.|+++|. ++.|..|.+...... .+ --......+.|++|||+...++++-
T Consensus 304 LIr~~L~~~s~A~~iL~~~~P~A~E~F~-S~~L~~ViEr~~~N~~~~~~~~~~~~~~s~~s~~~s~~Q~~~~~~~~~VE~ 382 (482)
T KOG4437|consen 304 LIKHDLKMNSGAKHVLDALDPNAYEAFK-SRNLQDVVERVLHNAQEVEKEPGQRRALSVQASLMTPVQPMLAEACKSVEY 382 (482)
T ss_pred HHHHHhccCCChhHHHhccCCCcHHHHH-hcCHHHHHHHHHHhHHHHhhCccccccccchhhhcCCcChhhhhhhhhHHH
Confidence 9999999999999999999999999996 466777776554221 11 0011123567999999998888776
Q ss_pred HHHHcCCCceEEEEecceEEEEEEEeCCEEEEEeCCCCCCCcchhhHHHHHHhhc-cccceeeeceEEEeeCCCCccccc
Q 005331 238 AWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNV-LVDRCILDGEMLVWDTSLNRFAEF 316 (702)
Q Consensus 238 ~~~~~~~~~~~~E~K~DG~R~qvh~~g~~v~~~SR~g~d~t~~~p~l~~~~~~~~-~~~~~ILDGE~v~~d~~~~~~~~F 316 (702)
+.++..+ +..-|.||||+|.|+|.+|+.|.+|||--....++ .+.+.+.+ ...+.++|||....+..+++++||
T Consensus 383 s~~~~~~-~~~S~~~~D~E~~~~~~~~D~~S~~S~~~~~~s~F----K~~~P~~~~~G~~~~~~~~~~~I~~K~~~P~~~ 457 (482)
T KOG4437|consen 383 AMKKCPN-GMFSEIKYDGERVQVHKNGDHFSYFSRLPHKVAHF----KDYIPQAFPGGHSMILDSEVLLIDNKTGKPLPF 457 (482)
T ss_pred HhccCCC-CccccccCCCceeeccCCCcchhhhccChHhhhhh----hhcCchhcCCCccccccccccceecccCCCCCc
Confidence 6666655 57799999999999999999999999966544321 11111222 256899999999999999999999
Q ss_pred cchHHHHHHhhcCCCCCCceEEEEEEEee
Q 005331 317 GSNQEIAKAARDGLSSDRQLCYFAFDVLY 345 (702)
Q Consensus 317 ~~lq~~~~~~r~~~~~~~~~~~~vFDiL~ 345 (702)
+++.-..+..+. +...|.++||+.|
T Consensus 458 ~~~~~~~K~~~~----~~~~~~~~~~~~~ 482 (482)
T KOG4437|consen 458 GTLGVHKKAAFQ----DANVCLFVFDCIY 482 (482)
T ss_pred hhcchhhHHHhc----CcchheeecccCC
Confidence 988765554442 3567899999865
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=7.4e-27 Score=215.58 Aligned_cols=121 Identities=30% Similarity=0.566 Sum_probs=105.5
Q ss_pred CcceEEEEEEEecCCCCCCccceEEEEEecCCCCCCCCcceEEEEEecCCCCHHHHHHHHHhhccccccccCCCCCCCCc
Q 005331 450 SDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSF 529 (702)
Q Consensus 450 ~~~DlvVIG~~~G~G~r~g~~gs~llg~~d~~~~~~~~~~~~~v~kVgtG~s~~~~~~l~~~l~~~~~~~~~~~~~pp~~ 529 (702)
|++|+||+|+++|.|+++|.+|+||||+|++++ ++|+++|+||||||++++++|.++|+++++.
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 ccccCCCCCCCcEEEeCCCceEEEEEeeeceeecccccCCCceeeccEEEEEecCCCccCCCCHHHHH
Q 005331 530 YQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDKPWHDCLDVQSFV 597 (702)
Q Consensus 530 ~~~~~~~~~~pdvwi~~P~~s~v~ev~a~~~~~~s~~~~~g~tLRfPr~~riR~DK~~~d~~t~~el~ 597 (702)
..+|++|++ | .+|+||++.. +..++.|++|++||||||+++|+||+|+||+|++||.
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 4799998643 3467889999999999999999999999999999985
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=8.1e-26 Score=210.48 Aligned_cols=122 Identities=42% Similarity=0.787 Sum_probs=103.0
Q ss_pred CcceEEEEEEEecCCCCCCccceEEEEEecCCCCCCCCcceEEEEEecCCCCHHHHHHHHHhhccccccccCCCCCCCCc
Q 005331 450 SDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSF 529 (702)
Q Consensus 450 ~~~DlvVIG~~~G~G~r~g~~gs~llg~~d~~~~~~~~~~~~~v~kVgtG~s~~~~~~l~~~l~~~~~~~~~~~~~pp~~ 529 (702)
|++|+||+|+++|+|+++|.+|+||||++++++ ++|+++|+||||||++++++|.++|.+++... .|| +
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 479999999999999999999999999997643 38999999999999999999999999988651 133 2
Q ss_pred ccccCCCCCCCcEEEeCCCceEEEEEeeeceeecccccCC-------CceeeccEEEEEecCCCccCC
Q 005331 530 YQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSA-------PYSLRFPRIDRVRYDKPWHDC 590 (702)
Q Consensus 530 ~~~~~~~~~~pdvwi~~P~~s~v~ev~a~~~~~~s~~~~~-------g~tLRfPr~~riR~DK~~~d~ 590 (702)
. ....+|++||+ | ++|+||+++.. ..|+.|++ |++||||||+++|+||+|+||
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 23468999999 7 68999986432 35777887 899999999999999999998
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=99.84 E-value=1.9e-20 Score=171.24 Aligned_cols=114 Identities=27% Similarity=0.460 Sum_probs=89.3
Q ss_pred cceEEEEEEEecCCCCCCccceEEEEEecCCCCCCCCcceEEEEEecCCCCHHHHHHHHHhhccccccccCCCCCCCCcc
Q 005331 451 DLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFY 530 (702)
Q Consensus 451 ~~DlvVIG~~~G~G~r~g~~gs~llg~~d~~~~~~~~~~~~~v~kVgtG~s~~~~~~l~~~l~~~~~~~~~~~~~pp~~~ 530 (702)
+.|++|+|++.+.| ++|.+|+||||+++++ .|+++|+||||||++++++|.++|.+++.. .|| |.
T Consensus 2 ~~~~vI~G~~~~~g-~~~~~gslllg~~~~~-------~l~~vG~vgtG~s~~~~~~l~~~l~~~~~~------~~p-~~ 66 (115)
T cd07971 2 RQEFVIGGYTPPKG-SRGGFGSLLLGVYDGG-------RLVYVGRVGTGFSAATLRELRERLAPLERK------TSP-FA 66 (115)
T ss_pred CceEEEEEEECCCC-CCCcccEEEEEEEcCC-------EEEEeeeEcCCCCHHHHHHHHHHhhcccCC------CCC-Cc
Confidence 46776666666666 7788999999999753 799999999999999999999999988654 133 21
Q ss_pred cccCCCCCCCcEEEeCCCceEEEEEeeeceeecccccCCCceeeccEEEEEecCCCccCC
Q 005331 531 QVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDKPWHDC 590 (702)
Q Consensus 531 ~~~~~~~~~pdvwi~~P~~s~v~ev~a~~~~~~s~~~~~g~tLRfPr~~riR~DK~~~d~ 590 (702)
.. ......+++|++ |. +|+||++. .++.+++||||+|+++|+||+|+||
T Consensus 67 ~~-~~~~~~~~~wv~-P~--lv~eV~~~-------~~t~~~~LR~P~f~~~R~Dk~~~~~ 115 (115)
T cd07971 67 DP-PPADARGAVWVK-PE--LVAEVEFA-------EWTPDGRLRHPVFKGLREDKPAAEV 115 (115)
T ss_pred cc-ccccCCCCEEec-CC--EEEEEEEE-------EecCCCcEECCeeeEeeCCCCcccC
Confidence 11 112457899999 74 78899753 2456779999999999999999997
No 40
>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=99.80 E-value=6.3e-19 Score=159.40 Aligned_cols=108 Identities=22% Similarity=0.315 Sum_probs=86.9
Q ss_pred CcceEEEEEEEecCCCCCCccceEEEEEecCCCCCCCCcceEEEEEecCCCCHHHHHHHHHhhccccccccCCCCCCCCc
Q 005331 450 SDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSF 529 (702)
Q Consensus 450 ~~~DlvVIG~~~G~G~r~g~~gs~llg~~d~~~~~~~~~~~~~v~kVgtG~s~~~~~~l~~~l~~~~~~~~~~~~~pp~~ 529 (702)
+++|+||+|+++|.|+++|.+|+||||+++++ .+.++|+||||||++++++|.+++++++... . |+++
T Consensus 1 ~~~d~vV~G~~~~~g~~~~~~gslllg~~~~~-------~~~~vg~vgtGf~~~~~~~l~~~l~~~~~~~----~-~~~~ 68 (108)
T cd08040 1 KTAEAVIIGMRAGFGNRSDVMGSLLLGYYGED-------GLQAVFSVGTGFSADERRDLWQNLEPLVTSF----D-DHPV 68 (108)
T ss_pred CceeEEEEEeEeCCCCCCCceEEEEEEEECCC-------ceEEEEEEcCCCCHHHHHHHHHhcchhccCC----C-CCcc
Confidence 47899999999999999999999999999754 4779999999999999999999999887541 1 2211
Q ss_pred ccccCCCCCCCcEEEeCCCceEEEEEeeeceeecccccCCCceeeccEEEEEe
Q 005331 530 YQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVR 582 (702)
Q Consensus 530 ~~~~~~~~~~pdvwi~~P~~s~v~ev~a~~~~~~s~~~~~g~tLRfPr~~riR 582 (702)
......+|++|++ | ++|+||++. .++.+++||||||+++|
T Consensus 69 ---~~~~~~~~~vwv~-P--~lv~eV~~~-------~~t~~~~lR~P~f~~~R 108 (108)
T cd08040 69 ---WNVGKDLSFVPLY-P--GKVVEVKYF-------EMGSKDCLRFPVFIGIR 108 (108)
T ss_pred ---cccccCCCCEEee-c--eEEEEEEeE-------EeeCCCeEECCeEEEeC
Confidence 1123457899999 7 479999753 24568999999999997
No 41
>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=99.80 E-value=3.1e-19 Score=158.25 Aligned_cols=97 Identities=41% Similarity=0.719 Sum_probs=72.4
Q ss_pred CCCccceEEEEEecCCCCCCCCcceEEEEEecCCCCHHHHHHHHHhhccccccccCCCCCCCCcccccCCCCCCCcEEEe
Q 005331 466 RGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDVWIE 545 (702)
Q Consensus 466 r~g~~gs~llg~~d~~~~~~~~~~~~~v~kVgtG~s~~~~~~l~~~l~~~~~~~~~~~~~pp~~~~~~~~~~~~pdvwi~ 545 (702)
|+|.+|+||||+++++. +.|.+||+||||||++++++|.++|.+++... ||...... ...+|++||+
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 46889999999999762 38999999999999999999999999998652 33211111 1268999998
Q ss_pred CCCceEEEEEeeeceeecccccCCCceeeccEEEEEecCC
Q 005331 546 SPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDK 585 (702)
Q Consensus 546 ~P~~s~v~ev~a~~~~~~s~~~~~g~tLRfPr~~riR~DK 585 (702)
|+. |+||+++.. ..+ | +||||||+++|+||
T Consensus 68 -P~~--V~eV~~~e~-t~~-----G-~lR~P~~~~~R~DK 97 (97)
T PF04679_consen 68 -PEL--VVEVKFAEI-TPS-----G-SLRFPRFKRIREDK 97 (97)
T ss_dssp -ST---EEEEEESEE-EEE-----S-EEESEEEEEEETTS
T ss_pred -CCE--EEEEEEEEE-cCC-----C-eEECCEEeEEeCCC
Confidence 865 999986432 222 6 99999999999998
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=99.74 E-value=1.8e-17 Score=177.73 Aligned_cols=163 Identities=20% Similarity=0.243 Sum_probs=120.3
Q ss_pred CceEEEEecceEEEEEEEeCCEEEEEeCCCCCC---CcchhhHHHHHHhhccccceeeeceEEEeeCCCCccccccchHH
Q 005331 245 KEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDH---SEYGHAMSKIIEQNVLVDRCILDGEMLVWDTSLNRFAEFGSNQE 321 (702)
Q Consensus 245 ~~~~~E~K~DG~R~qvh~~g~~v~~~SR~g~d~---t~~~p~l~~~~~~~~~~~~~ILDGE~v~~d~~~~~~~~F~~lq~ 321 (702)
++|++|+||||.|+++|+.++++..+||+|... |+.+|++...-.. ...++++||||+++.+. ||- +.
T Consensus 48 ~~~~vEEKlDG~nvri~~~~G~v~a~TR~G~i~e~~T~~~~eiv~~~~~-~~~p~~iLdGElvg~~~------p~v--~~ 118 (342)
T cd07894 48 GPVAVEEKMNGYNVRIVRIGGKVLAFTRGGFICPFTTDRLRDLIDPEFF-DDHPDLVLCGEVVGPEN------PYV--PG 118 (342)
T ss_pred CCEEEEEeECCcEEEEEEECCEEEEEeCCCccCccchhhHhhhchHHhh-ccCCCEEEEEEEEecCC------ccc--cc
Confidence 589999999999999999999999999998644 6777877322110 11367999999998652 220 00
Q ss_pred HHHHhhcCCCCCCceEEEEEEEeeeCCccccCCCHHHHHHHHHhhccCCCCcccccccCCCCCccccCCCCCccccccCC
Q 005331 322 IAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHN 401 (702)
Q Consensus 322 ~~~~~r~~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~~~~~~~~p~~~~~~~v~~~~~~~~~~~~~~ 401 (702)
......++.|++|||++.|+ ...+|+.+|+++|+++.-+....+ ......+
T Consensus 119 -------~~~~~~~v~F~vFDI~~~~~--~~~lp~~eR~~lLe~lg~~~v~~~--------------------~~~~~~d 169 (342)
T cd07894 119 -------SYPEVEDVGFFVFDIRKKNT--GRPLPVEERRELLEKYGLPTVRLF--------------------GEFTADE 169 (342)
T ss_pred -------cCccccccEEEEEeeEEcCC--CCCCCHHHHHHHHHhcCCCCcceE--------------------EEEecCC
Confidence 01112578999999999885 568999999999999733221111 0233456
Q ss_pred HHHHHHHHHHHHHCCCceEEEecCCC-----CcccCCCCCCeEEEcccc
Q 005331 402 VDEVEKFFKETIENRDEGIVLKDLGS-----KWEPGDRSGKWLKLKPEY 445 (702)
Q Consensus 402 ~~~i~~~~~~ai~~g~EGlV~K~~ds-----~Y~~G~Rs~~WlKvK~~y 445 (702)
.+++.++++++.++|.||||+|++++ +|.....+-++|++.-.|
T Consensus 170 ~~~l~~~l~~~~~~G~EGVVlK~~~~~~~~~Ky~t~~~~~~di~~~~~~ 218 (342)
T cd07894 170 IEELKEIIRELDKEGREGVVLKDPDMRVPPLKYTTSYSNCSDIRYAFRY 218 (342)
T ss_pred HHHHHHHHHHHHHCCCceEEEeccccccCcceeecCCCCcHHHHHHhhh
Confidence 88999999999999999999999999 687766666777776665
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=99.72 E-value=6e-17 Score=149.18 Aligned_cols=120 Identities=22% Similarity=0.259 Sum_probs=86.1
Q ss_pred CcceEEEEEEEecCCCCCCccceEEEEEecCCCCCCCCcceEEEEEecCCCCHHHHHHHHHhhccccccccCCCCCCCCc
Q 005331 450 SDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSF 529 (702)
Q Consensus 450 ~~~DlvVIG~~~G~G~r~g~~gs~llg~~d~~~~~~~~~~~~~v~kVgtG~s~~~~~~l~~~l~~~~~~~~~~~~~pp~~ 529 (702)
++.|++|+|+.++. +.+||+|||+|+++ ++|+++|+| ||||++++++|.++|+++.....++ ..++.+
T Consensus 1 ~~~e~vI~G~~~~~----~~~gsLlLg~~~~~------g~l~yvG~v-tGf~~~~~~~L~~~l~~l~~~~p~~-~~~~~~ 68 (122)
T cd07970 1 RTADCVVGGVRGHK----DRPGSLLLGLYDDG------GRLRHVGRT-SPLAAAERRELAELLEPARAGHPWT-GRAPGF 68 (122)
T ss_pred CcEeEEEEEEECCC----CCccEEEEEEECCC------CCEEEEEEE-CCCCHHHHHHHHHHHHHhhcCCCCc-cccccc
Confidence 36787766655544 46999999999754 279999999 9999999999999999876542111 111212
Q ss_pred ccccCCCCCCCcEEEeCCCceEEEEEeeeceeecccccCCCceeecc-EEEEEecCCCccCCC
Q 005331 530 YQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFP-RIDRVRYDKPWHDCL 591 (702)
Q Consensus 530 ~~~~~~~~~~pdvwi~~P~~s~v~ev~a~~~~~~s~~~~~g~tLRfP-r~~riR~DK~~~d~~ 591 (702)
..........+.+|++ |. +|+||++. .|+.++.|||| +|+++|+||+++||+
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 68888642 35566799999 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=5.2e-13 Score=133.31 Aligned_cols=173 Identities=17% Similarity=0.269 Sum_probs=105.1
Q ss_pred cCCCceEEEEecceEEEEEEEeCCEEEEEeCCCCCCC---cchhhHHHHHHhhccccceeeeceEEEeeCCCCccccccc
Q 005331 242 LHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHS---EYGHAMSKIIEQNVLVDRCILDGEMLVWDTSLNRFAEFGS 318 (702)
Q Consensus 242 ~~~~~~~~E~K~DG~R~qvh~~g~~v~~~SR~g~d~t---~~~p~l~~~~~~~~~~~~~ILDGE~v~~d~~~~~~~~F~~ 318 (702)
+...+|++.+|-||.|+++.+.++.+.+++|+..-+. -.+|.-.+.. ......+.+||||||. |...
T Consensus 13 l~~~~Y~V~eKaDG~Ryll~i~~~~~ylidr~~~~~~v~~~~~p~~~~~~-~~~~~~~TLLDGElV~-d~~~-------- 82 (192)
T PF01331_consen 13 LQQKDYFVCEKADGTRYLLLITDNGVYLIDRKNNVFKVDNLHFPSKKDSS-DGRHHQDTLLDGELVL-DKDP-------- 82 (192)
T ss_dssp HHHS-EEEEEEESSEEEEEEEEEEEEEEEETTS-EEEESSST-ECTTC---TTCEGCSEEEEEEEEE-EECT--------
T ss_pred HhhCCcEEEECCCCcEEEEEEecceEEEEeCCCcEEEecCcccccccccc-cccccCCEEEEEEEEc-ccCC--------
Confidence 3346899999999999999998889999999876432 1233211000 0123568999999987 3211
Q ss_pred hHHHHHHhhcCCCCCCceEEEEEEEeeeCCccccCCCHHHHHHHHHhhccCCCCcccc---cccCCCCCccccCCCCCcc
Q 005331 319 NQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLET---LVPDHGLNSHVRPQGEPCW 395 (702)
Q Consensus 319 lq~~~~~~r~~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~~~~~~---~~p~~~~~~~v~~~~~~~~ 395 (702)
....++|++||+|++||+++++.||.+|...|++.+......... .......++.++.. .
T Consensus 83 -------------~~~~~~flifD~l~~~G~~v~~~~~~~Rl~~l~~~i~~p~~~~~~~~~~~~~~~~pf~i~~K---~- 145 (192)
T PF01331_consen 83 -------------GEKKPRFLIFDILAINGQNVTDKPLDERLAYLQEEIIEPRKNAELKSGIIKKKKEPFSIRIK---D- 145 (192)
T ss_dssp -------------TCEEEEEEEEEEEEETTEEGCCSBHHHHHHHHHHHTHHHHHHHHCHTTSCTCTTSSSEEEE------
T ss_pred -------------CCCceEEEEEeeehhCCcEeccCCHHHHHHHHHHHHHHHHHhhccccccccccccceeeecc---c-
Confidence 124578999999999999999999999999997744321110000 00000112222110 0
Q ss_pred ccccCCHHH-HHHHHHHHHHCCCceEEEecCCCCcccCCCCCCeEEEc
Q 005331 396 SLVAHNVDE-VEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLK 442 (702)
Q Consensus 396 ~~~~~~~~~-i~~~~~~ai~~g~EGlV~K~~ds~Y~~G~Rs~~WlKvK 442 (702)
.......+. +...+..-+.+...|||+-..+.+|.+| +..+++|||
T Consensus 146 ~~~~~~~~~~~~~~~~~~l~h~~DGLIFtp~~~pY~~G-t~~~llKWK 192 (192)
T PF01331_consen 146 FFPIYQIEKLLFEEFIPKLPHETDGLIFTPVNTPYVPG-TCPNLLKWK 192 (192)
T ss_dssp -EEGGGHHHHCHHCCCCCTTSTEEEEEEEESSSB--SE-EEEEEEEE-
T ss_pred cHHHHhhHHHHHHHhhccCCCCCCEEEEecCCCCccCC-CCCccEeeC
Confidence 111122222 1222333456788999999999999999 677999998
No 45
>COG5226 CEG1 mRNA capping enzyme, guanylyltransferase (alpha) subunit [RNA processing and modification]
Probab=99.13 E-value=1.1e-10 Score=118.87 Aligned_cols=183 Identities=20% Similarity=0.303 Sum_probs=118.6
Q ss_pred cCCCceEEEEecceEEEEEEEeC------CEEEEEeCCCCCCC---cchhhHHHHHHhhccccceeeeceEEEeeCCCCc
Q 005331 242 LHGKEVVIECKFDGDRIQIHKNG------SEIHYFSRSFLDHS---EYGHAMSKIIEQNVLVDRCILDGEMLVWDTSLNR 312 (702)
Q Consensus 242 ~~~~~~~~E~K~DG~R~qvh~~g------~~v~~~SR~g~d~t---~~~p~l~~~~~~~~~~~~~ILDGE~v~~d~~~~~ 312 (702)
+...+|++.+|-||.||++.+.. -...+|.|..+-|. ..+|-+...........+..||||+|. |
T Consensus 59 Ll~~dy~VCEKsDGvR~Ll~vte~p~tg~~~~y~~DR~nnfY~v~~~f~p~~~~~k~ge~l~~dtlldgelV~-d----- 132 (404)
T COG5226 59 LLNNDYLVCEKSDGVRALLLVTEEPVTGAFRGYFYDRRNNFYEVHTSFPPCSTVLKDGEVLLEDTLLDGELVF-D----- 132 (404)
T ss_pred HHhCCeEEEEccCCeEEEEEEEecccCCCcceEEEeccCceEEeccccCCcccccccCcEEeccceecceEEE-E-----
Confidence 44568999999999999988742 25778999887542 233433221111123467789999987 2
Q ss_pred cccccchHHHHHHhhcCCCCCCceEEEEEEEeeeCCccccCCCHHHHHHHHHhhccCCCCcccccccCCC--CCccccCC
Q 005331 313 FAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHG--LNSHVRPQ 390 (702)
Q Consensus 313 ~~~F~~lq~~~~~~r~~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~~~~~~~~p~~~--~~~~v~~~ 390 (702)
..|.+.++ ++.|.+||+|.+||.-+..++.++|.+.|.+-+.....+.....+... .++|
T Consensus 133 ~~p~~k~~--------------qlryl~fdcLa~~g~~~~~~~~s~Rl~~l~Ke~~kp~~~~r~s~~~~~~~fpf~---- 194 (404)
T COG5226 133 CLPYEKVP--------------QLRYLLFDCLAYAGMFVERMEKSERLKTLQKEDEKPRERKRVSIEIDSGSFPFH---- 194 (404)
T ss_pred eccccchH--------------HHHHHHHHHhhhcceeEeecchhhHHHHhhhhhcccHhhhhheeecccccccee----
Confidence 25655444 356899999999999999999999999998755422111111111110 1111
Q ss_pred CCCccccccCCH---HHHHHHHHHH--HHCCCceEEEecCCCCcccCCCCCCeEEEccccccCCCcceEEEEE
Q 005331 391 GEPCWSLVAHNV---DEVEKFFKET--IENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLIIG 458 (702)
Q Consensus 391 ~~~~~~~~~~~~---~~i~~~~~~a--i~~g~EGlV~K~~ds~Y~~G~Rs~~WlKvK~~y~~~g~~~DlvVIG 458 (702)
+..... -.+-++++.. +.+|..|||+-..+.||..|++ +..+|+||.-+ .++|+..|-
T Consensus 195 ------~s~K~M~~syg~~ki~k~ip~L~HgnDGLIFTp~~~PY~~Gkd-~~lLKWKP~~~---NTiDF~lvl 257 (404)
T COG5226 195 ------FSVKQMLKSYGFWKIYKKIPELKHGNDGLIFTPADEPYSVGKD-GALLKWKPASL---NTIDFRLVL 257 (404)
T ss_pred ------eeHHHHHhhhhHHHHHhhcccccCCCCceEeccCCCCcccCcc-ceeeecCcccc---Cceeeeeee
Confidence 111111 1233444322 4689999999999999999965 58999999854 478886654
No 46
>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=99.11 E-value=2.5e-10 Score=96.78 Aligned_cols=76 Identities=25% Similarity=0.392 Sum_probs=60.2
Q ss_pred cceEEEEEEEecCCCCCCccceEEEEEecCCCCCCCCcceEEEEEecCCCCHHHHHHHHHhhccccccccCCCCCCCCcc
Q 005331 451 DLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFY 530 (702)
Q Consensus 451 ~~DlvVIG~~~G~G~r~g~~gs~llg~~d~~~~~~~~~~~~~v~kVgtG~s~~~~~~l~~~l~~~~~~~~~~~~~pp~~~ 530 (702)
+.|++|+|.++|.|++.|.+|+|+|+.++. . .++||||||+++++++. | +
T Consensus 2 ~~e~vIvG~~~g~g~~~~~~g~llv~~~~g--------~---~~~vgtG~t~~~r~~~~-----------------~-~- 51 (77)
T cd08041 2 DAEARVVGYEEGKGKYEGMLGALVVETKDG--------I---RFKIGSGFSDEQRRNPP-----------------P-I- 51 (77)
T ss_pred ceeEEEEEEEcCCCccCCcEEEEEEEecCC--------C---EEEEcCCCCHHHHhcCC-----------------C-C-
Confidence 679999999999999999999999998752 1 45899999999998552 1 0
Q ss_pred cccCCCCCCCcEEEeCCCceEEEEEeeeceeecccccCCCceeeccEEEEEe
Q 005331 531 QVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVR 582 (702)
Q Consensus 531 ~~~~~~~~~pdvwi~~P~~s~v~ev~a~~~~~~s~~~~~g~tLRfPr~~riR 582 (702)
..|++|++ ..++.++.||||+|+++|
T Consensus 52 -------------------g~v~~V~y-------~e~t~~g~lR~P~f~g~R 77 (77)
T cd08041 52 -------------------GSIITYKY-------QGLTKNGLPRFPVFLRVR 77 (77)
T ss_pred -------------------CCEEEEEE-------EecCCCCcccCCEEEecC
Confidence 12667754 346678899999999997
No 47
>COG1423 ATP-dependent DNA ligase, homolog of eukaryotic ligase III [DNA replication, recombination, and repair]
Probab=98.87 E-value=3.6e-08 Score=102.86 Aligned_cols=150 Identities=23% Similarity=0.328 Sum_probs=104.8
Q ss_pred HcCCCceEEEEecceEEEEEEEeCCEEEEEeCCCCC--CC-cchhhHHHH-HHhhccccceeeeceEEEeeCCCCccccc
Q 005331 241 KLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLD--HS-EYGHAMSKI-IEQNVLVDRCILDGEMLVWDTSLNRFAEF 316 (702)
Q Consensus 241 ~~~~~~~~~E~K~DG~R~qvh~~g~~v~~~SR~g~d--~t-~~~p~l~~~-~~~~~~~~~~ILDGE~v~~d~~~~~~~~F 316 (702)
.|+.+.+++|+|+||+.+-|.+-+|.+...||.|.- || +..+.+.+. +... .++.+|-|||+.-++ -+.|
T Consensus 84 ~F~~~~v~VEEKmnGYNVRV~k~~g~vyAiTRgG~ICPfTT~r~~~l~~~eff~d--~p~lvlcgEmvG~en---PYv~- 157 (382)
T COG1423 84 HFGRGKVVVEEKMNGYNVRVVKLGGEVYAITRGGLICPFTTERLRDLIDLEFFDD--YPDLVLCGEMVGPEN---PYVP- 157 (382)
T ss_pred hcCCCcEEEEEeccCceEEEEEECCEEEEEecCceecCchhHHHHhhcchhhHhh--CCCcEEEEEeccCCC---CCCC-
Confidence 465678999999999999999999999999999984 44 344444321 2222 378999999998542 2222
Q ss_pred cchHHHHHHhhcCCCCCCceEEEEEEEeeeCCccccCCCHHHHHHHHHhhccCCCCcccccccCCCCCccccCCCCCccc
Q 005331 317 GSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWS 396 (702)
Q Consensus 317 ~~lq~~~~~~r~~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~~~~~~~~p~~~~~~~v~~~~~~~~~ 396 (702)
+ ..-....+.|++||+--.|.. ..+|..||++++++.--+ ||.+.+ .
T Consensus 158 ~-----------~~y~~e~v~fFvFDire~~tg--r~Lp~eer~~l~ekYgl~----------------~V~~fg----~ 204 (382)
T COG1423 158 G-----------PYYEKEDVGFFVFDIREKNTG--RPLPVEERLELAEKYGLP----------------HVEIFG----E 204 (382)
T ss_pred C-----------CCCccCCceEEEEEEEecCCC--CCCCHHHHHHHHHHcCCC----------------ceEEee----e
Confidence 0 111235689999999987642 357999999999985322 111111 1
Q ss_pred cccCCH-HHHHHHHHHHHHCCCceEEEecCCCCc
Q 005331 397 LVAHNV-DEVEKFFKETIENRDEGIVLKDLGSKW 429 (702)
Q Consensus 397 ~~~~~~-~~i~~~~~~ai~~g~EGlV~K~~ds~Y 429 (702)
+..++. +++.+..++.-.+|.||+|+|+++..=
T Consensus 205 ~~~~e~~eei~eIve~L~keGREGVV~Kdpdm~~ 238 (382)
T COG1423 205 FPADEAGEEIYEIVERLNKEGREGVVMKDPDMRV 238 (382)
T ss_pred echhHhHHHHHHHHHHHhhcCCcceEecCccccc
Confidence 223334 788888999999999999999987643
No 48
>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=98.83 E-value=5.9e-08 Score=104.32 Aligned_cols=148 Identities=22% Similarity=0.273 Sum_probs=96.7
Q ss_pred HcCCCceEEEEecceEEEEEEEeCCEEEEEeCCCCCCC--c-chhhHHHHHHhhccc--cceeeeceEEEeeCCCCcccc
Q 005331 241 KLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHS--E-YGHAMSKIIEQNVLV--DRCILDGEMLVWDTSLNRFAE 315 (702)
Q Consensus 241 ~~~~~~~~~E~K~DG~R~qvh~~g~~v~~~SR~g~d~t--~-~~p~l~~~~~~~~~~--~~~ILDGE~v~~d~~~~~~~~ 315 (702)
.+.++.+++|+|+||+.+-|..-+|++..+||.|...+ . .++.+.+ ..++. ++.+|.|||+.-+. .+.+
T Consensus 75 ~f~~~~v~vEEKlDG~Nvri~~~~g~l~a~tRGgyicp~tt~r~~~~~~---~~~~~d~p~l~LcGE~iGpen---pY~~ 148 (374)
T TIGR01209 75 HFKDPEVVVEEKMNGYNVRIVKYGGNVYALTRGGFICPFTTERLPDLID---LEFFDDNPDLVLCGEMAGPEN---PYTP 148 (374)
T ss_pred hcCCCcEEEEEeecCceEEEEeECCEEEEEccCcccCCCcHHHHHHHhh---HHhhccCCCeEEEEEEcCCCC---CCcc
Confidence 35565699999999999999888899999999998642 1 2233322 22333 78999999997332 1111
Q ss_pred ccchHHHHHHhhcCC-CCCCceEEEEEEEeeeCCccccCCCHHHHHHHHHhhccCCCCcccccccCCCCCccccCCCCCc
Q 005331 316 FGSNQEIAKAARDGL-SSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPC 394 (702)
Q Consensus 316 F~~lq~~~~~~r~~~-~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~~~~~~~~p~~~~~~~v~~~~~~~ 394 (702)
. .. ....+..|++|||.- ...-.-+|..+|++++++.--+.-..+ .
T Consensus 149 h------------s~~y~~l~~~FfvFDI~d--~~t~~~L~~~er~~l~e~yglp~Vpvl-----------g-------- 195 (374)
T TIGR01209 149 E------------YYPEVKEDLGFFLFDIRE--GKTNRSLPVEERLELAEKYGLPHVEIL-----------G-------- 195 (374)
T ss_pred c------------CccccCCCceEEEEEEEE--CCCCccCCHHHHHHHHHHCCCCcccee-----------e--------
Confidence 0 11 112467899999973 334457899999999998632211000 0
Q ss_pred cccccCC-HHHHHHHHHHHHHCCCceEEEecCCCC
Q 005331 395 WSLVAHN-VDEVEKFFKETIENRDEGIVLKDLGSK 428 (702)
Q Consensus 395 ~~~~~~~-~~~i~~~~~~ai~~g~EGlV~K~~ds~ 428 (702)
.+...+ .+++.+..+..=++|.||||+|+++..
T Consensus 196 -~~~~~~~~~~~~eii~~L~~~gREGVVlK~~~~~ 229 (374)
T TIGR01209 196 -VYTADEAVEEIYEIIERLNKEGREGVVMKDPEMR 229 (374)
T ss_pred -EEcHHHHHHHHHHHHHHhhhcCcceEEEcCcccc
Confidence 111122 226667777777899999999998654
No 49
>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=98.48 E-value=8e-07 Score=87.93 Aligned_cols=176 Identities=15% Similarity=0.126 Sum_probs=118.9
Q ss_pred ccccccccCChHHHHHHcCCCceEEEEecceEEEEEEEeCCEEEEEeCCCCCCCc---chhhHHHHHHhhccccceeeec
Q 005331 225 RPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSE---YGHAMSKIIEQNVLVDRCILDG 301 (702)
Q Consensus 225 ~PmLA~~~~~~~~~~~~~~~~~~~~E~K~DG~R~qvh~~g~~v~~~SR~g~d~t~---~~p~l~~~~~~~~~~~~~ILDG 301 (702)
+.||++-...+++-+ ..+|++=+===|-||+|....|.+.+++|+|.-+.. .+|.-.. .+ -+||
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 357888888899999999999999999999976421 2332110 11 4566
Q ss_pred eEEEeeCCCCccccccchHHHHHHhhcCCCCCCceEEEEEEEeeeCCccccCCCHHHHHHHHHhhccCCCCcccccccCC
Q 005331 302 EMLVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDH 381 (702)
Q Consensus 302 E~v~~d~~~~~~~~F~~lq~~~~~~r~~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~~~~~~~~p~~ 381 (702)
|+|. |-.-+ +...+|+|+|||.+||.++.+.+...|...|++-+.+....-. ...
T Consensus 72 ~tIL-Dci~~---------------------~~~~~yyVlDii~w~g~~l~d~~~~~Rf~wl~skl~E~~~~~~---~~~ 126 (186)
T cd09232 72 YTIL-DCIYN---------------------EDDRTYYVLDVLCWNGHPLYDCETEFRFFWLRSKLEELPELDE---PSE 126 (186)
T ss_pred CEEE-EEecC---------------------CCCCEEEEEEEeeeCCcccccCCcchhHHHHHhhCCCcccccc---ccc
Confidence 6653 31100 1124799999999999999999999999999998776542110 000
Q ss_pred CCCccccCCCCCccccccCCHHHHHHHHHHHH---HCCCceEEEecCCCCcccCCCCCCeEEEccc
Q 005331 382 GLNSHVRPQGEPCWSLVAHNVDEVEKFFKETI---ENRDEGIVLKDLGSKWEPGDRSGKWLKLKPE 444 (702)
Q Consensus 382 ~~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai---~~g~EGlV~K~~ds~Y~~G~Rs~~WlKvK~~ 444 (702)
.-++.+++. + .+.+ +.+.+++.|...+ ..-..||++-..++.|.+| +++.|+|+||.
T Consensus 127 ~~~~~f~~~--p--~~~~-~~~~l~~~~~~~~~~~~~e~DGLlFyhk~~~Y~~G-~tPlvl~wKp~ 186 (186)
T cd09232 127 KNPFRFVPL--P--YFPC-TKESLQSAYSGPLNDDPYELDGLLFYHKESHYTPG-STPLVLWLKDY 186 (186)
T ss_pred cCCceEEec--C--cccC-cHHHHHHHHhcccccCCCCCceEEEEeCCCcccCc-CCCcEEEecCC
Confidence 011222211 1 2222 3367888888888 8899999999999999998 78999999983
No 50
>PF14743 DNA_ligase_OB_2: DNA ligase OB-like domain; PDB: 2Q2U_D 2Q2T_A 1FVI_A 1P8L_A.
Probab=98.21 E-value=1.5e-06 Score=71.11 Aligned_cols=65 Identities=25% Similarity=0.443 Sum_probs=39.6
Q ss_pred cCCCCCCccceEEEEEecCCCCCCCCcceEEEEEecCCCCHHHHHHHHHhhccccccccCCCCCCCCcccccCCCCCCCc
Q 005331 462 GSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERPD 541 (702)
Q Consensus 462 G~G~r~g~~gs~llg~~d~~~~~~~~~~~~~v~kVgtG~s~~~~~~l~~~l~~~~~~~~~~~~~pp~~~~~~~~~~~~pd 541 (702)
|+|+..|++|+|+|-..+ + ..++||||||+++++++. .
T Consensus 2 G~Gk~~g~~Galv~~~~~--G---------~~f~iGsG~td~~R~~~~------~------------------------- 39 (66)
T PF14743_consen 2 GKGKFKGMLGALVCETED--G---------VEFKIGSGFTDEEREEPP------Y------------------------- 39 (66)
T ss_dssp ---EEEEEEEEEEEEE-T--T---------EEEEE-SS--HHHHHHHH------H-------------------------
T ss_pred CccccCCCEEEEEEEeCC--C---------CEEEECCCCCHHHHhcCC------C-------------------------
Confidence 778889999999997643 1 366899999999998663 0
Q ss_pred EEEeCCCceEEEEEeeeceeecccccCCCceeeccEEEEEe
Q 005331 542 VWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVR 582 (702)
Q Consensus 542 vwi~~P~~s~v~ev~a~~~~~~s~~~~~g~tLRfPr~~riR 582 (702)
..-+++|++. ..+....+|||+|.++|
T Consensus 40 -------iG~iit~ky~-------~~t~~g~pRfP~f~~~R 66 (66)
T PF14743_consen 40 -------IGKIITVKYQ-------GLTKDGSPRFPVFVRVR 66 (66)
T ss_dssp -------TT-EEEEEEE--------TTSSSS-EEEEEEEE-
T ss_pred -------CCCEEEEEEE-------ccCCCCccccCEEEEeC
Confidence 0124566652 23456699999999998
No 51
>smart00532 LIGANc Ligase N family.
Probab=97.88 E-value=0.00033 Score=78.36 Aligned_cols=223 Identities=18% Similarity=0.255 Sum_probs=130.1
Q ss_pred ceEEEEecceEEEEEEEeCCE-EEEEeC----CCCCCCcchhhH---HHHHHhhccccceeeeceEEEeeCCCC------
Q 005331 246 EVVIECKFDGDRIQIHKNGSE-IHYFSR----SFLDHSEYGHAM---SKIIEQNVLVDRCILDGEMLVWDTSLN------ 311 (702)
Q Consensus 246 ~~~~E~K~DG~R~qvh~~g~~-v~~~SR----~g~d~t~~~p~l---~~~~~~~~~~~~~ILDGE~v~~d~~~~------ 311 (702)
.|++|+|+||.-+.+.+.+|. ++..|| .|+|+|+....+ ...+. ...+..+.+-||++.-...-.
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 699999999999999988776 889999 788998633222 11121 001345889999997321100
Q ss_pred ---ccccccchHHHH-HHhhc---CCCCCCceEEEEEEEeeeCCccccCCCHHHHHHHHHhhccCCCCcccccccCCCCC
Q 005331 312 ---RFAEFGSNQEIA-KAARD---GLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLN 384 (702)
Q Consensus 312 ---~~~~F~~lq~~~-~~~r~---~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~~~~~~~~p~~~~~ 384 (702)
.-.+|..-+..+ ...+. ......++.|++|++...++.. ...+..++.+.|.++-=+...
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 002343222221 11111 1112358999999986443311 124678888888876321110
Q ss_pred ccccCCCCCccccccCCHHHHHHHHHHHHH------CCCceEEEecCCCCccc--C--CCCCCe---EEEccccccCCCc
Q 005331 385 SHVRPQGEPCWSLVAHNVDEVEKFFKETIE------NRDEGIVLKDLGSKWEP--G--DRSGKW---LKLKPEYIRAGSD 451 (702)
Q Consensus 385 ~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~------~g~EGlV~K~~ds~Y~~--G--~Rs~~W---lKvK~~y~~~g~~ 451 (702)
....+.+.+++.++++...+ -.-.|||+|--+-.+.. | .+.+.| +|+.++ .
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 12234678889988887665 36689999987766544 3 356778 455554 4
Q ss_pred ceEEEEEEEecCCCCCCccceEEEEEecCCC-CCCCCcceEEEEEecCCCCHHHHHHH
Q 005331 452 LDVLIIGGYYGSGRRGGEVAQFLVALAERPA-PDTYPRRFISFCRVGTGLSDEELDAV 508 (702)
Q Consensus 452 ~DlvVIG~~~G~G~r~g~~gs~llg~~d~~~-~~~~~~~~~~v~kVgtG~s~~~~~~l 508 (702)
..-.|.+-.|..|| .|.+.-. |..++-. + + .+|.++ |..+.+..+++
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 55567777787765 4555432 2222210 0 1 234444 77777777665
No 52
>PF00533 BRCT: BRCA1 C Terminus (BRCT) domain; InterPro: IPR001357 The BRCT domain (after the C_terminal domain of a breast cancer susceptibility protein) is found predominantly in proteins involved in cell cycle checkpoint functions responsive to DNA damage [], for example as found in the breast cancer DNA-repair protein BRCA1. The domain is an approximately 100 amino acid tandem repeat, which appears to act as a phospho-protein binding domain []. A chitin biosynthesis protein from yeast also seems to belong to this group. ; GO: 0005622 intracellular; PDB: 3L46_A 3AL3_A 3AL2_A 1WF6_A 3II6_X 2NTE_B 3FA2_A 2R1Z_A 2COK_A 2K7F_A ....
Probab=97.76 E-value=3.2e-05 Score=64.76 Aligned_cols=48 Identities=21% Similarity=0.395 Sum_probs=43.2
Q ss_pred cccccCCcEEEEEeCCCCCCHHHHHHHHHHcCCEEEEecCCCeeEEEec
Q 005331 653 ETSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAN 701 (702)
Q Consensus 653 ~s~~f~g~~f~v~~~~~~~~k~~l~~~i~~~gG~~~~n~~~~~~~~i~~ 701 (702)
.+.+|+|+.||| ++....++++|+++|++|||++.+...+.+||+|+.
T Consensus 2 ~~~~F~g~~f~i-~~~~~~~~~~l~~~i~~~GG~v~~~~~~~~thvI~~ 49 (78)
T PF00533_consen 2 KPKIFEGCTFCI-SGFDSDEREELEQLIKKHGGTVSNSFSKKTTHVIVG 49 (78)
T ss_dssp STTTTTTEEEEE-SSTSSSHHHHHHHHHHHTTEEEESSSSTTSSEEEES
T ss_pred CCCCCCCEEEEE-ccCCCCCHHHHHHHHHHcCCEEEeecccCcEEEEeC
Confidence 367999999999 666778899999999999999999998889999975
No 53
>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=97.75 E-value=0.00042 Score=74.10 Aligned_cols=167 Identities=17% Similarity=0.256 Sum_probs=100.9
Q ss_pred ceEEEEecceEEEEEEEeCCE-EEEEeC----CCCCCCcchhhH---HHHHHhhccccceeeeceEEEeeCCCCc-----
Q 005331 246 EVVIECKFDGDRIQIHKNGSE-IHYFSR----SFLDHSEYGHAM---SKIIEQNVLVDRCILDGEMLVWDTSLNR----- 312 (702)
Q Consensus 246 ~~~~E~K~DG~R~qvh~~g~~-v~~~SR----~g~d~t~~~p~l---~~~~~~~~~~~~~ILDGE~v~~d~~~~~----- 312 (702)
.|++|+|+||.-+.+.+.+|+ ++..|| .|+|+|+....+ ...+. . .+..+.+=||++.-...-.+
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 678888633222 11221 1 14468899999974211000
Q ss_pred ----cccccchHHHH-HHhhc---CCCCCCceEEEEEEEeeeCCccccCCCHHHHHHHHHhhccCCCCcccccccCCCCC
Q 005331 313 ----FAEFGSNQEIA-KAARD---GLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLN 384 (702)
Q Consensus 313 ----~~~F~~lq~~~-~~~r~---~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~~~~~~~~p~~~~~ 384 (702)
-.+|..-+..+ ...|. ......++.|++|++...++.. .....++.+.|.++-=++..
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 01333222211 11111 1112468999999996544211 34678888888876322211
Q ss_pred ccccCCCCCccccccCCHHHHHHHHHHHHHC------CCceEEEecCCCCcc----cCCCCCCe
Q 005331 385 SHVRPQGEPCWSLVAHNVDEVEKFFKETIEN------RDEGIVLKDLGSKWE----PGDRSGKW 438 (702)
Q Consensus 385 ~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~------g~EGlV~K~~ds~Y~----~G~Rs~~W 438 (702)
....+.+.+++.++++..... .-.|||+|--+-.+. ...+++.|
T Consensus 246 ----------~~~~~~~~~ev~~~~~~~~~~R~~l~y~iDGiViKvn~~~~~~~lG~tsk~PrW 299 (307)
T cd00114 246 ----------ETRLCKNIEEVLAFYDEIEAKRDSLPYEIDGVVVKVDDLALQRELGFTSKAPRW 299 (307)
T ss_pred ----------CeEEeCCHHHHHHHHHHHHHhhhcCCCCCCcEEEEEeCHHHHHHhCccCCCCCc
Confidence 123456788999988877433 668999997665543 23455777
No 54
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=97.70 E-value=0.00056 Score=78.32 Aligned_cols=211 Identities=16% Similarity=0.202 Sum_probs=120.5
Q ss_pred cccccccc-cCChHHHHHHcCC--CceEEEEecceEEEEEEEeCCE-EEEEeC----CCCCCCcch---hhHHHHHHhhc
Q 005331 224 VRPQLAMR-IGDAHAAWRKLHG--KEVVIECKFDGDRIQIHKNGSE-IHYFSR----SFLDHSEYG---HAMSKIIEQNV 292 (702)
Q Consensus 224 ~~PmLA~~-~~~~~~~~~~~~~--~~~~~E~K~DG~R~qvh~~g~~-v~~~SR----~g~d~t~~~---p~l~~~~~~~~ 292 (702)
-.|||+-. +-+.++. .++.. ..|++|+|+||.-+.+.+.+|. ++..|| -|+|+|+.. +.+...+. .
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 45898543 2233332 22211 2699999999999999887665 688999 678888632 22222221 1
Q ss_pred cccceeeeceEEEeeCCCCcc-ccccchHHH-HHHhhc--CCCCCCceEEEEEEEeeeCCccccCCCHHHHHHHHHhhcc
Q 005331 293 LVDRCILDGEMLVWDTSLNRF-AEFGSNQEI-AKAARD--GLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVK 368 (702)
Q Consensus 293 ~~~~~ILDGE~v~~d~~~~~~-~~F~~lq~~-~~~~r~--~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~ 368 (702)
.+..+.+-||++.-...-.+. ..|..-+.. +...|. ......++.|++|++. +| .....++.+.|.++-=
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 123588999999743210000 001110111 111110 0011467999999983 44 2467788888887642
Q ss_pred CCCCcccccccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHH----CCCceEEEecCCCCcccC--CCCCCe---E
Q 005331 369 PSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIE----NRDEGIVLKDLGSKWEPG--DRSGKW---L 439 (702)
Q Consensus 369 ~~~~~~~~~~p~~~~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~----~g~EGlV~K~~ds~Y~~G--~Rs~~W---l 439 (702)
+.... ....+.+.+++.++++.... -.-.|+|+|--+-.|..| .+.+.| +
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 11234677888887776543 367899999776666543 467788 4
Q ss_pred EEccccccCCCcceEEEEEEEecCCCCCCccc
Q 005331 440 KLKPEYIRAGSDLDVLIIGGYYGSGRRGGEVA 471 (702)
Q Consensus 440 KvK~~y~~~g~~~DlvVIG~~~G~G~r~g~~g 471 (702)
|+.++ +..-.|.+-.|..|| .|.+.
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 55554 455577787887775 45554
No 55
>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=97.67 E-value=0.0008 Score=79.09 Aligned_cols=195 Identities=18% Similarity=0.257 Sum_probs=116.2
Q ss_pred ceEEEEecceEEEEEEEeCCE-EEEEeC----CCCCCCcchhhH---HHHHHhhccccceeeeceEEEeeCCCC------
Q 005331 246 EVVIECKFDGDRIQIHKNGSE-IHYFSR----SFLDHSEYGHAM---SKIIEQNVLVDRCILDGEMLVWDTSLN------ 311 (702)
Q Consensus 246 ~~~~E~K~DG~R~qvh~~g~~-v~~~SR----~g~d~t~~~p~l---~~~~~~~~~~~~~ILDGE~v~~d~~~~------ 311 (702)
.|++|+|+||.-+.+.+.+|+ ++..|| .|+|+|+-...+ ...+.....+..+.+-||++.-...-.
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 788888632222 212210001345889999997421100
Q ss_pred ---ccccccchHHHH-HHhhc---CCCCCCceEEEEEEEeeeCCccccCCCHHHHHHHHHhhccCCCCcccccccCCCCC
Q 005331 312 ---RFAEFGSNQEIA-KAARD---GLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLN 384 (702)
Q Consensus 312 ---~~~~F~~lq~~~-~~~r~---~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~~~~~~~~p~~~~~ 384 (702)
.-.+|..-+..+ ...|. ......++.|++|++...+ ........++.+.|.++-=+...
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 001343323221 11121 1112468999999985322 21124778888888876322211
Q ss_pred ccccCCCCCccccccCCHHHHHHHHHHHHH------CCCceEEEecCCCCcc----cCCCCCCe---EEEccccccCCCc
Q 005331 385 SHVRPQGEPCWSLVAHNVDEVEKFFKETIE------NRDEGIVLKDLGSKWE----PGDRSGKW---LKLKPEYIRAGSD 451 (702)
Q Consensus 385 ~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~------~g~EGlV~K~~ds~Y~----~G~Rs~~W---lKvK~~y~~~g~~ 451 (702)
....+.+.+++.+++++..+ -.-.|+|+|--+-.+. ...+++.| +|+.++ +
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 12235678899988887643 3678999997665543 12357788 566654 4
Q ss_pred ceEEEEEEEecCCCCCCccc
Q 005331 452 LDVLIIGGYYGSGRRGGEVA 471 (702)
Q Consensus 452 ~DlvVIG~~~G~G~r~g~~g 471 (702)
..-.|.+-.|..|| .|.+.
T Consensus 307 ~~T~l~~I~~qVGR-TG~iT 325 (652)
T TIGR00575 307 AQTKLLDVVVQVGR-TGAIT 325 (652)
T ss_pred eeEEEEEEEEecCC-Cceee
Confidence 55577787887775 45554
No 56
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=97.63 E-value=0.0012 Score=77.81 Aligned_cols=195 Identities=21% Similarity=0.294 Sum_probs=116.6
Q ss_pred ceEEEEecceEEEEEEEeCCE-EEEEeC----CCCCCCcch---hhHHHHHHhhccccceeeeceEEEeeCCCC------
Q 005331 246 EVVIECKFDGDRIQIHKNGSE-IHYFSR----SFLDHSEYG---HAMSKIIEQNVLVDRCILDGEMLVWDTSLN------ 311 (702)
Q Consensus 246 ~~~~E~K~DG~R~qvh~~g~~-v~~~SR----~g~d~t~~~---p~l~~~~~~~~~~~~~ILDGE~v~~d~~~~------ 311 (702)
.|++|+|+||.-+.+.+.+|. ++..|| .|+|+|+-. +.+...+... .+..+.+-||++.-...-.
T Consensus 109 ~~~~epKiDGlsisL~Y~~G~L~~a~TRGDG~~GeDvT~n~~~I~~IP~~l~~~-~p~~levRGEv~m~~~~F~~lN~~~ 187 (665)
T PRK07956 109 TYLCELKIDGLAVSLLYENGVLVRAATRGDGTTGEDITANVRTIRSIPLRLHGN-EPERLEVRGEVFMPKADFEALNEER 187 (665)
T ss_pred ceEEEEecccEEEEEEEECCEEEEEEecCCCccchhHhhhhhhhccCChhhccc-CCCeEEEEEEEEEEHHHHHHHHHHH
Confidence 599999999999999887765 688999 788998632 2222222101 1345889999997421100
Q ss_pred ---ccccccchHHHH-HHhhcC---CCCCCceEEEEEEEeeeCCccccCCCHHHHHHHHHhhccCCCCcccccccCCCCC
Q 005331 312 ---RFAEFGSNQEIA-KAARDG---LSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLN 384 (702)
Q Consensus 312 ---~~~~F~~lq~~~-~~~r~~---~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~~~~~~~~p~~~~~ 384 (702)
.-.+|..-+..+ ...|.. .....++.|++|++...++ ........++.+.|.++-=++..
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 002333222221 111110 1124689999999864431 11134678888888876322211
Q ss_pred ccccCCCCCccccccCCHHHHHHHHHHHHH------CCCceEEEecCCCCccc--C--CCCCCe---EEEccccccCCCc
Q 005331 385 SHVRPQGEPCWSLVAHNVDEVEKFFKETIE------NRDEGIVLKDLGSKWEP--G--DRSGKW---LKLKPEYIRAGSD 451 (702)
Q Consensus 385 ~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~------~g~EGlV~K~~ds~Y~~--G--~Rs~~W---lKvK~~y~~~g~~ 451 (702)
....+.+.+++.+++++..+ -.-.|||+|--+-.|.. | .+.+.| +|+.++ +
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 12235678889888887653 36689999976644421 2 356788 566664 4
Q ss_pred ceEEEEEEEecCCCCCCccc
Q 005331 452 LDVLIIGGYYGSGRRGGEVA 471 (702)
Q Consensus 452 ~DlvVIG~~~G~G~r~g~~g 471 (702)
..-.|.+-.|..|| .|.+.
T Consensus 319 ~~T~l~~I~~qVGR-TG~iT 337 (665)
T PRK07956 319 ATTKLLDIEVQVGR-TGAVT 337 (665)
T ss_pred eEEEEEEEEEecCC-Cceee
Confidence 55677777787775 45454
No 57
>smart00292 BRCT breast cancer carboxy-terminal domain.
Probab=97.61 E-value=0.00014 Score=60.16 Aligned_cols=48 Identities=21% Similarity=0.381 Sum_probs=42.5
Q ss_pred cccCCcEEEEEeCCCCCCHHHHHHHHHHcCCEEEEecCC-CeeEEEecC
Q 005331 655 SIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNN-SVTHCVANH 702 (702)
Q Consensus 655 ~~f~g~~f~v~~~~~~~~k~~l~~~i~~~gG~~~~n~~~-~~~~~i~~~ 702 (702)
.+|+|+.||+.......++++|+++|.++||+++.+... ..||+|+.+
T Consensus 1 ~~f~g~~~~~~g~~~~~~~~~l~~~i~~~Gg~~~~~~~~~~~thvi~~~ 49 (80)
T smart00292 1 KLFKGKVFVITGKFDKNERDELKELIEALGGKVTSSLSSKTTTHVIVGS 49 (80)
T ss_pred CccCCeEEEEeCCCCCccHHHHHHHHHHcCCEEecccCccceeEEEEcC
Confidence 479999999987567788999999999999999999886 799999863
No 58
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=97.61 E-value=0.00098 Score=78.54 Aligned_cols=193 Identities=20% Similarity=0.223 Sum_probs=115.2
Q ss_pred CceEEEEecceEEEEEEEeCCE-EEEEeC----CCCCCCcchhhH---HHHHHhhccccceeeeceEEEeeCC-------
Q 005331 245 KEVVIECKFDGDRIQIHKNGSE-IHYFSR----SFLDHSEYGHAM---SKIIEQNVLVDRCILDGEMLVWDTS------- 309 (702)
Q Consensus 245 ~~~~~E~K~DG~R~qvh~~g~~-v~~~SR----~g~d~t~~~p~l---~~~~~~~~~~~~~ILDGE~v~~d~~------- 309 (702)
..|++|+|+||.-+-+.+.+|+ ++..|| .|.|+|+-...+ ...+. ...+..+.+=||++.-...
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 4699999999999998887665 788999 788998633222 11121 1113457888999974221
Q ss_pred ---CCccccccchHHHH-HHhhcC---CCCCCceEEEEEEEeeeCCccccCCCHHHHHHHHHhhccCCCCcccccccCCC
Q 005331 310 ---LNRFAEFGSNQEIA-KAARDG---LSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHG 382 (702)
Q Consensus 310 ---~~~~~~F~~lq~~~-~~~r~~---~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~~~~~~~~p~~~ 382 (702)
.+. .+|..-+..+ ...|.. .....++.|++|++...++. .....++.+.|..+-=+....
T Consensus 211 ~~~~g~-~~faNpRN~aAGslR~ldp~~~~~r~L~f~~y~~~~~~~~---~~t~~e~l~~L~~~GF~v~~~--------- 277 (689)
T PRK14351 211 RIERGE-EPFANPRNAAAGTLRQLDPSVVAERPLDIFFFDVLDASEL---FDSHWEELERFPEWGLRVTDR--------- 277 (689)
T ss_pred HHHcCC-CCcCCHHHHHhhHhhccChHHHhcCCceEEEEecccCCCC---CCCHHHHHHHHHHCCCCcCCc---------
Confidence 010 1233222221 111111 11236899999998654431 246678888888763222111
Q ss_pred CCccccCCCCCccccccCCHHHHHHHHHHHHH------CCCceEEEecCCCCccc----CCCCCCe---EEEccccccCC
Q 005331 383 LNSHVRPQGEPCWSLVAHNVDEVEKFFKETIE------NRDEGIVLKDLGSKWEP----GDRSGKW---LKLKPEYIRAG 449 (702)
Q Consensus 383 ~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~------~g~EGlV~K~~ds~Y~~----G~Rs~~W---lKvK~~y~~~g 449 (702)
...+.+.+++.++++...+ -.-.|||+|--+-.+.. ..+.+.| +|+.++
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 1235678888887776643 45689999976655421 2467788 455554
Q ss_pred CcceEEEEEEEecCCCCCCccc
Q 005331 450 SDLDVLIIGGYYGSGRRGGEVA 471 (702)
Q Consensus 450 ~~~DlvVIG~~~G~G~r~g~~g 471 (702)
...-.|.+-.|..|| .|.+.
T Consensus 340 -~~~T~l~~I~~qVGR-TG~iT 359 (689)
T PRK14351 340 -AEETTIRDIVVQVGR-TGRLT 359 (689)
T ss_pred -eeEEEEEEEEEecCC-Cceee
Confidence 455577777787765 45554
No 59
>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=97.45 E-value=3.5e-05 Score=82.70 Aligned_cols=169 Identities=21% Similarity=0.310 Sum_probs=95.0
Q ss_pred ceEEEEecceEEEEEEEeCCE-EEEEeC----CCCCCCcchhhHHHHHHhhcc--ccceeeeceEEEeeCCCC-------
Q 005331 246 EVVIECKFDGDRIQIHKNGSE-IHYFSR----SFLDHSEYGHAMSKIIEQNVL--VDRCILDGEMLVWDTSLN------- 311 (702)
Q Consensus 246 ~~~~E~K~DG~R~qvh~~g~~-v~~~SR----~g~d~t~~~p~l~~~~~~~~~--~~~~ILDGE~v~~d~~~~------- 311 (702)
.|++|+|+||.-+.+++.+|. ++..|| -|.|+|+....+.. +...+. +..+.+=||++.-...-.
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 499999999999999998776 688999 56778753222211 111111 357788899986211000
Q ss_pred --ccccccchHHHH-HHhhcC---CCCCCceEEEEEEEeeeCCccccCCCHHHHHHHHHhhccCCCCcccccccCCCCCc
Q 005331 312 --RFAEFGSNQEIA-KAARDG---LSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNS 385 (702)
Q Consensus 312 --~~~~F~~lq~~~-~~~r~~---~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~~~~~~~~p~~~~~~ 385 (702)
.-.+|..-+..+ ...+.. .....++.|++|++.+.+| +..-....++.+.|.++-=++...
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 001222222221 111111 0123689999999999887 333446788888888753222110
Q ss_pred cccCCCCCccccccCCHHHHHHHHHHHHHC------CCceEEEecCCCCccc--C--CCCCCe
Q 005331 386 HVRPQGEPCWSLVAHNVDEVEKFFKETIEN------RDEGIVLKDLGSKWEP--G--DRSGKW 438 (702)
Q Consensus 386 ~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~------g~EGlV~K~~ds~Y~~--G--~Rs~~W 438 (702)
...+.+.+++.++++...+. .-.|||+|--+-.+.. | .+++.|
T Consensus 254 ----------~~~~~~~~~v~~~~~~~~~~R~~l~y~iDGiVikvn~~~~~~~LG~t~~~Prw 306 (315)
T PF01653_consen 254 ----------IRFCKSIEEVEEYIEEWEERREELPYPIDGIVIKVNDLALQERLGYTSKHPRW 306 (315)
T ss_dssp ----------EEEESSHHHHHHHHHHHHHHGCCSSS-EEEEEEEESBHHHHHHH-BESSSBSS
T ss_pred ----------eEecCCHHHHHHHHHHHHhhhhccccccCcEEEEecCHHHHHhcCCcCCCCCe
Confidence 22356889999988887653 5579999976554433 2 345667
No 60
>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=97.03 E-value=0.0015 Score=52.55 Aligned_cols=44 Identities=18% Similarity=0.394 Sum_probs=38.2
Q ss_pred CcEEEEEeCCCCCCHHHHHHHHHHcCCEEEEecCCCeeEEEecC
Q 005331 659 DMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVANH 702 (702)
Q Consensus 659 g~~f~v~~~~~~~~k~~l~~~i~~~gG~~~~n~~~~~~~~i~~~ 702 (702)
|+.||+.......++++|+++|.++||+++......+||+|+.+
T Consensus 1 ~~~~~i~g~~~~~~~~~l~~~i~~~Gg~v~~~~~~~~thvI~~~ 44 (72)
T cd00027 1 GLTFVITGDLPSEERDELKELIEKLGGKVTSSVSKKTTHVIVGS 44 (72)
T ss_pred CCEEEEEecCCCcCHHHHHHHHHHcCCEEeccccCCceEEEECC
Confidence 57888887665789999999999999999999887799999863
No 61
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=96.99 E-value=0.0084 Score=70.54 Aligned_cols=196 Identities=17% Similarity=0.171 Sum_probs=110.5
Q ss_pred ceEEEEecceEEEEEEEeCCE-EEEEeC----CCCCCCcchhhHHHHHHhhcc-ccceeeeceEEEeeCCCC-----ccc
Q 005331 246 EVVIECKFDGDRIQIHKNGSE-IHYFSR----SFLDHSEYGHAMSKIIEQNVL-VDRCILDGEMLVWDTSLN-----RFA 314 (702)
Q Consensus 246 ~~~~E~K~DG~R~qvh~~g~~-v~~~SR----~g~d~t~~~p~l~~~~~~~~~-~~~~ILDGE~v~~d~~~~-----~~~ 314 (702)
+|++|+|+||.-+.+.+.+|. ++..|| .|.|+|+-...+.. +...+. ...+.+-||++.-...-. .-.
T Consensus 111 ~~~~epKiDGlaisL~YenG~L~~a~TRGDG~~GEDVT~n~~~I~~-IP~~l~~~~~levRGEv~m~~~~F~~lN~~~~~ 189 (669)
T PRK14350 111 GISVEPKIDGCSIVLYYKDGILEKALTRGDGRFGNDVTENVRTIRN-VPLFIDEKVELVLRGEIYITKENFLKINKTLEK 189 (669)
T ss_pred eEEEEEecccEEEEEEEECCEEEEEEecCCCCcchhHhhhhhhhcc-cchhcCCCceEEEEEEEEeeHHHHHHHHHhhhc
Confidence 599999999999999887665 688999 68888863222111 111111 245788999987321100 012
Q ss_pred cccchHHHH-HHhhc---CCCCCCceEEEEEEEeeeCCccccCCCHHHHHHHHHhhccCCCCcccccccCCCCCccccCC
Q 005331 315 EFGSNQEIA-KAARD---GLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQ 390 (702)
Q Consensus 315 ~F~~lq~~~-~~~r~---~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~~~~~~~~p~~~~~~~v~~~ 390 (702)
+|..-+..+ ...|. ......++.|++|++...++ ...+..++.+.|.++-=+.......
T Consensus 190 ~faNpRNaaAGsLr~~d~~~~a~r~L~f~~y~~~~~~~---~~~t~~e~l~~L~~~GF~v~~~~~~-------------- 252 (669)
T PRK14350 190 PYTNARNLASGILRRIDSREVANFPLDIFVYDILYSSL---ELKTNHDAFDKLKKFGFKVNPFCRF-------------- 252 (669)
T ss_pred cCCChhHHHHHHHHccCchhhhcCceEEEEEEcccCCC---CCCCHHHHHHHHHHCCCCCCcceEE--------------
Confidence 343322221 11111 11124589999999853222 1236778888888763222111000
Q ss_pred CCCccccccCCHHHHHHHHHHHHH------CCCceEEEecCCCCccc--C--CCCCCe---EEEccccccCCCcceEEEE
Q 005331 391 GEPCWSLVAHNVDEVEKFFKETIE------NRDEGIVLKDLGSKWEP--G--DRSGKW---LKLKPEYIRAGSDLDVLII 457 (702)
Q Consensus 391 ~~~~~~~~~~~~~~i~~~~~~ai~------~g~EGlV~K~~ds~Y~~--G--~Rs~~W---lKvK~~y~~~g~~~DlvVI 457 (702)
.....+.+++.++++++.. -.-.|||+|--+-.+.. | .+.+.| +|+.++ +..-.|.
T Consensus 253 -----~~~~~~~~e~~~~~~~~~~~R~~l~y~iDGiViKvn~~~~q~~lG~ts~~PrWaiA~Kf~~~------~~~T~l~ 321 (669)
T PRK14350 253 -----FDGKNSIEEILNYVKDIEKKRNSFEYEIDGVVLKVSDFALREILGYTSHHPKWSMAYKFESL------SGFSKVN 321 (669)
T ss_pred -----EcCCCcHHHHHHHHHHHHHHHhcCCCCCCcEEEEecCHHHHHhcCCcCCCCCceEEEcCCCc------eeEEEEE
Confidence 0011236777777765533 45689999975543322 2 356788 566664 4555777
Q ss_pred EEEecCCCCCCccc
Q 005331 458 GGYYGSGRRGGEVA 471 (702)
Q Consensus 458 G~~~G~G~r~g~~g 471 (702)
+-.|..|| .|.+.
T Consensus 322 ~I~~qVGR-TG~iT 334 (669)
T PRK14350 322 DIVVQVGR-SGKIT 334 (669)
T ss_pred EEEEecCC-ceeee
Confidence 77777765 44443
No 62
>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=96.96 E-value=0.012 Score=63.04 Aligned_cols=106 Identities=16% Similarity=0.110 Sum_probs=64.6
Q ss_pred cCCCceEEEEecceEEEEEEEeCC-EEEEEeCCCCCCC-----c---chhhHHHHHH-------hh--ccccceeeeceE
Q 005331 242 LHGKEVVIECKFDGDRIQIHKNGS-EIHYFSRSFLDHS-----E---YGHAMSKIIE-------QN--VLVDRCILDGEM 303 (702)
Q Consensus 242 ~~~~~~~~E~K~DG~R~qvh~~g~-~v~~~SR~g~d~t-----~---~~p~l~~~~~-------~~--~~~~~~ILDGE~ 303 (702)
+.+.+|.+.+|.||...-+.++++ .+++.||++.-.. . ..+.+...+. .. ....++++=||+
T Consensus 22 l~~~ewvatEKlhGaNfsi~~~~~~~i~~akR~~~l~~~e~f~G~~~i~~~l~~~~~~l~~~l~~~~~~~~~~v~IyGEl 101 (325)
T TIGR02307 22 LGLTEWVAREKIHGTNFSIIIERDFKVTCAKRTGIILPNEDFFGYHILIKNYTASVKAIQDILETKAIIVVVSVQVFGEL 101 (325)
T ss_pred cCCceEEEEEEecCcceEEEEeCCceEEEeecccccCcccccccHHHHHHHHHHHHHHHHHHHhhhcccccceEEEEEEe
Confidence 445689999999999998888877 8999999965321 1 1122221111 10 123678999999
Q ss_pred EEeeCCCCccccccchHHHHHHhhcCCCCCCceEEEEEEEeeeCCccccCCCHHHHHHHHHhh
Q 005331 304 LVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKV 366 (702)
Q Consensus 304 v~~d~~~~~~~~F~~lq~~~~~~r~~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~ 366 (702)
+.|.-..+.. +. ...|++|||..-...+-.-+++.+-.+.....
T Consensus 102 ~G~~~q~~~~----------------Y~---~~~fyaFdI~~~~~~~~~~L~~d~~~e~~~~~ 145 (325)
T TIGR02307 102 AGPGYQKPVV----------------YS---DKDFYAFDIKYTETSDDVTLVDDYMMESFCNV 145 (325)
T ss_pred ecCcccCccc----------------cc---cccEEEEEEEEeccCcceEecHHHHHHHHHHc
Confidence 9864211100 11 35799999955312123456676666666554
No 63
>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=96.93 E-value=0.0018 Score=64.10 Aligned_cols=106 Identities=23% Similarity=0.344 Sum_probs=61.8
Q ss_pred ceEEEEecceEEEEEEEe-CCEEEEEeCCCC-----CCCcc------hhhHH---HHHHh-h-----ccccceeeeceEE
Q 005331 246 EVVIECKFDGDRIQIHKN-GSEIHYFSRSFL-----DHSEY------GHAMS---KIIEQ-N-----VLVDRCILDGEML 304 (702)
Q Consensus 246 ~~~~E~K~DG~R~qvh~~-g~~v~~~SR~g~-----d~t~~------~p~l~---~~~~~-~-----~~~~~~ILDGE~v 304 (702)
+|++++|+||.-+.+... ++.+++.+|++. ++... +.... ..+.. . ....++++=||++
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 699999999999998875 445999999982 11111 11111 01111 1 1356889999999
Q ss_pred EeeCCCCccccccchHHHHHHhhcCCCCCCceEEEEEEEeeeCCc-cccCCCHHHHHHHHHhh
Q 005331 305 VWDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDT-SVIHQSLKERHELLQKV 366 (702)
Q Consensus 305 ~~d~~~~~~~~F~~lq~~~~~~r~~~~~~~~~~~~vFDiL~lng~-~l~~~pl~eRr~~L~~~ 366 (702)
.|-+.-.. ... + ...+..|++|||...+.. ...-++..+.+.+++.+
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 012578999999988532 22445778888888765
No 64
>PRK01109 ATP-dependent DNA ligase; Provisional
Probab=96.92 E-value=0.0038 Score=72.95 Aligned_cols=97 Identities=14% Similarity=0.112 Sum_probs=79.8
Q ss_pred CCCCcHHHHHHHHHHHHhcC---ChhHHHHHHHHHhhhcCCCchHhhhHhhcCCCCCCCccccCCCHHHHHHHHHHHhCC
Q 005331 4 TEETEVIVLVSLFNWIQKTK---PAAKKRSKFRKFLDTYCDSVDYFSALRLILPSLDRERGSYGLKESVLANCLIDALGM 80 (702)
Q Consensus 4 ~~~~~F~~l~~~~e~i~~~~---~~~~k~~~l~~~l~~~~~~~~~~~~lrLllp~~d~~r~~ygike~~L~k~~~~~~~l 80 (702)
.++++|.++++.|++|++++ ++.+|..+|.++|.+. .+.+...++||++-.+. .|++++++.++|+.+++.
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 7789999999999986 67889999999999882 899999999999999983
Q ss_pred CcChHHHHHHhhhhcCCCCCCCCCHHHHHHHHhh
Q 005331 81 SKDSADAVRLINWRKGGAAPNAGNFPMVAAEVLQ 114 (702)
Q Consensus 81 ~~~s~~~~~L~~wk~~~~~~~~gD~~~~~~~v~~ 114 (702)
.....+..++.+ ..||++.+|..+..
T Consensus 186 ~~~~~~ve~~y~--------~~~Dlg~va~~l~~ 211 (590)
T PRK01109 186 AVARELVERAYN--------LRADLGYIAKILAE 211 (590)
T ss_pred ccchHHHHHHHH--------hCCCHHHHHHHHHh
Confidence 223344444443 47999999887653
No 65
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=95.85 E-value=0.2 Score=58.22 Aligned_cols=176 Identities=20% Similarity=0.303 Sum_probs=108.5
Q ss_pred CceEEEEecceEEEEEEEeCCE-EEEEeCC----CCCCCcchhhHHHHHHhhc--cccceeeeceEEEeeCCC-------
Q 005331 245 KEVVIECKFDGDRIQIHKNGSE-IHYFSRS----FLDHSEYGHAMSKIIEQNV--LVDRCILDGEMLVWDTSL------- 310 (702)
Q Consensus 245 ~~~~~E~K~DG~R~qvh~~g~~-v~~~SR~----g~d~t~~~p~l~~~~~~~~--~~~~~ILDGE~v~~d~~~------- 310 (702)
..|++|+|.||.-+-+.+.+|. ++--||. |+|+|.-...+.. +...+ .+..+-+=||++.--..-
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 4799999999999988887665 6777875 6788864444432 11122 255678899998731100
Q ss_pred --CccccccchHHHH-HHhhc---CCCCCCceEEEEEEEeeeCCccccCCCHHHHHHHHHhhccCCCCcccccccCCCCC
Q 005331 311 --NRFAEFGSNQEIA-KAARD---GLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLN 384 (702)
Q Consensus 311 --~~~~~F~~lq~~~-~~~r~---~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~~~~~~~~p~~~~~ 384 (702)
..-.+|..-+..+ ...|. .....+++.++++.+-...+. ..-.+..++.+.|.++-=+...
T Consensus 188 ~~~g~~~faNpRNaAAGsLRqlD~~ita~R~L~~f~y~~~~~~~~-~~~~t~~e~l~~L~~~GF~v~~------------ 254 (667)
T COG0272 188 EEEGEKPFANPRNAAAGSLRQLDPKITAKRKLGFFIYAVGDGEEG-LLADTQSERLAFLKAWGFPVNP------------ 254 (667)
T ss_pred HHhCCCCcCChhhhhhhhhhccCHHHHhcCCceEEEEeCCccCCC-CCccCHHHHHHHHHHcCCCCCc------------
Confidence 0002222211111 11110 011346899999998866554 5566788999999886433221
Q ss_pred ccccCCCCCccccccCCHHHHHHHHHHHHHC------CCceEEEecCCCCccc--C--CCCCCe---EEEccc
Q 005331 385 SHVRPQGEPCWSLVAHNVDEVEKFFKETIEN------RDEGIVLKDLGSKWEP--G--DRSGKW---LKLKPE 444 (702)
Q Consensus 385 ~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~------g~EGlV~K~~ds~Y~~--G--~Rs~~W---lKvK~~ 444 (702)
....+.+.+++.++++..... --.|+|+|--+-.... | .|++.| +|+.++
T Consensus 255 ----------~~~~~~~~~ev~~~~~~~~~~R~~L~y~IDGvViKvn~l~~q~~lG~tsk~PrWAiAyKFpa~ 317 (667)
T COG0272 255 ----------YTRLCKNADEVLAFYEEWEKKRASLPYDIDGVVIKVNDLALQRELGFTSKAPRWAIAYKFPAE 317 (667)
T ss_pred ----------HhhhcCCHHHHHHHHHHHHhhcccCCCccceEEEEeccHHHHHHhCCccCCCceeeeecCCch
Confidence 123467899999999988774 4579999965432211 2 367889 688776
No 66
>PHA02142 putative RNA ligase
Probab=95.73 E-value=0.19 Score=54.78 Aligned_cols=104 Identities=15% Similarity=0.158 Sum_probs=65.3
Q ss_pred cCCCceEEEEecceEEEEEEEe---------------------CCEEEEEeCCCC-CCC--cchhhH------HHHHHhh
Q 005331 242 LHGKEVVIECKFDGDRIQIHKN---------------------GSEIHYFSRSFL-DHS--EYGHAM------SKIIEQN 291 (702)
Q Consensus 242 ~~~~~~~~E~K~DG~R~qvh~~---------------------g~~v~~~SR~g~-d~t--~~~p~l------~~~~~~~ 291 (702)
..+..|.+-+|+||.-|.+.+. .+++...|||.. ++. ..+-.+ .+.+.+
T Consensus 166 ~~~~~f~~TeKLDGsS~tvy~~~~~~~~~~~~~~~~~~~~~~~~~~~gv~srn~~l~~~~~~~~W~~a~~~~i~~~l~~- 244 (366)
T PHA02142 166 YADVKFAKSLKLDGSSITMAWVTDPDLFLDLGTEDEPYAHDYDDAQFIVASRNQVLRYNADSKWWKGVENYQIVDRLKE- 244 (366)
T ss_pred hcCceEEEEEEecceeEEEEEecCCcccccccccccccccccCCCceeEeeccccccccCCchHHHHHHHcCcHHHHHh-
Confidence 4467799999999999988732 567788899875 221 111111 112211
Q ss_pred ccccceeeeceEEEeeCCCCccccccchHHHHHHhhcCCCCCCceEEEEEEEeeeCCccccCCCHHHHHHHHHhhc
Q 005331 292 VLVDRCILDGEMLVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVV 367 (702)
Q Consensus 292 ~~~~~~ILDGE~v~~d~~~~~~~~F~~lq~~~~~~r~~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~ 367 (702)
...++.+=||++.-.-.++. ..-....|++|||-.+++.. =+++.++.++++++-
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 13578899999972211111 00112479999998777654 568899999888763
No 67
>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=94.43 E-value=0.53 Score=51.10 Aligned_cols=104 Identities=17% Similarity=0.179 Sum_probs=58.7
Q ss_pred CCceEEEEecceEEEEEEEeCC--EE-----EEEeCCCCCC---Cc-ch-----hhHHHHHHhhccccceeeeceEEEee
Q 005331 244 GKEVVIECKFDGDRIQIHKNGS--EI-----HYFSRSFLDH---SE-YG-----HAMSKIIEQNVLVDRCILDGEMLVWD 307 (702)
Q Consensus 244 ~~~~~~E~K~DG~R~qvh~~g~--~v-----~~~SR~g~d~---t~-~~-----p~l~~~~~~~~~~~~~ILDGE~v~~d 307 (702)
+..|.+-+|+||.-|.+.+..+ .+ -+-|||..-. +. |. ..+.+.+.+.....++.+=||++.-.
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 5689999999999998876332 22 2447876521 11 11 12233332222345788999998722
Q ss_pred CCCCccccccchHHHHHHhhcCCCCCCceEEEEEEEeeeCCccccCCCHHHHHHHHHhh
Q 005331 308 TSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKV 366 (702)
Q Consensus 308 ~~~~~~~~F~~lq~~~~~~r~~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~ 366 (702)
-.++. +..+.+-.|++|++ +.+|.. .=+++.++.++++++
T Consensus 238 IQ~n~-----------------Yg~~~~~~~f~F~v-~~~~~~-ryld~~~~~~~~~~~ 277 (341)
T TIGR02306 238 IQKNR-----------------YGFDKYRTVFAFRA-FFDGEQ-RFLTDEDFQDLCLTL 277 (341)
T ss_pred ccCCc-----------------CCCCCCceEEEEEE-EEcCcc-eecCHHHHHHHHHhc
Confidence 11110 11112222788887 555543 345889999888875
No 68
>KOG3132 consensus m3G-cap-specific nuclear import receptor (Snurportin1) [RNA processing and modification]
Probab=94.19 E-value=0.35 Score=48.99 Aligned_cols=173 Identities=13% Similarity=0.128 Sum_probs=111.6
Q ss_pred ccccccccCChHHHHHHcCCCceEEEEecceEEEEEEEeCCEEEEEeCCCCCCCcchhhHHHH-HHhhcc-ccceeeece
Q 005331 225 RPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKI-IEQNVL-VDRCILDGE 302 (702)
Q Consensus 225 ~PmLA~~~~~~~~~~~~~~~~~~~~E~K~DG~R~qvh~~g~~v~~~SR~g~d~t~~~p~l~~~-~~~~~~-~~~~ILDGE 302 (702)
+-||.+-+-++++. + +.+|++=.-=-|-||+|.-..|....|.|+|..+. .||..... -.++.. ..=.|||+
T Consensus 100 qlMLsEWliDvP~~---L-sqdW~vv~~PvGKR~lvVaSrG~Tvay~k~G~~v~-rF~S~LPGGnrr~~~a~~ytILDC- 173 (325)
T KOG3132|consen 100 QLMLSEWLIDVPDN---L-SQDWYVVARPVGKRCLVVASRGTTVAYVKNGSTVH-RFPSALPGGNRRKGPANSYTILDC- 173 (325)
T ss_pred HhhhHHHhccCccc---c-CcceEEEEeecCceEEEEecCCceEEEecCCeeEe-eccccCCCCCcCCCCcccceeeee-
Confidence 34666554444332 2 46799988899999999888888889999998764 23331110 001111 12247775
Q ss_pred EEEeeCCCCccccccchHHHHHHhhcCCCCCCceEEEEEEEeeeCCccccCCCHHHHHHHHHhhccCCCCcccccccCCC
Q 005331 303 MLVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHG 382 (702)
Q Consensus 303 ~v~~d~~~~~~~~F~~lq~~~~~~r~~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~~~~~~~~p~~~ 382 (702)
+|+. ..-.|+|.|++..+|.++.+.|+.-|.-.|++-+.+.++-- .|.-.
T Consensus 174 --Iy~e-------------------------snQTYYVlD~~cWrgh~~yec~~dFRffwl~SKL~E~~~l~---~~t~~ 223 (325)
T KOG3132|consen 174 --IYHE-------------------------SNQTYYVLDMVCWRGHSLYECTSDFRFFWLQSKLAETGALD---PPTVY 223 (325)
T ss_pred --eecc-------------------------cCceEEEEEEEeecCcccccCchHHHHHHHhhhccccccCC---CCCcC
Confidence 2321 12269999999999999999999999999998776654210 01000
Q ss_pred CC--ccccCCCCCccccccCCHHHHHHHHHHHHHCCCceEEEecCCCCcccCCC-CCCeEE
Q 005331 383 LN--SHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDR-SGKWLK 440 (702)
Q Consensus 383 ~~--~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EGlV~K~~ds~Y~~G~R-s~~WlK 440 (702)
-. +.+.| .+ ..+.+.+-+++.-.+.-...||.+-...-.|.||.- =-+|+|
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 00 11111 12 236777788888778888899999999999999963 236864
No 69
>PRK09247 ATP-dependent DNA ligase; Validated
Probab=89.42 E-value=0.55 Score=54.49 Aligned_cols=82 Identities=17% Similarity=0.261 Sum_probs=69.7
Q ss_pred HHHHHHHHHHHhhhchHhHHHHHHHHHHhCCHHHHHHHHHHHhhhhc-cCcccccccccc----Cc---CHHHHHhhhCC
Q 005331 127 KELNDLLDRLASSENRAEKISVLSTLIKKTNAQEMKWIIMIILKDLK-LGISEKSIFHEF----HP---DAEDLFNVTCD 198 (702)
Q Consensus 127 ~eVn~~Ld~La~~~~~~~k~~~l~~ll~~~t~~E~k~l~RiIlk~lr-iG~~e~~il~~~----hp---da~~~~~~~~d 198 (702)
.+.-+++++|+..+++.+|.++|..+|...++.+.-|.+++++..+. .|++++.+.+++ .. ...+.|+-..|
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 45677889999999999999999999999999999999999999885 999999988755 21 24556788899
Q ss_pred HHHHHHHHhh
Q 005331 199 LKLVCEKLKD 208 (702)
Q Consensus 199 L~~V~~~L~~ 208 (702)
|+.||..+..
T Consensus 82 lg~~~~~~~~ 91 (539)
T PRK09247 82 LAETIALLLP 91 (539)
T ss_pred HHHHHHHhcc
Confidence 9999988864
No 70
>PF12738 PTCB-BRCT: twin BRCT domain; PDB: 3PA6_A 3KTF_C 2WT8_C 3EF1_A 3EF0_A.
Probab=89.20 E-value=0.41 Score=38.41 Aligned_cols=30 Identities=27% Similarity=0.510 Sum_probs=25.5
Q ss_pred CHHHHHHHHHHcCCEEEEecCCCeeEEEec
Q 005331 672 SLDSLHKMVVENGGTFSMNLNNSVTHCVAN 701 (702)
Q Consensus 672 ~k~~l~~~i~~~gG~~~~n~~~~~~~~i~~ 701 (702)
.+++|.++|..+||++..+....+||.|+.
T Consensus 12 ~~~~l~~~i~~~Gg~~~~~lt~~~THLI~~ 41 (63)
T PF12738_consen 12 ERSQLRKLIEALGGKYSKDLTKKTTHLICS 41 (63)
T ss_dssp TCCHHHHHHHCTT-EEESSSSTT-SEEEEE
T ss_pred HHHHHHHHHHHCCCEEeccccCCceEEEEe
Confidence 378999999999999999998889999984
No 71
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=86.51 E-value=1.1 Score=48.24 Aligned_cols=49 Identities=22% Similarity=0.257 Sum_probs=40.7
Q ss_pred cccccCCcEEEEEeCCCCCCHHHHHHHHHHcCCEEEEecCCCeeEEEec
Q 005331 653 ETSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAN 701 (702)
Q Consensus 653 ~s~~f~g~~f~v~~~~~~~~k~~l~~~i~~~gG~~~~n~~~~~~~~i~~ 701 (702)
.+..|.|+.||+--.-..+++.+++++|+++||++..+.+...++.|+.
T Consensus 217 ~~~~l~g~~~vfTG~l~~~~R~~~~~~~~~~Gg~v~~sVs~~t~~lV~G 265 (309)
T PRK06195 217 GFTAFKEEVVVFTGGLASMTRDEAMILVRRLGGTVGSSVTKKTTYLVTN 265 (309)
T ss_pred CCccccCCEEEEccccCCCCHHHHHHHHHHhCCEecCCcccCceEEEEC
Confidence 4567999999876555678999999999999999999988867777764
No 72
>KOG2386 consensus mRNA capping enzyme, guanylyltransferase (alpha) subunit [RNA processing and modification]
Probab=86.27 E-value=0.42 Score=52.44 Aligned_cols=98 Identities=18% Similarity=0.295 Sum_probs=63.1
Q ss_pred CceEEEEecceEEEEEEEeCCE-EEEEeCCCCCCC---cchhhHHHHHHhhccccceeeeceEEEeeCCCCccccccchH
Q 005331 245 KEVVIECKFDGDRIQIHKNGSE-IHYFSRSFLDHS---EYGHAMSKIIEQNVLVDRCILDGEMLVWDTSLNRFAEFGSNQ 320 (702)
Q Consensus 245 ~~~~~E~K~DG~R~qvh~~g~~-v~~~SR~g~d~t---~~~p~l~~~~~~~~~~~~~ILDGE~v~~d~~~~~~~~F~~lq 320 (702)
..|.+.+|.||.|..+-.+++. +..+-|.-...- -+++.-.. ........++||||+. |..+.
T Consensus 285 ~~y~~~We~dg~~~~~L~~~~~~~~~~dR~~~~~~~~~~~~~~~~~---~~~~~~~tl~dge~~l-D~l~~--------- 351 (393)
T KOG2386|consen 285 EYYEASWEADGTRYMMLIDGDGEYYDFDRWRFVKGRENLRKIREDS---DTKVLHQTLLDGEMIL-DRLKE--------- 351 (393)
T ss_pred hhhhhhhcccCcEEEEEecCCceeEechhhhHHHhhhhhhcccccc---cchhhhhhhcccceec-ccccc---------
Confidence 3467899999999998887755 555554332111 01110000 0011346789999998 64321
Q ss_pred HHHHHhhcCCCCCCceEEEEEEEeeeCCccccCCCHHHHHHHHHh-hcc
Q 005331 321 EIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQK-VVK 368 (702)
Q Consensus 321 ~~~~~~r~~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~-~~~ 368 (702)
...+.|.++|++-+|++.+...|+. |.+.+++ ++.
T Consensus 352 ------------~~~~r~l~Yd~~r~n~~~v~~~~f~-r~~~~~~evi~ 387 (393)
T KOG2386|consen 352 ------------EAIPRYLIYDMVRFNSQKVEKRPFS-RWQIIEKEVID 387 (393)
T ss_pred ------------ccchhheeeeeeeccCcccccCcch-HHHHHHHHhcC
Confidence 1135699999999999999999999 8886654 443
No 73
>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=84.96 E-value=0.81 Score=44.80 Aligned_cols=85 Identities=24% Similarity=0.418 Sum_probs=61.1
Q ss_pred CHHHHHHHHHHHHhhhchHhHHHHHHHHHHhCCHHHHHHHHHHHhhhh-------ccCcccccccccc----Cc---CHH
Q 005331 125 TIKELNDLLDRLASSENRAEKISVLSTLIKKTNAQEMKWIIMIILKDL-------KLGISEKSIFHEF----HP---DAE 190 (702)
Q Consensus 125 Ti~eVn~~Ld~La~~~~~~~k~~~l~~ll~~~t~~E~k~l~RiIlk~l-------riG~~e~~il~~~----hp---da~ 190 (702)
+-.++-++|++|+..+++.+|..+|+.++....+.+..|.+..+++-+ ..|++++++.+++ +- ...
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 346777899999999999999999999999988777888888888844 5899999887644 42 244
Q ss_pred HHHhhhCCHHHHHHHHhhh
Q 005331 191 DLFNVTCDLKLVCEKLKDR 209 (702)
Q Consensus 191 ~~~~~~~dL~~V~~~L~~~ 209 (702)
+.|.-..|++.|+..+...
T Consensus 82 ~~~~~~GD~g~~~~~~~~~ 100 (177)
T PF04675_consen 82 ESYKKVGDLGEVAEEVLQK 100 (177)
T ss_dssp HHHHHHS-HHHHHHHHHHH
T ss_pred HHHHhcCcHHHHHHHHHhh
Confidence 5677899999999988753
No 74
>COG5275 BRCT domain type II [General function prediction only]
Probab=84.53 E-value=2 Score=42.99 Aligned_cols=54 Identities=22% Similarity=0.238 Sum_probs=45.3
Q ss_pred CccccccccCCcEEEEEeCCCCCCHHHHHHHHHHcCCEEEEecCCCeeEEEecC
Q 005331 649 DIKGETSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVANH 702 (702)
Q Consensus 649 ~~~~~s~~f~g~~f~v~~~~~~~~k~~l~~~i~~~gG~~~~n~~~~~~~~i~~~ 702 (702)
....+++.+.|+.|++--.-..++.++-+.+|+.+||++..-|....+|+|+.+
T Consensus 149 ~peg~~~cL~G~~fVfTG~l~TlsR~~a~~lvk~yGgrvT~~pSskTtflvlGd 202 (276)
T COG5275 149 VPEGERECLKGKVFVFTGDLKTLSRDDAKTLVKVYGGRVTAVPSSKTTFLVLGD 202 (276)
T ss_pred CCCCCcccccccEEEEecccccccchhHHHHHHHhCCeeecccccceeEEEecC
Confidence 334678999999987766667789999999999999999999988788888764
No 75
>PRK03180 ligB ATP-dependent DNA ligase; Reviewed
Probab=83.86 E-value=6.5 Score=45.38 Aligned_cols=93 Identities=20% Similarity=0.236 Sum_probs=72.6
Q ss_pred CCcHHHHHHHHHHHHhcC---ChhHHHHHHHHHhhhcCCCchHhhhHhhcCCCCCCCccccCCCHHHHHHHHHHHhCCCc
Q 005331 6 ETEVIVLVSLFNWIQKTK---PAAKKRSKFRKFLDTYCDSVDYFSALRLILPSLDRERGSYGLKESVLANCLIDALGMSK 82 (702)
Q Consensus 6 ~~~F~~l~~~~e~i~~~~---~~~~k~~~l~~~l~~~~~~~~~~~~lrLllp~~d~~r~~ygike~~L~k~~~~~~~l~~ 82 (702)
+.+-.++-+.|++|.+.+ +..+|..+|..++.+. .+.+..-++|+|+-.+. .|+++.++..+++.+++++.
T Consensus 72 ~ltl~~V~~~l~~ia~~~g~~s~~~k~~~l~~ll~~~-~~~E~~~l~r~i~~~lR-----iGv~~~~v~~Ala~a~~~~~ 145 (508)
T PRK03180 72 TLTVADVDAALSEIAAVAGAGSQARRAALLAALFAAA-TEDEQRFLRRLLTGELR-----QGALDGVMADAVARAAGVPA 145 (508)
T ss_pred CCcHHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHhC-CHHHHHHHHHHHhCCCc-----ccccHHHHHHHHHHHhCCCH
Confidence 466777778999988875 4478889999999985 57788889999999883 89999999999999998764
Q ss_pred ChHHHHHHhhhhcCCCCCCCCCHHHHHHHHhh
Q 005331 83 DSADAVRLINWRKGGAAPNAGNFPMVAAEVLQ 114 (702)
Q Consensus 83 ~s~~~~~L~~wk~~~~~~~~gD~~~~~~~v~~ 114 (702)
. +..+..+| .+|++.++...+.
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 5899988876553
No 76
>PLN03122 Poly [ADP-ribose] polymerase; Provisional
Probab=78.16 E-value=3.8 Score=49.52 Aligned_cols=47 Identities=19% Similarity=0.237 Sum_probs=37.9
Q ss_pred cccccCCcEEEEEeCCCCCCHHHHHHHHHHcCCEEEEecCCCeeEEEec
Q 005331 653 ETSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAN 701 (702)
Q Consensus 653 ~s~~f~g~~f~v~~~~~~~~k~~l~~~i~~~gG~~~~n~~~~~~~~i~~ 701 (702)
....|.|+.|||.-.-.. +++++.++|.++||+++-.... .||||++
T Consensus 186 ~~kpL~G~~fviTGtl~~-sr~elK~~Ie~~GGkvsssVs~-~T~lIvt 232 (815)
T PLN03122 186 PGKPFSGMMISLSGRLSR-THQYWKKDIEKHGGKVANSVEG-VTCLVVS 232 (815)
T ss_pred cCCCcCCcEEEEeCCCCC-CHHHHHHHHHHcCCEEcccccc-ceEEEEc
Confidence 445699999887643333 8999999999999999988854 8999975
No 77
>PLN03113 DNA ligase 1; Provisional
Probab=76.52 E-value=5 Score=48.23 Aligned_cols=86 Identities=13% Similarity=0.291 Sum_probs=72.1
Q ss_pred CCCCHHHHHHHHHHHHhhhchHhHHHHHHHHHHhC---CHHHHHHHHHHHhhhhc-------cCcccccccccc----Cc
Q 005331 122 GGLTIKELNDLLDRLASSENRAEKISVLSTLIKKT---NAQEMKWIIMIILKDLK-------LGISEKSIFHEF----HP 187 (702)
Q Consensus 122 ~~lTi~eVn~~Ld~La~~~~~~~k~~~l~~ll~~~---t~~E~k~l~RiIlk~lr-------iG~~e~~il~~~----hp 187 (702)
.++.-.++-+.++.|...+++.++..+|..+|... +|.+.-|.+.++.+.+- +|++++.+.+++ ..
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 46788999999999999999999999999999985 99999999999887664 699999988765 21
Q ss_pred ---CHHHHHhhhCCHHHHHHHHh
Q 005331 188 ---DAEDLFNVTCDLKLVCEKLK 207 (702)
Q Consensus 188 ---da~~~~~~~~dL~~V~~~L~ 207 (702)
.....|.-..||+.|+..+.
T Consensus 207 ~~~~ik~~y~~~GDlG~vA~~~~ 229 (744)
T PLN03113 207 TEKQVKKQYKELGDLGLVAKASR 229 (744)
T ss_pred CHHHHHHHHHHhCCHHHHHHhhh
Confidence 24556788899999998665
No 78
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=76.06 E-value=4.5 Score=43.70 Aligned_cols=47 Identities=13% Similarity=0.220 Sum_probs=38.7
Q ss_pred ccccCCcEEEEEeCCCCCCHHHHHHHHHHcCCEEEEecCCCeeEEEec
Q 005331 654 TSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAN 701 (702)
Q Consensus 654 s~~f~g~~f~v~~~~~~~~k~~l~~~i~~~gG~~~~n~~~~~~~~i~~ 701 (702)
..+|.|+.||+- |.-.++++|++++|.++||++.-+.+...+++|++
T Consensus 230 ~~l~~g~~~v~T-G~l~~~R~e~~~~~~~~G~~v~~sVs~~t~~lv~g 276 (313)
T PRK06063 230 RPLVQGMRVALS-AEVSRTHEELVERILHAGLAYSDSVDRDTSLVVCN 276 (313)
T ss_pred CcccCCCEEEEe-cCCCCCHHHHHHHHHHcCCEecCccccCccEEEEC
Confidence 568999998764 33336999999999999999999988877888875
No 79
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=74.93 E-value=2.6 Score=49.38 Aligned_cols=40 Identities=25% Similarity=0.361 Sum_probs=36.1
Q ss_pred ccccCCcEEEEEeCCCCCCHHHHHHHHHHcCCEEEEecCC
Q 005331 654 TSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNN 693 (702)
Q Consensus 654 s~~f~g~~f~v~~~~~~~~k~~l~~~i~~~gG~~~~n~~~ 693 (702)
-.||+|++||++..-....+++|.++|+..||++.+-++.
T Consensus 585 ~kLf~gl~~~~~g~fs~~p~~~l~~l~~~~gg~~l~~~~~ 624 (684)
T KOG4362|consen 585 PKLFEGLKFYFVGDFSNPPKEQLQELVHLAGGTILQVPRV 624 (684)
T ss_pred cchhcCCcceeecccccCcHHHHHHHHhhcCcceeeccCc
Confidence 4699999999999888889999999999999999988643
No 80
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=74.75 E-value=4.6 Score=48.19 Aligned_cols=48 Identities=15% Similarity=0.306 Sum_probs=40.0
Q ss_pred ccccCCcEEEEEeCCCCCCHHHHHHHHHHcCCEEEEecCCCeeEEEec
Q 005331 654 TSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAN 701 (702)
Q Consensus 654 s~~f~g~~f~v~~~~~~~~k~~l~~~i~~~gG~~~~n~~~~~~~~i~~ 701 (702)
...|.|+.|||--.-..+++++++++|.++||++..+.+...++.|+.
T Consensus 607 ~~~l~g~~~v~TG~l~~~~R~~~~~~i~~~Gg~v~~sVs~kt~~Lv~G 654 (689)
T PRK14351 607 GDALDGLTFVFTGSLSGYTRSEAQELVEAHGGNATGSVSGNTDYLVVG 654 (689)
T ss_pred CCCCCCcEEEEccCCCCCCHHHHHHHHHHcCCEEcCCcCCCccEEEEc
Confidence 457999999886555567999999999999999999988867777764
No 81
>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=73.03 E-value=6 Score=47.02 Aligned_cols=48 Identities=15% Similarity=0.236 Sum_probs=39.1
Q ss_pred ccccCCcEEEEEeCCCCCCHHHHHHHHHHcCCEEEEecCCCeeEEEec
Q 005331 654 TSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAN 701 (702)
Q Consensus 654 s~~f~g~~f~v~~~~~~~~k~~l~~~i~~~gG~~~~n~~~~~~~~i~~ 701 (702)
+..|.|+.||+--.-...++++++++|.++||+++.+.+....+.|+.
T Consensus 582 ~~~l~gk~~v~TG~l~~~~R~~~~~~i~~~G~~v~~sVs~kt~~lv~G 629 (652)
T TIGR00575 582 GSPLAGKTFVLTGTLSQMSRDEAKELLENLGGKVASSVSKKTDYVIAG 629 (652)
T ss_pred CCCccCcEEEEeccCCCCCHHHHHHHHHHcCCEEeCCcCCCccEEEEC
Confidence 456999999876444567899999999999999999998866666664
No 82
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=69.25 E-value=8 Score=46.03 Aligned_cols=48 Identities=15% Similarity=0.212 Sum_probs=37.5
Q ss_pred ccccCCcEEEEEeCCCCCCHHHHHHHHHHcCCEEEEecCCCeeEEEec
Q 005331 654 TSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAN 701 (702)
Q Consensus 654 s~~f~g~~f~v~~~~~~~~k~~l~~~i~~~gG~~~~n~~~~~~~~i~~ 701 (702)
...|.|+.|||--.-..++.++++++|.++||+++-..+....+.||.
T Consensus 591 ~~~l~gktfV~TG~l~~~~R~e~~~lie~~Ggkv~ssVSkktd~LV~G 638 (669)
T PRK14350 591 NSFLFGKKFCITGSFNGYSRSVLIDKLTKKGAIFNTCVTKYLDFLLVG 638 (669)
T ss_pred CCccCCcEEEEecccCCCCHHHHHHHHHHcCCEEeccccCCCcEEEEC
Confidence 457999999875333456889999999999999998888755555553
No 83
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=67.01 E-value=8.5 Score=45.86 Aligned_cols=46 Identities=13% Similarity=0.091 Sum_probs=37.8
Q ss_pred ccCCcEEEEEeCCCCCCHHHHHHHHHHcCCEEEEecCCCeeEEEec
Q 005331 656 IFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAN 701 (702)
Q Consensus 656 ~f~g~~f~v~~~~~~~~k~~l~~~i~~~gG~~~~n~~~~~~~~i~~ 701 (702)
.|.|+.|||--.-..+++++++++|.++||+++.+.+....+.|+.
T Consensus 590 ~~~g~~~v~TG~l~~~~R~e~~~~i~~~G~~v~~sVs~kt~~lv~G 635 (665)
T PRK07956 590 DLAGKTVVLTGTLEQLSRDEAKEKLEALGAKVSGSVSKKTDLVVAG 635 (665)
T ss_pred CccccEEEEeCCCCCCCHHHHHHHHHHcCCEEeCcccCCCCEEEEC
Confidence 4999999886544567999999999999999999988766666654
No 84
>COG4566 TtrR Response regulator [Signal transduction mechanisms]
Probab=66.25 E-value=22 Score=35.44 Aligned_cols=81 Identities=19% Similarity=0.327 Sum_probs=54.4
Q ss_pred CCCHHHHHHHHhhhccCCCCCCCCHHHHHHHHHH----HHhhhchHhHHHHHHHHHHhCCHHHHHHHHHHHhhhhc----
Q 005331 102 AGNFPMVAAEVLQRRQGMISGGLTIKELNDLLDR----LASSENRAEKISVLSTLIKKTNAQEMKWIIMIILKDLK---- 173 (702)
Q Consensus 102 ~gD~~~~~~~v~~~r~~~~~~~lTi~eVn~~Ld~----La~~~~~~~k~~~l~~ll~~~t~~E~k~l~RiIlk~lr---- 173 (702)
.||.+..++.+...--..-.+|.+-+++-+.+.. .+..........-+...|..+||.|...|-+++.+-+.
T Consensus 85 hgDIpmaV~AmK~GAvDFLeKP~~~q~Lldav~~Al~~~~~~~~~~~~~~~~~~~l~tLT~RERqVl~~vV~G~~NKqIA 164 (202)
T COG4566 85 HGDIPMAVQAMKAGAVDFLEKPFSEQDLLDAVERALARDASRRAEADRQAAIRARLATLTPRERQVLDLVVRGLMNKQIA 164 (202)
T ss_pred CCChHHHHHHHHcchhhHHhCCCchHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhcCHHHHHHHHHHHcCcccHHHH
Confidence 5899988877644322222455555555444443 33333344555678889999999999999999977553
Q ss_pred --cCccccccc
Q 005331 174 --LGISEKSIF 182 (702)
Q Consensus 174 --iG~~e~~il 182 (702)
+|+++.||-
T Consensus 165 ~dLgiS~rTVe 175 (202)
T COG4566 165 FDLGISERTVE 175 (202)
T ss_pred HHcCCchhhHH
Confidence 689998884
No 85
>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=64.13 E-value=22 Score=41.12 Aligned_cols=93 Identities=22% Similarity=0.253 Sum_probs=71.4
Q ss_pred CCCcHHHHHHHHHHHHhcC---ChhHHHHHHHHHhhhcCCCchHhhhHhhcCCCCCCCccccCCCHHHHHHHHHHHhCCC
Q 005331 5 EETEVIVLVSLFNWIQKTK---PAAKKRSKFRKFLDTYCDSVDYFSALRLILPSLDRERGSYGLKESVLANCLIDALGMS 81 (702)
Q Consensus 5 ~~~~F~~l~~~~e~i~~~~---~~~~k~~~l~~~l~~~~~~~~~~~~lrLllp~~d~~r~~ygike~~L~k~~~~~~~l~ 81 (702)
.+..-.++-+.|++|.+.+ ++.+|..+|..++.+. ++.+..=++|+|+-++. .|++++++..+++.+++++
T Consensus 53 ~~lti~eV~~~L~~ia~~~g~~s~~~k~~~l~~ll~~~-~~~e~k~l~r~i~~~lr-----iG~~~~~il~al~~~~~~~ 126 (514)
T TIGR00574 53 APLTVKEVYETLKNIAETSGEGSQDKKIKLLKSLLKRA-SPLEAKYLIRTILGDLR-----IGIAEKTILDALAKAFLLS 126 (514)
T ss_pred CCcCHHHHHHHHHHHHHhhCCCcHHHHHHHHHHHHHhC-CHHHHHHHHHHHhhhcc-----cCccHHHHHHHHHHHhccc
Confidence 3466778888888888775 3567888999999874 57788889999998882 8999999999999999876
Q ss_pred cChHHHHHHhhhhcCCCCCCCCCHHHHHHHHh
Q 005331 82 KDSADAVRLINWRKGGAAPNAGNFPMVAAEVL 113 (702)
Q Consensus 82 ~~s~~~~~L~~wk~~~~~~~~gD~~~~~~~v~ 113 (702)
.. +..++ | ....|++.++.++.
T Consensus 127 ~~--~~~~~--~------~~~~dl~~v~~~l~ 148 (514)
T TIGR00574 127 HP--DVERA--F------NLTNDLGKVAKILL 148 (514)
T ss_pred hH--HHHHH--H------HhCCCHHHHHHHHH
Confidence 43 33333 2 24678998888765
No 86
>PLN03123 poly [ADP-ribose] polymerase; Provisional
Probab=50.13 E-value=29 Score=43.18 Aligned_cols=48 Identities=17% Similarity=0.313 Sum_probs=38.8
Q ss_pred ccccccCCcEEEEEeCCCCCCHHHHHHHHHHcCCEEEEecCCCeeEEEe
Q 005331 652 GETSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVA 700 (702)
Q Consensus 652 ~~s~~f~g~~f~v~~~~~~~~k~~l~~~i~~~gG~~~~n~~~~~~~~i~ 700 (702)
.....|.|+.|+++-.- ..++.++.++|.+|||+++......+||+|+
T Consensus 389 ~~~~~l~~~~i~i~G~~-~~~~~~~k~~Ie~~GG~~s~~v~~~~t~l~t 436 (981)
T PLN03123 389 SESEFLGDLKVSIVGAS-KEKVTEWKAKIEEAGGVFHATVKKDTNCLVV 436 (981)
T ss_pred ccCCCcCCeEEEEecCC-CCcHHHHHHHHHhcCCEEeeeccCCceEEEc
Confidence 56788999998887432 3567999999999999999988776777665
No 87
>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=47.81 E-value=2.1e+02 Score=29.11 Aligned_cols=31 Identities=26% Similarity=0.165 Sum_probs=23.1
Q ss_pred ceEEEEecceEEE-EEEEeCCEEEEEeCCCCC
Q 005331 246 EVVIECKFDGDRI-QIHKNGSEIHYFSRSFLD 276 (702)
Q Consensus 246 ~~~~E~K~DG~R~-qvh~~g~~v~~~SR~g~d 276 (702)
++.+-.|+||.=+ .....+|.+.+-|+++-+
T Consensus 46 p~~v~~K~dGsli~~~~~~~g~~~~~SK~s~~ 77 (221)
T PF09511_consen 46 PVEVYEKEDGSLIFIPYLDDGELIVASKGSFD 77 (221)
T ss_dssp EEEEEEE--SEEE-EEEEETTEEEEEETTBSS
T ss_pred cEEEEEecCcEEEEEeeecCCeEEEEecCccc
Confidence 7999999999544 334578899999999864
No 88
>COG5163 NOP7 Protein required for biogenesis of the 60S ribosomal subunit [Translation, ribosomal structure and biogenesis]
Probab=38.73 E-value=22 Score=38.82 Aligned_cols=37 Identities=27% Similarity=0.380 Sum_probs=30.1
Q ss_pred ccccccCCcEEEEEeCCCCCCHHHHHHHHHHcCCEEEEec
Q 005331 652 GETSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNL 691 (702)
Q Consensus 652 ~~s~~f~g~~f~v~~~~~~~~k~~l~~~i~~~gG~~~~n~ 691 (702)
+...||+|+.|||-..- ....||-+|.++||.++-.|
T Consensus 346 s~~slFS~f~FyisreV---p~dsLefiilscGG~V~~~p 382 (591)
T COG5163 346 SLKSLFSGFKFYISREV---PGDSLEFIILSCGGSVVGSP 382 (591)
T ss_pred chhhhhhceEEEEeccc---cchHHHHHHHHcCCcccCch
Confidence 35679999999997543 33679999999999998766
No 89
>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=36.63 E-value=78 Score=33.32 Aligned_cols=67 Identities=19% Similarity=0.217 Sum_probs=50.1
Q ss_pred EEeeeCCc--cccCCCHHHHHHHHHhhccCCCCcccccccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHCCCce
Q 005331 342 DVLYVGDT--SVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEG 419 (702)
Q Consensus 342 DiL~lng~--~l~~~pl~eRr~~L~~~~~~~~~~~~~~~p~~~~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EG 419 (702)
|-++++|. ....++..||+++++.+.....+++.++. .....+..+..++.+.+.+.|..|
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 34555653 23678999999999998887766654431 223457788899999999999999
Q ss_pred EEEecC
Q 005331 420 IVLKDL 425 (702)
Q Consensus 420 lV~K~~ 425 (702)
+|+=.+
T Consensus 99 v~~~~P 104 (284)
T cd00950 99 ALVVTP 104 (284)
T ss_pred EEEccc
Confidence 999865
No 90
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=33.19 E-value=79 Score=37.43 Aligned_cols=46 Identities=17% Similarity=0.182 Sum_probs=36.7
Q ss_pred cccCCcEEEEEeCCCCCCHHHHHHHHHHcCCEEEEecCCCeeEEEe
Q 005331 655 SIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVA 700 (702)
Q Consensus 655 ~~f~g~~f~v~~~~~~~~k~~l~~~i~~~gG~~~~n~~~~~~~~i~ 700 (702)
+.|.|+.||+--.=..+|.++...++.+.||++.-+.+....++||
T Consensus 593 ~~l~gkt~V~TGtL~~~sR~eak~~le~lGakv~~SVSkktD~vva 638 (667)
T COG0272 593 SPLAGKTFVLTGTLEGMSRDEAKALLEALGAKVSGSVSKKTDYVVA 638 (667)
T ss_pred cccCCCEEEEeccCCCCCHHHHHHHHHHcCCEEeceecccccEEEE
Confidence 7899999876544467999999999999999999888774444444
No 91
>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=31.71 E-value=1.1e+02 Score=32.18 Aligned_cols=65 Identities=22% Similarity=0.305 Sum_probs=47.4
Q ss_pred eeeCCc--cccCCCHHHHHHHHHhhccCCCCcccccccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHCCCceEE
Q 005331 344 LYVGDT--SVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIV 421 (702)
Q Consensus 344 L~lng~--~l~~~pl~eRr~~L~~~~~~~~~~~~~~~p~~~~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EGlV 421 (702)
++++|. ....++.+||+++++.+.....+++.++. .....+..+..++.+.+.+.|-.|+|
T Consensus 35 i~~~GstGE~~~ls~~Er~~l~~~~~~~~~~~~~vi~-----------------gv~~~~~~~~i~~a~~a~~~Gad~v~ 97 (281)
T cd00408 35 LVVLGTTGEAPTLTDEERKEVIEAVVEAVAGRVPVIA-----------------GVGANSTREAIELARHAEEAGADGVL 97 (281)
T ss_pred EEECCCCcccccCCHHHHHHHHHHHHHHhCCCCeEEE-----------------ecCCccHHHHHHHHHHHHHcCCCEEE
Confidence 445553 23577899999999999887666654331 22345677888999999999999999
Q ss_pred EecC
Q 005331 422 LKDL 425 (702)
Q Consensus 422 ~K~~ 425 (702)
+=.+
T Consensus 98 v~pP 101 (281)
T cd00408 98 VVPP 101 (281)
T ss_pred ECCC
Confidence 9653
No 92
>KOG2481 consensus Protein required for normal rRNA processing [RNA processing and modification]
Probab=31.68 E-value=46 Score=37.81 Aligned_cols=37 Identities=24% Similarity=0.399 Sum_probs=30.6
Q ss_pred ccccccCCcEEEEEeCCCCCCHHHHHHHHHHcCCEEEEec
Q 005331 652 GETSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNL 691 (702)
Q Consensus 652 ~~s~~f~g~~f~v~~~~~~~~k~~l~~~i~~~gG~~~~n~ 691 (702)
....+|+|+.|++=... .++.|+-+|..+||.|+--+
T Consensus 323 ~~kslF~glkFfl~reV---PresL~fiI~s~GG~V~wd~ 359 (570)
T KOG2481|consen 323 SHKSLFSGLKFFLNREV---PRESLEFIIRSFGGKVSWDP 359 (570)
T ss_pred hHHHHhhcceeeeeccC---chHHHHHHHHHcCCceecCc
Confidence 45679999999986544 45889999999999998775
No 93
>PRK03170 dihydrodipicolinate synthase; Provisional
Probab=31.38 E-value=1e+02 Score=32.57 Aligned_cols=65 Identities=20% Similarity=0.240 Sum_probs=48.1
Q ss_pred eeeCCc--cccCCCHHHHHHHHHhhccCCCCcccccccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHCCCceEE
Q 005331 344 LYVGDT--SVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIV 421 (702)
Q Consensus 344 L~lng~--~l~~~pl~eRr~~L~~~~~~~~~~~~~~~p~~~~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EGlV 421 (702)
++++|. ....++..||+++++.+.....+++.++. .....+.++..++.+.+.+.|..|+|
T Consensus 39 i~~~Gs~GE~~~ls~~Er~~~~~~~~~~~~~~~~vi~-----------------gv~~~~~~~~i~~a~~a~~~G~d~v~ 101 (292)
T PRK03170 39 LVVVGTTGESPTLTHEEHEELIRAVVEAVNGRVPVIA-----------------GTGSNSTAEAIELTKFAEKAGADGAL 101 (292)
T ss_pred EEECCcCCccccCCHHHHHHHHHHHHHHhCCCCcEEe-----------------ecCCchHHHHHHHHHHHHHcCCCEEE
Confidence 444542 23678999999999999887777654331 12345678888999999999999999
Q ss_pred EecC
Q 005331 422 LKDL 425 (702)
Q Consensus 422 ~K~~ 425 (702)
+=.+
T Consensus 102 ~~pP 105 (292)
T PRK03170 102 VVTP 105 (292)
T ss_pred ECCC
Confidence 9764
No 94
>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=31.09 E-value=92 Score=21.83 Aligned_cols=28 Identities=25% Similarity=0.408 Sum_probs=19.7
Q ss_pred HHhhhccCCCCCCCCHHHHHHHHHHHHh
Q 005331 111 EVLQRRQGMISGGLTIKELNDLLDRLAS 138 (702)
Q Consensus 111 ~v~~~r~~~~~~~lTi~eVn~~Ld~La~ 138 (702)
+|...+...........||+++|+++|.
T Consensus 5 dIr~~~F~~~~rGY~~~eVD~fLd~v~~ 32 (34)
T TIGR03544 5 DIRNKRFKKKLRGYDAAEVDAFLDRVAD 32 (34)
T ss_pred HHhhCcCCCCCCCCCHHHHHHHHHHHHH
Confidence 4444443333467899999999999985
No 95
>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=30.85 E-value=1.1e+02 Score=32.48 Aligned_cols=66 Identities=20% Similarity=0.239 Sum_probs=48.0
Q ss_pred EEeeeCCc--cccCCCHHHHHHHHHhhccCCCCcccccccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHCCCce
Q 005331 342 DVLYVGDT--SVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEG 419 (702)
Q Consensus 342 DiL~lng~--~l~~~pl~eRr~~L~~~~~~~~~~~~~~~p~~~~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EG 419 (702)
|-++++|. ....++.+||.++++..+....+++.++. .....+.++..++-+.+.+.|-.|
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 34556652 23467999999999998887777654331 123356788889999999999999
Q ss_pred EEEec
Q 005331 420 IVLKD 424 (702)
Q Consensus 420 lV~K~ 424 (702)
+|+=.
T Consensus 100 v~v~~ 104 (290)
T TIGR00683 100 LSAVT 104 (290)
T ss_pred EEEeC
Confidence 99954
No 96
>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=30.11 E-value=1.1e+02 Score=32.47 Aligned_cols=65 Identities=22% Similarity=0.202 Sum_probs=48.0
Q ss_pred eeeCCc--cccCCCHHHHHHHHHhhccCCCCcccccccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHCCCceEE
Q 005331 344 LYVGDT--SVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIV 421 (702)
Q Consensus 344 L~lng~--~l~~~pl~eRr~~L~~~~~~~~~~~~~~~p~~~~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EGlV 421 (702)
++.+|. ....++..||+++++.++....+++.++. .....+..+..++-+.+.+.|..|+|
T Consensus 38 i~v~GstGE~~~Ls~~Er~~l~~~~~~~~~g~~pvi~-----------------gv~~~~t~~ai~~a~~A~~~Gad~v~ 100 (294)
T TIGR02313 38 ISVGGTSGEPGSLTLEERKQAIENAIDQIAGRIPFAP-----------------GTGALNHDETLELTKFAEEAGADAAM 100 (294)
T ss_pred EEECccCcccccCCHHHHHHHHHHHHHHhCCCCcEEE-----------------ECCcchHHHHHHHHHHHHHcCCCEEE
Confidence 444542 23578999999999999887777654431 12345677888888999999999999
Q ss_pred EecC
Q 005331 422 LKDL 425 (702)
Q Consensus 422 ~K~~ 425 (702)
+=.+
T Consensus 101 v~pP 104 (294)
T TIGR02313 101 VIVP 104 (294)
T ss_pred EcCc
Confidence 9864
No 97
>PF14909 SPATA6: Spermatogenesis-assoc protein 6
Probab=29.83 E-value=1.4e+02 Score=28.28 Aligned_cols=59 Identities=20% Similarity=0.429 Sum_probs=42.9
Q ss_pred CCcEEEeCCCceEEEEEeeeceeecccccCCCceeeccEE--EEEecCCCccCCCCHHHHHHHHHc
Q 005331 539 RPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRI--DRVRYDKPWHDCLDVQSFVELVHS 602 (702)
Q Consensus 539 ~pdvwi~~P~~s~v~ev~a~~~~~~s~~~~~g~tLRfPr~--~riR~DK~~~d~~t~~el~~l~~~ 602 (702)
-|.||.. +...+-+.|..-.++.++ .-..-.||-+ .++|.+|....|.+..++.++.+.
T Consensus 11 CPGv~L~-~~~~vyL~v~~lg~~~~T----~~~ppvFPllfhek~~FeK~F~~~~dp~~l~~~Le~ 71 (140)
T PF14909_consen 11 CPGVWLC-DKGDVYLSVCILGQYKRT----RCLPPVFPLLFHEKFRFEKVFPNAVDPAQLADLLED 71 (140)
T ss_pred cCCeEeC-CCCCEEEEEEEcccEeec----ccCCCcCCeeEeeEEEeEEEecCCCCHHHHHHHhhc
Confidence 5789997 677777777542232222 2334679966 479999999999999999998863
No 98
>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=27.82 E-value=1.3e+02 Score=31.78 Aligned_cols=58 Identities=16% Similarity=0.174 Sum_probs=45.3
Q ss_pred cCCCHHHHHHHHHhhccCCCCcccccccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHCCCceEEEecCC
Q 005331 352 IHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLG 426 (702)
Q Consensus 352 ~~~pl~eRr~~L~~~~~~~~~~~~~~~p~~~~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EGlV~K~~d 426 (702)
..++..||+++++.++....+++.++. ...+.+.++..++-+.+.+.|..|+|+=.+-
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 578999999999998887776654331 2234577888899999999999999997643
No 99
>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=27.82 E-value=1.3e+02 Score=32.29 Aligned_cols=65 Identities=15% Similarity=0.238 Sum_probs=49.2
Q ss_pred eeeCCc--cccCCCHHHHHHHHHhhccCCCCcccccccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHCCCceEE
Q 005331 344 LYVGDT--SVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIV 421 (702)
Q Consensus 344 L~lng~--~l~~~pl~eRr~~L~~~~~~~~~~~~~~~p~~~~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EGlV 421 (702)
++++|. ....++.+||+++++..+....+++-++. ...+.+.++..++.+.+.+.|-.|+|
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 445552 34678999999999999887777754321 22345778999999999999999999
Q ss_pred EecC
Q 005331 422 LKDL 425 (702)
Q Consensus 422 ~K~~ 425 (702)
+=.+
T Consensus 109 v~~P 112 (309)
T cd00952 109 LGRP 112 (309)
T ss_pred ECCC
Confidence 9875
No 100
>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=27.13 E-value=1.1e+02 Score=32.32 Aligned_cols=65 Identities=20% Similarity=0.311 Sum_probs=47.6
Q ss_pred eeeCCc--cccCCCHHHHHHHHHhhccCCCCcccccccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHCCCceEE
Q 005331 344 LYVGDT--SVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIV 421 (702)
Q Consensus 344 L~lng~--~l~~~pl~eRr~~L~~~~~~~~~~~~~~~p~~~~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EGlV 421 (702)
+++.|. ....++..||+++++.++....+++.++. ...+.+.++..++.+.+.+.|..|+|
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 445542 24678999999999998877666654331 33456889999999999999999999
Q ss_pred EecC
Q 005331 422 LKDL 425 (702)
Q Consensus 422 ~K~~ 425 (702)
+=.|
T Consensus 102 v~~P 105 (289)
T PF00701_consen 102 VIPP 105 (289)
T ss_dssp EEES
T ss_pred Eecc
Confidence 9765
No 101
>PRK02289 4-oxalocrotonate tautomerase; Provisional
Probab=26.33 E-value=1.3e+02 Score=23.72 Aligned_cols=25 Identities=16% Similarity=0.139 Sum_probs=19.3
Q ss_pred EEEecCCCCHHHHHHHHHhhccccc
Q 005331 493 FCRVGTGLSDEELDAVVTKLKPYFR 517 (702)
Q Consensus 493 v~kVgtG~s~~~~~~l~~~l~~~~~ 517 (702)
-+++..|.|+++.++|.+.+..-..
T Consensus 5 ~i~~~~Grs~EqK~~L~~~it~a~~ 29 (60)
T PRK02289 5 RIDLFEGRSQEQKNALAREVTEVVS 29 (60)
T ss_pred EEEECCCCCHHHHHHHHHHHHHHHH
Confidence 3456679999999999988765543
No 102
>PLN02417 dihydrodipicolinate synthase
Probab=25.80 E-value=1.5e+02 Score=31.22 Aligned_cols=58 Identities=10% Similarity=0.008 Sum_probs=45.2
Q ss_pred ccCCCHHHHHHHHHhhccCCCCcccccccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHCCCceEEEecC
Q 005331 351 VIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDL 425 (702)
Q Consensus 351 l~~~pl~eRr~~L~~~~~~~~~~~~~~~p~~~~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EGlV~K~~ 425 (702)
...++..||+++++.++....+++.++. .....+..+..++.+.+.+.|..|+|+-.+
T Consensus 48 ~~~ls~~Er~~~~~~~~~~~~~~~pvi~-----------------gv~~~~t~~~i~~a~~a~~~Gadav~~~~P 105 (280)
T PLN02417 48 GQLMSWDEHIMLIGHTVNCFGGKIKVIG-----------------NTGSNSTREAIHATEQGFAVGMHAALHINP 105 (280)
T ss_pred hhhCCHHHHHHHHHHHHHHhCCCCcEEE-----------------ECCCccHHHHHHHHHHHHHcCCCEEEEcCC
Confidence 3567899999999998887777654321 223457788899999999999999999765
No 103
>PRK04147 N-acetylneuraminate lyase; Provisional
Probab=25.72 E-value=1.6e+02 Score=31.30 Aligned_cols=57 Identities=19% Similarity=0.247 Sum_probs=45.0
Q ss_pred cCCCHHHHHHHHHhhccCCCCcccccccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHCCCceEEEecC
Q 005331 352 IHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDL 425 (702)
Q Consensus 352 ~~~pl~eRr~~L~~~~~~~~~~~~~~~p~~~~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EGlV~K~~ 425 (702)
..++..||+++++.++....+++.++. ...+.+..+..++.+.+.+.|..|+|+=.+
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 567889999999999887777654331 223457788899999999999999998753
No 104
>KOG3673 consensus FtsJ-like RNA methyltransferase [RNA processing and modification]
Probab=24.82 E-value=72 Score=36.57 Aligned_cols=38 Identities=18% Similarity=0.149 Sum_probs=33.1
Q ss_pred CCCceEEEEEEEeeeCCccccCCCHHHHHHHHHhhccC
Q 005331 332 SDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKP 369 (702)
Q Consensus 332 ~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~ 369 (702)
...+..+++.|.+.|+|.++.+.||.||.++-++.+..
T Consensus 654 ~~~~~avhIiD~~vL~G~Dvr~~py~eR~~~aeKFv~a 691 (845)
T KOG3673|consen 654 SSEPQAVHIIDAAVLFGDDVRNLPYEERMKAAEKFVAA 691 (845)
T ss_pred cccchheeeeeeeeecCchhhcccHHHHHHHHHHHHHH
Confidence 34566799999999999999999999999999987654
No 105
>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=24.78 E-value=1.7e+02 Score=30.88 Aligned_cols=67 Identities=22% Similarity=0.298 Sum_probs=48.7
Q ss_pred EEeeeCCc--cccCCCHHHHHHHHHhhccCCCCcccccccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHCCCce
Q 005331 342 DVLYVGDT--SVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEG 419 (702)
Q Consensus 342 DiL~lng~--~l~~~pl~eRr~~L~~~~~~~~~~~~~~~p~~~~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EG 419 (702)
|-+.++|. ....++.+||+++++..+....+++.++. .....+..+..++.+.+.+.|-.|
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 34555552 23577899999999998877666653321 123457788899999999999999
Q ss_pred EEEecC
Q 005331 420 IVLKDL 425 (702)
Q Consensus 420 lV~K~~ 425 (702)
+|+=.+
T Consensus 100 v~~~~P 105 (288)
T cd00954 100 ISAITP 105 (288)
T ss_pred EEEeCC
Confidence 998764
No 106
>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=24.50 E-value=1.7e+02 Score=31.05 Aligned_cols=63 Identities=14% Similarity=0.246 Sum_probs=45.8
Q ss_pred eeeCCc--cccCCCHHHHHHHHHhhccCCCCcccccccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHCCCceEE
Q 005331 344 LYVGDT--SVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIV 421 (702)
Q Consensus 344 L~lng~--~l~~~pl~eRr~~L~~~~~~~~~~~~~~~p~~~~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EGlV 421 (702)
++++|. ....++.+||.++++.++....+++.++. .... +..+..++.+.+.+.|..|+|
T Consensus 38 i~v~GstGE~~~Ls~eEr~~l~~~~~~~~~~~~pvi~-----------------gv~~-~t~~~i~~a~~a~~~Gad~v~ 99 (289)
T cd00951 38 LFAAGGTGEFFSLTPDEYAQVVRAAVEETAGRVPVLA-----------------GAGY-GTATAIAYAQAAEKAGADGIL 99 (289)
T ss_pred EEECcCCcCcccCCHHHHHHHHHHHHHHhCCCCCEEE-----------------ecCC-CHHHHHHHHHHHHHhCCCEEE
Confidence 445552 23578999999999998887766654331 1222 667888899999999999999
Q ss_pred Eec
Q 005331 422 LKD 424 (702)
Q Consensus 422 ~K~ 424 (702)
+=.
T Consensus 100 ~~p 102 (289)
T cd00951 100 LLP 102 (289)
T ss_pred ECC
Confidence 954
No 107
>KOG2386 consensus mRNA capping enzyme, guanylyltransferase (alpha) subunit [RNA processing and modification]
Probab=22.51 E-value=3.7e+02 Score=30.05 Aligned_cols=175 Identities=15% Similarity=0.153 Sum_probs=88.3
Q ss_pred HHHHHHcCCCceEEEEecceEEEEEEEe-----CCEEEEEeCCCCCCC--c---chhhHHHHHHhhccccceeeeceEEE
Q 005331 236 HAAWRKLHGKEVVIECKFDGDRIQIHKN-----GSEIHYFSRSFLDHS--E---YGHAMSKIIEQNVLVDRCILDGEMLV 305 (702)
Q Consensus 236 ~~~~~~~~~~~~~~E~K~DG~R~qvh~~-----g~~v~~~SR~g~d~t--~---~~p~l~~~~~~~~~~~~~ILDGE~v~ 305 (702)
.+.+..+....+.+-.|.||.|++..++ +..+.+.=++-.-.- . +-..+...+ +. ...++-+|||+|.
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 3445555556799999999999999883 234555555533221 1 111112221 11 2467789999998
Q ss_pred eeCCCCccccccchHHHHHHhhcCCCCCCceEEEEEEEeeeCCccccCCCHHHHHHHHHhhccCCC---CcccccccCC-
Q 005331 306 WDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSK---GRLETLVPDH- 381 (702)
Q Consensus 306 ~d~~~~~~~~F~~lq~~~~~~r~~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~---~~~~~~~p~~- 381 (702)
..- |-|- ...-|.+|+.|.-+|. +...++.+.++..-.+.- ..+.-+.+..
T Consensus 129 vhc------thG~---------------NrtgyLI~~yL~~~~~----~s~~~aik~f~~~r~~gi~k~dyi~~L~~~~~ 183 (393)
T KOG2386|consen 129 VHC------THGL---------------NRTGYLICAYLADVGG----YSSSEAIKRFADARPPGIEKQDYIDALYSRYH 183 (393)
T ss_pred EeC------CCcc---------------cccceeeeeeeeeccC----ccHHHHHHHHHHhCCCccCchHHHHHHhhccc
Confidence 542 2111 1245999999987764 344444444544322110 0000000000
Q ss_pred -CCCccccCCCCCccccccCCHHHHHHHHHHHHH-CCCceEEEecCCCCcc-cCCCCCCeEEEcccc
Q 005331 382 -GLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIE-NRDEGIVLKDLGSKWE-PGDRSGKWLKLKPEY 445 (702)
Q Consensus 382 -~~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~-~g~EGlV~K~~ds~Y~-~G~Rs~~WlKvK~~y 445 (702)
..+..+... ...+............. ++..|++.-...-+|. .| +...-+|+|++-
T Consensus 184 ~~~p~~vs~p-------~~~~~~~~~~~~~~~~~~~~~Dg~i~t~~~~pg~~~g-~~~~~~k~k~~~ 242 (393)
T KOG2386|consen 184 DIFPFKVSCP-------SMPDWKRSIKLKKPVHKLHGNDGLIFTPAEIPGSKNG-KQEALLKWKPFS 242 (393)
T ss_pred ccccccccCC-------CCcchhhhhhhccccccccccCCCcCCcccCcccccc-chhhhhcCCchh
Confidence 000111100 00111111112221111 7888999888888894 45 445789999973
No 108
>PF11459 DUF2893: Protein of unknwon function (DUF2893); InterPro: IPR021561 This is a bacterial family of uncharacterised proteins.
Probab=21.97 E-value=2.4e+02 Score=23.48 Aligned_cols=45 Identities=16% Similarity=0.333 Sum_probs=37.5
Q ss_pred CCCCCHHHHHHHHHHHHhhhchHhHHHHHHHHHHhCCHHHHHHHHHHHhh
Q 005331 121 SGGLTIKELNDLLDRLASSENRAEKISVLSTLIKKTNAQEMKWIIMIILK 170 (702)
Q Consensus 121 ~~~lTi~eVn~~Ld~La~~~~~~~k~~~l~~ll~~~t~~E~k~l~RiIlk 170 (702)
+...++.+++++++.|.+.+ ...++.||..|+....+.++..+-.
T Consensus 15 p~~~s~e~a~~l~egL~nLr-----p~~lq~LL~~C~svKvkRLfl~lA~ 59 (69)
T PF11459_consen 15 PKRQSFEEADELMEGLRNLR-----PRVLQELLEHCTSVKVKRLFLYLAE 59 (69)
T ss_pred CccCCHHHHHHHHHHHhhcC-----HHHHHHHHHHCccHHHHHHHHHHHH
Confidence 46789999999999998765 3689999999999999998876543
No 109
>COG0329 DapA Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]
Probab=21.24 E-value=2e+02 Score=30.76 Aligned_cols=64 Identities=25% Similarity=0.334 Sum_probs=48.5
Q ss_pred eeeCCc--cccCCCHHHHHHHHHhhccCCCCcccccccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHCCCceEE
Q 005331 344 LYVGDT--SVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIV 421 (702)
Q Consensus 344 L~lng~--~l~~~pl~eRr~~L~~~~~~~~~~~~~~~p~~~~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EGlV 421 (702)
|+.+|. ....++..||+++++..+....+++-++. ...+.+.++..++-+.+-+.|-.|+|
T Consensus 42 i~~~GttGE~~~Ls~eEr~~v~~~~v~~~~grvpvia-----------------G~g~~~t~eai~lak~a~~~Gad~il 104 (299)
T COG0329 42 LVVLGTTGESPTLTLEERKEVLEAVVEAVGGRVPVIA-----------------GVGSNSTAEAIELAKHAEKLGADGIL 104 (299)
T ss_pred EEECCCCccchhcCHHHHHHHHHHHHHHHCCCCcEEE-----------------ecCCCcHHHHHHHHHHHHhcCCCEEE
Confidence 445552 23578999999999999988877753321 23356788889999999999999999
Q ss_pred Eec
Q 005331 422 LKD 424 (702)
Q Consensus 422 ~K~ 424 (702)
+=.
T Consensus 105 ~v~ 107 (299)
T COG0329 105 VVP 107 (299)
T ss_pred EeC
Confidence 974
No 110
>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=21.06 E-value=1e+02 Score=25.29 Aligned_cols=56 Identities=20% Similarity=0.267 Sum_probs=28.4
Q ss_pred HHHHHHHHHhCCCcChHHHHHHhhhhcCCCCCCCCCHHHHHHHHhhhc----cCCCCCCCCHHHHHHHHH
Q 005331 69 VLANCLIDALGMSKDSADAVRLINWRKGGAAPNAGNFPMVAAEVLQRR----QGMISGGLTIKELNDLLD 134 (702)
Q Consensus 69 ~L~k~~~~~~~l~~~s~~~~~L~~wk~~~~~~~~gD~~~~~~~v~~~r----~~~~~~~lTi~eVn~~Ld 134 (702)
.-+|.+++.+|++.=+.++.+.+. -|.--.+.++++.- ....-..||.+|||..|.
T Consensus 7 esvk~iAes~Gi~~l~de~a~~La----------~dveyrlreiiq~a~kfm~hskR~~Lt~~Di~~ALr 66 (66)
T PF02969_consen 7 ESVKDIAESLGISNLSDEAAKALA----------EDVEYRLREIIQEALKFMRHSKRTKLTTDDINSALR 66 (66)
T ss_dssp HHHHHHHHHTT---B-HHHHHHHH----------HHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHH-
T ss_pred HHHHHHHHHcCCCCCCHHHHHHHH----------HHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhC
Confidence 346889999999765555555442 23333333443321 011236799999999874
Done!