Query 006003
Match_columns 665
No_of_seqs 392 out of 1868
Neff 7.4
Searched_HMMs 46136
Date Thu Mar 28 16:57:34 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/006003.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/006003hhsearch_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 2E-131 4E-136 1081.3 49.3 624 3-665 1-642 (881)
2 PLN03113 DNA ligase 1; Provisi 100.0 1E-107 2E-112 932.1 54.5 551 5-604 127-731 (744)
3 PRK01109 ATP-dependent DNA lig 100.0 1E-104 3E-109 903.2 53.4 544 7-604 1-583 (590)
4 KOG0967 ATP-dependent DNA liga 100.0 3E-102 7E-107 834.8 36.5 551 5-603 97-704 (714)
5 TIGR00574 dnl1 DNA ligase I, A 100.0 6E-97 1E-101 830.8 50.7 494 62-600 1-513 (514)
6 PRK09247 ATP-dependent DNA lig 100.0 9.5E-95 2.1E-99 812.4 50.6 523 9-603 1-538 (539)
7 PRK03180 ligB ATP-dependent DN 100.0 2.1E-94 4.5E-99 803.5 49.1 493 7-600 1-506 (508)
8 PHA02587 30 DNA ligase; Provis 100.0 7.5E-66 1.6E-70 572.3 41.4 447 13-597 3-484 (488)
9 COG1793 CDC9 ATP-dependent DNA 100.0 7.2E-64 1.6E-68 548.0 30.8 422 99-600 17-443 (444)
10 TIGR02779 NHEJ_ligase_lig DNA 100.0 6.7E-60 1.4E-64 496.5 32.8 288 243-591 10-297 (298)
11 PRK09632 ATP-dependent DNA lig 100.0 1.7E-59 3.6E-64 535.6 31.8 307 218-591 455-761 (764)
12 PRK08224 ligC ATP-dependent DN 100.0 1.7E-57 3.8E-62 484.7 33.9 317 217-591 2-330 (350)
13 PRK05972 ligD ATP-dependent DN 100.0 3.7E-56 8.1E-61 512.4 31.4 304 222-591 232-536 (860)
14 PRK09633 ligD ATP-dependent DN 100.0 6.7E-55 1.4E-59 492.0 31.9 310 224-601 1-318 (610)
15 PRK07636 ligB ATP-dependent DN 100.0 1.5E-50 3.2E-55 419.8 29.7 272 224-582 3-274 (275)
16 cd07900 Adenylation_DNA_ligase 100.0 1.6E-48 3.5E-53 392.3 22.6 213 216-445 2-219 (219)
17 TIGR02776 NHEJ_ligase_prk DNA 100.0 8.8E-47 1.9E-51 421.8 24.4 258 271-592 1-259 (552)
18 cd07903 Adenylation_DNA_ligase 100.0 1.9E-45 4.1E-50 372.8 21.9 214 215-446 3-224 (225)
19 cd07902 Adenylation_DNA_ligase 100.0 2E-44 4.3E-49 361.7 21.6 206 216-445 6-213 (213)
20 cd07901 Adenylation_DNA_ligase 100.0 2.6E-44 5.7E-49 359.6 22.0 205 220-444 1-207 (207)
21 PRK09125 DNA ligase; Provision 100.0 3.5E-44 7.7E-49 372.8 23.5 254 224-585 28-282 (282)
22 PHA00454 ATP-dependent DNA lig 100.0 3.6E-43 7.9E-48 371.9 28.3 284 225-583 7-314 (315)
23 cd07898 Adenylation_DNA_ligase 100.0 9E-43 1.9E-47 347.1 22.1 199 224-444 1-201 (201)
24 cd07897 Adenylation_DNA_ligase 100.0 6.5E-43 1.4E-47 349.2 20.7 200 222-444 3-205 (207)
25 cd08039 Adenylation_DNA_ligase 100.0 1.3E-42 2.9E-47 351.6 22.1 201 233-445 10-235 (235)
26 cd07905 Adenylation_DNA_ligase 100.0 1.2E-40 2.6E-45 329.8 19.8 190 224-444 1-193 (194)
27 PF01068 DNA_ligase_A_M: ATP d 100.0 1.2E-40 2.5E-45 332.0 17.7 199 226-442 1-202 (202)
28 cd07906 Adenylation_DNA_ligase 100.0 8.5E-40 1.8E-44 322.9 18.5 189 224-443 1-189 (190)
29 cd07967 OBF_DNA_ligase_III The 100.0 4.7E-34 1E-38 265.5 15.2 137 449-595 2-139 (139)
30 cd07896 Adenylation_kDNA_ligas 100.0 2E-33 4.4E-38 273.6 13.8 173 224-443 1-174 (174)
31 cd06846 Adenylation_DNA_ligase 100.0 1.4E-31 3.1E-36 262.5 17.8 177 226-443 2-182 (182)
32 PF04675 DNA_ligase_A_N: DNA l 100.0 5.3E-32 1.1E-36 264.4 13.5 169 7-187 1-177 (177)
33 cd07968 OBF_DNA_ligase_IV The 100.0 7.5E-30 1.6E-34 239.0 14.5 139 449-593 1-140 (140)
34 cd07969 OBF_DNA_ligase_I The O 100.0 1.5E-28 3.2E-33 230.8 15.9 134 449-601 1-143 (144)
35 cd07895 Adenylation_mRNA_cappi 100.0 6.3E-28 1.4E-32 242.9 14.8 175 239-443 35-215 (215)
36 cd07972 OBF_DNA_ligase_Arch_Li 99.9 4.4E-27 9.5E-32 215.2 14.1 121 450-597 1-121 (122)
37 KOG4437 ATP-dependent DNA liga 99.9 2.1E-26 4.5E-31 231.6 19.1 318 7-345 155-482 (482)
38 cd07893 OBF_DNA_ligase The Oli 99.9 4.8E-26 1E-30 210.2 15.0 122 450-590 1-129 (129)
39 cd07971 OBF_DNA_ligase_LigD Th 99.8 1.5E-20 3.2E-25 170.5 13.2 114 451-590 2-115 (115)
40 PF04679 DNA_ligase_A_C: ATP d 99.8 2.4E-19 5.3E-24 157.5 11.1 97 466-585 1-97 (97)
41 cd08040 OBF_DNA_ligase_family 99.8 6.3E-19 1.4E-23 158.0 12.8 108 450-582 1-108 (108)
42 cd07894 Adenylation_RNA_ligase 99.7 1.3E-17 2.9E-22 177.2 14.6 163 245-445 48-218 (342)
43 cd07970 OBF_DNA_ligase_LigC Th 99.7 5.9E-17 1.3E-21 147.9 12.9 120 450-591 1-121 (122)
44 PF01331 mRNA_cap_enzyme: mRNA 99.3 5.3E-13 1.1E-17 132.1 1.2 174 241-442 12-192 (192)
45 COG5226 CEG1 mRNA capping enzy 99.2 4.3E-11 9.3E-16 120.7 7.9 183 242-458 59-257 (404)
46 cd08041 OBF_kDNA_ligase_like T 99.1 1.8E-10 3.9E-15 96.7 7.9 76 451-582 2-77 (77)
47 COG1423 ATP-dependent DNA liga 98.8 4.5E-08 9.7E-13 101.3 14.4 150 241-429 84-238 (382)
48 TIGR01209 RNA ligase, Pab1020 98.8 5.8E-08 1.3E-12 103.5 15.1 148 241-428 75-229 (374)
49 cd09232 Snurportin-1_C C-termi 98.6 4.7E-07 1E-11 88.7 11.1 176 225-444 5-186 (186)
50 PF14743 DNA_ligase_OB_2: DNA 98.2 1.1E-06 2.4E-11 71.2 3.5 37 462-509 2-38 (66)
51 smart00532 LIGANc Ligase N fam 97.9 0.00021 4.5E-09 79.3 14.5 224 246-509 104-362 (441)
52 cd00114 LIGANc NAD+ dependent 97.8 0.00022 4.8E-09 75.6 13.7 167 246-438 102-299 (307)
53 PF01653 DNA_ligase_aden: NAD- 97.8 7.3E-05 1.6E-09 79.6 8.2 169 246-438 108-306 (315)
54 PRK08097 ligB NAD-dependent DN 97.7 0.00075 1.6E-08 76.6 14.9 212 224-472 95-330 (562)
55 TIGR00575 dnlj DNA ligase, NAD 97.6 0.00047 1E-08 80.3 13.4 196 246-472 97-326 (652)
56 PRK14351 ligA NAD-dependent DN 97.6 0.0014 2.9E-08 76.7 15.5 223 245-509 132-389 (689)
57 PRK07956 ligA NAD-dependent DN 97.5 0.0013 2.9E-08 76.7 14.8 196 246-472 109-338 (665)
58 PRK14350 ligA NAD-dependent DN 97.2 0.0049 1.1E-07 71.8 14.5 196 246-471 111-334 (669)
59 PF09414 RNA_ligase: RNA ligas 97.0 0.0016 3.4E-08 64.0 6.7 106 246-366 2-129 (186)
60 TIGR02307 RNA_lig_RNL2 RNA lig 96.9 0.013 2.8E-07 62.1 13.3 106 242-366 22-145 (325)
61 PRK01109 ATP-dependent DNA lig 96.8 0.005 1.1E-07 71.3 10.3 97 4-114 112-211 (590)
62 COG0272 Lig NAD-dependent DNA 96.6 0.049 1.1E-06 62.5 15.9 195 245-470 109-336 (667)
63 PHA02142 putative RNA ligase 95.7 0.18 3.9E-06 54.5 13.8 112 234-367 157-299 (366)
64 KOG3132 m3G-cap-specific nucle 94.5 0.28 6E-06 49.2 9.8 173 225-440 100-277 (325)
65 TIGR02306 RNA_lig_DRB0094 RNA 93.2 1 2.2E-05 48.6 12.2 104 244-366 158-277 (341)
66 PRK09247 ATP-dependent DNA lig 89.8 0.5 1.1E-05 54.3 5.8 82 127-208 2-91 (539)
67 KOG2386 mRNA capping enzyme, g 89.4 0.22 4.8E-06 54.1 2.4 98 245-368 285-387 (393)
68 PF04675 DNA_ligase_A_N: DNA l 87.5 0.64 1.4E-05 45.1 4.0 85 125-209 2-100 (177)
69 PRK03180 ligB ATP-dependent DN 84.0 5.5 0.00012 45.6 9.8 92 6-113 72-166 (508)
70 PLN03113 DNA ligase 1; Provisi 78.1 4.4 9.6E-05 48.3 6.6 86 122-207 127-229 (744)
71 COG4566 TtrR Response regulato 72.3 15 0.00032 36.2 7.4 81 102-182 85-175 (202)
72 TIGR00574 dnl1 DNA ligase I, A 67.4 18 0.00039 41.5 8.2 93 5-113 53-148 (514)
73 PF09511 RNA_lig_T4_1: RNA lig 42.4 2.8E+02 0.0061 27.8 11.1 31 246-276 46-77 (221)
74 cd00950 DHDPS Dihydrodipicolin 38.2 70 0.0015 33.4 6.2 66 343-425 37-104 (284)
75 cd00408 DHDPS-like Dihydrodipi 34.8 88 0.0019 32.5 6.3 65 344-425 35-101 (281)
76 TIGR00683 nanA N-acetylneurami 32.8 97 0.0021 32.6 6.2 65 343-424 38-104 (290)
77 PRK03170 dihydrodipicolinate s 32.3 96 0.0021 32.5 6.1 58 351-425 48-105 (292)
78 PF14909 SPATA6: Spermatogenes 32.2 1.2E+02 0.0026 28.5 5.9 60 538-602 10-71 (140)
79 cd00952 CHBPH_aldolase Trans-o 31.6 1E+02 0.0022 32.8 6.2 58 351-425 55-112 (309)
80 TIGR03544 DivI1A_domain DivIVA 30.9 94 0.002 21.5 3.8 28 111-138 5-32 (34)
81 TIGR00674 dapA dihydrodipicoli 29.7 1.1E+02 0.0025 31.9 6.1 58 352-426 46-103 (285)
82 TIGR02313 HpaI-NOT-DapA 2,4-di 29.4 1.2E+02 0.0027 31.9 6.4 59 351-426 47-105 (294)
83 PLN02417 dihydrodipicolinate s 26.8 1.5E+02 0.0032 31.0 6.4 57 352-425 49-105 (280)
84 PF00701 DHDPS: Dihydrodipicol 26.1 1.2E+02 0.0025 31.8 5.4 58 351-425 48-105 (289)
85 PF11459 DUF2893: Protein of u 26.0 1.9E+02 0.0042 23.7 5.4 45 121-170 15-59 (69)
86 cd00954 NAL N-Acetylneuraminic 25.4 1.8E+02 0.004 30.4 6.8 67 342-425 37-105 (288)
87 PRK04147 N-acetylneuraminate l 25.0 1.8E+02 0.0038 30.7 6.5 57 352-425 52-108 (293)
88 KOG2386 mRNA capping enzyme, g 24.5 4.3E+02 0.0092 29.3 9.3 175 236-445 51-242 (393)
89 cd00951 KDGDH 5-dehydro-4-deox 24.1 1.8E+02 0.0039 30.5 6.4 56 351-424 47-102 (289)
90 COG0329 DapA Dihydrodipicolina 23.1 1.9E+02 0.004 30.7 6.3 58 351-425 51-108 (299)
91 PRK02289 4-oxalocrotonate taut 22.9 1.4E+02 0.0031 23.2 4.1 25 493-517 5-29 (60)
92 PF14538 Raptor_N: Raptor N-te 22.4 99 0.0021 29.5 3.6 40 298-345 106-145 (154)
93 PF13099 DUF3944: Domain of un 22.3 1.2E+02 0.0025 21.6 2.9 24 151-175 8-31 (35)
94 KOG3673 FtsJ-like RNA methyltr 21.7 89 0.0019 35.6 3.5 38 332-369 654-691 (845)
No 1
>KOG0966 consensus ATP-dependent DNA ligase IV [Replication, recombination and repair]
Probab=100.00 E-value=1.8e-131 Score=1081.33 Aligned_cols=624 Identities=46% Similarity=0.776 Sum_probs=545.1
Q ss_pred CCCCCcHHHHHHHHHHHHhcCChhHHHHHHHHHhhhcCCC----chHhhhHhhcCCCCCCCccccCCCHHHHHHHHHHHh
Q 006003 3 KTEETEVIVLVSLFNWIQKTKPAAKKRSKFRKFLDTYCDS----VDYFSALRLILPSLDRERGSYGLKESVLANCLIDAL 78 (665)
Q Consensus 3 ~~~~~~F~~l~~~~e~i~~~~~~~~k~~~l~~~~~~~~~~----~~~~~~lrLllp~~d~~r~~yglke~~L~k~~~~~~ 78 (665)
||+++.|+.+|++|+.|+.+.....|++++++++++|+.+ +|+||+|||+||++||+|+.|||||..||++|+++|
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 CCCcChHHHHHHhhhhcCCCCCCCCCHHHHHHHHhhhccCCCC-CCCCHHHHHHHHHHHHhhhhHHhHH-HHHHHHHHhC
Q 006003 79 GMSKDSADAVRLINWRKGGAAPNAGNFPMVAAEVLQRRQGMIS-GGLTIKELNDLLDRLASSENRAEKI-SVLSTLIKKT 156 (665)
Q Consensus 79 ~~~~~~~~~~~L~~wk~~~~~~~~gD~~~~~~~v~~~r~~~~~-~~lTi~eV~~~Ld~la~~~~~~~k~-~~l~~ll~~~ 156 (665)
+++++|.||++|+||+.++..+ |||+.++++++++|+...+ +.|||.|||++||.||+......+. ..|..++++|
T Consensus 81 ~lprds~Da~rL~nwr~~~~~~--Gdfs~i~~~vl~~R~~~~~s~alTi~evN~lLD~LA~~~~~~~~~~~~l~~lv~~~ 158 (881)
T KOG0966|consen 81 HLPRDSADAVRLKNWRASTGAR--GDFSLILYEVLQRRCENPSSGALTIKEVNDLLDSLASGPSEDGKKFKKLSQLVEQC 158 (881)
T ss_pred cCCCCcHHHHHHHhhccCCCcC--ccHHHHHHHHHHHHhcCCCCCceeHHHHHHHHHHHcCCchhhhhhhHHHHHHHHhC
Confidence 9999999999999999987655 9999999999999987654 4599999999999999887765554 8999999999
Q ss_pred CHHHHHHHHHHHHhhhccCCcccccccccCcCHHHHHhhhCCHHHHHHHHhhhhhccccCC--ccCCCccccccccccCC
Q 006003 157 NAQEMKWIIMIILKDLKLGISEKSIFHEFHPDAEDLFNVTCDLKLVCEKLKDRNQRHKRQD--IEVGKAVRPQLAMRIGD 234 (665)
Q Consensus 157 t~~E~k~l~RiilkdlriG~~e~til~~~hp~a~~~~~~~~dL~~v~~~l~~~~~~~~~~~--i~~g~~~~PmLA~~~~~ 234 (665)
||.|+|||+|||||++++|++|++||.+|||||+++||+|+||+.||+.|.||+.+++..+ |++|..|+||||++.+.
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-HHHHHhcCCceEEEEeeceeEEEEEEeCCEEEEEecCCCCCCcch-h----h-hHHHHHhhc--cccceeeeceEEE
Q 006003 235 AH-AAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYG-H----A-MSKIIEQNV--LVDRCILDGEMLV 305 (665)
Q Consensus 235 ~~-~~~~~~~~~~~~~E~K~DG~R~qih~~g~~v~~~SR~g~d~t~~~-p----~-l~~~~~~~~--~~~~~ILDGElv~ 305 (665)
.. +++++|++++|++|+|+||||+|+|++|+.++||||||.|||..| . + +...+...+ ....||||||||+
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 55 689999999999999999999999999999999999999999422 1 1 222222212 3789999999999
Q ss_pred eeCCCCccccccchHHHHHHhhcCCCCCCceEEEEEEEEeeCCccccCCCHHHHHHHHHhhcCCCCCcceecccCCCCCc
Q 006003 306 WDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNS 385 (665)
Q Consensus 306 ~d~~~~~~~~F~~lq~~~~~~~~~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~~~~~~~~p~~~~~~ 385 (665)
||+.+.++.|||+++++...... +...++||+|||+||+||++|.+.||.+|++.|+.++.+.+++++++.
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 99999999999999988765432 356789999999999999999999999999999999999999987752
Q ss_pred cccCCCCCccccccCCHHHHHHHHHHHHHcCCceEEeecCCCCCccCCCCCCeEEEcccccc-CCCcceEEEEEEEecCC
Q 006003 386 HVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIR-AGSDLDVLIIGGYYGSG 464 (665)
Q Consensus 386 ~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EGlV~K~~~s~Y~~GkRs~~WlKiK~~y~~-~g~~~DlvVIG~~~G~g 464 (665)
+..+++.++++++|++|+++|.||||+|.++|.|.||.|+++|+|+||+|+. +|+++|++|||||||+|
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 CCCCccceEEEEEeeCCCCCCCCcceEEEEEeccCCCHHHHHHHHHhhccccccccCCCCCCCCceeecCCCCCCCcEEE
Q 006003 465 RRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDVWI 544 (665)
Q Consensus 465 ~r~g~~~sfllg~~d~~~~~~~~~~~~~~~kVgsG~s~~~~~~l~~~l~~~~~~~~~~~~~pp~~~~~~~~~~~~pd~wi 544 (665)
+|+|++.+|+||+.++..++.+|.+|.++|+||+|+|++|+..+.++++++|.+ .++..+|+.++..+ ...||+||
T Consensus 460 ~rgg~~~~fl~a~~ek~~p~~~p~~f~sfcrvg~g~s~~e~~~v~~klr~~w~~-~~~~apP~s~l~~t---k~~Pd~wI 535 (881)
T KOG0966|consen 460 DRGGKVLSFLCALAEKAPPNSRPEKFCSFCRVGNGISQKERDTVREKLRGHWKP-TSLEAPPESFLFGT---KKIPDVWI 535 (881)
T ss_pred CCCCeeeeeeehhcccCCCCCccceeeEeeEecCCccHHHHHHHHHhhhhhccc-ccccCCCHHHHhcc---cCCCceeE
Confidence 999999999999998877777889999999999999999999999999999987 34444444444432 34799999
Q ss_pred eCCCceEEEEEeeeceecccCccCCCeeeeccEEEEEecCCCccCCCCHHHHHHHHHccCCCcccCCccCCCCCCCcccc
Q 006003 545 ESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDKPWHDCLDVQSFVELVHSSNGTTQKGKEYGGLQDDKPKQF 624 (665)
Q Consensus 545 ~~P~~s~v~ev~a~~~~~~s~~~~~g~sLRfPr~~riR~DK~~~d~~t~~el~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 624 (665)
+ |..|+|++|++. +++++..|.++|||||||+.++|+||+|+||+|+.+|.++...+. ++.+. +.+++
T Consensus 536 ~-P~~SiIlqikaa-~i~~s~~f~tn~tLrfPr~ekvR~DK~W~ec~tl~~l~~l~~~~~-------~d~~~---~~kk~ 603 (881)
T KOG0966|consen 536 D-PDNSIILQIKAA-EIVPSSNFVTNYTLRFPRIEKVRLDKPWHECLTLNELGDLVNVSK-------SDVED---KEKKK 603 (881)
T ss_pred C-CCCceEEEeehh-eeeecccccccceeecceeeeeecCCcHHHHhhHHHHHHHhcccc-------CCcch---hhhhc
Confidence 9 999999999953 345789999999999999999999999999999999999985321 11011 11111
Q ss_pred ccccccccccceecCCcccCCCcCCcccccCccCCceEEEC
Q 006003 625 RSSRKGEKKNVSIVPSHFLQTDVSDIKGETSIFSDMVFCIL 665 (665)
Q Consensus 625 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~g~~f~v~ 665 (665)
+...+ .+++....-|-..++.+.+.+.|++|+|++|||+
T Consensus 604 ~~t~~--~~k~~~~~i~~~~~~~~~~~~~s~if~gl~f~Vl 642 (881)
T KOG0966|consen 604 RDTLK--VRKRTRKAIHDSAPNRSKVAKISNIFDGLEFCVL 642 (881)
T ss_pred ccchh--hhhhhhhhhcccccchhcccchhhhhcCeeEEEe
Confidence 11111 1111112344556677889999999999999996
No 2
>PLN03113 DNA ligase 1; Provisional
Probab=100.00 E-value=1e-107 Score=932.07 Aligned_cols=551 Identities=24% Similarity=0.419 Sum_probs=471.8
Q ss_pred CCCcHHHHHHHHHHHHhcCChhHHHHHHHHHhhhc--CCCchHhhhHhh----cCCCCCCCccccCCCHHHHHHHHHHHh
Q 006003 5 EETEVIVLVSLFNWIQKTKPAAKKRSKFRKFLDTY--CDSVDYFSALRL----ILPSLDRERGSYGLKESVLANCLIDAL 78 (665)
Q Consensus 5 ~~~~F~~l~~~~e~i~~~~~~~~k~~~l~~~~~~~--~~~~~~~~~lrL----llp~~d~~r~~yglke~~L~k~~~~~~ 78 (665)
.+|||..||++|++|++++++.+|+.+|.+||... .+++|++++++| ++|.. ++.+|||+++.|+|+|++++
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 56999999999999999999999999999999986 367899999999 56664 46799999999999999999
Q ss_pred CCCcChHHHHHHhhhhcCCCCCCCCCHHHHHHHHhhhccC-CCCCCCCHHHHHHHHHHHHhhhh---HHhHHHHHHHHHH
Q 006003 79 GMSKDSADAVRLINWRKGGAAPNAGNFPMVAAEVLQRRQG-MISGGLTIKELNDLLDRLASSEN---RAEKISVLSTLIK 154 (665)
Q Consensus 79 ~~~~~~~~~~~L~~wk~~~~~~~~gD~~~~~~~v~~~r~~-~~~~~lTi~eV~~~Ld~la~~~~---~~~k~~~l~~ll~ 154 (665)
|++..... . .| ...||+|++|+.+.+++.. ..+.+|||.+|++.|++||..+| +++|..+|..|+.
T Consensus 205 g~~~~~ik---~-~y------~~~GDlG~vA~~~~~~q~~~~~~~~LTi~~V~~~L~~IA~~~G~~sq~~K~~~i~~Ll~ 274 (744)
T PLN03113 205 GRTEKQVK---K-QY------KELGDLGLVAKASRSSQSMMRKPEPLTVVKVFNTFQQIAKESGKDSQEKKKNRIKALLV 274 (744)
T ss_pred CcCHHHHH---H-HH------HHhCCHHHHHHhhhcccccccCCCCCCHHHHHHHHHHHHhhhCccCHHHHHHHHHHHHH
Confidence 99875432 2 33 3579999999987665543 34678999999999999999886 5678899999999
Q ss_pred hCCHHHHHHHHHHHHhhhccCCcccccccccCcCH------------------------HHHHhhhCCHHHHHHHHhhhh
Q 006003 155 KTNAQEMKWIIMIILKDLKLGISEKSIFHEFHPDA------------------------EDLFNVTCDLKLVCEKLKDRN 210 (665)
Q Consensus 155 ~~t~~E~k~l~RiilkdlriG~~e~til~~~hp~a------------------------~~~~~~~~dL~~v~~~l~~~~ 210 (665)
.+++.|++||+|+|+++||||++++||+.++|+.+ .++|+.++|+..|+..|....
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 256788888888887776533
Q ss_pred -hcc-ccCCccCCCccccccccccCCHHHHHHHhcCCceEEEEeeceeEEEEEE-eCCEEEEEecCCCCCCcchhhhHHH
Q 006003 211 -QRH-KRQDIEVGKAVRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHK-NGSEIHYFSRSFLDHSEYGHAMSKI 287 (665)
Q Consensus 211 -~~~-~~~~i~~g~~~~PmLA~~~~~~~~~~~~~~~~~~~~E~K~DG~R~qih~-~g~~v~~~SR~g~d~t~~~p~l~~~ 287 (665)
..+ ....+++|.||+||||++.+++.+++++|.+.+|++|+||||+|||+|+ .+++|++|||||+|+|..||++.+.
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 223 5567999999999999999999899999988899999999999999998 5789999999999999999999886
Q ss_pred HHhhc--cccceeeeceEEEeeCCCCccccccchHHHHHHhhcCC---CCCCceEEEEEEEEeeCCccccCCCHHHHHHH
Q 006003 288 IEQNV--LVDRCILDGEMLVWDTSLNRFAEFGSNQEIAKAARDGL---SSDRQLCYFAFDVLYVGDTSVIHQSLKERHEL 362 (665)
Q Consensus 288 ~~~~~--~~~~~ILDGElv~~d~~~~~~~~F~~lq~~~~~~~~~~---~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~ 362 (665)
+.... .+++||||||+|+||..+++++||+.+|... ++.. +...++||+||||||+||++|++.||.+||++
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 64322 1578999999999999888899998877642 2221 22478999999999999999999999999999
Q ss_pred HHhhcCCCCCcceecccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHcCCceEEeecC--CCCCccCCCCCCeEE
Q 006003 363 LQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDL--GSKWEPGDRSGKWLK 440 (665)
Q Consensus 363 L~~~~~~~~~~~~~~~p~~~~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EGlV~K~~--~s~Y~~GkRs~~WlK 440 (665)
|++++.+.+++++++. ....++.++++++|++++++|+||||+|++ +|+|+||+|+.+|+|
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 234568999999999999999999999986 899999999999999
Q ss_pred EccccccC-CCcceEEEEEEEecCCCCCCccceEEEEEeeCCCCCCCCcceEEEEEeccCCCHHHHHHHHHhhccccccc
Q 006003 441 LKPEYIRA-GSDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKY 519 (665)
Q Consensus 441 iK~~y~~~-g~~~DlvVIG~~~G~g~r~g~~~sfllg~~d~~~~~~~~~~~~~~~kVgsG~s~~~~~~l~~~l~~~~~~~ 519 (665)
+|++|+++ ++++|+||||||+|+|+|+|.+|+|||||||+++ ++|++|||||||||++++++|.+.|++++..
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 cCCCCCCCCceeecCCCCCCCcEEEeCCCceEEEEEeeeceecccCccC---------CCeeeeccEEEEEecCCCccCC
Q 006003 520 EYPKRAPPSFYQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFS---------APYSLRFPRIDRVRYDKPWHDC 590 (665)
Q Consensus 520 ~~~~~~pp~~~~~~~~~~~~pd~wi~~P~~s~v~ev~a~~~~~~s~~~~---------~g~sLRfPr~~riR~DK~~~d~ 590 (665)
.||+|+... ...+||+||+ |. .|+||+++.. ..|+.|+ .|++||||||+|+|+||+|+||
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 244455442 2458999999 74 5999985432 2577776 4899999999999999999999
Q ss_pred CCHHHHHHHHHccC
Q 006003 591 LDVQSFVELVHSSN 604 (665)
Q Consensus 591 ~t~~el~~l~~~~~ 604 (665)
+|++++.+||+.+.
T Consensus 718 tt~~~l~~ly~~Q~ 731 (744)
T PLN03113 718 TSSEQVADMYNAQK 731 (744)
T ss_pred CCHHHHHHHHHHHH
Confidence 99999999997554
No 3
>PRK01109 ATP-dependent DNA ligase; Provisional
Probab=100.00 E-value=1.2e-104 Score=903.19 Aligned_cols=544 Identities=28% Similarity=0.482 Sum_probs=472.3
Q ss_pred CcHHHHHHHHHHHHhcCChhHHHHHHHHHhhhcCCCc----hHhhhHhhcCCCCCCCccccCCCHHHHHHHHHHHhCCCc
Q 006003 7 TEVIVLVSLFNWIQKTKPAAKKRSKFRKFLDTYCDSV----DYFSALRLILPSLDRERGSYGLKESVLANCLIDALGMSK 82 (665)
Q Consensus 7 ~~F~~l~~~~e~i~~~~~~~~k~~~l~~~~~~~~~~~----~~~~~lrLllp~~d~~r~~yglke~~L~k~~~~~~~~~~ 82 (665)
|+|+.||++|++|++++++.+|+.+|.+||.+.. ++ .+|+++++++|..+. .+|||+++.|+++|++++|++.
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 467777778899874 5899999999999999999998
Q ss_pred ChHHHHHHhhhhcCCCCCCCCCHHHHHHHHhhhccCC------CCCCCCHHHHHHHHHHHHhhh---hHHhHHHHHHHHH
Q 006003 83 DSADAVRLINWRKGGAAPNAGNFPMVAAEVLQRRQGM------ISGGLTIKELNDLLDRLASSE---NRAEKISVLSTLI 153 (665)
Q Consensus 83 ~~~~~~~L~~wk~~~~~~~~gD~~~~~~~v~~~r~~~------~~~~lTi~eV~~~Ld~la~~~---~~~~k~~~l~~ll 153 (665)
+..+. + | ...||||.+|+.++++++.. .+++||+.+|++.|++||+.+ ++.+|..+|..||
T Consensus 78 ~~~~~--~--~------~~~GDlg~~a~~~~~~~~~~~~~~~~~~~~lti~eV~~~L~~Ia~~sg~~s~~~k~~iL~~Ll 147 (590)
T PRK01109 78 KEVEN--L--Y------KKTGDLGEVARRLKSKKKQKSLLAFFSKEPLTVKEVYDTLVKIALATGEGSQDLKIKLLAGLL 147 (590)
T ss_pred HHHHH--H--H------HhcCCHHHHHHHHHhhcccccccccCCCCCcCHHHHHHHHHHHHhhhCCCcHHHHHHHHHHHH
Confidence 76552 1 3 34799999999999876532 357899999999999999987 4678899999999
Q ss_pred HhCCHHHHHHHHHHHHhhhccCCccccccc----cc-----CcCHHHHHhhhCCHHHHHHHHhhhh-hccccCCccCCCc
Q 006003 154 KKTNAQEMKWIIMIILKDLKLGISEKSIFH----EF-----HPDAEDLFNVTCDLKLVCEKLKDRN-QRHKRQDIEVGKA 223 (665)
Q Consensus 154 ~~~t~~E~k~l~RiilkdlriG~~e~til~----~~-----hp~a~~~~~~~~dL~~v~~~l~~~~-~~~~~~~i~~g~~ 223 (665)
.+++++|++||+|+|+++||+|+++++|++ ++ |++++++|+.++||+.||+.+.++. ..+....+++|.|
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 999999999999999999999999999987 34 4788999999999999999998764 3456678999999
Q ss_pred cccccccccCCHHHHHHHhcCCceEEEEeeceeEEEEEEeCCEEEEEecCCCCCCcchhhhHHHHHhhccccceeeeceE
Q 006003 224 VRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDGEM 303 (665)
Q Consensus 224 ~~PmLA~~~~~~~~~~~~~~~~~~~~E~K~DG~R~qih~~g~~v~~~SR~g~d~t~~~p~l~~~~~~~~~~~~~ILDGEl 303 (665)
|+||||++.+.++++++++.+ +|++|+||||+|||+|+++++|++|||||+|+|..||++.+.+..++..++|||||||
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 999999999988888888854 6999999999999999999999999999999999999999877655656899999999
Q ss_pred EEeeCCCCccccccchHHHHHHhhcC----CCCCCceEEEEEEEEeeCCccccCCCHHHHHHHHHhhcCCCCCcceeccc
Q 006003 304 LVWDTSLNRFAEFGSNQEIAKAARDG----LSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVP 379 (665)
Q Consensus 304 v~~d~~~~~~~~F~~lq~~~~~~~~~----~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~~~~~~~~p 379 (665)
|+||+.+++++||+.+|.. .++. .....|+||+||||||+||+++++.||.+||++|++++.+.+. +.+.
T Consensus 307 v~~d~~~g~~~~F~~l~~R---~r~~~~~~~~~~~p~~~~vFDiL~l~g~~l~~~pl~eRr~~L~~~~~~~~~-~~~~-- 380 (590)
T PRK01109 307 VAVDPETGEMRPFQELMHR---KRKYDIEEAIKEYPVNVFLFDLLYVDGEDLTDKPLPERRKKLEEIVKENDK-VKLA-- 380 (590)
T ss_pred EEEECCCCcccChHHHhhc---ccccchhhhcccCceEEEEEEEEEECCcchhhCcHHHHHHHHHHhcCCCCc-eEEe--
Confidence 9999777888999877654 1111 1124689999999999999999999999999999999987543 4332
Q ss_pred CCCCCccccCCCCCccccccCCHHHHHHHHHHHHHcCCceEEeecC--CCCCccCCCCCCeEEEccccccC-CCcceEEE
Q 006003 380 DHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDL--GSKWEPGDRSGKWLKLKPEYIRA-GSDLDVLI 456 (665)
Q Consensus 380 ~~~~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EGlV~K~~--~s~Y~~GkRs~~WlKiK~~y~~~-g~~~DlvV 456 (665)
....+++.+++.++|++++++|+||||+|++ +|+|+||+|+.+|+|+|++|+++ ++++|+||
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 1334678899999999999999999999999 99999999999999999999984 78999999
Q ss_pred EEEEecCCCCCCccceEEEEEeeCCCCCCCCcceEEEEEeccCCCHHHHHHHHHhhccccccccCCCCCCCCceeecCCC
Q 006003 457 IGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNS 536 (665)
Q Consensus 457 IG~~~G~g~r~g~~~sfllg~~d~~~~~~~~~~~~~~~kVgsG~s~~~~~~l~~~l~~~~~~~~~~~~~pp~~~~~~~~~ 536 (665)
||++||+|+|+|.+|+|+||+||+++ ++|+++|+||||||++++++|.+.+.+++.+. .|| +. ..
T Consensus 446 iG~~~g~Gkr~~~~g~~ll~~~d~~~-----~~~~~v~kvgtG~sd~~~~~l~~~l~~~~~~~-----~~~-~~----~~ 510 (590)
T PRK01109 446 VGAFYGRGRRGGKYGSLLMAAYDPKT-----DTFETVCKVGSGFTDEDLDELPKMLKPYKIDH-----KHP-RV----VS 510 (590)
T ss_pred EEeEeCCCccCCccccEEEEEEcCCC-----CeEEEEEEECCCCCHHHHHHHHHHhhhhcccC-----CCc-cc----cc
Confidence 99999999999999999999998643 48999999999999999999999999988641 233 22 13
Q ss_pred CCCCcEEEeCCCceEEEEEeeeceecccCccC---------CCeeeeccEEEEEecCCCccCCCCHHHHHHHHHccC
Q 006003 537 KERPDVWIESPEKSIILSITSDIRTIRSEVFS---------APYSLRFPRIDRVRYDKPWHDCLDVQSFVELVHSSN 604 (665)
Q Consensus 537 ~~~pd~wi~~P~~s~v~ev~a~~~~~~s~~~~---------~g~sLRfPr~~riR~DK~~~d~~t~~el~~l~~~~~ 604 (665)
..+||+||+ | ++|+||+++..+ .|+.|+ .|++||||||+++|+||+|+||+|++++.+||+++.
T Consensus 511 ~~~pdvwv~-P--~~V~eV~~~~it-~S~~~~~~~~~~~~~~g~~LRfPr~~~~R~DK~~~d~~t~~~~~~ly~~q~ 583 (590)
T PRK01109 511 KMEPDVWVE-P--KLVAEIIGAEIT-LSPLHTCCLGVVEKGAGLAIRFPRFIRWRDDKSPEDATTTEEILEMYKRQK 583 (590)
T ss_pred ccCCcEEEe-c--cEEEEEEeeecc-cCcceecccccccCCCceeEEcCeeeEeeCCCChhhCcCHHHHHHHHHHhh
Confidence 568999999 7 689999865433 577777 689999999999999999999999999999997554
No 4
>KOG0967 consensus ATP-dependent DNA ligase I [Replication, recombination and repair]
Probab=100.00 E-value=3.3e-102 Score=834.79 Aligned_cols=551 Identities=27% Similarity=0.496 Sum_probs=477.5
Q ss_pred CCCcHHHHHHHHHHHHhcCChhHHHHHHHHHhhhcC--CCchHhhhHhhcCCCC--CCCccccCCCHHHHHHHHHHHhCC
Q 006003 5 EETEVIVLVSLFNWIQKTKPAAKKRSKFRKFLDTYC--DSVDYFSALRLILPSL--DRERGSYGLKESVLANCLIDALGM 80 (665)
Q Consensus 5 ~~~~F~~l~~~~e~i~~~~~~~~k~~~l~~~~~~~~--~~~~~~~~lrLllp~~--d~~r~~yglke~~L~k~~~~~~~~ 80 (665)
+.+||.++|.+|++|+++++|.+...++.+||.+.. +|+|+.|+++|.+.++ |.++.++|++|+.|.|+|++++|.
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 569999999999999999999999999999999864 6899999999988877 677899999999999999999999
Q ss_pred CcChHHHHHHhhhhcCCCCCCCCCHHHHHHHHhhhcc-CCCCCCCCHHHHHHHHHHHHhhhh---HHhHHHHHHHHHHhC
Q 006003 81 SKDSADAVRLINWRKGGAAPNAGNFPMVAAEVLQRRQ-GMISGGLTIKELNDLLDRLASSEN---RAEKISVLSTLIKKT 156 (665)
Q Consensus 81 ~~~~~~~~~L~~wk~~~~~~~~gD~~~~~~~v~~~r~-~~~~~~lTi~eV~~~Ld~la~~~~---~~~k~~~l~~ll~~~ 156 (665)
+...+ |+. +...||+|.||+....... +..|.+|||.+|++.|.+||..+| +..|..++..||..|
T Consensus 177 t~~~v---k~~-------~~~~GDLG~VA~~sR~sQ~~m~~P~pLtV~~VF~~Lr~IAk~sG~~S~~kK~~lik~Llvac 246 (714)
T KOG0967|consen 177 TLSHV---KNQ-------YNKLGDLGLVAQGSRSSQRMMFKPKPLTVRDVFSTLRKIAKESGKGSQNKKKDLIKALLVAC 246 (714)
T ss_pred cHHHH---HHH-------HHhcCcHHHHHhhcccccccccCCCCccHHHHHHHHHHHHHhhCcchhHHHHHHHHHHHHhc
Confidence 97643 332 2457999999998755433 346789999999999999999887 578899999999999
Q ss_pred CHHHHHHHHHHHHhhhccCCccccccccc------C----------cC------------HHHHHhhhCCHHHHHHHHhh
Q 006003 157 NAQEMKWIIMIILKDLKLGISEKSIFHEF------H----------PD------------AEDLFNVTCDLKLVCEKLKD 208 (665)
Q Consensus 157 t~~E~k~l~RiilkdlriG~~e~til~~~------h----------p~------------a~~~~~~~~dL~~v~~~l~~ 208 (665)
++.|+|||+|.|.++||||++++|||.++ + ++ ..++|+.++|+..++..|.+
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 99999999999999999999999998543 1 22 23579999999999988766
Q ss_pred hhh--ccccCCccCCCccccccccccCCHHHHHHHhcCCceEEEEeeceeEEEEEE-eCCEEEEEecCCCCCCcchhhhH
Q 006003 209 RNQ--RHKRQDIEVGKAVRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHK-NGSEIHYFSRSFLDHSEYGHAMS 285 (665)
Q Consensus 209 ~~~--~~~~~~i~~g~~~~PmLA~~~~~~~~~~~~~~~~~~~~E~K~DG~R~qih~-~g~~v~~~SR~g~d~t~~~p~l~ 285 (665)
... ..+.+.+.||.|++||||++.+.+.++++++.+..|.+|+||||+|+|||. .+|.|.+||||+++.|..||++.
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 345678999999999999999999999999999999999999999999997 57899999999999999999998
Q ss_pred HHHHhhc--cccceeeeceEEEeeCCCCccccccchHHHHHHhhcCCC---CCCceEEEEEEEEeeCCccccCCCHHHHH
Q 006003 286 KIIEQNV--LVDRCILDGEMLVWDTSLNRFAEFGSNQEIAKAARDGLS---SDRQLCYFAFDVLYVGDTSVIHQSLKERH 360 (665)
Q Consensus 286 ~~~~~~~--~~~~~ILDGElv~~d~~~~~~~~F~~lq~~~~~~~~~~~---~~~~~~~~vFDiL~lng~~l~~~pl~eRr 360 (665)
..+.... .+.++|||||+|+||...++++||+.|. .+.|+..+ ....+|.++||+||+||++|.++||.+||
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 7664322 3579999999999999988999995443 34444432 34689999999999999999999999999
Q ss_pred HHHHhhcCCCCCcceecccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHcCCceEEeecC--CCCCccCCCCCCe
Q 006003 361 ELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDL--GSKWEPGDRSGKW 438 (665)
Q Consensus 361 ~~L~~~~~~~~~~~~~~~p~~~~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EGlV~K~~--~s~Y~~GkRs~~W 438 (665)
++|.+.+...+|.++++. ...+.+.++++++|++++.+++||+|+|.+ ++.|+|.+||.+|
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 345688999999999999999999999976 4789999999999
Q ss_pred EEEccccccC-CCcceEEEEEEEecCCCCCCccceEEEEEeeCCCCCCCCcceEEEEEeccCCCHHHHHHHHHhhccccc
Q 006003 439 LKLKPEYIRA-GSDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFR 517 (665)
Q Consensus 439 lKiK~~y~~~-g~~~DlvVIG~~~G~g~r~g~~~sfllg~~d~~~~~~~~~~~~~~~kVgsG~s~~~~~~l~~~l~~~~~ 517 (665)
+|+|++|+++ |+++||||||+|||.|+|.|++|+||+|||+++. +.|.++||+||||||+++.++.+.|.....
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 9999999995 8999999999999999999999999999999875 589999999999999999999998865432
Q ss_pred cccCCCCCCCCceeecCCCCCCCcEEEeCCCceEEEEEe-eeceecccCccC---------CCeeeeccEEEEEecCCCc
Q 006003 518 KYEYPKRAPPSFYQVTNNSKERPDVWIESPEKSIILSIT-SDIRTIRSEVFS---------APYSLRFPRIDRVRYDKPW 587 (665)
Q Consensus 518 ~~~~~~~~pp~~~~~~~~~~~~pd~wi~~P~~s~v~ev~-a~~~~~~s~~~~---------~g~sLRfPr~~riR~DK~~ 587 (665)
..|+++|.+. ...+||+|++ |. .||||+ ||+. + |+.|. .|.|||||||.|+|+||.+
T Consensus 622 ------~~~~~~y~~d--~s~kPd~wf~-p~--~VwEvk~Adlt-~-SPiy~Aa~Glv~~dkGISlRFPRfiRiR~DK~p 688 (714)
T KOG0967|consen 622 ------DSPKPYYRFD--ESLKPDVWFE-PT--EVWEVKAADLT-L-SPIYKAALGLVDPDKGISLRFPRFIRIRDDKNP 688 (714)
T ss_pred ------cCcHhhcccC--ccCCCccccC-HH--HHHHHhhcccc-c-cchhHhhhcCcCCCCceeEecceeeEeeccCCh
Confidence 2456677775 4567999999 75 489997 5653 2 45443 5899999999999999999
Q ss_pred cCCCCHHHHHHHHHcc
Q 006003 588 HDCLDVQSFVELVHSS 603 (665)
Q Consensus 588 ~d~~t~~el~~l~~~~ 603 (665)
+||+|.+++.+||+++
T Consensus 689 eeAtts~qiaemY~~Q 704 (714)
T KOG0967|consen 689 EEATTSSQIAEMYQAQ 704 (714)
T ss_pred hhcccHHHHHHHHHHH
Confidence 9999999999999776
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=6e-97 Score=830.83 Aligned_cols=494 Identities=34% Similarity=0.608 Sum_probs=427.5
Q ss_pred ccCCCHHHHHHHHHHHhCCCcChHHHHHHhhhhcCCCCCCCCCHHHHHHHHhhhcc--CCCCCCCCHHHHHHHHHHHHhh
Q 006003 62 SYGLKESVLANCLIDALGMSKDSADAVRLINWRKGGAAPNAGNFPMVAAEVLQRRQ--GMISGGLTIKELNDLLDRLASS 139 (665)
Q Consensus 62 ~yglke~~L~k~~~~~~~~~~~~~~~~~L~~wk~~~~~~~~gD~~~~~~~v~~~r~--~~~~~~lTi~eV~~~Ld~la~~ 139 (665)
+|||||+.|+|++++++|+++++.++..+ ..||+|.+++.++.+.. ...+++|||.+||+.|++||+.
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 49999999999999999999998887544 34899999998886553 2346889999999999999998
Q ss_pred hh---HHhHHHHHHHHHHhCCHHHHHHHHHHHHhhhccCCcccccccccCcCH-------HHHHhhhCCHHHHHHHHhhh
Q 006003 140 EN---RAEKISVLSTLIKKTNAQEMKWIIMIILKDLKLGISEKSIFHEFHPDA-------EDLFNVTCDLKLVCEKLKDR 209 (665)
Q Consensus 140 ~~---~~~k~~~l~~ll~~~t~~E~k~l~RiilkdlriG~~e~til~~~hp~a-------~~~~~~~~dL~~v~~~l~~~ 209 (665)
++ +.+|..+|..|+.+|+|.|++||+|+|+++||||+++++|+.++|+++ +++|++|+||+.||+.|.++
T Consensus 71 ~g~~s~~~k~~~l~~ll~~~~~~e~k~l~r~i~~~lriG~~~~~il~al~~~~~~~~~~~~~~~~~~~dl~~v~~~l~~~ 150 (514)
T TIGR00574 71 SGEGSQDKKIKLLKSLLKRASPLEAKYLIRTILGDLRIGIAEKTILDALAKAFLLSHPDVERAFNLTNDLGKVAKILLEP 150 (514)
T ss_pred hCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHhhhcccCccHHHHHHHHHHHhccchHHHHHHHHhCCCHHHHHHHHHhc
Confidence 75 578889999999999999999999999999999999999999998877 99999999999999999876
Q ss_pred hhcc--ccCCccCCCccccccccccCCHHHHHHHhcCCceEEEEeeceeEEEEEEeCCEEEEEecCCCCCCcchhhh-HH
Q 006003 210 NQRH--KRQDIEVGKAVRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAM-SK 286 (665)
Q Consensus 210 ~~~~--~~~~i~~g~~~~PmLA~~~~~~~~~~~~~~~~~~~~E~K~DG~R~qih~~g~~v~~~SR~g~d~t~~~p~l-~~ 286 (665)
..+. ....+++|.||+||||+++.+++++++++.+ +|++|+||||+|||+|+++++|++|||||+++|..+|++ .+
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 3367999999999999999988888888764 899999999999999999999999999999999999998 66
Q ss_pred HHHhhcc-ccceeeeceEEEeeCCCCccccccchHHHHHHhh-cCCCCCCceEEEEEEEEeeCCccccCCCHHHHHHHHH
Q 006003 287 IIEQNVL-VDRCILDGEMLVWDTSLNRFAEFGSNQEIAKAAR-DGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQ 364 (665)
Q Consensus 287 ~~~~~~~-~~~~ILDGElv~~d~~~~~~~~F~~lq~~~~~~~-~~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~ 364 (665)
.+...+. ..+||||||||+||+.+++++||+.++...+... .....+.+++|++|||||+||+++++.||.+|+++|+
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 1112356899999999999999999999999999999
Q ss_pred hhcCCCCCcceecccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHcCCceEEeecCCCCCccCCCCCCeEEEccc
Q 006003 365 KVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPE 444 (665)
Q Consensus 365 ~~~~~~~~~~~~~~p~~~~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EGlV~K~~~s~Y~~GkRs~~WlKiK~~ 444 (665)
+++.+.++++.++. ...+++.+++.++|++++++|+||||+|+++|+|+||+|+.+|+|+|++
T Consensus 310 ~~~~~~~~~i~~~~-----------------~~~~~~~e~~~~~~~~~~~~g~EGlv~K~~ds~Y~~G~Rs~~WlK~K~~ 372 (514)
T TIGR00574 310 SILKPIPNRIEIAE-----------------MKITSNVEELEKFLNEAISEGCEGLMLKDLKSIYEPGKRGWLWLKFKPE 372 (514)
T ss_pred HhccCCCCcEEEEE-----------------EEecCCHHHHHHHHHHHHHcCCceEEEecCCCcccCCCCCCcceeCchh
Confidence 99988777665431 3446789999999999999999999999999999999999999999999
Q ss_pred cccC-CCcceEEEEEEEecCCCCCCccceEEEEEeeCCCCCCCCcceEEEEEeccCCCHHHHHHHHHhhccccccccCCC
Q 006003 445 YIRA-GSDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPK 523 (665)
Q Consensus 445 y~~~-g~~~DlvVIG~~~G~g~r~g~~~sfllg~~d~~~~~~~~~~~~~~~kVgsG~s~~~~~~l~~~l~~~~~~~~~~~ 523 (665)
|+++ ++++|++|||+++|+|+++|.+|+|+||++|++. ++|+++|+||||||++++++|.+++.++|.... +.
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 389999999999999999999999999986521 11
Q ss_pred CCCCCceeecCCCCCCCcEEEeCCCceEEEEEeeeceecccCccCC-CeeeeccEEEEEecCCCccCCCCHHHHHHHH
Q 006003 524 RAPPSFYQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSA-PYSLRFPRIDRVRYDKPWHDCLDVQSFVELV 600 (665)
Q Consensus 524 ~~pp~~~~~~~~~~~~pd~wi~~P~~s~v~ev~a~~~~~~s~~~~~-g~sLRfPr~~riR~DK~~~d~~t~~el~~l~ 600 (665)
.+|.+ ....|++|++ | ++|+||+++.. ..|+.|++ |++||||||+++|+||+|+||+|++++.+||
T Consensus 447 -~~~~~------~~~~~~~w~~-p--~~V~eV~~~e~-t~s~~~~~~g~~LRfPr~~~~R~DK~~~d~~~~~~~~~ly 513 (514)
T TIGR00574 447 -RVPSI------LSDEPDIWFD-P--AIVWEVTGAEI-TRSPTYKANGISLRFPRFSRIRDDKGPEDATTIEEIKELY 513 (514)
T ss_pred -CCccc------ccCCCeEEec-C--CeEEEEEhhhe-eecCcccccceEEEcceEEEEcCCCChHHCCCHHHHHHHh
Confidence 12222 1257899999 7 57999986543 36888998 9999999999999999999999999999998
No 6
>PRK09247 ATP-dependent DNA ligase; Validated
Probab=100.00 E-value=9.5e-95 Score=812.40 Aligned_cols=523 Identities=20% Similarity=0.255 Sum_probs=438.2
Q ss_pred HHHHHHHHHHHHhcCChhHHHHHHHHHhhhcCCCchHhhhHhhcCCCCCCCccccCCCHHHHHHHHHHHhCCCcChHHHH
Q 006003 9 VIVLVSLFNWIQKTKPAAKKRSKFRKFLDTYCDSVDYFSALRLILPSLDRERGSYGLKESVLANCLIDALGMSKDSADAV 88 (665)
Q Consensus 9 F~~l~~~~e~i~~~~~~~~k~~~l~~~~~~~~~~~~~~~~lrLllp~~d~~r~~yglke~~L~k~~~~~~~~~~~~~~~~ 88 (665)
+.+||++|++|++++++.+|+++|.+||.++ +++++.++++|+++... .|||+++.|.+++++++|++....+.
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 48999999999999999999765442
Q ss_pred HHhhhhcCCCCCCCCCHHHHHHHHhhhccCCC---CCCCCHHHHHHHHHHHHhhhhHHhHHHHHHHHHHhCCHHHHHHHH
Q 006003 89 RLINWRKGGAAPNAGNFPMVAAEVLQRRQGMI---SGGLTIKELNDLLDRLASSENRAEKISVLSTLIKKTNAQEMKWII 165 (665)
Q Consensus 89 ~L~~wk~~~~~~~~gD~~~~~~~v~~~r~~~~---~~~lTi~eV~~~Ld~la~~~~~~~k~~~l~~ll~~~t~~E~k~l~ 165 (665)
. +...||+|++|+.++++++... +.++||.+|.+.|.++|.. +|...|..|+.+++|.|++||+
T Consensus 75 ---~------~~~~GDlg~~~~~~~~~~~~~~~~~~~~~tv~~v~~~l~~~~~~----~k~~~l~~ll~~~~~~e~~~i~ 141 (539)
T PRK09247 75 ---S------YDYVGDLAETIALLLPAPSDEASDLPLAPWLEEVLLPLRGLGRE----ELRAALADLWDRLDEDGRFALN 141 (539)
T ss_pred ---H------HHhcCCHHHHHHHhcccccccccCCCccccHHHHHHHHHhhhHH----HHHHHHHHHHHhCCHHHHHHHH
Confidence 1 2457999999999987765321 3579999999998888753 4778899999999999999999
Q ss_pred HHHHhhhccCCcccccccccC----cC---HHHHHhh--hCCHHHHHHHHhhhhhccccCCccCCCccccccccccCCHH
Q 006003 166 MIILKDLKLGISEKSIFHEFH----PD---AEDLFNV--TCDLKLVCEKLKDRNQRHKRQDIEVGKAVRPQLAMRIGDAH 236 (665)
Q Consensus 166 RiilkdlriG~~e~til~~~h----p~---a~~~~~~--~~dL~~v~~~l~~~~~~~~~~~i~~g~~~~PmLA~~~~~~~ 236 (665)
|+|+++||||++++||+.+++ .+ ++++|+. ++|++.+++.+.... ....+++|.|++||||++..+..
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 3445655 778888877665421 45678999999999999998765
Q ss_pred HHHHHhcCCceEEEEeeceeEEEEEEeCCEEEEEecCCCCCCcchhhhHHHHHhhccccceeeeceEEEeeCCCCccccc
Q 006003 237 AAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDGEMLVWDTSLNRFAEF 316 (665)
Q Consensus 237 ~~~~~~~~~~~~~E~K~DG~R~qih~~g~~v~~~SR~g~d~t~~~p~l~~~~~~~~~~~~~ILDGElv~~d~~~~~~~~F 316 (665)
+.. +...+|++|+||||+|||+|++++++++|||||+++|..||++.+.+. .+ +.+||||||||+||+.++.+.||
T Consensus 219 ~~~--~~~~~~~~E~K~DG~R~qih~~~~~v~lfSR~g~d~t~~fPei~~~~~-~l-~~~~ILDGElv~~~~~~~~~~~F 294 (539)
T PRK09247 219 LTL--GDPADWQAEWKWDGIRVQLVRRGGEVRLWSRGEELITERFPELAEAAE-AL-PDGTVLDGELLVWRPEDGRPQPF 294 (539)
T ss_pred hhh--cCCCcEEEEEeEcceEEEEEEeCCEEEEEeCCCccchhhhHHHHHHHH-hC-CCCEEEEeEEEEEECCCCCcCCH
Confidence 432 334589999999999999999999999999999999999999988653 33 46799999999999766778999
Q ss_pred cchHHHHHHhhc--CCCCCCceEEEEEEEEeeCCccccCCCHHHHHHHHHhhcCCCCC-cceecccCCCCCccccCCCCC
Q 006003 317 GSNQEIAKAARD--GLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKG-RLETLVPDHGLNSHVRPQGEP 393 (665)
Q Consensus 317 ~~lq~~~~~~~~--~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~~-~~~~~~p~~~~~~~v~~~~~~ 393 (665)
+.+|....+... ....+.++||++|||||+||+++++.||.+||++|++++.+.++ ++.++.
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 888765332111 01124689999999999999999999999999999999977643 444321
Q ss_pred ccccccCCHHHHHHHHHHHHHcCCceEEeecCCCCCccCCCCCCeEEEccccccCCCcceEEEEEEEecCCCCCCccceE
Q 006003 394 CWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLIIGGYYGSGRRGGEVAQF 473 (665)
Q Consensus 394 ~~~~~~~~~~~i~~~~~~ai~~g~EGlV~K~~~s~Y~~GkRs~~WlKiK~~y~~~g~~~DlvVIG~~~G~g~r~g~~~sf 473 (665)
...+.+.+++.++|++++++|+||||+|+++|+|+||+|+..|+|+|++| .++|+||||+++|+|+|+|.+|+|
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 EEEEeeCCCCCCCCcceEEEEEeccCCCHHHHHHHHHhhccccccccCCCCCCCCceeecCCCCCCCcEEEeCCCceEEE
Q 006003 474 LVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDVWIESPEKSIIL 553 (665)
Q Consensus 474 llg~~d~~~~~~~~~~~~~~~kVgsG~s~~~~~~l~~~l~~~~~~~~~~~~~pp~~~~~~~~~~~~pd~wi~~P~~s~v~ 553 (665)
+||+++++.+ ...|++|||||||||++++++|.+.++++... ...|++|++ |. +|+
T Consensus 434 lla~~~~~~~---~~~~~~v~kvgsGftd~~l~~l~~~l~~~~~~------------------~~~~~~~v~-P~--~V~ 489 (539)
T PRK09247 434 TFGVWDGPEG---GRQLVPFAKAYSGLTDEEIKQLDRWVRKNTVE------------------RFGPVRSVR-PE--LVF 489 (539)
T ss_pred EEEEEcCCCC---ceeEEEEEEECCCCCHHHHHHHHHHHhhcccc------------------cCCCceEec-Cc--eEE
Confidence 9999976531 13699999999999999999999877653211 125799999 74 799
Q ss_pred EEeeeceecccCccCCCeeeeccEEEEEecCCCccCCCCHHHHHHHHHcc
Q 006003 554 SITSDIRTIRSEVFSAPYSLRFPRIDRVRYDKPWHDCLDVQSFVELVHSS 603 (665)
Q Consensus 554 ev~a~~~~~~s~~~~~g~sLRfPr~~riR~DK~~~d~~t~~el~~l~~~~ 603 (665)
||+++.. ..|+.|++|++||||||+++|+||+|+||+|++++.+||+.+
T Consensus 490 EV~~~ei-t~S~~~~~G~~LRfPr~~~~R~DK~~~ea~t~~~l~~l~~~~ 538 (539)
T PRK09247 490 EIAFEGI-QRSKRHKSGIAVRFPRILRWRWDKPAREADTLETLQALLDAE 538 (539)
T ss_pred EEEecee-eecCCcCCCcEEEcceEEEEeCCCChHHCcCHHHHHHHHhcC
Confidence 9986532 368889999999999999999999999999999999999643
No 7
>PRK03180 ligB ATP-dependent DNA ligase; Reviewed
Probab=100.00 E-value=2.1e-94 Score=803.49 Aligned_cols=493 Identities=21% Similarity=0.350 Sum_probs=424.0
Q ss_pred CcHHHHHHHHHHHHhcCChhHHHHHHHHHhhhcCCCchHhhhHhhcCCCCCCCccccCCCHHHHHHHHHHHhCCCcChHH
Q 006003 7 TEVIVLVSLFNWIQKTKPAAKKRSKFRKFLDTYCDSVDYFSALRLILPSLDRERGSYGLKESVLANCLIDALGMSKDSAD 86 (665)
Q Consensus 7 ~~F~~l~~~~e~i~~~~~~~~k~~~l~~~~~~~~~~~~~~~~lrLllp~~d~~r~~yglke~~L~k~~~~~~~~~~~~~~ 86 (665)
|+|++||++|++|++|+++.+|+++|++||.+. .++++.++++|+...+. .++.|++++.+.++++.
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 689999999999999999999999999999987 56799999999998886 34799998666665321
Q ss_pred HHHHhhhhcCCCCCCCCCHHHHHHHHhhhccCCCCCCCCHHHHHHHHHHHHhhhh---HHhHHHHHHHHHHhCCHHHHHH
Q 006003 87 AVRLINWRKGGAAPNAGNFPMVAAEVLQRRQGMISGGLTIKELNDLLDRLASSEN---RAEKISVLSTLIKKTNAQEMKW 163 (665)
Q Consensus 87 ~~~L~~wk~~~~~~~~gD~~~~~~~v~~~r~~~~~~~lTi~eV~~~Ld~la~~~~---~~~k~~~l~~ll~~~t~~E~k~ 163 (665)
..+++|||.+||+.|++||..+| +++|..+|..|+.+|+|.|++|
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 01257999999999999999865 5788899999999999999999
Q ss_pred HHHHHHhhhccCCccccccccc-------CcCHHHHHhhhCCHHHHHHHHh-hhhhccccCCccCCCccccccccccCCH
Q 006003 164 IIMIILKDLKLGISEKSIFHEF-------HPDAEDLFNVTCDLKLVCEKLK-DRNQRHKRQDIEVGKAVRPQLAMRIGDA 235 (665)
Q Consensus 164 l~RiilkdlriG~~e~til~~~-------hp~a~~~~~~~~dL~~v~~~l~-~~~~~~~~~~i~~g~~~~PmLA~~~~~~ 235 (665)
|+|+|+++||||+++++|+.++ +++++++|++|+|++.||+.+. ++...+....|++|.||+||||++..++
T Consensus 116 l~r~i~~~lRiGv~~~~v~~Ala~a~~~~~~~v~~a~~~~~dl~~v~~~~l~~~~~~~~~~~i~~~~P~~PMLA~~~~~~ 195 (508)
T PRK03180 116 LRRLLTGELRQGALDGVMADAVARAAGVPAAAVRRAAMLAGDLPAVAAAALTGGAAALARFRLEVGRPVRPMLAQTATSV 195 (508)
T ss_pred HHHHHhCCCcccccHHHHHHHHHHHhCCCHHHHHHHHHHcCCHHHHHHHHHhcCccccccCCCCCCCCCCCccCCcCCCh
Confidence 9999999999999999999877 3567889999999999999655 4455566778999999999999999888
Q ss_pred HHHHHHhcCCceEEEEeeceeEEEEEEeCCEEEEEecCCCCCCcchhhhHHHHHhhccccceeeeceEEEeeCCCCcccc
Q 006003 236 HAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDGEMLVWDTSLNRFAE 315 (665)
Q Consensus 236 ~~~~~~~~~~~~~~E~K~DG~R~qih~~g~~v~~~SR~g~d~t~~~p~l~~~~~~~~~~~~~ILDGElv~~d~~~~~~~~ 315 (665)
++++++++ .+|++|+||||+|||+|++++++++|||||+++|..+|++.+.+. .+..++||||||||+||+. +++.|
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 88888885 579999999999999999999999999999999999999987653 3445789999999999974 67889
Q ss_pred ccchHHHHHHhhc--CCCCCCceEEEEEEEEeeCCccccCCCHHHHHHHHHhhcCCCCCcceecccCCCCCccccCCCCC
Q 006003 316 FGSNQEIAKAARD--GLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEP 393 (665)
Q Consensus 316 F~~lq~~~~~~~~--~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~~~~~~~~p~~~~~~~v~~~~~~ 393 (665)
|+.++....+... ......+++|++|||||+||++++++||.+||++|++++.+.. .+ |
T Consensus 273 F~~l~~R~~~k~~~~~~~~~~pv~~~~FDlL~l~G~dl~~~pl~eRr~~L~~~~~~~~-~~----~-------------- 333 (508)
T PRK03180 273 FQVTASRFGRRVDVAAARATQPLSPFFFDALHLDGRDLLDAPLSERLAALDALVPAAH-RV----P-------------- 333 (508)
T ss_pred HHHHHHHhccccchhhhcccCceEEEEEeehhcCCcchhcCCHHHHHHHHHHhhcccc-cc----c--------------
Confidence 9776654322110 0112468999999999999999999999999999999986421 10 0
Q ss_pred ccccccCCHHHHHHHHHHHHHcCCceEEeecCCCCCccCCCCCCeEEEccccccCCCcceEEEEEEEecCCCCCCccceE
Q 006003 394 CWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLIIGGYYGSGRRGGEVAQF 473 (665)
Q Consensus 394 ~~~~~~~~~~~i~~~~~~ai~~g~EGlV~K~~~s~Y~~GkRs~~WlKiK~~y~~~g~~~DlvVIG~~~G~g~r~g~~~sf 473 (665)
....++.++++++|++++++|+||||+|+++|+|+||+|+.+|+|+|+. +++|+||||+++|+|+|+|.+|+|
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 2234678999999999999999999999999999999999999999996 499999999999999999999999
Q ss_pred EEEEeeCCCCCCCCcceEEEEEeccCCCHHHHHHHHHhhccccccccCCCCCCCCceeecCCCCCCCcEEEeCCCceEEE
Q 006003 474 LVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDVWIESPEKSIIL 553 (665)
Q Consensus 474 llg~~d~~~~~~~~~~~~~~~kVgsG~s~~~~~~l~~~l~~~~~~~~~~~~~pp~~~~~~~~~~~~pd~wi~~P~~s~v~ 553 (665)
+||+||+++ ++|++|||||||||++++++|.+.+.++... ...|++||+ |. +|+
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 135799999 75 699
Q ss_pred EEeeeceecccCccCCCeeeeccEEEEEecCCCccCCCCHHHHHHHH
Q 006003 554 SITSDIRTIRSEVFSAPYSLRFPRIDRVRYDKPWHDCLDVQSFVELV 600 (665)
Q Consensus 554 ev~a~~~~~~s~~~~~g~sLRfPr~~riR~DK~~~d~~t~~el~~l~ 600 (665)
||+++.. ..|+.|++|++||||||+|+|+||+|+||+|++++.+||
T Consensus 461 EV~~~~i-t~S~~~~~G~~LRfPr~~r~R~DK~~~ea~tl~~~~~l~ 506 (508)
T PRK03180 461 EIAFDGV-QRSTRYPGGVALRFARVLRYRPDKTPAEADTIDTVRALL 506 (508)
T ss_pred EEEeeEe-eeCCcccCCeEEECCeeeEeeCCCChHHCcCHHHHHHHh
Confidence 9986543 367889999999999999999999999999999999998
No 8
>PHA02587 30 DNA ligase; Provisional
Probab=100.00 E-value=7.5e-66 Score=572.33 Aligned_cols=447 Identities=20% Similarity=0.280 Sum_probs=334.8
Q ss_pred HHHHHHHHhcCChhHHHHHHHHHhhhcCCCchHhhhHhhcCCCCCCCccccCCCHHHHHHHHHHHhCCCcChHHHHHHhh
Q 006003 13 VSLFNWIQKTKPAAKKRSKFRKFLDTYCDSVDYFSALRLILPSLDRERGSYGLKESVLANCLIDALGMSKDSADAVRLIN 92 (665)
Q Consensus 13 ~~~~e~i~~~~~~~~k~~~l~~~~~~~~~~~~~~~~lrLllp~~d~~r~~yglke~~L~k~~~~~~~~~~~~~~~~~L~~ 92 (665)
-+++++|+++.++++|.+||.+..+ .+.+--+++|.+...- .|||+.
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 4789999999999999998887744 3567778888766653 577432
Q ss_pred hhcCCCCCCCCCHHHHHHHHhhhccCCCCCCCCHHH-HHHHHHHHHhhhh-HHhHHHHHHHHHHhCCHHHHHHHHHHHHh
Q 006003 93 WRKGGAAPNAGNFPMVAAEVLQRRQGMISGGLTIKE-LNDLLDRLASSEN-RAEKISVLSTLIKKTNAQEMKWIIMIILK 170 (665)
Q Consensus 93 wk~~~~~~~~gD~~~~~~~v~~~r~~~~~~~lTi~e-V~~~Ld~la~~~~-~~~k~~~l~~ll~~~t~~E~k~l~Riilk 170 (665)
|..++.. ....+.+++.+ +..+..+||+..- .+.++..|..++.+|||.|++||+|+|++
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 1111100 01124567777 5556667887654 56778899999999999999999999999
Q ss_pred hhccCCcccccccccCcCHHHHHhhhCCHHHHHHHHhhhhhccccCCccCCCcccc-ccccccCCHHHHHHHhcCCceEE
Q 006003 171 DLKLGISEKSIFHEFHPDAEDLFNVTCDLKLVCEKLKDRNQRHKRQDIEVGKAVRP-QLAMRIGDAHAAWRKLHGKEVVI 249 (665)
Q Consensus 171 dlriG~~e~til~~~hp~a~~~~~~~~dL~~v~~~l~~~~~~~~~~~i~~g~~~~P-mLA~~~~~~~~~~~~~~~~~~~~ 249 (665)
+||||+++++|+++||+ +.|++| |||++... ++++++-+.+|++
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 99999999999988854 578888 99998543 4566633448999
Q ss_pred EEeeceeEEEEEEeCCEEEEEecCCCCCCcchhhhHHHHHhhcc-----ccceeeeceEEEeeCCCCccccc--------
Q 006003 250 ECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVL-----VDRCILDGEMLVWDTSLNRFAEF-------- 316 (665)
Q Consensus 250 E~K~DG~R~qih~~g~~v~~~SR~g~d~t~~~p~l~~~~~~~~~-----~~~~ILDGElv~~d~~~~~~~~F-------- 316 (665)
|+||||+|||+|++++++++|||||++++. +|++.+.+.+... ++++|||||+|+||+.++.+.+|
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 999999999999999999999999999985 5887765543211 47899999999998765533333
Q ss_pred -----cchHHHHH------Hh-hcC--CCCCCceEEEEEEEEeeC---CccccCCCHHHHHHHHHhhcCC-CCCcceecc
Q 006003 317 -----GSNQEIAK------AA-RDG--LSSDRQLCYFAFDVLYVG---DTSVIHQSLKERHELLQKVVKP-SKGRLETLV 378 (665)
Q Consensus 317 -----~~lq~~~~------~~-~~~--~~~~~~~~~~vFDiL~ln---g~~l~~~pl~eRr~~L~~~~~~-~~~~~~~~~ 378 (665)
+.++.... .. +.. .....+++|+|||||++| |.++++.||.+||++|++++.. ..+++.++.
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 4457889999999999999863 233443221
Q ss_pred cCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHcCCceEEeecCCCCCccCCCCCCeEEEccccccCCCcceEEEEE
Q 006003 379 PDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLIIG 458 (665)
Q Consensus 379 p~~~~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EGlV~K~~~s~Y~~GkRs~~WlKiK~~y~~~g~~~DlvVIG 458 (665)
...+++.+++.++|++++++|+||||+|+++|+|++| |+.+|+|+|+.+ ++|++|||
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 EEecCCCCCCccceEEEEEeeCCCCCCCCcceEEEEEeccCCCHHHHHHHHHhhccccccccCCCCCCCCceeecCCCCC
Q 006003 459 GYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKE 538 (665)
Q Consensus 459 ~~~G~g~r~g~~~sfllg~~d~~~~~~~~~~~~~~~kVgsG~s~~~~~~l~~~l~~~~~~~~~~~~~pp~~~~~~~~~~~ 538 (665)
+|+|. +++|.+|+|+|++++ + . .+|+||||||++++++|...+. . +| +... ....
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 567889999997642 1 2 4799999999999998865532 1 11 1111 1223
Q ss_pred CCcEEEeCCC-ceEEEEEeeeceecccCccCCCeeeeccEEEEEecCCCccCCCCHHHHH
Q 006003 539 RPDVWIESPE-KSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDKPWHDCLDVQSFV 597 (665)
Q Consensus 539 ~pd~wi~~P~-~s~v~ev~a~~~~~~s~~~~~g~sLRfPr~~riR~DK~~~d~~t~~el~ 597 (665)
++.+|..++. ...|+||+++.. ..|..|++|++||||||+|+|+||+ +|+|++++.
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 246999986543 3688899999999999999999999 999999875
No 9
>COG1793 CDC9 ATP-dependent DNA ligase [DNA replication, recombination, and repair]
Probab=100.00 E-value=7.2e-64 Score=547.99 Aligned_cols=422 Identities=27% Similarity=0.413 Sum_probs=344.2
Q ss_pred CCCCCCHHHHHHHHhhhccCCCCCCCCHHHHHHHHHHHHhhhhHHhHHHHHHHHHHhCCHHHHHHHHHHHHhhhccCCcc
Q 006003 99 APNAGNFPMVAAEVLQRRQGMISGGLTIKELNDLLDRLASSENRAEKISVLSTLIKKTNAQEMKWIIMIILKDLKLGISE 178 (665)
Q Consensus 99 ~~~~gD~~~~~~~v~~~r~~~~~~~lTi~eV~~~Ld~la~~~~~~~k~~~l~~ll~~~t~~E~k~l~RiilkdlriG~~e 178 (665)
+...||+|..+..+.. +.+|+..|..++...+ .+ .++..|+..++ +|+++
T Consensus 17 ~~~~Gdlg~~~~~~~~-----------v~~v~~~~~~~~~~~g-~~--~~~~~L~~~~~----------------~gv~~ 66 (444)
T COG1793 17 YIPQGDLGEGAVLLWD-----------VEGVYLTLSKVAERTG-QE--RLLWLLLDEAD----------------IGVSE 66 (444)
T ss_pred ccccCccchhheeeee-----------cccchhhHHHHHhhcC-ch--hHHHHHHHhcc----------------cchhh
Confidence 3567999988765432 8899999999999888 22 78888888888 99999
Q ss_pred cccccccCcCHHHHHhhhCCHHHHHHHHhhh-hhccccCCccCCCccccccccccCCHHHHHHHhcCCceEEEEeeceeE
Q 006003 179 KSIFHEFHPDAEDLFNVTCDLKLVCEKLKDR-NQRHKRQDIEVGKAVRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDR 257 (665)
Q Consensus 179 ~til~~~hp~a~~~~~~~~dL~~v~~~l~~~-~~~~~~~~i~~g~~~~PmLA~~~~~~~~~~~~~~~~~~~~E~K~DG~R 257 (665)
++++.++..-.+..|+.++|+..++..+... ..++....+.+|.|+.||||.......+...+..+ .|.+|+||||+|
T Consensus 67 ~~~~~ala~~~~~~~~~~~d~g~~a~~~~~~~~~~~~~~~~~~~~p~~~~la~~~~~~~~~~~~~~~-~w~~E~K~DG~R 145 (444)
T COG1793 67 GTVLDALAEAVERAYLWHNDLGALAKILLTLGAEALDKATLLPGRPLPPMLAPMLASLEEALPRDGG-DWAYEEKFDGYR 145 (444)
T ss_pred HHHHHHHHHHhhhhhccCCCchhhhhhhhhcccccccccccccCCccchhhccccccccccCCCCCC-CEEEEEeeceEE
Confidence 9999877555788899999999988876543 23344556789999999999998776555444433 599999999999
Q ss_pred EEEEEeCCEEEEEecCCCCCCcchhhhHHHHHhhccccceeeeceEEEeeCCCCccccccchHHHHHHhhc--CCCCCCc
Q 006003 258 IQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDGEMLVWDTSLNRFAEFGSNQEIAKAARD--GLSSDRQ 335 (665)
Q Consensus 258 ~qih~~g~~v~~~SR~g~d~t~~~p~l~~~~~~~~~~~~~ILDGElv~~d~~~~~~~~F~~lq~~~~~~~~--~~~~~~~ 335 (665)
+|+|++++.|++|||||.|+|.+||++...+...+..+++|||||+|++|+. ...||+.+|...++..+ ......+
T Consensus 146 ~q~h~~~~~vrl~SR~g~d~T~~fP~~~~~~~~~l~~~~~iiDGE~V~~~~~--~~~~F~~Lq~r~~~k~~v~~~~~~~~ 223 (444)
T COG1793 146 VQIHIDGGKVRLYSRNGEDWTGRFPDILEAAAEALPADDFILDGEIVVLDEE--GRLDFQALQQRLRRKYDVAKLRRETP 223 (444)
T ss_pred EEEEEcCCEEEEEeCCCccchhhChHHHHHHHhcCCCCceEEeeeEEEECCC--CCCCHHHHHHHhhhccchhhhccCCc
Confidence 9999999999999999999999999765555555667899999999999975 45899888876543211 1234578
Q ss_pred eEEEEEEEEeeCCccccCCCHHHHHHHHHhhcCCCCCcceecccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHc
Q 006003 336 LCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIEN 415 (665)
Q Consensus 336 ~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~~~~~~~~p~~~~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~ 415 (665)
++|++|||||+||++|+++||.+||+.|++++... +.+.+.. ....++.+++..+|+.+++.
T Consensus 224 ~~~~aFDlL~~dG~dL~~~pl~eRr~~Le~lv~~~-~~~~~~~-----------------~i~~~~~~~~~~~~~~a~~~ 285 (444)
T COG1793 224 LVLFAFDLLYLDGEDLRGLPLEERRALLEELVKSS-DKIEIAE-----------------RIPFSDAEEGEAFLEAAIEL 285 (444)
T ss_pred eEEEEEEEEeECCcccccCchHHHHHHHHHHhccc-ccccccc-----------------ceeccChhhHHHHHHHHHhc
Confidence 99999999999999999999999999999999874 2222110 12237889999999999999
Q ss_pred CCceEEeecCCCCCccCCCCCCeEEEccccccCCCcceEEEEEEEecCCCCCCccceEEEEEeeCCCCCCCCcceEEEEE
Q 006003 416 RDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCR 495 (665)
Q Consensus 416 g~EGlV~K~~~s~Y~~GkRs~~WlKiK~~y~~~g~~~DlvVIG~~~G~g~r~g~~~sfllg~~d~~~~~~~~~~~~~~~k 495 (665)
|+||||+|+++|+|++|+|+..|+|+|++ +++|+||+|+++|.|+++ .+|+|+||+|++++ +.|+++|+
T Consensus 286 g~EGvv~K~~ds~Y~~g~R~~~W~K~K~~-----~~~d~vv~G~~~g~Gkr~-~~~slll~~~~~~~-----~~~~~v~k 354 (444)
T COG1793 286 GLEGVVAKRPDSPYRAGGRSNKWLKVKRD-----ETLDLVVVGAEYGKGKRS-LYGSLLLGVYDGDG-----GGLLYVGK 354 (444)
T ss_pred CceEEEEeCCCCCcCCCCCCCcceEeccC-----CcccEEEEEEEecCCccc-ccceEEEEEEcCCC-----ceEEEEec
Confidence 99999999999999999999999999998 489999999999999999 89999999998764 37999999
Q ss_pred eccCCCHHHHHHHHHhhccccccccCCCCCCCCceeecCCCCCCCcEEEeCCCceEEEEEeeeceecccCccCC--Ceee
Q 006003 496 VGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSA--PYSL 573 (665)
Q Consensus 496 VgsG~s~~~~~~l~~~l~~~~~~~~~~~~~pp~~~~~~~~~~~~pd~wi~~P~~s~v~ev~a~~~~~~s~~~~~--g~sL 573 (665)
|||||+++++++|.++|++++... .+++ .+..|..+| .+|+||.++..+ .+..|.. |.+|
T Consensus 355 VgtGf~~~~l~~l~~~l~~~~~~~----~~~~-----------~~~~~~~~p--~~V~EV~~~~~t-~~~~~r~~~~~~l 416 (444)
T COG1793 355 VGTGFSDAELEELTERLEPLIVSR----FNGK-----------VPGKVVPPP--GLVAEVRFAEIT-KSGRLRHASGLGL 416 (444)
T ss_pred ccCCCCHHHHHHHHHHHHHhccCc----CCCc-----------cCceeecCC--cEEEEEEEeecc-cCCceecccCccc
Confidence 999999999999999999987541 1111 111155546 479999865432 4566655 8999
Q ss_pred eccEEEEEecCCCccCCCCHHHHHHHH
Q 006003 574 RFPRIDRVRYDKPWHDCLDVQSFVELV 600 (665)
Q Consensus 574 RfPr~~riR~DK~~~d~~t~~el~~l~ 600 (665)
||||+.++|.||.|.+++|++++.+++
T Consensus 417 Rfpr~~rvr~dk~~~~a~t~~~~~~~~ 443 (444)
T COG1793 417 RFPRFVRVRDDKLPEDADTIEEIEALY 443 (444)
T ss_pred CcCcccccccccCcccccccccchhhc
Confidence 999999999999999999999988775
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=6.7e-60 Score=496.49 Aligned_cols=288 Identities=28% Similarity=0.410 Sum_probs=240.3
Q ss_pred cCCceEEEEeeceeEEEEEEeCCEEEEEecCCCCCCcchhhhHHHHHhhccccceeeeceEEEeeCCCCccccccchHHH
Q 006003 243 HGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDGEMLVWDTSLNRFAEFGSNQEI 322 (665)
Q Consensus 243 ~~~~~~~E~K~DG~R~qih~~g~~v~~~SR~g~d~t~~~p~l~~~~~~~~~~~~~ILDGElv~~d~~~~~~~~F~~lq~~ 322 (665)
.+.+|++|+||||+|||+|+++++|++|||||+++|..||++...+ ..+..++||||||||+||..+ + .+|+.+|..
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-AALPILPAVLDGEIVVLDESG-R-SDFSALQNR 86 (298)
T ss_pred CCCCEEEEEEEceEEEEEEEeCCEEEEEeCCCCchHhHhHHHHHHH-HhCCCCcEEEEeEEEEECCCC-C-CCHHHHHhh
Confidence 4678999999999999999999999999999999999889987754 344567999999999999753 3 589777764
Q ss_pred HHHhhcCCCCCCceEEEEEEEEeeCCccccCCCHHHHHHHHHhhcCCCCCcceecccCCCCCccccCCCCCccccccCCH
Q 006003 323 AKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNV 402 (665)
Q Consensus 323 ~~~~~~~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~~~~~~~~p~~~~~~~v~~~~~~~~~~~~~~~ 402 (665)
.+. ....+++|++||||++||++++++||.+|+++|++++.+.++...+.. . ..++.
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 124789999999999999999999999999999999977554332110 0 24567
Q ss_pred HHHHHHHHHHHHcCCceEEeecCCCCCccCCCCCCeEEEccccccCCCcceEEEEEEEecCCCCCCccceEEEEEeeCCC
Q 006003 403 DEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLIIGGYYGSGRRGGEVAQFLVALAERPA 482 (665)
Q Consensus 403 ~~i~~~~~~ai~~g~EGlV~K~~~s~Y~~GkRs~~WlKiK~~y~~~g~~~DlvVIG~~~G~g~r~g~~~sfllg~~d~~~ 482 (665)
+++.++|++++++|+||||+|+++|+|++|+ |.+|+|+|+.+ +.|++|+|++.|.|++ |.+|+|+||++++.
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 7899888888899988 77999999999642
Q ss_pred CCCCCcceEEEEEeccCCCHHHHHHHHHhhccccccccCCCCCCCCceeecCCCCCCCcEEEeCCCceEEEEEeeeceec
Q 006003 483 PDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDVWIESPEKSIILSITSDIRTI 562 (665)
Q Consensus 483 ~~~~~~~~~~~~kVgsG~s~~~~~~l~~~l~~~~~~~~~~~~~pp~~~~~~~~~~~~pd~wi~~P~~s~v~ev~a~~~~~ 562 (665)
.|.++|+||||||++++++|.++|.+++... .+|. .....|++|++ | .+|+||++.
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 12346789999 7 478899753
Q ss_pred ccCccCCCeeeeccEEEEEecCCCccCCC
Q 006003 563 RSEVFSAPYSLRFPRIDRVRYDKPWHDCL 591 (665)
Q Consensus 563 ~s~~~~~g~sLRfPr~~riR~DK~~~d~~ 591 (665)
.++.|++||||||+++|+||+|+||+
T Consensus 272 ---~~t~~~~lR~P~~~~~R~Dk~~~~~~ 297 (298)
T TIGR02779 272 ---GWTRDGRLRQASFVGLREDKPASEVT 297 (298)
T ss_pred ---ccCCCCeEeccEEEeeeCCCCHHHcc
Confidence 34568899999999999999999996
No 11
>PRK09632 ATP-dependent DNA ligase; Reviewed
Probab=100.00 E-value=1.7e-59 Score=535.56 Aligned_cols=307 Identities=25% Similarity=0.382 Sum_probs=253.7
Q ss_pred ccCCCccccccccccCCHHHHHHHhcCCceEEEEeeceeEEEEEEeCCEEEEEecCCCCCCcchhhhHHHHHhhccccce
Q 006003 218 IEVGKAVRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRC 297 (665)
Q Consensus 218 i~~g~~~~PmLA~~~~~~~~~~~~~~~~~~~~E~K~DG~R~qih~~g~~v~~~SR~g~d~t~~~p~l~~~~~~~~~~~~~ 297 (665)
..++.+|+||||+..... .+.+.+|++|+||||+|||+|++++.|++|||||+++|..||++.+.. ..+...+|
T Consensus 455 ~~~~~~v~PMLA~~~~~~-----~~~~~~w~~E~K~DG~R~~~~~~~g~vrL~SRnG~d~T~~fPel~~~~-~~l~~~~~ 528 (764)
T PRK09632 455 AEEADDLAPMLATAGTVA-----GLKASQWAFEGKWDGYRLLAEADHGALRLRSRSGRDVTAEYPELAALA-EDLADHHV 528 (764)
T ss_pred CCCCCCCcCccCCcCCCC-----CCCCCCEEEEEEECceeEEEEEeCCEEEEEeCCCCCccccchhHHHHH-hhCCCcce
Confidence 578899999999976422 245678999999999999999999999999999999999999998743 44556799
Q ss_pred eeeceEEEeeCCCCccccccchHHHHHHhhcCCCCCCceEEEEEEEEeeCCccccCCCHHHHHHHHHhhcCCCCCcceec
Q 006003 298 ILDGEMLVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETL 377 (665)
Q Consensus 298 ILDGElv~~d~~~~~~~~F~~lq~~~~~~~~~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~~~~~~~ 377 (665)
|||||||+||+.+ + .+|+.+|... ...+++|++|||||+||++|+++||.+||++|++++.+ .+.+.+.
T Consensus 529 ILDGEiVvld~~G-~-~~F~~Lq~r~--------~~~~v~y~vFDLL~lnG~dL~~~Pl~eRR~~L~~l~~~-~~~i~~s 597 (764)
T PRK09632 529 VLDGEIVALDDSG-V-PSFGLLQNRG--------RDTRVEFWAFDLLYLDGRSLLRKPYRDRRKLLEALAPS-GGSLTVP 597 (764)
T ss_pred eeeeEEEEeCCCC-C-CCHHHHhhhh--------hcCCeEEEEEeeeccCCcccccCCHHHHHHHHHHhhCC-CCcEEec
Confidence 9999999999754 3 5898777641 23689999999999999999999999999999999863 2233211
Q ss_pred ccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHcCCceEEeecCCCCCccCCCCCCeEEEccccccCCCcceEEEE
Q 006003 378 VPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLII 457 (665)
Q Consensus 378 ~p~~~~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EGlV~K~~~s~Y~~GkRs~~WlKiK~~y~~~g~~~DlvVI 457 (665)
.....++.++|+.++++|.||||+|+++|+|++|+||.+|+|+|+.| +.|+||+
T Consensus 598 ---------------------~~~~~~~~~~l~~a~~~GlEGIVaKr~dS~Y~pGrRs~~WlKiK~~~-----~~e~VI~ 651 (764)
T PRK09632 598 ---------------------PLLPGDGAEALAYSRELGWEGVVAKRRDSTYQPGRRSSSWIKDKHWR-----TQEVVIG 651 (764)
T ss_pred ---------------------ceecccHHHHHHHHHHcCCcEEEEeCCCCCCCCCCcCCCeEEEecCC-----ceEEEEE
Confidence 11123578899999999999999999999999999999999999986 7899888
Q ss_pred EEEecCCCCCCccceEEEEEeeCCCCCCCCcceEEEEEeccCCCHHHHHHHHHhhccccccccCCCCCCCCceeecCCCC
Q 006003 458 GGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSK 537 (665)
Q Consensus 458 G~~~G~g~r~g~~~sfllg~~d~~~~~~~~~~~~~~~kVgsG~s~~~~~~l~~~l~~~~~~~~~~~~~pp~~~~~~~~~~ 537 (665)
|+++|+|+++|.+|+||||+++.+ .|.++|+||||||++++++|.++|.++.++ .|| |........
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 589999999999999999999999987643 122 321111124
Q ss_pred CCCcEEEeCCCceEEEEEeeeceecccCccCCCeeeeccEEEEEecCCCccCCC
Q 006003 538 ERPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDKPWHDCL 591 (665)
Q Consensus 538 ~~pd~wi~~P~~s~v~ev~a~~~~~~s~~~~~g~sLRfPr~~riR~DK~~~d~~ 591 (665)
.+|++||+ |. +|+||++. .++.+++||||||+++|+||+++||+
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 75 68888642 35567899999999999999999986
No 12
>PRK08224 ligC ATP-dependent DNA ligase; Reviewed
Probab=100.00 E-value=1.7e-57 Score=484.69 Aligned_cols=317 Identities=22% Similarity=0.353 Sum_probs=248.8
Q ss_pred CccCCCccccccccccCCHHHHHHHhcCCceEEEEeeceeEEEEEEeCCEEEEEecCCCCCCcchhhhHHHHHhhccccc
Q 006003 217 DIEVGKAVRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDR 296 (665)
Q Consensus 217 ~i~~g~~~~PmLA~~~~~~~~~~~~~~~~~~~~E~K~DG~R~qih~~g~~v~~~SR~g~d~t~~~p~l~~~~~~~~~~~~ 296 (665)
+..+|.|++||||.....++ .+.+|++|+||||+|||+|+++++|++|||||+++|..||++.+.+. ...+.+
T Consensus 2 ~~~~~~~i~PMLA~~~~~~~------~~~~w~~E~K~DG~R~~~~~~~~~v~l~SRng~d~t~~fPel~~~~~-~~~~~~ 74 (350)
T PRK08224 2 DLPVMPPVEPMLAKSVDAIP------PGDGWSYEPKWDGFRCLVFRDGDEVELGSRNGKPLTRYFPELVAALR-AELPER 74 (350)
T ss_pred CCCCCCCcCCccCCccCCCC------CCCcEEEEEeECeeEEEEEEECCEEEEEeCCCCCchhhhHHHHHHHH-hhCCCC
Confidence 56789999999999876442 34579999999999999999999999999999999999999988764 345679
Q ss_pred eeeeceEEEeeCCCCccccccchHHHHHHhhc---CCCCCCceEEEEEEEEeeCCccccCCCHHHHHHHHHhhcCCCCCc
Q 006003 297 CILDGEMLVWDTSLNRFAEFGSNQEIAKAARD---GLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGR 373 (665)
Q Consensus 297 ~ILDGElv~~d~~~~~~~~F~~lq~~~~~~~~---~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~~~ 373 (665)
||||||||++|.. + .+|+.+|........ ......+++|++|||||+||++++++||.+|+++|++++... +.
T Consensus 75 ~vLDGEiVv~~~~-~--~~F~~Lq~r~~~~~~~~~~~~~~~pv~~~vFDlL~l~G~dl~~~Pl~eRr~~L~~l~~~~-~~ 150 (350)
T PRK08224 75 CVLDGEIVVARDG-G--LDFEALQQRIHPAASRVRKLAEETPASFVAFDLLALGDRDLTGRPFAERRAALEAAAAGS-GP 150 (350)
T ss_pred EEEeeEEEEeCCC-C--CCHHHHHhhhhccccchhhhhhcCCEEEEEEeeeeECCcChhhCCHHHHHHHHHHhcCCC-Cc
Confidence 9999999999853 2 799888765321110 112346899999999999999999999999999999998643 22
Q ss_pred ceecccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHcCCceEEeecCCCCCccCCCCCCeEEEccccccCCCcce
Q 006003 374 LETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLD 453 (665)
Q Consensus 374 ~~~~~p~~~~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EGlV~K~~~s~Y~~GkRs~~WlKiK~~y~~~g~~~D 453 (665)
+.+. ....+.++++++|++++++|.||||+|+++|+|++|+|+ |+|+|+.+ +.|
T Consensus 151 i~~~-------------------~~~~~~~~~~~~~~~a~~~G~EGIV~Kr~dS~Y~~Grr~--WlKiK~~~-----~~d 204 (350)
T PRK08224 151 VHLT-------------------PATTDPATARRWFEEFEGAGLDGVIAKPLDGPYQPGKRA--MFKVKHER-----TAD 204 (350)
T ss_pred EEEe-------------------cccCCHHHHHHHHHHHHhCCCcEEEEeCCCCCcCCCCcC--EEEEccCC-----cEE
Confidence 3221 012456789999999999999999999999999999886 99999974 899
Q ss_pred EEEEEEEecCCCCCCccceEEEEEeeCCCCCCCCcceEEEEEeccCCCHHHHHHHHHhhcccccccc-CCCCCCCCceee
Q 006003 454 VLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYE-YPKRAPPSFYQV 532 (665)
Q Consensus 454 lvVIG~~~G~g~r~g~~~sfllg~~d~~~~~~~~~~~~~~~kVgsG~s~~~~~~l~~~l~~~~~~~~-~~~~~pp~~~~~ 532 (665)
++|+|+++|+|+ |.+|+|+||+|++++ +++++|+|| |||++++++|.++|.+++.+.. +|.+.. +|...
T Consensus 205 ~vI~G~~~g~~~--~~~gslllg~~d~~g------~l~~vG~v~-Gf~~~~~~~L~~~l~~l~~~~~~~p~~~~-pf~~~ 274 (350)
T PRK08224 205 CVVAGYRYHKSG--PVVGSLLLGLYDDDG------QLHHVGVTS-AFPMARRRELTAELEPLRTPFGDHPWNWA-AFTGR 274 (350)
T ss_pred EEEEEEEcCCCC--CccccEEEEEECCCC------cEEEEEEEC-CCCHHHHHHHHHHHHhhhcCCCCCccccC-ccccc
Confidence 999998888875 789999999997543 789999985 9999999999999998875421 010000 12111
Q ss_pred cCC-----CCCCCcEE--EeCCCceEEEEEeeeceecccCccCCCeeeecc-EEEEEecCCCccCCC
Q 006003 533 TNN-----SKERPDVW--IESPEKSIILSITSDIRTIRSEVFSAPYSLRFP-RIDRVRYDKPWHDCL 591 (665)
Q Consensus 533 ~~~-----~~~~pd~w--i~~P~~s~v~ev~a~~~~~~s~~~~~g~sLRfP-r~~riR~DK~~~d~~ 591 (665)
... ...+..+| ++ |. +|+||.+ ..++ +..|||| +|+++|.||+++||+
T Consensus 275 ~~~~~~~~~~~~~~~w~~v~-P~--lv~eV~~-------~~~t-~~~lR~p~~f~g~r~Dk~p~~v~ 330 (350)
T PRK08224 275 APGGPSRWSAGKDLSWVPLR-PE--RVVEVRY-------DHME-GGRFRHTAQFLRWRPDRDPRSCT 330 (350)
T ss_pred CCCccccccccCCcEEEeee-EE--EEEEEec-------Cccc-CCeecCCCeeEEEcCCCChHHCC
Confidence 000 11235689 99 75 5778754 3455 4599998 999999999999997
No 13
>PRK05972 ligD ATP-dependent DNA ligase; Reviewed
Probab=100.00 E-value=3.7e-56 Score=512.37 Aligned_cols=304 Identities=26% Similarity=0.397 Sum_probs=244.5
Q ss_pred CccccccccccCCHHHHHHHhcCCceEEEEeeceeEEEEEEeCCEEEEEecCCCCCCcchhhhHHHHHhhccccceeeec
Q 006003 222 KAVRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDG 301 (665)
Q Consensus 222 ~~~~PmLA~~~~~~~~~~~~~~~~~~~~E~K~DG~R~qih~~g~~v~~~SR~g~d~t~~~p~l~~~~~~~~~~~~~ILDG 301 (665)
..++||||.....++ .+.+|++|+||||+|||+|++++++++|||||+|+|..||+|.+.+. .+..++|||||
T Consensus 232 ~~i~PMLAt~~~~~p------~g~~W~~E~K~DG~R~~a~~~gg~vrL~SRnG~d~T~~fPel~~~~~-~l~~~~~ILDG 304 (860)
T PRK05972 232 DFLAPQLATLVDRPP------SGDGWIYEIKFDGYRILARIEGGEVRLFTRNGLDWTAKLPALAKAAA-ALGLPDAWLDG 304 (860)
T ss_pred cccCcccCccCCCCC------CcCceEEEeeeCcEEEEEEEECCEEEEEeCCCCccccccHHHHHHHH-hcCCCceeEeE
Confidence 458999999877653 35689999999999999999999999999999999999999988764 45568999999
Q ss_pred eEEEeeCCCCccccccchHHHHHHhhcCCCCCCceEEEEEEEEeeCCccccCCCHHHHHHHHHhhcCCCCC-cceecccC
Q 006003 302 EMLVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKG-RLETLVPD 380 (665)
Q Consensus 302 Elv~~d~~~~~~~~F~~lq~~~~~~~~~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~~-~~~~~~p~ 380 (665)
|||+||..+ + .+|+.+|...+. ....+++|++|||||+||++|+++||.+|+++|++++.+.++ .+.+
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 999999754 3 589887764432 124689999999999999999999999999999999976432 2322
Q ss_pred CCCCccccCCCCCccccccCCHHHHHHHHHHHHHcCCceEEeecCCCCCccCCCCCCeEEEccccccCCCcceEEEEEEE
Q 006003 381 HGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLIIGGY 460 (665)
Q Consensus 381 ~~~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EGlV~K~~~s~Y~~GkRs~~WlKiK~~y~~~g~~~DlvVIG~~ 460 (665)
+.+...++.++|+.++++|+||||+|+.+|+|++| ||.+|+|+|+.+ +.|+||+|.+
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 11223457889999999999999999999999987 899999999985 5576555544
Q ss_pred ecCCCCCCccceEEEEEeeCCCCCCCCcceEEEEEeccCCCHHHHHHHHHhhccccccccCCCCCCCCceeecCCCCCCC
Q 006003 461 YGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERP 540 (665)
Q Consensus 461 ~G~g~r~g~~~sfllg~~d~~~~~~~~~~~~~~~kVgsG~s~~~~~~l~~~l~~~~~~~~~~~~~pp~~~~~~~~~~~~p 540 (665)
.|.|+++| +|+||||++++. +|+++|+||||||++++++|.++|.++.+. .+| |..........+
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 321111122345
Q ss_pred cEEEeCCCceEEEEEeeeceecccCccCCCeeeeccEEEEEecCCCccCCC
Q 006003 541 DVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDKPWHDCL 591 (665)
Q Consensus 541 d~wi~~P~~s~v~ev~a~~~~~~s~~~~~g~sLRfPr~~riR~DK~~~d~~ 591 (665)
++||+ |+ +|+||++. .++.++.||||+|+++|+||+++||+
T Consensus 496 ~~WV~-P~--LV~EV~f~-------e~T~~g~LR~P~F~glR~DK~p~ev~ 536 (860)
T PRK05972 496 VHWVK-PE--LVAEVEFA-------GWTRDGIVRQAVFKGLREDKPAREVV 536 (860)
T ss_pred CEEEc-cC--EEEEEEEe-------eccCCCCCccceEEEeecCCChHHhC
Confidence 79999 85 68898753 24556699999999999999999997
No 14
>PRK09633 ligD ATP-dependent DNA ligase; Reviewed
Probab=100.00 E-value=6.7e-55 Score=492.03 Aligned_cols=310 Identities=22% Similarity=0.271 Sum_probs=241.3
Q ss_pred cccccccccCCHHHHHHHhcCCceEEEEeeceeEEEEEEeCCEEEEEecCCCCCCcchhhhHHHHHhhcc----ccceee
Q 006003 224 VRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVL----VDRCIL 299 (665)
Q Consensus 224 ~~PmLA~~~~~~~~~~~~~~~~~~~~E~K~DG~R~qih~~g~~v~~~SR~g~d~t~~~p~l~~~~~~~~~----~~~~IL 299 (665)
++||||.....++ .+.+|++|+||||+|||+|++++.|++|||||+++|..||++.+.+..... ..+|||
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 4799998876542 467899999999999999999999999999999999999999876532111 137999
Q ss_pred eceEEEeeCCCCccccccchHHHHHHhhcC----CCCCCceEEEEEEEEeeCCccccCCCHHHHHHHHHhhcCCCCCcce
Q 006003 300 DGEMLVWDTSLNRFAEFGSNQEIAKAARDG----LSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLE 375 (665)
Q Consensus 300 DGElv~~d~~~~~~~~F~~lq~~~~~~~~~----~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~~~~~ 375 (665)
|||||+||..+. .+|+.+|...+..+.. .....+++|+||||||+||+++++.||.+||++|++++.+.....+
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 999999986533 5888777653321111 1224689999999999999999999999999999999875421000
Q ss_pred ecccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHcCCceEEeecCCCCCccCCCCCCeEEEccccccCCCcceEE
Q 006003 376 TLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVL 455 (665)
Q Consensus 376 ~~~p~~~~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EGlV~K~~~s~Y~~GkRs~~WlKiK~~y~~~g~~~Dlv 455 (665)
+ + +...+.+. .+.+.++++++|++++++|.||||+|+.+|+|++|+||.+|+|+|+.+ +.|++
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 EEEEEecCCCCCCccceEEEEEeeCCCCCCCCcceEEEEEeccCCCHHHHHHHHHhhccccccccCCCCCCCCceeecCC
Q 006003 456 IIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNN 535 (665)
Q Consensus 456 VIG~~~G~g~r~g~~~sfllg~~d~~~~~~~~~~~~~~~kVgsG~s~~~~~~l~~~l~~~~~~~~~~~~~pp~~~~~~~~ 535 (665)
|+|...|. |.|++|+++. ++++++|+||||||++++++|.++|.++.+.
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 3688898843 3799999999999999999999999876432
Q ss_pred CCCCCcEEEeCCCceEEEEEeeeceecccCccCCCeeeeccEEEEEecCCCccCCCCHHHHHHHHH
Q 006003 536 SKERPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDKPWHDCLDVQSFVELVH 601 (665)
Q Consensus 536 ~~~~pd~wi~~P~~s~v~ev~a~~~~~~s~~~~~g~sLRfPr~~riR~DK~~~d~~t~~el~~l~~ 601 (665)
...+.+|++ |. +|+||++.. ++ |+.||||+|+++|+||+++||++.++..+++.
T Consensus 265 -~~~~~~wV~-P~--LV~EV~~~e-------~t-~g~LR~P~f~glR~DK~~~ev~~~~~~~~~~~ 318 (610)
T PRK09633 265 -TKSGEYTLE-PS--ICVTVACIT-------FD-GGTLREPSFVSFLFDMDPTECTYQQLQRQLAP 318 (610)
T ss_pred -CCCCcEEEe-ee--EEEEEEEee-------cC-CCeEEeeEEeEEEcCCChHHcchhhhhhhhcc
Confidence 123579999 75 588887532 32 78999999999999999999999888777663
No 15
>PRK07636 ligB ATP-dependent DNA ligase; Reviewed
Probab=100.00 E-value=1.5e-50 Score=419.82 Aligned_cols=272 Identities=24% Similarity=0.328 Sum_probs=214.4
Q ss_pred cccccccccCCHHHHHHHhcCCceEEEEeeceeEEEEEEeCCEEEEEecCCCCCCcchhhhHHHHHhhccccceeeeceE
Q 006003 224 VRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDGEM 303 (665)
Q Consensus 224 ~~PmLA~~~~~~~~~~~~~~~~~~~~E~K~DG~R~qih~~g~~v~~~SR~g~d~t~~~p~l~~~~~~~~~~~~~ILDGEl 303 (665)
++||||...... +.+.+|++|+||||+|||+|++++++++|||||+++|..+|++.+.. ..++|||||||
T Consensus 3 ~~PmLa~~~~~~------~~~~~~~~E~K~DG~R~~~~~~~~~v~l~SR~g~~~t~~fPe~~~~~----~~~~~vLDGEl 72 (275)
T PRK07636 3 ISPMLLESAKEP------FNSENYITEPKFDGIRLIASKNNGLIRLYTRHNNEVTAKFPELLNLD----IPDGTVLDGEL 72 (275)
T ss_pred cCCccCCcCCCC------CCCCcEEEEEEEceeEEEEEEeCCEEEEEeCCCCCchhhhhhHHhhh----cCCCEEEEeEE
Confidence 789999887643 45678999999999999999999999999999999999999987642 24679999999
Q ss_pred EEeeCCCCccccccchHHHHHHhhcCCCCCCceEEEEEEEEeeCCccccCCCHHHHHHHHHhhcCCCCCcceecccCCCC
Q 006003 304 LVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGL 383 (665)
Q Consensus 304 v~~d~~~~~~~~F~~lq~~~~~~~~~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~~~~~~~~p~~~~ 383 (665)
|+||..+ + .+|+.+|...+.. ......+++|+|||||++||++++++||.+|+++|++++.+.+ .+.+
T Consensus 73 v~~d~~g-~-~~F~~l~~r~~~~--~~~~~~~~~~~vFDlL~~~g~~l~~~pl~eRr~~L~~~~~~~~-~~~~------- 140 (275)
T PRK07636 73 IVLGSTG-A-PDFEAVMERFQSK--KSTKIHPVVFCVFDVLYINGVSLTALPLSERKEILASLLLPHP-NVKI------- 140 (275)
T ss_pred EEECCCC-C-CCHHHHHHHhccc--cccccCceEEEEEEeEEECceehhhCCHHHHHHHHHHhcCCCC-CEEE-------
Confidence 9999753 3 4797776643321 1122478999999999999999999999999999999986543 2221
Q ss_pred CccccCCCCCccccccCCHHHHHHHHHHHHHcCCceEEeecCCCCCccCCCCCCeEEEccccccCCCcceEEEEEEEecC
Q 006003 384 NSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLIIGGYYGS 463 (665)
Q Consensus 384 ~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EGlV~K~~~s~Y~~GkRs~~WlKiK~~y~~~g~~~DlvVIG~~~G~ 463 (665)
+....+++.++|++++++|.||||+|+++|+|.+|+||.+|+|+|+. ++.|++|+|+..
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 11223467889999999999999999999999999999999999974 588987766422
Q ss_pred CCCCCccceEEEEEeeCCCCCCCCcceEEEEEeccCCCHHHHHHHHHhhccccccccCCCCCCCCceeecCCCCCCCcEE
Q 006003 464 GRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDVW 543 (665)
Q Consensus 464 g~r~g~~~sfllg~~d~~~~~~~~~~~~~~~kVgsG~s~~~~~~l~~~l~~~~~~~~~~~~~pp~~~~~~~~~~~~pd~w 543 (665)
+.+|++ +|+++ + + ++|+||| |+++++++|.+.+.+.... ..++.+|
T Consensus 200 ----~~~g~l-lg~~~--g------~--~~G~vgt-~~~~~~~~l~~~l~~~~~~------------------~~~~~~w 245 (275)
T PRK07636 200 ----EEFGLL-LSYLD--G------R--SAGIMEF-MPYDARKKFYKRAKRLVVG------------------EDKKFVY 245 (275)
T ss_pred ----CCCcEE-EEecC--C------e--EEEEECC-CCHHHHHHHHHHhhhhccC------------------ccCCCEE
Confidence 225655 78764 2 3 6899999 9999999999888665321 2356899
Q ss_pred EeCCCceEEEEEeeeceecccCccCCCeeeeccEEEEEe
Q 006003 544 IESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVR 582 (665)
Q Consensus 544 i~~P~~s~v~ev~a~~~~~~s~~~~~g~sLRfPr~~riR 582 (665)
++ |. +|.||++. .++.++.||||+|+++|
T Consensus 246 v~-P~--lv~eV~~~-------e~t~~g~lR~p~f~g~r 274 (275)
T PRK07636 246 IE-PI--IGCRVKHR-------FKTKNGMLRIPSFVEWR 274 (275)
T ss_pred eC-Cc--EEEEEEEE-------EecCCCCEEccEEEEEe
Confidence 99 74 57777542 34555669999999998
No 16
>cd07900 Adenylation_DNA_ligase_I_Euk Adenylation domain of eukaryotic DNA Ligase I. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. Some organisms express a variety of different ligases which appear to be targeted to specific functions. There are three classes of ATP-dependent DNA ligases in eukaryotic cells (I, III and IV). DNA ligase I is required for the ligation of Okazaki fragments during lagging-strand DNA synthesis and for base excision repair (BER). DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains. The adenylation and C-terminal oligonucleotide/oligo
Probab=100.00 E-value=1.6e-48 Score=392.33 Aligned_cols=213 Identities=30% Similarity=0.547 Sum_probs=184.0
Q ss_pred CCccCCCccccccccccCCHHHHHHHhcCCceEEEEeeceeEEEEEEeC-CEEEEEecCCCCCCcchhhhHHHHHhhc--
Q 006003 216 QDIEVGKAVRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNG-SEIHYFSRSFLDHSEYGHAMSKIIEQNV-- 292 (665)
Q Consensus 216 ~~i~~g~~~~PmLA~~~~~~~~~~~~~~~~~~~~E~K~DG~R~qih~~g-~~v~~~SR~g~d~t~~~p~l~~~~~~~~-- 292 (665)
..|++|.||+||||++..+++++++++.+.+|++|+||||+|||+|+++ +.|++|||||+++|..+|++.+.+...+
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 3588999999999999888888888898889999999999999999976 8999999999999999999988765443
Q ss_pred cccceeeeceEEEeeCCCCccccccchHHHHHHhhcCCCCCCceEEEEEEEEeeCCccccCCCHHHHHHHHHhhcCCCCC
Q 006003 293 LVDRCILDGEMLVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKG 372 (665)
Q Consensus 293 ~~~~~ILDGElv~~d~~~~~~~~F~~lq~~~~~~~~~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~~ 372 (665)
..++||||||||+||..++.+.+|+.+|...+..........+++|++|||||+||++|+++||.+|+++|++++.+.++
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 36789999999999987677889988876532211111234789999999999999999999999999999999987776
Q ss_pred cceecccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHcCCceEEeecCC--CCCccCCCCCCeEEEcccc
Q 006003 373 RLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLG--SKWEPGDRSGKWLKLKPEY 445 (665)
Q Consensus 373 ~~~~~~p~~~~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EGlV~K~~~--s~Y~~GkRs~~WlKiK~~y 445 (665)
++.++. ...+++.+++.++|++++++|.||||+|+++ |+|.||+||.+|+|+|++|
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 2346789999999999999999999999999 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=8.8e-47 Score=421.77 Aligned_cols=258 Identities=26% Similarity=0.406 Sum_probs=204.5
Q ss_pred ecCCCCCCcchhhhHHHHHhhccccceeeeceEEEeeCCCCccccccchHHHHHHhhcCCCCCCceEEEEEEEEeeCCcc
Q 006003 271 SRSFLDHSEYGHAMSKIIEQNVLVDRCILDGEMLVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTS 350 (665)
Q Consensus 271 SR~g~d~t~~~p~l~~~~~~~~~~~~~ILDGElv~~d~~~~~~~~F~~lq~~~~~~~~~~~~~~~~~~~vFDiL~lng~~ 350 (665)
||||+|+|..||++.+.+. .+..++||||||||+||.. ++ .+|+.+|.+.+. ....+++|++|||||+||++
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 4556899999999999975 33 579888775432 13468999999999999999
Q ss_pred ccCCCHHHHHHHHHhhcCCCCC-cceecccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHcCCceEEeecCCCCC
Q 006003 351 VIHQSLKERHELLQKVVKPSKG-RLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKW 429 (665)
Q Consensus 351 l~~~pl~eRr~~L~~~~~~~~~-~~~~~~p~~~~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EGlV~K~~~s~Y 429 (665)
++++||.+|+++|++++.+... .+.+. .+..++..++|++++++|.||||+|+++|+|
T Consensus 73 L~~~Pl~eRr~~L~~ll~~~~~~~i~~~---------------------~~~~~~~~~~~~~a~~~G~EGIV~K~~dS~Y 131 (552)
T TIGR02776 73 LRDLPLEERKKRLKQLLKAQDEPAIRYS---------------------DHFESDGDALLESACRLGLEGVVSKRLDSPY 131 (552)
T ss_pred cccCCHHHHHHHHHHHhhhcCCCcEEEe---------------------eeecccHHHHHHHHHHCCCceEEEeCCCCCC
Confidence 9999999999999999976532 22211 0112344589999999999999999999999
Q ss_pred ccCCCCCCeEEEccccccCCCcceEEEEEEEecCCCCCCccceEEEEEeeCCCCCCCCcceEEEEEeccCCCHHHHHHHH
Q 006003 430 EPGDRSGKWLKLKPEYIRAGSDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVV 509 (665)
Q Consensus 430 ~~GkRs~~WlKiK~~y~~~g~~~DlvVIG~~~G~g~r~g~~~sfllg~~d~~~~~~~~~~~~~~~kVgsG~s~~~~~~l~ 509 (665)
++| ||.+|+|+|+.| +.|++ ||||++.+ |.+|+|+||+++. ++|+++|+||||||++++++|.
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 55565544 2399999999972 3799999999999999999999
Q ss_pred HhhccccccccCCCCCCCCceeecCCCCCCCcEEEeCCCceEEEEEeeeceecccCccCCCeeeeccEEEEEecCCCccC
Q 006003 510 TKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDKPWHD 589 (665)
Q Consensus 510 ~~l~~~~~~~~~~~~~pp~~~~~~~~~~~~pd~wi~~P~~s~v~ev~a~~~~~~s~~~~~g~sLRfPr~~riR~DK~~~d 589 (665)
++|++++... +| |.. .......|++|++ |. +|+||++. .++.+++||||||+++|+||+|+|
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 9999987541 11 111 1112346799999 75 68899753 345688999999999999999999
Q ss_pred CCC
Q 006003 590 CLD 592 (665)
Q Consensus 590 ~~t 592 (665)
|+.
T Consensus 257 ~t~ 259 (552)
T TIGR02776 257 VTL 259 (552)
T ss_pred cch
Confidence 963
No 18
>cd07903 Adenylation_DNA_ligase_IV Adenylation domain of DNA Ligase IV. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. There are three classes of ATP-dependent DNA ligase in eukaryotic cells (I, III and IV). DNA ligase IV is required for DNA non-homologous end joining pathways, including recombination of the V(D)J immunoglobulin gene segments in cells of the mammalian immune system. DNA ligase IV is stabilized by forming a complex with XRCC4, a nuclear phosphoprotein, which is phosphorylated by DNA-dependent protein kinase. DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more di
Probab=100.00 E-value=1.9e-45 Score=372.79 Aligned_cols=214 Identities=43% Similarity=0.708 Sum_probs=181.9
Q ss_pred cCCccCCCccccccccccCCHHHHHHHhcCCceEEEEeeceeEEEEEEeCCEEEEEecCCCCCCcchhhhHHHH------
Q 006003 215 RQDIEVGKAVRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKII------ 288 (665)
Q Consensus 215 ~~~i~~g~~~~PmLA~~~~~~~~~~~~~~~~~~~~E~K~DG~R~qih~~g~~v~~~SR~g~d~t~~~p~l~~~~------ 288 (665)
..++++|.||+||||++.......+..+.+.+|++|+||||+|||+|++++++++|||||+++|..+|++.+..
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 35689999999999999987766656777889999999999999999999999999999999999888876532
Q ss_pred H--hhccccceeeeceEEEeeCCCCccccccchHHHHHHhhcCCCCCCceEEEEEEEEeeCCccccCCCHHHHHHHHHhh
Q 006003 289 E--QNVLVDRCILDGEMLVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKV 366 (665)
Q Consensus 289 ~--~~~~~~~~ILDGElv~~d~~~~~~~~F~~lq~~~~~~~~~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~ 366 (665)
. .....++||||||||+||..++.+.+|+.+++...... ......+++|+|||||++||++++++||.+|+++|+++
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 0 11235789999999999987778899998876543211 11235689999999999999999999999999999999
Q ss_pred cCCCCCcceecccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHcCCceEEeecCCCCCccCCCCCCeEEEccccc
Q 006003 367 VKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYI 446 (665)
Q Consensus 367 ~~~~~~~~~~~~p~~~~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EGlV~K~~~s~Y~~GkRs~~WlKiK~~y~ 446 (665)
+.+.++++.++. ...+++.+++.++|++++++|.||||+|+++|+|++|+||.+|+|+||+|+
T Consensus 162 ~~~~~~~i~~~~-----------------~~~~~~~~~~~~~~~~~~~~g~EGlv~K~~~s~Y~~g~Rs~~wlK~K~~Y~ 224 (225)
T cd07903 162 ITPIPGRLEVVK-----------------RTEASTKEEIEEALNEAIDNREEGIVVKDLDSKYKPGKRGGGWIKIKPEYL 224 (225)
T ss_pred cCCCCCeEEEEE-----------------EEeCCCHHHHHHHHHHHHHcCCceEEEecCCCCCccCCcCCCcEEechhhc
Confidence 988766665431 234578899999999999999999999999999999999999999999996
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=2e-44 Score=361.69 Aligned_cols=206 Identities=30% Similarity=0.484 Sum_probs=173.7
Q ss_pred CCccCCCccccccccccCCHHHHHHHhcCCceEEEEeeceeEEEEEEeCCEEEEEecCCCCCCc-chhhhHHHHHhhcc-
Q 006003 216 QDIEVGKAVRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSE-YGHAMSKIIEQNVL- 293 (665)
Q Consensus 216 ~~i~~g~~~~PmLA~~~~~~~~~~~~~~~~~~~~E~K~DG~R~qih~~g~~v~~~SR~g~d~t~-~~p~l~~~~~~~~~- 293 (665)
.++++|.||+||||++....+++++++. .+|++|+||||+|||+|++++++++|||||+++|. .+|++.+.+.+.+.
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 57877776554443
Q ss_pred ccceeeeceEEEeeCCCCccccccchHHHHHHhhcCCCCCCceEEEEEEEEeeCCccccCCCHHHHHHHHHhhcCCCCCc
Q 006003 294 VDRCILDGEMLVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGR 373 (665)
Q Consensus 294 ~~~~ILDGElv~~d~~~~~~~~F~~lq~~~~~~~~~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~~~ 373 (665)
.++||||||||+||..++++++|+.++...+. .....+++|++||||++||.+++++||.+|+++|++++.+.+++
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 67899999999999877788899887653221 11345799999999999999999999999999999999876655
Q ss_pred ceecccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHcCCceEEeecCCCCCccCCCCCCeEEEcccc
Q 006003 374 LETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEY 445 (665)
Q Consensus 374 ~~~~~p~~~~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EGlV~K~~~s~Y~~GkRs~~WlKiK~~y 445 (665)
+.+.. ...+.+.+++.++|++++++|.||||+|+++|+|.+|+| +|+|+|+||
T Consensus 161 ~~~~~-----------------~~~~~~~~~l~~~~~~~~~~g~EGvV~K~~~s~Y~~G~r--~W~K~K~dY 213 (213)
T cd07902 161 IMLSE-----------------MKFVKKADDLSAMIARVIKEGLEGLVLKDLKSVYEPGKR--HWLKVKKDY 213 (213)
T ss_pred EEEEE-----------------EEEcCCHHHHHHHHHHHHHCCCCeEEEeCCCCCccCCCC--CceEeCCCC
Confidence 44321 234568899999999999999999999999999999987 699999998
No 20
>cd07901 Adenylation_DNA_ligase_Arch_LigB Adenylation domain of archaeal and bacterial LigB-like DNA ligases. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. Bacterial DNA ligases are divided into two broad classes: NAD-dependent and ATP-dependent. All bacterial species have a NAD-dependent DNA ligase (LigA). Some bacterial genomes contain multiple genes for DNA ligases that are predicted to use ATP as their cofactor, including Mycobacterium tuberculosis LigB, LigC, and LigD. This group is composed of archaeal DNA ligases and bacterial proteins similar to Mycobacterium tuberculosis LigB. Members of this group contain adeny
Probab=100.00 E-value=2.6e-44 Score=359.63 Aligned_cols=205 Identities=33% Similarity=0.568 Sum_probs=171.5
Q ss_pred CCCccccccccccCCHHHHHHHhcCCceEEEEeeceeEEEEEEeCCEEEEEecCCCCCCcchhhhHHHHHhhccccceee
Q 006003 220 VGKAVRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCIL 299 (665)
Q Consensus 220 ~g~~~~PmLA~~~~~~~~~~~~~~~~~~~~E~K~DG~R~qih~~g~~v~~~SR~g~d~t~~~p~l~~~~~~~~~~~~~IL 299 (665)
||.||+||||+....+++++++. +.+|++|+||||+|||+|++++.+++|||||+++|..+|++.+.+......++|||
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--CCCCCCceEEEEEEEEeeCCccccCCCHHHHHHHHHhhcCCCCCcceec
Q 006003 300 DGEMLVWDTSLNRFAEFGSNQEIAKAARD--GLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETL 377 (665)
Q Consensus 300 DGElv~~d~~~~~~~~F~~lq~~~~~~~~--~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~~~~~~~ 377 (665)
|||||+||+ .+.+.+|+.+|....+... ......+++|+|||||++||++++++||.+|+++|++++.+. +.+.++
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 5667799887765332110 001235899999999999999999999999999999999865 344332
Q ss_pred ccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHcCCceEEeecCCCCCccCCCCCCeEEEccc
Q 006003 378 VPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPE 444 (665)
Q Consensus 378 ~p~~~~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EGlV~K~~~s~Y~~GkRs~~WlKiK~~ 444 (665)
. ...+++.+++.++|++++++|.||||+|+++|+|.+|+||.+|+|+||+
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 21
>PRK09125 DNA ligase; Provisional
Probab=100.00 E-value=3.5e-44 Score=372.84 Aligned_cols=254 Identities=24% Similarity=0.362 Sum_probs=194.0
Q ss_pred cccccccccCCHHHHHHHhcCCceEEEEeeceeEEEEEEeCCEEEEEecCCCCCCcchhhhHHHHHhhccccceeeeceE
Q 006003 224 VRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDGEM 303 (665)
Q Consensus 224 ~~PmLA~~~~~~~~~~~~~~~~~~~~E~K~DG~R~qih~~g~~v~~~SR~g~d~t~~~p~l~~~~~~~~~~~~~ILDGEl 303 (665)
+.||||...... +.+.+|++|+||||+|||+ + .+++|||||+++|. |+.. ...+ +++|||||+
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 689999887531 2346899999999999975 3 48999999999987 4422 2222 489999999
Q ss_pred EEeeCCCCccccccchHHHHHHhhcCCCCCCceEEEEEEEEeeCCccccCCCHHHHHHHHHhhcCCCC-CcceecccCCC
Q 006003 304 LVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSK-GRLETLVPDHG 382 (665)
Q Consensus 304 v~~d~~~~~~~~F~~lq~~~~~~~~~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~-~~~~~~~p~~~ 382 (665)
|+++ .+|+.++.+.++.........+++|++||+|++|| ||.+|+++|++++.+.+ +.+.++
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 36876666543321111112589999999999986 99999999999997652 233221
Q ss_pred CCccccCCCCCccccccCCHHHHHHHHHHHHHcCCceEEeecCCCCCccCCCCCCeEEEccccccCCCcceEEEEEEEec
Q 006003 383 LNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLIIGGYYG 462 (665)
Q Consensus 383 ~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EGlV~K~~~s~Y~~GkRs~~WlKiK~~y~~~g~~~DlvVIG~~~G 462 (665)
....+++.++++++|++++++|+||||+|+++|+|++| |+.+|+|+|+.+ +.|++|||+++|
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 CCCCCCccceEEEEEeeCCCCCCCCcceEEEEEeccCCCHHHHHHHHHhhccccccccCCCCCCCCceeecCCCCCCCcE
Q 006003 463 SGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDV 542 (665)
Q Consensus 463 ~g~r~g~~~sfllg~~d~~~~~~~~~~~~~~~kVgsG~s~~~~~~l~~~l~~~~~~~~~~~~~pp~~~~~~~~~~~~pd~ 542 (665)
+|+++|.+|+|+|+..+ + ..| +||||||+++++. ||.+
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 99999999999998543 2 122 7899999998641 1211
Q ss_pred EEeCCCceEEEEEeeeceecccCccCCCeeeeccEEEEEecCC
Q 006003 543 WIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDK 585 (665)
Q Consensus 543 wi~~P~~s~v~ev~a~~~~~~s~~~~~g~sLRfPr~~riR~DK 585 (665)
..+++|++ ..++..+.||||+|+++|+|.
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 335567889999999999983
No 22
>PHA00454 ATP-dependent DNA ligase
Probab=100.00 E-value=3.6e-43 Score=371.90 Aligned_cols=284 Identities=20% Similarity=0.291 Sum_probs=208.2
Q ss_pred ccccccccCC--HHHHHHHhcCCceEEEEeeceeEEEEEEeCC-EEEEEecCCCCCCcchhhhHH------HHHh---hc
Q 006003 225 RPQLAMRIGD--AHAAWRKLHGKEVVIECKFDGDRIQIHKNGS-EIHYFSRSFLDHSEYGHAMSK------IIEQ---NV 292 (665)
Q Consensus 225 ~PmLA~~~~~--~~~~~~~~~~~~~~~E~K~DG~R~qih~~g~-~v~~~SR~g~d~t~~~p~l~~------~~~~---~~ 292 (665)
+|++|...+. +.+++.+++ .|++|+||||+|||+|++++ .+++|||||+++++.. ++.. .+.. +.
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 6889988775 778888773 89999999999999999876 4999999999876421 1110 0111 12
Q ss_pred cccceeeeceEEEeeCCCCccccccchHHHHHHhhc--CCCCCCceEEEEEEEEeeC----Cccc---cCCCHHHHHHHH
Q 006003 293 LVDRCILDGEMLVWDTSLNRFAEFGSNQEIAKAARD--GLSSDRQLCYFAFDVLYVG----DTSV---IHQSLKERHELL 363 (665)
Q Consensus 293 ~~~~~ILDGElv~~d~~~~~~~~F~~lq~~~~~~~~--~~~~~~~~~~~vFDiL~ln----g~~l---~~~pl~eRr~~L 363 (665)
.++++|||||+|+.+ .+|+.++.+.++... ......+++|+|||+|++| |+++ ..+||.+|+++|
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 467555554432110 1123468999999999999 6665 789999999999
Q ss_pred HhhcCCCCC-cceecccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHcCCceEEeecCCCCCccCCCCCCeEEEc
Q 006003 364 QKVVKPSKG-RLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLK 442 (665)
Q Consensus 364 ~~~~~~~~~-~~~~~~p~~~~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EGlV~K~~~s~Y~~GkRs~~WlKiK 442 (665)
++++...+. .+.++ ..+.+.+.+++.++|++++++|.||||+|+++|+|++|+|+. |+|+|
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 134567899999999999999999999999999999998875 88999
Q ss_pred cccccCCCcceEEEEEEEecCCCC--CCccceEEEEEeeCCCCCCCCcceEEEEEeccCCCHHHHHHHHHhhcccccccc
Q 006003 443 PEYIRAGSDLDVLIIGGYYGSGRR--GGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYE 520 (665)
Q Consensus 443 ~~y~~~g~~~DlvVIG~~~G~g~r--~g~~~sfllg~~d~~~~~~~~~~~~~~~kVgsG~s~~~~~~l~~~l~~~~~~~~ 520 (665)
+.+ ++|++|||+++|.|++ .|.+++|+|++ ++ +.+.+ |||||++++++|.+++.++...
T Consensus 220 ~~~-----~~d~vIvG~~~g~g~~~~~g~~~~~~~~~--~~------g~l~~----gtGfs~~~~~~l~~~l~~~~~~-- 280 (315)
T PHA00454 220 PEC-----EADGTIVGVVWGTPGLANEGKVIGFRVLL--ED------GRVVN----ATGISRALMEEFTANVKEHGED-- 280 (315)
T ss_pred ccC-----ceeEEEEEEEECCCCccCCceEEEEEEEe--CC------CcEEE----ccCCCHHHHHHHHHHHHhhccC--
Confidence 985 8999999999998643 36677777754 22 24443 8999999999999998775321
Q ss_pred CCCCCCCCceeecCCCCCCCcEEEeCCCceEEEEEeeeceecccCccCCCeeeeccEEEEEec
Q 006003 521 YPKRAPPSFYQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRY 583 (665)
Q Consensus 521 ~~~~~pp~~~~~~~~~~~~pd~wi~~P~~s~v~ev~a~~~~~~s~~~~~g~sLRfPr~~riR~ 583 (665)
...| |....|+||++ ..+|.+++||||+|+++|+
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 22224677754 2366778999999999995
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=9e-43 Score=347.14 Aligned_cols=199 Identities=33% Similarity=0.525 Sum_probs=167.6
Q ss_pred cccccccccCCHHHHHHHhcCCceEEEEeeceeEEEEEEeCCEEEEEecCCCCCCcchhhhHHHHHhhccccceeeeceE
Q 006003 224 VRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDGEM 303 (665)
Q Consensus 224 ~~PmLA~~~~~~~~~~~~~~~~~~~~E~K~DG~R~qih~~g~~v~~~SR~g~d~t~~~p~l~~~~~~~~~~~~~ILDGEl 303 (665)
|+||||+++..+.++ .++.+.+|++|+||||+|||+|+++++|++|||||+++|..+|++.+.+.. .+++|||||||
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 566788999999999999999999999999999999999989998876542 35899999999
Q ss_pred EEeeCCCCccccccchHHHHHHhhcC--CCCCCceEEEEEEEEeeCCccccCCCHHHHHHHHHhhcCCCCCcceecccCC
Q 006003 304 LVWDTSLNRFAEFGSNQEIAKAARDG--LSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDH 381 (665)
Q Consensus 304 v~~d~~~~~~~~F~~lq~~~~~~~~~--~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~~~~~~~~p~~ 381 (665)
|+||..+. .||..++....+.... .....+++|+|||||++||++++++||.||+++|++++.+.++++.++.
T Consensus 78 v~~~~~~~--~~f~~~~~~~~~~~~~~~~~~~~~~~~~vFDil~~~g~~l~~~p~~eR~~~L~~~~~~~~~~i~~~~--- 152 (201)
T cd07898 78 LAWDDNRG--LPFSELFKRLGRKFRDKFLDEDVPVVLMAFDLLYLNGESLLDRPLRERRQLLEELFVEIPGRIRIAP--- 152 (201)
T ss_pred EEEeCCCC--CcHHHHHHHhcccccchhhhccCcEEEEEEeEEeECCcchhhCCHHHHHHHHHHhhcCCCCcEEEee---
Confidence 99986533 5887776544322111 1234679999999999999999999999999999999988766665421
Q ss_pred CCCccccCCCCCccccccCCHHHHHHHHHHHHHcCCceEEeecCCCCCccCCCCCCeEEEccc
Q 006003 382 GLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPE 444 (665)
Q Consensus 382 ~~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EGlV~K~~~s~Y~~GkRs~~WlKiK~~ 444 (665)
...+++.+++.++|++++++|.||||+|+++|+|++|+||.+|+|+|||
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 2345788899999999999999999999999999999999999999996
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=6.5e-43 Score=349.22 Aligned_cols=200 Identities=25% Similarity=0.316 Sum_probs=166.4
Q ss_pred CccccccccccCCHHHHHHHhcCCceEEEEeeceeEEEEEEeCCEEEEEecCCCCCCcchhhhHHHHHhhccccceeeec
Q 006003 222 KAVRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDG 301 (665)
Q Consensus 222 ~~~~PmLA~~~~~~~~~~~~~~~~~~~~E~K~DG~R~qih~~g~~v~~~SR~g~d~t~~~p~l~~~~~~~~~~~~~ILDG 301 (665)
.|+.||||+++....+.+ ....+|++|+||||+|||+|++++.+++|||||+++|..+|++.+.+. . .+.+|||||
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 589999999998766543 345689999999999999999999999999999999999999987653 2 357899999
Q ss_pred eEEEeeCCCCccccccchHHHHHHhhcC--CCCCCceEEEEEEEEeeCCccccCCCHHHHHHHHHhhcCCCC-Ccceecc
Q 006003 302 EMLVWDTSLNRFAEFGSNQEIAKAARDG--LSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSK-GRLETLV 378 (665)
Q Consensus 302 Elv~~d~~~~~~~~F~~lq~~~~~~~~~--~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~-~~~~~~~ 378 (665)
|||+||. +...+|+.++....+.... .....+++|++|||||+||+++++.||.+|+++|++++.+.+ +++.+.
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 4568998887654321110 112468999999999999999999999999999999997763 343321
Q ss_pred cCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHcCCceEEeecCCCCCccCCCCCCeEEEccc
Q 006003 379 PDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPE 444 (665)
Q Consensus 379 p~~~~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EGlV~K~~~s~Y~~GkRs~~WlKiK~~ 444 (665)
....+++.+++.++|++++++|+||||+|+++|+|++|+|+++|+|+|+|
T Consensus 156 ----------------~~~~~~~~~~~~~~~~~~~~~g~EGiv~K~~~s~Y~~Grr~~~W~K~K~d 205 (207)
T cd07897 156 ----------------PLIAFADWEELAALRAQSRERGAEGLMLKRRDSPYLVGRKKGDWWKWKID 205 (207)
T ss_pred ----------------ceEecCCHHHHHHHHHHHHHcCCeEEEEeCCCCCcCCCCcCCCeeEeCCC
Confidence 13346788999999999999999999999999999999999999999997
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=1.3e-42 Score=351.59 Aligned_cols=201 Identities=26% Similarity=0.407 Sum_probs=163.1
Q ss_pred CCHHHHHHHhcCCceEEEEeeceeEEEEEEe----CCEEEEEecCCCCCCcchhhhHHHHHhhc--------cccceeee
Q 006003 233 GDAHAAWRKLHGKEVVIECKFDGDRIQIHKN----GSEIHYFSRSFLDHSEYGHAMSKIIEQNV--------LVDRCILD 300 (665)
Q Consensus 233 ~~~~~~~~~~~~~~~~~E~K~DG~R~qih~~----g~~v~~~SR~g~d~t~~~p~l~~~~~~~~--------~~~~~ILD 300 (665)
.++..+++.+.+.+|++|+||||+|||+|++ ++.|++|||||+|+|..+|++.+.+...+ .+++||||
T Consensus 10 ~~~~~~~~~~~~~~~~~E~K~DG~R~qih~~~~~~~~~v~lfSR~~~d~T~~~pel~~~~~~~~~~~~~~~~~~~~~ILD 89 (235)
T cd08039 10 RSIKHCCKMIGSRRMWVETKYDGEYCQIHIDLSKDSSPIRIFSKSGKDSTADRAGVHSIIRKALRIGKPGCKFSKNCILE 89 (235)
T ss_pred cCHHHHHHHhCCCcEEEEEeecceEEEEEEecccCCCEEEEEeCCCCcccccchhHHHHHHHHhhccccccCCCccEEEE
Confidence 3467788888999999999999999999997 88999999999999999999887654332 25789999
Q ss_pred ceEEEeeCCCCccccccchHHHHHHhhc--------CCCCCCceEEEEEEEEeeCCccccCCCHHHHHHHHHhhcCCCCC
Q 006003 301 GEMLVWDTSLNRFAEFGSNQEIAKAARD--------GLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKG 372 (665)
Q Consensus 301 GElv~~d~~~~~~~~F~~lq~~~~~~~~--------~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~~ 372 (665)
||||+||+.++++.||+.+|........ ......++||+||||||+||+++++.||.+|+++|++++.+.++
T Consensus 90 GEiVv~d~~~g~~~~F~~L~~~~~~~~~~~~~~~~~~~~~~~~v~~~vFDlL~lnG~~l~~~pl~eRr~~L~~l~~~~~~ 169 (235)
T cd08039 90 GEMVVWSDRQGKIDPFHKIRKHVERSGSFIGTDNDSPPHEYEHLMIVFFDVLLLDDESLLSKPYSERRDLLESLVHVIPG 169 (235)
T ss_pred eEEEEEECCCCccCCHHHHHhhcccccchhccccccccccccceEEEEEEEEEECChhhhcCCHHHHHHHHHHhcccCCC
Confidence 9999999877788999988765321110 01124679999999999999999999999999999999988777
Q ss_pred cceecccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHcCCceEEeecCCCCCccCCC-----CCCeEEEcccc
Q 006003 373 RLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDR-----SGKWLKLKPEY 445 (665)
Q Consensus 373 ~~~~~~p~~~~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EGlV~K~~~s~Y~~GkR-----s~~WlKiK~~y 445 (665)
+++++.. ..+. .....+.++++++|++++++|+||||+|+++|+|.||++ +.+|+|+|+||
T Consensus 170 ~~~~~~~-----~~i~-------~~~~~~~~~l~~~~~~a~~~g~EGIv~K~~~S~Y~pgr~~~~~r~~~WlKlK~dY 235 (235)
T cd08039 170 YAGLSER-----FPID-------FSRSSGYERLRQIFARAIAERWEGLVLKGDEEPYFDLFLEQGSFSGCWIKLKKDY 235 (235)
T ss_pred cEEEEEE-----Eeec-------ccCCCCHHHHHHHHHHHHHcCCceEEEecCCCCcccCcccccccCCCeEEeCCCC
Confidence 6654321 0110 011246789999999999999999999999999999743 58999999998
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=1.2e-40 Score=329.79 Aligned_cols=190 Identities=26% Similarity=0.390 Sum_probs=157.0
Q ss_pred cccccccccCCHHHHHHHhcCCceEEEEeeceeEEEEEEeCCEEEEEecCCCCCCcchhhhHHHHHhhccccceeeeceE
Q 006003 224 VRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDGEM 303 (665)
Q Consensus 224 ~~PmLA~~~~~~~~~~~~~~~~~~~~E~K~DG~R~qih~~g~~v~~~SR~g~d~t~~~p~l~~~~~~~~~~~~~ILDGEl 303 (665)
|+||||+....+++ +.+|++|+||||+|||+|++++.+++|||||+++|..+|++.+++.. ..+.+|||||||
T Consensus 1 i~PmLa~~~~~~~~------~~~~~~E~K~DG~R~~~~~~~~~v~l~SR~g~~~t~~~p~~~~~~~~-~~~~~~iLDGEl 73 (194)
T cd07905 1 VEPMLARAVDALPE------PGGWQYEPKWDGFRCLAFRDGDEVRLQSRSGKPLTRYFPELVAAARA-LLPPGCVLDGEL 73 (194)
T ss_pred CCceeCCccCCCCC------CCceEEEeeeceEEEEEEEeCCEEEEEeCCCCchhhhhHHHHHHHHh-hCCCCEEEEeEE
Confidence 58999998876432 56899999999999999999999999999999999999999887643 346789999999
Q ss_pred EEeeCCCCccccccchHHHHHHhhcC---CCCCCceEEEEEEEEeeCCccccCCCHHHHHHHHHhhcCCCCCcceecccC
Q 006003 304 LVWDTSLNRFAEFGSNQEIAKAARDG---LSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPD 380 (665)
Q Consensus 304 v~~d~~~~~~~~F~~lq~~~~~~~~~---~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~~~~~~~~p~ 380 (665)
|+||+.+ .+|+.+|......... .....+++|+|||||++||+++++.||.+|+++|++++.+..+++.++.
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 9998643 4998887654321111 1234789999999999999999999999999999999987644444320
Q ss_pred CCCCccccCCCCCccccccCCHHHHHHHHHHHHHcCCceEEeecCCCCCccCCCCCCeEEEccc
Q 006003 381 HGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPE 444 (665)
Q Consensus 381 ~~~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EGlV~K~~~s~Y~~GkRs~~WlKiK~~ 444 (665)
...+.+++.++|++++++|+||||+|+++|+|++|+| +|+|+|+.
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 1246789999999999999999999999999999974 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=1.2e-40 Score=331.97 Aligned_cols=199 Identities=31% Similarity=0.529 Sum_probs=166.1
Q ss_pred cccccccCCHHHHHHHhcCCceEEEEeeceeEEEEEEeCCEEEEEecCCCCCCcchhhhHHHHHhhccc--cceeeeceE
Q 006003 226 PQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLV--DRCILDGEM 303 (665)
Q Consensus 226 PmLA~~~~~~~~~~~~~~~~~~~~E~K~DG~R~qih~~g~~v~~~SR~g~d~t~~~p~l~~~~~~~~~~--~~~ILDGEl 303 (665)
||||++..+++++++++ +.+|++|+||||+|||+|+.++.+++|||+|+++|..+|++...+...+.. +++||||||
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 99999999888899888 678999999999999999999999999999999999889988776554433 479999999
Q ss_pred EEeeCCCCccccccchHHHHHHhhcCCC-CCCceEEEEEEEEeeCCccccCCCHHHHHHHHHhhcCCCCCcceecccCCC
Q 006003 304 LVWDTSLNRFAEFGSNQEIAKAARDGLS-SDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHG 382 (665)
Q Consensus 304 v~~d~~~~~~~~F~~lq~~~~~~~~~~~-~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~~~~~~~~p~~~ 382 (665)
|+||+.++.+.||+.++....+...... ...+++|+|||+|++||.++++.||.+|+++|++++.+..+.+.++.
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 9999988888999766654421110000 14689999999999999999999999999999999965555554431
Q ss_pred CCccccCCCCCccccccCCHHHHHHHHHHHHHcCCceEEeecCCCCCccCCCCCCeEEEc
Q 006003 383 LNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLK 442 (665)
Q Consensus 383 ~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EGlV~K~~~s~Y~~GkRs~~WlKiK 442 (665)
+..+++.+++.++|++++++|+||+|+|+++|+|++|+||.+|+|+|
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=8.5e-40 Score=322.91 Aligned_cols=189 Identities=29% Similarity=0.456 Sum_probs=155.8
Q ss_pred cccccccccCCHHHHHHHhcCCceEEEEeeceeEEEEEEeCCEEEEEecCCCCCCcchhhhHHHHHhhccccceeeeceE
Q 006003 224 VRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDGEM 303 (665)
Q Consensus 224 ~~PmLA~~~~~~~~~~~~~~~~~~~~E~K~DG~R~qih~~g~~v~~~SR~g~d~t~~~p~l~~~~~~~~~~~~~ILDGEl 303 (665)
++||||+++.... .+.+|++|+||||+|||+|++++.+++|||+|+++|..+|++...+.+ +...++||||||
T Consensus 1 i~pmLa~~~~~~~------~~~~~~~e~K~DG~R~~i~~~~~~v~~~SR~g~~~t~~~p~l~~~~~~-~~~~~~iLDGEl 73 (190)
T cd07906 1 IEPMLATLVDEPP------DGEDWLYEIKWDGYRALARVDGGRVRLYSRNGLDWTARFPELAEALAA-LPVRDAVLDGEI 73 (190)
T ss_pred CCCeECCcCCCCC------CCCCeEEEEeEceEEEEEEEECCEEEEEcCCCCcchhhhHHHHHHHHh-cCCCCEEEEeEE
Confidence 5899999988652 357899999999999999999999999999999999989998876543 356899999999
Q ss_pred EEeeCCCCccccccchHHHHHHhhcCCCCCCceEEEEEEEEeeCCccccCCCHHHHHHHHHhhcCCCCCcceecccCCCC
Q 006003 304 LVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGL 383 (665)
Q Consensus 304 v~~d~~~~~~~~F~~lq~~~~~~~~~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~~~~~~~~p~~~~ 383 (665)
|+||.... .+|+.++...++.. ......+++|+|||||++||+++.++||.||+++|++++.+..+++.++.
T Consensus 74 v~~~~~~~--~~F~~l~~~~~~~~-~~~~~~~~~~~vFDil~~~~~~~~~~p~~eR~~~L~~~~~~~~~~i~~~~----- 145 (190)
T cd07906 74 VVLDEGGR--PDFQALQNRLRLRR-RLARTVPVVYYAFDLLYLDGEDLRGLPLLERKELLEELLPAGSPRLRVSE----- 145 (190)
T ss_pred EEECCCCC--CCHHHHHHhhcccc-hhcccCceEEEEEeeeeeCCcchhhCCHHHHHHHHHHHhccCCCcEEECc-----
Confidence 99997542 58876665443211 12245789999999999999999999999999999999987755554321
Q ss_pred CccccCCCCCccccccCCHHHHHHHHHHHHHcCCceEEeecCCCCCccCCCCCCeEEEcc
Q 006003 384 NSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKP 443 (665)
Q Consensus 384 ~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EGlV~K~~~s~Y~~GkRs~~WlKiK~ 443 (665)
+.. .+..++|++++++|.||||+|+++|+|++|+||.+|+|+|+
T Consensus 146 ------------~~~----~~~~~~~~~~~~~g~EGiv~K~~~s~Y~~g~rs~~wlK~K~ 189 (190)
T cd07906 146 ------------HFE----GGGAALFAAACELGLEGIVAKRADSPYRSGRRSRDWLKIKC 189 (190)
T ss_pred ------------eEc----CCHHHHHHHHHHcCCcEEEEecCCCCcCCCCCCCccEEEec
Confidence 111 12378999999999999999999999999999999999997
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=4.7e-34 Score=265.50 Aligned_cols=137 Identities=26% Similarity=0.530 Sum_probs=118.1
Q ss_pred CCcceEEEEEEEecCCCCCCccceEEEEEeeCCCCCCCCcceEEEEEeccCCCHHHHHHHHHhhccccccccCCCCCCCC
Q 006003 449 GSDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPS 528 (665)
Q Consensus 449 g~~~DlvVIG~~~G~g~r~g~~~sfllg~~d~~~~~~~~~~~~~~~kVgsG~s~~~~~~l~~~l~~~~~~~~~~~~~pp~ 528 (665)
+|++||||||||+|+|+++|.+|+||||++++++ ++|+++||||||||++++++|.++|+++++. .+...||.
T Consensus 2 ~dtlDlVViG~~~g~G~r~~~~gslLlg~~d~~~-----~~l~~vgkVGTGfs~~~l~~l~~~L~~l~~~--~~~~~~p~ 74 (139)
T cd07967 2 ADTADLVVLGAYYGTGSKGGMMSVFLMGCYDPNS-----KKWCTVTKCGNGHDDATLARLQKELKMVKIS--KDPSKVPS 74 (139)
T ss_pred CceEeEEEEEEEECCCCCCCccceEEEEEEeCCC-----CEEEEEeEECCCCCHHHHHHHHHHhhhhccc--cCCcCCCc
Confidence 4799999999999999999999999999998653 4899999999999999999999999999876 23335677
Q ss_pred ceeecCCCCCCCcEEEeCCCceEEEEEeeeceecccCccC-CCeeeeccEEEEEecCCCccCCCCHHH
Q 006003 529 FYQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFS-APYSLRFPRIDRVRYDKPWHDCLDVQS 595 (665)
Q Consensus 529 ~~~~~~~~~~~pd~wi~~P~~s~v~ev~a~~~~~~s~~~~-~g~sLRfPr~~riR~DK~~~d~~t~~e 595 (665)
|+.+. ...+||+||.+|+.|+|+||+++..+ .|+.|. +|+|||||||++||+||+|+||+|++|
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 87753 35799999977999999999965433 467676 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=2e-33 Score=273.61 Aligned_cols=173 Identities=20% Similarity=0.312 Sum_probs=135.0
Q ss_pred cccccccccCCHHHHHHHhcCCceEEEEeeceeEEEEEEeCCEEEEEecCCCCCCcchhhhHHHHHhhccccceeeeceE
Q 006003 224 VRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDGEM 303 (665)
Q Consensus 224 ~~PmLA~~~~~~~~~~~~~~~~~~~~E~K~DG~R~qih~~g~~v~~~SR~g~d~t~~~p~l~~~~~~~~~~~~~ILDGEl 303 (665)
++||||++.....+ +.+|++|+||||+|||+|. + ++|||+|+++|.. +. +...+ .++||||||
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 58999998875432 4589999999999999873 2 8999999999974 22 22222 349999999
Q ss_pred EEeeCCCCccccccchHHHHHHhhcCCCCCCceEEEEEEEEeeCCccccCCCHHHHHHHHHhhcCCCC-CcceecccCCC
Q 006003 304 LVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSK-GRLETLVPDHG 382 (665)
Q Consensus 304 v~~d~~~~~~~~F~~lq~~~~~~~~~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~-~~~~~~~p~~~ 382 (665)
|++++ ||+.++.+.+..........+++|++||||+ ++.||.+|+++|++++.+.+ +.+.++.
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 7877766544322111134689999999999 67899999999999997652 3333321
Q ss_pred CCccccCCCCCccccccCCHHHHHHHHHHHHHcCCceEEeecCCCCCccCCCCCCeEEEcc
Q 006003 383 LNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKP 443 (665)
Q Consensus 383 ~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EGlV~K~~~s~Y~~GkRs~~WlKiK~ 443 (665)
...+.+.+++.+++++++++|+||||+|+++|+|++| |+.+|+|+||
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 3456788999999999999999999999999999987 8899999997
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=1.4e-31 Score=262.51 Aligned_cols=177 Identities=23% Similarity=0.333 Sum_probs=139.4
Q ss_pred cccccccCCHHHHHHHhcCCceEEEEeeceeEEEEEEeCCEEEEEecCCCCCCcchhhhHHHHHhhccccceeeeceEEE
Q 006003 226 PQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDGEMLV 305 (665)
Q Consensus 226 PmLA~~~~~~~~~~~~~~~~~~~~E~K~DG~R~qih~~g~~v~~~SR~g~d~t~~~p~l~~~~~~~~~~~~~ILDGElv~ 305 (665)
||||.......+ ..+.+.+|++|+||||+|||+|++++.+++|||||+++|..+|.+..... .....++|||||||+
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 788887765422 24567899999999999999999999999999999999987777643111 123578999999999
Q ss_pred eeCCCCccccccchHHHHHHhhcCCCCCCceEEEEEEEEeeCCccccCCCHHHHHHHHHhhcCCCCC--cceecccCCCC
Q 006003 306 WDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKG--RLETLVPDHGL 383 (665)
Q Consensus 306 ~d~~~~~~~~F~~lq~~~~~~~~~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~~--~~~~~~p~~~~ 383 (665)
++... ...+++|++||+|++||.+++++||.+|+++|++++.+.++ .+.+..
T Consensus 79 ~~~~~---------------------~~~~~~~~~FDil~~~~~~~~~~p~~eR~~~L~~~v~~~~~~~~~~i~~----- 132 (182)
T cd06846 79 ENREV---------------------ANPKPTYYAFDVVPLSGVGLRDLPYSDRFAYLKSLLKEFEGLDPVKLVP----- 132 (182)
T ss_pred ccCCC---------------------ccceeEEEEEEEEEECCCccccCCHHHHHHHHHHHhhhhccCCceeEEE-----
Confidence 86531 13578999999999999999999999999999999987542 222210
Q ss_pred CccccCCCCCccccccCCHHHHHHHHHHHHHcCCceEEeecCCCCC--ccCCCCCCeEEEcc
Q 006003 384 NSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKW--EPGDRSGKWLKLKP 443 (665)
Q Consensus 384 ~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EGlV~K~~~s~Y--~~GkRs~~WlKiK~ 443 (665)
+. ... ...+++.+++++++++|.||||+|+++|+| .+| |+..|+|+||
T Consensus 133 ---~~-------~~~-~~~~~~~~~~~~~~~~g~EGvi~K~~~s~Y~~~~g-r~~~wlK~Kp 182 (182)
T cd06846 133 ---LE-------NAP-SYDETLDDLLEKLKKKGKEGLVFKHPDAPYKGRPG-SSGNQLKLKP 182 (182)
T ss_pred ---ee-------ccc-ccchHHHHHHHHhhhcCCceEEEEcCCCCccccCC-CCCceEeecC
Confidence 00 111 123338999999999999999999999999 887 8999999997
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=5.3e-32 Score=264.38 Aligned_cols=169 Identities=37% Similarity=0.661 Sum_probs=137.1
Q ss_pred CcHHHHHHHHHHHHhcCChhHHHHHHHHHhhhcCCC---chHhhhHhhcCCCCCCCccccCCCHHHHHHHHHHHhCCCcC
Q 006003 7 TEVIVLVSLFNWIQKTKPAAKKRSKFRKFLDTYCDS---VDYFSALRLILPSLDRERGSYGLKESVLANCLIDALGMSKD 83 (665)
Q Consensus 7 ~~F~~l~~~~e~i~~~~~~~~k~~~l~~~~~~~~~~---~~~~~~lrLllp~~d~~r~~yglke~~L~k~~~~~~~~~~~ 83 (665)
|+|++||++|++|++++++.+|+++|++||..+... .++|+++++++|+.| +| +|||+++.|++++++++|++++
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 799999999999999999999999999999998654 689999999999999 56 9999999999999999999998
Q ss_pred hHHHHHHhhhhcCCCCCCCCCHHHHHHHHhhhccCC--CCCCCCHHHHHHHHHHHHhhh---hHHhHHHHHHHHHHhCCH
Q 006003 84 SADAVRLINWRKGGAAPNAGNFPMVAAEVLQRRQGM--ISGGLTIKELNDLLDRLASSE---NRAEKISVLSTLIKKTNA 158 (665)
Q Consensus 84 ~~~~~~L~~wk~~~~~~~~gD~~~~~~~v~~~r~~~--~~~~lTi~eV~~~Ld~la~~~---~~~~k~~~l~~ll~~~t~ 158 (665)
+.++ +|+. .||||.+++++++++... .+++|||.+||+.||+||..+ ++..|..+|..|+++|||
T Consensus 79 ~~~~----~~~~------~GD~g~~~~~~~~~~~~~~~~~~~lTi~~V~~~L~~la~~~g~~s~~~k~~~l~~ll~~~s~ 148 (177)
T PF04675_consen 79 SIDE----SYKK------VGDLGEVAEEVLQKRKSETSKPSPLTISEVNETLDELAAASGKGSQDEKIDILKELLRRCSP 148 (177)
T ss_dssp HHHH----HHHH------HS-HHHHHHHHHHHHTTTS--SS--BHHHHHHHHHHHHH--STTHHHHHHHHHHHHHTTS-H
T ss_pred HHHH----HHHh------cCcHHHHHHHHHhhccccccCCCCCCHHHHHHHHHHHHHhhCccchHHHHHHHHHHHHhCCH
Confidence 7775 4443 799999999999888743 368999999999999999987 478899999999999999
Q ss_pred HHHHHHHHHHHhhhccCCcccccccccCc
Q 006003 159 QEMKWIIMIILKDLKLGISEKSIFHEFHP 187 (665)
Q Consensus 159 ~E~k~l~RiilkdlriG~~e~til~~~hp 187 (665)
.|++||+|||+|+||||+++++|+++|||
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 99999999999999999999999999987
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=99.97 E-value=7.5e-30 Score=238.97 Aligned_cols=139 Identities=53% Similarity=1.053 Sum_probs=113.5
Q ss_pred CCcceEEEEEEEecCCCCCCccceEEEEEeeCCCC-CCCCcceEEEEEeccCCCHHHHHHHHHhhccccccccCCCCCCC
Q 006003 449 GSDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAP-DTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPP 527 (665)
Q Consensus 449 g~~~DlvVIG~~~G~g~r~g~~~sfllg~~d~~~~-~~~~~~~~~~~kVgsG~s~~~~~~l~~~l~~~~~~~~~~~~~pp 527 (665)
++++||||||||+|+|+++|.+|+||||+++.++. +..+.+|+++|+||||||++++++|.++|.++|.+ .+...||
T Consensus 1 ~~~lDlvViG~~~g~g~~~~~~~slllG~~~~~~~~~~~~~~l~~vgkVgtGfs~~~~~~L~~~l~~~~~~--~~~~~~P 78 (140)
T cd07968 1 GEDLDLLIIGGYYGEGRRGGKVSSFLCGVAEDDDPESDKPSVFYSFCKVGSGFSDEELDEIRRKLKPHWKP--FDKKAPP 78 (140)
T ss_pred CCcEeEEEEccEeCCCCcCCccccEEEEEEcCCCCCCCCCCEEEEEEEEccCCCHHHHHHHHHHhcCcEEE--cCcCCCC
Confidence 47999999999999999999999999999976431 11234899999999999999999999999999876 2333344
Q ss_pred CceeecCCCCCCCcEEEeCCCceEEEEEeeeceecccCccCCCeeeeccEEEEEecCCCccCCCCH
Q 006003 528 SFYQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDKPWHDCLDV 593 (665)
Q Consensus 528 ~~~~~~~~~~~~pd~wi~~P~~s~v~ev~a~~~~~~s~~~~~g~sLRfPr~~riR~DK~~~d~~t~ 593 (665)
.+ .......+|++||+ |..|+|+||++... ..+..|++|++||||||+++|+||+|+||+|+
T Consensus 79 ~~--~~~~~~~~~~~Wv~-P~~slV~EV~~~e~-t~s~~~~~g~~LR~Pr~~~~R~DK~~~e~~t~ 140 (140)
T cd07968 79 SS--LLKFGKEKPDVWIE-PKDSVVLEVKAAEI-VPSDSYKTGYTLRFPRCEKIRYDKDWHDCLTL 140 (140)
T ss_pred cc--cccccccCCcEEEe-cCCCEEEEEEeeeE-eecCcccCCcEEEcceEeEEECCCCHHHccCC
Confidence 33 11224568999999 88899999996543 35788889999999999999999999999984
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=1.5e-28 Score=230.75 Aligned_cols=134 Identities=37% Similarity=0.590 Sum_probs=113.3
Q ss_pred CCcceEEEEEEEecCCCCCCccceEEEEEeeCCCCCCCCcceEEEEEeccCCCHHHHHHHHHhhccccccccCCCCCCCC
Q 006003 449 GSDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPS 528 (665)
Q Consensus 449 g~~~DlvVIG~~~G~g~r~g~~~sfllg~~d~~~~~~~~~~~~~~~kVgsG~s~~~~~~l~~~l~~~~~~~~~~~~~pp~ 528 (665)
++++|+||||+++|+|++.+.+|+||||++++++ ++|+++|+||||||++++++|.++|.+++... +||.
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 4789999999999999998999999999998653 48999999999999999999999999998651 2332
Q ss_pred ceeecCCCCCCCcEEEeCCCceEEEEEeeeceecccCccCC---------CeeeeccEEEEEecCCCccCCCCHHHHHHH
Q 006003 529 FYQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSA---------PYSLRFPRIDRVRYDKPWHDCLDVQSFVEL 599 (665)
Q Consensus 529 ~~~~~~~~~~~pd~wi~~P~~s~v~ev~a~~~~~~s~~~~~---------g~sLRfPr~~riR~DK~~~d~~t~~el~~l 599 (665)
+ . ...+|++||+ | .+|+||+++.. ..|+.|++ |++||||||+++|+||+|+||+++++|.+|
T Consensus 71 ~-~----~~~~~~vWv~-P--~lV~EV~~~e~-t~s~~~~~~~~~~~~~~g~~LRfPr~~~~R~Dk~~~~~~~~~~l~~l 141 (144)
T cd07969 71 V-D----SSLEPDVWFE-P--KEVWEVKAADL-TLSPVHTAAIGLVDEEKGISLRFPRFIRVRDDKKPEDATTSEQIAEM 141 (144)
T ss_pred c-c----ccCCCcEEEe-e--eEEEEEEEeEe-ecCcceeccccccccCCceEEEeeEEEEeeCCCChHHCCCHHHHHHH
Confidence 2 1 1258999999 7 47999986543 35677765 889999999999999999999999999999
Q ss_pred HH
Q 006003 600 VH 601 (665)
Q Consensus 600 ~~ 601 (665)
|+
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=6.3e-28 Score=242.94 Aligned_cols=175 Identities=21% Similarity=0.289 Sum_probs=130.4
Q ss_pred HHHhcCCceEEEEeeceeEEEEEEeC-CEEEEEecCCCCCCcchhhhHHHHHhhccccceeeeceEEEeeCCCCcccccc
Q 006003 239 WRKLHGKEVVIECKFDGDRIQIHKNG-SEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDGEMLVWDTSLNRFAEFG 317 (665)
Q Consensus 239 ~~~~~~~~~~~E~K~DG~R~qih~~g-~~v~~~SR~g~d~t~~~p~l~~~~~~~~~~~~~ILDGElv~~d~~~~~~~~F~ 317 (665)
+..+...+|++|+||||+|+|+|+.+ +.+.++||+++.++..+|.+.+.........++|||||||+++...
T Consensus 35 ~~~~~~~~y~ve~K~DG~R~~l~~~~~~~v~l~sR~~~~~~~~~~~~~~~~~~~~~~~~~ilDGElv~~~~~~------- 107 (215)
T cd07895 35 LELLKQNDYFVCEKSDGVRYLLLITGRGEVYLIDRKNDVFKVPGLFFPRRKNLEPHHQGTLLDGELVIDKVPG------- 107 (215)
T ss_pred HHHHhhCCeEEEEeEcCeEEEEEEecCCcEEEEeCCCCeEEeccccCCCcccccccccCeeeEEEEEEEcCCC-------
Confidence 34456678999999999999999998 9999999999998877776542111112357899999999986431
Q ss_pred chHHHHHHhhcCCCCCCceEEEEEEEEeeCCccccCCCHHHHHHHHHhhcCCCCCcce-e-cccCCCCCccccCCCCCcc
Q 006003 318 SNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLE-T-LVPDHGLNSHVRPQGEPCW 395 (665)
Q Consensus 318 ~lq~~~~~~~~~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~~~~~-~-~~p~~~~~~~v~~~~~~~~ 395 (665)
..+++|+|||||++||+++++.||.+|+++|++++........ . ........+.|+.
T Consensus 108 ---------------~~~~~~~vFDiL~~~g~~l~~~pl~~R~~~L~~~i~~~~~~~~~~~~~~~~~~~~~i~~------ 166 (215)
T cd07895 108 ---------------KKRPRYLIFDILAFNGQSVTEKPLSERLKYIKKEVIEPRNELLKKGPIDKAKEPFSVRL------ 166 (215)
T ss_pred ---------------ceEEEEEEEEEEEECCcCccCCCHHHHHHHHHHhchhHHHHhhhcChhhcCCCCeEEEe------
Confidence 2478999999999999999999999999999999854321100 0 0000000011110
Q ss_pred ccccCCHHHHHHHHHHH---HHcCCceEEeecCCCCCccCCCCCCeEEEcc
Q 006003 396 SLVAHNVDEVEKFFKET---IENRDEGIVLKDLGSKWEPGDRSGKWLKLKP 443 (665)
Q Consensus 396 ~~~~~~~~~i~~~~~~a---i~~g~EGlV~K~~~s~Y~~GkRs~~WlKiK~ 443 (665)
......+++.++++.+ +.+|.||||+|+.+++|.+| |+.+|+|+||
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
>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=99.95 E-value=4.4e-27 Score=215.19 Aligned_cols=121 Identities=31% Similarity=0.570 Sum_probs=105.3
Q ss_pred CcceEEEEEEEecCCCCCCccceEEEEEeeCCCCCCCCcceEEEEEeccCCCHHHHHHHHHhhccccccccCCCCCCCCc
Q 006003 450 SDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSF 529 (665)
Q Consensus 450 ~~~DlvVIG~~~G~g~r~g~~~sfllg~~d~~~~~~~~~~~~~~~kVgsG~s~~~~~~l~~~l~~~~~~~~~~~~~pp~~ 529 (665)
|++|+||+|+++|.|+++|.+|+||||++++++ ++|+++|+||||||++++++|.++|+++++.
T Consensus 1 ~t~d~vi~G~~~~~g~~~~~~~slllg~~d~~~-----g~l~~vg~vgtG~~~~~~~~l~~~l~~~~~~----------- 64 (122)
T cd07972 1 ETLDLVVIGAEWGEGRRAGLLGSYTLAVRDEET-----GELVPVGKVATGLTDEELEELTERLRELIIE----------- 64 (122)
T ss_pred CceeEEEEeeEeCCCCcCCCcccEEEEEEcCCC-----CeEEEEEEEccCCCHHHHHHHHHHhhhhhcc-----------
Confidence 479999999999999999999999999997652 3899999999999999999999999887643
Q ss_pred eeecCCCCCCCcEEEeCCCceEEEEEeeeceecccCccCCCeeeeccEEEEEecCCCccCCCCHHHHH
Q 006003 530 YQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDKPWHDCLDVQSFV 597 (665)
Q Consensus 530 ~~~~~~~~~~pd~wi~~P~~s~v~ev~a~~~~~~s~~~~~g~sLRfPr~~riR~DK~~~d~~t~~el~ 597 (665)
..+|++|++ |. +|+||++... ..++.|++|++||||||+++|+||+|+||+|++||.
T Consensus 65 -------~~~~~~wv~-P~--lV~eV~~~e~-t~s~~~~~g~~LR~Prf~~~R~Dk~~~~~~t~~~~~ 121 (122)
T cd07972 65 -------KFGPVVSVK-PE--LVFEVAFEEI-QRSPRYKSGYALRFPRIVRIRDDKDPDEADTLERVE 121 (122)
T ss_pred -------ccCCcEEEe-ce--EEEEEEeeEE-EecCccccCceEEccEEeEEeCCCChHHCcCHHHHh
Confidence 125789999 74 7999986432 367888999999999999999999999999999985
No 37
>KOG4437 consensus ATP-dependent DNA ligase III [Replication, recombination and repair]
Probab=99.94 E-value=2.1e-26 Score=231.58 Aligned_cols=318 Identities=24% Similarity=0.344 Sum_probs=244.6
Q ss_pred CcHHHHHHHHHHHHhcCChhHHHHHHHHHhhhcCCCchHhhhHhhcCCCCCCCccccCCCHHHHHHHHHHHhCCCcChHH
Q 006003 7 TEVIVLVSLFNWIQKTKPAAKKRSKFRKFLDTYCDSVDYFSALRLILPSLDRERGSYGLKESVLANCLIDALGMSKDSAD 86 (665)
Q Consensus 7 ~~F~~l~~~~e~i~~~~~~~~k~~~l~~~~~~~~~~~~~~~~lrLllp~~d~~r~~yglke~~L~k~~~~~~~~~~~~~~ 86 (665)
.+|.+|..+|.-++..+....|+++|..+|.+---+.|+|.+|++|+-+.|. +.|+|.++.|+++++++|.+...+.
T Consensus 155 N~F~ef~kiCS~L~~~p~~~~Kt~VI~~LL~kdNFDGDL~LWL~FLIRESD~--R~YNl~DkKLI~lfsKiLn~~~~~~- 231 (482)
T KOG4437|consen 155 NLFREFRKLCSMLADNPSYNTKTQVIQDLLRKDNFDGDLYLWLKFLIRESDK--RVYNLNDKKLIKLFSKILNCNPDDM- 231 (482)
T ss_pred hHHHHHHHHHHHHHhCcCccchhHHHHHHHhccCCCcchhhhhhhhhccccc--ccccccHHHHHHHHHHHHccChHHH-
Confidence 3577777777777777777789999999997532257999999999999986 5899999999999999999986532
Q ss_pred HHHHhhhhcCCCCCCCCCHHHHHHHHhhhccCCCCCCCCHHHHHHHHHHHHhhhhHHhHHHHHHHHHHhCCHHHHHHHHH
Q 006003 87 AVRLINWRKGGAAPNAGNFPMVAAEVLQRRQGMISGGLTIKELNDLLDRLASSENRAEKISVLSTLIKKTNAQEMKWIIM 166 (665)
Q Consensus 87 ~~~L~~wk~~~~~~~~gD~~~~~~~v~~~r~~~~~~~lTi~eV~~~Ld~la~~~~~~~k~~~l~~ll~~~t~~E~k~l~R 166 (665)
+..|-. .+.+.+..+...-.+..++..+-+||++|+++|.+|+..+..++.+..|+....+|++.|.+.|+|
T Consensus 232 ---~~~Y~~-----~S~~~~i~i~~~~~K~~~~~K~~~siQ~~D~~L~rLSKi~~~D~~~~~L~~~A~R~~~~~L~~iIR 303 (482)
T KOG4437|consen 232 ---ARDYEQ-----GSVSETIRVFFEQSKSFPPAKSLLTIQEVDEFLLRLSKLTKEDEQQQALQDIASRCTANDLKCIIR 303 (482)
T ss_pred ---HHHHHh-----ccchhhhhhhHhhccCCCCcccceeHHHHHHHHHHHhcccchHHHHHHHHHHHHhcccchHHHHHH
Confidence 223322 223555555444444455667899999999999999999999999999999999999999999999
Q ss_pred HHHhhhccCCcccccccccCcCHHHHHhhhCCHHHHHHHHhhh--------hhc-cccCCccCCCccccccccccCCHHH
Q 006003 167 IILKDLKLGISEKSIFHEFHPDAEDLFNVTCDLKLVCEKLKDR--------NQR-HKRQDIEVGKAVRPQLAMRIGDAHA 237 (665)
Q Consensus 167 iilkdlriG~~e~til~~~hp~a~~~~~~~~dL~~v~~~l~~~--------~~~-~~~~~i~~g~~~~PmLA~~~~~~~~ 237 (665)
+|-++|+...+.+.||++.||.|+++|. ++.|.-|.+..... ..+ .-........|++|||+....+++-
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 45677777654321 111 0011134567999999998888776
Q ss_pred HHHHhcCCceEEEEeeceeEEEEEEeCCEEEEEecCCCCCCcchhhhHHHHHhhc-cccceeeeceEEEeeCCCCccccc
Q 006003 238 AWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNV-LVDRCILDGEMLVWDTSLNRFAEF 316 (665)
Q Consensus 238 ~~~~~~~~~~~~E~K~DG~R~qih~~g~~v~~~SR~g~d~t~~~p~l~~~~~~~~-~~~~~ILDGElv~~d~~~~~~~~F 316 (665)
+.++..| +..-|.||||+|.|+|.+++.+.+|||--....++ .+.+.+.+ ...+.++|||....+..+++++||
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 57789999999999999999999999965443321 11111122 357899999999999999999999
Q ss_pred cchHHHHHHhhcCCCCCCceEEEEEEEEe
Q 006003 317 GSNQEIAKAARDGLSSDRQLCYFAFDVLY 345 (665)
Q Consensus 317 ~~lq~~~~~~~~~~~~~~~~~~~vFDiL~ 345 (665)
+++.-..+..+. +..+|..+||+.|
T Consensus 458 ~~~~~~~K~~~~----~~~~~~~~~~~~~ 482 (482)
T KOG4437|consen 458 GTLGVHKKAAFQ----DANVCLFVFDCIY 482 (482)
T ss_pred hhcchhhHHHhc----CcchheeecccCC
Confidence 988655444432 3567899999865
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=99.94 E-value=4.8e-26 Score=210.20 Aligned_cols=122 Identities=42% Similarity=0.787 Sum_probs=102.8
Q ss_pred CcceEEEEEEEecCCCCCCccceEEEEEeeCCCCCCCCcceEEEEEeccCCCHHHHHHHHHhhccccccccCCCCCCCCc
Q 006003 450 SDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSF 529 (665)
Q Consensus 450 ~~~DlvVIG~~~G~g~r~g~~~sfllg~~d~~~~~~~~~~~~~~~kVgsG~s~~~~~~l~~~l~~~~~~~~~~~~~pp~~ 529 (665)
|++|+||+|+++|+|+++|.+|+||||++++++ ++|+++|+||||||++++++|.++|.+++... .|| +
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 48999999999999999999999999988641 133 2
Q ss_pred eeecCCCCCCCcEEEeCCCceEEEEEeeeceecccCccCC-------CeeeeccEEEEEecCCCccCC
Q 006003 530 YQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSA-------PYSLRFPRIDRVRYDKPWHDC 590 (665)
Q Consensus 530 ~~~~~~~~~~pd~wi~~P~~s~v~ev~a~~~~~~s~~~~~-------g~sLRfPr~~riR~DK~~~d~ 590 (665)
. ....+|++||+ | ++|+||+++.. ..|+.|++ |++||||||+++|+||+|+||
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 68999986533 25777877 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=1.5e-20 Score=170.50 Aligned_cols=114 Identities=27% Similarity=0.458 Sum_probs=88.9
Q ss_pred cceEEEEEEEecCCCCCCccceEEEEEeeCCCCCCCCcceEEEEEeccCCCHHHHHHHHHhhccccccccCCCCCCCCce
Q 006003 451 DLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFY 530 (665)
Q Consensus 451 ~~DlvVIG~~~G~g~r~g~~~sfllg~~d~~~~~~~~~~~~~~~kVgsG~s~~~~~~l~~~l~~~~~~~~~~~~~pp~~~ 530 (665)
+.|++|+|++.+.| +.|.+|+||||++++. +|+++|+||||||++++++|.++|++++.. .|| |.
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 46776666666667 7788999999999753 799999999999999999999999988644 133 21
Q ss_pred eecCCCCCCCcEEEeCCCceEEEEEeeeceecccCccCCCeeeeccEEEEEecCCCccCC
Q 006003 531 QVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDKPWHDC 590 (665)
Q Consensus 531 ~~~~~~~~~pd~wi~~P~~s~v~ev~a~~~~~~s~~~~~g~sLRfPr~~riR~DK~~~d~ 590 (665)
.. ......+++|++ |. +|+||++.. ++.+++||||+|+++|+||+|+||
T Consensus 67 ~~-~~~~~~~~~wv~-P~--lv~eV~~~~-------~t~~~~LR~P~f~~~R~Dk~~~~~ 115 (115)
T cd07971 67 DP-PPADARGAVWVK-PE--LVAEVEFAE-------WTPDGRLRHPVFKGLREDKPAAEV 115 (115)
T ss_pred cc-ccccCCCCEEec-CC--EEEEEEEEE-------ecCCCcEECCeeeEeeCCCCcccC
Confidence 11 112457899999 74 688997532 345779999999999999999987
No 40
>PF04679 DNA_ligase_A_C: ATP dependent DNA ligase C terminal region ; InterPro: IPR012309 DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA fragments by catalysing the formation of an internucleotide ester bond between phosphate and deoxyribose. It is active during DNA replication, DNA repair and DNA recombination. There are two forms of DNA ligase, one requires ATP (6.5.1.1 from EC), the other NAD (6.5.1.2 from EC), the latter being restricted to eubacteria. Eukaryotic, archaebacterial, viral and some eubacterial DNA ligases are ATP-dependent. The first step in the ligation reaction is the formation of a covalent enzyme-AMP complex. The co-factor ATP is cleaved to pyrophosphate and AMP, with the AMP being covalently joined to a highly conserved lysine residue in the active site of the ligase. The activated AMP residue is then transferred to the 5'phosphate of the nick, before the nick is sealed by phosphodiester-bond formation and AMP elimination [,]. Vertebrate cells encode three well-characterised DNA ligases (DNA ligases I, III and IV), all of which are related in structure and sequence. With the exception of the atypically small PBCV-1 viral enzyme, two regions of primary sequence are common to all members of the family. The catalytic region comprises six conserved sequence motifs (I, III, IIIa, IV, V-VI), motif I includes the lysine residue that is adenylated in the first step of the ligation reaction. The function of the second, less well-conserved region is unknown. When folded, each protein comprises of two distinct sub-domains: a large amino-terminal sub-domain ('domain 1') and a smaller carboxy-terminal sub-domain ('domain 2'). The ATP-binding site of the enzyme lies in the cleft between the two sub-domains. Domain 1 consists of two antiparallel beta sheets flanked by alpha helices, whereas domain 2 consists of a five-stranded beta barrel and a single alpha helix, which form the oligonucleotide-binding fold [, ]. This region is found in many but not all ATP-dependent DNA ligase enzymes (6.5.1.1 from EC). It is thought to constitute part of the catalytic core of ATP dependent DNA ligase []. ; GO: 0003910 DNA ligase (ATP) activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 3RR5_A 2CFM_A 1X9N_A 1VS0_B 3GDE_A 2HIX_A 2HIV_A 3L2P_A 4EQ5_A.
Probab=99.80 E-value=2.4e-19 Score=157.52 Aligned_cols=97 Identities=42% Similarity=0.730 Sum_probs=72.6
Q ss_pred CCCccceEEEEEeeCCCCCCCCcceEEEEEeccCCCHHHHHHHHHhhccccccccCCCCCCCCceeecCCCCCCCcEEEe
Q 006003 466 RGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDVWIE 545 (665)
Q Consensus 466 r~g~~~sfllg~~d~~~~~~~~~~~~~~~kVgsG~s~~~~~~l~~~l~~~~~~~~~~~~~pp~~~~~~~~~~~~pd~wi~ 545 (665)
|+|.+|+||||+++++. ++|.++|+||||||++++++|.++|.+++... ||...... ...+|++||+
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 46889999999999862 48999999999999999999999999998652 33221221 2268999999
Q ss_pred CCCceEEEEEeeeceecccCccCCCeeeeccEEEEEecCC
Q 006003 546 SPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDK 585 (665)
Q Consensus 546 ~P~~s~v~ev~a~~~~~~s~~~~~g~sLRfPr~~riR~DK 585 (665)
|++ |+||+++..+ .+ | +||||||+++|+||
T Consensus 68 -P~~--V~eV~~~e~t-~~-----G-~lR~P~~~~~R~DK 97 (97)
T PF04679_consen 68 -PEL--VVEVKFAEIT-PS-----G-SLRFPRFKRIREDK 97 (97)
T ss_dssp -ST---EEEEEESEEE-EE-----S-EEESEEEEEEETTS
T ss_pred -CCE--EEEEEEEEEc-CC-----C-eEECCEEeEEeCCC
Confidence 865 9999865432 22 6 99999999999998
No 41
>cd08040 OBF_DNA_ligase_family The Oligonucleotide/oligosaccharide binding (OB)-fold domain is a DNA-binding module that is part of the catalytic core unit of ATP dependent DNA ligases. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP dependent DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains including a DNA-binding domain, an adenylation (nucleotidyltransferase (NTase)) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The adenylation and C-terminal OB-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The catalytic core unit contains six conserved sequence motifs (I, III, IIIa, IV,
Probab=99.79 E-value=6.3e-19 Score=158.04 Aligned_cols=108 Identities=23% Similarity=0.354 Sum_probs=86.5
Q ss_pred CcceEEEEEEEecCCCCCCccceEEEEEeeCCCCCCCCcceEEEEEeccCCCHHHHHHHHHhhccccccccCCCCCCCCc
Q 006003 450 SDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSF 529 (665)
Q Consensus 450 ~~~DlvVIG~~~G~g~r~g~~~sfllg~~d~~~~~~~~~~~~~~~kVgsG~s~~~~~~l~~~l~~~~~~~~~~~~~pp~~ 529 (665)
+++|+||+|+++|.|+++|.+|+||||+++++ .+.++|+||||||++++++|.+++++++... .++|.+
T Consensus 1 ~~~d~vV~G~~~~~g~~~~~~gslllg~~~~~-------~~~~vg~vgtGf~~~~~~~l~~~l~~~~~~~----~~~~~~ 69 (108)
T cd08040 1 KTAEAVIIGMRAGFGNRSDVMGSLLLGYYGED-------GLQAVFSVGTGFSADERRDLWQNLEPLVTSF----DDHPVW 69 (108)
T ss_pred CceeEEEEEeEeCCCCCCCceEEEEEEEECCC-------ceEEEEEEcCCCCHHHHHHHHHhcchhccCC----CCCccc
Confidence 47899999999999999899999999998754 4779999999999999999999999887541 112211
Q ss_pred eeecCCCCCCCcEEEeCCCceEEEEEeeeceecccCccCCCeeeeccEEEEEe
Q 006003 530 YQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVR 582 (665)
Q Consensus 530 ~~~~~~~~~~pd~wi~~P~~s~v~ev~a~~~~~~s~~~~~g~sLRfPr~~riR 582 (665)
.....+|++|++ | ++|+||+++. ++.+++||||||+++|
T Consensus 70 ----~~~~~~~~vwv~-P--~lv~eV~~~~-------~t~~~~lR~P~f~~~R 108 (108)
T cd08040 70 ----NVGKDLSFVPLY-P--GKVVEVKYFE-------MGSKDCLRFPVFIGIR 108 (108)
T ss_pred ----ccccCCCCEEee-c--eEEEEEEeEE-------eeCCCeEECCeEEEeC
Confidence 123457899999 7 4789997532 3458999999999997
No 42
>cd07894 Adenylation_RNA_ligase Adenylation domain of RNA circularization proteins. RNA circularization proteins are capable of circularizing RNA molecules in an ATP-dependent reaction. RNA circularization may protect RNA from exonuclease activity. This model comprises the adenylation domain, the minimal catalytic unit that is common to all members of the ATP-dependent DNA ligase family, and the carboxy-terminal extension of RNA circularization protein that serves as a dimerization module. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation of nicked nucleic acid substrates using the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. The adenylation domain binds ATP and contains many active site residues.
Probab=99.74 E-value=1.3e-17 Score=177.24 Aligned_cols=163 Identities=20% Similarity=0.250 Sum_probs=120.3
Q ss_pred CceEEEEeeceeEEEEEEeCCEEEEEecCCCCC---CcchhhhHHHHHhhccccceeeeceEEEeeCCCCccccccchHH
Q 006003 245 KEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDH---SEYGHAMSKIIEQNVLVDRCILDGEMLVWDTSLNRFAEFGSNQE 321 (665)
Q Consensus 245 ~~~~~E~K~DG~R~qih~~g~~v~~~SR~g~d~---t~~~p~l~~~~~~~~~~~~~ILDGElv~~d~~~~~~~~F~~lq~ 321 (665)
.+|++|+|+||.|+++|+.++++..+||+|... |+.+|++...-.. ...++++||||+++.+. ||. +.
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 6777777322110 12367999999998652 221 00
Q ss_pred HHHHhhcCCCCCCceEEEEEEEEeeCCccccCCCHHHHHHHHHhhcCCCCCcceecccCCCCCccccCCCCCccccccCC
Q 006003 322 IAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHN 401 (665)
Q Consensus 322 ~~~~~~~~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~~~~~~~~p~~~~~~~v~~~~~~~~~~~~~~ 401 (665)
......++.|++|||++.|+ ...+|+.+|+++|+++.-+....+. .....+
T Consensus 119 -------~~~~~~~v~F~vFDI~~~~~--~~~lp~~eR~~lLe~lg~~~v~~~~--------------------~~~~~d 169 (342)
T cd07894 119 -------SYPEVEDVGFFVFDIRKKNT--GRPLPVEERRELLEKYGLPTVRLFG--------------------EFTADE 169 (342)
T ss_pred -------cCccccccEEEEEeeEEcCC--CCCCCHHHHHHHHHhcCCCCcceEE--------------------EEecCC
Confidence 01112578999999999885 5679999999999998432211110 223456
Q ss_pred HHHHHHHHHHHHHcCCceEEeecCCC-----CCccCCCCCCeEEEcccc
Q 006003 402 VDEVEKFFKETIENRDEGIVLKDLGS-----KWEPGDRSGKWLKLKPEY 445 (665)
Q Consensus 402 ~~~i~~~~~~ai~~g~EGlV~K~~~s-----~Y~~GkRs~~WlKiK~~y 445 (665)
.+++.++++++.++|.||||+|++++ .|.....+-++|++.-.|
T Consensus 170 ~~~l~~~l~~~~~~G~EGVVlK~~~~~~~~~Ky~t~~~~~~di~~~~~~ 218 (342)
T cd07894 170 IEELKEIIRELDKEGREGVVLKDPDMRVPPLKYTTSYSNCSDIRYAFRY 218 (342)
T ss_pred HHHHHHHHHHHHHCCCceEEEeccccccCcceeecCCCCcHHHHHHhhh
Confidence 88999999999999999999999999 687666666777776665
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=5.9e-17 Score=147.90 Aligned_cols=120 Identities=22% Similarity=0.259 Sum_probs=85.7
Q ss_pred CcceEEEEEEEecCCCCCCccceEEEEEeeCCCCCCCCcceEEEEEeccCCCHHHHHHHHHhhccccccccCCCCCCCCc
Q 006003 450 SDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSF 529 (665)
Q Consensus 450 ~~~DlvVIG~~~G~g~r~g~~~sfllg~~d~~~~~~~~~~~~~~~kVgsG~s~~~~~~l~~~l~~~~~~~~~~~~~pp~~ 529 (665)
++.|++|+|+.++. +.+|++|||+++.+ ++|+++|+| ||||++++++|.++|+++......+ ..++.|
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 36788776665554 45999999999754 379999999 9999999999999999876542111 111213
Q ss_pred eeecCCCCCCCcEEEeCCCceEEEEEeeeceecccCccCCCeeeecc-EEEEEecCCCccCCC
Q 006003 530 YQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFP-RIDRVRYDKPWHDCL 591 (665)
Q Consensus 530 ~~~~~~~~~~pd~wi~~P~~s~v~ev~a~~~~~~s~~~~~g~sLRfP-r~~riR~DK~~~d~~ 591 (665)
..........+.+|++ |. +|+||++. .++.++.|||| ||+++|+||+++||+
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 75 58888643 34456699999 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=99.30 E-value=5.3e-13 Score=132.15 Aligned_cols=174 Identities=17% Similarity=0.268 Sum_probs=105.5
Q ss_pred HhcCCceEEEEeeceeEEEEEEeCCEEEEEecCCCCCC---cchhhhHHHHHhhccccceeeeceEEEeeCCCCcccccc
Q 006003 241 KLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHS---EYGHAMSKIIEQNVLVDRCILDGEMLVWDTSLNRFAEFG 317 (665)
Q Consensus 241 ~~~~~~~~~E~K~DG~R~qih~~g~~v~~~SR~g~d~t---~~~p~l~~~~~~~~~~~~~ILDGElv~~d~~~~~~~~F~ 317 (665)
.+...+|++.+|-||.|+++.+.++.+.+++|+.+-+. -.+|.-.+.. ......+.+||||||. |...
T Consensus 12 ~l~~~~Y~V~eKaDG~Ryll~i~~~~~ylidr~~~~~~v~~~~~p~~~~~~-~~~~~~~TLLDGElV~-d~~~------- 82 (192)
T PF01331_consen 12 LLQQKDYFVCEKADGTRYLLLITDNGVYLIDRKNNVFKVDNLHFPSKKDSS-DGRHHQDTLLDGELVL-DKDP------- 82 (192)
T ss_dssp HHHHS-EEEEEEESSEEEEEEEEEEEEEEEETTS-EEEESSST-ECTTC---TTCEGCSEEEEEEEEE-EECT-------
T ss_pred HHhhCCcEEEECCCCcEEEEEEecceEEEEeCCCcEEEecCcccccccccc-cccccCCEEEEEEEEc-ccCC-------
Confidence 34446899999999999999998889999999876442 1233211000 0123568999999987 3211
Q ss_pred chHHHHHHhhcCCCCCCceEEEEEEEEeeCCccccCCCHHHHHHHHHhhcCCCCCccee---cccCCCCCccccCCCCCc
Q 006003 318 SNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLET---LVPDHGLNSHVRPQGEPC 394 (665)
Q Consensus 318 ~lq~~~~~~~~~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~~~~~~---~~p~~~~~~~v~~~~~~~ 394 (665)
....++|++||+|++||+++++.|+.+|...|++.+......... .......++.++.. +
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 124678999999999999999999999999998744321100000 00000011111110 0
Q ss_pred cccccCCHHH-HHHHHHHHHHcCCceEEeecCCCCCccCCCCCCeEEEc
Q 006003 395 WSLVAHNVDE-VEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLK 442 (665)
Q Consensus 395 ~~~~~~~~~~-i~~~~~~ai~~g~EGlV~K~~~s~Y~~GkRs~~WlKiK 442 (665)
.......+. +...+..-+.+...|||+-..+.+|.+| +..+++|||
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 2222333456788999999999999998 678999998
No 45
>COG5226 CEG1 mRNA capping enzyme, guanylyltransferase (alpha) subunit [RNA processing and modification]
Probab=99.18 E-value=4.3e-11 Score=120.67 Aligned_cols=183 Identities=20% Similarity=0.301 Sum_probs=118.6
Q ss_pred hcCCceEEEEeeceeEEEEEEeC------CEEEEEecCCCCCC---cchhhhHHHHHhhccccceeeeceEEEeeCCCCc
Q 006003 242 LHGKEVVIECKFDGDRIQIHKNG------SEIHYFSRSFLDHS---EYGHAMSKIIEQNVLVDRCILDGEMLVWDTSLNR 312 (665)
Q Consensus 242 ~~~~~~~~E~K~DG~R~qih~~g------~~v~~~SR~g~d~t---~~~p~l~~~~~~~~~~~~~ILDGElv~~d~~~~~ 312 (665)
+...+|++.+|-||.||++.+.. -...+|.|..+-|. ..+|-+...........+..||||+|. |
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 44568999999999999998742 25778999876542 233432221111123567899999986 3
Q ss_pred cccccchHHHHHHhhcCCCCCCceEEEEEEEEeeCCccccCCCHHHHHHHHHhhcCCCCCcceecccCC--CCCccccCC
Q 006003 313 FAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDH--GLNSHVRPQ 390 (665)
Q Consensus 313 ~~~F~~lq~~~~~~~~~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~~~~~~~~p~~--~~~~~v~~~ 390 (665)
..|.+.++ ++.|.+||+|.+||.-+..++.++|.+.|++-+...-.+.....+.. ..++|
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 25665444 34588999999999999999999999999875532211111111111 01111
Q ss_pred CCCccccccCCHH---HHHHHHHHH--HHcCCceEEeecCCCCCccCCCCCCeEEEccccccCCCcceEEEEE
Q 006003 391 GEPCWSLVAHNVD---EVEKFFKET--IENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLIIG 458 (665)
Q Consensus 391 ~~~~~~~~~~~~~---~i~~~~~~a--i~~g~EGlV~K~~~s~Y~~GkRs~~WlKiK~~y~~~g~~~DlvVIG 458 (665)
+.....+ .+-++++.. +.+|..|||+-..+.||..|++ +..+|+||.-+ .|+|+..|-
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 1111111 223344222 4689999999999999999966 58999999865 488886654
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=99.12 E-value=1.8e-10 Score=96.74 Aligned_cols=76 Identities=25% Similarity=0.392 Sum_probs=59.8
Q ss_pred cceEEEEEEEecCCCCCCccceEEEEEeeCCCCCCCCcceEEEEEeccCCCHHHHHHHHHhhccccccccCCCCCCCCce
Q 006003 451 DLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFY 530 (665)
Q Consensus 451 ~~DlvVIG~~~G~g~r~g~~~sfllg~~d~~~~~~~~~~~~~~~kVgsG~s~~~~~~l~~~l~~~~~~~~~~~~~pp~~~ 530 (665)
+.|++|+|.++|.|++.|.+|+|+|+.++. . .++||||||+++++++. | +
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 46899999999998552 1 0
Q ss_pred eecCCCCCCCcEEEeCCCceEEEEEeeeceecccCccCCCeeeeccEEEEEe
Q 006003 531 QVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVR 582 (665)
Q Consensus 531 ~~~~~~~~~pd~wi~~P~~s~v~ev~a~~~~~~s~~~~~g~sLRfPr~~riR 582 (665)
..|++|++ ..++.++.||||+|+++|
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 02667754 335668899999999997
No 47
>COG1423 ATP-dependent DNA ligase, homolog of eukaryotic ligase III [DNA replication, recombination, and repair]
Probab=98.85 E-value=4.5e-08 Score=101.29 Aligned_cols=150 Identities=23% Similarity=0.308 Sum_probs=105.1
Q ss_pred HhcCCceEEEEeeceeEEEEEEeCCEEEEEecCCCC--CC-cchhhhHHH-HHhhccccceeeeceEEEeeCCCCccccc
Q 006003 241 KLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLD--HS-EYGHAMSKI-IEQNVLVDRCILDGEMLVWDTSLNRFAEF 316 (665)
Q Consensus 241 ~~~~~~~~~E~K~DG~R~qih~~g~~v~~~SR~g~d--~t-~~~p~l~~~-~~~~~~~~~~ILDGElv~~d~~~~~~~~F 316 (665)
.|+...+++|+|+||+.+-|.+-+|++.-.||.|.- || +..+.+.+. +.. .-++.+|.|||+.-+. .+.|
T Consensus 84 ~F~~~~v~VEEKmnGYNVRV~k~~g~vyAiTRgG~ICPfTT~r~~~l~~~eff~--d~p~lvlcgEmvG~en---PYv~- 157 (382)
T COG1423 84 HFGRGKVVVEEKMNGYNVRVVKLGGEVYAITRGGLICPFTTERLRDLIDLEFFD--DYPDLVLCGEMVGPEN---PYVP- 157 (382)
T ss_pred hcCCCcEEEEEeccCceEEEEEECCEEEEEecCceecCchhHHHHhhcchhhHh--hCCCcEEEEEeccCCC---CCCC-
Confidence 455678999999999999999989999999999984 44 344444322 111 2378999999998542 2222
Q ss_pred cchHHHHHHhhcCCCCCCceEEEEEEEEeeCCccccCCCHHHHHHHHHhhcCCCCCcceecccCCCCCccccCCCCCccc
Q 006003 317 GSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWS 396 (665)
Q Consensus 317 ~~lq~~~~~~~~~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~~~~~~~~p~~~~~~~v~~~~~~~~~ 396 (665)
+ .......+.|++||+--.|.. ..+|..+|++++++.--+. +++ .+ .
T Consensus 158 ~-----------~~y~~e~v~fFvFDire~~tg--r~Lp~eer~~l~ekYgl~~---V~~-------------fg----~ 204 (382)
T COG1423 158 G-----------PYYEKEDVGFFVFDIREKNTG--RPLPVEERLELAEKYGLPH---VEI-------------FG----E 204 (382)
T ss_pred C-----------CCCccCCceEEEEEEEecCCC--CCCCHHHHHHHHHHcCCCc---eEE-------------ee----e
Confidence 0 111235789999999987642 3579999999999864321 111 11 1
Q ss_pred cccCCH-HHHHHHHHHHHHcCCceEEeecCCCCC
Q 006003 397 LVAHNV-DEVEKFFKETIENRDEGIVLKDLGSKW 429 (665)
Q Consensus 397 ~~~~~~-~~i~~~~~~ai~~g~EGlV~K~~~s~Y 429 (665)
+..++. +++.++.++.-.+|.||+|+|+++..=
T Consensus 205 ~~~~e~~eei~eIve~L~keGREGVV~Kdpdm~~ 238 (382)
T COG1423 205 FPADEAGEEIYEIVERLNKEGREGVVMKDPDMRV 238 (382)
T ss_pred echhHhHHHHHHHHHHHhhcCCcceEecCccccc
Confidence 222334 788888999999999999999987653
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=5.8e-08 Score=103.47 Aligned_cols=148 Identities=22% Similarity=0.289 Sum_probs=96.9
Q ss_pred HhcCCceEEEEeeceeEEEEEEeCCEEEEEecCCCCCC--c-chhhhHHHHHhhccc--cceeeeceEEEeeCCCCcccc
Q 006003 241 KLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHS--E-YGHAMSKIIEQNVLV--DRCILDGEMLVWDTSLNRFAE 315 (665)
Q Consensus 241 ~~~~~~~~~E~K~DG~R~qih~~g~~v~~~SR~g~d~t--~-~~p~l~~~~~~~~~~--~~~ILDGElv~~d~~~~~~~~ 315 (665)
.+.++.+++|+|+||..+-|..-+|++..+||.|...+ . .++.+.+ ..+.. ++.+|.|||+.-+. |
T Consensus 75 ~f~~~~v~vEEKlDG~Nvri~~~~g~l~a~tRGgyicp~tt~r~~~~~~---~~~~~d~p~l~LcGE~iGpen------p 145 (374)
T TIGR01209 75 HFKDPEVVVEEKMNGYNVRIVKYGGNVYALTRGGFICPFTTERLPDLID---LEFFDDNPDLVLCGEMAGPEN------P 145 (374)
T ss_pred hcCCCcEEEEEeecCceEEEEeECCEEEEEccCcccCCCcHHHHHHHhh---HHhhccCCCeEEEEEEcCCCC------C
Confidence 35566699999999999999888899999999998642 1 2233322 22333 78999999997332 2
Q ss_pred ccchHHHHHHhhcCC-CCCCceEEEEEEEEeeCCccccCCCHHHHHHHHHhhcCCCCCcceecccCCCCCccccCCCCCc
Q 006003 316 FGSNQEIAKAARDGL-SSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPC 394 (665)
Q Consensus 316 F~~lq~~~~~~~~~~-~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~~~~~~~~p~~~~~~~v~~~~~~~ 394 (665)
+. +... ....+..|++|||. +...-.-+|..+|++++++.--+.-..+ .
T Consensus 146 Y~---------~hs~~y~~l~~~FfvFDI~--d~~t~~~L~~~er~~l~e~yglp~Vpvl-----------g-------- 195 (374)
T TIGR01209 146 YT---------PEYYPEVKEDLGFFLFDIR--EGKTNRSLPVEERLELAEKYGLPHVEIL-----------G-------- 195 (374)
T ss_pred Cc---------ccCccccCCCceEEEEEEE--ECCCCccCCHHHHHHHHHHCCCCcccee-----------e--------
Confidence 10 0011 12246789999997 3434457899999999998732211100 0
Q ss_pred cccccCC-HHHHHHHHHHHHHcCCceEEeecCCCC
Q 006003 395 WSLVAHN-VDEVEKFFKETIENRDEGIVLKDLGSK 428 (665)
Q Consensus 395 ~~~~~~~-~~~i~~~~~~ai~~g~EGlV~K~~~s~ 428 (665)
.+.... .+++.++.+..-++|.||||+|+++..
T Consensus 196 -~~~~~~~~~~~~eii~~L~~~gREGVVlK~~~~~ 229 (374)
T TIGR01209 196 -VYTADEAVEEIYEIIERLNKEGREGVVMKDPEMR 229 (374)
T ss_pred -EEcHHHHHHHHHHHHHHhhhcCcceEEEcCcccc
Confidence 011122 236667777777899999999998654
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=98.56 E-value=4.7e-07 Score=88.73 Aligned_cols=176 Identities=15% Similarity=0.125 Sum_probs=119.1
Q ss_pred ccccccccCCHHHHHHHhcCCceEEEEeeceeEEEEEEeCCEEEEEecCCCCCCc---chhhhHHHHHhhccccceeeec
Q 006003 225 RPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSE---YGHAMSKIIEQNVLVDRCILDG 301 (665)
Q Consensus 225 ~PmLA~~~~~~~~~~~~~~~~~~~~E~K~DG~R~qih~~g~~v~~~SR~g~d~t~---~~p~l~~~~~~~~~~~~~ILDG 301 (665)
+.||++-...+++-+ ..+|++=+===|-||++....|.+.+++|+|.-+.. .+|.-.. .+ -+||
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 356665544433211 357888888889999999999999999999987532 2332110 11 4566
Q ss_pred eEEEeeCCCCccccccchHHHHHHhhcCCCCCCceEEEEEEEEeeCCccccCCCHHHHHHHHHhhcCCCCCcceecccCC
Q 006003 302 EMLVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDH 381 (665)
Q Consensus 302 Elv~~d~~~~~~~~F~~lq~~~~~~~~~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~~~~~~~~p~~ 381 (665)
|+|. |..-+ +...+|+|+|||..||.++.+.+...|...|++-+.+....-. ...
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 6663 32111 1234799999999999999999999999999998876542110 000
Q ss_pred CCCccccCCCCCccccccCCHHHHHHHHHHHH---HcCCceEEeecCCCCCccCCCCCCeEEEccc
Q 006003 382 GLNSHVRPQGEPCWSLVAHNVDEVEKFFKETI---ENRDEGIVLKDLGSKWEPGDRSGKWLKLKPE 444 (665)
Q Consensus 382 ~~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai---~~g~EGlV~K~~~s~Y~~GkRs~~WlKiK~~ 444 (665)
.-++.+++. | .+.++ .+.+.+.|...+ ..-..||++-..++.|.+| +++.|+|+||.
T Consensus 127 ~~~~~f~~~--p--~~~~~-~~~l~~~~~~~~~~~~~e~DGLlFyhk~~~Y~~G-~tPlvl~wKp~ 186 (186)
T cd09232 127 KNPFRFVPL--P--YFPCT-KESLQSAYSGPLNDDPYELDGLLFYHKESHYTPG-STPLVLWLKDY 186 (186)
T ss_pred cCCceEEec--C--cccCc-HHHHHHHHhcccccCCCCCceEEEEeCCCcccCc-CCCcEEEecCC
Confidence 011122211 1 22233 367888888888 8888999999999999998 78999999983
No 50
>PF14743 DNA_ligase_OB_2: DNA ligase OB-like domain; PDB: 2Q2U_D 2Q2T_A 1FVI_A 1P8L_A.
Probab=98.20 E-value=1.1e-06 Score=71.19 Aligned_cols=37 Identities=22% Similarity=0.462 Sum_probs=24.1
Q ss_pred cCCCCCCccceEEEEEeeCCCCCCCCcceEEEEEeccCCCHHHHHHHH
Q 006003 462 GSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVV 509 (665)
Q Consensus 462 G~g~r~g~~~sfllg~~d~~~~~~~~~~~~~~~kVgsG~s~~~~~~l~ 509 (665)
|+|+..|++|+|+|-..+ + ..++|||||||++++++.
T Consensus 2 G~Gk~~g~~Galv~~~~~--G---------~~f~iGsG~td~~R~~~~ 38 (66)
T PF14743_consen 2 GKGKFKGMLGALVCETED--G---------VEFKIGSGFTDEEREEPP 38 (66)
T ss_dssp ---EEEEEEEEEEEEE-T--T---------EEEEE-SS--HHHHHHHH
T ss_pred CccccCCCEEEEEEEeCC--C---------CEEEECCCCCHHHHhcCC
Confidence 778889999999997632 1 367899999999998663
No 51
>smart00532 LIGANc Ligase N family.
Probab=97.87 E-value=0.00021 Score=79.30 Aligned_cols=224 Identities=18% Similarity=0.250 Sum_probs=130.5
Q ss_pred ceEEEEeeceeEEEEEEeCCE-EEEEec----CCCCCCcchhh---hHHHHHhhccccceeeeceEEEeeCCCC------
Q 006003 246 EVVIECKFDGDRIQIHKNGSE-IHYFSR----SFLDHSEYGHA---MSKIIEQNVLVDRCILDGEMLVWDTSLN------ 311 (665)
Q Consensus 246 ~~~~E~K~DG~R~qih~~g~~-v~~~SR----~g~d~t~~~p~---l~~~~~~~~~~~~~ILDGElv~~d~~~~------ 311 (665)
.|++|+|+||.-+.+.+.+|. ++..|| .|+|+|+.... +...+. .-.+..+.+-||++.-...-.
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 699999999999999998776 889999 78899863322 211111 001345889999987321100
Q ss_pred ---ccccccchHHHH-HHhh---cCCCCCCceEEEEEEEEeeCCccccCCCHHHHHHHHHhhcCCCCCcceecccCCCCC
Q 006003 312 ---RFAEFGSNQEIA-KAAR---DGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLN 384 (665)
Q Consensus 312 ---~~~~F~~lq~~~-~~~~---~~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~~~~~~~~p~~~~~ 384 (665)
.-.+|..-...+ ...+ ......+++.|++|++...++.. ...+..++.+.|.++-=+...
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 001233222211 1111 11112458999999986443321 124678888888886321110
Q ss_pred ccccCCCCCccccccCCHHHHHHHHHHHHHc------CCceEEeecCCCCCcc--C--CCCCCe---EEEccccccCCCc
Q 006003 385 SHVRPQGEPCWSLVAHNVDEVEKFFKETIEN------RDEGIVLKDLGSKWEP--G--DRSGKW---LKLKPEYIRAGSD 451 (665)
Q Consensus 385 ~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~------g~EGlV~K~~~s~Y~~--G--kRs~~W---lKiK~~y~~~g~~ 451 (665)
....+.+.+++.++++...+. .-.|||+|--+-.+.. | .+++.| +|+.++ .
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 122356788899988877653 5579999987766544 3 345667 466564 4
Q ss_pred ceEEEEEEEecCCCCCCccceEEEEEeeCCC-CCCCCcceEEEEEeccCCCHHHHHHHH
Q 006003 452 LDVLIIGGYYGSGRRGGEVAQFLVALAERPA-PDTYPRRFISFCRVGTGLSDEELDAVV 509 (665)
Q Consensus 452 ~DlvVIG~~~G~g~r~g~~~sfllg~~d~~~-~~~~~~~~~~~~kVgsG~s~~~~~~l~ 509 (665)
..-.|.+..|..|| .|.+.-. |..++-. + + .+|.++ |..+.+..+++.
T Consensus 314 ~~T~l~~I~~qVGR-TG~iTPv--A~lePV~l~----G--~tVsrA-TLhN~~~i~~~~ 362 (441)
T smart00532 314 AETKLLDIIVQVGR-TGKITPV--AELEPVFLA----G--STVSRA-TLHNEDEIEEKD 362 (441)
T ss_pred eEEEEEEEEEecCC-CceeeEE--EEEEeEEEC----C--EEEEec-ccCCHHHHHHcC
Confidence 45577788887775 4555432 2222210 0 1 234444 777777777653
No 52
>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=97.85 E-value=0.00022 Score=75.58 Aligned_cols=167 Identities=17% Similarity=0.253 Sum_probs=99.9
Q ss_pred ceEEEEeeceeEEEEEEeCCE-EEEEec----CCCCCCcchhhh---HHHHHhhccccceeeeceEEEeeCCCCc-----
Q 006003 246 EVVIECKFDGDRIQIHKNGSE-IHYFSR----SFLDHSEYGHAM---SKIIEQNVLVDRCILDGEMLVWDTSLNR----- 312 (665)
Q Consensus 246 ~~~~E~K~DG~R~qih~~g~~-v~~~SR----~g~d~t~~~p~l---~~~~~~~~~~~~~ILDGElv~~d~~~~~----- 312 (665)
.|++|+|+||.-+.+.+.+|. ++..|| .|+|+|+....+ ...+. . .+..+.+=||++.-...-.+
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 11111 1 14468899999974211000
Q ss_pred ----cccccchHHH-HHHhh---cCCCCCCceEEEEEEEEeeCCccccCCCHHHHHHHHHhhcCCCCCcceecccCCCCC
Q 006003 313 ----FAEFGSNQEI-AKAAR---DGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLN 384 (665)
Q Consensus 313 ----~~~F~~lq~~-~~~~~---~~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~~~~~~~~p~~~~~ 384 (665)
-.+|..-... +...+ .......++.|++|++...++.. .....++.+.|+++-=++..
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 0133322221 11111 11112468999999996544312 34778899998886322211
Q ss_pred ccccCCCCCccccccCCHHHHHHHHHHHHHc------CCceEEeecCCCCCc----cCCCCCCe
Q 006003 385 SHVRPQGEPCWSLVAHNVDEVEKFFKETIEN------RDEGIVLKDLGSKWE----PGDRSGKW 438 (665)
Q Consensus 385 ~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~------g~EGlV~K~~~s~Y~----~GkRs~~W 438 (665)
....+.+.+++.++++..... .-.|||+|--+..+. ...+++.|
T Consensus 246 ----------~~~~~~~~~ev~~~~~~~~~~R~~l~y~iDGiViKvn~~~~~~~lG~tsk~PrW 299 (307)
T cd00114 246 ----------ETRLCKNIEEVLAFYDEIEAKRDSLPYEIDGVVVKVDDLALQRELGFTSKAPRW 299 (307)
T ss_pred ----------CeEEeCCHHHHHHHHHHHHHhhhcCCCCCCcEEEEEeCHHHHHHhCccCCCCCc
Confidence 123356788999988877443 557999997665543 22345666
No 53
>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=97.75 E-value=7.3e-05 Score=79.55 Aligned_cols=169 Identities=21% Similarity=0.329 Sum_probs=94.5
Q ss_pred ceEEEEeeceeEEEEEEeCCE-EEEEec----CCCCCCcchhhhHHHHHhhcc--ccceeeeceEEEeeCCCCc------
Q 006003 246 EVVIECKFDGDRIQIHKNGSE-IHYFSR----SFLDHSEYGHAMSKIIEQNVL--VDRCILDGEMLVWDTSLNR------ 312 (665)
Q Consensus 246 ~~~~E~K~DG~R~qih~~g~~-v~~~SR----~g~d~t~~~p~l~~~~~~~~~--~~~~ILDGElv~~d~~~~~------ 312 (665)
.|++|+|+||.-+.+++.+|. ++..|| -|.|+|+....+.. +...+. +..+.+=||++.-...-.+
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 56777753222211 111111 3677888999862110000
Q ss_pred ---cccccchHHHH-HHhhcC---CCCCCceEEEEEEEEeeCCccccCCCHHHHHHHHHhhcCCCCCcceecccCCCCCc
Q 006003 313 ---FAEFGSNQEIA-KAARDG---LSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNS 385 (665)
Q Consensus 313 ---~~~F~~lq~~~-~~~~~~---~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~~~~~~~~p~~~~~~ 385 (665)
-.+|..-+..+ ...+.. ....+++.|++|++.+.+| +..-....++.+.|.++-=++...
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 01222111111 111110 0123689999999999988 333457788999888753222110
Q ss_pred cccCCCCCccccccCCHHHHHHHHHHHHHcC------CceEEeecCCCCCcc--C--CCCCCe
Q 006003 386 HVRPQGEPCWSLVAHNVDEVEKFFKETIENR------DEGIVLKDLGSKWEP--G--DRSGKW 438 (665)
Q Consensus 386 ~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g------~EGlV~K~~~s~Y~~--G--kRs~~W 438 (665)
...+.+.+++.++++...+.+ -.|||+|--+-.+.. | .+++.|
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 223568899999998877643 359999976544432 2 245556
No 54
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=97.66 E-value=0.00075 Score=76.64 Aligned_cols=212 Identities=16% Similarity=0.207 Sum_probs=120.5
Q ss_pred cccccccc-cCCHHHHHHHhcC--CceEEEEeeceeEEEEEEeCCE-EEEEec----CCCCCCcch---hhhHHHHHhhc
Q 006003 224 VRPQLAMR-IGDAHAAWRKLHG--KEVVIECKFDGDRIQIHKNGSE-IHYFSR----SFLDHSEYG---HAMSKIIEQNV 292 (665)
Q Consensus 224 ~~PmLA~~-~~~~~~~~~~~~~--~~~~~E~K~DG~R~qih~~g~~-v~~~SR----~g~d~t~~~---p~l~~~~~~~~ 292 (665)
-.|||.-. +.+.++. .++.. ..|++|+|+||.-+.+.+.+|. ++..|| -|+|+|+.. +.+...+. .
T Consensus 95 ~~PMlSL~k~~s~eel-~~w~~~~~~~~vepKiDGlsisL~Ye~G~Lv~a~TRGDG~~GEDVT~nv~~I~~IP~~l~-~- 171 (562)
T PRK08097 95 PVAHTGVKKLADKQAL-ARWMAGRSDLWVQPKVDGVAVTLVYRDGKLVQAISRGNGLKGEDWTAKARLIPAIPQQLP-G- 171 (562)
T ss_pred CCCcccccccCCHHHH-HHHHhhccceEEEEecccEEEEEEEECCEEEEEEecCCCccchhHHhhHhhhcccchhhc-C-
Confidence 35898543 2233332 22211 2699999999999999887665 678999 577888532 22222121 1
Q ss_pred cccceeeeceEEEeeCCCCcc-ccccchHHH-HHHhh--cCCCCCCceEEEEEEEEeeCCccccCCCHHHHHHHHHhhcC
Q 006003 293 LVDRCILDGEMLVWDTSLNRF-AEFGSNQEI-AKAAR--DGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVK 368 (665)
Q Consensus 293 ~~~~~ILDGElv~~d~~~~~~-~~F~~lq~~-~~~~~--~~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~ 368 (665)
.+..+.+-||++.-...-.+. ..|..-+.. +...+ +.....+++.|++|++. +| .....++.+.|.++-=
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 133588999998742210000 001100111 11111 00011468999999983 44 2467888888887642
Q ss_pred CCCCcceecccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHH----cCCceEEeecCCCCCccC--CCCCCe---E
Q 006003 369 PSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIE----NRDEGIVLKDLGSKWEPG--DRSGKW---L 439 (665)
Q Consensus 369 ~~~~~~~~~~p~~~~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~----~g~EGlV~K~~~s~Y~~G--kRs~~W---l 439 (665)
+.... ....+.+.+++.++++.... -.-.|+|+|--+..|..| .+.+.| +
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 11234678888887776543 356799999766665543 456677 4
Q ss_pred EEccccccCCCcceEEEEEEEecCCCCCCccce
Q 006003 440 KLKPEYIRAGSDLDVLIIGGYYGSGRRGGEVAQ 472 (665)
Q Consensus 440 KiK~~y~~~g~~~DlvVIG~~~G~g~r~g~~~s 472 (665)
|+.++ +..-.+.+..|..|| .|.+.-
T Consensus 305 Kf~~~------~~~T~l~~I~~qVGR-TG~iTP 330 (562)
T PRK08097 305 KYPPV------QQVAEVRAVQFAVGR-TGKITV 330 (562)
T ss_pred cCCCc------EEEEEEEEEEEecCC-CceeeE
Confidence 55554 455577788887775 455543
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=97.64 E-value=0.00047 Score=80.28 Aligned_cols=196 Identities=18% Similarity=0.266 Sum_probs=115.8
Q ss_pred ceEEEEeeceeEEEEEEeCCE-EEEEec----CCCCCCcchh---hhHHHHHhhccccceeeeceEEEeeCCCCc-----
Q 006003 246 EVVIECKFDGDRIQIHKNGSE-IHYFSR----SFLDHSEYGH---AMSKIIEQNVLVDRCILDGEMLVWDTSLNR----- 312 (665)
Q Consensus 246 ~~~~E~K~DG~R~qih~~g~~-v~~~SR----~g~d~t~~~p---~l~~~~~~~~~~~~~ILDGElv~~d~~~~~----- 312 (665)
.|++|+|+||.-+.+.+.+|+ ++..|| .|+|+|+... .+...+.....+..+.+-||++.-...-.+
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 599999999999999997665 779999 6888886322 221111100013458899999873211000
Q ss_pred ----cccccchHHH-HHHhhc---CCCCCCceEEEEEEEEeeCCccccCCCHHHHHHHHHhhcCCCCCcceecccCCCCC
Q 006003 313 ----FAEFGSNQEI-AKAARD---GLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLN 384 (665)
Q Consensus 313 ----~~~F~~lq~~-~~~~~~---~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~~~~~~~~p~~~~~ 384 (665)
-.+|..-+.. +...+. .....+++.|++|++...+ ........++.+.|.++-=+...
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 0134322221 111111 1112468999999985322 21124778888888876322211
Q ss_pred ccccCCCCCccccccCCHHHHHHHHHHHHHc------CCceEEeecCCCCCcc----CCCCCCe---EEEccccccCCCc
Q 006003 385 SHVRPQGEPCWSLVAHNVDEVEKFFKETIEN------RDEGIVLKDLGSKWEP----GDRSGKW---LKLKPEYIRAGSD 451 (665)
Q Consensus 385 ~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~------g~EGlV~K~~~s~Y~~----GkRs~~W---lKiK~~y~~~g~~ 451 (665)
....+.+.+++.+++++..+. .-.|+|+|--+-.+.. ..+++.| +|+.++ +
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 122356788999988876433 5579999976555431 2356677 566664 4
Q ss_pred ceEEEEEEEecCCCCCCccce
Q 006003 452 LDVLIIGGYYGSGRRGGEVAQ 472 (665)
Q Consensus 452 ~DlvVIG~~~G~g~r~g~~~s 472 (665)
..-.|.+..|..|| .|.+.-
T Consensus 307 ~~T~l~~I~~qVGR-TG~iTP 326 (652)
T TIGR00575 307 AQTKLLDVVVQVGR-TGAITP 326 (652)
T ss_pred eeEEEEEEEEecCC-Cceeee
Confidence 55577888887775 455543
No 56
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=97.55 E-value=0.0014 Score=76.71 Aligned_cols=223 Identities=19% Similarity=0.215 Sum_probs=127.1
Q ss_pred CceEEEEeeceeEEEEEEeCCE-EEEEec----CCCCCCcchhhh---HHHHHhhccccceeeeceEEEeeCCCCc----
Q 006003 245 KEVVIECKFDGDRIQIHKNGSE-IHYFSR----SFLDHSEYGHAM---SKIIEQNVLVDRCILDGEMLVWDTSLNR---- 312 (665)
Q Consensus 245 ~~~~~E~K~DG~R~qih~~g~~-v~~~SR----~g~d~t~~~p~l---~~~~~~~~~~~~~ILDGElv~~d~~~~~---- 312 (665)
..|++|+|+||.=+-+.+.+|+ ++..|| .|+|+|+....+ ...+. ...+..+.+=||++.-...-.+
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 4699999999999999887665 678999 688988632222 11111 1113457888999874221000
Q ss_pred -----cccccchHHHH-HHhhcC---CCCCCceEEEEEEEEeeCCccccCCCHHHHHHHHHhhcCCCCCcceecccCCCC
Q 006003 313 -----FAEFGSNQEIA-KAARDG---LSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGL 383 (665)
Q Consensus 313 -----~~~F~~lq~~~-~~~~~~---~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~~~~~~~~p~~~~ 383 (665)
-.+|..-+..+ ...|.. .....++.|++|++...++. .....++.+.|.++-=+....
T Consensus 211 ~~~~g~~~faNpRN~aAGslR~ldp~~~~~r~L~f~~y~~~~~~~~---~~t~~e~l~~L~~~GF~v~~~---------- 277 (689)
T PRK14351 211 RIERGEEPFANPRNAAAGTLRQLDPSVVAERPLDIFFFDVLDASEL---FDSHWEELERFPEWGLRVTDR---------- 277 (689)
T ss_pred HHHcCCCCcCCHHHHHhhHhhccChHHHhcCCceEEEEecccCCCC---CCCHHHHHHHHHHCCCCcCCc----------
Confidence 01232222111 111110 11246899999999655431 246778888888763222111
Q ss_pred CccccCCCCCccccccCCHHHHHHHHHHHHH------cCCceEEeecCCCCCcc----CCCCCCe---EEEccccccCCC
Q 006003 384 NSHVRPQGEPCWSLVAHNVDEVEKFFKETIE------NRDEGIVLKDLGSKWEP----GDRSGKW---LKLKPEYIRAGS 450 (665)
Q Consensus 384 ~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~------~g~EGlV~K~~~s~Y~~----GkRs~~W---lKiK~~y~~~g~ 450 (665)
...+.+.+++.++++...+ -.-.|||+|--+-.+.. ..+.+.| +|+.++
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 34569999976654421 2356777 466654
Q ss_pred cceEEEEEEEecCCCCCCccceEEEEEeeCCC-CCCCCcceEEEEEeccCCCHHHHHHHH
Q 006003 451 DLDVLIIGGYYGSGRRGGEVAQFLVALAERPA-PDTYPRRFISFCRVGTGLSDEELDAVV 509 (665)
Q Consensus 451 ~~DlvVIG~~~G~g~r~g~~~sfllg~~d~~~-~~~~~~~~~~~~kVgsG~s~~~~~~l~ 509 (665)
...-.|.+..|..|| .|.+.-. |..+|-. + + .+|.++ |..+.++.+.+.
T Consensus 340 ~~~T~l~~I~~qVGR-TG~iTPV--A~lePV~l~----G--~tVsra-tLhN~~~i~~~d 389 (689)
T PRK14351 340 AEETTIRDIVVQVGR-TGRLTPV--ALLDPVDVG----G--VTVSRA-SLHNPAEIEELG 389 (689)
T ss_pred eeEEEEEEEEEecCC-CceeeeE--EEEEeEEEC----C--EEEEEe-ccCCHHHHHHcC
Confidence 445577788887775 4555432 2222210 0 1 134444 666777776653
No 57
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=97.51 E-value=0.0013 Score=76.69 Aligned_cols=196 Identities=20% Similarity=0.293 Sum_probs=116.3
Q ss_pred ceEEEEeeceeEEEEEEeCCE-EEEEec----CCCCCCcch---hhhHHHHHhhccccceeeeceEEEeeCCCCc-----
Q 006003 246 EVVIECKFDGDRIQIHKNGSE-IHYFSR----SFLDHSEYG---HAMSKIIEQNVLVDRCILDGEMLVWDTSLNR----- 312 (665)
Q Consensus 246 ~~~~E~K~DG~R~qih~~g~~-v~~~SR----~g~d~t~~~---p~l~~~~~~~~~~~~~ILDGElv~~d~~~~~----- 312 (665)
.|++|+|+||.-+.+.+.+|. ++..|| .|+|+|+.. +.+...+.. ..+..+.+-||++.-...-.+
T Consensus 109 ~~~~epKiDGlsisL~Y~~G~L~~a~TRGDG~~GeDvT~n~~~I~~IP~~l~~-~~p~~levRGEv~m~~~~F~~lN~~~ 187 (665)
T PRK07956 109 TYLCELKIDGLAVSLLYENGVLVRAATRGDGTTGEDITANVRTIRSIPLRLHG-NEPERLEVRGEVFMPKADFEALNEER 187 (665)
T ss_pred ceEEEEecccEEEEEEEECCEEEEEEecCCCccchhHhhhhhhhccCChhhcc-cCCCeEEEEEEEEEEHHHHHHHHHHH
Confidence 599999999999999987765 678999 688888632 222222210 113458899999874211000
Q ss_pred ----cccccchHHHH-HHhhc---CCCCCCceEEEEEEEEeeCCccccCCCHHHHHHHHHhhcCCCCCcceecccCCCCC
Q 006003 313 ----FAEFGSNQEIA-KAARD---GLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLN 384 (665)
Q Consensus 313 ----~~~F~~lq~~~-~~~~~---~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~~~~~~~~p~~~~~ 384 (665)
-.+|..-+..+ ...+. .....+++.|++|++...++ ........++.+.|.++-=+...
T Consensus 188 ~~~g~~~faNpRNaaAGslr~ld~~~~~~r~L~f~~y~~~~~~~-~~~~~t~~e~l~~L~~~GF~v~~------------ 254 (665)
T PRK07956 188 REEGEKPFANPRNAAAGSLRQLDPKITAKRPLSFFAYGVGEVEG-GELPDSQSEALEFLKAWGFPVNP------------ 254 (665)
T ss_pred HhcCCCcccChHHHHhhhhhccChHHHhcCCCEEEEEecccccC-CCCCCCHHHHHHHHHHCCCCcCC------------
Confidence 01232212111 11110 01124689999999964432 11134778888888886322211
Q ss_pred ccccCCCCCccccccCCHHHHHHHHHHHHHc------CCceEEeecCCCCCcc--C--CCCCCe---EEEccccccCCCc
Q 006003 385 SHVRPQGEPCWSLVAHNVDEVEKFFKETIEN------RDEGIVLKDLGSKWEP--G--DRSGKW---LKLKPEYIRAGSD 451 (665)
Q Consensus 385 ~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~------g~EGlV~K~~~s~Y~~--G--kRs~~W---lKiK~~y~~~g~~ 451 (665)
....+.+.+++.++++...+. .-.|||+|--+-.|.. | .+.+.| +|+.++ .
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 122356788999988877543 4579999976644321 2 345667 566665 4
Q ss_pred ceEEEEEEEecCCCCCCccce
Q 006003 452 LDVLIIGGYYGSGRRGGEVAQ 472 (665)
Q Consensus 452 ~DlvVIG~~~G~g~r~g~~~s 472 (665)
..-.|.+..|..|| .|.+.-
T Consensus 319 ~~T~l~~I~~qVGR-TG~iTP 338 (665)
T PRK07956 319 ATTKLLDIEVQVGR-TGAVTP 338 (665)
T ss_pred eEEEEEEEEEecCC-Cceeee
Confidence 55577788887775 455543
No 58
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=97.20 E-value=0.0049 Score=71.84 Aligned_cols=196 Identities=17% Similarity=0.171 Sum_probs=110.3
Q ss_pred ceEEEEeeceeEEEEEEeCCE-EEEEec----CCCCCCcchhhhHHHHHhhcc-ccceeeeceEEEeeCCCC-----ccc
Q 006003 246 EVVIECKFDGDRIQIHKNGSE-IHYFSR----SFLDHSEYGHAMSKIIEQNVL-VDRCILDGEMLVWDTSLN-----RFA 314 (665)
Q Consensus 246 ~~~~E~K~DG~R~qih~~g~~-v~~~SR----~g~d~t~~~p~l~~~~~~~~~-~~~~ILDGElv~~d~~~~-----~~~ 314 (665)
+|++|+|+||.-+.+.+.+|. ++..|| .|+|+|+..-.+.. +...+. ...+.+-||++.-...-. .-.
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 678999 68888863221111 111111 245788999987321100 002
Q ss_pred cccchHHHH-HHhhc---CCCCCCceEEEEEEEEeeCCccccCCCHHHHHHHHHhhcCCCCCcceecccCCCCCccccCC
Q 006003 315 EFGSNQEIA-KAARD---GLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQ 390 (665)
Q Consensus 315 ~F~~lq~~~-~~~~~---~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~~~~~~~~p~~~~~~~v~~~ 390 (665)
+|..-+..+ ...+. .....+++.|++|++...++ ...+..++.+.|.++-=+.......
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 333222211 11111 11124689999999853222 1236788888888763222111000
Q ss_pred CCCccccccCCHHHHHHHHHHHHH------cCCceEEeecCCCCCcc--C--CCCCCe---EEEccccccCCCcceEEEE
Q 006003 391 GEPCWSLVAHNVDEVEKFFKETIE------NRDEGIVLKDLGSKWEP--G--DRSGKW---LKLKPEYIRAGSDLDVLII 457 (665)
Q Consensus 391 ~~~~~~~~~~~~~~i~~~~~~ai~------~g~EGlV~K~~~s~Y~~--G--kRs~~W---lKiK~~y~~~g~~~DlvVI 457 (665)
.....+.+++.++++++.. -.-.|||+|--+-.+.. | .+++.| +|+.++ +..-.|.
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 0001346778777765533 34579999975543321 2 246677 566665 4555777
Q ss_pred EEEecCCCCCCccc
Q 006003 458 GGYYGSGRRGGEVA 471 (665)
Q Consensus 458 G~~~G~g~r~g~~~ 471 (665)
+..|..|| .|.+.
T Consensus 322 ~I~~qVGR-TG~iT 334 (669)
T PRK14350 322 DIVVQVGR-SGKIT 334 (669)
T ss_pred EEEEecCC-ceeee
Confidence 88887775 45554
No 59
>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=96.98 E-value=0.0016 Score=64.03 Aligned_cols=106 Identities=22% Similarity=0.331 Sum_probs=62.2
Q ss_pred ceEEEEeeceeEEEEEEe-CCEEEEEecCCCC-----CCcc------hhhhHH---HHHh-h-----ccccceeeeceEE
Q 006003 246 EVVIECKFDGDRIQIHKN-GSEIHYFSRSFLD-----HSEY------GHAMSK---IIEQ-N-----VLVDRCILDGEML 304 (665)
Q Consensus 246 ~~~~E~K~DG~R~qih~~-g~~v~~~SR~g~d-----~t~~------~p~l~~---~~~~-~-----~~~~~~ILDGElv 304 (665)
+|++++|+||.-+.+... ++.+++.+|++.- +... +..... .+.. . ....++++=||++
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 699999999999998885 4459999999821 1110 111110 1111 1 1356889999999
Q ss_pred EeeCCCCccccccchHHHHHHhhcCCCCCCceEEEEEEEEeeCCc-cccCCCHHHHHHHHHhh
Q 006003 305 VWDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDT-SVIHQSLKERHELLQKV 366 (665)
Q Consensus 305 ~~d~~~~~~~~F~~lq~~~~~~~~~~~~~~~~~~~vFDiL~lng~-~l~~~pl~eRr~~L~~~ 366 (665)
.|-+.-. . ... + ...+..|++|||...+.. ...-++..+.+.+++.+
T Consensus 82 G~~~~Iq---~-~~~---------~--~~~~~~F~~Fdi~~~~~~~~~~~l~~~~~~~~~~~~ 129 (186)
T PF09414_consen 82 GAKPSIQ---K-NRY---------Q--LDPPKDFYVFDIYDIDEQGEIRYLSWDEVREFAEEL 129 (186)
T ss_dssp CEECTTC---S-S---------------ECCCEEEEEEEEEEETCCGEEE-HHHHHHHHHCCC
T ss_pred eeccccc---c-ccc---------c--cCCCceEEEEEEEEcCCCCeeEECCHHHHHHHHHHC
Confidence 8753211 0 000 0 012678999999998543 22455788888888775
No 60
>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=96.92 E-value=0.013 Score=62.09 Aligned_cols=106 Identities=16% Similarity=0.101 Sum_probs=64.5
Q ss_pred hcCCceEEEEeeceeEEEEEEeCC-EEEEEecCCCCCC-----c---chhhhHHHHH---hh------ccccceeeeceE
Q 006003 242 LHGKEVVIECKFDGDRIQIHKNGS-EIHYFSRSFLDHS-----E---YGHAMSKIIE---QN------VLVDRCILDGEM 303 (665)
Q Consensus 242 ~~~~~~~~E~K~DG~R~qih~~g~-~v~~~SR~g~d~t-----~---~~p~l~~~~~---~~------~~~~~~ILDGEl 303 (665)
+.+.+|.+.+|.||.-.-+.++++ .+++.||++.-.. . ..+.+...+. .. ....++++=||+
T Consensus 22 l~~~ewvatEKlhGaNfsi~~~~~~~i~~akR~~~l~~~e~f~G~~~i~~~l~~~~~~l~~~l~~~~~~~~~~v~IyGEl 101 (325)
T TIGR02307 22 LGLTEWVAREKIHGTNFSIIIERDFKVTCAKRTGIILPNEDFFGYHILIKNYTASVKAIQDILETKAIIVVVSVQVFGEL 101 (325)
T ss_pred cCCceEEEEEEecCcceEEEEeCCceEEEeecccccCcccccccHHHHHHHHHHHHHHHHHHHhhhcccccceEEEEEEe
Confidence 445689999999999999988877 8999999965321 1 1122211111 11 123678999999
Q ss_pred EEeeCCCCccccccchHHHHHHhhcCCCCCCceEEEEEEEEeeCCccccCCCHHHHHHHHHhh
Q 006003 304 LVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKV 366 (665)
Q Consensus 304 v~~d~~~~~~~~F~~lq~~~~~~~~~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~ 366 (665)
+.|.-..+.. .. ...|++|||......+-.-+++.+-.+.....
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 35799999955322123455666666666554
No 61
>PRK01109 ATP-dependent DNA ligase; Provisional
Probab=96.84 E-value=0.005 Score=71.31 Aligned_cols=97 Identities=14% Similarity=0.112 Sum_probs=79.1
Q ss_pred CCCCcHHHHHHHHHHHHhcC---ChhHHHHHHHHHhhhcCCCchHhhhHhhcCCCCCCCccccCCCHHHHHHHHHHHhCC
Q 006003 4 TEETEVIVLVSLFNWIQKTK---PAAKKRSKFRKFLDTYCDSVDYFSALRLILPSLDRERGSYGLKESVLANCLIDALGM 80 (665)
Q Consensus 4 ~~~~~F~~l~~~~e~i~~~~---~~~~k~~~l~~~~~~~~~~~~~~~~lrLllp~~d~~r~~yglke~~L~k~~~~~~~~ 80 (665)
.++++|.+++++|++|++++ ++.+|..+|.++|.+. ++.+...++||++-.+. .|++++++.++|+++++.
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 36789999999999999997 7789999999999986 67889999999999882 899999999999999983
Q ss_pred CcChHHHHHHhhhhcCCCCCCCCCHHHHHHHHhh
Q 006003 81 SKDSADAVRLINWRKGGAAPNAGNFPMVAAEVLQ 114 (665)
Q Consensus 81 ~~~~~~~~~L~~wk~~~~~~~~gD~~~~~~~v~~ 114 (665)
.....+..++.+ ..||++.+|..+..
T Consensus 186 ~~~~~~ve~~y~--------~~~Dlg~va~~l~~ 211 (590)
T PRK01109 186 AVARELVERAYN--------LRADLGYIAKILAE 211 (590)
T ss_pred ccchHHHHHHHH--------hCCCHHHHHHHHHh
Confidence 223334444433 46899998877653
No 62
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=96.63 E-value=0.049 Score=62.49 Aligned_cols=195 Identities=21% Similarity=0.290 Sum_probs=116.4
Q ss_pred CceEEEEeeceeEEEEEEeCCE-EEEEecC----CCCCCcchhhhHHHHHhhc--cccceeeeceEEEeeCCCC------
Q 006003 245 KEVVIECKFDGDRIQIHKNGSE-IHYFSRS----FLDHSEYGHAMSKIIEQNV--LVDRCILDGEMLVWDTSLN------ 311 (665)
Q Consensus 245 ~~~~~E~K~DG~R~qih~~g~~-v~~~SR~----g~d~t~~~p~l~~~~~~~~--~~~~~ILDGElv~~d~~~~------ 311 (665)
..|++|+|.||.-+-+.+.+|. ++--||. |+|+|.-...+... ...+ .+..+-+=||++.--..-.
T Consensus 109 ~~y~~EpKiDGlsisL~YenG~Lv~aaTRGdG~~GEDiT~NvrtI~~I-P~~l~~~p~~lEVRGEvfm~k~~F~~lN~~~ 187 (667)
T COG0272 109 VEYVVEPKIDGLAISLVYENGKLVRAATRGDGTTGEDITANVRTIRSI-PLKLPGAPAVLEVRGEVFMPKEDFEALNEER 187 (667)
T ss_pred cceEEEeecceEEEEEEEECCEEEEeeccCCCccccchhhhhhhHhhh-hhhccCCCceEEEEeEEEEeHHHHHHHHHHH
Confidence 4799999999999998887664 6777875 67888644444332 1112 2566788999886311000
Q ss_pred ---ccccccchHHHH-HHhh---cCCCCCCceEEEEEEEEeeCCccccCCCHHHHHHHHHhhcCCCCCcceecccCCCCC
Q 006003 312 ---RFAEFGSNQEIA-KAAR---DGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLN 384 (665)
Q Consensus 312 ---~~~~F~~lq~~~-~~~~---~~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~~~~~~~~p~~~~~ 384 (665)
.-.+|..-...+ ...| ......+++.++++.+-...+. ..-.+..++.+.|.++-=+...
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 001222111110 0011 0011246899999998866554 5566788999999887433211
Q ss_pred ccccCCCCCccccccCCHHHHHHHHHHHHHcC------CceEEeecCCCCCcc--C--CCCCCe---EEEccccccCCCc
Q 006003 385 SHVRPQGEPCWSLVAHNVDEVEKFFKETIENR------DEGIVLKDLGSKWEP--G--DRSGKW---LKLKPEYIRAGSD 451 (665)
Q Consensus 385 ~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g------~EGlV~K~~~s~Y~~--G--kRs~~W---lKiK~~y~~~g~~ 451 (665)
....+.+.+++.++++.....+ -.|+|+|--+-.... | .|++.| +|+.++-
T Consensus 255 ----------~~~~~~~~~ev~~~~~~~~~~R~~L~y~IDGvViKvn~l~~q~~lG~tsk~PrWAiAyKFpa~e------ 318 (667)
T COG0272 255 ----------YTRLCKNADEVLAFYEEWEKKRASLPYDIDGVVIKVNDLALQRELGFTSKAPRWAIAYKFPAEE------ 318 (667)
T ss_pred ----------HhhhcCCHHHHHHHHHHHHhhcccCCCccceEEEEeccHHHHHHhCCccCCCceeeeecCCchh------
Confidence 1234678999999999887743 459999965432211 2 367788 6888863
Q ss_pred ceEEEEEEEecCCCCCCcc
Q 006003 452 LDVLIIGGYYGSGRRGGEV 470 (665)
Q Consensus 452 ~DlvVIG~~~G~g~r~g~~ 470 (665)
.--.+.+..+.-|| .|.+
T Consensus 319 ~~T~l~dI~~qVGR-TG~i 336 (667)
T COG0272 319 AVTKLLDIEVQVGR-TGAI 336 (667)
T ss_pred eeeEEEEEEEecCC-ceee
Confidence 22244455555554 4444
No 63
>PHA02142 putative RNA ligase
Probab=95.74 E-value=0.18 Score=54.45 Aligned_cols=112 Identities=15% Similarity=0.221 Sum_probs=68.4
Q ss_pred CHHHHHH-HhcCCceEEEEeeceeEEEEEE---------------------eCCEEEEEecCCCC-CC--c-chh-----
Q 006003 234 DAHAAWR-KLHGKEVVIECKFDGDRIQIHK---------------------NGSEIHYFSRSFLD-HS--E-YGH----- 282 (665)
Q Consensus 234 ~~~~~~~-~~~~~~~~~E~K~DG~R~qih~---------------------~g~~v~~~SR~g~d-~t--~-~~p----- 282 (665)
++.+.+. +..+..|.+-+|+||.-|.+.+ +.+.+...|||..- +. . +..
T Consensus 157 n~~~~~~~~~~~~~f~~TeKLDGsS~tvy~~~~~~~~~~~~~~~~~~~~~~~~~~~gv~srn~~l~~~~~~~~W~~a~~~ 236 (366)
T PHA02142 157 NIFNRYKEKYADVKFAKSLKLDGSSITMAWVTDPDLFLDLGTEDEPYAHDYDDAQFIVASRNQVLRYNADSKWWKGVENY 236 (366)
T ss_pred hhhhhhhhhhcCceEEEEEEecceeEEEEEecCCcccccccccccccccccCCCceeEeeccccccccCCchHHHHHHHc
Confidence 3444432 2446789999999999998873 24677889998752 21 1 111
Q ss_pred hhHHHHHhhccccceeeeceEEEeeCCCCccccccchHHHHHHhhcCCCCCCceEEEEEEEEeeCCccccCCCHHHHHHH
Q 006003 283 AMSKIIEQNVLVDRCILDGEMLVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHEL 362 (665)
Q Consensus 283 ~l~~~~~~~~~~~~~ILDGElv~~d~~~~~~~~F~~lq~~~~~~~~~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~ 362 (665)
.+.+.+.+ ...++.+=||++.-.-+++. ..-....|++|||-.++++. =+++.++.++
T Consensus 237 ~i~~~l~~--~~~~iaIqGEl~Gp~IQ~N~------------------~~~~~~~F~vF~v~~i~~~~--yl~~~e~~~~ 294 (366)
T PHA02142 237 QIVDRLKE--LGMSVAIQGELMGPGIQKNR------------------ENFDKYRIFAFRAWFIDEQR--FATDEEFQDL 294 (366)
T ss_pred CcHHHHHh--hCCcEEEEEEEecccccCcc------------------ccCCCCceEEEEEEEeccce--eCCHHHHHHH
Confidence 11111211 23678899999972211110 00112479999998777765 5688999998
Q ss_pred HHhhc
Q 006003 363 LQKVV 367 (665)
Q Consensus 363 L~~~~ 367 (665)
++++-
T Consensus 295 ~~~~g 299 (366)
T PHA02142 295 CRTLG 299 (366)
T ss_pred HHHcC
Confidence 88763
No 64
>KOG3132 consensus m3G-cap-specific nuclear import receptor (Snurportin1) [RNA processing and modification]
Probab=94.47 E-value=0.28 Score=49.24 Aligned_cols=173 Identities=13% Similarity=0.141 Sum_probs=111.7
Q ss_pred ccccccccCCHHHHHHHhcCCceEEEEeeceeEEEEEEeCCEEEEEecCCCCCCcchhhhHHH-HHhhc-cccceeeece
Q 006003 225 RPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKI-IEQNV-LVDRCILDGE 302 (665)
Q Consensus 225 ~PmLA~~~~~~~~~~~~~~~~~~~~E~K~DG~R~qih~~g~~v~~~SR~g~d~t~~~p~l~~~-~~~~~-~~~~~ILDGE 302 (665)
+-||.+-.-++++. + +.+|++=.-==|-||+|.-..|...-|.|||..+.. ||..... -.++. ...=.|||+
T Consensus 100 qlMLsEWliDvP~~---L-sqdW~vv~~PvGKR~lvVaSrG~Tvay~k~G~~v~r-F~S~LPGGnrr~~~a~~ytILDC- 173 (325)
T KOG3132|consen 100 QLMLSEWLIDVPDN---L-SQDWYVVARPVGKRCLVVASRGTTVAYVKNGSTVHR-FPSALPGGNRRKGPANSYTILDC- 173 (325)
T ss_pred HhhhHHHhccCccc---c-CcceEEEEeecCceEEEEecCCceEEEecCCeeEee-ccccCCCCCcCCCCcccceeeee-
Confidence 34665544444332 2 468999999999999998888888899999987653 3322110 00111 112257775
Q ss_pred EEEeeCCCCccccccchHHHHHHhhcCCCCCCceEEEEEEEEeeCCccccCCCHHHHHHHHHhhcCCCCCcceecccCCC
Q 006003 303 MLVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHG 382 (665)
Q Consensus 303 lv~~d~~~~~~~~F~~lq~~~~~~~~~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~~~~~~~~p~~~ 382 (665)
+|++ ..-.|+|.|++..+|.++.+.|+.-|.-.|++-+.+.++-- .|...
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 2322 11259999999999999999999999999998776654210 00000
Q ss_pred --CCccccCCCCCccccccCCHHHHHHHHHHHHHcCCceEEeecCCCCCccCCC-CCCeEE
Q 006003 383 --LNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDR-SGKWLK 440 (665)
Q Consensus 383 --~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EGlV~K~~~s~Y~~GkR-s~~WlK 440 (665)
..+.+.| .+ .-+.+.+.+++.-.+.-...||.+-.-.-.|.||.- --+|+|
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 0011111 11 236777888888778888899999998999999953 237865
No 65
>TIGR02306 RNA_lig_DRB0094 RNA ligase, DRB0094 family. The member of this family from Deinococcus radiodurans, a species that withstands and recovers from extensive radiation or dessication damage, is an apparent RNA ligase. It repairs RNA stand breaks in nicked DNA:RNA and RNA:RNA but not DNA:DNA duplexes. It has adenylyltransferase activity associated with the C-terminal domain. Related proteins also in this family are found in Streptomyces avermitilis MA-4680 and in bacteriophage 44RR2.8t. The phage example is unsurprising since one mechanism of host cell defense against phage is cleavage and inactivation of certain tRNA molecules. A fungal sequence from Neurospora crassa scores between trusted and noise cutofffs and may be similar in function.
Probab=93.24 E-value=1 Score=48.59 Aligned_cols=104 Identities=17% Similarity=0.190 Sum_probs=58.1
Q ss_pred CCceEEEEeeceeEEEEEEeC--CE-----EEEEecCCCCC---Cc-ch-----hhhHHHHHhhccccceeeeceEEEee
Q 006003 244 GKEVVIECKFDGDRIQIHKNG--SE-----IHYFSRSFLDH---SE-YG-----HAMSKIIEQNVLVDRCILDGEMLVWD 307 (665)
Q Consensus 244 ~~~~~~E~K~DG~R~qih~~g--~~-----v~~~SR~g~d~---t~-~~-----p~l~~~~~~~~~~~~~ILDGElv~~d 307 (665)
+..|.+-+|+||.-|.+.+-. +. +-+-|||..-. +. |. ..+.+.+.+.....++.+=||++.-.
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 568999999999999887632 22 22457886521 11 11 12223332222345688999998722
Q ss_pred CCCCccccccchHHHHHHhhcCCCCCCceEEEEEEEEeeCCccccCCCHHHHHHHHHhh
Q 006003 308 TSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKV 366 (665)
Q Consensus 308 ~~~~~~~~F~~lq~~~~~~~~~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~ 366 (665)
-+++ .. + .+.+-.+++|++ +.+|.. .=+++.++.+++.++
T Consensus 238 IQ~n---~Y------------g--~~~~~~~f~F~v-~~~~~~-ryld~~~~~~~~~~~ 277 (341)
T TIGR02306 238 IQKN---RY------------G--FDKYRTVFAFRA-FFDGEQ-RFLTDEDFQDLCLTL 277 (341)
T ss_pred ccCC---cC------------C--CCCCceEEEEEE-EEcCcc-eecCHHHHHHHHHhc
Confidence 1111 00 1 111212778887 555543 345889999888875
No 66
>PRK09247 ATP-dependent DNA ligase; Validated
Probab=89.77 E-value=0.5 Score=54.31 Aligned_cols=82 Identities=17% Similarity=0.261 Sum_probs=69.5
Q ss_pred HHHHHHHHHHHhhhhHHhHHHHHHHHHHhCCHHHHHHHHHHHHhhhc-cCCccccccccc----Cc---CHHHHHhhhCC
Q 006003 127 KELNDLLDRLASSENRAEKISVLSTLIKKTNAQEMKWIIMIILKDLK-LGISEKSIFHEF----HP---DAEDLFNVTCD 198 (665)
Q Consensus 127 ~eV~~~Ld~la~~~~~~~k~~~l~~ll~~~t~~E~k~l~Riilkdlr-iG~~e~til~~~----hp---~a~~~~~~~~d 198 (665)
.++-+.+++|++.+++.+|..+|..+|+..++.+.-|.++++++.+. .|++++.+.+++ .. ...+.|+-..|
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 35667889999999999999999999999999999999999999886 999999988755 21 23556788899
Q ss_pred HHHHHHHHhh
Q 006003 199 LKLVCEKLKD 208 (665)
Q Consensus 199 L~~v~~~l~~ 208 (665)
|+.||..+..
T Consensus 82 lg~~~~~~~~ 91 (539)
T PRK09247 82 LAETIALLLP 91 (539)
T ss_pred HHHHHHHhcc
Confidence 9999988764
No 67
>KOG2386 consensus mRNA capping enzyme, guanylyltransferase (alpha) subunit [RNA processing and modification]
Probab=89.41 E-value=0.22 Score=54.05 Aligned_cols=98 Identities=18% Similarity=0.306 Sum_probs=63.5
Q ss_pred CceEEEEeeceeEEEEEEeCCE-EEEEecCCCCCCc---chhhhHHHHHhhccccceeeeceEEEeeCCCCccccccchH
Q 006003 245 KEVVIECKFDGDRIQIHKNGSE-IHYFSRSFLDHSE---YGHAMSKIIEQNVLVDRCILDGEMLVWDTSLNRFAEFGSNQ 320 (665)
Q Consensus 245 ~~~~~E~K~DG~R~qih~~g~~-v~~~SR~g~d~t~---~~p~l~~~~~~~~~~~~~ILDGElv~~d~~~~~~~~F~~lq 320 (665)
..|.+++|.||.|+.+-.+++. +..+-|.-...-. +++.-.. ........++||||+. |..+.
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 3567999999999998887654 5555554322110 1110000 0011346789999998 64322
Q ss_pred HHHHHhhcCCCCCCceEEEEEEEEeeCCccccCCCHHHHHHHHHh-hcC
Q 006003 321 EIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQK-VVK 368 (665)
Q Consensus 321 ~~~~~~~~~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~-~~~ 368 (665)
...+.|.++|++.+|++.+...|+. |.+.+.+ ++.
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 1134689999999999999999999 8886654 443
No 68
>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=87.46 E-value=0.64 Score=45.14 Aligned_cols=85 Identities=24% Similarity=0.418 Sum_probs=61.5
Q ss_pred CHHHHHHHHHHHHhhhhHHhHHHHHHHHHHhCCHHHHHHHHHHHHhhh-------ccCCccccccccc----Cc---CHH
Q 006003 125 TIKELNDLLDRLASSENRAEKISVLSTLIKKTNAQEMKWIIMIILKDL-------KLGISEKSIFHEF----HP---DAE 190 (665)
Q Consensus 125 Ti~eV~~~Ld~la~~~~~~~k~~~l~~ll~~~t~~E~k~l~Riilkdl-------riG~~e~til~~~----hp---~a~ 190 (665)
+..++-++|++|+..+++.+|..+|+.++....+.+..|.+..+++-+ ..|++++++.+++ +- ...
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 456777899999999999999999999999998887888888888844 5899999887644 42 234
Q ss_pred HHHhhhCCHHHHHHHHhhh
Q 006003 191 DLFNVTCDLKLVCEKLKDR 209 (665)
Q Consensus 191 ~~~~~~~dL~~v~~~l~~~ 209 (665)
+.|....|++.++..+...
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 69
>PRK03180 ligB ATP-dependent DNA ligase; Reviewed
Probab=83.98 E-value=5.5 Score=45.58 Aligned_cols=92 Identities=21% Similarity=0.230 Sum_probs=71.2
Q ss_pred CCcHHHHHHHHHHHHhcC---ChhHHHHHHHHHhhhcCCCchHhhhHhhcCCCCCCCccccCCCHHHHHHHHHHHhCCCc
Q 006003 6 ETEVIVLVSLFNWIQKTK---PAAKKRSKFRKFLDTYCDSVDYFSALRLILPSLDRERGSYGLKESVLANCLIDALGMSK 82 (665)
Q Consensus 6 ~~~F~~l~~~~e~i~~~~---~~~~k~~~l~~~~~~~~~~~~~~~~lrLllp~~d~~r~~yglke~~L~k~~~~~~~~~~ 82 (665)
+.+-.++-+.|++|.+.+ +..+|..+|..++.+. ++.+..-++|+|+-.+ ..|+++.++..+++++++++.
T Consensus 72 ~ltl~~V~~~l~~ia~~~g~~s~~~k~~~l~~ll~~~-~~~E~~~l~r~i~~~l-----RiGv~~~~v~~Ala~a~~~~~ 145 (508)
T PRK03180 72 TLTVADVDAALSEIAAVAGAGSQARRAALLAALFAAA-TEDEQRFLRRLLTGEL-----RQGALDGVMADAVARAAGVPA 145 (508)
T ss_pred CCcHHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHhC-CHHHHHHHHHHHhCCC-----cccccHHHHHHHHHHHhCCCH
Confidence 456677777999988875 4478888999999985 5778888999999988 299999999999999998764
Q ss_pred ChHHHHHHhhhhcCCCCCCCCCHHHHHHHHh
Q 006003 83 DSADAVRLINWRKGGAAPNAGNFPMVAAEVL 113 (665)
Q Consensus 83 ~~~~~~~L~~wk~~~~~~~~gD~~~~~~~v~ 113 (665)
. +..+..+ ..||++.++...+
T Consensus 146 ~--~v~~a~~--------~~~dl~~v~~~~l 166 (508)
T PRK03180 146 A--AVRRAAM--------LAGDLPAVAAAAL 166 (508)
T ss_pred H--HHHHHHH--------HcCCHHHHHHHHH
Confidence 3 3333333 2578988887554
No 70
>PLN03113 DNA ligase 1; Provisional
Probab=78.13 E-value=4.4 Score=48.25 Aligned_cols=86 Identities=13% Similarity=0.291 Sum_probs=72.0
Q ss_pred CCCCHHHHHHHHHHHHhhhhHHhHHHHHHHHHHhC---CHHHHHHHHHHHHhhhc-------cCCccccccccc----Cc
Q 006003 122 GGLTIKELNDLLDRLASSENRAEKISVLSTLIKKT---NAQEMKWIIMIILKDLK-------LGISEKSIFHEF----HP 187 (665)
Q Consensus 122 ~~lTi~eV~~~Ld~la~~~~~~~k~~~l~~ll~~~---t~~E~k~l~Riilkdlr-------iG~~e~til~~~----hp 187 (665)
.++.-.++-+.+++|...+++.++..+|..+|+.. +|.+.-|.+.++.+.+- +|++++.+.+++ ..
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 99999999999887764 599999988765 21
Q ss_pred ---CHHHHHhhhCCHHHHHHHHh
Q 006003 188 ---DAEDLFNVTCDLKLVCEKLK 207 (665)
Q Consensus 188 ---~a~~~~~~~~dL~~v~~~l~ 207 (665)
.....|....||+.|+..+.
T Consensus 207 ~~~~ik~~y~~~GDlG~vA~~~~ 229 (744)
T PLN03113 207 TEKQVKKQYKELGDLGLVAKASR 229 (744)
T ss_pred CHHHHHHHHHHhCCHHHHHHhhh
Confidence 23556788899999998664
No 71
>COG4566 TtrR Response regulator [Signal transduction mechanisms]
Probab=72.27 E-value=15 Score=36.22 Aligned_cols=81 Identities=19% Similarity=0.327 Sum_probs=55.1
Q ss_pred CCCHHHHHHHHhhhccCCCCCCCCHHHHHHHHHH----HHhhhhHHhHHHHHHHHHHhCCHHHHHHHHHHHHhhhc----
Q 006003 102 AGNFPMVAAEVLQRRQGMISGGLTIKELNDLLDR----LASSENRAEKISVLSTLIKKTNAQEMKWIIMIILKDLK---- 173 (665)
Q Consensus 102 ~gD~~~~~~~v~~~r~~~~~~~lTi~eV~~~Ld~----la~~~~~~~k~~~l~~ll~~~t~~E~k~l~Riilkdlr---- 173 (665)
.||.++.+..+...-...-..|.+-+++.+.+.. .+..........-+...|..+||.|...|-+++.+-+.
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 5899988877544332222456666665555544 33333344555778899999999999999999987553
Q ss_pred --cCCcccccc
Q 006003 174 --LGISEKSIF 182 (665)
Q Consensus 174 --iG~~e~til 182 (665)
+|+|++||-
T Consensus 165 ~dLgiS~rTVe 175 (202)
T COG4566 165 FDLGISERTVE 175 (202)
T ss_pred HHcCCchhhHH
Confidence 699999883
No 72
>TIGR00574 dnl1 DNA ligase I, ATP-dependent (dnl1). All proteins in this family with known functions are ATP-dependent DNA ligases. Functions include DNA repair, DNA replication, and DNA recombination (or any process requiring ligation of two single-stranded DNA sections). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=67.43 E-value=18 Score=41.46 Aligned_cols=93 Identities=22% Similarity=0.253 Sum_probs=70.7
Q ss_pred CCCcHHHHHHHHHHHHhcC---ChhHHHHHHHHHhhhcCCCchHhhhHhhcCCCCCCCccccCCCHHHHHHHHHHHhCCC
Q 006003 5 EETEVIVLVSLFNWIQKTK---PAAKKRSKFRKFLDTYCDSVDYFSALRLILPSLDRERGSYGLKESVLANCLIDALGMS 81 (665)
Q Consensus 5 ~~~~F~~l~~~~e~i~~~~---~~~~k~~~l~~~~~~~~~~~~~~~~lrLllp~~d~~r~~yglke~~L~k~~~~~~~~~ 81 (665)
.+..-.++-+.|++|.+.+ +..+|..+|..++.+. ++.+..=++|+|+-++. .|++++++..+++.+++++
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 3456678888888888775 3567888999999874 67788889999998872 8999999999999999876
Q ss_pred cChHHHHHHhhhhcCCCCCCCCCHHHHHHHHh
Q 006003 82 KDSADAVRLINWRKGGAAPNAGNFPMVAAEVL 113 (665)
Q Consensus 82 ~~~~~~~~L~~wk~~~~~~~~gD~~~~~~~v~ 113 (665)
.. +..++ | ....|++.++.++.
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 33232 2 24578888887765
No 73
>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=42.36 E-value=2.8e+02 Score=27.81 Aligned_cols=31 Identities=26% Similarity=0.165 Sum_probs=22.9
Q ss_pred ceEEEEeeceeEE-EEEEeCCEEEEEecCCCC
Q 006003 246 EVVIECKFDGDRI-QIHKNGSEIHYFSRSFLD 276 (665)
Q Consensus 246 ~~~~E~K~DG~R~-qih~~g~~v~~~SR~g~d 276 (665)
++.+-.|+||.=+ .....+|.+.+-|+++-+
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 7999999999444 334578899999999864
No 74
>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=38.25 E-value=70 Score=33.36 Aligned_cols=66 Identities=18% Similarity=0.196 Sum_probs=49.4
Q ss_pred EEeeCCc--cccCCCHHHHHHHHHhhcCCCCCcceecccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHcCCceE
Q 006003 343 VLYVGDT--SVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGI 420 (665)
Q Consensus 343 iL~lng~--~l~~~pl~eRr~~L~~~~~~~~~~~~~~~p~~~~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EGl 420 (665)
-++++|. ....++..||+++++.+.....+++.++. .....+.++..++.+.+.+.|..|+
T Consensus 37 gl~v~GstGE~~~lt~~Er~~l~~~~~~~~~~~~~vi~-----------------gv~~~~~~~~~~~a~~a~~~G~d~v 99 (284)
T cd00950 37 GLVVCGTTGESPTLSDEEHEAVIEAVVEAVNGRVPVIA-----------------GTGSNNTAEAIELTKRAEKAGADAA 99 (284)
T ss_pred EEEECCCCcchhhCCHHHHHHHHHHHHHHhCCCCcEEe-----------------ccCCccHHHHHHHHHHHHHcCCCEE
Confidence 4455552 23678999999999998877766655432 1234577888999999999999999
Q ss_pred EeecC
Q 006003 421 VLKDL 425 (665)
Q Consensus 421 V~K~~ 425 (665)
|+=.|
T Consensus 100 ~~~~P 104 (284)
T cd00950 100 LVVTP 104 (284)
T ss_pred EEccc
Confidence 99876
No 75
>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=34.77 E-value=88 Score=32.50 Aligned_cols=65 Identities=22% Similarity=0.305 Sum_probs=47.2
Q ss_pred EeeCCc--cccCCCHHHHHHHHHhhcCCCCCcceecccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHcCCceEE
Q 006003 344 LYVGDT--SVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIV 421 (665)
Q Consensus 344 L~lng~--~l~~~pl~eRr~~L~~~~~~~~~~~~~~~p~~~~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EGlV 421 (665)
++++|. ....++..||+++++.+.....+++.++. .....+..+..++.+.+.+.|..|+|
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 444542 23567899999999998877666655432 22345677888899999999999999
Q ss_pred eecC
Q 006003 422 LKDL 425 (665)
Q Consensus 422 ~K~~ 425 (665)
+=.|
T Consensus 98 v~pP 101 (281)
T cd00408 98 VVPP 101 (281)
T ss_pred ECCC
Confidence 9654
No 76
>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=32.76 E-value=97 Score=32.63 Aligned_cols=65 Identities=18% Similarity=0.219 Sum_probs=47.3
Q ss_pred EEeeCCc--cccCCCHHHHHHHHHhhcCCCCCcceecccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHcCCceE
Q 006003 343 VLYVGDT--SVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGI 420 (665)
Q Consensus 343 iL~lng~--~l~~~pl~eRr~~L~~~~~~~~~~~~~~~p~~~~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EGl 420 (665)
-++++|. ....++.+||.++++.++....+++.++. .....+.++..++-+.+.+.|-.|+
T Consensus 38 gi~~~GstGE~~~Lt~eEr~~~~~~~~~~~~~~~pvi~-----------------gv~~~~t~~~i~la~~a~~~Gad~v 100 (290)
T TIGR00683 38 GLYVGGSTGENFMLSTEEKKEIFRIAKDEAKDQIALIA-----------------QVGSVNLKEAVELGKYATELGYDCL 100 (290)
T ss_pred EEEECCcccccccCCHHHHHHHHHHHHHHhCCCCcEEE-----------------ecCCCCHHHHHHHHHHHHHhCCCEE
Confidence 3455542 23467999999999998887777664432 1223567888889999999999999
Q ss_pred Eeec
Q 006003 421 VLKD 424 (665)
Q Consensus 421 V~K~ 424 (665)
|+=.
T Consensus 101 ~v~~ 104 (290)
T TIGR00683 101 SAVT 104 (290)
T ss_pred EEeC
Confidence 9954
No 77
>PRK03170 dihydrodipicolinate synthase; Provisional
Probab=32.33 E-value=96 Score=32.54 Aligned_cols=58 Identities=17% Similarity=0.235 Sum_probs=45.2
Q ss_pred ccCCCHHHHHHHHHhhcCCCCCcceecccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHcCCceEEeecC
Q 006003 351 VIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDL 425 (665)
Q Consensus 351 l~~~pl~eRr~~L~~~~~~~~~~~~~~~p~~~~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EGlV~K~~ 425 (665)
...++..||+++++.+.....+++.++. .....+.++..++.+.+.+.|..|+|+=.|
T Consensus 48 ~~~ls~~Er~~~~~~~~~~~~~~~~vi~-----------------gv~~~~~~~~i~~a~~a~~~G~d~v~~~pP 105 (292)
T PRK03170 48 SPTLTHEEHEELIRAVVEAVNGRVPVIA-----------------GTGSNSTAEAIELTKFAEKAGADGALVVTP 105 (292)
T ss_pred cccCCHHHHHHHHHHHHHHhCCCCcEEe-----------------ecCCchHHHHHHHHHHHHHcCCCEEEECCC
Confidence 3578999999999999887777665431 123356788888999999999999999765
No 78
>PF14909 SPATA6: Spermatogenesis-assoc protein 6
Probab=32.21 E-value=1.2e+02 Score=28.49 Aligned_cols=60 Identities=20% Similarity=0.422 Sum_probs=43.0
Q ss_pred CCCcEEEeCCCceEEEEEeeeceecccCccCCCeeeeccEE--EEEecCCCccCCCCHHHHHHHHHc
Q 006003 538 ERPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRI--DRVRYDKPWHDCLDVQSFVELVHS 602 (665)
Q Consensus 538 ~~pd~wi~~P~~s~v~ev~a~~~~~~s~~~~~g~sLRfPr~--~riR~DK~~~d~~t~~el~~l~~~ 602 (665)
.-|.+|.. +...+-+.|..-.++.+ +.-..-.||-+ .++|.+|....|.+..++.++.+.
T Consensus 10 TCPGv~L~-~~~~vyL~v~~lg~~~~----T~~~ppvFPllfhek~~FeK~F~~~~dp~~l~~~Le~ 71 (140)
T PF14909_consen 10 TCPGVWLC-DKGDVYLSVCILGQYKR----TRCLPPVFPLLFHEKFRFEKVFPNAVDPAQLADLLED 71 (140)
T ss_pred ecCCeEeC-CCCCEEEEEEEcccEee----cccCCCcCCeeEeeEEEeEEEecCCCCHHHHHHHhhc
Confidence 35789997 66667777753222222 23345689966 479999999999999999998864
No 79
>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=31.61 E-value=1e+02 Score=32.82 Aligned_cols=58 Identities=16% Similarity=0.255 Sum_probs=46.4
Q ss_pred ccCCCHHHHHHHHHhhcCCCCCcceecccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHcCCceEEeecC
Q 006003 351 VIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDL 425 (665)
Q Consensus 351 l~~~pl~eRr~~L~~~~~~~~~~~~~~~p~~~~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EGlV~K~~ 425 (665)
...++.+||+++++..+....+++.++. .....+.++..++-+.+.+.|-.|+|+=.|
T Consensus 55 ~~~Lt~eEr~~v~~~~~~~~~grvpvi~-----------------Gv~~~~t~~ai~~a~~A~~~Gad~vlv~~P 112 (309)
T cd00952 55 CATLTWEEKQAFVATVVETVAGRVPVFV-----------------GATTLNTRDTIARTRALLDLGADGTMLGRP 112 (309)
T ss_pred chhCCHHHHHHHHHHHHHHhCCCCCEEE-----------------EeccCCHHHHHHHHHHHHHhCCCEEEECCC
Confidence 4578999999999999887777765432 223457788999999999999999999876
No 80
>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=30.88 E-value=94 Score=21.55 Aligned_cols=28 Identities=25% Similarity=0.408 Sum_probs=19.3
Q ss_pred HHhhhccCCCCCCCCHHHHHHHHHHHHh
Q 006003 111 EVLQRRQGMISGGLTIKELNDLLDRLAS 138 (665)
Q Consensus 111 ~v~~~r~~~~~~~lTi~eV~~~Ld~la~ 138 (665)
+|.+.+...........||+++|+++|.
T Consensus 5 dIr~~~F~~~~rGY~~~eVD~fLd~v~~ 32 (34)
T TIGR03544 5 DIRNKRFKKKLRGYDAAEVDAFLDRVAD 32 (34)
T ss_pred HHhhCcCCCCCCCCCHHHHHHHHHHHHH
Confidence 3434433333467899999999999985
No 81
>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=29.72 E-value=1.1e+02 Score=31.91 Aligned_cols=58 Identities=16% Similarity=0.174 Sum_probs=45.5
Q ss_pred cCCCHHHHHHHHHhhcCCCCCcceecccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHcCCceEEeecCC
Q 006003 352 IHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLG 426 (665)
Q Consensus 352 ~~~pl~eRr~~L~~~~~~~~~~~~~~~p~~~~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EGlV~K~~~ 426 (665)
..++..||+++++.++....+++.++. ...+.+.++..++-+.+.+.|..|+|+=.|.
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 578999999999998877777665431 2234577888899999999999999997643
No 82
>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=29.40 E-value=1.2e+02 Score=31.89 Aligned_cols=59 Identities=19% Similarity=0.123 Sum_probs=45.6
Q ss_pred ccCCCHHHHHHHHHhhcCCCCCcceecccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHcCCceEEeecCC
Q 006003 351 VIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLG 426 (665)
Q Consensus 351 l~~~pl~eRr~~L~~~~~~~~~~~~~~~p~~~~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EGlV~K~~~ 426 (665)
...++..||+++++.++....+++.++. .....+.++..++-+.+.+.|..|+|+=.|-
T Consensus 47 ~~~Ls~~Er~~l~~~~~~~~~g~~pvi~-----------------gv~~~~t~~ai~~a~~A~~~Gad~v~v~pP~ 105 (294)
T TIGR02313 47 PGSLTLEERKQAIENAIDQIAGRIPFAP-----------------GTGALNHDETLELTKFAEEAGADAAMVIVPY 105 (294)
T ss_pred cccCCHHHHHHHHHHHHHHhCCCCcEEE-----------------ECCcchHHHHHHHHHHHHHcCCCEEEEcCcc
Confidence 3567999999999999887777765431 1234567788888899999999999998753
No 83
>PLN02417 dihydrodipicolinate synthase
Probab=26.84 E-value=1.5e+02 Score=31.02 Aligned_cols=57 Identities=11% Similarity=0.028 Sum_probs=44.9
Q ss_pred cCCCHHHHHHHHHhhcCCCCCcceecccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHcCCceEEeecC
Q 006003 352 IHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDL 425 (665)
Q Consensus 352 ~~~pl~eRr~~L~~~~~~~~~~~~~~~p~~~~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EGlV~K~~ 425 (665)
..++..||+++++.++....+++.++. .....+..+..++.+.+.+.|..|+|+-.|
T Consensus 49 ~~ls~~Er~~~~~~~~~~~~~~~pvi~-----------------gv~~~~t~~~i~~a~~a~~~Gadav~~~~P 105 (280)
T PLN02417 49 QLMSWDEHIMLIGHTVNCFGGKIKVIG-----------------NTGSNSTREAIHATEQGFAVGMHAALHINP 105 (280)
T ss_pred hhCCHHHHHHHHHHHHHHhCCCCcEEE-----------------ECCCccHHHHHHHHHHHHHcCCCEEEEcCC
Confidence 567899999999998877777665431 223457788899999999999999999765
No 84
>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=26.06 E-value=1.2e+02 Score=31.82 Aligned_cols=58 Identities=19% Similarity=0.327 Sum_probs=44.8
Q ss_pred ccCCCHHHHHHHHHhhcCCCCCcceecccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHcCCceEEeecC
Q 006003 351 VIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDL 425 (665)
Q Consensus 351 l~~~pl~eRr~~L~~~~~~~~~~~~~~~p~~~~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EGlV~K~~ 425 (665)
...++..||+++++.++...++++.++. ...+.+.++..++.+.+.+.|..|+|+=.|
T Consensus 48 ~~~Lt~~Er~~l~~~~~~~~~~~~~vi~-----------------gv~~~st~~~i~~a~~a~~~Gad~v~v~~P 105 (289)
T PF00701_consen 48 FYSLTDEERKELLEIVVEAAAGRVPVIA-----------------GVGANSTEEAIELARHAQDAGADAVLVIPP 105 (289)
T ss_dssp GGGS-HHHHHHHHHHHHHHHTTSSEEEE-----------------EEESSSHHHHHHHHHHHHHTT-SEEEEEES
T ss_pred cccCCHHHHHHHHHHHHHHccCceEEEe-----------------cCcchhHHHHHHHHHHHhhcCceEEEEecc
Confidence 4578999999999998877666665432 334568899999999999999999999765
No 85
>PF11459 DUF2893: Protein of unknwon function (DUF2893); InterPro: IPR021561 This is a bacterial family of uncharacterised proteins.
Probab=26.02 E-value=1.9e+02 Score=23.72 Aligned_cols=45 Identities=16% Similarity=0.346 Sum_probs=37.2
Q ss_pred CCCCCHHHHHHHHHHHHhhhhHHhHHHHHHHHHHhCCHHHHHHHHHHHHh
Q 006003 121 SGGLTIKELNDLLDRLASSENRAEKISVLSTLIKKTNAQEMKWIIMIILK 170 (665)
Q Consensus 121 ~~~lTi~eV~~~Ld~la~~~~~~~k~~~l~~ll~~~t~~E~k~l~Riilk 170 (665)
+...++.+++++++.|.+.+. ..++.||..|+....+.+...+-.
T Consensus 15 p~~~s~e~a~~l~egL~nLrp-----~~lq~LL~~C~svKvkRLfl~lA~ 59 (69)
T PF11459_consen 15 PKRQSFEEADELMEGLRNLRP-----RVLQELLEHCTSVKVKRLFLYLAE 59 (69)
T ss_pred CccCCHHHHHHHHHHHhhcCH-----HHHHHHHHHCccHHHHHHHHHHHH
Confidence 467899999999999986653 689999999999999988876543
No 86
>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=25.43 E-value=1.8e+02 Score=30.44 Aligned_cols=67 Identities=22% Similarity=0.298 Sum_probs=48.4
Q ss_pred EEEeeCCc--cccCCCHHHHHHHHHhhcCCCCCcceecccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHcCCce
Q 006003 342 DVLYVGDT--SVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEG 419 (665)
Q Consensus 342 DiL~lng~--~l~~~pl~eRr~~L~~~~~~~~~~~~~~~p~~~~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EG 419 (665)
|-+.++|. ....++.+||+++++..+....+++.++. .....+.++..++-+.+.+.|..|
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 33444542 22577899999999998877666654432 122456788899999999999999
Q ss_pred EEeecC
Q 006003 420 IVLKDL 425 (665)
Q Consensus 420 lV~K~~ 425 (665)
+|+=.|
T Consensus 100 v~~~~P 105 (288)
T cd00954 100 ISAITP 105 (288)
T ss_pred EEEeCC
Confidence 998765
No 87
>PRK04147 N-acetylneuraminate lyase; Provisional
Probab=25.00 E-value=1.8e+02 Score=30.66 Aligned_cols=57 Identities=19% Similarity=0.247 Sum_probs=45.0
Q ss_pred cCCCHHHHHHHHHhhcCCCCCcceecccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHcCCceEEeecC
Q 006003 352 IHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDL 425 (665)
Q Consensus 352 ~~~pl~eRr~~L~~~~~~~~~~~~~~~p~~~~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EGlV~K~~ 425 (665)
..++..||+++++.++....+++.++. ...+.+.++..++-+.+.+.|..|+|+=.|
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 467889999999999887777765432 223457788889999999999999999764
No 88
>KOG2386 consensus mRNA capping enzyme, guanylyltransferase (alpha) subunit [RNA processing and modification]
Probab=24.46 E-value=4.3e+02 Score=29.27 Aligned_cols=175 Identities=17% Similarity=0.196 Sum_probs=89.0
Q ss_pred HHHHHHhcCCceEEEEeeceeEEEEEEe-----CCEEEEEecCCC--CCC---cchhhhHHHHHhhccccceeeeceEEE
Q 006003 236 HAAWRKLHGKEVVIECKFDGDRIQIHKN-----GSEIHYFSRSFL--DHS---EYGHAMSKIIEQNVLVDRCILDGEMLV 305 (665)
Q Consensus 236 ~~~~~~~~~~~~~~E~K~DG~R~qih~~-----g~~v~~~SR~g~--d~t---~~~p~l~~~~~~~~~~~~~ILDGElv~ 305 (665)
.+.+..+....+.+-.|.||.|++..++ +..+.+.=++-. ... .+...+...+ +. ...++-+|||+|.
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 4455666667899999999999999883 234555555432 211 1111122222 11 2466789999998
Q ss_pred eeCCCCccccccchHHHHHHhhcCCCCCCceEEEEEEEEeeCCccccCCCHHHHHHHHHhhcCCCC---CcceecccC--
Q 006003 306 WDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSK---GRLETLVPD-- 380 (665)
Q Consensus 306 ~d~~~~~~~~F~~lq~~~~~~~~~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~---~~~~~~~p~-- 380 (665)
..- |-|. .+..|++|+.|.-+|. ....++.+.++..-.+.- ..+.-+.+.
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 2221 2345999999988764 344455555544332210 000000000
Q ss_pred CCCCccccCCCCCccccccCCHHHHHHHHHHHHH-cCCceEEeecCCCCCc-cCCCCCCeEEEcccc
Q 006003 381 HGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIE-NRDEGIVLKDLGSKWE-PGDRSGKWLKLKPEY 445 (665)
Q Consensus 381 ~~~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~-~g~EGlV~K~~~s~Y~-~GkRs~~WlKiK~~y 445 (665)
...+..+.....|.| ............ ++..|++.-...-+|. .| +...-+|+|++-
T Consensus 184 ~~~p~~vs~p~~~~~-------~~~~~~~~~~~~~~~~Dg~i~t~~~~pg~~~g-~~~~~~k~k~~~ 242 (393)
T KOG2386|consen 184 DIFPFKVSCPSMPDW-------KRSIKLKKPVHKLHGNDGLIFTPAEIPGSKNG-KQEALLKWKPFS 242 (393)
T ss_pred ccccccccCCCCcch-------hhhhhhccccccccccCCCcCCcccCcccccc-chhhhhcCCchh
Confidence 000001100000111 111111111111 7888999888888994 45 446789999974
No 89
>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=24.06 E-value=1.8e+02 Score=30.52 Aligned_cols=56 Identities=14% Similarity=0.223 Sum_probs=43.0
Q ss_pred ccCCCHHHHHHHHHhhcCCCCCcceecccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHcCCceEEeec
Q 006003 351 VIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKD 424 (665)
Q Consensus 351 l~~~pl~eRr~~L~~~~~~~~~~~~~~~p~~~~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EGlV~K~ 424 (665)
...++..||.++++.++....+++.++. .... +..+..++.+.+.+.|..|+|+=.
T Consensus 47 ~~~Ls~eEr~~l~~~~~~~~~~~~pvi~-----------------gv~~-~t~~~i~~a~~a~~~Gad~v~~~p 102 (289)
T cd00951 47 FFSLTPDEYAQVVRAAVEETAGRVPVLA-----------------GAGY-GTATAIAYAQAAEKAGADGILLLP 102 (289)
T ss_pred cccCCHHHHHHHHHHHHHHhCCCCCEEE-----------------ecCC-CHHHHHHHHHHHHHhCCCEEEECC
Confidence 3577999999999998887777664432 1222 667888899999999999999954
No 90
>COG0329 DapA Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]
Probab=23.09 E-value=1.9e+02 Score=30.74 Aligned_cols=58 Identities=22% Similarity=0.328 Sum_probs=46.0
Q ss_pred ccCCCHHHHHHHHHhhcCCCCCcceecccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHcCCceEEeecC
Q 006003 351 VIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDL 425 (665)
Q Consensus 351 l~~~pl~eRr~~L~~~~~~~~~~~~~~~p~~~~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EGlV~K~~ 425 (665)
...++..||+++++.++....+++.++. ...+.+.++..++-+.+-+.|-.|+|+=.|
T Consensus 51 ~~~Ls~eEr~~v~~~~v~~~~grvpvia-----------------G~g~~~t~eai~lak~a~~~Gad~il~v~P 108 (299)
T COG0329 51 SPTLTLEERKEVLEAVVEAVGGRVPVIA-----------------GVGSNSTAEAIELAKHAEKLGADGILVVPP 108 (299)
T ss_pred chhcCHHHHHHHHHHHHHHHCCCCcEEE-----------------ecCCCcHHHHHHHHHHHHhcCCCEEEEeCC
Confidence 3567899999999999988888765432 233467788889999999999999999753
No 91
>PRK02289 4-oxalocrotonate tautomerase; Provisional
Probab=22.93 E-value=1.4e+02 Score=23.22 Aligned_cols=25 Identities=16% Similarity=0.139 Sum_probs=19.2
Q ss_pred EEEeccCCCHHHHHHHHHhhccccc
Q 006003 493 FCRVGTGLSDEELDAVVTKLKPYFR 517 (665)
Q Consensus 493 ~~kVgsG~s~~~~~~l~~~l~~~~~ 517 (665)
.+++..|.|+++.++|.+.+.....
T Consensus 5 ~i~~~~Grs~EqK~~L~~~it~a~~ 29 (60)
T PRK02289 5 RIDLFEGRSQEQKNALAREVTEVVS 29 (60)
T ss_pred EEEECCCCCHHHHHHHHHHHHHHHH
Confidence 3456679999999999988765543
No 92
>PF14538 Raptor_N: Raptor N-terminal CASPase like domain
Probab=22.39 E-value=99 Score=29.52 Aligned_cols=40 Identities=13% Similarity=0.293 Sum_probs=24.8
Q ss_pred eeeceEEEeeCCCCccccccchHHHHHHhhcCCCCCCceEEEEEEEEe
Q 006003 298 ILDGEMLVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLY 345 (665)
Q Consensus 298 ILDGElv~~d~~~~~~~~F~~lq~~~~~~~~~~~~~~~~~~~vFDiL~ 345 (665)
+-+||++++|+....+.|.. +.++.... ..+..+|||+=.
T Consensus 106 t~~GeIw~f~~~~tqyip~s-i~dL~~~l-------g~Psi~V~DC~~ 145 (154)
T PF14538_consen 106 TENGEIWVFNKNYTQYIPLS-IYDLQSWL-------GSPSIYVFDCSN 145 (154)
T ss_pred CCCCeEEEEcCCCCcceEEE-HHHHHHhc-------CCCEEEEEECCc
Confidence 45789999988766665542 23333221 245788999853
No 93
>PF13099 DUF3944: Domain of unknown function (DUF3944)
Probab=22.26 E-value=1.2e+02 Score=21.58 Aligned_cols=24 Identities=21% Similarity=0.422 Sum_probs=20.2
Q ss_pred HHHHhCCHHHHHHHHHHHHhhhccC
Q 006003 151 TLIKKTNAQEMKWIIMIILKDLKLG 175 (665)
Q Consensus 151 ~ll~~~t~~E~k~l~RiilkdlriG 175 (665)
.+|..|+.++.+-|+++|..| +-|
T Consensus 8 eFL~~cs~edL~~L~~~Lt~d-kdG 31 (35)
T PF13099_consen 8 EFLAECSNEDLKDLVDILTHD-KDG 31 (35)
T ss_pred HHHHHCCHHHHHHHHHHHhcC-CCC
Confidence 468889999999999999987 443
No 94
>KOG3673 consensus FtsJ-like RNA methyltransferase [RNA processing and modification]
Probab=21.68 E-value=89 Score=35.55 Aligned_cols=38 Identities=18% Similarity=0.149 Sum_probs=33.0
Q ss_pred CCCceEEEEEEEEeeCCccccCCCHHHHHHHHHhhcCC
Q 006003 332 SDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKP 369 (665)
Q Consensus 332 ~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~ 369 (665)
...+-.+++.|.+.|+|.++.+.||.||.++-++.+..
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 34566789999999999999999999999999887654
Done!