Query 003632
Match_columns 806
No_of_seqs 303 out of 1839
Neff 6.0
Searched_HMMs 46136
Date Fri Mar 29 03:05:33 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/003632.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/003632hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0967 ATP-dependent DNA liga 100.0 3E-159 7E-164 1321.7 49.9 632 161-792 69-704 (714)
2 PLN03113 DNA ligase 1; Provisi 100.0 1E-151 3E-156 1331.6 76.2 741 53-806 1-744 (744)
3 PRK01109 ATP-dependent DNA lig 100.0 6E-122 1E-126 1072.4 61.6 580 191-796 1-586 (590)
4 PRK09247 ATP-dependent DNA lig 100.0 9E-106 2E-110 926.5 57.1 528 194-792 2-538 (539)
5 PRK03180 ligB ATP-dependent DN 100.0 9E-106 2E-110 920.2 53.3 505 191-790 1-507 (508)
6 TIGR00574 dnl1 DNA ligase I, A 100.0 4E-105 8E-110 920.1 54.4 511 250-790 1-514 (514)
7 KOG0966 ATP-dependent DNA liga 100.0 3.7E-91 8E-96 791.2 38.3 561 189-791 3-591 (881)
8 COG1793 CDC9 ATP-dependent DNA 100.0 1.2E-71 2.7E-76 627.6 38.0 439 260-789 2-443 (444)
9 PHA02587 30 DNA ligase; Provis 100.0 2.3E-69 4.9E-74 617.5 43.7 448 196-787 2-485 (488)
10 TIGR02779 NHEJ_ligase_lig DNA 100.0 4E-62 8.8E-67 527.6 34.0 289 450-780 9-297 (298)
11 PRK09632 ATP-dependent DNA lig 100.0 1.3E-60 2.8E-65 561.5 35.4 307 425-780 454-761 (764)
12 PRK08224 ligC ATP-dependent DN 100.0 3E-59 6.6E-64 513.6 34.4 310 425-780 2-330 (350)
13 PRK05972 ligD ATP-dependent DN 100.0 4.6E-58 1E-62 544.4 35.2 303 430-781 232-537 (860)
14 PRK09633 ligD ATP-dependent DN 100.0 5.9E-58 1.3E-62 532.3 33.8 303 432-791 1-319 (610)
15 PRK07636 ligB ATP-dependent DN 100.0 2.3E-52 5E-57 446.5 31.8 272 432-771 3-274 (275)
16 cd07900 Adenylation_DNA_ligase 100.0 4E-51 8.7E-56 423.7 24.8 217 423-641 1-219 (219)
17 TIGR02776 NHEJ_ligase_prk DNA 100.0 2.5E-49 5.5E-54 455.7 28.5 257 480-781 1-259 (552)
18 PHA00454 ATP-dependent DNA lig 100.0 1.1E-46 2.5E-51 410.1 31.8 284 433-772 7-314 (315)
19 PRK09125 DNA ligase; Provision 100.0 9.3E-47 2E-51 404.4 28.2 254 432-774 28-282 (282)
20 cd07903 Adenylation_DNA_ligase 100.0 1.6E-45 3.5E-50 383.0 23.3 216 423-642 3-224 (225)
21 cd07901 Adenylation_DNA_ligase 100.0 4.1E-45 8.8E-50 375.7 24.2 205 428-640 1-207 (207)
22 cd07902 Adenylation_DNA_ligase 100.0 4.3E-45 9.3E-50 377.3 23.2 208 423-641 5-213 (213)
23 cd07897 Adenylation_DNA_ligase 100.0 1E-43 2.3E-48 365.4 22.6 201 430-641 3-206 (207)
24 cd08039 Adenylation_DNA_ligase 100.0 3.2E-43 7E-48 367.8 24.1 199 441-641 10-235 (235)
25 cd07898 Adenylation_DNA_ligase 100.0 7.4E-43 1.6E-47 357.2 23.9 199 432-640 1-201 (201)
26 PF01068 DNA_ligase_A_M: ATP d 100.0 3.6E-42 7.8E-47 350.4 21.0 201 434-638 1-202 (202)
27 cd07905 Adenylation_DNA_ligase 100.0 7.6E-41 1.6E-45 340.8 20.8 190 432-640 1-193 (194)
28 cd07906 Adenylation_DNA_ligase 100.0 5.8E-40 1.3E-44 333.0 21.4 189 432-639 1-189 (190)
29 cd07967 OBF_DNA_ligase_III The 100.0 3.1E-35 6.7E-40 284.1 13.7 132 645-784 1-139 (139)
30 PF04675 DNA_ligase_A_N: DNA l 100.0 1.4E-34 2.9E-39 290.1 17.2 176 191-369 1-177 (177)
31 cd07896 Adenylation_kDNA_ligas 100.0 1.2E-33 2.6E-38 282.8 16.7 173 432-639 1-174 (174)
32 cd07969 OBF_DNA_ligase_I The O 100.0 1.4E-33 3E-38 274.5 15.7 144 646-791 1-144 (144)
33 cd06846 Adenylation_DNA_ligase 100.0 3.9E-31 8.5E-36 266.3 18.2 175 434-639 2-182 (182)
34 cd07893 OBF_DNA_ligase The Oli 100.0 1.2E-30 2.6E-35 249.6 14.8 129 647-779 1-129 (129)
35 cd07968 OBF_DNA_ligase_IV The 100.0 5E-30 1.1E-34 248.7 12.9 128 646-782 1-140 (140)
36 cd07972 OBF_DNA_ligase_Arch_Li 100.0 8.9E-30 1.9E-34 241.4 14.0 121 647-786 1-121 (122)
37 cd07895 Adenylation_mRNA_cappi 99.9 1E-26 2.3E-31 240.5 14.4 162 450-639 38-215 (215)
38 KOG4437 ATP-dependent DNA liga 99.9 1.4E-24 3E-29 227.9 16.9 326 192-556 156-482 (482)
39 cd07971 OBF_DNA_ligase_LigD Th 99.9 2.1E-23 4.6E-28 195.8 14.2 114 648-779 2-115 (115)
40 PF04679 DNA_ligase_A_C: ATP d 99.9 5.4E-23 1.2E-27 187.3 10.3 97 663-774 1-97 (97)
41 cd08040 OBF_DNA_ligase_family 99.9 9.6E-22 2.1E-26 182.6 13.1 108 647-771 1-108 (108)
42 cd07970 OBF_DNA_ligase_LigC Th 99.8 1.6E-19 3.4E-24 171.4 13.0 114 647-781 1-122 (122)
43 cd07894 Adenylation_RNA_ligase 99.8 9.4E-18 2E-22 184.5 15.5 163 453-641 48-218 (342)
44 cd08041 OBF_kDNA_ligase_like T 99.3 2E-12 4.4E-17 113.2 7.5 76 648-771 2-77 (77)
45 PF01331 mRNA_cap_enzyme: mRNA 99.3 3.6E-12 7.8E-17 129.9 5.9 158 452-638 15-192 (192)
46 COG1423 ATP-dependent DNA liga 98.8 5E-08 1.1E-12 105.4 15.2 148 448-619 83-234 (382)
47 PF14743 DNA_ligase_OB_2: DNA 98.7 1.8E-08 3.9E-13 85.8 5.3 66 658-771 1-66 (66)
48 TIGR01209 RNA ligase, Pab1020 98.7 4.3E-07 9.2E-12 100.8 15.5 147 449-619 75-226 (374)
49 COG5226 CEG1 mRNA capping enzy 98.5 7E-08 1.5E-12 102.2 5.2 172 452-655 61-257 (404)
50 cd09232 Snurportin-1_C C-termi 98.5 6.3E-07 1.4E-11 91.4 11.1 152 453-639 21-185 (186)
51 PRK08097 ligB NAD-dependent DN 98.1 0.00025 5.4E-09 83.3 21.6 230 434-699 97-357 (562)
52 PRK01109 ATP-dependent DNA lig 98.1 1E-05 2.2E-10 96.2 9.4 93 189-291 113-210 (590)
53 smart00532 LIGANc Ligase N fam 98.0 0.00013 2.9E-09 83.7 17.6 239 433-700 74-361 (441)
54 cd00114 LIGANc NAD+ dependent 97.9 0.00028 6.1E-09 77.5 15.8 185 433-634 72-299 (307)
55 PF01653 DNA_ligase_aden: NAD- 97.9 2.4E-05 5.2E-10 86.1 7.3 173 433-619 77-289 (315)
56 TIGR00575 dnlj DNA ligase, NAD 97.9 0.00049 1.1E-08 82.8 18.8 238 433-700 67-354 (652)
57 PRK14350 ligA NAD-dependent DN 97.8 0.0011 2.5E-08 79.6 20.4 240 433-701 78-364 (669)
58 PRK07956 ligA NAD-dependent DN 97.7 0.00072 1.6E-08 81.5 17.4 239 433-700 78-366 (665)
59 PRK14351 ligA NAD-dependent DN 97.7 0.0014 3E-08 79.2 19.1 237 433-700 104-388 (689)
60 PF09414 RNA_ligase: RNA ligas 97.4 0.00035 7.5E-09 70.8 7.7 159 454-638 2-186 (186)
61 TIGR02307 RNA_lig_RNL2 RNA lig 97.3 0.0025 5.4E-08 70.2 12.1 162 451-640 23-217 (325)
62 COG0272 Lig NAD-dependent DNA 96.9 0.034 7.4E-07 66.2 17.8 193 453-668 109-337 (667)
63 PHA02142 putative RNA ligase 96.2 0.049 1.1E-06 61.1 12.8 163 441-639 156-357 (366)
64 PRK03180 ligB ATP-dependent DN 94.7 0.15 3.2E-06 60.1 10.1 91 189-289 71-164 (508)
65 KOG3132 m3G-cap-specific nucle 94.1 0.23 4.9E-06 52.3 8.8 152 452-636 115-277 (325)
66 TIGR02306 RNA_lig_DRB0094 RNA 93.5 1.3 2.7E-05 49.8 13.9 154 452-639 158-335 (341)
67 TIGR00574 dnl1 DNA ligase I, A 92.5 0.53 1.2E-05 55.6 9.7 93 189-291 53-148 (514)
68 KOG2386 mRNA capping enzyme, g 91.2 0.13 2.9E-06 58.1 2.6 95 454-576 286-383 (393)
69 PRK09247 ATP-dependent DNA lig 89.0 1.4 3E-05 52.5 8.8 87 307-413 3-90 (539)
70 PF04675 DNA_ligase_A_N: DNA l 88.5 0.84 1.8E-05 45.8 5.8 65 189-263 109-176 (177)
71 PLN03113 DNA ligase 1; Provisi 81.5 6.1 0.00013 48.8 9.5 71 189-269 239-312 (744)
72 PF09511 RNA_lig_T4_1: RNA lig 56.6 1.9E+02 0.0041 30.3 12.9 149 454-641 46-218 (221)
73 cd00408 DHDPS-like Dihydrodipi 56.3 28 0.00061 37.5 6.8 65 555-619 35-101 (281)
74 PRK03170 dihydrodipicolinate s 54.8 27 0.00058 38.1 6.4 65 555-619 39-105 (292)
75 cd00950 DHDPS Dihydrodipicolin 54.7 27 0.00059 37.8 6.4 67 553-619 36-104 (284)
76 PF00701 DHDPS: Dihydrodipicol 54.3 32 0.00069 37.4 6.8 65 555-619 39-105 (289)
77 COG4566 TtrR Response regulato 54.1 34 0.00073 35.6 6.4 89 279-370 84-179 (202)
78 TIGR02313 HpaI-NOT-DapA 2,4-di 53.4 30 0.00066 37.9 6.5 65 555-619 38-104 (294)
79 TIGR00683 nanA N-acetylneurami 53.0 32 0.0007 37.6 6.7 66 554-619 38-105 (290)
80 cd00952 CHBPH_aldolase Trans-o 52.1 35 0.00076 37.8 6.8 65 555-619 46-112 (309)
81 TIGR00674 dapA dihydrodipicoli 50.9 36 0.00079 37.0 6.6 57 563-619 46-102 (285)
82 cd00951 KDGDH 5-dehydro-4-deox 48.9 39 0.00085 36.9 6.5 64 555-619 38-103 (289)
83 PLN02417 dihydrodipicolinate s 48.4 40 0.00087 36.7 6.4 57 563-619 49-105 (280)
84 PRK04147 N-acetylneuraminate l 47.1 40 0.00088 36.8 6.3 57 563-619 52-108 (293)
85 cd00954 NAL N-Acetylneuraminic 46.5 49 0.0011 36.0 6.8 67 553-619 37-105 (288)
86 COG0329 DapA Dihydrodipicolina 44.0 66 0.0014 35.5 7.3 65 555-619 42-108 (299)
87 PRK03620 5-dehydro-4-deoxygluc 39.7 67 0.0014 35.4 6.6 65 554-619 44-110 (303)
88 TIGR03249 KdgD 5-dehydro-4-deo 39.6 69 0.0015 35.1 6.6 66 553-619 41-108 (296)
89 KOG2386 mRNA capping enzyme, g 38.5 57 0.0012 37.5 5.8 167 444-640 51-241 (393)
90 KOG3673 FtsJ-like RNA methyltr 34.7 51 0.0011 39.1 4.6 62 545-606 656-723 (845)
91 KOG0967 ATP-dependent DNA liga 34.6 2.4E+02 0.0052 34.4 10.1 89 190-288 210-322 (714)
92 PRK14956 DNA polymerase III su 32.9 51 0.0011 38.9 4.4 26 119-144 434-459 (484)
93 cd08205 RuBisCO_IV_RLP Ribulos 28.5 1.2E+02 0.0027 34.5 6.5 55 564-619 174-232 (367)
94 KOG0971 Microtubule-associated 27.2 1.2E+02 0.0026 38.1 6.2 18 151-168 217-234 (1243)
95 cd00953 KDG_aldolase KDG (2-ke 23.5 2.4E+02 0.0052 30.7 7.3 62 555-619 37-100 (279)
No 1
>KOG0967 consensus ATP-dependent DNA ligase I [Replication, recombination and repair]
Probab=100.00 E-value=3.3e-159 Score=1321.68 Aligned_cols=632 Identities=64% Similarity=1.067 Sum_probs=616.7
Q ss_pred HHHhhhhhccccCCCCCCCcccccccCCCccchHHHHHHHHHHHhccchHHHHHHHHHHHHhhhcCCCCchHhHHHHHhC
Q 003632 161 AELKSNIVLLKKKAGEFDPKMVACWEKGERVPFIFLSLVFDMISNETGRILITDIVCNMLRTVMETTPEDLVPVVYLAAN 240 (806)
Q Consensus 161 ~~~~~~~~~~~~~~~~~~p~~~~~w~~~~~~~F~~la~~~~~I~~tssr~~k~~iL~~~~r~~i~~~p~dl~~~vyL~~~ 240 (806)
.+.+...+.+.++|..|+|++.+||..|+++||++||++|+.|+.|++|+++++||+|||+.+++.+|+||+++|||++|
T Consensus 69 ~~~~~~~~~~~~~~~~y~~~~~a~wk~~~~~py~~~a~tF~kIe~~s~Rl~i~~il~n~f~~v~~~sP~dLlp~vYLsiN 148 (714)
T KOG0967|consen 69 ADSKSDSGLLKKSPEDYLPSENACWKDGSKVPYLELARTFEKIEETSGRLEIIDILSNFLRSVLATSPDDLLPTVYLSIN 148 (714)
T ss_pred ccccccccccCCCccccchhhhhhccccCcCcHHHHHHHHHHHHhhccceeHHHHHHHHHHHHHhcCchhhhhHHHHhhh
Confidence 34555667789999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CcCCCccccccCCCHHHHHHHHHHHhCCCHHHHHHHHhhcCCHHHHHhhcccccCccCCCCCCCHHHHHHHHHHHHHHhC
Q 003632 241 KIAPAHEGLELGIGDASIIKALAEACGRTESHVKKQYQEMGDLGLVAKASRSSQSMMRKPDPLTITKVFDTFRLIAKEAG 320 (806)
Q Consensus 241 ~l~P~~e~~elgIg~~~L~Kal~~~~g~s~~~ik~~~~~~GDlg~va~~~r~~q~~l~~~~~LTI~eV~~~L~~IA~~~G 320 (806)
+|.|+|+|.|||||++.|+|||+++||++..+++..|++.||||+||+.+|.+|++|++|+||||.+|+..|++||+.+|
T Consensus 149 ~l~P~yeGlELGvGes~l~KAi~EatGrt~~~vk~~~~~~GDLG~VA~~sR~sQ~~m~~P~pLtV~~VF~~Lr~IAk~sG 228 (714)
T KOG0967|consen 149 KLAPDYEGLELGVGESLLMKAIAEATGRTLSHVKNQYNKLGDLGLVAQGSRSSQRMMFKPKPLTVRDVFSTLRKIAKESG 228 (714)
T ss_pred ccCccccCccccccHHHHHHHHHHHhCccHHHHHHHHHhcCcHHHHHhhcccccccccCCCCccHHHHHHHHHHHHHhhC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CChHHHHHHHHHHHHHhcCCChHHHHHHHHhhcccCcccHHHHHHHHHhhhcccC----CCCCCCCCCcccHHHHHHHHH
Q 003632 321 KDSQEKKKNRIKALLVAATDCEPQYLIRLLQSKLRIGLAEQTLLAALGQAAVYNE----QHSKPPPNIQSPLEEAAKIVK 396 (806)
Q Consensus 321 ~~sq~~k~~~L~~Ll~~~t~~E~k~LiRiIlkdLRiG~~e~til~ala~A~~~~~----~~~~~~~~l~~~l~~a~~~~k 396 (806)
++||.+|++++..||.+|++.|+|||+|.|.++||||++++|||.||++|+.++. .+++.+..+++.|+.+..+|+
T Consensus 229 ~~S~~kK~~lik~Llvac~~~E~kyLiRsL~gkLRiGlaeqTvL~AL~~A~~~~~~~~~~~~~~~d~~kd~le~~~~ivk 308 (714)
T KOG0967|consen 229 KGSQNKKKDLIKALLVACRGIEAKYLIRSLEGKLRIGLAEQTVLAALGQAFVLNDNNDEEKSKKPDSLKDPLEEAAQIVK 308 (714)
T ss_pred cchhHHHHHHHHHHHHhcccccHHHHHHHHHhhhhhhhhHHHHHHHHHHHHhccCchhhhccCCcchhhhhhHHHHHHHH
Confidence 9999999999999999999999999999999999999999999999999998763 345666778999999999999
Q ss_pred HHhhcCCchhhhHhhhhhcCccccCCccccCCCCCCcccccccCCChHHHHhhcCCCceeEeeecceEeEEEEEecCCeE
Q 003632 397 QVFSVLPVYEKIVPALLTDGVWNLSNTCSFTPGIPIGPMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHYLEDGSV 476 (806)
Q Consensus 397 ~~y~~~p~~~~v~~~ll~~g~~~l~~~~~l~~g~Pv~PMLA~~~~~i~~~l~k~~g~~~~~E~KyDG~R~qih~~~~g~V 476 (806)
++|+++|||+.|+++|+++|+++|.++|.++||+|++||||+|++++.+++++|++..|.|||||||+|+|||+.++|.|
T Consensus 309 ~afcq~P~ydiivp~lL~~Gie~L~e~c~l~PGIPlKPMLAkpTK~i~evl~rf~~~~FTCEyKYDGeRAQIH~~edG~v 388 (714)
T KOG0967|consen 309 QAFCQLPDYDIIVPALLEHGIENLPETCKLTPGIPLKPMLAKPTKGIQEVLERFQDKAFTCEYKYDGERAQIHKLEDGTV 388 (714)
T ss_pred HHHhcCCchhhhHHHHHHhhhhhccccCccCCCCCCcchhcCcchhHHHHHHHhhCceeEEEeecCceeeeeEEccCCcE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEecCCCcCCCCcchHHHHHHhhcCCCCCCeEEEEEEEEEecCCCccCChHHHHHhhhccCCccccccceEEEEeeeee
Q 003632 477 EIYSRNAERNTGKFPDVVLAVSRLKKPSVRSFVLDCEIVAYDREKQKILPFQTLSTRARKNVSLSDIKVDVCIYAFDILY 556 (806)
Q Consensus 477 ~ifSR~gk~~T~~~Pel~~~l~~~~~~~v~~~ILDGElVa~d~~~g~~~pFq~L~~r~rk~~~~~~~~~~v~~~vFDiLy 556 (806)
.|||||++++|.+||||...+..+..+.+.+||||||+|+||++.|+++|||.|++|.||+++.+++++.||+|+|||||
T Consensus 389 ~IfSRN~E~~T~kYPDi~~~~~~~~kp~v~sFIlD~EvVA~Dr~~~~IlpFQvLSTRkRk~v~v~dikV~Vcvf~FDily 468 (714)
T KOG0967|consen 389 EIFSRNSENNTGKYPDIIEVISKLKKPSVKSFILDCEVVAWDREKGKILPFQVLSTRKRKNVDVNDIKVKVCVFVFDILY 468 (714)
T ss_pred EEEecccccccccCccHHHHHHHhhCCccceeEEeeeEEEEeccCCccCchhhhhhhhccccchhhceEEEEEEEEeeee
Confidence 99999999999999999999999888899999999999999999999999999999999999999999999999999999
Q ss_pred cCCccccCCcHHHHHHHHHHhhccCCCcEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEEeCCCCCCccCCCCCCCeEE
Q 003632 557 RNGQPLLQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLK 636 (806)
Q Consensus 557 lnG~~L~~~Pl~eRr~~L~~l~~~~~~~i~~~~~~~~~~~eei~~~~~~ai~~g~EGlmlK~~~~ds~Y~pGkRs~~WlK 636 (806)
+||++|+++||.+||++|.+.|.+++|+++++....+++.+++++||++++..+|||+|+|.+|.+++|+|.+||.+|+|
T Consensus 469 ~ng~~Li~~pL~eRR~~l~e~f~e~~g~f~fat~~~tn~~~eiq~Fl~~sv~~~cEGlMvKtLd~~atYep~kRs~~WlK 548 (714)
T KOG0967|consen 469 LNGESLIQEPLRERRELLHESFKEIPGEFQFATSLDTNDIDEIQEFLEESVQNSCEGLMVKTLDTNATYEPSKRSNNWLK 548 (714)
T ss_pred eCChhhhhhhHHHHHHHHHhhcccCCCceeEeeeeccCCHHHHHHHHHHhhccCcceeEEEeeccccccCchhhccchhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EccccccccCCcccEEEEEEEeCCCCCCCcccEEEEEEeeCCCCeEEEeeeccCCCCHHHHHHHHHhhccccCCCCCCCc
Q 003632 637 LKKDYIESIGDSLDLVPIAAFHGRGKRTGVYGAFLLACYDSNNEEFQSICKIGTGFSEAMLEERSSSLRSKVIPKPRPYY 716 (806)
Q Consensus 637 lK~dY~~~~~dtlDlvVIGa~~G~Gkr~g~~gsfLla~~d~~~g~~~~v~kVgtGftd~~l~~l~~~l~~~~~~~p~~~~ 716 (806)
+|+||++|+||++||||||+|+|+|||+||+|+||+||||+++++|++|||+||||||++++++++.+....+..|++||
T Consensus 549 lKkDYldgvgdslDLv~iga~~G~GrrtG~yg~fLlacyn~dteefqsiCKigtGFsD~~l~e~~~~l~~~~~~~~~~~y 628 (714)
T KOG0967|consen 549 LKKDYLDGVGDSLDLVVIGAYYGRGRRTGWYGGFLLACYNPDTEEFQSICKIGTGFSDEFLQELHESLSSTVIDSPKPYY 628 (714)
T ss_pred hhhhhhcccccceeeeeeeeeeccccccccccceeEEeecCchHHHHHHHhhcCCCCHHHHHHHHHHhhhccccCcHhhc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999888899999
Q ss_pred ccCCCCCCcEEecCceEEEEEeceeecCccccccccccCCCCCceeeccEEeEEecCCCccCCCCHHHHHHHHHHh
Q 003632 717 RFADTISPDVWFEPTEVWEVKAADLTISPVHRAAIGVVDPDKGISLRFPRLIRVREDKTPEQASSSEQVAEMYTAQ 792 (806)
Q Consensus 717 ~~~~~~~pdvwieP~~V~EV~~~eit~S~~~~a~~g~~~~~~G~sLRFPRf~riR~DK~~~da~t~~el~ely~~q 792 (806)
.++...+||+||+|..||||++++||.||.|+||.|++++++|+|||||||+|+|+||.++||+|.+||++||++|
T Consensus 629 ~~d~s~kPd~wf~p~~VwEvk~Adlt~SPiy~Aa~Glv~~dkGISlRFPRfiRiR~DK~peeAtts~qiaemY~~Q 704 (714)
T KOG0967|consen 629 RFDESLKPDVWFEPTEVWEVKAADLTLSPIYKAALGLVDPDKGISLRFPRFIRIRDDKNPEEATTSSQIAEMYQAQ 704 (714)
T ss_pred ccCccCCCccccCHHHHHHHhhccccccchhHhhhcCcCCCCceeEecceeeEeeccCChhhcccHHHHHHHHHHH
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999999999
No 2
>PLN03113 DNA ligase 1; Provisional
Probab=100.00 E-value=1.2e-151 Score=1331.58 Aligned_cols=741 Identities=79% Similarity=1.209 Sum_probs=660.3
Q ss_pred cCCCCCcHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccch---hhcccCCCCCCCCCCCCCCCC
Q 003632 53 MSSSAPNAFQVLMSAAAKKKPSPQPNSSSSSSSPKKRRTLDTQTPKTTNSVVGEKI---QEVAEEPSNDLVKPISNQIDN 129 (806)
Q Consensus 53 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~ 129 (806)
|| |+||||||||+-++...++....+++.+++||+++...++++....-+.-+.- -+..-++.++.+.++....++
T Consensus 1 ~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 79 (744)
T PLN03113 1 MS-SRPSAFDALMSNARAAAKKKQPQTQSQSSSPKKRKIGETQDANLGKTNVSEGTLPKTEDTIEPKSDSAKPRSSTSSI 79 (744)
T ss_pred CC-CCccHHHHHHHHHHHHhhccCCCccCCCCccccccccCCCCCCcCCcccccccccccccCCCCCCCccccccccccc
Confidence 44 59999999999444433344444466677778887776555544333333332 122334444555555555554
Q ss_pred CCCcccCCCCCCCCCcccceeeeccchhhhHHHHhhhhhccccCCCCCCCcccccccCCCccchHHHHHHHHHHHhccch
Q 003632 130 PIDSEKESQPTPPSPKKRKVNVNSVSAKEKIAELKSNIVLLKKKAGEFDPKMVACWEKGERVPFIFLSLVFDMISNETGR 209 (806)
Q Consensus 130 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~w~~~~~~~F~~la~~~~~I~~tssr 209 (806)
.++.++. +++.. +.... +.+++...+..+.+++..|||...++|..|.+|||..||++|++|+.|++|
T Consensus 80 ~~~~~~~-------~~~~~-~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~w~~~~~~~f~~l~~~~~~Ie~tt~r 147 (744)
T PLN03113 80 AEDSKTG-------TKKAQ-TLSKP----KKDEMKSKIGLLKKKPNDFDPEKVAYWEKGERVPFLFVALAFDLISNETGR 147 (744)
T ss_pred ccccCCC-------ccccc-ccccc----cccchhhhHhhccCCccccCcchhhcccCCCCccHHHHHHHHHHHHhccCH
Confidence 4443322 22221 11111 114556666678999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHhhhcCCCCchHhHHHHHhCCcCCCccccccCCCHHHHHHHHHHHhCCCHHHHHHHHhhcCCHHHHHhh
Q 003632 210 ILITDIVCNMLRTVMETTPEDLVPVVYLAANKIAPAHEGLELGIGDASIIKALAEACGRTESHVKKQYQEMGDLGLVAKA 289 (806)
Q Consensus 210 ~~k~~iL~~~~r~~i~~~p~dl~~~vyL~~~~l~P~~e~~elgIg~~~L~Kal~~~~g~s~~~ik~~~~~~GDlg~va~~ 289 (806)
++|+++|+|||+.++..+|+|+.++|||++|+|+|+|++.|||||++.|+|+|++++|++++.+++.|++.||+|+||+.
T Consensus 148 lek~~~L~~~~r~~~~~~p~dl~~~vyL~~~~l~P~~e~~elgige~~L~kai~e~~g~~~~~ik~~y~~~GDlG~vA~~ 227 (744)
T PLN03113 148 IVITDIVCNMLRTVMATTPEDLVAVVYLLANRIAPAHEGVELGIGEATIIKALAEAFGRTEKQVKKQYKELGDLGLVAKA 227 (744)
T ss_pred HHHHHHHHHHHHHhccCChHHHHHHHHHHhCCCCccccCcccCcCHHHHHHHHHHHHCcCHHHHHHHHHHhCCHHHHHHh
Confidence 99999999999999888999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccccCccCCCCCCCHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHhcCCChHHHHHHHHhhcccCcccHHHHHHHHHh
Q 003632 290 SRSSQSMMRKPDPLTITKVFDTFRLIAKEAGKDSQEKKKNRIKALLVAATDCEPQYLIRLLQSKLRIGLAEQTLLAALGQ 369 (806)
Q Consensus 290 ~r~~q~~l~~~~~LTI~eV~~~L~~IA~~~G~~sq~~k~~~L~~Ll~~~t~~E~k~LiRiIlkdLRiG~~e~til~ala~ 369 (806)
+++.|.+++++++|||.+||+.|.+||+.+|.+||++|..+|..||..|+++|++||+|+|+++||||++++||+.|||+
T Consensus 228 ~~~~q~~~~~~~~LTi~~V~~~L~~IA~~~G~~sq~~K~~~i~~Ll~~~~~~E~k~liR~l~g~LRIGv~e~tVl~ALa~ 307 (744)
T PLN03113 228 SRSSQSMMRKPEPLTVVKVFNTFQQIAKESGKDSQEKKKNRIKALLVAATDCEPLYLIRLLQTKLRIGLAGQTLLAALGQ 307 (744)
T ss_pred hhcccccccCCCCCCHHHHHHHHHHHHhhhCccCHHHHHHHHHHHHHhCCHHHHHHHHHHHhccccccccHHHHHHHHHH
Confidence 98888887888999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhcccCCCCCCCCCCcccHHHHHHHHHHHhhcCCchhhhHhhhhhcCccccCCccccCCCCCCcccccccCCChHHHHhh
Q 003632 370 AAVYNEQHSKPPPNIQSPLEEAAKIVKQVFSVLPVYEKIVPALLTDGVWNLSNTCSFTPGIPIGPMLAKPTKGVSEIVNK 449 (806)
Q Consensus 370 A~~~~~~~~~~~~~l~~~l~~a~~~~k~~y~~~p~~~~v~~~ll~~g~~~l~~~~~l~~g~Pv~PMLA~~~~~i~~~l~k 449 (806)
||.++..+.....++.++|++++.+++++|+.+|+|+.|++.++++|+.++..+|.++||+||+||||++++++++++++
T Consensus 308 a~~~~~~~~~~~~~~~~~l~~~~~~v~~a~~~~p~~~~i~~~ll~~g~~~l~~~~~i~~g~Pi~PMLA~~~~~~~eil~~ 387 (744)
T PLN03113 308 AAVYNEEHSTPPPNIQSPLEEAAKIVKQVYSVLPVYDKIVPALLSGGVWNLPKTCSFTPGVPVGPMLAKPTKGVSEIVNK 387 (744)
T ss_pred HhcccccccccccccchhhHHHHHHHHHHhccCCCHHHHHHHHHhCCcccccccccccCCCCCCCccCCCCCChHHHhhc
Confidence 99876654444456788899999999999999999999999999999999988999999999999999999999999999
Q ss_pred cCCCceeEeeecceEeEEEEEecCCeEEEEecCCCcCCCCcchHHHHHHhhcCCCCCCeEEEEEEEEEecCCCccCChHH
Q 003632 450 FQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAVSRLKKPSVRSFVLDCEIVAYDREKQKILPFQT 529 (806)
Q Consensus 450 ~~g~~~~~E~KyDG~R~qih~~~~g~V~ifSR~gk~~T~~~Pel~~~l~~~~~~~v~~~ILDGElVa~d~~~g~~~pFq~ 529 (806)
|+|.+|++|+||||+|||||+..+|.|++|||||+++|++|||+++++..+..+.+++||||||+|+||+.+|+++|||.
T Consensus 388 ~~g~~~~~E~KyDGeR~QiH~~~~g~v~lfSRn~ed~T~~fPel~~~~~~~~~~~~~~~ILDGEiVa~d~~~~~~lpFq~ 467 (744)
T PLN03113 388 FQDMEFTCEYKYDGERAQIHFLEDGSVEIYSRNAERNTGKYPDVVVAISRLKKPSVKSFILDCELVAYDREKKKILPFQI 467 (744)
T ss_pred cCCCCEEEEEeeccceEEEEEecCCEEEEEeCCCCcccccchhHHHHHHHhccccCCCEEEEeEEEEEECCCCCcCCHHH
Confidence 98889999999999999999866789999999999999999999998888775567899999999999998888999999
Q ss_pred HHHhhhccCCccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCCCcEEEEeEEecCCHHHHHHHHHHHHHc
Q 003632 530 LSTRARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAAVDA 609 (806)
Q Consensus 530 L~~r~rk~~~~~~~~~~v~~~vFDiLylnG~~L~~~Pl~eRr~~L~~l~~~~~~~i~~~~~~~~~~~eei~~~~~~ai~~ 609 (806)
|++|.|+++...+.+.++||+||||||+||++|++.||.+||++|++++.+.++++++++...+++.++++++|+++++.
T Consensus 468 Lq~R~rk~~~~~~~~~pv~~~aFDlLylnG~~L~~~PL~eRR~~L~~~~~~~~~~i~~~~~~~~~~~ee~~~~~~~ai~~ 547 (744)
T PLN03113 468 LSTRARKNVVMSDIKVDVCIFAFDMLYLNGQPLIQEQLKIRREHLYESFEEDPGFFQFATAITSNDLEEIQKFLDAAVDA 547 (744)
T ss_pred HHhhhccccchhccccceEEEEEeccccCccChhcCCHHHHHHHHHHHhccCCCcEEEeeeeccCCHHHHHHHHHHHHHc
Confidence 99999887665556789999999999999999999999999999999999888899999999999999999999999999
Q ss_pred CCceeEEEeCCCCCCccCCCCCCCeEEEccccccccCCcccEEEEEEEeCCCCCCCcccEEEEEEeeCCCCeEEEeeecc
Q 003632 610 SCEGLIIKTMDRDATYEPSKRSLNWLKLKKDYIESIGDSLDLVPIAAFHGRGKRTGVYGAFLLACYDSNNEEFQSICKIG 689 (806)
Q Consensus 610 g~EGlmlK~~~~ds~Y~pGkRs~~WlKlK~dY~~~~~dtlDlvVIGa~~G~Gkr~g~~gsfLla~~d~~~g~~~~v~kVg 689 (806)
|+||||+|+++.+|+|+||+|+.+|+|+|++|+++|+|++|+||||||+|+|+|+|++|+|||||||+++|+|++|||||
T Consensus 548 g~EGlmvK~l~~dS~Y~pGkRs~~WlKlK~dy~~~~~dtlDlVvIGa~~G~GkR~g~~g~fLla~yd~~~~~~~~v~Kvg 627 (744)
T PLN03113 548 SCEGLIIKTLNKDATYEPSKRSNNWLKLKKDYMESIGDSLDLVPIAAFHGRGKRTGVYGAFLLACYDSNKEEFQSICKIG 627 (744)
T ss_pred CCceEEEeccCCCCCccCCCCCCCeEEEechhhccccccccEEEEEEEeCCCCcCCccceEEEEEEcCCCCEEEEeeEEC
Confidence 99999999976589999999999999999999999999999999999999999999999999999998888999999999
Q ss_pred CCCCHHHHHHHHHhhccccCCCCCCCcccCCCCCCcEEecCceEEEEEeceeecCccccccccccCCCCCceeeccEEeE
Q 003632 690 TGFSEAMLEERSSSLRSKVIPKPRPYYRFADTISPDVWFEPTEVWEVKAADLTISPVHRAAIGVVDPDKGISLRFPRLIR 769 (806)
Q Consensus 690 tGftd~~l~~l~~~l~~~~~~~p~~~~~~~~~~~pdvwieP~~V~EV~~~eit~S~~~~a~~g~~~~~~G~sLRFPRf~r 769 (806)
|||||++++++.+.|++++++.|++|+.++....||+||+|..||||+|+|||.||+|+||+|.+.+++|++||||||+|
T Consensus 628 TGfsd~~l~~l~~~L~~~~~~~~~~~~~~~~~~~pdvwveP~~V~EV~~aeit~Sp~h~a~~g~~~~~~G~sLRFPRf~r 707 (744)
T PLN03113 628 TGFSEAVLEERSASLRSQVIPTPKSYYRYGDSIKPDVWFEPTEVWEVKAADLTISPVHRAAVGIVDPDKGISLRFPRLVR 707 (744)
T ss_pred CCCCHHHHHHHHHHHHHhcccCCCcccccCCCCCCcEEECCceEEEEEeeeeccCcccccccccccCCCCeEEECCEEEE
Confidence 99999999999999999999888888888777789999999999999999999999999999999999999999999999
Q ss_pred EecCCCccCCCCHHHHHHHHHHhhhcCCCCCCCCCCC
Q 003632 770 VREDKTPEQASSSEQVAEMYTAQKLNHPNNQDDNEDD 806 (806)
Q Consensus 770 iR~DK~~~da~t~~el~ely~~q~~~~~~~~~~~~~~ 806 (806)
+|+||+|+||+|+++|.+||++|...++.+++++|||
T Consensus 708 iR~DK~~~datt~~~l~~ly~~Q~~~~~~~~~~~~~~ 744 (744)
T PLN03113 708 VREDKSPEQATSSEQVADMYNAQKHNHPSNQDDNDDD 744 (744)
T ss_pred EECCCChHHCCCHHHHHHHHHHHHHhhcccCCCCCCC
Confidence 9999999999999999999999999999998888886
No 3
>PRK01109 ATP-dependent DNA ligase; Provisional
Probab=100.00 E-value=6e-122 Score=1072.35 Aligned_cols=580 Identities=36% Similarity=0.627 Sum_probs=533.5
Q ss_pred cchHHHHHHHHHHHhccchHHHHHHHHHHHHhhhcCCCCchHhHHHHHhCCcCCCccccccCCCHHHHHHHHHHHhCCCH
Q 003632 191 VPFIFLSLVFDMISNETGRILITDIVCNMLRTVMETTPEDLVPVVYLAANKIAPAHEGLELGIGDASIIKALAEACGRTE 270 (806)
Q Consensus 191 ~~F~~la~~~~~I~~tssr~~k~~iL~~~~r~~i~~~p~dl~~~vyL~~~~l~P~~e~~elgIg~~~L~Kal~~~~g~s~ 270 (806)
|+|..||++|++|++|+||++|+++|++||+.+ +|+++.+++||++|+|+|+|++.+|||+++.|+|+|++++|++.
T Consensus 1 m~f~~l~~~~~~i~~t~~r~~k~~~l~~~~~~~---~~~~~~~~~~l~~~~~~p~~~~~~~gi~~~~l~k~i~~~~g~~~ 77 (590)
T PRK01109 1 MEFSELAEYFERLEKTTSRTQLTKLLADLLKKT---PPEIIDKVVYLIQGKLWPDWLGLELGVGEKLLIKAISMATGISE 77 (590)
T ss_pred CcHHHHHHHHHHHHhhhchHHHHHHHHHHHHhC---CHHhhhhhHHHHhCCcCccccCcccCcCHHHHHHHHHHHHCcCH
Confidence 789999999999999999999999999999997 78999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhhcCCHHHHHhhccccc--Cc---cCCCCCCCHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHhcCCChHHH
Q 003632 271 SHVKKQYQEMGDLGLVAKASRSSQ--SM---MRKPDPLTITKVFDTFRLIAKEAGKDSQEKKKNRIKALLVAATDCEPQY 345 (806)
Q Consensus 271 ~~ik~~~~~~GDlg~va~~~r~~q--~~---l~~~~~LTI~eV~~~L~~IA~~~G~~sq~~k~~~L~~Ll~~~t~~E~k~ 345 (806)
+.+++.|.++||+|+||+.+++.+ .+ ++.+++||+.+|++.|++||+.+|.+|+..|+++|..||.+|++.|++|
T Consensus 78 ~~~~~~~~~~GDlg~~a~~~~~~~~~~~~~~~~~~~~lti~eV~~~L~~Ia~~sg~~s~~~k~~iL~~Ll~~~~~~E~k~ 157 (590)
T PRK01109 78 KEVENLYKKTGDLGEVARRLKSKKKQKSLLAFFSKEPLTVKEVYDTLVKIALATGEGSQDLKIKLLAGLLKDASPLEAKY 157 (590)
T ss_pred HHHHHHHHhcCCHHHHHHHHHhhcccccccccCCCCCcCHHHHHHHHHHHHhhhCCCcHHHHHHHHHHHHHhCCHHHHHH
Confidence 999999999999999999876543 32 2457899999999999999999999999999999999999999999999
Q ss_pred HHHHHhhcccCcccHHHHHHHHHhhhcccCCCCCCCCCCcccHHHHHHHHHHHhhcCCchhhhHhhhhhcCccccCCccc
Q 003632 346 LIRLLQSKLRIGLAEQTLLAALGQAAVYNEQHSKPPPNIQSPLEEAAKIVKQVFSVLPVYEKIVPALLTDGVWNLSNTCS 425 (806)
Q Consensus 346 LiRiIlkdLRiG~~e~til~ala~A~~~~~~~~~~~~~l~~~l~~a~~~~k~~y~~~p~~~~v~~~ll~~g~~~l~~~~~ 425 (806)
|+|+|+++||||+++++|++||+.|+.... ....++++|+.|||++.++..+..+|+..+ .++.
T Consensus 158 iirli~g~lriGv~e~~il~ALa~A~~~~~---------------~~~~ve~~y~~~~Dlg~va~~l~~~g~~~~-~~~~ 221 (590)
T PRK01109 158 IARFVEGRLRLGVGDATILDALAIAFGGAV---------------ARELVERAYNLRADLGYIAKILAEGGIEAL-KKVK 221 (590)
T ss_pred HHHHHhhhhhcCccHHHHHHHHHHHHhccc---------------chHHHHHHHHhCCCHHHHHHHHHhcchhhh-ccCc
Confidence 999999999999999999999999875211 123567899999999999999999887666 4689
Q ss_pred cCCCCCCcccccccCCChHHHHhhcCCCceeEeeecceEeEEEEEecCCeEEEEecCCCcCCCCcchHHHHHHhhcCCCC
Q 003632 426 FTPGIPIGPMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAVSRLKKPSV 505 (806)
Q Consensus 426 l~~g~Pv~PMLA~~~~~i~~~l~k~~g~~~~~E~KyDG~R~qih~~~~g~V~ifSR~gk~~T~~~Pel~~~l~~~~~~~v 505 (806)
++||+||+||||+++++++++++++++ .|++|+||||+|||+|+. +|.|++|||||+++|..||++.++++..++ .
T Consensus 222 i~~~~Pv~PmLA~~~~~~~~~~~~~~~-~~~~E~K~DG~R~qih~~-~~~v~l~SR~~~d~T~~~pel~~~~~~~~~--~ 297 (590)
T PRK01109 222 PQVGIPIRPMLAERLSSPKEILKKMGG-EALVEYKYDGERAQIHKK-GDKVKIFSRRLENITHQYPDVVEYAKEAIK--A 297 (590)
T ss_pred ccCCCCCCcccCCccCCHHHHHHHcCC-CeEEEecCCceEEEEEEc-CCEEEEEeCCchhhccccchHHHHHHHhcC--c
Confidence 999999999999999999999999865 799999999999999995 789999999999999999999999887664 3
Q ss_pred CCeEEEEEEEEEecCCCccCChHHHHHhhhccCC-ccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCCCc
Q 003632 506 RSFVLDCEIVAYDREKQKILPFQTLSTRARKNVS-LSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEPGF 584 (806)
Q Consensus 506 ~~~ILDGElVa~d~~~g~~~pFq~L~~r~rk~~~-~~~~~~~v~~~vFDiLylnG~~L~~~Pl~eRr~~L~~l~~~~~~~ 584 (806)
++||||||+|+||+++|+++|||.|++|.|++.. ......++||+||||||+||+++++.||.+||++|++++.+.+ .
T Consensus 298 ~~~ILDGElv~~d~~~g~~~~F~~l~~R~r~~~~~~~~~~~p~~~~vFDiL~l~g~~l~~~pl~eRr~~L~~~~~~~~-~ 376 (590)
T PRK01109 298 EEAIVEGEIVAVDPETGEMRPFQELMHRKRKYDIEEAIKEYPVNVFLFDLLYVDGEDLTDKPLPERRKKLEEIVKEND-K 376 (590)
T ss_pred cceEEeeeEEEEECCCCcccChHHHhhcccccchhhhcccCceEEEEEEEEEECCcchhhCcHHHHHHHHHHhcCCCC-c
Confidence 7999999999999888998999999999655421 1123578999999999999999999999999999999998765 5
Q ss_pred EEEEeEEecCCHHHHHHHHHHHHHcCCceeEEEeCCCCCCccCCCCCCCeEEEccccccccCCcccEEEEEEEeCCCCCC
Q 003632 585 FQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLKKDYIESIGDSLDLVPIAAFHGRGKRT 664 (806)
Q Consensus 585 i~~~~~~~~~~~eei~~~~~~ai~~g~EGlmlK~~~~ds~Y~pGkRs~~WlKlK~dY~~~~~dtlDlvVIGa~~G~Gkr~ 664 (806)
+++++...+++.+++.++|++++++|+||||+|+++++|+|+||+|+.+|+|+|+||+++++|++|+||||+++|+|+|+
T Consensus 377 ~~~~~~~~~~~~~~~~~~~~~a~~~g~EGiv~K~~~~ds~Y~~g~Rs~~WlK~K~dy~~~~~~~~DlvviG~~~g~Gkr~ 456 (590)
T PRK01109 377 VKLAERIITDDVEELEKFFHRAIEEGCEGLMAKSLGKDSIYQAGARGWLWIKYKRDYQSEMADTVDLVVVGAFYGRGRRG 456 (590)
T ss_pred eEEeeeEecCCHHHHHHHHHHHHHcCCceEEEecCCCCCCcCCCCCCccHHHhhHHhhcccCCceeEEEEEeEeCCCccC
Confidence 89999999999999999999999999999999999778999999999999999999999999999999999999999999
Q ss_pred CcccEEEEEEeeCCCCeEEEeeeccCCCCHHHHHHHHHhhccccCCCCCCCcccCCCCCCcEEecCceEEEEEeceeecC
Q 003632 665 GVYGAFLLACYDSNNEEFQSICKIGTGFSEAMLEERSSSLRSKVIPKPRPYYRFADTISPDVWFEPTEVWEVKAADLTIS 744 (806)
Q Consensus 665 g~~gsfLla~~d~~~g~~~~v~kVgtGftd~~l~~l~~~l~~~~~~~p~~~~~~~~~~~pdvwieP~~V~EV~~~eit~S 744 (806)
|++|+|+|||||+++|+|++||||||||||+++++|.+.+++++++.+++++ .....||+||+|..||||+|++||.|
T Consensus 457 ~~~g~~ll~~~d~~~~~~~~v~kvgtG~sd~~~~~l~~~l~~~~~~~~~~~~--~~~~~pdvwv~P~~V~eV~~~~it~S 534 (590)
T PRK01109 457 GKYGSLLMAAYDPKTDTFETVCKVGSGFTDEDLDELPKMLKPYKIDHKHPRV--VSKMEPDVWVEPKLVAEIIGAEITLS 534 (590)
T ss_pred CccccEEEEEEcCCCCeEEEEEEECCCCCHHHHHHHHHHhhhhcccCCCccc--ccccCCcEEEeccEEEEEEeeecccC
Confidence 9999999999998788999999999999999999999999999987655543 23458999999999999999999999
Q ss_pred ccccccccccCCCCCceeeccEEeEEecCCCccCCCCHHHHHHHHHHhhhcC
Q 003632 745 PVHRAAIGVVDPDKGISLRFPRLIRVREDKTPEQASSSEQVAEMYTAQKLNH 796 (806)
Q Consensus 745 ~~~~a~~g~~~~~~G~sLRFPRf~riR~DK~~~da~t~~el~ely~~q~~~~ 796 (806)
|+|+||+|.+.++.|++||||||+++|+||+|+||+|+++|.+||++|+.+.
T Consensus 535 ~~~~~~~~~~~~~~g~~LRfPr~~~~R~DK~~~d~~t~~~~~~ly~~q~~~~ 586 (590)
T PRK01109 535 PLHTCCLGVVEKGAGLAIRFPRFIRWRDDKSPEDATTTEEILEMYKRQKKKK 586 (590)
T ss_pred cceecccccccCCCceeEEcCeeeEeeCCCChhhCcCHHHHHHHHHHhhhcc
Confidence 9999999999888999999999999999999999999999999999998864
No 4
>PRK09247 ATP-dependent DNA ligase; Validated
Probab=100.00 E-value=9e-106 Score=926.47 Aligned_cols=528 Identities=21% Similarity=0.317 Sum_probs=464.7
Q ss_pred HHHHHHHHHHHhccchHHHHHHHHHHHHhhhcCCCCchHhHHHHHhCCcCCCccccccCCCHHHHHHHHHHHhCCCHHHH
Q 003632 194 IFLSLVFDMISNETGRILITDIVCNMLRTVMETTPEDLVPVVYLAANKIAPAHEGLELGIGDASIIKALAEACGRTESHV 273 (806)
Q Consensus 194 ~~la~~~~~I~~tssr~~k~~iL~~~~r~~i~~~p~dl~~~vyL~~~~l~P~~e~~elgIg~~~L~Kal~~~~g~s~~~i 273 (806)
..||++|++|++|++|++|+++|++||+.+ +|+|+.+++||++|++. ++||+++.|+|++++++|++++.+
T Consensus 2 ~~fa~~~~~i~~t~~~~ek~~~l~~~~~~~---~~~d~~~~~~ll~g~~~------~~~i~~~~l~k~~~~~~g~~~~~~ 72 (539)
T PRK09247 2 KAFAELLDRLDLTTSTNAKLALLADYFRSA---PDPDRAWALALLTGGLP------RRLVKTRLLRELAAERADLPPWLF 72 (539)
T ss_pred hHHHHHHHHHHhccCHHHHHHHHHHHHHhC---CHHHHHHHHHHhcCCcc------cCCCCHHHHHHHHHHHHCcCHHHH
Confidence 689999999999999999999999999997 78899999999999987 479999999999999999999999
Q ss_pred HHHHhhcCCHHHHHhhcccccC--ccCCCCCCCHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHhcCCChHHHHHHHHh
Q 003632 274 KKQYQEMGDLGLVAKASRSSQS--MMRKPDPLTITKVFDTFRLIAKEAGKDSQEKKKNRIKALLVAATDCEPQYLIRLLQ 351 (806)
Q Consensus 274 k~~~~~~GDlg~va~~~r~~q~--~l~~~~~LTI~eV~~~L~~IA~~~G~~sq~~k~~~L~~Ll~~~t~~E~k~LiRiIl 351 (806)
++.|.++||+|+||..+...+. .++.+.++||.+|++.|.+|++.+ |+..|..||.+|++.|++||+|+|+
T Consensus 73 ~~~~~~~GDlg~~~~~~~~~~~~~~~~~~~~~tv~~v~~~l~~~~~~~-------k~~~l~~ll~~~~~~e~~~i~rli~ 145 (539)
T PRK09247 73 EESYDYVGDLAETIALLLPAPSDEASDLPLAPWLEEVLLPLRGLGREE-------LRAALADLWDRLDEDGRFALNKLIT 145 (539)
T ss_pred HHHHHhcCCHHHHHHHhcccccccccCCCccccHHHHHHHHHhhhHHH-------HHHHHHHHHHhCCHHHHHHHHHHhh
Confidence 9999999999999988643322 223346799999999999997542 6788999999999999999999999
Q ss_pred hcccCcccHHHHHHHHHhhhcccCCCCCCCCCCcccHHHHHHHHHHHhhc--CCchhhhHhhhhhcCccccCCccccCCC
Q 003632 352 SKLRIGLAEQTLLAALGQAAVYNEQHSKPPPNIQSPLEEAAKIVKQVFSV--LPVYEKIVPALLTDGVWNLSNTCSFTPG 429 (806)
Q Consensus 352 kdLRiG~~e~til~ala~A~~~~~~~~~~~~~l~~~l~~a~~~~k~~y~~--~p~~~~v~~~ll~~g~~~l~~~~~l~~g 429 (806)
++||||+++++|+.||++|+..+ .+.+.++|+. +|+++.+. .++..|. ..|.++||
T Consensus 146 g~lRiG~~~~~v~~ala~a~~~~-----------------~~~v~~~~~~~~~~~~~~~~-~~~~~~~----~~~~~~~~ 203 (539)
T PRK09247 146 GGFRVGVSARLVTRALAELGGVD-----------------EARIAQRLMGLWPPYADLFA-WLIGPEE----DPLPADPG 203 (539)
T ss_pred CccccchhHHHHHHHHHHHhCCC-----------------HHHHHHHHhCCCCCcHHHHH-HHhhCCc----cccCCCCC
Confidence 99999999999999999998421 1234556666 66665544 4555565 46899999
Q ss_pred CCCcccccccCCChHHHHhhcCCCceeEeeecceEeEEEEEecCCeEEEEecCCCcCCCCcchHHHHHHhhcCCCCCCeE
Q 003632 430 IPIGPMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAVSRLKKPSVRSFV 509 (806)
Q Consensus 430 ~Pv~PMLA~~~~~i~~~l~k~~g~~~~~E~KyDG~R~qih~~~~g~V~ifSR~gk~~T~~~Pel~~~l~~~~~~~v~~~I 509 (806)
+|++||||+++.++.+... ...+|++|+||||+|||+|+. +|.|++|||||+++|..||++.+++.. ++ .+||
T Consensus 204 ~P~~pMLA~~~~~~~~~~~--~~~~~~~E~K~DG~R~qih~~-~~~v~lfSR~g~d~t~~fPei~~~~~~-l~---~~~I 276 (539)
T PRK09247 204 QPYPFFLAHPLEDEDLTLG--DPADWQAEWKWDGIRVQLVRR-GGEVRLWSRGEELITERFPELAEAAEA-LP---DGTV 276 (539)
T ss_pred CcCCCeeCCcCCCchhhhc--CCCcEEEEEeEcceEEEEEEe-CCEEEEEeCCCccchhhhHHHHHHHHh-CC---CCEE
Confidence 9999999999988765443 334899999999999999995 789999999999999999999987764 32 5799
Q ss_pred EEEEEEEEecCCCccCChHHHHHhhh-ccCCcc-ccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCCC-cEE
Q 003632 510 LDCEIVAYDREKQKILPFQTLSTRAR-KNVSLS-DIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEPG-FFQ 586 (806)
Q Consensus 510 LDGElVa~d~~~g~~~pFq~L~~r~r-k~~~~~-~~~~~v~~~vFDiLylnG~~L~~~Pl~eRr~~L~~l~~~~~~-~i~ 586 (806)
||||+|+||+.+|.++|||.|++|.+ ++.... ....++||+||||||+||+++++.||.+||++|++++.+.++ ++.
T Consensus 277 LDGElv~~~~~~~~~~~F~~l~~R~~rk~~~~~~~~~~pv~~~vFDiL~l~g~~l~~~Pl~eRr~~L~~~~~~~~~~~i~ 356 (539)
T PRK09247 277 LDGELLVWRPEDGRPQPFADLQQRIGRKTVGKKLLADYPAFLRAYDLLEDGGEDLRALPLAERRARLEALIARLPDPRLD 356 (539)
T ss_pred EEeEEEEEECCCCCcCCHHHHHHHhcccccchhhhhcCCeEEEEEEeeeeCCcchhhCCHHHHHHHHHHHhcccCCCeEE
Confidence 99999999977778899999999954 433211 125789999999999999999999999999999999987654 899
Q ss_pred EEeEEecCCHHHHHHHHHHHHHcCCceeEEEeCCCCCCccCCCCCCCeEEEccccccccCCcccEEEEEEEeCCCCCCCc
Q 003632 587 FATTLTSIDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLKKDYIESIGDSLDLVPIAAFHGRGKRTGV 666 (806)
Q Consensus 587 ~~~~~~~~~~eei~~~~~~ai~~g~EGlmlK~~~~ds~Y~pGkRs~~WlKlK~dY~~~~~dtlDlvVIGa~~G~Gkr~g~ 666 (806)
+++...+++.+++.++|++++++|+||||+|++ +|+|+||+|+..|+|+|++| +++|+||||+++|+|+|+|+
T Consensus 357 ~~~~~~~~~~~e~~~~~~~a~~~g~EGlm~K~~--~s~Y~~Grr~~~WlK~K~~~-----~t~DlVvig~~~G~Gkr~g~ 429 (539)
T PRK09247 357 LSPLVPFSDWDELAALRAAARERGVEGLMLKRR--DSPYLVGRKKGPWWKWKRDP-----LTIDAVLMYAQRGHGRRASL 429 (539)
T ss_pred ecCceecCCHHHHHHHHHHHHHCCCceEEEecC--CCCcCCCCCcchhhcccCCC-----CcEEEEEEEeecCCCCcCCc
Confidence 999999999999999999999999999999999 99999999999999999997 48999999999999999999
Q ss_pred ccEEEEEEeeCCC--CeEEEeeeccCCCCHHHHHHHHHhhccccCCCCCCCcccCCCCCCcEEecCceEEEEEeceeecC
Q 003632 667 YGAFLLACYDSNN--EEFQSICKIGTGFSEAMLEERSSSLRSKVIPKPRPYYRFADTISPDVWFEPTEVWEVKAADLTIS 744 (806)
Q Consensus 667 ~gsfLla~~d~~~--g~~~~v~kVgtGftd~~l~~l~~~l~~~~~~~p~~~~~~~~~~~pdvwieP~~V~EV~~~eit~S 744 (806)
+|+|+|||||++. ++|++||||||||||+++++|.+.++++.+.. ..|++||+|..||||+|+|||.|
T Consensus 430 ~~~~lla~~~~~~~~~~~~~v~kvgsGftd~~l~~l~~~l~~~~~~~----------~~~~~~v~P~~V~EV~~~eit~S 499 (539)
T PRK09247 430 YTDYTFGVWDGPEGGRQLVPFAKAYSGLTDEEIKQLDRWVRKNTVER----------FGPVRSVRPELVFEIAFEGIQRS 499 (539)
T ss_pred cccEEEEEEcCCCCceeEEEEEEECCCCCHHHHHHHHHHHhhccccc----------CCCceEecCceEEEEEeceeeec
Confidence 9999999998753 36999999999999999999998887654332 25899999999999999999999
Q ss_pred ccccccccccCCCCCceeeccEEeEEecCCCccCCCCHHHHHHHHHHh
Q 003632 745 PVHRAAIGVVDPDKGISLRFPRLIRVREDKTPEQASSSEQVAEMYTAQ 792 (806)
Q Consensus 745 ~~~~a~~g~~~~~~G~sLRFPRf~riR~DK~~~da~t~~el~ely~~q 792 (806)
|+|++ |++||||||+|+|+||+|+||+|+++|.+||++|
T Consensus 500 ~~~~~---------G~~LRfPr~~~~R~DK~~~ea~t~~~l~~l~~~~ 538 (539)
T PRK09247 500 KRHKS---------GIAVRFPRILRWRWDKPAREADTLETLQALLDAE 538 (539)
T ss_pred CCcCC---------CcEEEcceEEEEeCCCChHHCcCHHHHHHHHhcC
Confidence 99986 8999999999999999999999999999999876
No 5
>PRK03180 ligB ATP-dependent DNA ligase; Reviewed
Probab=100.00 E-value=8.5e-106 Score=920.23 Aligned_cols=505 Identities=29% Similarity=0.407 Sum_probs=455.1
Q ss_pred cchHHHHHHHHHHHhccchHHHHHHHHHHHHhhhcCCCCchHhHHHHHhCCcCCCccccccCCCHHHHHHHHHHHhCCCH
Q 003632 191 VPFIFLSLVFDMISNETGRILITDIVCNMLRTVMETTPEDLVPVVYLAANKIAPAHEGLELGIGDASIIKALAEACGRTE 270 (806)
Q Consensus 191 ~~F~~la~~~~~I~~tssr~~k~~iL~~~~r~~i~~~p~dl~~~vyL~~~~l~P~~e~~elgIg~~~L~Kal~~~~g~s~ 270 (806)
|+|..||++|++|++|++|++|+++|++||+.+ +++|+.+++||++|++. +.++|++++.+.++++.
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 689999999999999999999999999999997 78899999999999997 56899998777766432
Q ss_pred HHHHHHHhhcCCHHHHHhhcccccCccCCCCCCCHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHhcCCChHHHHHHHH
Q 003632 271 SHVKKQYQEMGDLGLVAKASRSSQSMMRKPDPLTITKVFDTFRLIAKEAGKDSQEKKKNRIKALLVAATDCEPQYLIRLL 350 (806)
Q Consensus 271 ~~ik~~~~~~GDlg~va~~~r~~q~~l~~~~~LTI~eV~~~L~~IA~~~G~~sq~~k~~~L~~Ll~~~t~~E~k~LiRiI 350 (806)
..+++|||.+||+.|++||..+|.+|++.|..+|+.||.+|++.|++||+|+|
T Consensus 68 ---------------------------~~~~~ltl~~V~~~l~~ia~~~g~~s~~~k~~~l~~ll~~~~~~E~~~l~r~i 120 (508)
T PRK03180 68 ---------------------------AAEPTLTVADVDAALSEIAAVAGAGSQARRAALLAALFAAATEDEQRFLRRLL 120 (508)
T ss_pred ---------------------------cCCCCCcHHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHH
Confidence 01367999999999999999999999999999999999999999999999999
Q ss_pred hhcccCcccHHHHHHHHHhhhcccCCCCCCCCCCcccHHHHHHHHHHHhhcCCchhhhHhhhhhcCccccCCccccCCCC
Q 003632 351 QSKLRIGLAEQTLLAALGQAAVYNEQHSKPPPNIQSPLEEAAKIVKQVFSVLPVYEKIVPALLTDGVWNLSNTCSFTPGI 430 (806)
Q Consensus 351 lkdLRiG~~e~til~ala~A~~~~~~~~~~~~~l~~~l~~a~~~~k~~y~~~p~~~~v~~~ll~~g~~~l~~~~~l~~g~ 430 (806)
+++||||+++++|+.|||+|+..+ ...+.++|+.|+|++.+++.++++|...+ ..|.+++|+
T Consensus 121 ~~~lRiGv~~~~v~~Ala~a~~~~-----------------~~~v~~a~~~~~dl~~v~~~~l~~~~~~~-~~~~i~~~~ 182 (508)
T PRK03180 121 TGELRQGALDGVMADAVARAAGVP-----------------AAAVRRAAMLAGDLPAVAAAALTGGAAAL-ARFRLEVGR 182 (508)
T ss_pred hCCCcccccHHHHHHHHHHHhCCC-----------------HHHHHHHHHHcCCHHHHHHHHHhcCcccc-ccCCCCCCC
Confidence 999999999999999999998532 23567899999999999999998887665 579999999
Q ss_pred CCcccccccCCChHHHHhhcCCCceeEeeecceEeEEEEEecCCeEEEEecCCCcCCCCcchHHHHHHhhcCCCCCCeEE
Q 003632 431 PIGPMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAVSRLKKPSVRSFVL 510 (806)
Q Consensus 431 Pv~PMLA~~~~~i~~~l~k~~g~~~~~E~KyDG~R~qih~~~~g~V~ifSR~gk~~T~~~Pel~~~l~~~~~~~v~~~IL 510 (806)
|++||||++.+++++++++++ .+|++|+||||+|||+|+. +|+|++|||||+++|+.||++.+.+... ++++|||
T Consensus 183 P~~PMLA~~~~~~~~~~~~~~-~~~~~E~K~DG~R~qih~~-~~~v~l~SR~~~d~T~~fPei~~~~~~~---~~~~~IL 257 (508)
T PRK03180 183 PVRPMLAQTATSVAEALARLG-GPAAVEAKLDGARVQVHRD-GDDVRVYTRTLDDITARLPEVVEAVRAL---PVRSLVL 257 (508)
T ss_pred CCCCccCCcCCChHHHHHHhC-CCeEEEEEEceeEEEEEEE-CCEEEEEeCCCCcchhhhHHHHHHHHhC---CCcceee
Confidence 999999999999988888885 4899999999999999995 7899999999999999999999877653 2478999
Q ss_pred EEEEEEEecCCCccCChHHHHHhhhccCCc--cccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCCCcEEEE
Q 003632 511 DCEIVAYDREKQKILPFQTLSTRARKNVSL--SDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEPGFFQFA 588 (806)
Q Consensus 511 DGElVa~d~~~g~~~pFq~L~~r~rk~~~~--~~~~~~v~~~vFDiLylnG~~L~~~Pl~eRr~~L~~l~~~~~~~i~~~ 588 (806)
|||+|+||+ +|+++|||.+++|.++.... .....+++|++|||||+||+++++.||.+||++|++++.+. ..+
T Consensus 258 DGElv~~d~-~g~~~~F~~l~~R~~~k~~~~~~~~~~pv~~~~FDlL~l~G~dl~~~pl~eRr~~L~~~~~~~----~~~ 332 (508)
T PRK03180 258 DGEAIALRP-DGRPRPFQVTASRFGRRVDVAAARATQPLSPFFFDALHLDGRDLLDAPLSERLAALDALVPAA----HRV 332 (508)
T ss_pred cceEEEECC-CCCcCCHHHHHHHhccccchhhhcccCceEEEEEeehhcCCcchhcCCHHHHHHHHHHhhccc----ccc
Confidence 999999996 57889999999997553322 12357899999999999999999999999999999998642 123
Q ss_pred eEEecCCHHHHHHHHHHHHHcCCceeEEEeCCCCCCccCCCCCCCeEEEccccccccCCcccEEEEEEEeCCCCCCCccc
Q 003632 589 TTLTSIDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLKKDYIESIGDSLDLVPIAAFHGRGKRTGVYG 668 (806)
Q Consensus 589 ~~~~~~~~eei~~~~~~ai~~g~EGlmlK~~~~ds~Y~pGkRs~~WlKlK~dY~~~~~dtlDlvVIGa~~G~Gkr~g~~g 668 (806)
+....++.+++.++|++++++|+||||+|++ +|+|+||+|+.+|+|+|+. +++|+||||+++|+|||+|++|
T Consensus 333 ~~~~~~~~~~~~~~~~~a~~~g~EGlm~K~~--ds~Y~~GrR~~~WlK~K~~------~t~D~VviG~~~G~Gkr~g~~~ 404 (508)
T PRK03180 333 PRLVTADPAAAAAFLAAALAAGHEGVMVKSL--DAPYAAGRRGAGWLKVKPV------HTLDLVVLAAEWGSGRRTGKLS 404 (508)
T ss_pred cceecCCHHHHHHHHHHHHHcCCceEEEeCC--CCCcCCCCCCCCcEEEcCC------CceEEEEEeeecCCCCCCCCcc
Confidence 4556788999999999999999999999999 9999999999999999995 5999999999999999999999
Q ss_pred EEEEEEeeCCCCeEEEeeeccCCCCHHHHHHHHHhhccccCCCCCCCcccCCCCCCcEEecCceEEEEEeceeecCcccc
Q 003632 669 AFLLACYDSNNEEFQSICKIGTGFSEAMLEERSSSLRSKVIPKPRPYYRFADTISPDVWFEPTEVWEVKAADLTISPVHR 748 (806)
Q Consensus 669 sfLla~~d~~~g~~~~v~kVgtGftd~~l~~l~~~l~~~~~~~p~~~~~~~~~~~pdvwieP~~V~EV~~~eit~S~~~~ 748 (806)
+|+|||||+++|+|++||||||||||++++++.+.+.++.+.. ..|++||+|..||||+|++||.||.|+
T Consensus 405 ~~llg~~d~~~~~l~~vgkv~sG~td~~l~~l~~~l~~~~~~~----------~~~~vwv~P~~V~EV~~~~it~S~~~~ 474 (508)
T PRK03180 405 NLHLGARDPATGGFVMLGKTFKGMTDAMLAWQTERFLELAVGR----------DGWTVYVRPELVVEIAFDGVQRSTRYP 474 (508)
T ss_pred ceEEEEEeCCCCeEEEecCccCCCCHHHHHHHHHHHHhhccCC----------CCCCEEeeCCEEEEEEeeEeeeCCccc
Confidence 9999999987799999999999999999999999998775542 268999999999999999999999998
Q ss_pred ccccccCCCCCceeeccEEeEEecCCCccCCCCHHHHHHHHH
Q 003632 749 AAIGVVDPDKGISLRFPRLIRVREDKTPEQASSSEQVAEMYT 790 (806)
Q Consensus 749 a~~g~~~~~~G~sLRFPRf~riR~DK~~~da~t~~el~ely~ 790 (806)
+ |++||||||+|+|+||+|+||+|+++|.+||.
T Consensus 475 ~---------G~~LRfPr~~r~R~DK~~~ea~tl~~~~~l~~ 507 (508)
T PRK03180 475 G---------GVALRFARVLRYRPDKTPAEADTIDTVRALLP 507 (508)
T ss_pred C---------CeEEECCeeeEeeCCCChHHCcCHHHHHHHhc
Confidence 6 79999999999999999999999999999994
No 6
>TIGR00574 dnl1 DNA ligase I, ATP-dependent (dnl1). All proteins in this family with known functions are ATP-dependent DNA ligases. Functions include DNA repair, DNA replication, and DNA recombination (or any process requiring ligation of two single-stranded DNA sections). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=100.00 E-value=3.7e-105 Score=920.13 Aligned_cols=511 Identities=42% Similarity=0.700 Sum_probs=466.5
Q ss_pred ccCCCHHHHHHHHHHHhCCCHHHHHHHHhhcCCHHHHHhhcccccC-ccCCCCCCCHHHHHHHHHHHHHHhCCChHHHHH
Q 003632 250 ELGIGDASIIKALAEACGRTESHVKKQYQEMGDLGLVAKASRSSQS-MMRKPDPLTITKVFDTFRLIAKEAGKDSQEKKK 328 (806)
Q Consensus 250 elgIg~~~L~Kal~~~~g~s~~~ik~~~~~~GDlg~va~~~r~~q~-~l~~~~~LTI~eV~~~L~~IA~~~G~~sq~~k~ 328 (806)
+||||++.|+|++++++|++.+.+++.|.+.||+|+++..++..+. ....+.+|||.+||+.|++||+.+|.+|+++|.
T Consensus 1 ~~gi~~~~l~k~~~~~~~~~~~~~~~~~~~~gd~g~~~~~~~~~~~~~~~~~~~lti~eV~~~L~~ia~~~g~~s~~~k~ 80 (514)
T TIGR00574 1 EYGIGEKLLIKAISKALGIPKDEIEEKVKEDGDLGEVIEGLFSKQKQTSFFSAPLTVKEVYETLKNIAETSGEGSQDKKI 80 (514)
T ss_pred CCCCcHHHHHHHHHHHHCcCHHHHHHHHHhcCCHHHHHHHHhccccccccCCCCcCHHHHHHHHHHHHHhhCCCcHHHHH
Confidence 6999999999999999999999999999999999999988766554 345678999999999999999999999999999
Q ss_pred HHHHHHHHhcCCChHHHHHHHHhhcccCcccHHHHHHHHHhhhcccCCCCCCCCCCcccHHHHHHHHHHHhhcCCchhhh
Q 003632 329 NRIKALLVAATDCEPQYLIRLLQSKLRIGLAEQTLLAALGQAAVYNEQHSKPPPNIQSPLEEAAKIVKQVFSVLPVYEKI 408 (806)
Q Consensus 329 ~~L~~Ll~~~t~~E~k~LiRiIlkdLRiG~~e~til~ala~A~~~~~~~~~~~~~l~~~l~~a~~~~k~~y~~~p~~~~v 408 (806)
.+|..||.+|++.|++||+|+|+++||||+++++|+.|||+||..+ ...+.++|+.|||++.|
T Consensus 81 ~~l~~ll~~~~~~e~k~l~r~i~~~lriG~~~~~il~al~~~~~~~-----------------~~~~~~~~~~~~dl~~v 143 (514)
T TIGR00574 81 KLLKSLLKRASPLEAKYLIRTILGDLRIGIAEKTILDALAKAFLLS-----------------HPDVERAFNLTNDLGKV 143 (514)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHhhhcccCccHHHHHHHHHHHhccc-----------------hHHHHHHHHhCCCHHHH
Confidence 9999999999999999999999999999999999999999998532 13457789999999999
Q ss_pred HhhhhhcCccccCCccccCCCCCCcccccccCCChHHHHhhcCCCceeEeeecceEeEEEEEecCCeEEEEecCCCcCCC
Q 003632 409 VPALLTDGVWNLSNTCSFTPGIPIGPMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTG 488 (806)
Q Consensus 409 ~~~ll~~g~~~l~~~~~l~~g~Pv~PMLA~~~~~i~~~l~k~~g~~~~~E~KyDG~R~qih~~~~g~V~ifSR~gk~~T~ 488 (806)
+..+.++|...+..++.+++|+|++||||++++++.++++++++ +|++|+||||+|||+|+. +|+|++|||||+++|.
T Consensus 144 ~~~l~~~~~~~~~~~~~i~~~~p~~PMLA~~~~~~~~~~~~~~~-~~~~E~K~DG~R~qih~~-~~~v~l~SR~g~~~t~ 221 (514)
T TIGR00574 144 AKILLEPGLRGLDKDLSIQLGIPFKPMLAERAKSIEEALKKKGN-KFYVEYKYDGERVQIHKD-GDKFKIFSRRLENYTY 221 (514)
T ss_pred HHHHHhcChhhhcccceeecCCcCccccCCccCCHHHHHHHhCC-ceEEEEeecceEEEEEEc-CCEEEEEcCCCccccc
Confidence 99999999877767799999999999999999999888888865 899999999999999994 7899999999999999
Q ss_pred CcchH-HHHHHhhcCCCCCCeEEEEEEEEEecCCCccCChHHHHHhhhccC-CccccccceEEEEeeeeecCCccccCCc
Q 003632 489 KFPDV-VLAVSRLKKPSVRSFVLDCEIVAYDREKQKILPFQTLSTRARKNV-SLSDIKVDVCIYAFDILYRNGQPLLQEQ 566 (806)
Q Consensus 489 ~~Pel-~~~l~~~~~~~v~~~ILDGElVa~d~~~g~~~pFq~L~~r~rk~~-~~~~~~~~v~~~vFDiLylnG~~L~~~P 566 (806)
.||++ .+.+...++. ..+||||||||+||+.+|+++||+.+++|.++.. .......++||++|||||+||+++++.|
T Consensus 222 ~~pei~~~~~~~~~~~-~~~~ILDGElv~~d~~~g~~~~F~~l~~r~~~~~~~~~~~~~~~~~~vFDiL~l~g~~l~~~p 300 (514)
T TIGR00574 222 AYPEIFTEFIKEAFPG-IKSCILDGEMVAIDPETGKILPFQTLLRRKRRYDIDSMEKKVPVCLFVFDILYLNGESLIDEP 300 (514)
T ss_pred ccchhHHHHHHHhcCc-cceeeecceEEEEEcCCCCCcCcHhHHhhhhhccccccccccceEEEEEEEEEECCcchhcCc
Confidence 99999 8888876653 5689999999999988888999999999977521 1123357899999999999999999999
Q ss_pred HHHHHHHHHHhhccCCCcEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEEeCCCCCCccCCCCCCCeEEEccccccccC
Q 003632 567 LRVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLKKDYIESIG 646 (806)
Q Consensus 567 l~eRr~~L~~l~~~~~~~i~~~~~~~~~~~eei~~~~~~ai~~g~EGlmlK~~~~ds~Y~pGkRs~~WlKlK~dY~~~~~ 646 (806)
|.||+++|++++.+.++.+++++...+++.+++.++|++++++|+||||+|++ +|+|+||+|+.+|+|+|++|+++++
T Consensus 301 l~eRr~~L~~~~~~~~~~i~~~~~~~~~~~e~~~~~~~~~~~~g~EGlv~K~~--ds~Y~~G~Rs~~WlK~K~~y~~~~~ 378 (514)
T TIGR00574 301 LIERREILESILKPIPNRIEIAEMKITSNVEELEKFLNEAISEGCEGLMLKDL--KSIYEPGKRGWLWLKFKPEYLEGMG 378 (514)
T ss_pred HHHHHHHHHHhccCCCCcEEEEEEEecCCHHHHHHHHHHHHHcCCceEEEecC--CCcccCCCCCCcceeCchhhccccc
Confidence 99999999999998888999999999999999999999999999999999999 9999999999999999999999999
Q ss_pred CcccEEEEEEEeCCCCCCCcccEEEEEEeeCCCCeEEEeeeccCCCCHHHHHHHHHhhccccCCCCCCCcccCCCCCCcE
Q 003632 647 DSLDLVPIAAFHGRGKRTGVYGAFLLACYDSNNEEFQSICKIGTGFSEAMLEERSSSLRSKVIPKPRPYYRFADTISPDV 726 (806)
Q Consensus 647 dtlDlvVIGa~~G~Gkr~g~~gsfLla~~d~~~g~~~~v~kVgtGftd~~l~~l~~~l~~~~~~~p~~~~~~~~~~~pdv 726 (806)
|++|+||||+++|+|+++|++|+|+|||||+++++|++||||||||||+++++|.+.+.++++..+++.+.......|++
T Consensus 379 ~~~D~vvig~~~g~gk~~g~~~~~l~g~~d~~~~~~~~v~kvgsG~sd~~l~~l~~~l~~~~~~~~~~~~~~~~~~~~~~ 458 (514)
T TIGR00574 379 DTLDLVVIGAYYGKGKRTGMYGSFLLACYDPESEEFKTITKVGTGFTDADLQELGKKLPPLWIDPPGSRVPSILSDEPDI 458 (514)
T ss_pred CceeEEEEeeEecCCccCCceeEEEEEEEcCCCCeEEEEEEECCCCCHHHHHHHHHhccCcEecCCCCCCcccccCCCeE
Confidence 99999999999999999999999999999987789999999999999999999999999998875443322111236899
Q ss_pred EecCceEEEEEeceeecCccccccccccCCCCCceeeccEEeEEecCCCccCCCCHHHHHHHHH
Q 003632 727 WFEPTEVWEVKAADLTISPVHRAAIGVVDPDKGISLRFPRLIRVREDKTPEQASSSEQVAEMYT 790 (806)
Q Consensus 727 wieP~~V~EV~~~eit~S~~~~a~~g~~~~~~G~sLRFPRf~riR~DK~~~da~t~~el~ely~ 790 (806)
|++|..||||+|+|+|.||+|+++ |++||||||+++|+||+|+||+|+++|.+||+
T Consensus 459 w~~p~~V~eV~~~e~t~s~~~~~~--------g~~LRfPr~~~~R~DK~~~d~~~~~~~~~ly~ 514 (514)
T TIGR00574 459 WFDPAIVWEVTGAEITRSPTYKAN--------GISLRFPRFSRIRDDKGPEDATTIEEIKELYE 514 (514)
T ss_pred EecCCeEEEEEhhheeecCccccc--------ceEEEcceEEEEcCCCChHHCCCHHHHHHHhC
Confidence 999999999999999999999974 78999999999999999999999999999994
No 7
>KOG0966 consensus ATP-dependent DNA ligase IV [Replication, recombination and repair]
Probab=100.00 E-value=3.7e-91 Score=791.19 Aligned_cols=561 Identities=25% Similarity=0.405 Sum_probs=477.5
Q ss_pred CccchHHHHHHHHHHHhccchHHHHHHHHHHHHhhhcCCCCchHhHHHHHhCCcCCCcccc--ccCCCHHHHHHHHHHHh
Q 003632 189 ERVPFIFLSLVFDMISNETGRILITDIVCNMLRTVMETTPEDLVPVVYLAANKIAPAHEGL--ELGIGDASIIKALAEAC 266 (806)
Q Consensus 189 ~~~~F~~la~~~~~I~~tssr~~k~~iL~~~~r~~i~~~p~dl~~~vyL~~~~l~P~~e~~--elgIg~~~L~Kal~~~~ 266 (806)
+++.|+.++++|+.|..++.-+.|++++..++..+- .|-+....+|.++++++|.+++. .|||++..|++.+++++
T Consensus 3 ~~~~F~~~~~~f~~i~~t~~~~~k~~~~~k~~~s~~--~~~e~~sd~y~~lRL~lp~lDReR~~Yglket~La~l~i~~l 80 (881)
T KOG0966|consen 3 SPQNFSEVVDFFNKIRRTSNVKSKQAKFRKNFESWC--RPCEVGSDMYVALRLILPDLDRERGSYGLKETVLARLYIRAL 80 (881)
T ss_pred CccccchHHHHHHHHHHhhhhHhHHHHHhhcccccc--ccccCCcchhhhhhhcccchhhcccccCchHHHHHHHHHHHh
Confidence 578899999999999999999999999999998863 34334455666667788999654 89999999999999999
Q ss_pred CCCH---HHHHHH-Hh----hcCCHHHHHhhcccccCccCCCCCCCHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHhc
Q 003632 267 GRTE---SHVKKQ-YQ----EMGDLGLVAKASRSSQSMMRKPDPLTITKVFDTFRLIAKEAGKDSQEKKKNRIKALLVAA 338 (806)
Q Consensus 267 g~s~---~~ik~~-~~----~~GDlg~va~~~r~~q~~l~~~~~LTI~eV~~~L~~IA~~~G~~sq~~k~~~L~~Ll~~~ 338 (806)
+++. +.++.. |+ ..||++.+++.+.+.+.....++.|||++||+.||.||.... ...++.+.|..|.++|
T Consensus 81 ~lprds~Da~rL~nwr~~~~~~Gdfs~i~~~vl~~R~~~~~s~alTi~evN~lLD~LA~~~~--~~~~~~~~l~~lv~~~ 158 (881)
T KOG0966|consen 81 HLPRDSADAVRLKNWRASTGARGDFSLILYEVLQRRCENPSSGALTIKEVNDLLDSLASGPS--EDGKKFKKLSQLVEQC 158 (881)
T ss_pred cCCCCcHHHHHHHhhccCCCcCccHHHHHHHHHHHHhcCCCCCceeHHHHHHHHHHHcCCch--hhhhhhHHHHHHHHhC
Confidence 9976 334332 22 348999998876544333223445999999999999985332 2223348899999999
Q ss_pred CCChHHHHHHHHhhcccCcccHHHHHHHHHhhhcccCCCCCCCCCCcccHHHHHHHHHHHhhcCCchhhhHhhhhhcCcc
Q 003632 339 TDCEPQYLIRLLQSKLRIGLAEQTLLAALGQAAVYNEQHSKPPPNIQSPLEEAAKIVKQVFSVLPVYEKIVPALLTDGVW 418 (806)
Q Consensus 339 t~~E~k~LiRiIlkdLRiG~~e~til~ala~A~~~~~~~~~~~~~l~~~l~~a~~~~k~~y~~~p~~~~v~~~ll~~g~~ 418 (806)
++.|+|||+|||+|++.+|+++++|+..||+.| .++|++|.|++.||..|.+....
T Consensus 159 S~~ElkWliriiLK~lklG~se~~Il~vfHPdA------------------------~dl~~vtsDLk~Vc~~L~Dp~~~ 214 (881)
T KOG0966|consen 159 SPLELKWLIRIILKNLKLGASEKKILSVFHPDA------------------------QDLYNVTSDLKAVCKKLYDPSVG 214 (881)
T ss_pred CHHHHHHHHHHHHHhhhcCCccchhhhhcCccH------------------------HHHHHHhhhHHHHHHHhcCCccC
Confidence 999999999999999999999999999998743 25789999999999999875432
Q ss_pred ccCCccccCCCCCCcccccccCCChH-HHHhhcCCCceeEeeecceEeEEEEEecCCeEEEEecCCCcCCCCcch-----
Q 003632 419 NLSNTCSFTPGIPIGPMLAKPTKGVS-EIVNKFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPD----- 492 (806)
Q Consensus 419 ~l~~~~~l~~g~Pv~PMLA~~~~~i~-~~l~k~~g~~~~~E~KyDG~R~qih~~~~g~V~ifSR~gk~~T~~~Pe----- 492 (806)
--.....+.+|..++||||...+... +++++|++.+|++|.|+||+|+|+|++ +|.+++|||||.+||..|..
T Consensus 215 l~~~~~~i~lfsa~~PqLa~~~~~~~~~~~e~m~~~~f~lEtK~DGERiQlHk~-g~~~~yfSRNg~dyT~~yg~s~~~g 293 (881)
T KOG0966|consen 215 LKELDEDIELFSAFRPQLAQKQKLGDWAIIEKMGGQDFYLETKFDGERIQLHKD-GGEYKYFSRNGNDYTYEYGASYAHG 293 (881)
T ss_pred ccccccceeehhhcCHHHHhhhccchHHHHHHhcCCceEEEeeccCceEEEEec-CCEEEEEecCCcchhhhcCcccccc
Confidence 21112358999999999998765443 689999999999999999999999996 78999999999999987732
Q ss_pred -HHHHHHhhcCCCCCCeEEEEEEEEEecCCCccCChHHHHHhhhccCCccccccceEEEEeeeeecCCccccCCcHHHHH
Q 003632 493 -VVLAVSRLKKPSVRSFVLDCEIVAYDREKQKILPFQTLSTRARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRR 571 (806)
Q Consensus 493 -l~~~l~~~~~~~v~~~ILDGElVa~d~~~g~~~pFq~L~~r~rk~~~~~~~~~~v~~~vFDiLylnG~~L~~~Pl~eRr 571 (806)
+...|+.++...+.+||||||||+||+.+.++.||+..+...+.. ..+...++||+|||+||+||++|...||..|+
T Consensus 294 ~lt~~i~~~f~~~v~~cILDGEMm~wD~~~~~f~~~G~~~dik~~~--~~~~~~qp~yvvfDLLylNgksL~~~~l~qR~ 371 (881)
T KOG0966|consen 294 TLTQRIHGAFNKEVESCILDGEMMTWDTKTKRFCPFGSNSDIKELS--SRDGSQQPCYVVFDLLYLNGKSLFGAPLHQRL 371 (881)
T ss_pred cccHHHHhhhhhcchheEecceEEEeecchhhhccCCchhhHHHhh--ccccCCCceEEEeeeeeecCcccCCccHHHHH
Confidence 456788888778999999999999999999999999876433211 11346789999999999999999999999999
Q ss_pred HHHHHhhccCCCcEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEEeCCCCCCccCCCCCCCeEEEccccccccCCcccE
Q 003632 572 EHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLKKDYIESIGDSLDL 651 (806)
Q Consensus 572 ~~L~~l~~~~~~~i~~~~~~~~~~~eei~~~~~~ai~~g~EGlmlK~~~~ds~Y~pGkRs~~WlKlK~dY~~~~~dtlDl 651 (806)
++|..++.+.+++++++.+..+++.++++++|++|+++|.||||+|.+ +|.|.||.|+++|+|+||+|+.|+|+++|+
T Consensus 372 e~L~~v~~p~~~~iei~~~~~~~~~edi~~~f~~ai~~~~EGIVlK~~--~S~Y~pg~R~~gW~K~KPeYlkg~g~dLD~ 449 (881)
T KOG0966|consen 372 EILKKVIVPKSGRIEIVRSEVGSTKEDIEQFFEEAIDNGEEGIVLKKP--DSSYVPGQRSNGWIKLKPEYLKGFGEDLDL 449 (881)
T ss_pred HHHHhcccCCCCeeEEeehhhcccHHHHHHHHHHHHhcCCCceEEecc--CcccCccccCCCcEeecHHHHhhcCccccE
Confidence 999999999999999999999999999999999999999999999999 999999999999999999999999999999
Q ss_pred EEEEEEeCCCCCCCcccEEEEEEeeCC-----CCeEEEeeeccCCCCHHHHHHHHHhhccccCC----CCCCCcccCCCC
Q 003632 652 VPIAAFHGRGKRTGVYGAFLLACYDSN-----NEEFQSICKIGTGFSEAMLEERSSSLRSKVIP----KPRPYYRFADTI 722 (806)
Q Consensus 652 vVIGa~~G~Gkr~g~~gsfLla~~d~~-----~g~~~~v~kVgtGftd~~l~~l~~~l~~~~~~----~p~~~~~~~~~~ 722 (806)
+|||+|||+|+|+|.+.+|+||+.+.. ..+|.++|+||+|+|+.++..+...++++|.+ .||...-+++..
T Consensus 450 lIiGgy~G~g~rgg~~~~fl~a~~ek~~p~~~p~~f~sfcrvg~g~s~~e~~~v~~klr~~w~~~~~~apP~s~l~~tk~ 529 (881)
T KOG0966|consen 450 LIIGGYYGRGDRGGKVLSFLCALAEKAPPNSRPEKFCSFCRVGNGISQKERDTVREKLRGHWKPTSLEAPPESFLFGTKK 529 (881)
T ss_pred EEEecccCCCCCCCeeeeeeehhcccCCCCCccceeeEeeEecCCccHHHHHHHHHhhhhhcccccccCCCHHHHhcccC
Confidence 999999999999999999999997542 24599999999999999999999999998865 333333344444
Q ss_pred CCcEEecCc--eEEEEEeceeecCccccccccccCCCCCceeeccEEeEEecCCCccCCCCHHHHHHHHHH
Q 003632 723 SPDVWFEPT--EVWEVKAADLTISPVHRAAIGVVDPDKGISLRFPRLIRVREDKTPEQASSSEQVAEMYTA 791 (806)
Q Consensus 723 ~pdvwieP~--~V~EV~~~eit~S~~~~a~~g~~~~~~G~sLRFPRf~riR~DK~~~da~t~~el~ely~~ 791 (806)
.||+||+|. .|++|++++++.|..|.+ +++|||||+.++|+||+|+||.|+.++.++...
T Consensus 530 ~Pd~wI~P~~SiIlqikaa~i~~s~~f~t---------n~tLrfPr~ekvR~DK~W~ec~tl~~l~~l~~~ 591 (881)
T KOG0966|consen 530 IPDVWIDPDNSIILQIKAAEIVPSSNFVT---------NYTLRFPRIEKVRLDKPWHECLTLNELGDLVNV 591 (881)
T ss_pred CCceeECCCCceEEEeehheeeecccccc---------cceeecceeeeeecCCcHHHHhhHHHHHHHhcc
Confidence 799999997 799999999999999875 689999999999999999999999999999874
No 8
>COG1793 CDC9 ATP-dependent DNA ligase [DNA replication, recombination, and repair]
Probab=100.00 E-value=1.2e-71 Score=627.62 Aligned_cols=439 Identities=36% Similarity=0.555 Sum_probs=381.5
Q ss_pred HHHHHHhCCCHHHHHHHHhhcCCHHHHHhhcccccCccCCCCCCCHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHhcC
Q 003632 260 KALAEACGRTESHVKKQYQEMGDLGLVAKASRSSQSMMRKPDPLTITKVFDTFRLIAKEAGKDSQEKKKNRIKALLVAAT 339 (806)
Q Consensus 260 Kal~~~~g~s~~~ik~~~~~~GDlg~va~~~r~~q~~l~~~~~LTI~eV~~~L~~IA~~~G~~sq~~k~~~L~~Ll~~~t 339 (806)
+|+....| ...+.+.|...||+|.++..++. +.+|+..|.+++...| |+ .++..|+..++
T Consensus 2 ~av~~~~~--~~~~~~~~~~~Gdlg~~~~~~~~------------v~~v~~~~~~~~~~~g---~~---~~~~~L~~~~~ 61 (444)
T COG1793 2 KAVSEEDG--EYEIFEGYIPQGDLGEGAVLLWD------------VEGVYLTLSKVAERTG---QE---RLLWLLLDEAD 61 (444)
T ss_pred cchhhhcc--chhhhhcccccCccchhheeeee------------cccchhhHHHHHhhcC---ch---hHHHHHHHhcc
Confidence 35566666 66777889999999999876653 8899999999999988 32 78888888888
Q ss_pred CChHHHHHHHHhhcccCcccHHHHHHHHHhhhcccCCCCCCCCCCcccHHHHHHHHHHHhhcCCchhhhHhhhhhcCccc
Q 003632 340 DCEPQYLIRLLQSKLRIGLAEQTLLAALGQAAVYNEQHSKPPPNIQSPLEEAAKIVKQVFSVLPVYEKIVPALLTDGVWN 419 (806)
Q Consensus 340 ~~E~k~LiRiIlkdLRiG~~e~til~ala~A~~~~~~~~~~~~~l~~~l~~a~~~~k~~y~~~p~~~~v~~~ll~~g~~~ 419 (806)
+|++++++++||+.| ++.+|+.++|+..++..++..|...
T Consensus 62 ----------------~gv~~~~~~~ala~~------------------------~~~~~~~~~d~g~~a~~~~~~~~~~ 101 (444)
T COG1793 62 ----------------IGVSEGTVLDALAEA------------------------VERAYLWHNDLGALAKILLTLGAEA 101 (444)
T ss_pred ----------------cchhhHHHHHHHHHH------------------------hhhhhccCCCchhhhhhhhhccccc
Confidence 999999999999875 3567888999999999888888666
Q ss_pred cCCccccCCCCCCcccccccCCChHHHHhhcCCCceeEeeecceEeEEEEEecCCeEEEEecCCCcCCCCcchHHHHHHh
Q 003632 420 LSNTCSFTPGIPIGPMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAVSR 499 (806)
Q Consensus 420 l~~~~~l~~g~Pv~PMLA~~~~~i~~~l~k~~g~~~~~E~KyDG~R~qih~~~~g~V~ifSR~gk~~T~~~Pel~~~l~~ 499 (806)
+ ..+.+.+|.|+.|||+.....+.+...+..+ .|.+|+||||+|+|+|+. +|.|++|||+|+++|++||++.+++..
T Consensus 102 ~-~~~~~~~~~p~~~~la~~~~~~~~~~~~~~~-~w~~E~K~DG~R~q~h~~-~~~vrl~SR~g~d~T~~fP~~~~~~~~ 178 (444)
T COG1793 102 L-DKATLLPGRPLPPMLAPMLASLEEALPRDGG-DWAYEEKFDGYRVQIHID-GGKVRLYSRNGEDWTGRFPDILEAAAE 178 (444)
T ss_pred c-cccccccCCccchhhccccccccccCCCCCC-CEEEEEeeceEEEEEEEc-CCEEEEEeCCCccchhhChHHHHHHHh
Confidence 6 5677899999999999988877666655544 599999999999999995 779999999999999999987766666
Q ss_pred hcCCCCCCeEEEEEEEEEecCCCccCChHHHHHhhhccCC--ccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHh
Q 003632 500 LKKPSVRSFVLDCEIVAYDREKQKILPFQTLSTRARKNVS--LSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDS 577 (806)
Q Consensus 500 ~~~~~v~~~ILDGElVa~d~~~g~~~pFq~L~~r~rk~~~--~~~~~~~v~~~vFDiLylnG~~L~~~Pl~eRr~~L~~l 577 (806)
.+. .+++|||||+|++|+. ...|||.|++|.++... ......+++|++|||||+||++|.++||.|||+.|+++
T Consensus 179 ~l~--~~~~iiDGE~V~~~~~--~~~~F~~Lq~r~~~k~~v~~~~~~~~~~~~aFDlL~~dG~dL~~~pl~eRr~~Le~l 254 (444)
T COG1793 179 ALP--ADDFILDGEIVVLDEE--GRLDFQALQQRLRRKYDVAKLRRETPLVLFAFDLLYLDGEDLRGLPLEERRALLEEL 254 (444)
T ss_pred cCC--CCceEEeeeEEEECCC--CCCCHHHHHHHhhhccchhhhccCCceEEEEEEEEeECCcccccCchHHHHHHHHHH
Confidence 554 3789999999999975 45899999999866533 23346799999999999999999999999999999999
Q ss_pred hccCCCcEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEEeCCCCCCccCCCCCCCeEEEccccccccCCcccEEEEEEE
Q 003632 578 FEEEPGFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLKKDYIESIGDSLDLVPIAAF 657 (806)
Q Consensus 578 ~~~~~~~i~~~~~~~~~~~eei~~~~~~ai~~g~EGlmlK~~~~ds~Y~pGkRs~~WlKlK~dY~~~~~dtlDlvVIGa~ 657 (806)
+... +.+..++.....+.+++..+|+.+++.|+||||+|++ +|+|++|+|+..|+|+|++ +++|+||+|++
T Consensus 255 v~~~-~~~~~~~~i~~~~~~~~~~~~~~a~~~g~EGvv~K~~--ds~Y~~g~R~~~W~K~K~~------~~~d~vv~G~~ 325 (444)
T COG1793 255 VKSS-DKIEIAERIPFSDAEEGEAFLEAAIELGLEGVVAKRP--DSPYRAGGRSNKWLKVKRD------ETLDLVVVGAE 325 (444)
T ss_pred hccc-cccccccceeccChhhHHHHHHHHHhcCceEEEEeCC--CCCcCCCCCCCcceEeccC------CcccEEEEEEE
Confidence 9875 4566666666689999999999999999999999999 9999999999999999996 49999999999
Q ss_pred eCCCCCCCcccEEEEEEeeCCCCeEEEeeeccCCCCHHHHHHHHHhhccccCCCCCCCcccCCCCCCc-EEecCceEEEE
Q 003632 658 HGRGKRTGVYGAFLLACYDSNNEEFQSICKIGTGFSEAMLEERSSSLRSKVIPKPRPYYRFADTISPD-VWFEPTEVWEV 736 (806)
Q Consensus 658 ~G~Gkr~g~~gsfLla~~d~~~g~~~~v~kVgtGftd~~l~~l~~~l~~~~~~~p~~~~~~~~~~~pd-vwieP~~V~EV 736 (806)
+|+|+|+ ++|+|+||+|+++++.|+++|+|||||+++++++|+++++++.+..+... .+. +|++|..|+||
T Consensus 326 ~g~Gkr~-~~~slll~~~~~~~~~~~~v~kVgtGf~~~~l~~l~~~l~~~~~~~~~~~-------~~~~~~~~p~~V~EV 397 (444)
T COG1793 326 YGKGKRS-LYGSLLLGVYDGDGGGLLYVGKVGTGFSDAELEELTERLEPLIVSRFNGK-------VPGKVVPPPGLVAEV 397 (444)
T ss_pred ecCCccc-ccceEEEEEEcCCCceEEEEecccCCCCHHHHHHHHHHHHHhccCcCCCc-------cCceeecCCcEEEEE
Confidence 9999999 89999999999988889999999999999999999999999987642110 111 67777999999
Q ss_pred EeceeecCccccccccccCCCCCceeeccEEeEEecCCCccCCCCHHHHHHHH
Q 003632 737 KAADLTISPVHRAAIGVVDPDKGISLRFPRLIRVREDKTPEQASSSEQVAEMY 789 (806)
Q Consensus 737 ~~~eit~S~~~~a~~g~~~~~~G~sLRFPRf~riR~DK~~~da~t~~el~ely 789 (806)
+|+++|.|+.|+++ .|++||||||.++|.||.+++++|++++.+||
T Consensus 398 ~~~~~t~~~~~r~~-------~~~~lRfpr~~rvr~dk~~~~a~t~~~~~~~~ 443 (444)
T COG1793 398 RFAEITKSGRLRHA-------SGLGLRFPRFVRVRDDKLPEDADTIEEIEALY 443 (444)
T ss_pred EEeecccCCceecc-------cCcccCcCcccccccccCcccccccccchhhc
Confidence 99999999999985 58999999999999999999999999999987
No 9
>PHA02587 30 DNA ligase; Provisional
Probab=100.00 E-value=2.3e-69 Score=617.47 Aligned_cols=448 Identities=20% Similarity=0.236 Sum_probs=352.1
Q ss_pred HHHHHHHHHhccchHHHHHHHHHHHHhhhcCCCCchHhHHHHHhCCcCCCccccccCCCHHHHHHHHHHHhCCCHHHHHH
Q 003632 196 LSLVFDMISNETGRILITDIVCNMLRTVMETTPEDLVPVVYLAANKIAPAHEGLELGIGDASIIKALAEACGRTESHVKK 275 (806)
Q Consensus 196 la~~~~~I~~tssr~~k~~iL~~~~r~~i~~~p~dl~~~vyL~~~~l~P~~e~~elgIg~~~L~Kal~~~~g~s~~~ik~ 275 (806)
+-+++++|++|+|+++|.+||.+.- +-+.|-.+++|+++. ...|||+...
T Consensus 2 i~~il~~~~~~~~~~~k~~il~~~~------~n~~l~~~~~~~~~~------~~~~~~~~~~------------------ 51 (488)
T PHA02587 2 ILDILNELASTDSTKEKEAILKENK------DNELLKEVFRLTYNK------QINFGIKKWP------------------ 51 (488)
T ss_pred hHHHHHHHHhccCcchHHHHHHhcc------cChHHHHHHHHHhCc------ceeEeeeEcC------------------
Confidence 3478999999999999999998542 334455566687773 3467765211
Q ss_pred HHhhcCCHHHHHhhcccccCccCCCCCCCHHH-HHHHHHHHHHHhCCChHHHHHHHHHHHHHhcCCChHHHHHHHHhhcc
Q 003632 276 QYQEMGDLGLVAKASRSSQSMMRKPDPLTITK-VFDTFRLIAKEAGKDSQEKKKNRIKALLVAATDCEPQYLIRLLQSKL 354 (806)
Q Consensus 276 ~~~~~GDlg~va~~~r~~q~~l~~~~~LTI~e-V~~~L~~IA~~~G~~sq~~k~~~L~~Ll~~~t~~E~k~LiRiIlkdL 354 (806)
.-+. ......++++.+ +...+.+||+..-.+.. .+..|..++.+|++.|++||+|+|+++|
T Consensus 52 ------~~~~----------~~~~~~~~~~~~~~~~~~~~l~~r~~~~~~--~~~~l~~ll~~~~~~e~~~l~rli~~~l 113 (488)
T PHA02587 52 ------KPGH----------VEGSDGMLSLEDLLDFLEFDLATRKLTGNA--AIEELAQILSSMNEDDAEVLRRVLMRDL 113 (488)
T ss_pred ------CCcc----------ccCCCCceeHHHHHHHHHHHHHHhhcchhH--HHHHHHHHHHhCCHHHHHHHHHHHhccc
Confidence 0000 001235577888 44456688876655543 5789999999999999999999999999
Q ss_pred cCcccHHHHHHHHHhhhcccCCCCCCCCCCcccHHHHHHHHHHHhhcCCchhhhHhhhhhcCccccCCccccCCCCCCcc
Q 003632 355 RIGLAEQTLLAALGQAAVYNEQHSKPPPNIQSPLEEAAKIVKQVFSVLPVYEKIVPALLTDGVWNLSNTCSFTPGIPIGP 434 (806)
Q Consensus 355 RiG~~e~til~ala~A~~~~~~~~~~~~~l~~~l~~a~~~~k~~y~~~p~~~~v~~~ll~~g~~~l~~~~~l~~g~Pv~P 434 (806)
|||+++++|++||+ .++|++|
T Consensus 114 riGvs~~~i~~~~~-----------------------------------------------------------~~~P~~p 134 (488)
T PHA02587 114 ECGASEKIANKVWK-----------------------------------------------------------GLIPEQP 134 (488)
T ss_pred CCCccHHHHHHHhc-----------------------------------------------------------CCccCCC
Confidence 99999999997651 0478887
Q ss_pred -cccccCCChHHHHhh-cCCCceeEeeecceEeEEEEEecCCeEEEEecCCCcCCCCcchHHHHHHhhcC---CCCCCeE
Q 003632 435 -MLAKPTKGVSEIVNK-FQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAVSRLKK---PSVRSFV 509 (806)
Q Consensus 435 -MLA~~~~~i~~~l~k-~~g~~~~~E~KyDG~R~qih~~~~g~V~ifSR~gk~~T~~~Pel~~~l~~~~~---~~v~~~I 509 (806)
|||++... +++++ +. .+|++|+||||+|||+|++ +|.|++|||+|++++. ||++.+.+.++.. ....++|
T Consensus 135 ~mLA~~~~~--~~~~~~~~-~~~~~E~K~DG~R~q~h~~-~~~v~l~SR~g~~~~~-~p~i~~~l~~~~~~~~~~~~~~V 209 (488)
T PHA02587 135 QMLASSFSE--KLIKKNIK-FPAYAQLKADGARCFADID-ADGIEIRSRNGNEYLG-LDLLKEELKKMTAEARQRPGGVV 209 (488)
T ss_pred CccCCCCCH--HHHHhhcc-CcEEEEEccCceEEEEEEe-CCEEEEEecCCccccC-ChhHHHHHHHHhhhhcccCCcEE
Confidence 99998543 45655 44 3899999999999999996 6899999999999975 7999887776543 1237899
Q ss_pred EEEEEEEEecCCCccCCh-------------HHHHHhhhccCCcc---------ccccceEEEEeeeeecC---CccccC
Q 003632 510 LDCEIVAYDREKQKILPF-------------QTLSTRARKNVSLS---------DIKVDVCIYAFDILYRN---GQPLLQ 564 (806)
Q Consensus 510 LDGElVa~d~~~g~~~pF-------------q~L~~r~rk~~~~~---------~~~~~v~~~vFDiLyln---G~~L~~ 564 (806)
||||+|+||..++.+.+| |.++.|.+++...+ ....+++|+|||||+++ |..+++
T Consensus 210 LDGElv~~~~~~~~~~~~~f~~~~~~~~~f~q~l~~R~~~~~i~~~~l~~~~~~~~~~pv~~~vFDiL~ld~y~~~~~~~ 289 (488)
T PHA02587 210 IDGELVYVEVETKKPNGLSFLFDDSKAKEFVGVVADRATGNGIVNKSLKGTISKEEAQEIVFQVWDIVPLEVYYGKEKSD 289 (488)
T ss_pred EEeEEEEEecccCCCccchhhcccccccchhhhhhhhhhccchhhhhhccccchhhccceEEEEEEeechhhccCCcccc
Confidence 999999998766655555 78888876542111 23578999999999653 444788
Q ss_pred CcHHHHHHHHHHhhcc-CCCcEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEEeCCCCCCccCCCCCCCeEEEcccccc
Q 003632 565 EQLRVRREHLYDSFEE-EPGFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLKKDYIE 643 (806)
Q Consensus 565 ~Pl~eRr~~L~~l~~~-~~~~i~~~~~~~~~~~eei~~~~~~ai~~g~EGlmlK~~~~ds~Y~pGkRs~~WlKlK~dY~~ 643 (806)
.||.+||++|++++.. ..+++++++...+++.+++.++|+++++.|+||||+|++ +|+|++| |+.+|+|+|+.
T Consensus 290 ~pl~eRr~~L~~l~~~~~~~~i~l~~~~~~~~~ee~~~~~~~a~~~G~EGimlK~~--ds~Y~~G-Rs~~WlKiK~~--- 363 (488)
T PHA02587 290 MPYDDRFSKLAQMFEDCGYDRVELIENQVVNNLEEAKEIYKRYVDQGLEGIILKNT--DGLWEDG-RSKDQIKFKEV--- 363 (488)
T ss_pred CCHHHHHHHHHHHHhhcCCCcEEEEeeEEcCCHHHHHHHHHHHHhCCCCeEEEECC--CCCCCCC-CCCCcEEecCC---
Confidence 9999999999999963 356899999888999999999999999999999999999 9999998 88899999985
Q ss_pred ccCCcccEEEEEEEeCCCCCCCcccEEEEEEeeCCCCeEEEeeeccCCCCHHHHHHHHHhhccccCCCCCCCcccCCCCC
Q 003632 644 SIGDSLDLVPIAAFHGRGKRTGVYGAFLLACYDSNNEEFQSICKIGTGFSEAMLEERSSSLRSKVIPKPRPYYRFADTIS 723 (806)
Q Consensus 644 ~~~dtlDlvVIGa~~G~Gkr~g~~gsfLla~~d~~~g~~~~v~kVgtGftd~~l~~l~~~l~~~~~~~p~~~~~~~~~~~ 723 (806)
+++|++|||+++|. +++|.+|+|+|++++ |. .+|+|||||||++++++.+..+ .. ++.......+
T Consensus 364 ---~~~dlvVvG~~~~~-k~~~~~gs~ll~~~~---g~--~~~~vgsGftd~~~~~l~~~~~----~~--p~~~~~~~~r 428 (488)
T PHA02587 364 ---IDIDLEIVGVYEHK-KDPNKVGGFTLESAC---GK--ITVNTGSGLTDTTHRKKDGKKV----VI--PLSERHELDR 428 (488)
T ss_pred ---CceEEEEEeEEeCC-CCCCceeEEEEEecC---Cc--EEEEECCCCChHHhhhhccccc----ee--cccccchhcc
Confidence 48999999999964 678899999998764 44 4699999999999999876643 11 1212222335
Q ss_pred CcEEecCc----eEEEEEeceeecCccccccccccCCCCCceeeccEEeEEecCCCccCCCCHHHHHH
Q 003632 724 PDVWFEPT----EVWEVKAADLTISPVHRAAIGVVDPDKGISLRFPRLIRVREDKTPEQASSSEQVAE 787 (806)
Q Consensus 724 pdvwieP~----~V~EV~~~eit~S~~~~a~~g~~~~~~G~sLRFPRf~riR~DK~~~da~t~~el~e 787 (806)
+.+|.+|. .||||+|++||.||+|++ |++||||||+|+|+||+ +|+|+++|..
T Consensus 429 ~~~~~~~~~~~~~V~EV~~~~it~S~~~~~---------g~sLRfPrf~r~R~DK~--~Adt~~~v~~ 485 (488)
T PHA02587 429 EELMANKGKYIGKIAECECNGLQRSKGRKD---------KVSLFLPIIKRIRIDKT--EANTLEDVFA 485 (488)
T ss_pred hhhhhCcccccceEEEEEeceEEeCCCCCC---------CeeEEccceeEEeCCCC--cccCHHHHhh
Confidence 67787654 799999999999999986 79999999999999999 9999999864
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=4e-62 Score=527.62 Aligned_cols=289 Identities=30% Similarity=0.405 Sum_probs=251.3
Q ss_pred cCCCceeEeeecceEeEEEEEecCCeEEEEecCCCcCCCCcchHHHHHHhhcCCCCCCeEEEEEEEEEecCCCccCChHH
Q 003632 450 FQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAVSRLKKPSVRSFVLDCEIVAYDREKQKILPFQT 529 (806)
Q Consensus 450 ~~g~~~~~E~KyDG~R~qih~~~~g~V~ifSR~gk~~T~~~Pel~~~l~~~~~~~v~~~ILDGElVa~d~~~g~~~pFq~ 529 (806)
+.+.+|++|+||||+|||+|++ +|+|++|||||+++|..||++...+... ...+||||||+|+||.. |+ .+|+.
T Consensus 9 ~~~~~~~~E~K~DG~R~~~~~~-~~~v~l~SR~g~~~t~~~p~l~~~~~~~---~~~~~iLDGElv~~d~~-g~-~~F~~ 82 (298)
T TIGR02779 9 PTGDDWRYEVKYDGYRCLARIE-GGKVRLISRNGHDWTEKFPILAAALAAL---PILPAVLDGEIVVLDES-GR-SDFSA 82 (298)
T ss_pred CCCCCEEEEEEEceEEEEEEEe-CCEEEEEeCCCCchHhHhHHHHHHHHhC---CCCcEEEEeEEEEECCC-CC-CCHHH
Confidence 3566899999999999999996 7899999999999999999998865543 24689999999999964 54 69999
Q ss_pred HHHhhhccCCccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCCCcEEEEeEEecCCHHHHHHHHHHHHHc
Q 003632 530 LSTRARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAAVDA 609 (806)
Q Consensus 530 L~~r~rk~~~~~~~~~~v~~~vFDiLylnG~~L~~~Pl~eRr~~L~~l~~~~~~~i~~~~~~~~~~~eei~~~~~~ai~~ 609 (806)
|++|.+... ..+++|+||||||+||++++++||.+||++|++++.+.++.+.+... ...+.+++.++|++++++
T Consensus 83 l~~r~~~~~-----~~~~~~~vFDiL~l~g~~l~~~pl~eRr~~L~~l~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~ 156 (298)
T TIGR02779 83 LQNRLRAGR-----DRPATYYAFDLLYLDGEDLRDLPLSERKKLLEELLKAIKGPLAPDRY-SVHFEGDGQALLEAACRL 156 (298)
T ss_pred HHhhhhcCC-----CCceEEEEEeeeeECceehhcCCHHHHHHHHHHHhcccCCCceeEec-ccCchhHHHHHHHHHHHc
Confidence 999976532 37899999999999999999999999999999999876555443322 456778999999999999
Q ss_pred CCceeEEEeCCCCCCccCCCCCCCeEEEccccccccCCcccEEEEEEEeCCCCCCCcccEEEEEEeeCCCCeEEEeeecc
Q 003632 610 SCEGLIIKTMDRDATYEPSKRSLNWLKLKKDYIESIGDSLDLVPIAAFHGRGKRTGVYGAFLLACYDSNNEEFQSICKIG 689 (806)
Q Consensus 610 g~EGlmlK~~~~ds~Y~pGkRs~~WlKlK~dY~~~~~dtlDlvVIGa~~G~Gkr~g~~gsfLla~~d~~~g~~~~v~kVg 689 (806)
|+||||+|++ +|+|+||+ +.+|+|+|+.+ +.|++|+|++.|+|++ |.+|+|+||+||+ +.|++||+||
T Consensus 157 g~EGiv~K~~--ds~Y~~Gr-s~~WlK~K~~~------~~d~vV~G~~~g~g~~-~~~gslll~~~~~--~~l~~vg~vg 224 (298)
T TIGR02779 157 GLEGVVAKRR--DSPYRSGR-SADWLKLKCRR------RQEFVIGGYTPPNGSR-SGFGALLLGVYEG--GGLRYVGRVG 224 (298)
T ss_pred CCceEEEeCC--CCCCCCCC-CCCcEEEccCC------CCEEEEEEEECCCCCC-CccceEEEEEECC--CeEEEEeEec
Confidence 9999999999 99999995 99999999975 8999999999999998 7899999999975 5799999999
Q ss_pred CCCCHHHHHHHHHhhccccCCCCCCCcccCCCCCCcEEecCceEEEEEeceeecCccccccccccCCCCCceeeccEEeE
Q 003632 690 TGFSEAMLEERSSSLRSKVIPKPRPYYRFADTISPDVWFEPTEVWEVKAADLTISPVHRAAIGVVDPDKGISLRFPRLIR 769 (806)
Q Consensus 690 tGftd~~l~~l~~~l~~~~~~~p~~~~~~~~~~~pdvwieP~~V~EV~~~eit~S~~~~a~~g~~~~~~G~sLRFPRf~r 769 (806)
||||++++++|++.+.+++++..+++ .....+++||+|.+||||+|.++|. |.+||||||++
T Consensus 225 sG~s~~~~~~l~~~l~~~~~~~~~~~---~~~~~~~~wv~P~lV~eV~~~~~t~---------------~~~lR~P~~~~ 286 (298)
T TIGR02779 225 TGFSEAELATIKERLKPLESKPDKPG---AREKRGVHWVKPELVAEVEFAGWTR---------------DGRLRQASFVG 286 (298)
T ss_pred CCCCHHHHHHHHHHHHhhccCcCCCC---cccCCCCEEeCCeEEEEEEecccCC---------------CCeEeccEEEe
Confidence 99999999999999999876542222 2233688999999999999999985 45999999999
Q ss_pred EecCCCccCCC
Q 003632 770 VREDKTPEQAS 780 (806)
Q Consensus 770 iR~DK~~~da~ 780 (806)
+|+||+|+||+
T Consensus 287 ~R~Dk~~~~~~ 297 (298)
T TIGR02779 287 LREDKPASEVT 297 (298)
T ss_pred eeCCCCHHHcc
Confidence 99999999996
No 11
>PRK09632 ATP-dependent DNA ligase; Reviewed
Probab=100.00 E-value=1.3e-60 Score=561.48 Aligned_cols=307 Identities=27% Similarity=0.381 Sum_probs=264.7
Q ss_pred ccCCCCCCcccccccCCChHHHHhhcCCCceeEeeecceEeEEEEEecCCeEEEEecCCCcCCCCcchHHHHHHhhcCCC
Q 003632 425 SFTPGIPIGPMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAVSRLKKPS 504 (806)
Q Consensus 425 ~l~~g~Pv~PMLA~~~~~i~~~l~k~~g~~~~~E~KyDG~R~qih~~~~g~V~ifSR~gk~~T~~~Pel~~~l~~~~~~~ 504 (806)
...++.||+||||+..... .+.+.+|++|+||||+|||+|+. +|.|++|||||+++|..||++.+.+.. +.
T Consensus 454 ~~~~~~~v~PMLA~~~~~~-----~~~~~~w~~E~K~DG~R~~~~~~-~g~vrL~SRnG~d~T~~fPel~~~~~~-l~-- 524 (764)
T PRK09632 454 KAEEADDLAPMLATAGTVA-----GLKASQWAFEGKWDGYRLLAEAD-HGALRLRSRSGRDVTAEYPELAALAED-LA-- 524 (764)
T ss_pred cCCCCCCCcCccCCcCCCC-----CCCCCCEEEEEEECceeEEEEEe-CCEEEEEeCCCCCccccchhHHHHHhh-CC--
Confidence 3578999999999876421 24567899999999999999995 789999999999999999999885544 43
Q ss_pred CCCeEEEEEEEEEecCCCccCChHHHHHhhhccCCccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCCCc
Q 003632 505 VRSFVLDCEIVAYDREKQKILPFQTLSTRARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEPGF 584 (806)
Q Consensus 505 v~~~ILDGElVa~d~~~g~~~pFq~L~~r~rk~~~~~~~~~~v~~~vFDiLylnG~~L~~~Pl~eRr~~L~~l~~~~~~~ 584 (806)
..+||||||||+||+. |+ .+|+.|++|.+ ..+++|+||||||+||++|+++||.+||++|++++.. .+.
T Consensus 525 ~~~~ILDGEiVvld~~-G~-~~F~~Lq~r~~--------~~~v~y~vFDLL~lnG~dL~~~Pl~eRR~~L~~l~~~-~~~ 593 (764)
T PRK09632 525 DHHVVLDGEIVALDDS-GV-PSFGLLQNRGR--------DTRVEFWAFDLLYLDGRSLLRKPYRDRRKLLEALAPS-GGS 593 (764)
T ss_pred CcceeeeeEEEEeCCC-CC-CCHHHHhhhhh--------cCCeEEEEEeeeccCCcccccCCHHHHHHHHHHhhCC-CCc
Confidence 3689999999999974 54 59999999832 4679999999999999999999999999999999874 456
Q ss_pred EEEEeEEecCCHHHHHHHHHHHHHcCCceeEEEeCCCCCCccCCCCCCCeEEEccccccccCCcccEEEEEEEeCCCCCC
Q 003632 585 FQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLKKDYIESIGDSLDLVPIAAFHGRGKRT 664 (806)
Q Consensus 585 i~~~~~~~~~~~eei~~~~~~ai~~g~EGlmlK~~~~ds~Y~pGkRs~~WlKlK~dY~~~~~dtlDlvVIGa~~G~Gkr~ 664 (806)
+.+++.... ++.++|+.++++|+||||+|++ +|+|++|+||.+|+|+|+.| +.|+||+|+++|+|+|+
T Consensus 594 i~~s~~~~~----~~~~~l~~a~~~GlEGIVaKr~--dS~Y~pGrRs~~WlKiK~~~------~~e~VI~G~~~g~G~r~ 661 (764)
T PRK09632 594 LTVPPLLPG----DGAEALAYSRELGWEGVVAKRR--DSTYQPGRRSSSWIKDKHWR------TQEVVIGGWRPGEGGRS 661 (764)
T ss_pred EEecceecc----cHHHHHHHHHHcCCcEEEEeCC--CCCCCCCCcCCCeEEEecCC------ceEEEEEEEEcCCCCcC
Confidence 777776542 4778999999999999999999 99999999999999999986 89999999999999999
Q ss_pred CcccEEEEEEeeCCCCeEEEeeeccCCCCHHHHHHHHHhhccccCCCCCCCccc-CCCCCCcEEecCceEEEEEeceeec
Q 003632 665 GVYGAFLLACYDSNNEEFQSICKIGTGFSEAMLEERSSSLRSKVIPKPRPYYRF-ADTISPDVWFEPTEVWEVKAADLTI 743 (806)
Q Consensus 665 g~~gsfLla~~d~~~g~~~~v~kVgtGftd~~l~~l~~~l~~~~~~~p~~~~~~-~~~~~pdvwieP~~V~EV~~~eit~ 743 (806)
|.+|+||||+||+ +.|++||+||||||++++++|.++|+++....||..... .....+++||+|.+||||+|+++|.
T Consensus 662 g~~gsLLlGv~d~--~~L~yvGkVGTGftd~~l~~L~~~L~~l~~~~~Pf~~~~~~~~~~~~~WV~P~LV~EV~f~e~T~ 739 (764)
T PRK09632 662 SGIGSLLLGIPDP--GGLRYVGRVGTGFTERELASLKETLAPLHRDTSPFDADLPAADAKGATWVRPELVGEVRYSEWTP 739 (764)
T ss_pred CceeeEEEEEEcC--CeeEEEEEEeCCCCHHHHHHHHHHHHhhccCCCCcccccccccCCCcEEEeccEEEEEEEeeccC
Confidence 9999999999985 569999999999999999999999999877654321111 1234689999999999999999995
Q ss_pred CccccccccccCCCCCceeeccEEeEEecCCCccCCC
Q 003632 744 SPVHRAAIGVVDPDKGISLRFPRLIRVREDKTPEQAS 780 (806)
Q Consensus 744 S~~~~a~~g~~~~~~G~sLRFPRf~riR~DK~~~da~ 780 (806)
+ | .||||||+++|+||+++||+
T Consensus 740 ~--------------g-~LR~P~f~glR~DK~p~dv~ 761 (764)
T PRK09632 740 D--------------G-RLRQPSWRGLRPDKKPGDVV 761 (764)
T ss_pred C--------------C-ceecceEEEeeCCCCHHHcc
Confidence 3 4 99999999999999999986
No 12
>PRK08224 ligC ATP-dependent DNA ligase; Reviewed
Probab=100.00 E-value=3e-59 Score=513.62 Aligned_cols=310 Identities=25% Similarity=0.365 Sum_probs=261.4
Q ss_pred ccCCCCCCcccccccCCChHHHHhhcCCCceeEeeecceEeEEEEEecCCeEEEEecCCCcCCCCcchHHHHHHhhcCCC
Q 003632 425 SFTPGIPIGPMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAVSRLKKPS 504 (806)
Q Consensus 425 ~l~~g~Pv~PMLA~~~~~i~~~l~k~~g~~~~~E~KyDG~R~qih~~~~g~V~ifSR~gk~~T~~~Pel~~~l~~~~~~~ 504 (806)
.++++.|++||||+....++ .+.+|++|+||||+|||+|++ +|+|++|||||+++|..||+|.+++...+.
T Consensus 2 ~~~~~~~i~PMLA~~~~~~~------~~~~w~~E~K~DG~R~~~~~~-~~~v~l~SRng~d~t~~fPel~~~~~~~~~-- 72 (350)
T PRK08224 2 DLPVMPPVEPMLAKSVDAIP------PGDGWSYEPKWDGFRCLVFRD-GDEVELGSRNGKPLTRYFPELVAALRAELP-- 72 (350)
T ss_pred CCCCCCCcCCccCCccCCCC------CCCcEEEEEeECeeEEEEEEE-CCEEEEEeCCCCCchhhhHHHHHHHHhhCC--
Confidence 46789999999998765442 345799999999999999996 789999999999999999999988876643
Q ss_pred CCCeEEEEEEEEEecCCCccCChHHHHHhhhccCC---ccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccC
Q 003632 505 VRSFVLDCEIVAYDREKQKILPFQTLSTRARKNVS---LSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEE 581 (806)
Q Consensus 505 v~~~ILDGElVa~d~~~g~~~pFq~L~~r~rk~~~---~~~~~~~v~~~vFDiLylnG~~L~~~Pl~eRr~~L~~l~~~~ 581 (806)
.++|||||+|++|. +. .+|+.|++|.+.... ......+++|+||||||+||++|++.||.+|+++|++++..
T Consensus 73 -~~~vLDGEiVv~~~--~~-~~F~~Lq~r~~~~~~~~~~~~~~~pv~~~vFDlL~l~G~dl~~~Pl~eRr~~L~~l~~~- 147 (350)
T PRK08224 73 -ERCVLDGEIVVARD--GG-LDFEALQQRIHPAASRVRKLAEETPASFVAFDLLALGDRDLTGRPFAERRAALEAAAAG- 147 (350)
T ss_pred -CCEEEeeEEEEeCC--CC-CCHHHHHhhhhccccchhhhhhcCCEEEEEEeeeeECCcChhhCCHHHHHHHHHHhcCC-
Confidence 68999999999984 22 799999998753311 11225789999999999999999999999999999999865
Q ss_pred CCcEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEEeCCCCCCccCCCCCCCeEEEccccccccCCcccEEEEEEEeCCC
Q 003632 582 PGFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLKKDYIESIGDSLDLVPIAAFHGRG 661 (806)
Q Consensus 582 ~~~i~~~~~~~~~~~eei~~~~~~ai~~g~EGlmlK~~~~ds~Y~pGkRs~~WlKlK~dY~~~~~dtlDlvVIGa~~G~G 661 (806)
.+.+++++. ..+.+++.++|++++++|+||||+|+. +|+|++|+|+ |+|+|+.+ ++|+||+|+++|+|
T Consensus 148 ~~~i~~~~~--~~~~~~~~~~~~~a~~~G~EGIV~Kr~--dS~Y~~Grr~--WlKiK~~~------~~d~vI~G~~~g~~ 215 (350)
T PRK08224 148 SGPVHLTPA--TTDPATARRWFEEFEGAGLDGVIAKPL--DGPYQPGKRA--MFKVKHER------TADCVVAGYRYHKS 215 (350)
T ss_pred CCcEEEecc--cCCHHHHHHHHHHHHhCCCcEEEEeCC--CCCcCCCCcC--EEEEccCC------cEEEEEEEEEcCCC
Confidence 345777764 356789999999999999999999999 9999999987 99999964 89999999999987
Q ss_pred CCCCcccEEEEEEeeCCCCeEEEeeeccCCCCHHHHHHHHHhhccccCCCC--C----CCcccC-------CCCCCcEE-
Q 003632 662 KRTGVYGAFLLACYDSNNEEFQSICKIGTGFSEAMLEERSSSLRSKVIPKP--R----PYYRFA-------DTISPDVW- 727 (806)
Q Consensus 662 kr~g~~gsfLla~~d~~~g~~~~v~kVgtGftd~~l~~l~~~l~~~~~~~p--~----~~~~~~-------~~~~pdvw- 727 (806)
+ |.+|+|+||+||+ +|++++||+|| |||++++++|++.+.++..+.+ | +|.... ......+|
T Consensus 216 ~--~~~gslllg~~d~-~g~l~~vG~v~-Gf~~~~~~~L~~~l~~l~~~~~~~p~~~~pf~~~~~~~~~~~~~~~~~~w~ 291 (350)
T PRK08224 216 G--PVVGSLLLGLYDD-DGQLHHVGVTS-AFPMARRRELTAELEPLRTPFGDHPWNWAAFTGRAPGGPSRWSAGKDLSWV 291 (350)
T ss_pred C--CccccEEEEEECC-CCcEEEEEEEC-CCCHHHHHHHHHHHHhhhcCCCCCccccCcccccCCCccccccccCCcEEE
Confidence 6 7899999999975 47899999985 9999999999999998876544 2 331110 01135689
Q ss_pred -ecCceEEEEEeceeecCccccccccccCCCCCceeecc-EEeEEecCCCccCCC
Q 003632 728 -FEPTEVWEVKAADLTISPVHRAAIGVVDPDKGISLRFP-RLIRVREDKTPEQAS 780 (806)
Q Consensus 728 -ieP~~V~EV~~~eit~S~~~~a~~g~~~~~~G~sLRFP-Rf~riR~DK~~~da~ 780 (806)
++|.+|+||+|.++| . | .||+| +|+++|.||+++||+
T Consensus 292 ~v~P~lv~eV~~~~~t-~--------------~-~lR~p~~f~g~r~Dk~p~~v~ 330 (350)
T PRK08224 292 PLRPERVVEVRYDHME-G--------------G-RFRHTAQFLRWRPDRDPRSCT 330 (350)
T ss_pred eeeEEEEEEEecCccc-C--------------C-eecCCCeeEEEcCCCChHHCC
Confidence 999999999999998 3 5 89998 999999999999998
No 13
>PRK05972 ligD ATP-dependent DNA ligase; Reviewed
Probab=100.00 E-value=4.6e-58 Score=544.38 Aligned_cols=303 Identities=27% Similarity=0.375 Sum_probs=261.0
Q ss_pred CCCcccccccCCChHHHHhhcCCCceeEeeecceEeEEEEEecCCeEEEEecCCCcCCCCcchHHHHHHhhcCCCCCCeE
Q 003632 430 IPIGPMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAVSRLKKPSVRSFV 509 (806)
Q Consensus 430 ~Pv~PMLA~~~~~i~~~l~k~~g~~~~~E~KyDG~R~qih~~~~g~V~ifSR~gk~~T~~~Pel~~~l~~~~~~~v~~~I 509 (806)
..++||||.....++ .+.+|++|+||||+|||+|+. +|.|++|||||+++|.+||+|.+++..+ ++.+||
T Consensus 232 ~~i~PMLAt~~~~~p------~g~~W~~E~K~DG~R~~a~~~-gg~vrL~SRnG~d~T~~fPel~~~~~~l---~~~~~I 301 (860)
T PRK05972 232 DFLAPQLATLVDRPP------SGDGWIYEIKFDGYRILARIE-GGEVRLFTRNGLDWTAKLPALAKAAAAL---GLPDAW 301 (860)
T ss_pred cccCcccCccCCCCC------CcCceEEEeeeCcEEEEEEEE-CCEEEEEeCCCCccccccHHHHHHHHhc---CCCcee
Confidence 358999998766542 356899999999999999995 7899999999999999999999988764 347899
Q ss_pred EEEEEEEEecCCCccCChHHHHHhhhccCCccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCC-CcEEEE
Q 003632 510 LDCEIVAYDREKQKILPFQTLSTRARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEP-GFFQFA 588 (806)
Q Consensus 510 LDGElVa~d~~~g~~~pFq~L~~r~rk~~~~~~~~~~v~~~vFDiLylnG~~L~~~Pl~eRr~~L~~l~~~~~-~~i~~~ 588 (806)
||||+|++|.. |+ .+|+.|++|.+... ..+++|++|||||+||++|+++||.+||++|++++.+.+ +.++++
T Consensus 302 LDGEIVvld~~-G~-~~F~~Lq~r~~~~~-----~~~v~f~vFDLL~l~G~dL~~~PL~eRr~~L~~ll~~~~~~~i~~s 374 (860)
T PRK05972 302 LDGEIVVLDED-GV-PDFQALQNAFDEGR-----TEDLVYFAFDLPFLGGEDLRELPLEERRARLRALLEAARSDRIRFS 374 (860)
T ss_pred EeEEEEEECCC-CC-CCHHHHHHHhhccC-----CCceEEEEEeccccCCcccccCCHHHHHHHHHHHhhhcCCCcEEEe
Confidence 99999999964 54 59999999876432 468999999999999999999999999999999997653 468888
Q ss_pred eEEecCCHHHHHHHHHHHHHcCCceeEEEeCCCCCCccCCCCCCCeEEEccccccccCCcccEEEEEEEeCCCCCCCccc
Q 003632 589 TTLTSIDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLKKDYIESIGDSLDLVPIAAFHGRGKRTGVYG 668 (806)
Q Consensus 589 ~~~~~~~~eei~~~~~~ai~~g~EGlmlK~~~~ds~Y~pGkRs~~WlKlK~dY~~~~~dtlDlvVIGa~~G~Gkr~g~~g 668 (806)
++.. .+..++|+.+++.|+||||+|++ +|+|++| |+.+|+|+|+.+ +.|+||+|++.|+|+|.| +|
T Consensus 375 ~~~~----~~g~~ll~~a~~~GlEGIVaKr~--dS~Y~~G-Rs~~WlKiK~~~------~~E~VIgGy~~~~Gkr~g-~g 440 (860)
T PRK05972 375 EHFD----AGGDAVLASACRLGLEGVIGKRA--DSPYVSG-RSEDWIKLKCRA------RQEFVIGGYTDPKGSRSG-FG 440 (860)
T ss_pred ceec----chHHHHHHHHHHcCCceEEEeCC--CCCCCCC-CCCCcEEEecCC------CceEEEEEEeCCCCcccc-ce
Confidence 7654 34678999999999999999999 9999987 899999999975 678888888888999988 89
Q ss_pred EEEEEEeeCCCCeEEEeeeccCCCCHHHHHHHHHhhccccCCCCCCCcccC-C-CCCCcEEecCceEEEEEeceeecCcc
Q 003632 669 AFLLACYDSNNEEFQSICKIGTGFSEAMLEERSSSLRSKVIPKPRPYYRFA-D-TISPDVWFEPTEVWEVKAADLTISPV 746 (806)
Q Consensus 669 sfLla~~d~~~g~~~~v~kVgtGftd~~l~~l~~~l~~~~~~~p~~~~~~~-~-~~~pdvwieP~~V~EV~~~eit~S~~ 746 (806)
+||||+||+ ++|++||+||||||++++++|.++|.++..+.++ |.... . ...+++||+|.+||||+|++||.+
T Consensus 441 SLLlGvyd~--~~L~yvGkVGTGfsd~~l~~L~~~L~~l~~~~~P-f~~~~~~~~~~~~~WV~P~LV~EV~f~e~T~~-- 515 (860)
T PRK05972 441 SLLLGVHDD--DHLRYAGRVGTGFGAATLKTLLPRLKALATDKSP-FAGKPAPRKARGVHWVKPELVAEVEFAGWTRD-- 515 (860)
T ss_pred eEEEEEecC--CEEEEEEEECCCCCHHHHHHHHHHHHhhccCCCC-ccccCccccCCCCEEEccCEEEEEEEeeccCC--
Confidence 999999986 6999999999999999999999999998776553 42211 1 123579999999999999999965
Q ss_pred ccccccccCCCCCceeeccEEeEEecCCCccCCCC
Q 003632 747 HRAAIGVVDPDKGISLRFPRLIRVREDKTPEQASS 781 (806)
Q Consensus 747 ~~a~~g~~~~~~G~sLRFPRf~riR~DK~~~da~t 781 (806)
| .||||+|+++|+||+++||+-
T Consensus 516 ------------g-~LR~P~F~glR~DK~p~ev~~ 537 (860)
T PRK05972 516 ------------G-IVRQAVFKGLREDKPAREVVA 537 (860)
T ss_pred ------------C-CCccceEEEeecCCChHHhCh
Confidence 5 899999999999999999873
No 14
>PRK09633 ligD ATP-dependent DNA ligase; Reviewed
Probab=100.00 E-value=5.9e-58 Score=532.31 Aligned_cols=303 Identities=19% Similarity=0.277 Sum_probs=255.3
Q ss_pred CcccccccCCChHHHHhhcCCCceeEeeecceEeEEEEEecCCeEEEEecCCCcCCCCcchHHHHHHhhcCC--CCCCeE
Q 003632 432 IGPMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAVSRLKKP--SVRSFV 509 (806)
Q Consensus 432 v~PMLA~~~~~i~~~l~k~~g~~~~~E~KyDG~R~qih~~~~g~V~ifSR~gk~~T~~~Pel~~~l~~~~~~--~v~~~I 509 (806)
++||||.....+ +.+.+|++|+||||+|||+|++ +|.|++|||||+++|.+||+|++++..+... ...+||
T Consensus 1 ~~PMLa~~~~~~------p~g~~w~~E~K~DG~R~~~h~~-~~~V~L~SRng~d~T~~fPel~~~~~~~~~~~~~~~~~I 73 (610)
T PRK09633 1 MKPMQPTLTTSI------PIGDEWRYEVKYDGFRCLLIID-ETGITLISRNGRELTNTFPEIIEFCESNFEHLKEELPLT 73 (610)
T ss_pred CCCCcCCcCCCC------CCCCcEEEEEeEcceEEEEEEE-CCEEEEEeCCCCcchhhhhHHHHHHHhhhhccccCCcee
Confidence 579999877654 3567899999999999999995 7899999999999999999999877665421 124799
Q ss_pred EEEEEEEEecCCCccCChHHHHHhhhccCC--c--cccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCC---
Q 003632 510 LDCEIVAYDREKQKILPFQTLSTRARKNVS--L--SDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEP--- 582 (806)
Q Consensus 510 LDGElVa~d~~~g~~~pFq~L~~r~rk~~~--~--~~~~~~v~~~vFDiLylnG~~L~~~Pl~eRr~~L~~l~~~~~--- 582 (806)
||||+|++|.. |. .+|+.|++|.+.... . .....+++|+||||||+||++|++.||.+||++|++++.+.+
T Consensus 74 LDGEiVvld~~-g~-~~F~~Lq~R~~~~~~~~i~~~~~~~pv~~~vFDlL~lnG~dL~~~PL~eRr~~L~~ll~~~~~~~ 151 (610)
T PRK09633 74 LDGELVCLVNP-YR-SDFEHVQQRGRLKNTEVIAKSANARPCQLLAFDLLELKGESLTSLPYLERKKQLDKLMKAAKLPA 151 (610)
T ss_pred eeeEEEEecCC-CC-CCHHHHHhhhhccccchhhhhhcccceEEEEEeecccCCcccccCCHHHHHHHHHHHhhhccccc
Confidence 99999999854 33 699999999653211 1 123578999999999999999999999999999999997642
Q ss_pred -------CcEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEEeCCCCCCccCCCCCCCeEEEccccccccCCcccEEEEE
Q 003632 583 -------GFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLKKDYIESIGDSLDLVPIA 655 (806)
Q Consensus 583 -------~~i~~~~~~~~~~~eei~~~~~~ai~~g~EGlmlK~~~~ds~Y~pGkRs~~WlKlK~dY~~~~~dtlDlvVIG 655 (806)
..+++ +.+.+++.++|+.+++.|+||||+|++ +|+|++|+||.+|+|+|+. ++.|+||+|
T Consensus 152 ~~~~~~~~~i~~-----~~~~~~~~~l~~~a~~~g~EGIV~Kr~--dS~Y~~G~Rs~~WlKiK~~------~~~d~vI~G 218 (610)
T PRK09633 152 SPDPYAKARIQY-----IPSTTDFDALWEAVKRYDGEGIVAKKK--TSKWLENKRSKDWLKIKNW------RYVHVIVTG 218 (610)
T ss_pred ccccccccceEE-----cCCHHHHHHHHHHHHHcCCceEEEeCC--CCCCCCCCCCCCeEEEecc------CCceeEEEE
Confidence 13333 346778999999999999999999999 9999999999999999995 389999999
Q ss_pred EEeCCCCCCCcccEEEEEEeeCCCCeEEEeeeccCCCCHHHHHHHHHhhccccCCCCCCCcccCCCCCCcEEecCceEEE
Q 003632 656 AFHGRGKRTGVYGAFLLACYDSNNEEFQSICKIGTGFSEAMLEERSSSLRSKVIPKPRPYYRFADTISPDVWFEPTEVWE 735 (806)
Q Consensus 656 a~~G~Gkr~g~~gsfLla~~d~~~g~~~~v~kVgtGftd~~l~~l~~~l~~~~~~~p~~~~~~~~~~~pdvwieP~~V~E 735 (806)
+..|+ |.|++|+|+ +|+|++||+||||||++++++|++.|+++.+... .+.+|++|.+|||
T Consensus 219 ~~~~~-------g~~llgv~~--~g~l~~vGkvgtGft~~~~~~L~~~l~~l~~~~~----------~~~~wV~P~LV~E 279 (610)
T PRK09633 219 YDPSN-------GYFTGSVYK--DGQLTEVGSVKHGMEDEERQTLRAIFKQNGTKTK----------SGEYTLEPSICVT 279 (610)
T ss_pred EecCC-------ceEEEEEec--CCeEEEEEEecCCCCHHHHHHHHHHHHHhccCCC----------CCcEEEeeeEEEE
Confidence 87654 368899995 4899999999999999999999999988765431 4679999999999
Q ss_pred EEeceeecCccccccccccCCCCCceeeccEEeEEecCCCccCCCCHHHHHHHHHH
Q 003632 736 VKAADLTISPVHRAAIGVVDPDKGISLRFPRLIRVREDKTPEQASSSEQVAEMYTA 791 (806)
Q Consensus 736 V~~~eit~S~~~~a~~g~~~~~~G~sLRFPRf~riR~DK~~~da~t~~el~ely~~ 791 (806)
|+|++|| |..||||+|+++|+||+++||++.+++.++|..
T Consensus 280 V~~~e~t----------------~g~LR~P~f~glR~DK~~~ev~~~~~~~~~~~~ 319 (610)
T PRK09633 280 VACITFD----------------GGTLREPSFVSFLFDMDPTECTYQQLQRQLAPL 319 (610)
T ss_pred EEEeecC----------------CCeEEeeEEeEEEcCCChHHcchhhhhhhhccC
Confidence 9999996 348999999999999999999999888877754
No 15
>PRK07636 ligB ATP-dependent DNA ligase; Reviewed
Probab=100.00 E-value=2.3e-52 Score=446.52 Aligned_cols=272 Identities=25% Similarity=0.362 Sum_probs=228.0
Q ss_pred CcccccccCCChHHHHhhcCCCceeEeeecceEeEEEEEecCCeEEEEecCCCcCCCCcchHHHHHHhhcCCCCCCeEEE
Q 003632 432 IGPMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAVSRLKKPSVRSFVLD 511 (806)
Q Consensus 432 v~PMLA~~~~~i~~~l~k~~g~~~~~E~KyDG~R~qih~~~~g~V~ifSR~gk~~T~~~Pel~~~l~~~~~~~v~~~ILD 511 (806)
++||||...... +.+.+|++|+||||+|||+|+. +|+|++|||+|+++|..||++.+.. ++ ++||||
T Consensus 3 ~~PmLa~~~~~~------~~~~~~~~E~K~DG~R~~~~~~-~~~v~l~SR~g~~~t~~fPe~~~~~---~~---~~~vLD 69 (275)
T PRK07636 3 ISPMLLESAKEP------FNSENYITEPKFDGIRLIASKN-NGLIRLYTRHNNEVTAKFPELLNLD---IP---DGTVLD 69 (275)
T ss_pred cCCccCCcCCCC------CCCCcEEEEEEEceeEEEEEEe-CCEEEEEeCCCCCchhhhhhHHhhh---cC---CCEEEE
Confidence 689999876532 4566899999999999999995 7899999999999999999997642 32 579999
Q ss_pred EEEEEEecCCCccCChHHHHHhhhccCCccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCCCcEEEEeEE
Q 003632 512 CEIVAYDREKQKILPFQTLSTRARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEPGFFQFATTL 591 (806)
Q Consensus 512 GElVa~d~~~g~~~pFq~L~~r~rk~~~~~~~~~~v~~~vFDiLylnG~~L~~~Pl~eRr~~L~~l~~~~~~~i~~~~~~ 591 (806)
||+|++|.. |+ .+|+.+++|.+.... ....+++|+||||||+||++++++||.+|+++|++++.+.+ .+++++..
T Consensus 70 GElv~~d~~-g~-~~F~~l~~r~~~~~~--~~~~~~~~~vFDlL~~~g~~l~~~pl~eRr~~L~~~~~~~~-~~~~~~~~ 144 (275)
T PRK07636 70 GELIVLGST-GA-PDFEAVMERFQSKKS--TKIHPVVFCVFDVLYINGVSLTALPLSERKEILASLLLPHP-NVKIIEGI 144 (275)
T ss_pred eEEEEECCC-CC-CCHHHHHHHhccccc--cccCceEEEEEEeEEECceehhhCCHHHHHHHHHHhcCCCC-CEEEcccc
Confidence 999999964 54 589999998764321 22578999999999999999999999999999999997644 46666543
Q ss_pred ecCCHHHHHHHHHHHHHcCCceeEEEeCCCCCCccCCCCCCCeEEEccccccccCCcccEEEEEEEeCCCCCCCcccEEE
Q 003632 592 TSIDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLKKDYIESIGDSLDLVPIAAFHGRGKRTGVYGAFL 671 (806)
Q Consensus 592 ~~~~~eei~~~~~~ai~~g~EGlmlK~~~~ds~Y~pGkRs~~WlKlK~dY~~~~~dtlDlvVIGa~~G~Gkr~g~~gsfL 671 (806)
. +++.++|+.++++|.||||+|++ +|+|.+|+||.+|+|+|+ | +++|+||+|+..| .+|.+
T Consensus 145 ~----~~~~~~~~~~~~~g~EGiV~K~~--ds~Y~~g~Rs~~WlKiK~-~-----~~~e~vV~G~~~~------~~g~l- 205 (275)
T PRK07636 145 E----GHGTAYFELVEERELEGIVIKKA--NSPYEINKRSDNWLKVIN-Y-----QYTDVLITGYRKE------EFGLL- 205 (275)
T ss_pred c----ccHHHHHHHHHHcCCcEEEEeCC--CCCCCCCCCCCCeEEEec-C-----CeEEEEEEEEecC------CCcEE-
Confidence 2 46788999999999999999999 999999999999999997 3 6899999988543 25655
Q ss_pred EEEeeCCCCeEEEeeeccCCCCHHHHHHHHHhhccccCCCCCCCcccCCCCCCcEEecCceEEEEEeceeecCccccccc
Q 003632 672 LACYDSNNEEFQSICKIGTGFSEAMLEERSSSLRSKVIPKPRPYYRFADTISPDVWFEPTEVWEVKAADLTISPVHRAAI 751 (806)
Q Consensus 672 la~~d~~~g~~~~v~kVgtGftd~~l~~l~~~l~~~~~~~p~~~~~~~~~~~pdvwieP~~V~EV~~~eit~S~~~~a~~ 751 (806)
||+|+ |. ++|+||| |+++++++|.+.+.++.... ..+.+|++|.+|+||+|+|+|.+
T Consensus 206 lg~~~---g~--~~G~vgt-~~~~~~~~l~~~l~~~~~~~----------~~~~~wv~P~lv~eV~~~e~t~~------- 262 (275)
T PRK07636 206 LSYLD---GR--SAGIMEF-MPYDARKKFYKRAKRLVVGE----------DKKFVYIEPIIGCRVKHRFKTKN------- 262 (275)
T ss_pred EEecC---Ce--EEEEECC-CCHHHHHHHHHHhhhhccCc----------cCCCEEeCCcEEEEEEEEEecCC-------
Confidence 79886 44 7799999 99999999999887664432 25789999999999999999965
Q ss_pred cccCCCCCceeeccEEeEEe
Q 003632 752 GVVDPDKGISLRFPRLIRVR 771 (806)
Q Consensus 752 g~~~~~~G~sLRFPRf~riR 771 (806)
|. ||||+|+++|
T Consensus 263 -------g~-lR~p~f~g~r 274 (275)
T PRK07636 263 -------GM-LRIPSFVEWR 274 (275)
T ss_pred -------CC-EEccEEEEEe
Confidence 64 9999999998
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=4e-51 Score=423.74 Aligned_cols=217 Identities=67% Similarity=1.102 Sum_probs=200.9
Q ss_pred ccccCCCCCCcccccccCCChHHHHhhcCCCceeEeeecceEeEEEEEecCCeEEEEecCCCcCCCCcchHHHHHHhhcC
Q 003632 423 TCSFTPGIPIGPMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAVSRLKK 502 (806)
Q Consensus 423 ~~~l~~g~Pv~PMLA~~~~~i~~~l~k~~g~~~~~E~KyDG~R~qih~~~~g~V~ifSR~gk~~T~~~Pel~~~l~~~~~ 502 (806)
++.+++|+||+||||+++.+++++++++++.+|++|+||||+|||+|+..+|.|++|||||+++|..||++.+.+...+.
T Consensus 1 ~~~~~~~~pi~PMLA~~~~~~~~~~~~~~~~~~~~E~K~DG~R~~~h~~~~~~v~l~SR~g~~~t~~~pel~~~~~~~~~ 80 (219)
T cd07900 1 HCKLTPGIPVKPMLAKPTKGVSEVLDRFEDKEFTCEYKYDGERAQIHLLEDGKVKIFSRNLENNTEKYPDIVAVLPKSLK 80 (219)
T ss_pred CceeecCCccccccCCccCCHHHHHHHhCCCeEEEEEeecceEEEEEEcCCCeEEEECCCCccccchhhHHHHHHHHHhc
Confidence 36789999999999999999999999998889999999999999999975589999999999999999999999988875
Q ss_pred CCCCCeEEEEEEEEEecCCCccCChHHHHHhhhccCCccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCC
Q 003632 503 PSVRSFVLDCEIVAYDREKQKILPFQTLSTRARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEP 582 (806)
Q Consensus 503 ~~v~~~ILDGElVa~d~~~g~~~pFq~L~~r~rk~~~~~~~~~~v~~~vFDiLylnG~~L~~~Pl~eRr~~L~~l~~~~~ 582 (806)
++..+||||||||+||..+|...+|+.+++|.+++........+++|++|||||+||++|++.||.+||++|++++.+.+
T Consensus 81 ~~~~~~iLDGElv~~~~~~g~~~~F~~l~~r~~~~~~~~~~~~~~~~~vFDiL~l~g~~l~~~pl~eRr~~L~~~~~~~~ 160 (219)
T cd07900 81 PSVKSFILDSEIVAYDRETGKILPFQVLSTRKRKDVDANDIKVQVCVFAFDLLYLNGESLLKKPLRERRELLHSLFKEVP 160 (219)
T ss_pred ccCccEEEeeEEEEEEcCCCCCcChHHHhhhcccccccccCcccEEEEEEEEEEECCchhhcCCHHHHHHHHHHhcCCCC
Confidence 55689999999999998778888999999998766544445689999999999999999999999999999999998888
Q ss_pred CcEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEEeCCCC--CCccCCCCCCCeEEEcccc
Q 003632 583 GFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTMDRD--ATYEPSKRSLNWLKLKKDY 641 (806)
Q Consensus 583 ~~i~~~~~~~~~~~eei~~~~~~ai~~g~EGlmlK~~~~d--s~Y~pGkRs~~WlKlK~dY 641 (806)
+++.+++...+++.++++++|++++++|+||||+|++ + |+|+||+|+.+|+|+|+||
T Consensus 161 ~~~~~~~~~~~~~~~~~~~~~~~~~~~g~EGiv~K~~--~~~s~Y~~g~Rs~~W~K~K~dY 219 (219)
T cd07900 161 GRFQFATSKDSEDTEEIQEFLEEAVKNNCEGLMVKTL--DSDATYEPSKRSHNWLKLKKDY 219 (219)
T ss_pred CeEEEEEEEecCCHHHHHHHHHHHHHcCCceEEEecC--CCCCccCCCCcCCCceEeCCCC
Confidence 8999999999999999999999999999999999999 8 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=2.5e-49 Score=455.68 Aligned_cols=257 Identities=25% Similarity=0.393 Sum_probs=218.3
Q ss_pred ecCCCcCCCCcchHHHHHHhhcCCCCCCeEEEEEEEEEecCCCccCChHHHHHhhhccCCccccccceEEEEeeeeecCC
Q 003632 480 SRNAERNTGKFPDVVLAVSRLKKPSVRSFVLDCEIVAYDREKQKILPFQTLSTRARKNVSLSDIKVDVCIYAFDILYRNG 559 (806)
Q Consensus 480 SR~gk~~T~~~Pel~~~l~~~~~~~v~~~ILDGElVa~d~~~g~~~pFq~L~~r~rk~~~~~~~~~~v~~~vFDiLylnG 559 (806)
||||+++|.+||+|++++..+ .+.+||||||+|++|. +|+ .+|+.|+++.+.. ...++||+||||||+||
T Consensus 1 SRng~d~T~~fPel~~~~~~l---~~~~~ILDGElVvld~-~G~-~~F~~Lq~~~~~~-----~~~pv~~~vFDlL~l~G 70 (552)
T TIGR02776 1 TRNGHDWTKRFPEIVKALALL---KLLPAWIDGEIVVLDE-RGR-ADFAALQNALSAG-----ASRPLTYYAFDLLFLSG 70 (552)
T ss_pred CCCcCcchhhhHHHHHHHhhC---CCCCEEEEEEEEEECC-CCC-CCHHHHHHHHHhc-----ccCceEEEEEeccccCC
Confidence 899999999999999988743 3478999999999996 354 5799999986532 24789999999999999
Q ss_pred ccccCCcHHHHHHHHHHhhccCC-CcEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEEeCCCCCCccCCCCCCCeEEEc
Q 003632 560 QPLLQEQLRVRREHLYDSFEEEP-GFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLK 638 (806)
Q Consensus 560 ~~L~~~Pl~eRr~~L~~l~~~~~-~~i~~~~~~~~~~~eei~~~~~~ai~~g~EGlmlK~~~~ds~Y~pGkRs~~WlKlK 638 (806)
++++++||.+||++|++++.+.. +.++++++. . ++..++|++++++|+||||+|++ +|+|++| ||.+|+|+|
T Consensus 71 ~dL~~~Pl~eRr~~L~~ll~~~~~~~i~~~~~~-~---~~~~~~~~~a~~~G~EGIV~K~~--dS~Y~~G-Rs~~WlKlK 143 (552)
T TIGR02776 71 EDLRDLPLEERKKRLKQLLKAQDEPAIRYSDHF-E---SDGDALLESACRLGLEGVVSKRL--DSPYRSG-RSKDWLKLK 143 (552)
T ss_pred cccccCCHHHHHHHHHHHhhhcCCCcEEEeeee-c---ccHHHHHHHHHHCCCceEEEeCC--CCCCCCC-CCcchhccc
Confidence 99999999999999999998753 357777663 2 33459999999999999999999 9999999 999999999
Q ss_pred cccccccCCcccEEEEEEEeCCCCCCCcccEEEEEEeeCCCCeEEEeeeccCCCCHHHHHHHHHhhccccCCCCCCCccc
Q 003632 639 KDYIESIGDSLDLVPIAAFHGRGKRTGVYGAFLLACYDSNNEEFQSICKIGTGFSEAMLEERSSSLRSKVIPKPRPYYRF 718 (806)
Q Consensus 639 ~dY~~~~~dtlDlvVIGa~~G~Gkr~g~~gsfLla~~d~~~g~~~~v~kVgtGftd~~l~~l~~~l~~~~~~~p~~~~~~ 718 (806)
++| +.|++|+|++.|.| .+|+|+||+|| +|+|+++|+||||||++++++|++.+++++...++ |...
T Consensus 144 ~~~------~~e~vI~Gy~~~~r----~~gslLlg~~d--~g~l~~vgkVgsGfsd~~~~~L~~~l~~~~~~~~P-f~~~ 210 (552)
T TIGR02776 144 CRR------RQEFVITGYTPPNR----RFGALLVGVYE--GGQLVYAGKVGTGFGADTLKTLLARLKALGAKASP-FSGP 210 (552)
T ss_pred ccc------cceEEEEEEecCCC----ceeeEEEEEec--CCeEEEEEEEcCCCCHHHHHHHHHHHHhhcccCCC-ccCC
Confidence 976 77888888776652 29999999997 48999999999999999999999999998876543 3221
Q ss_pred -CCCCCCcEEecCceEEEEEeceeecCccccccccccCCCCCceeeccEEeEEecCCCccCCCC
Q 003632 719 -ADTISPDVWFEPTEVWEVKAADLTISPVHRAAIGVVDPDKGISLRFPRLIRVREDKTPEQASS 781 (806)
Q Consensus 719 -~~~~~pdvwieP~~V~EV~~~eit~S~~~~a~~g~~~~~~G~sLRFPRf~riR~DK~~~da~t 781 (806)
.....+++||+|.+||||+|++||. |.+||||||+++|+||+|+||+.
T Consensus 211 ~~~~~~~~~Wv~P~lV~EV~~~e~T~---------------~g~LR~Prf~~~R~DK~~~e~t~ 259 (552)
T TIGR02776 211 AGAKTRGVHWVRPSLVAEVEYAGITR---------------DGILREASFKGLREDKPAEEVTL 259 (552)
T ss_pred ccccCCCcEEEccCEEEEEEeeeccC---------------CCeeEccEEEEEeCCCCHHHcch
Confidence 1123579999999999999999995 35999999999999999999974
No 18
>PHA00454 ATP-dependent DNA ligase
Probab=100.00 E-value=1.1e-46 Score=410.08 Aligned_cols=284 Identities=20% Similarity=0.247 Sum_probs=227.2
Q ss_pred cccccccCCC--hHHHHhhcCCCceeEeeecceEeEEEEEecCCeEEEEecCCCcCCCCcchHHHHH------HhhcCC-
Q 003632 433 GPMLAKPTKG--VSEIVNKFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAV------SRLKKP- 503 (806)
Q Consensus 433 ~PMLA~~~~~--i~~~l~k~~g~~~~~E~KyDG~R~qih~~~~g~V~ifSR~gk~~T~~~Pel~~~l------~~~~~~- 503 (806)
+||+|..... +++++++++ .|++|+||||+|||+|+++++.|++|||||+. ||++.... .+++..
T Consensus 7 ~~~~~~~~~~~~i~~~~~~~g--~~~~E~K~DG~R~~~~~~~~~~v~l~SR~g~~----~p~l~~~~~~~~~~~~~~~~~ 80 (315)
T PHA00454 7 NPFRAVDFNESAIEKALEKAG--YLIADVKYDGVRGNIVVDNTADHGWLSREGKT----IPALEHLNGFDRRWAKLLNDD 80 (315)
T ss_pred CccccccCCHHHHHHHHHhCC--cEEEEEccceEEEEEEEcCCCeEEEEeCCCCc----ccchhhhhhhhhhhhhhhhhh
Confidence 5888877654 889998874 89999999999999999643459999999985 67665432 222221
Q ss_pred ---CCCCeEEEEEEEEEecCCCccCChHHHHHhhhccCC--ccccccceEEEEeeeeecC----Cccc---cCCcHHHHH
Q 003632 504 ---SVRSFVLDCEIVAYDREKQKILPFQTLSTRARKNVS--LSDIKVDVCIYAFDILYRN----GQPL---LQEQLRVRR 571 (806)
Q Consensus 504 ---~v~~~ILDGElVa~d~~~g~~~pFq~L~~r~rk~~~--~~~~~~~v~~~vFDiLyln----G~~L---~~~Pl~eRr 571 (806)
..+++|||||+|+.+ .+|+.+++|.++... ......+++|+|||||++| |+++ ...||.+|+
T Consensus 81 ~~~l~~~~vLDGElv~~~------~~f~~~~~~l~~k~~~~~~~~~~~v~~~vFDll~l~~~~~g~~l~~l~~~pl~~Rr 154 (315)
T PHA00454 81 RCIFPDGFMLDGELMVKG------VDFNTGSGLLRRKWKVLFELHLKKLHVVVYDVTPLDVLESGEDYDVMSLLMYEHVR 154 (315)
T ss_pred hhcCCCCeEEEEEEEecC------CCHHHHHHHhccCccchhhhccCceEEEEEEeeEeccccCCccccccccccHHHHH
Confidence 115899999999974 589999999764321 1223578999999999999 5554 689999999
Q ss_pred HHHHHhhccCCC-cEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEEeCCCCCCccCCCCCCCeEEEccccccccCCccc
Q 003632 572 EHLYDSFEEEPG-FFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLKKDYIESIGDSLD 650 (806)
Q Consensus 572 ~~L~~l~~~~~~-~i~~~~~~~~~~~eei~~~~~~ai~~g~EGlmlK~~~~ds~Y~pGkRs~~WlKlK~dY~~~~~dtlD 650 (806)
++|++++...+. .++++++..+.+.+++.++|+++++.|+||||+|++ +|+|++|+|+. |+|+|+.+ ++|
T Consensus 155 ~~L~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~EGiv~K~~--ds~Y~~Grr~~-~~K~K~~~------~~d 225 (315)
T PHA00454 155 AMVPLLMEYFPEIDWFLSESYEVYDMESLQELYEKKRAEGHEGLVVKDP--SLIYRRGKKSG-WWKMKPEC------EAD 225 (315)
T ss_pred HHHHHHHhhCCCcceEeeceEEcCCHHHHHHHHHHHHhCCCceEEEeCC--CCCCCCCCccC-cEEEcccC------cee
Confidence 999999876554 488999999999999999999999999999999999 99999998875 88999964 999
Q ss_pred EEEEEEEeCCCCC--CCcccEEEEEEeeCCCCeEEEeeeccCCCCHHHHHHHHHhhccccCCCCCCCcccCCCCCCcEEe
Q 003632 651 LVPIAAFHGRGKR--TGVYGAFLLACYDSNNEEFQSICKIGTGFSEAMLEERSSSLRSKVIPKPRPYYRFADTISPDVWF 728 (806)
Q Consensus 651 lvVIGa~~G~Gkr--~g~~gsfLla~~d~~~g~~~~v~kVgtGftd~~l~~l~~~l~~~~~~~p~~~~~~~~~~~pdvwi 728 (806)
+||||+++|+|++ .|.+++|+|++. +|.++. |||||++++++|++.+.++....+ ...
T Consensus 226 ~vIvG~~~g~g~~~~~g~~~~~~~~~~---~g~l~~----gtGfs~~~~~~l~~~l~~~~~~~~-------------~~p 285 (315)
T PHA00454 226 GTIVGVVWGTPGLANEGKVIGFRVLLE---DGRVVN----ATGISRALMEEFTANVKEHGEDYE-------------AMP 285 (315)
T ss_pred EEEEEEEECCCCccCCceEEEEEEEeC---CCcEEE----ccCCCHHHHHHHHHHHHhhccCcc-------------ccC
Confidence 9999999998643 478888888652 366653 899999999999999987643321 001
Q ss_pred cCceEEEEEeceeecCccccccccccCCCCCceeeccEEeEEec
Q 003632 729 EPTEVWEVKAADLTISPVHRAAIGVVDPDKGISLRFPRLIRVRE 772 (806)
Q Consensus 729 eP~~V~EV~~~eit~S~~~~a~~g~~~~~~G~sLRFPRf~riR~ 772 (806)
.|..|+||+|.++|.+ | .||||+|+++|+
T Consensus 286 ~~~~v~eV~y~e~T~~--------------g-~lR~P~F~g~Rd 314 (315)
T PHA00454 286 YNGRACQVSYMERTPD--------------G-SLRHPSFDRFRD 314 (315)
T ss_pred CCCeEEEEEEEEcCCC--------------C-cccCceeeeeec
Confidence 2456999999999953 5 999999999995
No 19
>PRK09125 DNA ligase; Provisional
Probab=100.00 E-value=9.3e-47 Score=404.37 Aligned_cols=254 Identities=30% Similarity=0.386 Sum_probs=210.0
Q ss_pred CcccccccCCChHHHHhhcCCCceeEeeecceEeEEEEEecCCeEEEEecCCCcCCCCcchHHHHHHhhcCCCCCCeEEE
Q 003632 432 IGPMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAVSRLKKPSVRSFVLD 511 (806)
Q Consensus 432 v~PMLA~~~~~i~~~l~k~~g~~~~~E~KyDG~R~qih~~~~g~V~ifSR~gk~~T~~~Pel~~~l~~~~~~~v~~~ILD 511 (806)
+.||||..... .+++.+|++|+||||+|||+ + .+++|||+|+++|. |+.. ... ..++|||
T Consensus 28 ~~~~LA~~~~~------~~~~~~~~~E~K~DG~R~~~----~-~v~l~SR~g~~it~--p~~~---~~~----~~~~vLD 87 (282)
T PRK09125 28 PDLQLATVYDK------GQDISGYLVSEKLDGVRAYW----D-GKQLLTRQGNPIAA--PAWF---TAG----FPPFPLD 87 (282)
T ss_pred CCceechhccc------CCChhhEEEEeeeeeEeEEE----C-CeEEEcCCCCcCCC--chhH---Hhc----CCCccEe
Confidence 46999987642 13445899999999999974 2 38999999999998 5532 222 2489999
Q ss_pred EEEEEEecCCCccCChHHHHHhhhccCCccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccC-CCcEEEEeE
Q 003632 512 CEIVAYDREKQKILPFQTLSTRARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEE-PGFFQFATT 590 (806)
Q Consensus 512 GElVa~d~~~g~~~pFq~L~~r~rk~~~~~~~~~~v~~~vFDiLylnG~~L~~~Pl~eRr~~L~~l~~~~-~~~i~~~~~ 590 (806)
||+|+++ .+|+.+++|.++.........+++|++||||++|| ||.+|+++|++++.+. .+.+++++.
T Consensus 88 GElv~~~------~~F~~l~~r~~~k~~~~~~~~~v~~~vFDll~~~g------pl~eRr~~L~~li~~~~~~~i~~~~~ 155 (282)
T PRK09125 88 GELWAGR------GQFEAISSIVRDKTPDDAAWRKVRFMVFDLPDAPG------DFEERLAVLKKLLAKLPSPYIKIIEQ 155 (282)
T ss_pred EEEEeCC------CCHHHHHHHHccCCcchhhhcccEEEEEEcCCCCC------CHHHHHHHHHHHHhhCCCCcEEEEeE
Confidence 9999853 47999999987543322224689999999999986 9999999999999875 457889999
Q ss_pred EecCCHHHHHHHHHHHHHcCCceeEEEeCCCCCCccCCCCCCCeEEEccccccccCCcccEEEEEEEeCCCCCCCcccEE
Q 003632 591 LTSIDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLKKDYIESIGDSLDLVPIAAFHGRGKRTGVYGAF 670 (806)
Q Consensus 591 ~~~~~~eei~~~~~~ai~~g~EGlmlK~~~~ds~Y~pGkRs~~WlKlK~dY~~~~~dtlDlvVIGa~~G~Gkr~g~~gsf 670 (806)
..+.+.++++++|++++++|+||||+|++ +|+|++| |+.+|+|+|+.| +.|++|||+++|+|+++|++|+|
T Consensus 156 ~~~~~~~~~~~~~~~~~~~G~EGiV~K~~--ds~Y~~G-Rs~~wlKiK~~~------~~d~vIvG~~~g~Gk~~g~~gsl 226 (282)
T PRK09125 156 IRVRSEAALQQFLDQIVAAGGEGLMLHRP--DAPYEAG-RSDDLLKLKPYY------DAEATVIGHLPGKGKFAGMLGAL 226 (282)
T ss_pred EEcCCHHHHHHHHHHHHHcCCCEEEEeCC--CCCCcCC-CCCCcEEEEecC------CCcEEEEEEEcCCCcccCceeeE
Confidence 99999999999999999999999999999 9999999 899999999976 78999999999999999999999
Q ss_pred EEEEeeCCCCeEEEeeeccCCCCHHHHHHHHHhhccccCCCCCCCcccCCCCCCcEEecCceEEEEEeceeecCcccccc
Q 003632 671 LLACYDSNNEEFQSICKIGTGFSEAMLEERSSSLRSKVIPKPRPYYRFADTISPDVWFEPTEVWEVKAADLTISPVHRAA 750 (806)
Q Consensus 671 Lla~~d~~~g~~~~v~kVgtGftd~~l~~l~~~l~~~~~~~p~~~~~~~~~~~pdvwieP~~V~EV~~~eit~S~~~~a~ 750 (806)
+|+.+|+ ..| +||||||+++++. ++ + + ..+++|+|.++|.+
T Consensus 227 lv~~~~g--~~~----~VgsG~t~~~r~~------------~~-~------------~--g~~~~V~y~e~t~~------ 267 (282)
T PRK09125 227 LVETPDG--REF----KIGSGFSDAEREN------------PP-K------------I--GSIITYKYRGLTKN------ 267 (282)
T ss_pred EEEeCCC--CEE----EeCCCCCHHHhcC------------CC-C------------C--CCEEEEEecccCCC------
Confidence 9996542 233 7899999998651 11 1 1 35899999999854
Q ss_pred ccccCCCCCceeeccEEeEEecCC
Q 003632 751 IGVVDPDKGISLRFPRLIRVREDK 774 (806)
Q Consensus 751 ~g~~~~~~G~sLRFPRf~riR~DK 774 (806)
| .||||+|+++|+|.
T Consensus 268 --------g-~lR~P~f~g~R~D~ 282 (282)
T PRK09125 268 --------G-LPRFASFLRVREDE 282 (282)
T ss_pred --------C-cccCCEEEEEecCC
Confidence 5 89999999999983
No 20
>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=1.6e-45 Score=382.97 Aligned_cols=216 Identities=31% Similarity=0.486 Sum_probs=189.9
Q ss_pred ccccCCCCCCcccccccCCChHHHHhhcCCCceeEeeecceEeEEEEEecCCeEEEEecCCCcCCCCcchHHHHH-----
Q 003632 423 TCSFTPGIPIGPMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAV----- 497 (806)
Q Consensus 423 ~~~l~~g~Pv~PMLA~~~~~i~~~l~k~~g~~~~~E~KyDG~R~qih~~~~g~V~ifSR~gk~~T~~~Pel~~~l----- 497 (806)
.+.+++|.||+||||+++++..+++..+.+.+|++|+||||+|||+|++ +|.|++|||+|+++|..||++....
T Consensus 3 ~~~~~~~~p~~PmLa~~~~~~~~~~~~~~~~~~~~E~K~DG~R~~i~~~-~~~v~l~SR~g~~~t~~~p~~~~~~~~~~~ 81 (225)
T cd07903 3 DLSIELFSPFRPMLAERLNIGYVEIKLLKGKPFYIETKLDGERIQLHKD-GNEFKYFSRNGNDYTYLYGASLTPGSLTPY 81 (225)
T ss_pred CceeecCCcCccccCCCCCCHHHHHHhhcCCeEEEEEeeCceEEEEEec-CCEEEEEeCCCccccccccccccccccchh
Confidence 4678999999999999999877665677788999999999999999996 7899999999999999999987642
Q ss_pred -HhhcCCCCCCeEEEEEEEEEecCCCccCChHHHHHhhhccCCccccccceEEEEeeeeecCCccccCCcHHHHHHHHHH
Q 003632 498 -SRLKKPSVRSFVLDCEIVAYDREKQKILPFQTLSTRARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYD 576 (806)
Q Consensus 498 -~~~~~~~v~~~ILDGElVa~d~~~g~~~pFq~L~~r~rk~~~~~~~~~~v~~~vFDiLylnG~~L~~~Pl~eRr~~L~~ 576 (806)
...+.....+||||||||+||..++.+.+|+.++++.+... ......+++|+|||||++||++++++||.+|+++|++
T Consensus 82 l~~~~~~~~~~~iLDGElv~~~~~~~~~~~f~~l~~~~~~~~-~~~~~~~~~~~vFDiL~~~g~~l~~~pl~eR~~~L~~ 160 (225)
T cd07903 82 IHLAFNPKVKSCILDGEMVVWDKETKRFLPFGTLKDVAKLRE-VEDSDLQPCFVVFDILYLNGKSLTNLPLHERKKLLEK 160 (225)
T ss_pred hhhhccccCcEEEeceEEEEEEcCcCeeccchHHHHHHhhcc-cccCCccEEEEEEEEEEECCeecccCcHHHHHHHHHH
Confidence 22233345899999999999987777899999977644211 0123578999999999999999999999999999999
Q ss_pred hhccCCCcEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEEeCCCCCCccCCCCCCCeEEEccccc
Q 003632 577 SFEEEPGFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLKKDYI 642 (806)
Q Consensus 577 l~~~~~~~i~~~~~~~~~~~eei~~~~~~ai~~g~EGlmlK~~~~ds~Y~pGkRs~~WlKlK~dY~ 642 (806)
++.+.++++.++++..+++.+++.++|++++++|+||||+|++ +|+|++|+|+.+|+|+|++|+
T Consensus 161 ~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~g~EGlv~K~~--~s~Y~~g~Rs~~wlK~K~~Y~ 224 (225)
T cd07903 161 IITPIPGRLEVVKRTEASTKEEIEEALNEAIDNREEGIVVKDL--DSKYKPGKRGGGWIKIKPEYL 224 (225)
T ss_pred hcCCCCCeEEEEEEEeCCCHHHHHHHHHHHHHcCCceEEEecC--CCCCccCCcCCCcEEechhhc
Confidence 9988778999999999999999999999999999999999999 999999999999999999996
No 21
>cd07901 Adenylation_DNA_ligase_Arch_LigB Adenylation domain of archaeal and bacterial LigB-like DNA ligases. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. Bacterial DNA ligases are divided into two broad classes: NAD-dependent and ATP-dependent. All bacterial species have a NAD-dependent DNA ligase (LigA). Some bacterial genomes contain multiple genes for DNA ligases that are predicted to use ATP as their cofactor, including Mycobacterium tuberculosis LigB, LigC, and LigD. This group is composed of archaeal DNA ligases and bacterial proteins similar to Mycobacterium tuberculosis LigB. Members of this group contain adeny
Probab=100.00 E-value=4.1e-45 Score=375.69 Aligned_cols=205 Identities=38% Similarity=0.591 Sum_probs=182.4
Q ss_pred CCCCCcccccccCCChHHHHhhcCCCceeEeeecceEeEEEEEecCCeEEEEecCCCcCCCCcchHHHHHHhhcCCCCCC
Q 003632 428 PGIPIGPMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAVSRLKKPSVRS 507 (806)
Q Consensus 428 ~g~Pv~PMLA~~~~~i~~~l~k~~g~~~~~E~KyDG~R~qih~~~~g~V~ifSR~gk~~T~~~Pel~~~l~~~~~~~v~~ 507 (806)
||+||+||||+++.++++++++. +.+|++|+||||+|||+|++ ++.|++|||+|+++|..||++.+++...+. ..+
T Consensus 1 ~~~p~~PmLA~~~~~~~~~~~~~-~~~~~~E~K~DG~R~~~~~~-~~~v~~~SR~~~~~t~~~pel~~~~~~~~~--~~~ 76 (207)
T cd07901 1 VGRPVRPMLAQRAPSVEEALIKE-GGEAAVEYKYDGIRVQIHKD-GDEVRIFSRRLEDITNALPEVVEAVRELVK--AED 76 (207)
T ss_pred CCCCCccccCCCCCCHHHHHHhc-CCcEEEEEeEcceeEEEEEe-CCEEEEEeCCCccccchhhHHHHHHHhcCC--CCC
Confidence 68999999999998888776665 45899999999999999996 679999999999999999999998887753 368
Q ss_pred eEEEEEEEEEecCCCccCChHHHHHhhhccCCcc--ccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCCCcE
Q 003632 508 FVLDCEIVAYDREKQKILPFQTLSTRARKNVSLS--DIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEPGFF 585 (806)
Q Consensus 508 ~ILDGElVa~d~~~g~~~pFq~L~~r~rk~~~~~--~~~~~v~~~vFDiLylnG~~L~~~Pl~eRr~~L~~l~~~~~~~i 585 (806)
||||||||+||+ +|++++|+.+++|.++..... ....+++|+||||||+||++++++||.+|+++|++++.+. +.+
T Consensus 77 ~iLDGElv~~~~-~g~~~~F~~l~~r~~~~~~~~~~~~~~~~~~~vFDil~~~g~~l~~~pl~eR~~~L~~~~~~~-~~i 154 (207)
T cd07901 77 AILDGEAVAYDP-DGRPLPFQETLRRFRRKYDVEEAAEEIPLTLFLFDILYLDGEDLLDLPLSERRKILEEIVPET-EAI 154 (207)
T ss_pred EEEeCEEEEECC-CCCccCHHHHHHHhccccchhhhhccCcEEEEEEEEEEECCcchhcCCHHHHHHHHHHhcCcC-CcE
Confidence 999999999996 687789999999965432211 1246899999999999999999999999999999999875 678
Q ss_pred EEEeEEecCCHHHHHHHHHHHHHcCCceeEEEeCCCCCCccCCCCCCCeEEEccc
Q 003632 586 QFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLKKD 640 (806)
Q Consensus 586 ~~~~~~~~~~~eei~~~~~~ai~~g~EGlmlK~~~~ds~Y~pGkRs~~WlKlK~d 640 (806)
.+++...+++.+++.++|++++++|+||||+|++ +|+|++|+|+.+|+|+|+|
T Consensus 155 ~~~~~~~~~~~~~~~~~~~~~~~~g~EGiv~K~~--~s~Y~~g~Rs~~wlK~K~~ 207 (207)
T cd07901 155 LLAPRIVTDDPEEAEEFFEEALEAGHEGVMVKSL--DSPYQAGRRGKNWLKVKPD 207 (207)
T ss_pred EEEEEEecCCHHHHHHHHHHHHHcCCceEEEeCC--CCCcCCCCCCCCeEEecCC
Confidence 9999988999999999999999999999999999 9999999999999999985
No 22
>cd07902 Adenylation_DNA_ligase_III Adenylation domain of DNA Ligase III. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three-step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. There are three classes of ATP-dependent DNA ligases in eukaryotic cells (I, III and IV). DNA ligase III is not found in lower eukaryotes and is present both in the nucleus and mitochondria. It has several isoforms; two splice forms, III-alpha and III-beta, differ in their carboxy-terminal sequences. DNA ligase III-beta is believed to play a role in homologous recombination during meiotic prophase. DNA ligase III-alpha interacts with X-ray Cross Complementing factor 1 (XRCC1) and functions in single nuc
Probab=100.00 E-value=4.3e-45 Score=377.26 Aligned_cols=208 Identities=31% Similarity=0.538 Sum_probs=185.7
Q ss_pred ccccCCCCCCcccccccCCChHHHHhhcCCCceeEeeecceEeEEEEEecCCeEEEEecCCCcCCC-CcchHHHHHHhhc
Q 003632 423 TCSFTPGIPIGPMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTG-KFPDVVLAVSRLK 501 (806)
Q Consensus 423 ~~~l~~g~Pv~PMLA~~~~~i~~~l~k~~g~~~~~E~KyDG~R~qih~~~~g~V~ifSR~gk~~T~-~~Pel~~~l~~~~ 501 (806)
.+.+++|+||+||||+++.+++++++++. ..|++|+||||+|||+|++ +|+|++|||||+++|. .+|++.+.+.+.+
T Consensus 5 ~~~~~~~~p~~PmLA~~~~~~~~~i~~~~-~~~~~E~K~DG~R~~i~~~-~~~v~l~SR~g~~~t~~~~~~~~~~~~~~~ 82 (213)
T cd07902 5 SVRASLMTPVKPMLAEACKSVEDAMKKCP-NGMYAEIKYDGERVQVHKQ-GDNFKFFSRSLKPVLPHKVAHFKDYIPKAF 82 (213)
T ss_pred eEEeEcCCcccCccCCcCCCHHHHHHhcC-CceEEEeccCCEEEEEEEc-CCEEEEEcCCCcccccchhHHHHHHHHHhc
Confidence 46789999999999999988887777653 3699999999999999996 6899999999999996 6899888777766
Q ss_pred CCCCCCeEEEEEEEEEecCCCccCChHHHHHhhhccCCccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccC
Q 003632 502 KPSVRSFVLDCEIVAYDREKQKILPFQTLSTRARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEE 581 (806)
Q Consensus 502 ~~~v~~~ILDGElVa~d~~~g~~~pFq~L~~r~rk~~~~~~~~~~v~~~vFDiLylnG~~L~~~Pl~eRr~~L~~l~~~~ 581 (806)
.. ..+||||||+|+||..+|++++|+.++.|.+... ...+++|+|||||++||+++++.||.+|+++|++++.+.
T Consensus 83 ~~-~~~~iLDGEiv~~d~~~g~~~~F~~l~~~~~~~~----~~~~v~~~vFDiL~l~g~~l~~~pl~eR~~~L~~~~~~~ 157 (213)
T cd07902 83 PH-GHSMILDSEVLLVDTKTGKPLPFGTLGIHKKSAF----KDANVCLFVFDCLYYNGESLMDKPLRERRKILEDNMVEI 157 (213)
T ss_pred cc-ccceeeeeEEEEEECCCCcccccchhhhhhcccc----ccCceEEEEEEEeeeCCcchhcCcHHHHHHHHHHhccCC
Confidence 42 5799999999999988888889999987765321 235799999999999999999999999999999999887
Q ss_pred CCcEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEEeCCCCCCccCCCCCCCeEEEcccc
Q 003632 582 PGFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLKKDY 641 (806)
Q Consensus 582 ~~~i~~~~~~~~~~~eei~~~~~~ai~~g~EGlmlK~~~~ds~Y~pGkRs~~WlKlK~dY 641 (806)
++++.+++...+.+.+++.++|++++++|+||||+|++ +|+|++|+| +|+|+|+||
T Consensus 158 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~g~EGvV~K~~--~s~Y~~G~r--~W~K~K~dY 213 (213)
T cd07902 158 PNRIMLSEMKFVKKADDLSAMIARVIKEGLEGLVLKDL--KSVYEPGKR--HWLKVKKDY 213 (213)
T ss_pred CCeEEEEEEEEcCCHHHHHHHHHHHHHCCCCeEEEeCC--CCCccCCCC--CceEeCCCC
Confidence 77899999888999999999999999999999999999 999999988 799999998
No 23
>cd07897 Adenylation_DNA_ligase_Bac1 Adenylation domain of putative bacterial ATP-dependent DNA ligases. Bacterial DNA ligases are divided into two broad classes: NAD-dependent and ATP-dependent. All bacterial species have a NAD-dependent DNA ligase (LigA). Some bacterial genomes contain multiple genes for DNA ligases that are predicted to use ATP as their cofactor, including Mycobacterium tuberculosis LigB, LigC, and LigD. This group is composed of predicted bacterial ATP-dependent DNA ligases. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three-step reaction mechanism. The adenylation and C-terminal oligonucleotide/oligosaccharide binding (OB)-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family, including this group. The adenylation domain binds ATP and contains many of the active site residues.
Probab=100.00 E-value=1e-43 Score=365.43 Aligned_cols=201 Identities=28% Similarity=0.426 Sum_probs=176.0
Q ss_pred CCCcccccccCCChHHHHhhcCCCceeEeeecceEeEEEEEecCCeEEEEecCCCcCCCCcchHHHHHHhhcCCCCCCeE
Q 003632 430 IPIGPMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAVSRLKKPSVRSFV 509 (806)
Q Consensus 430 ~Pv~PMLA~~~~~i~~~l~k~~g~~~~~E~KyDG~R~qih~~~~g~V~ifSR~gk~~T~~~Pel~~~l~~~~~~~v~~~I 509 (806)
+|+.||||+++.++.+.+. ....|++|+||||+|||+|+. ++.|++|||||+++|..||++.+++..+ + .+||
T Consensus 3 ~~~~pmLA~~~~~~~~~~~--~~~~~~~E~K~DG~R~~~~~~-~~~v~l~SR~g~~~t~~~p~l~~~~~~l-~---~~~i 75 (207)
T cd07897 3 RPYPFMLAHPLEDDPEDLG--DPSDWQAEWKWDGIRGQLIRR-GGEVFLWSRGEELITGSFPELLAAAEAL-P---DGTV 75 (207)
T ss_pred CCCCceeCCcCCCchhhhc--CcccEEEEEeEceEEEEEEEc-CCEEEEEeCCCCcccccchHHHHHHHhC-C---CCeE
Confidence 7999999999988766542 345899999999999999985 7899999999999999999998876543 2 5899
Q ss_pred EEEEEEEEecCCCccCChHHHHHhhhccCCcc--ccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccC-CCcEE
Q 003632 510 LDCEIVAYDREKQKILPFQTLSTRARKNVSLS--DIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEE-PGFFQ 586 (806)
Q Consensus 510 LDGElVa~d~~~g~~~pFq~L~~r~rk~~~~~--~~~~~v~~~vFDiLylnG~~L~~~Pl~eRr~~L~~l~~~~-~~~i~ 586 (806)
||||||+||. +...+|+.+++|.++..... ....+++|+||||||+||+++++.||.+|+++|++++.+. .+++.
T Consensus 76 LDGElv~~~~--~~~~~F~~l~~r~~~~~~~~~~~~~~~~~~~vFDil~l~g~~l~~~pl~eRr~~L~~l~~~~~~~~i~ 153 (207)
T cd07897 76 LDGELLVWRD--GRPLPFNDLQQRLGRKTVGKKLLAEAPAAFRAYDLLELNGEDLRALPLRERRARLEALLARLPPPRLD 153 (207)
T ss_pred EEeEEEEecC--CCccCHHHHHHHhcccccchhhHhhCCeEEEEEeeeeECceEhhhCCHHHHHHHHHHhhhhcCCCcee
Confidence 9999999986 45689999999865332211 1246899999999999999999999999999999999876 46788
Q ss_pred EEeEEecCCHHHHHHHHHHHHHcCCceeEEEeCCCCCCccCCCCCCCeEEEcccc
Q 003632 587 FATTLTSIDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLKKDY 641 (806)
Q Consensus 587 ~~~~~~~~~~eei~~~~~~ai~~g~EGlmlK~~~~ds~Y~pGkRs~~WlKlK~dY 641 (806)
+++...+++.+++.++|++++++|+||||+|++ +|+|++|+|+.+|+|+|+|-
T Consensus 154 ~~~~~~~~~~~~~~~~~~~~~~~g~EGiv~K~~--~s~Y~~Grr~~~W~K~K~d~ 206 (207)
T cd07897 154 LSPLIAFADWEELAALRAQSRERGAEGLMLKRR--DSPYLVGRKKGDWWKWKIDP 206 (207)
T ss_pred ecceEecCCHHHHHHHHHHHHHcCCeEEEEeCC--CCCcCCCCcCCCeeEeCCCC
Confidence 999999999999999999999999999999999 99999999999999999974
No 24
>cd08039 Adenylation_DNA_ligase_Fungal Adenylation domain of uncharacterized fungal ATP-dependent DNA ligase-like proteins. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. This group is composed of uncharacterized fungal proteins with similarity to ATP-dependent DNA ligases. ATP dependent DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains including a DNA-binding domain, an adenylation (nucleotidyltransferase (NTase)) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The adenylation domain binds ATP and contains many of the active-site res
Probab=100.00 E-value=3.2e-43 Score=367.79 Aligned_cols=199 Identities=23% Similarity=0.375 Sum_probs=171.1
Q ss_pred CChHHHHhhcCCCceeEeeecceEeEEEEEec---CCeEEEEecCCCcCCCCcchHHHHHHhhcC------CCCCCeEEE
Q 003632 441 KGVSEIVNKFQDMEFTCEYKYDGERAQIHYLE---DGSVEIYSRNAERNTGKFPDVVLAVSRLKK------PSVRSFVLD 511 (806)
Q Consensus 441 ~~i~~~l~k~~g~~~~~E~KyDG~R~qih~~~---~g~V~ifSR~gk~~T~~~Pel~~~l~~~~~------~~v~~~ILD 511 (806)
+++..+++.+++..|++|+||||+|||+|+.. ++.|++|||||+++|..||++.+.+...+. +.+++||||
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 45777888899999999999999999999851 678999999999999999999887766542 125799999
Q ss_pred EEEEEEecCCCccCChHHHHHhhhccC--------CccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCCC
Q 003632 512 CEIVAYDREKQKILPFQTLSTRARKNV--------SLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEPG 583 (806)
Q Consensus 512 GElVa~d~~~g~~~pFq~L~~r~rk~~--------~~~~~~~~v~~~vFDiLylnG~~L~~~Pl~eRr~~L~~l~~~~~~ 583 (806)
||||+||..+|++.||+.|++|.+... .......++||+||||||+||+++++.||.+||++|++++.++++
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 999999988888899999998864221 111235789999999999999999999999999999999988888
Q ss_pred cEEEEeEEec-----CCHHHHHHHHHHHHHcCCceeEEEeCCCCCCccCCCC-----CCCeEEEcccc
Q 003632 584 FFQFATTLTS-----IDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKR-----SLNWLKLKKDY 641 (806)
Q Consensus 584 ~i~~~~~~~~-----~~~eei~~~~~~ai~~g~EGlmlK~~~~ds~Y~pGkR-----s~~WlKlK~dY 641 (806)
++.+++...+ .+.+++.++|++++++|+||||+|++ +|+|.||++ +..|+|+|+||
T Consensus 170 ~~~~~~~~~i~~~~~~~~~~l~~~~~~a~~~g~EGIv~K~~--~S~Y~pgr~~~~~r~~~WlKlK~dY 235 (235)
T cd08039 170 YAGLSERFPIDFSRSSGYERLRQIFARAIAERWEGLVLKGD--EEPYFDLFLEQGSFSGCWIKLKKDY 235 (235)
T ss_pred cEEEEEEEeecccCCCCHHHHHHHHHHHHHcCCceEEEecC--CCCcccCcccccccCCCeEEeCCCC
Confidence 8888776553 37899999999999999999999999 999999753 58999999998
No 25
>cd07898 Adenylation_DNA_ligase Adenylation domain of ATP-dependent DNA Ligases. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. Some organisms express a variety of different ligases which appear to be targeted to specific functions. ATP-dependent DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains including a DNA-binding domain, an adenylation (nucleotidyltransferase (NTase)) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The adenylation domain binds ATP and contains many of the active-site residues. The adenylation and C-terminal OB-f
Probab=100.00 E-value=7.4e-43 Score=357.20 Aligned_cols=199 Identities=40% Similarity=0.619 Sum_probs=176.0
Q ss_pred CcccccccCCChHHHHhhcCCCceeEeeecceEeEEEEEecCCeEEEEecCCCcCCCCcchHHHHHHhhcCCCCCCeEEE
Q 003632 432 IGPMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAVSRLKKPSVRSFVLD 511 (806)
Q Consensus 432 v~PMLA~~~~~i~~~l~k~~g~~~~~E~KyDG~R~qih~~~~g~V~ifSR~gk~~T~~~Pel~~~l~~~~~~~v~~~ILD 511 (806)
|+||||+++++++++ .++.+.+|++|+||||+|||+|+. +++|++|||+|+++|..||++.+++... .++||||
T Consensus 1 i~pmLa~~~~~~~~~-~~~~~~~~~~E~K~DG~R~~~~~~-~~~v~l~SR~g~~~t~~~p~i~~~~~~~----~~~~vLD 74 (201)
T cd07898 1 IKPMLAHPEESAEAA-KAKKPAAAWVEDKYDGIRAQVHKD-GGRVEIFSRSLEDITDQFPELAAAAKAL----PHEFILD 74 (201)
T ss_pred CCCeecCcCCChHHH-HhhCCCeEEEEEeeceEEEEEEEe-CCEEEEEcCCChhchhhhhhHHHHHHhC----CCCEEEE
Confidence 689999999988665 556788999999999999999996 6899999999999999999998876642 2789999
Q ss_pred EEEEEEecCCCccCChHHHHHhhhccCCcc--ccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCCCcEEEEe
Q 003632 512 CEIVAYDREKQKILPFQTLSTRARKNVSLS--DIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEPGFFQFAT 589 (806)
Q Consensus 512 GElVa~d~~~g~~~pFq~L~~r~rk~~~~~--~~~~~v~~~vFDiLylnG~~L~~~Pl~eRr~~L~~l~~~~~~~i~~~~ 589 (806)
||||+||... ..+|+.+++|.++..... ....+++|+|||||++||++++++||.||+++|++++.+.++++.+++
T Consensus 75 GElv~~~~~~--~~~f~~~~~~~~~~~~~~~~~~~~~~~~~vFDil~~~g~~l~~~p~~eR~~~L~~~~~~~~~~i~~~~ 152 (201)
T cd07898 75 GEILAWDDNR--GLPFSELFKRLGRKFRDKFLDEDVPVVLMAFDLLYLNGESLLDRPLRERRQLLEELFVEIPGRIRIAP 152 (201)
T ss_pred EEEEEEeCCC--CCcHHHHHHHhcccccchhhhccCcEEEEEEeEEeECCcchhhCCHHHHHHHHHHhhcCCCCcEEEee
Confidence 9999998643 369999998865432211 235789999999999999999999999999999999988888999999
Q ss_pred EEecCCHHHHHHHHHHHHHcCCceeEEEeCCCCCCccCCCCCCCeEEEccc
Q 003632 590 TLTSIDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLKKD 640 (806)
Q Consensus 590 ~~~~~~~eei~~~~~~ai~~g~EGlmlK~~~~ds~Y~pGkRs~~WlKlK~d 640 (806)
...+++.+++.++|++++++|+||||+|++ +|+|++|+|+.+|+|+|+|
T Consensus 153 ~~~~~~~~~~~~~~~~~~~~g~EGim~K~~--~s~Y~~g~Rs~~wlK~K~~ 201 (201)
T cd07898 153 ALPVESAEELEAAFARARARGNEGLMLKDP--DSPYEPGRRGLAWLKLKKE 201 (201)
T ss_pred eEEcCCHHHHHHHHHHHHHcCCceEEEeCC--CCCcCCCCcCCCcEEeCCC
Confidence 999999999999999999999999999999 9999999999999999985
No 26
>PF01068 DNA_ligase_A_M: ATP dependent DNA ligase domain; InterPro: IPR012310 DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA fragments by catalysing the formation of an internucleotide ester bond between phosphate and deoxyribose. It is active during DNA replication, DNA repair and DNA recombination. There are two forms of DNA ligase, one requires ATP (6.5.1.1 from EC), the other NAD (6.5.1.2 from EC), the latter being restricted to eubacteria. Eukaryotic, archaebacterial, viral and some eubacterial DNA ligases are ATP-dependent. The first step in the ligation reaction is the formation of a covalent enzyme-AMP complex. The co-factor ATP is cleaved to pyrophosphate and AMP, with the AMP being covalently joined to a highly conserved lysine residue in the active site of the ligase. The activated AMP residue is then transferred to the 5'phosphate of the nick, before the nick is sealed by phosphodiester-bond formation and AMP elimination [,]. Vertebrate cells encode three well-characterised DNA ligases (DNA ligases I, III and IV), all of which are related in structure and sequence. With the exception of the atypically small PBCV-1 viral enzyme, two regions of primary sequence are common to all members of the family. The catalytic region comprises six conserved sequence motifs (I, III, IIIa, IV, V-VI), motif I includes the lysine residue that is adenylated in the first step of the ligation reaction. The function of the second, less well-conserved region is unknown. When folded, each protein comprises of two distinct sub-domains: a large amino-terminal sub-domain ('domain 1') and a smaller carboxy-terminal sub-domain ('domain 2'). The ATP-binding site of the enzyme lies in the cleft between the two sub-domains. Domain 1 consists of two antiparallel beta sheets flanked by alpha helices, whereas domain 2 consists of a five-stranded beta barrel and a single alpha helix, which form the oligonucleotide-binding fold [, ]. This domain belongs to a more diverse superfamily, including catalytic domain of the mRNA capping enzyme (IPR001339 from INTERPRO) and NAD-dependent DNA ligase (IPR001679 from INTERPRO) []. ; GO: 0003910 DNA ligase (ATP) activity, 0005524 ATP binding, 0006281 DNA repair, 0006310 DNA recombination; PDB: 3RR5_A 1X9N_A 2CFM_A 3QWU_B 3GDE_A 2Q2U_C 2Q2T_A 1FVI_A 1P8L_A 2VUG_A ....
Probab=100.00 E-value=3.6e-42 Score=350.37 Aligned_cols=201 Identities=36% Similarity=0.607 Sum_probs=180.3
Q ss_pred ccccccCCChHHHHhhcCCCceeEeeecceEeEEEEEecCCeEEEEecCCCcCCCCcchHHHHHHhhcCCCCCCeEEEEE
Q 003632 434 PMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAVSRLKKPSVRSFVLDCE 513 (806)
Q Consensus 434 PMLA~~~~~i~~~l~k~~g~~~~~E~KyDG~R~qih~~~~g~V~ifSR~gk~~T~~~Pel~~~l~~~~~~~v~~~ILDGE 513 (806)
||||+++++++++++++ +.+|++|+||||+|||||+ .+|.|++|||+|+++|..||++.+.+...+.++..+||||||
T Consensus 1 PmLA~~~~~~~~~~~~~-~~~~~~e~K~DG~R~~i~~-~~~~v~~~SR~g~~~~~~~~~l~~~l~~~~~~~~~~~vLDGE 78 (202)
T PF01068_consen 1 PMLAQPFDSIEKALKKF-GGPWYVEPKYDGVRCQIHK-DGGGVRLFSRNGKDITSQFPELAEALRELLFPDGPDFVLDGE 78 (202)
T ss_dssp -EEEEEESSHHHHHHHT-TSCEEEEEEESSEEEEEEE-ETTEEEEEETTSSB-GGGHHHHHHHHHHHBCTSCTEEEEEEE
T ss_pred CcCCccccCHHHHHHhc-CCCeEEEEeEeeEEeeeee-ccccceeecccccchhhHHHHHHHHHHHHhcCCCCceEEEEE
Confidence 89999999999999988 6689999999999999998 488999999999999999999999998887665678999999
Q ss_pred EEEEecCCCccCChHHHHHhhh-ccCCccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCCCcEEEEeEEe
Q 003632 514 IVAYDREKQKILPFQTLSTRAR-KNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEPGFFQFATTLT 592 (806)
Q Consensus 514 lVa~d~~~g~~~pFq~L~~r~r-k~~~~~~~~~~v~~~vFDiLylnG~~L~~~Pl~eRr~~L~~l~~~~~~~i~~~~~~~ 592 (806)
+|+||+.++...||+.++++.+ +.........+++|+|||||++||.++++.||.+|+++|++++....+.+.+++...
T Consensus 79 lv~~d~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~vFDil~l~~~~l~~~p~~eR~~~L~~~~~~~~~~i~~~~~~~ 158 (202)
T PF01068_consen 79 LVVLDPNTGSPLPFQELSGRLNRRSKKIPEQSEPLQFVVFDILYLDGKDLLDLPYEERRELLEELLEPPPPRIRIVESYV 158 (202)
T ss_dssp EEEBETTTSSBCCHHHHHHHHBHSSSCHHHHHSCEEEEEEEEEEETTEECTTSCHHHHHHHHHHHBG-BTSSEEEEEEEE
T ss_pred EEEEecCCCcchhHHHHhhhhhhhcccchhccCcEEEEEEEEEEeCCeEeeeccHHHHHHHHHHhhccCCCceeEeeeec
Confidence 9999999888999999999983 333222226799999999999999999999999999999999976678899999999
Q ss_pred cCCHHHHHHHHHHHHHcCCceeEEEeCCCCCCccCCCCCCCeEEEc
Q 003632 593 SIDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLK 638 (806)
Q Consensus 593 ~~~~eei~~~~~~ai~~g~EGlmlK~~~~ds~Y~pGkRs~~WlKlK 638 (806)
+.+.++++++|++++++|+||+|+|++ +++|++|+|+.+|+|+|
T Consensus 159 ~~~~~~~~~~~~~~~~~g~EG~v~K~~--~~~Y~~Gkrs~~w~K~K 202 (202)
T PF01068_consen 159 VNSKEELEELFEEAIDQGFEGLVLKDP--DSPYEPGKRSSGWLKVK 202 (202)
T ss_dssp ESSHHHHHHHHHHHHHTTSSEEEEEET--TSSC-TTEEEEEEEEEE
T ss_pred CCCHHHHHHHHHHHHHcCCceEEEECC--CCccCCCCcCCCcEEEC
Confidence 999999999999999999999999999 99999999999999998
No 27
>cd07905 Adenylation_DNA_ligase_LigC Adenylation domain of Mycobacterium tuberculosis LigC-like ATP-dependent DNA ligases. Bacterial DNA ligases are divided into two broad classes: NAD-dependent and ATP-dependent. All bacterial species have a NAD-dependent DNA ligase (LigA). Some bacterial genomes contain multiple genes for DNA ligases that are predicted to use ATP as their cofactor, including Mycobacterium tuberculosis LigB, LigC, and LigD. This group is composed of ATP-dependent DNA ligases similar to Mycobacterium tuberculosis LigC. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. Members of this group contain adenylation and C-terminal oligonucleotide/oligosaccharide binding (OB)-fold domains, comprising a catalytic core unit that is
Probab=100.00 E-value=7.6e-41 Score=340.84 Aligned_cols=190 Identities=28% Similarity=0.396 Sum_probs=164.1
Q ss_pred CcccccccCCChHHHHhhcCCCceeEeeecceEeEEEEEecCCeEEEEecCCCcCCCCcchHHHHHHhhcCCCCCCeEEE
Q 003632 432 IGPMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAVSRLKKPSVRSFVLD 511 (806)
Q Consensus 432 v~PMLA~~~~~i~~~l~k~~g~~~~~E~KyDG~R~qih~~~~g~V~ifSR~gk~~T~~~Pel~~~l~~~~~~~v~~~ILD 511 (806)
|+||||..+.++++ +.+|++|+||||+|||+|++ ++.|++|||||+++|+.||++.+++...+. .+||||
T Consensus 1 i~PmLa~~~~~~~~------~~~~~~E~K~DG~R~~~~~~-~~~v~l~SR~g~~~t~~~p~~~~~~~~~~~---~~~iLD 70 (194)
T cd07905 1 VEPMLARAVDALPE------PGGWQYEPKWDGFRCLAFRD-GDEVRLQSRSGKPLTRYFPELVAAARALLP---PGCVLD 70 (194)
T ss_pred CCceeCCccCCCCC------CCceEEEeeeceEEEEEEEe-CCEEEEEeCCCCchhhhhHHHHHHHHhhCC---CCEEEE
Confidence 58999998876532 56899999999999999995 679999999999999999999998887643 589999
Q ss_pred EEEEEEecCCCccCChHHHHHhhhccCC---ccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCCCcEEEE
Q 003632 512 CEIVAYDREKQKILPFQTLSTRARKNVS---LSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEPGFFQFA 588 (806)
Q Consensus 512 GElVa~d~~~g~~~pFq~L~~r~rk~~~---~~~~~~~v~~~vFDiLylnG~~L~~~Pl~eRr~~L~~l~~~~~~~i~~~ 588 (806)
||+|+||+ +. .+|+.+++|.++... ......+++|+||||||+||+++++.||.+|+++|++++.+..+.++++
T Consensus 71 GElv~~~~--~~-~~F~~l~~r~~~~~~~~~~~~~~~~~~~~vFDiL~l~g~~l~~~pl~eRr~~L~~~~~~~~~~i~~~ 147 (194)
T cd07905 71 GELVVWRG--GR-LDFDALQQRIHPAASRVRRLAEETPASFVAFDLLALGGRDLRGRPLRERRAALEALLAGWGPPLHLS 147 (194)
T ss_pred eEEEEEcC--CC-CCHHHHHHHhcccccchhhhhccCCEEEEEEeeeeeCCcccccCCHHHHHHHHHHHhcccCCCeEEC
Confidence 99999985 33 499999999754321 1123678999999999999999999999999999999998766778888
Q ss_pred eEEecCCHHHHHHHHHHHHHcCCceeEEEeCCCCCCccCCCCCCCeEEEccc
Q 003632 589 TTLTSIDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLKKD 640 (806)
Q Consensus 589 ~~~~~~~~eei~~~~~~ai~~g~EGlmlK~~~~ds~Y~pGkRs~~WlKlK~d 640 (806)
+. +.+.+++.++|++++++|+||||+|++ +|+|++|+| +|+|+|+.
T Consensus 148 ~~--~~~~~~~~~~~~~~~~~g~EGiv~K~~--~s~Y~~Gr~--~WlK~K~~ 193 (194)
T cd07905 148 PA--TTDRAEAREWLEEFEGAGLEGVVAKRL--DGPYRPGER--AMLKVKHR 193 (194)
T ss_pred Cc--cCCHHHHHHHHHHHHHCCCceEEEeCC--CCCcCCCCC--cEEEEecc
Confidence 75 467889999999999999999999999 999999974 89999983
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=5.8e-40 Score=333.03 Aligned_cols=189 Identities=33% Similarity=0.469 Sum_probs=164.5
Q ss_pred CcccccccCCChHHHHhhcCCCceeEeeecceEeEEEEEecCCeEEEEecCCCcCCCCcchHHHHHHhhcCCCCCCeEEE
Q 003632 432 IGPMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAVSRLKKPSVRSFVLD 511 (806)
Q Consensus 432 v~PMLA~~~~~i~~~l~k~~g~~~~~E~KyDG~R~qih~~~~g~V~ifSR~gk~~T~~~Pel~~~l~~~~~~~v~~~ILD 511 (806)
|+||||+++.++. .+.+|++|+||||+|||+|+. ++.|++|||+|+++|..||++..++.++ ...++|||
T Consensus 1 i~pmLa~~~~~~~------~~~~~~~e~K~DG~R~~i~~~-~~~v~~~SR~g~~~t~~~p~l~~~~~~~---~~~~~iLD 70 (190)
T cd07906 1 IEPMLATLVDEPP------DGEDWLYEIKWDGYRALARVD-GGRVRLYSRNGLDWTARFPELAEALAAL---PVRDAVLD 70 (190)
T ss_pred CCCeECCcCCCCC------CCCCeEEEEeEceEEEEEEEE-CCEEEEEcCCCCcchhhhHHHHHHHHhc---CCCCEEEE
Confidence 5899999988652 356899999999999999996 6799999999999999999998877764 34789999
Q ss_pred EEEEEEecCCCccCChHHHHHhhhccCCccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCCCcEEEEeEE
Q 003632 512 CEIVAYDREKQKILPFQTLSTRARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEPGFFQFATTL 591 (806)
Q Consensus 512 GElVa~d~~~g~~~pFq~L~~r~rk~~~~~~~~~~v~~~vFDiLylnG~~L~~~Pl~eRr~~L~~l~~~~~~~i~~~~~~ 591 (806)
||||+||... ..+|+.+++|.++.. ......+++|+|||||++||++++++||.||+++|++++.+.++.+++++..
T Consensus 71 GElv~~~~~~--~~~F~~l~~~~~~~~-~~~~~~~~~~~vFDil~~~~~~~~~~p~~eR~~~L~~~~~~~~~~i~~~~~~ 147 (190)
T cd07906 71 GEIVVLDEGG--RPDFQALQNRLRLRR-RLARTVPVVYYAFDLLYLDGEDLRGLPLLERKELLEELLPAGSPRLRVSEHF 147 (190)
T ss_pred eEEEEECCCC--CCCHHHHHHhhcccc-hhcccCceEEEEEeeeeeCCcchhhCCHHHHHHHHHHHhccCCCcEEECceE
Confidence 9999998643 269999999986543 2234678999999999999999999999999999999998877788888766
Q ss_pred ecCCHHHHHHHHHHHHHcCCceeEEEeCCCCCCccCCCCCCCeEEEcc
Q 003632 592 TSIDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLKK 639 (806)
Q Consensus 592 ~~~~~eei~~~~~~ai~~g~EGlmlK~~~~ds~Y~pGkRs~~WlKlK~ 639 (806)
.. +.+++|++++++|+||||+|++ +|+|++|+|+.+|+|+|+
T Consensus 148 ~~----~~~~~~~~~~~~g~EGiv~K~~--~s~Y~~g~rs~~wlK~K~ 189 (190)
T cd07906 148 EG----GGAALFAAACELGLEGIVAKRA--DSPYRSGRRSRDWLKIKC 189 (190)
T ss_pred cC----CHHHHHHHHHHcCCcEEEEecC--CCCcCCCCCCCccEEEec
Confidence 43 2378999999999999999999 999999999999999997
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=3.1e-35 Score=284.09 Aligned_cols=132 Identities=34% Similarity=0.675 Sum_probs=119.9
Q ss_pred cCCcccEEEEEEEeCCCCCCCcccEEEEEEeeCCCCeEEEeeeccCCCCHHHHHHHHHhhccccCCC----CCCCcccCC
Q 003632 645 IGDSLDLVPIAAFHGRGKRTGVYGAFLLACYDSNNEEFQSICKIGTGFSEAMLEERSSSLRSKVIPK----PRPYYRFAD 720 (806)
Q Consensus 645 ~~dtlDlvVIGa~~G~Gkr~g~~gsfLla~~d~~~g~~~~v~kVgtGftd~~l~~l~~~l~~~~~~~----p~~~~~~~~ 720 (806)
|+|++||||||+|+|+|+|+|++|+||||+||+++++|++|||||||||++++++|.++|+++++.. ++.|+.++.
T Consensus 1 ~~dtlDlVViG~~~g~G~r~~~~gslLlg~~d~~~~~l~~vgkVGTGfs~~~l~~l~~~L~~l~~~~~~~~~p~~~~~~~ 80 (139)
T cd07967 1 MADTADLVVLGAYYGTGSKGGMMSVFLMGCYDPNSKKWCTVTKCGNGHDDATLARLQKELKMVKISKDPSKVPSWLKCNK 80 (139)
T ss_pred CCceEeEEEEEEEECCCCCCCccceEEEEEEeCCCCEEEEEeEECCCCCHHHHHHHHHHhhhhccccCCcCCCceEeecC
Confidence 4689999999999999999999999999999987889999999999999999999999999988754 345666666
Q ss_pred CCCCcEEec-C--ceEEEEEeceeecCccccccccccCCCCCceeeccEEeEEecCCCccCCCCHHH
Q 003632 721 TISPDVWFE-P--TEVWEVKAADLTISPVHRAAIGVVDPDKGISLRFPRLIRVREDKTPEQASSSEQ 784 (806)
Q Consensus 721 ~~~pdvwie-P--~~V~EV~~~eit~S~~~~a~~g~~~~~~G~sLRFPRf~riR~DK~~~da~t~~e 784 (806)
...||+||+ | ..||||+|+|||.||+|.++ |++||||||++||+||+|+||+|++|
T Consensus 81 ~~~Pdv~~~~P~~s~V~EV~~aeit~S~~~~a~--------G~tLRFPr~~~iR~DK~~~d~~t~~~ 139 (139)
T cd07967 81 SLVPDFIVKDPKKAPVWEITGAEFSKSEAHTAD--------GISIRFPRVTRIRDDKDWKTATSLPE 139 (139)
T ss_pred CCCCCEEEeCCCccEEEEEEeeeEEecCccccc--------CEEEEccEEEEEeCCCCHHHCccccC
Confidence 678999994 8 58999999999999999863 89999999999999999999999864
No 30
>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=100.00 E-value=1.4e-34 Score=290.07 Aligned_cols=176 Identities=35% Similarity=0.577 Sum_probs=146.1
Q ss_pred cchHHHHHHHHHHHhccchHHHHHHHHHHHHhhhcCCCCchHhHHHHHhCCcCCCccccccCCCHHHHHHHHHHHhCCCH
Q 003632 191 VPFIFLSLVFDMISNETGRILITDIVCNMLRTVMETTPEDLVPVVYLAANKIAPAHEGLELGIGDASIIKALAEACGRTE 270 (806)
Q Consensus 191 ~~F~~la~~~~~I~~tssr~~k~~iL~~~~r~~i~~~p~dl~~~vyL~~~~l~P~~e~~elgIg~~~L~Kal~~~~g~s~ 270 (806)
|+|++||++|++|+++++|++|+++|++||+.+. +.++.+++|+++++|+|+|++++|||+++.|+|++++++|+++
T Consensus 1 m~F~~l~~l~~~l~~~~~~~~k~~~l~~~~~~~~---~~~~~~~~~~~~~~l~P~~d~r~~~i~~~~L~k~~~~~~~~~~ 77 (177)
T PF04675_consen 1 MPFSDLCELFEKLESTSSRLEKIAILSNFFRSWR---EEDLGPDLYLLLRLLFPEYDGREYGIGEKLLAKAIAEALGLPE 77 (177)
T ss_dssp GBHHHHHHHHHHHHT---HHHHHHHHHHHHHTSH---CCGHHCHHHHHHTHSSTTTCS---S--HHHHHHHHHHHHTS-H
T ss_pred CcHHHHHHHHHHHHhccCHHHHHHHHHHHHHHcc---cchhhhHHHHHhcccccchhhhHhccchhHHHHHHHHHHcCCH
Confidence 7999999999999999999999999999999984 3448999999999999999999999999999999999999999
Q ss_pred HHHHHHHhhcCCHHHHHhhcccccC-ccCCCCCCCHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHhcCCChHHHHHHH
Q 003632 271 SHVKKQYQEMGDLGLVAKASRSSQS-MMRKPDPLTITKVFDTFRLIAKEAGKDSQEKKKNRIKALLVAATDCEPQYLIRL 349 (806)
Q Consensus 271 ~~ik~~~~~~GDlg~va~~~r~~q~-~l~~~~~LTI~eV~~~L~~IA~~~G~~sq~~k~~~L~~Ll~~~t~~E~k~LiRi 349 (806)
+.+.+.|++.||+|++|+.+...+. ....+.+|||.+||+.|++||..+|.+|++.|..+|..|+++|++.|++||+||
T Consensus 78 ~~~~~~~~~~GD~g~~~~~~~~~~~~~~~~~~~lTi~~V~~~L~~la~~~g~~s~~~k~~~l~~ll~~~s~~E~k~i~Ri 157 (177)
T PF04675_consen 78 KSIDESYKKVGDLGEVAEEVLQKRKSETSKPSPLTISEVNETLDELAAASGKGSQDEKIDILKELLRRCSPEEAKWIVRI 157 (177)
T ss_dssp HHHHHHHHHHS-HHHHHHHHHHHHTTTS--SS--BHHHHHHHHHHHHH--STTHHHHHHHHHHHHHTTS-HHHHHHHHHH
T ss_pred HHHHHHHHhcCcHHHHHHHHHhhccccccCCCCCCHHHHHHHHHHHHHhhCccchHHHHHHHHHHHHhCCHHHHHHHHHH
Confidence 9999999999999999998765544 333478999999999999999999999999999999999999999999999999
Q ss_pred HhhcccCcccHHHHHHHHHh
Q 003632 350 LQSKLRIGLAEQTLLAALGQ 369 (806)
Q Consensus 350 IlkdLRiG~~e~til~ala~ 369 (806)
|+++||||+++++|+.|||+
T Consensus 158 il~~lriG~~~~~il~ala~ 177 (177)
T PF04675_consen 158 ILKDLRIGVSEKTILDALAP 177 (177)
T ss_dssp HTT--SSS--HHHHHHHHHH
T ss_pred HhCCCeeCccHHHHHHHhCc
Confidence 99999999999999999985
No 31
>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=1.2e-33 Score=282.83 Aligned_cols=173 Identities=24% Similarity=0.250 Sum_probs=145.5
Q ss_pred CcccccccCCChHHHHhhcCCCceeEeeecceEeEEEEEecCCeEEEEecCCCcCCCCcchHHHHHHhhcCCCCCCeEEE
Q 003632 432 IGPMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAVSRLKKPSVRSFVLD 511 (806)
Q Consensus 432 v~PMLA~~~~~i~~~l~k~~g~~~~~E~KyDG~R~qih~~~~g~V~ifSR~gk~~T~~~Pel~~~l~~~~~~~v~~~ILD 511 (806)
++||||++.....+ +.+|++|+||||+|||+|. + ++|||+|+++|.. + .+...+ .++|||
T Consensus 1 ~~pmla~~~~~~~~------~~~~~~e~K~DG~R~~~~~---~--~~~SR~g~~~t~~-~----~~~~~l----~~~ilD 60 (174)
T cd07896 1 PELLLAKTYDEGED------ISGYLVSEKLDGVRAYWDG---K--QLLSRSGKPIAAP-A----WFTAGL----PPFPLD 60 (174)
T ss_pred CccccccccccCCC------hHHeeechhhceEEEEEec---c--EEEecCCcCCCCC-H----HHHhhC----CCCccC
Confidence 47999998765432 3589999999999999862 2 9999999999975 2 222223 359999
Q ss_pred EEEEEEecCCCccCChHHHHHhhhccCCccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccC-CCcEEEEeE
Q 003632 512 CEIVAYDREKQKILPFQTLSTRARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEE-PGFFQFATT 590 (806)
Q Consensus 512 GElVa~d~~~g~~~pFq~L~~r~rk~~~~~~~~~~v~~~vFDiLylnG~~L~~~Pl~eRr~~L~~l~~~~-~~~i~~~~~ 590 (806)
||+|+++ .||+.+++|.++.........+++|++||||+ .+.||.+|+++|++++... ++.+++++.
T Consensus 61 GElv~~~------~~f~~l~~~~~~~~~~~~~~~~~~f~vFDil~------~~~p~~eR~~~L~~~i~~~~~~~~~~~~~ 128 (174)
T cd07896 61 GELWIGR------GQFEQTSSIVRSKKPDDEDWRKVKFMVFDLPS------AKGPFEERLERLKNLLEKIPNPHIKIVPQ 128 (174)
T ss_pred ceEEcCC------CCHHHHHHHHhcCCCChhhcccceEEEEeCCC------CCCCHHHHHHHHHHHHHhCCCCcEEEEee
Confidence 9999985 39999999987654322345789999999998 5789999999999999876 467899999
Q ss_pred EecCCHHHHHHHHHHHHHcCCceeEEEeCCCCCCccCCCCCCCeEEEcc
Q 003632 591 LTSIDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLKK 639 (806)
Q Consensus 591 ~~~~~~eei~~~~~~ai~~g~EGlmlK~~~~ds~Y~pGkRs~~WlKlK~ 639 (806)
..+.+.+++.+++++++++|+||+|+|++ +++|++| |+.+|+|+||
T Consensus 129 ~~~~~~~~i~~~~~~~~~~g~EGlv~K~~--ds~Y~~g-R~~~wlK~Kp 174 (174)
T cd07896 129 IPVKSNEALDQYLDEVVAAGGEGLMLRRP--DAPYETG-RSDNLLKLKP 174 (174)
T ss_pred eeeCCHHHHHHHHHHHHhcCCCeEEEecC--CCcccCC-cCCCceeeCC
Confidence 99999999999999999999999999999 9999987 7899999997
No 32
>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=100.00 E-value=1.4e-33 Score=274.51 Aligned_cols=144 Identities=69% Similarity=1.178 Sum_probs=131.5
Q ss_pred CCcccEEEEEEEeCCCCCCCcccEEEEEEeeCCCCeEEEeeeccCCCCHHHHHHHHHhhccccCCCCCCCcccCCCCCCc
Q 003632 646 GDSLDLVPIAAFHGRGKRTGVYGAFLLACYDSNNEEFQSICKIGTGFSEAMLEERSSSLRSKVIPKPRPYYRFADTISPD 725 (806)
Q Consensus 646 ~dtlDlvVIGa~~G~Gkr~g~~gsfLla~~d~~~g~~~~v~kVgtGftd~~l~~l~~~l~~~~~~~p~~~~~~~~~~~pd 725 (806)
+|++|+||||+++|+|++.+.+|+|+||+||+++++|++|||||||||++++++|.++|.+++++.++.... ....|+
T Consensus 1 ~~t~D~vViG~~~g~g~~~~~~~slllG~~~~~~~~l~~vgkvgtGft~~~~~~L~~~l~~~~~~~~p~~~~--~~~~~~ 78 (144)
T cd07969 1 GDTLDLVPIGAYYGKGKRTGVYGAFLLACYDPETEEFQTVCKIGTGFSDEFLEELYESLKEHVIPKKPYRVD--SSLEPD 78 (144)
T ss_pred CCceeEEEEEEEECCCCCCCCcceEEEEEEeCCCCEEEEEeEEccCCCHHHHHHHHHHhhhhccccCCcccc--ccCCCc
Confidence 479999999999999999999999999999987789999999999999999999999999998876544321 224799
Q ss_pred EEecCceEEEEEeceeecCccccccccccCCCCCceeeccEEeEEecCCCccCCCCHHHHHHHHHH
Q 003632 726 VWFEPTEVWEVKAADLTISPVHRAAIGVVDPDKGISLRFPRLIRVREDKTPEQASSSEQVAEMYTA 791 (806)
Q Consensus 726 vwieP~~V~EV~~~eit~S~~~~a~~g~~~~~~G~sLRFPRf~riR~DK~~~da~t~~el~ely~~ 791 (806)
+||+|.+||||+|++||.|++|++|.|.+..+.|++||||||+++|+||+|+||+++++|.+||++
T Consensus 79 vWv~P~lV~EV~~~e~t~s~~~~~~~~~~~~~~g~~LRfPr~~~~R~Dk~~~~~~~~~~l~~l~~~ 144 (144)
T cd07969 79 VWFEPKEVWEVKAADLTLSPVHTAAIGLVDEEKGISLRFPRFIRVRDDKKPEDATTSEQIAEMYKK 144 (144)
T ss_pred EEEeeeEEEEEEEeEeecCcceeccccccccCCceEEEeeEEEEeeCCCChHHCCCHHHHHHHHhC
Confidence 999999999999999999999999999887778999999999999999999999999999999973
No 33
>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=3.9e-31 Score=266.34 Aligned_cols=175 Identities=28% Similarity=0.287 Sum_probs=140.9
Q ss_pred ccccccCCChHHHHhhcCCCceeEeeecceEeEEEEEecCCeEEEEecCCCcCCCCcchHHHHHHhhcCCCCCCeEEEEE
Q 003632 434 PMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAVSRLKKPSVRSFVLDCE 513 (806)
Q Consensus 434 PMLA~~~~~i~~~l~k~~g~~~~~E~KyDG~R~qih~~~~g~V~ifSR~gk~~T~~~Pel~~~l~~~~~~~v~~~ILDGE 513 (806)
|||+.......+. .+.+.+|++|+||||+|||+|+. +|.+++|||+|+++|..||++... ... ....++|||||
T Consensus 2 ~~~~~~~~~~~~~--~~~~~~~~~e~K~DG~R~~~~~~-~~~v~~~sR~g~~~~~~~~~~~~~--~~~-~~~~~~ilDGE 75 (182)
T cd06846 2 QLLNPILEEALSE--YDEQDEYYVQEKYDGKRALIVAL-NGGVFAISRTGLEVPLPSILIPGR--ELL-TLKPGFILDGE 75 (182)
T ss_pred CccchhhhHHHhh--ccccCcEEEEEccCceEEEEEEc-CCeEEEEeCCCCEEecccccccch--HHh-ccCCCeeEEEE
Confidence 7888876655332 35567899999999999999996 689999999999999999987541 111 12368999999
Q ss_pred EEEEecCCCccCChHHHHHhhhccCCccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCCC--cEEEEeE-
Q 003632 514 IVAYDREKQKILPFQTLSTRARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEPG--FFQFATT- 590 (806)
Q Consensus 514 lVa~d~~~g~~~pFq~L~~r~rk~~~~~~~~~~v~~~vFDiLylnG~~L~~~Pl~eRr~~L~~l~~~~~~--~i~~~~~- 590 (806)
+|+++.. + ...+++|++||||++||.+++++||.+|+++|++++...++ .+.+...
T Consensus 76 lv~~~~~------~---------------~~~~~~~~~FDil~~~~~~~~~~p~~eR~~~L~~~v~~~~~~~~~~i~~~~ 134 (182)
T cd06846 76 LVVENRE------V---------------ANPKPTYYAFDVVPLSGVGLRDLPYSDRFAYLKSLLKEFEGLDPVKLVPLE 134 (182)
T ss_pred EEeccCC------C---------------ccceeEEEEEEEEEECCCccccCCHHHHHHHHHHHhhhhccCCceeEEEee
Confidence 9998642 1 14579999999999999999999999999999999987642 3444433
Q ss_pred -EecCCHHHHHHHHHHHHHcCCceeEEEeCCCCCCc--cCCCCCCCeEEEcc
Q 003632 591 -LTSIDLDEIQKFLDAAVDASCEGLIIKTMDRDATY--EPSKRSLNWLKLKK 639 (806)
Q Consensus 591 -~~~~~~eei~~~~~~ai~~g~EGlmlK~~~~ds~Y--~pGkRs~~WlKlK~ 639 (806)
..+.+ +++.++|++++++|+||||+|++ +++| .+| |+..|+|+||
T Consensus 135 ~~~~~~-~~~~~~~~~~~~~g~EGvi~K~~--~s~Y~~~~g-r~~~wlK~Kp 182 (182)
T cd06846 135 NAPSYD-ETLDDLLEKLKKKGKEGLVFKHP--DAPYKGRPG-SSGNQLKLKP 182 (182)
T ss_pred cccccc-hHHHHHHHHhhhcCCceEEEEcC--CCCccccCC-CCCceEeecC
Confidence 23333 33899999999999999999999 9999 877 8999999997
No 34
>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=99.97 E-value=1.2e-30 Score=249.56 Aligned_cols=129 Identities=47% Similarity=0.835 Sum_probs=117.3
Q ss_pred CcccEEEEEEEeCCCCCCCcccEEEEEEeeCCCCeEEEeeeccCCCCHHHHHHHHHhhccccCCCCCCCcccCCCCCCcE
Q 003632 647 DSLDLVPIAAFHGRGKRTGVYGAFLLACYDSNNEEFQSICKIGTGFSEAMLEERSSSLRSKVIPKPRPYYRFADTISPDV 726 (806)
Q Consensus 647 dtlDlvVIGa~~G~Gkr~g~~gsfLla~~d~~~g~~~~v~kVgtGftd~~l~~l~~~l~~~~~~~p~~~~~~~~~~~pdv 726 (806)
|++|+||+|+++|+|+++|++|+||||+||+++++|++|||||||||++++++|.++|.+++++.+++. ......|++
T Consensus 1 d~~D~VI~G~~~~~g~~~~~~~slLlg~~d~~~~~l~~vgkvgtGfs~~~~~~l~~~l~~~~~~~~p~~--~~~~~~~~~ 78 (129)
T cd07893 1 DTLDLVIVGAYYGKGRRGGGIGAFLCAVYDPERDEFQTICKVGSGFTDEELEELRELLKELKTPEKPPR--VNSIEKPDF 78 (129)
T ss_pred CcEEEEEEeeEcCCCCcCCCcceEEEEEEcCCCCEEEEEeEECCCCCHHHHHHHHHHhhcccccCCCCc--ccccCCCcE
Confidence 589999999999999999999999999999777899999999999999999999999999988765442 233457999
Q ss_pred EecCceEEEEEeceeecCccccccccccCCCCCceeeccEEeEEecCCCccCC
Q 003632 727 WFEPTEVWEVKAADLTISPVHRAAIGVVDPDKGISLRFPRLIRVREDKTPEQA 779 (806)
Q Consensus 727 wieP~~V~EV~~~eit~S~~~~a~~g~~~~~~G~sLRFPRf~riR~DK~~~da 779 (806)
||+|..||||+|++||.|+.|++++|. .++|++||||||+++|+||+|+||
T Consensus 79 wv~P~lV~EV~~~e~t~s~~~~~~~~~--~~~g~~LRfPr~~~~R~Dk~~~e~ 129 (129)
T cd07893 79 WVEPKVVVEVLADEITRSPMHTAGRGE--EEEGYALRFPRFVRIRDDKGPEDA 129 (129)
T ss_pred EEeeeEEEEEEeeeeeeCccccccccc--CCCceEEECCEEEEEeCCCChhhC
Confidence 999999999999999999999998877 468899999999999999999987
No 35
>cd07968 OBF_DNA_ligase_IV The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase IV is a DNA-binding module that is part of the catalytic core unit. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriohages, eukarya, archaea and bacteria. There are three classes of ATP-dependent DNA ligases in eukaryotic cells (I, III and IV). DNA ligase IV is required for DNA non-homologous end joining pathways, including recombination of the V(D)J immunoglobulin gene segments in cells of the mammalian immune system. DNA ligase IV is stabilized by forming a complex with XRCC4, a nuclear phosphoprotein, which is phosphorylated by DNA-dependent pro
Probab=99.96 E-value=5e-30 Score=248.67 Aligned_cols=128 Identities=36% Similarity=0.600 Sum_probs=111.4
Q ss_pred CCcccEEEEEEEeCCCCCCCcccEEEEEEeeCCCC------eEEEeeeccCCCCHHHHHHHHHhhccccCCC---CCCCc
Q 003632 646 GDSLDLVPIAAFHGRGKRTGVYGAFLLACYDSNNE------EFQSICKIGTGFSEAMLEERSSSLRSKVIPK---PRPYY 716 (806)
Q Consensus 646 ~dtlDlvVIGa~~G~Gkr~g~~gsfLla~~d~~~g------~~~~v~kVgtGftd~~l~~l~~~l~~~~~~~---p~~~~ 716 (806)
+|++||||||+++|+|+++|.+|+||||+||.+.+ +|++|||||||||++++++|.++|++++++. .+++.
T Consensus 1 ~~~lDlvViG~~~g~g~~~~~~~slllG~~~~~~~~~~~~~~l~~vgkVgtGfs~~~~~~L~~~l~~~~~~~~~~~~P~~ 80 (140)
T cd07968 1 GEDLDLLIIGGYYGEGRRGGKVSSFLCGVAEDDDPESDKPSVFYSFCKVGSGFSDEELDEIRRKLKPHWKPFDKKAPPSS 80 (140)
T ss_pred CCcEeEEEEccEeCCCCcCCccccEEEEEEcCCCCCCCCCCEEEEEEEEccCCCHHHHHHHHHHhcCcEEEcCcCCCCcc
Confidence 47999999999999999999999999999987544 8999999999999999999999999987642 12221
Q ss_pred -ccCCCCCCcEEecCc--eEEEEEeceeecCccccccccccCCCCCceeeccEEeEEecCCCccCCCCH
Q 003632 717 -RFADTISPDVWFEPT--EVWEVKAADLTISPVHRAAIGVVDPDKGISLRFPRLIRVREDKTPEQASSS 782 (806)
Q Consensus 717 -~~~~~~~pdvwieP~--~V~EV~~~eit~S~~~~a~~g~~~~~~G~sLRFPRf~riR~DK~~~da~t~ 782 (806)
.......|++||+|. +||||+|+|||.|+.|++ |++||||||+++|+||+|+||+|+
T Consensus 81 ~~~~~~~~~~~Wv~P~~slV~EV~~~e~t~s~~~~~---------g~~LR~Pr~~~~R~DK~~~e~~t~ 140 (140)
T cd07968 81 LLKFGKEKPDVWIEPKDSVVLEVKAAEIVPSDSYKT---------GYTLRFPRCEKIRYDKDWHDCLTL 140 (140)
T ss_pred cccccccCCcEEEecCCCEEEEEEeeeEeecCcccC---------CcEEEcceEeEEECCCCHHHccCC
Confidence 112334799999999 999999999999999985 789999999999999999999984
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=99.96 E-value=8.9e-30 Score=241.37 Aligned_cols=121 Identities=39% Similarity=0.683 Sum_probs=112.2
Q ss_pred CcccEEEEEEEeCCCCCCCcccEEEEEEeeCCCCeEEEeeeccCCCCHHHHHHHHHhhccccCCCCCCCcccCCCCCCcE
Q 003632 647 DSLDLVPIAAFHGRGKRTGVYGAFLLACYDSNNEEFQSICKIGTGFSEAMLEERSSSLRSKVIPKPRPYYRFADTISPDV 726 (806)
Q Consensus 647 dtlDlvVIGa~~G~Gkr~g~~gsfLla~~d~~~g~~~~v~kVgtGftd~~l~~l~~~l~~~~~~~p~~~~~~~~~~~pdv 726 (806)
|++|+||+|+++|+|+++|++|+||||+||+++|+|++||+||||||++++++|.+.++++.+.. ..|++
T Consensus 1 ~t~d~vi~G~~~~~g~~~~~~~slllg~~d~~~g~l~~vg~vgtG~~~~~~~~l~~~l~~~~~~~----------~~~~~ 70 (122)
T cd07972 1 ETLDLVVIGAEWGEGRRAGLLGSYTLAVRDEETGELVPVGKVATGLTDEELEELTERLRELIIEK----------FGPVV 70 (122)
T ss_pred CceeEEEEeeEeCCCCcCCCcccEEEEEEcCCCCeEEEEEEEccCCCHHHHHHHHHHhhhhhccc----------cCCcE
Confidence 58999999999999999999999999999876689999999999999999999999998876542 15899
Q ss_pred EecCceEEEEEeceeecCccccccccccCCCCCceeeccEEeEEecCCCccCCCCHHHHH
Q 003632 727 WFEPTEVWEVKAADLTISPVHRAAIGVVDPDKGISLRFPRLIRVREDKTPEQASSSEQVA 786 (806)
Q Consensus 727 wieP~~V~EV~~~eit~S~~~~a~~g~~~~~~G~sLRFPRf~riR~DK~~~da~t~~el~ 786 (806)
|++|.+||||+|++||.|+.|++ |++||||||+++|+||+|+||+|+++|.
T Consensus 71 wv~P~lV~eV~~~e~t~s~~~~~---------g~~LR~Prf~~~R~Dk~~~~~~t~~~~~ 121 (122)
T cd07972 71 SVKPELVFEVAFEEIQRSPRYKS---------GYALRFPRIVRIRDDKDPDEADTLERVE 121 (122)
T ss_pred EEeceEEEEEEeeEEEecCcccc---------CceEEccEEeEEeCCCChHHCcCHHHHh
Confidence 99999999999999999999985 7899999999999999999999999985
No 37
>cd07895 Adenylation_mRNA_capping Adenylation domain of GTP-dependent mRNA capping enzymes. RNA capping enzymes transfer GMP from GTP to the 5'-diphosphate end of nascent mRNAs to form a G(5')ppp(5')RNA cap structure. The RNA cap is found only in eukarya. RNA capping is chemically analogous to the first two steps of polynucleotide ligation. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation of nicked nucleic acid substrates using the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. Structural studies reveal a shared structure for DNA ligases and capping enzymes, with a common catalytic core composed of an adenylation or nucleotidyltransferase domain and a C-terminal OB-fold domain containing conserved sequence motifs. The adenylation domain binds ATP and contains many active site residues.
Probab=99.94 E-value=1e-26 Score=240.45 Aligned_cols=162 Identities=22% Similarity=0.207 Sum_probs=127.9
Q ss_pred cCCCceeEeeecceEeEEEEEecC-CeEEEEecCCCcCCCCcchHHHHHHhhcCCCCCCeEEEEEEEEEecCCCccCChH
Q 003632 450 FQDMEFTCEYKYDGERAQIHYLED-GSVEIYSRNAERNTGKFPDVVLAVSRLKKPSVRSFVLDCEIVAYDREKQKILPFQ 528 (806)
Q Consensus 450 ~~g~~~~~E~KyDG~R~qih~~~~-g~V~ifSR~gk~~T~~~Pel~~~l~~~~~~~v~~~ILDGElVa~d~~~g~~~pFq 528 (806)
+...+|++|+||||+|+|+|+. + +.+.+|||+++.++..+|++.+... ......++|||||+|+++.. +
T Consensus 38 ~~~~~y~ve~K~DG~R~~l~~~-~~~~v~l~sR~~~~~~~~~~~~~~~~~--~~~~~~~~ilDGElv~~~~~-~------ 107 (215)
T cd07895 38 LKQNDYFVCEKSDGVRYLLLIT-GRGEVYLIDRKNDVFKVPGLFFPRRKN--LEPHHQGTLLDGELVIDKVP-G------ 107 (215)
T ss_pred HhhCCeEEEEeEcCeEEEEEEe-cCCcEEEEeCCCCeEEeccccCCCccc--ccccccCeeeEEEEEEEcCC-C------
Confidence 4456899999999999999996 5 7899999999999988888653211 11134789999999998642 1
Q ss_pred HHHHhhhccCCccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCCCc-E-----------EEEeEEecCCH
Q 003632 529 TLSTRARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEPGF-F-----------QFATTLTSIDL 596 (806)
Q Consensus 529 ~L~~r~rk~~~~~~~~~~v~~~vFDiLylnG~~L~~~Pl~eRr~~L~~l~~~~~~~-i-----------~~~~~~~~~~~ 596 (806)
..+++|+|||||++||+++.+.||.+|+++|++++...... + ..+........
T Consensus 108 ---------------~~~~~~~vFDiL~~~g~~l~~~pl~~R~~~L~~~i~~~~~~~~~~~~~~~~~~~~~i~~k~~~~~ 172 (215)
T cd07895 108 ---------------KKRPRYLIFDILAFNGQSVTEKPLSERLKYIKKEVIEPRNELLKKGPIDKAKEPFSVRLKDFFPL 172 (215)
T ss_pred ---------------ceEEEEEEEEEEEECCcCccCCCHHHHHHHHHHhchhHHHHhhhcChhhcCCCCeEEEecceEeH
Confidence 24789999999999999999999999999999998542111 0 01111222234
Q ss_pred HHHHHHHHHH---HHcCCceeEEEeCCCCCCccCCCCCCCeEEEcc
Q 003632 597 DEIQKFLDAA---VDASCEGLIIKTMDRDATYEPSKRSLNWLKLKK 639 (806)
Q Consensus 597 eei~~~~~~a---i~~g~EGlmlK~~~~ds~Y~pGkRs~~WlKlK~ 639 (806)
+++..+|+.+ +.+|.||||+|+. +++|.+| |+..|+|+||
T Consensus 173 ~~~~~~~~~~~~~~~~~~EGlIfk~~--~~~Y~~G-r~~~~lKwKp 215 (215)
T cd07895 173 YKIEKLFEKIIPKLPHENDGLIFTPN--DEPYVPG-TDKNLLKWKP 215 (215)
T ss_pred HhHHHHHHhccccCCCCCCCEEEccC--CCCccCc-cCCcceeeCC
Confidence 5778888888 5999999999999 9999999 9999999997
No 38
>KOG4437 consensus ATP-dependent DNA ligase III [Replication, recombination and repair]
Probab=99.92 E-value=1.4e-24 Score=227.89 Aligned_cols=326 Identities=20% Similarity=0.298 Sum_probs=237.0
Q ss_pred chHHHHHHHHHHHhccchHHHHHHHHHHHHhhhcCCCCchHhHHHHHhCCcCCCccccccCCCHHHHHHHHHHHhCCCHH
Q 003632 192 PFIFLSLVFDMISNETGRILITDIVCNMLRTVMETTPEDLVPVVYLAANKIAPAHEGLELGIGDASIIKALAEACGRTES 271 (806)
Q Consensus 192 ~F~~la~~~~~I~~tssr~~k~~iL~~~~r~~i~~~p~dl~~~vyL~~~~l~P~~e~~elgIg~~~L~Kal~~~~g~s~~ 271 (806)
+|..|.++|..|+..+....|++.++.+|++- +.|++-++|.-|| ..+.+.+.|||.++.||+.+++++++...
T Consensus 156 ~F~ef~kiCS~L~~~p~~~~Kt~VI~~LL~kd-NFDGDL~LWL~FL-----IRESD~R~YNl~DkKLI~lfsKiLn~~~~ 229 (482)
T KOG4437|consen 156 LFREFRKLCSMLADNPSYNTKTQVIQDLLRKD-NFDGDLYLWLKFL-----IRESDKRVYNLNDKKLIKLFSKILNCNPD 229 (482)
T ss_pred HHHHHHHHHHHHHhCcCccchhHHHHHHHhcc-CCCcchhhhhhhh-----hcccccccccccHHHHHHHHHHHHccChH
Confidence 59999999999999999999999999999873 3455656655554 56778999999999999999999999976
Q ss_pred HHHHHHh-hcCCHHHHHhhcccccCccCCCCCCCHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHhcCCChHHHHHHHH
Q 003632 272 HVKKQYQ-EMGDLGLVAKASRSSQSMMRKPDPLTITKVFDTFRLIAKEAGKDSQEKKKNRIKALLVAATDCEPQYLIRLL 350 (806)
Q Consensus 272 ~ik~~~~-~~GDlg~va~~~r~~q~~l~~~~~LTI~eV~~~L~~IA~~~G~~sq~~k~~~L~~Ll~~~t~~E~k~LiRiI 350 (806)
..-..|. ...|.+.-+...-.+ +.....+-+||++|+++|.+|++++..+. .++.|+....+|+..|.++|||+|
T Consensus 230 ~~~~~Y~~~S~~~~i~i~~~~~K-~~~~~K~~~siQ~~D~~L~rLSKi~~~D~---~~~~L~~~A~R~~~~~L~~iIRLI 305 (482)
T KOG4437|consen 230 DMARDYEQGSVSETIRVFFEQSK-SFPPAKSLLTIQEVDEFLLRLSKLTKEDE---QQQALQDIASRCTANDLKCIIRLI 305 (482)
T ss_pred HHHHHHHhccchhhhhhhHhhcc-CCCCcccceeHHHHHHHHHHHhcccchHH---HHHHHHHHHHhcccchHHHHHHHH
Confidence 6655553 344554433221111 11113467999999999999999886554 468899999999999999999999
Q ss_pred hhcccCcccHHHHHHHHHhhhcccCCCCCCCCCCcccHHHHHHHHHHHhhcCCchhhhHhhhhhcCccccCCccccCCCC
Q 003632 351 QSKLRIGLAEQTLLAALGQAAVYNEQHSKPPPNIQSPLEEAAKIVKQVFSVLPVYEKIVPALLTDGVWNLSNTCSFTPGI 430 (806)
Q Consensus 351 lkdLRiG~~e~til~ala~A~~~~~~~~~~~~~l~~~l~~a~~~~k~~y~~~p~~~~v~~~ll~~g~~~l~~~~~l~~g~ 430 (806)
.++|....+.+.||+++++-++.-.. .++|++.+++. |+ |++.+. .+.|..+.. ...-.+..
T Consensus 306 r~~L~~~s~A~~iL~~~~P~A~E~F~----S~~L~~ViEr~-------~~---N~~~~~---~~~~~~~~~-s~~s~~~s 367 (482)
T KOG4437|consen 306 KHDLKMNSGAKHVLDALDPNAYEAFK----SRNLQDVVERV-------LH---NAQEVE---KEPGQRRAL-SVQASLMT 367 (482)
T ss_pred HHHhccCCChhHHHhccCCCcHHHHH----hcCHHHHHHHH-------HH---hHHHHh---hCccccccc-cchhhhcC
Confidence 99999999999999999875432111 12344444433 32 233332 133333211 11234568
Q ss_pred CCcccccccCCChHHHHhhcCCCceeEeeecceEeEEEEEecCCeEEEEecCCCcCCCCcchHHHHHHhhcCCCCCCeEE
Q 003632 431 PIGPMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAVSRLKKPSVRSFVL 510 (806)
Q Consensus 431 Pv~PMLA~~~~~i~~~l~k~~g~~~~~E~KyDG~R~qih~~~~g~V~ifSR~gk~~T~~~Pel~~~l~~~~~~~v~~~IL 510 (806)
|++|||+..+++++-..++.+| +...|.||||+|.|+|.+ ++.|.+|||--+... ...+.+.+.+. +..+.++
T Consensus 368 ~~Q~~~~~~~~~VE~s~~~~~~-~~~S~~~~D~E~~~~~~~-~D~~S~~S~~~~~~s----~FK~~~P~~~~-~G~~~~~ 440 (482)
T KOG4437|consen 368 PVQPMLAEACKSVEYAMKKCPN-GMFSEIKYDGERVQVHKN-GDHFSYFSRLPHKVA----HFKDYIPQAFP-GGHSMIL 440 (482)
T ss_pred CcChhhhhhhhhHHHHhccCCC-CccccccCCCceeeccCC-CcchhhhccChHhhh----hhhhcCchhcC-CCccccc
Confidence 9999999999999888877776 566899999999999985 668999998765432 12233444443 4578999
Q ss_pred EEEEEEEecCCCccCChHHHHHhhhccCCccccccceEEEEeeeee
Q 003632 511 DCEIVAYDREKQKILPFQTLSTRARKNVSLSDIKVDVCIYAFDILY 556 (806)
Q Consensus 511 DGElVa~d~~~g~~~pFq~L~~r~rk~~~~~~~~~~v~~~vFDiLy 556 (806)
|||...++..+|+++||+++.-..+-.. ...++|.++||++|
T Consensus 441 ~~~~~~I~~K~~~P~~~~~~~~~~K~~~----~~~~~~~~~~~~~~ 482 (482)
T KOG4437|consen 441 DSEVLLIDNKTGKPLPFGTLGVHKKAAF----QDANVCLFVFDCIY 482 (482)
T ss_pred cccccceecccCCCCCchhcchhhHHHh----cCcchheeecccCC
Confidence 9999999999999999998854321110 13568999999875
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=99.90 E-value=2.1e-23 Score=195.79 Aligned_cols=114 Identities=28% Similarity=0.355 Sum_probs=97.9
Q ss_pred cccEEEEEEEeCCCCCCCcccEEEEEEeeCCCCeEEEeeeccCCCCHHHHHHHHHhhccccCCCCCCCcccCCCCCCcEE
Q 003632 648 SLDLVPIAAFHGRGKRTGVYGAFLLACYDSNNEEFQSICKIGTGFSEAMLEERSSSLRSKVIPKPRPYYRFADTISPDVW 727 (806)
Q Consensus 648 tlDlvVIGa~~G~Gkr~g~~gsfLla~~d~~~g~~~~v~kVgtGftd~~l~~l~~~l~~~~~~~p~~~~~~~~~~~pdvw 727 (806)
+.|+||+|++.+.| +.|.+|+||||+||+ ++|++||+||||||++++++|++.+.++..+.|+..........+++|
T Consensus 2 ~~~~vI~G~~~~~g-~~~~~gslllg~~~~--~~l~~vG~vgtG~s~~~~~~l~~~l~~~~~~~~p~~~~~~~~~~~~~w 78 (115)
T cd07971 2 RQEFVIGGYTPPKG-SRGGFGSLLLGVYDG--GRLVYVGRVGTGFSAATLRELRERLAPLERKTSPFADPPPADARGAVW 78 (115)
T ss_pred CceEEEEEEECCCC-CCCcccEEEEEEEcC--CEEEEeeeEcCCCCHHHHHHHHHHhhcccCCCCCCcccccccCCCCEE
Confidence 57899999888888 788999999999986 489999999999999999999999999887765432211223468999
Q ss_pred ecCceEEEEEeceeecCccccccccccCCCCCceeeccEEeEEecCCCccCC
Q 003632 728 FEPTEVWEVKAADLTISPVHRAAIGVVDPDKGISLRFPRLIRVREDKTPEQA 779 (806)
Q Consensus 728 ieP~~V~EV~~~eit~S~~~~a~~g~~~~~~G~sLRFPRf~riR~DK~~~da 779 (806)
|+|.+||||+|+++|.+ .+||||||+++|+||+|+||
T Consensus 79 v~P~lv~eV~~~~~t~~---------------~~LR~P~f~~~R~Dk~~~~~ 115 (115)
T cd07971 79 VKPELVAEVEFAEWTPD---------------GRLRHPVFKGLREDKPAAEV 115 (115)
T ss_pred ecCCEEEEEEEEEecCC---------------CcEECCeeeEeeCCCCcccC
Confidence 99999999999999953 49999999999999999987
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=99.89 E-value=5.4e-23 Score=187.34 Aligned_cols=97 Identities=45% Similarity=0.678 Sum_probs=81.1
Q ss_pred CCCcccEEEEEEeeCCCCeEEEeeeccCCCCHHHHHHHHHhhccccCCCCCCCcccCCCCCCcEEecCceEEEEEeceee
Q 003632 663 RTGVYGAFLLACYDSNNEEFQSICKIGTGFSEAMLEERSSSLRSKVIPKPRPYYRFADTISPDVWFEPTEVWEVKAADLT 742 (806)
Q Consensus 663 r~g~~gsfLla~~d~~~g~~~~v~kVgtGftd~~l~~l~~~l~~~~~~~p~~~~~~~~~~~pdvwieP~~V~EV~~~eit 742 (806)
|+|.+|+||||+||+++++|++||+||||||++++++|.+.|.+++++.++..........|++||+|..||||+|+|||
T Consensus 1 R~g~~~slllg~~d~~~~~l~~vg~vgtG~~~~~~~~l~~~l~~~~~~~~p~~~~~~~~~~~~~wv~P~~V~eV~~~e~t 80 (97)
T PF04679_consen 1 RGGGIGSLLLGVYDPDSGRLVYVGKVGTGFSDEELRELRERLEPLWIKKPPFDVKPPSRERPDVWVEPELVVEVKFAEIT 80 (97)
T ss_dssp GTTSEEEEEEEEEETTTTEEEEEEEE-SS--HHHHHHHHHHHGGGEEEEETTTCCECCSCTTEEEE-ST-EEEEEESEEE
T ss_pred CCCccceEEEEEEcCCCCcEEEEEEECCCCCHHHHHHHHHHhhCccccCCCCccccccCccCcEEeCCCEEEEEEEEEEc
Confidence 56889999999999988999999999999999999999999999987766443333333579999999999999999999
Q ss_pred cCccccccccccCCCCCceeeccEEeEEecCC
Q 003632 743 ISPVHRAAIGVVDPDKGISLRFPRLIRVREDK 774 (806)
Q Consensus 743 ~S~~~~a~~g~~~~~~G~sLRFPRf~riR~DK 774 (806)
.+ | +||||||+++|+||
T Consensus 81 ~~--------------G-~lR~P~~~~~R~DK 97 (97)
T PF04679_consen 81 PS--------------G-SLRFPRFKRIREDK 97 (97)
T ss_dssp EE--------------S-EEESEEEEEEETTS
T ss_pred CC--------------C-eEECCEEeEEeCCC
Confidence 76 8 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=99.87 E-value=9.6e-22 Score=182.55 Aligned_cols=108 Identities=28% Similarity=0.330 Sum_probs=92.2
Q ss_pred CcccEEEEEEEeCCCCCCCcccEEEEEEeeCCCCeEEEeeeccCCCCHHHHHHHHHhhccccCCCCCCCcccCCCCCCcE
Q 003632 647 DSLDLVPIAAFHGRGKRTGVYGAFLLACYDSNNEEFQSICKIGTGFSEAMLEERSSSLRSKVIPKPRPYYRFADTISPDV 726 (806)
Q Consensus 647 dtlDlvVIGa~~G~Gkr~g~~gsfLla~~d~~~g~~~~v~kVgtGftd~~l~~l~~~l~~~~~~~p~~~~~~~~~~~pdv 726 (806)
|++|+||+|+++|.|+++|.+|+||||+||++ .++++|+||||||++++++|++.++++..+.++..........+++
T Consensus 1 ~~~d~vV~G~~~~~g~~~~~~gslllg~~~~~--~~~~vg~vgtGf~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~v 78 (108)
T cd08040 1 KTAEAVIIGMRAGFGNRSDVMGSLLLGYYGED--GLQAVFSVGTGFSADERRDLWQNLEPLVTSFDDHPVWNVGKDLSFV 78 (108)
T ss_pred CceeEEEEEeEeCCCCCCCceEEEEEEEECCC--ceEEEEEEcCCCCHHHHHHHHHhcchhccCCCCCcccccccCCCCE
Confidence 58999999999999999999999999999863 4889999999999999999999999887765432211222346899
Q ss_pred EecCceEEEEEeceeecCccccccccccCCCCCceeeccEEeEEe
Q 003632 727 WFEPTEVWEVKAADLTISPVHRAAIGVVDPDKGISLRFPRLIRVR 771 (806)
Q Consensus 727 wieP~~V~EV~~~eit~S~~~~a~~g~~~~~~G~sLRFPRf~riR 771 (806)
|++|.+||||+|+++|. |.+||||||+++|
T Consensus 79 wv~P~lv~eV~~~~~t~---------------~~~lR~P~f~~~R 108 (108)
T cd08040 79 PLYPGKVVEVKYFEMGS---------------KDCLRFPVFIGIR 108 (108)
T ss_pred EeeceEEEEEEeEEeeC---------------CCeEECCeEEEeC
Confidence 99999999999999984 4699999999997
No 42
>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=99.81 E-value=1.6e-19 Score=171.38 Aligned_cols=114 Identities=25% Similarity=0.308 Sum_probs=94.3
Q ss_pred CcccEEEEEEEeCCCCCCCcccEEEEEEeeCCCCeEEEeeeccCCCCHHHHHHHHHhhccccCCCCCC-----Cc-ccC-
Q 003632 647 DSLDLVPIAAFHGRGKRTGVYGAFLLACYDSNNEEFQSICKIGTGFSEAMLEERSSSLRSKVIPKPRP-----YY-RFA- 719 (806)
Q Consensus 647 dtlDlvVIGa~~G~Gkr~g~~gsfLla~~d~~~g~~~~v~kVgtGftd~~l~~l~~~l~~~~~~~p~~-----~~-~~~- 719 (806)
|+.|+||+|+.++. +.+|++|||+||+ .|+|++||+| ||||++++++|.+.|+++.++.|+. |. .++
T Consensus 1 ~~~e~vI~G~~~~~----~~~gsLlLg~~~~-~g~l~yvG~v-tGf~~~~~~~L~~~l~~l~~~~p~~~~~~~~~~~~~~ 74 (122)
T cd07970 1 RTADCVVGGVRGHK----DRPGSLLLGLYDD-GGRLRHVGRT-SPLAAAERRELAELLEPARAGHPWTGRAPGFPSRWGT 74 (122)
T ss_pred CcEeEEEEEEECCC----CCccEEEEEEECC-CCCEEEEEEE-CCCCHHHHHHHHHHHHHhhcCCCCcccccccccccCc
Confidence 47899999998776 5689999999975 4689999999 9999999999999999987665431 11 011
Q ss_pred CCCCCcEEecCceEEEEEeceeecCccccccccccCCCCCceeecc-EEeEEecCCCccCCCC
Q 003632 720 DTISPDVWFEPTEVWEVKAADLTISPVHRAAIGVVDPDKGISLRFP-RLIRVREDKTPEQASS 781 (806)
Q Consensus 720 ~~~~pdvwieP~~V~EV~~~eit~S~~~~a~~g~~~~~~G~sLRFP-Rf~riR~DK~~~da~t 781 (806)
....+.+|++|.+|+||+|+++|.+ | .|||| ||+++|+||+++||+.
T Consensus 75 ~~~~~~~wv~P~lV~eV~~~e~t~~--------------G-~LRhP~~f~glR~Dk~~~~v~~ 122 (122)
T cd07970 75 RKSLEWVPVRPELVVEVSADTAEGG--------------G-RFRHPLRFLRWRPDKSPEDCTL 122 (122)
T ss_pred ccCCCeEEeeccEEEEEEeeEEecC--------------C-ceeCCceeEEEcCCCCHHHCcC
Confidence 1134789999999999999999964 6 99999 8999999999999863
No 43
>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=99.75 E-value=9.4e-18 Score=184.49 Aligned_cols=163 Identities=20% Similarity=0.263 Sum_probs=123.0
Q ss_pred CceeEeeecceEeEEEEEecCCeEEEEecCCCc---CCCCcchHHHHHHhhcCCCCCCeEEEEEEEEEecCCCccCChHH
Q 003632 453 MEFTCEYKYDGERAQIHYLEDGSVEIYSRNAER---NTGKFPDVVLAVSRLKKPSVRSFVLDCEIVAYDREKQKILPFQT 529 (806)
Q Consensus 453 ~~~~~E~KyDG~R~qih~~~~g~V~ifSR~gk~---~T~~~Pel~~~l~~~~~~~v~~~ILDGElVa~d~~~g~~~pFq~ 529 (806)
.+|++|+|+||.|+++|++ +|++.+|||+|.. .|+.+|++.. ..++. ...++|||||+++.+. ||..
T Consensus 48 ~~~~vEEKlDG~nvri~~~-~G~v~a~TR~G~i~e~~T~~~~eiv~--~~~~~-~~p~~iLdGElvg~~~------p~v~ 117 (342)
T cd07894 48 GPVAVEEKMNGYNVRIVRI-GGKVLAFTRGGFICPFTTDRLRDLID--PEFFD-DHPDLVLCGEVVGPEN------PYVP 117 (342)
T ss_pred CCEEEEEeECCcEEEEEEE-CCEEEEEeCCCccCccchhhHhhhch--HHhhc-cCCCEEEEEEEEecCC------cccc
Confidence 5899999999999999996 7899999999864 4888888842 22222 2367999999998752 3311
Q ss_pred HHHhhhccCCccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCCCcEEEEeEEecCCHHHHHHHHHHHHHc
Q 003632 530 LSTRARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAAVDA 609 (806)
Q Consensus 530 L~~r~rk~~~~~~~~~~v~~~vFDiLylnG~~L~~~Pl~eRr~~L~~l~~~~~~~i~~~~~~~~~~~eei~~~~~~ai~~ 609 (806)
.... ...++.|++|||++.|+ ...+|+.+|+++|+++.-+. ...+....+.+.+++.++++++.++
T Consensus 118 ------~~~~---~~~~v~F~vFDI~~~~~--~~~lp~~eR~~lLe~lg~~~---v~~~~~~~~~d~~~l~~~l~~~~~~ 183 (342)
T cd07894 118 ------GSYP---EVEDVGFFVFDIRKKNT--GRPLPVEERRELLEKYGLPT---VRLFGEFTADEIEELKEIIRELDKE 183 (342)
T ss_pred ------ccCc---cccccEEEEEeeEEcCC--CCCCCHHHHHHHHHhcCCCC---cceEEEEecCCHHHHHHHHHHHHHC
Confidence 0000 12588999999999885 55789999999999983221 2223345677789999999999999
Q ss_pred CCceeEEEeCCCCC-----CccCCCCCCCeEEEcccc
Q 003632 610 SCEGLIIKTMDRDA-----TYEPSKRSLNWLKLKKDY 641 (806)
Q Consensus 610 g~EGlmlK~~~~ds-----~Y~pGkRs~~WlKlK~dY 641 (806)
|+||||+|++ ++ .|......-++|++.-.|
T Consensus 184 G~EGVVlK~~--~~~~~~~Ky~t~~~~~~di~~~~~~ 218 (342)
T cd07894 184 GREGVVLKDP--DMRVPPLKYTTSYSNCSDIRYAFRY 218 (342)
T ss_pred CCceEEEecc--ccccCcceeecCCCCcHHHHHHhhh
Confidence 9999999999 77 687666666777777666
No 44
>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=99.34 E-value=2e-12 Score=113.16 Aligned_cols=76 Identities=30% Similarity=0.469 Sum_probs=65.1
Q ss_pred cccEEEEEEEeCCCCCCCcccEEEEEEeeCCCCeEEEeeeccCCCCHHHHHHHHHhhccccCCCCCCCcccCCCCCCcEE
Q 003632 648 SLDLVPIAAFHGRGKRTGVYGAFLLACYDSNNEEFQSICKIGTGFSEAMLEERSSSLRSKVIPKPRPYYRFADTISPDVW 727 (806)
Q Consensus 648 tlDlvVIGa~~G~Gkr~g~~gsfLla~~d~~~g~~~~v~kVgtGftd~~l~~l~~~l~~~~~~~p~~~~~~~~~~~pdvw 727 (806)
+.|++|+|+++|.|++.|.+|+|+|+.+|. . +++||||||++++++++.
T Consensus 2 ~~e~vIvG~~~g~g~~~~~~g~llv~~~~g---~---~~~vgtG~t~~~r~~~~~------------------------- 50 (77)
T cd08041 2 DAEARVVGYEEGKGKYEGMLGALVVETKDG---I---RFKIGSGFSDEQRRNPPP------------------------- 50 (77)
T ss_pred ceeEEEEEEEcCCCccCCcEEEEEEEecCC---C---EEEEcCCCCHHHHhcCCC-------------------------
Confidence 689999999999999999999999999873 2 358999999999986651
Q ss_pred ecCceEEEEEeceeecCccccccccccCCCCCceeeccEEeEEe
Q 003632 728 FEPTEVWEVKAADLTISPVHRAAIGVVDPDKGISLRFPRLIRVR 771 (806)
Q Consensus 728 ieP~~V~EV~~~eit~S~~~~a~~g~~~~~~G~sLRFPRf~riR 771 (806)
| ..|+||+|.++|.. | .||||+|+++|
T Consensus 51 ~--g~v~~V~y~e~t~~--------------g-~lR~P~f~g~R 77 (77)
T cd08041 51 I--GSIITYKYQGLTKN--------------G-LPRFPVFLRVR 77 (77)
T ss_pred C--CCEEEEEEEecCCC--------------C-cccCCEEEecC
Confidence 1 25999999999953 4 99999999997
No 45
>PF01331 mRNA_cap_enzyme: mRNA capping enzyme, catalytic domain; InterPro: IPR001339 The mRNA capping enzyme in yeasts is composed of two separate chains, alpha a mRNA guanyltransferase and beta an RNA 5'-triphosphate. X-ray crystallography reveals a large conformational change during guanyl transfer by mRNA capping enzymes []. Binding of the enzyme to nucleotides is specific to the GMP moiety of GTP. The viral mRNA capping enzyme is a monomer that transfers a GMP cap onto the end of mRNA that terminates with a 5'-diphosphate tail.; GO: 0004484 mRNA guanylyltransferase activity, 0006370 mRNA capping, 0006397 mRNA processing; PDB: 3RTX_A 3KYH_D 3S24_G 1CKN_B 1CKO_A 1CKM_B 1P16_B.
Probab=99.27 E-value=3.6e-12 Score=129.95 Aligned_cols=158 Identities=23% Similarity=0.287 Sum_probs=104.0
Q ss_pred CCceeEeeecceEeEEEEEecCCeEEEEecCCCcCC---CCcchHHHHHHhhcCCCCCCeEEEEEEEEEecCCCccCChH
Q 003632 452 DMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNT---GKFPDVVLAVSRLKKPSVRSFVLDCEIVAYDREKQKILPFQ 528 (806)
Q Consensus 452 g~~~~~E~KyDG~R~qih~~~~g~V~ifSR~gk~~T---~~~Pel~~~l~~~~~~~v~~~ILDGElVa~d~~~g~~~pFq 528 (806)
..+|+|.+|-||.|+++.+. ++.+.++.|+.+-+. -.+|--.+- .......+.+||||||. |...+
T Consensus 15 ~~~Y~V~eKaDG~Ryll~i~-~~~~ylidr~~~~~~v~~~~~p~~~~~---~~~~~~~~TLLDGElV~-d~~~~------ 83 (192)
T PF01331_consen 15 QKDYFVCEKADGTRYLLLIT-DNGVYLIDRKNNVFKVDNLHFPSKKDS---SDGRHHQDTLLDGELVL-DKDPG------ 83 (192)
T ss_dssp HS-EEEEEEESSEEEEEEEE-EEEEEEEETTS-EEEESSST-ECTTC-----TTCEGCSEEEEEEEEE-EECTT------
T ss_pred hCCcEEEECCCCcEEEEEEe-cceEEEEeCCCcEEEecCccccccccc---ccccccCCEEEEEEEEc-ccCCC------
Confidence 34799999999999999986 458999999987643 123321100 00112368999999986 32211
Q ss_pred HHHHhhhccCCccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhcc----------------CCCcEEEEeEEe
Q 003632 529 TLSTRARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEE----------------EPGFFQFATTLT 592 (806)
Q Consensus 529 ~L~~r~rk~~~~~~~~~~v~~~vFDiLylnG~~L~~~Pl~eRr~~L~~l~~~----------------~~~~i~~~~~~~ 592 (806)
...++|++||+|++||+++.+.||.+|...|++.+.. .|-.+.+-....
T Consensus 84 ---------------~~~~~flifD~l~~~G~~v~~~~~~~Rl~~l~~~i~~p~~~~~~~~~~~~~~~~pf~i~~K~~~~ 148 (192)
T PF01331_consen 84 ---------------EKKPRFLIFDILAINGQNVTDKPLDERLAYLQEEIIEPRKNAELKSGIIKKKKEPFSIRIKDFFP 148 (192)
T ss_dssp ---------------CEEEEEEEEEEEEETTEEGCCSBHHHHHHHHHHHTHHHHHHHHCHTTSCTCTTSSSEEEE---EE
T ss_pred ---------------CCceEEEEEeeehhCCcEeccCCHHHHHHHHHHHHHHHHHhhccccccccccccceeeeccccHH
Confidence 3468999999999999999999999999999764421 011233333444
Q ss_pred cCCHHH-HHHHHHHHHHcCCceeEEEeCCCCCCccCCCCCCCeEEEc
Q 003632 593 SIDLDE-IQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLK 638 (806)
Q Consensus 593 ~~~~ee-i~~~~~~ai~~g~EGlmlK~~~~ds~Y~pGkRs~~WlKlK 638 (806)
....+. +...+..-+.++..|||.-.. +.+|.+| +..+++|||
T Consensus 149 ~~~~~~~~~~~~~~~l~h~~DGLIFtp~--~~pY~~G-t~~~llKWK 192 (192)
T PF01331_consen 149 IYQIEKLLFEEFIPKLPHETDGLIFTPV--NTPYVPG-TCPNLLKWK 192 (192)
T ss_dssp GGGHHHHCHHCCCCCTTSTEEEEEEEES--SSB--SE-EEEEEEEE-
T ss_pred HHhhHHHHHHHhhccCCCCCCEEEEecC--CCCccCC-CCCccEeeC
Confidence 444444 222333345678899999999 8999999 678999998
No 46
>COG1423 ATP-dependent DNA ligase, homolog of eukaryotic ligase III [DNA replication, recombination, and repair]
Probab=98.84 E-value=5e-08 Score=105.37 Aligned_cols=148 Identities=20% Similarity=0.224 Sum_probs=107.4
Q ss_pred hhcCCCceeEeeecceEeEEEEEecCCeEEEEecCCCcC---CCCcchHHHHHHhhcCCCCCCeEEEEEEEEEecCCCcc
Q 003632 448 NKFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERN---TGKFPDVVLAVSRLKKPSVRSFVLDCEIVAYDREKQKI 524 (806)
Q Consensus 448 ~k~~g~~~~~E~KyDG~R~qih~~~~g~V~ifSR~gk~~---T~~~Pel~~~l~~~~~~~v~~~ILDGElVa~d~~~g~~ 524 (806)
+.|+.+.+++|.|.||+.+.|.+. +|++.-.||.|--. |.+.+++.+. +.+.+ ..+.||.|||+..++
T Consensus 83 ~~F~~~~v~VEEKmnGYNVRV~k~-~g~vyAiTRgG~ICPfTT~r~~~l~~~--eff~d-~p~lvlcgEmvG~en----- 153 (382)
T COG1423 83 KHFGRGKVVVEEKMNGYNVRVVKL-GGEVYAITRGGLICPFTTERLRDLIDL--EFFDD-YPDLVLCGEMVGPEN----- 153 (382)
T ss_pred hhcCCCcEEEEEeccCceEEEEEE-CCEEEEEecCceecCchhHHHHhhcch--hhHhh-CCCcEEEEEeccCCC-----
Confidence 457677999999999999999986 78999999999864 3455555432 33332 368999999998642
Q ss_pred CChHHHHHhhhccCCccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCCCcEEEEeEEecCCH-HHHHHHH
Q 003632 525 LPFQTLSTRARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDL-DEIQKFL 603 (806)
Q Consensus 525 ~pFq~L~~r~rk~~~~~~~~~~v~~~vFDiLylnG~~L~~~Pl~eRr~~L~~l~~~~~~~i~~~~~~~~~~~-eei~~~~ 603 (806)
|+-. . .--...++.|++|||.-.|.. ..+|.+||++++++.-- + ++.+......++. +++.++.
T Consensus 154 -PYv~------~---~~y~~e~v~fFvFDire~~tg--r~Lp~eer~~l~ekYgl--~-~V~~fg~~~~~e~~eei~eIv 218 (382)
T COG1423 154 -PYVP------G---PYYEKEDVGFFVFDIREKNTG--RPLPVEERLELAEKYGL--P-HVEIFGEFPADEAGEEIYEIV 218 (382)
T ss_pred -CCCC------C---CCCccCCceEEEEEEEecCCC--CCCCHHHHHHHHHHcCC--C-ceEEeeeechhHhHHHHHHHH
Confidence 2210 0 011256899999999987643 24699999999998632 2 2344444445555 8889999
Q ss_pred HHHHHcCCceeEEEeC
Q 003632 604 DAAVDASCEGLIIKTM 619 (806)
Q Consensus 604 ~~ai~~g~EGlmlK~~ 619 (806)
++.-.+|.||||+|++
T Consensus 219 e~L~keGREGVV~Kdp 234 (382)
T COG1423 219 ERLNKEGREGVVMKDP 234 (382)
T ss_pred HHHhhcCCcceEecCc
Confidence 9999999999999999
No 47
>PF14743 DNA_ligase_OB_2: DNA ligase OB-like domain; PDB: 2Q2U_D 2Q2T_A 1FVI_A 1P8L_A.
Probab=98.71 E-value=1.8e-08 Score=85.77 Aligned_cols=66 Identities=39% Similarity=0.602 Sum_probs=44.6
Q ss_pred eCCCCCCCcccEEEEEEeeCCCCeEEEeeeccCCCCHHHHHHHHHhhccccCCCCCCCcccCCCCCCcEEecCceEEEEE
Q 003632 658 HGRGKRTGVYGAFLLACYDSNNEEFQSICKIGTGFSEAMLEERSSSLRSKVIPKPRPYYRFADTISPDVWFEPTEVWEVK 737 (806)
Q Consensus 658 ~G~Gkr~g~~gsfLla~~d~~~g~~~~v~kVgtGftd~~l~~l~~~l~~~~~~~p~~~~~~~~~~~pdvwieP~~V~EV~ 737 (806)
.|+||..|++|+++|...| | ..++|||||||+++++++- + ..+++|+
T Consensus 1 ~G~Gk~~g~~Galv~~~~~---G---~~f~iGsG~td~~R~~~~~---------------i------------G~iit~k 47 (66)
T PF14743_consen 1 EGKGKFKGMLGALVCETED---G---VEFKIGSGFTDEEREEPPY---------------I------------GKIITVK 47 (66)
T ss_dssp ----EEEEEEEEEEEEE-T---T---EEEEE-SS--HHHHHHHHH---------------T------------T-EEEEE
T ss_pred CCccccCCCEEEEEEEeCC---C---CEEEECCCCCHHHHhcCCC---------------C------------CCEEEEE
Confidence 3789999999999998644 4 3468999999999998770 0 2588999
Q ss_pred eceeecCccccccccccCCCCCceeeccEEeEEe
Q 003632 738 AADLTISPVHRAAIGVVDPDKGISLRFPRLIRVR 771 (806)
Q Consensus 738 ~~eit~S~~~~a~~g~~~~~~G~sLRFPRf~riR 771 (806)
|.++|.+ | .+|||+|+++|
T Consensus 48 y~~~t~~--------------g-~pRfP~f~~~R 66 (66)
T PF14743_consen 48 YQGLTKD--------------G-SPRFPVFVRVR 66 (66)
T ss_dssp EE-TTSS--------------S-S-EEEEEEEE-
T ss_pred EEccCCC--------------C-ccccCEEEEeC
Confidence 9999964 6 99999999998
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=98.66 E-value=4.3e-07 Score=100.75 Aligned_cols=147 Identities=21% Similarity=0.278 Sum_probs=97.3
Q ss_pred hcCCCceeEeeecceEeEEEEEecCCeEEEEecCCCcC---CCCcchHHHHHHhhcCCCCCCeEEEEEEEEEecCCCccC
Q 003632 449 KFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERN---TGKFPDVVLAVSRLKKPSVRSFVLDCEIVAYDREKQKIL 525 (806)
Q Consensus 449 k~~g~~~~~E~KyDG~R~qih~~~~g~V~ifSR~gk~~---T~~~Pel~~~l~~~~~~~v~~~ILDGElVa~d~~~g~~~ 525 (806)
.|.++.+++|+|+||..+-|.. -+|++..+||.|-.. |.+++++.+ ...+.+ ..+.+|.||++.-+.
T Consensus 75 ~f~~~~v~vEEKlDG~Nvri~~-~~g~l~a~tRGgyicp~tt~r~~~~~~--~~~~~d-~p~l~LcGE~iGpen------ 144 (374)
T TIGR01209 75 HFKDPEVVVEEKMNGYNVRIVK-YGGNVYALTRGGFICPFTTERLPDLID--LEFFDD-NPDLVLCGEMAGPEN------ 144 (374)
T ss_pred hcCCCcEEEEEeecCceEEEEe-ECCEEEEEccCcccCCCcHHHHHHHhh--HHhhcc-CCCeEEEEEEcCCCC------
Confidence 4666669999999999999966 478999999999875 122344433 234442 368999999996432
Q ss_pred ChHHHHHhhhccCCccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhh-ccCCCcEEEEeEEecCC-HHHHHHHH
Q 003632 526 PFQTLSTRARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSF-EEEPGFFQFATTLTSID-LDEIQKFL 603 (806)
Q Consensus 526 pFq~L~~r~rk~~~~~~~~~~v~~~vFDiLylnG~~L~~~Pl~eRr~~L~~l~-~~~~~~i~~~~~~~~~~-~eei~~~~ 603 (806)
|+. +.. ......+..|++|||.. ...-.-+|..+|+++++.+- ..+| .+.. ....+ .+++.+..
T Consensus 145 pY~------~hs--~~y~~l~~~FfvFDI~d--~~t~~~L~~~er~~l~e~yglp~Vp-vlg~---~~~~~~~~~~~eii 210 (374)
T TIGR01209 145 PYT------PEY--YPEVKEDLGFFLFDIRE--GKTNRSLPVEERLELAEKYGLPHVE-ILGV---YTADEAVEEIYEII 210 (374)
T ss_pred CCc------ccC--ccccCCCceEEEEEEEE--CCCCccCCHHHHHHHHHHCCCCccc-eeeE---EcHHHHHHHHHHHH
Confidence 210 000 11123477999999973 33334579999999999873 2222 1111 22223 23666777
Q ss_pred HHHHHcCCceeEEEeC
Q 003632 604 DAAVDASCEGLIIKTM 619 (806)
Q Consensus 604 ~~ai~~g~EGlmlK~~ 619 (806)
+..-++|.||||+|++
T Consensus 211 ~~L~~~gREGVVlK~~ 226 (374)
T TIGR01209 211 ERLNKEGREGVVMKDP 226 (374)
T ss_pred HHhhhcCcceEEEcCc
Confidence 7778899999999998
No 49
>COG5226 CEG1 mRNA capping enzyme, guanylyltransferase (alpha) subunit [RNA processing and modification]
Probab=98.54 E-value=7e-08 Score=102.24 Aligned_cols=172 Identities=23% Similarity=0.278 Sum_probs=114.4
Q ss_pred CCceeEeeecceEeEEEEEecC---C--eEEEEecCCCcC---CCCcchHHHHHH-hhcCCCCCCeEEEEEEEEEecCCC
Q 003632 452 DMEFTCEYKYDGERAQIHYLED---G--SVEIYSRNAERN---TGKFPDVVLAVS-RLKKPSVRSFVLDCEIVAYDREKQ 522 (806)
Q Consensus 452 g~~~~~E~KyDG~R~qih~~~~---g--~V~ifSR~gk~~---T~~~Pel~~~l~-~~~~~~v~~~ILDGElVa~d~~~g 522 (806)
..+|++.+|-||.||++.+.++ | .+.+|.|..+-| +..||-+..... +.+ ..+..||||+|. |
T Consensus 61 ~~dy~VCEKsDGvR~Ll~vte~p~tg~~~~y~~DR~nnfY~v~~~f~p~~~~~k~ge~l---~~dtlldgelV~-d---- 132 (404)
T COG5226 61 NNDYLVCEKSDGVRALLLVTEEPVTGAFRGYFYDRRNNFYEVHTSFPPCSTVLKDGEVL---LEDTLLDGELVF-D---- 132 (404)
T ss_pred hCCeEEEEccCCeEEEEEEEecccCCCcceEEEeccCceEEeccccCCcccccccCcEE---eccceecceEEE-E----
Confidence 3479999999999999887642 2 478899988754 233443321111 111 256789999986 3
Q ss_pred ccCChHHHHHhhhccCCccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhcc-CC----------CcEEEEeEE
Q 003632 523 KILPFQTLSTRARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEE-EP----------GFFQFATTL 591 (806)
Q Consensus 523 ~~~pFq~L~~r~rk~~~~~~~~~~v~~~vFDiLylnG~~L~~~Pl~eRr~~L~~l~~~-~~----------~~i~~~~~~ 591 (806)
..|...+ .++.|.+||+|-++|.-+..++..+|...|++-+.. .. +.+.+--
T Consensus 133 -~~p~~k~--------------~qlryl~fdcLa~~g~~~~~~~~s~Rl~~l~Ke~~kp~~~~r~s~~~~~~~fpf~~-- 195 (404)
T COG5226 133 -CLPYEKV--------------PQLRYLLFDCLAYAGMFVERMEKSERLKTLQKEDEKPRERKRVSIEIDSGSFPFHF-- 195 (404)
T ss_pred -eccccch--------------HHHHHHHHHHhhhcceeEeecchhhHHHHhhhhhcccHhhhhheeeccccccceee--
Confidence 1343322 356778999999999999999999999999886542 10 1111100
Q ss_pred ecCCHH---HHHHHHHHH--HHcCCceeEEEeCCCCCCccCCCCCCCeEEEccccccccCCcccEEEEE
Q 003632 592 TSIDLD---EIQKFLDAA--VDASCEGLIIKTMDRDATYEPSKRSLNWLKLKKDYIESIGDSLDLVPIA 655 (806)
Q Consensus 592 ~~~~~e---ei~~~~~~a--i~~g~EGlmlK~~~~ds~Y~pGkRs~~WlKlK~dY~~~~~dtlDlvVIG 655 (806)
...-++ .+-++|+.. +.+|..|+|.-.. +.+|..|++ ...|||||.-++ |+|+..|=
T Consensus 196 s~K~M~~syg~~ki~k~ip~L~HgnDGLIFTp~--~~PY~~Gkd-~~lLKWKP~~~N----TiDF~lvl 257 (404)
T COG5226 196 SVKQMLKSYGFWKIYKKIPELKHGNDGLIFTPA--DEPYSVGKD-GALLKWKPASLN----TIDFRLVL 257 (404)
T ss_pred eHHHHHhhhhHHHHHhhcccccCCCCceEeccC--CCCcccCcc-ceeeecCccccC----ceeeeeee
Confidence 011111 234455332 3679999999999 999999966 589999998754 88887654
No 50
>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=98.51 E-value=6.3e-07 Score=91.37 Aligned_cols=152 Identities=20% Similarity=0.204 Sum_probs=111.1
Q ss_pred CceeEeeecceEeEEEEEecCCeEEEEecCCCcCCCCcchHHHHHHhhcCCCCCCeEEEEEEEEEecCCCccCChHHHHH
Q 003632 453 MEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAVSRLKKPSVRSFVLDCEIVAYDREKQKILPFQTLST 532 (806)
Q Consensus 453 ~~~~~E~KyDG~R~qih~~~~g~V~ifSR~gk~~T~~~Pel~~~l~~~~~~~v~~~ILDGElVa~d~~~g~~~pFq~L~~ 532 (806)
.+|++=+===|-||+|... +|.+.+++|+|..+. .|+- .++.+-..--+|||+|. |-.-+
T Consensus 21 ~~w~~~~~P~G~R~lvv~~-~g~t~~~~r~g~~~~-~f~s-------~lP~g~~~~~~~g~tIL-Dci~~---------- 80 (186)
T cd09232 21 EEWLVVPCPVGKRCLVVAS-KGKTVARSKNGRTLH-RFSS-------ALPGGSRKTSNSGYTIL-DCIYN---------- 80 (186)
T ss_pred cceEEEECcCceEEEEEEe-CCEEEEEeCCCCEEE-eccc-------CCCCCCcCCCCCCCEEE-EEecC----------
Confidence 4677777777999999986 899999999998752 1211 11111000023444442 21111
Q ss_pred hhhccCCccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCC----------CcEEEEeEEecCCHHHHHHH
Q 003632 533 RARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEP----------GFFQFATTLTSIDLDEIQKF 602 (806)
Q Consensus 533 r~rk~~~~~~~~~~v~~~vFDiLylnG~~L~~~Pl~eRr~~L~~l~~~~~----------~~i~~~~~~~~~~~eei~~~ 602 (806)
.....|+|+|||.+||.++.+.++..|...|++-+.+.+ -.+...+...++. +.+++.
T Consensus 81 -----------~~~~~yyVlDii~w~g~~l~d~~~~~Rf~wl~skl~E~~~~~~~~~~~~~~f~~~p~~~~~~-~~l~~~ 148 (186)
T cd09232 81 -----------EDDRTYYVLDVLCWNGHPLYDCETEFRFFWLRSKLEELPELDEPSEKNPFRFVPLPYFPCTK-ESLQSA 148 (186)
T ss_pred -----------CCCCEEEEEEEeeeCCcccccCCcchhHHHHHhhCCCccccccccccCCceEEecCcccCcH-HHHHHH
Confidence 123489999999999999999999999999999887643 1455566666655 778888
Q ss_pred HHHHH---HcCCceeEEEeCCCCCCccCCCCCCCeEEEcc
Q 003632 603 LDAAV---DASCEGLIIKTMDRDATYEPSKRSLNWLKLKK 639 (806)
Q Consensus 603 ~~~ai---~~g~EGlmlK~~~~ds~Y~pGkRs~~WlKlK~ 639 (806)
|...+ ..-..|++.-.. ++.|++| +++.|+|+|+
T Consensus 149 ~~~~~~~~~~e~DGLlFyhk--~~~Y~~G-~tPlvl~wKp 185 (186)
T cd09232 149 YSGPLNDDPYELDGLLFYHK--ESHYTPG-STPLVLWLKD 185 (186)
T ss_pred HhcccccCCCCCceEEEEeC--CCcccCc-CCCcEEEecC
Confidence 88888 888999999999 8899999 7899999997
No 51
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=98.11 E-value=0.00025 Score=83.32 Aligned_cols=230 Identities=13% Similarity=0.126 Sum_probs=138.1
Q ss_pred ccccc-cCCChHHHHhhcCC--CceeEeeecceEeEEEEEecCCe-EEEEec----CCCcCCCCcchHHHHHHhhcCCCC
Q 003632 434 PMLAK-PTKGVSEIVNKFQD--MEFTCEYKYDGERAQIHYLEDGS-VEIYSR----NAERNTGKFPDVVLAVSRLKKPSV 505 (806)
Q Consensus 434 PMLA~-~~~~i~~~l~k~~g--~~~~~E~KyDG~R~qih~~~~g~-V~ifSR----~gk~~T~~~Pel~~~l~~~~~~~v 505 (806)
|||.- .+.+.+++.+ |-. ..|++|+|+||.-+.+.+. +|. ++..|| -|+|+|+..--+ ..|...++...
T Consensus 97 PMlSL~k~~s~eel~~-w~~~~~~~~vepKiDGlsisL~Ye-~G~Lv~a~TRGDG~~GEDVT~nv~~I-~~IP~~l~~~~ 173 (562)
T PRK08097 97 AHTGVKKLADKQALAR-WMAGRSDLWVQPKVDGVAVTLVYR-DGKLVQAISRGNGLKGEDWTAKARLI-PAIPQQLPGAL 173 (562)
T ss_pred CcccccccCCHHHHHH-HHhhccceEEEEecccEEEEEEEE-CCEEEEEEecCCCccchhHHhhHhhh-cccchhhcCCC
Confidence 99973 3456666533 311 2599999999999999995 665 688999 788888753222 11222222112
Q ss_pred CCeEEEEEEEEEecCCCccCChHHH-----------HHhhhccCCccccccceEEEEeeeeecCCccccCCcHHHHHHHH
Q 003632 506 RSFVLDCEIVAYDREKQKILPFQTL-----------STRARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHL 574 (806)
Q Consensus 506 ~~~ILDGElVa~d~~~g~~~pFq~L-----------~~r~rk~~~~~~~~~~v~~~vFDiLylnG~~L~~~Pl~eRr~~L 574 (806)
..+.+-||++.-. ..|+.. ++-.|.. +......++.|++|++. +| .....++.+.|
T Consensus 174 ~~levRGEv~m~~------~~F~~~~~g~aNPRN~AAGsLr~~-d~~~~~r~L~~f~y~~~--~~----~~t~~e~l~~L 240 (562)
T PRK08097 174 ANLVLQGELFLRR------EGHIQQQMGGINARAKVAGLMMRK-DPSPTLNQIGVFVWAWP--DG----PASMPERLAQL 240 (562)
T ss_pred CeEEEEEEEEEeH------HHHHHHhcCcCCchHHHhHHHhhc-CcHhhhccceEEEEECC--CC----CCCHHHHHHHH
Confidence 3588999999743 234432 1222211 11112568999999983 44 24678888888
Q ss_pred HHhhccCCC-cEEEEeEEecCCHHHHHHHHHHHHH----cCCceeEEEeCCCCCCccC--CCCCCCe---EEEccccccc
Q 003632 575 YDSFEEEPG-FFQFATTLTSIDLDEIQKFLDAAVD----ASCEGLIIKTMDRDATYEP--SKRSLNW---LKLKKDYIES 644 (806)
Q Consensus 575 ~~l~~~~~~-~i~~~~~~~~~~~eei~~~~~~ai~----~g~EGlmlK~~~~ds~Y~p--GkRs~~W---lKlK~dY~~~ 644 (806)
..+-=++.. .. ..+.+.+++.++++.... -.-.|+|+|-- +-.|.. ..+.+.| +|+.++
T Consensus 241 ~~~GF~v~~~~~-----~~~~~~~~i~~~~~~~~r~~l~y~iDGiViKvn--~~~~~~~~ts~~PrWAiAyKf~~~---- 309 (562)
T PRK08097 241 ATAGFPLTQRYT-----HPVKNAEEVARWRERWYRAPLPFVTDGVVVRQA--KEPPGRYWQPGQGEWAVAWKYPPV---- 309 (562)
T ss_pred HHCCCCcCccce-----EeeCCHHHHHHHHHHHhhccCCCCCCcEEEEec--CHHHHhhccCCCCCceEEEcCCCc----
Confidence 887433322 11 225678888887776543 36789999976 444432 3456788 566553
Q ss_pred cCCcccEEEEEEEeCCCCCCCcccEEEEEEeeCC--CCeEEEeeeccCCCCHHHHHH
Q 003632 645 IGDSLDLVPIAAFHGRGKRTGVYGAFLLACYDSN--NEEFQSICKIGTGFSEAMLEE 699 (806)
Q Consensus 645 ~~dtlDlvVIGa~~G~Gkr~g~~gsfLla~~d~~--~g~~~~v~kVgtGftd~~l~~ 699 (806)
+..-.+.+..|.-|| +|.++. +|..+|- .|. +|.++ |-...+..++
T Consensus 310 ---~~~T~l~~I~~qVGR-TG~iTP--VA~lePV~l~Gt--tVsrA-TLhN~~~i~~ 357 (562)
T PRK08097 310 ---QQVAEVRAVQFAVGR-TGKITV--VLELEPVMLDDK--RVSRV-NIGSVRRWQQ 357 (562)
T ss_pred ---EEEEEEEEEEEecCC-CceeeE--EEEEEEEEeCCE--EEEEe-ecCCHHHHHH
Confidence 566677887777664 666654 3444431 244 34454 5566666554
No 52
>PRK01109 ATP-dependent DNA ligase; Provisional
Probab=98.07 E-value=1e-05 Score=96.16 Aligned_cols=93 Identities=26% Similarity=0.373 Sum_probs=86.0
Q ss_pred CccchHHHHHHHHHHHhcc---chHHHHHHHHHHHHhhhcCCCCchHhHHHHHhCCcCCCccccccCCCHHHHHHHHHHH
Q 003632 189 ERVPFIFLSLVFDMISNET---GRILITDIVCNMLRTVMETTPEDLVPVVYLAANKIAPAHEGLELGIGDASIIKALAEA 265 (806)
Q Consensus 189 ~~~~F~~la~~~~~I~~ts---sr~~k~~iL~~~~r~~i~~~p~dl~~~vyL~~~~l~P~~e~~elgIg~~~L~Kal~~~ 265 (806)
++++|.++.+.|++|++++ ++.+|+++|.++|+.+ +|+++.+.++++++.+. +|++++++.+||+++
T Consensus 113 ~~lti~eV~~~L~~Ia~~sg~~s~~~k~~iL~~Ll~~~---~~~E~k~iirli~g~lr-------iGv~e~~il~ALa~A 182 (590)
T PRK01109 113 EPLTVKEVYDTLVKIALATGEGSQDLKIKLLAGLLKDA---SPLEAKYIARFVEGRLR-------LGVGDATILDALAIA 182 (590)
T ss_pred CCcCHHHHHHHHHHHHhhhCCCcHHHHHHHHHHHHHhC---CHHHHHHHHHHHhhhhh-------cCccHHHHHHHHHHH
Confidence 5799999999999999997 8999999999999997 78999999999999765 899999999999999
Q ss_pred hC--CCHHHHHHHHhhcCCHHHHHhhcc
Q 003632 266 CG--RTESHVKKQYQEMGDLGLVAKASR 291 (806)
Q Consensus 266 ~g--~s~~~ik~~~~~~GDlg~va~~~r 291 (806)
+| .+...+++.|...||+|.||..+.
T Consensus 183 ~~~~~~~~~ve~~y~~~~Dlg~va~~l~ 210 (590)
T PRK01109 183 FGGAVARELVERAYNLRADLGYIAKILA 210 (590)
T ss_pred HhcccchHHHHHHHHhCCCHHHHHHHHH
Confidence 99 999999999999999999987653
No 53
>smart00532 LIGANc Ligase N family.
Probab=98.05 E-value=0.00013 Score=83.70 Aligned_cols=239 Identities=15% Similarity=0.180 Sum_probs=142.4
Q ss_pred cccccc-cCCChHHHH---hhcC---C--CceeEeeecceEeEEEEEecCCe-EEEEec----CCCcCCCCcchHHHHHH
Q 003632 433 GPMLAK-PTKGVSEIV---NKFQ---D--MEFTCEYKYDGERAQIHYLEDGS-VEIYSR----NAERNTGKFPDVVLAVS 498 (806)
Q Consensus 433 ~PMLA~-~~~~i~~~l---~k~~---g--~~~~~E~KyDG~R~qih~~~~g~-V~ifSR----~gk~~T~~~Pel~~~l~ 498 (806)
.|||.- .+.+.+++. ++.. + -.|++|+|+||.-+.+.+. +|+ ++..|| .|+|+|....-+.. +.
T Consensus 74 ~pMlSL~k~~~~~el~~f~~~~~~~~~~~~~~~~epKiDGlsisL~Ye-~G~l~~a~TRGDG~~GeDVT~nv~~i~~-iP 151 (441)
T smart00532 74 VPMLSLDNAFDEDELRAFDERIEKALGSPFAYVVEPKIDGLSVSLLYE-NGKLVQAATRGDGTVGEDVTQNVKTIRS-IP 151 (441)
T ss_pred CcccCccccCCHHHHHHHHHHHHHhcCCCceEEEEEecccEEEEEEEE-CCEEEEEEecCCCCcceehhhhhhhhcC-cC
Confidence 399973 344555542 2221 1 2689999999999999995 776 889999 89999985432211 11
Q ss_pred hhcCC-CCCCeEEEEEEEEEecCCCccCChHHHHH-------------------hhhccCCccccccceEEEEeeeeecC
Q 003632 499 RLKKP-SVRSFVLDCEIVAYDREKQKILPFQTLST-------------------RARKNVSLSDIKVDVCIYAFDILYRN 558 (806)
Q Consensus 499 ~~~~~-~v~~~ILDGElVa~d~~~g~~~pFq~L~~-------------------r~rk~~~~~~~~~~v~~~vFDiLyln 558 (806)
..+.. ....+.+-||++.-. ..|+.+-. -+|..........++.|++|++...+
T Consensus 152 ~~i~~~~p~~leiRGEv~~~~------~~F~~ln~~~~~~g~~~faNpRN~aAG~lr~ld~~~~~~r~L~~~~y~~~~~~ 225 (441)
T smart00532 152 LRLSGDVPERLEVRGEVFMPK------EDFLALNEELEEEGEKPFANPRNAAAGSLRQLDPRITAKRKLRAFFYGLGTGE 225 (441)
T ss_pred hhhcccCCCeEEEEceEEEEH------HHHHHHHHHHHhcCCCcccChHHHHHHHHHhcCchhhhhccceEEEEEcccCC
Confidence 11211 013588999999742 23444311 11111000112458999999986444
Q ss_pred CccccCCcHHHHHHHHHHhhccCCCcEEEEeEEecCCHHHHHHHHHHHHH------cCCceeEEEeCCCCCCccC--C--
Q 003632 559 GQPLLQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAAVD------ASCEGLIIKTMDRDATYEP--S-- 628 (806)
Q Consensus 559 G~~L~~~Pl~eRr~~L~~l~~~~~~~i~~~~~~~~~~~eei~~~~~~ai~------~g~EGlmlK~~~~ds~Y~p--G-- 628 (806)
+... .....++.+.|.++-=++..... .+.+.+++.++++...+ -...|||+|-- +-.+.. |
T Consensus 226 ~~~~-~~t~~e~l~~L~~~GF~v~~~~~-----~~~~~~ei~~~~~~~~~~r~~l~y~iDGiViKvn--~~~~~~~lG~t 297 (441)
T smart00532 226 ELFL-PKTQSEALKWLKELGFPVSPHTR-----LCKNADEVIEYYEEWEEKRAELPYEIDGVVVKVD--DLALQRELGFT 297 (441)
T ss_pred CCCC-ccCHHHHHHHHHHCCCCCCCCeE-----eeCCHHHHHHHHHHHHHhcccCCCCcCcEEEEec--CHHHHHHhCcc
Confidence 3211 24678899999887322322222 35678899998887765 36789999986 444432 2
Q ss_pred CCCCCe---EEEccccccccCCcccEEEEEEEeCCCCCCCcccEEEEEEeeCC--CCeEEEeeeccCCCCHHHHHHH
Q 003632 629 KRSLNW---LKLKKDYIESIGDSLDLVPIAAFHGRGKRTGVYGAFLLACYDSN--NEEFQSICKIGTGFSEAMLEER 700 (806)
Q Consensus 629 kRs~~W---lKlK~dY~~~~~dtlDlvVIGa~~G~Gkr~g~~gsfLla~~d~~--~g~~~~v~kVgtGftd~~l~~l 700 (806)
.+.+.| +|+..+ ...-.|.+..|--|| +|.++.. |..++- .|. +|.++ |..+.++++++
T Consensus 298 s~~PrwaiA~Kf~~~-------~~~T~l~~I~~qVGR-TG~iTPv--A~lePV~l~G~--tVsrA-TLhN~~~i~~~ 361 (441)
T smart00532 298 SKAPRWAIAYKFPAE-------EAETKLLDIIVQVGR-TGKITPV--AELEPVFLAGS--TVSRA-TLHNEDEIEEK 361 (441)
T ss_pred CCCCCeeEEECCCCc-------eeEEEEEEEEEecCC-CceeeEE--EEEEeEEECCE--EEEec-ccCCHHHHHHc
Confidence 346778 566654 566677777776664 5666543 444431 244 44555 67777777653
No 54
>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=97.89 E-value=0.00028 Score=77.51 Aligned_cols=185 Identities=15% Similarity=0.205 Sum_probs=111.5
Q ss_pred cccccc-cCCChHHHH---hhcC-----CCceeEeeecceEeEEEEEecCCe-EEEEec----CCCcCCCCcchHHHHHH
Q 003632 433 GPMLAK-PTKGVSEIV---NKFQ-----DMEFTCEYKYDGERAQIHYLEDGS-VEIYSR----NAERNTGKFPDVVLAVS 498 (806)
Q Consensus 433 ~PMLA~-~~~~i~~~l---~k~~-----g~~~~~E~KyDG~R~qih~~~~g~-V~ifSR----~gk~~T~~~Pel~~~l~ 498 (806)
.|||.- .+.+.+++. ++.. ...|+||+|+||.-+.+.+. +|+ ++..|| .|+|+|....-|. .|.
T Consensus 72 ~pMlSL~k~~~~~el~~~~~r~~~~~~~~~~~~vepKiDGlsisL~Y~-~G~L~~a~TRGdG~~GeDVT~nv~~I~-~IP 149 (307)
T cd00114 72 VPMLSLDNAFDEEELRAFDERIKRFLGEEPAYVVEPKIDGLSISLRYE-NGVLVQAATRGDGTTGEDVTENVRTIR-SIP 149 (307)
T ss_pred CcCccccccCCHHHHHHHHHHHHHhcCCCCcEEEEEeccceEEEEEEE-CCEEEEEEecCCCcchhhHHhhHhhhc-ccC
Confidence 489873 334444432 2221 12699999999999999995 666 789999 7889987543221 122
Q ss_pred hhcCCCCCCeEEEEEEEEEecCCCccCChHHHHH-------------------hhhccCCccccccceEEEEeeeeecCC
Q 003632 499 RLKKPSVRSFVLDCEIVAYDREKQKILPFQTLST-------------------RARKNVSLSDIKVDVCIYAFDILYRNG 559 (806)
Q Consensus 499 ~~~~~~v~~~ILDGElVa~d~~~g~~~pFq~L~~-------------------r~rk~~~~~~~~~~v~~~vFDiLylnG 559 (806)
..++.....+.+-||++.-. ..|+.+-. -+|..........++.|++|++...++
T Consensus 150 ~~i~~~~~~levRGEv~m~~------~~F~~~n~~~~~~~~~~faNpRNaaAGsLr~ld~~~~~~r~L~f~~y~~~~~~~ 223 (307)
T cd00114 150 LTLAGAPETLEVRGEVFMPK------ADFEALNKEREERGEKPFANPRNAAAGSLRQLDPKITAKRPLRFFIYGLGEAEG 223 (307)
T ss_pred hhhcCCCCeEEEEEEEEEEH------HHHHHHHHHHHHcCCCCccChHHHHHHHHHhcCcchhhcCcceEEEEecccccC
Confidence 22211124589999999742 23433321 111110001115689999999865443
Q ss_pred ccccCCcHHHHHHHHHHhhccCCCcEEEEeEEecCCHHHHHHHHHHHHHc------CCceeEEEeCCCCCCcc----CCC
Q 003632 560 QPLLQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAAVDA------SCEGLIIKTMDRDATYE----PSK 629 (806)
Q Consensus 560 ~~L~~~Pl~eRr~~L~~l~~~~~~~i~~~~~~~~~~~eei~~~~~~ai~~------g~EGlmlK~~~~ds~Y~----pGk 629 (806)
.. -....++.+.|.++-=+++.... .+.+.+++.+++++..+. ...|||+|-- +-.+. ...
T Consensus 224 ~~--~~t~~e~l~~L~~~GF~v~~~~~-----~~~~~~ev~~~~~~~~~~R~~l~y~iDGiViKvn--~~~~~~~lG~ts 294 (307)
T cd00114 224 LG--PKTQSEALAFLKEWGFPVSPETR-----LCKNIEEVLAFYDEIEAKRDSLPYEIDGVVVKVD--DLALQRELGFTS 294 (307)
T ss_pred CC--CCCHHHHHHHHHHCCCCCCCCeE-----EeCCHHHHHHHHHHHHHhhhcCCCCCCcEEEEEe--CHHHHHHhCccC
Confidence 12 24678899999887434333222 356789999998877433 6789999986 43332 233
Q ss_pred CCCCe
Q 003632 630 RSLNW 634 (806)
Q Consensus 630 Rs~~W 634 (806)
+.+.|
T Consensus 295 k~PrW 299 (307)
T cd00114 295 KAPRW 299 (307)
T ss_pred CCCCc
Confidence 45666
No 55
>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=97.88 E-value=2.4e-05 Score=86.15 Aligned_cols=173 Identities=17% Similarity=0.231 Sum_probs=99.0
Q ss_pred cccccc-cCCChHHHH---hh----cCCC--ceeEeeecceEeEEEEEecCCe-EEEEec----CCCcCCCCcchHHHHH
Q 003632 433 GPMLAK-PTKGVSEIV---NK----FQDM--EFTCEYKYDGERAQIHYLEDGS-VEIYSR----NAERNTGKFPDVVLAV 497 (806)
Q Consensus 433 ~PMLA~-~~~~i~~~l---~k----~~g~--~~~~E~KyDG~R~qih~~~~g~-V~ifSR----~gk~~T~~~Pel~~~l 497 (806)
.|||.- .+.+.+++. ++ ++.. .|+||+|+||.-+.+++. +|. ++..|| -|+|+|.....+. .|
T Consensus 77 ~pMlSL~k~~s~eel~~w~~r~~~~~~~~~~~~~~e~KiDGlsi~L~Y~-~G~L~~a~TRGdG~~GeDvT~n~~~i~-~i 154 (315)
T PF01653_consen 77 VPMLSLDKAYSEEELRKWLKRVEKALGEEEEEFVVEPKIDGLSISLIYE-NGKLVRAATRGDGEVGEDVTHNVRTIK-SI 154 (315)
T ss_dssp S-----EEESSHHHHHHHHHHHHHHCSS-SSEEEEEEEESSEEEEEEEE-TTEEEEEEEETTSSEEEB-HHHHCTST-TS
T ss_pred ccccCccccCCHHHHHHHHHHHHHHhcccccceeEeeccceeEEEEEEe-CCEEEEEEEcCCCccchhHHHHHHHHh-cC
Confidence 489863 344444442 22 2222 599999999999999995 776 689999 6788876432221 12
Q ss_pred HhhcCCCCCCeEEEEEEEEEecCCCccCChHHHHHh-------------------hhccCCccccccceEEEEeeeeecC
Q 003632 498 SRLKKPSVRSFVLDCEIVAYDREKQKILPFQTLSTR-------------------ARKNVSLSDIKVDVCIYAFDILYRN 558 (806)
Q Consensus 498 ~~~~~~~v~~~ILDGElVa~d~~~g~~~pFq~L~~r-------------------~rk~~~~~~~~~~v~~~vFDiLyln 558 (806)
...+......+.+=||++.-. ..|..+-.. +|..........++.|++|++.+.+
T Consensus 155 P~~i~~~p~~~eVRGEv~m~~------~~F~~ln~~~~~~~~~~faNpRN~aAGsLr~~d~~~~~~r~L~f~~y~~~~~~ 228 (315)
T PF01653_consen 155 PLRIPEKPGRLEVRGEVYMSK------SDFEKLNEEREEEGEKPFANPRNAAAGSLRQKDPSITAERKLSFFAYGIGEPE 228 (315)
T ss_dssp -SB-SSSSSEEEEEEEEE--H------HHHHHHHHHHHHTTS---SSHHHHHHHHHTSSSHHHHHTS--EEEEEEEEEET
T ss_pred chhhccCCcceEEEEEEEEeh------hhHHHHHHHHHHhccchhhhhhHHHHHhhhhccchhhhcCeeEEEEEEecccc
Confidence 222221125788999999632 245554311 1110000012458999999999988
Q ss_pred CccccCCcHHHHHHHHHHhhccCCCcEEEEeEEecCCHHHHHHHHHHHHHc------CCceeEEEeC
Q 003632 559 GQPLLQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAAVDA------SCEGLIIKTM 619 (806)
Q Consensus 559 G~~L~~~Pl~eRr~~L~~l~~~~~~~i~~~~~~~~~~~eei~~~~~~ai~~------g~EGlmlK~~ 619 (806)
| ...-....++.+.|.++-=++...+. .+.+.+++.++++...+. ...|||+|--
T Consensus 229 ~-~~~~~t~~e~l~~L~~~GF~v~~~~~-----~~~~~~~v~~~~~~~~~~R~~l~y~iDGiVikvn 289 (315)
T PF01653_consen 229 G-DLGFNTQSERLQFLKEWGFPVNPYIR-----FCKSIEEVEEYIEEWEERREELPYPIDGIVIKVN 289 (315)
T ss_dssp T-STT-SBHHHHHHHHHHTT--B-TTEE-----EESSHHHHHHHHHHHHHHGCCSSS-EEEEEEEES
T ss_pred c-ccChHHHHHHHHHHHHcCCCCCcceE-----ecCCHHHHHHHHHHHHhhhhccccccCcEEEEec
Confidence 7 23334678899999886333333333 356889999998887764 4679999985
No 56
>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=97.87 E-value=0.00049 Score=82.78 Aligned_cols=238 Identities=16% Similarity=0.194 Sum_probs=142.2
Q ss_pred cccccc-cCCChHHHHh---hcC---C--CceeEeeecceEeEEEEEecCCe-EEEEec----CCCcCCCCcchHHHHHH
Q 003632 433 GPMLAK-PTKGVSEIVN---KFQ---D--MEFTCEYKYDGERAQIHYLEDGS-VEIYSR----NAERNTGKFPDVVLAVS 498 (806)
Q Consensus 433 ~PMLA~-~~~~i~~~l~---k~~---g--~~~~~E~KyDG~R~qih~~~~g~-V~ifSR----~gk~~T~~~Pel~~~l~ 498 (806)
.|||.- .+.+.+++.+ +.. + -.|+||+|+||.-+.+.+. +|+ ++..|| .|+|+|...-.+. .|.
T Consensus 67 ~pMlSL~k~~~~~el~~~~~r~~~~~~~~~~~~~epKiDGlaisL~Ye-~G~L~~a~TRGDG~~GeDvT~nv~~I~-~iP 144 (652)
T TIGR00575 67 TPMLSLDNAFDEDELAAFIKRIRRQLGLKVEYVVEPKIDGLSVSLTYE-NGVLVRALTRGDGTVGEDVTANVRTIR-SIP 144 (652)
T ss_pred CcCcCccccCCHHHHHHHHHHHHHhcCCCceEEEEEeccceEEEEEEE-CCEEEEEEecCCCccchhHhhhhhhhc-ccc
Confidence 499873 3444454422 221 1 2599999999999999994 676 789999 7899987533221 122
Q ss_pred hhcCC--CCCCeEEEEEEEEEecCCCccCChHHHH-------------------HhhhccCCccccccceEEEEeeeeec
Q 003632 499 RLKKP--SVRSFVLDCEIVAYDREKQKILPFQTLS-------------------TRARKNVSLSDIKVDVCIYAFDILYR 557 (806)
Q Consensus 499 ~~~~~--~v~~~ILDGElVa~d~~~g~~~pFq~L~-------------------~r~rk~~~~~~~~~~v~~~vFDiLyl 557 (806)
..+.. ....+.+-||++.-. ..|+.+- +-+|.-........++.|++|++...
T Consensus 145 ~~i~~~~~p~~levRGEv~m~~------~~F~~~N~~~~~~g~~~faNpRN~aAGslr~ld~~~~~~r~L~~~~y~~~~~ 218 (652)
T TIGR00575 145 LRLAGDNPPERLEVRGEVFMPK------EDFEALNEERREQGEKPFANPRNAAAGSLRQLDPRITAKRKLRFFAYGLGEG 218 (652)
T ss_pred hhhcCCCCCceEEEEEEEEEEH------HHHHHHHHHHHHcCCCCCCCcHHHHHHHHHcCCchhhhcCccEEEEEecccc
Confidence 22220 113588999999742 2344331 11111100011256899999998532
Q ss_pred CCccccCCcHHHHHHHHHHhhccCCCcEEEEeEEecCCHHHHHHHHHHHHH------cCCceeEEEeCCCCCCcc----C
Q 003632 558 NGQPLLQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAAVD------ASCEGLIIKTMDRDATYE----P 627 (806)
Q Consensus 558 nG~~L~~~Pl~eRr~~L~~l~~~~~~~i~~~~~~~~~~~eei~~~~~~ai~------~g~EGlmlK~~~~ds~Y~----p 627 (806)
+ ........++.+.|.++-=++..... .+.+.+++.+++++..+ -.-.|+|+|-- +-.|. .
T Consensus 219 ~--~~~~~t~~e~l~~L~~~GF~v~~~~~-----~~~~~~ei~~~~~~~~~~R~~l~y~iDGiViKvn--~~~~~~~lG~ 289 (652)
T TIGR00575 219 L--ELPDATQYEALAWLKKWGFPVSPHIR-----LCDSIEEVLEYYREIEEKRDSLPYEIDGVVVKVD--DLALQDELGF 289 (652)
T ss_pred C--CCCCCCHHHHHHHHHHCCCCCCCCeE-----eeCCHHHHHHHHHHHHHhhhcCCCCCCcEEEEec--CHHHHHHhCc
Confidence 2 21124778889999887333333222 35678999999887743 36789999975 43332 1
Q ss_pred CCCCCCe---EEEccccccccCCcccEEEEEEEeCCCCCCCcccEEEEEEeeCC--CCeEEEeeeccCCCCHHHHHHH
Q 003632 628 SKRSLNW---LKLKKDYIESIGDSLDLVPIAAFHGRGKRTGVYGAFLLACYDSN--NEEFQSICKIGTGFSEAMLEER 700 (806)
Q Consensus 628 GkRs~~W---lKlK~dY~~~~~dtlDlvVIGa~~G~Gkr~g~~gsfLla~~d~~--~g~~~~v~kVgtGftd~~l~~l 700 (806)
..+.+.| +|+.++ ...-.|.+..|--|| +|.++.. |..+|- .|. +|.++ |..+.++++++
T Consensus 290 t~~~PrwaiA~Kf~~~-------~~~T~l~~I~~qVGR-TG~iTPv--A~lePV~l~G~--~VsrA-tLhN~~~i~~~ 354 (652)
T TIGR00575 290 TSKAPRWAIAYKFPAE-------EAQTKLLDVVVQVGR-TGAITPV--AKLEPVFVAGT--TVSRA-TLHNEDEIEEL 354 (652)
T ss_pred cCCCCCceEEEcCCCc-------eeeEEEEEEEEecCC-CceeeeE--EEEeeEEECCE--EEEEe-ecCCHHHHHHc
Confidence 2356788 666664 566678887776664 6666643 444431 244 44554 67777777654
No 57
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=97.81 E-value=0.0011 Score=79.64 Aligned_cols=240 Identities=17% Similarity=0.173 Sum_probs=139.8
Q ss_pred cccccc-cCCChHHHH---hhcC------C--CceeEeeecceEeEEEEEecCCe-EEEEec----CCCcCCCCcchHHH
Q 003632 433 GPMLAK-PTKGVSEIV---NKFQ------D--MEFTCEYKYDGERAQIHYLEDGS-VEIYSR----NAERNTGKFPDVVL 495 (806)
Q Consensus 433 ~PMLA~-~~~~i~~~l---~k~~------g--~~~~~E~KyDG~R~qih~~~~g~-V~ifSR----~gk~~T~~~Pel~~ 495 (806)
.|||.- .+.+.+++. +++. + .+|+||+|+||.-+.+.+. +|+ ++..|| .|+|+|+..--+ .
T Consensus 78 ~pMlSL~k~~~~~el~~~~~r~~~~~~~~~~~~~~~~epKiDGlaisL~Ye-nG~L~~a~TRGDG~~GEDVT~n~~~I-~ 155 (669)
T PRK14350 78 FPILSLDKVYDLKLLKLWIEKMDLENSNLGFDFGISVEPKIDGCSIVLYYK-DGILEKALTRGDGRFGNDVTENVRTI-R 155 (669)
T ss_pred CccccccccCCHHHHHHHHHHHHHhhccCCCCceEEEEEecccEEEEEEEE-CCEEEEEEecCCCCcchhHhhhhhhh-c
Confidence 399863 344555542 2221 1 2599999999999999995 676 688999 789998753221 1
Q ss_pred HHHhhcCCCCCCeEEEEEEEEEecCCCccCChHHHHHh---------------hhccCCccccccceEEEEeeeeecCCc
Q 003632 496 AVSRLKKPSVRSFVLDCEIVAYDREKQKILPFQTLSTR---------------ARKNVSLSDIKVDVCIYAFDILYRNGQ 560 (806)
Q Consensus 496 ~l~~~~~~~v~~~ILDGElVa~d~~~g~~~pFq~L~~r---------------~rk~~~~~~~~~~v~~~vFDiLylnG~ 560 (806)
-|...++. ...+.+-||++.-. ..|+.+-.. .|..........++.|++|++...++.
T Consensus 156 ~IP~~l~~-~~~levRGEv~m~~------~~F~~lN~~~~~~faNpRNaaAGsLr~~d~~~~a~r~L~f~~y~~~~~~~~ 228 (669)
T PRK14350 156 NVPLFIDE-KVELVLRGEIYITK------ENFLKINKTLEKPYTNARNLASGILRRIDSREVANFPLDIFVYDILYSSLE 228 (669)
T ss_pred ccchhcCC-CceEEEEEEEEeeH------HHHHHHHHhhhccCCChhHHHHHHHHccCchhhhcCceEEEEEEcccCCCC
Confidence 12222221 14588999999742 235443211 111000011245899999998532221
Q ss_pred cccCCcHHHHHHHHHHhhccCCCcEEEEeEEecCCHHHHHHHHHHHHH------cCCceeEEEeCCCCCCcc----CCCC
Q 003632 561 PLLQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAAVD------ASCEGLIIKTMDRDATYE----PSKR 630 (806)
Q Consensus 561 ~L~~~Pl~eRr~~L~~l~~~~~~~i~~~~~~~~~~~eei~~~~~~ai~------~g~EGlmlK~~~~ds~Y~----pGkR 630 (806)
..+..++.+.|.++-=++.....++.. ..+.+++.++++++.. -...|||+|-- +-.+. ...+
T Consensus 229 ---~~t~~e~l~~L~~~GF~v~~~~~~~~~--~~~~~e~~~~~~~~~~~R~~l~y~iDGiViKvn--~~~~q~~lG~ts~ 301 (669)
T PRK14350 229 ---LKTNHDAFDKLKKFGFKVNPFCRFFDG--KNSIEEILNYVKDIEKKRNSFEYEIDGVVLKVS--DFALREILGYTSH 301 (669)
T ss_pred ---CCCHHHHHHHHHHCCCCCCcceEEEcC--CCcHHHHHHHHHHHHHHHhcCCCCCCcEEEEec--CHHHHHhcCCcCC
Confidence 236778888888874333333333221 2347888888876633 35689999985 32221 1234
Q ss_pred CCCe---EEEccccccccCCcccEEEEEEEeCCCCCCCcccEEEEEEeeCC--CCeEEEeeeccCCCCHHHHHHHH
Q 003632 631 SLNW---LKLKKDYIESIGDSLDLVPIAAFHGRGKRTGVYGAFLLACYDSN--NEEFQSICKIGTGFSEAMLEERS 701 (806)
Q Consensus 631 s~~W---lKlK~dY~~~~~dtlDlvVIGa~~G~Gkr~g~~gsfLla~~d~~--~g~~~~v~kVgtGftd~~l~~l~ 701 (806)
.+.| +|+.++ ...-.|.+..|--|| +|.++.. |..+|- .|. +|.++ |..+.++.+++.
T Consensus 302 ~PrWaiA~Kf~~~-------~~~T~l~~I~~qVGR-TG~iTPV--A~l~PV~l~G~--tVsrA-TLhN~~~I~~~d 364 (669)
T PRK14350 302 HPKWSMAYKFESL-------SGFSKVNDIVVQVGR-SGKITPV--ANIEKVFVAGA--FITNA-SLHNQDYIDSIG 364 (669)
T ss_pred CCCceEEEcCCCc-------eeEEEEEEEEEecCC-ceeeeEE--EEEEeEEECCE--EEEEe-ccCCHHHHHHcC
Confidence 6788 666664 566677777776654 6665543 444431 244 45555 677877776543
No 58
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=97.75 E-value=0.00072 Score=81.46 Aligned_cols=239 Identities=16% Similarity=0.225 Sum_probs=142.0
Q ss_pred cccccc-cCCChHHHH---hhcC------CCceeEeeecceEeEEEEEecCCe-EEEEec----CCCcCCCCcchHHHHH
Q 003632 433 GPMLAK-PTKGVSEIV---NKFQ------DMEFTCEYKYDGERAQIHYLEDGS-VEIYSR----NAERNTGKFPDVVLAV 497 (806)
Q Consensus 433 ~PMLA~-~~~~i~~~l---~k~~------g~~~~~E~KyDG~R~qih~~~~g~-V~ifSR----~gk~~T~~~Pel~~~l 497 (806)
.|||.- .+.+.+++. ++.. ...|+||+|+||.-+.+.+. +|+ ++..|| .|+|+|+..--+. -|
T Consensus 78 ~pMlSL~k~~~~~el~~w~~r~~~~~~~~~~~~~~epKiDGlsisL~Y~-~G~L~~a~TRGDG~~GeDvT~n~~~I~-~I 155 (665)
T PRK07956 78 VPMLSLDNAFSEEELRAFDKRVRKRLPDPPLTYLCELKIDGLAVSLLYE-NGVLVRAATRGDGTTGEDITANVRTIR-SI 155 (665)
T ss_pred CcCcCccccCCHHHHHHHHHHHHHhcCCCCcceEEEEecccEEEEEEEE-CCEEEEEEecCCCccchhHhhhhhhhc-cC
Confidence 389863 344445542 2222 12599999999999999995 665 688999 7999987532221 12
Q ss_pred HhhcC-CCCCCeEEEEEEEEEecCCCccCChHHHHHh-------------------hhccCCccccccceEEEEeeeeec
Q 003632 498 SRLKK-PSVRSFVLDCEIVAYDREKQKILPFQTLSTR-------------------ARKNVSLSDIKVDVCIYAFDILYR 557 (806)
Q Consensus 498 ~~~~~-~~v~~~ILDGElVa~d~~~g~~~pFq~L~~r-------------------~rk~~~~~~~~~~v~~~vFDiLyl 557 (806)
...++ +....+++-||++.-. ..|+.+-.+ +|..........++.|++|++...
T Consensus 156 P~~l~~~~p~~levRGEv~m~~------~~F~~lN~~~~~~g~~~faNpRNaaAGslr~ld~~~~~~r~L~f~~y~~~~~ 229 (665)
T PRK07956 156 PLRLHGNEPERLEVRGEVFMPK------ADFEALNEERREEGEKPFANPRNAAAGSLRQLDPKITAKRPLSFFAYGVGEV 229 (665)
T ss_pred ChhhcccCCCeEEEEEEEEEEH------HHHHHHHHHHHhcCCCcccChHHHHhhhhhccChHHHhcCCCEEEEEecccc
Confidence 22221 1114588999999742 235544221 111000001246899999998644
Q ss_pred CCccccCCcHHHHHHHHHHhhccCCCcEEEEeEEecCCHHHHHHHHHHHHH------cCCceeEEEeCCCCCCcc----C
Q 003632 558 NGQPLLQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAAVD------ASCEGLIIKTMDRDATYE----P 627 (806)
Q Consensus 558 nG~~L~~~Pl~eRr~~L~~l~~~~~~~i~~~~~~~~~~~eei~~~~~~ai~------~g~EGlmlK~~~~ds~Y~----p 627 (806)
++. .......++.+.|.++-=++..... .+.+.+++.+++++..+ -...|||+|-- +-.|. .
T Consensus 230 ~~~-~~~~t~~e~l~~L~~~GF~v~~~~~-----~~~~~~ei~~~~~~~~~~R~~l~y~iDGiViKvn--~~~~~~~lG~ 301 (665)
T PRK07956 230 EGG-ELPDSQSEALEFLKAWGFPVNPYRK-----LCTSIEEVLAFYEEIEEERHDLPYDIDGVVIKVD--DLALQEELGF 301 (665)
T ss_pred cCC-CCCCCHHHHHHHHHHCCCCcCCceE-----eeCCHHHHHHHHHHHHHhhccCCCCCCcEEEEec--CHHHHHhcCc
Confidence 321 1124678899999887333332222 35678999999887763 36789999986 42221 1
Q ss_pred CCCCCCe---EEEccccccccCCcccEEEEEEEeCCCCCCCcccEEEEEEeeCC--CCeEEEeeeccCCCCHHHHHHH
Q 003632 628 SKRSLNW---LKLKKDYIESIGDSLDLVPIAAFHGRGKRTGVYGAFLLACYDSN--NEEFQSICKIGTGFSEAMLEER 700 (806)
Q Consensus 628 GkRs~~W---lKlK~dY~~~~~dtlDlvVIGa~~G~Gkr~g~~gsfLla~~d~~--~g~~~~v~kVgtGftd~~l~~l 700 (806)
..+.+.| +|+.++ ...-.|.+..|.-|| +|.++.. |..+|- .|. +|.++ |..+.++++++
T Consensus 302 t~~~PrWaiA~Kf~~~-------~~~T~l~~I~~qVGR-TG~iTPV--A~l~PV~l~G~--tVsrA-tLhN~~~i~~~ 366 (665)
T PRK07956 302 TAKAPRWAIAYKFPAE-------EATTKLLDIEVQVGR-TGAVTPV--ARLEPVEVAGV--TVSRA-TLHNADEIERK 366 (665)
T ss_pred cCCCCCceeEecCCCc-------eeEEEEEEEEEecCC-CceeeeE--EEEEeEEECCE--EEEEe-ecCCHHHHHHc
Confidence 2346778 676664 566677787777664 6666543 444431 244 44554 67777777653
No 59
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=97.71 E-value=0.0014 Score=79.18 Aligned_cols=237 Identities=18% Similarity=0.229 Sum_probs=141.7
Q ss_pred cccccc-cCCChHHHH---hh----cCCCceeEeeecceEeEEEEEecCCe-EEEEec----CCCcCCCCcchHHHHHHh
Q 003632 433 GPMLAK-PTKGVSEIV---NK----FQDMEFTCEYKYDGERAQIHYLEDGS-VEIYSR----NAERNTGKFPDVVLAVSR 499 (806)
Q Consensus 433 ~PMLA~-~~~~i~~~l---~k----~~g~~~~~E~KyDG~R~qih~~~~g~-V~ifSR----~gk~~T~~~Pel~~~l~~ 499 (806)
.|||.- .+.+.+++. ++ +....|+||+|+||.-+-+.+. +|+ ++..|| .|+|+|+....+. .|..
T Consensus 104 ~pMlSL~k~~~~~el~~f~~r~~~~~~~~~~~~epKiDGlaisL~Ye-~G~L~~a~TRGDG~~GeDVT~nv~~I~-~IP~ 181 (689)
T PRK14351 104 APMLSIDQSGEADDVREFDERVRREVGAVEYVCEPKFDGLSVEVVYE-DGEYQRAATRGDGREGDDVTANVRTIR-SVPQ 181 (689)
T ss_pred CcccccCccCCHHHHHHHHHHHHHhcCCceEEEEEecccEEEEEEEE-CCEEEEEEecCCCCcceeHhhhhhhhc-ccch
Confidence 389863 344555542 11 2223699999999999999995 665 789999 7999997543221 1222
Q ss_pred hcCC-CCCCeEEEEEEEEEecCCCccCChHHHHH-------------------hhhccCCccccccceEEEEeeeeecCC
Q 003632 500 LKKP-SVRSFVLDCEIVAYDREKQKILPFQTLST-------------------RARKNVSLSDIKVDVCIYAFDILYRNG 559 (806)
Q Consensus 500 ~~~~-~v~~~ILDGElVa~d~~~g~~~pFq~L~~-------------------r~rk~~~~~~~~~~v~~~vFDiLylnG 559 (806)
.+.. ....+++=||++.-. ..|+.+-. -.|+.........++.|++|++...++
T Consensus 182 ~l~~~~p~~levRGEv~m~~------~~F~~lN~~~~~~g~~~faNpRN~aAGslR~ldp~~~~~r~L~f~~y~~~~~~~ 255 (689)
T PRK14351 182 KLRGDYPDFLAVRGEVYMPK------DAFQAYNRERIERGEEPFANPRNAAAGTLRQLDPSVVAERPLDIFFFDVLDASE 255 (689)
T ss_pred hhcccCCCeEEEEEEEEEEH------HHHHHHHHHHHHcCCCCcCCHHHHHhhHhhccChHHHhcCCceEEEEecccCCC
Confidence 2211 113478889999743 23444321 111110000114689999999865544
Q ss_pred ccccCCcHHHHHHHHHHhhccCCCcEEEEeEEecCCHHHHHHHHHHHHH------cCCceeEEEeCCCCCCcc----CCC
Q 003632 560 QPLLQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAAVD------ASCEGLIIKTMDRDATYE----PSK 629 (806)
Q Consensus 560 ~~L~~~Pl~eRr~~L~~l~~~~~~~i~~~~~~~~~~~eei~~~~~~ai~------~g~EGlmlK~~~~ds~Y~----pGk 629 (806)
. .....++.+.|..+-=++..... .+.+.+++.+++++..+ -...|||+|-- +-.+. ...
T Consensus 256 ~---~~t~~e~l~~L~~~GF~v~~~~~-----~~~~~~~~~~~~~~~~~~R~~l~y~iDGiViKvn--~~~~q~~lG~ts 325 (689)
T PRK14351 256 L---FDSHWEELERFPEWGLRVTDRTE-----RVDDIDDAIAYRDRLLAARDDLNYEIDGVVIKVD--DRDAREELGATA 325 (689)
T ss_pred C---CCCHHHHHHHHHHCCCCcCCceE-----eeCCHHHHHHHHHHHHHhhhcCCCCCceEEEEeC--CHHHHHHhCccC
Confidence 2 24677888888887433333222 35778888888876643 35689999986 43331 123
Q ss_pred CCCCe---EEEccccccccCCcccEEEEEEEeCCCCCCCcccEEEEEEeeCC--CCeEEEeeeccCCCCHHHHHHH
Q 003632 630 RSLNW---LKLKKDYIESIGDSLDLVPIAAFHGRGKRTGVYGAFLLACYDSN--NEEFQSICKIGTGFSEAMLEER 700 (806)
Q Consensus 630 Rs~~W---lKlK~dY~~~~~dtlDlvVIGa~~G~Gkr~g~~gsfLla~~d~~--~g~~~~v~kVgtGftd~~l~~l 700 (806)
+.+.| +|+.++ ...-.|.+..|--|| +|.++.. |..+|- .|. +|.++ |..+.++++++
T Consensus 326 ~~PrWaiA~Kf~~~-------~~~T~l~~I~~qVGR-TG~iTPV--A~lePV~l~G~--tVsra-tLhN~~~i~~~ 388 (689)
T PRK14351 326 RAPRWAFAYKFPAR-------AEETTIRDIVVQVGR-TGRLTPV--ALLDPVDVGGV--TVSRA-SLHNPAEIEEL 388 (689)
T ss_pred CCCCceEEEcCCCc-------eeEEEEEEEEEecCC-CceeeeE--EEEEeEEECCE--EEEEe-ccCCHHHHHHc
Confidence 56788 566653 556677777776654 6666543 444431 244 45555 67777777653
No 60
>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=97.44 E-value=0.00035 Score=70.80 Aligned_cols=159 Identities=21% Similarity=0.167 Sum_probs=83.4
Q ss_pred ceeEeeecceEeEEEEEecCCeEEEEecCCCc-----C------CCCcchHHHH---HHhh---c-CCCCCCeEEEEEEE
Q 003632 454 EFTCEYKYDGERAQIHYLEDGSVEIYSRNAER-----N------TGKFPDVVLA---VSRL---K-KPSVRSFVLDCEIV 515 (806)
Q Consensus 454 ~~~~E~KyDG~R~qih~~~~g~V~ifSR~gk~-----~------T~~~Pel~~~---l~~~---~-~~~v~~~ILDGElV 515 (806)
+|++++|+||.-+.+.+..++.+.+.+|++.. + ...|...... +... . .....++++=||++
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 69999999999999988766679999999832 1 1112222111 1111 1 01347899999999
Q ss_pred EEecCCCccCChHHHHHhhhccCCccccccceEEEEeeeeecCCc-cccCCcHHHHHHHHHHhhccCCCcEEEEeEEecC
Q 003632 516 AYDREKQKILPFQTLSTRARKNVSLSDIKVDVCIYAFDILYRNGQ-PLLQEQLRVRREHLYDSFEEEPGFFQFATTLTSI 594 (806)
Q Consensus 516 a~d~~~g~~~pFq~L~~r~rk~~~~~~~~~~v~~~vFDiLylnG~-~L~~~Pl~eRr~~L~~l~~~~~~~i~~~~~~~~~ 594 (806)
.+-+.-. ++.. ....+..|++|||...+.. ...=.+..+.+.+++.+- +..++.....
T Consensus 82 G~~~~Iq-------------~~~~--~~~~~~~F~~Fdi~~~~~~~~~~~l~~~~~~~~~~~~g------l~~VPvl~~g 140 (186)
T PF09414_consen 82 GAKPSIQ-------------KNRY--QLDPPKDFYVFDIYDIDEQGEIRYLSWDEVREFAEELG------LKTVPVLYRG 140 (186)
T ss_dssp CEECTTC-------------SS------ECCCEEEEEEEEEEETCCGEEE-HHHHHHHHHCCCT-------EES-ECEEE
T ss_pred eeccccc-------------cccc--ccCCCceEEEEEEEEcCCCCeeEECCHHHHHHHHHHCC------CCEeCEEEEE
Confidence 8642100 0000 0013689999999988543 223457777777776651 2223322111
Q ss_pred CHHHHHH------HH-HHHHHcCCceeEEEeCCCCCCccCCCCCCCeEEEc
Q 003632 595 DLDEIQK------FL-DAAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLK 638 (806)
Q Consensus 595 ~~eei~~------~~-~~ai~~g~EGlmlK~~~~ds~Y~pGkRs~~WlKlK 638 (806)
...+... .. ...-..-.||+|+|.. +..+ .+.| .-+|.|
T Consensus 141 ~~~~~~~~~~~~~~~~~~~~~~~~EGiVik~~--~~~~-~~~r--~~~K~k 186 (186)
T PF09414_consen 141 TFTELDDLDDLFESGKPSGEGNIREGIVIKPE--DEFH-DGSR--VIFKAK 186 (186)
T ss_dssp CHHHHCTS-CCGBBTTS-STT-B--EEEEEET--TTT--TTEB--SEEEEE
T ss_pred ccchhhhhhHHHhhcccCCCCCccCEEEEEEe--EecC-CCce--EEEEEC
Confidence 2222211 10 1122356899999998 6656 4545 566665
No 61
>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=97.25 E-value=0.0025 Score=70.20 Aligned_cols=162 Identities=21% Similarity=0.182 Sum_probs=91.9
Q ss_pred CCCceeEeeecceEeEEEEEecCCeEEEEecCCCcCC-CCc-------chHHHHHH---hhcC----CCCCCeEEEEEEE
Q 003632 451 QDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNT-GKF-------PDVVLAVS---RLKK----PSVRSFVLDCEIV 515 (806)
Q Consensus 451 ~g~~~~~E~KyDG~R~qih~~~~g~V~ifSR~gk~~T-~~~-------Pel~~~l~---~~~~----~~v~~~ILDGElV 515 (806)
.+.+|.+.+|.||...-+.+++++.+++.||++.--- ..| +++...++ +.+. ....++++=||++
T Consensus 23 ~~~ewvatEKlhGaNfsi~~~~~~~i~~akR~~~l~~~e~f~G~~~i~~~l~~~~~~l~~~l~~~~~~~~~~v~IyGEl~ 102 (325)
T TIGR02307 23 GLTEWVAREKIHGTNFSIIIERDFKVTCAKRTGIILPNEDFFGYHILIKNYTASVKAIQDILETKAIIVVVSVQVFGELA 102 (325)
T ss_pred CCceEEEEEEecCcceEEEEeCCceEEEeecccccCcccccccHHHHHHHHHHHHHHHHHHHhhhcccccceEEEEEEee
Confidence 4568999999999999888864438999999964321 111 22222222 2221 1357899999999
Q ss_pred EEecCCCccCChHHHHHhhhccCCccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCCCcEEEEeEEecCC
Q 003632 516 AYDREKQKILPFQTLSTRARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEPGFFQFATTLTSID 595 (806)
Q Consensus 516 a~d~~~g~~~pFq~L~~r~rk~~~~~~~~~~v~~~vFDiLylnG~~L~~~Pl~eRr~~L~~l~~~~~~~i~~~~~~~~~~ 595 (806)
.+.-..+. . -.+..|++|||.+....+..=+++.+-.+...... + +..++.....+
T Consensus 103 G~~~q~~~---------------~----Y~~~~fyaFdI~~~~~~~~~~L~~d~~~e~~~~~~----~-l~~ap~L~rGt 158 (325)
T TIGR02307 103 GPGYQKPV---------------V----YSDKDFYAFDIKYTETSDDVTLVDDYMMESFCNVP----K-LKYAPLLGRGT 158 (325)
T ss_pred cCcccCcc---------------c----cccccEEEEEEEEeccCcceEecHHHHHHHHHHcC----C-cccchhhcccC
Confidence 87321110 0 11568999999553121223345655555554431 1 23333333456
Q ss_pred HHHHHHH---HHHH-----H--------HcCCceeEEEeCCCCC-CccC-CCCCCCeEEEccc
Q 003632 596 LDEIQKF---LDAA-----V--------DASCEGLIIKTMDRDA-TYEP-SKRSLNWLKLKKD 640 (806)
Q Consensus 596 ~eei~~~---~~~a-----i--------~~g~EGlmlK~~~~ds-~Y~p-GkRs~~WlKlK~d 640 (806)
.+++.++ +..+ + .+=+||+|+|.. .. .|.. |.| .-+|.|.+
T Consensus 159 ~~e~l~~~~~~~s~~ip~l~~~~~~~~~~n~aEGvViKp~--~~~~~~~~g~r--~iiK~kn~ 217 (325)
T TIGR02307 159 LDELLAFDVENFTTDHPALVDAGNYPLEGNTAEGYVVKHC--RPGKWLRNGNR--TIIKCKNS 217 (325)
T ss_pred HHHHHhcccccccccCcccccccccCCCCCeeeeEEEeec--cccccccCCce--EEEEEecH
Confidence 6666655 1111 1 122899999998 42 2432 333 57888874
No 62
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=96.90 E-value=0.034 Score=66.21 Aligned_cols=193 Identities=18% Similarity=0.201 Sum_probs=122.6
Q ss_pred CceeEeeecceEeEEEEEecCCe-EEEEecC----CCcCCCCcchHHHHHHhhcCCCCCCeEEEEEEEEEecCCCccCCh
Q 003632 453 MEFTCEYKYDGERAQIHYLEDGS-VEIYSRN----AERNTGKFPDVVLAVSRLKKPSVRSFVLDCEIVAYDREKQKILPF 527 (806)
Q Consensus 453 ~~~~~E~KyDG~R~qih~~~~g~-V~ifSR~----gk~~T~~~Pel~~~l~~~~~~~v~~~ILDGElVa~d~~~g~~~pF 527 (806)
..|+||+|+||.-+-+.+ ++|. ++--||. |+|+|....-|.. |...++......-+-||++.-- ..|
T Consensus 109 ~~y~~EpKiDGlsisL~Y-enG~Lv~aaTRGdG~~GEDiT~NvrtI~~-IP~~l~~~p~~lEVRGEvfm~k------~~F 180 (667)
T COG0272 109 VEYVVEPKIDGLAISLVY-ENGKLVRAATRGDGTTGEDITANVRTIRS-IPLKLPGAPAVLEVRGEVFMPK------EDF 180 (667)
T ss_pred cceEEEeecceEEEEEEE-ECCEEEEeeccCCCccccchhhhhhhHhh-hhhhccCCCceEEEEeEEEEeH------HHH
Confidence 479999999999999988 4665 6777875 8899986554442 4433331235678999998741 346
Q ss_pred HHHHHhhhcc------------------CCcc-ccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCCCcEEEE
Q 003632 528 QTLSTRARKN------------------VSLS-DIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEPGFFQFA 588 (806)
Q Consensus 528 q~L~~r~rk~------------------~~~~-~~~~~v~~~vFDiLylnG~~L~~~Pl~eRr~~L~~l~~~~~~~i~~~ 588 (806)
+.+-...... .+.. ..+.++.+++|.+-+..+. ..-....++.+.|..+-=++...
T Consensus 181 ~~lN~~~~~~g~~~faNpRNaAAGsLRqlD~~ita~R~L~~f~y~~~~~~~~-~~~~t~~e~l~~L~~~GF~v~~~---- 255 (667)
T COG0272 181 EALNEEREEEGEKPFANPRNAAAGSLRQLDPKITAKRKLGFFIYAVGDGEEG-LLADTQSERLAFLKAWGFPVNPY---- 255 (667)
T ss_pred HHHHHHHHHhCCCCcCChhhhhhhhhhccCHHHHhcCCceEEEEeCCccCCC-CCccCHHHHHHHHHHcCCCCCcH----
Confidence 6654322110 0111 1145899999998865544 55567889999999874333222
Q ss_pred eEEecCCHHHHHHHHHHHHHc------CCceeEEEeCCCCCCcc---CCCCCCCe---EEEccccccccCCcccEEEEEE
Q 003632 589 TTLTSIDLDEIQKFLDAAVDA------SCEGLIIKTMDRDATYE---PSKRSLNW---LKLKKDYIESIGDSLDLVPIAA 656 (806)
Q Consensus 589 ~~~~~~~~eei~~~~~~ai~~------g~EGlmlK~~~~ds~Y~---pGkRs~~W---lKlK~dY~~~~~dtlDlvVIGa 656 (806)
...+.+.+++.++++..... --.|+|+|--| -..|+ .-.|++.| +|+.+.- .--.+.+.
T Consensus 256 -~~~~~~~~ev~~~~~~~~~~R~~L~y~IDGvViKvn~-l~~q~~lG~tsk~PrWAiAyKFpa~e-------~~T~l~dI 326 (667)
T COG0272 256 -TRLCKNADEVLAFYEEWEKKRASLPYDIDGVVIKVND-LALQRELGFTSKAPRWAIAYKFPAEE-------AVTKLLDI 326 (667)
T ss_pred -hhhcCCHHHHHHHHHHHHhhcccCCCccceEEEEecc-HHHHHHhCCccCCCceeeeecCCchh-------eeeEEEEE
Confidence 23478999999999998764 46799999752 23332 12357889 7877753 22344444
Q ss_pred EeCCCCCCCccc
Q 003632 657 FHGRGKRTGVYG 668 (806)
Q Consensus 657 ~~G~Gkr~g~~g 668 (806)
.+.-| |+|.++
T Consensus 327 ~~qVG-RTG~iT 337 (667)
T COG0272 327 EVQVG-RTGAIT 337 (667)
T ss_pred EEecC-Cceeee
Confidence 44443 455544
No 63
>PHA02142 putative RNA ligase
Probab=96.25 E-value=0.049 Score=61.09 Aligned_cols=163 Identities=17% Similarity=0.176 Sum_probs=93.6
Q ss_pred CChHHHHh-hcCCCceeEeeecceEeEEEEEe--------------------cCCeEEEEecCCCc---CCCCcchH---
Q 003632 441 KGVSEIVN-KFQDMEFTCEYKYDGERAQIHYL--------------------EDGSVEIYSRNAER---NTGKFPDV--- 493 (806)
Q Consensus 441 ~~i~~~l~-k~~g~~~~~E~KyDG~R~qih~~--------------------~~g~V~ifSR~gk~---~T~~~Pel--- 493 (806)
.++.++++ +..+..|.+-.|+||.-|-+.+. ..|.+...|||... -+..|-.+
T Consensus 156 Qn~~~~~~~~~~~~~f~~TeKLDGsS~tvy~~~~~~~~~~~~~~~~~~~~~~~~~~~gv~srn~~l~~~~~~~~W~~a~~ 235 (366)
T PHA02142 156 QNIFNRYKEKYADVKFAKSLKLDGSSITMAWVTDPDLFLDLGTEDEPYAHDYDDAQFIVASRNQVLRYNADSKWWKGVEN 235 (366)
T ss_pred hhhhhhhhhhhcCceEEEEEEecceeEEEEEecCCcccccccccccccccccCCCceeEeeccccccccCCchHHHHHHH
Confidence 34555432 24567899999999999987732 24677889999862 12222222
Q ss_pred ---HHHHHhhcCCCCCCeEEEEEEEEEecCCCccCChHHHHHhhhccCCccccccceEEEEeeeeecCCccccCCcHHHH
Q 003632 494 ---VLAVSRLKKPSVRSFVLDCEIVAYDREKQKILPFQTLSTRARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVR 570 (806)
Q Consensus 494 ---~~~l~~~~~~~v~~~ILDGElVa~d~~~g~~~pFq~L~~r~rk~~~~~~~~~~v~~~vFDiLylnG~~L~~~Pl~eR 570 (806)
.+.|+.+ -.++.+=||++.-.-.++ .. ......|++|||-.++++. =+++.++
T Consensus 236 ~~i~~~l~~~----~~~iaIqGEl~Gp~IQ~N---------------~~---~~~~~~F~vF~v~~i~~~~--yl~~~e~ 291 (366)
T PHA02142 236 YQIVDRLKEL----GMSVAIQGELMGPGIQKN---------------RE---NFDKYRIFAFRAWFIDEQR--FATDEEF 291 (366)
T ss_pred cCcHHHHHhh----CCcEEEEEEEecccccCc---------------cc---cCCCCceEEEEEEEeccce--eCCHHHH
Confidence 2233332 257889999997422111 00 0112479999997777665 3678899
Q ss_pred HHHHHHhhccCCCcEEEEeEEe-------cCCHHHHHHHHHH--HHHcCCceeEEEeCCCCCCccCCCCCCCeEEEcc
Q 003632 571 REHLYDSFEEEPGFFQFATTLT-------SIDLDEIQKFLDA--AVDASCEGLIIKTMDRDATYEPSKRSLNWLKLKK 639 (806)
Q Consensus 571 r~~L~~l~~~~~~~i~~~~~~~-------~~~~eei~~~~~~--ai~~g~EGlmlK~~~~ds~Y~pGkRs~~WlKlK~ 639 (806)
+++++++--+ .++... ..+.+++.++-+- .-..-+||+|+|.. . =..|.| -|+|.|.
T Consensus 292 ~~~~~~~gl~------~VPvL~~~~~~~~~~s~eE~L~~A~~p~~~~~~~EGiViKp~--~--~~~g~r--~~fK~is 357 (366)
T PHA02142 292 QDLCRTLGME------IVPQLGYSYPFQEFTNVKEMLAAADIPSINHKIAEGVVYKSV--E--LVNGRM--VHFKAIN 357 (366)
T ss_pred HHHHHHcCCc------eeeeecccccccccCCHHHHHhhcCCCcccccccceEEEeec--c--ccCCce--EEEEEcC
Confidence 9988876221 222211 1244444433210 00123799999987 3 112323 5999886
No 64
>PRK03180 ligB ATP-dependent DNA ligase; Reviewed
Probab=94.66 E-value=0.15 Score=60.14 Aligned_cols=91 Identities=19% Similarity=0.216 Sum_probs=78.7
Q ss_pred CccchHHHHHHHHHHHhcc---chHHHHHHHHHHHHhhhcCCCCchHhHHHHHhCCcCCCccccccCCCHHHHHHHHHHH
Q 003632 189 ERVPFIFLSLVFDMISNET---GRILITDIVCNMLRTVMETTPEDLVPVVYLAANKIAPAHEGLELGIGDASIIKALAEA 265 (806)
Q Consensus 189 ~~~~F~~la~~~~~I~~ts---sr~~k~~iL~~~~r~~i~~~p~dl~~~vyL~~~~l~P~~e~~elgIg~~~L~Kal~~~ 265 (806)
.+++..++=+.|++|+..+ +..+|.++|..+|..+ +|.+.-+.+.++++. ..+|+++.++..|++++
T Consensus 71 ~~ltl~~V~~~l~~ia~~~g~~s~~~k~~~l~~ll~~~---~~~E~~~l~r~i~~~-------lRiGv~~~~v~~Ala~a 140 (508)
T PRK03180 71 PTLTVADVDAALSEIAAVAGAGSQARRAALLAALFAAA---TEDEQRFLRRLLTGE-------LRQGALDGVMADAVARA 140 (508)
T ss_pred CCCcHHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHhC---CHHHHHHHHHHHhCC-------CcccccHHHHHHHHHHH
Confidence 3566778777888888865 5689999999999986 888888888888874 46999999999999999
Q ss_pred hCCCHHHHHHHHhhcCCHHHHHhh
Q 003632 266 CGRTESHVKKQYQEMGDLGLVAKA 289 (806)
Q Consensus 266 ~g~s~~~ik~~~~~~GDlg~va~~ 289 (806)
++.+...++..|...||++.++..
T Consensus 141 ~~~~~~~v~~a~~~~~dl~~v~~~ 164 (508)
T PRK03180 141 AGVPAAAVRRAAMLAGDLPAVAAA 164 (508)
T ss_pred hCCCHHHHHHHHHHcCCHHHHHHH
Confidence 999999999999999999999864
No 65
>KOG3132 consensus m3G-cap-specific nuclear import receptor (Snurportin1) [RNA processing and modification]
Probab=94.14 E-value=0.23 Score=52.32 Aligned_cols=152 Identities=20% Similarity=0.369 Sum_probs=104.4
Q ss_pred CCceeEeeecceEeEEEEEecCCeEEEEecCCCcCCCCcchHHHHHHhhcCCCCCCeEEEEEEEEEecCCCccCChHHHH
Q 003632 452 DMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAVSRLKKPSVRSFVLDCEIVAYDREKQKILPFQTLS 531 (806)
Q Consensus 452 g~~~~~E~KyDG~R~qih~~~~g~V~ifSR~gk~~T~~~Pel~~~l~~~~~~~v~~~ILDGElVa~d~~~g~~~pFq~L~ 531 (806)
+.+|++=.-==|-||.|.-. .|...-|.|+|..+. +||....-=.....+.-.=.||||= ++
T Consensus 115 sqdW~vv~~PvGKR~lvVaS-rG~Tvay~k~G~~v~-rF~S~LPGGnrr~~~a~~ytILDCI---y~------------- 176 (325)
T KOG3132|consen 115 SQDWYVVARPVGKRCLVVAS-RGTTVAYVKNGSTVH-RFPSALPGGNRRKGPANSYTILDCI---YH------------- 176 (325)
T ss_pred CcceEEEEeecCceEEEEec-CCceEEEecCCeeEe-eccccCCCCCcCCCCcccceeeeee---ec-------------
Confidence 35788888888999998764 788889999998763 4554211000000011122356652 21
Q ss_pred HhhhccCCccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCCC--------cEEEE--eEEecCCHHHHHH
Q 003632 532 TRARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEPG--------FFQFA--TTLTSIDLDEIQK 601 (806)
Q Consensus 532 ~r~rk~~~~~~~~~~v~~~vFDiLylnG~~L~~~Pl~eRr~~L~~l~~~~~~--------~i~~~--~~~~~~~~eei~~ 601 (806)
+.+-.|+|.|++..+|.++.+.++.-|.-.|++-+.+.++ .+.|+ +... .+.+.+.+
T Consensus 177 ------------esnQTYYVlD~~cWrgh~~yec~~dFRffwl~SKL~E~~~l~~~t~~~~f~Fs~vp~~p-C~q~~l~~ 243 (325)
T KOG3132|consen 177 ------------ESNQTYYVLDMVCWRGHSLYECTSDFRFFWLQSKLAETGALDPPTVYHKFRFSVVPFYP-CDQSGLHS 243 (325)
T ss_pred ------------ccCceEEEEEEEeecCcccccCchHHHHHHHhhhccccccCCCCCcCccceecccCCCC-CCHHHHHH
Confidence 1234789999999999999999999999999998876432 33443 3333 36777888
Q ss_pred HHHHHHHcCCceeEEEeCCCCCCccCCCC-CCCeEE
Q 003632 602 FLDAAVDASCEGLIIKTMDRDATYEPSKR-SLNWLK 636 (806)
Q Consensus 602 ~~~~ai~~g~EGlmlK~~~~ds~Y~pGkR-s~~WlK 636 (806)
.|.-.+--...|+..-.- .-.|.||.. --+|||
T Consensus 244 ~~~~~~pf~~DGLLFYhk--s~~yqpgqsplvgwlk 277 (325)
T KOG3132|consen 244 AYTGSLPFVRDGLLFYHK--SVVYQPGQSPLVGWLK 277 (325)
T ss_pred HHcCCCceeeeeEEEeec--ceeeCCCCCccccccc
Confidence 888777778899999987 788999964 247875
No 66
>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=93.52 E-value=1.3 Score=49.78 Aligned_cols=154 Identities=14% Similarity=0.176 Sum_probs=83.0
Q ss_pred CCceeEeeecceEeEEEEEec-CCeEE-----EEecCCCc---CCCCcch------HHHHHHhhcCCCCCCeEEEEEEEE
Q 003632 452 DMEFTCEYKYDGERAQIHYLE-DGSVE-----IYSRNAER---NTGKFPD------VVLAVSRLKKPSVRSFVLDCEIVA 516 (806)
Q Consensus 452 g~~~~~E~KyDG~R~qih~~~-~g~V~-----ifSR~gk~---~T~~~Pe------l~~~l~~~~~~~v~~~ILDGElVa 516 (806)
+..|++-.|+||--|.+.+.. .+.+. +-|||.+. -+..|-. |.+.+.+.. .-.++.+=||++.
T Consensus 158 ~~~~~~TeKldGss~tv~~~~~~~~~~~~~~Gvcsr~~~l~~~~~~~~W~~a~~~~i~~~l~~~~--~~~~vaiqGEl~G 235 (341)
T TIGR02306 158 GEKVAKTEKLHGTSITVAWVTDEERFLVLSKGVASRNLVLRENADNKYWKAVENYQIVDRAKAAE--LRMSVAIFGEVMG 235 (341)
T ss_pred CceEEEEEEecceeEEEEEecCCcccccccceeecCCcccccCCCchhHHHHHhcChHHHHhhcc--cCceEEEEEEEeC
Confidence 578999999999999776532 23322 44788762 2223322 233343211 1257889999997
Q ss_pred EecCCCccCChHHHHHhhhccCCccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCCCcEEEEeEEecCCH
Q 003632 517 YDREKQKILPFQTLSTRARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDL 596 (806)
Q Consensus 517 ~d~~~g~~~pFq~L~~r~rk~~~~~~~~~~v~~~vFDiLylnG~~L~~~Pl~eRr~~L~~l~~~~~~~i~~~~~~~~~~~ 596 (806)
-.-.++. .. ...+-.+++|++ +.+|+. .=++++++.+++..+. +|- + + ..+.
T Consensus 236 ~gIQ~n~--------------Yg---~~~~~~~f~F~v-~~~~~~-ryld~~~~~~~~~~~~--VPv-L-~-----~g~~ 287 (341)
T TIGR02306 236 PGIQKNR--------------YG---FDKYRTVFAFRA-FFDGEQ-RFLTDEDFQDLCLTLI--VPQ-L-Y-----EGPF 287 (341)
T ss_pred ccccCCc--------------CC---CCCCceEEEEEE-EEcCcc-eecCHHHHHHHHHhcc--cce-E-E-----Eech
Confidence 3221110 00 011222788887 444442 2247889998888752 221 1 1 1122
Q ss_pred HHHHHHHHHHHHc----C-----CceeEEEeCCCCCCccCCCCCCCeEEEcc
Q 003632 597 DEIQKFLDAAVDA----S-----CEGLIIKTMDRDATYEPSKRSLNWLKLKK 639 (806)
Q Consensus 597 eei~~~~~~ai~~----g-----~EGlmlK~~~~ds~Y~pGkRs~~WlKlK~ 639 (806)
++. ..++.++.. | +||+|+|.. ...|-... +.-|+|.|.
T Consensus 288 de~-~~~~~~ig~a~~~~~~~~irEGvViKp~--~~~~~~~G-~r~~fK~is 335 (341)
T TIGR02306 288 DEF-TVVKDMLGAETVSGIGLHIREGVVYKSV--ELRFAVDG-RMVHFKAIS 335 (341)
T ss_pred hHh-hhhhhhhcccccCccccceeceEEEeec--cccccCCC-ceEEEEEcC
Confidence 221 333333322 2 899999998 65553221 235999886
No 67
>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=92.50 E-value=0.53 Score=55.63 Aligned_cols=93 Identities=19% Similarity=0.265 Sum_probs=78.9
Q ss_pred CccchHHHHHHHHHHHhcc---chHHHHHHHHHHHHhhhcCCCCchHhHHHHHhCCcCCCccccccCCCHHHHHHHHHHH
Q 003632 189 ERVPFIFLSLVFDMISNET---GRILITDIVCNMLRTVMETTPEDLVPVVYLAANKIAPAHEGLELGIGDASIIKALAEA 265 (806)
Q Consensus 189 ~~~~F~~la~~~~~I~~ts---sr~~k~~iL~~~~r~~i~~~p~dl~~~vyL~~~~l~P~~e~~elgIg~~~L~Kal~~~ 265 (806)
.++.-.++-..++.|++.+ ++.+|.++|.++|+.. +|.+.-+.+.++++. ...|++++++.++|+.+
T Consensus 53 ~~lti~eV~~~L~~ia~~~g~~s~~~k~~~l~~ll~~~---~~~e~k~l~r~i~~~-------lriG~~~~~il~al~~~ 122 (514)
T TIGR00574 53 APLTVKEVYETLKNIAETSGEGSQDKKIKLLKSLLKRA---SPLEAKYLIRTILGD-------LRIGIAEKTILDALAKA 122 (514)
T ss_pred CCcCHHHHHHHHHHHHHhhCCCcHHHHHHHHHHHHHhC---CHHHHHHHHHHHhhh-------cccCccHHHHHHHHHHH
Confidence 4566788888888888765 5789999999999886 888888888888774 45899999999999999
Q ss_pred hCCCHHHHHHHHhhcCCHHHHHhhcc
Q 003632 266 CGRTESHVKKQYQEMGDLGLVAKASR 291 (806)
Q Consensus 266 ~g~s~~~ik~~~~~~GDlg~va~~~r 291 (806)
++.+...+...|....|++.|+..+.
T Consensus 123 ~~~~~~~~~~~~~~~~dl~~v~~~l~ 148 (514)
T TIGR00574 123 FLLSHPDVERAFNLTNDLGKVAKILL 148 (514)
T ss_pred hccchHHHHHHHHhCCCHHHHHHHHH
Confidence 99998999999999999999987653
No 68
>KOG2386 consensus mRNA capping enzyme, guanylyltransferase (alpha) subunit [RNA processing and modification]
Probab=91.24 E-value=0.13 Score=58.11 Aligned_cols=95 Identities=17% Similarity=0.163 Sum_probs=64.8
Q ss_pred ceeEeeecceEeEEEEEecCCeEEEEecCCCcCC---CCcchHHHHHHhhcCCCCCCeEEEEEEEEEecCCCccCChHHH
Q 003632 454 EFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNT---GKFPDVVLAVSRLKKPSVRSFVLDCEIVAYDREKQKILPFQTL 530 (806)
Q Consensus 454 ~~~~E~KyDG~R~qih~~~~g~V~ifSR~gk~~T---~~~Pel~~~l~~~~~~~v~~~ILDGElVa~d~~~g~~~pFq~L 530 (806)
.|.+.+|.||.|...-++.+|.+..|-|.-...- -.++.- ....+.....++|||++. |.-++
T Consensus 286 ~y~~~We~dg~~~~~L~~~~~~~~~~dR~~~~~~~~~~~~~~~-----~~~~~~~~~tl~dge~~l-D~l~~-------- 351 (393)
T KOG2386|consen 286 YYEASWEADGTRYMMLIDGDGEYYDFDRWRFVKGRENLRKIRE-----DSDTKVLHQTLLDGEMIL-DRLKE-------- 351 (393)
T ss_pred hhhhhhcccCcEEEEEecCCceeEechhhhHHHhhhhhhcccc-----cccchhhhhhhcccceec-ccccc--------
Confidence 4678999999999888876666777765543221 011110 001113356789999998 65432
Q ss_pred HHhhhccCCccccccceEEEEeeeeecCCccccCCcHHHHHHHHHH
Q 003632 531 STRARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYD 576 (806)
Q Consensus 531 ~~r~rk~~~~~~~~~~v~~~vFDiLylnG~~L~~~Pl~eRr~~L~~ 576 (806)
.....+.+||++-+|++.+...|+. |.+.+.+
T Consensus 352 -------------~~~~r~l~Yd~~r~n~~~v~~~~f~-r~~~~~~ 383 (393)
T KOG2386|consen 352 -------------EAIPRYLIYDMVRFNSQKVEKRPFS-RWQIIEK 383 (393)
T ss_pred -------------ccchhheeeeeeeccCcccccCcch-HHHHHHH
Confidence 1245678999999999999999999 9887755
No 69
>PRK09247 ATP-dependent DNA ligase; Validated
Probab=89.02 E-value=1.4 Score=52.55 Aligned_cols=87 Identities=13% Similarity=0.127 Sum_probs=66.4
Q ss_pred HHHHHHHHHHHHhCCChHHHHHHHHHHHHHhcCCChHHHHHHHHhhccc-CcccHHHHHHHHHhhhcccCCCCCCCCCCc
Q 003632 307 KVFDTFRLIAKEAGKDSQEKKKNRIKALLVAATDCEPQYLIRLLQSKLR-IGLAEQTLLAALGQAAVYNEQHSKPPPNIQ 385 (806)
Q Consensus 307 eV~~~L~~IA~~~G~~sq~~k~~~L~~Ll~~~t~~E~k~LiRiIlkdLR-iG~~e~til~ala~A~~~~~~~~~~~~~l~ 385 (806)
+.-+.+++|+..+ +...|.++|..+|..+++.+.-|.++++++.+. .|++++.+.++++.++..+.
T Consensus 3 ~fa~~~~~i~~t~---~~~ek~~~l~~~~~~~~~~d~~~~~~ll~g~~~~~~i~~~~l~k~~~~~~g~~~---------- 69 (539)
T PRK09247 3 AFAELLDRLDLTT---STNAKLALLADYFRSAPDPDRAWALALLTGGLPRRLVKTRLLRELAAERADLPP---------- 69 (539)
T ss_pred HHHHHHHHHHhcc---CHHHHHHHHHHHHHhCCHHHHHHHHHHhcCCcccCCCCHHHHHHHHHHHHCcCH----------
Confidence 4456666776543 455789999999999999999999999999885 99999999999999876432
Q ss_pred ccHHHHHHHHHHHhhcCCchhhhHhhhh
Q 003632 386 SPLEEAAKIVKQVFSVLPVYEKIVPALL 413 (806)
Q Consensus 386 ~~l~~a~~~~k~~y~~~p~~~~v~~~ll 413 (806)
..+++.|...-|++.++..++
T Consensus 70 -------~~~~~~~~~~GDlg~~~~~~~ 90 (539)
T PRK09247 70 -------WLFEESYDYVGDLAETIALLL 90 (539)
T ss_pred -------HHHHHHHHhcCCHHHHHHHhc
Confidence 233456666667777665554
No 70
>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=88.54 E-value=0.84 Score=45.83 Aligned_cols=65 Identities=22% Similarity=0.359 Sum_probs=50.8
Q ss_pred CccchHHHHHHHHHHHhcc---chHHHHHHHHHHHHhhhcCCCCchHhHHHHHhCCcCCCccccccCCCHHHHHHHHH
Q 003632 189 ERVPFIFLSLVFDMISNET---GRILITDIVCNMLRTVMETTPEDLVPVVYLAANKIAPAHEGLELGIGDASIIKALA 263 (806)
Q Consensus 189 ~~~~F~~la~~~~~I~~ts---sr~~k~~iL~~~~r~~i~~~p~dl~~~vyL~~~~l~P~~e~~elgIg~~~L~Kal~ 263 (806)
.++...++-+++++|+..+ ++.+|.++|.++++++ +|.+..+.+.++++ ...+|++++.+..+++
T Consensus 109 ~~lTi~~V~~~L~~la~~~g~~s~~~k~~~l~~ll~~~---s~~E~k~i~Riil~-------~lriG~~~~~il~ala 176 (177)
T PF04675_consen 109 SPLTISEVNETLDELAAASGKGSQDEKIDILKELLRRC---SPEEAKWIVRIILK-------DLRIGVSEKTILDALA 176 (177)
T ss_dssp S--BHHHHHHHHHHHHH--STTHHHHHHHHHHHHHTTS----HHHHHHHHHHHTT---------SSS--HHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHHhhCccchHHHHHHHHHHHHhC---CHHHHHHHHHHHhC-------CCeeCccHHHHHHHhC
Confidence 5778899999999999987 7899999999999986 89999999999887 3569999999998875
No 71
>PLN03113 DNA ligase 1; Provisional
Probab=81.49 E-value=6.1 Score=48.84 Aligned_cols=71 Identities=18% Similarity=0.268 Sum_probs=56.3
Q ss_pred CccchHHHHHHHHHHHhcc---chHHHHHHHHHHHHhhhcCCCCchHhHHHHHhCCcCCCccccccCCCHHHHHHHHHHH
Q 003632 189 ERVPFIFLSLVFDMISNET---GRILITDIVCNMLRTVMETTPEDLVPVVYLAANKIAPAHEGLELGIGDASIIKALAEA 265 (806)
Q Consensus 189 ~~~~F~~la~~~~~I~~ts---sr~~k~~iL~~~~r~~i~~~p~dl~~~vyL~~~~l~P~~e~~elgIg~~~L~Kal~~~ 265 (806)
.+.+-.++-..|..|+..+ +..+|..+|..++..+ .+.+.-..+.++++. ..+|+++.++..||+.+
T Consensus 239 ~~LTi~~V~~~L~~IA~~~G~~sq~~K~~~i~~Ll~~~---~~~E~k~liR~l~g~-------LRIGv~e~tVl~ALa~a 308 (744)
T PLN03113 239 EPLTVVKVFNTFQQIAKESGKDSQEKKKNRIKALLVAA---TDCEPLYLIRLLQTK-------LRIGLAGQTLLAALGQA 308 (744)
T ss_pred CCCCHHHHHHHHHHHHhhhCccCHHHHHHHHHHHHHhC---CHHHHHHHHHHHhcc-------ccccccHHHHHHHHHHH
Confidence 3456677777777787765 5668899999999886 677888888888874 46999999999999999
Q ss_pred hCCC
Q 003632 266 CGRT 269 (806)
Q Consensus 266 ~g~s 269 (806)
++.+
T Consensus 309 ~~~~ 312 (744)
T PLN03113 309 AVYN 312 (744)
T ss_pred hccc
Confidence 8654
No 72
>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=56.60 E-value=1.9e+02 Score=30.29 Aligned_cols=149 Identities=17% Similarity=0.218 Sum_probs=57.4
Q ss_pred ceeEeeecceEeEEEEEecCCeEEEEecCCCcCCCCcchH----------------HHHHHhhcCCCCCCeEEEEEEEEE
Q 003632 454 EFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDV----------------VLAVSRLKKPSVRSFVLDCEIVAY 517 (806)
Q Consensus 454 ~~~~E~KyDG~R~qih~~~~g~V~ifSR~gk~~T~~~Pel----------------~~~l~~~~~~~v~~~ILDGElVa~ 517 (806)
++.+-.|+||.=+.+....+|.+.+-|+++-... +-.. .+..+.++. .++-+=.|++.
T Consensus 46 p~~v~~K~dGsli~~~~~~~g~~~~~SK~s~~s~--~a~~a~~~l~~~~~~~~~~~~~l~~~~~~---~~~T~~fE~~~- 119 (221)
T PF09511_consen 46 PVEVYEKEDGSLIFIPYLDDGELIVASKGSFDSD--HADWARELLEKQLEKEGKNLEELAEELLE---PNYTFIFELCS- 119 (221)
T ss_dssp EEEEEEE--SEEE-EEEEETTEEEEEETTBSSSH--HHHHHHHHHHSGGGHH---HHHHHHHHHH---TTEEEEEEEE--
T ss_pred cEEEEEecCcEEEEEeeecCCeEEEEecCcccch--HHHHHHHHHHHHhhhhhHHHHHHHHHHhh---CCcEEEEEEec-
Confidence 7899999999444233335789999999985321 1111 111111222 34555556553
Q ss_pred ecC-CCccCChHHHHHhhhccCCccccccceEEEEeeeeecC-CccccCCcHHHHHHHHHHhhccCCCcEEEEeEEecCC
Q 003632 518 DRE-KQKILPFQTLSTRARKNVSLSDIKVDVCIYAFDILYRN-GQPLLQEQLRVRREHLYDSFEEEPGFFQFATTLTSID 595 (806)
Q Consensus 518 d~~-~g~~~pFq~L~~r~rk~~~~~~~~~~v~~~vFDiLyln-G~~L~~~Pl~eRr~~L~~l~~~~~~~i~~~~~~~~~~ 595 (806)
+. ..-+++ ...-.+.+++.+.-+ .-.....|+. .+..+.... .+..++.....+
T Consensus 120 -p~~~~~Vi~-----------------Y~~~~~~l~l~i~n~~tg~~~~l~~~----~~~~~a~~~--g~~~~~~~~~~~ 175 (221)
T PF09511_consen 120 -PEFNRHVIE-----------------YEEEQLILLLAIRNNNTGEYITLPYD----ELDKIAKKF--GFPRVKSFTFEN 175 (221)
T ss_dssp -TT-S-SSS-------------------SS-EEEE-EEEEETTT--B--HHHH----HH-TTTGGG--B--EEE-S---S
T ss_pred -CcCCceeEe-----------------cCCccceEEEEEEEcCCCceEecCHH----HHHHHHHHh--CCCceeEeeccc
Confidence 22 111111 112233344444322 1111223333 333332221 233444445666
Q ss_pred HHHHHHHHHH------HHHcCCceeEEEeCCCCCCccCCCCCCCeEEEcccc
Q 003632 596 LDEIQKFLDA------AVDASCEGLIIKTMDRDATYEPSKRSLNWLKLKKDY 641 (806)
Q Consensus 596 ~eei~~~~~~------ai~~g~EGlmlK~~~~ds~Y~pGkRs~~WlKlK~dY 641 (806)
.+++.++++. ....+.||.|+... + .++..+|+|-+|
T Consensus 176 ~~e~~~~~~~~~~~~~~~~~~~EG~Vv~~~--~-------~~g~~~KiK~~~ 218 (221)
T PF09511_consen 176 WEELKEFLEDEIIDGAYNGEEIEGFVVRFE--D-------QSGFMFKIKTPW 218 (221)
T ss_dssp ---------TTHHHHHHH-SS--EEEEEET--T---------S-EEEEE-HH
T ss_pred ccccccchhhhhhhhhccCccCcEEEEEEE--C-------CCccEEEEcccc
Confidence 7777777643 23568999999997 4 445779999754
No 73
>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=56.28 E-value=28 Score=37.53 Aligned_cols=65 Identities=15% Similarity=0.122 Sum_probs=52.0
Q ss_pred eecCCc--cccCCcHHHHHHHHHHhhccCCCcEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEEeC
Q 003632 555 LYRNGQ--PLLQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTM 619 (806)
Q Consensus 555 LylnG~--~L~~~Pl~eRr~~L~~l~~~~~~~i~~~~~~~~~~~eei~~~~~~ai~~g~EGlmlK~~ 619 (806)
++++|. .-..++.+||+++++.+.....+++.++-.....+.++..++.+.+.+.|..|+|+=.+
T Consensus 35 i~~~GstGE~~~ls~~Er~~l~~~~~~~~~~~~~vi~gv~~~~~~~~i~~a~~a~~~Gad~v~v~pP 101 (281)
T cd00408 35 LVVLGTTGEAPTLTDEERKEVIEAVVEAVAGRVPVIAGVGANSTREAIELARHAEEAGADGVLVVPP 101 (281)
T ss_pred EEECCCCcccccCCHHHHHHHHHHHHHHhCCCCeEEEecCCccHHHHHHHHHHHHHcCCCEEEECCC
Confidence 445553 23467899999999999888777777776666678888999999999999999999765
No 74
>PRK03170 dihydrodipicolinate synthase; Provisional
Probab=54.76 E-value=27 Score=38.05 Aligned_cols=65 Identities=17% Similarity=0.070 Sum_probs=52.4
Q ss_pred eecCCc--cccCCcHHHHHHHHHHhhccCCCcEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEEeC
Q 003632 555 LYRNGQ--PLLQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTM 619 (806)
Q Consensus 555 LylnG~--~L~~~Pl~eRr~~L~~l~~~~~~~i~~~~~~~~~~~eei~~~~~~ai~~g~EGlmlK~~ 619 (806)
++++|. ....++..||+++++.+.....+++.++-.....+.++..++.+.+.+.|..|+|+=.+
T Consensus 39 i~~~Gs~GE~~~ls~~Er~~~~~~~~~~~~~~~~vi~gv~~~~~~~~i~~a~~a~~~G~d~v~~~pP 105 (292)
T PRK03170 39 LVVVGTTGESPTLTHEEHEELIRAVVEAVNGRVPVIAGTGSNSTAEAIELTKFAEKAGADGALVVTP 105 (292)
T ss_pred EEECCcCCccccCCHHHHHHHHHHHHHHhCCCCcEEeecCCchHHHHHHHHHHHHHcCCCEEEECCC
Confidence 444552 23568999999999999988777777666666668889999999999999999999876
No 75
>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=54.70 E-value=27 Score=37.77 Aligned_cols=67 Identities=15% Similarity=0.025 Sum_probs=53.8
Q ss_pred eeeecCCc--cccCCcHHHHHHHHHHhhccCCCcEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEEeC
Q 003632 553 DILYRNGQ--PLLQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTM 619 (806)
Q Consensus 553 DiLylnG~--~L~~~Pl~eRr~~L~~l~~~~~~~i~~~~~~~~~~~eei~~~~~~ai~~g~EGlmlK~~ 619 (806)
|-++++|. ....++..||+++++.+.....+++.++-.....+.++..++.+.+.+.|..|+|+=.+
T Consensus 36 ~gl~v~GstGE~~~lt~~Er~~l~~~~~~~~~~~~~vi~gv~~~~~~~~~~~a~~a~~~G~d~v~~~~P 104 (284)
T cd00950 36 DGLVVCGTTGESPTLSDEEHEAVIEAVVEAVNGRVPVIAGTGSNNTAEAIELTKRAEKAGADAALVVTP 104 (284)
T ss_pred CEEEECCCCcchhhCCHHHHHHHHHHHHHHhCCCCcEEeccCCccHHHHHHHHHHHHHcCCCEEEEccc
Confidence 34555653 33578999999999999888777776666655678899999999999999999999876
No 76
>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=54.28 E-value=32 Score=37.38 Aligned_cols=65 Identities=17% Similarity=0.145 Sum_probs=52.1
Q ss_pred eecCCc--cccCCcHHHHHHHHHHhhccCCCcEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEEeC
Q 003632 555 LYRNGQ--PLLQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTM 619 (806)
Q Consensus 555 LylnG~--~L~~~Pl~eRr~~L~~l~~~~~~~i~~~~~~~~~~~eei~~~~~~ai~~g~EGlmlK~~ 619 (806)
+++.|. .-..++..||+++++.+....++++.++-.....+.++..++.+.+.+.|..|+|+=.+
T Consensus 39 l~~~GstGE~~~Lt~~Er~~l~~~~~~~~~~~~~vi~gv~~~st~~~i~~a~~a~~~Gad~v~v~~P 105 (289)
T PF00701_consen 39 LVVLGSTGEFYSLTDEERKELLEIVVEAAAGRVPVIAGVGANSTEEAIELARHAQDAGADAVLVIPP 105 (289)
T ss_dssp EEESSTTTTGGGS-HHHHHHHHHHHHHHHTTSSEEEEEEESSSHHHHHHHHHHHHHTT-SEEEEEES
T ss_pred EEECCCCcccccCCHHHHHHHHHHHHHHccCceEEEecCcchhHHHHHHHHHHHhhcCceEEEEecc
Confidence 444442 34578999999999999887777777777777889999999999999999999999776
No 77
>COG4566 TtrR Response regulator [Signal transduction mechanisms]
Probab=54.12 E-value=34 Score=35.60 Aligned_cols=89 Identities=20% Similarity=0.327 Sum_probs=59.6
Q ss_pred hcCCHHHHHhhcccccCccCCCCCCCHHHHHHHHHHHHH-HhCCChHHHHHHHHHHHHHhcCCChHHHHHHHHhhccc--
Q 003632 279 EMGDLGLVAKASRSSQSMMRKPDPLTITKVFDTFRLIAK-EAGKDSQEKKKNRIKALLVAATDCEPQYLIRLLQSKLR-- 355 (806)
Q Consensus 279 ~~GDlg~va~~~r~~q~~l~~~~~LTI~eV~~~L~~IA~-~~G~~sq~~k~~~L~~Ll~~~t~~E~k~LiRiIlkdLR-- 355 (806)
-+||+..+++..+..- .-|-.+|..-+++.+.+..--. .............+..+|+.+|+.|...|-+++.+.+.
T Consensus 84 GhgDIpmaV~AmK~GA-vDFLeKP~~~q~Lldav~~Al~~~~~~~~~~~~~~~~~~~l~tLT~RERqVl~~vV~G~~NKq 162 (202)
T COG4566 84 GHGDIPMAVQAMKAGA-VDFLEKPFSEQDLLDAVERALARDASRRAEADRQAAIRARLATLTPRERQVLDLVVRGLMNKQ 162 (202)
T ss_pred CCCChHHHHHHHHcch-hhHHhCCCchHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhcCHHHHHHHHHHHcCcccHH
Confidence 4689998887765332 2234577777777776554322 11112222345778999999999999999999988663
Q ss_pred ----CcccHHHHHHHHHhh
Q 003632 356 ----IGLAEQTLLAALGQA 370 (806)
Q Consensus 356 ----iG~~e~til~ala~A 370 (806)
+|+++.||- +|+|
T Consensus 163 IA~dLgiS~rTVe--~HRa 179 (202)
T COG4566 163 IAFDLGISERTVE--LHRA 179 (202)
T ss_pred HHHHcCCchhhHH--HHHH
Confidence 688888886 3454
No 78
>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=53.43 E-value=30 Score=37.92 Aligned_cols=65 Identities=15% Similarity=0.225 Sum_probs=52.6
Q ss_pred eecCCc--cccCCcHHHHHHHHHHhhccCCCcEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEEeC
Q 003632 555 LYRNGQ--PLLQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTM 619 (806)
Q Consensus 555 LylnG~--~L~~~Pl~eRr~~L~~l~~~~~~~i~~~~~~~~~~~eei~~~~~~ai~~g~EGlmlK~~ 619 (806)
++.+|. .-..++..||+++++.+.....+++.++-.....+.++..++-+.+.+.|..|+|+=.+
T Consensus 38 i~v~GstGE~~~Ls~~Er~~l~~~~~~~~~g~~pvi~gv~~~~t~~ai~~a~~A~~~Gad~v~v~pP 104 (294)
T TIGR02313 38 ISVGGTSGEPGSLTLEERKQAIENAIDQIAGRIPFAPGTGALNHDETLELTKFAEEAGADAAMVIVP 104 (294)
T ss_pred EEECccCcccccCCHHHHHHHHHHHHHHhCCCCcEEEECCcchHHHHHHHHHHHHHcCCCEEEEcCc
Confidence 344542 23467999999999999888888877776666678888899999999999999999877
No 79
>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=53.02 E-value=32 Score=37.62 Aligned_cols=66 Identities=17% Similarity=0.137 Sum_probs=51.8
Q ss_pred eeecCCc--cccCCcHHHHHHHHHHhhccCCCcEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEEeC
Q 003632 554 ILYRNGQ--PLLQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTM 619 (806)
Q Consensus 554 iLylnG~--~L~~~Pl~eRr~~L~~l~~~~~~~i~~~~~~~~~~~eei~~~~~~ai~~g~EGlmlK~~ 619 (806)
-++++|. .-..++.+||.++++.......+++.++-..-..+.++..++-+.+.+.|..|+|+=.+
T Consensus 38 gi~~~GstGE~~~Lt~eEr~~~~~~~~~~~~~~~pvi~gv~~~~t~~~i~la~~a~~~Gad~v~v~~P 105 (290)
T TIGR00683 38 GLYVGGSTGENFMLSTEEKKEIFRIAKDEAKDQIALIAQVGSVNLKEAVELGKYATELGYDCLSAVTP 105 (290)
T ss_pred EEEECCcccccccCCHHHHHHHHHHHHHHhCCCCcEEEecCCCCHHHHHHHHHHHHHhCCCEEEEeCC
Confidence 3555552 23457999999999999888777777666655678889999999999999999999554
No 80
>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=52.10 E-value=35 Score=37.75 Aligned_cols=65 Identities=11% Similarity=0.113 Sum_probs=52.8
Q ss_pred eecCCc--cccCCcHHHHHHHHHHhhccCCCcEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEEeC
Q 003632 555 LYRNGQ--PLLQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTM 619 (806)
Q Consensus 555 LylnG~--~L~~~Pl~eRr~~L~~l~~~~~~~i~~~~~~~~~~~eei~~~~~~ai~~g~EGlmlK~~ 619 (806)
++++|. ....++.+||+++++.......+++.++-.....+.++..++-+.+.+.|..|+|+=.+
T Consensus 46 i~v~GstGE~~~Lt~eEr~~v~~~~~~~~~grvpvi~Gv~~~~t~~ai~~a~~A~~~Gad~vlv~~P 112 (309)
T cd00952 46 ILTMGTFGECATLTWEEKQAFVATVVETVAGRVPVFVGATTLNTRDTIARTRALLDLGADGTMLGRP 112 (309)
T ss_pred EEECcccccchhCCHHHHHHHHHHHHHHhCCCCCEEEEeccCCHHHHHHHHHHHHHhCCCEEEECCC
Confidence 445552 34568999999999999888888777766666678899999999999999999999876
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=50.88 E-value=36 Score=36.98 Aligned_cols=57 Identities=12% Similarity=0.049 Sum_probs=49.2
Q ss_pred cCCcHHHHHHHHHHhhccCCCcEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEEeC
Q 003632 563 LQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTM 619 (806)
Q Consensus 563 ~~~Pl~eRr~~L~~l~~~~~~~i~~~~~~~~~~~eei~~~~~~ai~~g~EGlmlK~~ 619 (806)
..++..||+++++.+.....+++.++-.....+.++..++-+.+.+.|..|+|+=.+
T Consensus 46 ~~Ls~~Er~~~~~~~~~~~~~~~~vi~gv~~~s~~~~i~~a~~a~~~Gad~v~v~pP 102 (285)
T TIGR00674 46 PTLSHEEHKKVIEFVVDLVNGRVPVIAGTGSNATEEAISLTKFAEDVGADGFLVVTP 102 (285)
T ss_pred ccCCHHHHHHHHHHHHHHhCCCCeEEEeCCCccHHHHHHHHHHHHHcCCCEEEEcCC
Confidence 567999999999999887777777766666678899999999999999999999876
No 82
>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=48.91 E-value=39 Score=36.92 Aligned_cols=64 Identities=14% Similarity=0.176 Sum_probs=49.7
Q ss_pred eecCCc--cccCCcHHHHHHHHHHhhccCCCcEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEEeC
Q 003632 555 LYRNGQ--PLLQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTM 619 (806)
Q Consensus 555 LylnG~--~L~~~Pl~eRr~~L~~l~~~~~~~i~~~~~~~~~~~eei~~~~~~ai~~g~EGlmlK~~ 619 (806)
++++|. ....++.+||.++++.++....+++.++-.... +.++..++.+.+.+.|..|+|+=.+
T Consensus 38 i~v~GstGE~~~Ls~eEr~~l~~~~~~~~~~~~pvi~gv~~-~t~~~i~~a~~a~~~Gad~v~~~pP 103 (289)
T cd00951 38 LFAAGGTGEFFSLTPDEYAQVVRAAVEETAGRVPVLAGAGY-GTATAIAYAQAAEKAGADGILLLPP 103 (289)
T ss_pred EEECcCCcCcccCCHHHHHHHHHHHHHHhCCCCCEEEecCC-CHHHHHHHHHHHHHhCCCEEEECCC
Confidence 445552 235679999999999998887777666655544 7788899999999999999999554
No 83
>PLN02417 dihydrodipicolinate synthase
Probab=48.37 E-value=40 Score=36.68 Aligned_cols=57 Identities=5% Similarity=-0.134 Sum_probs=47.4
Q ss_pred cCCcHHHHHHHHHHhhccCCCcEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEEeC
Q 003632 563 LQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTM 619 (806)
Q Consensus 563 ~~~Pl~eRr~~L~~l~~~~~~~i~~~~~~~~~~~eei~~~~~~ai~~g~EGlmlK~~ 619 (806)
..++..||+++++.......+++.++-..-..+.++..++.+.+.+.|..|+|+=.+
T Consensus 49 ~~ls~~Er~~~~~~~~~~~~~~~pvi~gv~~~~t~~~i~~a~~a~~~Gadav~~~~P 105 (280)
T PLN02417 49 QLMSWDEHIMLIGHTVNCFGGKIKVIGNTGSNSTREAIHATEQGFAVGMHAALHINP 105 (280)
T ss_pred hhCCHHHHHHHHHHHHHHhCCCCcEEEECCCccHHHHHHHHHHHHHcCCCEEEEcCC
Confidence 467899999999998887777777766666667888899999999999999999766
No 84
>PRK04147 N-acetylneuraminate lyase; Provisional
Probab=47.07 E-value=40 Score=36.80 Aligned_cols=57 Identities=16% Similarity=0.152 Sum_probs=48.9
Q ss_pred cCCcHHHHHHHHHHhhccCCCcEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEEeC
Q 003632 563 LQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTM 619 (806)
Q Consensus 563 ~~~Pl~eRr~~L~~l~~~~~~~i~~~~~~~~~~~eei~~~~~~ai~~g~EGlmlK~~ 619 (806)
..++..||+++++.++....+++.++-..-..+.++..++-+.+.+.|..|+|+=.+
T Consensus 52 ~~Ls~eEr~~~~~~~~~~~~~~~~viagvg~~~t~~ai~~a~~a~~~Gad~v~v~~P 108 (293)
T PRK04147 52 FLLSTEEKKQVLEIVAEEAKGKVKLIAQVGSVNTAEAQELAKYATELGYDAISAVTP 108 (293)
T ss_pred ccCCHHHHHHHHHHHHHHhCCCCCEEecCCCCCHHHHHHHHHHHHHcCCCEEEEeCC
Confidence 467889999999999988877777666666678899999999999999999999876
No 85
>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=46.48 E-value=49 Score=36.05 Aligned_cols=67 Identities=21% Similarity=0.198 Sum_probs=52.3
Q ss_pred eeeecCCc--cccCCcHHHHHHHHHHhhccCCCcEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEEeC
Q 003632 553 DILYRNGQ--PLLQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTM 619 (806)
Q Consensus 553 DiLylnG~--~L~~~Pl~eRr~~L~~l~~~~~~~i~~~~~~~~~~~eei~~~~~~ai~~g~EGlmlK~~ 619 (806)
|-++++|. ....++.+||+++++.......+++.++-.....+.++..++-+.+.+.|..|+|+=.+
T Consensus 37 ~gi~~~GstGE~~~Lt~~Er~~~~~~~~~~~~~~~~viagv~~~~~~~ai~~a~~a~~~Gad~v~~~~P 105 (288)
T cd00954 37 DGLYVNGSTGEGFLLSVEERKQIAEIVAEAAKGKVTLIAHVGSLNLKESQELAKHAEELGYDAISAITP 105 (288)
T ss_pred CEEEECcCCcCcccCCHHHHHHHHHHHHHHhCCCCeEEeccCCCCHHHHHHHHHHHHHcCCCEEEEeCC
Confidence 33445552 23567899999999999887777766665555678889999999999999999998876
No 86
>COG0329 DapA Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]
Probab=43.96 E-value=66 Score=35.51 Aligned_cols=65 Identities=18% Similarity=0.140 Sum_probs=54.0
Q ss_pred eecCCc--cccCCcHHHHHHHHHHhhccCCCcEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEEeC
Q 003632 555 LYRNGQ--PLLQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTM 619 (806)
Q Consensus 555 LylnG~--~L~~~Pl~eRr~~L~~l~~~~~~~i~~~~~~~~~~~eei~~~~~~ai~~g~EGlmlK~~ 619 (806)
++.+|. .-..++..||+++++..+....+++.++-..-.++.++..++-+.+.+.|-.|+|+=.+
T Consensus 42 i~~~GttGE~~~Ls~eEr~~v~~~~v~~~~grvpviaG~g~~~t~eai~lak~a~~~Gad~il~v~P 108 (299)
T COG0329 42 LVVLGTTGESPTLTLEERKEVLEAVVEAVGGRVPVIAGVGSNSTAEAIELAKHAEKLGADGILVVPP 108 (299)
T ss_pred EEECCCCccchhcCHHHHHHHHHHHHHHHCCCCcEEEecCCCcHHHHHHHHHHHHhcCCCEEEEeCC
Confidence 445553 23567999999999999988888877776677788899999999999999999999876
No 87
>PRK03620 5-dehydro-4-deoxyglucarate dehydratase; Provisional
Probab=39.75 E-value=67 Score=35.38 Aligned_cols=65 Identities=12% Similarity=0.154 Sum_probs=50.4
Q ss_pred eeecCCc--cccCCcHHHHHHHHHHhhccCCCcEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEEeC
Q 003632 554 ILYRNGQ--PLLQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTM 619 (806)
Q Consensus 554 iLylnG~--~L~~~Pl~eRr~~L~~l~~~~~~~i~~~~~~~~~~~eei~~~~~~ai~~g~EGlmlK~~ 619 (806)
-++++|. ....++.+||+++++.+...+.+++.++-..- .+.++..++.+.+.+.|..|+|+=.+
T Consensus 44 Gi~~~GstGE~~~Lt~eEr~~~~~~~~~~~~~~~pvi~gv~-~~t~~~i~~~~~a~~~Gadav~~~pP 110 (303)
T PRK03620 44 ALFAAGGTGEFFSLTPDEYSQVVRAAVETTAGRVPVIAGAG-GGTAQAIEYAQAAERAGADGILLLPP 110 (303)
T ss_pred EEEECcCCcCcccCCHHHHHHHHHHHHHHhCCCCcEEEecC-CCHHHHHHHHHHHHHhCCCEEEECCC
Confidence 3455553 34567999999999999887777766665544 47888899999999999999999654
No 88
>TIGR03249 KdgD 5-dehydro-4-deoxyglucarate dehydratase. 5-dehydro-4-deoxyglucarate dehydratase not only catalyzes the dehydration of the substrate (diol to ketone + water), but causes the decarboxylation of the intermediate product to yield 2-oxoglutarate semialdehyde (2,5-dioxopentanoate). The gene for the enzyme is usually observed in the vicinity of transporters and dehydratases handling D-galactarate and D-gluconate as well as aldehyde dehydrogenases which convert the product to alpha-ketoglutarate.
Probab=39.61 E-value=69 Score=35.08 Aligned_cols=66 Identities=11% Similarity=0.106 Sum_probs=50.5
Q ss_pred eeeecCCc--cccCCcHHHHHHHHHHhhccCCCcEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEEeC
Q 003632 553 DILYRNGQ--PLLQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTM 619 (806)
Q Consensus 553 DiLylnG~--~L~~~Pl~eRr~~L~~l~~~~~~~i~~~~~~~~~~~eei~~~~~~ai~~g~EGlmlK~~ 619 (806)
|-++++|. .-..++.+||+++++.......+++.++-..- .+.++..++.+.+.+.|..|+|+=.+
T Consensus 41 ~gi~v~GstGE~~~Lt~eEr~~v~~~~~~~~~g~~pvi~gv~-~~t~~ai~~a~~a~~~Gadav~~~pP 108 (296)
T TIGR03249 41 EALFAAGGTGEFFSLTPAEYEQVVEIAVSTAKGKVPVYTGVG-GNTSDAIEIARLAEKAGADGYLLLPP 108 (296)
T ss_pred CEEEECCCCcCcccCCHHHHHHHHHHHHHHhCCCCcEEEecC-ccHHHHHHHHHHHHHhCCCEEEECCC
Confidence 33555553 33567999999999999888777766655543 46888889999999999999999554
No 89
>KOG2386 consensus mRNA capping enzyme, guanylyltransferase (alpha) subunit [RNA processing and modification]
Probab=38.48 E-value=57 Score=37.45 Aligned_cols=167 Identities=16% Similarity=0.162 Sum_probs=83.6
Q ss_pred HHHHhhcCCCceeEeeecceEeEEEEEec----CCeEEEEecCCCcCCCCcchH------HHHHHhhcCCCCCCeEEEEE
Q 003632 444 SEIVNKFQDMEFTCEYKYDGERAQIHYLE----DGSVEIYSRNAERNTGKFPDV------VLAVSRLKKPSVRSFVLDCE 513 (806)
Q Consensus 444 ~~~l~k~~g~~~~~E~KyDG~R~qih~~~----~g~V~ifSR~gk~~T~~~Pel------~~~l~~~~~~~v~~~ILDGE 513 (806)
.+.+..+....+.+-.|.||.|++..+.. ...+.+.-|+-.-. .-+|.. +..+... +.++-+|||
T Consensus 51 ~dl~~~l~~~~~~vgl~iDltnt~ryy~~~~~~~~g~~Y~K~~c~g~-~~vp~~~~v~~fv~~v~~f----~~~~~~~~~ 125 (393)
T KOG2386|consen 51 KDLFELLKEHNYKVGLKIDLTNTLRYYDKPELEERGVKYLKRNCPGR-GVVPRTELVDKFVKLVKGF----VDDTKLDDE 125 (393)
T ss_pred HHHHHHHHhcCceEEEEEeccceeeeeccccccccceeEEEeccCCc-ccCCCccchHHHHHHHHHH----HhcccCCCC
Confidence 44555554557899999999999988842 11244444332211 113322 2233333 256788999
Q ss_pred EEEEecCCCccCChHHHHHhhhccCCccccccceEEEEeeeeecCCccccCC-----------cHHHHHHHHHHhhccCC
Q 003632 514 IVAYDREKQKILPFQTLSTRARKNVSLSDIKVDVCIYAFDILYRNGQPLLQE-----------QLRVRREHLYDSFEEEP 582 (806)
Q Consensus 514 lVa~d~~~g~~~pFq~L~~r~rk~~~~~~~~~~v~~~vFDiLylnG~~L~~~-----------Pl~eRr~~L~~l~~~~~ 582 (806)
+|...-..| ....-|.+|+.|..+|. .... |..+|...+.++...-.
T Consensus 126 LI~vhcthG---------------------~NrtgyLI~~yL~~~~~-~s~~~aik~f~~~r~~gi~k~dyi~~L~~~~~ 183 (393)
T KOG2386|consen 126 LIGVHCTHG---------------------LNRTGYLICAYLADVGG-YSSSEAIKRFADARPPGIEKQDYIDALYSRYH 183 (393)
T ss_pred EEEEeCCCc---------------------ccccceeeeeeeeeccC-ccHHHHHHHHHHhCCCccCchHHHHHHhhccc
Confidence 998753322 12346889999987764 2222 22233333333322111
Q ss_pred CcEEE-EeEEecCCHHHHHHHHHHHHH-cCCceeEEEeCCCCCCcc-CCCCCCCeEEEccc
Q 003632 583 GFFQF-ATTLTSIDLDEIQKFLDAAVD-ASCEGLIIKTMDRDATYE-PSKRSLNWLKLKKD 640 (806)
Q Consensus 583 ~~i~~-~~~~~~~~~eei~~~~~~ai~-~g~EGlmlK~~~~ds~Y~-pGkRs~~WlKlK~d 640 (806)
..+.+ +......+............. .+..|.+.-.. ..+|. -| +...-+|+|++
T Consensus 184 ~~~p~~vs~p~~~~~~~~~~~~~~~~~~~~~Dg~i~t~~--~~pg~~~g-~~~~~~k~k~~ 241 (393)
T KOG2386|consen 184 DIFPFKVSCPSMPDWKRSIKLKKPVHKLHGNDGLIFTPA--EIPGSKNG-KQEALLKWKPF 241 (393)
T ss_pred ccccccccCCCCcchhhhhhhccccccccccCCCcCCcc--cCcccccc-chhhhhcCCch
Confidence 11101 111111222222222222211 56677776666 67783 44 44678999985
No 90
>KOG3673 consensus FtsJ-like RNA methyltransferase [RNA processing and modification]
Probab=34.66 E-value=51 Score=39.12 Aligned_cols=62 Identities=10% Similarity=0.025 Sum_probs=43.6
Q ss_pred cceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCC--Cc----EEEEeEEecCCHHHHHHHHHHH
Q 003632 545 VDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEP--GF----FQFATTLTSIDLDEIQKFLDAA 606 (806)
Q Consensus 545 ~~v~~~vFDiLylnG~~L~~~Pl~eRr~~L~~l~~~~~--~~----i~~~~~~~~~~~eei~~~~~~a 606 (806)
..-.+++.|.+.|+|.++.+.||+||.++-++.+..+. .+ +.-.....+...+++.++|...
T Consensus 656 ~~~avhIiD~~vL~G~Dvr~~py~eR~~~aeKFv~al~kp~Rkd~~~~a~r~Kp~yrL~em~~ff~nl 723 (845)
T KOG3673|consen 656 EPQAVHIIDAAVLFGDDVRNLPYEERMKAAEKFVAALKKPNRKDKKHRAERIKPTYRLAEMDEFFSNL 723 (845)
T ss_pred cchheeeeeeeeecCchhhcccHHHHHHHHHHHHHHhcCCCCccccccceecccceeHHHHHHHHHhh
Confidence 45578899999999999999999999999998876532 11 1111122345567777777654
No 91
>KOG0967 consensus ATP-dependent DNA ligase I [Replication, recombination and repair]
Probab=34.57 E-value=2.4e+02 Score=34.44 Aligned_cols=89 Identities=15% Similarity=0.223 Sum_probs=63.2
Q ss_pred ccchHHHHHHHHHHHhcc---chHHHHHHHHHHHHhhhcCCCCchHhHHHHHhCCcCCCccccccCCCHHHHHHHHHHHh
Q 003632 190 RVPFIFLSLVFDMISNET---GRILITDIVCNMLRTVMETTPEDLVPVVYLAANKIAPAHEGLELGIGDASIIKALAEAC 266 (806)
Q Consensus 190 ~~~F~~la~~~~~I~~ts---sr~~k~~iL~~~~r~~i~~~p~dl~~~vyL~~~~l~P~~e~~elgIg~~~L~Kal~~~~ 266 (806)
+..-..+-+.|-+|+..+ +.++|.+++..+|... .+.+..-.++++.+. ..+|+.+.++.-||++++
T Consensus 210 pLtV~~VF~~Lr~IAk~sG~~S~~kK~~lik~Llvac---~~~E~kyLiRsL~gk-------LRiGlaeqTvL~AL~~A~ 279 (714)
T KOG0967|consen 210 PLTVRDVFSTLRKIAKESGKGSQNKKKDLIKALLVAC---RGIEAKYLIRSLEGK-------LRIGLAEQTVLAALGQAF 279 (714)
T ss_pred CccHHHHHHHHHHHHHhhCcchhHHHHHHHHHHHHhc---ccccHHHHHHHHHhh-------hhhhhhHHHHHHHHHHHH
Confidence 444566777777777755 5789999999999886 556666666766664 468999999999999987
Q ss_pred CCC----------HH-----------HHHHHHhhcCCHHHHHh
Q 003632 267 GRT----------ES-----------HVKKQYQEMGDLGLVAK 288 (806)
Q Consensus 267 g~s----------~~-----------~ik~~~~~~GDlg~va~ 288 (806)
.+. ++ .+++.|-+.-|+..++.
T Consensus 280 ~~~~~~~~~~~~~~d~~kd~le~~~~ivk~afcq~P~ydiivp 322 (714)
T KOG0967|consen 280 VLNDNNDEEKSKKPDSLKDPLEEAAQIVKQAFCQLPDYDIIVP 322 (714)
T ss_pred hccCchhhhccCCcchhhhhhHHHHHHHHHHHhcCCchhhhHH
Confidence 654 12 34556666677766553
No 92
>PRK14956 DNA polymerase III subunits gamma and tau; Provisional
Probab=32.85 E-value=51 Score=38.94 Aligned_cols=26 Identities=42% Similarity=0.509 Sum_probs=21.8
Q ss_pred CCCCCCCCCCCCCCcccCCCCCCCCC
Q 003632 119 LVKPISNQIDNPIDSEKESQPTPPSP 144 (806)
Q Consensus 119 ~~~~~~~~~~~~~~~~~~~~~~~~~~ 144 (806)
+.++.++-.++|-.|+.+||.+|||.
T Consensus 434 ~~~~~~~~~~~~~~~~~~~~~~~~~~ 459 (484)
T PRK14956 434 SNQQDSNLDNNPLPSKSESQSEPPSS 459 (484)
T ss_pred cccccccCCCCCCCCcccccCCCCCC
Confidence 34677778888999999999999986
No 93
>cd08205 RuBisCO_IV_RLP Ribulose bisphosphate carboxylase like proteins, Rubisco-Form IV. Ribulose bisphosphate carboxylase (Rubisco) plays an important role in the Calvin reductive pentose phosphate pathway. It catalyzes the primary CO2 fixation step. Rubisco is activated by carbamylation of an active site lysine, stabilized by a divalent cation, which then catalyzes the proton abstraction from the substrate ribulose 1,5 bisphosphate (RuBP) and leads to the formation of two molecules of 3-phosphoglycerate. Members of the Rubisco family can be divided into 4 subgroups, Form I-IV, which differ in their taxonomic distribution and subunit composition. Form I-III have Rubisco activity, while Form IV, also called Rubisco-like proteins (RLP), are missing critical active site residues and therefore do not catalyze CO2 fixation. They are believed to utilize a related enzymatic mechanism, but have divergent functions, like for example 2,3-diketo-5-methylthiopentyl-1-phosphate enolase or 5-methyl
Probab=28.48 E-value=1.2e+02 Score=34.48 Aligned_cols=55 Identities=22% Similarity=0.288 Sum_probs=42.4
Q ss_pred CCcHHHHHHHHHHhhccCC---Cc-EEEEeEEecCCHHHHHHHHHHHHHcCCceeEEEeC
Q 003632 564 QEQLRVRREHLYDSFEEEP---GF-FQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTM 619 (806)
Q Consensus 564 ~~Pl~eRr~~L~~l~~~~~---~~-i~~~~~~~~~~~eei~~~~~~ai~~g~EGlmlK~~ 619 (806)
-.|++||.++..+.+.... ++ ..++.. .+.+.+++.+..+.+.+.|..|+|+-.+
T Consensus 174 ~~~~eER~~~v~~av~~a~~~TG~~~~y~~n-it~~~~e~i~~a~~a~~~Gad~vmv~~~ 232 (367)
T cd08205 174 YAPFEERVRACMEAVRRANEETGRKTLYAPN-ITGDPDELRRRADRAVEAGANALLINPN 232 (367)
T ss_pred cCCHHHHHHHHHHHHHHHHHhhCCcceEEEE-cCCCHHHHHHHHHHHHHcCCCEEEEecc
Confidence 4699999999999887654 33 333333 3355689999999999999999999876
No 94
>KOG0971 consensus Microtubule-associated protein dynactin DCTN1/Glued [Cell cycle control, cell division, chromosome partitioning; Cytoskeleton]
Probab=27.21 E-value=1.2e+02 Score=38.15 Aligned_cols=18 Identities=28% Similarity=0.281 Sum_probs=8.5
Q ss_pred eeccchhhhHHHHhhhhh
Q 003632 151 VNSVSAKEKIAELKSNIV 168 (806)
Q Consensus 151 ~~~~~~~~~~~~~~~~~~ 168 (806)
.+|.++..++.++...+-
T Consensus 217 v~l~saskte~eLr~Qvr 234 (1243)
T KOG0971|consen 217 VPLPSASKTEEELRAQVR 234 (1243)
T ss_pred CCCCccccchHHHHHHHH
Confidence 444444445544544443
No 95
>cd00953 KDG_aldolase KDG (2-keto-3-deoxygluconate) aldolases found in archaea. This subfamily of enzymes is adapted for high thermostability and shows specificity for non-phosphorylated substrates. The enzyme catalyses the reversible aldol cleavage of 2-keto-3-dexoygluconate to pyruvate and glyceraldehyde, the third step of a modified non-phosphorylated Entner-Doudoroff pathway of glucose oxidation. KDG aldolase shows no significant sequence similarity to microbial 2-keto-3-deoxyphosphogluconate (KDPG) aldolases, and the enzyme shows no activity with glyceraldehyde 3-phosphate as substrate. The enzyme is a tetramer and a member of the DHDPS family of Schiff-base-dependent class I aldolases.
Probab=23.46 E-value=2.4e+02 Score=30.66 Aligned_cols=62 Identities=13% Similarity=0.023 Sum_probs=46.7
Q ss_pred eecCCc--cccCCcHHHHHHHHHHhhccCCCcEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEEeC
Q 003632 555 LYRNGQ--PLLQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTM 619 (806)
Q Consensus 555 LylnG~--~L~~~Pl~eRr~~L~~l~~~~~~~i~~~~~~~~~~~eei~~~~~~ai~~g~EGlmlK~~ 619 (806)
++++|. .-..++.+||+++++.+..... . ++-..-..+.++..++-+.+.+.|..|+|+=.+
T Consensus 37 l~~~GstGE~~~Lt~eEr~~l~~~~~~~~~-~--vi~gvg~~~~~~ai~~a~~a~~~Gad~v~v~~P 100 (279)
T cd00953 37 VFVAGTTGLGPSLSFQEKLELLKAYSDITD-K--VIFQVGSLNLEESIELARAAKSFGIYAIASLPP 100 (279)
T ss_pred EEEcccCCCcccCCHHHHHHHHHHHHHHcC-C--EEEEeCcCCHHHHHHHHHHHHHcCCCEEEEeCC
Confidence 445552 2356789999999999887653 3 233344567889999999999999999999766
Done!