Query 004212
Match_columns 768
No_of_seqs 340 out of 1927
Neff 5.8
Searched_HMMs 46136
Date Thu Mar 28 19:29:15 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/004212.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/004212hhsearch_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 6E-141 1E-145 1170.9 44.4 590 161-750 69-662 (714)
2 PLN03113 DNA ligase 1; Provisi 100.0 6E-137 1E-141 1200.4 71.3 683 53-748 1-686 (744)
3 PRK01109 ATP-dependent DNA lig 100.0 2E-110 5E-115 968.7 57.0 532 191-748 1-538 (590)
4 PRK09247 ATP-dependent DNA lig 100.0 6.5E-96 1E-100 839.2 53.4 493 194-748 2-503 (539)
5 PRK03180 ligB ATP-dependent DN 100.0 4E-96 9E-101 835.1 48.6 472 191-748 1-474 (508)
6 TIGR00574 dnl1 DNA ligase I, A 100.0 2.3E-95 5E-100 833.1 51.9 477 250-748 1-480 (514)
7 KOG0966 ATP-dependent DNA liga 100.0 1.8E-80 3.9E-85 701.2 36.6 530 189-751 3-560 (881)
8 COG1793 CDC9 ATP-dependent DNA 100.0 4.2E-67 9E-72 587.3 36.7 407 260-752 2-411 (444)
9 PHA02587 30 DNA ligase; Provis 100.0 5.5E-62 1.2E-66 553.3 40.6 420 196-748 2-457 (488)
10 PRK08224 ligC ATP-dependent DN 100.0 3.5E-57 7.6E-62 494.3 32.6 288 425-742 2-307 (350)
11 PRK09632 ATP-dependent DNA lig 100.0 4.5E-57 9.8E-62 528.6 33.7 284 425-743 454-739 (764)
12 TIGR02779 NHEJ_ligase_lig DNA 100.0 9.1E-57 2E-61 482.7 32.4 267 450-743 9-275 (298)
13 PRK05972 ligD ATP-dependent DN 100.0 9E-55 1.9E-59 513.5 33.4 282 430-745 232-516 (860)
14 PRK09633 ligD ATP-dependent DN 100.0 2.6E-53 5.6E-58 490.6 31.5 270 432-742 1-286 (610)
15 PRK07636 ligB ATP-dependent DN 100.0 1.9E-51 4.2E-56 436.6 29.3 260 432-744 3-262 (275)
16 cd07900 Adenylation_DNA_ligase 100.0 1.5E-51 3.2E-56 424.3 24.7 217 423-641 1-219 (219)
17 cd07903 Adenylation_DNA_ligase 100.0 7.3E-46 1.6E-50 382.8 23.1 216 423-642 3-224 (225)
18 cd07901 Adenylation_DNA_ligase 100.0 1.2E-45 2.6E-50 377.0 23.7 205 428-640 1-207 (207)
19 cd07902 Adenylation_DNA_ligase 100.0 1.8E-45 3.9E-50 377.6 23.1 208 423-641 5-213 (213)
20 PHA00454 ATP-dependent DNA lig 100.0 7E-44 1.5E-48 385.7 29.7 271 433-744 7-301 (315)
21 TIGR02776 NHEJ_ligase_prk DNA 100.0 2.3E-44 5E-49 412.2 26.9 235 480-744 1-237 (552)
22 cd07897 Adenylation_DNA_ligase 100.0 1.5E-44 3.2E-49 369.2 22.1 201 430-641 3-206 (207)
23 cd08039 Adenylation_DNA_ligase 100.0 9.1E-44 2E-48 369.7 23.8 198 442-641 11-235 (235)
24 cd07898 Adenylation_DNA_ligase 100.0 1.6E-43 3.5E-48 359.6 23.5 199 432-640 1-201 (201)
25 PRK09125 DNA ligase; Provision 100.0 5.4E-43 1.2E-47 373.1 25.9 239 432-744 28-267 (282)
26 PF01068 DNA_ligase_A_M: ATP d 100.0 2.2E-42 4.8E-47 349.2 20.2 201 434-638 1-202 (202)
27 cd07905 Adenylation_DNA_ligase 100.0 1E-41 2.2E-46 345.0 20.8 190 432-640 1-193 (194)
28 cd07906 Adenylation_DNA_ligase 100.0 1.5E-40 3.3E-45 335.0 20.9 189 432-639 1-189 (190)
29 PF04675 DNA_ligase_A_N: DNA l 100.0 6.1E-35 1.3E-39 290.5 17.5 176 191-369 1-177 (177)
30 cd07896 Adenylation_kDNA_ligas 100.0 6.4E-34 1.4E-38 282.8 16.4 173 432-639 1-174 (174)
31 cd06846 Adenylation_DNA_ligase 100.0 1.6E-31 3.5E-36 267.2 18.2 176 434-639 2-182 (182)
32 cd07895 Adenylation_mRNA_cappi 99.9 2.2E-27 4.8E-32 243.8 13.7 159 450-639 38-215 (215)
33 KOG4437 ATP-dependent DNA liga 99.9 1.7E-23 3.8E-28 219.0 18.2 327 191-556 155-482 (482)
34 cd07967 OBF_DNA_ligase_III The 99.9 5.1E-24 1.1E-28 205.1 12.8 103 645-747 1-110 (139)
35 cd07893 OBF_DNA_ligase The Oli 99.9 1.6E-21 3.4E-26 185.8 12.4 100 647-748 1-100 (129)
36 cd07969 OBF_DNA_ligase_I The O 99.9 2.4E-21 5.1E-26 187.9 12.6 105 646-752 1-105 (144)
37 cd07968 OBF_DNA_ligase_IV The 99.8 6.7E-21 1.5E-25 183.9 12.0 103 646-748 1-115 (140)
38 cd07972 OBF_DNA_ligase_Arch_Li 99.8 1.1E-19 2.4E-24 171.5 11.5 92 647-748 1-92 (122)
39 cd07894 Adenylation_RNA_ligase 99.8 3.8E-18 8.2E-23 186.5 15.3 166 450-642 46-219 (342)
40 cd08040 OBF_DNA_ligase_family 99.8 6.1E-18 1.3E-22 156.2 11.8 95 647-743 1-95 (108)
41 cd07971 OBF_DNA_ligase_LigD Th 99.7 5.7E-17 1.2E-21 151.4 12.1 94 648-744 2-95 (115)
42 PF04679 DNA_ligase_A_C: ATP d 99.7 1E-16 2.2E-21 145.3 8.9 82 663-744 1-82 (97)
43 cd07970 OBF_DNA_ligase_LigC Th 99.5 3.4E-14 7.3E-19 134.3 11.7 93 647-745 1-100 (122)
44 PF01331 mRNA_cap_enzyme: mRNA 99.3 1.9E-12 4.2E-17 131.0 5.8 158 452-638 15-192 (192)
45 COG1423 ATP-dependent DNA liga 98.9 1.6E-08 3.4E-13 108.7 14.3 148 448-619 83-234 (382)
46 TIGR01209 RNA ligase, Pab1020 98.8 7.6E-08 1.6E-12 106.1 13.7 148 449-619 75-226 (374)
47 COG5226 CEG1 mRNA capping enzy 98.7 1.7E-08 3.6E-13 106.5 5.5 171 453-655 62-257 (404)
48 cd08041 OBF_kDNA_ligase_like T 98.6 6.2E-08 1.3E-12 84.5 6.9 63 648-743 2-64 (77)
49 cd09232 Snurportin-1_C C-termi 98.6 3.6E-07 7.8E-12 92.7 10.9 152 453-639 21-185 (186)
50 smart00532 LIGANc Ligase N fam 98.2 0.0001 2.3E-09 84.0 20.3 239 434-701 75-362 (441)
51 PRK08097 ligB NAD-dependent DN 98.1 0.0002 4.4E-09 83.6 21.6 232 434-701 97-359 (562)
52 PRK01109 ATP-dependent DNA lig 98.1 7E-06 1.5E-10 96.9 9.8 93 189-291 113-210 (590)
53 PRK07956 ligA NAD-dependent DN 98.0 0.0004 8.6E-09 83.2 20.3 219 454-701 109-367 (665)
54 PF01653 DNA_ligase_aden: NAD- 97.9 1.5E-05 3.3E-10 87.2 7.2 173 433-619 77-289 (315)
55 cd00114 LIGANc NAD+ dependent 97.9 0.00018 4E-09 78.5 15.3 164 454-634 102-299 (307)
56 PRK14351 ligA NAD-dependent DN 97.9 0.00088 1.9E-08 80.4 21.6 237 434-701 105-389 (689)
57 PRK14350 ligA NAD-dependent DN 97.9 0.00072 1.6E-08 80.9 20.5 219 454-701 111-364 (669)
58 TIGR00575 dnlj DNA ligase, NAD 97.9 0.00081 1.7E-08 80.5 20.9 218 454-701 97-355 (652)
59 PF09414 RNA_ligase: RNA ligas 97.4 0.00017 3.6E-09 72.6 4.2 159 454-638 2-186 (186)
60 TIGR02307 RNA_lig_RNL2 RNA lig 97.2 0.0042 9E-08 68.2 12.8 162 451-640 23-217 (325)
61 COG0272 Lig NAD-dependent DNA 96.7 0.035 7.5E-07 65.8 16.1 173 453-640 109-317 (667)
62 PF14743 DNA_ligase_OB_2: DNA 96.0 0.0063 1.4E-07 51.9 3.2 38 658-701 1-38 (66)
63 PHA02142 putative RNA ligase 95.8 0.098 2.1E-06 58.5 12.6 162 442-639 157-357 (366)
64 PRK03180 ligB ATP-dependent DN 94.9 0.13 2.8E-06 60.2 10.3 91 189-289 71-164 (508)
65 KOG3132 m3G-cap-specific nucle 94.6 0.15 3.3E-06 53.4 8.6 152 452-636 115-277 (325)
66 TIGR02306 RNA_lig_DRB0094 RNA 93.5 1.3 2.8E-05 49.5 13.8 155 452-640 158-336 (341)
67 TIGR00574 dnl1 DNA ligase I, A 92.8 0.52 1.1E-05 55.3 10.1 93 189-291 53-148 (514)
68 PRK09247 ATP-dependent DNA lig 91.4 0.43 9.4E-06 56.3 7.3 87 307-413 3-90 (539)
69 KOG2386 mRNA capping enzyme, g 91.2 0.14 3E-06 57.7 2.8 97 454-578 286-385 (393)
70 PF04675 DNA_ligase_A_N: DNA l 90.8 0.62 1.3E-05 46.5 6.7 91 305-415 3-100 (177)
71 PLN03113 DNA ligase 1; Provisi 85.9 2.3 5E-05 52.1 8.4 70 302-374 128-207 (744)
72 COG4566 TtrR Response regulato 61.8 23 0.00049 36.7 6.6 86 279-365 84-176 (202)
73 cd00408 DHDPS-like Dihydrodipi 55.5 30 0.00065 37.0 6.8 57 563-619 45-101 (281)
74 cd00950 DHDPS Dihydrodipicolin 54.1 29 0.00063 37.3 6.4 66 554-619 37-104 (284)
75 PRK03170 dihydrodipicolinate s 53.8 29 0.00063 37.5 6.4 57 563-619 49-105 (292)
76 TIGR00683 nanA N-acetylneurami 50.9 37 0.00081 36.9 6.7 57 563-619 49-105 (290)
77 KOG0967 ATP-dependent DNA liga 50.1 1.2E+02 0.0025 36.9 10.6 91 301-411 97-197 (714)
78 cd00952 CHBPH_aldolase Trans-o 49.6 41 0.00089 37.0 6.8 58 562-619 55-112 (309)
79 PF09511 RNA_lig_T4_1: RNA lig 49.1 2.2E+02 0.0048 29.6 11.9 32 454-485 46-77 (221)
80 TIGR02313 HpaI-NOT-DapA 2,4-di 48.8 33 0.00071 37.4 5.8 57 563-619 48-104 (294)
81 PF00701 DHDPS: Dihydrodipicol 48.4 37 0.00081 36.6 6.2 58 562-619 48-105 (289)
82 cd00951 KDGDH 5-dehydro-4-deox 46.9 44 0.00096 36.2 6.5 57 562-619 47-103 (289)
83 TIGR00674 dapA dihydrodipicoli 45.6 40 0.00087 36.4 5.9 57 563-619 46-102 (285)
84 PRK04147 N-acetylneuraminate l 44.4 38 0.00082 36.8 5.5 57 563-619 52-108 (293)
85 PLN02417 dihydrodipicolinate s 44.1 43 0.00094 36.2 5.8 57 563-619 49-105 (280)
86 COG0329 DapA Dihydrodipicolina 44.0 67 0.0015 35.2 7.3 58 562-619 51-108 (299)
87 cd00954 NAL N-Acetylneuraminic 41.6 51 0.0011 35.7 5.9 57 563-619 49-105 (288)
88 TIGR03249 KdgD 5-dehydro-4-deo 37.3 80 0.0017 34.4 6.6 65 554-619 42-108 (296)
89 PRK03620 5-dehydro-4-deoxygluc 37.0 80 0.0017 34.6 6.6 64 555-619 45-110 (303)
90 KOG3673 FtsJ-like RNA methyltr 34.5 53 0.0012 38.8 4.8 63 544-606 655-723 (845)
91 PF11588 DUF3243: Protein of u 28.4 25 0.00054 31.4 0.7 25 328-352 53-77 (81)
92 PRK14956 DNA polymerase III su 27.5 69 0.0015 37.7 4.3 27 119-145 434-460 (484)
93 cd08205 RuBisCO_IV_RLP Ribulos 25.1 1.6E+02 0.0034 33.4 6.5 56 563-619 173-232 (367)
94 cd00953 KDG_aldolase KDG (2-ke 24.0 2.4E+02 0.0051 30.5 7.4 55 562-619 46-100 (279)
95 KOG0971 Microtubule-associated 22.1 1.9E+02 0.004 36.5 6.5 16 151-166 217-232 (1243)
96 COG1510 Predicted transcriptio 21.8 4.4E+02 0.0096 27.0 8.1 80 260-343 45-125 (177)
No 1
>KOG0967 consensus ATP-dependent DNA ligase I [Replication, recombination and repair]
Probab=100.00 E-value=5.8e-141 Score=1170.91 Aligned_cols=590 Identities=62% Similarity=1.013 Sum_probs=572.0
Q ss_pred HHHhhhhhhcccCCCCCCCcccccccCCCccchHHHHHHHHHHHhhhchHHHHHHHHHHHHhhhcCCCCchHHHHHHHhC
Q 004212 161 AELKSNIVLLKKKAGEFDPKMVACWEKGERVPFIFLSLVFDMISNETGRILITDIVCNMLRTVMETTPEDLVPVVYLAAN 240 (768)
Q Consensus 161 ~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~F~~la~l~e~I~~tssr~~k~~iL~~~fr~~i~~~p~dl~~~vyl~~~ 240 (768)
.+.+...+.+.++|..|.|...+||..|+++||++||.+|+.|+.|++|+++++||+|||+.+++.+|+||+++|||++|
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 35556677899999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccCCCccccccCCCHHHHHHHHHHHhCCCHHHHHHHHhhhCChHHHHhhhcccCCccCCCCCCcHHHHHHHHHHHHHHhC
Q 004212 241 KIAPAHEGLELGIGDASIIKALAEACGRTESHVKKQYQEMGDLGLVAKASRSSQSMMRKPDPLTITKVFDTFRLIAKEAG 320 (768)
Q Consensus 241 ~l~P~~e~~elGIg~~~L~Kal~~a~G~s~~~ik~~y~~~GDlg~vA~~~r~~q~~l~~~~~LTI~eV~~~L~kIA~~~G 320 (768)
+|.|+|++.|||||+++|+|||+++||++..+++..|++.||+|+||+.+|.+|++|++|+||||.+|+..|++||+.+|
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 CChHHHHHHHHHHHHHhcCCChHHHHHHHHhhcccCcccHHHHHHHHHhhhccCCC----CCCCCCCCcchHHHHHHHHH
Q 004212 321 KDSQEKKKNRIKALLVAATDCEPQYLIRLLQSKLRIGLAEQTLLAALGQAAVYNEQ----HSKPPPNIQSPLEEAAKIVK 396 (768)
Q Consensus 321 ~~Sq~~K~~~l~~Ll~~~t~~E~k~lvRiIlkdLRiGi~e~tVl~ala~a~~~~~~----~~~~~~~l~~~l~~a~~~vk 396 (768)
++||.+|+++|+.||.+|++.|+|||+|.|.++||||++++|||.||++|+.++.. ++..+..+++.|+.+..+|+
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 99999999999999999999999999999999999999999999999999987632 44556678999999999999
Q ss_pred HHhhcCCchhhhhhhhhhcCccccCCccccCCCCCCccccccccCChHHHHhhcCCCceEEeeecceEeEEEEEecCCeE
Q 004212 397 QVFSVLPVYEKIVPALLTDGVWNLSNTCSFTPGIPIGPMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHYLEDGSV 476 (768)
Q Consensus 397 ~~y~~~pd~~~v~~~ll~~g~~~l~~~~~i~~g~PvkPMLA~~~~~i~~il~k~~g~~~~~E~KyDG~R~qih~~~~g~V 476 (768)
++|+++|||+.|++.|+++|++++.++|.++||+|++||||++++++.+++++|++..|.|||||||+|+|||+.++|+|
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 EEEcCCcccCCCCCchHHHHHHhhcCCCCCCeEEEEEEEEEecCCCcccChhhHHhhhhccCCccccccceEEEEeeeee
Q 004212 477 EIYSRNAERNTGKFPDVVLAVSRLKKPSVRSFVLDCEIVAYDREKQKILPFQTLSTRARKNVSLSDIKVDVCIYAFDILY 556 (768)
Q Consensus 477 ~lfSR~g~d~T~~fPel~~~l~~~~~~~~~~~ILDGElVa~d~~~g~~~pFq~L~~R~rk~~~~~~~~~~v~~~vFDiLy 556 (768)
.|||||+++.|.+||||...+..+..+.+.+||||||+|+||.+.|+++|||.|++|.|++++.+++++.||+|+|||||
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 99999999999999999999998888888999999999999999999999999999999999999999999999999999
Q ss_pred cCCccccCCcHHHHHHHHHHhhccCCCeEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEeeCCCCCCccCCCCCCCeEE
Q 004212 557 RNGQPLLQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLK 636 (768)
Q Consensus 557 lnG~~L~~~Pl~ERr~lL~~l~~~~~~~i~l~~~~~~~~~eei~~~~~~ai~~G~EGlVlK~~~~dS~Y~pGkRs~~WlK 636 (768)
+||++|+++|+.+||++|.+.|.+.++.++++....+++.+++++||+++++.+|||+|+|.+|.+++|+|.+||.+|+|
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 99999999999999999999999999999999999999999999999999999999999999988999999999999999
Q ss_pred EccccccccCCcccEEEEEEEcCCCCCCCccceEEEEEeeCCCCeEEEEEEeccCCCHHHHHHHHHHhccccCCCCCCCc
Q 004212 637 LKKDYIESIGDSLDLVPIAAFHGRGKRTGVYGAFLLACYDSNNEEFQSICKIGTGFSEAMLEERSSSLRSKVIPKPRPYY 716 (768)
Q Consensus 637 vK~dy~~~~~dtlDlvVIG~~~G~Gkr~g~~gsfLlg~~d~~~g~l~~vgkVGTGfsd~~l~~L~~~l~~~~~~~p~~~~ 716 (768)
+|+||++|+||++||||||+|+|+|||+|++|+||+||||+++++|++|||+||||||++++++.+.+....+..+++||
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 99999999999999999999999999999999999999999999999999999999999999999999999888888999
Q ss_pred cCCCCCCCcEEecCcceEEEEecceeecCCCccc
Q 004212 717 RFADTISPDVWFEPTERPETSNSPASIVYDSQIT 750 (768)
Q Consensus 717 ~~~~~~~pdvWv~P~~V~EV~~aeit~Sp~~~~~ 750 (768)
++.+..+||+||+|..||||++||+|.||.|+..
T Consensus 629 ~~d~s~kPd~wf~p~~VwEvk~Adlt~SPiy~Aa 662 (714)
T KOG0967|consen 629 RFDESLKPDVWFEPTEVWEVKAADLTLSPIYKAA 662 (714)
T ss_pred ccCccCCCccccCHHHHHHHhhccccccchhHhh
Confidence 9998889999999999999999999999999543
No 2
>PLN03113 DNA ligase 1; Provisional
Probab=100.00 E-value=6.1e-137 Score=1200.39 Aligned_cols=683 Identities=76% Similarity=1.162 Sum_probs=601.3
Q ss_pred cCCCCCcHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccchh---hcccCCCCCCCCCCCCCCCC
Q 004212 53 MSSSAPNAFQVLMSAAAKKKPSPQPNSSSSSSSPKKRRTLDTQTPKTTNSVVGEKIQ---EVAEEPSNDLVKPISNQIDN 129 (768)
Q Consensus 53 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~ 129 (768)
|| |+||||||||+-++...++....+++.+++||+++...++++....-+.-+.-+ +..-++.++.+.++....++
T Consensus 1 ~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 79 (744)
T PLN03113 1 MS-SRPSAFDALMSNARAAAKKKQPQTQSQSSSPKKRKIGETQDANLGKTNVSEGTLPKTEDTIEPKSDSAKPRSSTSSI 79 (744)
T ss_pred CC-CCccHHHHHHHHHHHHhhccCCCccCCCCccccccccCCCCCCcCCcccccccccccccCCCCCCCccccccccccc
Confidence 44 599999999994444333444444666777888877765555444333333321 22334444555555555544
Q ss_pred CCCcccCCCCCCCCCccccccccccchhhhHHHHhhhhhhcccCCCCCCCcccccccCCCccchHHHHHHHHHHHhhhch
Q 004212 130 PIDSEKESQPTPPSPKKRKVNVNSVSAKEKIAELKSNIVLLKKKAGEFDPKMVACWEKGERVPFIFLSLVFDMISNETGR 209 (768)
Q Consensus 130 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~F~~la~l~e~I~~tssr 209 (768)
.++.++. +... .+.. . .+.+++...+..+..++..|||..+++|..|.+|||..||++|++|+.|++|
T Consensus 80 ~~~~~~~-----~~~~---~~~~---~-~~~~~~~~~~~~~~~~~~~~~~~~~~~w~~~~~~~f~~l~~~~~~Ie~tt~r 147 (744)
T PLN03113 80 AEDSKTG-----TKKA---QTLS---K-PKKDEMKSKIGLLKKKPNDFDPEKVAYWEKGERVPFLFVALAFDLISNETGR 147 (744)
T ss_pred ccccCCC-----cccc---cccc---c-ccccchhhhHhhccCCccccCcchhhcccCCCCccHHHHHHHHHHHHhccCH
Confidence 4443322 1111 1111 1 1114556666678999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHhhhcCCCCchHHHHHHHhCccCCCccccccCCCHHHHHHHHHHHhCCCHHHHHHHHhhhCChHHHHhh
Q 004212 210 ILITDIVCNMLRTVMETTPEDLVPVVYLAANKIAPAHEGLELGIGDASIIKALAEACGRTESHVKKQYQEMGDLGLVAKA 289 (768)
Q Consensus 210 ~~k~~iL~~~fr~~i~~~p~dl~~~vyl~~~~l~P~~e~~elGIg~~~L~Kal~~a~G~s~~~ik~~y~~~GDlg~vA~~ 289 (768)
++|+++|+|||+.++..+|+|+.+++||++|+|+|+|++.|||||++.|+|+|++++|++++.+++.|+++||+|+||+.
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 hcccCCccCCCCCCcHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHhcCCChHHHHHHHHhhcccCcccHHHHHHHHHh
Q 004212 290 SRSSQSMMRKPDPLTITKVFDTFRLIAKEAGKDSQEKKKNRIKALLVAATDCEPQYLIRLLQSKLRIGLAEQTLLAALGQ 369 (768)
Q Consensus 290 ~r~~q~~l~~~~~LTI~eV~~~L~kIA~~~G~~Sq~~K~~~l~~Ll~~~t~~E~k~lvRiIlkdLRiGi~e~tVl~ala~ 369 (768)
+++.|.+++++++|||.+||+.|.+||+.+|.+||++|+.+|..||..|+++|++||+|+|+++||||++++||+.|||+
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 99888888888999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhccCCCCCCCCCCCcchHHHHHHHHHHHhhcCCchhhhhhhhhhcCccccCCccccCCCCCCccccccccCChHHHHhh
Q 004212 370 AAVYNEQHSKPPPNIQSPLEEAAKIVKQVFSVLPVYEKIVPALLTDGVWNLSNTCSFTPGIPIGPMLAKPTKGVSEIVNK 449 (768)
Q Consensus 370 a~~~~~~~~~~~~~l~~~l~~a~~~vk~~y~~~pd~~~v~~~ll~~g~~~l~~~~~i~~g~PvkPMLA~~~~~i~~il~k 449 (768)
||.++..+.....+..++|+++..+++++|+.+|||+.|++.++++|+.++..+|.+++|+||+||||++++++++++++
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 99876543333445678899999999999999999999999999999999988999999999999999999999999999
Q ss_pred cCCCceEEeeecceEeEEEEEecCCeEEEEcCCcccCCCCCchHHHHHHhhcCCCCCCeEEEEEEEEEecCCCcccChhh
Q 004212 450 FQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAVSRLKKPSVRSFVLDCEIVAYDREKQKILPFQT 529 (768)
Q Consensus 450 ~~g~~~~~E~KyDG~R~qih~~~~g~V~lfSR~g~d~T~~fPel~~~l~~~~~~~~~~~ILDGElVa~d~~~g~~~pFq~ 529 (768)
|+|.+|+||+||||+|+|||+..+|+|++|||||+++|++|||+++++..++.+.+++||||||+|+||.++|+++|||.
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 98889999999999999999855789999999999999999999998888765557899999999999988888999999
Q ss_pred HHhhhhccCCccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCCCeEEEEeEEecCCHHHHHHHHHHHHHc
Q 004212 530 LSTRARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAAVDA 609 (768)
Q Consensus 530 L~~R~rk~~~~~~~~~~v~~~vFDiLylnG~~L~~~Pl~ERr~lL~~l~~~~~~~i~l~~~~~~~~~eei~~~~~~ai~~ 609 (768)
|++|.|+++...+.+.++||+||||||+||++|+++||.|||++|++++.+.++++++++...+++.++++++|+++++.
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 99998887655556789999999999999999999999999999999998877899999999899999999999999999
Q ss_pred CCceeEEeeCCCCCCccCCCCCCCeEEEccccccccCCcccEEEEEEEcCCCCCCCccceEEEEEeeCCCCeEEEEEEec
Q 004212 610 SCEGLIIKTMDRDATYEPSKRSLNWLKLKKDYIESIGDSLDLVPIAAFHGRGKRTGVYGAFLLACYDSNNEEFQSICKIG 689 (768)
Q Consensus 610 G~EGlVlK~~~~dS~Y~pGkRs~~WlKvK~dy~~~~~dtlDlvVIG~~~G~Gkr~g~~gsfLlg~~d~~~g~l~~vgkVG 689 (768)
|+||||+|+++.+|+|+||+|+.+|+|+|++|+++++|++|+||||||+|+|+|+|++|+|||||||+++|+|++|||||
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 99999999975589999999999999999999999999999999999999999999999999999998778999999999
Q ss_pred cCCCHHHHHHHHHHhccccCCCCCCCccCCCCCCCcEEecCcceEEEEecceeecCCCc
Q 004212 690 TGFSEAMLEERSSSLRSKVIPKPRPYYRFADTISPDVWFEPTERPETSNSPASIVYDSQ 748 (768)
Q Consensus 690 TGfsd~~l~~L~~~l~~~~~~~p~~~~~~~~~~~pdvWv~P~~V~EV~~aeit~Sp~~~ 748 (768)
|||||+++++|.+.|++++++.|++|+.++....|++||+|.+||||+|+|||.||+|+
T Consensus 628 TGfsd~~l~~l~~~L~~~~~~~~~~~~~~~~~~~pdvwveP~~V~EV~~aeit~Sp~h~ 686 (744)
T PLN03113 628 TGFSEAVLEERSASLRSQVIPTPKSYYRYGDSIKPDVWFEPTEVWEVKAADLTISPVHR 686 (744)
T ss_pred CCCCHHHHHHHHHHHHHhcccCCCcccccCCCCCCcEEECCceEEEEEeeeeccCcccc
Confidence 99999999999999999998888888888776789999999999999999999999994
No 3
>PRK01109 ATP-dependent DNA ligase; Provisional
Probab=100.00 E-value=2.3e-110 Score=968.66 Aligned_cols=532 Identities=34% Similarity=0.578 Sum_probs=486.5
Q ss_pred cchHHHHHHHHHHHhhhchHHHHHHHHHHHHhhhcCCCCchHHHHHHHhCccCCCccccccCCCHHHHHHHHHHHhCCCH
Q 004212 191 VPFIFLSLVFDMISNETGRILITDIVCNMLRTVMETTPEDLVPVVYLAANKIAPAHEGLELGIGDASIIKALAEACGRTE 270 (768)
Q Consensus 191 ~~F~~la~l~e~I~~tssr~~k~~iL~~~fr~~i~~~p~dl~~~vyl~~~~l~P~~e~~elGIg~~~L~Kal~~a~G~s~ 270 (768)
|+|..||++|++|++|+||++|+++|++||+.+ +++++.+++||++|+|+|+|++++|||++++|+|+|++++|++.
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 789999999999999999999999999999996 78999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhhhCChHHHHhhhcccC--Cc---cCCCCCCcHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHhcCCChHHH
Q 004212 271 SHVKKQYQEMGDLGLVAKASRSSQ--SM---MRKPDPLTITKVFDTFRLIAKEAGKDSQEKKKNRIKALLVAATDCEPQY 345 (768)
Q Consensus 271 ~~ik~~y~~~GDlg~vA~~~r~~q--~~---l~~~~~LTI~eV~~~L~kIA~~~G~~Sq~~K~~~l~~Ll~~~t~~E~k~ 345 (768)
+.+++.|+++||+|++|+.+++.+ .+ ++.+++||+.+|++.|++||..+|.+|+.+|+++|..||.+|+++|++|
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 22 2456899999999999999999999999999999999999999999999
Q ss_pred HHHHHhhcccCcccHHHHHHHHHhhhccCCCCCCCCCCCcchHHHHHHHHHHHhhcCCchhhhhhhhhhcCccccCCccc
Q 004212 346 LIRLLQSKLRIGLAEQTLLAALGQAAVYNEQHSKPPPNIQSPLEEAAKIVKQVFSVLPVYEKIVPALLTDGVWNLSNTCS 425 (768)
Q Consensus 346 lvRiIlkdLRiGi~e~tVl~ala~a~~~~~~~~~~~~~l~~~l~~a~~~vk~~y~~~pd~~~v~~~ll~~g~~~l~~~~~ 425 (768)
|+|+|+++||||+++++|++|||.|+.... ....++++|+.+||++.++..+.++|+..+ .++.
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 999999999999999999999999986211 123567899999999999999999887666 4689
Q ss_pred cCCCCCCccccccccCChHHHHhhcCCCceEEeeecceEeEEEEEecCCeEEEEcCCcccCCCCCchHHHHHHhhcCCCC
Q 004212 426 FTPGIPIGPMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAVSRLKKPSV 505 (768)
Q Consensus 426 i~~g~PvkPMLA~~~~~i~~il~k~~g~~~~~E~KyDG~R~qih~~~~g~V~lfSR~g~d~T~~fPel~~~l~~~~~~~~ 505 (768)
+++|+|++||||+++++++++++++++ +|++|+||||+|||+|+. +|+|++|||||+++|..||||++.+...++ .
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 999999999999999999999998864 799999999999999995 789999999999999999999998887664 3
Q ss_pred CCeEEEEEEEEEecCCCcccChhhHHhhhhccCC-ccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCCCe
Q 004212 506 RSFVLDCEIVAYDREKQKILPFQTLSTRARKNVS-LSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEPGF 584 (768)
Q Consensus 506 ~~~ILDGElVa~d~~~g~~~pFq~L~~R~rk~~~-~~~~~~~v~~~vFDiLylnG~~L~~~Pl~ERr~lL~~l~~~~~~~ 584 (768)
++||||||||+||+++|+++|||.|++|.|+... ......++||+||||||+||++|++.||.|||++|++++.+.+ .
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 7899999999999878888999999999554421 1223679999999999999999999999999999999998754 5
Q ss_pred EEEEeEEecCCHHHHHHHHHHHHHcCCceeEEeeCCCCCCccCCCCCCCeEEEccccccccCCcccEEEEEEEcCCCCCC
Q 004212 585 FQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLKKDYIESIGDSLDLVPIAAFHGRGKRT 664 (768)
Q Consensus 585 i~l~~~~~~~~~eei~~~~~~ai~~G~EGlVlK~~~~dS~Y~pGkRs~~WlKvK~dy~~~~~dtlDlvVIG~~~G~Gkr~ 664 (768)
+++++...+++.++++++|+.++++|+||||+|+++++|+|+||+|+.+|+|+|++|+++++|++|+||||+++|+|+|+
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 CccceEEEEEeeCCCCeEEEEEEeccCCCHHHHHHHHHHhccccCCCCCCCccCCCCCCCcEEecCcceEEEEecceeec
Q 004212 665 GVYGAFLLACYDSNNEEFQSICKIGTGFSEAMLEERSSSLRSKVIPKPRPYYRFADTISPDVWFEPTERPETSNSPASIV 744 (768)
Q Consensus 665 g~~gsfLlg~~d~~~g~l~~vgkVGTGfsd~~l~~L~~~l~~~~~~~p~~~~~~~~~~~pdvWv~P~~V~EV~~aeit~S 744 (768)
|++|+|+||+||+++|+|++||||||||||+++++|.+.+++++++.+++++ .....||+||+|.+||||+|+|||.|
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 9999999999998778999999999999999999999999999988765553 23457999999999999999999999
Q ss_pred CCCc
Q 004212 745 YDSQ 748 (768)
Q Consensus 745 p~~~ 748 (768)
|+|+
T Consensus 535 ~~~~ 538 (590)
T PRK01109 535 PLHT 538 (590)
T ss_pred ccee
Confidence 9993
No 4
>PRK09247 ATP-dependent DNA ligase; Validated
Probab=100.00 E-value=6.5e-96 Score=839.17 Aligned_cols=493 Identities=20% Similarity=0.273 Sum_probs=430.7
Q ss_pred HHHHHHHHHHHhhhchHHHHHHHHHHHHhhhcCCCCchHHHHHHHhCccCCCccccccCCCHHHHHHHHHHHhCCCHHHH
Q 004212 194 IFLSLVFDMISNETGRILITDIVCNMLRTVMETTPEDLVPVVYLAANKIAPAHEGLELGIGDASIIKALAEACGRTESHV 273 (768)
Q Consensus 194 ~~la~l~e~I~~tssr~~k~~iL~~~fr~~i~~~p~dl~~~vyl~~~~l~P~~e~~elGIg~~~L~Kal~~a~G~s~~~i 273 (768)
..||++|++|++|++|++|+++|++||+.+ +|+|+.+++||++|++. ++||+++.|+|+|++++|++++.+
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 HHHHhhhCChHHHHhhhcccCC--ccCCCCCCcHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHhcCCChHHHHHHHHh
Q 004212 274 KKQYQEMGDLGLVAKASRSSQS--MMRKPDPLTITKVFDTFRLIAKEAGKDSQEKKKNRIKALLVAATDCEPQYLIRLLQ 351 (768)
Q Consensus 274 k~~y~~~GDlg~vA~~~r~~q~--~l~~~~~LTI~eV~~~L~kIA~~~G~~Sq~~K~~~l~~Ll~~~t~~E~k~lvRiIl 351 (768)
++.|.++||+|+||..+...+. .++.+.++||.+|++.|.+|++. .|+..|..||.+|++.|++||+|+|+
T Consensus 73 ~~~~~~~GDlg~~~~~~~~~~~~~~~~~~~~~tv~~v~~~l~~~~~~-------~k~~~l~~ll~~~~~~e~~~i~rli~ 145 (539)
T PRK09247 73 EESYDYVGDLAETIALLLPAPSDEASDLPLAPWLEEVLLPLRGLGRE-------ELRAALADLWDRLDEDGRFALNKLIT 145 (539)
T ss_pred HHHHHhcCCHHHHHHHhcccccccccCCCccccHHHHHHHHHhhhHH-------HHHHHHHHHHHhCCHHHHHHHHHHhh
Confidence 9999999999999988644322 22334679999999999998754 26789999999999999999999999
Q ss_pred hcccCcccHHHHHHHHHhhhccCCCCCCCCCCCcchHHHHHHHHHHHhhc--CCchhhhhhhhhhcCccccCCccccCCC
Q 004212 352 SKLRIGLAEQTLLAALGQAAVYNEQHSKPPPNIQSPLEEAAKIVKQVFSV--LPVYEKIVPALLTDGVWNLSNTCSFTPG 429 (768)
Q Consensus 352 kdLRiGi~e~tVl~ala~a~~~~~~~~~~~~~l~~~l~~a~~~vk~~y~~--~pd~~~v~~~ll~~g~~~l~~~~~i~~g 429 (768)
++||||++++||++|||+||..+ .+.+.++|+. .|+++.+.. ++..|. .+|.++||
T Consensus 146 g~lRiG~~~~~v~~ala~a~~~~-----------------~~~v~~~~~~~~~~~~~~~~~-~~~~~~----~~~~~~~~ 203 (539)
T PRK09247 146 GGFRVGVSARLVTRALAELGGVD-----------------EARIAQRLMGLWPPYADLFAW-LIGPEE----DPLPADPG 203 (539)
T ss_pred CccccchhHHHHHHHHHHHhCCC-----------------HHHHHHHHhCCCCCcHHHHHH-HhhCCc----cccCCCCC
Confidence 99999999999999999998532 1234556666 666665544 455565 46889999
Q ss_pred CCCccccccccCChHHHHhhcCCCceEEeeecceEeEEEEEecCCeEEEEcCCcccCCCCCchHHHHHHhhcCCCCCCeE
Q 004212 430 IPIGPMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAVSRLKKPSVRSFV 509 (768)
Q Consensus 430 ~PvkPMLA~~~~~i~~il~k~~g~~~~~E~KyDG~R~qih~~~~g~V~lfSR~g~d~T~~fPel~~~l~~~~~~~~~~~I 509 (768)
+|++||||++++++.+... ...+|++|+||||+|+|+|+. +|+|++|||||+++|.+||++.+++..+ + .+||
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-GGEVRLWSRGEELITERFPELAEAAEAL-P---DGTV 276 (539)
T ss_pred CcCCCeeCCcCCCchhhhc--CCCcEEEEEeEcceEEEEEEe-CCEEEEEeCCCccchhhhHHHHHHHHhC-C---CCEE
Confidence 9999999999988755443 334899999999999999994 7899999999999999999999877643 2 5799
Q ss_pred EEEEEEEEecCCCcccChhhHHhhhh-ccCCcc-ccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCC-CeEE
Q 004212 510 LDCEIVAYDREKQKILPFQTLSTRAR-KNVSLS-DIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEP-GFFQ 586 (768)
Q Consensus 510 LDGElVa~d~~~g~~~pFq~L~~R~r-k~~~~~-~~~~~v~~~vFDiLylnG~~L~~~Pl~ERr~lL~~l~~~~~-~~i~ 586 (768)
||||+|+||+++|.++||+.|++|.+ +..... ..+.++||+||||||+||++++++||.+||++|++++.+.+ ++++
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 99999999976778899999999954 333211 12579999999999999999999999999999999998764 4899
Q ss_pred EEeEEecCCHHHHHHHHHHHHHcCCceeEEeeCCCCCCccCCCCCCCeEEEccccccccCCcccEEEEEEEcCCCCCCCc
Q 004212 587 FATTLTSIDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLKKDYIESIGDSLDLVPIAAFHGRGKRTGV 666 (768)
Q Consensus 587 l~~~~~~~~~eei~~~~~~ai~~G~EGlVlK~~~~dS~Y~pGkRs~~WlKvK~dy~~~~~dtlDlvVIG~~~G~Gkr~g~ 666 (768)
+++...+.+.+++.++|++++++|+||||+|++ +|+|+||+|+..|+|+|++| +++|+||||+++|+|+|+|+
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 999998999999999999999999999999999 99999999999999999997 48999999999999999999
Q ss_pred cceEEEEEeeCCC--CeEEEEEEeccCCCHHHHHHHHHHhccccCCCCCCCccCCCCCCCcEEecCcceEEEEecceeec
Q 004212 667 YGAFLLACYDSNN--EEFQSICKIGTGFSEAMLEERSSSLRSKVIPKPRPYYRFADTISPDVWFEPTERPETSNSPASIV 744 (768)
Q Consensus 667 ~gsfLlg~~d~~~--g~l~~vgkVGTGfsd~~l~~L~~~l~~~~~~~p~~~~~~~~~~~pdvWv~P~~V~EV~~aeit~S 744 (768)
+|+|+|||||++. ++|++||||||||||+++++|.+.++++.... ..|++||+|.+||||+|+|||.|
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 36999999999999999999999887654332 15899999999999999999999
Q ss_pred CCCc
Q 004212 745 YDSQ 748 (768)
Q Consensus 745 p~~~ 748 (768)
|+|+
T Consensus 500 ~~~~ 503 (539)
T PRK09247 500 KRHK 503 (539)
T ss_pred CCcC
Confidence 9995
No 5
>PRK03180 ligB ATP-dependent DNA ligase; Reviewed
Probab=100.00 E-value=4e-96 Score=835.12 Aligned_cols=472 Identities=27% Similarity=0.376 Sum_probs=422.3
Q ss_pred cchHHHHHHHHHHHhhhchHHHHHHHHHHHHhhhcCCCCchHHHHHHHhCccCCCccccccCCCHHHHHHHHHHHhCCCH
Q 004212 191 VPFIFLSLVFDMISNETGRILITDIVCNMLRTVMETTPEDLVPVVYLAANKIAPAHEGLELGIGDASIIKALAEACGRTE 270 (768)
Q Consensus 191 ~~F~~la~l~e~I~~tssr~~k~~iL~~~fr~~i~~~p~dl~~~vyl~~~~l~P~~e~~elGIg~~~L~Kal~~a~G~s~ 270 (768)
|+|..||++|++|++|++|++|+++|++||+.+ +++|+.+++||++|++. ++++|++++.+.++++.
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 56899998777766422
Q ss_pred HHHHHHHhhhCChHHHHhhhcccCCccCCCCCCcHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHhcCCChHHHHHHHH
Q 004212 271 SHVKKQYQEMGDLGLVAKASRSSQSMMRKPDPLTITKVFDTFRLIAKEAGKDSQEKKKNRIKALLVAATDCEPQYLIRLL 350 (768)
Q Consensus 271 ~~ik~~y~~~GDlg~vA~~~r~~q~~l~~~~~LTI~eV~~~L~kIA~~~G~~Sq~~K~~~l~~Ll~~~t~~E~k~lvRiI 350 (768)
..+++|||.+||+.|++||..+|.+|++.|+.+|+.||.+|++.|++||+|+|
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 hhcccCcccHHHHHHHHHhhhccCCCCCCCCCCCcchHHHHHHHHHHHhhcCCchhhhhhhhhhcCccccCCccccCCCC
Q 004212 351 QSKLRIGLAEQTLLAALGQAAVYNEQHSKPPPNIQSPLEEAAKIVKQVFSVLPVYEKIVPALLTDGVWNLSNTCSFTPGI 430 (768)
Q Consensus 351 lkdLRiGi~e~tVl~ala~a~~~~~~~~~~~~~l~~~l~~a~~~vk~~y~~~pd~~~v~~~ll~~g~~~l~~~~~i~~g~ 430 (768)
+++||||+++++|+.|||+||..+ ...++++|+.|+|++.++..++++|...+ ..|.|++|+
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 999999999999999999998542 13467889999999999999998887665 578999999
Q ss_pred CCccccccccCChHHHHhhcCCCceEEeeecceEeEEEEEecCCeEEEEcCCcccCCCCCchHHHHHHhhcCCCCCCeEE
Q 004212 431 PIGPMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAVSRLKKPSVRSFVL 510 (768)
Q Consensus 431 PvkPMLA~~~~~i~~il~k~~g~~~~~E~KyDG~R~qih~~~~g~V~lfSR~g~d~T~~fPel~~~l~~~~~~~~~~~IL 510 (768)
|++||||++++++++++++++ .+|++|+||||+|||+|+. +|+|++|||||+++|++|||+.+.+... ..++|||
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 999999999999988888875 4799999999999999995 7899999999999999999999876653 2368999
Q ss_pred EEEEEEEecCCCcccChhhHHhhhhccCCc--cccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCCCeEEEE
Q 004212 511 DCEIVAYDREKQKILPFQTLSTRARKNVSL--SDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEPGFFQFA 588 (768)
Q Consensus 511 DGElVa~d~~~g~~~pFq~L~~R~rk~~~~--~~~~~~v~~~vFDiLylnG~~L~~~Pl~ERr~lL~~l~~~~~~~i~l~ 588 (768)
|||||+||+ +|++.|||.+++|.+++... ...+.+++|++|||||+||++++++||.+||++|++++.+. ..+
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 47888999999997543221 22357999999999999999999999999999999998742 123
Q ss_pred eEEecCCHHHHHHHHHHHHHcCCceeEEeeCCCCCCccCCCCCCCeEEEccccccccCCcccEEEEEEEcCCCCCCCccc
Q 004212 589 TTLTSIDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLKKDYIESIGDSLDLVPIAAFHGRGKRTGVYG 668 (768)
Q Consensus 589 ~~~~~~~~eei~~~~~~ai~~G~EGlVlK~~~~dS~Y~pGkRs~~WlKvK~dy~~~~~dtlDlvVIG~~~G~Gkr~g~~g 668 (768)
+.....+.++++++|++++++|+||||+|++ +|+|+||+|+.+|+|+|+. +++|+||||+++|+|+|+|++|
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 4455678999999999999999999999999 9999999999999999995 5999999999999999999999
Q ss_pred eEEEEEeeCCCCeEEEEEEeccCCCHHHHHHHHHHhccccCCCCCCCccCCCCCCCcEEecCcceEEEEecceeecCCCc
Q 004212 669 AFLLACYDSNNEEFQSICKIGTGFSEAMLEERSSSLRSKVIPKPRPYYRFADTISPDVWFEPTERPETSNSPASIVYDSQ 748 (768)
Q Consensus 669 sfLlg~~d~~~g~l~~vgkVGTGfsd~~l~~L~~~l~~~~~~~p~~~~~~~~~~~pdvWv~P~~V~EV~~aeit~Sp~~~ 748 (768)
+|+|||||+++|+|++||||||||||++++++++.+.++.+..+ .|++||+|.+||||+|++||.||.|+
T Consensus 405 ~~llg~~d~~~~~l~~vgkv~sG~td~~l~~l~~~l~~~~~~~~----------~~~vwv~P~~V~EV~~~~it~S~~~~ 474 (508)
T PRK03180 405 NLHLGARDPATGGFVMLGKTFKGMTDAMLAWQTERFLELAVGRD----------GWTVYVRPELVVEIAFDGVQRSTRYP 474 (508)
T ss_pred ceEEEEEeCCCCeEEEecCccCCCCHHHHHHHHHHHHhhccCCC----------CCCEEeeCCEEEEEEeeEeeeCCccc
Confidence 99999999877899999999999999999999999988765432 68999999999999999999999983
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=2.3e-95 Score=833.07 Aligned_cols=477 Identities=39% Similarity=0.653 Sum_probs=433.6
Q ss_pred ccCCCHHHHHHHHHHHhCCCHHHHHHHHhhhCChHHHHhhhcccCC-ccCCCCCCcHHHHHHHHHHHHHHhCCChHHHHH
Q 004212 250 ELGIGDASIIKALAEACGRTESHVKKQYQEMGDLGLVAKASRSSQS-MMRKPDPLTITKVFDTFRLIAKEAGKDSQEKKK 328 (768)
Q Consensus 250 elGIg~~~L~Kal~~a~G~s~~~ik~~y~~~GDlg~vA~~~r~~q~-~l~~~~~LTI~eV~~~L~kIA~~~G~~Sq~~K~ 328 (768)
+||||++.|+|++++++|++.+.+++.|.+.||+|+++..++..+. ....+.+|||.+|++.|++||..+|.+|+++|.
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 6999999999999999999999999999999999999998766554 344568999999999999999999999999999
Q ss_pred HHHHHHHHhcCCChHHHHHHHHhhcccCcccHHHHHHHHHhhhccCCCCCCCCCCCcchHHHHHHHHHHHhhcCCchhhh
Q 004212 329 NRIKALLVAATDCEPQYLIRLLQSKLRIGLAEQTLLAALGQAAVYNEQHSKPPPNIQSPLEEAAKIVKQVFSVLPVYEKI 408 (768)
Q Consensus 329 ~~l~~Ll~~~t~~E~k~lvRiIlkdLRiGi~e~tVl~ala~a~~~~~~~~~~~~~l~~~l~~a~~~vk~~y~~~pd~~~v 408 (768)
.+|..||.+|++.|++||+|+|+++||||+++++|+.|||++|..+. ..+.++|+.|||++.|
T Consensus 81 ~~l~~ll~~~~~~e~k~l~r~i~~~lriG~~~~~il~al~~~~~~~~-----------------~~~~~~~~~~~dl~~v 143 (514)
T TIGR00574 81 KLLKSLLKRASPLEAKYLIRTILGDLRIGIAEKTILDALAKAFLLSH-----------------PDVERAFNLTNDLGKV 143 (514)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHhhhcccCccHHHHHHHHHHHhccch-----------------HHHHHHHHhCCCHHHH
Confidence 99999999999999999999999999999999999999999986431 2456789999999999
Q ss_pred hhhhhhcCccccCCccccCCCCCCccccccccCChHHHHhhcCCCceEEeeecceEeEEEEEecCCeEEEEcCCcccCCC
Q 004212 409 VPALLTDGVWNLSNTCSFTPGIPIGPMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTG 488 (768)
Q Consensus 409 ~~~ll~~g~~~l~~~~~i~~g~PvkPMLA~~~~~i~~il~k~~g~~~~~E~KyDG~R~qih~~~~g~V~lfSR~g~d~T~ 488 (768)
+..+.++|+..+..++.+++|+|++||||+++++++++++++.+ +|++|+||||+|||+|+ .+|+|++|||||+++|.
T Consensus 144 ~~~l~~~~~~~~~~~~~i~~~~p~~PMLA~~~~~~~~~~~~~~~-~~~~E~K~DG~R~qih~-~~~~v~l~SR~g~~~t~ 221 (514)
T TIGR00574 144 AKILLEPGLRGLDKDLSIQLGIPFKPMLAERAKSIEEALKKKGN-KFYVEYKYDGERVQIHK-DGDKFKIFSRRLENYTY 221 (514)
T ss_pred HHHHHhcChhhhcccceeecCCcCccccCCccCCHHHHHHHhCC-ceEEEEeecceEEEEEE-cCCEEEEEcCCCccccc
Confidence 99999999877767799999999999999999999888888764 89999999999999999 57899999999999999
Q ss_pred CCchH-HHHHHhhcCCCCCCeEEEEEEEEEecCCCcccChhhHHhhhhcc-CCccccccceEEEEeeeeecCCccccCCc
Q 004212 489 KFPDV-VLAVSRLKKPSVRSFVLDCEIVAYDREKQKILPFQTLSTRARKN-VSLSDIKVDVCIYAFDILYRNGQPLLQEQ 566 (768)
Q Consensus 489 ~fPel-~~~l~~~~~~~~~~~ILDGElVa~d~~~g~~~pFq~L~~R~rk~-~~~~~~~~~v~~~vFDiLylnG~~L~~~P 566 (768)
.||++ .+.+...++. ..+||||||||+||.++|+++||+.|++|.++. ........+++|++|||||+||++++++|
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 8878776653 468999999999998778889999999997642 11223467899999999999999999999
Q ss_pred HHHHHHHHHHhhccCCCeEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEeeCCCCCCccCCCCCCCeEEEccccccccC
Q 004212 567 LRVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLKKDYIESIG 646 (768)
Q Consensus 567 l~ERr~lL~~l~~~~~~~i~l~~~~~~~~~eei~~~~~~ai~~G~EGlVlK~~~~dS~Y~pGkRs~~WlKvK~dy~~~~~ 646 (768)
|.|||++|++++.+.++.+++++...+++.+++.++|++++++|+||||+|++ +|+|+||+|+.+|+|+|++|+++++
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 99999999999988888999999999999999999999999999999999999 9999999999999999999999999
Q ss_pred CcccEEEEEEEcCCCCCCCccceEEEEEeeCCCCeEEEEEEeccCCCHHHHHHHHHHhccccCCCCCCCccCCCCCCCcE
Q 004212 647 DSLDLVPIAAFHGRGKRTGVYGAFLLACYDSNNEEFQSICKIGTGFSEAMLEERSSSLRSKVIPKPRPYYRFADTISPDV 726 (768)
Q Consensus 647 dtlDlvVIG~~~G~Gkr~g~~gsfLlg~~d~~~g~l~~vgkVGTGfsd~~l~~L~~~l~~~~~~~p~~~~~~~~~~~pdv 726 (768)
+++|+||||+++|+|+++|++|+|+||+||+++++|++||||||||||+++++|.+.+.+++++.+++.+.......|++
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 99999999999999999999999999999987789999999999999999999999999998876544322112246899
Q ss_pred EecCcceEEEEecceeecCCCc
Q 004212 727 WFEPTERPETSNSPASIVYDSQ 748 (768)
Q Consensus 727 Wv~P~~V~EV~~aeit~Sp~~~ 748 (768)
|++|.+||||+|+|||.||+|+
T Consensus 459 w~~p~~V~eV~~~e~t~s~~~~ 480 (514)
T TIGR00574 459 WFDPAIVWEVTGAEITRSPTYK 480 (514)
T ss_pred EecCCeEEEEEhhheeecCccc
Confidence 9999999999999999999983
No 7
>KOG0966 consensus ATP-dependent DNA ligase IV [Replication, recombination and repair]
Probab=100.00 E-value=1.8e-80 Score=701.18 Aligned_cols=530 Identities=24% Similarity=0.377 Sum_probs=443.3
Q ss_pred CccchHHHHHHHHHHHhhhchHHHHHHHHHHHHhhhcCCCCchHHHHHHHhCccCCCcccc--ccCCCHHHHHHHHHHHh
Q 004212 189 ERVPFIFLSLVFDMISNETGRILITDIVCNMLRTVMETTPEDLVPVVYLAANKIAPAHEGL--ELGIGDASIIKALAEAC 266 (768)
Q Consensus 189 ~~~~F~~la~l~e~I~~tssr~~k~~iL~~~fr~~i~~~p~dl~~~vyl~~~~l~P~~e~~--elGIg~~~L~Kal~~a~ 266 (768)
+++.|+.++++|+.|..+..-+.|++++..++-... .|-+....+|.+++.++|.+++. .|||++..|++.+++++
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 578899999999999999999999999999997764 34334444555556678999654 99999999999999999
Q ss_pred CCCH---HHHHHH-Hh----hhCChHHHHhhhcccCCccCCCCCCcHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHhc
Q 004212 267 GRTE---SHVKKQ-YQ----EMGDLGLVAKASRSSQSMMRKPDPLTITKVFDTFRLIAKEAGKDSQEKKKNRIKALLVAA 338 (768)
Q Consensus 267 G~s~---~~ik~~-y~----~~GDlg~vA~~~r~~q~~l~~~~~LTI~eV~~~L~kIA~~~G~~Sq~~K~~~l~~Ll~~~ 338 (768)
+++. +.++.. |+ ..||++.++.++...+.....++.|||.+||+.||.||...- ...++.+.|..|.++|
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 333322 22 348999998876544333323455999999999999985332 2223348899999999
Q ss_pred CCChHHHHHHHHhhcccCcccHHHHHHHHHhhhccCCCCCCCCCCCcchHHHHHHHHHHHhhcCCchhhhhhhhhhcCcc
Q 004212 339 TDCEPQYLIRLLQSKLRIGLAEQTLLAALGQAAVYNEQHSKPPPNIQSPLEEAAKIVKQVFSVLPVYEKIVPALLTDGVW 418 (768)
Q Consensus 339 t~~E~k~lvRiIlkdLRiGi~e~tVl~ala~a~~~~~~~~~~~~~l~~~l~~a~~~vk~~y~~~pd~~~v~~~ll~~g~~ 418 (768)
++.|+|||+|||+|++.+|+++++|+..||+.| . +.|++|.|+..||..|......
T Consensus 159 S~~ElkWliriiLK~lklG~se~~Il~vfHPdA--------------------~----dl~~vtsDLk~Vc~~L~Dp~~~ 214 (881)
T KOG0966|consen 159 SPLELKWLIRIILKNLKLGASEKKILSVFHPDA--------------------Q----DLYNVTSDLKAVCKKLYDPSVG 214 (881)
T ss_pred CHHHHHHHHHHHHHhhhcCCccchhhhhcCccH--------------------H----HHHHHhhhHHHHHHHhcCCccC
Confidence 999999999999999999999999999986532 2 3588999999999998875432
Q ss_pred ccCCccccCCCCCCccccccccCChH-HHHhhcCCCceEEeeecceEeEEEEEecCCeEEEEcCCcccCCCCCch-----
Q 004212 419 NLSNTCSFTPGIPIGPMLAKPTKGVS-EIVNKFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPD----- 492 (768)
Q Consensus 419 ~l~~~~~i~~g~PvkPMLA~~~~~i~-~il~k~~g~~~~~E~KyDG~R~qih~~~~g~V~lfSR~g~d~T~~fPe----- 492 (768)
--.....+.+|.-++||||...+... +++++|++.+|++|.|+||+|+|+|++ +|++++|||||.|+|..|..
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 21122358999999999998766443 688899999999999999999999995 88999999999999987732
Q ss_pred -HHHHHHhhcCCCCCCeEEEEEEEEEecCCCcccChhhHHhhhhccCCccccccceEEEEeeeeecCCccccCCcHHHHH
Q 004212 493 -VVLAVSRLKKPSVRSFVLDCEIVAYDREKQKILPFQTLSTRARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRR 571 (768)
Q Consensus 493 -l~~~l~~~~~~~~~~~ILDGElVa~d~~~g~~~pFq~L~~R~rk~~~~~~~~~~v~~~vFDiLylnG~~L~~~Pl~ERr 571 (768)
+...|+.++..++.+||||||||+||+.+.++.||+..+.-.+.. ..+...++||++||+||+||++|.+.||..|+
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 456788888777899999999999999999999999876432211 11346789999999999999999999999999
Q ss_pred HHHHHhhccCCCeEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEeeCCCCCCccCCCCCCCeEEEccccccccCCcccE
Q 004212 572 EHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLKKDYIESIGDSLDL 651 (768)
Q Consensus 572 ~lL~~l~~~~~~~i~l~~~~~~~~~eei~~~~~~ai~~G~EGlVlK~~~~dS~Y~pGkRs~~WlKvK~dy~~~~~dtlDl 651 (768)
++|+.++.+.+++++++.+..++..++++++|+.|++.|.||||+|.+ +|.|.||.|+++|+|+||+|+.|+++++|+
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 EEEEEEcCCCCCCCccceEEEEEeeCC-----CCeEEEEEEeccCCCHHHHHHHHHHhccccCC----CCCCCccCCCCC
Q 004212 652 VPIAAFHGRGKRTGVYGAFLLACYDSN-----NEEFQSICKIGTGFSEAMLEERSSSLRSKVIP----KPRPYYRFADTI 722 (768)
Q Consensus 652 vVIG~~~G~Gkr~g~~gsfLlg~~d~~-----~g~l~~vgkVGTGfsd~~l~~L~~~l~~~~~~----~p~~~~~~~~~~ 722 (768)
+|||+|+|+|+|+|.+.+|+||+.+.. ..+|.++|+||+|+|+.++..+...++++|.+ .||...-++...
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 23599999999999999999999999999865 233322233344
Q ss_pred CCcEEecCc--ceEEEEecceeecCCCcccc
Q 004212 723 SPDVWFEPT--ERPETSNSPASIVYDSQITC 751 (768)
Q Consensus 723 ~pdvWv~P~--~V~EV~~aeit~Sp~~~~~~ 751 (768)
.||+|++|. +|++|+.++++.|..+...|
T Consensus 530 ~Pd~wI~P~~SiIlqikaa~i~~s~~f~tn~ 560 (881)
T KOG0966|consen 530 IPDVWIDPDNSIILQIKAAEIVPSSNFVTNY 560 (881)
T ss_pred CCceeECCCCceEEEeehheeeecccccccc
Confidence 799999997 79999999999998886555
No 8
>COG1793 CDC9 ATP-dependent DNA ligase [DNA replication, recombination, and repair]
Probab=100.00 E-value=4.2e-67 Score=587.33 Aligned_cols=407 Identities=34% Similarity=0.492 Sum_probs=349.6
Q ss_pred HHHHHHhCCCHHHHHHHHhhhCChHHHHhhhcccCCccCCCCCCcHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHhcC
Q 004212 260 KALAEACGRTESHVKKQYQEMGDLGLVAKASRSSQSMMRKPDPLTITKVFDTFRLIAKEAGKDSQEKKKNRIKALLVAAT 339 (768)
Q Consensus 260 Kal~~a~G~s~~~ik~~y~~~GDlg~vA~~~r~~q~~l~~~~~LTI~eV~~~L~kIA~~~G~~Sq~~K~~~l~~Ll~~~t 339 (768)
+|+....| ...+.+.|...||+|.++..+.. +.+|+..|..++...| ++ +++..|+..++
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 45666677 66778899999999999876543 8899999999999988 32 78888888888
Q ss_pred CChHHHHHHHHhhcccCcccHHHHHHHHHhhhccCCCCCCCCCCCcchHHHHHHHHHHHhhcCCchhhhhhhhhhcCccc
Q 004212 340 DCEPQYLIRLLQSKLRIGLAEQTLLAALGQAAVYNEQHSKPPPNIQSPLEEAAKIVKQVFSVLPVYEKIVPALLTDGVWN 419 (768)
Q Consensus 340 ~~E~k~lvRiIlkdLRiGi~e~tVl~ala~a~~~~~~~~~~~~~l~~~l~~a~~~vk~~y~~~pd~~~v~~~ll~~g~~~ 419 (768)
+|++++++++||+.| ++.+|+.+||++.++...+..|...
T Consensus 62 ----------------~gv~~~~~~~ala~~------------------------~~~~~~~~~d~g~~a~~~~~~~~~~ 101 (444)
T COG1793 62 ----------------IGVSEGTVLDALAEA------------------------VERAYLWHNDLGALAKILLTLGAEA 101 (444)
T ss_pred ----------------cchhhHHHHHHHHHH------------------------hhhhhccCCCchhhhhhhhhccccc
Confidence 999999999999775 3467888999999999888887666
Q ss_pred cCCccccCCCCCCccccccccCChHHHHhhcCCCceEEeeecceEeEEEEEecCCeEEEEcCCcccCCCCCchHHHHHHh
Q 004212 420 LSNTCSFTPGIPIGPMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAVSR 499 (768)
Q Consensus 420 l~~~~~i~~g~PvkPMLA~~~~~i~~il~k~~g~~~~~E~KyDG~R~qih~~~~g~V~lfSR~g~d~T~~fPel~~~l~~ 499 (768)
+ ..+.++++.|++|||+.....+.+.+.+..+ +|++|+||||+|+|+|+. +|+|++|||||+|+|++||++.+++..
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 5 4577899999999999988877666555443 599999999999999995 789999999999999999987766666
Q ss_pred hcCCCCCCeEEEEEEEEEecCCCcccChhhHHhhhhccCC--ccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHh
Q 004212 500 LKKPSVRSFVLDCEIVAYDREKQKILPFQTLSTRARKNVS--LSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDS 577 (768)
Q Consensus 500 ~~~~~~~~~ILDGElVa~d~~~g~~~pFq~L~~R~rk~~~--~~~~~~~v~~~vFDiLylnG~~L~~~Pl~ERr~lL~~l 577 (768)
.+. ..++|||||+|++|+. ...|||.||+|.+.+.. ......+++|++|||||+||++|+++||.|||++|+++
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 3689999999999975 46899999999865532 23457899999999999999999999999999999999
Q ss_pred hccCCCeEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEeeCCCCCCccCCCCCCCeEEEccccccccCCcccEEEEEEE
Q 004212 578 FEEEPGFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLKKDYIESIGDSLDLVPIAAF 657 (768)
Q Consensus 578 ~~~~~~~i~l~~~~~~~~~eei~~~~~~ai~~G~EGlVlK~~~~dS~Y~pGkRs~~WlKvK~dy~~~~~dtlDlvVIG~~ 657 (768)
+... +.+.+++.+...+.++++.+|+.+++.|+||||+|++ ||+|++|+|+..|+|+|++ +++|+||+|++
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 9874 4555666666688999999999999999999999999 9999999999999999997 59999999999
Q ss_pred cCCCCCCCccceEEEEEeeCCCCeEEEEEEeccCCCHHHHHHHHHHhccccCCCCCCCccCCCCCCCc-EEecCcceEEE
Q 004212 658 HGRGKRTGVYGAFLLACYDSNNEEFQSICKIGTGFSEAMLEERSSSLRSKVIPKPRPYYRFADTISPD-VWFEPTERPET 736 (768)
Q Consensus 658 ~G~Gkr~g~~gsfLlg~~d~~~g~l~~vgkVGTGfsd~~l~~L~~~l~~~~~~~p~~~~~~~~~~~pd-vWv~P~~V~EV 736 (768)
+|+|+|+ .+|+|+||+|++++|.|+++|+|||||+++++++|+++++++......+. .+. +|++|.+|+||
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 89999999999987889999999999999999999999999987752111 111 66777999999
Q ss_pred EecceeecCCCccccc
Q 004212 737 SNSPASIVYDSQITCL 752 (768)
Q Consensus 737 ~~aeit~Sp~~~~~~~ 752 (768)
+|++||.|+.| +|+
T Consensus 398 ~~~~~t~~~~~--r~~ 411 (444)
T COG1793 398 RFAEITKSGRL--RHA 411 (444)
T ss_pred EEeecccCCce--ecc
Confidence 99999999998 665
No 9
>PHA02587 30 DNA ligase; Provisional
Probab=100.00 E-value=5.5e-62 Score=553.27 Aligned_cols=420 Identities=17% Similarity=0.214 Sum_probs=325.0
Q ss_pred HHHHHHHHHhhhchHHHHHHHHHHHHhhhcCCCCchHHHHHHHhCccCCCc-cccccCCCHHHHHHHHHHHhCCCHHHHH
Q 004212 196 LSLVFDMISNETGRILITDIVCNMLRTVMETTPEDLVPVVYLAANKIAPAH-EGLELGIGDASIIKALAEACGRTESHVK 274 (768)
Q Consensus 196 la~l~e~I~~tssr~~k~~iL~~~fr~~i~~~p~dl~~~vyl~~~~l~P~~-e~~elGIg~~~L~Kal~~a~G~s~~~ik 274 (768)
+-+++++|++|.|+++|.+||.+.- .++++..||-++ | ....|||+...
T Consensus 2 i~~il~~~~~~~~~~~k~~il~~~~-------~n~~l~~~~~~~------~~~~~~~~~~~~~----------------- 51 (488)
T PHA02587 2 ILDILNELASTDSTKEKEAILKENK-------DNELLKEVFRLT------YNKQINFGIKKWP----------------- 51 (488)
T ss_pred hHHHHHHHHhccCcchHHHHHHhcc-------cChHHHHHHHHH------hCcceeEeeeEcC-----------------
Confidence 4578999999999999999998542 344444444333 3 24577766311
Q ss_pred HHHhhhCChHHHHhhhcccCCccCCCCCCcHHHHHH-HHHHHHHHhCCChHHHHHHHHHHHHHhcCCChHHHHHHHHhhc
Q 004212 275 KQYQEMGDLGLVAKASRSSQSMMRKPDPLTITKVFD-TFRLIAKEAGKDSQEKKKNRIKALLVAATDCEPQYLIRLLQSK 353 (768)
Q Consensus 275 ~~y~~~GDlg~vA~~~r~~q~~l~~~~~LTI~eV~~-~L~kIA~~~G~~Sq~~K~~~l~~Ll~~~t~~E~k~lvRiIlkd 353 (768)
+.|- .-....++++.++.+ .+.++|+..-.+. ..++.|..++.+|++.|++||+|+|+++
T Consensus 52 ----~~~~-------------~~~~~~~~~~~~~~~~~~~~l~~r~~~~~--~~~~~l~~ll~~~~~~e~~~l~rli~~~ 112 (488)
T PHA02587 52 ----KPGH-------------VEGSDGMLSLEDLLDFLEFDLATRKLTGN--AAIEELAQILSSMNEDDAEVLRRVLMRD 112 (488)
T ss_pred ----CCcc-------------ccCCCCceeHHHHHHHHHHHHHHhhcchh--HHHHHHHHHHHhCCHHHHHHHHHHHhcc
Confidence 1010 001235678888444 5567787665443 3478999999999999999999999999
Q ss_pred ccCcccHHHHHHHHHhhhccCCCCCCCCCCCcchHHHHHHHHHHHhhcCCchhhhhhhhhhcCccccCCccccCCCCCCc
Q 004212 354 LRIGLAEQTLLAALGQAAVYNEQHSKPPPNIQSPLEEAAKIVKQVFSVLPVYEKIVPALLTDGVWNLSNTCSFTPGIPIG 433 (768)
Q Consensus 354 LRiGi~e~tVl~ala~a~~~~~~~~~~~~~l~~~l~~a~~~vk~~y~~~pd~~~v~~~ll~~g~~~l~~~~~i~~g~Pvk 433 (768)
||||+++++|++||+ .++|++
T Consensus 113 lriGvs~~~i~~~~~-----------------------------------------------------------~~~P~~ 133 (488)
T PHA02587 113 LECGASEKIANKVWK-----------------------------------------------------------GLIPEQ 133 (488)
T ss_pred cCCCccHHHHHHHhc-----------------------------------------------------------CCccCC
Confidence 999999999997641 047888
Q ss_pred c-ccccccCChHHHHhhcCCCceEEeeecceEeEEEEEecCCeEEEEcCCcccCCCCCchHHHHHHhhcC---CCCCCeE
Q 004212 434 P-MLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAVSRLKK---PSVRSFV 509 (768)
Q Consensus 434 P-MLA~~~~~i~~il~k~~g~~~~~E~KyDG~R~qih~~~~g~V~lfSR~g~d~T~~fPel~~~l~~~~~---~~~~~~I 509 (768)
| |||++... +++++.-+.+|++|+||||+|||+|+. +|+|++|||||++++. ||++.+.+.++.. ....++|
T Consensus 134 p~mLA~~~~~--~~~~~~~~~~~~~E~K~DG~R~q~h~~-~~~v~l~SR~g~~~~~-~p~i~~~l~~~~~~~~~~~~~~V 209 (488)
T PHA02587 134 PQMLASSFSE--KLIKKNIKFPAYAQLKADGARCFADID-ADGIEIRSRNGNEYLG-LDLLKEELKKMTAEARQRPGGVV 209 (488)
T ss_pred CCccCCCCCH--HHHHhhccCcEEEEEccCceEEEEEEe-CCEEEEEecCCccccC-ChhHHHHHHHHhhhhcccCCcEE
Confidence 7 99998543 456552234899999999999999995 7899999999999975 8999887766543 1136899
Q ss_pred EEEEEEEEecCCCcccCh-------------hhHHhhhhccCCc---------cccccceEEEEeeeeecC---CccccC
Q 004212 510 LDCEIVAYDREKQKILPF-------------QTLSTRARKNVSL---------SDIKVDVCIYAFDILYRN---GQPLLQ 564 (768)
Q Consensus 510 LDGElVa~d~~~g~~~pF-------------q~L~~R~rk~~~~---------~~~~~~v~~~vFDiLyln---G~~L~~ 564 (768)
||||+|+||.+++.+.+| |.+++|.+++... .....+++|+|||||++| |.++++
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 999999998766554454 7888887544211 123578999999999653 445788
Q ss_pred CcHHHHHHHHHHhhcc-CCCeEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEeeCCCCCCccCCCCCCCeEEEcccccc
Q 004212 565 EQLRVRREHLYDSFEE-EPGFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLKKDYIE 643 (768)
Q Consensus 565 ~Pl~ERr~lL~~l~~~-~~~~i~l~~~~~~~~~eei~~~~~~ai~~G~EGlVlK~~~~dS~Y~pGkRs~~WlKvK~dy~~ 643 (768)
.||.+||++|++++.. ..+++++++...+++.+++.++|+++++.|+||||+|++ +|+|++| |+.+|+|+|+.
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 346889999888899999999999999999999999999 9999998 78899999986
Q ss_pred ccCCcccEEEEEEEcCCCCCCCccceEEEEEeeCCCCeEEEEEEeccCCCHHHHHHHHHHhccccCCCCCCCccCCCCCC
Q 004212 644 SIGDSLDLVPIAAFHGRGKRTGVYGAFLLACYDSNNEEFQSICKIGTGFSEAMLEERSSSLRSKVIPKPRPYYRFADTIS 723 (768)
Q Consensus 644 ~~~dtlDlvVIG~~~G~Gkr~g~~gsfLlg~~d~~~g~l~~vgkVGTGfsd~~l~~L~~~l~~~~~~~p~~~~~~~~~~~ 723 (768)
+++|++|||+++|. +++|.+|+|+|++++ |. .+|+|||||||++++++.+... . .|+....+..+
T Consensus 364 ---~~~dlvVvG~~~~~-k~~~~~gs~ll~~~~---g~--~~~~vgsGftd~~~~~l~~~~~----~--~p~~~~~~~~r 428 (488)
T PHA02587 364 ---IDIDLEIVGVYEHK-KDPNKVGGFTLESAC---GK--ITVNTGSGLTDTTHRKKDGKKV----V--IPLSERHELDR 428 (488)
T ss_pred ---CceEEEEEeEEeCC-CCCCceeEEEEEecC---Cc--EEEEECCCCChHHhhhhccccc----e--ecccccchhcc
Confidence 48999999999864 677899999998764 44 4699999999999999977653 1 22333334446
Q ss_pred CcEEecCc----ceEEEEecceeecCCCc
Q 004212 724 PDVWFEPT----ERPETSNSPASIVYDSQ 748 (768)
Q Consensus 724 pdvWv~P~----~V~EV~~aeit~Sp~~~ 748 (768)
+.+|.+|. .||||+|++||.||+|+
T Consensus 429 ~~~~~~~~~~~~~V~EV~~~~it~S~~~~ 457 (488)
T PHA02587 429 EELMANKGKYIGKIAECECNGLQRSKGRK 457 (488)
T ss_pred hhhhhCcccccceEEEEEeceEEeCCCCC
Confidence 78898764 79999999999999993
No 10
>PRK08224 ligC ATP-dependent DNA ligase; Reviewed
Probab=100.00 E-value=3.5e-57 Score=494.31 Aligned_cols=288 Identities=24% Similarity=0.323 Sum_probs=243.4
Q ss_pred ccCCCCCCccccccccCChHHHHhhcCCCceEEeeecceEeEEEEEecCCeEEEEcCCcccCCCCCchHHHHHHhhcCCC
Q 004212 425 SFTPGIPIGPMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAVSRLKKPS 504 (768)
Q Consensus 425 ~i~~g~PvkPMLA~~~~~i~~il~k~~g~~~~~E~KyDG~R~qih~~~~g~V~lfSR~g~d~T~~fPel~~~l~~~~~~~ 504 (768)
.+.++.|++||||+....+ +.+.+|++|+||||+|||+|++ +|+|++|||||+++|.+||+|++++...+.
T Consensus 2 ~~~~~~~i~PMLA~~~~~~------~~~~~w~~E~K~DG~R~~~~~~-~~~v~l~SRng~d~t~~fPel~~~~~~~~~-- 72 (350)
T PRK08224 2 DLPVMPPVEPMLAKSVDAI------PPGDGWSYEPKWDGFRCLVFRD-GDEVELGSRNGKPLTRYFPELVAALRAELP-- 72 (350)
T ss_pred CCCCCCCcCCccCCccCCC------CCCCcEEEEEeECeeEEEEEEE-CCEEEEEeCCCCCchhhhHHHHHHHHhhCC--
Confidence 3578999999999987654 2445799999999999999995 789999999999999999999988876543
Q ss_pred CCCeEEEEEEEEEecCCCcccChhhHHhhhhccCC---ccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccC
Q 004212 505 VRSFVLDCEIVAYDREKQKILPFQTLSTRARKNVS---LSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEE 581 (768)
Q Consensus 505 ~~~~ILDGElVa~d~~~g~~~pFq~L~~R~rk~~~---~~~~~~~v~~~vFDiLylnG~~L~~~Pl~ERr~lL~~l~~~~ 581 (768)
.++|||||||++|. +. .+|+.||+|.+.... ......+++|+||||||+||++|+++||.|||++|++++..
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 68999999999983 22 899999998753311 11235789999999999999999999999999999999965
Q ss_pred CCeEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEeeCCCCCCccCCCCCCCeEEEccccccccCCcccEEEEEEEcCCC
Q 004212 582 PGFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLKKDYIESIGDSLDLVPIAAFHGRG 661 (768)
Q Consensus 582 ~~~i~l~~~~~~~~~eei~~~~~~ai~~G~EGlVlK~~~~dS~Y~pGkRs~~WlKvK~dy~~~~~dtlDlvVIG~~~G~G 661 (768)
.+.+++++. ..+.++++++|++++++|+||||+|++ ||+|++|+|+ |+|+|+. +++|+||+|+++|+|
T Consensus 148 ~~~i~~~~~--~~~~~~~~~~~~~a~~~G~EGIV~Kr~--dS~Y~~Grr~--WlKiK~~------~~~d~vI~G~~~g~~ 215 (350)
T PRK08224 148 SGPVHLTPA--TTDPATARRWFEEFEGAGLDGVIAKPL--DGPYQPGKRA--MFKVKHE------RTADCVVAGYRYHKS 215 (350)
T ss_pred CCcEEEecc--cCCHHHHHHHHHHHHhCCCcEEEEeCC--CCCcCCCCcC--EEEEccC------CcEEEEEEEEEcCCC
Confidence 345777764 346788999999999999999999999 9999999987 9999996 489999999999987
Q ss_pred CCCCccceEEEEEeeCCCCeEEEEEEeccCCCHHHHHHHHHHhccccCCCC--C----CCccCC-------CCCCCcEE-
Q 004212 662 KRTGVYGAFLLACYDSNNEEFQSICKIGTGFSEAMLEERSSSLRSKVIPKP--R----PYYRFA-------DTISPDVW- 727 (768)
Q Consensus 662 kr~g~~gsfLlg~~d~~~g~l~~vgkVGTGfsd~~l~~L~~~l~~~~~~~p--~----~~~~~~-------~~~~pdvW- 727 (768)
+ |.+|+|+||+||+ +|+|++||+|| |||++++++|++.|+++..+.+ | +|.... ...+..+|
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 5 7899999999975 47899999985 9999999999999999887654 2 342211 11236789
Q ss_pred -ecCcceEEEEeccee
Q 004212 728 -FEPTERPETSNSPAS 742 (768)
Q Consensus 728 -v~P~~V~EV~~aeit 742 (768)
|+|.+|+||+|.+||
T Consensus 292 ~v~P~lv~eV~~~~~t 307 (350)
T PRK08224 292 PLRPERVVEVRYDHME 307 (350)
T ss_pred eeeEEEEEEEecCccc
Confidence 999999999999999
No 11
>PRK09632 ATP-dependent DNA ligase; Reviewed
Probab=100.00 E-value=4.5e-57 Score=528.60 Aligned_cols=284 Identities=26% Similarity=0.374 Sum_probs=246.5
Q ss_pred ccCCCCCCccccccccCChHHHHhhcCCCceEEeeecceEeEEEEEecCCeEEEEcCCcccCCCCCchHHHHHHhhcCCC
Q 004212 425 SFTPGIPIGPMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAVSRLKKPS 504 (768)
Q Consensus 425 ~i~~g~PvkPMLA~~~~~i~~il~k~~g~~~~~E~KyDG~R~qih~~~~g~V~lfSR~g~d~T~~fPel~~~l~~~~~~~ 504 (768)
...++.|++||||+..... .+.+.+|++|+||||+|||+|+. +|+|++|||||+++|.+||+|.+.+.. +.
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 3578999999999976532 24667899999999999999995 789999999999999999999885444 43
Q ss_pred CCCeEEEEEEEEEecCCCcccChhhHHhhhhccCCccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCCCe
Q 004212 505 VRSFVLDCEIVAYDREKQKILPFQTLSTRARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEPGF 584 (768)
Q Consensus 505 ~~~~ILDGElVa~d~~~g~~~pFq~L~~R~rk~~~~~~~~~~v~~~vFDiLylnG~~L~~~Pl~ERr~lL~~l~~~~~~~ 584 (768)
..++|||||||++|.. |. .+|+.||+|.+ ..+++|+||||||+||++|+++||.+||++|++++.. .+.
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 2689999999999964 43 69999999842 4689999999999999999999999999999999974 457
Q ss_pred EEEEeEEecCCHHHHHHHHHHHHHcCCceeEEeeCCCCCCccCCCCCCCeEEEccccccccCCcccEEEEEEEcCCCCCC
Q 004212 585 FQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLKKDYIESIGDSLDLVPIAAFHGRGKRT 664 (768)
Q Consensus 585 i~l~~~~~~~~~eei~~~~~~ai~~G~EGlVlK~~~~dS~Y~pGkRs~~WlKvK~dy~~~~~dtlDlvVIG~~~G~Gkr~ 664 (768)
+++++.... +++++|+.++++|+||||+|++ +|+|++|+||.+|+|+|+++ ++|+||+|+++|+|+|+
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 777776543 4788999999999999999999 99999999999999999986 89999999999999999
Q ss_pred CccceEEEEEeeCCCCeEEEEEEeccCCCHHHHHHHHHHhccccCCCCCCCcc-C-CCCCCCcEEecCcceEEEEeccee
Q 004212 665 GVYGAFLLACYDSNNEEFQSICKIGTGFSEAMLEERSSSLRSKVIPKPRPYYR-F-ADTISPDVWFEPTERPETSNSPAS 742 (768)
Q Consensus 665 g~~gsfLlg~~d~~~g~l~~vgkVGTGfsd~~l~~L~~~l~~~~~~~p~~~~~-~-~~~~~pdvWv~P~~V~EV~~aeit 742 (768)
|.+|+|+||+||+ +.|++||+||||||++++++|.+.|+++..+.+ ||.. . ....++++||+|.+||||+|++||
T Consensus 662 g~~gsLLlGv~d~--~~L~yvGkVGTGftd~~l~~L~~~L~~l~~~~~-Pf~~~~~~~~~~~~~WV~P~LV~EV~f~e~T 738 (764)
T PRK09632 662 SGIGSLLLGIPDP--GGLRYVGRVGTGFTERELASLKETLAPLHRDTS-PFDADLPAADAKGATWVRPELVGEVRYSEWT 738 (764)
T ss_pred CceeeEEEEEEcC--CeeEEEEEEeCCCCHHHHHHHHHHHHhhccCCC-CcccccccccCCCcEEEeccEEEEEEEeecc
Confidence 9999999999985 569999999999999999999999999987765 4421 2 123468999999999999999998
Q ss_pred e
Q 004212 743 I 743 (768)
Q Consensus 743 ~ 743 (768)
.
T Consensus 739 ~ 739 (764)
T PRK09632 739 P 739 (764)
T ss_pred C
Confidence 4
No 12
>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=9.1e-57 Score=482.74 Aligned_cols=267 Identities=29% Similarity=0.387 Sum_probs=230.9
Q ss_pred cCCCceEEeeecceEeEEEEEecCCeEEEEcCCcccCCCCCchHHHHHHhhcCCCCCCeEEEEEEEEEecCCCcccChhh
Q 004212 450 FQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAVSRLKKPSVRSFVLDCEIVAYDREKQKILPFQT 529 (768)
Q Consensus 450 ~~g~~~~~E~KyDG~R~qih~~~~g~V~lfSR~g~d~T~~fPel~~~l~~~~~~~~~~~ILDGElVa~d~~~g~~~pFq~ 529 (768)
+.|.+|++|+||||+|||+|+. +|+|++|||||+++|.+||++.+.+... ...++|||||||++|.. |. .+|+.
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 4677899999999999999995 7899999999999999999998765443 23689999999999964 43 69999
Q ss_pred HHhhhhccCCccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCCCeEEEEeEEecCCHHHHHHHHHHHHHc
Q 004212 530 LSTRARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAAVDA 609 (768)
Q Consensus 530 L~~R~rk~~~~~~~~~~v~~~vFDiLylnG~~L~~~Pl~ERr~lL~~l~~~~~~~i~l~~~~~~~~~eei~~~~~~ai~~ 609 (768)
|++|.+... ..+++|++||||++||++++++||.+||++|++++.+.++.+.+... ...+.+++.++|++++++
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 999976432 37899999999999999999999999999999999875554433322 355678999999999999
Q ss_pred CCceeEEeeCCCCCCccCCCCCCCeEEEccccccccCCcccEEEEEEEcCCCCCCCccceEEEEEeeCCCCeEEEEEEec
Q 004212 610 SCEGLIIKTMDRDATYEPSKRSLNWLKLKKDYIESIGDSLDLVPIAAFHGRGKRTGVYGAFLLACYDSNNEEFQSICKIG 689 (768)
Q Consensus 610 G~EGlVlK~~~~dS~Y~pGkRs~~WlKvK~dy~~~~~dtlDlvVIG~~~G~Gkr~g~~gsfLlg~~d~~~g~l~~vgkVG 689 (768)
|+||||+|++ ||+|+||+ +.+|+|+|+++ +.|++|+|++.|+|++ |.+|+|+||+||+ +.|++||+||
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 8999999999999988 8899999999975 6799999999
Q ss_pred cCCCHHHHHHHHHHhccccCCCCCCCccCCCCCCCcEEecCcceEEEEecceee
Q 004212 690 TGFSEAMLEERSSSLRSKVIPKPRPYYRFADTISPDVWFEPTERPETSNSPASI 743 (768)
Q Consensus 690 TGfsd~~l~~L~~~l~~~~~~~p~~~~~~~~~~~pdvWv~P~~V~EV~~aeit~ 743 (768)
||||++++++|++.+.+++++..+++ .....+++||+|.+||||+|.+||.
T Consensus 225 sG~s~~~~~~l~~~l~~~~~~~~~~~---~~~~~~~~wv~P~lV~eV~~~~~t~ 275 (298)
T TIGR02779 225 TGFSEAELATIKERLKPLESKPDKPG---AREKRGVHWVKPELVAEVEFAGWTR 275 (298)
T ss_pred CCCCHHHHHHHHHHHHhhccCcCCCC---cccCCCCEEeCCeEEEEEEecccCC
Confidence 99999999999999999876652222 2233689999999999999999985
No 13
>PRK05972 ligD ATP-dependent DNA ligase; Reviewed
Probab=100.00 E-value=9e-55 Score=513.54 Aligned_cols=282 Identities=26% Similarity=0.354 Sum_probs=243.1
Q ss_pred CCCccccccccCChHHHHhhcCCCceEEeeecceEeEEEEEecCCeEEEEcCCcccCCCCCchHHHHHHhhcCCCCCCeE
Q 004212 430 IPIGPMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAVSRLKKPSVRSFV 509 (768)
Q Consensus 430 ~PvkPMLA~~~~~i~~il~k~~g~~~~~E~KyDG~R~qih~~~~g~V~lfSR~g~d~T~~fPel~~~l~~~~~~~~~~~I 509 (768)
..++||||+....+ +.+.+|++|+||||+|||+|+. +|+|++|||||+++|.+||+|++++..+ ...++|
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 DFLAPQLATLVDRP------PSGDGWIYEIKFDGYRILARIE-GGEVRLFTRNGLDWTAKLPALAKAAAAL---GLPDAW 301 (860)
T ss_pred cccCcccCccCCCC------CCcCceEEEeeeCcEEEEEEEE-CCEEEEEeCCCCccccccHHHHHHHHhc---CCCcee
Confidence 35899999987764 3456899999999999999995 7899999999999999999999887764 346899
Q ss_pred EEEEEEEEecCCCcccChhhHHhhhhccCCccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCC-CeEEEE
Q 004212 510 LDCEIVAYDREKQKILPFQTLSTRARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEP-GFFQFA 588 (768)
Q Consensus 510 LDGElVa~d~~~g~~~pFq~L~~R~rk~~~~~~~~~~v~~~vFDiLylnG~~L~~~Pl~ERr~lL~~l~~~~~-~~i~l~ 588 (768)
||||||++|.. |. .+|+.||+|.+... ..+++|++|||||+||++|+++||.+||++|++++.+.+ +.++++
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 44 59999999875431 368999999999999999999999999999999997653 478888
Q ss_pred eEEecCCHHHHHHHHHHHHHcCCceeEEeeCCCCCCccCCCCCCCeEEEccccccccCCcccEEEEEEEcCCCCCCCccc
Q 004212 589 TTLTSIDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLKKDYIESIGDSLDLVPIAAFHGRGKRTGVYG 668 (768)
Q Consensus 589 ~~~~~~~~eei~~~~~~ai~~G~EGlVlK~~~~dS~Y~pGkRs~~WlKvK~dy~~~~~dtlDlvVIG~~~G~Gkr~g~~g 668 (768)
++... +++++|+.++++|+||||+|++ ||+|++| |+.+|+|+|+.+ +.|+||+|++.|.|+|.| +|
T Consensus 375 ~~~~~----~g~~ll~~a~~~GlEGIVaKr~--dS~Y~~G-Rs~~WlKiK~~~------~~E~VIgGy~~~~Gkr~g-~g 440 (860)
T PRK05972 375 EHFDA----GGDAVLASACRLGLEGVIGKRA--DSPYVSG-RSEDWIKLKCRA------RQEFVIGGYTDPKGSRSG-FG 440 (860)
T ss_pred ceecc----hHHHHHHHHHHcCCceEEEeCC--CCCCCCC-CCCCcEEEecCC------CceEEEEEEeCCCCcccc-ce
Confidence 76642 5788999999999999999999 9999987 899999999975 678888888888999987 99
Q ss_pred eEEEEEeeCCCCeEEEEEEeccCCCHHHHHHHHHHhccccCCCCCCCccCC--CCCCCcEEecCcceEEEEecceeecC
Q 004212 669 AFLLACYDSNNEEFQSICKIGTGFSEAMLEERSSSLRSKVIPKPRPYYRFA--DTISPDVWFEPTERPETSNSPASIVY 745 (768)
Q Consensus 669 sfLlg~~d~~~g~l~~vgkVGTGfsd~~l~~L~~~l~~~~~~~p~~~~~~~--~~~~pdvWv~P~~V~EV~~aeit~Sp 745 (768)
+|+||+||+ ++|++||+||||||++++++|.+.|+++..+.+ ||.... ....+++||+|.+||||+|++||.+.
T Consensus 441 SLLlGvyd~--~~L~yvGkVGTGfsd~~l~~L~~~L~~l~~~~~-Pf~~~~~~~~~~~~~WV~P~LV~EV~f~e~T~~g 516 (860)
T PRK05972 441 SLLLGVHDD--DHLRYAGRVGTGFGAATLKTLLPRLKALATDKS-PFAGKPAPRKARGVHWVKPELVAEVEFAGWTRDG 516 (860)
T ss_pred eEEEEEecC--CEEEEEEEECCCCCHHHHHHHHHHHHhhccCCC-CccccCccccCCCCEEEccCEEEEEEEeeccCCC
Confidence 999999985 699999999999999999999999999988765 453321 12245899999999999999999764
No 14
>PRK09633 ligD ATP-dependent DNA ligase; Reviewed
Probab=100.00 E-value=2.6e-53 Score=490.64 Aligned_cols=270 Identities=19% Similarity=0.253 Sum_probs=227.7
Q ss_pred CccccccccCChHHHHhhcCCCceEEeeecceEeEEEEEecCCeEEEEcCCcccCCCCCchHHHHHHhhcCC--CCCCeE
Q 004212 432 IGPMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAVSRLKKP--SVRSFV 509 (768)
Q Consensus 432 vkPMLA~~~~~i~~il~k~~g~~~~~E~KyDG~R~qih~~~~g~V~lfSR~g~d~T~~fPel~~~l~~~~~~--~~~~~I 509 (768)
++||||..+..+ +.|.+|++|+||||+|||+|+. +|+|++|||||+++|.+||+|++++..+... ...+||
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 579999887764 3577899999999999999994 7899999999999999999999877665421 124799
Q ss_pred EEEEEEEEecCCCcccChhhHHhhhhccCC----ccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCC---
Q 004212 510 LDCEIVAYDREKQKILPFQTLSTRARKNVS----LSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEP--- 582 (768)
Q Consensus 510 LDGElVa~d~~~g~~~pFq~L~~R~rk~~~----~~~~~~~v~~~vFDiLylnG~~L~~~Pl~ERr~lL~~l~~~~~--- 582 (768)
||||||++|.. | ..+|+.||+|.+.... ......+++|+||||||+||++|++.||.+||++|++++.+.+
T Consensus 74 LDGEiVvld~~-g-~~~F~~Lq~R~~~~~~~~i~~~~~~~pv~~~vFDlL~lnG~dL~~~PL~eRr~~L~~ll~~~~~~~ 151 (610)
T PRK09633 74 LDGELVCLVNP-Y-RSDFEHVQQRGRLKNTEVIAKSANARPCQLLAFDLLELKGESLTSLPYLERKKQLDKLMKAAKLPA 151 (610)
T ss_pred eeeEEEEecCC-C-CCCHHHHHhhhhccccchhhhhhcccceEEEEEeecccCCcccccCCHHHHHHHHHHHhhhccccc
Confidence 99999999854 3 3699999999653211 1123578999999999999999999999999999999997532
Q ss_pred -------CeEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEeeCCCCCCccCCCCCCCeEEEccccccccCCcccEEEEE
Q 004212 583 -------GFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLKKDYIESIGDSLDLVPIA 655 (768)
Q Consensus 583 -------~~i~l~~~~~~~~~eei~~~~~~ai~~G~EGlVlK~~~~dS~Y~pGkRs~~WlKvK~dy~~~~~dtlDlvVIG 655 (768)
..+++ +.+.++++++|++++++|+||||+|++ +|+|++|+||.+|+|+|+. +++|+||+|
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 13444 345678999999999999999999999 9999999999999999995 489999999
Q ss_pred EEcCCCCCCCccceEEEEEeeCCCCeEEEEEEeccCCCHHHHHHHHHHhccccCCCCCCCccCCCCCCCcEEecCcceEE
Q 004212 656 AFHGRGKRTGVYGAFLLACYDSNNEEFQSICKIGTGFSEAMLEERSSSLRSKVIPKPRPYYRFADTISPDVWFEPTERPE 735 (768)
Q Consensus 656 ~~~G~Gkr~g~~gsfLlg~~d~~~g~l~~vgkVGTGfsd~~l~~L~~~l~~~~~~~p~~~~~~~~~~~pdvWv~P~~V~E 735 (768)
+..|. |+|++|+|+ +|+|++||+||||||++++++|++.|+++.+... .+.+||+|.+|||
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 468899995 4899999999999999999999999998866532 4689999999999
Q ss_pred EEeccee
Q 004212 736 TSNSPAS 742 (768)
Q Consensus 736 V~~aeit 742 (768)
|+|++||
T Consensus 280 V~~~e~t 286 (610)
T PRK09633 280 VACITFD 286 (610)
T ss_pred EEEeecC
Confidence 9999996
No 15
>PRK07636 ligB ATP-dependent DNA ligase; Reviewed
Probab=100.00 E-value=1.9e-51 Score=436.62 Aligned_cols=260 Identities=23% Similarity=0.303 Sum_probs=218.9
Q ss_pred CccccccccCChHHHHhhcCCCceEEeeecceEeEEEEEecCCeEEEEcCCcccCCCCCchHHHHHHhhcCCCCCCeEEE
Q 004212 432 IGPMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAVSRLKKPSVRSFVLD 511 (768)
Q Consensus 432 vkPMLA~~~~~i~~il~k~~g~~~~~E~KyDG~R~qih~~~~g~V~lfSR~g~d~T~~fPel~~~l~~~~~~~~~~~ILD 511 (768)
++||||...+.. +++.+|++|+||||+|||+|+. +|+|++|||||+++|..||++.+.. +. +++|||
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 689999876643 5667899999999999999985 7899999999999999999998642 32 479999
Q ss_pred EEEEEEecCCCcccChhhHHhhhhccCCccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCCCeEEEEeEE
Q 004212 512 CEIVAYDREKQKILPFQTLSTRARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEPGFFQFATTL 591 (768)
Q Consensus 512 GElVa~d~~~g~~~pFq~L~~R~rk~~~~~~~~~~v~~~vFDiLylnG~~L~~~Pl~ERr~lL~~l~~~~~~~i~l~~~~ 591 (768)
||||++|.. |. .+|+.|++|.+.... ....+++|+||||||+||++++++||.|||++|++++.+. ..+++++..
T Consensus 70 GElv~~d~~-g~-~~F~~l~~r~~~~~~--~~~~~~~~~vFDlL~~~g~~l~~~pl~eRr~~L~~~~~~~-~~~~~~~~~ 144 (275)
T PRK07636 70 GELIVLGST-GA-PDFEAVMERFQSKKS--TKIHPVVFCVFDVLYINGVSLTALPLSERKEILASLLLPH-PNVKIIEGI 144 (275)
T ss_pred eEEEEECCC-CC-CCHHHHHHHhccccc--cccCceEEEEEEeEEECceehhhCCHHHHHHHHHHhcCCC-CCEEEcccc
Confidence 999999964 44 589999998754311 2257899999999999999999999999999999999764 356666653
Q ss_pred ecCCHHHHHHHHHHHHHcCCceeEEeeCCCCCCccCCCCCCCeEEEccccccccCCcccEEEEEEEcCCCCCCCccceEE
Q 004212 592 TSIDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLKKDYIESIGDSLDLVPIAAFHGRGKRTGVYGAFL 671 (768)
Q Consensus 592 ~~~~~eei~~~~~~ai~~G~EGlVlK~~~~dS~Y~pGkRs~~WlKvK~dy~~~~~dtlDlvVIG~~~G~Gkr~g~~gsfL 671 (768)
. ++++++|++++++|+||||+|++ ||+|.+|+||.+|+|+|+. +++|+||+|+..+ .+|.+
T Consensus 145 ~----~~~~~~~~~~~~~g~EGiV~K~~--ds~Y~~g~Rs~~WlKiK~~------~~~e~vV~G~~~~------~~g~l- 205 (275)
T PRK07636 145 E----GHGTAYFELVEERELEGIVIKKA--NSPYEINKRSDNWLKVINY------QYTDVLITGYRKE------EFGLL- 205 (275)
T ss_pred c----ccHHHHHHHHHHcCCcEEEEeCC--CCCCCCCCCCCCeEEEecC------CeEEEEEEEEecC------CCcEE-
Confidence 2 46788999999999999999999 9999999999999999973 6899999988543 25655
Q ss_pred EEEeeCCCCeEEEEEEeccCCCHHHHHHHHHHhccccCCCCCCCccCCCCCCCcEEecCcceEEEEecceeec
Q 004212 672 LACYDSNNEEFQSICKIGTGFSEAMLEERSSSLRSKVIPKPRPYYRFADTISPDVWFEPTERPETSNSPASIV 744 (768)
Q Consensus 672 lg~~d~~~g~l~~vgkVGTGfsd~~l~~L~~~l~~~~~~~p~~~~~~~~~~~pdvWv~P~~V~EV~~aeit~S 744 (768)
||+|| |. ++|+||| |+++++++|.+.+.++.... .++++|++|.+|+||+|+|||.+
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 8899999 99999999999997765432 25789999999999999999866
No 16
>cd07900 Adenylation_DNA_ligase_I_Euk Adenylation domain of eukaryotic DNA Ligase I. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. Some organisms express a variety of different ligases which appear to be targeted to specific functions. There are three classes of ATP-dependent DNA ligases in eukaryotic cells (I, III and IV). DNA ligase I is required for the ligation of Okazaki fragments during lagging-strand DNA synthesis and for base excision repair (BER). DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains. The adenylation and C-terminal oligonucleotide/oligo
Probab=100.00 E-value=1.5e-51 Score=424.34 Aligned_cols=217 Identities=67% Similarity=1.102 Sum_probs=199.6
Q ss_pred ccccCCCCCCccccccccCChHHHHhhcCCCceEEeeecceEeEEEEEecCCeEEEEcCCcccCCCCCchHHHHHHhhcC
Q 004212 423 TCSFTPGIPIGPMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAVSRLKK 502 (768)
Q Consensus 423 ~~~i~~g~PvkPMLA~~~~~i~~il~k~~g~~~~~E~KyDG~R~qih~~~~g~V~lfSR~g~d~T~~fPel~~~l~~~~~ 502 (768)
++.|++|+|++||||+++.+++++++++++.+|++|+||||+|||+|+..+|.|++|||||+++|.+||++++.+...+.
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 36789999999999999999988998898889999999999999999964589999999999999999999999888875
Q ss_pred CCCCCeEEEEEEEEEecCCCcccChhhHHhhhhccCCccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCC
Q 004212 503 PSVRSFVLDCEIVAYDREKQKILPFQTLSTRARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEP 582 (768)
Q Consensus 503 ~~~~~~ILDGElVa~d~~~g~~~pFq~L~~R~rk~~~~~~~~~~v~~~vFDiLylnG~~L~~~Pl~ERr~lL~~l~~~~~ 582 (768)
.+..+||||||||+||..+|..++|+.|++|.+++........+++|++|||||+||++|+++||.+||++|++++.+.+
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 45689999999999998778888999999998766543345689999999999999999999999999999999998877
Q ss_pred CeEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEeeCCCC--CCccCCCCCCCeEEEcccc
Q 004212 583 GFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTMDRD--ATYEPSKRSLNWLKLKKDY 641 (768)
Q Consensus 583 ~~i~l~~~~~~~~~eei~~~~~~ai~~G~EGlVlK~~~~d--S~Y~pGkRs~~WlKvK~dy 641 (768)
++++++++..+++.+++.++|++++++|+||||+|++ + |+|+||+||.+|+|+|+||
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 8899999999999999999999999999999999999 8 9999999999999999998
No 17
>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=7.3e-46 Score=382.85 Aligned_cols=216 Identities=31% Similarity=0.486 Sum_probs=189.0
Q ss_pred ccccCCCCCCccccccccCChHHHHhhcCCCceEEeeecceEeEEEEEecCCeEEEEcCCcccCCCCCchHHHHH-----
Q 004212 423 TCSFTPGIPIGPMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAV----- 497 (768)
Q Consensus 423 ~~~i~~g~PvkPMLA~~~~~i~~il~k~~g~~~~~E~KyDG~R~qih~~~~g~V~lfSR~g~d~T~~fPel~~~l----- 497 (768)
.+.+++|.||+||||++++...+.+..+.+.+|++|+||||+|||+|++ +|+|++|||||+++|..||++....
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 4678999999999999998876665677788999999999999999995 7899999999999999999987642
Q ss_pred -HhhcCCCCCCeEEEEEEEEEecCCCcccChhhHHhhhhccCCccccccceEEEEeeeeecCCccccCCcHHHHHHHHHH
Q 004212 498 -SRLKKPSVRSFVLDCEIVAYDREKQKILPFQTLSTRARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYD 576 (768)
Q Consensus 498 -~~~~~~~~~~~ILDGElVa~d~~~g~~~pFq~L~~R~rk~~~~~~~~~~v~~~vFDiLylnG~~L~~~Pl~ERr~lL~~ 576 (768)
...+.....++|||||||+||..++.+.+|+.|+++.+... ......+++|+|||||++||++++++||.+|+++|++
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 22232345799999999999987677899999987654211 0123578999999999999999999999999999999
Q ss_pred hhccCCCeEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEeeCCCCCCccCCCCCCCeEEEccccc
Q 004212 577 SFEEEPGFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLKKDYI 642 (768)
Q Consensus 577 l~~~~~~~i~l~~~~~~~~~eei~~~~~~ai~~G~EGlVlK~~~~dS~Y~pGkRs~~WlKvK~dy~ 642 (768)
++.+.++.+++++...+++.+++.++|+.++++|+||||+|++ +|+|++|+|+.+|+|+|++|+
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 999999999999999999995
No 18
>cd07901 Adenylation_DNA_ligase_Arch_LigB Adenylation domain of archaeal and bacterial LigB-like DNA ligases. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. Bacterial DNA ligases are divided into two broad classes: NAD-dependent and ATP-dependent. All bacterial species have a NAD-dependent DNA ligase (LigA). Some bacterial genomes contain multiple genes for DNA ligases that are predicted to use ATP as their cofactor, including Mycobacterium tuberculosis LigB, LigC, and LigD. This group is composed of archaeal DNA ligases and bacterial proteins similar to Mycobacterium tuberculosis LigB. Members of this group contain adeny
Probab=100.00 E-value=1.2e-45 Score=377.02 Aligned_cols=205 Identities=38% Similarity=0.591 Sum_probs=181.8
Q ss_pred CCCCCccccccccCChHHHHhhcCCCceEEeeecceEeEEEEEecCCeEEEEcCCcccCCCCCchHHHHHHhhcCCCCCC
Q 004212 428 PGIPIGPMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAVSRLKKPSVRS 507 (768)
Q Consensus 428 ~g~PvkPMLA~~~~~i~~il~k~~g~~~~~E~KyDG~R~qih~~~~g~V~lfSR~g~d~T~~fPel~~~l~~~~~~~~~~ 507 (768)
||+|++||||++...+++++++. +.+|++|+||||+|||+|+. ++.|++|||||+++|..||++.+++...+. ..+
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 68999999999998887776654 56899999999999999995 779999999999999999999998887753 368
Q ss_pred eEEEEEEEEEecCCCcccChhhHHhhhhccCCcc--ccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCCCeE
Q 004212 508 FVLDCEIVAYDREKQKILPFQTLSTRARKNVSLS--DIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEPGFF 585 (768)
Q Consensus 508 ~ILDGElVa~d~~~g~~~pFq~L~~R~rk~~~~~--~~~~~v~~~vFDiLylnG~~L~~~Pl~ERr~lL~~l~~~~~~~i 585 (768)
||||||||++|+ +|.+.+|+.|++|.++..... ..+.+++|+|||||++||++++++||.+|+++|++++.+. +.+
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 677789999999965332211 1246899999999999999999999999999999999875 678
Q ss_pred EEEeEEecCCHHHHHHHHHHHHHcCCceeEEeeCCCCCCccCCCCCCCeEEEccc
Q 004212 586 QFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLKKD 640 (768)
Q Consensus 586 ~l~~~~~~~~~eei~~~~~~ai~~G~EGlVlK~~~~dS~Y~pGkRs~~WlKvK~d 640 (768)
++++...+.+.+++.++|++++++|+||||+|++ +|+|++|+|+.+|+|+|+|
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 8999888899999999999999999999999999 9999999999999999985
No 19
>cd07902 Adenylation_DNA_ligase_III Adenylation domain of DNA Ligase III. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three-step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. There are three classes of ATP-dependent DNA ligases in eukaryotic cells (I, III and IV). DNA ligase III is not found in lower eukaryotes and is present both in the nucleus and mitochondria. It has several isoforms; two splice forms, III-alpha and III-beta, differ in their carboxy-terminal sequences. DNA ligase III-beta is believed to play a role in homologous recombination during meiotic prophase. DNA ligase III-alpha interacts with X-ray Cross Complementing factor 1 (XRCC1) and functions in single nuc
Probab=100.00 E-value=1.8e-45 Score=377.57 Aligned_cols=208 Identities=31% Similarity=0.538 Sum_probs=184.9
Q ss_pred ccccCCCCCCccccccccCChHHHHhhcCCCceEEeeecceEeEEEEEecCCeEEEEcCCcccCCC-CCchHHHHHHhhc
Q 004212 423 TCSFTPGIPIGPMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTG-KFPDVVLAVSRLK 501 (768)
Q Consensus 423 ~~~i~~g~PvkPMLA~~~~~i~~il~k~~g~~~~~E~KyDG~R~qih~~~~g~V~lfSR~g~d~T~-~fPel~~~l~~~~ 501 (768)
.+.+++|.|++||||+++++++++++++. .+|++|+||||+|||+|++ +|+|++|||||+++|. .||++.+.+.+.+
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 46789999999999999988877776653 3699999999999999995 6899999999999996 6899888777766
Q ss_pred CCCCCCeEEEEEEEEEecCCCcccChhhHHhhhhccCCccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccC
Q 004212 502 KPSVRSFVLDCEIVAYDREKQKILPFQTLSTRARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEE 581 (768)
Q Consensus 502 ~~~~~~~ILDGElVa~d~~~g~~~pFq~L~~R~rk~~~~~~~~~~v~~~vFDiLylnG~~L~~~Pl~ERr~lL~~l~~~~ 581 (768)
.. ..+||||||||+||.++|++++|+.++.|.+... ...+++|++||||++||++++++||.+|+++|++++.+.
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 5799999999999987788889999988765321 235799999999999999999999999999999999887
Q ss_pred CCeEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEeeCCCCCCccCCCCCCCeEEEcccc
Q 004212 582 PGFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLKKDY 641 (768)
Q Consensus 582 ~~~i~l~~~~~~~~~eei~~~~~~ai~~G~EGlVlK~~~~dS~Y~pGkRs~~WlKvK~dy 641 (768)
++.+.+++...+.+.+++.++|+.++++|+||||+|++ +|+|++|+| +|+|+|+||
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 77889999888899999999999999999999999999 999999988 799999998
No 20
>PHA00454 ATP-dependent DNA ligase
Probab=100.00 E-value=7e-44 Score=385.71 Aligned_cols=271 Identities=18% Similarity=0.202 Sum_probs=215.7
Q ss_pred ccccccccCC--hHHHHhhcCCCceEEeeecceEeEEEEEecCCeEEEEcCCcccCCCCCchHHHHH------HhhcCC-
Q 004212 433 GPMLAKPTKG--VSEIVNKFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAV------SRLKKP- 503 (768)
Q Consensus 433 kPMLA~~~~~--i~~il~k~~g~~~~~E~KyDG~R~qih~~~~g~V~lfSR~g~d~T~~fPel~~~l------~~~~~~- 503 (768)
+||+|..... +++++++++ .|++|+||||+|||+|+.++++|++|||||++ ||+++... .+++..
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 5889987664 888998864 89999999999999999533359999999975 67766432 222221
Q ss_pred ---CCCCeEEEEEEEEEecCCCcccChhhHHhhhhccCC--ccccccceEEEEeeeeecC----Cccc---cCCcHHHHH
Q 004212 504 ---SVRSFVLDCEIVAYDREKQKILPFQTLSTRARKNVS--LSDIKVDVCIYAFDILYRN----GQPL---LQEQLRVRR 571 (768)
Q Consensus 504 ---~~~~~ILDGElVa~d~~~g~~~pFq~L~~R~rk~~~--~~~~~~~v~~~vFDiLyln----G~~L---~~~Pl~ERr 571 (768)
...++|||||+|+.+ .+|+.+++|.++... ......+++|+|||||++| |+++ ..+||.+||
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 014899999999974 579999999764421 1223578999999999999 5665 789999999
Q ss_pred HHHHHhhccCCC-eEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEeeCCCCCCccCCCCCCCeEEEccccccccCCccc
Q 004212 572 EHLYDSFEEEPG-FFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLKKDYIESIGDSLD 650 (768)
Q Consensus 572 ~lL~~l~~~~~~-~i~l~~~~~~~~~eei~~~~~~ai~~G~EGlVlK~~~~dS~Y~pGkRs~~WlKvK~dy~~~~~dtlD 650 (768)
++|++++...+. .++++++..+.+.+++.++|++++++|+||||+|++ +|+|++|+|+. |+|+|+.+ ++|
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 999999876543 488999999999999999999999999999999999 99999998875 88999974 899
Q ss_pred EEEEEEEcCCCCC--CCccceEEEEEeeCCCCeEEEEEEeccCCCHHHHHHHHHHhccccCCCCCCCccCCCCCCCcEEe
Q 004212 651 LVPIAAFHGRGKR--TGVYGAFLLACYDSNNEEFQSICKIGTGFSEAMLEERSSSLRSKVIPKPRPYYRFADTISPDVWF 728 (768)
Q Consensus 651 lvVIG~~~G~Gkr--~g~~gsfLlg~~d~~~g~l~~vgkVGTGfsd~~l~~L~~~l~~~~~~~p~~~~~~~~~~~pdvWv 728 (768)
+||+|+++|.|++ .|.+++|+|.+. +|.+++ |||||++++++|++.+.++....+. ..
T Consensus 226 ~vIvG~~~g~g~~~~~g~~~~~~~~~~---~g~l~~----gtGfs~~~~~~l~~~l~~~~~~~~~-------------~p 285 (315)
T PHA00454 226 GTIVGVVWGTPGLANEGKVIGFRVLLE---DGRVVN----ATGISRALMEEFTANVKEHGEDYEA-------------MP 285 (315)
T ss_pred EEEEEEEECCCCccCCceEEEEEEEeC---CCcEEE----ccCCCHHHHHHHHHHHHhhccCccc-------------cC
Confidence 9999999998643 377888877652 367664 8999999999999999887443210 01
Q ss_pred cCcceEEEEecceeec
Q 004212 729 EPTERPETSNSPASIV 744 (768)
Q Consensus 729 ~P~~V~EV~~aeit~S 744 (768)
.|..|+||+|.+||..
T Consensus 286 ~~~~v~eV~y~e~T~~ 301 (315)
T PHA00454 286 YNGRACQVSYMERTPD 301 (315)
T ss_pred CCCeEEEEEEEEcCCC
Confidence 2446999999999854
No 21
>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=2.3e-44 Score=412.24 Aligned_cols=235 Identities=24% Similarity=0.389 Sum_probs=199.0
Q ss_pred cCCcccCCCCCchHHHHHHhhcCCCCCCeEEEEEEEEEecCCCcccChhhHHhhhhccCCccccccceEEEEeeeeecCC
Q 004212 480 SRNAERNTGKFPDVVLAVSRLKKPSVRSFVLDCEIVAYDREKQKILPFQTLSTRARKNVSLSDIKVDVCIYAFDILYRNG 559 (768)
Q Consensus 480 SR~g~d~T~~fPel~~~l~~~~~~~~~~~ILDGElVa~d~~~g~~~pFq~L~~R~rk~~~~~~~~~~v~~~vFDiLylnG 559 (768)
||||+++|.+||||++++..+ ...+||||||||++|.. |+ .+|+.|+++.+.. ...++||++|||||+||
T Consensus 1 SRng~d~T~~fPel~~~~~~l---~~~~~ILDGElVvld~~-G~-~~F~~Lq~~~~~~-----~~~pv~~~vFDlL~l~G 70 (552)
T TIGR02776 1 TRNGHDWTKRFPEIVKALALL---KLLPAWIDGEIVVLDER-GR-ADFAALQNALSAG-----ASRPLTYYAFDLLFLSG 70 (552)
T ss_pred CCCcCcchhhhHHHHHHHhhC---CCCCEEEEEEEEEECCC-CC-CCHHHHHHHHHhc-----ccCceEEEEEeccccCC
Confidence 899999999999999987743 34789999999999963 54 6799999976532 24789999999999999
Q ss_pred ccccCCcHHHHHHHHHHhhccCC-CeEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEeeCCCCCCccCCCCCCCeEEEc
Q 004212 560 QPLLQEQLRVRREHLYDSFEEEP-GFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLK 638 (768)
Q Consensus 560 ~~L~~~Pl~ERr~lL~~l~~~~~-~~i~l~~~~~~~~~eei~~~~~~ai~~G~EGlVlK~~~~dS~Y~pGkRs~~WlKvK 638 (768)
++|+++||.+||++|++++.+.. ..++++++.. ++..++|++++++|+||||+|++ +|+|++| ||.+|+|+|
T Consensus 71 ~dL~~~Pl~eRr~~L~~ll~~~~~~~i~~~~~~~----~~~~~~~~~a~~~G~EGIV~K~~--dS~Y~~G-Rs~~WlKlK 143 (552)
T TIGR02776 71 EDLRDLPLEERKKRLKQLLKAQDEPAIRYSDHFE----SDGDALLESACRLGLEGVVSKRL--DSPYRSG-RSKDWLKLK 143 (552)
T ss_pred cccccCCHHHHHHHHHHHhhhcCCCcEEEeeeec----ccHHHHHHHHHHCCCceEEEeCC--CCCCCCC-CCcchhccc
Confidence 99999999999999999998653 3577776632 34459999999999999999999 9999999 999999999
Q ss_pred cccccccCCcccEEEEEEEcCCCCCCCccceEEEEEeeCCCCeEEEEEEeccCCCHHHHHHHHHHhccccCCCCCCCccC
Q 004212 639 KDYIESIGDSLDLVPIAAFHGRGKRTGVYGAFLLACYDSNNEEFQSICKIGTGFSEAMLEERSSSLRSKVIPKPRPYYRF 718 (768)
Q Consensus 639 ~dy~~~~~dtlDlvVIG~~~G~Gkr~g~~gsfLlg~~d~~~g~l~~vgkVGTGfsd~~l~~L~~~l~~~~~~~p~~~~~~ 718 (768)
++| +.|+||+|++.|.| .+|+|+||+|| +|+|+++|+||||||++++++|++.|++++.+.+ ||...
T Consensus 144 ~~~------~~e~vI~Gy~~~~r----~~gslLlg~~d--~g~l~~vgkVgsGfsd~~~~~L~~~l~~~~~~~~-Pf~~~ 210 (552)
T TIGR02776 144 CRR------RQEFVITGYTPPNR----RFGALLVGVYE--GGQLVYAGKVGTGFGADTLKTLLARLKALGAKAS-PFSGP 210 (552)
T ss_pred ccc------cceEEEEEEecCCC----ceeeEEEEEec--CCeEEEEEEEcCCCCHHHHHHHHHHHHhhcccCC-CccCC
Confidence 976 78888888776652 29999999997 4899999999999999999999999999988764 34322
Q ss_pred C-CCCCCcEEecCcceEEEEecceeec
Q 004212 719 A-DTISPDVWFEPTERPETSNSPASIV 744 (768)
Q Consensus 719 ~-~~~~pdvWv~P~~V~EV~~aeit~S 744 (768)
. ....+++||+|.+||||+|++||.+
T Consensus 211 ~~~~~~~~~Wv~P~lV~EV~~~e~T~~ 237 (552)
T TIGR02776 211 AGAKTRGVHWVRPSLVAEVEYAGITRD 237 (552)
T ss_pred ccccCCCcEEEccCEEEEEEeeeccCC
Confidence 1 2335799999999999999999863
No 22
>cd07897 Adenylation_DNA_ligase_Bac1 Adenylation domain of putative bacterial ATP-dependent DNA ligases. Bacterial DNA ligases are divided into two broad classes: NAD-dependent and ATP-dependent. All bacterial species have a NAD-dependent DNA ligase (LigA). Some bacterial genomes contain multiple genes for DNA ligases that are predicted to use ATP as their cofactor, including Mycobacterium tuberculosis LigB, LigC, and LigD. This group is composed of predicted bacterial ATP-dependent DNA ligases. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three-step reaction mechanism. The adenylation and C-terminal oligonucleotide/oligosaccharide binding (OB)-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family, including this group. The adenylation domain binds ATP and contains many of the active site residues.
Probab=100.00 E-value=1.5e-44 Score=369.25 Aligned_cols=201 Identities=28% Similarity=0.431 Sum_probs=175.8
Q ss_pred CCCccccccccCChHHHHhhcCCCceEEeeecceEeEEEEEecCCeEEEEcCCcccCCCCCchHHHHHHhhcCCCCCCeE
Q 004212 430 IPIGPMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAVSRLKKPSVRSFV 509 (768)
Q Consensus 430 ~PvkPMLA~~~~~i~~il~k~~g~~~~~E~KyDG~R~qih~~~~g~V~lfSR~g~d~T~~fPel~~~l~~~~~~~~~~~I 509 (768)
+|+.||||+++.++++.+. ...+|++|+||||+|||+|+ .+++|++|||||+++|..||++.+++..+ + .+||
T Consensus 3 ~~~~pmLA~~~~~~~~~~~--~~~~~~~E~K~DG~R~~~~~-~~~~v~l~SR~g~~~t~~~p~l~~~~~~l-~---~~~i 75 (207)
T cd07897 3 RPYPFMLAHPLEDDPEDLG--DPSDWQAEWKWDGIRGQLIR-RGGEVFLWSRGEELITGSFPELLAAAEAL-P---DGTV 75 (207)
T ss_pred CCCCceeCCcCCCchhhhc--CcccEEEEEeEceEEEEEEE-cCCEEEEEeCCCCcccccchHHHHHHHhC-C---CCeE
Confidence 7999999999988766542 34589999999999999998 47899999999999999999999876543 2 5899
Q ss_pred EEEEEEEEecCCCcccChhhHHhhhhccCCcc--ccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccC-CCeEE
Q 004212 510 LDCEIVAYDREKQKILPFQTLSTRARKNVSLS--DIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEE-PGFFQ 586 (768)
Q Consensus 510 LDGElVa~d~~~g~~~pFq~L~~R~rk~~~~~--~~~~~v~~~vFDiLylnG~~L~~~Pl~ERr~lL~~l~~~~-~~~i~ 586 (768)
||||||+||. +...+|+.|++|.++..... ....+++|++|||||+||+++++.||.+||++|++++.+. .+.+.
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 9999999985 45789999999865332211 1256899999999999999999999999999999999876 36788
Q ss_pred EEeEEecCCHHHHHHHHHHHHHcCCceeEEeeCCCCCCccCCCCCCCeEEEcccc
Q 004212 587 FATTLTSIDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLKKDY 641 (768)
Q Consensus 587 l~~~~~~~~~eei~~~~~~ai~~G~EGlVlK~~~~dS~Y~pGkRs~~WlKvK~dy 641 (768)
+++...+.+.+++.++|++++++|+||||+|++ +|+|++|+|+.+|+|+|+|-
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 999888999999999999999999999999999 99999999999999999973
No 23
>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=9.1e-44 Score=369.73 Aligned_cols=198 Identities=23% Similarity=0.382 Sum_probs=169.0
Q ss_pred ChHHHHhhcCCCceEEeeecceEeEEEEEe---cCCeEEEEcCCcccCCCCCchHHHHHHhhcC------CCCCCeEEEE
Q 004212 442 GVSEIVNKFQDMEFTCEYKYDGERAQIHYL---EDGSVEIYSRNAERNTGKFPDVVLAVSRLKK------PSVRSFVLDC 512 (768)
Q Consensus 442 ~i~~il~k~~g~~~~~E~KyDG~R~qih~~---~~g~V~lfSR~g~d~T~~fPel~~~l~~~~~------~~~~~~ILDG 512 (768)
+++.+++.+++.+|++|+||||+|||+|+. .++.|++|||||+++|..||++.+.+...+. ...++|||||
T Consensus 11 ~~~~~~~~~~~~~~~~E~K~DG~R~qih~~~~~~~~~v~lfSR~~~d~T~~~pel~~~~~~~~~~~~~~~~~~~~~ILDG 90 (235)
T cd08039 11 SIKHCCKMIGSRRMWVETKYDGEYCQIHIDLSKDSSPIRIFSKSGKDSTADRAGVHSIIRKALRIGKPGCKFSKNCILEG 90 (235)
T ss_pred CHHHHHHHhCCCcEEEEEeecceEEEEEEecccCCCEEEEEeCCCCcccccchhHHHHHHHHhhccccccCCCccEEEEe
Confidence 466777788899999999999999999984 1678999999999999999999887766542 1247899999
Q ss_pred EEEEEecCCCcccChhhHHhhhhccC--------CccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCCCe
Q 004212 513 EIVAYDREKQKILPFQTLSTRARKNV--------SLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEPGF 584 (768)
Q Consensus 513 ElVa~d~~~g~~~pFq~L~~R~rk~~--------~~~~~~~~v~~~vFDiLylnG~~L~~~Pl~ERr~lL~~l~~~~~~~ 584 (768)
|||+||..+|++.||+.|++|.+... .......++||+||||||+||++|++.||.+||++|++++.+.+++
T Consensus 91 EiVv~d~~~g~~~~F~~L~~~~~~~~~~~~~~~~~~~~~~~~v~~~vFDlL~lnG~~l~~~pl~eRr~~L~~l~~~~~~~ 170 (235)
T cd08039 91 EMVVWSDRQGKIDPFHKIRKHVERSGSFIGTDNDSPPHEYEHLMIVFFDVLLLDDESLLSKPYSERRDLLESLVHVIPGY 170 (235)
T ss_pred EEEEEECCCCccCCHHHHHhhcccccchhccccccccccccceEEEEEEEEEECChhhhcCCHHHHHHHHHHhcccCCCc
Confidence 99999987788899999998864221 1112357899999999999999999999999999999999887777
Q ss_pred EEEEeEEec-----CCHHHHHHHHHHHHHcCCceeEEeeCCCCCCccCCCC-----CCCeEEEcccc
Q 004212 585 FQFATTLTS-----IDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKR-----SLNWLKLKKDY 641 (768)
Q Consensus 585 i~l~~~~~~-----~~~eei~~~~~~ai~~G~EGlVlK~~~~dS~Y~pGkR-----s~~WlKvK~dy 641 (768)
+.+++...+ .+.+++.++|++++++|+||||+|++ +|+|.||++ +.+|+|+|+||
T Consensus 171 ~~~~~~~~i~~~~~~~~~~l~~~~~~a~~~g~EGIv~K~~--~S~Y~pgr~~~~~r~~~WlKlK~dY 235 (235)
T cd08039 171 AGLSERFPIDFSRSSGYERLRQIFARAIAERWEGLVLKGD--EEPYFDLFLEQGSFSGCWIKLKKDY 235 (235)
T ss_pred EEEEEEEeecccCCCCHHHHHHHHHHHHHcCCceEEEecC--CCCcccCcccccccCCCeEEeCCCC
Confidence 778776543 36889999999999999999999999 999999753 58999999998
No 24
>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=1.6e-43 Score=359.57 Aligned_cols=199 Identities=40% Similarity=0.619 Sum_probs=175.6
Q ss_pred CccccccccCChHHHHhhcCCCceEEeeecceEeEEEEEecCCeEEEEcCCcccCCCCCchHHHHHHhhcCCCCCCeEEE
Q 004212 432 IGPMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAVSRLKKPSVRSFVLD 511 (768)
Q Consensus 432 vkPMLA~~~~~i~~il~k~~g~~~~~E~KyDG~R~qih~~~~g~V~lfSR~g~d~T~~fPel~~~l~~~~~~~~~~~ILD 511 (768)
|+||||++++.++++ ..+.+.+|++|+||||+|||+|+. +++|++|||+|+++|..||++.+++... .++||||
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 589999999988665 556788999999999999999995 6899999999999999999998876643 2689999
Q ss_pred EEEEEEecCCCcccChhhHHhhhhccCCcc--ccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCCCeEEEEe
Q 004212 512 CEIVAYDREKQKILPFQTLSTRARKNVSLS--DIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEPGFFQFAT 589 (768)
Q Consensus 512 GElVa~d~~~g~~~pFq~L~~R~rk~~~~~--~~~~~v~~~vFDiLylnG~~L~~~Pl~ERr~lL~~l~~~~~~~i~l~~ 589 (768)
||||+||..+ ..+|+.+++|.++..... ....+++|+|||||++||++++++||.||+++|++++.+.++.+.+++
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 9999998532 369999998865432211 235789999999999999999999999999999999988778899999
Q ss_pred EEecCCHHHHHHHHHHHHHcCCceeEEeeCCCCCCccCCCCCCCeEEEccc
Q 004212 590 TLTSIDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLKKD 640 (768)
Q Consensus 590 ~~~~~~~eei~~~~~~ai~~G~EGlVlK~~~~dS~Y~pGkRs~~WlKvK~d 640 (768)
...+++.+++.++|++++++|+||||+|++ +|+|++|+|+.+|+|+|+|
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 988999999999999999999999999999 9999999999999999985
No 25
>PRK09125 DNA ligase; Provisional
Probab=100.00 E-value=5.4e-43 Score=373.07 Aligned_cols=239 Identities=26% Similarity=0.311 Sum_probs=196.5
Q ss_pred CccccccccCChHHHHhhcCCCceEEeeecceEeEEEEEecCCeEEEEcCCcccCCCCCchHHHHHHhhcCCCCCCeEEE
Q 004212 432 IGPMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAVSRLKKPSVRSFVLD 511 (768)
Q Consensus 432 vkPMLA~~~~~i~~il~k~~g~~~~~E~KyDG~R~qih~~~~g~V~lfSR~g~d~T~~fPel~~~l~~~~~~~~~~~ILD 511 (768)
+.||||..... .+++.+|++|+||||+|||+ + .+++|||+|+++|. |+.. ... ..++|||
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 57999987643 13456899999999999973 2 38999999999998 6532 122 2489999
Q ss_pred EEEEEEecCCCcccChhhHHhhhhccCCccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccC-CCeEEEEeE
Q 004212 512 CEIVAYDREKQKILPFQTLSTRARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEE-PGFFQFATT 590 (768)
Q Consensus 512 GElVa~d~~~g~~~pFq~L~~R~rk~~~~~~~~~~v~~~vFDiLylnG~~L~~~Pl~ERr~lL~~l~~~~-~~~i~l~~~ 590 (768)
||+|+++ .+|+.+++|.+++........+++|++||||++|| ||.+|+++|++++.+. .+.+++++.
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 47999999987543322234689999999999986 9999999999999865 457889999
Q ss_pred EecCCHHHHHHHHHHHHHcCCceeEEeeCCCCCCccCCCCCCCeEEEccccccccCCcccEEEEEEEcCCCCCCCccceE
Q 004212 591 LTSIDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLKKDYIESIGDSLDLVPIAAFHGRGKRTGVYGAF 670 (768)
Q Consensus 591 ~~~~~~eei~~~~~~ai~~G~EGlVlK~~~~dS~Y~pGkRs~~WlKvK~dy~~~~~dtlDlvVIG~~~G~Gkr~g~~gsf 670 (768)
..+.+.++++++|++++++|+||||+|++ ||+|++| |+.+|+|+|+++ +.|++|||+++|+|+++|++|+|
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 EEEEeeCCCCeEEEEEEeccCCCHHHHHHHHHHhccccCCCCCCCccCCCCCCCcEEecCcceEEEEecceeec
Q 004212 671 LLACYDSNNEEFQSICKIGTGFSEAMLEERSSSLRSKVIPKPRPYYRFADTISPDVWFEPTERPETSNSPASIV 744 (768)
Q Consensus 671 Llg~~d~~~g~l~~vgkVGTGfsd~~l~~L~~~l~~~~~~~p~~~~~~~~~~~pdvWv~P~~V~EV~~aeit~S 744 (768)
+|+.+| |.. .+||||||+++++. + +++ ..+++|+|.++|..
T Consensus 227 lv~~~~---g~~---~~VgsG~t~~~r~~------------~-~~~--------------g~~~~V~y~e~t~~ 267 (282)
T PRK09125 227 LVETPD---GRE---FKIGSGFSDAEREN------------P-PKI--------------GSIITYKYRGLTKN 267 (282)
T ss_pred EEEeCC---CCE---EEeCCCCCHHHhcC------------C-CCC--------------CCEEEEEecccCCC
Confidence 999654 432 27899999998651 1 111 24899999999843
No 26
>PF01068 DNA_ligase_A_M: ATP dependent DNA ligase domain; InterPro: IPR012310 DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA fragments by catalysing the formation of an internucleotide ester bond between phosphate and deoxyribose. It is active during DNA replication, DNA repair and DNA recombination. There are two forms of DNA ligase, one requires ATP (6.5.1.1 from EC), the other NAD (6.5.1.2 from EC), the latter being restricted to eubacteria. Eukaryotic, archaebacterial, viral and some eubacterial DNA ligases are ATP-dependent. The first step in the ligation reaction is the formation of a covalent enzyme-AMP complex. The co-factor ATP is cleaved to pyrophosphate and AMP, with the AMP being covalently joined to a highly conserved lysine residue in the active site of the ligase. The activated AMP residue is then transferred to the 5'phosphate of the nick, before the nick is sealed by phosphodiester-bond formation and AMP elimination [,]. Vertebrate cells encode three well-characterised DNA ligases (DNA ligases I, III and IV), all of which are related in structure and sequence. With the exception of the atypically small PBCV-1 viral enzyme, two regions of primary sequence are common to all members of the family. The catalytic region comprises six conserved sequence motifs (I, III, IIIa, IV, V-VI), motif I includes the lysine residue that is adenylated in the first step of the ligation reaction. The function of the second, less well-conserved region is unknown. When folded, each protein comprises of two distinct sub-domains: a large amino-terminal sub-domain ('domain 1') and a smaller carboxy-terminal sub-domain ('domain 2'). The ATP-binding site of the enzyme lies in the cleft between the two sub-domains. Domain 1 consists of two antiparallel beta sheets flanked by alpha helices, whereas domain 2 consists of a five-stranded beta barrel and a single alpha helix, which form the oligonucleotide-binding fold [, ]. This domain belongs to a more diverse superfamily, including catalytic domain of the mRNA capping enzyme (IPR001339 from INTERPRO) and NAD-dependent DNA ligase (IPR001679 from INTERPRO) []. ; GO: 0003910 DNA ligase (ATP) activity, 0005524 ATP binding, 0006281 DNA repair, 0006310 DNA recombination; PDB: 3RR5_A 1X9N_A 2CFM_A 3QWU_B 3GDE_A 2Q2U_C 2Q2T_A 1FVI_A 1P8L_A 2VUG_A ....
Probab=100.00 E-value=2.2e-42 Score=349.23 Aligned_cols=201 Identities=36% Similarity=0.607 Sum_probs=179.1
Q ss_pred cccccccCChHHHHhhcCCCceEEeeecceEeEEEEEecCCeEEEEcCCcccCCCCCchHHHHHHhhcCCCCCCeEEEEE
Q 004212 434 PMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAVSRLKKPSVRSFVLDCE 513 (768)
Q Consensus 434 PMLA~~~~~i~~il~k~~g~~~~~E~KyDG~R~qih~~~~g~V~lfSR~g~d~T~~fPel~~~l~~~~~~~~~~~ILDGE 513 (768)
||||++.++++++++++ +.+|++|+||||+|||+|+ .+|.|++|||+|+++|..||++.+.+...+..+..++|||||
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 89999999999999888 6689999999999999998 588999999999999999999999898877655568999999
Q ss_pred EEEEecCCCcccChhhHHhhhh-ccCCccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCCCeEEEEeEEe
Q 004212 514 IVAYDREKQKILPFQTLSTRAR-KNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEPGFFQFATTLT 592 (768)
Q Consensus 514 lVa~d~~~g~~~pFq~L~~R~r-k~~~~~~~~~~v~~~vFDiLylnG~~L~~~Pl~ERr~lL~~l~~~~~~~i~l~~~~~ 592 (768)
+|+||..++...||+.++++.+ +.........+++|+|||||++||.++.+.||.||+++|++++....+.+.+++...
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 9999998888999999999873 332111126799999999999999999999999999999999966678899999999
Q ss_pred cCCHHHHHHHHHHHHHcCCceeEEeeCCCCCCccCCCCCCCeEEEc
Q 004212 593 SIDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLK 638 (768)
Q Consensus 593 ~~~~eei~~~~~~ai~~G~EGlVlK~~~~dS~Y~pGkRs~~WlKvK 638 (768)
+.+.++++++|++++++|+||+|+|++ +++|++|+|+.+|+|+|
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=1e-41 Score=344.95 Aligned_cols=190 Identities=28% Similarity=0.393 Sum_probs=164.0
Q ss_pred CccccccccCChHHHHhhcCCCceEEeeecceEeEEEEEecCCeEEEEcCCcccCCCCCchHHHHHHhhcCCCCCCeEEE
Q 004212 432 IGPMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAVSRLKKPSVRSFVLD 511 (768)
Q Consensus 432 vkPMLA~~~~~i~~il~k~~g~~~~~E~KyDG~R~qih~~~~g~V~lfSR~g~d~T~~fPel~~~l~~~~~~~~~~~ILD 511 (768)
|+||||..+.+++ .+.+|++|+||||+|||+|+. ++.|++|||||+++|+.||++.+++...+. .++|||
T Consensus 1 i~PmLa~~~~~~~------~~~~~~~E~K~DG~R~~~~~~-~~~v~l~SR~g~~~t~~~p~~~~~~~~~~~---~~~iLD 70 (194)
T cd07905 1 VEPMLARAVDALP------EPGGWQYEPKWDGFRCLAFRD-GDEVRLQSRSGKPLTRYFPELVAAARALLP---PGCVLD 70 (194)
T ss_pred CCceeCCccCCCC------CCCceEEEeeeceEEEEEEEe-CCEEEEEeCCCCchhhhhHHHHHHHHhhCC---CCEEEE
Confidence 5899999887653 256899999999999999995 789999999999999999999988877543 589999
Q ss_pred EEEEEEecCCCcccChhhHHhhhhccCC---ccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCCCeEEEE
Q 004212 512 CEIVAYDREKQKILPFQTLSTRARKNVS---LSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEPGFFQFA 588 (768)
Q Consensus 512 GElVa~d~~~g~~~pFq~L~~R~rk~~~---~~~~~~~v~~~vFDiLylnG~~L~~~Pl~ERr~lL~~l~~~~~~~i~l~ 588 (768)
||||++|.. . .+|+.|++|.+.... ......+++|+||||||+||+++++.||.+|+++|++++.+..+.++++
T Consensus 71 GElv~~~~~--~-~~F~~l~~r~~~~~~~~~~~~~~~~~~~~vFDiL~l~g~~l~~~pl~eRr~~L~~~~~~~~~~i~~~ 147 (194)
T cd07905 71 GELVVWRGG--R-LDFDALQQRIHPAASRVRRLAEETPASFVAFDLLALGGRDLRGRPLRERRAALEALLAGWGPPLHLS 147 (194)
T ss_pred eEEEEEcCC--C-CCHHHHHHHhcccccchhhhhccCCEEEEEEeeeeeCCcccccCCHHHHHHHHHHHhcccCCCeEEC
Confidence 999999853 3 499999999754321 1223678999999999999999999999999999999998766778888
Q ss_pred eEEecCCHHHHHHHHHHHHHcCCceeEEeeCCCCCCccCCCCCCCeEEEccc
Q 004212 589 TTLTSIDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLKKD 640 (768)
Q Consensus 589 ~~~~~~~~eei~~~~~~ai~~G~EGlVlK~~~~dS~Y~pGkRs~~WlKvK~d 640 (768)
+. ..+.+++.++|++++++|+||||+|++ +|+|++|+| +|+|+|+.
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 357789999999999999999999999 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=1.5e-40 Score=334.98 Aligned_cols=189 Identities=33% Similarity=0.469 Sum_probs=164.3
Q ss_pred CccccccccCChHHHHhhcCCCceEEeeecceEeEEEEEecCCeEEEEcCCcccCCCCCchHHHHHHhhcCCCCCCeEEE
Q 004212 432 IGPMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAVSRLKKPSVRSFVLD 511 (768)
Q Consensus 432 vkPMLA~~~~~i~~il~k~~g~~~~~E~KyDG~R~qih~~~~g~V~lfSR~g~d~T~~fPel~~~l~~~~~~~~~~~ILD 511 (768)
|+||||+++.++. .+.+|++|+||||+|||+|+. ++.|++|||+|+++|..||++...+.++ ...++|||
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 456899999999999999995 6799999999999999999998877664 23789999
Q ss_pred EEEEEEecCCCcccChhhHHhhhhccCCccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCCCeEEEEeEE
Q 004212 512 CEIVAYDREKQKILPFQTLSTRARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEPGFFQFATTL 591 (768)
Q Consensus 512 GElVa~d~~~g~~~pFq~L~~R~rk~~~~~~~~~~v~~~vFDiLylnG~~L~~~Pl~ERr~lL~~l~~~~~~~i~l~~~~ 591 (768)
||||+||..+ ..+|+.+++|.+... ......+++|+|||||++||++++++||.||+++|++++.+..+.+++++..
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 369999999976543 2234679999999999999999999999999999999998876788888766
Q ss_pred ecCCHHHHHHHHHHHHHcCCceeEEeeCCCCCCccCCCCCCCeEEEcc
Q 004212 592 TSIDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLKK 639 (768)
Q Consensus 592 ~~~~~eei~~~~~~ai~~G~EGlVlK~~~~dS~Y~pGkRs~~WlKvK~ 639 (768)
.. +.+++|++++++|+||||+|++ +|+|++|+|+.+|+|+|+
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
>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=6.1e-35 Score=290.49 Aligned_cols=176 Identities=35% Similarity=0.577 Sum_probs=146.2
Q ss_pred cchHHHHHHHHHHHhhhchHHHHHHHHHHHHhhhcCCCCchHHHHHHHhCccCCCccccccCCCHHHHHHHHHHHhCCCH
Q 004212 191 VPFIFLSLVFDMISNETGRILITDIVCNMLRTVMETTPEDLVPVVYLAANKIAPAHEGLELGIGDASIIKALAEACGRTE 270 (768)
Q Consensus 191 ~~F~~la~l~e~I~~tssr~~k~~iL~~~fr~~i~~~p~dl~~~vyl~~~~l~P~~e~~elGIg~~~L~Kal~~a~G~s~ 270 (768)
|+|++||++|++|+++++|++|+++|++||+.+. +.++.+++|+++|+|+|+|++++|||+++.|+|++++++|+++
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 4459999999999999999999999999999999999999999
Q ss_pred HHHHHHHhhhCChHHHHhhhcccCC-ccCCCCCCcHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHhcCCChHHHHHHH
Q 004212 271 SHVKKQYQEMGDLGLVAKASRSSQS-MMRKPDPLTITKVFDTFRLIAKEAGKDSQEKKKNRIKALLVAATDCEPQYLIRL 349 (768)
Q Consensus 271 ~~ik~~y~~~GDlg~vA~~~r~~q~-~l~~~~~LTI~eV~~~L~kIA~~~G~~Sq~~K~~~l~~Ll~~~t~~E~k~lvRi 349 (768)
+.+++.|+++||+|++|+.+...+. ....+.+|||.+||+.|++||..+|.+|++.|+++|..|+++|+|.|++||+||
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 333468999999999999999999999999999999999999999999999999
Q ss_pred HhhcccCcccHHHHHHHHHh
Q 004212 350 LQSKLRIGLAEQTLLAALGQ 369 (768)
Q Consensus 350 IlkdLRiGi~e~tVl~ala~ 369 (768)
|+++||||+++++|+.|||+
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 30
>cd07896 Adenylation_kDNA_ligase_like Adenylation domain of kDNA ligases and similar proteins. The mitochondrial DNA of parasitic protozoans is highly unusual. It is termed the kinetoplast DNA (kDNA) and consists of circular DNA molecules (maxicircles) and several thousand smaller circular molecules (minicircles). This group is composed of kDNA ligase, Chlorella virus DNA ligase, and similar proteins. kDNA ligase and Chlorella virus DNA ligase are the smallest known ATP-dependent ligases. They are involved in DNA replication or repair. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. They have a highly modular architecture consisting of a unique arrangement of two or more discrete domains. The adenylation and the C-terminal oligonucleotide/oligosaccharide binding (OB)-fold domains comprise a catalytic core unit that is common to most me
Probab=100.00 E-value=6.4e-34 Score=282.77 Aligned_cols=173 Identities=24% Similarity=0.247 Sum_probs=145.2
Q ss_pred CccccccccCChHHHHhhcCCCceEEeeecceEeEEEEEecCCeEEEEcCCcccCCCCCchHHHHHHhhcCCCCCCeEEE
Q 004212 432 IGPMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAVSRLKKPSVRSFVLD 511 (768)
Q Consensus 432 vkPMLA~~~~~i~~il~k~~g~~~~~E~KyDG~R~qih~~~~g~V~lfSR~g~d~T~~fPel~~~l~~~~~~~~~~~ILD 511 (768)
++||||++..... .+.+|++|+||||+|||+|. + ++|||+|+++|.. + .+...+ .++|||
T Consensus 1 ~~pmla~~~~~~~------~~~~~~~e~K~DG~R~~~~~---~--~~~SR~g~~~t~~-~----~~~~~l----~~~ilD 60 (174)
T cd07896 1 PELLLAKTYDEGE------DISGYLVSEKLDGVRAYWDG---K--QLLSRSGKPIAAP-A----WFTAGL----PPFPLD 60 (174)
T ss_pred CccccccccccCC------ChHHeeechhhceEEEEEec---c--EEEecCCcCCCCC-H----HHHhhC----CCCccC
Confidence 4799999877542 24589999999999999862 2 9999999999975 2 222323 359999
Q ss_pred EEEEEEecCCCcccChhhHHhhhhccCCccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccC-CCeEEEEeE
Q 004212 512 CEIVAYDREKQKILPFQTLSTRARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEE-PGFFQFATT 590 (768)
Q Consensus 512 GElVa~d~~~g~~~pFq~L~~R~rk~~~~~~~~~~v~~~vFDiLylnG~~L~~~Pl~ERr~lL~~l~~~~-~~~i~l~~~ 590 (768)
||+|+++ .+|+.+++|.++.........+++|++||||+ .+.||.+|+++|++++... .+.+++++.
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 9999975 48999999987654322345789999999998 5789999999999999876 467899999
Q ss_pred EecCCHHHHHHHHHHHHHcCCceeEEeeCCCCCCccCCCCCCCeEEEcc
Q 004212 591 LTSIDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLKK 639 (768)
Q Consensus 591 ~~~~~~eei~~~~~~ai~~G~EGlVlK~~~~dS~Y~pGkRs~~WlKvK~ 639 (768)
..+.+.+++.++++.++++|+||||+|++ +++|++| |+.+|+|+|+
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 7889999996
No 31
>cd06846 Adenylation_DNA_ligase_like Adenylation domain of proteins similar to ATP-dependent polynucleotide ligases. ATP-dependent polynucleotide ligases catalyze the phosphodiester bond formation of nicked nucleic acid substrates using ATP as a cofactor in a three step reaction mechanism. This family includes ATP-dependent DNA and RNA ligases. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent DNA ligases have a highly modular architecture, consisting of a unique arrangement of two or more discrete domains, including a DNA-binding domain, an adenylation or nucleotidyltransferase (NTase) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The adenylation domain binds ATP and contains many active site residues. Together with the C-terminal OB-fold domain, it comprises a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The catalytic core contains six conserved seq
Probab=99.97 E-value=1.6e-31 Score=267.20 Aligned_cols=176 Identities=27% Similarity=0.255 Sum_probs=140.8
Q ss_pred cccccccCChHHHHhhcCCCceEEeeecceEeEEEEEecCCeEEEEcCCcccCCCCCchHHHHHHhhcCCCCCCeEEEEE
Q 004212 434 PMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAVSRLKKPSVRSFVLDCE 513 (768)
Q Consensus 434 PMLA~~~~~i~~il~k~~g~~~~~E~KyDG~R~qih~~~~g~V~lfSR~g~d~T~~fPel~~~l~~~~~~~~~~~ILDGE 513 (768)
|||+.+.....+. .+.+.+|++|+||||+|||+|+. +|.+++|||+|+++|..||++... ... ....++|||||
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 7888776654332 35667899999999999999995 689999999999999999987541 111 12368999999
Q ss_pred EEEEecCCCcccChhhHHhhhhccCCccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCCC--eEEEEeEE
Q 004212 514 IVAYDREKQKILPFQTLSTRARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEPG--FFQFATTL 591 (768)
Q Consensus 514 lVa~d~~~g~~~pFq~L~~R~rk~~~~~~~~~~v~~~vFDiLylnG~~L~~~Pl~ERr~lL~~l~~~~~~--~i~l~~~~ 591 (768)
||+++.. + ...+++|++||||++||.+++++||.+|+++|++++.+.++ .+.+++..
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 13579999999999999999999999999999999987542 34444332
Q ss_pred ecC-CHHHHHHHHHHHHHcCCceeEEeeCCCCCCc--cCCCCCCCeEEEcc
Q 004212 592 TSI-DLDEIQKFLDAAVDASCEGLIIKTMDRDATY--EPSKRSLNWLKLKK 639 (768)
Q Consensus 592 ~~~-~~eei~~~~~~ai~~G~EGlVlK~~~~dS~Y--~pGkRs~~WlKvK~ 639 (768)
... +.+++.+++++++++|+||||+|++ +++| .+| |+.+|+|+||
T Consensus 135 ~~~~~~~~~~~~~~~~~~~g~EGvi~K~~--~s~Y~~~~g-r~~~wlK~Kp 182 (182)
T cd06846 135 NAPSYDETLDDLLEKLKKKGKEGLVFKHP--DAPYKGRPG-SSGNQLKLKP 182 (182)
T ss_pred cccccchHHHHHHHHhhhcCCceEEEEcC--CCCccccCC-CCCceEeecC
Confidence 222 2233899999999999999999999 9999 887 7999999997
No 32
>cd07895 Adenylation_mRNA_capping Adenylation domain of GTP-dependent mRNA capping enzymes. RNA capping enzymes transfer GMP from GTP to the 5'-diphosphate end of nascent mRNAs to form a G(5')ppp(5')RNA cap structure. The RNA cap is found only in eukarya. RNA capping is chemically analogous to the first two steps of polynucleotide ligation. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation of nicked nucleic acid substrates using the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. Structural studies reveal a shared structure for DNA ligases and capping enzymes, with a common catalytic core composed of an adenylation or nucleotidyltransferase domain and a C-terminal OB-fold domain containing conserved sequence motifs. The adenylation domain binds ATP and contains many active site residues.
Probab=99.95 E-value=2.2e-27 Score=243.77 Aligned_cols=159 Identities=23% Similarity=0.235 Sum_probs=128.2
Q ss_pred cCCCceEEeeecceEeEEEEEecC-CeEEEEcCCcccCCCCCchHHHHHHhhcCCCCCCeEEEEEEEEEecCCCcccChh
Q 004212 450 FQDMEFTCEYKYDGERAQIHYLED-GSVEIYSRNAERNTGKFPDVVLAVSRLKKPSVRSFVLDCEIVAYDREKQKILPFQ 528 (768)
Q Consensus 450 ~~g~~~~~E~KyDG~R~qih~~~~-g~V~lfSR~g~d~T~~fPel~~~l~~~~~~~~~~~ILDGElVa~d~~~g~~~pFq 528 (768)
+...+|++|+||||+|+|+|+. + +.+.++||+++.++..+|++.+... ......++|||||+|+++.. +
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 3456899999999999999995 6 7899999999999998888753211 11124789999999998642 1
Q ss_pred hHHhhhhccCCccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCCC---------------eEEEEeEEec
Q 004212 529 TLSTRARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEPG---------------FFQFATTLTS 593 (768)
Q Consensus 529 ~L~~R~rk~~~~~~~~~~v~~~vFDiLylnG~~L~~~Pl~ERr~lL~~l~~~~~~---------------~i~l~~~~~~ 593 (768)
..+++|+|||||++||+++.+.||.+|+++|++++..... .+...+.
T Consensus 108 ---------------~~~~~~~vFDiL~~~g~~l~~~pl~~R~~~L~~~i~~~~~~~~~~~~~~~~~~~~~i~~k~~--- 169 (215)
T cd07895 108 ---------------KKRPRYLIFDILAFNGQSVTEKPLSERLKYIKKEVIEPRNELLKKGPIDKAKEPFSVRLKDF--- 169 (215)
T ss_pred ---------------ceEEEEEEEEEEEECCcCccCCCHHHHHHHHHHhchhHHHHhhhcChhhcCCCCeEEEecce---
Confidence 2479999999999999999999999999999999864211 1222222
Q ss_pred CCHHHHHHHHHHH---HHcCCceeEEeeCCCCCCccCCCCCCCeEEEcc
Q 004212 594 IDLDEIQKFLDAA---VDASCEGLIIKTMDRDATYEPSKRSLNWLKLKK 639 (768)
Q Consensus 594 ~~~eei~~~~~~a---i~~G~EGlVlK~~~~dS~Y~pGkRs~~WlKvK~ 639 (768)
...+++.++|+.+ +.+|.||||+|+. +++|.+| |+.+|+|+|+
T Consensus 170 ~~~~~~~~~~~~~~~~~~~~~EGlIfk~~--~~~Y~~G-r~~~~lKwKp 215 (215)
T cd07895 170 FPLYKIEKLFEKIIPKLPHENDGLIFTPN--DEPYVPG-TDKNLLKWKP 215 (215)
T ss_pred EeHHhHHHHHHhccccCCCCCCCEEEccC--CCCccCc-cCCcceeeCC
Confidence 2345788888888 5999999999999 9999999 9999999996
No 33
>KOG4437 consensus ATP-dependent DNA ligase III [Replication, recombination and repair]
Probab=99.91 E-value=1.7e-23 Score=219.02 Aligned_cols=327 Identities=21% Similarity=0.307 Sum_probs=232.9
Q ss_pred cchHHHHHHHHHHHhhhchHHHHHHHHHHHHhhhcCCCCchHHHHHHHhCccCCCccccccCCCHHHHHHHHHHHhCCCH
Q 004212 191 VPFIFLSLVFDMISNETGRILITDIVCNMLRTVMETTPEDLVPVVYLAANKIAPAHEGLELGIGDASIIKALAEACGRTE 270 (768)
Q Consensus 191 ~~F~~la~l~e~I~~tssr~~k~~iL~~~fr~~i~~~p~dl~~~vyl~~~~l~P~~e~~elGIg~~~L~Kal~~a~G~s~ 270 (768)
-.|..|.++|..|+..+....|+++|+.+|+.- ..+.+-++|.-|| ..+-+++.|||.++.|++.+++++++..
T Consensus 155 N~F~ef~kiCS~L~~~p~~~~Kt~VI~~LL~kd-NFDGDL~LWL~FL-----IRESD~R~YNl~DkKLI~lfsKiLn~~~ 228 (482)
T KOG4437|consen 155 NLFREFRKLCSMLADNPSYNTKTQVIQDLLRKD-NFDGDLYLWLKFL-----IRESDKRVYNLNDKKLIKLFSKILNCNP 228 (482)
T ss_pred hHHHHHHHHHHHHHhCcCccchhHHHHHHHhcc-CCCcchhhhhhhh-----hcccccccccccHHHHHHHHHHHHccCh
Confidence 359999999999999999999999999999873 2244445554444 4577899999999999999999999987
Q ss_pred HHHHHHHh-hhCChHHHHhhhcccCCccCCCCCCcHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHhcCCChHHHHHHH
Q 004212 271 SHVKKQYQ-EMGDLGLVAKASRSSQSMMRKPDPLTITKVFDTFRLIAKEAGKDSQEKKKNRIKALLVAATDCEPQYLIRL 349 (768)
Q Consensus 271 ~~ik~~y~-~~GDlg~vA~~~r~~q~~l~~~~~LTI~eV~~~L~kIA~~~G~~Sq~~K~~~l~~Ll~~~t~~E~k~lvRi 349 (768)
...-..|. ...|.+..+...-.+ +.....+-+||++|.+.|.+|++.+..+. .++.|+....+|+.+|.+.|||+
T Consensus 229 ~~~~~~Y~~~S~~~~i~i~~~~~K-~~~~~K~~~siQ~~D~~L~rLSKi~~~D~---~~~~L~~~A~R~~~~~L~~iIRL 304 (482)
T KOG4437|consen 229 DDMARDYEQGSVSETIRVFFEQSK-SFPPAKSLLTIQEVDEFLLRLSKLTKEDE---QQQALQDIASRCTANDLKCIIRL 304 (482)
T ss_pred HHHHHHHHhccchhhhhhhHhhcc-CCCCcccceeHHHHHHHHHHHhcccchHH---HHHHHHHHHHhcccchHHHHHHH
Confidence 66555553 334554433221111 01112467999999999999999876554 47899999999999999999999
Q ss_pred HhhcccCcccHHHHHHHHHhhhccCCCCCCCCCCCcchHHHHHHHHHHHhhcCCchhhhhhhhhhcCccccCCccccCCC
Q 004212 350 LQSKLRIGLAEQTLLAALGQAAVYNEQHSKPPPNIQSPLEEAAKIVKQVFSVLPVYEKIVPALLTDGVWNLSNTCSFTPG 429 (768)
Q Consensus 350 IlkdLRiGi~e~tVl~ala~a~~~~~~~~~~~~~l~~~l~~a~~~vk~~y~~~pd~~~v~~~ll~~g~~~l~~~~~i~~g 429 (768)
|.++|....+.+.||++++.-++.... ...|++.++ ++|+ |++.+.. +.|..+.. ...-...
T Consensus 305 Ir~~L~~~s~A~~iL~~~~P~A~E~F~----S~~L~~ViE-------r~~~---N~~~~~~---~~~~~~~~-s~~s~~~ 366 (482)
T KOG4437|consen 305 IKHDLKMNSGAKHVLDALDPNAYEAFK----SRNLQDVVE-------RVLH---NAQEVEK---EPGQRRAL-SVQASLM 366 (482)
T ss_pred HHHHhccCCChhHHHhccCCCcHHHHH----hcCHHHHHH-------HHHH---hHHHHhh---Cccccccc-cchhhhc
Confidence 999999999999999998764432110 123444443 3333 2444422 33433211 1122356
Q ss_pred CCCccccccccCChHHHHhhcCCCceEEeeecceEeEEEEEecCCeEEEEcCCcccCCCCCchHHHHHHhhcCCCCCCeE
Q 004212 430 IPIGPMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAVSRLKKPSVRSFV 509 (768)
Q Consensus 430 ~PvkPMLA~~~~~i~~il~k~~g~~~~~E~KyDG~R~qih~~~~g~V~lfSR~g~d~T~~fPel~~~l~~~~~~~~~~~I 509 (768)
.|++|||+..+++++-..++.+| +..-|.||||+|.|+|.+ ++.|.+|||--+...+ |. +.+.+.+. +-++.+
T Consensus 367 s~~Q~~~~~~~~~VE~s~~~~~~-~~~S~~~~D~E~~~~~~~-~D~~S~~S~~~~~~s~-FK---~~~P~~~~-~G~~~~ 439 (482)
T KOG4437|consen 367 TPVQPMLAEACKSVEYAMKKCPN-GMFSEIKYDGERVQVHKN-GDHFSYFSRLPHKVAH-FK---DYIPQAFP-GGHSMI 439 (482)
T ss_pred CCcChhhhhhhhhHHHHhccCCC-CccccccCCCceeeccCC-CcchhhhccChHhhhh-hh---hcCchhcC-CCcccc
Confidence 89999999999888766666655 567899999999999984 6789999987665432 22 22334443 347999
Q ss_pred EEEEEEEEecCCCcccChhhHHhhhhccCCccccccceEEEEeeeee
Q 004212 510 LDCEIVAYDREKQKILPFQTLSTRARKNVSLSDIKVDVCIYAFDILY 556 (768)
Q Consensus 510 LDGElVa~d~~~g~~~pFq~L~~R~rk~~~~~~~~~~v~~~vFDiLy 556 (768)
+|||...++..+|+++||+++.-...... ...++|.++||+.|
T Consensus 440 ~~~~~~~I~~K~~~P~~~~~~~~~~K~~~----~~~~~~~~~~~~~~ 482 (482)
T KOG4437|consen 440 LDSEVLLIDNKTGKPLPFGTLGVHKKAAF----QDANVCLFVFDCIY 482 (482)
T ss_pred ccccccceecccCCCCCchhcchhhHHHh----cCcchheeecccCC
Confidence 99999999999999999999753321110 13578999999875
No 34
>cd07967 OBF_DNA_ligase_III The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase III is a DNA-binding module that is part of the catalytic core unit. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriohages, eukarya, archaea and bacteria. There are three classes of ATP-dependent DNA ligases in eukaryotic cells (I, III and IV). DNA ligase III is not found in lower eukaryotes and is present both in the nucleus and mitochondria. It has several isoforms; two splice forms, III-alpha and III-beta, differ in their carboxy-terminal sequences. DNA ligase III-beta is believed to play a role in homologous recombination during meiotic proph
Probab=99.91 E-value=5.1e-24 Score=205.06 Aligned_cols=103 Identities=26% Similarity=0.496 Sum_probs=92.6
Q ss_pred cCCcccEEEEEEEcCCCCCCCccceEEEEEeeCCCCeEEEEEEeccCCCHHHHHHHHHHhccccCCC----CCCCccCCC
Q 004212 645 IGDSLDLVPIAAFHGRGKRTGVYGAFLLACYDSNNEEFQSICKIGTGFSEAMLEERSSSLRSKVIPK----PRPYYRFAD 720 (768)
Q Consensus 645 ~~dtlDlvVIG~~~G~Gkr~g~~gsfLlg~~d~~~g~l~~vgkVGTGfsd~~l~~L~~~l~~~~~~~----p~~~~~~~~ 720 (768)
|+|++||||||+++|+|+|+|++|+||||+||+++|+|+++||||||||++++++|.+.|+++++.. ++.|+.++.
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 4689999999999999999999999999999987789999999999999999999999999998765 334555666
Q ss_pred CCCCcEEec-C--cceEEEEecceeecCCC
Q 004212 721 TISPDVWFE-P--TERPETSNSPASIVYDS 747 (768)
Q Consensus 721 ~~~pdvWv~-P--~~V~EV~~aeit~Sp~~ 747 (768)
..+||+||+ | .+||||+|+|||.||.|
T Consensus 81 ~~~Pdv~~~~P~~s~V~EV~~aeit~S~~~ 110 (139)
T cd07967 81 SLVPDFIVKDPKKAPVWEITGAEFSKSEAH 110 (139)
T ss_pred CCCCCEEEeCCCccEEEEEEeeeEEecCcc
Confidence 678999994 8 68999999999999998
No 35
>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=99.86 E-value=1.6e-21 Score=185.80 Aligned_cols=100 Identities=38% Similarity=0.653 Sum_probs=90.2
Q ss_pred CcccEEEEEEEcCCCCCCCccceEEEEEeeCCCCeEEEEEEeccCCCHHHHHHHHHHhccccCCCCCCCccCCCCCCCcE
Q 004212 647 DSLDLVPIAAFHGRGKRTGVYGAFLLACYDSNNEEFQSICKIGTGFSEAMLEERSSSLRSKVIPKPRPYYRFADTISPDV 726 (768)
Q Consensus 647 dtlDlvVIG~~~G~Gkr~g~~gsfLlg~~d~~~g~l~~vgkVGTGfsd~~l~~L~~~l~~~~~~~p~~~~~~~~~~~pdv 726 (768)
|++|+||+|+++|+|+++|.+|+||||+||+++|+|++||+||||||++++++|.+.|.+++++.+|+. ......|++
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 589999999999999999999999999999766899999999999999999999999999998876542 233457999
Q ss_pred EecCcceEEEEecceeecCCCc
Q 004212 727 WFEPTERPETSNSPASIVYDSQ 748 (768)
Q Consensus 727 Wv~P~~V~EV~~aeit~Sp~~~ 748 (768)
||+|.+||||+|++||.|+.|.
T Consensus 79 wv~P~lV~EV~~~e~t~s~~~~ 100 (129)
T cd07893 79 WVEPKVVVEVLADEITRSPMHT 100 (129)
T ss_pred EEeeeEEEEEEeeeeeeCcccc
Confidence 9999999999999999999984
No 36
>cd07969 OBF_DNA_ligase_I The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase I is a DNA-binding module that is part of the catalytic core unit. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriohages, eukarya, archaea and bacteria. There are three classes of ATP-dependent DNA ligases in eukaryotic cells (I, III and IV). This group is composed of eukaryotic DNA ligase I, Sulfolobus solfataricus DNA ligase and similar proteins. DNA ligase I is required for the ligation of Okazaki fragments during lagging-strand DNA synthesis and for base excision repair (BER). ATP dependent DNA ligases have a highly modular architecture consist
Probab=99.86 E-value=2.4e-21 Score=187.86 Aligned_cols=105 Identities=53% Similarity=0.898 Sum_probs=92.2
Q ss_pred CCcccEEEEEEEcCCCCCCCccceEEEEEeeCCCCeEEEEEEeccCCCHHHHHHHHHHhccccCCCCCCCccCCCCCCCc
Q 004212 646 GDSLDLVPIAAFHGRGKRTGVYGAFLLACYDSNNEEFQSICKIGTGFSEAMLEERSSSLRSKVIPKPRPYYRFADTISPD 725 (768)
Q Consensus 646 ~dtlDlvVIG~~~G~Gkr~g~~gsfLlg~~d~~~g~l~~vgkVGTGfsd~~l~~L~~~l~~~~~~~p~~~~~~~~~~~pd 725 (768)
+|++|+||||+++|+|++.+.+|+|+||+||+++|+|++|||||||||++++++|.+.|.+++++.+|+.. ....+|+
T Consensus 1 ~~t~D~vViG~~~g~g~~~~~~~slllG~~~~~~~~l~~vgkvgtGft~~~~~~L~~~l~~~~~~~~p~~~--~~~~~~~ 78 (144)
T cd07969 1 GDTLDLVPIGAYYGKGKRTGVYGAFLLACYDPETEEFQTVCKIGTGFSDEFLEELYESLKEHVIPKKPYRV--DSSLEPD 78 (144)
T ss_pred CCceeEEEEEEEECCCCCCCCcceEEEEEEeCCCCEEEEEeEEccCCCHHHHHHHHHHhhhhccccCCccc--cccCCCc
Confidence 47999999999999999999999999999998778999999999999999999999999999988754322 2224799
Q ss_pred EEecCcceEEEEecceeecCCCccccc
Q 004212 726 VWFEPTERPETSNSPASIVYDSQITCL 752 (768)
Q Consensus 726 vWv~P~~V~EV~~aeit~Sp~~~~~~~ 752 (768)
+||+|.+||||+|++||.|++|+..++
T Consensus 79 vWv~P~lV~EV~~~e~t~s~~~~~~~~ 105 (144)
T cd07969 79 VWFEPKEVWEVKAADLTLSPVHTAAIG 105 (144)
T ss_pred EEEeeeEEEEEEEeEeecCcceecccc
Confidence 999999999999999999999954333
No 37
>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=99.84 E-value=6.7e-21 Score=183.87 Aligned_cols=103 Identities=30% Similarity=0.514 Sum_probs=88.0
Q ss_pred CCcccEEEEEEEcCCCCCCCccceEEEEEeeCCCC------eEEEEEEeccCCCHHHHHHHHHHhccccCCC---CCCCc
Q 004212 646 GDSLDLVPIAAFHGRGKRTGVYGAFLLACYDSNNE------EFQSICKIGTGFSEAMLEERSSSLRSKVIPK---PRPYY 716 (768)
Q Consensus 646 ~dtlDlvVIG~~~G~Gkr~g~~gsfLlg~~d~~~g------~l~~vgkVGTGfsd~~l~~L~~~l~~~~~~~---p~~~~ 716 (768)
+|++||||||+++|+|+++|.+|+||||+||.+++ +|++|||||||||++++++|.+.|++++++. .+|+.
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 8999999999999999999999999986542 22332
Q ss_pred -cCCCCCCCcEEecCc--ceEEEEecceeecCCCc
Q 004212 717 -RFADTISPDVWFEPT--ERPETSNSPASIVYDSQ 748 (768)
Q Consensus 717 -~~~~~~~pdvWv~P~--~V~EV~~aeit~Sp~~~ 748 (768)
.......|++||+|. +||||+|+|||.|+.|.
T Consensus 81 ~~~~~~~~~~~Wv~P~~slV~EV~~~e~t~s~~~~ 115 (140)
T cd07968 81 LLKFGKEKPDVWIEPKDSVVLEVKAAEIVPSDSYK 115 (140)
T ss_pred cccccccCCcEEEecCCCEEEEEEeeeEeecCccc
Confidence 112344699999999 99999999999999884
No 38
>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=99.81 E-value=1.1e-19 Score=171.49 Aligned_cols=92 Identities=32% Similarity=0.454 Sum_probs=84.3
Q ss_pred CcccEEEEEEEcCCCCCCCccceEEEEEeeCCCCeEEEEEEeccCCCHHHHHHHHHHhccccCCCCCCCccCCCCCCCcE
Q 004212 647 DSLDLVPIAAFHGRGKRTGVYGAFLLACYDSNNEEFQSICKIGTGFSEAMLEERSSSLRSKVIPKPRPYYRFADTISPDV 726 (768)
Q Consensus 647 dtlDlvVIG~~~G~Gkr~g~~gsfLlg~~d~~~g~l~~vgkVGTGfsd~~l~~L~~~l~~~~~~~p~~~~~~~~~~~pdv 726 (768)
|++|+||+|+++|.|+++|++|+||||+||+++|+|++||+||||||++++++|.+.|+++.+.. .+|++
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 58999999999999999999999999999876689999999999999999999999999876543 15899
Q ss_pred EecCcceEEEEecceeecCCCc
Q 004212 727 WFEPTERPETSNSPASIVYDSQ 748 (768)
Q Consensus 727 Wv~P~~V~EV~~aeit~Sp~~~ 748 (768)
||+|.+||||+|++||.|+.|.
T Consensus 71 wv~P~lV~eV~~~e~t~s~~~~ 92 (122)
T cd07972 71 SVKPELVFEVAFEEIQRSPRYK 92 (122)
T ss_pred EEeceEEEEEEeeEEEecCccc
Confidence 9999999999999999999984
No 39
>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=99.77 E-value=3.8e-18 Score=186.54 Aligned_cols=166 Identities=20% Similarity=0.266 Sum_probs=125.8
Q ss_pred cCCCceEEeeecceEeEEEEEecCCeEEEEcCCccc---CCCCCchHHHHHHhhcCCCCCCeEEEEEEEEEecCCCcccC
Q 004212 450 FQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAER---NTGKFPDVVLAVSRLKKPSVRSFVLDCEIVAYDREKQKILP 526 (768)
Q Consensus 450 ~~g~~~~~E~KyDG~R~qih~~~~g~V~lfSR~g~d---~T~~fPel~~~l~~~~~~~~~~~ILDGElVa~d~~~g~~~p 526 (768)
|. .+|++|+|+||.|+++|++ +|++.++||+|.. .|+.+|+++. ..++. ...+++||||+++.+. |
T Consensus 46 f~-~~~~vEEKlDG~nvri~~~-~G~v~a~TR~G~i~e~~T~~~~eiv~--~~~~~-~~p~~iLdGElvg~~~------p 114 (342)
T cd07894 46 FK-GPVAVEEKMNGYNVRIVRI-GGKVLAFTRGGFICPFTTDRLRDLID--PEFFD-DHPDLVLCGEVVGPEN------P 114 (342)
T ss_pred CC-CCEEEEEeECCcEEEEEEE-CCEEEEEeCCCccCccchhhHhhhch--HHhhc-cCCCEEEEEEEEecCC------c
Confidence 44 5899999999999999985 7899999999864 4888998842 23332 2357999999998752 3
Q ss_pred hhhHHhhhhccCCccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCCCeEEEEeEEecCCHHHHHHHHHHH
Q 004212 527 FQTLSTRARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAA 606 (768)
Q Consensus 527 Fq~L~~R~rk~~~~~~~~~~v~~~vFDiLylnG~~L~~~Pl~ERr~lL~~l~~~~~~~i~l~~~~~~~~~eei~~~~~~a 606 (768)
|.. .... ...++.|++|||++.|+ ...+|+.+|+++|+++.-+.. ..+......+.+++.++++.+
T Consensus 115 ~v~------~~~~---~~~~v~F~vFDI~~~~~--~~~lp~~eR~~lLe~lg~~~v---~~~~~~~~~d~~~l~~~l~~~ 180 (342)
T cd07894 115 YVP------GSYP---EVEDVGFFVFDIRKKNT--GRPLPVEERRELLEKYGLPTV---RLFGEFTADEIEELKEIIREL 180 (342)
T ss_pred ccc------ccCc---cccccEEEEEeeEEcCC--CCCCCHHHHHHHHHhcCCCCc---ceEEEEecCCHHHHHHHHHHH
Confidence 311 0000 12589999999999885 557899999999999833211 222345567789999999999
Q ss_pred HHcCCceeEEeeCCCCC-----CccCCCCCCCeEEEccccc
Q 004212 607 VDASCEGLIIKTMDRDA-----TYEPSKRSLNWLKLKKDYI 642 (768)
Q Consensus 607 i~~G~EGlVlK~~~~dS-----~Y~pGkRs~~WlKvK~dy~ 642 (768)
.++|+||||+|++ ++ .|.....+-+++++.-.|.
T Consensus 181 ~~~G~EGVVlK~~--~~~~~~~Ky~t~~~~~~di~~~~~~~ 219 (342)
T cd07894 181 DKEGREGVVLKDP--DMRVPPLKYTTSYSNCSDIRYAFRYP 219 (342)
T ss_pred HHCCCceEEEecc--ccccCcceeecCCCCcHHHHHHhhhc
Confidence 9999999999999 77 7887767778888877664
No 40
>cd08040 OBF_DNA_ligase_family The Oligonucleotide/oligosaccharide binding (OB)-fold domain is a DNA-binding module that is part of the catalytic core unit of ATP dependent DNA ligases. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP dependent DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains including a DNA-binding domain, an adenylation (nucleotidyltransferase (NTase)) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The adenylation and C-terminal OB-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The catalytic core unit contains six conserved sequence motifs (I, III, IIIa, IV,
Probab=99.75 E-value=6.1e-18 Score=156.16 Aligned_cols=95 Identities=22% Similarity=0.217 Sum_probs=81.2
Q ss_pred CcccEEEEEEEcCCCCCCCccceEEEEEeeCCCCeEEEEEEeccCCCHHHHHHHHHHhccccCCCCCCCccCCCCCCCcE
Q 004212 647 DSLDLVPIAAFHGRGKRTGVYGAFLLACYDSNNEEFQSICKIGTGFSEAMLEERSSSLRSKVIPKPRPYYRFADTISPDV 726 (768)
Q Consensus 647 dtlDlvVIG~~~G~Gkr~g~~gsfLlg~~d~~~g~l~~vgkVGTGfsd~~l~~L~~~l~~~~~~~p~~~~~~~~~~~pdv 726 (768)
|++|+||+|+++|.|+++|.+|+||||+||++ .++++|+||||||++++++|++.++++..+.+++.........+++
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 47999999999999999999999999999863 4889999999999999999999999988776542211223346899
Q ss_pred EecCcceEEEEecceee
Q 004212 727 WFEPTERPETSNSPASI 743 (768)
Q Consensus 727 Wv~P~~V~EV~~aeit~ 743 (768)
|++|.+||||+|++||.
T Consensus 79 wv~P~lv~eV~~~~~t~ 95 (108)
T cd08040 79 PLYPGKVVEVKYFEMGS 95 (108)
T ss_pred EeeceEEEEEEeEEeeC
Confidence 99999999999999984
No 41
>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=99.71 E-value=5.7e-17 Score=151.43 Aligned_cols=94 Identities=22% Similarity=0.264 Sum_probs=79.9
Q ss_pred cccEEEEEEEcCCCCCCCccceEEEEEeeCCCCeEEEEEEeccCCCHHHHHHHHHHhccccCCCCCCCccCCCCCCCcEE
Q 004212 648 SLDLVPIAAFHGRGKRTGVYGAFLLACYDSNNEEFQSICKIGTGFSEAMLEERSSSLRSKVIPKPRPYYRFADTISPDVW 727 (768)
Q Consensus 648 tlDlvVIG~~~G~Gkr~g~~gsfLlg~~d~~~g~l~~vgkVGTGfsd~~l~~L~~~l~~~~~~~p~~~~~~~~~~~pdvW 727 (768)
+.|+||+|++.+.| +.|.+|+||||+||+ ++|++||+||||||++++++|++.|+++.++.+|..........+++|
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 589999999999999999999999999987765332222234468999
Q ss_pred ecCcceEEEEecceeec
Q 004212 728 FEPTERPETSNSPASIV 744 (768)
Q Consensus 728 v~P~~V~EV~~aeit~S 744 (768)
|+|.+||||+|++||.+
T Consensus 79 v~P~lv~eV~~~~~t~~ 95 (115)
T cd07971 79 VKPELVAEVEFAEWTPD 95 (115)
T ss_pred ecCCEEEEEEEEEecCC
Confidence 99999999999999854
No 42
>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=99.68 E-value=1e-16 Score=145.33 Aligned_cols=82 Identities=32% Similarity=0.458 Sum_probs=66.8
Q ss_pred CCCccceEEEEEeeCCCCeEEEEEEeccCCCHHHHHHHHHHhccccCCCCCCCccCCCCCCCcEEecCcceEEEEeccee
Q 004212 663 RTGVYGAFLLACYDSNNEEFQSICKIGTGFSEAMLEERSSSLRSKVIPKPRPYYRFADTISPDVWFEPTERPETSNSPAS 742 (768)
Q Consensus 663 r~g~~gsfLlg~~d~~~g~l~~vgkVGTGfsd~~l~~L~~~l~~~~~~~p~~~~~~~~~~~pdvWv~P~~V~EV~~aeit 742 (768)
|+|.+|+||||+||+++|+|++||+||||||++++++|.+.|++++++.+|.........+|++||+|.+||||+|+|||
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 56889999999999887999999999999999999999999999988776443333333579999999999999999999
Q ss_pred ec
Q 004212 743 IV 744 (768)
Q Consensus 743 ~S 744 (768)
.|
T Consensus 81 ~~ 82 (97)
T PF04679_consen 81 PS 82 (97)
T ss_dssp EE
T ss_pred CC
Confidence 88
No 43
>cd07970 OBF_DNA_ligase_LigC The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase LigC is a DNA-binding module that is part of the catalytic core unit. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriohages, eukarya, archaea and bacteria. Bacterial DNA ligases are divided into two broad classes: NAD-dependent and ATP-dependent. All bacterial species have a NAD-dependent DNA ligase (LigA). Some bacterial genomes contain multiple genes for DNA ligases that are predicted to use ATP as their cofactor, including Mycobacterium tuberculosis LigB, LigC, and LigD. This group is composed of Mycobacterium tuberculosis LigC and similar ba
Probab=99.55 E-value=3.4e-14 Score=134.34 Aligned_cols=93 Identities=17% Similarity=0.112 Sum_probs=75.1
Q ss_pred CcccEEEEEEEcCCCCCCCccceEEEEEeeCCCCeEEEEEEeccCCCHHHHHHHHHHhccccCCCCCC-----Ccc-CC-
Q 004212 647 DSLDLVPIAAFHGRGKRTGVYGAFLLACYDSNNEEFQSICKIGTGFSEAMLEERSSSLRSKVIPKPRP-----YYR-FA- 719 (768)
Q Consensus 647 dtlDlvVIG~~~G~Gkr~g~~gsfLlg~~d~~~g~l~~vgkVGTGfsd~~l~~L~~~l~~~~~~~p~~-----~~~-~~- 719 (768)
|+.|+||+|+.++. +.+|+++||+||+ +|+|+|||+| ||||++++++|++.|+++.++.|++ |.. ++
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 47899999988775 5689999999975 4789999999 9999999999999999987765421 211 11
Q ss_pred CCCCCcEEecCcceEEEEecceeecC
Q 004212 720 DTISPDVWFEPTERPETSNSPASIVY 745 (768)
Q Consensus 720 ~~~~pdvWv~P~~V~EV~~aeit~Sp 745 (768)
....+.+|++|.+||||+|.+||.+.
T Consensus 75 ~~~~~~~wv~P~lV~eV~~~e~t~~G 100 (122)
T cd07970 75 RKSLEWVPVRPELVVEVSADTAEGGG 100 (122)
T ss_pred ccCCCeEEeeccEEEEEEeeEEecCC
Confidence 12347899999999999999998754
No 44
>PF01331 mRNA_cap_enzyme: mRNA capping enzyme, catalytic domain; InterPro: IPR001339 The mRNA capping enzyme in yeasts is composed of two separate chains, alpha a mRNA guanyltransferase and beta an RNA 5'-triphosphate. X-ray crystallography reveals a large conformational change during guanyl transfer by mRNA capping enzymes []. Binding of the enzyme to nucleotides is specific to the GMP moiety of GTP. The viral mRNA capping enzyme is a monomer that transfers a GMP cap onto the end of mRNA that terminates with a 5'-diphosphate tail.; GO: 0004484 mRNA guanylyltransferase activity, 0006370 mRNA capping, 0006397 mRNA processing; PDB: 3RTX_A 3KYH_D 3S24_G 1CKN_B 1CKO_A 1CKM_B 1P16_B.
Probab=99.30 E-value=1.9e-12 Score=131.05 Aligned_cols=158 Identities=22% Similarity=0.275 Sum_probs=103.8
Q ss_pred CCceEEeeecceEeEEEEEecCCeEEEEcCCcccCC---CCCchHHHHHHhhcCCCCCCeEEEEEEEEEecCCCcccChh
Q 004212 452 DMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNT---GKFPDVVLAVSRLKKPSVRSFVLDCEIVAYDREKQKILPFQ 528 (768)
Q Consensus 452 g~~~~~E~KyDG~R~qih~~~~g~V~lfSR~g~d~T---~~fPel~~~l~~~~~~~~~~~ILDGElVa~d~~~g~~~pFq 528 (768)
..+|++.+|-||.|+++.+. ++.+.++.|+.+-+- -.+|--.+ ........+.+||||||. |...+
T Consensus 15 ~~~Y~V~eKaDG~Ryll~i~-~~~~ylidr~~~~~~v~~~~~p~~~~---~~~~~~~~~TLLDGElV~-d~~~~------ 83 (192)
T PF01331_consen 15 QKDYFVCEKADGTRYLLLIT-DNGVYLIDRKNNVFKVDNLHFPSKKD---SSDGRHHQDTLLDGELVL-DKDPG------ 83 (192)
T ss_dssp HS-EEEEEEESSEEEEEEEE-EEEEEEEETTS-EEEESSST-ECTTC-----TTCEGCSEEEEEEEEE-EECTT------
T ss_pred hCCcEEEECCCCcEEEEEEe-cceEEEEeCCCcEEEecCcccccccc---cccccccCCEEEEEEEEc-ccCCC------
Confidence 34799999999999999986 458999999987543 12333110 000112368999999986 32211
Q ss_pred hHHhhhhccCCccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccC----------------CCeEEEEeEEe
Q 004212 529 TLSTRARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEE----------------PGFFQFATTLT 592 (768)
Q Consensus 529 ~L~~R~rk~~~~~~~~~~v~~~vFDiLylnG~~L~~~Pl~ERr~lL~~l~~~~----------------~~~i~l~~~~~ 592 (768)
....+|++||+|++||+++.+.|+.+|...|++.+.+. +-.+.+-+...
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 24689999999999999999999999999997654320 11233333344
Q ss_pred cCCHHH-HHHHHHHHHHcCCceeEEeeCCCCCCccCCCCCCCeEEEc
Q 004212 593 SIDLDE-IQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLK 638 (768)
Q Consensus 593 ~~~~ee-i~~~~~~ai~~G~EGlVlK~~~~dS~Y~pGkRs~~WlKvK 638 (768)
....+. +...+..-+.++..|||.-.. +.+|.+| +..+++|||
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 443433 222223335678899999999 9999999 678999998
No 45
>COG1423 ATP-dependent DNA ligase, homolog of eukaryotic ligase III [DNA replication, recombination, and repair]
Probab=98.91 E-value=1.6e-08 Score=108.72 Aligned_cols=148 Identities=20% Similarity=0.211 Sum_probs=107.9
Q ss_pred hhcCCCceEEeeecceEeEEEEEecCCeEEEEcCCcccC---CCCCchHHHHHHhhcCCCCCCeEEEEEEEEEecCCCcc
Q 004212 448 NKFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERN---TGKFPDVVLAVSRLKKPSVRSFVLDCEIVAYDREKQKI 524 (768)
Q Consensus 448 ~k~~g~~~~~E~KyDG~R~qih~~~~g~V~lfSR~g~d~---T~~fPel~~~l~~~~~~~~~~~ILDGElVa~d~~~g~~ 524 (768)
+.|+.+.+++|.|.||+.+.|.+. +|++.-.||.|--+ |.+.+++.+. +.+. ...+.||.||||..++
T Consensus 83 ~~F~~~~v~VEEKmnGYNVRV~k~-~g~vyAiTRgG~ICPfTT~r~~~l~~~--eff~-d~p~lvlcgEmvG~en----- 153 (382)
T COG1423 83 KHFGRGKVVVEEKMNGYNVRVVKL-GGEVYAITRGGLICPFTTERLRDLIDL--EFFD-DYPDLVLCGEMVGPEN----- 153 (382)
T ss_pred hhcCCCcEEEEEeccCceEEEEEE-CCEEEEEecCceecCchhHHHHhhcch--hhHh-hCCCcEEEEEeccCCC-----
Confidence 357777999999999999999986 78999999999864 4555555432 3333 2478999999998652
Q ss_pred cChhhHHhhhhccCCccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCCCeEEEEeEEecCCH-HHHHHHH
Q 004212 525 LPFQTLSTRARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDL-DEIQKFL 603 (768)
Q Consensus 525 ~pFq~L~~R~rk~~~~~~~~~~v~~~vFDiLylnG~~L~~~Pl~ERr~lL~~l~~~~~~~i~l~~~~~~~~~-eei~~~~ 603 (768)
|+-. .. --...++.|++|||...|.. ..+|.+||++++++.--+ ++.+......++. +++.++.
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------GP---YYEKEDVGFFVFDIREKNTG--RPLPVEERLELAEKYGLP---HVEIFGEFPADEAGEEIYEIV 218 (382)
T ss_pred -CCCC------CC---CCccCCceEEEEEEEecCCC--CCCCHHHHHHHHHHcCCC---ceEEeeeechhHhHHHHHHHH
Confidence 2211 00 01246899999999987643 247999999999987432 2333333444455 7888888
Q ss_pred HHHHHcCCceeEEeeC
Q 004212 604 DAAVDASCEGLIIKTM 619 (768)
Q Consensus 604 ~~ai~~G~EGlVlK~~ 619 (768)
++.-.+|.||||+|++
T Consensus 219 e~L~keGREGVV~Kdp 234 (382)
T COG1423 219 ERLNKEGREGVVMKDP 234 (382)
T ss_pred HHHhhcCCcceEecCc
Confidence 8888999999999999
No 46
>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=98.76 E-value=7.6e-08 Score=106.10 Aligned_cols=148 Identities=21% Similarity=0.272 Sum_probs=97.6
Q ss_pred hcCCCceEEeeecceEeEEEEEecCCeEEEEcCCcccC---CCCCchHHHHHHhhcCCCCCCeEEEEEEEEEecCCCccc
Q 004212 449 KFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERN---TGKFPDVVLAVSRLKKPSVRSFVLDCEIVAYDREKQKIL 525 (768)
Q Consensus 449 k~~g~~~~~E~KyDG~R~qih~~~~g~V~lfSR~g~d~---T~~fPel~~~l~~~~~~~~~~~ILDGElVa~d~~~g~~~ 525 (768)
.|.+..+++|+|.||+.+-|.. -+|++..+||.|... |++++++.+ ...+.+ ..+.+|.||++.-+.
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 4667669999999999999966 478999999999875 222344433 244543 378999999997532
Q ss_pred ChhhHHhhhhccCCccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCCCeEEEEeEEecCC-HHHHHHHHH
Q 004212 526 PFQTLSTRARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEPGFFQFATTLTSID-LDEIQKFLD 604 (768)
Q Consensus 526 pFq~L~~R~rk~~~~~~~~~~v~~~vFDiLylnG~~L~~~Pl~ERr~lL~~l~~~~~~~i~l~~~~~~~~-~eei~~~~~ 604 (768)
|+.. .. ......+..|++|||.. ...-.-+|..+|+++++++--+....+.. ....+ .+++.++.+
T Consensus 145 pY~~------hs--~~y~~l~~~FfvFDI~d--~~t~~~L~~~er~~l~e~yglp~Vpvlg~---~~~~~~~~~~~eii~ 211 (374)
T TIGR01209 145 PYTP------EY--YPEVKEDLGFFLFDIRE--GKTNRSLPVEERLELAEKYGLPHVEILGV---YTADEAVEEIYEIIE 211 (374)
T ss_pred CCcc------cC--ccccCCCceEEEEEEEE--CCCCccCCHHHHHHHHHHCCCCccceeeE---EcHHHHHHHHHHHHH
Confidence 1110 00 11113478999999973 33345679999999999873221112111 12222 235666767
Q ss_pred HHHHcCCceeEEeeC
Q 004212 605 AAVDASCEGLIIKTM 619 (768)
Q Consensus 605 ~ai~~G~EGlVlK~~ 619 (768)
..-+.|.||||+|++
T Consensus 212 ~L~~~gREGVVlK~~ 226 (374)
T TIGR01209 212 RLNKEGREGVVMKDP 226 (374)
T ss_pred HhhhcCcceEEEcCc
Confidence 777899999999998
No 47
>COG5226 CEG1 mRNA capping enzyme, guanylyltransferase (alpha) subunit [RNA processing and modification]
Probab=98.69 E-value=1.7e-08 Score=106.55 Aligned_cols=171 Identities=23% Similarity=0.286 Sum_probs=115.4
Q ss_pred CceEEeeecceEeEEEEEecC---C--eEEEEcCCcccC---CCCCchHHHHHH-hhcCCCCCCeEEEEEEEEEecCCCc
Q 004212 453 MEFTCEYKYDGERAQIHYLED---G--SVEIYSRNAERN---TGKFPDVVLAVS-RLKKPSVRSFVLDCEIVAYDREKQK 523 (768)
Q Consensus 453 ~~~~~E~KyDG~R~qih~~~~---g--~V~lfSR~g~d~---T~~fPel~~~l~-~~~~~~~~~~ILDGElVa~d~~~g~ 523 (768)
.+|++.+|-||.||++.+.++ | .+.+|.|..+-| +..||.+..... +.+ ..+..||||+|. |
T Consensus 62 ~dy~VCEKsDGvR~Ll~vte~p~tg~~~~y~~DR~nnfY~v~~~f~p~~~~~k~ge~l---~~dtlldgelV~-d----- 132 (404)
T COG5226 62 NDYLVCEKSDGVRALLLVTEEPVTGAFRGYFYDRRNNFYEVHTSFPPCSTVLKDGEVL---LEDTLLDGELVF-D----- 132 (404)
T ss_pred CCeEEEEccCCeEEEEEEEecccCCCcceEEEeccCceEEeccccCCcccccccCcEE---eccceecceEEE-E-----
Confidence 479999999999999888642 2 478899988644 334453322111 111 257789999986 3
Q ss_pred ccChhhHHhhhhccCCccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCC-----------CeEEEEeEEe
Q 004212 524 ILPFQTLSTRARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEP-----------GFFQFATTLT 592 (768)
Q Consensus 524 ~~pFq~L~~R~rk~~~~~~~~~~v~~~vFDiLylnG~~L~~~Pl~ERr~lL~~l~~~~~-----------~~i~l~~~~~ 592 (768)
..|...+ .++.|.+||+|.+||..+..++..+|.+.|.+-+..-. +.+.+- +.
T Consensus 133 ~~p~~k~--------------~qlryl~fdcLa~~g~~~~~~~~s~Rl~~l~Ke~~kp~~~~r~s~~~~~~~fpf~--~s 196 (404)
T COG5226 133 CLPYEKV--------------PQLRYLLFDCLAYAGMFVERMEKSERLKTLQKEDEKPRERKRVSIEIDSGSFPFH--FS 196 (404)
T ss_pred eccccch--------------HHHHHHHHHHhhhcceeEeecchhhHHHHhhhhhcccHhhhhheeecccccccee--ee
Confidence 2344333 35678899999999999999999999999987664210 111110 00
Q ss_pred cCCH---HHHHHHHHHH--HHcCCceeEEeeCCCCCCccCCCCCCCeEEEccccccccCCcccEEEEE
Q 004212 593 SIDL---DEIQKFLDAA--VDASCEGLIIKTMDRDATYEPSKRSLNWLKLKKDYIESIGDSLDLVPIA 655 (768)
Q Consensus 593 ~~~~---eei~~~~~~a--i~~G~EGlVlK~~~~dS~Y~pGkRs~~WlKvK~dy~~~~~dtlDlvVIG 655 (768)
.... -.+.++|+.. +.+|..|+|.-.. +.+|..|++ ...|||||.-+ .|+|+..|=
T Consensus 197 ~K~M~~syg~~ki~k~ip~L~HgnDGLIFTp~--~~PY~~Gkd-~~lLKWKP~~~----NTiDF~lvl 257 (404)
T COG5226 197 VKQMLKSYGFWKIYKKIPELKHGNDGLIFTPA--DEPYSVGKD-GALLKWKPASL----NTIDFRLVL 257 (404)
T ss_pred HHHHHhhhhHHHHHhhcccccCCCCceEeccC--CCCcccCcc-ceeeecCcccc----Cceeeeeee
Confidence 1111 1344455332 3689999999999 999999976 48999999876 488987654
No 48
>cd08041 OBF_kDNA_ligase_like The Oligonucleotide/oligosaccharide binding (OB)-fold domain of kDNA ligase-like ATP-dependent DNA ligases is a DNA-binding module that is part of the catalytic core unit. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriohages, eukarya, archaea and bacteria. The mitochondrial DNA of parasitic protozoan is highly unusual. It is termed the kinetoplast DNA (kDNA) and consists of circular DNA molecules (maxicircles) and several thousand smaller circular molecules (minicircles). This group is composed of kDNA ligase, Chlorella virus DNA ligase, and similar proteins. kDNA ligase and Chlorella virus DNA ligase are the smallest known ATP-de
Probab=98.64 E-value=6.2e-08 Score=84.48 Aligned_cols=63 Identities=21% Similarity=0.261 Sum_probs=54.3
Q ss_pred cccEEEEEEEcCCCCCCCccceEEEEEeeCCCCeEEEEEEeccCCCHHHHHHHHHHhccccCCCCCCCccCCCCCCCcEE
Q 004212 648 SLDLVPIAAFHGRGKRTGVYGAFLLACYDSNNEEFQSICKIGTGFSEAMLEERSSSLRSKVIPKPRPYYRFADTISPDVW 727 (768)
Q Consensus 648 tlDlvVIG~~~G~Gkr~g~~gsfLlg~~d~~~g~l~~vgkVGTGfsd~~l~~L~~~l~~~~~~~p~~~~~~~~~~~pdvW 727 (768)
+.|++|+|+++|.|++.|.+|+|+|+.+| |. +++||||||++++++++. +
T Consensus 2 ~~e~vIvG~~~g~g~~~~~~g~llv~~~~---g~---~~~vgtG~t~~~r~~~~~------------~------------ 51 (77)
T cd08041 2 DAEARVVGYEEGKGKYEGMLGALVVETKD---GI---RFKIGSGFSDEQRRNPPP------------I------------ 51 (77)
T ss_pred ceeEEEEEEEcCCCccCCcEEEEEEEecC---CC---EEEEcCCCCHHHHhcCCC------------C------------
Confidence 68999999999999999999999999987 33 469999999999998871 0
Q ss_pred ecCcceEEEEecceee
Q 004212 728 FEPTERPETSNSPASI 743 (768)
Q Consensus 728 v~P~~V~EV~~aeit~ 743 (768)
..|+||+|.++|.
T Consensus 52 ---g~v~~V~y~e~t~ 64 (77)
T cd08041 52 ---GSIITYKYQGLTK 64 (77)
T ss_pred ---CCEEEEEEEecCC
Confidence 1499999999985
No 49
>cd09232 Snurportin-1_C C-terminal m3G cap-binding domain of nuclear import adaptor snurportin-1. Snurportin-1 (SPN1 or SNUPN) is a nuclear import adaptor for m3G-capped spliceosomal U small nucleoproteins (snRNPs), which are assembled in the cytoplasm. After capping and assembly, the U snRNPs are transported into the nucleus by SPN1 and importin beta; SPN1 is then returned to the cytoplasm by exportin 1 (CRM1), which also transports the non-capped U snRNPs. The U snRNPs are essential elements of the spliceosome, which catalyzes the excision of introns and the ligation of exons to form a mature mRNA. SPN1 contains two domains, an N-terminal importin beta-binding (IBB) domain and a C-terminal m3G cap-binding domain.
Probab=98.57 E-value=3.6e-07 Score=92.67 Aligned_cols=152 Identities=20% Similarity=0.204 Sum_probs=111.6
Q ss_pred CceEEeeecceEeEEEEEecCCeEEEEcCCcccCCCCCchHHHHHHhhcCCCCCCeEEEEEEEEEecCCCcccChhhHHh
Q 004212 453 MEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAVSRLKKPSVRSFVLDCEIVAYDREKQKILPFQTLST 532 (768)
Q Consensus 453 ~~~~~E~KyDG~R~qih~~~~g~V~lfSR~g~d~T~~fPel~~~l~~~~~~~~~~~ILDGElVa~d~~~g~~~pFq~L~~ 532 (768)
.+|.+=+-==|.|++|... +|.+.+++|+|.-+. .|+. .++.+...--+|||+|. |-.-+
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 4688888888999999986 889999999997742 2211 11111000034444442 21101
Q ss_pred hhhccCCccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCC----------CeEEEEeEEecCCHHHHHHH
Q 004212 533 RARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEP----------GFFQFATTLTSIDLDEIQKF 602 (768)
Q Consensus 533 R~rk~~~~~~~~~~v~~~vFDiLylnG~~L~~~Pl~ERr~lL~~l~~~~~----------~~i~l~~~~~~~~~eei~~~ 602 (768)
+...+|+|+|||.+||.++.+.+...|...|++-+.+.+ -.++..+...++. +.+++.
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 123589999999999999999999999999999887743 1455666666654 678888
Q ss_pred HHHHH---HcCCceeEEeeCCCCCCccCCCCCCCeEEEcc
Q 004212 603 LDAAV---DASCEGLIIKTMDRDATYEPSKRSLNWLKLKK 639 (768)
Q Consensus 603 ~~~ai---~~G~EGlVlK~~~~dS~Y~pGkRs~~WlKvK~ 639 (768)
|...+ ..-..|++.-.. ++.|++| +++.|+|+|+
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 889999999999 8899998 7899999997
No 50
>smart00532 LIGANc Ligase N family.
Probab=98.19 E-value=0.0001 Score=84.01 Aligned_cols=239 Identities=16% Similarity=0.201 Sum_probs=142.1
Q ss_pred ccccc-ccCChHHHH---hhcC---C--CceEEeeecceEeEEEEEecCCe-EEEEcC----CcccCCCCCchHHHHHHh
Q 004212 434 PMLAK-PTKGVSEIV---NKFQ---D--MEFTCEYKYDGERAQIHYLEDGS-VEIYSR----NAERNTGKFPDVVLAVSR 499 (768)
Q Consensus 434 PMLA~-~~~~i~~il---~k~~---g--~~~~~E~KyDG~R~qih~~~~g~-V~lfSR----~g~d~T~~fPel~~~l~~ 499 (768)
|||.- .+.+.+++. ++.. + ..|++|+|+||.-+.+.+ ++|+ ++..|| .|+|+|+...-+.. +..
T Consensus 75 pMlSL~k~~~~~el~~f~~~~~~~~~~~~~~~~epKiDGlsisL~Y-e~G~l~~a~TRGDG~~GeDVT~nv~~i~~-iP~ 152 (441)
T smart00532 75 PMLSLDNAFDEDELRAFDERIEKALGSPFAYVVEPKIDGLSVSLLY-ENGKLVQAATRGDGTVGEDVTQNVKTIRS-IPL 152 (441)
T ss_pred cccCccccCCHHHHHHHHHHHHHhcCCCceEEEEEecccEEEEEEE-ECCEEEEEEecCCCCcceehhhhhhhhcC-cCh
Confidence 99974 233444442 2211 1 268999999999999998 4777 889999 79999985432211 111
Q ss_pred hcCC-CCCCeEEEEEEEEEecCCCcccChhhH---------------Hhhh----hccCCccccccceEEEEeeeeecCC
Q 004212 500 LKKP-SVRSFVLDCEIVAYDREKQKILPFQTL---------------STRA----RKNVSLSDIKVDVCIYAFDILYRNG 559 (768)
Q Consensus 500 ~~~~-~~~~~ILDGElVa~d~~~g~~~pFq~L---------------~~R~----rk~~~~~~~~~~v~~~vFDiLylnG 559 (768)
.+.. ....+.+-||++.-. ..|+.+ .+.+ |..........++.|++|++...++
T Consensus 153 ~i~~~~p~~leiRGEv~~~~------~~F~~ln~~~~~~g~~~faNpRN~aAG~lr~ld~~~~~~r~L~~~~y~~~~~~~ 226 (441)
T smart00532 153 RLSGDVPERLEVRGEVFMPK------EDFLALNEELEEEGEKPFANPRNAAAGSLRQLDPRITAKRKLRAFFYGLGTGEE 226 (441)
T ss_pred hhcccCCCeEEEEceEEEEH------HHHHHHHHHHHhcCCCcccChHHHHHHHHHhcCchhhhhccceEEEEEcccCCC
Confidence 1111 013588999999743 234443 1111 1100011124589999999864443
Q ss_pred ccccCCcHHHHHHHHHHhhccCCCeEEEEeEEecCCHHHHHHHHHHHHH------cCCceeEEeeCCCCCCccC--C--C
Q 004212 560 QPLLQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAAVD------ASCEGLIIKTMDRDATYEP--S--K 629 (768)
Q Consensus 560 ~~L~~~Pl~ERr~lL~~l~~~~~~~i~l~~~~~~~~~eei~~~~~~ai~------~G~EGlVlK~~~~dS~Y~p--G--k 629 (768)
... .....++.+.|.++-=....... .+.+.+++.++++...+ -...|||+|-- +-.+.. | .
T Consensus 227 ~~~-~~t~~e~l~~L~~~GF~v~~~~~-----~~~~~~ei~~~~~~~~~~r~~l~y~iDGiViKvn--~~~~~~~lG~ts 298 (441)
T smart00532 227 LFL-PKTQSEALKWLKELGFPVSPHTR-----LCKNADEVIEYYEEWEEKRAELPYEIDGVVVKVD--DLALQRELGFTS 298 (441)
T ss_pred CCC-ccCHHHHHHHHHHCCCCCCCCeE-----eeCCHHHHHHHHHHHHHhcccCCCCcCcEEEEec--CHHHHHHhCccC
Confidence 211 24678899999887333322222 24678888888887654 47789999986 544442 2 3
Q ss_pred CCCCe---EEEccccccccCCcccEEEEEEEcCCCCCCCccceEEEEEeeCC--CCeEEEEEEeccCCCHHHHHHHH
Q 004212 630 RSLNW---LKLKKDYIESIGDSLDLVPIAAFHGRGKRTGVYGAFLLACYDSN--NEEFQSICKIGTGFSEAMLEERS 701 (768)
Q Consensus 630 Rs~~W---lKvK~dy~~~~~dtlDlvVIG~~~G~Gkr~g~~gsfLlg~~d~~--~g~l~~vgkVGTGfsd~~l~~L~ 701 (768)
+.+.| +|+..+ ...-.|.+..|--| |+|.+... |..++- .|. +|.++ |..+.+.++++.
T Consensus 299 ~~PrwaiA~Kf~~~-------~~~T~l~~I~~qVG-RTG~iTPv--A~lePV~l~G~--tVsrA-TLhN~~~i~~~~ 362 (441)
T smart00532 299 KAPRWAIAYKFPAE-------EAETKLLDIIVQVG-RTGKITPV--AELEPVFLAGS--TVSRA-TLHNEDEIEEKD 362 (441)
T ss_pred CCCCeeEEECCCCc-------eeEEEEEEEEEecC-CCceeeEE--EEEEeEEECCE--EEEec-ccCCHHHHHHcC
Confidence 46778 566654 45556666666555 45655543 333331 254 45665 788888887754
No 51
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=98.14 E-value=0.0002 Score=83.65 Aligned_cols=232 Identities=13% Similarity=0.127 Sum_probs=138.2
Q ss_pred ccccc-ccCChHHHHhhcCC--CceEEeeecceEeEEEEEecCCe-EEEEcC----CcccCCCCCchHHHHHHhhcCCCC
Q 004212 434 PMLAK-PTKGVSEIVNKFQD--MEFTCEYKYDGERAQIHYLEDGS-VEIYSR----NAERNTGKFPDVVLAVSRLKKPSV 505 (768)
Q Consensus 434 PMLA~-~~~~i~~il~k~~g--~~~~~E~KyDG~R~qih~~~~g~-V~lfSR----~g~d~T~~fPel~~~l~~~~~~~~ 505 (768)
|||.- .+.+.+++.+ |-. .+|++|+|+||.-+.+.+. +|+ ++..|| -|+|+|+..--+ ..+...++...
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 3445555532 211 2599999999999999984 676 789999 788888753222 11222222111
Q ss_pred CCeEEEEEEEEEecCCCcccChhhHH-----------hhhhccCCccccccceEEEEeeeeecCCccccCCcHHHHHHHH
Q 004212 506 RSFVLDCEIVAYDREKQKILPFQTLS-----------TRARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHL 574 (768)
Q Consensus 506 ~~~ILDGElVa~d~~~g~~~pFq~L~-----------~R~rk~~~~~~~~~~v~~~vFDiLylnG~~L~~~Pl~ERr~lL 574 (768)
..+.+-||++.-. ..|+... .-.|.. +......++.|++|++. +| .....++.+.|
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 2354322 111110 01112568999999983 44 24678888888
Q ss_pred HHhhccCCC-eEEEEeEEecCCHHHHHHHHHHHHH----cCCceeEEeeCCCCCCccC--CCCCCCe---EEEccccccc
Q 004212 575 YDSFEEEPG-FFQFATTLTSIDLDEIQKFLDAAVD----ASCEGLIIKTMDRDATYEP--SKRSLNW---LKLKKDYIES 644 (768)
Q Consensus 575 ~~l~~~~~~-~i~l~~~~~~~~~eei~~~~~~ai~----~G~EGlVlK~~~~dS~Y~p--GkRs~~W---lKvK~dy~~~ 644 (768)
+++-=+... ... .+.+.+++.++++.... -...|+|+|-- +-.|.. +.+.+.| +|+..+
T Consensus 241 ~~~GF~v~~~~~~-----~~~~~~~i~~~~~~~~r~~l~y~iDGiViKvn--~~~~~~~~ts~~PrWAiAyKf~~~---- 309 (562)
T PRK08097 241 ATAGFPLTQRYTH-----PVKNAEEVARWRERWYRAPLPFVTDGVVVRQA--KEPPGRYWQPGQGEWAVAWKYPPV---- 309 (562)
T ss_pred HHCCCCcCccceE-----eeCCHHHHHHHHHHHhhccCCCCCCcEEEEec--CHHHHhhccCCCCCceEEEcCCCc----
Confidence 887433332 211 24567888877765432 47889999986 545543 3456788 565553
Q ss_pred cCCcccEEEEEEEcCCCCCCCccceEEEEEeeCC--CCeEEEEEEeccCCCHHHHHHHH
Q 004212 645 IGDSLDLVPIAAFHGRGKRTGVYGAFLLACYDSN--NEEFQSICKIGTGFSEAMLEERS 701 (768)
Q Consensus 645 ~~dtlDlvVIG~~~G~Gkr~g~~gsfLlg~~d~~--~g~l~~vgkVGTGfsd~~l~~L~ 701 (768)
+..-.+.+..+.-| |+|.+... |..++- .|. +|.++ |-...+..+++.
T Consensus 310 ---~~~T~l~~I~~qVG-RTG~iTPV--A~lePV~l~Gt--tVsrA-TLhN~~~i~~~~ 359 (562)
T PRK08097 310 ---QQVAEVRAVQFAVG-RTGKITVV--LELEPVMLDDK--RVSRV-NIGSVRRWQQWD 359 (562)
T ss_pred ---EEEEEEEEEEEecC-CCceeeEE--EEEEEEEeCCE--EEEEe-ecCCHHHHHHcC
Confidence 45556777666655 45655543 333331 354 45565 667777776643
No 52
>PRK01109 ATP-dependent DNA ligase; Provisional
Probab=98.14 E-value=7e-06 Score=96.95 Aligned_cols=93 Identities=26% Similarity=0.373 Sum_probs=86.2
Q ss_pred CccchHHHHHHHHHHHhhh---chHHHHHHHHHHHHhhhcCCCCchHHHHHHHhCccCCCccccccCCCHHHHHHHHHHH
Q 004212 189 ERVPFIFLSLVFDMISNET---GRILITDIVCNMLRTVMETTPEDLVPVVYLAANKIAPAHEGLELGIGDASIIKALAEA 265 (768)
Q Consensus 189 ~~~~F~~la~l~e~I~~ts---sr~~k~~iL~~~fr~~i~~~p~dl~~~vyl~~~~l~P~~e~~elGIg~~~L~Kal~~a 265 (768)
.+++|.++.+.|++|++++ ++.+|+++|.++|+.+ +++++.+.+++++|.+. +|++++++.+||+++
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 5789999999999999998 8999999999999996 78999999999999765 899999999999999
Q ss_pred hC--CCHHHHHHHHhhhCChHHHHhhhc
Q 004212 266 CG--RTESHVKKQYQEMGDLGLVAKASR 291 (768)
Q Consensus 266 ~G--~s~~~ik~~y~~~GDlg~vA~~~r 291 (768)
+| .+...+++.|...||+|.||..+.
T Consensus 183 ~~~~~~~~~ve~~y~~~~Dlg~va~~l~ 210 (590)
T PRK01109 183 FGGAVARELVERAYNLRADLGYIAKILA 210 (590)
T ss_pred HhcccchHHHHHHHHhCCCHHHHHHHHH
Confidence 99 999999999999999999987654
No 53
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=97.97 E-value=0.0004 Score=83.17 Aligned_cols=219 Identities=17% Similarity=0.226 Sum_probs=133.2
Q ss_pred ceEEeeecceEeEEEEEecCCe-EEEEcC----CcccCCCCCchHHHHHHhhcC-CCCCCeEEEEEEEEEecCCCcccCh
Q 004212 454 EFTCEYKYDGERAQIHYLEDGS-VEIYSR----NAERNTGKFPDVVLAVSRLKK-PSVRSFVLDCEIVAYDREKQKILPF 527 (768)
Q Consensus 454 ~~~~E~KyDG~R~qih~~~~g~-V~lfSR----~g~d~T~~fPel~~~l~~~~~-~~~~~~ILDGElVa~d~~~g~~~pF 527 (768)
.|++|+|+||.-+.+.+. +|+ ++..|| .|+|+|+..--+. .|...+. .....+.+-||++.-. ..|
T Consensus 109 ~~~~epKiDGlsisL~Y~-~G~L~~a~TRGDG~~GeDvT~n~~~I~-~IP~~l~~~~p~~levRGEv~m~~------~~F 180 (665)
T PRK07956 109 TYLCELKIDGLAVSLLYE-NGVLVRAATRGDGTTGEDITANVRTIR-SIPLRLHGNEPERLEVRGEVFMPK------ADF 180 (665)
T ss_pred ceEEEEecccEEEEEEEE-CCEEEEEEecCCCccchhHhhhhhhhc-cCChhhcccCCCeEEEEEEEEEEH------HHH
Confidence 599999999999999984 676 788999 7899997532221 1111121 0114588999999742 235
Q ss_pred hhHHhh---------------h----hccCCccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCCCeEEEE
Q 004212 528 QTLSTR---------------A----RKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEPGFFQFA 588 (768)
Q Consensus 528 q~L~~R---------------~----rk~~~~~~~~~~v~~~vFDiLylnG~~L~~~Pl~ERr~lL~~l~~~~~~~i~l~ 588 (768)
+.+-.+ + |..........++.|++|++...++ ........++.+.|.++-=++.....
T Consensus 181 ~~lN~~~~~~g~~~faNpRNaaAGslr~ld~~~~~~r~L~f~~y~~~~~~~-~~~~~t~~e~l~~L~~~GF~v~~~~~-- 257 (665)
T PRK07956 181 EALNEERREEGEKPFANPRNAAAGSLRQLDPKITAKRPLSFFAYGVGEVEG-GELPDSQSEALEFLKAWGFPVNPYRK-- 257 (665)
T ss_pred HHHHHHHHhcCCCcccChHHHHhhhhhccChHHHhcCCCEEEEEecccccC-CCCCCCHHHHHHHHHHCCCCcCCceE--
Confidence 544221 1 1000001124689999999864432 11134778899999887433332222
Q ss_pred eEEecCCHHHHHHHHHHHHH------cCCceeEEeeCCCCCCcc----CCCCCCCe---EEEccccccccCCcccEEEEE
Q 004212 589 TTLTSIDLDEIQKFLDAAVD------ASCEGLIIKTMDRDATYE----PSKRSLNW---LKLKKDYIESIGDSLDLVPIA 655 (768)
Q Consensus 589 ~~~~~~~~eei~~~~~~ai~------~G~EGlVlK~~~~dS~Y~----pGkRs~~W---lKvK~dy~~~~~dtlDlvVIG 655 (768)
.+.+.+++.++++...+ -...|||+|-- +-.|. ...+.+.| +|+..+ ...-.|.+
T Consensus 258 ---~~~~~~ei~~~~~~~~~~R~~l~y~iDGiViKvn--~~~~~~~lG~t~~~PrWaiA~Kf~~~-------~~~T~l~~ 325 (665)
T PRK07956 258 ---LCTSIEEVLAFYEEIEEERHDLPYDIDGVVIKVD--DLALQEELGFTAKAPRWAIAYKFPAE-------EATTKLLD 325 (665)
T ss_pred ---eeCCHHHHHHHHHHHHHhhccCCCCCCcEEEEec--CHHHHHhcCccCCCCCceeEecCCCc-------eeEEEEEE
Confidence 24678889888877653 47789999986 43332 12356788 666664 45556777
Q ss_pred EEcCCCCCCCccceEEEEEeeCC--CCeEEEEEEeccCCCHHHHHHHH
Q 004212 656 AFHGRGKRTGVYGAFLLACYDSN--NEEFQSICKIGTGFSEAMLEERS 701 (768)
Q Consensus 656 ~~~G~Gkr~g~~gsfLlg~~d~~--~g~l~~vgkVGTGfsd~~l~~L~ 701 (768)
..+.-| |+|.+... |..++- .|. +|.++ |..+.++.+++.
T Consensus 326 I~~qVG-RTG~iTPV--A~l~PV~l~G~--tVsrA-tLhN~~~i~~~~ 367 (665)
T PRK07956 326 IEVQVG-RTGAVTPV--ARLEPVEVAGV--TVSRA-TLHNADEIERKD 367 (665)
T ss_pred EEEecC-CCceeeeE--EEEEeEEECCE--EEEEe-ecCCHHHHHHcC
Confidence 666655 45655543 333331 354 45665 788888887754
No 54
>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=97.95 E-value=1.5e-05 Score=87.15 Aligned_cols=173 Identities=18% Similarity=0.262 Sum_probs=98.5
Q ss_pred cccccc-ccCChHHHH---hh----cCCC--ceEEeeecceEeEEEEEecCCe-EEEEcC----CcccCCCCCchHHHHH
Q 004212 433 GPMLAK-PTKGVSEIV---NK----FQDM--EFTCEYKYDGERAQIHYLEDGS-VEIYSR----NAERNTGKFPDVVLAV 497 (768)
Q Consensus 433 kPMLA~-~~~~i~~il---~k----~~g~--~~~~E~KyDG~R~qih~~~~g~-V~lfSR----~g~d~T~~fPel~~~l 497 (768)
.|||.- .+.+.+++. ++ ++.. .|+||+|+||.-+.+++ ++|. ++..|| -|+|+|.....+. .+
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 VPMLSLDKAYSEEELRKWLKRVEKALGEEEEEFVVEPKIDGLSISLIY-ENGKLVRAATRGDGEVGEDVTHNVRTIK-SI 154 (315)
T ss_dssp S-----EEESSHHHHHHHHHHHHHHCSS-SSEEEEEEEESSEEEEEEE-ETTEEEEEEEETTSSEEEB-HHHHCTST-TS
T ss_pred ccccCccccCCHHHHHHHHHHHHHHhcccccceeEeeccceeEEEEEE-eCCEEEEEEEcCCCccchhHHHHHHHHh-cC
Confidence 389863 233444442 22 2222 49999999999999999 4777 689999 6888886432221 12
Q ss_pred HhhcCCCCCCeEEEEEEEEEecCCCcccChhhHHhhh-------------------hccCCccccccceEEEEeeeeecC
Q 004212 498 SRLKKPSVRSFVLDCEIVAYDREKQKILPFQTLSTRA-------------------RKNVSLSDIKVDVCIYAFDILYRN 558 (768)
Q Consensus 498 ~~~~~~~~~~~ILDGElVa~d~~~g~~~pFq~L~~R~-------------------rk~~~~~~~~~~v~~~vFDiLyln 558 (768)
...+......+.+=||++.-. ..|..+-.+. |..........++.|++|++.+.+
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 222221126788999999642 2455553111 100000112458999999999988
Q ss_pred CccccCCcHHHHHHHHHHhhccCCCeEEEEeEEecCCHHHHHHHHHHHHHc------CCceeEEeeC
Q 004212 559 GQPLLQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAAVDA------SCEGLIIKTM 619 (768)
Q Consensus 559 G~~L~~~Pl~ERr~lL~~l~~~~~~~i~l~~~~~~~~~eei~~~~~~ai~~------G~EGlVlK~~ 619 (768)
| +..-....++.+.|.++-=++...+.+ +.+.+++.++++...+. ...|||+|--
T Consensus 229 ~-~~~~~t~~e~l~~L~~~GF~v~~~~~~-----~~~~~~v~~~~~~~~~~R~~l~y~iDGiVikvn 289 (315)
T PF01653_consen 229 G-DLGFNTQSERLQFLKEWGFPVNPYIRF-----CKSIEEVEEYIEEWEERREELPYPIDGIVIKVN 289 (315)
T ss_dssp T-STT-SBHHHHHHHHHHTT--B-TTEEE-----ESSHHHHHHHHHHHHHHGCCSSS-EEEEEEEES
T ss_pred c-ccChHHHHHHHHHHHHcCCCCCcceEe-----cCCHHHHHHHHHHHHhhhhccccccCcEEEEec
Confidence 7 333457788999998764333333333 56788999888877653 5679999986
No 55
>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=97.93 E-value=0.00018 Score=78.49 Aligned_cols=164 Identities=15% Similarity=0.198 Sum_probs=102.6
Q ss_pred ceEEeeecceEeEEEEEecCCe-EEEEcC----CcccCCCCCchHHHHHHhhcCCCCCCeEEEEEEEEEecCCCcccChh
Q 004212 454 EFTCEYKYDGERAQIHYLEDGS-VEIYSR----NAERNTGKFPDVVLAVSRLKKPSVRSFVLDCEIVAYDREKQKILPFQ 528 (768)
Q Consensus 454 ~~~~E~KyDG~R~qih~~~~g~-V~lfSR----~g~d~T~~fPel~~~l~~~~~~~~~~~ILDGElVa~d~~~g~~~pFq 528 (768)
.|+||+|+||.-+.+.+. +|+ ++..|| .|+|+|....-|. .|...+......+.+-||++.-. ..|+
T Consensus 102 ~~~vepKiDGlsisL~Y~-~G~L~~a~TRGdG~~GeDVT~nv~~I~-~IP~~i~~~~~~levRGEv~m~~------~~F~ 173 (307)
T cd00114 102 AYVVEPKIDGLSISLRYE-NGVLVQAATRGDGTTGEDVTENVRTIR-SIPLTLAGAPETLEVRGEVFMPK------ADFE 173 (307)
T ss_pred cEEEEEeccceEEEEEEE-CCEEEEEEecCCCcchhhHHhhHhhhc-ccChhhcCCCCeEEEEEEEEEEH------HHHH
Confidence 699999999999999984 676 789999 7899998543221 12222211024689999999742 2344
Q ss_pred hHHh---------------h----hhccCCccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCCCeEEEEe
Q 004212 529 TLST---------------R----ARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEPGFFQFAT 589 (768)
Q Consensus 529 ~L~~---------------R----~rk~~~~~~~~~~v~~~vFDiLylnG~~L~~~Pl~ERr~lL~~l~~~~~~~i~l~~ 589 (768)
.+-. . .|..........++.|++|++...++.. -....++.+.|+++-=++.....+
T Consensus 174 ~~n~~~~~~~~~~faNpRNaaAGsLr~ld~~~~~~r~L~f~~y~~~~~~~~~--~~t~~e~l~~L~~~GF~v~~~~~~-- 249 (307)
T cd00114 174 ALNKEREERGEKPFANPRNAAAGSLRQLDPKITAKRPLRFFIYGLGEAEGLG--PKTQSEALAFLKEWGFPVSPETRL-- 249 (307)
T ss_pred HHHHHHHHcCCCCccChHHHHHHHHHhcCcchhhcCcceEEEEecccccCCC--CCCHHHHHHHHHHCCCCCCCCeEE--
Confidence 3321 1 1110001112568999999986544211 247788999998874444333222
Q ss_pred EEecCCHHHHHHHHHHHHH------cCCceeEEeeCCCCCCcc----CCCCCCCe
Q 004212 590 TLTSIDLDEIQKFLDAAVD------ASCEGLIIKTMDRDATYE----PSKRSLNW 634 (768)
Q Consensus 590 ~~~~~~~eei~~~~~~ai~------~G~EGlVlK~~~~dS~Y~----pGkRs~~W 634 (768)
+.+.+++.++++...+ -...|||+|-- +-.+. ...+.+.|
T Consensus 250 ---~~~~~ev~~~~~~~~~~R~~l~y~iDGiViKvn--~~~~~~~lG~tsk~PrW 299 (307)
T cd00114 250 ---CKNIEEVLAFYDEIEAKRDSLPYEIDGVVVKVD--DLALQRELGFTSKAPRW 299 (307)
T ss_pred ---eCCHHHHHHHHHHHHHhhhcCCCCCCcEEEEEe--CHHHHHHhCccCCCCCc
Confidence 5678899988887633 47789999986 44432 23345667
No 56
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=97.91 E-value=0.00088 Score=80.42 Aligned_cols=237 Identities=18% Similarity=0.234 Sum_probs=141.5
Q ss_pred cccccc-cCChHHHH---hh----cCCCceEEeeecceEeEEEEEecCCe-EEEEcC----CcccCCCCCchHHHHHHhh
Q 004212 434 PMLAKP-TKGVSEIV---NK----FQDMEFTCEYKYDGERAQIHYLEDGS-VEIYSR----NAERNTGKFPDVVLAVSRL 500 (768)
Q Consensus 434 PMLA~~-~~~i~~il---~k----~~g~~~~~E~KyDG~R~qih~~~~g~-V~lfSR----~g~d~T~~fPel~~~l~~~ 500 (768)
|||.-. +.+.+++. ++ +....|++|+|+||.-+-+.+. +|+ ++..|| .|+|+|+....+. .+...
T Consensus 105 pMlSL~k~~~~~el~~f~~r~~~~~~~~~~~~epKiDGlaisL~Ye-~G~L~~a~TRGDG~~GeDVT~nv~~I~-~IP~~ 182 (689)
T PRK14351 105 PMLSIDQSGEADDVREFDERVRREVGAVEYVCEPKFDGLSVEVVYE-DGEYQRAATRGDGREGDDVTANVRTIR-SVPQK 182 (689)
T ss_pred cccccCccCCHHHHHHHHHHHHHhcCCceEEEEEecccEEEEEEEE-CCEEEEEEecCCCCcceeHhhhhhhhc-ccchh
Confidence 898732 33444542 11 2223699999999999999984 676 789999 7999998543221 12222
Q ss_pred cCC-CCCCeEEEEEEEEEecCCCcccChhhHHh---------------h----hhccCCccccccceEEEEeeeeecCCc
Q 004212 501 KKP-SVRSFVLDCEIVAYDREKQKILPFQTLST---------------R----ARKNVSLSDIKVDVCIYAFDILYRNGQ 560 (768)
Q Consensus 501 ~~~-~~~~~ILDGElVa~d~~~g~~~pFq~L~~---------------R----~rk~~~~~~~~~~v~~~vFDiLylnG~ 560 (768)
+.. ....+++-||++.-. ..|+.+-. . .|..........++.|++|++...++.
T Consensus 183 l~~~~p~~levRGEv~m~~------~~F~~lN~~~~~~g~~~faNpRN~aAGslR~ldp~~~~~r~L~f~~y~~~~~~~~ 256 (689)
T PRK14351 183 LRGDYPDFLAVRGEVYMPK------DAFQAYNRERIERGEEPFANPRNAAAGTLRQLDPSVVAERPLDIFFFDVLDASEL 256 (689)
T ss_pred hcccCCCeEEEEEEEEEEH------HHHHHHHHHHHHcCCCCcCCHHHHHhhHhhccChHHHhcCCceEEEEecccCCCC
Confidence 211 113578899999743 23444321 1 111000001246899999998655442
Q ss_pred cccCCcHHHHHHHHHHhhccCCCeEEEEeEEecCCHHHHHHHHHHHH------HcCCceeEEeeCCCCCCcc----CCCC
Q 004212 561 PLLQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAAV------DASCEGLIIKTMDRDATYE----PSKR 630 (768)
Q Consensus 561 ~L~~~Pl~ERr~lL~~l~~~~~~~i~l~~~~~~~~~eei~~~~~~ai------~~G~EGlVlK~~~~dS~Y~----pGkR 630 (768)
.....++.+.|..+-=++..... .+.+.+++.++++... .-...|||+|-- +-.+. ...+
T Consensus 257 ---~~t~~e~l~~L~~~GF~v~~~~~-----~~~~~~~~~~~~~~~~~~R~~l~y~iDGiViKvn--~~~~q~~lG~ts~ 326 (689)
T PRK14351 257 ---FDSHWEELERFPEWGLRVTDRTE-----RVDDIDDAIAYRDRLLAARDDLNYEIDGVVIKVD--DRDAREELGATAR 326 (689)
T ss_pred ---CCCHHHHHHHHHHCCCCcCCceE-----eeCCHHHHHHHHHHHHHhhhcCCCCCceEEEEeC--CHHHHHHhCccCC
Confidence 24678888888887433333322 2567888888777654 346789999986 44332 1235
Q ss_pred CCCe---EEEccccccccCCcccEEEEEEEcCCCCCCCccceEEEEEeeCC--CCeEEEEEEeccCCCHHHHHHHH
Q 004212 631 SLNW---LKLKKDYIESIGDSLDLVPIAAFHGRGKRTGVYGAFLLACYDSN--NEEFQSICKIGTGFSEAMLEERS 701 (768)
Q Consensus 631 s~~W---lKvK~dy~~~~~dtlDlvVIG~~~G~Gkr~g~~gsfLlg~~d~~--~g~l~~vgkVGTGfsd~~l~~L~ 701 (768)
.+.| +|+..+ ...-.|.+..+--| |+|.+... |..++- .|. +|.++ |..+.++++++.
T Consensus 327 ~PrWaiA~Kf~~~-------~~~T~l~~I~~qVG-RTG~iTPV--A~lePV~l~G~--tVsra-tLhN~~~i~~~d 389 (689)
T PRK14351 327 APRWAFAYKFPAR-------AEETTIRDIVVQVG-RTGRLTPV--ALLDPVDVGGV--TVSRA-SLHNPAEIEELG 389 (689)
T ss_pred CCCceEEEcCCCc-------eeEEEEEEEEEecC-CCceeeeE--EEEEeEEECCE--EEEEe-ccCCHHHHHHcC
Confidence 6788 566654 45556767666555 45655543 333331 354 55666 678888877754
No 57
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=97.90 E-value=0.00072 Score=80.85 Aligned_cols=219 Identities=17% Similarity=0.179 Sum_probs=130.1
Q ss_pred ceEEeeecceEeEEEEEecCCe-EEEEcC----CcccCCCCCchHHHHHHhhcCCCCCCeEEEEEEEEEecCCCcccChh
Q 004212 454 EFTCEYKYDGERAQIHYLEDGS-VEIYSR----NAERNTGKFPDVVLAVSRLKKPSVRSFVLDCEIVAYDREKQKILPFQ 528 (768)
Q Consensus 454 ~~~~E~KyDG~R~qih~~~~g~-V~lfSR----~g~d~T~~fPel~~~l~~~~~~~~~~~ILDGElVa~d~~~g~~~pFq 528 (768)
+|+||+|+||.-+.+.+ ++|+ ++..|| .|+|+|+..--+. .+...+.. ...+.+-||++.-. ..|+
T Consensus 111 ~~~~epKiDGlaisL~Y-enG~L~~a~TRGDG~~GEDVT~n~~~I~-~IP~~l~~-~~~levRGEv~m~~------~~F~ 181 (669)
T PRK14350 111 GISVEPKIDGCSIVLYY-KDGILEKALTRGDGRFGNDVTENVRTIR-NVPLFIDE-KVELVLRGEIYITK------ENFL 181 (669)
T ss_pred eEEEEEecccEEEEEEE-ECCEEEEEEecCCCCcchhHhhhhhhhc-ccchhcCC-CceEEEEEEEEeeH------HHHH
Confidence 59999999999999998 4676 789999 7899997532221 12222211 14588999999742 2354
Q ss_pred hHHhh---------------hhccCCccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCCCeEEEEeEEec
Q 004212 529 TLSTR---------------ARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEPGFFQFATTLTS 593 (768)
Q Consensus 529 ~L~~R---------------~rk~~~~~~~~~~v~~~vFDiLylnG~~L~~~Pl~ERr~lL~~l~~~~~~~i~l~~~~~~ 593 (768)
.+-.. .|..........++.|++|++...++. ..+..++.+.|.++-=++.....+... .
T Consensus 182 ~lN~~~~~~faNpRNaaAGsLr~~d~~~~a~r~L~f~~y~~~~~~~~---~~t~~e~l~~L~~~GF~v~~~~~~~~~--~ 256 (669)
T PRK14350 182 KINKTLEKPYTNARNLASGILRRIDSREVANFPLDIFVYDILYSSLE---LKTNHDAFDKLKKFGFKVNPFCRFFDG--K 256 (669)
T ss_pred HHHHhhhccCCChhHHHHHHHHccCchhhhcCceEEEEEEcccCCCC---CCCHHHHHHHHHHCCCCCCcceEEEcC--C
Confidence 43211 111000111245899999998532221 236778888888874343333333221 2
Q ss_pred CCHHHHHHHHHHHH------HcCCceeEEeeCCCCCCcc--CC--CCCCCe---EEEccccccccCCcccEEEEEEEcCC
Q 004212 594 IDLDEIQKFLDAAV------DASCEGLIIKTMDRDATYE--PS--KRSLNW---LKLKKDYIESIGDSLDLVPIAAFHGR 660 (768)
Q Consensus 594 ~~~eei~~~~~~ai------~~G~EGlVlK~~~~dS~Y~--pG--kRs~~W---lKvK~dy~~~~~dtlDlvVIG~~~G~ 660 (768)
.+.+++.+++++.. .-...|||+|-- +-.+. -| .+.+.| +|+..+ ...-.|.+..+--
T Consensus 257 ~~~~e~~~~~~~~~~~R~~l~y~iDGiViKvn--~~~~q~~lG~ts~~PrWaiA~Kf~~~-------~~~T~l~~I~~qV 327 (669)
T PRK14350 257 NSIEEILNYVKDIEKKRNSFEYEIDGVVLKVS--DFALREILGYTSHHPKWSMAYKFESL-------SGFSKVNDIVVQV 327 (669)
T ss_pred CcHHHHHHHHHHHHHHHhcCCCCCCcEEEEec--CHHHHHhcCCcCCCCCceEEEcCCCc-------eeEEEEEEEEEec
Confidence 34778877776553 246789999986 33222 12 346788 666664 4555676666655
Q ss_pred CCCCCccceEEEEEeeCC--CCeEEEEEEeccCCCHHHHHHHH
Q 004212 661 GKRTGVYGAFLLACYDSN--NEEFQSICKIGTGFSEAMLEERS 701 (768)
Q Consensus 661 Gkr~g~~gsfLlg~~d~~--~g~l~~vgkVGTGfsd~~l~~L~ 701 (768)
| |+|.+... |..++- .|. +|.++ |..+.++.+++.
T Consensus 328 G-RTG~iTPV--A~l~PV~l~G~--tVsrA-TLhN~~~I~~~d 364 (669)
T PRK14350 328 G-RSGKITPV--ANIEKVFVAGA--FITNA-SLHNQDYIDSIG 364 (669)
T ss_pred C-CceeeeEE--EEEEeEEECCE--EEEEe-ccCCHHHHHHcC
Confidence 5 45655543 333331 354 56666 788888887754
No 58
>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=97.89 E-value=0.00081 Score=80.45 Aligned_cols=218 Identities=16% Similarity=0.197 Sum_probs=133.4
Q ss_pred ceEEeeecceEeEEEEEecCCe-EEEEcC----CcccCCCCCchHHHHHHhhcCC--CCCCeEEEEEEEEEecCCCcccC
Q 004212 454 EFTCEYKYDGERAQIHYLEDGS-VEIYSR----NAERNTGKFPDVVLAVSRLKKP--SVRSFVLDCEIVAYDREKQKILP 526 (768)
Q Consensus 454 ~~~~E~KyDG~R~qih~~~~g~-V~lfSR----~g~d~T~~fPel~~~l~~~~~~--~~~~~ILDGElVa~d~~~g~~~p 526 (768)
.|++|+|+||.-+.+.+ ++|+ ++..|| .|+|+|+..-.+. .+...+.. ....+.+-||++.-. ..
T Consensus 97 ~~~~epKiDGlaisL~Y-e~G~L~~a~TRGDG~~GeDvT~nv~~I~-~iP~~i~~~~~p~~levRGEv~m~~------~~ 168 (652)
T TIGR00575 97 EYVVEPKIDGLSVSLTY-ENGVLVRALTRGDGTVGEDVTANVRTIR-SIPLRLAGDNPPERLEVRGEVFMPK------ED 168 (652)
T ss_pred eEEEEEeccceEEEEEE-ECCEEEEEEecCCCccchhHhhhhhhhc-ccchhhcCCCCCceEEEEEEEEEEH------HH
Confidence 59999999999999999 4776 789999 7899998543221 12222210 113588999999742 23
Q ss_pred hhhH---------------Hhh----hhccCCccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCCCeEEE
Q 004212 527 FQTL---------------STR----ARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEPGFFQF 587 (768)
Q Consensus 527 Fq~L---------------~~R----~rk~~~~~~~~~~v~~~vFDiLylnG~~L~~~Pl~ERr~lL~~l~~~~~~~i~l 587 (768)
|+.+ .+. .|..........++.|++|++...+ ........++.+.|.++-=++.....+
T Consensus 169 F~~~N~~~~~~g~~~faNpRN~aAGslr~ld~~~~~~r~L~~~~y~~~~~~--~~~~~t~~e~l~~L~~~GF~v~~~~~~ 246 (652)
T TIGR00575 169 FEALNEERREQGEKPFANPRNAAAGSLRQLDPRITAKRKLRFFAYGLGEGL--ELPDATQYEALAWLKKWGFPVSPHIRL 246 (652)
T ss_pred HHHHHHHHHHcCCCCCCCcHHHHHHHHHcCCchhhhcCccEEEEEeccccC--CCCCCCHHHHHHHHHHCCCCCCCCeEe
Confidence 4433 111 1110001112568999999985322 211247788888888874333333222
Q ss_pred EeEEecCCHHHHHHHHHHHHH------cCCceeEEeeCCCCCCcc----CCCCCCCe---EEEccccccccCCcccEEEE
Q 004212 588 ATTLTSIDLDEIQKFLDAAVD------ASCEGLIIKTMDRDATYE----PSKRSLNW---LKLKKDYIESIGDSLDLVPI 654 (768)
Q Consensus 588 ~~~~~~~~~eei~~~~~~ai~------~G~EGlVlK~~~~dS~Y~----pGkRs~~W---lKvK~dy~~~~~dtlDlvVI 654 (768)
+.+.+++.++++...+ -.-.|+|+|-- +-.+. ...+.+.| +|+..+ ...-.|.
T Consensus 247 -----~~~~~ei~~~~~~~~~~R~~l~y~iDGiViKvn--~~~~~~~lG~t~~~PrwaiA~Kf~~~-------~~~T~l~ 312 (652)
T TIGR00575 247 -----CDSIEEVLEYYREIEEKRDSLPYEIDGVVVKVD--DLALQDELGFTSKAPRWAIAYKFPAE-------EAQTKLL 312 (652)
T ss_pred -----eCCHHHHHHHHHHHHHhhhcCCCCCCcEEEEec--CHHHHHHhCccCCCCCceEEEcCCCc-------eeeEEEE
Confidence 4678899988876642 47789999986 44442 12356788 666664 4555677
Q ss_pred EEEcCCCCCCCccceEEEEEeeCC--CCeEEEEEEeccCCCHHHHHHHH
Q 004212 655 AAFHGRGKRTGVYGAFLLACYDSN--NEEFQSICKIGTGFSEAMLEERS 701 (768)
Q Consensus 655 G~~~G~Gkr~g~~gsfLlg~~d~~--~g~l~~vgkVGTGfsd~~l~~L~ 701 (768)
+..+--| |+|.+... |..++- .|. +|.++ |..+.++.+++.
T Consensus 313 ~I~~qVG-RTG~iTPv--A~lePV~l~G~--~VsrA-tLhN~~~i~~~~ 355 (652)
T TIGR00575 313 DVVVQVG-RTGAITPV--AKLEPVFVAGT--TVSRA-TLHNEDEIEELD 355 (652)
T ss_pred EEEEecC-CCceeeeE--EEEeeEEECCE--EEEEe-ecCCHHHHHHcC
Confidence 7666655 45655543 333331 354 45665 788888887754
No 59
>PF09414 RNA_ligase: RNA ligase; InterPro: IPR021122 This entry represents the RNA ligase domain. RNA ligase enzyme repairs RNA strand breaks in nicked DNA:RNA and RNA:RNA but not in DNA:DNA duplexes []. Members of this RNA ligase family include: RNA editing ligase 1 (REL1) , which is essential for RNA editing and may be active in U-deletion editing [, , ]. RNA editing ligase 2 (REL2), which may be active in U-insertion editing []. RnlB RNA ligase 2 (or Rnl2), second RNA ligase of Enterobacteria phage T4 (Bacteriophage T4); unlike RNA ligase 1, RnlB prefers doule stranded substrates [, ]. ; PDB: 2HVS_B 2HVR_A 1S68_A 2HVQ_A 1XDN_A.
Probab=97.36 E-value=0.00017 Score=72.58 Aligned_cols=159 Identities=21% Similarity=0.175 Sum_probs=83.6
Q ss_pred ceEEeeecceEeEEEEEecCCeEEEEcCCccc-----C------CCCCchHHHH---HHhh---c-CCCCCCeEEEEEEE
Q 004212 454 EFTCEYKYDGERAQIHYLEDGSVEIYSRNAER-----N------TGKFPDVVLA---VSRL---K-KPSVRSFVLDCEIV 515 (768)
Q Consensus 454 ~~~~E~KyDG~R~qih~~~~g~V~lfSR~g~d-----~------T~~fPel~~~---l~~~---~-~~~~~~~ILDGElV 515 (768)
+|++++|+||.-+.+.+..++.+++.+|++.. + ...|...... +... . .....+++|=||++
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 69999999999999988766679999999932 1 1112222111 1111 1 01346899999999
Q ss_pred EEecCCCcccChhhHHhhhhccCCccccccceEEEEeeeeecCCc-cccCCcHHHHHHHHHHhhccCCCeEEEEeEEecC
Q 004212 516 AYDREKQKILPFQTLSTRARKNVSLSDIKVDVCIYAFDILYRNGQ-PLLQEQLRVRREHLYDSFEEEPGFFQFATTLTSI 594 (768)
Q Consensus 516 a~d~~~g~~~pFq~L~~R~rk~~~~~~~~~~v~~~vFDiLylnG~-~L~~~Pl~ERr~lL~~l~~~~~~~i~l~~~~~~~ 594 (768)
.+-+. + + ++.. ....+..|++|||...+.+ ...=++..+++.+++.+- +..+|.....
T Consensus 82 G~~~~---I------q----~~~~--~~~~~~~F~~Fdi~~~~~~~~~~~l~~~~~~~~~~~~g------l~~VPvl~~g 140 (186)
T PF09414_consen 82 GAKPS---I------Q----KNRY--QLDPPKDFYVFDIYDIDEQGEIRYLSWDEVREFAEELG------LKTVPVLYRG 140 (186)
T ss_dssp CEECT---T------C----SS------ECCCEEEEEEEEEEETCCGEEE-HHHHHHHHHCCCT-------EES-ECEEE
T ss_pred eeccc---c------c----cccc--ccCCCceEEEEEEEEcCCCCeeEECCHHHHHHHHHHCC------CCEeCEEEEE
Confidence 86421 0 0 0100 0013789999999988543 223457778888776652 1223322111
Q ss_pred CHHHHHH------HH-HHHHHcCCceeEEeeCCCCCCccCCCCCCCeEEEc
Q 004212 595 DLDEIQK------FL-DAAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLK 638 (768)
Q Consensus 595 ~~eei~~------~~-~~ai~~G~EGlVlK~~~~dS~Y~pGkRs~~WlKvK 638 (768)
...+... .. ...-..-.||+|+|.. +..+ .+.| .-+|.|
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 1122456899999998 6656 4544 566665
No 60
>TIGR02307 RNA_lig_RNL2 RNA ligase, Rnl2 family. Members of this family ligate (seal breaks in) RNA. Members so far include phage proteins that can counteract a host defense of cleavage of specific tRNA molecules, trypanosome ligases involved in RNA editing, but no prokaryotic host proteins.
Probab=97.18 E-value=0.0042 Score=68.16 Aligned_cols=162 Identities=21% Similarity=0.188 Sum_probs=92.0
Q ss_pred CCCceEEeeecceEeEEEEEecCCeEEEEcCCcccC-CCCC-------chHHHHHH---hhcC----CCCCCeEEEEEEE
Q 004212 451 QDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERN-TGKF-------PDVVLAVS---RLKK----PSVRSFVLDCEIV 515 (768)
Q Consensus 451 ~g~~~~~E~KyDG~R~qih~~~~g~V~lfSR~g~d~-T~~f-------Pel~~~l~---~~~~----~~~~~~ILDGElV 515 (768)
.+.+|.+.+|.||...-+.+++++++++.||++.-- .+.| +++...++ +.+. ....++++=||++
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 456899999999999988886433899999996432 1122 22222222 2221 1347899999999
Q ss_pred EEecCCCcccChhhHHhhhhccCCccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCCCeEEEEeEEecCC
Q 004212 516 AYDREKQKILPFQTLSTRARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEPGFFQFATTLTSID 595 (768)
Q Consensus 516 a~d~~~g~~~pFq~L~~R~rk~~~~~~~~~~v~~~vFDiLylnG~~L~~~Pl~ERr~lL~~l~~~~~~~i~l~~~~~~~~ 595 (768)
.+.-..+. . -. +..|++|||.+....+..=+++.+-.+...... + +..++..-..+
T Consensus 103 G~~~q~~~---------------~---Y~-~~~fyaFdI~~~~~~~~~~L~~d~~~e~~~~~~----~-l~~ap~L~rGt 158 (325)
T TIGR02307 103 GPGYQKPV---------------V---YS-DKDFYAFDIKYTETSDDVTLVDDYMMESFCNVP----K-LKYAPLLGRGT 158 (325)
T ss_pred cCcccCcc---------------c---cc-cccEEEEEEEEeccCcceEecHHHHHHHHHHcC----C-cccchhhcccC
Confidence 86321110 0 01 468999999553221233456666666555442 1 22333333345
Q ss_pred HHHHHHH---HHHH-----H--------HcCCceeEEeeCCCCC-CccC-CCCCCCeEEEccc
Q 004212 596 LDEIQKF---LDAA-----V--------DASCEGLIIKTMDRDA-TYEP-SKRSLNWLKLKKD 640 (768)
Q Consensus 596 ~eei~~~---~~~a-----i--------~~G~EGlVlK~~~~dS-~Y~p-GkRs~~WlKvK~d 640 (768)
.+++.++ +..+ . .+=+||+|+|.. .. .|.. |.| .-+|.|.+
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 5665554 1111 1 122899999998 42 2332 333 67888884
No 61
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=96.74 E-value=0.035 Score=65.82 Aligned_cols=173 Identities=17% Similarity=0.213 Sum_probs=113.2
Q ss_pred CceEEeeecceEeEEEEEecCCe-EEEEcCC----cccCCCCCchHHHHHHhhcCCCCCCeEEEEEEEEEecCCCcccCh
Q 004212 453 MEFTCEYKYDGERAQIHYLEDGS-VEIYSRN----AERNTGKFPDVVLAVSRLKKPSVRSFVLDCEIVAYDREKQKILPF 527 (768)
Q Consensus 453 ~~~~~E~KyDG~R~qih~~~~g~-V~lfSR~----g~d~T~~fPel~~~l~~~~~~~~~~~ILDGElVa~d~~~g~~~pF 527 (768)
..|+||+|.||.-+-+.+ ++|. ++--||. |+|+|....-|.. |...+........+-||++.-- ..|
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 4676 7788875 7999987655543 3333331135678999998641 346
Q ss_pred hhHHhhhhcc------------------CCcc-ccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCCCeEEEE
Q 004212 528 QTLSTRARKN------------------VSLS-DIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEPGFFQFA 588 (768)
Q Consensus 528 q~L~~R~rk~------------------~~~~-~~~~~v~~~vFDiLylnG~~L~~~Pl~ERr~lL~~l~~~~~~~i~l~ 588 (768)
+.+-...... .+.. ..+.++.+++|.+-+..+. ..-.+..|+.+.|+.+-=++....
T Consensus 181 ~~lN~~~~~~g~~~faNpRNaAAGsLRqlD~~ita~R~L~~f~y~~~~~~~~-~~~~t~~e~l~~L~~~GF~v~~~~--- 256 (667)
T COG0272 181 EALNEEREEEGEKPFANPRNAAAGSLRQLDPKITAKRKLGFFIYAVGDGEEG-LLADTQSERLAFLKAWGFPVNPYT--- 256 (667)
T ss_pred HHHHHHHHHhCCCCcCChhhhhhhhhhccCHHHHhcCCceEEEEeCCccCCC-CCccCHHHHHHHHHHcCCCCCcHh---
Confidence 6554221100 0111 1245899999998866544 555678899999988744332222
Q ss_pred eEEecCCHHHHHHHHHHHHH------cCCceeEEeeCCCCCCcc-CC--CCCCCe---EEEccc
Q 004212 589 TTLTSIDLDEIQKFLDAAVD------ASCEGLIIKTMDRDATYE-PS--KRSLNW---LKLKKD 640 (768)
Q Consensus 589 ~~~~~~~~eei~~~~~~ai~------~G~EGlVlK~~~~dS~Y~-pG--kRs~~W---lKvK~d 640 (768)
..+.+.+++.++++...+ .--.|+|+|--+ -..|+ -| .|++.| +|+.+.
T Consensus 257 --~~~~~~~ev~~~~~~~~~~R~~L~y~IDGvViKvn~-l~~q~~lG~tsk~PrWAiAyKFpa~ 317 (667)
T COG0272 257 --RLCKNADEVLAFYEEWEKKRASLPYDIDGVVIKVND-LALQRELGFTSKAPRWAIAYKFPAE 317 (667)
T ss_pred --hhcCCHHHHHHHHHHHHhhcccCCCccceEEEEecc-HHHHHHhCCccCCCceeeeecCCch
Confidence 236789999999988765 356799999852 12222 12 357889 777775
No 62
>PF14743 DNA_ligase_OB_2: DNA ligase OB-like domain; PDB: 2Q2U_D 2Q2T_A 1FVI_A 1P8L_A.
Probab=95.97 E-value=0.0063 Score=51.88 Aligned_cols=38 Identities=37% Similarity=0.594 Sum_probs=26.0
Q ss_pred cCCCCCCCccceEEEEEeeCCCCeEEEEEEeccCCCHHHHHHHH
Q 004212 658 HGRGKRTGVYGAFLLACYDSNNEEFQSICKIGTGFSEAMLEERS 701 (768)
Q Consensus 658 ~G~Gkr~g~~gsfLlg~~d~~~g~l~~vgkVGTGfsd~~l~~L~ 701 (768)
.|+||..|++|+|+|...| | ...+|||||||+++++++
T Consensus 1 ~G~Gk~~g~~Galv~~~~~---G---~~f~iGsG~td~~R~~~~ 38 (66)
T PF14743_consen 1 EGKGKFKGMLGALVCETED---G---VEFKIGSGFTDEEREEPP 38 (66)
T ss_dssp ----EEEEEEEEEEEEE-T---T---EEEEE-SS--HHHHHHHH
T ss_pred CCccccCCCEEEEEEEeCC---C---CEEEECCCCCHHHHhcCC
Confidence 3788999999999998644 5 357899999999999988
No 63
>PHA02142 putative RNA ligase
Probab=95.83 E-value=0.098 Score=58.48 Aligned_cols=162 Identities=18% Similarity=0.197 Sum_probs=92.9
Q ss_pred ChHHHHh-hcCCCceEEeeecceEeEEEEEe--------------------cCCeEEEEcCCccc---CCCCCchHH---
Q 004212 442 GVSEIVN-KFQDMEFTCEYKYDGERAQIHYL--------------------EDGSVEIYSRNAER---NTGKFPDVV--- 494 (768)
Q Consensus 442 ~i~~il~-k~~g~~~~~E~KyDG~R~qih~~--------------------~~g~V~lfSR~g~d---~T~~fPel~--- 494 (768)
++.++++ +..+..|.+-.|.||.-|-+.+. ..|.+..-|||... -+..|=+++
T Consensus 157 n~~~~~~~~~~~~~f~~TeKLDGsS~tvy~~~~~~~~~~~~~~~~~~~~~~~~~~~gv~srn~~l~~~~~~~~W~~a~~~ 236 (366)
T PHA02142 157 NIFNRYKEKYADVKFAKSLKLDGSSITMAWVTDPDLFLDLGTEDEPYAHDYDDAQFIVASRNQVLRYNADSKWWKGVENY 236 (366)
T ss_pred hhhhhhhhhhcCceEEEEEEecceeEEEEEecCCcccccccccccccccccCCCceeEeeccccccccCCchHHHHHHHc
Confidence 4444432 24467899999999999987732 24677788998752 122222222
Q ss_pred ---HHHHhhcCCCCCCeEEEEEEEEEecCCCcccChhhHHhhhhccCCccccccceEEEEeeeeecCCccccCCcHHHHH
Q 004212 495 ---LAVSRLKKPSVRSFVLDCEIVAYDREKQKILPFQTLSTRARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRR 571 (768)
Q Consensus 495 ---~~l~~~~~~~~~~~ILDGElVa~d~~~g~~~pFq~L~~R~rk~~~~~~~~~~v~~~vFDiLylnG~~L~~~Pl~ERr 571 (768)
+.|+.+ -.++.+=||++.-.-.++ ... -....|++|||-.++++. =+++.+++
T Consensus 237 ~i~~~l~~~----~~~iaIqGEl~Gp~IQ~N---------------~~~---~~~~~F~vF~v~~i~~~~--yl~~~e~~ 292 (366)
T PHA02142 237 QIVDRLKEL----GMSVAIQGELMGPGIQKN---------------REN---FDKYRIFAFRAWFIDEQR--FATDEEFQ 292 (366)
T ss_pred CcHHHHHhh----CCcEEEEEEEecccccCc---------------ccc---CCCCceEEEEEEEeccce--eCCHHHHH
Confidence 233332 157889999997321111 100 112479999997777665 36889999
Q ss_pred HHHHHhhccCCCeEEEEeEEe----cCCHHHHHHHHHHHH-----HcCCceeEEeeCCCCCCccCCCCCCCeEEEcc
Q 004212 572 EHLYDSFEEEPGFFQFATTLT----SIDLDEIQKFLDAAV-----DASCEGLIIKTMDRDATYEPSKRSLNWLKLKK 639 (768)
Q Consensus 572 ~lL~~l~~~~~~~i~l~~~~~----~~~~eei~~~~~~ai-----~~G~EGlVlK~~~~dS~Y~pGkRs~~WlKvK~ 639 (768)
++++++--+ .++... ....+.++++++.|- ..-+||+|+|.. . =..|+| -|+|.|.
T Consensus 293 ~~~~~~gl~------~VPvL~~~~~~~~~~s~eE~L~~A~~p~~~~~~~EGiViKp~--~--~~~g~r--~~fK~is 357 (366)
T PHA02142 293 DLCRTLGME------IVPQLGYSYPFQEFTNVKEMLAAADIPSINHKIAEGVVYKSV--E--LVNGRM--VHFKAIN 357 (366)
T ss_pred HHHHHcCCc------eeeeecccccccccCCHHHHHhhcCCCcccccccceEEEeec--c--ccCCce--EEEEEcC
Confidence 988876322 222211 111113344444431 123799999987 3 112322 5999886
No 64
>PRK03180 ligB ATP-dependent DNA ligase; Reviewed
Probab=94.88 E-value=0.13 Score=60.24 Aligned_cols=91 Identities=19% Similarity=0.216 Sum_probs=78.6
Q ss_pred CccchHHHHHHHHHHHhhh---chHHHHHHHHHHHHhhhcCCCCchHHHHHHHhCccCCCccccccCCCHHHHHHHHHHH
Q 004212 189 ERVPFIFLSLVFDMISNET---GRILITDIVCNMLRTVMETTPEDLVPVVYLAANKIAPAHEGLELGIGDASIIKALAEA 265 (768)
Q Consensus 189 ~~~~F~~la~l~e~I~~ts---sr~~k~~iL~~~fr~~i~~~p~dl~~~vyl~~~~l~P~~e~~elGIg~~~L~Kal~~a 265 (768)
.+.+-.++=+.|++|+..+ +..+|.++|..++..+ +|.+.-+.+.++++. ..+|+++.++..|++++
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 3566777777888888865 5689999999999886 889998889998875 46999999999999999
Q ss_pred hCCCHHHHHHHHhhhCChHHHHhh
Q 004212 266 CGRTESHVKKQYQEMGDLGLVAKA 289 (768)
Q Consensus 266 ~G~s~~~ik~~y~~~GDlg~vA~~ 289 (768)
++.+...++..|..+||++.++..
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=94.57 E-value=0.15 Score=53.43 Aligned_cols=152 Identities=20% Similarity=0.377 Sum_probs=105.4
Q ss_pred CCceEEeeecceEeEEEEEecCCeEEEEcCCcccCCCCCchHHHHHHhhcCCCCCCeEEEEEEEEEecCCCcccChhhHH
Q 004212 452 DMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAVSRLKKPSVRSFVLDCEIVAYDREKQKILPFQTLS 531 (768)
Q Consensus 452 g~~~~~E~KyDG~R~qih~~~~g~V~lfSR~g~d~T~~fPel~~~l~~~~~~~~~~~ILDGElVa~d~~~g~~~pFq~L~ 531 (768)
+.+|++=.-==|-||+|.- ..|...-|.|+|..+. +||....-=..--.+.-.-.||||= ++
T Consensus 115 sqdW~vv~~PvGKR~lvVa-SrG~Tvay~k~G~~v~-rF~S~LPGGnrr~~~a~~ytILDCI---y~------------- 176 (325)
T KOG3132|consen 115 SQDWYVVARPVGKRCLVVA-SRGTTVAYVKNGSTVH-RFPSALPGGNRRKGPANSYTILDCI---YH------------- 176 (325)
T ss_pred CcceEEEEeecCceEEEEe-cCCceEEEecCCeeEe-eccccCCCCCcCCCCcccceeeeee---ec-------------
Confidence 4589998888999999887 4788889999998753 4554211000000001123455542 21
Q ss_pred hhhhccCCccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCCC--------eEEEE--eEEecCCHHHHHH
Q 004212 532 TRARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEPG--------FFQFA--TTLTSIDLDEIQK 601 (768)
Q Consensus 532 ~R~rk~~~~~~~~~~v~~~vFDiLylnG~~L~~~Pl~ERr~lL~~l~~~~~~--------~i~l~--~~~~~~~~eei~~ 601 (768)
+.+-.|+|.|++.++|.++.+-++.=|.=.|++-+.+.++ .+.|+ +...+ +.+.+.+
T Consensus 177 ------------esnQTYYVlD~~cWrgh~~yec~~dFRffwl~SKL~E~~~l~~~t~~~~f~Fs~vp~~pC-~q~~l~~ 243 (325)
T KOG3132|consen 177 ------------ESNQTYYVLDMVCWRGHSLYECTSDFRFFWLQSKLAETGALDPPTVYHKFRFSVVPFYPC-DQSGLHS 243 (325)
T ss_pred ------------ccCceEEEEEEEeecCcccccCchHHHHHHHhhhccccccCCCCCcCccceecccCCCCC-CHHHHHH
Confidence 1345799999999999999999999999999998876431 33343 33333 5677777
Q ss_pred HHHHHHHcCCceeEEeeCCCCCCccCCCC-CCCeEE
Q 004212 602 FLDAAVDASCEGLIIKTMDRDATYEPSKR-SLNWLK 636 (768)
Q Consensus 602 ~~~~ai~~G~EGlVlK~~~~dS~Y~pGkR-s~~WlK 636 (768)
.+.-.+---..|+.+-.. .-.|.||.. --+|||
T Consensus 244 ~~~~~~pf~~DGLLFYhk--s~~yqpgqsplvgwlk 277 (325)
T KOG3132|consen 244 AYTGSLPFVRDGLLFYHK--SVVYQPGQSPLVGWLK 277 (325)
T ss_pred HHcCCCceeeeeEEEeec--ceeeCCCCCccccccc
Confidence 777777778899999988 889999964 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=93.49 E-value=1.3 Score=49.49 Aligned_cols=155 Identities=14% Similarity=0.173 Sum_probs=83.9
Q ss_pred CCceEEeeecceEeEEEEEec-CCeEE-----EEcCCccc---CCCCCch------HHHHHHhhcCCCCCCeEEEEEEEE
Q 004212 452 DMEFTCEYKYDGERAQIHYLE-DGSVE-----IYSRNAER---NTGKFPD------VVLAVSRLKKPSVRSFVLDCEIVA 516 (768)
Q Consensus 452 g~~~~~E~KyDG~R~qih~~~-~g~V~-----lfSR~g~d---~T~~fPe------l~~~l~~~~~~~~~~~ILDGElVa 516 (768)
+..|.+-.|+||.-+.+.+.. .+.+. +-|||.+. -+..|-. |.+.+.+.. ...++.+=||++.
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 568999999999999777532 23322 34688762 2223322 223333211 1257889999997
Q ss_pred EecCCCcccChhhHHhhhhccCCccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCCCeEEEEeEEecCCH
Q 004212 517 YDREKQKILPFQTLSTRARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDL 596 (768)
Q Consensus 517 ~d~~~g~~~pFq~L~~R~rk~~~~~~~~~~v~~~vFDiLylnG~~L~~~Pl~ERr~lL~~l~~~~~~~i~l~~~~~~~~~ 596 (768)
-.-.++ .- . ...+-.+++|++ +.+|+. .=++++++.++++++.. |- + + ....
T Consensus 236 ~gIQ~n----------~Y--g-----~~~~~~~f~F~v-~~~~~~-ryld~~~~~~~~~~~~V--Pv-L-~-----~g~~ 287 (341)
T TIGR02306 236 PGIQKN----------RY--G-----FDKYRTVFAFRA-FFDGEQ-RFLTDEDFQDLCLTLIV--PQ-L-Y-----EGPF 287 (341)
T ss_pred ccccCC----------cC--C-----CCCCceEEEEEE-EEcCcc-eecCHHHHHHHHHhccc--ce-E-E-----Eech
Confidence 321111 00 0 011222788888 555442 23588999998887622 21 1 1 1122
Q ss_pred HHHHHHHHHHHHc----C-----CceeEEeeCCCCCCccCCCCCCCeEEEccc
Q 004212 597 DEIQKFLDAAVDA----S-----CEGLIIKTMDRDATYEPSKRSLNWLKLKKD 640 (768)
Q Consensus 597 eei~~~~~~ai~~----G-----~EGlVlK~~~~dS~Y~pGkRs~~WlKvK~d 640 (768)
++ ...++.++.. | .||+|+|.. ...+-... +.-|+|.|.+
T Consensus 288 de-~~~~~~~ig~a~~~~~~~~irEGvViKp~--~~~~~~~G-~r~~fK~is~ 336 (341)
T TIGR02306 288 DE-FTVVKDMLGAETVSGIGLHIREGVVYKSV--ELRFAVDG-RMVHFKAISN 336 (341)
T ss_pred hH-hhhhhhhhcccccCccccceeceEEEeec--cccccCCC-ceEEEEEcCH
Confidence 22 2333333322 2 899999998 66553222 3369999863
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=92.79 E-value=0.52 Score=55.34 Aligned_cols=93 Identities=19% Similarity=0.265 Sum_probs=78.6
Q ss_pred CccchHHHHHHHHHHHhhh---chHHHHHHHHHHHHhhhcCCCCchHHHHHHHhCccCCCccccccCCCHHHHHHHHHHH
Q 004212 189 ERVPFIFLSLVFDMISNET---GRILITDIVCNMLRTVMETTPEDLVPVVYLAANKIAPAHEGLELGIGDASIIKALAEA 265 (768)
Q Consensus 189 ~~~~F~~la~l~e~I~~ts---sr~~k~~iL~~~fr~~i~~~p~dl~~~vyl~~~~l~P~~e~~elGIg~~~L~Kal~~a 265 (768)
.++.-.++-+.++.|++.+ ++.+|.++|.++|+.. +|.+.-+.+.++++. ...|++++++.++|+.+
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 3566778888888888765 5788999999999886 888988888888764 45899999999999999
Q ss_pred hCCCHHHHHHHHhhhCChHHHHhhhc
Q 004212 266 CGRTESHVKKQYQEMGDLGLVAKASR 291 (768)
Q Consensus 266 ~G~s~~~ik~~y~~~GDlg~vA~~~r 291 (768)
++.+...+...|....|++.|+..+.
T Consensus 123 ~~~~~~~~~~~~~~~~dl~~v~~~l~ 148 (514)
T TIGR00574 123 FLLSHPDVERAFNLTNDLGKVAKILL 148 (514)
T ss_pred hccchHHHHHHHHhCCCHHHHHHHHH
Confidence 99999999999999999999987653
No 68
>PRK09247 ATP-dependent DNA ligase; Validated
Probab=91.39 E-value=0.43 Score=56.34 Aligned_cols=87 Identities=13% Similarity=0.130 Sum_probs=65.8
Q ss_pred HHHHHHHHHHHHhCCChHHHHHHHHHHHHHhcCCChHHHHHHHHhhccc-CcccHHHHHHHHHhhhccCCCCCCCCCCCc
Q 004212 307 KVFDTFRLIAKEAGKDSQEKKKNRIKALLVAATDCEPQYLIRLLQSKLR-IGLAEQTLLAALGQAAVYNEQHSKPPPNIQ 385 (768)
Q Consensus 307 eV~~~L~kIA~~~G~~Sq~~K~~~l~~Ll~~~t~~E~k~lvRiIlkdLR-iGi~e~tVl~ala~a~~~~~~~~~~~~~l~ 385 (768)
+..+.+++|+..+ +...|.++|.++|..+++.+.-|.++++++.+. .|++++++.++++.++..+..
T Consensus 3 ~fa~~~~~i~~t~---~~~ek~~~l~~~~~~~~~~d~~~~~~ll~g~~~~~~i~~~~l~k~~~~~~g~~~~--------- 70 (539)
T PRK09247 3 AFAELLDRLDLTT---STNAKLALLADYFRSAPDPDRAWALALLTGGLPRRLVKTRLLRELAAERADLPPW--------- 70 (539)
T ss_pred HHHHHHHHHHhcc---CHHHHHHHHHHHHHhCCHHHHHHHHHHhcCCcccCCCCHHHHHHHHHHHHCcCHH---------
Confidence 4455666776544 456789999999999999999999999999886 999999999999998875432
Q ss_pred chHHHHHHHHHHHhhcCCchhhhhhhhh
Q 004212 386 SPLEEAAKIVKQVFSVLPVYEKIVPALL 413 (768)
Q Consensus 386 ~~l~~a~~~vk~~y~~~pd~~~v~~~ll 413 (768)
.+++.|...-|++.++..++
T Consensus 71 --------~~~~~~~~~GDlg~~~~~~~ 90 (539)
T PRK09247 71 --------LFEESYDYVGDLAETIALLL 90 (539)
T ss_pred --------HHHHHHHhcCCHHHHHHHhc
Confidence 23445556666666655443
No 69
>KOG2386 consensus mRNA capping enzyme, guanylyltransferase (alpha) subunit [RNA processing and modification]
Probab=91.25 E-value=0.14 Score=57.66 Aligned_cols=97 Identities=16% Similarity=0.152 Sum_probs=65.6
Q ss_pred ceEEeeecceEeEEEEEecCCeEEEEcCCcccCC---CCCchHHHHHHhhcCCCCCCeEEEEEEEEEecCCCcccChhhH
Q 004212 454 EFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNT---GKFPDVVLAVSRLKKPSVRSFVLDCEIVAYDREKQKILPFQTL 530 (768)
Q Consensus 454 ~~~~E~KyDG~R~qih~~~~g~V~lfSR~g~d~T---~~fPel~~~l~~~~~~~~~~~ILDGElVa~d~~~g~~~pFq~L 530 (768)
.|.+.||+||.|...-++.+|.+..+-|.-...- -.++.-. ...+.....++|||++. |.-++
T Consensus 286 ~y~~~We~dg~~~~~L~~~~~~~~~~dR~~~~~~~~~~~~~~~~-----~~~~~~~~tl~dge~~l-D~l~~-------- 351 (393)
T KOG2386|consen 286 YYEASWEADGTRYMMLIDGDGEYYDFDRWRFVKGRENLRKIRED-----SDTKVLHQTLLDGEMIL-DRLKE-------- 351 (393)
T ss_pred hhhhhhcccCcEEEEEecCCceeEechhhhHHHhhhhhhccccc-----ccchhhhhhhcccceec-ccccc--------
Confidence 4678999999999888765666667766543221 1111100 01113356789999998 75332
Q ss_pred HhhhhccCCccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhh
Q 004212 531 STRARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSF 578 (768)
Q Consensus 531 ~~R~rk~~~~~~~~~~v~~~vFDiLylnG~~L~~~Pl~ERr~lL~~l~ 578 (768)
.....+.+||++.+|++.+...|+. |.+.+++-+
T Consensus 352 -------------~~~~r~l~Yd~~r~n~~~v~~~~f~-r~~~~~~ev 385 (393)
T KOG2386|consen 352 -------------EAIPRYLIYDMVRFNSQKVEKRPFS-RWQIIEKEV 385 (393)
T ss_pred -------------ccchhheeeeeeeccCcccccCcch-HHHHHHHHh
Confidence 1245788999999999999999999 988776543
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=90.78 E-value=0.62 Score=46.49 Aligned_cols=91 Identities=14% Similarity=0.205 Sum_probs=62.2
Q ss_pred HHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHhcCCChHHHHHHHHhhcc-------cCcccHHHHHHHHHhhhccCCCC
Q 004212 305 ITKVFDTFRLIAKEAGKDSQEKKKNRIKALLVAATDCEPQYLIRLLQSKL-------RIGLAEQTLLAALGQAAVYNEQH 377 (768)
Q Consensus 305 I~eV~~~L~kIA~~~G~~Sq~~K~~~l~~Ll~~~t~~E~k~lvRiIlkdL-------RiGi~e~tVl~ala~a~~~~~~~ 377 (768)
..++.+.|++|+.. .+..+|.++|.+++....+.+.-+.+.++++.+ ..|++++++.+++++++..++.
T Consensus 3 F~~l~~l~~~l~~~---~~~~~k~~~l~~~~~~~~~~~~~~~~~~~~~~l~P~~d~r~~~i~~~~L~k~~~~~~~~~~~- 78 (177)
T PF04675_consen 3 FSDLCELFEKLEST---SSRLEKIAILSNFFRSWREEDLGPDLYLLLRLLFPEYDGREYGIGEKLLAKAIAEALGLPEK- 78 (177)
T ss_dssp HHHHHHHHHHHHT------HHHHHHHHHHHHHTSHCCGHHCHHHHHHTHSSTTTCS---S--HHHHHHHHHHHHTS-HH-
T ss_pred HHHHHHHHHHHHhc---cCHHHHHHHHHHHHHHcccchhhhHHHHHhcccccchhhhHhccchhHHHHHHHHHHcCCHH-
Confidence 35666777777653 456678999999999999887777777777744 5899999999999999876532
Q ss_pred CCCCCCCcchHHHHHHHHHHHhhcCCchhhhhhhhhhc
Q 004212 378 SKPPPNIQSPLEEAAKIVKQVFSVLPVYEKIVPALLTD 415 (768)
Q Consensus 378 ~~~~~~l~~~l~~a~~~vk~~y~~~pd~~~v~~~ll~~ 415 (768)
.+.+.|...-|++.++..++..
T Consensus 79 ----------------~~~~~~~~~GD~g~~~~~~~~~ 100 (177)
T PF04675_consen 79 ----------------SIDESYKKVGDLGEVAEEVLQK 100 (177)
T ss_dssp ----------------HHHHHHHHHS-HHHHHHHHHHH
T ss_pred ----------------HHHHHHHhcCcHHHHHHHHHhh
Confidence 2334566677888887776643
No 71
>PLN03113 DNA ligase 1; Provisional
Probab=85.94 E-value=2.3 Score=52.13 Aligned_cols=70 Identities=23% Similarity=0.301 Sum_probs=57.4
Q ss_pred CCcHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHhc---CCChHHHHHHHHhhccc-------CcccHHHHHHHHHhhh
Q 004212 302 PLTITKVFDTFRLIAKEAGKDSQEKKKNRIKALLVAA---TDCEPQYLIRLLQSKLR-------IGLAEQTLLAALGQAA 371 (768)
Q Consensus 302 ~LTI~eV~~~L~kIA~~~G~~Sq~~K~~~l~~Ll~~~---t~~E~k~lvRiIlkdLR-------iGi~e~tVl~ala~a~ 371 (768)
++.-.++.+.|.+|...++ ...|.++|.++|..+ ++++.-|.+.++.+.+. +||+++.+.+|++.++
T Consensus 128 ~~~f~~l~~~~~~Ie~tt~---rlek~~~L~~~~r~~~~~~p~dl~~~vyL~~~~l~P~~e~~elgige~~L~kai~e~~ 204 (744)
T PLN03113 128 RVPFLFVALAFDLISNETG---RIVITDIVCNMLRTVMATTPEDLVAVVYLLANRIAPAHEGVELGIGEATIIKALAEAF 204 (744)
T ss_pred CccHHHHHHHHHHHHhccC---HHHHHHHHHHHHHHhccCChHHHHHHHHHHhCCCCccccCcccCcCHHHHHHHHHHHH
Confidence 4566777788888876655 346789999999985 88999999999988764 6999999999999998
Q ss_pred ccC
Q 004212 372 VYN 374 (768)
Q Consensus 372 ~~~ 374 (768)
+.+
T Consensus 205 g~~ 207 (744)
T PLN03113 205 GRT 207 (744)
T ss_pred CcC
Confidence 754
No 72
>COG4566 TtrR Response regulator [Signal transduction mechanisms]
Probab=61.80 E-value=23 Score=36.68 Aligned_cols=86 Identities=19% Similarity=0.299 Sum_probs=57.7
Q ss_pred hhCChHHHHhhhcccCCccCCCCCCcHHHHHHHHHHHHHH-hCCChHHHHHHHHHHHHHhcCCChHHHHHHHHhhccc--
Q 004212 279 EMGDLGLVAKASRSSQSMMRKPDPLTITKVFDTFRLIAKE-AGKDSQEKKKNRIKALLVAATDCEPQYLIRLLQSKLR-- 355 (768)
Q Consensus 279 ~~GDlg~vA~~~r~~q~~l~~~~~LTI~eV~~~L~kIA~~-~G~~Sq~~K~~~l~~Ll~~~t~~E~k~lvRiIlkdLR-- 355 (768)
-+||+..+++..+..- .-|-.+|..-+++.+.+.+--.. .-..........+..+|..+|+.|...+-+++.+-+.
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 4789988777655332 12335677777777765543221 1112222345788999999999999999999988663
Q ss_pred ----CcccHHHHHH
Q 004212 356 ----IGLAEQTLLA 365 (768)
Q Consensus 356 ----iGi~e~tVl~ 365 (768)
+|+++.||--
T Consensus 163 IA~dLgiS~rTVe~ 176 (202)
T COG4566 163 IAFDLGISERTVEL 176 (202)
T ss_pred HHHHcCCchhhHHH
Confidence 6888888863
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=55.46 E-value=30 Score=37.01 Aligned_cols=57 Identities=14% Similarity=0.123 Sum_probs=48.2
Q ss_pred cCCcHHHHHHHHHHhhccCCCeEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEeeC
Q 004212 563 LQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTM 619 (768)
Q Consensus 563 ~~~Pl~ERr~lL~~l~~~~~~~i~l~~~~~~~~~eei~~~~~~ai~~G~EGlVlK~~ 619 (768)
..++.+||+++++.......+++.++-.....+.++..++.+.+.+.|..|+|+=.+
T Consensus 45 ~~ls~~Er~~l~~~~~~~~~~~~~vi~gv~~~~~~~~i~~a~~a~~~Gad~v~v~pP 101 (281)
T cd00408 45 PTLTDEERKEVIEAVVEAVAGRVPVIAGVGANSTREAIELARHAEEAGADGVLVVPP 101 (281)
T ss_pred ccCCHHHHHHHHHHHHHHhCCCCeEEEecCCccHHHHHHHHHHHHHcCCCEEEECCC
Confidence 467899999999999987777776766666677888899999999999999999766
No 74
>cd00950 DHDPS Dihydrodipicolinate synthase (DHDPS) is a key enzyme in lysine biosynthesis. It catalyzes the aldol condensation of L-aspartate-beta- semialdehyde and pyruvate to dihydropicolinic acid via a Schiff base formation between pyruvate and a lysine residue. The functional enzyme is a homotetramer consisting of a dimer of dimers. DHDPS is member of dihydrodipicolinate synthase family that comprises several pyruvate-dependent class I aldolases that use the same catalytic step to catalyze different reactions in different pathways.
Probab=54.10 E-value=29 Score=37.30 Aligned_cols=66 Identities=14% Similarity=0.002 Sum_probs=52.5
Q ss_pred eeecCCc--cccCCcHHHHHHHHHHhhccCCCeEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEeeC
Q 004212 554 ILYRNGQ--PLLQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTM 619 (768)
Q Consensus 554 iLylnG~--~L~~~Pl~ERr~lL~~l~~~~~~~i~l~~~~~~~~~eei~~~~~~ai~~G~EGlVlK~~ 619 (768)
-++++|. ....++..||+++++...+...+++.++-.....+.++..++.+.+.+.|..|+|+=.+
T Consensus 37 gl~v~GstGE~~~lt~~Er~~l~~~~~~~~~~~~~vi~gv~~~~~~~~~~~a~~a~~~G~d~v~~~~P 104 (284)
T cd00950 37 GLVVCGTTGESPTLSDEEHEAVIEAVVEAVNGRVPVIAGTGSNNTAEAIELTKRAEKAGADAALVVTP 104 (284)
T ss_pred EEEECCCCcchhhCCHHHHHHHHHHHHHHhCCCCcEEeccCCccHHHHHHHHHHHHHcCCCEEEEccc
Confidence 3455542 23578999999999999887777666665555667889999999999999999999887
No 75
>PRK03170 dihydrodipicolinate synthase; Provisional
Probab=53.77 E-value=29 Score=37.52 Aligned_cols=57 Identities=16% Similarity=0.064 Sum_probs=48.6
Q ss_pred cCCcHHHHHHHHHHhhccCCCeEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEeeC
Q 004212 563 LQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTM 619 (768)
Q Consensus 563 ~~~Pl~ERr~lL~~l~~~~~~~i~l~~~~~~~~~eei~~~~~~ai~~G~EGlVlK~~ 619 (768)
..++.+||+++++.+.....+++.++-.....+.++..++.+.+.+.|..|+|+=.+
T Consensus 49 ~~ls~~Er~~~~~~~~~~~~~~~~vi~gv~~~~~~~~i~~a~~a~~~G~d~v~~~pP 105 (292)
T PRK03170 49 PTLTHEEHEELIRAVVEAVNGRVPVIAGTGSNSTAEAIELTKFAEKAGADGALVVTP 105 (292)
T ss_pred ccCCHHHHHHHHHHHHHHhCCCCcEEeecCCchHHHHHHHHHHHHHcCCCEEEECCC
Confidence 568999999999999988777766666665667889999999999999999999876
No 76
>TIGR00683 nanA N-acetylneuraminate lyase. N-acetylneuraminate lyase is also known as N-acetylneuraminic acid aldolase, sialic acid aldolase, or sialate lyase. It is an intracellular enzyme. The structure of this homotetrameric enzyme related to dihydrodipicolinate synthase is known. In Clostridium tertium, the enzyme appears to be in an operon with a secreted sialidase that releases sialic acid from host sialoglycoconjugates. In several E. coli strains, however, this enzyme is responsible for N-acetyl-D-neuraminic acid synthesis for capsule production by condensing N-acetyl-D-mannosamine and pyruvate.
Probab=50.92 E-value=37 Score=36.92 Aligned_cols=57 Identities=14% Similarity=0.106 Sum_probs=47.5
Q ss_pred cCCcHHHHHHHHHHhhccCCCeEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEeeC
Q 004212 563 LQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTM 619 (768)
Q Consensus 563 ~~~Pl~ERr~lL~~l~~~~~~~i~l~~~~~~~~~eei~~~~~~ai~~G~EGlVlK~~ 619 (768)
..++.+||+++++.......+++.++-.....+.++..++-+.+.+.|..|+|+=.+
T Consensus 49 ~~Lt~eEr~~~~~~~~~~~~~~~pvi~gv~~~~t~~~i~la~~a~~~Gad~v~v~~P 105 (290)
T TIGR00683 49 FMLSTEEKKEIFRIAKDEAKDQIALIAQVGSVNLKEAVELGKYATELGYDCLSAVTP 105 (290)
T ss_pred ccCCHHHHHHHHHHHHHHhCCCCcEEEecCCCCHHHHHHHHHHHHHhCCCEEEEeCC
Confidence 457999999999999988777766666655667888899999999999999999655
No 77
>KOG0967 consensus ATP-dependent DNA ligase I [Replication, recombination and repair]
Probab=50.12 E-value=1.2e+02 Score=36.85 Aligned_cols=91 Identities=20% Similarity=0.275 Sum_probs=63.2
Q ss_pred CCCcHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHh---cCCChH---HHH-HHHHh---hcccCcccHHHHHHHHHhh
Q 004212 301 DPLTITKVFDTFRLIAKEAGKDSQEKKKNRIKALLVA---ATDCEP---QYL-IRLLQ---SKLRIGLAEQTLLAALGQA 370 (768)
Q Consensus 301 ~~LTI~eV~~~L~kIA~~~G~~Sq~~K~~~l~~Ll~~---~t~~E~---k~l-vRiIl---kdLRiGi~e~tVl~ala~a 370 (768)
+..+-.++..+|.+|...+|.-. -+.++.++|.. .+|++. -|| +.-|- ..|.+|+++.++.+|++.|
T Consensus 97 ~~~py~~~a~tF~kIe~~s~Rl~---i~~il~n~f~~v~~~sP~dLlp~vYLsiN~l~P~yeGlELGvGes~l~KAi~Ea 173 (714)
T KOG0967|consen 97 SKVPYLELARTFEKIEETSGRLE---IIDILSNFLRSVLATSPDDLLPTVYLSINKLAPDYEGLELGVGESLLMKAIAEA 173 (714)
T ss_pred CcCcHHHHHHHHHHHHhhcccee---HHHHHHHHHHHHHhcCchhhhhHHHHhhhccCccccCccccccHHHHHHHHHHH
Confidence 56777889999999988776532 24566666654 455554 222 12221 3678999999999999999
Q ss_pred hccCCCCCCCCCCCcchHHHHHHHHHHHhhcCCchhhhhhh
Q 004212 371 AVYNEQHSKPPPNIQSPLEEAAKIVKQVFSVLPVYEKIVPA 411 (768)
Q Consensus 371 ~~~~~~~~~~~~~l~~~l~~a~~~vk~~y~~~pd~~~v~~~ 411 (768)
.+-. ...|+.-|+..-|++.|+..
T Consensus 174 tGrt-----------------~~~vk~~~~~~GDLG~VA~~ 197 (714)
T KOG0967|consen 174 TGRT-----------------LSHVKNQYNKLGDLGLVAQG 197 (714)
T ss_pred hCcc-----------------HHHHHHHHHhcCcHHHHHhh
Confidence 8743 34578889999999888653
No 78
>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=49.60 E-value=41 Score=36.98 Aligned_cols=58 Identities=10% Similarity=0.090 Sum_probs=49.4
Q ss_pred ccCCcHHHHHHHHHHhhccCCCeEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEeeC
Q 004212 562 LLQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTM 619 (768)
Q Consensus 562 L~~~Pl~ERr~lL~~l~~~~~~~i~l~~~~~~~~~eei~~~~~~ai~~G~EGlVlK~~ 619 (768)
...++.+||+++++...+...+++.++-.....+.++..++-+.+.+.|..|+|+=.+
T Consensus 55 ~~~Lt~eEr~~v~~~~~~~~~grvpvi~Gv~~~~t~~ai~~a~~A~~~Gad~vlv~~P 112 (309)
T cd00952 55 CATLTWEEKQAFVATVVETVAGRVPVFVGATTLNTRDTIARTRALLDLGADGTMLGRP 112 (309)
T ss_pred chhCCHHHHHHHHHHHHHHhCCCCCEEEEeccCCHHHHHHHHHHHHHhCCCEEEECCC
Confidence 4568999999999999988777776666666678889999999999999999999876
No 79
>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=49.11 E-value=2.2e+02 Score=29.59 Aligned_cols=32 Identities=28% Similarity=0.331 Sum_probs=22.1
Q ss_pred ceEEeeecceEeEEEEEecCCeEEEEcCCccc
Q 004212 454 EFTCEYKYDGERAQIHYLEDGSVEIYSRNAER 485 (768)
Q Consensus 454 ~~~~E~KyDG~R~qih~~~~g~V~lfSR~g~d 485 (768)
++.+-.|+||.=+.+....+|.+.+-|+++-.
T Consensus 46 p~~v~~K~dGsli~~~~~~~g~~~~~SK~s~~ 77 (221)
T PF09511_consen 46 PVEVYEKEDGSLIFIPYLDDGELIVASKGSFD 77 (221)
T ss_dssp EEEEEEE--SEEE-EEEEETTEEEEEETTBSS
T ss_pred cEEEEEecCcEEEEEeeecCCeEEEEecCccc
Confidence 68999999995552233357899999999853
No 80
>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=48.75 E-value=33 Score=37.44 Aligned_cols=57 Identities=16% Similarity=0.238 Sum_probs=48.6
Q ss_pred cCCcHHHHHHHHHHhhccCCCeEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEeeC
Q 004212 563 LQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTM 619 (768)
Q Consensus 563 ~~~Pl~ERr~lL~~l~~~~~~~i~l~~~~~~~~~eei~~~~~~ai~~G~EGlVlK~~ 619 (768)
..++..||+++++.......+++.++-.....+.++..++-+.+.+.|..|+|+=.+
T Consensus 48 ~~Ls~~Er~~l~~~~~~~~~g~~pvi~gv~~~~t~~ai~~a~~A~~~Gad~v~v~pP 104 (294)
T TIGR02313 48 GSLTLEERKQAIENAIDQIAGRIPFAPGTGALNHDETLELTKFAEEAGADAAMVIVP 104 (294)
T ss_pred ccCCHHHHHHHHHHHHHHhCCCCcEEEECCcchHHHHHHHHHHHHHcCCCEEEEcCc
Confidence 457999999999999888778777776666677888888999999999999999887
No 81
>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=48.36 E-value=37 Score=36.59 Aligned_cols=58 Identities=16% Similarity=0.138 Sum_probs=48.4
Q ss_pred ccCCcHHHHHHHHHHhhccCCCeEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEeeC
Q 004212 562 LLQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTM 619 (768)
Q Consensus 562 L~~~Pl~ERr~lL~~l~~~~~~~i~l~~~~~~~~~eei~~~~~~ai~~G~EGlVlK~~ 619 (768)
-..++..||+++++.......+++.++-.....+.++..++.+.+.+.|..|+|+=.+
T Consensus 48 ~~~Lt~~Er~~l~~~~~~~~~~~~~vi~gv~~~st~~~i~~a~~a~~~Gad~v~v~~P 105 (289)
T PF00701_consen 48 FYSLTDEERKELLEIVVEAAAGRVPVIAGVGANSTEEAIELARHAQDAGADAVLVIPP 105 (289)
T ss_dssp GGGS-HHHHHHHHHHHHHHHTTSSEEEEEEESSSHHHHHHHHHHHHHTT-SEEEEEES
T ss_pred cccCCHHHHHHHHHHHHHHccCceEEEecCcchhHHHHHHHHHHHhhcCceEEEEecc
Confidence 3468999999999999887777777777777788999999999999999999999776
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=46.92 E-value=44 Score=36.24 Aligned_cols=57 Identities=12% Similarity=0.120 Sum_probs=46.4
Q ss_pred ccCCcHHHHHHHHHHhhccCCCeEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEeeC
Q 004212 562 LLQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTM 619 (768)
Q Consensus 562 L~~~Pl~ERr~lL~~l~~~~~~~i~l~~~~~~~~~eei~~~~~~ai~~G~EGlVlK~~ 619 (768)
...++.+||+++++..++...+++.++-.... +.++..++-+.+.+.|..|+|+=.+
T Consensus 47 ~~~Ls~eEr~~l~~~~~~~~~~~~pvi~gv~~-~t~~~i~~a~~a~~~Gad~v~~~pP 103 (289)
T cd00951 47 FFSLTPDEYAQVVRAAVEETAGRVPVLAGAGY-GTATAIAYAQAAEKAGADGILLLPP 103 (289)
T ss_pred cccCCHHHHHHHHHHHHHHhCCCCCEEEecCC-CHHHHHHHHHHHHHhCCCEEEECCC
Confidence 35689999999999998877776656555544 7788889999999999999999655
No 83
>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=45.58 E-value=40 Score=36.40 Aligned_cols=57 Identities=12% Similarity=0.049 Sum_probs=48.5
Q ss_pred cCCcHHHHHHHHHHhhccCCCeEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEeeC
Q 004212 563 LQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTM 619 (768)
Q Consensus 563 ~~~Pl~ERr~lL~~l~~~~~~~i~l~~~~~~~~~eei~~~~~~ai~~G~EGlVlK~~ 619 (768)
..++.+||+++++.......+++.++-.....+.++..++-+.+.+.|..|+|+=.+
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 467999999999999887777776666666677888999999999999999999876
No 84
>PRK04147 N-acetylneuraminate lyase; Provisional
Probab=44.41 E-value=38 Score=36.79 Aligned_cols=57 Identities=16% Similarity=0.152 Sum_probs=47.5
Q ss_pred cCCcHHHHHHHHHHhhccCCCeEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEeeC
Q 004212 563 LQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTM 619 (768)
Q Consensus 563 ~~~Pl~ERr~lL~~l~~~~~~~i~l~~~~~~~~~eei~~~~~~ai~~G~EGlVlK~~ 619 (768)
..++.+||+++++..+....+++.++-.....+.++..++-+.+.+.|..|+|+=.+
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 357889999999999888777766666665677889999999999999999998876
No 85
>PLN02417 dihydrodipicolinate synthase
Probab=44.13 E-value=43 Score=36.20 Aligned_cols=57 Identities=5% Similarity=-0.134 Sum_probs=45.6
Q ss_pred cCCcHHHHHHHHHHhhccCCCeEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEeeC
Q 004212 563 LQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTM 619 (768)
Q Consensus 563 ~~~Pl~ERr~lL~~l~~~~~~~i~l~~~~~~~~~eei~~~~~~ai~~G~EGlVlK~~ 619 (768)
..++.+||+++++...+...+++.++-.....+.++..++.+.+.+.|..|+|+=.+
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 356889999999888877777766666655667888888888889999999998766
No 86
>COG0329 DapA Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]
Probab=44.05 E-value=67 Score=35.24 Aligned_cols=58 Identities=17% Similarity=0.134 Sum_probs=50.8
Q ss_pred ccCCcHHHHHHHHHHhhccCCCeEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEeeC
Q 004212 562 LLQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTM 619 (768)
Q Consensus 562 L~~~Pl~ERr~lL~~l~~~~~~~i~l~~~~~~~~~eei~~~~~~ai~~G~EGlVlK~~ 619 (768)
-..++.+||+++++..++...+++.++-..-+++.++..++-+.+.+.|-.|+|+=.+
T Consensus 51 ~~~Ls~eEr~~v~~~~v~~~~grvpviaG~g~~~t~eai~lak~a~~~Gad~il~v~P 108 (299)
T COG0329 51 SPTLTLEERKEVLEAVVEAVGGRVPVIAGVGSNSTAEAIELAKHAEKLGADGILVVPP 108 (299)
T ss_pred chhcCHHHHHHHHHHHHHHHCCCCcEEEecCCCcHHHHHHHHHHHHhcCCCEEEEeCC
Confidence 3568999999999999998888877776667778899999999999999999999887
No 87
>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=41.63 E-value=51 Score=35.71 Aligned_cols=57 Identities=16% Similarity=0.141 Sum_probs=47.0
Q ss_pred cCCcHHHHHHHHHHhhccCCCeEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEeeC
Q 004212 563 LQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTM 619 (768)
Q Consensus 563 ~~~Pl~ERr~lL~~l~~~~~~~i~l~~~~~~~~~eei~~~~~~ai~~G~EGlVlK~~ 619 (768)
..++.+||+++++.......+++.++-.....+.++..++-+.+.+.|..|+|+=.+
T Consensus 49 ~~Lt~~Er~~~~~~~~~~~~~~~~viagv~~~~~~~ai~~a~~a~~~Gad~v~~~~P 105 (288)
T cd00954 49 FLLSVEERKQIAEIVAEAAKGKVTLIAHVGSLNLKESQELAKHAEELGYDAISAITP 105 (288)
T ss_pred ccCCHHHHHHHHHHHHHHhCCCCeEEeccCCCCHHHHHHHHHHHHHcCCCEEEEeCC
Confidence 457899999999998887777766655555567888999999999999999998776
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=37.34 E-value=80 Score=34.36 Aligned_cols=65 Identities=11% Similarity=0.093 Sum_probs=49.3
Q ss_pred eeecCCc--cccCCcHHHHHHHHHHhhccCCCeEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEeeC
Q 004212 554 ILYRNGQ--PLLQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTM 619 (768)
Q Consensus 554 iLylnG~--~L~~~Pl~ERr~lL~~l~~~~~~~i~l~~~~~~~~~eei~~~~~~ai~~G~EGlVlK~~ 619 (768)
-++++|. .-..++.+||+++++.......+++.++-... .+.++..++.+.+.+.|..|+|+=.+
T Consensus 42 gi~v~GstGE~~~Lt~eEr~~v~~~~~~~~~g~~pvi~gv~-~~t~~ai~~a~~a~~~Gadav~~~pP 108 (296)
T TIGR03249 42 ALFAAGGTGEFFSLTPAEYEQVVEIAVSTAKGKVPVYTGVG-GNTSDAIEIARLAEKAGADGYLLLPP 108 (296)
T ss_pred EEEECCCCcCcccCCHHHHHHHHHHHHHHhCCCCcEEEecC-ccHHHHHHHHHHHHHhCCCEEEECCC
Confidence 3445542 23568999999999999887777665555543 46788888999999999999999654
No 89
>PRK03620 5-dehydro-4-deoxyglucarate dehydratase; Provisional
Probab=36.98 E-value=80 Score=34.57 Aligned_cols=64 Identities=13% Similarity=0.161 Sum_probs=49.2
Q ss_pred eecCCc--cccCCcHHHHHHHHHHhhccCCCeEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEeeC
Q 004212 555 LYRNGQ--PLLQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTM 619 (768)
Q Consensus 555 LylnG~--~L~~~Pl~ERr~lL~~l~~~~~~~i~l~~~~~~~~~eei~~~~~~ai~~G~EGlVlK~~ 619 (768)
++.+|. ....++.+||+++++.......+++.++-... .+.++..++.+.+.+.|..|+|+=.+
T Consensus 45 i~~~GstGE~~~Lt~eEr~~~~~~~~~~~~~~~pvi~gv~-~~t~~~i~~~~~a~~~Gadav~~~pP 110 (303)
T PRK03620 45 LFAAGGTGEFFSLTPDEYSQVVRAAVETTAGRVPVIAGAG-GGTAQAIEYAQAAERAGADGILLLPP 110 (303)
T ss_pred EEECcCCcCcccCCHHHHHHHHHHHHHHhCCCCcEEEecC-CCHHHHHHHHHHHHHhCCCEEEECCC
Confidence 445552 23568999999999999887777666655554 37788889999999999999999655
No 90
>KOG3673 consensus FtsJ-like RNA methyltransferase [RNA processing and modification]
Probab=34.51 E-value=53 Score=38.79 Aligned_cols=63 Identities=10% Similarity=0.017 Sum_probs=44.5
Q ss_pred ccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCCC------eEEEEeEEecCCHHHHHHHHHHH
Q 004212 544 KVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEPG------FFQFATTLTSIDLDEIQKFLDAA 606 (768)
Q Consensus 544 ~~~v~~~vFDiLylnG~~L~~~Pl~ERr~lL~~l~~~~~~------~i~l~~~~~~~~~eei~~~~~~a 606 (768)
..+-.+.+.|.+.|+|.++.++||+||.++-++.+..... ...-.....+...++..++|...
T Consensus 655 ~~~~avhIiD~~vL~G~Dvr~~py~eR~~~aeKFv~al~kp~Rkd~~~~a~r~Kp~yrL~em~~ff~nl 723 (845)
T KOG3673|consen 655 SEPQAVHIIDAAVLFGDDVRNLPYEERMKAAEKFVAALKKPNRKDKKHRAERIKPTYRLAEMDEFFSNL 723 (845)
T ss_pred ccchheeeeeeeeecCchhhcccHHHHHHHHHHHHHHhcCCCCccccccceecccceeHHHHHHHHHhh
Confidence 3456788999999999999999999999999998765321 11111122345567777777654
No 91
>PF11588 DUF3243: Protein of unknown function (DUF3243); InterPro: IPR021637 This family of proteins with unknown function includes uncharacterised proteins ymfJ and yflH. The family appears to be restricted to Firmicutes.; PDB: 3D0W_B.
Probab=28.41 E-value=25 Score=31.44 Aligned_cols=25 Identities=24% Similarity=0.258 Sum_probs=21.0
Q ss_pred HHHHHHHHHhcCCChHHHHHHHHhh
Q 004212 328 KNRIKALLVAATDCEPQYLIRLLQS 352 (768)
Q Consensus 328 ~~~l~~Ll~~~t~~E~k~lvRiIlk 352 (768)
.++|+.|+..++.+|.+-|.+++.|
T Consensus 53 erlLkELW~va~e~Eq~~LA~lmvK 77 (81)
T PF11588_consen 53 ERLLKELWDVADEEEQHALANLMVK 77 (81)
T ss_dssp HHHHHHHHHC--HHHHHHHHHHHHH
T ss_pred HHHHHHHHHhCCHHHHHHHHHHHHH
Confidence 5799999999999999999999876
No 92
>PRK14956 DNA polymerase III subunits gamma and tau; Provisional
Probab=27.48 E-value=69 Score=37.69 Aligned_cols=27 Identities=44% Similarity=0.529 Sum_probs=21.6
Q ss_pred CCCCCCCCCCCCCCcccCCCCCCCCCc
Q 004212 119 LVKPISNQIDNPIDSEKESQPTPPSPK 145 (768)
Q Consensus 119 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 145 (768)
+.++.++-.++|-.|+.+||.+||+.+
T Consensus 434 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 460 (484)
T PRK14956 434 SNQQDSNLDNNPLPSKSESQSEPPSSK 460 (484)
T ss_pred cccccccCCCCCCCCcccccCCCCCCh
Confidence 346777788889999999999999543
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=25.11 E-value=1.6e+02 Score=33.42 Aligned_cols=56 Identities=20% Similarity=0.243 Sum_probs=42.6
Q ss_pred cCCcHHHHHHHHHHhhccCC----CeEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEeeC
Q 004212 563 LQEQLRVRREHLYDSFEEEP----GFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTM 619 (768)
Q Consensus 563 ~~~Pl~ERr~lL~~l~~~~~----~~i~l~~~~~~~~~eei~~~~~~ai~~G~EGlVlK~~ 619 (768)
.-.|++||.+...+.+.... ....++... +.+.+++.+..+.+.+.|..|+|+-.+
T Consensus 173 ~~~~~eER~~~v~~av~~a~~~TG~~~~y~~ni-t~~~~e~i~~a~~a~~~Gad~vmv~~~ 232 (367)
T cd08205 173 PYAPFEERVRACMEAVRRANEETGRKTLYAPNI-TGDPDELRRRADRAVEAGANALLINPN 232 (367)
T ss_pred ccCCHHHHHHHHHHHHHHHHHhhCCcceEEEEc-CCCHHHHHHHHHHHHHcCCCEEEEecc
Confidence 34799999999999887654 333344333 344688999999999999999999886
No 94
>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=24.04 E-value=2.4e+02 Score=30.50 Aligned_cols=55 Identities=13% Similarity=-0.028 Sum_probs=43.8
Q ss_pred ccCCcHHHHHHHHHHhhccCCCeEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEeeC
Q 004212 562 LLQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTM 619 (768)
Q Consensus 562 L~~~Pl~ERr~lL~~l~~~~~~~i~l~~~~~~~~~eei~~~~~~ai~~G~EGlVlK~~ 619 (768)
-..++.+||+++++...+... . ++-...+.+.++..++-+.+.+.|..|+|+=.+
T Consensus 46 ~~~Lt~eEr~~l~~~~~~~~~-~--vi~gvg~~~~~~ai~~a~~a~~~Gad~v~v~~P 100 (279)
T cd00953 46 GPSLSFQEKLELLKAYSDITD-K--VIFQVGSLNLEESIELARAAKSFGIYAIASLPP 100 (279)
T ss_pred cccCCHHHHHHHHHHHHHHcC-C--EEEEeCcCCHHHHHHHHHHHHHcCCCEEEEeCC
Confidence 356899999999999887653 3 233444567889999999999999999998776
No 95
>KOG0971 consensus Microtubule-associated protein dynactin DCTN1/Glued [Cell cycle control, cell division, chromosome partitioning; Cytoskeleton]
Probab=22.07 E-value=1.9e+02 Score=36.48 Aligned_cols=16 Identities=31% Similarity=0.293 Sum_probs=7.0
Q ss_pred ccccchhhhHHHHhhh
Q 004212 151 VNSVSAKEKIAELKSN 166 (768)
Q Consensus 151 ~~~~~~~~~~~~~~~~ 166 (768)
.++.++++++.++...
T Consensus 217 v~l~saskte~eLr~Q 232 (1243)
T KOG0971|consen 217 VPLPSASKTEEELRAQ 232 (1243)
T ss_pred CCCCccccchHHHHHH
Confidence 3444444444444443
No 96
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=21.78 E-value=4.4e+02 Score=27.01 Aligned_cols=80 Identities=23% Similarity=0.221 Sum_probs=50.9
Q ss_pred HHHHHHhCCCHHHHHHHHhhhCChHHHHhhhccc-CCccCCCCCCcHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHhc
Q 004212 260 KALAEACGRTESHVKKQYQEMGDLGLVAKASRSS-QSMMRKPDPLTITKVFDTFRLIAKEAGKDSQEKKKNRIKALLVAA 338 (768)
Q Consensus 260 Kal~~a~G~s~~~ik~~y~~~GDlg~vA~~~r~~-q~~l~~~~~LTI~eV~~~L~kIA~~~G~~Sq~~K~~~l~~Ll~~~ 338 (768)
.-|++++|.|...+-...++.-|++.|-....+. ++.. -.+..++++.+..++...-...-+.-...++.++..+
T Consensus 45 ~Ei~E~lg~Sks~vS~~lkkL~~~~lV~~~~~~G~Rk~~----F~a~~df~~~f~t~f~ek~~ReId~t~e~l~k~~~e~ 120 (177)
T COG1510 45 DEIAEALGMSKSNVSMGLKKLQDWNLVKKVFEKGDRKDY----FEAEKDFSQIFRTLFEEKWKREIDPTKEALKKLLEEL 120 (177)
T ss_pred HHHHHHHCCCcchHHHHHHHHHhcchHHhhhccCcchhh----hcccchHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHc
Confidence 3478999999998888777777777664332211 1112 2456788888888876544333344456777777777
Q ss_pred CCChH
Q 004212 339 TDCEP 343 (768)
Q Consensus 339 t~~E~ 343 (768)
.+++-
T Consensus 121 ~~~~~ 125 (177)
T COG1510 121 NEDLD 125 (177)
T ss_pred ccccc
Confidence 76444
Done!