Query 003762
Match_columns 797
No_of_seqs 317 out of 1942
Neff 5.9
Searched_HMMs 46136
Date Thu Mar 28 11:35:51 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/003762.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/003762hhsearch_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 1E-151 2E-156 1260.9 47.5 612 161-772 69-684 (714)
2 PLN03113 DNA ligase 1; Provisi 100.0 2E-144 5E-149 1267.8 73.0 715 53-780 1-720 (744)
3 PRK01109 ATP-dependent DNA lig 100.0 7E-117 2E-121 1027.5 58.4 564 191-780 1-572 (590)
4 PRK03180 ligB ATP-dependent DN 100.0 1E-101 3E-106 883.7 51.2 495 191-780 1-499 (508)
5 PRK09247 ATP-dependent DNA lig 100.0 4E-101 1E-105 885.8 54.7 516 194-780 2-528 (539)
6 TIGR00574 dnl1 DNA ligase I, A 100.0 9E-101 2E-105 881.7 52.6 501 250-780 1-506 (514)
7 KOG0966 ATP-dependent DNA liga 100.0 3.7E-88 7.9E-93 766.3 36.5 548 189-778 3-580 (881)
8 COG1793 CDC9 ATP-dependent DNA 100.0 3E-69 6.4E-74 607.3 37.0 422 260-772 2-426 (444)
9 PHA02587 30 DNA ligase; Provis 100.0 1.1E-65 2.4E-70 586.2 43.3 435 196-772 2-472 (488)
10 TIGR02779 NHEJ_ligase_lig DNA 100.0 3.2E-60 6.9E-65 511.8 33.4 287 450-778 9-297 (298)
11 PRK09632 ATP-dependent DNA lig 100.0 9.2E-59 2E-63 545.1 34.6 304 425-778 454-761 (764)
12 PRK08224 ligC ATP-dependent DN 100.0 1.2E-57 2.6E-62 500.2 33.7 309 425-779 2-331 (350)
13 PRK05972 ligD ATP-dependent DN 100.0 3.4E-56 7.5E-61 527.7 34.2 299 431-778 233-536 (860)
14 PRK09633 ligD ATP-dependent DN 100.0 2.1E-55 4.5E-60 510.3 32.8 292 432-780 1-310 (610)
15 PRK07636 ligB ATP-dependent DN 100.0 1.1E-52 2.3E-57 448.3 31.4 272 432-771 3-274 (275)
16 cd07900 Adenylation_DNA_ligase 100.0 7.8E-51 1.7E-55 420.9 24.9 217 423-641 1-219 (219)
17 TIGR02776 NHEJ_ligase_prk DNA 100.0 1.6E-47 3.5E-52 440.1 27.7 255 480-779 1-259 (552)
18 PHA00454 ATP-dependent DNA lig 100.0 1.4E-46 2.9E-51 408.7 31.4 284 433-772 7-314 (315)
19 PRK09125 DNA ligase; Provision 100.0 1E-45 2.2E-50 395.7 27.5 252 432-772 28-280 (282)
20 cd07903 Adenylation_DNA_ligase 100.0 2.9E-45 6.4E-50 380.2 23.3 216 423-642 3-224 (225)
21 cd07901 Adenylation_DNA_ligase 100.0 8.2E-45 1.8E-49 372.7 24.0 205 428-640 1-207 (207)
22 cd07902 Adenylation_DNA_ligase 100.0 9.8E-45 2.1E-49 373.9 23.4 208 423-641 5-213 (213)
23 cd07897 Adenylation_DNA_ligase 100.0 1.9E-43 4.2E-48 362.7 22.7 201 430-641 3-206 (207)
24 cd08039 Adenylation_DNA_ligase 100.0 5.1E-43 1.1E-47 365.7 24.1 199 441-641 10-235 (235)
25 cd07898 Adenylation_DNA_ligase 100.0 1.3E-42 2.7E-47 354.7 23.8 199 432-640 1-201 (201)
26 PF01068 DNA_ligase_A_M: ATP d 100.0 6.5E-42 1.4E-46 347.6 21.1 201 434-638 1-202 (202)
27 cd07905 Adenylation_DNA_ligase 100.0 9.7E-41 2.1E-45 339.4 20.6 190 432-640 1-193 (194)
28 cd07906 Adenylation_DNA_ligase 100.0 8.5E-40 1.8E-44 331.1 21.3 189 432-639 1-189 (190)
29 PF04675 DNA_ligase_A_N: DNA l 100.0 5.5E-35 1.2E-39 292.3 17.1 176 191-369 1-177 (177)
30 cd07896 Adenylation_kDNA_ligas 100.0 2.2E-33 4.9E-38 280.2 16.3 173 432-639 1-174 (174)
31 cd06846 Adenylation_DNA_ligase 100.0 3.4E-31 7.5E-36 266.2 18.2 175 434-639 2-182 (182)
32 cd07967 OBF_DNA_ligase_III The 100.0 1.7E-31 3.6E-36 257.9 13.9 128 645-780 1-137 (139)
33 cd07969 OBF_DNA_ligase_I The O 100.0 7.1E-29 1.5E-33 241.3 14.3 133 646-780 1-135 (144)
34 cd07893 OBF_DNA_ligase The Oli 100.0 9.9E-29 2.1E-33 236.1 14.3 127 647-777 1-129 (129)
35 cd07968 OBF_DNA_ligase_IV The 99.9 1.8E-27 3.8E-32 230.6 13.2 126 646-780 1-140 (140)
36 cd07895 Adenylation_mRNA_cappi 99.9 6.8E-27 1.5E-31 241.3 14.7 162 450-639 38-215 (215)
37 cd07972 OBF_DNA_ligase_Arch_Li 99.9 4.1E-26 8.9E-31 216.1 12.9 115 647-780 1-117 (122)
38 KOG4437 ATP-dependent DNA liga 99.9 6.1E-23 1.3E-27 215.7 18.6 324 190-556 154-482 (482)
39 cd08040 OBF_DNA_ligase_family 99.9 5.3E-22 1.1E-26 184.0 13.0 108 647-771 1-108 (108)
40 cd07971 OBF_DNA_ligase_LigD Th 99.9 1.3E-21 2.9E-26 183.3 13.6 112 648-777 2-115 (115)
41 PF04679 DNA_ligase_A_C: ATP d 99.8 2.7E-21 5.9E-26 175.9 9.3 95 663-772 1-95 (97)
42 cd07894 Adenylation_RNA_ligase 99.8 9.3E-18 2E-22 184.3 15.6 165 450-641 46-218 (342)
43 cd07970 OBF_DNA_ligase_LigC Th 99.7 2.6E-17 5.6E-22 156.1 12.3 110 647-777 1-120 (122)
44 PF01331 mRNA_cap_enzyme: mRNA 99.3 1.3E-12 2.9E-17 132.8 7.1 158 452-638 15-192 (192)
45 cd08041 OBF_kDNA_ligase_like T 99.3 2.4E-12 5.1E-17 112.7 6.9 76 648-771 2-77 (77)
46 COG1423 ATP-dependent DNA liga 98.9 3.5E-08 7.5E-13 106.5 14.6 148 448-619 83-234 (382)
47 COG5226 CEG1 mRNA capping enzy 98.8 4.4E-09 9.6E-14 111.2 5.6 174 452-655 61-257 (404)
48 PF14743 DNA_ligase_OB_2: DNA 98.7 1.6E-08 3.6E-13 86.0 5.5 66 658-771 1-66 (66)
49 cd09232 Snurportin-1_C C-termi 98.6 1.8E-07 3.8E-12 95.3 11.0 149 453-639 21-185 (186)
50 TIGR01209 RNA ligase, Pab1020 98.6 5.8E-07 1.3E-11 99.6 15.3 148 449-619 75-226 (374)
51 PRK08097 ligB NAD-dependent DN 98.3 5.9E-05 1.3E-09 88.4 20.7 206 434-670 97-331 (562)
52 PRK01109 ATP-dependent DNA lig 98.1 8E-06 1.7E-10 96.9 9.5 93 189-291 113-210 (590)
53 smart00532 LIGANc Ligase N fam 98.1 9.1E-05 2E-09 84.9 17.0 237 434-699 75-360 (441)
54 PRK07956 ligA NAD-dependent DN 98.0 0.00012 2.7E-09 87.8 17.0 238 433-699 78-365 (665)
55 cd00114 LIGANc NAD+ dependent 98.0 0.00011 2.5E-09 80.5 14.8 185 433-634 72-299 (307)
56 PRK14351 ligA NAD-dependent DN 97.9 0.00042 9.1E-09 83.5 18.6 235 434-699 105-387 (689)
57 TIGR00575 dnlj DNA ligase, NAD 97.8 0.00053 1.2E-08 82.3 18.0 237 433-699 67-353 (652)
58 PRK14350 ligA NAD-dependent DN 97.8 0.00048 1E-08 82.6 17.5 217 454-699 111-362 (669)
59 PF01653 DNA_ligase_aden: NAD- 97.7 8.2E-05 1.8E-09 81.9 8.3 173 433-619 77-289 (315)
60 PF09414 RNA_ligase: RNA ligas 97.4 0.00015 3.2E-09 73.3 4.0 159 454-638 2-186 (186)
61 TIGR02307 RNA_lig_RNL2 RNA lig 97.2 0.0027 5.8E-08 70.0 12.2 162 451-640 23-217 (325)
62 COG0272 Lig NAD-dependent DNA 97.0 0.026 5.7E-07 67.1 17.5 173 453-640 109-317 (667)
63 PHA02142 putative RNA ligase 95.9 0.089 1.9E-06 59.1 12.7 163 442-640 157-358 (366)
64 KOG3132 m3G-cap-specific nucle 95.8 0.039 8.6E-07 57.8 8.5 152 452-636 115-277 (325)
65 PRK03180 ligB ATP-dependent DN 94.6 0.16 3.5E-06 59.7 10.1 91 189-289 71-164 (508)
66 TIGR02306 RNA_lig_DRB0094 RNA 93.4 1.6 3.6E-05 48.9 14.6 155 452-640 158-336 (341)
67 TIGR00574 dnl1 DNA ligase I, A 92.4 0.58 1.3E-05 55.2 9.8 93 189-291 53-148 (514)
68 KOG2386 mRNA capping enzyme, g 92.2 0.091 2E-06 59.3 2.7 97 454-578 286-385 (393)
69 PRK09247 ATP-dependent DNA lig 91.4 0.55 1.2E-05 55.8 8.2 87 307-413 3-90 (539)
70 PF04675 DNA_ligase_A_N: DNA l 90.1 0.75 1.6E-05 46.1 6.7 91 305-415 3-100 (177)
71 PLN03113 DNA ligase 1; Provisi 85.4 3.3 7.3E-05 51.0 9.4 92 301-412 127-228 (744)
72 COG4566 TtrR Response regulato 62.5 19 0.00042 37.3 6.3 86 279-365 84-176 (202)
73 PF09511 RNA_lig_T4_1: RNA lig 61.9 79 0.0017 33.1 11.1 47 586-641 166-218 (221)
74 cd00408 DHDPS-like Dihydrodipi 53.4 33 0.00073 36.9 6.8 58 562-619 44-101 (281)
75 cd00950 DHDPS Dihydrodipicolin 53.2 30 0.00065 37.4 6.4 66 554-619 37-104 (284)
76 PRK03170 dihydrodipicolinate s 51.0 34 0.00073 37.2 6.4 58 562-619 48-105 (292)
77 PF00701 DHDPS: Dihydrodipicol 50.3 40 0.00087 36.6 6.8 58 562-619 48-105 (289)
78 TIGR02313 HpaI-NOT-DapA 2,4-di 49.7 38 0.00083 37.1 6.6 58 562-619 47-104 (294)
79 TIGR00683 nanA N-acetylneurami 49.3 40 0.00088 36.8 6.6 66 554-619 38-105 (290)
80 TIGR00674 dapA dihydrodipicoli 47.2 45 0.00098 36.2 6.6 57 563-619 46-102 (285)
81 cd00952 CHBPH_aldolase Trans-o 46.0 50 0.0011 36.5 6.8 58 562-619 55-112 (309)
82 cd00951 KDGDH 5-dehydro-4-deox 44.8 50 0.0011 36.1 6.5 57 562-619 47-103 (289)
83 PLN02417 dihydrodipicolinate s 44.5 50 0.0011 35.9 6.5 57 563-619 49-105 (280)
84 PRK04147 N-acetylneuraminate l 44.2 48 0.001 36.2 6.2 57 563-619 52-108 (293)
85 cd00954 NAL N-Acetylneuraminic 42.9 61 0.0013 35.3 6.8 57 563-619 49-105 (288)
86 COG0329 DapA Dihydrodipicolina 40.5 81 0.0018 34.8 7.3 65 555-619 42-108 (299)
87 PRK03620 5-dehydro-4-deoxygluc 34.5 91 0.002 34.3 6.6 64 555-619 45-110 (303)
88 TIGR03249 KdgD 5-dehydro-4-deo 34.3 95 0.0021 34.0 6.6 64 555-619 43-108 (296)
89 KOG3673 FtsJ-like RNA methyltr 32.9 59 0.0013 38.6 4.8 62 545-606 656-723 (845)
90 KOG0967 ATP-dependent DNA liga 32.2 2.1E+02 0.0045 34.9 9.1 91 300-410 96-196 (714)
91 PRK14956 DNA polymerase III su 30.9 58 0.0012 38.5 4.4 27 119-145 434-460 (484)
92 KOG0971 Microtubule-associated 28.8 1.2E+02 0.0025 38.3 6.4 21 151-171 217-237 (1243)
93 cd08205 RuBisCO_IV_RLP Ribulos 28.4 1.3E+02 0.0027 34.4 6.5 56 563-619 173-232 (367)
94 KOG2386 mRNA capping enzyme, g 28.3 1.7E+02 0.0037 33.8 7.4 169 444-641 51-242 (393)
95 cd00953 KDG_aldolase KDG (2-ke 24.0 2.3E+02 0.0051 30.7 7.4 55 562-619 46-100 (279)
96 COG1510 Predicted transcriptio 23.7 3.5E+02 0.0076 27.8 7.9 114 212-343 11-125 (177)
97 PF11588 DUF3243: Protein of u 23.7 31 0.00068 30.9 0.5 25 328-352 53-77 (81)
No 1
>KOG0967 consensus ATP-dependent DNA ligase I [Replication, recombination and repair]
Probab=100.00 E-value=1.1e-151 Score=1260.92 Aligned_cols=612 Identities=63% Similarity=1.042 Sum_probs=596.4
Q ss_pred HHHhhhhhhcccCCCCCCCcccccccCCCccchHHHHHHHHHHHhccchHHHHHHHHHHHHhhhcCCCCchHHHHHHHhC
Q 003762 161 AELKSNIVLLKKKAGEFDPKMVACWEKGERVPFIFLSLVFDMISNETGRILITDIVCNMLRTVMETTPEDLVPVVYLAAN 240 (797)
Q Consensus 161 ~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~F~~la~~~e~I~~tssR~~k~~iL~~~fr~~i~~~p~dl~~~vyL~~~ 240 (797)
.+.+...+.+..+|..|.|.+.+||..|+++||+++|.+|+.|+.+++|+++++||+|||+.+++.+|+||+++|||++|
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 35556677889999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccCCCccccccCCChHHHHHHHHHHhCCCHHHHHHHHHhcCCHHHHHhhccccCCCCCCCCCCCHHHHHHHHHHHHHHhC
Q 003762 241 KIAPAHEGLELGIGDASIIKALAEACGRTESHVKKQYQEMGDLGLVAKASRSSQSMMRKPDPLTITKVFDTFRLIAKEAG 320 (797)
Q Consensus 241 ~l~P~~e~~elGIge~~L~kal~~a~G~s~~~ik~~y~~~GDlg~vA~~~r~~q~~l~~~~~LTI~eV~~~L~kIA~~~G 320 (797)
+|.|+|+|.|||||+++|+|||+++||++..++|..|++.||||+||+.+|.+|++|+.|+||||.+|+..|++||..+|
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 CChHHHHHHHHHHHHHhcCCChHHHHHHHHhhhccCcccHHHHHHHHHHhhccCC----CCCCCCCCCcchHHHHHHHHH
Q 003762 321 KDSQEKKKNRIKALLVAATDCEPQYLIRLLQSKLRIGLAEQTLLAALGQAAVYNE----QHSKPPPNIQSPLEEAAKIVK 396 (797)
Q Consensus 321 ~~s~~~K~~~L~~LL~~~t~~E~k~LiRiIlkdLRiGi~e~tvl~Ala~a~~~~~----~~~~~~~~l~~~l~~a~~~vk 396 (797)
++|+.+|+++++.||.+|++.|+|||+|.|.++||||++++|||.||++|+.++. .+++.+..+++.++.+..+|+
T Consensus 229 ~~S~~kK~~lik~Llvac~~~E~kyLiRsL~gkLRiGlaeqTvL~AL~~A~~~~~~~~~~~~~~~d~~kd~le~~~~ivk 308 (714)
T KOG0967|consen 229 KGSQNKKKDLIKALLVACRGIEAKYLIRSLEGKLRIGLAEQTVLAALGQAFVLNDNNDEEKSKKPDSLKDPLEEAAQIVK 308 (714)
T ss_pred cchhHHHHHHHHHHHHhcccccHHHHHHHHHhhhhhhhhHHHHHHHHHHHHhccCchhhhccCCcchhhhhhHHHHHHHH
Confidence 9999999999999999999999999999999999999999999999999998763 244566678999999999999
Q ss_pred HHhhcCCchhhhHhhhhhcCccccCCccccCCCCCCccccccccCChHHHHhhcCCCceEEEeecceEEEEEEEecCCeE
Q 003762 397 QVFSVLPVYEKIVPALLTDGVWNLSNTCSFTPGIPIGPMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHYLEDGSV 476 (797)
Q Consensus 397 ~~y~~~pd~~~v~~~l~~~g~~~l~~~~~l~~g~Pv~PMLA~~~~~i~~~l~k~~g~~~~~E~KyDG~R~qih~~~~g~V 476 (797)
++|+++|||+.|++.|+++|+++|.++|.++||+|++||||++++++.+++++|++..|.|||||||+|+|||+.++|.|
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 EEEecCCCccCCCcchHHHHHHhhcCCCCCCeEEEEEEEEEecCCCcccChhhHHhhhcccCCccccccceEEEEeeeee
Q 003762 477 EIYSRNAERNTGKFPDVVLAVSRLKKPSVRSFVLDCEIVAYDREKQKILPFQTLSTRARKNVSLSDIKVDVCIYAFDILY 556 (797)
Q Consensus 477 ~ifSR~gkd~T~~yPel~~~l~~~~~~~v~~~ILDGElVa~d~~~g~~lpFq~L~~R~Rk~~~~~~~~~~v~~~vFDILy 556 (797)
.|||||++++|.+||||...+..+..+.+.+||||||+|+||++.|+++|||.|++|.||+++..+++++||+|+|||||
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 99999999999999999999999888889999999999999999999999999999999999989999999999999999
Q ss_pred cCCccccCCcHHHHHHHHHHhhccCCCcEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEEeCCCCCCccCCCCCCCeEE
Q 003762 557 RNGQPLLQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLK 636 (797)
Q Consensus 557 lnG~~L~~~Pl~ERr~lL~~l~~~~~~~i~~v~~~~~~~~eei~~~f~~ai~~g~EGlmvK~~~~ds~Y~pGkRs~~WlK 636 (797)
+||++|+++|+.+||++|.+.|.+++|+++++....+++.+++++||+++++.+|||+|+|.+|.+++|+|.+||.+|+|
T Consensus 469 ~ng~~Li~~pL~eRR~~l~e~f~e~~g~f~fat~~~tn~~~eiq~Fl~~sv~~~cEGlMvKtLd~~atYep~kRs~~WlK 548 (714)
T KOG0967|consen 469 LNGESLIQEPLRERRELLHESFKEIPGEFQFATSLDTNDIDEIQEFLEESVQNSCEGLMVKTLDTNATYEPSKRSNNWLK 548 (714)
T ss_pred eCChhhhhhhHHHHHHHHHhhcccCCCceeEeeeeccCCHHHHHHHHHHhhccCcceeEEEeeccccccCchhhccchhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EccccccccCCccceEEEeEEeCCCCcCCccceEEEEEecCCCceEEEeccccCCCCHHHHHHHHHhhccccCCCCCCCc
Q 003762 637 LKKDYIESIGDSLDLVPIAAFHGRGKRTGVYGAFLLACYDSNNEEFQSICKIGTGFSEAMLEERSSSLRSKVIPKPRPYY 716 (797)
Q Consensus 637 lK~dY~~~~~dtlDlvVIGa~~G~Gkr~g~~gsfllg~~d~~~g~~~~vgkVGTGfSd~~l~~l~~~l~~~~~~~p~~~~ 716 (797)
+|+||++|+||++||||||+|+|+|||+|+||+||+||||+++++|++|||+||||||++++++++.+....+..|++||
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 99999999999999999999999999999999999999999999999999999999999999999999998888888999
Q ss_pred ccCCCCCCceEeccceEEEEEeeeeecCCcccccccccCCCCCceeeeceEeeEeC
Q 003762 717 RFADTISPDVWFEPTEVWEVKAADLTISPVHRAAIGVVDPDKVFTVRFSVLAHLSF 772 (797)
Q Consensus 717 ~~~~~~~pdvw~eP~~V~EV~~~eit~S~~~~aa~g~v~~~~G~sLRFPRf~riR~ 772 (797)
++....+||+||+|..||||+++|||.||.|+||.|+|++++|+|||||||+|+|+
T Consensus 629 ~~d~s~kPd~wf~p~~VwEvk~Adlt~SPiy~Aa~Glv~~dkGISlRFPRfiRiR~ 684 (714)
T KOG0967|consen 629 RFDESLKPDVWFEPTEVWEVKAADLTLSPIYKAALGLVDPDKGISLRFPRFIRIRD 684 (714)
T ss_pred ccCccCCCccccCHHHHHHHhhccccccchhHhhhcCcCCCCceeEecceeeEeec
Confidence 99998899999999999999999999999999999999999999999999999999
No 2
>PLN03113 DNA ligase 1; Provisional
Probab=100.00 E-value=2.5e-144 Score=1267.80 Aligned_cols=715 Identities=76% Similarity=1.167 Sum_probs=633.6
Q ss_pred cCCCCCcHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccch---hhcccCCCCCCCCCCCCCCCC
Q 003762 53 MSSSAPNAFQVLMSAAAKKKPSPQPNSSSSSSSPKKRRTLDTQTPKTTNSVVGEKI---QEVAEEPSNDLVKPISNQIDN 129 (797)
Q Consensus 53 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~ 129 (797)
|| |+||||||||+-++...++....+++.++++|+++...++++....-+.-+.- -+..-++.++.+.++....++
T Consensus 1 ~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 79 (744)
T PLN03113 1 MS-SRPSAFDALMSNARAAAKKKQPQTQSQSSSPKKRKIGETQDANLGKTNVSEGTLPKTEDTIEPKSDSAKPRSSTSSI 79 (744)
T ss_pred CC-CCccHHHHHHHHHHHHhhccCCCccCCCCccccccccCCCCCCcCCcccccccccccccCCCCCCCccccccccccc
Confidence 44 59999999999444433344444466677788887776555544433333332 122334444555555555554
Q ss_pred CCCcccCCCCCCCCCccccccccccchhhhHHHHhhhhhhcccCCCCCCCcccccccCCCccchHHHHHHHHHHHhccch
Q 003762 130 PIDSEKESQPTPPSPKKRKVNVNSVSAKEKIAELKSNIVLLKKKAGEFDPKMVACWEKGERVPFIFLSLVFDMISNETGR 209 (797)
Q Consensus 130 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~F~~la~~~e~I~~tssR 209 (797)
.++.++. +... .+.+... .++....+..+..++..|||..+++|..|.+|+|..||++|++|++|++|
T Consensus 80 ~~~~~~~-----~~~~---~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~w~~~~~~~f~~l~~~~~~Ie~tt~r 147 (744)
T PLN03113 80 AEDSKTG-----TKKA---QTLSKPK----KDEMKSKIGLLKKKPNDFDPEKVAYWEKGERVPFLFVALAFDLISNETGR 147 (744)
T ss_pred ccccCCC-----cccc---ccccccc----ccchhhhHhhccCCccccCcchhhcccCCCCccHHHHHHHHHHHHhccCH
Confidence 4443322 1111 1111111 14455556678999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHhhhcCCCCchHHHHHHHhCccCCCccccccCCChHHHHHHHHHHhCCCHHHHHHHHHhcCCHHHHHhh
Q 003762 210 ILITDIVCNMLRTVMETTPEDLVPVVYLAANKIAPAHEGLELGIGDASIIKALAEACGRTESHVKKQYQEMGDLGLVAKA 289 (797)
Q Consensus 210 ~~k~~iL~~~fr~~i~~~p~dl~~~vyL~~~~l~P~~e~~elGIge~~L~kal~~a~G~s~~~ik~~y~~~GDlg~vA~~ 289 (797)
++|+++|+|||+.++..+|+|+.++|||++|+|+|+|++.|||||++.|+|+|++++|++++.+++.|+++||||+||+.
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 ccccCCCCCCCCCCCHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHhcCCChHHHHHHHHhhhccCcccHHHHHHHHHH
Q 003762 290 SRSSQSMMRKPDPLTITKVFDTFRLIAKEAGKDSQEKKKNRIKALLVAATDCEPQYLIRLLQSKLRIGLAEQTLLAALGQ 369 (797)
Q Consensus 290 ~r~~q~~l~~~~~LTI~eV~~~L~kIA~~~G~~s~~~K~~~L~~LL~~~t~~E~k~LiRiIlkdLRiGi~e~tvl~Ala~ 369 (797)
+++.|.+++++++|||.+||+.|.+||+.+|++|+++|+.+|..||.+|+++|++||+|+|+++||||++++||+.|||+
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 98888888888999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhccCCCCCCCCCCCcchHHHHHHHHHHHhhcCCchhhhHhhhhhcCccccCCccccCCCCCCccccccccCChHHHHhh
Q 003762 370 AAVYNEQHSKPPPNIQSPLEEAAKIVKQVFSVLPVYEKIVPALLTDGVWNLSNTCSFTPGIPIGPMLAKPTKGVSEIVNK 449 (797)
Q Consensus 370 a~~~~~~~~~~~~~l~~~l~~a~~~vk~~y~~~pd~~~v~~~l~~~g~~~l~~~~~l~~g~Pv~PMLA~~~~~i~~~l~k 449 (797)
||.++..+.....+..++|++++.+++++|+.+|||+.|++.++++|+.++..+|.|+||+||+||||++++++.+++++
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 99877644444456778899999999999999999999999999999999988999999999999999999999999999
Q ss_pred cCCCceEEEeecceEEEEEEEecCCeEEEEecCCCccCCCcchHHHHHHhhcCCCCCCeEEEEEEEEEecCCCcccChhh
Q 003762 450 FQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAVSRLKKPSVRSFVLDCEIVAYDREKQKILPFQT 529 (797)
Q Consensus 450 ~~g~~~~~E~KyDG~R~qih~~~~g~V~ifSR~gkd~T~~yPel~~~l~~~~~~~v~~~ILDGElVa~d~~~g~~lpFq~ 529 (797)
|++.+|+||+||||+|+|||+..+|.|++|||||+++|++|||+++++..+..+++++||||||+|+||.++++++|||.
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 98889999999999999999866789999999999999999999998888775567899999999999998889999999
Q ss_pred HHhhhcccCCccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCCCcEEEEeEEecCCHHHHHHHHHHHHHc
Q 003762 530 LSTRARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAAVDA 609 (797)
Q Consensus 530 L~~R~Rk~~~~~~~~~~v~~~vFDILylnG~~L~~~Pl~ERr~lL~~l~~~~~~~i~~v~~~~~~~~eei~~~f~~ai~~ 609 (797)
|++|.|+++...+.+.++||+||||||+||++|+++||.|||++|++++.+.++++++++...+++.++++++|+++++.
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 99999887655556789999999999999999999999999999999998888899999999999999999999999999
Q ss_pred CCceeEEEeCCCCCCccCCCCCCCeEEEccccccccCCccceEEEeEEeCCCCcCCccceEEEEEecCCCceEEEecccc
Q 003762 610 SCEGLIIKTMDRDATYEPSKRSLNWLKLKKDYIESIGDSLDLVPIAAFHGRGKRTGVYGAFLLACYDSNNEEFQSICKIG 689 (797)
Q Consensus 610 g~EGlmvK~~~~ds~Y~pGkRs~~WlKlK~dY~~~~~dtlDlvVIGa~~G~Gkr~g~~gsfllg~~d~~~g~~~~vgkVG 689 (797)
|+||||+|+++.+|+|+||+|+.+|+|+|++|+++|+|++|+||||||+|+|+|+|++|+|||||||+++++|++|||||
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 99999999976689999999999999999999999999999999999999999999999999999998778999999999
Q ss_pred CCCCHHHHHHHHHhhccccCCCCCCCcccCCCCCCceEeccceEEEEEeeeeecCCcccccccccCCCCCceeeeceEee
Q 003762 690 TGFSEAMLEERSSSLRSKVIPKPRPYYRFADTISPDVWFEPTEVWEVKAADLTISPVHRAAIGVVDPDKVFTVRFSVLAH 769 (797)
Q Consensus 690 TGfSd~~l~~l~~~l~~~~~~~p~~~~~~~~~~~pdvw~eP~~V~EV~~~eit~S~~~~aa~g~v~~~~G~sLRFPRf~r 769 (797)
|||||++++++.+.+++++++.|++|+.++....|||||+|..||||+|+|||.||+|+||+|.+++++|++||||||+|
T Consensus 628 TGfsd~~l~~l~~~L~~~~~~~~~~~~~~~~~~~pdvwveP~~V~EV~~aeit~Sp~h~a~~g~~~~~~G~sLRFPRf~r 707 (744)
T PLN03113 628 TGFSEAVLEERSASLRSQVIPTPKSYYRYGDSIKPDVWFEPTEVWEVKAADLTISPVHRAAVGIVDPDKGISLRFPRLVR 707 (744)
T ss_pred CCCCHHHHHHHHHHHHHhcccCCCcccccCCCCCCcEEECCceEEEEEeeeeccCcccccccccccCCCCeEEECCEEEE
Confidence 99999999999999999998888889888877789999999999999999999999999999999999999999999999
Q ss_pred EeC--CcccccCC
Q 003762 770 LSF--PLLFCLGN 780 (797)
Q Consensus 770 iR~--~~~~~~~~ 780 (797)
||+ .|++|...
T Consensus 708 iR~DK~~~datt~ 720 (744)
T PLN03113 708 VREDKSPEQATSS 720 (744)
T ss_pred EECCCChHHCCCH
Confidence 999 99999654
No 3
>PRK01109 ATP-dependent DNA ligase; Provisional
Probab=100.00 E-value=7.5e-117 Score=1027.47 Aligned_cols=564 Identities=34% Similarity=0.580 Sum_probs=517.4
Q ss_pred cchHHHHHHHHHHHhccchHHHHHHHHHHHHhhhcCCCCchHHHHHHHhCccCCCccccccCCChHHHHHHHHHHhCCCH
Q 003762 191 VPFIFLSLVFDMISNETGRILITDIVCNMLRTVMETTPEDLVPVVYLAANKIAPAHEGLELGIGDASIIKALAEACGRTE 270 (797)
Q Consensus 191 ~~F~~la~~~e~I~~tssR~~k~~iL~~~fr~~i~~~p~dl~~~vyL~~~~l~P~~e~~elGIge~~L~kal~~a~G~s~ 270 (797)
|+|..||++|++|++|+||++|+++|++||+.+ +++++.+++||++|+|+|+|++.+|||++++|+|+|++++|+++
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 HHHHHHHHhcCCHHHHHhhcccc--CCC---CCCCCCCCHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHhcCCChHHH
Q 003762 271 SHVKKQYQEMGDLGLVAKASRSS--QSM---MRKPDPLTITKVFDTFRLIAKEAGKDSQEKKKNRIKALLVAATDCEPQY 345 (797)
Q Consensus 271 ~~ik~~y~~~GDlg~vA~~~r~~--q~~---l~~~~~LTI~eV~~~L~kIA~~~G~~s~~~K~~~L~~LL~~~t~~E~k~ 345 (797)
+.+++.|+++||||++|+.+++. |.+ ++.+++||+.+|++.|++||+.+|.+|+.+|+++|..||.+|+++|++|
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 99999999999999999987654 332 2456899999999999999999999999999999999999999999999
Q ss_pred HHHHHhhhccCcccHHHHHHHHHHhhccCCCCCCCCCCCcchHHHHHHHHHHHhhcCCchhhhHhhhhhcCccccCCccc
Q 003762 346 LIRLLQSKLRIGLAEQTLLAALGQAAVYNEQHSKPPPNIQSPLEEAAKIVKQVFSVLPVYEKIVPALLTDGVWNLSNTCS 425 (797)
Q Consensus 346 LiRiIlkdLRiGi~e~tvl~Ala~a~~~~~~~~~~~~~l~~~l~~a~~~vk~~y~~~pd~~~v~~~l~~~g~~~l~~~~~ 425 (797)
|+|+|+++||||+++++|++|||.|+.... ....++++|+.+||++.++..+.++|+..+ .++.
T Consensus 158 iirli~g~lriGv~e~~il~ALa~A~~~~~---------------~~~~ve~~y~~~~Dlg~va~~l~~~g~~~~-~~~~ 221 (590)
T PRK01109 158 IARFVEGRLRLGVGDATILDALAIAFGGAV---------------ARELVERAYNLRADLGYIAKILAEGGIEAL-KKVK 221 (590)
T ss_pred HHHHHhhhhhcCccHHHHHHHHHHHHhccc---------------chHHHHHHHHhCCCHHHHHHHHHhcchhhh-ccCc
Confidence 999999999999999999999999875211 123467889999999999999999888666 4699
Q ss_pred cCCCCCCccccccccCChHHHHhhcCCCceEEEeecceEEEEEEEecCCeEEEEecCCCccCCCcchHHHHHHhhcCCCC
Q 003762 426 FTPGIPIGPMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAVSRLKKPSV 505 (797)
Q Consensus 426 l~~g~Pv~PMLA~~~~~i~~~l~k~~g~~~~~E~KyDG~R~qih~~~~g~V~ifSR~gkd~T~~yPel~~~l~~~~~~~v 505 (797)
+++|+|++||||+++++++++++++++ +|++|+||||+|||+|++ +|.|++|||||+++|..||++++++.+.++ .
T Consensus 222 i~~~~Pv~PmLA~~~~~~~~~~~~~~~-~~~~E~K~DG~R~qih~~-~~~v~l~SR~~~d~T~~~pel~~~~~~~~~--~ 297 (590)
T PRK01109 222 PQVGIPIRPMLAERLSSPKEILKKMGG-EALVEYKYDGERAQIHKK-GDKVKIFSRRLENITHQYPDVVEYAKEAIK--A 297 (590)
T ss_pred ccCCCCCCcccCCccCCHHHHHHHcCC-CeEEEecCCceEEEEEEc-CCEEEEEeCCchhhccccchHHHHHHHhcC--c
Confidence 999999999999999999999999865 799999999999999995 789999999999999999999998887664 3
Q ss_pred CCeEEEEEEEEEecCCCcccChhhHHhhhcccCC-ccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCCCc
Q 003762 506 RSFVLDCEIVAYDREKQKILPFQTLSTRARKNVS-LSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEPGF 584 (797)
Q Consensus 506 ~~~ILDGElVa~d~~~g~~lpFq~L~~R~Rk~~~-~~~~~~~v~~~vFDILylnG~~L~~~Pl~ERr~lL~~l~~~~~~~ 584 (797)
++||||||+|+||+++|+++|||.|++|.|+... ......++||++|||||+||++|++.||.+||++|++++.+.+ .
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 7999999999999888889999999999655421 1223578999999999999999999999999999999998755 5
Q ss_pred EEEEeEEecCCHHHHHHHHHHHHHcCCceeEEEeCCCCCCccCCCCCCCeEEEccccccccCCccceEEEeEEeCCCCcC
Q 003762 585 FQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLKKDYIESIGDSLDLVPIAAFHGRGKRT 664 (797)
Q Consensus 585 i~~v~~~~~~~~eei~~~f~~ai~~g~EGlmvK~~~~ds~Y~pGkRs~~WlKlK~dY~~~~~dtlDlvVIGa~~G~Gkr~ 664 (797)
+++++...+++.++++++|++++++|+||||+|+++++|+|+||+|+.+|+|+|++|+++++|++|+||||+++|+|+|+
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 CccceEEEEEecCCCceEEEeccccCCCCHHHHHHHHHhhccccCCCCCCCcccCCCCCCceEeccceEEEEEeeeeecC
Q 003762 665 GVYGAFLLACYDSNNEEFQSICKIGTGFSEAMLEERSSSLRSKVIPKPRPYYRFADTISPDVWFEPTEVWEVKAADLTIS 744 (797)
Q Consensus 665 g~~gsfllg~~d~~~g~~~~vgkVGTGfSd~~l~~l~~~l~~~~~~~p~~~~~~~~~~~pdvw~eP~~V~EV~~~eit~S 744 (797)
|++|+|+||+||+++|+|++||||||||||+++++|.+.+++++++.+++++ ....+|||||+|.+||||+|++||.|
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 9999999999998778999999999999999999999999999987655543 23458999999999999999999999
Q ss_pred CcccccccccCCCCCceeeeceEeeEeC--CcccccCC
Q 003762 745 PVHRAAIGVVDPDKVFTVRFSVLAHLSF--PLLFCLGN 780 (797)
Q Consensus 745 ~~~~aa~g~v~~~~G~sLRFPRf~riR~--~~~~~~~~ 780 (797)
|+|+||.|.+.++.|++||||||+|+|+ +|++|...
T Consensus 535 ~~~~~~~~~~~~~~g~~LRfPr~~~~R~DK~~~d~~t~ 572 (590)
T PRK01109 535 PLHTCCLGVVEKGAGLAIRFPRFIRWRDDKSPEDATTT 572 (590)
T ss_pred cceecccccccCCCceeEEcCeeeEeeCCCChhhCcCH
Confidence 9999999999988999999999999999 99999654
No 4
>PRK03180 ligB ATP-dependent DNA ligase; Reviewed
Probab=100.00 E-value=1.4e-101 Score=883.75 Aligned_cols=495 Identities=27% Similarity=0.360 Sum_probs=443.9
Q ss_pred cchHHHHHHHHHHHhccchHHHHHHHHHHHHhhhcCCCCchHHHHHHHhCccCCCccccccCCChHHHHHHHHHHhCCCH
Q 003762 191 VPFIFLSLVFDMISNETGRILITDIVCNMLRTVMETTPEDLVPVVYLAANKIAPAHEGLELGIGDASIIKALAEACGRTE 270 (797)
Q Consensus 191 ~~F~~la~~~e~I~~tssR~~k~~iL~~~fr~~i~~~p~dl~~~vyL~~~~l~P~~e~~elGIge~~L~kal~~a~G~s~ 270 (797)
|+|.+||++|++|++|++|++|+++|++||+.+ +++|+.+++||++|++. +.++|++++.+.++++.
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 46899998777666432
Q ss_pred HHHHHHHHhcCCHHHHHhhccccCCCCCCCCCCCHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHhcCCChHHHHHHHH
Q 003762 271 SHVKKQYQEMGDLGLVAKASRSSQSMMRKPDPLTITKVFDTFRLIAKEAGKDSQEKKKNRIKALLVAATDCEPQYLIRLL 350 (797)
Q Consensus 271 ~~ik~~y~~~GDlg~vA~~~r~~q~~l~~~~~LTI~eV~~~L~kIA~~~G~~s~~~K~~~L~~LL~~~t~~E~k~LiRiI 350 (797)
..+.+|||.+||+.|++||..+|.+|++.|+.+|+.||.+|++.|++||+|+|
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 hhhccCcccHHHHHHHHHHhhccCCCCCCCCCCCcchHHHHHHHHHHHhhcCCchhhhHhhhhhcCccccCCccccCCCC
Q 003762 351 QSKLRIGLAEQTLLAALGQAAVYNEQHSKPPPNIQSPLEEAAKIVKQVFSVLPVYEKIVPALLTDGVWNLSNTCSFTPGI 430 (797)
Q Consensus 351 lkdLRiGi~e~tvl~Ala~a~~~~~~~~~~~~~l~~~l~~a~~~vk~~y~~~pd~~~v~~~l~~~g~~~l~~~~~l~~g~ 430 (797)
+++||||+++++|+.|||+||..+ ...+.++|+.|+|++.+++.++++|...+ ..|.|++|+
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 13467889999999999999999887666 569999999
Q ss_pred CCccccccccCChHHHHhhcCCCceEEEeecceEEEEEEEecCCeEEEEecCCCccCCCcchHHHHHHhhcCCCCCCeEE
Q 003762 431 PIGPMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAVSRLKKPSVRSFVL 510 (797)
Q Consensus 431 Pv~PMLA~~~~~i~~~l~k~~g~~~~~E~KyDG~R~qih~~~~g~V~ifSR~gkd~T~~yPel~~~l~~~~~~~v~~~IL 510 (797)
|++||||++.+++++++++++ .+|++|+||||+|||+|++ +|+|++|||||+++|+.||++.+.+... ..++|||
T Consensus 183 P~~PMLA~~~~~~~~~~~~~~-~~~~~E~K~DG~R~qih~~-~~~v~l~SR~~~d~T~~fPei~~~~~~~---~~~~~IL 257 (508)
T PRK03180 183 PVRPMLAQTATSVAEALARLG-GPAAVEAKLDGARVQVHRD-GDDVRVYTRTLDDITARLPEVVEAVRAL---PVRSLVL 257 (508)
T ss_pred CCCCccCCcCCChHHHHHHhC-CCeEEEEEEceeEEEEEEE-CCEEEEEeCCCCcchhhhHHHHHHHHhC---CCcceee
Confidence 999999999999988888885 4899999999999999995 7899999999999999999999877653 2478999
Q ss_pred EEEEEEEecCCCcccChhhHHhhhcccCCc--cccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCCCcEEEE
Q 003762 511 DCEIVAYDREKQKILPFQTLSTRARKNVSL--SDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEPGFFQFA 588 (797)
Q Consensus 511 DGElVa~d~~~g~~lpFq~L~~R~Rk~~~~--~~~~~~v~~~vFDILylnG~~L~~~Pl~ERr~lL~~l~~~~~~~i~~v 588 (797)
|||+|+||. +|+++|||.+++|.+++... .....+++|++|||||+||++++++||.+||++|++++.+. ..+
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 57888999999997554322 22357899999999999999999999999999999998742 123
Q ss_pred eEEecCCHHHHHHHHHHHHHcCCceeEEEeCCCCCCccCCCCCCCeEEEccccccccCCccceEEEeEEeCCCCcCCccc
Q 003762 589 TTLTSIDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLKKDYIESIGDSLDLVPIAAFHGRGKRTGVYG 668 (797)
Q Consensus 589 ~~~~~~~~eei~~~f~~ai~~g~EGlmvK~~~~ds~Y~pGkRs~~WlKlK~dY~~~~~dtlDlvVIGa~~G~Gkr~g~~g 668 (797)
+....++.++++++|++++++|+||||+|++ +|+|+||+|+.+|+|+|+. +++|+||||+++|+|||+|++|
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 4556778999999999999999999999999 9999999999999999995 5999999999999999999999
Q ss_pred eEEEEEecCCCceEEEeccccCCCCHHHHHHHHHhhccccCCCCCCCcccCCCCCCceEeccceEEEEEeeeeecCCccc
Q 003762 669 AFLLACYDSNNEEFQSICKIGTGFSEAMLEERSSSLRSKVIPKPRPYYRFADTISPDVWFEPTEVWEVKAADLTISPVHR 748 (797)
Q Consensus 669 sfllg~~d~~~g~~~~vgkVGTGfSd~~l~~l~~~l~~~~~~~p~~~~~~~~~~~pdvw~eP~~V~EV~~~eit~S~~~~ 748 (797)
+|+|||||+++|+|++||||||||||++++++.+.+.++.+.. ..|++||+|.+||||+|++||.||+|+
T Consensus 405 ~~llg~~d~~~~~l~~vgkv~sG~td~~l~~l~~~l~~~~~~~----------~~~~vwv~P~~V~EV~~~~it~S~~~~ 474 (508)
T PRK03180 405 NLHLGARDPATGGFVMLGKTFKGMTDAMLAWQTERFLELAVGR----------DGWTVYVRPELVVEIAFDGVQRSTRYP 474 (508)
T ss_pred ceEEEEEeCCCCeEEEecCccCCCCHHHHHHHHHHHHhhccCC----------CCCCEEeeCCEEEEEEeeEeeeCCccc
Confidence 9999999987789999999999999999999999998775542 268999999999999999999999998
Q ss_pred ccccccCCCCCceeeeceEeeEeC--CcccccCC
Q 003762 749 AAIGVVDPDKVFTVRFSVLAHLSF--PLLFCLGN 780 (797)
Q Consensus 749 aa~g~v~~~~G~sLRFPRf~riR~--~~~~~~~~ 780 (797)
+ |++||||||+|||+ +|.+|...
T Consensus 475 ~---------G~~LRfPr~~r~R~DK~~~ea~tl 499 (508)
T PRK03180 475 G---------GVALRFARVLRYRPDKTPAEADTI 499 (508)
T ss_pred C---------CeEEECCeeeEeeCCCChHHCcCH
Confidence 6 89999999999999 99999764
No 5
>PRK09247 ATP-dependent DNA ligase; Validated
Probab=100.00 E-value=4.5e-101 Score=885.77 Aligned_cols=516 Identities=20% Similarity=0.282 Sum_probs=452.0
Q ss_pred HHHHHHHHHHHhccchHHHHHHHHHHHHhhhcCCCCchHHHHHHHhCccCCCccccccCCChHHHHHHHHHHhCCCHHHH
Q 003762 194 IFLSLVFDMISNETGRILITDIVCNMLRTVMETTPEDLVPVVYLAANKIAPAHEGLELGIGDASIIKALAEACGRTESHV 273 (797)
Q Consensus 194 ~~la~~~e~I~~tssR~~k~~iL~~~fr~~i~~~p~dl~~~vyL~~~~l~P~~e~~elGIge~~L~kal~~a~G~s~~~i 273 (797)
..||++|++|++|++|++|+++|++||+.+ +|+|+.+++||++|++. ++||+++.|+|+|++++|++++.+
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 HHHHHhcCCHHHHHhhccccC-CC-CCCCCCCCHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHhcCCChHHHHHHHHh
Q 003762 274 KKQYQEMGDLGLVAKASRSSQ-SM-MRKPDPLTITKVFDTFRLIAKEAGKDSQEKKKNRIKALLVAATDCEPQYLIRLLQ 351 (797)
Q Consensus 274 k~~y~~~GDlg~vA~~~r~~q-~~-l~~~~~LTI~eV~~~L~kIA~~~G~~s~~~K~~~L~~LL~~~t~~E~k~LiRiIl 351 (797)
++.|.++||+|+||..+...+ .+ .+.+.++||.+|++.|.+|++.+ |+..|..||.+|++.|++||+|+|+
T Consensus 73 ~~~~~~~GDlg~~~~~~~~~~~~~~~~~~~~~tv~~v~~~l~~~~~~~-------k~~~l~~ll~~~~~~e~~~i~rli~ 145 (539)
T PRK09247 73 EESYDYVGDLAETIALLLPAPSDEASDLPLAPWLEEVLLPLRGLGREE-------LRAALADLWDRLDEDGRFALNKLIT 145 (539)
T ss_pred HHHHHhcCCHHHHHHHhcccccccccCCCccccHHHHHHHHHhhhHHH-------HHHHHHHHHHhCCHHHHHHHHHHhh
Confidence 999999999999998864332 22 22346799999999999997542 6789999999999999999999999
Q ss_pred hhccCcccHHHHHHHHHHhhccCCCCCCCCCCCcchHHHHHHHHHHHhhc--CCchhhhHhhhhhcCccccCCccccCCC
Q 003762 352 SKLRIGLAEQTLLAALGQAAVYNEQHSKPPPNIQSPLEEAAKIVKQVFSV--LPVYEKIVPALLTDGVWNLSNTCSFTPG 429 (797)
Q Consensus 352 kdLRiGi~e~tvl~Ala~a~~~~~~~~~~~~~l~~~l~~a~~~vk~~y~~--~pd~~~v~~~l~~~g~~~l~~~~~l~~g 429 (797)
++||||++++||+.|||.||..+ .+.+.++|+. .|+++.+.. +...|. ..+.++||
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 1234456666 677765554 444565 46889999
Q ss_pred CCCccccccccCChHHHHhhcCCCceEEEeecceEEEEEEEecCCeEEEEecCCCccCCCcchHHHHHHhhcCCCCCCeE
Q 003762 430 IPIGPMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAVSRLKKPSVRSFV 509 (797)
Q Consensus 430 ~Pv~PMLA~~~~~i~~~l~k~~g~~~~~E~KyDG~R~qih~~~~g~V~ifSR~gkd~T~~yPel~~~l~~~~~~~v~~~I 509 (797)
+|++||||++++++.+... ...+|++|+||||+|+|+|+. +|.|++|||||+++|..||++.+++.. ++ .+||
T Consensus 204 ~P~~pMLA~~~~~~~~~~~--~~~~~~~E~K~DG~R~qih~~-~~~v~lfSR~g~d~t~~fPei~~~~~~-l~---~~~I 276 (539)
T PRK09247 204 QPYPFFLAHPLEDEDLTLG--DPADWQAEWKWDGIRVQLVRR-GGEVRLWSRGEELITERFPELAEAAEA-LP---DGTV 276 (539)
T ss_pred CcCCCeeCCcCCCchhhhc--CCCcEEEEEeEcceEEEEEEe-CCEEEEEeCCCccchhhhHHHHHHHHh-CC---CCEE
Confidence 9999999999988765443 335899999999999999995 789999999999999999999987764 33 5799
Q ss_pred EEEEEEEEecCCCcccChhhHHhhhc-ccCCcc-ccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCC-CcEE
Q 003762 510 LDCEIVAYDREKQKILPFQTLSTRAR-KNVSLS-DIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEP-GFFQ 586 (797)
Q Consensus 510 LDGElVa~d~~~g~~lpFq~L~~R~R-k~~~~~-~~~~~v~~~vFDILylnG~~L~~~Pl~ERr~lL~~l~~~~~-~~i~ 586 (797)
||||+|+||++++.++||+.|++|.+ ++.... ....++||++|||||+||++++++||.+||++|++++.+.+ ++++
T Consensus 277 LDGElv~~~~~~~~~~~F~~l~~R~~rk~~~~~~~~~~pv~~~vFDiL~l~g~~l~~~Pl~eRr~~L~~~~~~~~~~~i~ 356 (539)
T PRK09247 277 LDGELLVWRPEDGRPQPFADLQQRIGRKTVGKKLLADYPAFLRAYDLLEDGGEDLRALPLAERRARLEALIARLPDPRLD 356 (539)
T ss_pred EEeEEEEEECCCCCcCCHHHHHHHhcccccchhhhhcCCeEEEEEEeeeeCCcchhhCCHHHHHHHHHHHhcccCCCeEE
Confidence 99999999977778899999999954 433211 12579999999999999999999999999999999998764 4899
Q ss_pred EEeEEecCCHHHHHHHHHHHHHcCCceeEEEeCCCCCCccCCCCCCCeEEEccccccccCCccceEEEeEEeCCCCcCCc
Q 003762 587 FATTLTSIDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLKKDYIESIGDSLDLVPIAAFHGRGKRTGV 666 (797)
Q Consensus 587 ~v~~~~~~~~eei~~~f~~ai~~g~EGlmvK~~~~ds~Y~pGkRs~~WlKlK~dY~~~~~dtlDlvVIGa~~G~Gkr~g~ 666 (797)
+++...+++.++++++|++++++|+||||+|++ +|+|+||+|+..|+|+|++| +++|+||||+++|+|+|+|+
T Consensus 357 ~~~~~~~~~~~e~~~~~~~a~~~g~EGlm~K~~--~s~Y~~Grr~~~WlK~K~~~-----~t~DlVvig~~~G~Gkr~g~ 429 (539)
T PRK09247 357 LSPLVPFSDWDELAALRAAARERGVEGLMLKRR--DSPYLVGRKKGPWWKWKRDP-----LTIDAVLMYAQRGHGRRASL 429 (539)
T ss_pred ecCceecCCHHHHHHHHHHHHHCCCceEEEecC--CCCcCCCCCcchhhcccCCC-----CcEEEEEEEeecCCCCcCCc
Confidence 999999999999999999999999999999999 99999999999999999997 48999999999999999999
Q ss_pred cceEEEEEecCCC--ceEEEeccccCCCCHHHHHHHHHhhccccCCCCCCCcccCCCCCCceEeccceEEEEEeeeeecC
Q 003762 667 YGAFLLACYDSNN--EEFQSICKIGTGFSEAMLEERSSSLRSKVIPKPRPYYRFADTISPDVWFEPTEVWEVKAADLTIS 744 (797)
Q Consensus 667 ~gsfllg~~d~~~--g~~~~vgkVGTGfSd~~l~~l~~~l~~~~~~~p~~~~~~~~~~~pdvw~eP~~V~EV~~~eit~S 744 (797)
+|+|+|||||++. ++|++||||||||||+++++|.+.++++.+.. ..|++|++|.+||||+|+|||.|
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 25899999999999999999999
Q ss_pred CcccccccccCCCCCceeeeceEeeEeC--CcccccCC
Q 003762 745 PVHRAAIGVVDPDKVFTVRFSVLAHLSF--PLLFCLGN 780 (797)
Q Consensus 745 ~~~~aa~g~v~~~~G~sLRFPRf~riR~--~~~~~~~~ 780 (797)
|+|++ |++||||||+|+|+ +|.+|...
T Consensus 500 ~~~~~---------G~~LRfPr~~~~R~DK~~~ea~t~ 528 (539)
T PRK09247 500 KRHKS---------GIAVRFPRILRWRWDKPAREADTL 528 (539)
T ss_pred CCcCC---------CcEEEcceEEEEeCCCChHHCcCH
Confidence 99985 89999999999999 99999654
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=9.2e-101 Score=881.71 Aligned_cols=501 Identities=40% Similarity=0.655 Sum_probs=455.0
Q ss_pred ccCCChHHHHHHHHHHhCCCHHHHHHHHHhcCCHHHHHhhccccCC-CCCCCCCCCHHHHHHHHHHHHHHhCCChHHHHH
Q 003762 250 ELGIGDASIIKALAEACGRTESHVKKQYQEMGDLGLVAKASRSSQS-MMRKPDPLTITKVFDTFRLIAKEAGKDSQEKKK 328 (797)
Q Consensus 250 elGIge~~L~kal~~a~G~s~~~ik~~y~~~GDlg~vA~~~r~~q~-~l~~~~~LTI~eV~~~L~kIA~~~G~~s~~~K~ 328 (797)
+||||++.|+|++++++|++++.+++.|.+.||+|+++..++..+. +...+.+|||.+|++.|++||..+|.+|+++|.
T Consensus 1 ~~gi~~~~l~k~~~~~~~~~~~~~~~~~~~~gd~g~~~~~~~~~~~~~~~~~~~lti~eV~~~L~~ia~~~g~~s~~~k~ 80 (514)
T TIGR00574 1 EYGIGEKLLIKAISKALGIPKDEIEEKVKEDGDLGEVIEGLFSKQKQTSFFSAPLTVKEVYETLKNIAETSGEGSQDKKI 80 (514)
T ss_pred CCCCcHHHHHHHHHHHHCcCHHHHHHHHHhcCCHHHHHHHHhccccccccCCCCcCHHHHHHHHHHHHHhhCCCcHHHHH
Confidence 6999999999999999999999999999999999999988766554 344578999999999999999999999999999
Q ss_pred HHHHHHHHhcCCChHHHHHHHHhhhccCcccHHHHHHHHHHhhccCCCCCCCCCCCcchHHHHHHHHHHHhhcCCchhhh
Q 003762 329 NRIKALLVAATDCEPQYLIRLLQSKLRIGLAEQTLLAALGQAAVYNEQHSKPPPNIQSPLEEAAKIVKQVFSVLPVYEKI 408 (797)
Q Consensus 329 ~~L~~LL~~~t~~E~k~LiRiIlkdLRiGi~e~tvl~Ala~a~~~~~~~~~~~~~l~~~l~~a~~~vk~~y~~~pd~~~v 408 (797)
.+|..||.+|++.|++||+|+|+++||||+++++|+.|||.+|..+. ..+.++|+.|||++.|
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 HhhhhhcCccccCCccccCCCCCCccccccccCChHHHHhhcCCCceEEEeecceEEEEEEEecCCeEEEEecCCCccCC
Q 003762 409 VPALLTDGVWNLSNTCSFTPGIPIGPMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTG 488 (797)
Q Consensus 409 ~~~l~~~g~~~l~~~~~l~~g~Pv~PMLA~~~~~i~~~l~k~~g~~~~~E~KyDG~R~qih~~~~g~V~ifSR~gkd~T~ 488 (797)
+..+.++|+..+..++.+++|+|++||||++++++.++++++++ +|++|+||||+|||+|+ .+|+|++|||||+++|.
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 99999999877767799999999999999999999888888765 89999999999999999 47899999999999999
Q ss_pred CcchH-HHHHHhhcCCCCCCeEEEEEEEEEecCCCcccChhhHHhhhccc-CCccccccceEEEEeeeeecCCccccCCc
Q 003762 489 KFPDV-VLAVSRLKKPSVRSFVLDCEIVAYDREKQKILPFQTLSTRARKN-VSLSDIKVDVCIYAFDILYRNGQPLLQEQ 566 (797)
Q Consensus 489 ~yPel-~~~l~~~~~~~v~~~ILDGElVa~d~~~g~~lpFq~L~~R~Rk~-~~~~~~~~~v~~~vFDILylnG~~L~~~P 566 (797)
.||++ .+.+...++. ..+||||||+|+||.++|+++||+.+++|.++. ........+++|++|||||+||++++++|
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 468999999999998878899999999997752 11223457899999999999999999999
Q ss_pred HHHHHHHHHHhhccCCCcEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEEeCCCCCCccCCCCCCCeEEEccccccccC
Q 003762 567 LRVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLKKDYIESIG 646 (797)
Q Consensus 567 l~ERr~lL~~l~~~~~~~i~~v~~~~~~~~eei~~~f~~ai~~g~EGlmvK~~~~ds~Y~pGkRs~~WlKlK~dY~~~~~ 646 (797)
|.||+++|++++.+.++.+++++...+++.+++.++|++++++|+||||+|++ +|+|++|+|+.+|+|+|++|+++|+
T Consensus 301 l~eRr~~L~~~~~~~~~~i~~~~~~~~~~~e~~~~~~~~~~~~g~EGlv~K~~--ds~Y~~G~Rs~~WlK~K~~y~~~~~ 378 (514)
T TIGR00574 301 LIERREILESILKPIPNRIEIAEMKITSNVEELEKFLNEAISEGCEGLMLKDL--KSIYEPGKRGWLWLKFKPEYLEGMG 378 (514)
T ss_pred HHHHHHHHHHhccCCCCcEEEEEEEecCCHHHHHHHHHHHHHcCCceEEEecC--CCcccCCCCCCcceeCchhhccccc
Confidence 99999999999998888999999999999999999999999999999999999 9999999999999999999999999
Q ss_pred CccceEEEeEEeCCCCcCCccceEEEEEecCCCceEEEeccccCCCCHHHHHHHHHhhccccCCCCCCCcccCCCCCCce
Q 003762 647 DSLDLVPIAAFHGRGKRTGVYGAFLLACYDSNNEEFQSICKIGTGFSEAMLEERSSSLRSKVIPKPRPYYRFADTISPDV 726 (797)
Q Consensus 647 dtlDlvVIGa~~G~Gkr~g~~gsfllg~~d~~~g~~~~vgkVGTGfSd~~l~~l~~~l~~~~~~~p~~~~~~~~~~~pdv 726 (797)
+++|+||||+++|+|+++|++|+|+||++|+++++|++||||||||||+++++|.+.+.++++..+++.+.......|++
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 99999999999999999999999999999987789999999999999999999999999998765433321111247999
Q ss_pred EeccceEEEEEeeeeecCCcccccccccCCCCCceeeeceEeeEeC--CcccccCC
Q 003762 727 WFEPTEVWEVKAADLTISPVHRAAIGVVDPDKVFTVRFSVLAHLSF--PLLFCLGN 780 (797)
Q Consensus 727 w~eP~~V~EV~~~eit~S~~~~aa~g~v~~~~G~sLRFPRf~riR~--~~~~~~~~ 780 (797)
|++|.+||||+|+|+|.||+|+++ |++||||||+++|+ .|.+|...
T Consensus 459 w~~p~~V~eV~~~e~t~s~~~~~~--------g~~LRfPr~~~~R~DK~~~d~~~~ 506 (514)
T TIGR00574 459 WFDPAIVWEVTGAEITRSPTYKAN--------GISLRFPRFSRIRDDKGPEDATTI 506 (514)
T ss_pred EecCCeEEEEEhhheeecCccccc--------ceEEEcceEEEEcCCCChHHCCCH
Confidence 999999999999999999999863 79999999999999 78888654
No 7
>KOG0966 consensus ATP-dependent DNA ligase IV [Replication, recombination and repair]
Probab=100.00 E-value=3.7e-88 Score=766.31 Aligned_cols=548 Identities=25% Similarity=0.409 Sum_probs=461.8
Q ss_pred CccchHHHHHHHHHHHhccchHHHHHHHHHHHHhhhcCCCCchHHHHHHHhCccCCCcccc--ccCCChHHHHHHHHHHh
Q 003762 189 ERVPFIFLSLVFDMISNETGRILITDIVCNMLRTVMETTPEDLVPVVYLAANKIAPAHEGL--ELGIGDASIIKALAEAC 266 (797)
Q Consensus 189 ~~~~F~~la~~~e~I~~tssR~~k~~iL~~~fr~~i~~~p~dl~~~vyL~~~~l~P~~e~~--elGIge~~L~kal~~a~ 266 (797)
+++.|+.++++|+.|..+..-+.|++.+..++..+.+ |-+....+|.++++++|.+++. .|||++..|++.+++++
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 SPQNFSEVVDFFNKIRRTSNVKSKQAKFRKNFESWCR--PCEVGSDMYVALRLILPDLDRERGSYGLKETVLARLYIRAL 80 (881)
T ss_pred CccccchHHHHHHHHHHhhhhHhHHHHHhhccccccc--cccCCcchhhhhhhcccchhhcccccCchHHHHHHHHHHHh
Confidence 5788999999999999999999999999999988753 3223333444455578988544 99999999999999999
Q ss_pred CCCH---HHHHHH-HH----hcCCHHHHHhhccccCCCCCCCCCCCHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHhc
Q 003762 267 GRTE---SHVKKQ-YQ----EMGDLGLVAKASRSSQSMMRKPDPLTITKVFDTFRLIAKEAGKDSQEKKKNRIKALLVAA 338 (797)
Q Consensus 267 G~s~---~~ik~~-y~----~~GDlg~vA~~~r~~q~~l~~~~~LTI~eV~~~L~kIA~~~G~~s~~~K~~~L~~LL~~~ 338 (797)
+++. +.++.. |+ ..||++.+++.+.+.+.....++.|||.+||+.||.||.... ...++.+.|..|.++|
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 344332 33 348999999876443333334456999999999999985432 2223348999999999
Q ss_pred CCChHHHHHHHHhhhccCcccHHHHHHHHHHhhccCCCCCCCCCCCcchHHHHHHHHHHHhhcCCchhhhHhhhhhcCcc
Q 003762 339 TDCEPQYLIRLLQSKLRIGLAEQTLLAALGQAAVYNEQHSKPPPNIQSPLEEAAKIVKQVFSVLPVYEKIVPALLTDGVW 418 (797)
Q Consensus 339 t~~E~k~LiRiIlkdLRiGi~e~tvl~Ala~a~~~~~~~~~~~~~l~~~l~~a~~~vk~~y~~~pd~~~v~~~l~~~g~~ 418 (797)
++.|+|||+|||+|++.+|+++++|+..||+.| ..+|++|.|++.||..|.+....
T Consensus 159 S~~ElkWliriiLK~lklG~se~~Il~vfHPdA------------------------~dl~~vtsDLk~Vc~~L~Dp~~~ 214 (881)
T KOG0966|consen 159 SPLELKWLIRIILKNLKLGASEKKILSVFHPDA------------------------QDLYNVTSDLKAVCKKLYDPSVG 214 (881)
T ss_pred CHHHHHHHHHHHHHhhhcCCccchhhhhcCccH------------------------HHHHHHhhhHHHHHHHhcCCccC
Confidence 999999999999999999999999999987642 24688999999999999876543
Q ss_pred ccCCccccCCCCCCccccccccCChH-HHHhhcCCCceEEEeecceEEEEEEEecCCeEEEEecCCCccCCCcch-----
Q 003762 419 NLSNTCSFTPGIPIGPMLAKPTKGVS-EIVNKFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPD----- 492 (797)
Q Consensus 419 ~l~~~~~l~~g~Pv~PMLA~~~~~i~-~~l~k~~g~~~~~E~KyDG~R~qih~~~~g~V~ifSR~gkd~T~~yPe----- 492 (797)
--.....+.+|..++||||...+... +++++|++++|++|.|+||+|+|+|++ +|.+++|||||.|||..|..
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 21112359999999999998765443 688999999999999999999999996 78999999999999987732
Q ss_pred -HHHHHHhhcCCCCCCeEEEEEEEEEecCCCcccChhhHHhhhcccCCccccccceEEEEeeeeecCCccccCCcHHHHH
Q 003762 493 -VVLAVSRLKKPSVRSFVLDCEIVAYDREKQKILPFQTLSTRARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRR 571 (797)
Q Consensus 493 -l~~~l~~~~~~~v~~~ILDGElVa~d~~~g~~lpFq~L~~R~Rk~~~~~~~~~~v~~~vFDILylnG~~L~~~Pl~ERr 571 (797)
+...|+.++..++++|||||||++||+.+.++.||+..+...+-. ..+...++||++||+||+||++|.+.||..|+
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 455777777778899999999999999999999999876433211 11346789999999999999999999999999
Q ss_pred HHHHHhhccCCCcEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEEeCCCCCCccCCCCCCCeEEEccccccccCCccce
Q 003762 572 EHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLKKDYIESIGDSLDL 651 (797)
Q Consensus 572 ~lL~~l~~~~~~~i~~v~~~~~~~~eei~~~f~~ai~~g~EGlmvK~~~~ds~Y~pGkRs~~WlKlK~dY~~~~~dtlDl 651 (797)
++|+.++.+.+++++++.+..+++.++++++|++|++.|.||||+|.+ +|.|.||.|+++|+|+||+|+.|+|+++|+
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 EEEeEEeCCCCcCCccceEEEEEecCC-----CceEEEeccccCCCCHHHHHHHHHhhccccCC----CCCCCcccCCCC
Q 003762 652 VPIAAFHGRGKRTGVYGAFLLACYDSN-----NEEFQSICKIGTGFSEAMLEERSSSLRSKVIP----KPRPYYRFADTI 722 (797)
Q Consensus 652 vVIGa~~G~Gkr~g~~gsfllg~~d~~-----~g~~~~vgkVGTGfSd~~l~~l~~~l~~~~~~----~p~~~~~~~~~~ 722 (797)
+|||++||+|+|+|.+.+|+||+.+.. ..+|.++|+||+|+|+.++..+...++++|.+ .||..+-++...
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 24699999999999999999999999999864 233322233333
Q ss_pred CCceEeccc--eEEEEEeeeeecCCcccccccccCCCCCceeeeceEeeEeC--Cccccc
Q 003762 723 SPDVWFEPT--EVWEVKAADLTISPVHRAAIGVVDPDKVFTVRFSVLAHLSF--PLLFCL 778 (797)
Q Consensus 723 ~pdvw~eP~--~V~EV~~~eit~S~~~~aa~g~v~~~~G~sLRFPRf~riR~--~~~~~~ 778 (797)
.||+||+|. +|++|++++++.|.+|.+ +++|||||+.+||. |||+|.
T Consensus 530 ~Pd~wI~P~~SiIlqikaa~i~~s~~f~t---------n~tLrfPr~ekvR~DK~W~ec~ 580 (881)
T KOG0966|consen 530 IPDVWIDPDNSIILQIKAAEIVPSSNFVT---------NYTLRFPRIEKVRLDKPWHECL 580 (881)
T ss_pred CCceeECCCCceEEEeehheeeecccccc---------cceeecceeeeeecCCcHHHHh
Confidence 799999996 799999999999999975 79999999999999 999994
No 8
>COG1793 CDC9 ATP-dependent DNA ligase [DNA replication, recombination, and repair]
Probab=100.00 E-value=3e-69 Score=607.33 Aligned_cols=422 Identities=35% Similarity=0.507 Sum_probs=365.6
Q ss_pred HHHHHHhCCCHHHHHHHHHhcCCHHHHHhhccccCCCCCCCCCCCHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHhcC
Q 003762 260 KALAEACGRTESHVKKQYQEMGDLGLVAKASRSSQSMMRKPDPLTITKVFDTFRLIAKEAGKDSQEKKKNRIKALLVAAT 339 (797)
Q Consensus 260 kal~~a~G~s~~~ik~~y~~~GDlg~vA~~~r~~q~~l~~~~~LTI~eV~~~L~kIA~~~G~~s~~~K~~~L~~LL~~~t 339 (797)
+|+....| ...+.+.|...||+|.++..++. +.+|+..|.+++...| ++ .++..|+..++
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 45666667 66778899999999999977653 8899999999999988 32 78888998888
Q ss_pred CChHHHHHHHHhhhccCcccHHHHHHHHHHhhccCCCCCCCCCCCcchHHHHHHHHHHHhhcCCchhhhHhhhhhcCccc
Q 003762 340 DCEPQYLIRLLQSKLRIGLAEQTLLAALGQAAVYNEQHSKPPPNIQSPLEEAAKIVKQVFSVLPVYEKIVPALLTDGVWN 419 (797)
Q Consensus 340 ~~E~k~LiRiIlkdLRiGi~e~tvl~Ala~a~~~~~~~~~~~~~l~~~l~~a~~~vk~~y~~~pd~~~v~~~l~~~g~~~ 419 (797)
+|++++++++||+.| ++.+|+.+||++.++...+..|...
T Consensus 62 ----------------~gv~~~~~~~ala~~------------------------~~~~~~~~~d~g~~a~~~~~~~~~~ 101 (444)
T COG1793 62 ----------------IGVSEGTVLDALAEA------------------------VERAYLWHNDLGALAKILLTLGAEA 101 (444)
T ss_pred ----------------cchhhHHHHHHHHHH------------------------hhhhhccCCCchhhhhhhhhccccc
Confidence 999999999999775 2457889999999999888888766
Q ss_pred cCCccccCCCCCCccccccccCChHHHHhhcCCCceEEEeecceEEEEEEEecCCeEEEEecCCCccCCCcchHHHHHHh
Q 003762 420 LSNTCSFTPGIPIGPMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAVSR 499 (797)
Q Consensus 420 l~~~~~l~~g~Pv~PMLA~~~~~i~~~l~k~~g~~~~~E~KyDG~R~qih~~~~g~V~ifSR~gkd~T~~yPel~~~l~~ 499 (797)
+ ..+.+++|.|+.|||+....++.+...+..+ +|.+|+||||+|+|+|+. +|.|++|||+|+++|++||++.+++..
T Consensus 102 ~-~~~~~~~~~p~~~~la~~~~~~~~~~~~~~~-~w~~E~K~DG~R~q~h~~-~~~vrl~SR~g~d~T~~fP~~~~~~~~ 178 (444)
T COG1793 102 L-DKATLLPGRPLPPMLAPMLASLEEALPRDGG-DWAYEEKFDGYRVQIHID-GGKVRLYSRNGEDWTGRFPDILEAAAE 178 (444)
T ss_pred c-cccccccCCccchhhccccccccccCCCCCC-CEEEEEeeceEEEEEEEc-CCEEEEEeCCCccchhhChHHHHHHHh
Confidence 6 4677899999999999988877666655543 599999999999999995 779999999999999999987666666
Q ss_pred hcCCCCCCeEEEEEEEEEecCCCcccChhhHHhhhcccCC--ccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHh
Q 003762 500 LKKPSVRSFVLDCEIVAYDREKQKILPFQTLSTRARKNVS--LSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDS 577 (797)
Q Consensus 500 ~~~~~v~~~ILDGElVa~d~~~g~~lpFq~L~~R~Rk~~~--~~~~~~~v~~~vFDILylnG~~L~~~Pl~ERr~lL~~l 577 (797)
.+. .+++|||||+|++|++ ...+||.|++|.++... ......+++|++|||||+||++|+++||.|||++|+++
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 46899999999866532 23446899999999999999999999999999999999
Q ss_pred hccCCCcEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEEeCCCCCCccCCCCCCCeEEEccccccccCCccceEEEeEE
Q 003762 578 FEEEPGFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLKKDYIESIGDSLDLVPIAAF 657 (797)
Q Consensus 578 ~~~~~~~i~~v~~~~~~~~eei~~~f~~ai~~g~EGlmvK~~~~ds~Y~pGkRs~~WlKlK~dY~~~~~dtlDlvVIGa~ 657 (797)
+... +.+..++....++.++++.+|+.+++.|+||||+|+. ||+|++|+|+..|+|+|++ +++|+||+|++
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 4556666666689999999999999999999999999 9999999999999999997 59999999999
Q ss_pred eCCCCcCCccceEEEEEecCCCceEEEeccccCCCCHHHHHHHHHhhccccCCCCCCCcccCCCCCCc-eEeccceEEEE
Q 003762 658 HGRGKRTGVYGAFLLACYDSNNEEFQSICKIGTGFSEAMLEERSSSLRSKVIPKPRPYYRFADTISPD-VWFEPTEVWEV 736 (797)
Q Consensus 658 ~G~Gkr~g~~gsfllg~~d~~~g~~~~vgkVGTGfSd~~l~~l~~~l~~~~~~~p~~~~~~~~~~~pd-vw~eP~~V~EV 736 (797)
+|+|+|. ++|+|+||+|+++++.|+++|+|||||+|+++++|+++++++....+.+. .+. +|++|..|+||
T Consensus 326 ~g~Gkr~-~~~slll~~~~~~~~~~~~v~kVgtGf~~~~l~~l~~~l~~~~~~~~~~~-------~~~~~~~~p~~V~EV 397 (444)
T COG1793 326 YGKGKRS-LYGSLLLGVYDGDGGGLLYVGKVGTGFSDAELEELTERLEPLIVSRFNGK-------VPGKVVPPPGLVAEV 397 (444)
T ss_pred ecCCccc-ccceEEEEEEcCCCceEEEEecccCCCCHHHHHHHHHHHHHhccCcCCCc-------cCceeecCCcEEEEE
Confidence 9999999 89999999999988889999999999999999999999999987642110 112 77778999999
Q ss_pred EeeeeecCCcccccccccCCCCCceeeeceEeeEeC
Q 003762 737 KAADLTISPVHRAAIGVVDPDKVFTVRFSVLAHLSF 772 (797)
Q Consensus 737 ~~~eit~S~~~~aa~g~v~~~~G~sLRFPRf~riR~ 772 (797)
+|+++|.|++|+++ .|++||||||.|+|+
T Consensus 398 ~~~~~t~~~~~r~~-------~~~~lRfpr~~rvr~ 426 (444)
T COG1793 398 RFAEITKSGRLRHA-------SGLGLRFPRFVRVRD 426 (444)
T ss_pred EEeecccCCceecc-------cCcccCcCccccccc
Confidence 99999999999985 579999999999998
No 9
>PHA02587 30 DNA ligase; Provisional
Probab=100.00 E-value=1.1e-65 Score=586.15 Aligned_cols=435 Identities=18% Similarity=0.213 Sum_probs=339.8
Q ss_pred HHHHHHHHHhccchHHHHHHHHHHHHhhhcCCCCchHHHHHHHhCccCCCccccccCCChHHHHHHHHHHhCCCHHHHHH
Q 003762 196 LSLVFDMISNETGRILITDIVCNMLRTVMETTPEDLVPVVYLAANKIAPAHEGLELGIGDASIIKALAEACGRTESHVKK 275 (797)
Q Consensus 196 la~~~e~I~~tssR~~k~~iL~~~fr~~i~~~p~dl~~~vyL~~~~l~P~~e~~elGIge~~L~kal~~a~G~s~~~ik~ 275 (797)
+-+++++|++|+|+++|.+||.+-- +.+.|..+++|+.+. ...|||+..
T Consensus 2 i~~il~~~~~~~~~~~k~~il~~~~------~n~~l~~~~~~~~~~------~~~~~~~~~------------------- 50 (488)
T PHA02587 2 ILDILNELASTDSTKEKEAILKENK------DNELLKEVFRLTYNK------QINFGIKKW------------------- 50 (488)
T ss_pred hHHHHHHHHhccCcchHHHHHHhcc------cChHHHHHHHHHhCc------ceeEeeeEc-------------------
Confidence 4578999999999999999998542 233355555555432 346776521
Q ss_pred HHHhcCCHHHHHhhccccCCCCCCCCCCCHHHH-HHHHHHHHHHhCCChHHHHHHHHHHHHHhcCCChHHHHHHHHhhhc
Q 003762 276 QYQEMGDLGLVAKASRSSQSMMRKPDPLTITKV-FDTFRLIAKEAGKDSQEKKKNRIKALLVAATDCEPQYLIRLLQSKL 354 (797)
Q Consensus 276 ~y~~~GDlg~vA~~~r~~q~~l~~~~~LTI~eV-~~~L~kIA~~~G~~s~~~K~~~L~~LL~~~t~~E~k~LiRiIlkdL 354 (797)
.+.|- .-....++++.++ ...+.++|+..-.+.. .+..|..++.+|++.|++||+|+|+++|
T Consensus 51 --~~~~~-------------~~~~~~~~~~~~~~~~~~~~l~~r~~~~~~--~~~~l~~ll~~~~~~e~~~l~rli~~~l 113 (488)
T PHA02587 51 --PKPGH-------------VEGSDGMLSLEDLLDFLEFDLATRKLTGNA--AIEELAQILSSMNEDDAEVLRRVLMRDL 113 (488)
T ss_pred --CCCcc-------------ccCCCCceeHHHHHHHHHHHHHHhhcchhH--HHHHHHHHHHhCCHHHHHHHHHHHhccc
Confidence 11110 0012355788884 4455678876655443 4789999999999999999999999999
Q ss_pred cCcccHHHHHHHHHHhhccCCCCCCCCCCCcchHHHHHHHHHHHhhcCCchhhhHhhhhhcCccccCCccccCCCCCCcc
Q 003762 355 RIGLAEQTLLAALGQAAVYNEQHSKPPPNIQSPLEEAAKIVKQVFSVLPVYEKIVPALLTDGVWNLSNTCSFTPGIPIGP 434 (797)
Q Consensus 355 RiGi~e~tvl~Ala~a~~~~~~~~~~~~~l~~~l~~a~~~vk~~y~~~pd~~~v~~~l~~~g~~~l~~~~~l~~g~Pv~P 434 (797)
|||++++||++||+ .++|++|
T Consensus 114 riGvs~~~i~~~~~-----------------------------------------------------------~~~P~~p 134 (488)
T PHA02587 114 ECGASEKIANKVWK-----------------------------------------------------------GLIPEQP 134 (488)
T ss_pred CCCccHHHHHHHhc-----------------------------------------------------------CCccCCC
Confidence 99999999997651 0578888
Q ss_pred -ccccccCChHHHHhh-cCCCceEEEeecceEEEEEEEecCCeEEEEecCCCccCCCcchHHHHHHhhcC---CCCCCeE
Q 003762 435 -MLAKPTKGVSEIVNK-FQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAVSRLKK---PSVRSFV 509 (797)
Q Consensus 435 -MLA~~~~~i~~~l~k-~~g~~~~~E~KyDG~R~qih~~~~g~V~ifSR~gkd~T~~yPel~~~l~~~~~---~~v~~~I 509 (797)
|||++... +++++ +. .+|++|+||||+|||+|++ +|.|++|||+|++++ .||++.+.+.++.. ....++|
T Consensus 135 ~mLA~~~~~--~~~~~~~~-~~~~~E~K~DG~R~q~h~~-~~~v~l~SR~g~~~~-~~p~i~~~l~~~~~~~~~~~~~~V 209 (488)
T PHA02587 135 QMLASSFSE--KLIKKNIK-FPAYAQLKADGARCFADID-ADGIEIRSRNGNEYL-GLDLLKEELKKMTAEARQRPGGVV 209 (488)
T ss_pred CccCCCCCH--HHHHhhcc-CcEEEEEccCceEEEEEEe-CCEEEEEecCCcccc-CChhHHHHHHHHhhhhcccCCcEE
Confidence 99998543 45655 43 3899999999999999995 789999999999997 58999887766543 1237899
Q ss_pred EEEEEEEEecCCCcccCh-------------hhHHhhhcccCCc---------cccccceEEEEeeeeecC---CccccC
Q 003762 510 LDCEIVAYDREKQKILPF-------------QTLSTRARKNVSL---------SDIKVDVCIYAFDILYRN---GQPLLQ 564 (797)
Q Consensus 510 LDGElVa~d~~~g~~lpF-------------q~L~~R~Rk~~~~---------~~~~~~v~~~vFDILyln---G~~L~~ 564 (797)
||||+|+||.+++.+.+| |.++.|.+++... .....+++|++||||++| |.++++
T Consensus 210 LDGElv~~~~~~~~~~~~~f~~~~~~~~~f~q~l~~R~~~~~i~~~~l~~~~~~~~~~pv~~~vFDiL~ld~y~~~~~~~ 289 (488)
T PHA02587 210 IDGELVYVEVETKKPNGLSFLFDDSKAKEFVGVVADRATGNGIVNKSLKGTISKEEAQEIVFQVWDIVPLEVYYGKEKSD 289 (488)
T ss_pred EEeEEEEEecccCCCccchhhcccccccchhhhhhhhhhccchhhhhhccccchhhccceEEEEEEeechhhccCCcccc
Confidence 999999998766655555 7888887654211 123578999999999653 445788
Q ss_pred CcHHHHHHHHHHhhcc-CCCcEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEEeCCCCCCccCCCCCCCeEEEcccccc
Q 003762 565 EQLRVRREHLYDSFEE-EPGFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLKKDYIE 643 (797)
Q Consensus 565 ~Pl~ERr~lL~~l~~~-~~~~i~~v~~~~~~~~eei~~~f~~ai~~g~EGlmvK~~~~ds~Y~pGkRs~~WlKlK~dY~~ 643 (797)
.||.+||++|++++.. ..+++++++...+++.+++.++|+++++.|+||||+|++ +|+|++| |+.+|+|+|+.
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 346889999888999999999999999999999999999 9999998 88899999986
Q ss_pred ccCCccceEEEeEEeCCCCcCCccceEEEEEecCCCceEEEeccccCCCCHHHHHHHHHhhccccCCCCCCCcccCCCCC
Q 003762 644 SIGDSLDLVPIAAFHGRGKRTGVYGAFLLACYDSNNEEFQSICKIGTGFSEAMLEERSSSLRSKVIPKPRPYYRFADTIS 723 (797)
Q Consensus 644 ~~~dtlDlvVIGa~~G~Gkr~g~~gsfllg~~d~~~g~~~~vgkVGTGfSd~~l~~l~~~l~~~~~~~p~~~~~~~~~~~ 723 (797)
+++|++|||+++|. +++|.+|+|+|++++ |. .+|+|||||||++++++..... . .++-......+
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 48999999999964 677899999997764 44 3689999999999999876653 1 11222233346
Q ss_pred CceEeccc----eEEEEEeeeeecCCcccccccccCCCCCceeeeceEeeEeC
Q 003762 724 PDVWFEPT----EVWEVKAADLTISPVHRAAIGVVDPDKVFTVRFSVLAHLSF 772 (797)
Q Consensus 724 pdvw~eP~----~V~EV~~~eit~S~~~~aa~g~v~~~~G~sLRFPRf~riR~ 772 (797)
+.+|.+|. .||||+|++||.||+|++ |++||||||+|+|+
T Consensus 429 ~~~~~~~~~~~~~V~EV~~~~it~S~~~~~---------g~sLRfPrf~r~R~ 472 (488)
T PHA02587 429 EELMANKGKYIGKIAECECNGLQRSKGRKD---------KVSLFLPIIKRIRI 472 (488)
T ss_pred hhhhhCcccccceEEEEEeceEEeCCCCCC---------CeeEEccceeEEeC
Confidence 77887754 799999999999999986 79999999999999
No 10
>TIGR02779 NHEJ_ligase_lig DNA polymerase LigD, ligase domain. DNA repair of double-stranded breaks by non-homologous end joining (NHEJ) is accomplished by a two-protein system that is present in a minority of prokaryotes. One component is the Ku protein (see TIGR02772), which binds DNA ends. The other is a DNA ligase, a protein that is a multidomain polypeptide in most of those bacteria that have NHEJ, a permuted polypeptide in Mycobacterium tuberculosis and a few other species, and the product of tandem genes in some other bacteria. This model represents the ligase domain.
Probab=100.00 E-value=3.2e-60 Score=511.83 Aligned_cols=287 Identities=29% Similarity=0.371 Sum_probs=248.1
Q ss_pred cCCCceEEEeecceEEEEEEEecCCeEEEEecCCCccCCCcchHHHHHHhhcCCCCCCeEEEEEEEEEecCCCcccChhh
Q 003762 450 FQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAVSRLKKPSVRSFVLDCEIVAYDREKQKILPFQT 529 (797)
Q Consensus 450 ~~g~~~~~E~KyDG~R~qih~~~~g~V~ifSR~gkd~T~~yPel~~~l~~~~~~~v~~~ILDGElVa~d~~~g~~lpFq~ 529 (797)
+.+.+|++|+||||+|||+|++ +|+|++|||||+++|..||++.+.+... ...++|||||+|++|.. |. .+|+.
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 3567899999999999999995 7899999999999999999998865443 23689999999999864 43 59999
Q ss_pred HHhhhcccCCccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCCCcEEEEeEEecCCHHHHHHHHHHHHHc
Q 003762 530 LSTRARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAAVDA 609 (797)
Q Consensus 530 L~~R~Rk~~~~~~~~~~v~~~vFDILylnG~~L~~~Pl~ERr~lL~~l~~~~~~~i~~v~~~~~~~~eei~~~f~~ai~~ 609 (797)
|++|.+... ..+++|++||||++||++++++||.+|+++|++++.+.++.+.+... ...+.+++.++|++++++
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 999986532 37899999999999999999999999999999999876554433322 456778999999999999
Q ss_pred CCceeEEEeCCCCCCccCCCCCCCeEEEccccccccCCccceEEEeEEeCCCCcCCccceEEEEEecCCCceEEEecccc
Q 003762 610 SCEGLIIKTMDRDATYEPSKRSLNWLKLKKDYIESIGDSLDLVPIAAFHGRGKRTGVYGAFLLACYDSNNEEFQSICKIG 689 (797)
Q Consensus 610 g~EGlmvK~~~~ds~Y~pGkRs~~WlKlK~dY~~~~~dtlDlvVIGa~~G~Gkr~g~~gsfllg~~d~~~g~~~~vgkVG 689 (797)
|+||||+|++ +|+|++|+ +.+|+|+|+++ +.|++|+|++.|+|++ |.+|+|+||+||+ +.|+++|+||
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 5799999999
Q ss_pred CCCCHHHHHHHHHhhccccCCCCCCCcccCCCCCCceEeccceEEEEEeeeeecCCcccccccccCCCCCceeeeceEee
Q 003762 690 TGFSEAMLEERSSSLRSKVIPKPRPYYRFADTISPDVWFEPTEVWEVKAADLTISPVHRAAIGVVDPDKVFTVRFSVLAH 769 (797)
Q Consensus 690 TGfSd~~l~~l~~~l~~~~~~~p~~~~~~~~~~~pdvw~eP~~V~EV~~~eit~S~~~~aa~g~v~~~~G~sLRFPRf~r 769 (797)
||||++++++|++.+.++++...+++ .....+++||+|.+||||+|.++|. |.+||||||+|
T Consensus 225 sG~s~~~~~~l~~~l~~~~~~~~~~~---~~~~~~~~wv~P~lV~eV~~~~~t~---------------~~~lR~P~~~~ 286 (298)
T TIGR02779 225 TGFSEAELATIKERLKPLESKPDKPG---AREKRGVHWVKPELVAEVEFAGWTR---------------DGRLRQASFVG 286 (298)
T ss_pred CCCCHHHHHHHHHHHHhhccCcCCCC---cccCCCCEEeCCeEEEEEEecccCC---------------CCeEeccEEEe
Confidence 99999999999999999876542222 2233689999999999999999984 57999999999
Q ss_pred EeC--Cccccc
Q 003762 770 LSF--PLLFCL 778 (797)
Q Consensus 770 iR~--~~~~~~ 778 (797)
+|. +|++|.
T Consensus 287 ~R~Dk~~~~~~ 297 (298)
T TIGR02779 287 LREDKPASEVT 297 (298)
T ss_pred eeCCCCHHHcc
Confidence 999 788874
No 11
>PRK09632 ATP-dependent DNA ligase; Reviewed
Probab=100.00 E-value=9.2e-59 Score=545.08 Aligned_cols=304 Identities=26% Similarity=0.346 Sum_probs=261.9
Q ss_pred ccCCCCCCccccccccCChHHHHhhcCCCceEEEeecceEEEEEEEecCCeEEEEecCCCccCCCcchHHHHHHhhcCCC
Q 003762 425 SFTPGIPIGPMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAVSRLKKPS 504 (797)
Q Consensus 425 ~l~~g~Pv~PMLA~~~~~i~~~l~k~~g~~~~~E~KyDG~R~qih~~~~g~V~ifSR~gkd~T~~yPel~~~l~~~~~~~ 504 (797)
...++.|++||||+..... .+.+.+|++|+||||+|+|+|++ +|.|++|||||+++|.+||++.+++.. +.
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 3578999999999876422 24567899999999999999995 789999999999999999999885544 43
Q ss_pred CCCeEEEEEEEEEecCCCcccChhhHHhhhcccCCccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCCCc
Q 003762 505 VRSFVLDCEIVAYDREKQKILPFQTLSTRARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEPGF 584 (797)
Q Consensus 505 v~~~ILDGElVa~d~~~g~~lpFq~L~~R~Rk~~~~~~~~~~v~~~vFDILylnG~~L~~~Pl~ERr~lL~~l~~~~~~~ 584 (797)
..++|||||||++|.. |. .+|+.|++|.+ ..+++|++|||||+||++|+++||.+||++|++++.. .+.
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 2689999999999864 43 59999999842 3679999999999999999999999999999999974 456
Q ss_pred EEEEeEEecCCHHHHHHHHHHHHHcCCceeEEEeCCCCCCccCCCCCCCeEEEccccccccCCccceEEEeEEeCCCCcC
Q 003762 585 FQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLKKDYIESIGDSLDLVPIAAFHGRGKRT 664 (797)
Q Consensus 585 i~~v~~~~~~~~eei~~~f~~ai~~g~EGlmvK~~~~ds~Y~pGkRs~~WlKlK~dY~~~~~dtlDlvVIGa~~G~Gkr~ 664 (797)
+++++.... +++++|+.++++|+||||+|++ +|+|++|+|+.+|+|+|++| +.|+||+|+++|+|++.
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 CccceEEEEEecCCCceEEEeccccCCCCHHHHHHHHHhhccccCCCCCCCc-cc-CCCCCCceEeccceEEEEEeeeee
Q 003762 665 GVYGAFLLACYDSNNEEFQSICKIGTGFSEAMLEERSSSLRSKVIPKPRPYY-RF-ADTISPDVWFEPTEVWEVKAADLT 742 (797)
Q Consensus 665 g~~gsfllg~~d~~~g~~~~vgkVGTGfSd~~l~~l~~~l~~~~~~~p~~~~-~~-~~~~~pdvw~eP~~V~EV~~~eit 742 (797)
|.+|+|+||+||+ +.|++||+||||||++++++|.+.|+++....+ +|. .. ....++++||+|.+|+||+|+++|
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 569999999999999999999999999877654 332 12 123468999999999999999999
Q ss_pred cCCcccccccccCCCCCceeeeceEeeEeC--Cccccc
Q 003762 743 ISPVHRAAIGVVDPDKVFTVRFSVLAHLSF--PLLFCL 778 (797)
Q Consensus 743 ~S~~~~aa~g~v~~~~G~sLRFPRf~riR~--~~~~~~ 778 (797)
. ++.||||||+++|. ++.+|.
T Consensus 739 ~---------------~g~LR~P~f~glR~DK~p~dv~ 761 (764)
T PRK09632 739 P---------------DGRLRQPSWRGLRPDKKPGDVV 761 (764)
T ss_pred C---------------CCceecceEEEeeCCCCHHHcc
Confidence 4 46899999999999 667764
No 12
>PRK08224 ligC ATP-dependent DNA ligase; Reviewed
Probab=100.00 E-value=1.2e-57 Score=500.18 Aligned_cols=309 Identities=24% Similarity=0.316 Sum_probs=258.8
Q ss_pred ccCCCCCCccccccccCChHHHHhhcCCCceEEEeecceEEEEEEEecCCeEEEEecCCCccCCCcchHHHHHHhhcCCC
Q 003762 425 SFTPGIPIGPMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAVSRLKKPS 504 (797)
Q Consensus 425 ~l~~g~Pv~PMLA~~~~~i~~~l~k~~g~~~~~E~KyDG~R~qih~~~~g~V~ifSR~gkd~T~~yPel~~~l~~~~~~~ 504 (797)
.+.+|.|++||||+....++ .+.+|++|+||||+|||+|++ +|+|++|||||+++|+.||+|.+++...+.
T Consensus 2 ~~~~~~~i~PMLA~~~~~~~------~~~~w~~E~K~DG~R~~~~~~-~~~v~l~SRng~d~t~~fPel~~~~~~~~~-- 72 (350)
T PRK08224 2 DLPVMPPVEPMLAKSVDAIP------PGDGWSYEPKWDGFRCLVFRD-GDEVELGSRNGKPLTRYFPELVAALRAELP-- 72 (350)
T ss_pred CCCCCCCcCCccCCccCCCC------CCCcEEEEEeECeeEEEEEEE-CCEEEEEeCCCCCchhhhHHHHHHHHhhCC--
Confidence 46789999999998876542 345799999999999999995 789999999999999999999988876543
Q ss_pred CCCeEEEEEEEEEecCCCcccChhhHHhhhcccCC---ccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccC
Q 003762 505 VRSFVLDCEIVAYDREKQKILPFQTLSTRARKNVS---LSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEE 581 (797)
Q Consensus 505 v~~~ILDGElVa~d~~~g~~lpFq~L~~R~Rk~~~---~~~~~~~v~~~vFDILylnG~~L~~~Pl~ERr~lL~~l~~~~ 581 (797)
.++|||||+|++|. ++ .+|+.|++|.+.... ......+++|++|||||+||++|+++||.||+++|++++..
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 68999999999974 22 799999998753311 11235789999999999999999999999999999999965
Q ss_pred CCcEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEEeCCCCCCccCCCCCCCeEEEccccccccCCccceEEEeEEeCCC
Q 003762 582 PGFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLKKDYIESIGDSLDLVPIAAFHGRG 661 (797)
Q Consensus 582 ~~~i~~v~~~~~~~~eei~~~f~~ai~~g~EGlmvK~~~~ds~Y~pGkRs~~WlKlK~dY~~~~~dtlDlvVIGa~~G~G 661 (797)
.+.+++++. ..+.++++++|++++++|+||||+|+. +|+|++|+|+ |+|+|+.+ ++|+||+|+++|+|
T Consensus 148 ~~~i~~~~~--~~~~~~~~~~~~~a~~~G~EGIV~Kr~--dS~Y~~Grr~--WlKiK~~~------~~d~vI~G~~~g~~ 215 (350)
T PRK08224 148 SGPVHLTPA--TTDPATARRWFEEFEGAGLDGVIAKPL--DGPYQPGKRA--MFKVKHER------TADCVVAGYRYHKS 215 (350)
T ss_pred CCcEEEecc--cCCHHHHHHHHHHHHhCCCcEEEEeCC--CCCcCCCCcC--EEEEccCC------cEEEEEEEEEcCCC
Confidence 345777764 356789999999999999999999999 9999999887 99999964 99999999999987
Q ss_pred CcCCccceEEEEEecCCCceEEEeccccCCCCHHHHHHHHHhhccccCCCC--C----CCcccC-------CCCCCceE-
Q 003762 662 KRTGVYGAFLLACYDSNNEEFQSICKIGTGFSEAMLEERSSSLRSKVIPKP--R----PYYRFA-------DTISPDVW- 727 (797)
Q Consensus 662 kr~g~~gsfllg~~d~~~g~~~~vgkVGTGfSd~~l~~l~~~l~~~~~~~p--~----~~~~~~-------~~~~pdvw- 727 (797)
+ |.+|+|+||+||+ +|++++||+|+ |||++++++|++.++++..+.+ | +|.... ...+..+|
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 9999999999999998876544 2 332211 01235689
Q ss_pred -eccceEEEEEeeeeecCCcccccccccCCCCCceeeec-eEeeEeC--CcccccC
Q 003762 728 -FEPTEVWEVKAADLTISPVHRAAIGVVDPDKVFTVRFS-VLAHLSF--PLLFCLG 779 (797)
Q Consensus 728 -~eP~~V~EV~~~eit~S~~~~aa~g~v~~~~G~sLRFP-Rf~riR~--~~~~~~~ 779 (797)
++|.+|+||+|.++| + | .||+| +|+++|. +..+|..
T Consensus 292 ~v~P~lv~eV~~~~~t-~--------------~-~lR~p~~f~g~r~Dk~p~~v~~ 331 (350)
T PRK08224 292 PLRPERVVEVRYDHME-G--------------G-RFRHTAQFLRWRPDRDPRSCTY 331 (350)
T ss_pred eeeEEEEEEEecCccc-C--------------C-eecCCCeeEEEcCCCChHHCCH
Confidence 999999999999998 2 3 79998 9999999 7788854
No 13
>PRK05972 ligD ATP-dependent DNA ligase; Reviewed
Probab=100.00 E-value=3.4e-56 Score=527.71 Aligned_cols=299 Identities=27% Similarity=0.364 Sum_probs=257.0
Q ss_pred CCccccccccCChHHHHhhcCCCceEEEeecceEEEEEEEecCCeEEEEecCCCccCCCcchHHHHHHhhcCCCCCCeEE
Q 003762 431 PIGPMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAVSRLKKPSVRSFVL 510 (797)
Q Consensus 431 Pv~PMLA~~~~~i~~~l~k~~g~~~~~E~KyDG~R~qih~~~~g~V~ifSR~gkd~T~~yPel~~~l~~~~~~~v~~~IL 510 (797)
.++||||.....++ .+.+|++|+||||+|||+|++ +|+|++|||||+++|.+||+|++++..+ +++++||
T Consensus 233 ~i~PMLAt~~~~~p------~g~~W~~E~K~DG~R~~a~~~-gg~vrL~SRnG~d~T~~fPel~~~~~~l---~~~~~IL 302 (860)
T PRK05972 233 FLAPQLATLVDRPP------SGDGWIYEIKFDGYRILARIE-GGEVRLFTRNGLDWTAKLPALAKAAAAL---GLPDAWL 302 (860)
T ss_pred ccCcccCccCCCCC------CcCceEEEeeeCcEEEEEEEE-CCEEEEEeCCCCccccccHHHHHHHHhc---CCCceeE
Confidence 48999998776542 456899999999999999995 7899999999999999999999987764 3478999
Q ss_pred EEEEEEEecCCCcccChhhHHhhhcccCCccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCC-CcEEEEe
Q 003762 511 DCEIVAYDREKQKILPFQTLSTRARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEP-GFFQFAT 589 (797)
Q Consensus 511 DGElVa~d~~~g~~lpFq~L~~R~Rk~~~~~~~~~~v~~~vFDILylnG~~L~~~Pl~ERr~lL~~l~~~~~-~~i~~v~ 589 (797)
|||+|++|.+ |. .+|+.|++|.+... ..+++|++|||||+||++|+++||.+|+++|++++.+.+ +.+++++
T Consensus 303 DGEIVvld~~-G~-~~F~~Lq~r~~~~~-----~~~v~f~vFDLL~l~G~dL~~~PL~eRr~~L~~ll~~~~~~~i~~s~ 375 (860)
T PRK05972 303 DGEIVVLDED-GV-PDFQALQNAFDEGR-----TEDLVYFAFDLPFLGGEDLRELPLEERRARLRALLEAARSDRIRFSE 375 (860)
T ss_pred eEEEEEECCC-CC-CCHHHHHHHhhccC-----CCceEEEEEeccccCCcccccCCHHHHHHHHHHHhhhcCCCcEEEec
Confidence 9999999864 44 59999999876432 368999999999999999999999999999999997653 4788887
Q ss_pred EEecCCHHHHHHHHHHHHHcCCceeEEEeCCCCCCccCCCCCCCeEEEccccccccCCccceEEEeEEeCCCCcCCccce
Q 003762 590 TLTSIDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLKKDYIESIGDSLDLVPIAAFHGRGKRTGVYGA 669 (797)
Q Consensus 590 ~~~~~~~eei~~~f~~ai~~g~EGlmvK~~~~ds~Y~pGkRs~~WlKlK~dY~~~~~dtlDlvVIGa~~G~Gkr~g~~gs 669 (797)
+... +++++|+.+++.|+||||+|++ ||+|++| |+.+|+|+|+.+ +.|+||+|++.|+|+|.| +|+
T Consensus 376 ~~~~----~g~~ll~~a~~~GlEGIVaKr~--dS~Y~~G-Rs~~WlKiK~~~------~~E~VIgGy~~~~Gkr~g-~gS 441 (860)
T PRK05972 376 HFDA----GGDAVLASACRLGLEGVIGKRA--DSPYVSG-RSEDWIKLKCRA------RQEFVIGGYTDPKGSRSG-FGS 441 (860)
T ss_pred eecc----hHHHHHHHHHHcCCceEEEeCC--CCCCCCC-CCCCcEEEecCC------CceEEEEEEeCCCCcccc-cee
Confidence 6543 5788999999999999999999 9999987 899999999975 678888888888999988 999
Q ss_pred EEEEEecCCCceEEEeccccCCCCHHHHHHHHHhhccccCCCCCCCcccCC--CCCCceEeccceEEEEEeeeeecCCcc
Q 003762 670 FLLACYDSNNEEFQSICKIGTGFSEAMLEERSSSLRSKVIPKPRPYYRFAD--TISPDVWFEPTEVWEVKAADLTISPVH 747 (797)
Q Consensus 670 fllg~~d~~~g~~~~vgkVGTGfSd~~l~~l~~~l~~~~~~~p~~~~~~~~--~~~pdvw~eP~~V~EV~~~eit~S~~~ 747 (797)
|+||+||+ ++|++||+||||||++++++|.+.|+++....++ |..... ....++||+|.+||||+|+++|.+
T Consensus 442 LLlGvyd~--~~L~yvGkVGTGfsd~~l~~L~~~L~~l~~~~~P-f~~~~~~~~~~~~~WV~P~LV~EV~f~e~T~~--- 515 (860)
T PRK05972 442 LLLGVHDD--DHLRYAGRVGTGFGAATLKTLLPRLKALATDKSP-FAGKPAPRKARGVHWVKPELVAEVEFAGWTRD--- 515 (860)
T ss_pred EEEEEecC--CEEEEEEEECCCCCHHHHHHHHHHHHhhccCCCC-ccccCccccCCCCEEEccCEEEEEEEeeccCC---
Confidence 99999985 6999999999999999999999999998876543 432211 124579999999999999999953
Q ss_pred cccccccCCCCCceeeeceEeeEeC--Cccccc
Q 003762 748 RAAIGVVDPDKVFTVRFSVLAHLSF--PLLFCL 778 (797)
Q Consensus 748 ~aa~g~v~~~~G~sLRFPRf~riR~--~~~~~~ 778 (797)
..||||+|+++|. ++.+|.
T Consensus 516 ------------g~LR~P~F~glR~DK~p~ev~ 536 (860)
T PRK05972 516 ------------GIVRQAVFKGLREDKPAREVV 536 (860)
T ss_pred ------------CCCccceEEEeecCCChHHhC
Confidence 4799999999999 788884
No 14
>PRK09633 ligD ATP-dependent DNA ligase; Reviewed
Probab=100.00 E-value=2.1e-55 Score=510.28 Aligned_cols=292 Identities=19% Similarity=0.255 Sum_probs=244.9
Q ss_pred CccccccccCChHHHHhhcCCCceEEEeecceEEEEEEEecCCeEEEEecCCCccCCCcchHHHHHHhhcCC--CCCCeE
Q 003762 432 IGPMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAVSRLKKP--SVRSFV 509 (797)
Q Consensus 432 v~PMLA~~~~~i~~~l~k~~g~~~~~E~KyDG~R~qih~~~~g~V~ifSR~gkd~T~~yPel~~~l~~~~~~--~v~~~I 509 (797)
++||||.....+ +.+.+|++|+||||+|||+|++ +|.|++|||||+++|.+||++++++..+... ...++|
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 479999877654 3567899999999999999995 7899999999999999999999877654321 124799
Q ss_pred EEEEEEEEecCCCcccChhhHHhhhcccCC----ccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCC---
Q 003762 510 LDCEIVAYDREKQKILPFQTLSTRARKNVS----LSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEP--- 582 (797)
Q Consensus 510 LDGElVa~d~~~g~~lpFq~L~~R~Rk~~~----~~~~~~~v~~~vFDILylnG~~L~~~Pl~ERr~lL~~l~~~~~--- 582 (797)
||||+|++|.+ |. .+|+.|++|.+.... ......+++|++|||||+||++|++.||.+||++|++++.+.+
T Consensus 74 LDGEiVvld~~-g~-~~F~~Lq~R~~~~~~~~i~~~~~~~pv~~~vFDlL~lnG~dL~~~PL~eRr~~L~~ll~~~~~~~ 151 (610)
T PRK09633 74 LDGELVCLVNP-YR-SDFEHVQQRGRLKNTEVIAKSANARPCQLLAFDLLELKGESLTSLPYLERKKQLDKLMKAAKLPA 151 (610)
T ss_pred eeeEEEEecCC-CC-CCHHHHHhhhhccccchhhhhhcccceEEEEEeecccCCcccccCCHHHHHHHHHHHhhhccccc
Confidence 99999999854 32 699999999653211 1123578999999999999999999999999999999997642
Q ss_pred -------CcEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEEeCCCCCCccCCCCCCCeEEEccccccccCCccceEEEe
Q 003762 583 -------GFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLKKDYIESIGDSLDLVPIA 655 (797)
Q Consensus 583 -------~~i~~v~~~~~~~~eei~~~f~~ai~~g~EGlmvK~~~~ds~Y~pGkRs~~WlKlK~dY~~~~~dtlDlvVIG 655 (797)
..+++ +.+.++++++|+++++.|+||||+|+. +|+|++|+||.+|+|+|+. ++.|++|+|
T Consensus 152 ~~~~~~~~~i~~-----~~~~~~~~~l~~~a~~~g~EGIV~Kr~--dS~Y~~G~Rs~~WlKiK~~------~~~d~vI~G 218 (610)
T PRK09633 152 SPDPYAKARIQY-----IPSTTDFDALWEAVKRYDGEGIVAKKK--TSKWLENKRSKDWLKIKNW------RYVHVIVTG 218 (610)
T ss_pred ccccccccceEE-----cCCHHHHHHHHHHHHHcCCceEEEeCC--CCCCCCCCCCCCeEEEecc------CCceeEEEE
Confidence 13333 346678999999999999999999999 9999999999999999995 489999999
Q ss_pred EEeCCCCcCCccceEEEEEecCCCceEEEeccccCCCCHHHHHHHHHhhccccCCCCCCCcccCCCCCCceEeccceEEE
Q 003762 656 AFHGRGKRTGVYGAFLLACYDSNNEEFQSICKIGTGFSEAMLEERSSSLRSKVIPKPRPYYRFADTISPDVWFEPTEVWE 735 (797)
Q Consensus 656 a~~G~Gkr~g~~gsfllg~~d~~~g~~~~vgkVGTGfSd~~l~~l~~~l~~~~~~~p~~~~~~~~~~~pdvw~eP~~V~E 735 (797)
+..|+| .|++|+|+ +|+|+++|+||||||++++++|++.++++.+... .+.+|++|.+|||
T Consensus 219 ~~~~~g-------~~llgv~~--~g~l~~vGkvgtGft~~~~~~L~~~l~~l~~~~~----------~~~~wV~P~LV~E 279 (610)
T PRK09633 219 YDPSNG-------YFTGSVYK--DGQLTEVGSVKHGMEDEERQTLRAIFKQNGTKTK----------SGEYTLEPSICVT 279 (610)
T ss_pred EecCCc-------eEEEEEec--CCeEEEEEEecCCCCHHHHHHHHHHHHHhccCCC----------CCcEEEeeeEEEE
Confidence 876543 67889995 4899999999999999999999999988765431 4689999999999
Q ss_pred EEeeeeecCCcccccccccCCCCCceeeeceEeeEeC--CcccccCC
Q 003762 736 VKAADLTISPVHRAAIGVVDPDKVFTVRFSVLAHLSF--PLLFCLGN 780 (797)
Q Consensus 736 V~~~eit~S~~~~aa~g~v~~~~G~sLRFPRf~riR~--~~~~~~~~ 780 (797)
|+|+++| |+.||||||+++|. +..+|...
T Consensus 280 V~~~e~t----------------~g~LR~P~f~glR~DK~~~ev~~~ 310 (610)
T PRK09633 280 VACITFD----------------GGTLREPSFVSFLFDMDPTECTYQ 310 (610)
T ss_pred EEEeecC----------------CCeEEeeEEeEEEcCCChHHcchh
Confidence 9999996 57899999999999 77888543
No 15
>PRK07636 ligB ATP-dependent DNA ligase; Reviewed
Probab=100.00 E-value=1.1e-52 Score=448.34 Aligned_cols=272 Identities=24% Similarity=0.316 Sum_probs=228.2
Q ss_pred CccccccccCChHHHHhhcCCCceEEEeecceEEEEEEEecCCeEEEEecCCCccCCCcchHHHHHHhhcCCCCCCeEEE
Q 003762 432 IGPMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAVSRLKKPSVRSFVLD 511 (797)
Q Consensus 432 v~PMLA~~~~~i~~~l~k~~g~~~~~E~KyDG~R~qih~~~~g~V~ifSR~gkd~T~~yPel~~~l~~~~~~~v~~~ILD 511 (797)
++||||...+.. +++.+|++|+||||+|||+|+. +|+|++|||||+++|..||++.+.. +. .++|||
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 689999876542 4566899999999999999995 7899999999999999999998742 32 479999
Q ss_pred EEEEEEecCCCcccChhhHHhhhcccCCccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCCCcEEEEeEE
Q 003762 512 CEIVAYDREKQKILPFQTLSTRARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEPGFFQFATTL 591 (797)
Q Consensus 512 GElVa~d~~~g~~lpFq~L~~R~Rk~~~~~~~~~~v~~~vFDILylnG~~L~~~Pl~ERr~lL~~l~~~~~~~i~~v~~~ 591 (797)
||+|++|.+ |+ .+|+.|++|.+.... ....+++|++||||++||++++++||.||+++|++++.+.+ .+++++..
T Consensus 70 GElv~~d~~-g~-~~F~~l~~r~~~~~~--~~~~~~~~~vFDlL~~~g~~l~~~pl~eRr~~L~~~~~~~~-~~~~~~~~ 144 (275)
T PRK07636 70 GELIVLGST-GA-PDFEAVMERFQSKKS--TKIHPVVFCVFDVLYINGVSLTALPLSERKEILASLLLPHP-NVKIIEGI 144 (275)
T ss_pred eEEEEECCC-CC-CCHHHHHHHhccccc--cccCceEEEEEEeEEECceehhhCCHHHHHHHHHHhcCCCC-CEEEcccc
Confidence 999999864 44 589999998764321 22578999999999999999999999999999999997644 56666643
Q ss_pred ecCCHHHHHHHHHHHHHcCCceeEEEeCCCCCCccCCCCCCCeEEEccccccccCCccceEEEeEEeCCCCcCCccceEE
Q 003762 592 TSIDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLKKDYIESIGDSLDLVPIAAFHGRGKRTGVYGAFL 671 (797)
Q Consensus 592 ~~~~~eei~~~f~~ai~~g~EGlmvK~~~~ds~Y~pGkRs~~WlKlK~dY~~~~~dtlDlvVIGa~~G~Gkr~g~~gsfl 671 (797)
. ++++++|++++++|.||||+|++ ||+|.+|+|+.+|+|+|+. +++|+||+|+..+ .+|.+
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 5899999988543 25655
Q ss_pred EEEecCCCceEEEeccccCCCCHHHHHHHHHhhccccCCCCCCCcccCCCCCCceEeccceEEEEEeeeeecCCcccccc
Q 003762 672 LACYDSNNEEFQSICKIGTGFSEAMLEERSSSLRSKVIPKPRPYYRFADTISPDVWFEPTEVWEVKAADLTISPVHRAAI 751 (797)
Q Consensus 672 lg~~d~~~g~~~~vgkVGTGfSd~~l~~l~~~l~~~~~~~p~~~~~~~~~~~pdvw~eP~~V~EV~~~eit~S~~~~aa~ 751 (797)
||+|+ |. ++|+||| |+++++++|.+.++++.... .++++|++|.+|+||+|.|+|.+
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 6899999 99999999999887764432 25789999999999999999964
Q ss_pred cccCCCCCceeeeceEeeEe
Q 003762 752 GVVDPDKVFTVRFSVLAHLS 771 (797)
Q Consensus 752 g~v~~~~G~sLRFPRf~riR 771 (797)
|. ||||+|+++|
T Consensus 263 -------g~-lR~p~f~g~r 274 (275)
T PRK07636 263 -------GM-LRIPSFVEWR 274 (275)
T ss_pred -------CC-EEccEEEEEe
Confidence 55 9999999998
No 16
>cd07900 Adenylation_DNA_ligase_I_Euk Adenylation domain of eukaryotic DNA Ligase I. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. Some organisms express a variety of different ligases which appear to be targeted to specific functions. There are three classes of ATP-dependent DNA ligases in eukaryotic cells (I, III and IV). DNA ligase I is required for the ligation of Okazaki fragments during lagging-strand DNA synthesis and for base excision repair (BER). DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains. The adenylation and C-terminal oligonucleotide/oligo
Probab=100.00 E-value=7.8e-51 Score=420.88 Aligned_cols=217 Identities=67% Similarity=1.102 Sum_probs=200.5
Q ss_pred ccccCCCCCCccccccccCChHHHHhhcCCCceEEEeecceEEEEEEEecCCeEEEEecCCCccCCCcchHHHHHHhhcC
Q 003762 423 TCSFTPGIPIGPMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAVSRLKK 502 (797)
Q Consensus 423 ~~~l~~g~Pv~PMLA~~~~~i~~~l~k~~g~~~~~E~KyDG~R~qih~~~~g~V~ifSR~gkd~T~~yPel~~~l~~~~~ 502 (797)
++.|++|+|++||||++..+++++++++++.+|++|+||||+|||+|+..+|.|++|||||+++|..||++++.+...+.
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 36799999999999999999999999998889999999999999999964589999999999999999999999888875
Q ss_pred CCCCCeEEEEEEEEEecCCCcccChhhHHhhhcccCCccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCC
Q 003762 503 PSVRSFVLDCEIVAYDREKQKILPFQTLSTRARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEP 582 (797)
Q Consensus 503 ~~v~~~ILDGElVa~d~~~g~~lpFq~L~~R~Rk~~~~~~~~~~v~~~vFDILylnG~~L~~~Pl~ERr~lL~~l~~~~~ 582 (797)
.+..+||||||+|+||.++|...+|+.+++|.+++........+++|++|||||+||++|+++||.+||++|++++.+.+
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 55689999999999998778888999999998776544445689999999999999999999999999999999998878
Q ss_pred CcEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEEeCCCC--CCccCCCCCCCeEEEcccc
Q 003762 583 GFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTMDRD--ATYEPSKRSLNWLKLKKDY 641 (797)
Q Consensus 583 ~~i~~v~~~~~~~~eei~~~f~~ai~~g~EGlmvK~~~~d--s~Y~pGkRs~~WlKlK~dY 641 (797)
++++++++..+++.++++++|++++++|+||||+|++ + |+|++|+|+.+|+|+|+||
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
>TIGR02776 NHEJ_ligase_prk DNA ligase D. Members of this protein family are DNA ligases involved in the repair of DNA double-stranded breaks by non-homologous end joining (NHEJ). The system of the bacterial Ku protein (TIGR02772) plus this DNA ligase is seen in about 20 % of bacterial genomes to date and at least one archaeon (Archeoglobus fulgidus). This model describes a central and a C-terminal domain. These two domains may be permuted, as in genus Mycobacterium, or divided into tandem ORFs, and therefore not be identified by this model. An additional N-terminal 3'-phosphoesterase (PE) domain present in some but not all examples of this ligase is not included in the seed alignment for this model; This alignment models only the central ATP-dependent ligase domain and the C-terminal polymerase domain. Most examples of genes for this ligase are adjacent to the gene for Ku.
Probab=100.00 E-value=1.6e-47 Score=440.09 Aligned_cols=255 Identities=24% Similarity=0.361 Sum_probs=215.9
Q ss_pred ecCCCccCCCcchHHHHHHhhcCCCCCCeEEEEEEEEEecCCCcccChhhHHhhhcccCCccccccceEEEEeeeeecCC
Q 003762 480 SRNAERNTGKFPDVVLAVSRLKKPSVRSFVLDCEIVAYDREKQKILPFQTLSTRARKNVSLSDIKVDVCIYAFDILYRNG 559 (797)
Q Consensus 480 SR~gkd~T~~yPel~~~l~~~~~~~v~~~ILDGElVa~d~~~g~~lpFq~L~~R~Rk~~~~~~~~~~v~~~vFDILylnG 559 (797)
||||+++|.+||+|++++..+ .+.+||||||+|++|.+ |+ .+|+.|+++.+.. ...+++|++|||||+||
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 34789999999999964 54 5799999986533 24689999999999999
Q ss_pred ccccCCcHHHHHHHHHHhhccCC-CcEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEEeCCCCCCccCCCCCCCeEEEc
Q 003762 560 QPLLQEQLRVRREHLYDSFEEEP-GFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLK 638 (797)
Q Consensus 560 ~~L~~~Pl~ERr~lL~~l~~~~~-~~i~~v~~~~~~~~eei~~~f~~ai~~g~EGlmvK~~~~ds~Y~pGkRs~~WlKlK 638 (797)
++|+++||.+||++|++++.+.. +.++++++.. ++..++|++++++|+||||+|++ +|+|++| |+.+|+|+|
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 99999999999999999998753 3577776632 34459999999999999999999 9999999 999999999
Q ss_pred cccccccCCccceEEEeEEeCCCCcCCccceEEEEEecCCCceEEEeccccCCCCHHHHHHHHHhhccccCCCCCCCccc
Q 003762 639 KDYIESIGDSLDLVPIAAFHGRGKRTGVYGAFLLACYDSNNEEFQSICKIGTGFSEAMLEERSSSLRSKVIPKPRPYYRF 718 (797)
Q Consensus 639 ~dY~~~~~dtlDlvVIGa~~G~Gkr~g~~gsfllg~~d~~~g~~~~vgkVGTGfSd~~l~~l~~~l~~~~~~~p~~~~~~ 718 (797)
++| +.|++|+|++.|.| .+|+|+||+|| +|+|+++|+||||||++++++|++.+++++...+ +|...
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 4799999999999999999999999999887654 23221
Q ss_pred -CCCCCCceEeccceEEEEEeeeeecCCcccccccccCCCCCceeeeceEeeEeC--CcccccC
Q 003762 719 -ADTISPDVWFEPTEVWEVKAADLTISPVHRAAIGVVDPDKVFTVRFSVLAHLSF--PLLFCLG 779 (797)
Q Consensus 719 -~~~~~pdvw~eP~~V~EV~~~eit~S~~~~aa~g~v~~~~G~sLRFPRf~riR~--~~~~~~~ 779 (797)
+....+++||+|.+||||+|++||. |++||||||+|+|. ++.+|..
T Consensus 211 ~~~~~~~~~Wv~P~lV~EV~~~e~T~---------------~g~LR~Prf~~~R~DK~~~e~t~ 259 (552)
T TIGR02776 211 AGAKTRGVHWVRPSLVAEVEYAGITR---------------DGILREASFKGLREDKPAEEVTL 259 (552)
T ss_pred ccccCCCcEEEccCEEEEEEeeeccC---------------CCeeEccEEEEEeCCCCHHHcch
Confidence 1123579999999999999999994 57999999999999 8899943
No 18
>PHA00454 ATP-dependent DNA ligase
Probab=100.00 E-value=1.4e-46 Score=408.72 Aligned_cols=284 Identities=18% Similarity=0.204 Sum_probs=227.2
Q ss_pred ccccccccCC--hHHHHhhcCCCceEEEeecceEEEEEEEecCCeEEEEecCCCccCCCcchHHHHH------HhhcCC-
Q 003762 433 GPMLAKPTKG--VSEIVNKFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAV------SRLKKP- 503 (797)
Q Consensus 433 ~PMLA~~~~~--i~~~l~k~~g~~~~~E~KyDG~R~qih~~~~g~V~ifSR~gkd~T~~yPel~~~l------~~~~~~- 503 (797)
+||+|...+. +++++++++ .|++|+||||+|||+|+++++.|++|||||++ ||++.... .+.+..
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 5888887665 899998874 89999999999999999533359999999985 57765432 222221
Q ss_pred ---CCCCeEEEEEEEEEecCCCcccChhhHHhhhcccCC--ccccccceEEEEeeeeecC----Cccc---cCCcHHHHH
Q 003762 504 ---SVRSFVLDCEIVAYDREKQKILPFQTLSTRARKNVS--LSDIKVDVCIYAFDILYRN----GQPL---LQEQLRVRR 571 (797)
Q Consensus 504 ---~v~~~ILDGElVa~d~~~g~~lpFq~L~~R~Rk~~~--~~~~~~~v~~~vFDILyln----G~~L---~~~Pl~ERr 571 (797)
...++|||||+|+.+ .+|+.+++|.++... ......++.|++||||++| |+++ ..+||.+|+
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 489999999764421 1223578999999999999 5564 789999999
Q ss_pred HHHHHhhccCCC-cEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEEeCCCCCCccCCCCCCCeEEEccccccccCCccc
Q 003762 572 EHLYDSFEEEPG-FFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLKKDYIESIGDSLD 650 (797)
Q Consensus 572 ~lL~~l~~~~~~-~i~~v~~~~~~~~eei~~~f~~ai~~g~EGlmvK~~~~ds~Y~pGkRs~~WlKlK~dY~~~~~dtlD 650 (797)
++|++++...+. .++++++..+.+.+++.++|++++++|+||||+|++ +|+|++|+|+. |||+|+.+ ++|
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 999999876553 488999999999999999999999999999999999 99999998875 88999974 999
Q ss_pred eEEEeEEeCCCCc--CCccceEEEEEecCCCceEEEeccccCCCCHHHHHHHHHhhccccCCCCCCCcccCCCCCCceEe
Q 003762 651 LVPIAAFHGRGKR--TGVYGAFLLACYDSNNEEFQSICKIGTGFSEAMLEERSSSLRSKVIPKPRPYYRFADTISPDVWF 728 (797)
Q Consensus 651 lvVIGa~~G~Gkr--~g~~gsfllg~~d~~~g~~~~vgkVGTGfSd~~l~~l~~~l~~~~~~~p~~~~~~~~~~~pdvw~ 728 (797)
++|||+++|+|++ .|.+++|+|.+. +|.++. |||||++++++|++.++++....+ ...
T Consensus 226 ~vIvG~~~g~g~~~~~g~~~~~~~~~~---~g~l~~----gtGfs~~~~~~l~~~l~~~~~~~~-------------~~p 285 (315)
T PHA00454 226 GTIVGVVWGTPGLANEGKVIGFRVLLE---DGRVVN----ATGISRALMEEFTANVKEHGEDYE-------------AMP 285 (315)
T ss_pred EEEEEEEECCCCccCCceEEEEEEEeC---CCcEEE----ccCCCHHHHHHHHHHHHhhccCcc-------------ccC
Confidence 9999999998643 367777777652 366653 899999999999999987643321 001
Q ss_pred ccceEEEEEeeeeecCCcccccccccCCCCCceeeeceEeeEeC
Q 003762 729 EPTEVWEVKAADLTISPVHRAAIGVVDPDKVFTVRFSVLAHLSF 772 (797)
Q Consensus 729 eP~~V~EV~~~eit~S~~~~aa~g~v~~~~G~sLRFPRf~riR~ 772 (797)
.|..|+||+|.++|. +..||||+|+++|+
T Consensus 286 ~~~~v~eV~y~e~T~---------------~g~lR~P~F~g~Rd 314 (315)
T PHA00454 286 YNGRACQVSYMERTP---------------DGSLRHPSFDRFRD 314 (315)
T ss_pred CCCeEEEEEEEEcCC---------------CCcccCceeeeeec
Confidence 245799999999984 46899999999996
No 19
>PRK09125 DNA ligase; Provisional
Probab=100.00 E-value=1e-45 Score=395.67 Aligned_cols=252 Identities=27% Similarity=0.338 Sum_probs=208.8
Q ss_pred CccccccccCChHHHHhhcCCCceEEEeecceEEEEEEEecCCeEEEEecCCCccCCCcchHHHHHHhhcCCCCCCeEEE
Q 003762 432 IGPMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAVSRLKKPSVRSFVLD 511 (797)
Q Consensus 432 v~PMLA~~~~~i~~~l~k~~g~~~~~E~KyDG~R~qih~~~~g~V~ifSR~gkd~T~~yPel~~~l~~~~~~~v~~~ILD 511 (797)
+.||||+.... .+++.+|++|+||||+|||+ + .+++|||+|+++|. |+.. .. ..+++|||
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---TA----GFPPFPLD 87 (282)
T ss_pred CCceechhccc------CCChhhEEEEeeeeeEeEEE----C-CeEEEcCCCCcCCC--chhH---Hh----cCCCccEe
Confidence 57999987642 13456899999999999974 2 48999999999987 5532 12 23589999
Q ss_pred EEEEEEecCCCcccChhhHHhhhcccCCccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccC-CCcEEEEeE
Q 003762 512 CEIVAYDREKQKILPFQTLSTRARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEE-PGFFQFATT 590 (797)
Q Consensus 512 GElVa~d~~~g~~lpFq~L~~R~Rk~~~~~~~~~~v~~~vFDILylnG~~L~~~Pl~ERr~lL~~l~~~~-~~~i~~v~~ 590 (797)
||+|+++ .+|+.+++|.+++........+++|++||||++|| ||.+|+++|++++.+. .+.+++++.
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 47999999987653322234689999999999986 9999999999999875 457889999
Q ss_pred EecCCHHHHHHHHHHHHHcCCceeEEEeCCCCCCccCCCCCCCeEEEccccccccCCccceEEEeEEeCCCCcCCccceE
Q 003762 591 LTSIDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLKKDYIESIGDSLDLVPIAAFHGRGKRTGVYGAF 670 (797)
Q Consensus 591 ~~~~~~eei~~~f~~ai~~g~EGlmvK~~~~ds~Y~pGkRs~~WlKlK~dY~~~~~dtlDlvVIGa~~G~Gkr~g~~gsf 670 (797)
..+++.++++++|++++++|+||||+|++ ||+|++| |+.+|+|+|+++ +.|++|||+++|+|+++|++|+|
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 9999998 899999999986 78999999999999999999999
Q ss_pred EEEEecCCCceEEEeccccCCCCHHHHHHHHHhhccccCCCCCCCcccCCCCCCceEeccceEEEEEeeeeecCCccccc
Q 003762 671 LLACYDSNNEEFQSICKIGTGFSEAMLEERSSSLRSKVIPKPRPYYRFADTISPDVWFEPTEVWEVKAADLTISPVHRAA 750 (797)
Q Consensus 671 llg~~d~~~g~~~~vgkVGTGfSd~~l~~l~~~l~~~~~~~p~~~~~~~~~~~pdvw~eP~~V~EV~~~eit~S~~~~aa 750 (797)
+|+.+|. ..| +||||||+++++. ++ ++ ..+++|+|.++|.
T Consensus 227 lv~~~~g--~~~----~VgsG~t~~~r~~------------~~-~~--------------g~~~~V~y~e~t~------- 266 (282)
T PRK09125 227 LVETPDG--REF----KIGSGFSDAEREN------------PP-KI--------------GSIITYKYRGLTK------- 266 (282)
T ss_pred EEEeCCC--CEE----EeCCCCCHHHhcC------------CC-CC--------------CCEEEEEecccCC-------
Confidence 9996542 234 7899999998751 11 11 3599999999984
Q ss_pred ccccCCCCCceeeeceEeeEeC
Q 003762 751 IGVVDPDKVFTVRFSVLAHLSF 772 (797)
Q Consensus 751 ~g~v~~~~G~sLRFPRf~riR~ 772 (797)
...||||+|+++|+
T Consensus 267 --------~g~lR~P~f~g~R~ 280 (282)
T PRK09125 267 --------NGLPRFASFLRVRE 280 (282)
T ss_pred --------CCcccCCEEEEEec
Confidence 35799999999997
No 20
>cd07903 Adenylation_DNA_ligase_IV Adenylation domain of DNA Ligase IV. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. There are three classes of ATP-dependent DNA ligase in eukaryotic cells (I, III and IV). DNA ligase IV is required for DNA non-homologous end joining pathways, including recombination of the V(D)J immunoglobulin gene segments in cells of the mammalian immune system. DNA ligase IV is stabilized by forming a complex with XRCC4, a nuclear phosphoprotein, which is phosphorylated by DNA-dependent protein kinase. DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more di
Probab=100.00 E-value=2.9e-45 Score=380.17 Aligned_cols=216 Identities=31% Similarity=0.486 Sum_probs=189.9
Q ss_pred ccccCCCCCCccccccccCChHHHHhhcCCCceEEEeecceEEEEEEEecCCeEEEEecCCCccCCCcchHHHHH-----
Q 003762 423 TCSFTPGIPIGPMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAV----- 497 (797)
Q Consensus 423 ~~~l~~g~Pv~PMLA~~~~~i~~~l~k~~g~~~~~E~KyDG~R~qih~~~~g~V~ifSR~gkd~T~~yPel~~~l----- 497 (797)
.+.+++|.||+||||++.++..+.+..+.+.+|++|+||||+|||+|++ +|.|++|||+|+++|..||++.+..
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 4679999999999999998876665677788999999999999999995 7899999999999999999987643
Q ss_pred -HhhcCCCCCCeEEEEEEEEEecCCCcccChhhHHhhhcccCCccccccceEEEEeeeeecCCccccCCcHHHHHHHHHH
Q 003762 498 -SRLKKPSVRSFVLDCEIVAYDREKQKILPFQTLSTRARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYD 576 (797)
Q Consensus 498 -~~~~~~~v~~~ILDGElVa~d~~~g~~lpFq~L~~R~Rk~~~~~~~~~~v~~~vFDILylnG~~L~~~Pl~ERr~lL~~ 576 (797)
...+.....++|||||+|+||..++.+.+|+.++++.+... ......+++|++||||++||++++++||.+|+++|++
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 22233345899999999999987777899999987654221 0123568999999999999999999999999999999
Q ss_pred hhccCCCcEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEEeCCCCCCccCCCCCCCeEEEccccc
Q 003762 577 SFEEEPGFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLKKDYI 642 (797)
Q Consensus 577 l~~~~~~~i~~v~~~~~~~~eei~~~f~~ai~~g~EGlmvK~~~~ds~Y~pGkRs~~WlKlK~dY~ 642 (797)
++.+.++++++++...+++.+++.++|++++++|+||||+|++ +++|++|+|+.+|+|+|++|+
T Consensus 161 ~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~g~EGlv~K~~--~s~Y~~g~Rs~~wlK~K~~Y~ 224 (225)
T cd07903 161 IITPIPGRLEVVKRTEASTKEEIEEALNEAIDNREEGIVVKDL--DSKYKPGKRGGGWIKIKPEYL 224 (225)
T ss_pred hcCCCCCeEEEEEEEeCCCHHHHHHHHHHHHHcCCceEEEecC--CCCCccCCcCCCcEEechhhc
Confidence 9988778999999999999999999999999999999999999 999999999999999999996
No 21
>cd07901 Adenylation_DNA_ligase_Arch_LigB Adenylation domain of archaeal and bacterial LigB-like DNA ligases. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. Bacterial DNA ligases are divided into two broad classes: NAD-dependent and ATP-dependent. All bacterial species have a NAD-dependent DNA ligase (LigA). Some bacterial genomes contain multiple genes for DNA ligases that are predicted to use ATP as their cofactor, including Mycobacterium tuberculosis LigB, LigC, and LigD. This group is composed of archaeal DNA ligases and bacterial proteins similar to Mycobacterium tuberculosis LigB. Members of this group contain adeny
Probab=100.00 E-value=8.2e-45 Score=372.70 Aligned_cols=205 Identities=38% Similarity=0.591 Sum_probs=182.3
Q ss_pred CCCCCccccccccCChHHHHhhcCCCceEEEeecceEEEEEEEecCCeEEEEecCCCccCCCcchHHHHHHhhcCCCCCC
Q 003762 428 PGIPIGPMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAVSRLKKPSVRS 507 (797)
Q Consensus 428 ~g~Pv~PMLA~~~~~i~~~l~k~~g~~~~~E~KyDG~R~qih~~~~g~V~ifSR~gkd~T~~yPel~~~l~~~~~~~v~~ 507 (797)
||+|++||||++..++++++++. +.+|++|+||||+|||+|++ ++.|++|||+|+++|..||++.+++...+. ..+
T Consensus 1 ~~~p~~PmLA~~~~~~~~~~~~~-~~~~~~E~K~DG~R~~~~~~-~~~v~~~SR~~~~~t~~~pel~~~~~~~~~--~~~ 76 (207)
T cd07901 1 VGRPVRPMLAQRAPSVEEALIKE-GGEAAVEYKYDGIRVQIHKD-GDEVRIFSRRLEDITNALPEVVEAVRELVK--AED 76 (207)
T ss_pred CCCCCccccCCCCCCHHHHHHhc-CCcEEEEEeEcceeEEEEEe-CCEEEEEeCCCccccchhhHHHHHHHhcCC--CCC
Confidence 68999999999998888776665 45899999999999999995 679999999999999999999998887653 368
Q ss_pred eEEEEEEEEEecCCCcccChhhHHhhhcccCCcc--ccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCCCcE
Q 003762 508 FVLDCEIVAYDREKQKILPFQTLSTRARKNVSLS--DIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEPGFF 585 (797)
Q Consensus 508 ~ILDGElVa~d~~~g~~lpFq~L~~R~Rk~~~~~--~~~~~v~~~vFDILylnG~~L~~~Pl~ERr~lL~~l~~~~~~~i 585 (797)
||||||+|++|. +|.+.+|+.+++|.++..... ....+++|+|||||++||++++++||.+|+++|++++.+. +.+
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 999999999986 677789999999965432211 1246899999999999999999999999999999999875 678
Q ss_pred EEEeEEecCCHHHHHHHHHHHHHcCCceeEEEeCCCCCCccCCCCCCCeEEEccc
Q 003762 586 QFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLKKD 640 (797)
Q Consensus 586 ~~v~~~~~~~~eei~~~f~~ai~~g~EGlmvK~~~~ds~Y~pGkRs~~WlKlK~d 640 (797)
++++...+++.+++.++|++++++|+||||+|+. +|+|++|+|+.+|+|+|+|
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 8999988999999999999999999999999999 9999999999999999985
No 22
>cd07902 Adenylation_DNA_ligase_III Adenylation domain of DNA Ligase III. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three-step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. There are three classes of ATP-dependent DNA ligases in eukaryotic cells (I, III and IV). DNA ligase III is not found in lower eukaryotes and is present both in the nucleus and mitochondria. It has several isoforms; two splice forms, III-alpha and III-beta, differ in their carboxy-terminal sequences. DNA ligase III-beta is believed to play a role in homologous recombination during meiotic prophase. DNA ligase III-alpha interacts with X-ray Cross Complementing factor 1 (XRCC1) and functions in single nuc
Probab=100.00 E-value=9.8e-45 Score=373.89 Aligned_cols=208 Identities=31% Similarity=0.538 Sum_probs=185.6
Q ss_pred ccccCCCCCCccccccccCChHHHHhhcCCCceEEEeecceEEEEEEEecCCeEEEEecCCCccCC-CcchHHHHHHhhc
Q 003762 423 TCSFTPGIPIGPMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTG-KFPDVVLAVSRLK 501 (797)
Q Consensus 423 ~~~l~~g~Pv~PMLA~~~~~i~~~l~k~~g~~~~~E~KyDG~R~qih~~~~g~V~ifSR~gkd~T~-~yPel~~~l~~~~ 501 (797)
.+.+++|+|++||||++.++++++++++. ..|++|+||||+|||+|++ +|.|++|||||+++|. .||++.+.+.+.+
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 46799999999999999988887777653 3699999999999999995 6899999999999996 6899988777766
Q ss_pred CCCCCCeEEEEEEEEEecCCCcccChhhHHhhhcccCCccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccC
Q 003762 502 KPSVRSFVLDCEIVAYDREKQKILPFQTLSTRARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEE 581 (797)
Q Consensus 502 ~~~v~~~ILDGElVa~d~~~g~~lpFq~L~~R~Rk~~~~~~~~~~v~~~vFDILylnG~~L~~~Pl~ERr~lL~~l~~~~ 581 (797)
.. ..+||||||+|+||.++|++++|+.++.|.+... ...+++|++||||++||++++++||.+|+++|++++.+.
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 5799999999999988888889999988765321 235799999999999999999999999999999999887
Q ss_pred CCcEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEEeCCCCCCccCCCCCCCeEEEcccc
Q 003762 582 PGFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLKKDY 641 (797)
Q Consensus 582 ~~~i~~v~~~~~~~~eei~~~f~~ai~~g~EGlmvK~~~~ds~Y~pGkRs~~WlKlK~dY 641 (797)
++++.+++...+.+.+++.++|++++++|+||||+|++ +|+|++|+| +|+|+|+||
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 77889999888999999999999999999999999999 999999988 699999998
No 23
>cd07897 Adenylation_DNA_ligase_Bac1 Adenylation domain of putative bacterial ATP-dependent DNA ligases. Bacterial DNA ligases are divided into two broad classes: NAD-dependent and ATP-dependent. All bacterial species have a NAD-dependent DNA ligase (LigA). Some bacterial genomes contain multiple genes for DNA ligases that are predicted to use ATP as their cofactor, including Mycobacterium tuberculosis LigB, LigC, and LigD. This group is composed of predicted bacterial ATP-dependent DNA ligases. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three-step reaction mechanism. The adenylation and C-terminal oligonucleotide/oligosaccharide binding (OB)-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family, including this group. The adenylation domain binds ATP and contains many of the active site residues.
Probab=100.00 E-value=1.9e-43 Score=362.74 Aligned_cols=201 Identities=28% Similarity=0.426 Sum_probs=176.0
Q ss_pred CCCccccccccCChHHHHhhcCCCceEEEeecceEEEEEEEecCCeEEEEecCCCccCCCcchHHHHHHhhcCCCCCCeE
Q 003762 430 IPIGPMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAVSRLKKPSVRSFV 509 (797)
Q Consensus 430 ~Pv~PMLA~~~~~i~~~l~k~~g~~~~~E~KyDG~R~qih~~~~g~V~ifSR~gkd~T~~yPel~~~l~~~~~~~v~~~I 509 (797)
+|+.||||+++.++.+.+. ...+|++|+||||+|||+|++ ++.|++|||||+++|..||++.+++... + .+||
T Consensus 3 ~~~~pmLA~~~~~~~~~~~--~~~~~~~E~K~DG~R~~~~~~-~~~v~l~SR~g~~~t~~~p~l~~~~~~l-~---~~~i 75 (207)
T cd07897 3 RPYPFMLAHPLEDDPEDLG--DPSDWQAEWKWDGIRGQLIRR-GGEVFLWSRGEELITGSFPELLAAAEAL-P---DGTV 75 (207)
T ss_pred CCCCceeCCcCCCchhhhc--CcccEEEEEeEceEEEEEEEc-CCEEEEEeCCCCcccccchHHHHHHHhC-C---CCeE
Confidence 7999999999988766542 345899999999999999994 7899999999999999999999876543 2 5899
Q ss_pred EEEEEEEEecCCCcccChhhHHhhhcccCCcc--ccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccC-CCcEE
Q 003762 510 LDCEIVAYDREKQKILPFQTLSTRARKNVSLS--DIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEE-PGFFQ 586 (797)
Q Consensus 510 LDGElVa~d~~~g~~lpFq~L~~R~Rk~~~~~--~~~~~v~~~vFDILylnG~~L~~~Pl~ERr~lL~~l~~~~-~~~i~ 586 (797)
||||+|+||. +...+|+.+++|.++..... ....+++|++|||||+||+++++.||.+|+++|++++.+. .+++.
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 45789999999965432211 1246899999999999999999999999999999999876 46788
Q ss_pred EEeEEecCCHHHHHHHHHHHHHcCCceeEEEeCCCCCCccCCCCCCCeEEEcccc
Q 003762 587 FATTLTSIDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLKKDY 641 (797)
Q Consensus 587 ~v~~~~~~~~eei~~~f~~ai~~g~EGlmvK~~~~ds~Y~pGkRs~~WlKlK~dY 641 (797)
+++...+++.+++.++|++++++|+||||+|++ +|+|++|+|+.+|+|+|+|-
T Consensus 154 ~~~~~~~~~~~~~~~~~~~~~~~g~EGiv~K~~--~s~Y~~Grr~~~W~K~K~d~ 206 (207)
T cd07897 154 LSPLIAFADWEELAALRAQSRERGAEGLMLKRR--DSPYLVGRKKGDWWKWKIDP 206 (207)
T ss_pred ecceEecCCHHHHHHHHHHHHHcCCeEEEEeCC--CCCcCCCCcCCCeeEeCCCC
Confidence 999999999999999999999999999999999 99999999999999999973
No 24
>cd08039 Adenylation_DNA_ligase_Fungal Adenylation domain of uncharacterized fungal ATP-dependent DNA ligase-like proteins. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. This group is composed of uncharacterized fungal proteins with similarity to ATP-dependent DNA ligases. ATP dependent DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains including a DNA-binding domain, an adenylation (nucleotidyltransferase (NTase)) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The adenylation domain binds ATP and contains many of the active-site res
Probab=100.00 E-value=5.1e-43 Score=365.73 Aligned_cols=199 Identities=23% Similarity=0.372 Sum_probs=170.7
Q ss_pred CChHHHHhhcCCCceEEEeecceEEEEEEEec---CCeEEEEecCCCccCCCcchHHHHHHhhcCC------CCCCeEEE
Q 003762 441 KGVSEIVNKFQDMEFTCEYKYDGERAQIHYLE---DGSVEIYSRNAERNTGKFPDVVLAVSRLKKP------SVRSFVLD 511 (797)
Q Consensus 441 ~~i~~~l~k~~g~~~~~E~KyDG~R~qih~~~---~g~V~ifSR~gkd~T~~yPel~~~l~~~~~~------~v~~~ILD 511 (797)
+++..+++.+++.+|++|+||||+|||+|+.. ++.|++|||||+++|+.||++.+.+...+.. ..++||||
T Consensus 10 ~~~~~~~~~~~~~~~~~E~K~DG~R~qih~~~~~~~~~v~lfSR~~~d~T~~~pel~~~~~~~~~~~~~~~~~~~~~ILD 89 (235)
T cd08039 10 RSIKHCCKMIGSRRMWVETKYDGEYCQIHIDLSKDSSPIRIFSKSGKDSTADRAGVHSIIRKALRIGKPGCKFSKNCILE 89 (235)
T ss_pred cCHHHHHHHhCCCcEEEEEeecceEEEEEEecccCCCEEEEEeCCCCcccccchhHHHHHHHHhhccccccCCCccEEEE
Confidence 45777888899999999999999999999851 6799999999999999999998877665421 24789999
Q ss_pred EEEEEEecCCCcccChhhHHhhhcccC--------CccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCCC
Q 003762 512 CEIVAYDREKQKILPFQTLSTRARKNV--------SLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEPG 583 (797)
Q Consensus 512 GElVa~d~~~g~~lpFq~L~~R~Rk~~--------~~~~~~~~v~~~vFDILylnG~~L~~~Pl~ERr~lL~~l~~~~~~ 583 (797)
||||+||..+|++.+|+.|++|.+... .......++||++|||||+||+++++.||.+||++|++++.+.++
T Consensus 90 GEiVv~d~~~g~~~~F~~L~~~~~~~~~~~~~~~~~~~~~~~~v~~~vFDlL~lnG~~l~~~pl~eRr~~L~~l~~~~~~ 169 (235)
T cd08039 90 GEMVVWSDRQGKIDPFHKIRKHVERSGSFIGTDNDSPPHEYEHLMIVFFDVLLLDDESLLSKPYSERRDLLESLVHVIPG 169 (235)
T ss_pred eEEEEEECCCCccCCHHHHHhhcccccchhccccccccccccceEEEEEEEEEECChhhhcCCHHHHHHHHHHhcccCCC
Confidence 999999988888899999998864221 111235789999999999999999999999999999999988888
Q ss_pred cEEEEeEEec-----CCHHHHHHHHHHHHHcCCceeEEEeCCCCCCccCCCC-----CCCeEEEcccc
Q 003762 584 FFQFATTLTS-----IDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKR-----SLNWLKLKKDY 641 (797)
Q Consensus 584 ~i~~v~~~~~-----~~~eei~~~f~~ai~~g~EGlmvK~~~~ds~Y~pGkR-----s~~WlKlK~dY 641 (797)
++.+++...+ .+.++++++|++++++|+||||+|++ +|+|.||++ +..|+|+|+||
T Consensus 170 ~~~~~~~~~i~~~~~~~~~~l~~~~~~a~~~g~EGIv~K~~--~S~Y~pgr~~~~~r~~~WlKlK~dY 235 (235)
T cd08039 170 YAGLSERFPIDFSRSSGYERLRQIFARAIAERWEGLVLKGD--EEPYFDLFLEQGSFSGCWIKLKKDY 235 (235)
T ss_pred cEEEEEEEeecccCCCCHHHHHHHHHHHHHcCCceEEEecC--CCCcccCcccccccCCCeEEeCCCC
Confidence 8888776553 37889999999999999999999999 999999753 58999999998
No 25
>cd07898 Adenylation_DNA_ligase Adenylation domain of ATP-dependent DNA Ligases. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. Some organisms express a variety of different ligases which appear to be targeted to specific functions. ATP-dependent DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains including a DNA-binding domain, an adenylation (nucleotidyltransferase (NTase)) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The adenylation domain binds ATP and contains many of the active-site residues. The adenylation and C-terminal OB-f
Probab=100.00 E-value=1.3e-42 Score=354.73 Aligned_cols=199 Identities=40% Similarity=0.619 Sum_probs=175.7
Q ss_pred CccccccccCChHHHHhhcCCCceEEEeecceEEEEEEEecCCeEEEEecCCCccCCCcchHHHHHHhhcCCCCCCeEEE
Q 003762 432 IGPMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAVSRLKKPSVRSFVLD 511 (797)
Q Consensus 432 v~PMLA~~~~~i~~~l~k~~g~~~~~E~KyDG~R~qih~~~~g~V~ifSR~gkd~T~~yPel~~~l~~~~~~~v~~~ILD 511 (797)
|+||||+++++++++ .++.+.+|++|+||||+|||+|++ ++.|++|||+|+++|..||++.+++... .++||||
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 6899999999999999999998876642 2689999
Q ss_pred EEEEEEecCCCcccChhhHHhhhcccCCcc--ccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCCCcEEEEe
Q 003762 512 CEIVAYDREKQKILPFQTLSTRARKNVSLS--DIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEPGFFQFAT 589 (797)
Q Consensus 512 GElVa~d~~~g~~lpFq~L~~R~Rk~~~~~--~~~~~v~~~vFDILylnG~~L~~~Pl~ERr~lL~~l~~~~~~~i~~v~ 589 (797)
||||+||... ..+|+.+++|.++..... ....+++|+|||||++||++++++||.||+++|++++.+.++.+.+++
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 9999998543 368999998865432211 235779999999999999999999999999999999988878999999
Q ss_pred EEecCCHHHHHHHHHHHHHcCCceeEEEeCCCCCCccCCCCCCCeEEEccc
Q 003762 590 TLTSIDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLKKD 640 (797)
Q Consensus 590 ~~~~~~~eei~~~f~~ai~~g~EGlmvK~~~~ds~Y~pGkRs~~WlKlK~d 640 (797)
...+++.+++.++|++++++|+||||+|++ +|+|++|+|+.+|+|+|+|
T Consensus 153 ~~~~~~~~~~~~~~~~~~~~g~EGim~K~~--~s~Y~~g~Rs~~wlK~K~~ 201 (201)
T cd07898 153 ALPVESAEELEAAFARARARGNEGLMLKDP--DSPYEPGRRGLAWLKLKKE 201 (201)
T ss_pred eEEcCCHHHHHHHHHHHHHcCCceEEEeCC--CCCcCCCCcCCCcEEeCCC
Confidence 999999999999999999999999999999 9999999999999999985
No 26
>PF01068 DNA_ligase_A_M: ATP dependent DNA ligase domain; InterPro: IPR012310 DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA fragments by catalysing the formation of an internucleotide ester bond between phosphate and deoxyribose. It is active during DNA replication, DNA repair and DNA recombination. There are two forms of DNA ligase, one requires ATP (6.5.1.1 from EC), the other NAD (6.5.1.2 from EC), the latter being restricted to eubacteria. Eukaryotic, archaebacterial, viral and some eubacterial DNA ligases are ATP-dependent. The first step in the ligation reaction is the formation of a covalent enzyme-AMP complex. The co-factor ATP is cleaved to pyrophosphate and AMP, with the AMP being covalently joined to a highly conserved lysine residue in the active site of the ligase. The activated AMP residue is then transferred to the 5'phosphate of the nick, before the nick is sealed by phosphodiester-bond formation and AMP elimination [,]. Vertebrate cells encode three well-characterised DNA ligases (DNA ligases I, III and IV), all of which are related in structure and sequence. With the exception of the atypically small PBCV-1 viral enzyme, two regions of primary sequence are common to all members of the family. The catalytic region comprises six conserved sequence motifs (I, III, IIIa, IV, V-VI), motif I includes the lysine residue that is adenylated in the first step of the ligation reaction. The function of the second, less well-conserved region is unknown. When folded, each protein comprises of two distinct sub-domains: a large amino-terminal sub-domain ('domain 1') and a smaller carboxy-terminal sub-domain ('domain 2'). The ATP-binding site of the enzyme lies in the cleft between the two sub-domains. Domain 1 consists of two antiparallel beta sheets flanked by alpha helices, whereas domain 2 consists of a five-stranded beta barrel and a single alpha helix, which form the oligonucleotide-binding fold [, ]. This domain belongs to a more diverse superfamily, including catalytic domain of the mRNA capping enzyme (IPR001339 from INTERPRO) and NAD-dependent DNA ligase (IPR001679 from INTERPRO) []. ; GO: 0003910 DNA ligase (ATP) activity, 0005524 ATP binding, 0006281 DNA repair, 0006310 DNA recombination; PDB: 3RR5_A 1X9N_A 2CFM_A 3QWU_B 3GDE_A 2Q2U_C 2Q2T_A 1FVI_A 1P8L_A 2VUG_A ....
Probab=100.00 E-value=6.5e-42 Score=347.56 Aligned_cols=201 Identities=36% Similarity=0.607 Sum_probs=180.1
Q ss_pred cccccccCChHHHHhhcCCCceEEEeecceEEEEEEEecCCeEEEEecCCCccCCCcchHHHHHHhhcCCCCCCeEEEEE
Q 003762 434 PMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAVSRLKKPSVRSFVLDCE 513 (797)
Q Consensus 434 PMLA~~~~~i~~~l~k~~g~~~~~E~KyDG~R~qih~~~~g~V~ifSR~gkd~T~~yPel~~~l~~~~~~~v~~~ILDGE 513 (797)
||||++.++++++++++ +.+|++|+||||+|||||+ .+|.|++|||+|+++|..||++.+++...+..+..++|||||
T Consensus 1 PmLA~~~~~~~~~~~~~-~~~~~~e~K~DG~R~~i~~-~~~~v~~~SR~g~~~~~~~~~l~~~l~~~~~~~~~~~vLDGE 78 (202)
T PF01068_consen 1 PMLAQPFDSIEKALKKF-GGPWYVEPKYDGVRCQIHK-DGGGVRLFSRNGKDITSQFPELAEALRELLFPDGPDFVLDGE 78 (202)
T ss_dssp -EEEEEESSHHHHHHHT-TSCEEEEEEESSEEEEEEE-ETTEEEEEETTSSB-GGGHHHHHHHHHHHBCTSCTEEEEEEE
T ss_pred CcCCccccCHHHHHHhc-CCCeEEEEeEeeEEeeeee-ccccceeecccccchhhHHHHHHHHHHHHhcCCCCceEEEEE
Confidence 89999999999999988 6689999999999999998 588999999999999999999999998887665678999999
Q ss_pred EEEEecCCCcccChhhHHhhhcc-cCCccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCCCcEEEEeEEe
Q 003762 514 IVAYDREKQKILPFQTLSTRARK-NVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEPGFFQFATTLT 592 (797)
Q Consensus 514 lVa~d~~~g~~lpFq~L~~R~Rk-~~~~~~~~~~v~~~vFDILylnG~~L~~~Pl~ERr~lL~~l~~~~~~~i~~v~~~~ 592 (797)
+|+||..++...||+.++++.++ .........+++|++||||++||.++++.||.||+++|++++....+.+.+++...
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 99999998889999999999843 32221126799999999999999999999999999999999966678899999999
Q ss_pred cCCHHHHHHHHHHHHHcCCceeEEEeCCCCCCccCCCCCCCeEEEc
Q 003762 593 SIDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLK 638 (797)
Q Consensus 593 ~~~~eei~~~f~~ai~~g~EGlmvK~~~~ds~Y~pGkRs~~WlKlK 638 (797)
+++.++++++|++++++|+||+|+|++ +++|++|+|+.+|+|+|
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=9.7e-41 Score=339.39 Aligned_cols=190 Identities=28% Similarity=0.393 Sum_probs=164.0
Q ss_pred CccccccccCChHHHHhhcCCCceEEEeecceEEEEEEEecCCeEEEEecCCCccCCCcchHHHHHHhhcCCCCCCeEEE
Q 003762 432 IGPMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAVSRLKKPSVRSFVLD 511 (797)
Q Consensus 432 v~PMLA~~~~~i~~~l~k~~g~~~~~E~KyDG~R~qih~~~~g~V~ifSR~gkd~T~~yPel~~~l~~~~~~~v~~~ILD 511 (797)
|+||||..+.+++ .+.+|++|+||||+|||+|++ ++.|++|||||+++|+.||++.+++...+. .++|||
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 679999999999999999999998877543 589999
Q ss_pred EEEEEEecCCCcccChhhHHhhhcccCC---ccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCCCcEEEE
Q 003762 512 CEIVAYDREKQKILPFQTLSTRARKNVS---LSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEPGFFQFA 588 (797)
Q Consensus 512 GElVa~d~~~g~~lpFq~L~~R~Rk~~~---~~~~~~~v~~~vFDILylnG~~L~~~Pl~ERr~lL~~l~~~~~~~i~~v 588 (797)
||+|++|.. . .+|+.+++|.++... ......+++|++|||||+||+++++.||.+|+++|++++.+..+.++++
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 2 499999999754321 1223578999999999999999999999999999999998766778888
Q ss_pred eEEecCCHHHHHHHHHHHHHcCCceeEEEeCCCCCCccCCCCCCCeEEEccc
Q 003762 589 TTLTSIDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLKKD 640 (797)
Q Consensus 589 ~~~~~~~~eei~~~f~~ai~~g~EGlmvK~~~~ds~Y~pGkRs~~WlKlK~d 640 (797)
+. +.+.+++.++|++++++|+||||+|++ +|+|++|+| +|+|+|+.
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 89999984
No 28
>cd07906 Adenylation_DNA_ligase_LigD_LigC Adenylation domain of Mycobacterium tuberculosis LigD and LigC-like ATP-dependent DNA ligases. Bacterial DNA ligases are divided into two broad classes: NAD-dependent and ATP-dependent. All bacterial species have a NAD-dependent DNA ligase (LigA). Some bacterial genomes contain multiple genes for DNA ligases that are predicted to use ATP as their cofactor, including Mycobacterium tuberculosis LigB, LigC, and LigD. This group is composed of ATP-dependent DNA ligases similar to Mycobacterium tuberculosis LigC. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. Members of this group contain adenylation and C-terminal oligonucleotide/oligosaccharide binding (OB)-fold domains, comprising a catalytic cor
Probab=100.00 E-value=8.5e-40 Score=331.15 Aligned_cols=189 Identities=33% Similarity=0.469 Sum_probs=164.5
Q ss_pred CccccccccCChHHHHhhcCCCceEEEeecceEEEEEEEecCCeEEEEecCCCccCCCcchHHHHHHhhcCCCCCCeEEE
Q 003762 432 IGPMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAVSRLKKPSVRSFVLD 511 (797)
Q Consensus 432 v~PMLA~~~~~i~~~l~k~~g~~~~~E~KyDG~R~qih~~~~g~V~ifSR~gkd~T~~yPel~~~l~~~~~~~v~~~ILD 511 (797)
++||||++..++. .+.+|++|+||||+|||+|++ ++.|++|||+|+++|+.||++..++.++ ...++|||
T Consensus 1 i~pmLa~~~~~~~------~~~~~~~e~K~DG~R~~i~~~-~~~v~~~SR~g~~~t~~~p~l~~~~~~~---~~~~~iLD 70 (190)
T cd07906 1 IEPMLATLVDEPP------DGEDWLYEIKWDGYRALARVD-GGRVRLYSRNGLDWTARFPELAEALAAL---PVRDAVLD 70 (190)
T ss_pred CCCeECCcCCCCC------CCCCeEEEEeEceEEEEEEEE-CCEEEEEcCCCCcchhhhHHHHHHHHhc---CCCCEEEE
Confidence 5899999988652 356899999999999999996 6799999999999999999998877664 34789999
Q ss_pred EEEEEEecCCCcccChhhHHhhhcccCCccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCCCcEEEEeEE
Q 003762 512 CEIVAYDREKQKILPFQTLSTRARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEPGFFQFATTL 591 (797)
Q Consensus 512 GElVa~d~~~g~~lpFq~L~~R~Rk~~~~~~~~~~v~~~vFDILylnG~~L~~~Pl~ERr~lL~~l~~~~~~~i~~v~~~ 591 (797)
||+|+||..+ ..+|+.+++|.++.. ......+++|+|||||++||++++++||.||+++|++++.+.++.+++++..
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 369999999986543 2234578999999999999999999999999999999998877788888776
Q ss_pred ecCCHHHHHHHHHHHHHcCCceeEEEeCCCCCCccCCCCCCCeEEEcc
Q 003762 592 TSIDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLKK 639 (797)
Q Consensus 592 ~~~~~eei~~~f~~ai~~g~EGlmvK~~~~ds~Y~pGkRs~~WlKlK~ 639 (797)
.. +.+++|++++++|+||||+|++ +|+|++|+|+.+|+|+|+
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=5.5e-35 Score=292.25 Aligned_cols=176 Identities=35% Similarity=0.577 Sum_probs=146.1
Q ss_pred cchHHHHHHHHHHHhccchHHHHHHHHHHHHhhhcCCCCchHHHHHHHhCccCCCccccccCCChHHHHHHHHHHhCCCH
Q 003762 191 VPFIFLSLVFDMISNETGRILITDIVCNMLRTVMETTPEDLVPVVYLAANKIAPAHEGLELGIGDASIIKALAEACGRTE 270 (797)
Q Consensus 191 ~~F~~la~~~e~I~~tssR~~k~~iL~~~fr~~i~~~p~dl~~~vyL~~~~l~P~~e~~elGIge~~L~kal~~a~G~s~ 270 (797)
|+|++||++|++|+++++|++|+++|++||+.+. +.++.+++|+++|+|+|+|++++|||+++.|++++++++|+++
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 HHHHHHHHhcCCHHHHHhhccccCC-CCCCCCCCCHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHhcCCChHHHHHHH
Q 003762 271 SHVKKQYQEMGDLGLVAKASRSSQS-MMRKPDPLTITKVFDTFRLIAKEAGKDSQEKKKNRIKALLVAATDCEPQYLIRL 349 (797)
Q Consensus 271 ~~ik~~y~~~GDlg~vA~~~r~~q~-~l~~~~~LTI~eV~~~L~kIA~~~G~~s~~~K~~~L~~LL~~~t~~E~k~LiRi 349 (797)
+.+++.|+++||+|++|+.+...+. ....+.+|||.+||+.|++||..+|.+|++.|+++|..|+++|++.|++||+||
T Consensus 78 ~~~~~~~~~~GD~g~~~~~~~~~~~~~~~~~~~lTi~~V~~~L~~la~~~g~~s~~~k~~~l~~ll~~~s~~E~k~i~Ri 157 (177)
T PF04675_consen 78 KSIDESYKKVGDLGEVAEEVLQKRKSETSKPSPLTISEVNETLDELAAASGKGSQDEKIDILKELLRRCSPEEAKWIVRI 157 (177)
T ss_dssp HHHHHHHHHHS-HHHHHHHHHHHHTTTS--SS--BHHHHHHHHHHHHH--STTHHHHHHHHHHHHHTTS-HHHHHHHHHH
T ss_pred HHHHHHHHhcCcHHHHHHHHHhhccccccCCCCCCHHHHHHHHHHHHHhhCccchHHHHHHHHHHHHhCCHHHHHHHHHH
Confidence 9999999999999999998765544 333478999999999999999999999999999999999999999999999999
Q ss_pred HhhhccCcccHHHHHHHHHH
Q 003762 350 LQSKLRIGLAEQTLLAALGQ 369 (797)
Q Consensus 350 IlkdLRiGi~e~tvl~Ala~ 369 (797)
|+|+||||+++++|+.|||+
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=2.2e-33 Score=280.21 Aligned_cols=173 Identities=24% Similarity=0.253 Sum_probs=145.6
Q ss_pred CccccccccCChHHHHhhcCCCceEEEeecceEEEEEEEecCCeEEEEecCCCccCCCcchHHHHHHhhcCCCCCCeEEE
Q 003762 432 IGPMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAVSRLKKPSVRSFVLD 511 (797)
Q Consensus 432 v~PMLA~~~~~i~~~l~k~~g~~~~~E~KyDG~R~qih~~~~g~V~ifSR~gkd~T~~yPel~~~l~~~~~~~v~~~ILD 511 (797)
++||||++.....+ +.+|++|+||||+|||+|. . ++|||+|+++|.. + .+...+ .++|||
T Consensus 1 ~~pmla~~~~~~~~------~~~~~~e~K~DG~R~~~~~----~-~~~SR~g~~~t~~-~----~~~~~l----~~~ilD 60 (174)
T cd07896 1 PELLLAKTYDEGED------ISGYLVSEKLDGVRAYWDG----K-QLLSRSGKPIAAP-A----WFTAGL----PPFPLD 60 (174)
T ss_pred CccccccccccCCC------hHHeeechhhceEEEEEec----c-EEEecCCcCCCCC-H----HHHhhC----CCCccC
Confidence 47999998775432 3489999999999999862 2 9999999999975 2 222222 459999
Q ss_pred EEEEEEecCCCcccChhhHHhhhcccCCccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccC-CCcEEEEeE
Q 003762 512 CEIVAYDREKQKILPFQTLSTRARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEE-PGFFQFATT 590 (797)
Q Consensus 512 GElVa~d~~~g~~lpFq~L~~R~Rk~~~~~~~~~~v~~~vFDILylnG~~L~~~Pl~ERr~lL~~l~~~~-~~~i~~v~~ 590 (797)
||+|+++ .+|+.+++|.++.........+++|++||||+ .+.||.+|+++|++++.+. .+.+++++.
T Consensus 61 GElv~~~------~~f~~l~~~~~~~~~~~~~~~~~~f~vFDil~------~~~p~~eR~~~L~~~i~~~~~~~~~~~~~ 128 (174)
T cd07896 61 GELWIGR------GQFEQTSSIVRSKKPDDEDWRKVKFMVFDLPS------AKGPFEERLERLKNLLEKIPNPHIKIVPQ 128 (174)
T ss_pred ceEEcCC------CCHHHHHHHHhcCCCChhhcccceEEEEeCCC------CCCCHHHHHHHHHHHHHhCCCCcEEEEee
Confidence 9999985 39999999987654332345789999999998 6789999999999999876 467899999
Q ss_pred EecCCHHHHHHHHHHHHHcCCceeEEEeCCCCCCccCCCCCCCeEEEcc
Q 003762 591 LTSIDLDEIQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLKK 639 (797)
Q Consensus 591 ~~~~~~eei~~~f~~ai~~g~EGlmvK~~~~ds~Y~pGkRs~~WlKlK~ 639 (797)
..+.+.+++.+++++++++|+||+|+|+. +++|++| |+.+|+|+||
T Consensus 129 ~~~~~~~~i~~~~~~~~~~g~EGlv~K~~--ds~Y~~g-R~~~wlK~Kp 174 (174)
T cd07896 129 IPVKSNEALDQYLDEVVAAGGEGLMLRRP--DAPYETG-RSDNLLKLKP 174 (174)
T ss_pred eeeCCHHHHHHHHHHHHhcCCCeEEEecC--CCcccCC-cCCCceeeCC
Confidence 99999999999999999999999999999 9999987 7899999997
No 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=3.4e-31 Score=266.16 Aligned_cols=175 Identities=28% Similarity=0.290 Sum_probs=141.0
Q ss_pred cccccccCChHHHHhhcCCCceEEEeecceEEEEEEEecCCeEEEEecCCCccCCCcchHHHHHHhhcCCCCCCeEEEEE
Q 003762 434 PMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAVSRLKKPSVRSFVLDCE 513 (797)
Q Consensus 434 PMLA~~~~~i~~~l~k~~g~~~~~E~KyDG~R~qih~~~~g~V~ifSR~gkd~T~~yPel~~~l~~~~~~~v~~~ILDGE 513 (797)
|||+.......+. .+.+.+|++|+||||+|+|+|++ +|.+++|||+|+++|..||++... ... ....++|||||
T Consensus 2 ~~~~~~~~~~~~~--~~~~~~~~~e~K~DG~R~~~~~~-~~~v~~~sR~g~~~~~~~~~~~~~--~~~-~~~~~~ilDGE 75 (182)
T cd06846 2 QLLNPILEEALSE--YDEQDEYYVQEKYDGKRALIVAL-NGGVFAISRTGLEVPLPSILIPGR--ELL-TLKPGFILDGE 75 (182)
T ss_pred CccchhhhHHHhh--ccccCcEEEEEccCceEEEEEEc-CCeEEEEeCCCCEEecccccccch--HHh-ccCCCeeEEEE
Confidence 7888876655332 35567899999999999999995 689999999999999999987541 111 12368999999
Q ss_pred EEEEecCCCcccChhhHHhhhcccCCccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCCC--cEEEEe--
Q 003762 514 IVAYDREKQKILPFQTLSTRARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEPG--FFQFAT-- 589 (797)
Q Consensus 514 lVa~d~~~g~~lpFq~L~~R~Rk~~~~~~~~~~v~~~vFDILylnG~~L~~~Pl~ERr~lL~~l~~~~~~--~i~~v~-- 589 (797)
+|+++.. + ...+++|++||||++||.+++++||.+|+++|++++.+.++ .+.++.
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 13578999999999999999999999999999999987642 344443
Q ss_pred EEecCCHHHHHHHHHHHHHcCCceeEEEeCCCCCCc--cCCCCCCCeEEEcc
Q 003762 590 TLTSIDLDEIQKFLDAAVDASCEGLIIKTMDRDATY--EPSKRSLNWLKLKK 639 (797)
Q Consensus 590 ~~~~~~~eei~~~f~~ai~~g~EGlmvK~~~~ds~Y--~pGkRs~~WlKlK~ 639 (797)
...+.+ +++.++|++++++|+||||+|++ +++| .+| |+..|+|+||
T Consensus 135 ~~~~~~-~~~~~~~~~~~~~g~EGvi~K~~--~s~Y~~~~g-r~~~wlK~Kp 182 (182)
T cd06846 135 NAPSYD-ETLDDLLEKLKKKGKEGLVFKHP--DAPYKGRPG-SSGNQLKLKP 182 (182)
T ss_pred cccccc-hHHHHHHHHhhhcCCceEEEEcC--CCCccccCC-CCCceEeecC
Confidence 333333 33999999999999999999999 9999 777 8999999997
No 32
>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=99.97 E-value=1.7e-31 Score=257.94 Aligned_cols=128 Identities=27% Similarity=0.540 Sum_probs=115.7
Q ss_pred cCCccceEEEeEEeCCCCcCCccceEEEEEecCCCceEEEeccccCCCCHHHHHHHHHhhccccCCC----CCCCcccCC
Q 003762 645 IGDSLDLVPIAAFHGRGKRTGVYGAFLLACYDSNNEEFQSICKIGTGFSEAMLEERSSSLRSKVIPK----PRPYYRFAD 720 (797)
Q Consensus 645 ~~dtlDlvVIGa~~G~Gkr~g~~gsfllg~~d~~~g~~~~vgkVGTGfSd~~l~~l~~~l~~~~~~~----p~~~~~~~~ 720 (797)
|+|++||||||+++|+|+|+|++|+||||+||+++++|+++||||||||++++++|.++|+++++.. ++.|+.++.
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 4689999999999999999999999999999987789999999999999999999999999987654 345666666
Q ss_pred CCCCceEec-c--ceEEEEEeeeeecCCcccccccccCCCCCceeeeceEeeEeC--CcccccCC
Q 003762 721 TISPDVWFE-P--TEVWEVKAADLTISPVHRAAIGVVDPDKVFTVRFSVLAHLSF--PLLFCLGN 780 (797)
Q Consensus 721 ~~~pdvw~e-P--~~V~EV~~~eit~S~~~~aa~g~v~~~~G~sLRFPRf~riR~--~~~~~~~~ 780 (797)
..+|||||+ | ..||||+|+|||.||+|.| .|+|||||||+|+|. +|++|.+.
T Consensus 81 ~~~Pdv~~~~P~~s~V~EV~~aeit~S~~~~a--------~G~tLRFPr~~~iR~DK~~~d~~t~ 137 (139)
T cd07967 81 SLVPDFIVKDPKKAPVWEITGAEFSKSEAHTA--------DGISIRFPRVTRIRDDKDWKTATSL 137 (139)
T ss_pred CCCCCEEEeCCCccEEEEEEeeeEEecCcccc--------cCEEEEccEEEEEeCCCCHHHCccc
Confidence 678999994 8 5899999999999999986 389999999999999 99999865
No 33
>cd07969 OBF_DNA_ligase_I The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase I is a DNA-binding module that is part of the catalytic core unit. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriohages, eukarya, archaea and bacteria. There are three classes of ATP-dependent DNA ligases in eukaryotic cells (I, III and IV). This group is composed of eukaryotic DNA ligase I, Sulfolobus solfataricus DNA ligase and similar proteins. DNA ligase I is required for the ligation of Okazaki fragments during lagging-strand DNA synthesis and for base excision repair (BER). ATP dependent DNA ligases have a highly modular architecture consist
Probab=99.96 E-value=7.1e-29 Score=241.29 Aligned_cols=133 Identities=59% Similarity=0.980 Sum_probs=120.2
Q ss_pred CCccceEEEeEEeCCCCcCCccceEEEEEecCCCceEEEeccccCCCCHHHHHHHHHhhccccCCCCCCCcccCCCCCCc
Q 003762 646 GDSLDLVPIAAFHGRGKRTGVYGAFLLACYDSNNEEFQSICKIGTGFSEAMLEERSSSLRSKVIPKPRPYYRFADTISPD 725 (797)
Q Consensus 646 ~dtlDlvVIGa~~G~Gkr~g~~gsfllg~~d~~~g~~~~vgkVGTGfSd~~l~~l~~~l~~~~~~~p~~~~~~~~~~~pd 725 (797)
+||+|+||||+++|+|++.+.+|+|+||+||+++++|++|||||||||++++++|.++|.+++++.++... ....+|+
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 47999999999999999999999999999997767999999999999999999999999999887654322 1224799
Q ss_pred eEeccceEEEEEeeeeecCCcccccccccCCCCCceeeeceEeeEeC--CcccccCC
Q 003762 726 VWFEPTEVWEVKAADLTISPVHRAAIGVVDPDKVFTVRFSVLAHLSF--PLLFCLGN 780 (797)
Q Consensus 726 vw~eP~~V~EV~~~eit~S~~~~aa~g~v~~~~G~sLRFPRf~riR~--~~~~~~~~ 780 (797)
+||+|.+||||+|+++|.|++|+++.|++..+.|++||||||+++|. +|++|...
T Consensus 79 vWv~P~lV~EV~~~e~t~s~~~~~~~~~~~~~~g~~LRfPr~~~~R~Dk~~~~~~~~ 135 (144)
T cd07969 79 VWFEPKEVWEVKAADLTLSPVHTAAIGLVDEEKGISLRFPRFIRVRDDKKPEDATTS 135 (144)
T ss_pred EEEeeeEEEEEEEeEeecCcceeccccccccCCceEEEeeEEEEeeCCCChHHCCCH
Confidence 99999999999999999999999999998878899999999999999 89999765
No 34
>cd07893 OBF_DNA_ligase The Oligonucleotide/oligosaccharide binding (OB)-fold domain is a DNA-binding module that is part of the catalytic core unit of ATP dependent DNA ligases. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP dependent DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains including a DNA-binding domain, an adenylation (nucleotidyltransferase (NTase)) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The adenylation and C-terminal OB-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The catalytic core unit contains six conserved sequence motifs (I, III, IIIa, IV, V and V
Probab=99.96 E-value=9.9e-29 Score=236.14 Aligned_cols=127 Identities=39% Similarity=0.659 Sum_probs=114.9
Q ss_pred CccceEEEeEEeCCCCcCCccceEEEEEecCCCceEEEeccccCCCCHHHHHHHHHhhccccCCCCCCCcccCCCCCCce
Q 003762 647 DSLDLVPIAAFHGRGKRTGVYGAFLLACYDSNNEEFQSICKIGTGFSEAMLEERSSSLRSKVIPKPRPYYRFADTISPDV 726 (797)
Q Consensus 647 dtlDlvVIGa~~G~Gkr~g~~gsfllg~~d~~~g~~~~vgkVGTGfSd~~l~~l~~~l~~~~~~~p~~~~~~~~~~~pdv 726 (797)
|++|+||+|+++|+|+++|.+|+||||+||+++++|+++|+||||||++++++|.+.+.+++++.+++. ......|++
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 589999999999999999999999999998766899999999999999999999999999988765442 233457999
Q ss_pred EeccceEEEEEeeeeecCCcccccccccCCCCCceeeeceEeeEeC--Ccccc
Q 003762 727 WFEPTEVWEVKAADLTISPVHRAAIGVVDPDKVFTVRFSVLAHLSF--PLLFC 777 (797)
Q Consensus 727 w~eP~~V~EV~~~eit~S~~~~aa~g~v~~~~G~sLRFPRf~riR~--~~~~~ 777 (797)
||+|.+||||+|++||.|+.|++++|. .++|++||||||+++|+ +|++|
T Consensus 79 wv~P~lV~EV~~~e~t~s~~~~~~~~~--~~~g~~LRfPr~~~~R~Dk~~~e~ 129 (129)
T cd07893 79 WVEPKVVVEVLADEITRSPMHTAGRGE--EEEGYALRFPRFVRIRDDKGPEDA 129 (129)
T ss_pred EEeeeEEEEEEeeeeeeCccccccccc--CCCceEEECCEEEEEeCCCChhhC
Confidence 999999999999999999999998887 47899999999999999 88877
No 35
>cd07968 OBF_DNA_ligase_IV The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase IV is a DNA-binding module that is part of the catalytic core unit. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriohages, eukarya, archaea and bacteria. There are three classes of ATP-dependent DNA ligases in eukaryotic cells (I, III and IV). DNA ligase IV is required for DNA non-homologous end joining pathways, including recombination of the V(D)J immunoglobulin gene segments in cells of the mammalian immune system. DNA ligase IV is stabilized by forming a complex with XRCC4, a nuclear phosphoprotein, which is phosphorylated by DNA-dependent pro
Probab=99.95 E-value=1.8e-27 Score=230.56 Aligned_cols=126 Identities=33% Similarity=0.571 Sum_probs=108.9
Q ss_pred CCccceEEEeEEeCCCCcCCccceEEEEEecCCCc------eEEEeccccCCCCHHHHHHHHHhhccccCCC---CCCCc
Q 003762 646 GDSLDLVPIAAFHGRGKRTGVYGAFLLACYDSNNE------EFQSICKIGTGFSEAMLEERSSSLRSKVIPK---PRPYY 716 (797)
Q Consensus 646 ~dtlDlvVIGa~~G~Gkr~g~~gsfllg~~d~~~g------~~~~vgkVGTGfSd~~l~~l~~~l~~~~~~~---p~~~~ 716 (797)
+||+||||||+++|+|++.+.+|+||||+||.+.+ +|++||+||||||++++++|.+.|++++++. .+++.
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 8999999999999999999999999987542 22332
Q ss_pred -ccCCCCCCceEeccc--eEEEEEeeeeecCCcccccccccCCCCCceeeeceEeeEeC--CcccccCC
Q 003762 717 -RFADTISPDVWFEPT--EVWEVKAADLTISPVHRAAIGVVDPDKVFTVRFSVLAHLSF--PLLFCLGN 780 (797)
Q Consensus 717 -~~~~~~~pdvw~eP~--~V~EV~~~eit~S~~~~aa~g~v~~~~G~sLRFPRf~riR~--~~~~~~~~ 780 (797)
.......|++||+|. +||||+|+|||.|+.|++ |++||||||+++|+ +|++|.++
T Consensus 81 ~~~~~~~~~~~Wv~P~~slV~EV~~~e~t~s~~~~~---------g~~LR~Pr~~~~R~DK~~~e~~t~ 140 (140)
T cd07968 81 LLKFGKEKPDVWIEPKDSVVLEVKAAEIVPSDSYKT---------GYTLRFPRCEKIRYDKDWHDCLTL 140 (140)
T ss_pred cccccccCCcEEEecCCCEEEEEEeeeEeecCcccC---------CcEEEcceEeEEECCCCHHHccCC
Confidence 112334799999999 999999999999999974 89999999999999 89999753
No 36
>cd07895 Adenylation_mRNA_capping Adenylation domain of GTP-dependent mRNA capping enzymes. RNA capping enzymes transfer GMP from GTP to the 5'-diphosphate end of nascent mRNAs to form a G(5')ppp(5')RNA cap structure. The RNA cap is found only in eukarya. RNA capping is chemically analogous to the first two steps of polynucleotide ligation. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation of nicked nucleic acid substrates using the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. Structural studies reveal a shared structure for DNA ligases and capping enzymes, with a common catalytic core composed of an adenylation or nucleotidyltransferase domain and a C-terminal OB-fold domain containing conserved sequence motifs. The adenylation domain binds ATP and contains many active site residues.
Probab=99.94 E-value=6.8e-27 Score=241.33 Aligned_cols=162 Identities=22% Similarity=0.195 Sum_probs=128.1
Q ss_pred cCCCceEEEeecceEEEEEEEecC-CeEEEEecCCCccCCCcchHHHHHHhhcCCCCCCeEEEEEEEEEecCCCcccChh
Q 003762 450 FQDMEFTCEYKYDGERAQIHYLED-GSVEIYSRNAERNTGKFPDVVLAVSRLKKPSVRSFVLDCEIVAYDREKQKILPFQ 528 (797)
Q Consensus 450 ~~g~~~~~E~KyDG~R~qih~~~~-g~V~ifSR~gkd~T~~yPel~~~l~~~~~~~v~~~ILDGElVa~d~~~g~~lpFq 528 (797)
+...+|++|+||||+|+|+|+. + +.+.+|||+++.++..+|++.+... ......++|||||+|+++.. +
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 4456899999999999999995 5 7999999999999988888653211 11124789999999998642 1
Q ss_pred hHHhhhcccCCccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCCCc------------EEEEeEEecCCH
Q 003762 529 TLSTRARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEPGF------------FQFATTLTSIDL 596 (797)
Q Consensus 529 ~L~~R~Rk~~~~~~~~~~v~~~vFDILylnG~~L~~~Pl~ERr~lL~~l~~~~~~~------------i~~v~~~~~~~~ 596 (797)
..+++|++||||++||+++.+.||.+|+++|++++...... ...+........
T Consensus 108 ---------------~~~~~~~vFDiL~~~g~~l~~~pl~~R~~~L~~~i~~~~~~~~~~~~~~~~~~~~~i~~k~~~~~ 172 (215)
T cd07895 108 ---------------KKRPRYLIFDILAFNGQSVTEKPLSERLKYIKKEVIEPRNELLKKGPIDKAKEPFSVRLKDFFPL 172 (215)
T ss_pred ---------------ceEEEEEEEEEEEECCcCccCCCHHHHHHHHHHhchhHHHHhhhcChhhcCCCCeEEEecceEeH
Confidence 24789999999999999999999999999999998553111 001122222234
Q ss_pred HHHHHHHHHH---HHcCCceeEEEeCCCCCCccCCCCCCCeEEEcc
Q 003762 597 DEIQKFLDAA---VDASCEGLIIKTMDRDATYEPSKRSLNWLKLKK 639 (797)
Q Consensus 597 eei~~~f~~a---i~~g~EGlmvK~~~~ds~Y~pGkRs~~WlKlK~ 639 (797)
+++.++|+.+ +.+|.||||+|+. +++|.+| |+..|+||||
T Consensus 173 ~~~~~~~~~~~~~~~~~~EGlIfk~~--~~~Y~~G-r~~~~lKwKp 215 (215)
T cd07895 173 YKIEKLFEKIIPKLPHENDGLIFTPN--DEPYVPG-TDKNLLKWKP 215 (215)
T ss_pred HhHHHHHHhccccCCCCCCCEEEccC--CCCccCc-cCCcceeeCC
Confidence 5788888888 5999999999999 9999998 9999999997
No 37
>cd07972 OBF_DNA_ligase_Arch_LigB The Oligonucleotide/oligosaccharide binding (OB)-fold domain of archaeal and bacterial ATP-dependent DNA ligases is a DNA-binding module that is part of the catalytic core unit. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriohages, eukarya, archaea and bacteria. Bacterial DNA ligases are divided into two broad classes: NAD-dependent and ATP-dependent. All bacterial species have a NAD-dependent DNA ligase (LigA). Some bacterial genomes contain multiple genes for DNA ligases that are predicted to use ATP as their cofactor, including Mycobacterium tuberculosis LigB, LigC, and LigD. This group is composed of Pyrococcus furiosus DN
Probab=99.93 E-value=4.1e-26 Score=216.08 Aligned_cols=115 Identities=30% Similarity=0.460 Sum_probs=105.3
Q ss_pred CccceEEEeEEeCCCCcCCccceEEEEEecCCCceEEEeccccCCCCHHHHHHHHHhhccccCCCCCCCcccCCCCCCce
Q 003762 647 DSLDLVPIAAFHGRGKRTGVYGAFLLACYDSNNEEFQSICKIGTGFSEAMLEERSSSLRSKVIPKPRPYYRFADTISPDV 726 (797)
Q Consensus 647 dtlDlvVIGa~~G~Gkr~g~~gsfllg~~d~~~g~~~~vgkVGTGfSd~~l~~l~~~l~~~~~~~p~~~~~~~~~~~pdv 726 (797)
|++|+||+|+++|+|+++|++|+||||+||+++|+|++||+||||||++++++|.+.++++.+.. .+|++
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 58999999999999999999999999999876679999999999999999999999998876543 25899
Q ss_pred EeccceEEEEEeeeeecCCcccccccccCCCCCceeeeceEeeEeC--CcccccCC
Q 003762 727 WFEPTEVWEVKAADLTISPVHRAAIGVVDPDKVFTVRFSVLAHLSF--PLLFCLGN 780 (797)
Q Consensus 727 w~eP~~V~EV~~~eit~S~~~~aa~g~v~~~~G~sLRFPRf~riR~--~~~~~~~~ 780 (797)
|++|.+||||+|+++|.|+.|++ |++||||||+++|. +|++|..-
T Consensus 71 wv~P~lV~eV~~~e~t~s~~~~~---------g~~LR~Prf~~~R~Dk~~~~~~t~ 117 (122)
T cd07972 71 SVKPELVFEVAFEEIQRSPRYKS---------GYALRFPRIVRIRDDKDPDEADTL 117 (122)
T ss_pred EEeceEEEEEEeeEEEecCcccc---------CceEEccEEeEEeCCCChHHCcCH
Confidence 99999999999999999999975 89999999999999 89999753
No 38
>KOG4437 consensus ATP-dependent DNA ligase III [Replication, recombination and repair]
Probab=99.90 E-value=6.1e-23 Score=215.68 Aligned_cols=324 Identities=21% Similarity=0.296 Sum_probs=235.7
Q ss_pred ccchHHHHHHHHHHHhccchHHHHHHHHHHHHhhhcCCCCchHHHHHHHhCccCCCccccccCCChHHHHHHHHHHhCCC
Q 003762 190 RVPFIFLSLVFDMISNETGRILITDIVCNMLRTVMETTPEDLVPVVYLAANKIAPAHEGLELGIGDASIIKALAEACGRT 269 (797)
Q Consensus 190 ~~~F~~la~~~e~I~~tssR~~k~~iL~~~fr~~i~~~p~dl~~~vyL~~~~l~P~~e~~elGIge~~L~kal~~a~G~s 269 (797)
=.+|..|.++|..|+..+....|+++++++|+.- .+...+||.+.-|..+.+.+.|||.++-|++.+++++++.
T Consensus 154 FN~F~ef~kiCS~L~~~p~~~~Kt~VI~~LL~kd------NFDGDL~LWL~FLIRESD~R~YNl~DkKLI~lfsKiLn~~ 227 (482)
T KOG4437|consen 154 FNLFREFRKLCSMLADNPSYNTKTQVIQDLLRKD------NFDGDLYLWLKFLIRESDKRVYNLNDKKLIKLFSKILNCN 227 (482)
T ss_pred chHHHHHHHHHHHHHhCcCccchhHHHHHHHhcc------CCCcchhhhhhhhhcccccccccccHHHHHHHHHHHHccC
Confidence 3579999999999999999999999999999872 2223334444445667899999999999999999999998
Q ss_pred HHHHHHHHH-hcCCHHHHHhh-ccccCCCCCCCCCCCHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHhcCCChHHHHH
Q 003762 270 ESHVKKQYQ-EMGDLGLVAKA-SRSSQSMMRKPDPLTITKVFDTFRLIAKEAGKDSQEKKKNRIKALLVAATDCEPQYLI 347 (797)
Q Consensus 270 ~~~ik~~y~-~~GDlg~vA~~-~r~~q~~l~~~~~LTI~eV~~~L~kIA~~~G~~s~~~K~~~L~~LL~~~t~~E~k~Li 347 (797)
.......|- ...|.+.-+.. ..++. ....+-+||++|++.|.+|++.+..+. .++.|+....+|+..|.+.||
T Consensus 228 ~~~~~~~Y~~~S~~~~i~i~~~~~K~~--~~~K~~~siQ~~D~~L~rLSKi~~~D~---~~~~L~~~A~R~~~~~L~~iI 302 (482)
T KOG4437|consen 228 PDDMARDYEQGSVSETIRVFFEQSKSF--PPAKSLLTIQEVDEFLLRLSKLTKEDE---QQQALQDIASRCTANDLKCII 302 (482)
T ss_pred hHHHHHHHHhccchhhhhhhHhhccCC--CCcccceeHHHHHHHHHHHhcccchHH---HHHHHHHHHHhcccchHHHHH
Confidence 666555553 34455543322 11111 113467999999999999999876544 478999999999999999999
Q ss_pred HHHhhhccCcccHHHHHHHHHHhhccCCCCCCCCCCCcchHHHHHHHHHHHhhcCCchhhhHhhhhhcCccccCCccccC
Q 003762 348 RLLQSKLRIGLAEQTLLAALGQAAVYNEQHSKPPPNIQSPLEEAAKIVKQVFSVLPVYEKIVPALLTDGVWNLSNTCSFT 427 (797)
Q Consensus 348 RiIlkdLRiGi~e~tvl~Ala~a~~~~~~~~~~~~~l~~~l~~a~~~vk~~y~~~pd~~~v~~~l~~~g~~~l~~~~~l~ 427 (797)
|+|.++|....+.+.||+++|+-+..-. ..++|++.+++ +|+ |++.+.. +.|..+.. ...-.
T Consensus 303 RLIr~~L~~~s~A~~iL~~~~P~A~E~F----~S~~L~~ViEr-------~~~---N~~~~~~---~~~~~~~~-s~~s~ 364 (482)
T KOG4437|consen 303 RLIKHDLKMNSGAKHVLDALDPNAYEAF----KSRNLQDVVER-------VLH---NAQEVEK---EPGQRRAL-SVQAS 364 (482)
T ss_pred HHHHHHhccCCChhHHHhccCCCcHHHH----HhcCHHHHHHH-------HHH---hHHHHhh---Cccccccc-cchhh
Confidence 9999999999999999999876432111 11234444443 333 2444422 34443211 11223
Q ss_pred CCCCCccccccccCChHHHHhhcCCCceEEEeecceEEEEEEEecCCeEEEEecCCCccCCCcchHHHHHHhhcCCCCCC
Q 003762 428 PGIPIGPMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAVSRLKKPSVRS 507 (797)
Q Consensus 428 ~g~Pv~PMLA~~~~~i~~~l~k~~g~~~~~E~KyDG~R~qih~~~~g~V~ifSR~gkd~T~~yPel~~~l~~~~~~~v~~ 507 (797)
...|++|||+...++++-..++.+| +...|.||||+|.|+|.+ ++.|.+|||--+... ...+.+.+.+. +.++
T Consensus 365 ~~s~~Q~~~~~~~~~VE~s~~~~~~-~~~S~~~~D~E~~~~~~~-~D~~S~~S~~~~~~s----~FK~~~P~~~~-~G~~ 437 (482)
T KOG4437|consen 365 LMTPVQPMLAEACKSVEYAMKKCPN-GMFSEIKYDGERVQVHKN-GDHFSYFSRLPHKVA----HFKDYIPQAFP-GGHS 437 (482)
T ss_pred hcCCcChhhhhhhhhHHHHhccCCC-CccccccCCCceeeccCC-CcchhhhccChHhhh----hhhhcCchhcC-CCcc
Confidence 5789999999998898877777665 567899999999999985 668999998766542 22333444454 4478
Q ss_pred eEEEEEEEEEecCCCcccChhhHHhh---hcccCCccccccceEEEEeeeee
Q 003762 508 FVLDCEIVAYDREKQKILPFQTLSTR---ARKNVSLSDIKVDVCIYAFDILY 556 (797)
Q Consensus 508 ~ILDGElVa~d~~~g~~lpFq~L~~R---~Rk~~~~~~~~~~v~~~vFDILy 556 (797)
.++|||....+..+|+++||+++.-. .+++ .++|.++||+.|
T Consensus 438 ~~~~~~~~~I~~K~~~P~~~~~~~~~~K~~~~~-------~~~~~~~~~~~~ 482 (482)
T KOG4437|consen 438 MILDSEVLLIDNKTGKPLPFGTLGVHKKAAFQD-------ANVCLFVFDCIY 482 (482)
T ss_pred ccccccccceecccCCCCCchhcchhhHHHhcC-------cchheeecccCC
Confidence 99999999999999999999987432 2322 467999999875
No 39
>cd08040 OBF_DNA_ligase_family The Oligonucleotide/oligosaccharide binding (OB)-fold domain is a DNA-binding module that is part of the catalytic core unit of ATP dependent DNA ligases. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP dependent DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains including a DNA-binding domain, an adenylation (nucleotidyltransferase (NTase)) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The adenylation and C-terminal OB-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The catalytic core unit contains six conserved sequence motifs (I, III, IIIa, IV,
Probab=99.87 E-value=5.3e-22 Score=184.03 Aligned_cols=108 Identities=25% Similarity=0.280 Sum_probs=92.8
Q ss_pred CccceEEEeEEeCCCCcCCccceEEEEEecCCCceEEEeccccCCCCHHHHHHHHHhhccccCCCCCCCcccCCCCCCce
Q 003762 647 DSLDLVPIAAFHGRGKRTGVYGAFLLACYDSNNEEFQSICKIGTGFSEAMLEERSSSLRSKVIPKPRPYYRFADTISPDV 726 (797)
Q Consensus 647 dtlDlvVIGa~~G~Gkr~g~~gsfllg~~d~~~g~~~~vgkVGTGfSd~~l~~l~~~l~~~~~~~p~~~~~~~~~~~pdv 726 (797)
|++|+||+|+++|.|++.|.+|+||||+||++ .++++|+||||||++++++|++.++++..+.++..........+++
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 58999999999999999999999999999864 4889999999999999999999999887765432111222346899
Q ss_pred EeccceEEEEEeeeeecCCcccccccccCCCCCceeeeceEeeEe
Q 003762 727 WFEPTEVWEVKAADLTISPVHRAAIGVVDPDKVFTVRFSVLAHLS 771 (797)
Q Consensus 727 w~eP~~V~EV~~~eit~S~~~~aa~g~v~~~~G~sLRFPRf~riR 771 (797)
|++|.+||||+|+++|. +.+||||||+++|
T Consensus 79 wv~P~lv~eV~~~~~t~---------------~~~lR~P~f~~~R 108 (108)
T cd08040 79 PLYPGKVVEVKYFEMGS---------------KDCLRFPVFIGIR 108 (108)
T ss_pred EeeceEEEEEEeEEeeC---------------CCeEECCeEEEeC
Confidence 99999999999999993 6899999999997
No 40
>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=99.87 E-value=1.3e-21 Score=183.33 Aligned_cols=112 Identities=26% Similarity=0.285 Sum_probs=94.6
Q ss_pred ccceEEEeEEeCCCCcCCccceEEEEEecCCCceEEEeccccCCCCHHHHHHHHHhhccccCCCCCCCcccCCCCCCceE
Q 003762 648 SLDLVPIAAFHGRGKRTGVYGAFLLACYDSNNEEFQSICKIGTGFSEAMLEERSSSLRSKVIPKPRPYYRFADTISPDVW 727 (797)
Q Consensus 648 tlDlvVIGa~~G~Gkr~g~~gsfllg~~d~~~g~~~~vgkVGTGfSd~~l~~l~~~l~~~~~~~p~~~~~~~~~~~pdvw 727 (797)
+.|+||+|++.+.| +.|.+|+||||+||+ ++|+++|+||||||++++++|++.++++.++.|+..........+++|
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 499999999999999999999999999887765322212233478999
Q ss_pred eccceEEEEEeeeeecCCcccccccccCCCCCceeeeceEeeEeC--Ccccc
Q 003762 728 FEPTEVWEVKAADLTISPVHRAAIGVVDPDKVFTVRFSVLAHLSF--PLLFC 777 (797)
Q Consensus 728 ~eP~~V~EV~~~eit~S~~~~aa~g~v~~~~G~sLRFPRf~riR~--~~~~~ 777 (797)
|+|.+||||+|+++|. +.+||||||+++|+ .+.+|
T Consensus 79 v~P~lv~eV~~~~~t~---------------~~~LR~P~f~~~R~Dk~~~~~ 115 (115)
T cd07971 79 VKPELVAEVEFAEWTP---------------DGRLRHPVFKGLREDKPAAEV 115 (115)
T ss_pred ecCCEEEEEEEEEecC---------------CCcEECCeeeEeeCCCCcccC
Confidence 9999999999999994 46999999999999 55555
No 41
>PF04679 DNA_ligase_A_C: ATP dependent DNA ligase C terminal region ; InterPro: IPR012309 DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA fragments by catalysing the formation of an internucleotide ester bond between phosphate and deoxyribose. It is active during DNA replication, DNA repair and DNA recombination. There are two forms of DNA ligase, one requires ATP (6.5.1.1 from EC), the other NAD (6.5.1.2 from EC), the latter being restricted to eubacteria. Eukaryotic, archaebacterial, viral and some eubacterial DNA ligases are ATP-dependent. The first step in the ligation reaction is the formation of a covalent enzyme-AMP complex. The co-factor ATP is cleaved to pyrophosphate and AMP, with the AMP being covalently joined to a highly conserved lysine residue in the active site of the ligase. The activated AMP residue is then transferred to the 5'phosphate of the nick, before the nick is sealed by phosphodiester-bond formation and AMP elimination [,]. Vertebrate cells encode three well-characterised DNA ligases (DNA ligases I, III and IV), all of which are related in structure and sequence. With the exception of the atypically small PBCV-1 viral enzyme, two regions of primary sequence are common to all members of the family. The catalytic region comprises six conserved sequence motifs (I, III, IIIa, IV, V-VI), motif I includes the lysine residue that is adenylated in the first step of the ligation reaction. The function of the second, less well-conserved region is unknown. When folded, each protein comprises of two distinct sub-domains: a large amino-terminal sub-domain ('domain 1') and a smaller carboxy-terminal sub-domain ('domain 2'). The ATP-binding site of the enzyme lies in the cleft between the two sub-domains. Domain 1 consists of two antiparallel beta sheets flanked by alpha helices, whereas domain 2 consists of a five-stranded beta barrel and a single alpha helix, which form the oligonucleotide-binding fold [, ]. This region is found in many but not all ATP-dependent DNA ligase enzymes (6.5.1.1 from EC). It is thought to constitute part of the catalytic core of ATP dependent DNA ligase []. ; GO: 0003910 DNA ligase (ATP) activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 3RR5_A 2CFM_A 1X9N_A 1VS0_B 3GDE_A 2HIX_A 2HIV_A 3L2P_A 4EQ5_A.
Probab=99.85 E-value=2.7e-21 Score=175.91 Aligned_cols=95 Identities=36% Similarity=0.518 Sum_probs=78.5
Q ss_pred cCCccceEEEEEecCCCceEEEeccccCCCCHHHHHHHHHhhccccCCCCCCCcccCCCCCCceEeccceEEEEEeeeee
Q 003762 663 RTGVYGAFLLACYDSNNEEFQSICKIGTGFSEAMLEERSSSLRSKVIPKPRPYYRFADTISPDVWFEPTEVWEVKAADLT 742 (797)
Q Consensus 663 r~g~~gsfllg~~d~~~g~~~~vgkVGTGfSd~~l~~l~~~l~~~~~~~p~~~~~~~~~~~pdvw~eP~~V~EV~~~eit 742 (797)
|+|.+|+||||+||+++++|++||+||||||++++++|.+.+++++++.++.........+|++||+|.+||||+|+|||
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 56789999999999877999999999999999999999999999987765443333333579999999999999999999
Q ss_pred cCCcccccccccCCCCCceeeeceEeeEeC
Q 003762 743 ISPVHRAAIGVVDPDKVFTVRFSVLAHLSF 772 (797)
Q Consensus 743 ~S~~~~aa~g~v~~~~G~sLRFPRf~riR~ 772 (797)
.| | +||||||+++|+
T Consensus 81 ~~--------------G-~lR~P~~~~~R~ 95 (97)
T PF04679_consen 81 PS--------------G-SLRFPRFKRIRE 95 (97)
T ss_dssp EE--------------S-EEESEEEEEEET
T ss_pred CC--------------C-eEECCEEeEEeC
Confidence 64 7 999999999997
No 42
>cd07894 Adenylation_RNA_ligase Adenylation domain of RNA circularization proteins. RNA circularization proteins are capable of circularizing RNA molecules in an ATP-dependent reaction. RNA circularization may protect RNA from exonuclease activity. This model comprises the adenylation domain, the minimal catalytic unit that is common to all members of the ATP-dependent DNA ligase family, and the carboxy-terminal extension of RNA circularization protein that serves as a dimerization module. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation of nicked nucleic acid substrates using the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. The adenylation domain binds ATP and contains many active site residues.
Probab=99.75 E-value=9.3e-18 Score=184.27 Aligned_cols=165 Identities=21% Similarity=0.264 Sum_probs=124.4
Q ss_pred cCCCceEEEeecceEEEEEEEecCCeEEEEecCCC---ccCCCcchHHHHHHhhcCCCCCCeEEEEEEEEEecCCCcccC
Q 003762 450 FQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAE---RNTGKFPDVVLAVSRLKKPSVRSFVLDCEIVAYDREKQKILP 526 (797)
Q Consensus 450 ~~g~~~~~E~KyDG~R~qih~~~~g~V~ifSR~gk---d~T~~yPel~~~l~~~~~~~v~~~ILDGElVa~d~~~g~~lp 526 (797)
|. .+|++|+|+||.|+++|+ .+|++.+|||+|. +.|+.+|++.. ..++. ..++++||||+++.+. |
T Consensus 46 f~-~~~~vEEKlDG~nvri~~-~~G~v~a~TR~G~i~e~~T~~~~eiv~--~~~~~-~~p~~iLdGElvg~~~------p 114 (342)
T cd07894 46 FK-GPVAVEEKMNGYNVRIVR-IGGKVLAFTRGGFICPFTTDRLRDLID--PEFFD-DHPDLVLCGEVVGPEN------P 114 (342)
T ss_pred CC-CCEEEEEeECCcEEEEEE-ECCEEEEEeCCCccCccchhhHhhhch--HHhhc-cCCCEEEEEEEEecCC------c
Confidence 44 589999999999999999 4789999999985 44888898842 23322 2367999999998751 3
Q ss_pred hhhHHhhhcccCCccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCCCcEEEEeEEecCCHHHHHHHHHHH
Q 003762 527 FQTLSTRARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAA 606 (797)
Q Consensus 527 Fq~L~~R~Rk~~~~~~~~~~v~~~vFDILylnG~~L~~~Pl~ERr~lL~~l~~~~~~~i~~v~~~~~~~~eei~~~f~~a 606 (797)
|.. .... ...++.|++|||++.|+ ...+|+.+|+++|+++.-+. +..+......+.+++.++++++
T Consensus 115 ~v~------~~~~---~~~~v~F~vFDI~~~~~--~~~lp~~eR~~lLe~lg~~~---v~~~~~~~~~d~~~l~~~l~~~ 180 (342)
T cd07894 115 YVP------GSYP---EVEDVGFFVFDIRKKNT--GRPLPVEERRELLEKYGLPT---VRLFGEFTADEIEELKEIIREL 180 (342)
T ss_pred ccc------ccCc---cccccEEEEEeeEEcCC--CCCCCHHHHHHHHHhcCCCC---cceEEEEecCCHHHHHHHHHHH
Confidence 311 0010 12578999999999885 55789999999999983221 1223345567789999999999
Q ss_pred HHcCCceeEEEeCCCCC-----CccCCCCCCCeEEEcccc
Q 003762 607 VDASCEGLIIKTMDRDA-----TYEPSKRSLNWLKLKKDY 641 (797)
Q Consensus 607 i~~g~EGlmvK~~~~ds-----~Y~pGkRs~~WlKlK~dY 641 (797)
.++|+||||+|++ ++ .|.....+-++|++.-.|
T Consensus 181 ~~~G~EGVVlK~~--~~~~~~~Ky~t~~~~~~di~~~~~~ 218 (342)
T cd07894 181 DKEGREGVVLKDP--DMRVPPLKYTTSYSNCSDIRYAFRY 218 (342)
T ss_pred HHCCCceEEEecc--ccccCcceeecCCCCcHHHHHHhhh
Confidence 9999999999999 77 687666666777777766
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=99.73 E-value=2.6e-17 Score=156.15 Aligned_cols=110 Identities=17% Similarity=0.125 Sum_probs=88.1
Q ss_pred CccceEEEeEEeCCCCcCCccceEEEEEecCCCceEEEeccccCCCCHHHHHHHHHhhccccCCCCCC-----Ccc-cC-
Q 003762 647 DSLDLVPIAAFHGRGKRTGVYGAFLLACYDSNNEEFQSICKIGTGFSEAMLEERSSSLRSKVIPKPRP-----YYR-FA- 719 (797)
Q Consensus 647 dtlDlvVIGa~~G~Gkr~g~~gsfllg~~d~~~g~~~~vgkVGTGfSd~~l~~l~~~l~~~~~~~p~~-----~~~-~~- 719 (797)
|+.|+||+|+.+++ +.+|+++||+||+ .|+|+++|+| ||||++++++|.+.++++.++.|+. |.. ++
T Consensus 1 ~~~e~vI~G~~~~~----~~~gsLlLg~~~~-~g~l~yvG~v-tGf~~~~~~~L~~~l~~l~~~~p~~~~~~~~~~~~~~ 74 (122)
T cd07970 1 RTADCVVGGVRGHK----DRPGSLLLGLYDD-GGRLRHVGRT-SPLAAAERRELAELLEPARAGHPWTGRAPGFPSRWGT 74 (122)
T ss_pred CcEeEEEEEEECCC----CCccEEEEEEECC-CCCEEEEEEE-CCCCHHHHHHHHHHHHHhhcCCCCcccccccccccCc
Confidence 47899999998776 4689999999975 4689999999 9999999999999999987765431 111 11
Q ss_pred CCCCCceEeccceEEEEEeeeeecCCcccccccccCCCCCceeeec-eEeeEeC--Ccccc
Q 003762 720 DTISPDVWFEPTEVWEVKAADLTISPVHRAAIGVVDPDKVFTVRFS-VLAHLSF--PLLFC 777 (797)
Q Consensus 720 ~~~~pdvw~eP~~V~EV~~~eit~S~~~~aa~g~v~~~~G~sLRFP-Rf~riR~--~~~~~ 777 (797)
....+.+|++|.+|+||+|+++|.+ | .|||| ||+++|. +..+|
T Consensus 75 ~~~~~~~wv~P~lV~eV~~~e~t~~--------------G-~LRhP~~f~glR~Dk~~~~v 120 (122)
T cd07970 75 RKSLEWVPVRPELVVEVSADTAEGG--------------G-RFRHPLRFLRWRPDKSPEDC 120 (122)
T ss_pred ccCCCeEEeeccEEEEEEeeEEecC--------------C-ceeCCceeEEEcCCCCHHHC
Confidence 1134789999999999999999952 4 89999 8999998 34444
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=99.34 E-value=1.3e-12 Score=132.81 Aligned_cols=158 Identities=22% Similarity=0.258 Sum_probs=104.6
Q ss_pred CCceEEEeecceEEEEEEEecCCeEEEEecCCCccC---CCcchHHHHHHhhcCCCCCCeEEEEEEEEEecCCCcccChh
Q 003762 452 DMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNT---GKFPDVVLAVSRLKKPSVRSFVLDCEIVAYDREKQKILPFQ 528 (797)
Q Consensus 452 g~~~~~E~KyDG~R~qih~~~~g~V~ifSR~gkd~T---~~yPel~~~l~~~~~~~v~~~ILDGElVa~d~~~g~~lpFq 528 (797)
..+|+|.+|-||.|+++.+. ++.+.+++|+.+-+. -.+|-..+- .......+.+||||||.-. ..+
T Consensus 15 ~~~Y~V~eKaDG~Ryll~i~-~~~~ylidr~~~~~~v~~~~~p~~~~~---~~~~~~~~TLLDGElV~d~-~~~------ 83 (192)
T PF01331_consen 15 QKDYFVCEKADGTRYLLLIT-DNGVYLIDRKNNVFKVDNLHFPSKKDS---SDGRHHQDTLLDGELVLDK-DPG------ 83 (192)
T ss_dssp HS-EEEEEEESSEEEEEEEE-EEEEEEEETTS-EEEESSST-ECTTC-----TTCEGCSEEEEEEEEEEE-CTT------
T ss_pred hCCcEEEECCCCcEEEEEEe-cceEEEEeCCCcEEEecCccccccccc---ccccccCCEEEEEEEEccc-CCC------
Confidence 35799999999999999996 458999999987653 123321100 0011236899999998732 211
Q ss_pred hHHhhhcccCCccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccC----------------CCcEEEEeEEe
Q 003762 529 TLSTRARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEE----------------PGFFQFATTLT 592 (797)
Q Consensus 529 ~L~~R~Rk~~~~~~~~~~v~~~vFDILylnG~~L~~~Pl~ERr~lL~~l~~~~----------------~~~i~~v~~~~ 592 (797)
....+|++||+|++||+++.+.||.+|...|++.+... |=.+.+-....
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 24679999999999999999999999999997644321 11222333444
Q ss_pred cCCHHH-HHHHHHHHHHcCCceeEEEeCCCCCCccCCCCCCCeEEEc
Q 003762 593 SIDLDE-IQKFLDAAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLK 638 (797)
Q Consensus 593 ~~~~ee-i~~~f~~ai~~g~EGlmvK~~~~ds~Y~pGkRs~~WlKlK 638 (797)
....+. +...+..-+.++..|||+-.. +.+|.+| +...++|||
T Consensus 149 ~~~~~~~~~~~~~~~l~h~~DGLIFtp~--~~pY~~G-t~~~llKWK 192 (192)
T PF01331_consen 149 IYQIEKLLFEEFIPKLPHETDGLIFTPV--NTPYVPG-TCPNLLKWK 192 (192)
T ss_dssp GGGHHHHCHHCCCCCTTSTEEEEEEEES--SSB--SE-EEEEEEEE-
T ss_pred HHhhHHHHHHHhhccCCCCCCEEEEecC--CCCccCC-CCCccEeeC
Confidence 444444 233333345688899999999 8999998 778999998
No 45
>cd08041 OBF_kDNA_ligase_like The Oligonucleotide/oligosaccharide binding (OB)-fold domain of kDNA ligase-like ATP-dependent DNA ligases is a DNA-binding module that is part of the catalytic core unit. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriohages, eukarya, archaea and bacteria. The mitochondrial DNA of parasitic protozoan is highly unusual. It is termed the kinetoplast DNA (kDNA) and consists of circular DNA molecules (maxicircles) and several thousand smaller circular molecules (minicircles). This group is composed of kDNA ligase, Chlorella virus DNA ligase, and similar proteins. kDNA ligase and Chlorella virus DNA ligase are the smallest known ATP-de
Probab=99.33 E-value=2.4e-12 Score=112.67 Aligned_cols=76 Identities=25% Similarity=0.338 Sum_probs=65.3
Q ss_pred ccceEEEeEEeCCCCcCCccceEEEEEecCCCceEEEeccccCCCCHHHHHHHHHhhccccCCCCCCCcccCCCCCCceE
Q 003762 648 SLDLVPIAAFHGRGKRTGVYGAFLLACYDSNNEEFQSICKIGTGFSEAMLEERSSSLRSKVIPKPRPYYRFADTISPDVW 727 (797)
Q Consensus 648 tlDlvVIGa~~G~Gkr~g~~gsfllg~~d~~~g~~~~vgkVGTGfSd~~l~~l~~~l~~~~~~~p~~~~~~~~~~~pdvw 727 (797)
+.|++|+|+++|+|++.|.+|+|+|+.+|. . .++||||||++++++++. +
T Consensus 2 ~~e~vIvG~~~g~g~~~~~~g~llv~~~~g---~---~~~vgtG~t~~~r~~~~~---------------~--------- 51 (77)
T cd08041 2 DAEARVVGYEEGKGKYEGMLGALVVETKDG---I---RFKIGSGFSDEQRRNPPP---------------I--------- 51 (77)
T ss_pred ceeEEEEEEEcCCCccCCcEEEEEEEecCC---C---EEEEcCCCCHHHHhcCCC---------------C---------
Confidence 689999999999999999999999998863 2 348999999999997661 1
Q ss_pred eccceEEEEEeeeeecCCcccccccccCCCCCceeeeceEeeEe
Q 003762 728 FEPTEVWEVKAADLTISPVHRAAIGVVDPDKVFTVRFSVLAHLS 771 (797)
Q Consensus 728 ~eP~~V~EV~~~eit~S~~~~aa~g~v~~~~G~sLRFPRf~riR 771 (797)
..|+||+|.++|. +..||||+|+++|
T Consensus 52 ---g~v~~V~y~e~t~---------------~g~lR~P~f~g~R 77 (77)
T cd08041 52 ---GSIITYKYQGLTK---------------NGLPRFPVFLRVR 77 (77)
T ss_pred ---CCEEEEEEEecCC---------------CCcccCCEEEecC
Confidence 2499999999994 4789999999998
No 46
>COG1423 ATP-dependent DNA ligase, homolog of eukaryotic ligase III [DNA replication, recombination, and repair]
Probab=98.86 E-value=3.5e-08 Score=106.54 Aligned_cols=148 Identities=20% Similarity=0.227 Sum_probs=108.0
Q ss_pred hhcCCCceEEEeecceEEEEEEEecCCeEEEEecCCCcc---CCCcchHHHHHHhhcCCCCCCeEEEEEEEEEecCCCcc
Q 003762 448 NKFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERN---TGKFPDVVLAVSRLKKPSVRSFVLDCEIVAYDREKQKI 524 (797)
Q Consensus 448 ~k~~g~~~~~E~KyDG~R~qih~~~~g~V~ifSR~gkd~---T~~yPel~~~l~~~~~~~v~~~ILDGElVa~d~~~g~~ 524 (797)
+.|+.+.+++|.|.||+.+.|.+. +|.+...||.|-.. |.+.+++.+. +.+. ..++.+|.|||+..+.
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 357677899999999999999985 79999999999864 4455555442 3333 3478999999998642
Q ss_pred cChhhHHhhhcccCCccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCCCcEEEEeEEecCCH-HHHHHHH
Q 003762 525 LPFQTLSTRARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDL-DEIQKFL 603 (797)
Q Consensus 525 lpFq~L~~R~Rk~~~~~~~~~~v~~~vFDILylnG~~L~~~Pl~ERr~lL~~l~~~~~~~i~~v~~~~~~~~-eei~~~f 603 (797)
|+-. . ..-...++.|++|||.-.|.. ..+|.+||++++++.-- + ++.+......++. +++.++.
T Consensus 154 -PYv~------~---~~y~~e~v~fFvFDire~~tg--r~Lp~eer~~l~ekYgl--~-~V~~fg~~~~~e~~eei~eIv 218 (382)
T COG1423 154 -PYVP------G---PYYEKEDVGFFVFDIREKNTG--RPLPVEERLELAEKYGL--P-HVEIFGEFPADEAGEEIYEIV 218 (382)
T ss_pred -CCCC------C---CCCccCCceEEEEEEEecCCC--CCCCHHHHHHHHHHcCC--C-ceEEeeeechhHhHHHHHHHH
Confidence 2211 0 011246789999999987643 24699999999998732 2 3444444445555 7888888
Q ss_pred HHHHHcCCceeEEEeC
Q 003762 604 DAAVDASCEGLIIKTM 619 (797)
Q Consensus 604 ~~ai~~g~EGlmvK~~ 619 (797)
++.-.+|.||||+|++
T Consensus 219 e~L~keGREGVV~Kdp 234 (382)
T COG1423 219 ERLNKEGREGVVMKDP 234 (382)
T ss_pred HHHhhcCCcceEecCc
Confidence 9989999999999998
No 47
>COG5226 CEG1 mRNA capping enzyme, guanylyltransferase (alpha) subunit [RNA processing and modification]
Probab=98.81 E-value=4.4e-09 Score=111.19 Aligned_cols=174 Identities=20% Similarity=0.209 Sum_probs=117.1
Q ss_pred CCceEEEeecceEEEEEEEecC---C--eEEEEecCCCcc---CCCcchHHHHHH-hhcCCCCCCeEEEEEEEEEecCCC
Q 003762 452 DMEFTCEYKYDGERAQIHYLED---G--SVEIYSRNAERN---TGKFPDVVLAVS-RLKKPSVRSFVLDCEIVAYDREKQ 522 (797)
Q Consensus 452 g~~~~~E~KyDG~R~qih~~~~---g--~V~ifSR~gkd~---T~~yPel~~~l~-~~~~~~v~~~ILDGElVa~d~~~g 522 (797)
..+|++.+|-||.||++.+..+ | .+.+|.|..+=| +..||.+..... +-+ ..+..||||+|.-
T Consensus 61 ~~dy~VCEKsDGvR~Ll~vte~p~tg~~~~y~~DR~nnfY~v~~~f~p~~~~~k~ge~l---~~dtlldgelV~d----- 132 (404)
T COG5226 61 NNDYLVCEKSDGVRALLLVTEEPVTGAFRGYFYDRRNNFYEVHTSFPPCSTVLKDGEVL---LEDTLLDGELVFD----- 132 (404)
T ss_pred hCCeEEEEccCCeEEEEEEEecccCCCcceEEEeccCceEEeccccCCcccccccCcEE---eccceecceEEEE-----
Confidence 3479999999999999888632 2 578999988644 334453322111 111 2578899999873
Q ss_pred cccChhhHHhhhcccCCccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCCCcEEEE--------eEE-ec
Q 003762 523 KILPFQTLSTRARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEPGFFQFA--------TTL-TS 593 (797)
Q Consensus 523 ~~lpFq~L~~R~Rk~~~~~~~~~~v~~~vFDILylnG~~L~~~Pl~ERr~lL~~l~~~~~~~i~~v--------~~~-~~ 593 (797)
..|...+ .++.|.+||+|.++|..+..++..+|...|.+-+..--.+.+.+ +.. ..
T Consensus 133 -~~p~~k~--------------~qlryl~fdcLa~~g~~~~~~~~s~Rl~~l~Ke~~kp~~~~r~s~~~~~~~fpf~~s~ 197 (404)
T COG5226 133 -CLPYEKV--------------PQLRYLLFDCLAYAGMFVERMEKSERLKTLQKEDEKPRERKRVSIEIDSGSFPFHFSV 197 (404)
T ss_pred -eccccch--------------HHHHHHHHHHhhhcceeEeecchhhHHHHhhhhhcccHhhhhheeeccccccceeeeH
Confidence 2344332 35678899999999999999999999999987654310000000 000 01
Q ss_pred CC---HHHHHHHHHHH--HHcCCceeEEEeCCCCCCccCCCCCCCeEEEccccccccCCccceEEEe
Q 003762 594 ID---LDEIQKFLDAA--VDASCEGLIIKTMDRDATYEPSKRSLNWLKLKKDYIESIGDSLDLVPIA 655 (797)
Q Consensus 594 ~~---~eei~~~f~~a--i~~g~EGlmvK~~~~ds~Y~pGkRs~~WlKlK~dY~~~~~dtlDlvVIG 655 (797)
.. .-.+.++|+.. +.+|..|+|+-.. +.+|..|++ +..|||||.-+ .|+|+..|-
T Consensus 198 K~M~~syg~~ki~k~ip~L~HgnDGLIFTp~--~~PY~~Gkd-~~lLKWKP~~~----NTiDF~lvl 257 (404)
T COG5226 198 KQMLKSYGFWKIYKKIPELKHGNDGLIFTPA--DEPYSVGKD-GALLKWKPASL----NTIDFRLVL 257 (404)
T ss_pred HHHHhhhhHHHHHhhcccccCCCCceEeccC--CCCcccCcc-ceeeecCcccc----Cceeeeeee
Confidence 11 12345556433 3689999999999 999999965 58999999876 589987653
No 48
>PF14743 DNA_ligase_OB_2: DNA ligase OB-like domain; PDB: 2Q2U_D 2Q2T_A 1FVI_A 1P8L_A.
Probab=98.72 E-value=1.6e-08 Score=86.03 Aligned_cols=66 Identities=33% Similarity=0.478 Sum_probs=43.9
Q ss_pred eCCCCcCCccceEEEEEecCCCceEEEeccccCCCCHHHHHHHHHhhccccCCCCCCCcccCCCCCCceEeccceEEEEE
Q 003762 658 HGRGKRTGVYGAFLLACYDSNNEEFQSICKIGTGFSEAMLEERSSSLRSKVIPKPRPYYRFADTISPDVWFEPTEVWEVK 737 (797)
Q Consensus 658 ~G~Gkr~g~~gsfllg~~d~~~g~~~~vgkVGTGfSd~~l~~l~~~l~~~~~~~p~~~~~~~~~~~pdvw~eP~~V~EV~ 737 (797)
.|+||..|++|+++|...| |. ..+|||||||+++++++ .+ ..+++|+
T Consensus 1 ~G~Gk~~g~~Galv~~~~~---G~---~f~iGsG~td~~R~~~~------~i---------------------G~iit~k 47 (66)
T PF14743_consen 1 EGKGKFKGMLGALVCETED---GV---EFKIGSGFTDEEREEPP------YI---------------------GKIITVK 47 (66)
T ss_dssp ----EEEEEEEEEEEEE-T---TE---EEEE-SS--HHHHHHHH------HT---------------------T-EEEEE
T ss_pred CCccccCCCEEEEEEEeCC---CC---EEEECCCCCHHHHhcCC------CC---------------------CCEEEEE
Confidence 3789999999999997644 42 34899999999999887 11 2489999
Q ss_pred eeeeecCCcccccccccCCCCCceeeeceEeeEe
Q 003762 738 AADLTISPVHRAAIGVVDPDKVFTVRFSVLAHLS 771 (797)
Q Consensus 738 ~~eit~S~~~~aa~g~v~~~~G~sLRFPRf~riR 771 (797)
|.++|.+ ..+|||+|+|+|
T Consensus 48 y~~~t~~---------------g~pRfP~f~~~R 66 (66)
T PF14743_consen 48 YQGLTKD---------------GSPRFPVFVRVR 66 (66)
T ss_dssp EE-TTSS---------------SS-EEEEEEEE-
T ss_pred EEccCCC---------------CccccCEEEEeC
Confidence 9999853 479999999998
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=98.63 E-value=1.8e-07 Score=95.31 Aligned_cols=149 Identities=21% Similarity=0.260 Sum_probs=112.6
Q ss_pred CceEEEeecceEEEEEEEecCCeEEEEecCCCccC---CCcchHHHHHHhhcCCCCCCeEEEEEEEEEecCCCcccChhh
Q 003762 453 MEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNT---GKFPDVVLAVSRLKKPSVRSFVLDCEIVAYDREKQKILPFQT 529 (797)
Q Consensus 453 ~~~~~E~KyDG~R~qih~~~~g~V~ifSR~gkd~T---~~yPel~~~l~~~~~~~v~~~ILDGElVa~d~~~g~~lpFq~ 529 (797)
.+|++=+-==|.|++|+.. +|.+.+++|+|..+. ..+|.-... +. ....+|||+-. +
T Consensus 21 ~~w~~~~~P~G~R~lvv~~-~g~t~~~~r~g~~~~~f~s~lP~g~~~--~~---~~g~tILDci~---~----------- 80 (186)
T cd09232 21 EEWLVVPCPVGKRCLVVAS-KGKTVARSKNGRTLHRFSSALPGGSRK--TS---NSGYTILDCIY---N----------- 80 (186)
T ss_pred cceEEEECcCceEEEEEEe-CCEEEEEeCCCCEEEecccCCCCCCcC--CC---CCCCEEEEEec---C-----------
Confidence 4687777778999999996 899999999998752 122221100 00 11345555532 1
Q ss_pred HHhhhcccCCccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCCC----------cEEEEeEEecCCHHHH
Q 003762 530 LSTRARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEPG----------FFQFATTLTSIDLDEI 599 (797)
Q Consensus 530 L~~R~Rk~~~~~~~~~~v~~~vFDILylnG~~L~~~Pl~ERr~lL~~l~~~~~~----------~i~~v~~~~~~~~eei 599 (797)
+...+|+|+|||.+||+++.+.+...|...|++-+.+.+. .++..+...++. +.+
T Consensus 81 --------------~~~~~yyVlDii~w~g~~l~d~~~~~Rf~wl~skl~E~~~~~~~~~~~~~~f~~~p~~~~~~-~~l 145 (186)
T cd09232 81 --------------EDDRTYYVLDVLCWNGHPLYDCETEFRFFWLRSKLEELPELDEPSEKNPFRFVPLPYFPCTK-ESL 145 (186)
T ss_pred --------------CCCCEEEEEEEeeeCCcccccCCcchhHHHHHhhCCCccccccccccCCceEEecCcccCcH-HHH
Confidence 1124899999999999999999999999999998877431 456666676665 778
Q ss_pred HHHHHHHH---HcCCceeEEEeCCCCCCccCCCCCCCeEEEcc
Q 003762 600 QKFLDAAV---DASCEGLIIKTMDRDATYEPSKRSLNWLKLKK 639 (797)
Q Consensus 600 ~~~f~~ai---~~g~EGlmvK~~~~ds~Y~pGkRs~~WlKlK~ 639 (797)
++.|...+ ..-..|+++-.. ++.|++| +++.|+|+|+
T Consensus 146 ~~~~~~~~~~~~~e~DGLlFyhk--~~~Y~~G-~tPlvl~wKp 185 (186)
T cd09232 146 QSAYSGPLNDDPYELDGLLFYHK--ESHYTPG-STPLVLWLKD 185 (186)
T ss_pred HHHHhcccccCCCCCceEEEEeC--CCcccCc-CCCcEEEecC
Confidence 88898888 889999999999 8899998 7899999998
No 50
>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=98.62 E-value=5.8e-07 Score=99.63 Aligned_cols=148 Identities=21% Similarity=0.272 Sum_probs=96.4
Q ss_pred hcCCCceEEEeecceEEEEEEEecCCeEEEEecCCCcc---CCCcchHHHHHHhhcCCCCCCeEEEEEEEEEecCCCccc
Q 003762 449 KFQDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERN---TGKFPDVVLAVSRLKKPSVRSFVLDCEIVAYDREKQKIL 525 (797)
Q Consensus 449 k~~g~~~~~E~KyDG~R~qih~~~~g~V~ifSR~gkd~---T~~yPel~~~l~~~~~~~v~~~ILDGElVa~d~~~g~~l 525 (797)
.|.+..+++|+|.||..+-|.. -+|++..+||.|-.. |+++++..+ ...+.+ .++.+|.||++.-+.
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 3566569999999999999965 588999999999865 122344333 234443 378999999997431
Q ss_pred ChhhHHhhhcccCCccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCCCcEEEEeEEecCC-HHHHHHHHH
Q 003762 526 PFQTLSTRARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEPGFFQFATTLTSID-LDEIQKFLD 604 (797)
Q Consensus 526 pFq~L~~R~Rk~~~~~~~~~~v~~~vFDILylnG~~L~~~Pl~ERr~lL~~l~~~~~~~i~~v~~~~~~~-~eei~~~f~ 604 (797)
|+.. -. ......+..|++|||.- ...-.-+|..+|+++++++--+.-..+. .....+ .+++.+..+
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--GKTNRSLPVEERLELAEKYGLPHVEILG---VYTADEAVEEIYEIIE 211 (374)
T ss_pred CCcc------cC--ccccCCCceEEEEEEEE--CCCCccCCHHHHHHHHHHCCCCccceee---EEcHHHHHHHHHHHHH
Confidence 1100 00 11113467999999973 3334457999999999987322111111 122222 235666667
Q ss_pred HHHHcCCceeEEEeC
Q 003762 605 AAVDASCEGLIIKTM 619 (797)
Q Consensus 605 ~ai~~g~EGlmvK~~ 619 (797)
..-++|.||||+|++
T Consensus 212 ~L~~~gREGVVlK~~ 226 (374)
T TIGR01209 212 RLNKEGREGVVMKDP 226 (374)
T ss_pred HhhhcCcceEEEcCc
Confidence 777899999999998
No 51
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=98.26 E-value=5.9e-05 Score=88.41 Aligned_cols=206 Identities=14% Similarity=0.129 Sum_probs=126.0
Q ss_pred ccccc-ccCChHHHHhhcCC--CceEEEeecceEEEEEEEecCCe-EEEEec----CCCccCCCcchHHHHHHhhcCCCC
Q 003762 434 PMLAK-PTKGVSEIVNKFQD--MEFTCEYKYDGERAQIHYLEDGS-VEIYSR----NAERNTGKFPDVVLAVSRLKKPSV 505 (797)
Q Consensus 434 PMLA~-~~~~i~~~l~k~~g--~~~~~E~KyDG~R~qih~~~~g~-V~ifSR----~gkd~T~~yPel~~~l~~~~~~~v 505 (797)
|||.- .+.+.+++.+ |-. ..|++|+|+||.-+.+.+. +|+ ++..|| .|+|+|+..--+ ..|+..++...
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 99863 3445555532 211 2599999999999999994 665 789999 688988753221 11222232111
Q ss_pred CCeEEEEEEEEEecCCCcccChhhHH-----------hhhcccCCccccccceEEEEeeeeecCCccccCCcHHHHHHHH
Q 003762 506 RSFVLDCEIVAYDREKQKILPFQTLS-----------TRARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHL 574 (797)
Q Consensus 506 ~~~ILDGElVa~d~~~g~~lpFq~L~-----------~R~Rk~~~~~~~~~~v~~~vFDILylnG~~L~~~Pl~ERr~lL 574 (797)
..+.+-||++.-. ..|+... .-.|... ......++.|++|++. +| .....++.+.|
T Consensus 174 ~~levRGEv~m~~------~~F~~~~~g~aNPRN~AAGsLr~~d-~~~~~r~L~~f~y~~~--~~----~~t~~e~l~~L 240 (562)
T PRK08097 174 ANLVLQGELFLRR------EGHIQQQMGGINARAKVAGLMMRKD-PSPTLNQIGVFVWAWP--DG----PASMPERLAQL 240 (562)
T ss_pred CeEEEEEEEEEeH------HHHHHHhcCcCCchHHHhHHHhhcC-cHhhhccceEEEEECC--CC----CCCHHHHHHHH
Confidence 3588999999853 2354422 1122111 1112568999999983 44 24678888888
Q ss_pred HHhhccCCC-cEEEEeEEecCCHHHHHHHHHHHHH----cCCceeEEEeCCCCCCccC--CCCCCCe---EEEccccccc
Q 003762 575 YDSFEEEPG-FFQFATTLTSIDLDEIQKFLDAAVD----ASCEGLIIKTMDRDATYEP--SKRSLNW---LKLKKDYIES 644 (797)
Q Consensus 575 ~~l~~~~~~-~i~~v~~~~~~~~eei~~~f~~ai~----~g~EGlmvK~~~~ds~Y~p--GkRs~~W---lKlK~dY~~~ 644 (797)
+++-=++.. .. ..+.+.+++.++++.... -.-.|+|+|-- +-.|.. ..+.+.| +|+..+
T Consensus 241 ~~~GF~v~~~~~-----~~~~~~~~i~~~~~~~~r~~l~y~iDGiViKvn--~~~~~~~~ts~~PrWAiAyKf~~~---- 309 (562)
T PRK08097 241 ATAGFPLTQRYT-----HPVKNAEEVARWRERWYRAPLPFVTDGVVVRQA--KEPPGRYWQPGQGEWAVAWKYPPV---- 309 (562)
T ss_pred HHCCCCcCccce-----EeeCCHHHHHHHHHHHhhccCCCCCCcEEEEec--CHHHHhhccCCCCCceEEEcCCCc----
Confidence 876323221 11 125678888887776542 36789999976 544443 2356778 566554
Q ss_pred cCCccceEEEeEEeCCCCcCCccceE
Q 003762 645 IGDSLDLVPIAAFHGRGKRTGVYGAF 670 (797)
Q Consensus 645 ~~dtlDlvVIGa~~G~Gkr~g~~gsf 670 (797)
+..-.+.+..|.-| |+|.++..
T Consensus 310 ---~~~T~l~~I~~qVG-RTG~iTPV 331 (562)
T PRK08097 310 ---QQVAEVRAVQFAVG-RTGKITVV 331 (562)
T ss_pred ---EEEEEEEEEEEecC-CCceeeEE
Confidence 45556777777666 56665543
No 52
>PRK01109 ATP-dependent DNA ligase; Provisional
Probab=98.11 E-value=8e-06 Score=96.91 Aligned_cols=93 Identities=26% Similarity=0.373 Sum_probs=86.2
Q ss_pred CccchHHHHHHHHHHHhcc---chHHHHHHHHHHHHhhhcCCCCchHHHHHHHhCccCCCccccccCCChHHHHHHHHHH
Q 003762 189 ERVPFIFLSLVFDMISNET---GRILITDIVCNMLRTVMETTPEDLVPVVYLAANKIAPAHEGLELGIGDASIIKALAEA 265 (797)
Q Consensus 189 ~~~~F~~la~~~e~I~~ts---sR~~k~~iL~~~fr~~i~~~p~dl~~~vyL~~~~l~P~~e~~elGIge~~L~kal~~a 265 (797)
++++|.++.+.|++|++++ ++.+|+++|+++|+.+ +++++.+.++++++.+. +|++++++.+||+++
T Consensus 113 ~~lti~eV~~~L~~Ia~~sg~~s~~~k~~iL~~Ll~~~---~~~E~k~iirli~g~lr-------iGv~e~~il~ALa~A 182 (590)
T PRK01109 113 EPLTVKEVYDTLVKIALATGEGSQDLKIKLLAGLLKDA---SPLEAKYIARFVEGRLR-------LGVGDATILDALAIA 182 (590)
T ss_pred CCcCHHHHHHHHHHHHhhhCCCcHHHHHHHHHHHHHhC---CHHHHHHHHHHHhhhhh-------cCccHHHHHHHHHHH
Confidence 5799999999999999997 8899999999999997 78999999999999875 899999999999999
Q ss_pred hC--CCHHHHHHHHHhcCCHHHHHhhcc
Q 003762 266 CG--RTESHVKKQYQEMGDLGLVAKASR 291 (797)
Q Consensus 266 ~G--~s~~~ik~~y~~~GDlg~vA~~~r 291 (797)
+| .+...+++.|...||+|.||..+.
T Consensus 183 ~~~~~~~~~ve~~y~~~~Dlg~va~~l~ 210 (590)
T PRK01109 183 FGGAVARELVERAYNLRADLGYIAKILA 210 (590)
T ss_pred HhcccchHHHHHHHHhCCCHHHHHHHHH
Confidence 99 999999999999999999997653
No 53
>smart00532 LIGANc Ligase N family.
Probab=98.08 E-value=9.1e-05 Score=84.89 Aligned_cols=237 Identities=16% Similarity=0.182 Sum_probs=139.6
Q ss_pred ccccc-ccCChHHHH---hhcC---C--CceEEEeecceEEEEEEEecCCe-EEEEec----CCCccCCCcchHHHHHHh
Q 003762 434 PMLAK-PTKGVSEIV---NKFQ---D--MEFTCEYKYDGERAQIHYLEDGS-VEIYSR----NAERNTGKFPDVVLAVSR 499 (797)
Q Consensus 434 PMLA~-~~~~i~~~l---~k~~---g--~~~~~E~KyDG~R~qih~~~~g~-V~ifSR----~gkd~T~~yPel~~~l~~ 499 (797)
|||.- .+.+.+++. ++.. + ..|++|+|+||.-+.+.+. +|+ ++..|| .|+|+|+...-+.. +..
T Consensus 75 pMlSL~k~~~~~el~~f~~~~~~~~~~~~~~~~epKiDGlsisL~Ye-~G~l~~a~TRGDG~~GeDVT~nv~~i~~-iP~ 152 (441)
T smart00532 75 PMLSLDNAFDEDELRAFDERIEKALGSPFAYVVEPKIDGLSVSLLYE-NGKLVQAATRGDGTVGEDVTQNVKTIRS-IPL 152 (441)
T ss_pred cccCccccCCHHHHHHHHHHHHHhcCCCceEEEEEecccEEEEEEEE-CCEEEEEEecCCCCcceehhhhhhhhcC-cCh
Confidence 89873 344555542 2221 1 2689999999999999994 776 889999 79999985432211 222
Q ss_pred hcCCC-CCCeEEEEEEEEEecCCCcccChhhHHh-------------------hhcccCCccccccceEEEEeeeeecCC
Q 003762 500 LKKPS-VRSFVLDCEIVAYDREKQKILPFQTLST-------------------RARKNVSLSDIKVDVCIYAFDILYRNG 559 (797)
Q Consensus 500 ~~~~~-v~~~ILDGElVa~d~~~g~~lpFq~L~~-------------------R~Rk~~~~~~~~~~v~~~vFDILylnG 559 (797)
.+... -..+.+-||++.-. ..|+.+-. -+|..........++.|++|++...++
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 22110 13588999999853 23444311 111111111124589999999864433
Q ss_pred ccccCCcHHHHHHHHHHhhccCCCcEEEEeEEecCCHHHHHHHHHHHHH------cCCceeEEEeCCCCCCccC--C--C
Q 003762 560 QPLLQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAAVD------ASCEGLIIKTMDRDATYEP--S--K 629 (797)
Q Consensus 560 ~~L~~~Pl~ERr~lL~~l~~~~~~~i~~v~~~~~~~~eei~~~f~~ai~------~g~EGlmvK~~~~ds~Y~p--G--k 629 (797)
.. ......++.+.|.++-=++..... .+.+.++++++++...+ -.-.|||+|-- +-.+.. | .
T Consensus 227 ~~-~~~t~~e~l~~L~~~GF~v~~~~~-----~~~~~~ei~~~~~~~~~~r~~l~y~iDGiViKvn--~~~~~~~lG~ts 298 (441)
T smart00532 227 LF-LPKTQSEALKWLKELGFPVSPHTR-----LCKNADEVIEYYEEWEEKRAELPYEIDGVVVKVD--DLALQRELGFTS 298 (441)
T ss_pred CC-CccCHHHHHHHHHHCCCCCCCCeE-----eeCCHHHHHHHHHHHHHhcccCCCCcCcEEEEec--CHHHHHHhCccC
Confidence 21 124688899999887222222222 35678899999887765 36789999986 544443 2 2
Q ss_pred CCCCe---EEEccccccccCCccceEEEeEEeCCCCcCCccceEEEEEecCC--CceEEEeccccCCCCHHHHHH
Q 003762 630 RSLNW---LKLKKDYIESIGDSLDLVPIAAFHGRGKRTGVYGAFLLACYDSN--NEEFQSICKIGTGFSEAMLEE 699 (797)
Q Consensus 630 Rs~~W---lKlK~dY~~~~~dtlDlvVIGa~~G~Gkr~g~~gsfllg~~d~~--~g~~~~vgkVGTGfSd~~l~~ 699 (797)
+.+.| +|+..+ ...-.|.+..|--| |+|.++.. |..++- .|.. |.++ |..+.++.++
T Consensus 299 ~~PrwaiA~Kf~~~-------~~~T~l~~I~~qVG-RTG~iTPv--A~lePV~l~G~t--VsrA-TLhN~~~i~~ 360 (441)
T smart00532 299 KAPRWAIAYKFPAE-------EAETKLLDIIVQVG-RTGKITPV--AELEPVFLAGST--VSRA-TLHNEDEIEE 360 (441)
T ss_pred CCCCeeEEECCCCc-------eeEEEEEEEEEecC-CCceeeEE--EEEEeEEECCEE--EEec-ccCCHHHHHH
Confidence 45678 566664 45556777777666 56665543 334331 2433 3343 5666666654
No 54
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=98.01 E-value=0.00012 Score=87.77 Aligned_cols=238 Identities=17% Similarity=0.219 Sum_probs=139.7
Q ss_pred cccccc-ccCChHHHH---hhcC------CCceEEEeecceEEEEEEEecCCe-EEEEec----CCCccCCCcchHHHHH
Q 003762 433 GPMLAK-PTKGVSEIV---NKFQ------DMEFTCEYKYDGERAQIHYLEDGS-VEIYSR----NAERNTGKFPDVVLAV 497 (797)
Q Consensus 433 ~PMLA~-~~~~i~~~l---~k~~------g~~~~~E~KyDG~R~qih~~~~g~-V~ifSR----~gkd~T~~yPel~~~l 497 (797)
.|||.- .+.+.+++. ++.. ...|+||+|+||.-+.+.+. +|+ ++..|| .|+|+|+..--+. .|
T Consensus 78 ~pMlSL~k~~~~~el~~w~~r~~~~~~~~~~~~~~epKiDGlsisL~Y~-~G~L~~a~TRGDG~~GeDvT~n~~~I~-~I 155 (665)
T PRK07956 78 VPMLSLDNAFSEEELRAFDKRVRKRLPDPPLTYLCELKIDGLAVSLLYE-NGVLVRAATRGDGTTGEDITANVRTIR-SI 155 (665)
T ss_pred CcCcCccccCCHHHHHHHHHHHHHhcCCCCcceEEEEecccEEEEEEEE-CCEEEEEEecCCCccchhHhhhhhhhc-cC
Confidence 389863 233444442 2222 12599999999999999994 676 788999 7899987532211 12
Q ss_pred HhhcC-CCCCCeEEEEEEEEEecCCCcccChhhHHhh-------------------hcccCCccccccceEEEEeeeeec
Q 003762 498 SRLKK-PSVRSFVLDCEIVAYDREKQKILPFQTLSTR-------------------ARKNVSLSDIKVDVCIYAFDILYR 557 (797)
Q Consensus 498 ~~~~~-~~v~~~ILDGElVa~d~~~g~~lpFq~L~~R-------------------~Rk~~~~~~~~~~v~~~vFDILyl 557 (797)
+..++ ..-..+.+-||++.-. ..|+.+-.+ .|..........++.|++|++...
T Consensus 156 P~~l~~~~p~~levRGEv~m~~------~~F~~lN~~~~~~g~~~faNpRNaaAGslr~ld~~~~~~r~L~f~~y~~~~~ 229 (665)
T PRK07956 156 PLRLHGNEPERLEVRGEVFMPK------ADFEALNEERREEGEKPFANPRNAAAGSLRQLDPKITAKRPLSFFAYGVGEV 229 (665)
T ss_pred ChhhcccCCCeEEEEEEEEEEH------HHHHHHHHHHHhcCCCcccChHHHHhhhhhccChHHHhcCCCEEEEEecccc
Confidence 22221 0113588999999852 235544221 111100011246899999998644
Q ss_pred CCccccCCcHHHHHHHHHHhhccCCCcEEEEeEEecCCHHHHHHHHHHHHH------cCCceeEEEeCCCCCCcc----C
Q 003762 558 NGQPLLQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAAVD------ASCEGLIIKTMDRDATYE----P 627 (797)
Q Consensus 558 nG~~L~~~Pl~ERr~lL~~l~~~~~~~i~~v~~~~~~~~eei~~~f~~ai~------~g~EGlmvK~~~~ds~Y~----p 627 (797)
++ ........++.+.|.++-=++..... .+.+.+++.+++++..+ -.-.|||+|-- +-.|. .
T Consensus 230 ~~-~~~~~t~~e~l~~L~~~GF~v~~~~~-----~~~~~~ei~~~~~~~~~~R~~l~y~iDGiViKvn--~~~~~~~lG~ 301 (665)
T PRK07956 230 EG-GELPDSQSEALEFLKAWGFPVNPYRK-----LCTSIEEVLAFYEEIEEERHDLPYDIDGVVIKVD--DLALQEELGF 301 (665)
T ss_pred cC-CCCCCCHHHHHHHHHHCCCCcCCceE-----eeCCHHHHHHHHHHHHHhhccCCCCCCcEEEEec--CHHHHHhcCc
Confidence 32 11134778899999887323322222 35678999999887763 36689999985 43332 1
Q ss_pred CCCCCCe---EEEccccccccCCccceEEEeEEeCCCCcCCccceEEEEEecCC--CceEEEeccccCCCCHHHHHH
Q 003762 628 SKRSLNW---LKLKKDYIESIGDSLDLVPIAAFHGRGKRTGVYGAFLLACYDSN--NEEFQSICKIGTGFSEAMLEE 699 (797)
Q Consensus 628 GkRs~~W---lKlK~dY~~~~~dtlDlvVIGa~~G~Gkr~g~~gsfllg~~d~~--~g~~~~vgkVGTGfSd~~l~~ 699 (797)
..+.+.| +|+..+ ...-.|.+..|.-| |+|.++.. |..+|- .|.. |.++ |..+.++.++
T Consensus 302 t~~~PrWaiA~Kf~~~-------~~~T~l~~I~~qVG-RTG~iTPV--A~l~PV~l~G~t--VsrA-tLhN~~~i~~ 365 (665)
T PRK07956 302 TAKAPRWAIAYKFPAE-------EATTKLLDIEVQVG-RTGAVTPV--ARLEPVEVAGVT--VSRA-TLHNADEIER 365 (665)
T ss_pred cCCCCCceeEecCCCc-------eeEEEEEEEEEecC-CCceeeeE--EEEEeEEECCEE--EEEe-ecCCHHHHHH
Confidence 2356778 666664 45556777777666 56666544 334331 2433 3343 5666666654
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=97.98 E-value=0.00011 Score=80.45 Aligned_cols=185 Identities=15% Similarity=0.205 Sum_probs=111.9
Q ss_pred cccccc-ccCChHHHH---hhcC-----CCceEEEeecceEEEEEEEecCCe-EEEEec----CCCccCCCcchHHHHHH
Q 003762 433 GPMLAK-PTKGVSEIV---NKFQ-----DMEFTCEYKYDGERAQIHYLEDGS-VEIYSR----NAERNTGKFPDVVLAVS 498 (797)
Q Consensus 433 ~PMLA~-~~~~i~~~l---~k~~-----g~~~~~E~KyDG~R~qih~~~~g~-V~ifSR----~gkd~T~~yPel~~~l~ 498 (797)
.|||.- .+.+.+++. ++.. ...|+||+|+||.-+.+.+. +|+ ++..|| .|+|+|....-|. .|.
T Consensus 72 ~pMlSL~k~~~~~el~~~~~r~~~~~~~~~~~~vepKiDGlsisL~Y~-~G~L~~a~TRGdG~~GeDVT~nv~~I~-~IP 149 (307)
T cd00114 72 VPMLSLDNAFDEEELRAFDERIKRFLGEEPAYVVEPKIDGLSISLRYE-NGVLVQAATRGDGTTGEDVTENVRTIR-SIP 149 (307)
T ss_pred CcCccccccCCHHHHHHHHHHHHHhcCCCCcEEEEEeccceEEEEEEE-CCEEEEEEecCCCcchhhHHhhHhhhc-ccC
Confidence 489863 233444432 2221 12699999999999999994 676 789999 7899987543221 122
Q ss_pred hhcCCCCCCeEEEEEEEEEecCCCcccChhhHHh-------------------hhcccCCccccccceEEEEeeeeecCC
Q 003762 499 RLKKPSVRSFVLDCEIVAYDREKQKILPFQTLST-------------------RARKNVSLSDIKVDVCIYAFDILYRNG 559 (797)
Q Consensus 499 ~~~~~~v~~~ILDGElVa~d~~~g~~lpFq~L~~-------------------R~Rk~~~~~~~~~~v~~~vFDILylnG 559 (797)
..++.....+.+-||++.-. ..|+.+-. -+|..........++.|++|++...++
T Consensus 150 ~~i~~~~~~levRGEv~m~~------~~F~~~n~~~~~~~~~~faNpRNaaAGsLr~ld~~~~~~r~L~f~~y~~~~~~~ 223 (307)
T cd00114 150 LTLAGAPETLEVRGEVFMPK------ADFEALNKEREERGEKPFANPRNAAAGSLRQLDPKITAKRPLRFFIYGLGEAEG 223 (307)
T ss_pred hhhcCCCCeEEEEEEEEEEH------HHHHHHHHHHHHcCCCCccChHHHHHHHHHhcCcchhhcCcceEEEEecccccC
Confidence 22211124689999999852 13443321 111111111125689999999865442
Q ss_pred ccccCCcHHHHHHHHHHhhccCCCcEEEEeEEecCCHHHHHHHHHHHHHc------CCceeEEEeCCCCCCcc----CCC
Q 003762 560 QPLLQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAAVDA------SCEGLIIKTMDRDATYE----PSK 629 (797)
Q Consensus 560 ~~L~~~Pl~ERr~lL~~l~~~~~~~i~~v~~~~~~~~eei~~~f~~ai~~------g~EGlmvK~~~~ds~Y~----pGk 629 (797)
.. -....++.+.|+++-=+++.... .+.+.+++.+++++..+. .-.|||+|-- +-.+. ...
T Consensus 224 ~~--~~t~~e~l~~L~~~GF~v~~~~~-----~~~~~~ev~~~~~~~~~~R~~l~y~iDGiViKvn--~~~~~~~lG~ts 294 (307)
T cd00114 224 LG--PKTQSEALAFLKEWGFPVSPETR-----LCKNIEEVLAFYDEIEAKRDSLPYEIDGVVVKVD--DLALQRELGFTS 294 (307)
T ss_pred CC--CCCHHHHHHHHHHCCCCCCCCeE-----EeCCHHHHHHHHHHHHHhhhcCCCCCCcEEEEEe--CHHHHHHhCccC
Confidence 11 24778899999887333333222 356789999998887433 6789999985 44332 223
Q ss_pred CCCCe
Q 003762 630 RSLNW 634 (797)
Q Consensus 630 Rs~~W 634 (797)
+.+.|
T Consensus 295 k~PrW 299 (307)
T cd00114 295 KAPRW 299 (307)
T ss_pred CCCCc
Confidence 45667
No 56
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=97.89 E-value=0.00042 Score=83.46 Aligned_cols=235 Identities=18% Similarity=0.231 Sum_probs=139.0
Q ss_pred ccccc-ccCChHHHH---hh----cCCCceEEEeecceEEEEEEEecCCe-EEEEec----CCCccCCCcchHHHHHHhh
Q 003762 434 PMLAK-PTKGVSEIV---NK----FQDMEFTCEYKYDGERAQIHYLEDGS-VEIYSR----NAERNTGKFPDVVLAVSRL 500 (797)
Q Consensus 434 PMLA~-~~~~i~~~l---~k----~~g~~~~~E~KyDG~R~qih~~~~g~-V~ifSR----~gkd~T~~yPel~~~l~~~ 500 (797)
|||.- .+.+.+++. ++ ++...|+||+|+||.-+-+.+. +|+ ++..|| .|+|+|+....+. .|+..
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 89863 233455542 11 2324699999999999999995 665 789999 7999997543221 12222
Q ss_pred cCC-CCCCeEEEEEEEEEecCCCcccChhhHHh-------------------hhcccCCccccccceEEEEeeeeecCCc
Q 003762 501 KKP-SVRSFVLDCEIVAYDREKQKILPFQTLST-------------------RARKNVSLSDIKVDVCIYAFDILYRNGQ 560 (797)
Q Consensus 501 ~~~-~v~~~ILDGElVa~d~~~g~~lpFq~L~~-------------------R~Rk~~~~~~~~~~v~~~vFDILylnG~ 560 (797)
+.. .-..+.+=||++.-. ..|+.+-. -.|+.........++.|++|++...++.
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 113478889999853 23444421 1111110011246899999998655431
Q ss_pred cccCCcHHHHHHHHHHhhccCCCcEEEEeEEecCCHHHHHHHHHHHHH------cCCceeEEEeCCCCCCcc----CCCC
Q 003762 561 PLLQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAAVD------ASCEGLIIKTMDRDATYE----PSKR 630 (797)
Q Consensus 561 ~L~~~Pl~ERr~lL~~l~~~~~~~i~~v~~~~~~~~eei~~~f~~ai~------~g~EGlmvK~~~~ds~Y~----pGkR 630 (797)
.....++.+.|..+-=++..... .+.+.+++.++++...+ -.-.|||+|-- +-.+. ...+
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 24678888888887333333222 25778888888876643 35689999986 44332 1235
Q ss_pred CCCe---EEEccccccccCCccceEEEeEEeCCCCcCCccceEEEEEecCC--CceEEEeccccCCCCHHHHHH
Q 003762 631 SLNW---LKLKKDYIESIGDSLDLVPIAAFHGRGKRTGVYGAFLLACYDSN--NEEFQSICKIGTGFSEAMLEE 699 (797)
Q Consensus 631 s~~W---lKlK~dY~~~~~dtlDlvVIGa~~G~Gkr~g~~gsfllg~~d~~--~g~~~~vgkVGTGfSd~~l~~ 699 (797)
.+.| +|+..+ ...-.|.+..|--| |+|.++.. |..+|- .|.. |.++ |..+.++.++
T Consensus 327 ~PrWaiA~Kf~~~-------~~~T~l~~I~~qVG-RTG~iTPV--A~lePV~l~G~t--Vsra-tLhN~~~i~~ 387 (689)
T PRK14351 327 APRWAFAYKFPAR-------AEETTIRDIVVQVG-RTGRLTPV--ALLDPVDVGGVT--VSRA-SLHNPAEIEE 387 (689)
T ss_pred CCCceEEEcCCCc-------eeEEEEEEEEEecC-CCceeeeE--EEEEeEEECCEE--EEEe-ccCCHHHHHH
Confidence 6778 566654 45556777777666 56666543 334431 2433 3444 5566666654
No 57
>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=97.82 E-value=0.00053 Score=82.33 Aligned_cols=237 Identities=16% Similarity=0.197 Sum_probs=139.8
Q ss_pred cccccc-ccCChHHHH---hhcC---C--CceEEEeecceEEEEEEEecCCe-EEEEec----CCCccCCCcchHHHHHH
Q 003762 433 GPMLAK-PTKGVSEIV---NKFQ---D--MEFTCEYKYDGERAQIHYLEDGS-VEIYSR----NAERNTGKFPDVVLAVS 498 (797)
Q Consensus 433 ~PMLA~-~~~~i~~~l---~k~~---g--~~~~~E~KyDG~R~qih~~~~g~-V~ifSR----~gkd~T~~yPel~~~l~ 498 (797)
.|||.- .+.+.+++. ++.. + ..|+||+|+||.-+.+.+. +|+ ++..|| .|+|+|+..-.+. .|+
T Consensus 67 ~pMlSL~k~~~~~el~~~~~r~~~~~~~~~~~~~epKiDGlaisL~Ye-~G~L~~a~TRGDG~~GeDvT~nv~~I~-~iP 144 (652)
T TIGR00575 67 TPMLSLDNAFDEDELAAFIKRIRRQLGLKVEYVVEPKIDGLSVSLTYE-NGVLVRALTRGDGTVGEDVTANVRTIR-SIP 144 (652)
T ss_pred CcCcCccccCCHHHHHHHHHHHHHhcCCCceEEEEEeccceEEEEEEE-CCEEEEEEecCCCccchhHhhhhhhhc-ccc
Confidence 389863 233444442 2221 1 2599999999999999994 676 789999 7899987533221 122
Q ss_pred hhcCC--CCCCeEEEEEEEEEecCCCcccChhhHH-------------------hhhcccCCccccccceEEEEeeeeec
Q 003762 499 RLKKP--SVRSFVLDCEIVAYDREKQKILPFQTLS-------------------TRARKNVSLSDIKVDVCIYAFDILYR 557 (797)
Q Consensus 499 ~~~~~--~v~~~ILDGElVa~d~~~g~~lpFq~L~-------------------~R~Rk~~~~~~~~~~v~~~vFDILyl 557 (797)
..+.. .-..+.+-||++.-. ..|+.+- .-.|..........++.|++|++...
T Consensus 145 ~~i~~~~~p~~levRGEv~m~~------~~F~~~N~~~~~~g~~~faNpRN~aAGslr~ld~~~~~~r~L~~~~y~~~~~ 218 (652)
T TIGR00575 145 LRLAGDNPPERLEVRGEVFMPK------EDFEALNEERREQGEKPFANPRNAAAGSLRQLDPRITAKRKLRFFAYGLGEG 218 (652)
T ss_pred hhhcCCCCCceEEEEEEEEEEH------HHHHHHHHHHHHcCCCCCCCcHHHHHHHHHcCCchhhhcCccEEEEEecccc
Confidence 22221 113588999999852 1344431 11121111111256899999998532
Q ss_pred CCccccCCcHHHHHHHHHHhhccCCCcEEEEeEEecCCHHHHHHHHHHHHH------cCCceeEEEeCCCCCCcc----C
Q 003762 558 NGQPLLQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAAVD------ASCEGLIIKTMDRDATYE----P 627 (797)
Q Consensus 558 nG~~L~~~Pl~ERr~lL~~l~~~~~~~i~~v~~~~~~~~eei~~~f~~ai~------~g~EGlmvK~~~~ds~Y~----p 627 (797)
+ ........++.+.|+++-=++..... .+.+.+++.++++++.+ -.-.|+|+|-- +-.+. .
T Consensus 219 ~--~~~~~t~~e~l~~L~~~GF~v~~~~~-----~~~~~~ei~~~~~~~~~~R~~l~y~iDGiViKvn--~~~~~~~lG~ 289 (652)
T TIGR00575 219 L--ELPDATQYEALAWLKKWGFPVSPHIR-----LCDSIEEVLEYYREIEEKRDSLPYEIDGVVVKVD--DLALQDELGF 289 (652)
T ss_pred C--CCCCCCHHHHHHHHHHCCCCCCCCeE-----eeCCHHHHHHHHHHHHHhhhcCCCCCCcEEEEec--CHHHHHHhCc
Confidence 2 21124778889999887323333222 25678999999887743 36789999975 44442 1
Q ss_pred CCCCCCe---EEEccccccccCCccceEEEeEEeCCCCcCCccceEEEEEecCC--CceEEEeccccCCCCHHHHHH
Q 003762 628 SKRSLNW---LKLKKDYIESIGDSLDLVPIAAFHGRGKRTGVYGAFLLACYDSN--NEEFQSICKIGTGFSEAMLEE 699 (797)
Q Consensus 628 GkRs~~W---lKlK~dY~~~~~dtlDlvVIGa~~G~Gkr~g~~gsfllg~~d~~--~g~~~~vgkVGTGfSd~~l~~ 699 (797)
..+.+.| +|+.++ ...-.|.+..|--| |+|.++.. |..+|- .|.. |.++ |..+.++.++
T Consensus 290 t~~~PrwaiA~Kf~~~-------~~~T~l~~I~~qVG-RTG~iTPv--A~lePV~l~G~~--VsrA-tLhN~~~i~~ 353 (652)
T TIGR00575 290 TSKAPRWAIAYKFPAE-------EAQTKLLDVVVQVG-RTGAITPV--AKLEPVFVAGTT--VSRA-TLHNEDEIEE 353 (652)
T ss_pred cCCCCCceEEEcCCCc-------eeeEEEEEEEEecC-CCceeeeE--EEEeeEEECCEE--EEEe-ecCCHHHHHH
Confidence 2356778 666664 55557777777666 56666554 334431 2433 3343 5666666654
No 58
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=97.82 E-value=0.00048 Score=82.64 Aligned_cols=217 Identities=18% Similarity=0.178 Sum_probs=127.5
Q ss_pred ceEEEeecceEEEEEEEecCCe-EEEEec----CCCccCCCcchHHHHHHhhcCCCCCCeEEEEEEEEEecCCCcccChh
Q 003762 454 EFTCEYKYDGERAQIHYLEDGS-VEIYSR----NAERNTGKFPDVVLAVSRLKKPSVRSFVLDCEIVAYDREKQKILPFQ 528 (797)
Q Consensus 454 ~~~~E~KyDG~R~qih~~~~g~-V~ifSR----~gkd~T~~yPel~~~l~~~~~~~v~~~ILDGElVa~d~~~g~~lpFq 528 (797)
+|+||+|+||.-+-+.+. +|+ ++..|| .|+|+|+..--+ ..|+..++. ...+.+-||++.-. ..|+
T Consensus 111 ~~~~epKiDGlaisL~Ye-nG~L~~a~TRGDG~~GEDVT~n~~~I-~~IP~~l~~-~~~levRGEv~m~~------~~F~ 181 (669)
T PRK14350 111 GISVEPKIDGCSIVLYYK-DGILEKALTRGDGRFGNDVTENVRTI-RNVPLFIDE-KVELVLRGEIYITK------ENFL 181 (669)
T ss_pred eEEEEEecccEEEEEEEE-CCEEEEEEecCCCCcchhHhhhhhhh-cccchhcCC-CceEEEEEEEEeeH------HHHH
Confidence 599999999999999994 676 789999 789998753211 112222221 24688999999842 2354
Q ss_pred hHHhh---------------hcccCCccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCCCcEEEEeEEec
Q 003762 529 TLSTR---------------ARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEPGFFQFATTLTS 593 (797)
Q Consensus 529 ~L~~R---------------~Rk~~~~~~~~~~v~~~vFDILylnG~~L~~~Pl~ERr~lL~~l~~~~~~~i~~v~~~~~ 593 (797)
.+-.. .|..........++.|++|++...++. ..+..++.+.|+++-=++.....+... .
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 111111111245899999998532221 236788888888873333333333211 2
Q ss_pred CCHHHHHHHHHHHHH------cCCceeEEEeCCCCCCccC--C--CCCCCe---EEEccccccccCCccceEEEeEEeCC
Q 003762 594 IDLDEIQKFLDAAVD------ASCEGLIIKTMDRDATYEP--S--KRSLNW---LKLKKDYIESIGDSLDLVPIAAFHGR 660 (797)
Q Consensus 594 ~~~eei~~~f~~ai~------~g~EGlmvK~~~~ds~Y~p--G--kRs~~W---lKlK~dY~~~~~dtlDlvVIGa~~G~ 660 (797)
++.+++.++++++.+ -.-.|||+|-- +-.+.. | .+.+.| +|+.++ ...-.|.+..|--
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 347888888876643 35689999985 332221 2 246778 666664 4555677777766
Q ss_pred CCcCCccceEEEEEecCC--CceEEEeccccCCCCHHHHHH
Q 003762 661 GKRTGVYGAFLLACYDSN--NEEFQSICKIGTGFSEAMLEE 699 (797)
Q Consensus 661 Gkr~g~~gsfllg~~d~~--~g~~~~vgkVGTGfSd~~l~~ 699 (797)
| |+|.++.. |..+|- .|. +|.++ |..+.++.++
T Consensus 328 G-RTG~iTPV--A~l~PV~l~G~--tVsrA-TLhN~~~I~~ 362 (669)
T PRK14350 328 G-RSGKITPV--ANIEKVFVAGA--FITNA-SLHNQDYIDS 362 (669)
T ss_pred C-CceeeeEE--EEEEeEEECCE--EEEEe-ccCCHHHHHH
Confidence 5 56666543 334431 243 34444 5666666664
No 59
>PF01653 DNA_ligase_aden: NAD-dependent DNA ligase adenylation domain; InterPro: IPR013839 DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA fragments by catalyzing the formation of an internucleotide ester bond between phosphate and deoxyribose. It is active during DNA replication, DNA repair and DNA recombination. There are two forms of DNA ligase: one requires ATP (6.5.1.1 from EC), the other NAD (6.5.1.2 from EC). This entry represents the N-terminal adenylation domain of NAD-dependent DNA ligases. These are proteins of about 75 to 85 Kd whose sequence is well conserved [, ]. They also show similarity to yicF, an Escherichia coli hypothetical protein of 63 Kd. Despite a complete lack of detectable sequence similarity, the fold of the central core of this adenyaltion domain shares homology with the equivalent region of ATP-dependent DNA ligases [, ].; GO: 0003911 DNA ligase (NAD+) activity; PDB: 1ZAU_A 3SGI_A 1B04_A 3JSL_A 3JSN_A 1DGS_A 1V9P_A 3PN1_A 3BAC_A 3UQ8_A ....
Probab=97.72 E-value=8.2e-05 Score=81.88 Aligned_cols=173 Identities=18% Similarity=0.249 Sum_probs=99.1
Q ss_pred cccccc-ccCChHHHH---hh----cCCC--ceEEEeecceEEEEEEEecCCe-EEEEec----CCCccCCCcchHHHHH
Q 003762 433 GPMLAK-PTKGVSEIV---NK----FQDM--EFTCEYKYDGERAQIHYLEDGS-VEIYSR----NAERNTGKFPDVVLAV 497 (797)
Q Consensus 433 ~PMLA~-~~~~i~~~l---~k----~~g~--~~~~E~KyDG~R~qih~~~~g~-V~ifSR----~gkd~T~~yPel~~~l 497 (797)
.|||.- .+.+.+++. ++ ++.. .|+||+|+||.-+.+++. +|. ++..|| -|+|+|....-+. .|
T Consensus 77 ~pMlSL~k~~s~eel~~w~~r~~~~~~~~~~~~~~e~KiDGlsi~L~Y~-~G~L~~a~TRGdG~~GeDvT~n~~~i~-~i 154 (315)
T PF01653_consen 77 VPMLSLDKAYSEEELRKWLKRVEKALGEEEEEFVVEPKIDGLSISLIYE-NGKLVRAATRGDGEVGEDVTHNVRTIK-SI 154 (315)
T ss_dssp S-----EEESSHHHHHHHHHHHHHHCSS-SSEEEEEEEESSEEEEEEEE-TTEEEEEEEETTSSEEEB-HHHHCTST-TS
T ss_pred ccccCccccCCHHHHHHHHHHHHHHhcccccceeEeeccceeEEEEEEe-CCEEEEEEEcCCCccchhHHHHHHHHh-cC
Confidence 389863 234444442 22 2332 499999999999999994 776 689999 6788886432221 12
Q ss_pred HhhcCCCCCCeEEEEEEEEEecCCCcccChhhHHhh-------------------hcccCCccccccceEEEEeeeeecC
Q 003762 498 SRLKKPSVRSFVLDCEIVAYDREKQKILPFQTLSTR-------------------ARKNVSLSDIKVDVCIYAFDILYRN 558 (797)
Q Consensus 498 ~~~~~~~v~~~ILDGElVa~d~~~g~~lpFq~L~~R-------------------~Rk~~~~~~~~~~v~~~vFDILyln 558 (797)
...+......+.+=||++.-. ..|+.+-.. +|..........++.|++|++.+.+
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 222221126788999999742 245555311 1111000112468999999999988
Q ss_pred CccccCCcHHHHHHHHHHhhccCCCcEEEEeEEecCCHHHHHHHHHHHHHc------CCceeEEEeC
Q 003762 559 GQPLLQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAAVDA------SCEGLIIKTM 619 (797)
Q Consensus 559 G~~L~~~Pl~ERr~lL~~l~~~~~~~i~~v~~~~~~~~eei~~~f~~ai~~------g~EGlmvK~~ 619 (797)
| ...-....++.+.|.++-=++...+.+ +.+.+++.++++...+. .-.|||+|--
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 333457788999998763333333333 56889999999887763 5579999985
No 60
>PF09414 RNA_ligase: RNA ligase; InterPro: IPR021122 This entry represents the RNA ligase domain. RNA ligase enzyme repairs RNA strand breaks in nicked DNA:RNA and RNA:RNA but not in DNA:DNA duplexes []. Members of this RNA ligase family include: RNA editing ligase 1 (REL1) , which is essential for RNA editing and may be active in U-deletion editing [, , ]. RNA editing ligase 2 (REL2), which may be active in U-insertion editing []. RnlB RNA ligase 2 (or Rnl2), second RNA ligase of Enterobacteria phage T4 (Bacteriophage T4); unlike RNA ligase 1, RnlB prefers doule stranded substrates [, ]. ; PDB: 2HVS_B 2HVR_A 1S68_A 2HVQ_A 1XDN_A.
Probab=97.37 E-value=0.00015 Score=73.32 Aligned_cols=159 Identities=21% Similarity=0.177 Sum_probs=83.1
Q ss_pred ceEEEeecceEEEEEEEecCCeEEEEecCCCc-----c------CCCcchHHHHH---Hh---hc-CCCCCCeEEEEEEE
Q 003762 454 EFTCEYKYDGERAQIHYLEDGSVEIYSRNAER-----N------TGKFPDVVLAV---SR---LK-KPSVRSFVLDCEIV 515 (797)
Q Consensus 454 ~~~~E~KyDG~R~qih~~~~g~V~ifSR~gkd-----~------T~~yPel~~~l---~~---~~-~~~v~~~ILDGElV 515 (797)
+|++++|+||.-+.+.+..++.+.+.+|++.. + ...|......+ .. .. .....++++=||++
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 69999999999999998766679999999832 1 11122221111 11 11 01347899999999
Q ss_pred EEecCCCcccChhhHHhhhcccCCccccccceEEEEeeeeecCCc-cccCCcHHHHHHHHHHhhccCCCcEEEEeEEecC
Q 003762 516 AYDREKQKILPFQTLSTRARKNVSLSDIKVDVCIYAFDILYRNGQ-PLLQEQLRVRREHLYDSFEEEPGFFQFATTLTSI 594 (797)
Q Consensus 516 a~d~~~g~~lpFq~L~~R~Rk~~~~~~~~~~v~~~vFDILylnG~-~L~~~Pl~ERr~lL~~l~~~~~~~i~~v~~~~~~ 594 (797)
.+-+. + .++.. ....+..|++|||...+.+ ...=++..+++.+++.+- +..++.....
T Consensus 82 G~~~~---I----------q~~~~--~~~~~~~F~~Fdi~~~~~~~~~~~l~~~~~~~~~~~~g------l~~VPvl~~g 140 (186)
T PF09414_consen 82 GAKPS---I----------QKNRY--QLDPPKDFYVFDIYDIDEQGEIRYLSWDEVREFAEELG------LKTVPVLYRG 140 (186)
T ss_dssp CEECT---T----------CSS------ECCCEEEEEEEEEEETCCGEEE-HHHHHHHHHCCCT-------EES-ECEEE
T ss_pred eeccc---c----------ccccc--ccCCCceEEEEEEEEcCCCCeeEECCHHHHHHHHHHCC------CCEeCEEEEE
Confidence 86421 0 00000 0012679999999988543 223457777888776651 2223222111
Q ss_pred CHHHHHH------HH-HHHHHcCCceeEEEeCCCCCCccCCCCCCCeEEEc
Q 003762 595 DLDEIQK------FL-DAAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLK 638 (797)
Q Consensus 595 ~~eei~~------~f-~~ai~~g~EGlmvK~~~~ds~Y~pGkRs~~WlKlK 638 (797)
...+... .. ...-..-.||+|+|.. +..+ .+.| .-+|.|
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 5555 4444 566665
No 61
>TIGR02307 RNA_lig_RNL2 RNA ligase, Rnl2 family. Members of this family ligate (seal breaks in) RNA. Members so far include phage proteins that can counteract a host defense of cleavage of specific tRNA molecules, trypanosome ligases involved in RNA editing, but no prokaryotic host proteins.
Probab=97.24 E-value=0.0027 Score=69.96 Aligned_cols=162 Identities=21% Similarity=0.182 Sum_probs=92.7
Q ss_pred CCCceEEEeecceEEEEEEEecCCeEEEEecCCCccC-CCc-------chHHHHHH---hhcC----CCCCCeEEEEEEE
Q 003762 451 QDMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNT-GKF-------PDVVLAVS---RLKK----PSVRSFVLDCEIV 515 (797)
Q Consensus 451 ~g~~~~~E~KyDG~R~qih~~~~g~V~ifSR~gkd~T-~~y-------Pel~~~l~---~~~~----~~v~~~ILDGElV 515 (797)
.+.+|.+.+|.||...-+.+++++.+++.||++.-.- +.| +++...++ +.+. ....++++=||++
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 4568999999999999888864448999999964321 112 22222222 2221 1357899999999
Q ss_pred EEecCCCcccChhhHHhhhcccCCccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCCCcEEEEeEEecCC
Q 003762 516 AYDREKQKILPFQTLSTRARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEPGFFQFATTLTSID 595 (797)
Q Consensus 516 a~d~~~g~~lpFq~L~~R~Rk~~~~~~~~~~v~~~vFDILylnG~~L~~~Pl~ERr~lL~~l~~~~~~~i~~v~~~~~~~ 595 (797)
.+....+. . -.+..|++|||.+....+..=+++.+-.+...... + +..++.....+
T Consensus 103 G~~~q~~~---------------~----Y~~~~fyaFdI~~~~~~~~~~L~~d~~~e~~~~~~----~-l~~ap~L~rGt 158 (325)
T TIGR02307 103 GPGYQKPV---------------V----YSDKDFYAFDIKYTETSDDVTLVDDYMMESFCNVP----K-LKYAPLLGRGT 158 (325)
T ss_pred cCcccCcc---------------c----cccccEEEEEEEEeccCcceEecHHHHHHHHHHcC----C-cccchhhcccC
Confidence 87321110 0 11468999999553121233456666666555442 1 22333333355
Q ss_pred HHHHHHH---HHHH-----H--------HcCCceeEEEeCCCCC-CccC-CCCCCCeEEEccc
Q 003762 596 LDEIQKF---LDAA-----V--------DASCEGLIIKTMDRDA-TYEP-SKRSLNWLKLKKD 640 (797)
Q Consensus 596 ~eei~~~---f~~a-----i--------~~g~EGlmvK~~~~ds-~Y~p-GkRs~~WlKlK~d 640 (797)
.+++.++ +..+ + .+=+||+|+|.. .. .|.. |.| .-+|.|.+
T Consensus 159 ~~e~l~~~~~~~s~~ip~l~~~~~~~~~~n~aEGvViKp~--~~~~~~~~g~r--~iiK~kn~ 217 (325)
T TIGR02307 159 LDELLAFDVENFTTDHPALVDAGNYPLEGNTAEGYVVKHC--RPGKWLRNGNR--TIIKCKNS 217 (325)
T ss_pred HHHHHhcccccccccCcccccccccCCCCCeeeeEEEeec--cccccccCCce--EEEEEecH
Confidence 6666655 1111 1 122899999998 42 2432 333 57888884
No 62
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=96.97 E-value=0.026 Score=67.10 Aligned_cols=173 Identities=17% Similarity=0.223 Sum_probs=114.6
Q ss_pred CceEEEeecceEEEEEEEecCCe-EEEEecC----CCccCCCcchHHHHHHhhcCCCCCCeEEEEEEEEEecCCCcccCh
Q 003762 453 MEFTCEYKYDGERAQIHYLEDGS-VEIYSRN----AERNTGKFPDVVLAVSRLKKPSVRSFVLDCEIVAYDREKQKILPF 527 (797)
Q Consensus 453 ~~~~~E~KyDG~R~qih~~~~g~-V~ifSR~----gkd~T~~yPel~~~l~~~~~~~v~~~ILDGElVa~d~~~g~~lpF 527 (797)
..|+||+|+||.-+-+.+ ++|. ++--||. |+|+|....-|. .|+..+..-....-+-||++.-- ..|
T Consensus 109 ~~y~~EpKiDGlsisL~Y-enG~Lv~aaTRGdG~~GEDiT~NvrtI~-~IP~~l~~~p~~lEVRGEvfm~k------~~F 180 (667)
T COG0272 109 VEYVVEPKIDGLAISLVY-ENGKLVRAATRGDGTTGEDITANVRTIR-SIPLKLPGAPAVLEVRGEVFMPK------EDF 180 (667)
T ss_pred cceEEEeecceEEEEEEE-ECCEEEEeeccCCCccccchhhhhhhHh-hhhhhccCCCceEEEEeEEEEeH------HHH
Confidence 479999999999999998 4675 7788875 799998765554 34444432235778999998741 346
Q ss_pred hhHHhhhccc------------------CCcc-ccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCCCcEEEE
Q 003762 528 QTLSTRARKN------------------VSLS-DIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEPGFFQFA 588 (797)
Q Consensus 528 q~L~~R~Rk~------------------~~~~-~~~~~v~~~vFDILylnG~~L~~~Pl~ERr~lL~~l~~~~~~~i~~v 588 (797)
+.+-...... .+.. ..+.++.+++|.+-...+. ..-.+..|+.+.|+.+-=++....
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 6654321110 0000 1246899999998865544 556778899999988733322222
Q ss_pred eEEecCCHHHHHHHHHHHHHc------CCceeEEEeCCCCCCcc-CC--CCCCCe---EEEccc
Q 003762 589 TTLTSIDLDEIQKFLDAAVDA------SCEGLIIKTMDRDATYE-PS--KRSLNW---LKLKKD 640 (797)
Q Consensus 589 ~~~~~~~~eei~~~f~~ai~~------g~EGlmvK~~~~ds~Y~-pG--kRs~~W---lKlK~d 640 (797)
..+.+.+++.++++.+... --.|+|+|--+ -..|+ -| .|.+.| +|+.++
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 2478999999999998763 45799999752 22232 12 367888 677775
No 63
>PHA02142 putative RNA ligase
Probab=95.89 E-value=0.089 Score=59.06 Aligned_cols=163 Identities=17% Similarity=0.181 Sum_probs=92.9
Q ss_pred ChHHHHh-hcCCCceEEEeecceEEEEEEEe--------------------cCCeEEEEecCCCc---cCCCcchHH---
Q 003762 442 GVSEIVN-KFQDMEFTCEYKYDGERAQIHYL--------------------EDGSVEIYSRNAER---NTGKFPDVV--- 494 (797)
Q Consensus 442 ~i~~~l~-k~~g~~~~~E~KyDG~R~qih~~--------------------~~g~V~ifSR~gkd---~T~~yPel~--- 494 (797)
++.+.++ +..+..|.+-.|+||.-+-+.+. ..|.+.+.|||... -++.|=.++
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 24467899999999999887732 25677889999862 122332322
Q ss_pred ---HHHHhhcCCCCCCeEEEEEEEEEecCCCcccChhhHHhhhcccCCccccccceEEEEeeeeecCCccccCCcHHHHH
Q 003762 495 ---LAVSRLKKPSVRSFVLDCEIVAYDREKQKILPFQTLSTRARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRR 571 (797)
Q Consensus 495 ---~~l~~~~~~~v~~~ILDGElVa~d~~~g~~lpFq~L~~R~Rk~~~~~~~~~~v~~~vFDILylnG~~L~~~Pl~ERr 571 (797)
+.+.++ -.++.+=||++.-.-.++ .-. .....|++|||-.++++. =+++.+++
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 223332 157889999998422111 100 112479999997777765 36889999
Q ss_pred HHHHHhhccCCCcEEEEeEEe-------cCCHHHHHHHHH--HHHHcCCceeEEEeCCCCCCccCCCCCCCeEEEccc
Q 003762 572 EHLYDSFEEEPGFFQFATTLT-------SIDLDEIQKFLD--AAVDASCEGLIIKTMDRDATYEPSKRSLNWLKLKKD 640 (797)
Q Consensus 572 ~lL~~l~~~~~~~i~~v~~~~-------~~~~eei~~~f~--~ai~~g~EGlmvK~~~~ds~Y~pGkRs~~WlKlK~d 640 (797)
++++++--+ .|+... ..+.+|+.++-+ ..-.+-+||+|+|.. . =..|+| -|+|.|..
T Consensus 293 ~~~~~~gl~------~VPvL~~~~~~~~~~s~eE~L~~A~~p~~~~~~~EGiViKp~--~--~~~g~r--~~fK~is~ 358 (366)
T PHA02142 293 DLCRTLGME------IVPQLGYSYPFQEFTNVKEMLAAADIPSINHKIAEGVVYKSV--E--LVNGRM--VHFKAINN 358 (366)
T ss_pred HHHHHcCCc------eeeeecccccccccCCHHHHHhhcCCCcccccccceEEEeec--c--ccCCce--EEEEEcCH
Confidence 988876221 222211 114444433321 000133799999986 3 111322 58998863
No 64
>KOG3132 consensus m3G-cap-specific nuclear import receptor (Snurportin1) [RNA processing and modification]
Probab=95.75 E-value=0.039 Score=57.84 Aligned_cols=152 Identities=20% Similarity=0.357 Sum_probs=106.4
Q ss_pred CCceEEEeecceEEEEEEEecCCeEEEEecCCCccCCCcchHHHHHHhhcCCCCCCeEEEEEEEEEecCCCcccChhhHH
Q 003762 452 DMEFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNTGKFPDVVLAVSRLKKPSVRSFVLDCEIVAYDREKQKILPFQTLS 531 (797)
Q Consensus 452 g~~~~~E~KyDG~R~qih~~~~g~V~ifSR~gkd~T~~yPel~~~l~~~~~~~v~~~ILDGElVa~d~~~g~~lpFq~L~ 531 (797)
+.+|++=.-==|-||+|.- ..|....|.|+|..+ ++||....-=..--.+.-.-.||||= ++
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-SRGTTVAYVKNGSTV-HRFPSALPGGNRRKGPANSYTILDCI---YH------------- 176 (325)
T ss_pred CcceEEEEeecCceEEEEe-cCCceEEEecCCeeE-eeccccCCCCCcCCCCcccceeeeee---ec-------------
Confidence 3579888888999999887 478888999999876 35554211000000011133466652 21
Q ss_pred hhhcccCCccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCCC--------cEE--EEeEEecCCHHHHHH
Q 003762 532 TRARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEPG--------FFQ--FATTLTSIDLDEIQK 601 (797)
Q Consensus 532 ~R~Rk~~~~~~~~~~v~~~vFDILylnG~~L~~~Pl~ERr~lL~~l~~~~~~--------~i~--~v~~~~~~~~eei~~ 601 (797)
+.+-.|+|.|++.++|.++.+.++.-|.-.|++-+.+.++ .+. .++...| +.+.+.+
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 1234799999999999999999999999999998876432 233 3444444 5677888
Q ss_pred HHHHHHHcCCceeEEEeCCCCCCccCCCC-CCCeEE
Q 003762 602 FLDAAVDASCEGLIIKTMDRDATYEPSKR-SLNWLK 636 (797)
Q Consensus 602 ~f~~ai~~g~EGlmvK~~~~ds~Y~pGkR-s~~WlK 636 (797)
.+.-.+.-...|+.+-.. ...|.||.. --+|||
T Consensus 244 ~~~~~~pf~~DGLLFYhk--s~~yqpgqsplvgwlk 277 (325)
T KOG3132|consen 244 AYTGSLPFVRDGLLFYHK--SVVYQPGQSPLVGWLK 277 (325)
T ss_pred HHcCCCceeeeeEEEeec--ceeeCCCCCccccccc
Confidence 888888888999999988 888999964 246875
No 65
>PRK03180 ligB ATP-dependent DNA ligase; Reviewed
Probab=94.56 E-value=0.16 Score=59.72 Aligned_cols=91 Identities=18% Similarity=0.211 Sum_probs=78.7
Q ss_pred CccchHHHHHHHHHHHhcc---chHHHHHHHHHHHHhhhcCCCCchHHHHHHHhCccCCCccccccCCChHHHHHHHHHH
Q 003762 189 ERVPFIFLSLVFDMISNET---GRILITDIVCNMLRTVMETTPEDLVPVVYLAANKIAPAHEGLELGIGDASIIKALAEA 265 (797)
Q Consensus 189 ~~~~F~~la~~~e~I~~ts---sR~~k~~iL~~~fr~~i~~~p~dl~~~vyL~~~~l~P~~e~~elGIge~~L~kal~~a 265 (797)
.+.+..++=+.|++|+..+ +..+|.++|..+|..+ ++.+.-+.+.++++.+ .+|+++.++..||+++
T Consensus 71 ~~ltl~~V~~~l~~ia~~~g~~s~~~k~~~l~~ll~~~---~~~E~~~l~r~i~~~l-------RiGv~~~~v~~Ala~a 140 (508)
T PRK03180 71 PTLTVADVDAALSEIAAVAGAGSQARRAALLAALFAAA---TEDEQRFLRRLLTGEL-------RQGALDGVMADAVARA 140 (508)
T ss_pred CCCcHHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHhC---CHHHHHHHHHHHhCCC-------cccccHHHHHHHHHHH
Confidence 3566777777888888865 5589999999999986 7899999999998754 5899999999999999
Q ss_pred hCCCHHHHHHHHHhcCCHHHHHhh
Q 003762 266 CGRTESHVKKQYQEMGDLGLVAKA 289 (797)
Q Consensus 266 ~G~s~~~ik~~y~~~GDlg~vA~~ 289 (797)
++++...++..|..+||++.++..
T Consensus 141 ~~~~~~~v~~a~~~~~dl~~v~~~ 164 (508)
T PRK03180 141 AGVPAAAVRRAAMLAGDLPAVAAA 164 (508)
T ss_pred hCCCHHHHHHHHHHcCCHHHHHHH
Confidence 999999999999999999999864
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=93.43 E-value=1.6 Score=48.85 Aligned_cols=155 Identities=14% Similarity=0.183 Sum_probs=84.2
Q ss_pred CCceEEEeecceEEEEEEEec-CCeE-----EEEecCCC---ccCCCcchH------HHHHHhhcCCCCCCeEEEEEEEE
Q 003762 452 DMEFTCEYKYDGERAQIHYLE-DGSV-----EIYSRNAE---RNTGKFPDV------VLAVSRLKKPSVRSFVLDCEIVA 516 (797)
Q Consensus 452 g~~~~~E~KyDG~R~qih~~~-~g~V-----~ifSR~gk---d~T~~yPel------~~~l~~~~~~~v~~~ILDGElVa 516 (797)
+..|.+-.|+||.-+-+.+.. .+.+ -+-|||.+ +-++.|-.. .+.+.+.. .-.++.+=||++.
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 2332 24578876 222333222 23333211 1257889999997
Q ss_pred EecCCCcccChhhHHhhhcccCCccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCCCcEEEEeEEecCCH
Q 003762 517 YDREKQKILPFQTLSTRARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDL 596 (797)
Q Consensus 517 ~d~~~g~~lpFq~L~~R~Rk~~~~~~~~~~v~~~vFDILylnG~~L~~~Pl~ERr~lL~~l~~~~~~~i~~v~~~~~~~~ 596 (797)
-.-.++. + ....+-.+++|++ +.+|+. .=++++++.+++..+.. |- + + ..+.
T Consensus 236 ~gIQ~n~---Y--------------g~~~~~~~f~F~v-~~~~~~-ryld~~~~~~~~~~~~V--Pv-L-~-----~g~~ 287 (341)
T TIGR02306 236 PGIQKNR---Y--------------GFDKYRTVFAFRA-FFDGEQ-RFLTDEDFQDLCLTLIV--PQ-L-Y-----EGPF 287 (341)
T ss_pred ccccCCc---C--------------CCCCCceEEEEEE-EEcCcc-eecCHHHHHHHHHhccc--ce-E-E-----Eech
Confidence 4221110 0 0011222778887 555442 23588999998887522 21 1 1 1122
Q ss_pred HHHHHHHHHHHHc---------CCceeEEEeCCCCCCccCCCCCCCeEEEccc
Q 003762 597 DEIQKFLDAAVDA---------SCEGLIIKTMDRDATYEPSKRSLNWLKLKKD 640 (797)
Q Consensus 597 eei~~~f~~ai~~---------g~EGlmvK~~~~ds~Y~pGkRs~~WlKlK~d 640 (797)
++ ...++.++.. =+||+|+|.. ...|-... +.-|+|.|..
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 2899999998 66553322 2359998863
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=92.35 E-value=0.58 Score=55.19 Aligned_cols=93 Identities=18% Similarity=0.261 Sum_probs=78.7
Q ss_pred CccchHHHHHHHHHHHhcc---chHHHHHHHHHHHHhhhcCCCCchHHHHHHHhCccCCCccccccCCChHHHHHHHHHH
Q 003762 189 ERVPFIFLSLVFDMISNET---GRILITDIVCNMLRTVMETTPEDLVPVVYLAANKIAPAHEGLELGIGDASIIKALAEA 265 (797)
Q Consensus 189 ~~~~F~~la~~~e~I~~ts---sR~~k~~iL~~~fr~~i~~~p~dl~~~vyL~~~~l~P~~e~~elGIge~~L~kal~~a 265 (797)
.++.-.++-+.++.|++.+ ++.+|.++|.++|+.+ +|.+.-+.+.++++.+ ..|+++.++.++|+.+
T Consensus 53 ~~lti~eV~~~L~~ia~~~g~~s~~~k~~~l~~ll~~~---~~~e~k~l~r~i~~~l-------riG~~~~~il~al~~~ 122 (514)
T TIGR00574 53 APLTVKEVYETLKNIAETSGEGSQDKKIKLLKSLLKRA---SPLEAKYLIRTILGDL-------RIGIAEKTILDALAKA 122 (514)
T ss_pred CCcCHHHHHHHHHHHHHhhCCCcHHHHHHHHHHHHHhC---CHHHHHHHHHHHhhhc-------ccCccHHHHHHHHHHH
Confidence 3566777888888888764 5788999999999886 7899999998888743 5799999999999999
Q ss_pred hCCCHHHHHHHHHhcCCHHHHHhhcc
Q 003762 266 CGRTESHVKKQYQEMGDLGLVAKASR 291 (797)
Q Consensus 266 ~G~s~~~ik~~y~~~GDlg~vA~~~r 291 (797)
++++...+...|....|++.|+..+.
T Consensus 123 ~~~~~~~~~~~~~~~~dl~~v~~~l~ 148 (514)
T TIGR00574 123 FLLSHPDVERAFNLTNDLGKVAKILL 148 (514)
T ss_pred hccchHHHHHHHHhCCCHHHHHHHHH
Confidence 99999999999999999999987653
No 68
>KOG2386 consensus mRNA capping enzyme, guanylyltransferase (alpha) subunit [RNA processing and modification]
Probab=92.21 E-value=0.091 Score=59.32 Aligned_cols=97 Identities=16% Similarity=0.161 Sum_probs=67.0
Q ss_pred ceEEEeecceEEEEEEEecCCeEEEEecCCCccC---CCcchHHHHHHhhcCCCCCCeEEEEEEEEEecCCCcccChhhH
Q 003762 454 EFTCEYKYDGERAQIHYLEDGSVEIYSRNAERNT---GKFPDVVLAVSRLKKPSVRSFVLDCEIVAYDREKQKILPFQTL 530 (797)
Q Consensus 454 ~~~~E~KyDG~R~qih~~~~g~V~ifSR~gkd~T---~~yPel~~~l~~~~~~~v~~~ILDGElVa~d~~~g~~lpFq~L 530 (797)
.|.+.||.||.|...-++.+|.+..|-|.-...- -+++.- ..........++|||++. |.-++
T Consensus 286 ~y~~~We~dg~~~~~L~~~~~~~~~~dR~~~~~~~~~~~~~~~-----~~~~~~~~~tl~dge~~l-D~l~~-------- 351 (393)
T KOG2386|consen 286 YYEASWEADGTRYMMLIDGDGEYYDFDRWRFVKGRENLRKIRE-----DSDTKVLHQTLLDGEMIL-DRLKE-------- 351 (393)
T ss_pred hhhhhhcccCcEEEEEecCCceeEechhhhHHHhhhhhhcccc-----cccchhhhhhhcccceec-ccccc--------
Confidence 4678999999999988876777777776543221 011110 001123457899999998 64332
Q ss_pred HhhhcccCCccccccceEEEEeeeeecCCccccCCcHHHHHHHHHHhh
Q 003762 531 STRARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSF 578 (797)
Q Consensus 531 ~~R~Rk~~~~~~~~~~v~~~vFDILylnG~~L~~~Pl~ERr~lL~~l~ 578 (797)
.....|.+||++-+|++.+...|+. |.+.+..-+
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 1235788999999999999999999 998876543
No 69
>PRK09247 ATP-dependent DNA ligase; Validated
Probab=91.42 E-value=0.55 Score=55.78 Aligned_cols=87 Identities=13% Similarity=0.127 Sum_probs=67.0
Q ss_pred HHHHHHHHHHHHhCCChHHHHHHHHHHHHHhcCCChHHHHHHHHhhhcc-CcccHHHHHHHHHHhhccCCCCCCCCCCCc
Q 003762 307 KVFDTFRLIAKEAGKDSQEKKKNRIKALLVAATDCEPQYLIRLLQSKLR-IGLAEQTLLAALGQAAVYNEQHSKPPPNIQ 385 (797)
Q Consensus 307 eV~~~L~kIA~~~G~~s~~~K~~~L~~LL~~~t~~E~k~LiRiIlkdLR-iGi~e~tvl~Ala~a~~~~~~~~~~~~~l~ 385 (797)
+.-+.+++|+..+ +...|.++|..+|.++++.+.-|.++++++.+. .|++++.+.+|++.++..+.
T Consensus 3 ~fa~~~~~i~~t~---~~~ek~~~l~~~~~~~~~~d~~~~~~ll~g~~~~~~i~~~~l~k~~~~~~g~~~---------- 69 (539)
T PRK09247 3 AFAELLDRLDLTT---STNAKLALLADYFRSAPDPDRAWALALLTGGLPRRLVKTRLLRELAAERADLPP---------- 69 (539)
T ss_pred HHHHHHHHHHhcc---CHHHHHHHHHHHHHhCCHHHHHHHHHHhcCCcccCCCCHHHHHHHHHHHHCcCH----------
Confidence 4556677776544 456789999999999999999999999999885 99999999999999877542
Q ss_pred chHHHHHHHHHHHhhcCCchhhhHhhhh
Q 003762 386 SPLEEAAKIVKQVFSVLPVYEKIVPALL 413 (797)
Q Consensus 386 ~~l~~a~~~vk~~y~~~pd~~~v~~~l~ 413 (797)
..+++.|...-|++.++..++
T Consensus 70 -------~~~~~~~~~~GDlg~~~~~~~ 90 (539)
T PRK09247 70 -------WLFEESYDYVGDLAETIALLL 90 (539)
T ss_pred -------HHHHHHHHhcCCHHHHHHHhc
Confidence 233456666667777665543
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=90.11 E-value=0.75 Score=46.11 Aligned_cols=91 Identities=14% Similarity=0.205 Sum_probs=62.5
Q ss_pred HHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHhcCCChHHHHHHHHhhhc-------cCcccHHHHHHHHHHhhccCCCC
Q 003762 305 ITKVFDTFRLIAKEAGKDSQEKKKNRIKALLVAATDCEPQYLIRLLQSKL-------RIGLAEQTLLAALGQAAVYNEQH 377 (797)
Q Consensus 305 I~eV~~~L~kIA~~~G~~s~~~K~~~L~~LL~~~t~~E~k~LiRiIlkdL-------RiGi~e~tvl~Ala~a~~~~~~~ 377 (797)
..++.+.|++|++. .+..+|.++|..++..+.+.+..+.+.++++.+ ..|++++++.++++.++..++.
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 45667778888653 456678999999999999887777777777744 5899999999999999875432
Q ss_pred CCCCCCCcchHHHHHHHHHHHhhcCCchhhhHhhhhhc
Q 003762 378 SKPPPNIQSPLEEAAKIVKQVFSVLPVYEKIVPALLTD 415 (797)
Q Consensus 378 ~~~~~~l~~~l~~a~~~vk~~y~~~pd~~~v~~~l~~~ 415 (797)
.+.+.|...-|++.++..++..
T Consensus 79 ----------------~~~~~~~~~GD~g~~~~~~~~~ 100 (177)
T PF04675_consen 79 ----------------SIDESYKKVGDLGEVAEEVLQK 100 (177)
T ss_dssp ----------------HHHHHHHHHS-HHHHHHHHHHH
T ss_pred ----------------HHHHHHHhcCcHHHHHHHHHhh
Confidence 2334566678888887776643
No 71
>PLN03113 DNA ligase 1; Provisional
Probab=85.44 E-value=3.3 Score=50.98 Aligned_cols=92 Identities=23% Similarity=0.285 Sum_probs=69.0
Q ss_pred CCCCHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHhc---CCChHHHHHHHHhhhcc-------CcccHHHHHHHHHHh
Q 003762 301 DPLTITKVFDTFRLIAKEAGKDSQEKKKNRIKALLVAA---TDCEPQYLIRLLQSKLR-------IGLAEQTLLAALGQA 370 (797)
Q Consensus 301 ~~LTI~eV~~~L~kIA~~~G~~s~~~K~~~L~~LL~~~---t~~E~k~LiRiIlkdLR-------iGi~e~tvl~Ala~a 370 (797)
.++.-.++.++|++|...++ .-.|.++|..+|..+ ++++.-|.+.++.+.+. +|++++.+.+|++.+
T Consensus 127 ~~~~f~~l~~~~~~Ie~tt~---rlek~~~L~~~~r~~~~~~p~dl~~~vyL~~~~l~P~~e~~elgige~~L~kai~e~ 203 (744)
T PLN03113 127 ERVPFLFVALAFDLISNETG---RIVITDIVCNMLRTVMATTPEDLVAVVYLLANRIAPAHEGVELGIGEATIIKALAEA 203 (744)
T ss_pred CCccHHHHHHHHHHHHhccC---HHHHHHHHHHHHHHhccCChHHHHHHHHHHhCCCCccccCcccCcCHHHHHHHHHHH
Confidence 34567788888888876554 446889999999985 88999999999988774 699999999999998
Q ss_pred hccCCCCCCCCCCCcchHHHHHHHHHHHhhcCCchhhhHhhh
Q 003762 371 AVYNEQHSKPPPNIQSPLEEAAKIVKQVFSVLPVYEKIVPAL 412 (797)
Q Consensus 371 ~~~~~~~~~~~~~l~~~l~~a~~~vk~~y~~~pd~~~v~~~l 412 (797)
+..+.. .+++.|...-|++.++..+
T Consensus 204 ~g~~~~-----------------~ik~~y~~~GDlG~vA~~~ 228 (744)
T PLN03113 204 FGRTEK-----------------QVKKQYKELGDLGLVAKAS 228 (744)
T ss_pred HCcCHH-----------------HHHHHHHHhCCHHHHHHhh
Confidence 765421 2445555566666665543
No 72
>COG4566 TtrR Response regulator [Signal transduction mechanisms]
Probab=62.51 E-value=19 Score=37.31 Aligned_cols=86 Identities=19% Similarity=0.299 Sum_probs=58.1
Q ss_pred hcCCHHHHHhhccccCCCCCCCCCCCHHHHHHHHHHHHHH-hCCChHHHHHHHHHHHHHhcCCChHHHHHHHHhhhcc--
Q 003762 279 EMGDLGLVAKASRSSQSMMRKPDPLTITKVFDTFRLIAKE-AGKDSQEKKKNRIKALLVAATDCEPQYLIRLLQSKLR-- 355 (797)
Q Consensus 279 ~~GDlg~vA~~~r~~q~~l~~~~~LTI~eV~~~L~kIA~~-~G~~s~~~K~~~L~~LL~~~t~~E~k~LiRiIlkdLR-- 355 (797)
-+||+..+++.++..- .-|=.+|..-+++.+++.+--.. ............+..+|..+|+.|...|-+++.+.+.
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 3689988887765431 11234677777777766543221 1112223345789999999999999999999988663
Q ss_pred ----CcccHHHHHH
Q 003762 356 ----IGLAEQTLLA 365 (797)
Q Consensus 356 ----iGi~e~tvl~ 365 (797)
+|+++.||-.
T Consensus 163 IA~dLgiS~rTVe~ 176 (202)
T COG4566 163 IAFDLGISERTVEL 176 (202)
T ss_pred HHHHcCCchhhHHH
Confidence 6889998863
No 73
>PF09511 RNA_lig_T4_1: RNA ligase; InterPro: IPR019039 Members of this family include T4 phage proteins with ATP-dependent RNA ligase activity. Host defence to phage may include cleavage and inactivation of specific tRNA molecules; members of this family act to reverse this RNA damage. The enzyme is adenylated, transiently, on a Lys residue in a motif KXDGSL. This family also includes fungal tRNA ligases that have adenylyltransferase activity []. tRNA ligases are enzymes required for the splicing of precursor tRNA molecules containing introns. Please see the following relevant references: [, ]. ; PDB: 2C5U_B.
Probab=61.86 E-value=79 Score=33.13 Aligned_cols=47 Identities=21% Similarity=0.358 Sum_probs=18.2
Q ss_pred EEEeEEecCCHHHHHHHHHH------HHHcCCceeEEEeCCCCCCccCCCCCCCeEEEcccc
Q 003762 586 QFATTLTSIDLDEIQKFLDA------AVDASCEGLIIKTMDRDATYEPSKRSLNWLKLKKDY 641 (797)
Q Consensus 586 ~~v~~~~~~~~eei~~~f~~------ai~~g~EGlmvK~~~~ds~Y~pGkRs~~WlKlK~dY 641 (797)
..++.....+.+++.++++. .-..+.||.|+... + .++..+|+|-+|
T Consensus 166 ~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~EG~Vv~~~--~-------~~g~~~KiK~~~ 218 (221)
T PF09511_consen 166 PRVKSFTFENWEELKEFLEDEIIDGAYNGEEIEGFVVRFE--D-------QSGFMFKIKTPW 218 (221)
T ss_dssp -EEE-S---S---------TTHHHHHHH-SS--EEEEEET--T---------S-EEEEE-HH
T ss_pred CceeEeecccccccccchhhhhhhhhccCccCcEEEEEEE--C-------CCccEEEEcccc
Confidence 34444456667777777643 23568999999987 4 445789999754
No 74
>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=53.42 E-value=33 Score=36.86 Aligned_cols=58 Identities=14% Similarity=0.114 Sum_probs=48.5
Q ss_pred ccCCcHHHHHHHHHHhhccCCCcEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEEeC
Q 003762 562 LLQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTM 619 (797)
Q Consensus 562 L~~~Pl~ERr~lL~~l~~~~~~~i~~v~~~~~~~~eei~~~f~~ai~~g~EGlmvK~~ 619 (797)
-..++.+||+++++.+.....+++.++-.....+.++..++.+.+.+.|..|+|+=.+
T Consensus 44 ~~~ls~~Er~~l~~~~~~~~~~~~~vi~gv~~~~~~~~i~~a~~a~~~Gad~v~v~pP 101 (281)
T cd00408 44 APTLTDEERKEVIEAVVEAVAGRVPVIAGVGANSTREAIELARHAEEAGADGVLVVPP 101 (281)
T ss_pred cccCCHHHHHHHHHHHHHHhCCCCeEEEecCCccHHHHHHHHHHHHHcCCCEEEECCC
Confidence 3567899999999999887776776666666677888999999999999999999765
No 75
>cd00950 DHDPS Dihydrodipicolinate synthase (DHDPS) is a key enzyme in lysine biosynthesis. It catalyzes the aldol condensation of L-aspartate-beta- semialdehyde and pyruvate to dihydropicolinic acid via a Schiff base formation between pyruvate and a lysine residue. The functional enzyme is a homotetramer consisting of a dimer of dimers. DHDPS is member of dihydrodipicolinate synthase family that comprises several pyruvate-dependent class I aldolases that use the same catalytic step to catalyze different reactions in different pathways.
Probab=53.18 E-value=30 Score=37.36 Aligned_cols=66 Identities=14% Similarity=0.002 Sum_probs=52.5
Q ss_pred eeecCCc--cccCCcHHHHHHHHHHhhccCCCcEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEEeC
Q 003762 554 ILYRNGQ--PLLQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTM 619 (797)
Q Consensus 554 ILylnG~--~L~~~Pl~ERr~lL~~l~~~~~~~i~~v~~~~~~~~eei~~~f~~ai~~g~EGlmvK~~ 619 (797)
-++++|. ....++..||+++++.+.....+++.++-.....+.++..++.+.+.+.|..|+|+=.+
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 3455552 23578999999999999887777666665555668889999999999999999999876
No 76
>PRK03170 dihydrodipicolinate synthase; Provisional
Probab=51.00 E-value=34 Score=37.21 Aligned_cols=58 Identities=16% Similarity=0.051 Sum_probs=48.9
Q ss_pred ccCCcHHHHHHHHHHhhccCCCcEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEEeC
Q 003762 562 LLQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTM 619 (797)
Q Consensus 562 L~~~Pl~ERr~lL~~l~~~~~~~i~~v~~~~~~~~eei~~~f~~ai~~g~EGlmvK~~ 619 (797)
...++.+||+++++.+.....+++.++-.....+.++..++.+.+.+.|..|+|+=.+
T Consensus 48 ~~~ls~~Er~~~~~~~~~~~~~~~~vi~gv~~~~~~~~i~~a~~a~~~G~d~v~~~pP 105 (292)
T PRK03170 48 SPTLTHEEHEELIRAVVEAVNGRVPVIAGTGSNSTAEAIELTKFAEKAGADGALVVTP 105 (292)
T ss_pred cccCCHHHHHHHHHHHHHHhCCCCcEEeecCCchHHHHHHHHHHHHHcCCCEEEECCC
Confidence 3578999999999999888777766666655667889999999999999999999876
No 77
>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=50.30 E-value=40 Score=36.56 Aligned_cols=58 Identities=16% Similarity=0.138 Sum_probs=48.7
Q ss_pred ccCCcHHHHHHHHHHhhccCCCcEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEEeC
Q 003762 562 LLQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTM 619 (797)
Q Consensus 562 L~~~Pl~ERr~lL~~l~~~~~~~i~~v~~~~~~~~eei~~~f~~ai~~g~EGlmvK~~ 619 (797)
-..++.+||+++++..+...++++.++-.....+.++..++.+.+.+.|..|+|+=.+
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 4578999999999999887777777777777889999999999999999999999876
No 78
>TIGR02313 HpaI-NOT-DapA 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase. This model represents a subset of the DapA (dihydrodipicolinate synthase) family which has apparently evolved a separate function. The product of DapA, dihydrodipicolinate, results from the non-enzymatic cyclization and dehydration of 6-amino-2,4-dihydroxyhept-2-ene-1,7-dioic acid, which is different from the substrate of this reaction only in the presence of the amino group. In the absence of this amino group, and running the reaction in the opposite direction, the reaction corresponds to the HpaI aldolase component of the 4-hydroxyphenylacetic acid catabolism pathway (see TIGR02311). At present, this variant of DapA is found only in Oceanobacillus iheyensis HTE831 and Thermus thermophilus HB27. In both of these cases, one or more other DapA genes can be found and the one identified by this model is part of an operon for 4-hydroxyphenylacetic acid catabolism.
Probab=49.70 E-value=38 Score=37.10 Aligned_cols=58 Identities=16% Similarity=0.221 Sum_probs=49.3
Q ss_pred ccCCcHHHHHHHHHHhhccCCCcEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEEeC
Q 003762 562 LLQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTM 619 (797)
Q Consensus 562 L~~~Pl~ERr~lL~~l~~~~~~~i~~v~~~~~~~~eei~~~f~~ai~~g~EGlmvK~~ 619 (797)
-..++..||+++++.++....+++.++-.....+.++..++-+.+.+.|..|+|+=.+
T Consensus 47 ~~~Ls~~Er~~l~~~~~~~~~g~~pvi~gv~~~~t~~ai~~a~~A~~~Gad~v~v~pP 104 (294)
T TIGR02313 47 PGSLTLEERKQAIENAIDQIAGRIPFAPGTGALNHDETLELTKFAEEAGADAAMVIVP 104 (294)
T ss_pred cccCCHHHHHHHHHHHHHHhCCCCcEEEECCcchHHHHHHHHHHHHHcCCCEEEEcCc
Confidence 3468999999999999887777777766666678888899999999999999999876
No 79
>TIGR00683 nanA N-acetylneuraminate lyase. N-acetylneuraminate lyase is also known as N-acetylneuraminic acid aldolase, sialic acid aldolase, or sialate lyase. It is an intracellular enzyme. The structure of this homotetrameric enzyme related to dihydrodipicolinate synthase is known. In Clostridium tertium, the enzyme appears to be in an operon with a secreted sialidase that releases sialic acid from host sialoglycoconjugates. In several E. coli strains, however, this enzyme is responsible for N-acetyl-D-neuraminic acid synthesis for capsule production by condensing N-acetyl-D-mannosamine and pyruvate.
Probab=49.29 E-value=40 Score=36.83 Aligned_cols=66 Identities=17% Similarity=0.137 Sum_probs=51.1
Q ss_pred eeecCCc--cccCCcHHHHHHHHHHhhccCCCcEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEEeC
Q 003762 554 ILYRNGQ--PLLQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTM 619 (797)
Q Consensus 554 ILylnG~--~L~~~Pl~ERr~lL~~l~~~~~~~i~~v~~~~~~~~eei~~~f~~ai~~g~EGlmvK~~ 619 (797)
-++++|. .-..++.+||.++++.......+++.++-.....+.++..++-+.+.+.|-.|+|+=.+
T Consensus 38 gi~~~GstGE~~~Lt~eEr~~~~~~~~~~~~~~~pvi~gv~~~~t~~~i~la~~a~~~Gad~v~v~~P 105 (290)
T TIGR00683 38 GLYVGGSTGENFMLSTEEKKEIFRIAKDEAKDQIALIAQVGSVNLKEAVELGKYATELGYDCLSAVTP 105 (290)
T ss_pred EEEECCcccccccCCHHHHHHHHHHHHHHhCCCCcEEEecCCCCHHHHHHHHHHHHHhCCCEEEEeCC
Confidence 3445542 23457999999999999888777766665555667889999999999999999999655
No 80
>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=47.16 E-value=45 Score=36.17 Aligned_cols=57 Identities=12% Similarity=0.049 Sum_probs=48.8
Q ss_pred cCCcHHHHHHHHHHhhccCCCcEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEEeC
Q 003762 563 LQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTM 619 (797)
Q Consensus 563 ~~~Pl~ERr~lL~~l~~~~~~~i~~v~~~~~~~~eei~~~f~~ai~~g~EGlmvK~~ 619 (797)
..++.+||+++++.......+++.++-.....+.++..++-+.+.+.|..|+|+=.+
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 568999999999999887777776666666678889999999999999999999876
No 81
>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=46.04 E-value=50 Score=36.50 Aligned_cols=58 Identities=10% Similarity=0.090 Sum_probs=49.0
Q ss_pred ccCCcHHHHHHHHHHhhccCCCcEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEEeC
Q 003762 562 LLQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTM 619 (797)
Q Consensus 562 L~~~Pl~ERr~lL~~l~~~~~~~i~~v~~~~~~~~eei~~~f~~ai~~g~EGlmvK~~ 619 (797)
...++.+||+++++.......+++.++-.....+.++..++-+.+.+.|-.|+|+=.+
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 4568999999999999887777776665655678889999999999999999999876
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=44.79 E-value=50 Score=36.06 Aligned_cols=57 Identities=12% Similarity=0.120 Sum_probs=46.3
Q ss_pred ccCCcHHHHHHHHHHhhccCCCcEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEEeC
Q 003762 562 LLQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTM 619 (797)
Q Consensus 562 L~~~Pl~ERr~lL~~l~~~~~~~i~~v~~~~~~~~eei~~~f~~ai~~g~EGlmvK~~ 619 (797)
...++.+||.++++..+....+++.++-.... +.++..++-+.+.+.|..|+|+=.+
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 35689999999999998877676655555444 7788899999999999999999654
No 83
>PLN02417 dihydrodipicolinate synthase
Probab=44.54 E-value=50 Score=35.86 Aligned_cols=57 Identities=5% Similarity=-0.134 Sum_probs=47.3
Q ss_pred cCCcHHHHHHHHHHhhccCCCcEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEEeC
Q 003762 563 LQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTM 619 (797)
Q Consensus 563 ~~~Pl~ERr~lL~~l~~~~~~~i~~v~~~~~~~~eei~~~f~~ai~~g~EGlmvK~~ 619 (797)
..++.+||+++++.......+++.++-..-..+.++..++.+.+.+.|..|+|+-.+
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 467899999999998887777776666655667888899999999999999999766
No 84
>PRK04147 N-acetylneuraminate lyase; Provisional
Probab=44.18 E-value=48 Score=36.19 Aligned_cols=57 Identities=16% Similarity=0.152 Sum_probs=48.6
Q ss_pred cCCcHHHHHHHHHHhhccCCCcEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEEeC
Q 003762 563 LQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTM 619 (797)
Q Consensus 563 ~~~Pl~ERr~lL~~l~~~~~~~i~~v~~~~~~~~eei~~~f~~ai~~g~EGlmvK~~ 619 (797)
..++.+||+++++..+....+++.++-..-+.+.++..++-+.+.+.|..|+|+=.+
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 467889999999999988777776666665678899999999999999999999876
No 85
>cd00954 NAL N-Acetylneuraminic acid aldolase, also called N-acetylneuraminate lyase (NAL), which catalyses the reversible aldol reaction of N-acetyl-D-mannosamine and pyruvate to give N-acetyl-D-neuraminic acid (D-sialic acid). It has a widespread application as biocatalyst for the synthesis of sialic acid and its derivatives. This enzyme has been shown to be quite specific for pyruvate as the donor, but flexible to a variety of D- and, to some extent, L-hexoses and pentoses as acceptor substrates. NAL is member of dihydrodipicolinate synthase family that comprises several pyruvate-dependent class I aldolases.
Probab=42.94 E-value=61 Score=35.28 Aligned_cols=57 Identities=16% Similarity=0.141 Sum_probs=47.8
Q ss_pred cCCcHHHHHHHHHHhhccCCCcEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEEeC
Q 003762 563 LQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTM 619 (797)
Q Consensus 563 ~~~Pl~ERr~lL~~l~~~~~~~i~~v~~~~~~~~eei~~~f~~ai~~g~EGlmvK~~ 619 (797)
..++.+||+++++.......+++.++-.....+.++..++-+.+.+.|..|+|+=.+
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 568899999999998887777766655555567889999999999999999998876
No 86
>COG0329 DapA Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]
Probab=40.48 E-value=81 Score=34.79 Aligned_cols=65 Identities=18% Similarity=0.140 Sum_probs=53.3
Q ss_pred eecCCc--cccCCcHHHHHHHHHHhhccCCCcEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEEeC
Q 003762 555 LYRNGQ--PLLQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTM 619 (797)
Q Consensus 555 LylnG~--~L~~~Pl~ERr~lL~~l~~~~~~~i~~v~~~~~~~~eei~~~f~~ai~~g~EGlmvK~~ 619 (797)
++..|. ....++.+||+++++..+....+++-++-..-+++.++..++-+.+-+.|-.|+|+=.+
T Consensus 42 i~~~GttGE~~~Ls~eEr~~v~~~~v~~~~grvpviaG~g~~~t~eai~lak~a~~~Gad~il~v~P 108 (299)
T COG0329 42 LVVLGTTGESPTLTLEERKEVLEAVVEAVGGRVPVIAGVGSNSTAEAIELAKHAEKLGADGILVVPP 108 (299)
T ss_pred EEECCCCccchhcCHHHHHHHHHHHHHHHCCCCcEEEecCCCcHHHHHHHHHHHHhcCCCEEEEeCC
Confidence 444442 23568999999999999988888776666666778899999999999999999999876
No 87
>PRK03620 5-dehydro-4-deoxyglucarate dehydratase; Provisional
Probab=34.47 E-value=91 Score=34.28 Aligned_cols=64 Identities=13% Similarity=0.161 Sum_probs=49.1
Q ss_pred eecCCc--cccCCcHHHHHHHHHHhhccCCCcEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEEeC
Q 003762 555 LYRNGQ--PLLQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTM 619 (797)
Q Consensus 555 LylnG~--~L~~~Pl~ERr~lL~~l~~~~~~~i~~v~~~~~~~~eei~~~f~~ai~~g~EGlmvK~~ 619 (797)
++++|. ....++.+||+++++.+.....+++.++-... .+.++..++.+.+.+.|..|+|+=.+
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 34568999999999999887777665554443 47788889999999999999999655
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=34.26 E-value=95 Score=33.96 Aligned_cols=64 Identities=11% Similarity=0.099 Sum_probs=48.8
Q ss_pred eecCCc--cccCCcHHHHHHHHHHhhccCCCcEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEEeC
Q 003762 555 LYRNGQ--PLLQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTM 619 (797)
Q Consensus 555 LylnG~--~L~~~Pl~ERr~lL~~l~~~~~~~i~~v~~~~~~~~eei~~~f~~ai~~g~EGlmvK~~ 619 (797)
++++|. .-..++.+||+++++.......+++.++-..- .+.++..++.+.+.+.|..|+|+=.+
T Consensus 43 i~v~GstGE~~~Lt~eEr~~v~~~~~~~~~g~~pvi~gv~-~~t~~ai~~a~~a~~~Gadav~~~pP 108 (296)
T TIGR03249 43 LFAAGGTGEFFSLTPAEYEQVVEIAVSTAKGKVPVYTGVG-GNTSDAIEIARLAEKAGADGYLLLPP 108 (296)
T ss_pred EEECCCCcCcccCCHHHHHHHHHHHHHHhCCCCcEEEecC-ccHHHHHHHHHHHHHhCCCEEEECCC
Confidence 445542 23568999999999999887777665554443 46788889999999999999999654
No 89
>KOG3673 consensus FtsJ-like RNA methyltransferase [RNA processing and modification]
Probab=32.87 E-value=59 Score=38.59 Aligned_cols=62 Identities=10% Similarity=0.024 Sum_probs=44.6
Q ss_pred cceEEEEeeeeecCCccccCCcHHHHHHHHHHhhccCC--C----cEEEEeEEecCCHHHHHHHHHHH
Q 003762 545 VDVCIYAFDILYRNGQPLLQEQLRVRREHLYDSFEEEP--G----FFQFATTLTSIDLDEIQKFLDAA 606 (797)
Q Consensus 545 ~~v~~~vFDILylnG~~L~~~Pl~ERr~lL~~l~~~~~--~----~i~~v~~~~~~~~eei~~~f~~a 606 (797)
..-.+++.|.+.|+|.++.++||.||..+-++.+..+. . .........+...+++.++|...
T Consensus 656 ~~~avhIiD~~vL~G~Dvr~~py~eR~~~aeKFv~al~kp~Rkd~~~~a~r~Kp~yrL~em~~ff~nl 723 (845)
T KOG3673|consen 656 EPQAVHIIDAAVLFGDDVRNLPYEERMKAAEKFVAALKKPNRKDKKHRAERIKPTYRLAEMDEFFSNL 723 (845)
T ss_pred cchheeeeeeeeecCchhhcccHHHHHHHHHHHHHHhcCCCCccccccceecccceeHHHHHHHHHhh
Confidence 45578899999999999999999999999988876431 1 11122223355677888887654
No 90
>KOG0967 consensus ATP-dependent DNA ligase I [Replication, recombination and repair]
Probab=32.22 E-value=2.1e+02 Score=34.93 Aligned_cols=91 Identities=19% Similarity=0.246 Sum_probs=61.1
Q ss_pred CCCCCHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHh---cCCChH---HHHH-HHHh---hhccCcccHHHHHHHHHH
Q 003762 300 PDPLTITKVFDTFRLIAKEAGKDSQEKKKNRIKALLVA---ATDCEP---QYLI-RLLQ---SKLRIGLAEQTLLAALGQ 369 (797)
Q Consensus 300 ~~~LTI~eV~~~L~kIA~~~G~~s~~~K~~~L~~LL~~---~t~~E~---k~Li-RiIl---kdLRiGi~e~tvl~Ala~ 369 (797)
.+..+-.++..+|.+|.+.+|.-. -+.++..+|.. .+|++. -||- .-|- ..|.+|+++.++.+|++.
T Consensus 96 ~~~~py~~~a~tF~kIe~~s~Rl~---i~~il~n~f~~v~~~sP~dLlp~vYLsiN~l~P~yeGlELGvGes~l~KAi~E 172 (714)
T KOG0967|consen 96 GSKVPYLELARTFEKIEETSGRLE---IIDILSNFLRSVLATSPDDLLPTVYLSINKLAPDYEGLELGVGESLLMKAIAE 172 (714)
T ss_pred cCcCcHHHHHHHHHHHHhhcccee---HHHHHHHHHHHHHhcCchhhhhHHHHhhhccCccccCccccccHHHHHHHHHH
Confidence 356778899999999988776432 25666666655 355544 2322 2221 367899999999999999
Q ss_pred hhccCCCCCCCCCCCcchHHHHHHHHHHHhhcCCchhhhHh
Q 003762 370 AAVYNEQHSKPPPNIQSPLEEAAKIVKQVFSVLPVYEKIVP 410 (797)
Q Consensus 370 a~~~~~~~~~~~~~l~~~l~~a~~~vk~~y~~~pd~~~v~~ 410 (797)
|..-. ...|+.-|+..-|++.|+.
T Consensus 173 atGrt-----------------~~~vk~~~~~~GDLG~VA~ 196 (714)
T KOG0967|consen 173 ATGRT-----------------LSHVKNQYNKLGDLGLVAQ 196 (714)
T ss_pred HhCcc-----------------HHHHHHHHHhcCcHHHHHh
Confidence 97643 2345667777777777654
No 91
>PRK14956 DNA polymerase III subunits gamma and tau; Provisional
Probab=30.89 E-value=58 Score=38.51 Aligned_cols=27 Identities=44% Similarity=0.529 Sum_probs=21.7
Q ss_pred CCCCCCCCCCCCCCcccCCCCCCCCCc
Q 003762 119 LVKPISNQIDNPIDSEKESQPTPPSPK 145 (797)
Q Consensus 119 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 145 (797)
+.++.++-.++|-.|+.+||.+||+.+
T Consensus 434 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 460 (484)
T PRK14956 434 SNQQDSNLDNNPLPSKSESQSEPPSSK 460 (484)
T ss_pred cccccccCCCCCCCCcccccCCCCCCh
Confidence 346777788889999999999999443
No 92
>KOG0971 consensus Microtubule-associated protein dynactin DCTN1/Glued [Cell cycle control, cell division, chromosome partitioning; Cytoskeleton]
Probab=28.76 E-value=1.2e+02 Score=38.32 Aligned_cols=21 Identities=29% Similarity=0.243 Sum_probs=11.1
Q ss_pred ccccchhhhHHHHhhhhhhcc
Q 003762 151 VNSVSAKEKIAELKSNIVLLK 171 (797)
Q Consensus 151 ~~~~~~~~~~~~~~~~~~~~~ 171 (797)
.++.++..++.++.+++-.+.
T Consensus 217 v~l~saskte~eLr~QvrdLt 237 (1243)
T KOG0971|consen 217 VPLPSASKTEEELRAQVRDLT 237 (1243)
T ss_pred CCCCccccchHHHHHHHHHHH
Confidence 455555555555655554443
No 93
>cd08205 RuBisCO_IV_RLP Ribulose bisphosphate carboxylase like proteins, Rubisco-Form IV. Ribulose bisphosphate carboxylase (Rubisco) plays an important role in the Calvin reductive pentose phosphate pathway. It catalyzes the primary CO2 fixation step. Rubisco is activated by carbamylation of an active site lysine, stabilized by a divalent cation, which then catalyzes the proton abstraction from the substrate ribulose 1,5 bisphosphate (RuBP) and leads to the formation of two molecules of 3-phosphoglycerate. Members of the Rubisco family can be divided into 4 subgroups, Form I-IV, which differ in their taxonomic distribution and subunit composition. Form I-III have Rubisco activity, while Form IV, also called Rubisco-like proteins (RLP), are missing critical active site residues and therefore do not catalyze CO2 fixation. They are believed to utilize a related enzymatic mechanism, but have divergent functions, like for example 2,3-diketo-5-methylthiopentyl-1-phosphate enolase or 5-methyl
Probab=28.41 E-value=1.3e+02 Score=34.40 Aligned_cols=56 Identities=21% Similarity=0.288 Sum_probs=42.6
Q ss_pred cCCcHHHHHHHHHHhhccCC---C-cEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEEeC
Q 003762 563 LQEQLRVRREHLYDSFEEEP---G-FFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTM 619 (797)
Q Consensus 563 ~~~Pl~ERr~lL~~l~~~~~---~-~i~~v~~~~~~~~eei~~~f~~ai~~g~EGlmvK~~ 619 (797)
.-.|++||.+...+.+.... + ..-++... +.+.+++.+..+.+.+.|..|+|+-.+
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 34799999999998886544 3 33333333 345689999999999999999999876
No 94
>KOG2386 consensus mRNA capping enzyme, guanylyltransferase (alpha) subunit [RNA processing and modification]
Probab=28.32 E-value=1.7e+02 Score=33.77 Aligned_cols=169 Identities=15% Similarity=0.141 Sum_probs=85.1
Q ss_pred HHHHhhcCCCceEEEeecceEEEEEEEec----CCeEEEEecCCCccCCCcchH------HHHHHhhcCCCCCCeEEEEE
Q 003762 444 SEIVNKFQDMEFTCEYKYDGERAQIHYLE----DGSVEIYSRNAERNTGKFPDV------VLAVSRLKKPSVRSFVLDCE 513 (797)
Q Consensus 444 ~~~l~k~~g~~~~~E~KyDG~R~qih~~~----~g~V~ifSR~gkd~T~~yPel------~~~l~~~~~~~v~~~ILDGE 513 (797)
.+.+..+....+.+-.|.||.|++..++. .-.+.+.-++-.-. .-+|.. +.++.+. +.++-+|||
T Consensus 51 ~dl~~~l~~~~~~vgl~iDltnt~ryy~~~~~~~~g~~Y~K~~c~g~-~~vp~~~~v~~fv~~v~~f----~~~~~~~~~ 125 (393)
T KOG2386|consen 51 KDLFELLKEHNYKVGLKIDLTNTLRYYDKPELEERGVKYLKRNCPGR-GVVPRTELVDKFVKLVKGF----VDDTKLDDE 125 (393)
T ss_pred HHHHHHHHhcCceEEEEEeccceeeeeccccccccceeEEEeccCCc-ccCCCccchHHHHHHHHHH----HhcccCCCC
Confidence 34444444557899999999999998842 11233333332211 113322 2233333 256788999
Q ss_pred EEEEecCCCcccChhhHHhhhcccCCccccccceEEEEeeeeecCCccccCCcHH-----------HHHHHHHHhhccCC
Q 003762 514 IVAYDREKQKILPFQTLSTRARKNVSLSDIKVDVCIYAFDILYRNGQPLLQEQLR-----------VRREHLYDSFEEEP 582 (797)
Q Consensus 514 lVa~d~~~g~~lpFq~L~~R~Rk~~~~~~~~~~v~~~vFDILylnG~~L~~~Pl~-----------ERr~lL~~l~~~~~ 582 (797)
+|...-..| ....-|.+||.|.-+|. +...... +|...+.++.....
T Consensus 126 LI~vhcthG---------------------~NrtgyLI~~yL~~~~~-~s~~~aik~f~~~r~~gi~k~dyi~~L~~~~~ 183 (393)
T KOG2386|consen 126 LIGVHCTHG---------------------LNRTGYLICAYLADVGG-YSSSEAIKRFADARPPGIEKQDYIDALYSRYH 183 (393)
T ss_pred EEEEeCCCc---------------------ccccceeeeeeeeeccC-ccHHHHHHHHHHhCCCccCchHHHHHHhhccc
Confidence 998753222 12346889999987764 3222222 22223333322111
Q ss_pred CcE-EEEeEEecCCHHHHHHHHHHHHH-cCCceeEEEeCCCCCCccCCCCCCCeEEEcccc
Q 003762 583 GFF-QFATTLTSIDLDEIQKFLDAAVD-ASCEGLIIKTMDRDATYEPSKRSLNWLKLKKDY 641 (797)
Q Consensus 583 ~~i-~~v~~~~~~~~eei~~~f~~ai~-~g~EGlmvK~~~~ds~Y~pGkRs~~WlKlK~dY 641 (797)
..+ ..+......++............ ++..|.+.-.. ..+|..+.+...-+|+|++-
T Consensus 184 ~~~p~~vs~p~~~~~~~~~~~~~~~~~~~~~Dg~i~t~~--~~pg~~~g~~~~~~k~k~~~ 242 (393)
T KOG2386|consen 184 DIFPFKVSCPSMPDWKRSIKLKKPVHKLHGNDGLIFTPA--EIPGSKNGKQEALLKWKPFS 242 (393)
T ss_pred ccccccccCCCCcchhhhhhhccccccccccCCCcCCcc--cCccccccchhhhhcCCchh
Confidence 111 01111112222222222222222 67788888777 77884223456889999964
No 95
>cd00953 KDG_aldolase KDG (2-keto-3-deoxygluconate) aldolases found in archaea. This subfamily of enzymes is adapted for high thermostability and shows specificity for non-phosphorylated substrates. The enzyme catalyses the reversible aldol cleavage of 2-keto-3-dexoygluconate to pyruvate and glyceraldehyde, the third step of a modified non-phosphorylated Entner-Doudoroff pathway of glucose oxidation. KDG aldolase shows no significant sequence similarity to microbial 2-keto-3-deoxyphosphogluconate (KDPG) aldolases, and the enzyme shows no activity with glyceraldehyde 3-phosphate as substrate. The enzyme is a tetramer and a member of the DHDPS family of Schiff-base-dependent class I aldolases.
Probab=23.96 E-value=2.3e+02 Score=30.71 Aligned_cols=55 Identities=13% Similarity=-0.028 Sum_probs=43.8
Q ss_pred ccCCcHHHHHHHHHHhhccCCCcEEEEeEEecCCHHHHHHHHHHHHHcCCceeEEEeC
Q 003762 562 LLQEQLRVRREHLYDSFEEEPGFFQFATTLTSIDLDEIQKFLDAAVDASCEGLIIKTM 619 (797)
Q Consensus 562 L~~~Pl~ERr~lL~~l~~~~~~~i~~v~~~~~~~~eei~~~f~~ai~~g~EGlmvK~~ 619 (797)
-..++.+||+++++...+... . ++-..-+.+.++..++-+.+.+.|..|+|+=.+
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 333344567889999999999999999999876
No 96
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=23.73 E-value=3.5e+02 Score=27.84 Aligned_cols=114 Identities=20% Similarity=0.171 Sum_probs=67.3
Q ss_pred HHHHHHHHHHhhhcCCCCchHHHHHHHhCccCCCc-cccccCCChHHHHHHHHHHhCCCHHHHHHHHHhcCCHHHHHhhc
Q 003762 212 ITDIVCNMLRTVMETTPEDLVPVVYLAANKIAPAH-EGLELGIGDASIIKALAEACGRTESHVKKQYQEMGDLGLVAKAS 290 (797)
Q Consensus 212 k~~iL~~~fr~~i~~~p~dl~~~vyL~~~~l~P~~-e~~elGIge~~L~kal~~a~G~s~~~ik~~y~~~GDlg~vA~~~ 290 (797)
.+..+.+..+.+ +-+.....||-++ | .+..+. +.-|++++|+|..++-...++.-|++.|-...
T Consensus 11 ~Ie~fae~m~r~---G~nrtVG~iYgil------yls~~Pmt------l~Ei~E~lg~Sks~vS~~lkkL~~~~lV~~~~ 75 (177)
T COG1510 11 FIEHFAETMSRW---GINRTVGQIYGIL------YLSRKPLT------LDEIAEALGMSKSNVSMGLKKLQDWNLVKKVF 75 (177)
T ss_pred HHHHHHHHHHHh---CCcchHHHHhhhh------eecCCCcc------HHHHHHHHCCCcchHHHHHHHHHhcchHHhhh
Confidence 345555555555 3344555555433 2 122233 34478999999998877777766666554332
Q ss_pred cccCCCCCCCCCCCHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHhcCCChH
Q 003762 291 RSSQSMMRKPDPLTITKVFDTFRLIAKEAGKDSQEKKKNRIKALLVAATDCEP 343 (797)
Q Consensus 291 r~~q~~l~~~~~LTI~eV~~~L~kIA~~~G~~s~~~K~~~L~~LL~~~t~~E~ 343 (797)
.+. .++.--.+..++++.+..++...-....+.-...++.++..+.+++.
T Consensus 76 ~~G---~Rk~~F~a~~df~~~f~t~f~ek~~ReId~t~e~l~k~~~e~~~~~~ 125 (177)
T COG1510 76 EKG---DRKDYFEAEKDFSQIFRTLFEEKWKREIDPTKEALKKLLEELNEDLD 125 (177)
T ss_pred ccC---cchhhhcccchHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHcccccc
Confidence 211 11112245678999999887765544444456778888887776544
No 97
>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=23.67 E-value=31 Score=30.94 Aligned_cols=25 Identities=24% Similarity=0.258 Sum_probs=21.0
Q ss_pred HHHHHHHHHhcCCChHHHHHHHHhh
Q 003762 328 KNRIKALLVAATDCEPQYLIRLLQS 352 (797)
Q Consensus 328 ~~~L~~LL~~~t~~E~k~LiRiIlk 352 (797)
.++|+.|+.-++.+|++-|.+++.|
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
Done!