Query 012588
Match_columns 460
No_of_seqs 281 out of 889
Neff 6.6
Searched_HMMs 46136
Date Fri Mar 29 04:12:55 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/012588.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/012588hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG5226 CEG1 mRNA capping enzy 100.0 9.1E-68 2E-72 510.2 18.7 336 94-444 12-381 (404)
2 PF01331 mRNA_cap_enzyme: mRNA 100.0 8E-49 1.7E-53 369.8 13.4 190 132-330 1-192 (192)
3 cd07895 Adenylation_mRNA_cappi 100.0 3.6E-43 7.7E-48 336.9 21.2 212 105-331 3-215 (215)
4 KOG2386 mRNA capping enzyme, g 100.0 2.4E-36 5.3E-41 306.8 7.2 237 1-258 141-391 (393)
5 cd06846 Adenylation_DNA_ligase 100.0 3.4E-29 7.4E-34 233.9 18.2 178 129-331 1-182 (182)
6 cd07898 Adenylation_DNA_ligase 99.9 4.5E-26 9.9E-31 216.4 15.4 162 144-331 18-200 (201)
7 cd07903 Adenylation_DNA_ligase 99.9 2.9E-24 6.4E-29 207.3 16.6 167 142-334 28-224 (225)
8 PRK09247 ATP-dependent DNA lig 99.9 1.5E-23 3.4E-28 225.7 19.1 170 144-342 222-417 (539)
9 cd07897 Adenylation_DNA_ligase 99.9 1E-23 2.2E-28 201.4 15.3 161 144-332 21-205 (207)
10 cd07906 Adenylation_DNA_ligase 99.9 3.7E-23 8E-28 194.8 15.0 157 146-331 15-189 (190)
11 cd07901 Adenylation_DNA_ligase 99.9 5E-23 1.1E-27 196.5 15.0 157 146-331 24-206 (207)
12 cd07905 Adenylation_DNA_ligase 99.9 8.8E-23 1.9E-27 193.0 15.2 158 146-332 15-193 (194)
13 PF03919 mRNA_cap_C: mRNA capp 99.9 9.2E-24 2E-28 180.5 7.4 94 333-429 1-105 (105)
14 cd07900 Adenylation_DNA_ligase 99.9 1.2E-22 2.6E-27 195.6 14.3 164 143-332 27-218 (219)
15 cd09232 Snurportin-1_C C-termi 99.9 3.3E-22 7.1E-27 187.5 16.5 163 146-332 20-186 (186)
16 TIGR02779 NHEJ_ligase_lig DNA 99.9 2.7E-22 5.8E-27 201.7 16.4 169 146-342 11-192 (298)
17 PRK08224 ligC ATP-dependent DN 99.9 3E-22 6.6E-27 205.0 16.5 164 147-342 24-208 (350)
18 PRK07636 ligB ATP-dependent DN 99.9 6.7E-22 1.4E-26 196.6 18.2 162 146-342 17-195 (275)
19 cd08039 Adenylation_DNA_ligase 99.9 3.6E-22 7.9E-27 194.1 15.9 182 133-332 4-234 (235)
20 PRK09633 ligD ATP-dependent DN 99.9 6.3E-22 1.4E-26 214.9 17.9 277 146-444 15-362 (610)
21 PHA02587 30 DNA ligase; Provis 99.9 4.3E-21 9.4E-26 204.5 21.0 167 148-342 153-371 (488)
22 PRK05972 ligD ATP-dependent DN 99.9 5.2E-21 1.1E-25 212.8 21.8 166 147-342 249-427 (860)
23 cd07902 Adenylation_DNA_ligase 99.9 1.2E-21 2.5E-26 188.0 14.5 157 147-332 34-212 (213)
24 TIGR00574 dnl1 DNA ligase I, A 99.9 1.2E-21 2.7E-26 210.4 15.6 167 147-341 187-385 (514)
25 PRK03180 ligB ATP-dependent DN 99.9 4.3E-21 9.4E-26 205.3 14.9 164 147-342 204-390 (508)
26 PRK09632 ATP-dependent DNA lig 99.8 4E-20 8.6E-25 204.0 18.5 165 144-341 474-650 (764)
27 PLN03113 DNA ligase 1; Provisi 99.8 1.9E-20 4.1E-25 206.5 15.8 174 142-341 386-591 (744)
28 PRK01109 ATP-dependent DNA lig 99.8 1.7E-20 3.6E-25 204.4 14.8 166 147-341 248-445 (590)
29 PF01068 DNA_ligase_A_M: ATP d 99.8 1.3E-20 2.9E-25 177.9 11.7 159 146-330 18-202 (202)
30 COG1793 CDC9 ATP-dependent DNA 99.8 9.6E-20 2.1E-24 191.8 15.3 166 148-342 134-322 (444)
31 PHA00454 ATP-dependent DNA lig 99.8 4.1E-19 8.9E-24 179.9 15.8 182 129-341 6-228 (315)
32 PRK09125 DNA ligase; Provision 99.8 1.1E-17 2.3E-22 167.1 19.5 210 145-402 41-282 (282)
33 cd07896 Adenylation_kDNA_ligas 99.8 5.9E-18 1.3E-22 157.1 12.1 143 146-331 15-174 (174)
34 TIGR02776 NHEJ_ligase_prk DNA 99.7 1.8E-16 3.9E-21 170.8 13.0 140 173-342 1-153 (552)
35 KOG2386 mRNA capping enzyme, g 99.7 6.2E-18 1.3E-22 172.7 1.1 287 124-432 38-353 (393)
36 KOG0966 ATP-dependent DNA liga 99.6 1.5E-15 3.3E-20 163.5 13.7 210 105-335 198-441 (881)
37 KOG0967 ATP-dependent DNA liga 99.3 8.2E-12 1.8E-16 132.5 12.2 178 141-341 359-565 (714)
38 cd07894 Adenylation_RNA_ligase 99.1 5.3E-10 1.1E-14 114.5 13.6 147 147-321 48-205 (342)
39 KOG3132 m3G-cap-specific nucle 97.9 0.00021 4.6E-09 68.9 14.0 155 147-324 116-271 (325)
40 TIGR01209 RNA ligase, Pab1020 97.6 0.00057 1.2E-08 70.6 12.4 180 126-339 57-245 (374)
41 COG1423 ATP-dependent DNA liga 96.6 0.038 8.1E-07 56.4 12.8 142 146-316 87-236 (382)
42 PF01653 DNA_ligase_aden: NAD- 95.4 0.3 6.4E-06 50.0 13.5 159 148-332 108-313 (315)
43 KOG3673 FtsJ-like RNA methyltr 93.7 0.25 5.3E-06 53.2 8.2 96 199-306 634-732 (845)
44 smart00532 LIGANc Ligase N fam 93.5 3 6.4E-05 44.7 16.1 165 147-335 103-313 (441)
45 cd00114 LIGANc NAD+ dependent 93.5 2.7 5.8E-05 42.9 15.2 160 147-332 101-306 (307)
46 PRK07956 ligA NAD-dependent DN 92.5 5.7 0.00012 44.8 17.3 164 148-337 109-320 (665)
47 PF09414 RNA_ligase: RNA ligas 92.3 0.082 1.8E-06 49.3 2.2 103 147-250 1-128 (186)
48 PF05098 LEF-4: Late expressio 92.3 4.8 0.0001 42.9 15.3 207 145-406 232-450 (450)
49 PRK14351 ligA NAD-dependent DN 91.0 13 0.00028 42.2 18.0 167 147-339 132-344 (689)
50 PRK14350 ligA NAD-dependent DN 90.4 12 0.00025 42.4 16.9 167 147-338 110-318 (669)
51 PHA02142 putative RNA ligase 89.9 8.1 0.00018 40.3 14.1 103 146-251 168-298 (366)
52 TIGR00575 dnlj DNA ligase, NAD 89.9 21 0.00046 40.2 18.5 166 148-343 97-314 (652)
53 TIGR02307 RNA_lig_RNL2 RNA lig 88.8 2.9 6.3E-05 42.9 9.8 107 144-250 22-144 (325)
54 PRK08097 ligB NAD-dependent DN 88.0 17 0.00038 40.1 15.7 165 148-343 119-318 (562)
55 KOG1720 Protein tyrosine phosp 72.1 4.7 0.0001 38.8 3.9 35 1-35 164-200 (225)
56 COG0272 Lig NAD-dependent DNA 71.2 1E+02 0.0022 34.8 14.4 164 146-339 108-322 (667)
57 PF14671 DSPn: Dual specificit 64.2 3.5 7.6E-05 37.3 1.3 27 1-27 87-113 (141)
58 TIGR02306 RNA_lig_DRB0094 RNA 58.4 95 0.0021 32.3 10.6 103 147-251 159-277 (341)
59 PF10640 Pox_ATPase-GT: mRNA c 53.5 61 0.0013 32.9 8.0 93 105-210 184-282 (313)
60 KOG1716 Dual specificity phosp 39.6 37 0.0008 34.0 4.2 39 1-39 172-210 (285)
61 PF14555 UBA_4: UBA-like domai 38.7 27 0.00058 24.6 2.2 22 3-24 18-39 (43)
62 PRK12361 hypothetical protein; 36.0 45 0.00097 36.6 4.5 46 1-46 192-238 (547)
63 KOG2283 Clathrin coat dissocia 33.7 25 0.00054 37.7 1.9 25 1-25 124-149 (434)
64 PF03162 Y_phosphatase2: Tyros 27.6 43 0.00094 30.8 2.2 53 3-58 109-161 (164)
65 PF11396 DUF2874: Protein of u 24.4 66 0.0014 23.9 2.3 43 126-170 18-60 (61)
66 COG3640 CooC CO dehydrogenase 22.9 58 0.0013 32.2 2.2 67 95-171 46-116 (255)
No 1
>COG5226 CEG1 mRNA capping enzyme, guanylyltransferase (alpha) subunit [RNA processing and modification]
Probab=100.00 E-value=9.1e-68 Score=510.19 Aligned_cols=336 Identities=33% Similarity=0.457 Sum_probs=278.7
Q ss_pred CCCCCccccchHHHHHHHHHHHhcccCCCCCCCCCCCCcccccccccccccccCceEEEEcCCeeEEEEEEECC------
Q 012588 94 DVLGDEIPNDQQDAFRHFCYQTLKLNFGGRGNMQFPGSHPVSLNSDNLQLLRQRYYYATWKADGTRYMMLITID------ 167 (460)
Q Consensus 94 ~v~G~~~~~~~~~~~r~~~~~l~~~~~~~~~~~~FPGsqPVSl~r~nl~~l~~~~Y~V~~K~DG~R~Ll~i~~~------ 167 (460)
.++|+.+|++.++.|+-++.++++.. .+...|||||||||+.+|++.|..++|+||||+||+|+||+++.+
T Consensus 12 ~~pG~~~P~di~~~Lkt~i~klL~~~---~P~~tFpGsqPVsf~~~~i~~Ll~~dy~VCEKsDGvR~Ll~vte~p~tg~~ 88 (404)
T COG5226 12 FRPGNKVPPDIAEALKTKIYKLLCIT---EPRETFPGSQPVSFTLDNIGLLLNNDYLVCEKSDGVRALLLVTEEPVTGAF 88 (404)
T ss_pred ccCCCcCCchHHHHHHHHHHHHhCCC---CCcccCCCCcceeeehhhHHHHHhCCeEEEEccCCeEEEEEEEecccCCCc
Confidence 47899999999999999999999753 235999999999999999999999999999999999999999753
Q ss_pred EEEEEeCCCcccccc-CcCCcccCC-CCccccCCCceeeeeEEEEecCCCCCcceeEEEEeeeeecCCccccCCCHHHHH
Q 012588 168 GCYLIDRCFNFRRVQ-MRFPCRNSN-EGLGEKTHHFTLLDGEMIIDKLPDSRRQERRYLIYDMMAINQASVIERPFYERW 245 (460)
Q Consensus 168 ~vyLidR~~~~~~v~-~~FP~~~~~-~~l~~~~~~~TlLDGElV~d~~~~~~~~~~ryliFDiL~~~G~~l~~~pf~eRl 245 (460)
++|++||+|+|+.++ ..||..... +| +..+.+|+||||+|.|..+.++-++++|++||||+++|.-++.++.++|+
T Consensus 89 ~~y~~DR~nnfY~v~~~f~p~~~~~k~g--e~l~~dtlldgelV~d~~p~~k~~qlryl~fdcLa~~g~~~~~~~~s~Rl 166 (404)
T COG5226 89 RGYFYDRRNNFYEVHTSFPPCSTVLKDG--EVLLEDTLLDGELVFDCLPYEKVPQLRYLLFDCLAYAGMFVERMEKSERL 166 (404)
T ss_pred ceEEEeccCceEEeccccCCcccccccC--cEEeccceecceEEEEeccccchHHHHHHHHHHhhhcceeEeecchhhHH
Confidence 699999999998885 555544322 22 24578999999999998877643679999999999999999999999999
Q ss_pred HHHHHHhcCccchhhccccccCCCCccCCCCCeEEEeccceechhHHHHHHHhccccCCCCceEEEEcCCCCCccCCCCC
Q 012588 246 KMLEKEVIEPRNYERHNIYQSRNPYYRYDLEPFRVRRKDFWLLSTVNKLLKEFIPKLSHDADGLVFQGWDDPYVPRTHEG 325 (460)
Q Consensus 246 ~~L~~~i~~pr~~~~~~l~~~~~~~~~~~~~pf~I~~K~f~~~~~~~~ll~~~~~~l~h~~DGLIF~p~~spY~~G~~~~ 325 (460)
+.|++++.+|+..... +-.++....||.+.+|.|...++.-++++ -+|.|.|++|||||||+++||..|++..
T Consensus 167 ~~l~Ke~~kp~~~~r~------s~~~~~~~fpf~~s~K~M~~syg~~ki~k-~ip~L~HgnDGLIFTp~~~PY~~Gkd~~ 239 (404)
T COG5226 167 KTLQKEDEKPRERKRV------SIEIDSGSFPFHFSVKQMLKSYGFWKIYK-KIPELKHGNDGLIFTPADEPYSVGKDGA 239 (404)
T ss_pred HHhhhhhcccHhhhhh------eeeccccccceeeeHHHHHhhhhHHHHHh-hcccccCCCCceEeccCCCCcccCccce
Confidence 9999999999865442 22234456799999999999999999995 5799999999999999999999999999
Q ss_pred eEEEccCCCceEEEEEEEec----C--------CceeEEEEeCCcee-eecCceeEecC-------CCCCCCCceEEEEE
Q 012588 326 LLKWKYARMNSVDFLFEVTD----D--------DRQLLYVFERGKKK-LMEGSSVEFTD-------REPSFYSGKIIECT 385 (460)
Q Consensus 326 ~LKWKP~~~nTVDF~l~~~~----~--------~~~~L~v~~~g~~~-~~~~~~~~f~~-------~~~~~~dg~IvEC~ 385 (460)
+|||||.++|||||++.+.. + +...|+|+.+.+.. +|+. +...+ ..-..+.++||||.
T Consensus 240 lLKWKP~~~NTiDF~lvl~~~~~e~~Dyny~~~p~f~l~Vw~gRk~yrfFa~--~~v~d~ew~~lk~~~~pl~~rivEc~ 317 (404)
T COG5226 240 LLKWKPASLNTIDFRLVLHKKWSEVDDYNYVCSPKFGLDVWFGRKTYRFFAS--GEVIDGEWCELKYDCDPLYWRIVECV 317 (404)
T ss_pred eeecCccccCceeeeeeeccccccccCcceeecccccccEEecccceeeeee--eEechHHHHHHhhhcccchhhHHHHH
Confidence 99999999999999998762 1 12467777643322 3331 22222 23456999999999
Q ss_pred EeCCCCeeEEEEEecCCCCCChHHHHHHHHHhcccCCCHHHHHHHHHHhhc------Cccchhcc
Q 012588 386 WDPDVQLWKCMRIRTDKSTPNDINTYRKVMRSIRDNITEEVLLNEIQEIIR------LPMYADRI 444 (460)
Q Consensus 386 ~d~~~~~W~f~R~R~DK~~pN~~~tv~~v~~SI~~~Vt~e~Ll~~i~~~~~------~~~~~~~~ 444 (460)
.+. .|.|+++|+|+||..|||++||.+|++||+|+||.|+|..+..-|+. .||...|.
T Consensus 318 l~~-e~~W~~lrfRdDK~~~NhisvV~~VLeSi~D~vs~EdL~~~~~vire~~~~R~k~~~~~R~ 381 (404)
T COG5226 318 LKK-EGAWKLLRFRDDKDTPNHISVVCNVLESIRDNVSIEDLSTFYSVIRENSKRREKAMRRGRP 381 (404)
T ss_pred hcc-CCceEEEEeecCCCCCchhhHHHHHHHHHhccCcHHHHHHHHHHHHHHHHhhhhccccCCC
Confidence 984 56899999999999999999999999999999999999998877733 56655554
No 2
>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=100.00 E-value=8e-49 Score=369.79 Aligned_cols=190 Identities=46% Similarity=0.832 Sum_probs=157.8
Q ss_pred cccccccccccccccCceEEEEcCCeeEEEEEEECCEEEEEeCCCcccccc-CcCCcccCCCCccccCCCceeeeeEEEE
Q 012588 132 HPVSLNSDNLQLLRQRYYYATWKADGTRYMMLITIDGCYLIDRCFNFRRVQ-MRFPCRNSNEGLGEKTHHFTLLDGEMII 210 (460)
Q Consensus 132 qPVSl~r~nl~~l~~~~Y~V~~K~DG~R~Ll~i~~~~vyLidR~~~~~~v~-~~FP~~~~~~~l~~~~~~~TlLDGElV~ 210 (460)
|||||+|+||+.|.+++|+||||+||+||||+++++++|||||+++++.++ ++||...+. .....+++||||||||.
T Consensus 1 qPVS~~r~~l~~l~~~~Y~V~eKaDG~Ryll~i~~~~~ylidr~~~~~~v~~~~~p~~~~~--~~~~~~~~TLLDGElV~ 78 (192)
T PF01331_consen 1 QPVSFSRKNLQLLQQKDYFVCEKADGTRYLLLITDNGVYLIDRKNNVFKVDNLHFPSKKDS--SDGRHHQDTLLDGELVL 78 (192)
T ss_dssp EEEE--TTGHHHHHHS-EEEEEEESSEEEEEEEEEEEEEEEETTS-EEEESSST-ECTTC----TTCEGCSEEEEEEEEE
T ss_pred CCcccchhhHHHHhhCCcEEEECCCCcEEEEEEecceEEEEeCCCcEEEecCccccccccc--ccccccCCEEEEEEEEc
Confidence 899999999999999999999999999999999999999999999988886 999987531 01134689999999999
Q ss_pred ecCCCCCcceeEEEEeeeeecCCccccCCCHHHHHHHHHHHhcCccchhhccccccCCCCccCCCCCeEEEeccceechh
Q 012588 211 DKLPDSRRQERRYLIYDMMAINQASVIERPFYERWKMLEKEVIEPRNYERHNIYQSRNPYYRYDLEPFRVRRKDFWLLST 290 (460)
Q Consensus 211 d~~~~~~~~~~ryliFDiL~~~G~~l~~~pf~eRl~~L~~~i~~pr~~~~~~l~~~~~~~~~~~~~pf~I~~K~f~~~~~ 290 (460)
|+.++. ..++|||||||+++|++++++||.+|+++|++.|+.|+..+. + .++.+..+.+||.++.|+|++++.
T Consensus 79 d~~~~~--~~~~flifD~l~~~G~~v~~~~~~~Rl~~l~~~i~~p~~~~~--~---~~~~~~~~~~pf~i~~K~~~~~~~ 151 (192)
T PF01331_consen 79 DKDPGE--KKPRFLIFDILAINGQNVTDKPLDERLAYLQEEIIEPRKNAE--L---KSGIIKKKKEPFSIRIKDFFPIYQ 151 (192)
T ss_dssp EECTTC--EEEEEEEEEEEEETTEEGCCSBHHHHHHHHHHHTHHHHHHHH--C---HTTSCTCTTSSSEEEE---EEGGG
T ss_pred ccCCCC--CceEEEEEeeehhCCcEeccCCHHHHHHHHHHHHHHHHHhhc--c---ccccccccccceeeeccccHHHHh
Confidence 987653 589999999999999999999999999999999999987553 1 244455677999999999999999
Q ss_pred HHH-HHHHhccccCCCCceEEEEcCCCCCccCCCCCeEEEc
Q 012588 291 VNK-LLKEFIPKLSHDADGLVFQGWDDPYVPRTHEGLLKWK 330 (460)
Q Consensus 291 ~~~-ll~~~~~~l~h~~DGLIF~p~~spY~~G~~~~~LKWK 330 (460)
+++ +...+++.++|++|||||||.++||++|||..+||||
T Consensus 152 ~~~~~~~~~~~~l~h~~DGLIFtp~~~pY~~Gt~~~llKWK 192 (192)
T PF01331_consen 152 IEKLLFEEFIPKLPHETDGLIFTPVNTPYVPGTCPNLLKWK 192 (192)
T ss_dssp HHHHCHHCCCCCTTSTEEEEEEEESSSB--SEEEEEEEEE-
T ss_pred hHHHHHHHhhccCCCCCCEEEEecCCCCccCCCCCccEeeC
Confidence 998 4568889999999999999999999999999999998
No 3
>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=100.00 E-value=3.6e-43 Score=336.94 Aligned_cols=212 Identities=44% Similarity=0.703 Sum_probs=175.3
Q ss_pred HHHHHHHHHHHhcccCCCCCCCCCCCCcccccccccccccccCceEEEEcCCeeEEEEEEEC-CEEEEEeCCCccccccC
Q 012588 105 QDAFRHFCYQTLKLNFGGRGNMQFPGSHPVSLNSDNLQLLRQRYYYATWKADGTRYMMLITI-DGCYLIDRCFNFRRVQM 183 (460)
Q Consensus 105 ~~~~r~~~~~l~~~~~~~~~~~~FPGsqPVSl~r~nl~~l~~~~Y~V~~K~DG~R~Ll~i~~-~~vyLidR~~~~~~v~~ 183 (460)
...||..+..+|. .....+|||||||||+++|+..+...+|+||||+||+|++|++.+ +++||+||+++++ +.
T Consensus 3 ~~~l~~~~~~~~~----~~~~~~FpG~~pvs~~~~~~~~~~~~~y~ve~K~DG~R~~l~~~~~~~v~l~sR~~~~~--~~ 76 (215)
T cd07895 3 LSELRRKVAELCP----GWERGGFPGSQPVSFSRKNLELLKQNDYFVCEKSDGVRYLLLITGRGEVYLIDRKNDVF--KV 76 (215)
T ss_pred HHHHHHHHHHHhc----ccCCCCCCCCCccCccHHHHHHHhhCCeEEEEeEcCeEEEEEEecCCcEEEEeCCCCeE--Ee
Confidence 3567888888872 234699999999999999999999999999999999999999998 8999999999854 44
Q ss_pred cCCcccCCCCccccCCCceeeeeEEEEecCCCCCcceeEEEEeeeeecCCccccCCCHHHHHHHHHHHhcCccchhhccc
Q 012588 184 RFPCRNSNEGLGEKTHHFTLLDGEMIIDKLPDSRRQERRYLIYDMMAINQASVIERPFYERWKMLEKEVIEPRNYERHNI 263 (460)
Q Consensus 184 ~FP~~~~~~~l~~~~~~~TlLDGElV~d~~~~~~~~~~ryliFDiL~~~G~~l~~~pf~eRl~~L~~~i~~pr~~~~~~l 263 (460)
.||........ .....+|+||||||.+..++ ..+++|+|||||+++|+++++.||.+|+++|++.+..+....+
T Consensus 77 ~~~~~~~~~~~-~~~~~~~ilDGElv~~~~~~--~~~~~~~vFDiL~~~g~~l~~~pl~~R~~~L~~~i~~~~~~~~--- 150 (215)
T cd07895 77 PGLFFPRRKNL-EPHHQGTLLDGELVIDKVPG--KKRPRYLIFDILAFNGQSVTEKPLSERLKYIKKEVIEPRNELL--- 150 (215)
T ss_pred ccccCCCcccc-cccccCeeeEEEEEEEcCCC--ceEEEEEEEEEEEECCcCccCCCHHHHHHHHHHhchhHHHHhh---
Confidence 45544211001 12247899999999986543 2478999999999999999999999999999999877654322
Q ss_pred cccCCCCccCCCCCeEEEeccceechhHHHHHHHhccccCCCCceEEEEcCCCCCccCCCCCeEEEcc
Q 012588 264 YQSRNPYYRYDLEPFRVRRKDFWLLSTVNKLLKEFIPKLSHDADGLVFQGWDDPYVPRTHEGLLKWKY 331 (460)
Q Consensus 264 ~~~~~~~~~~~~~pf~I~~K~f~~~~~~~~ll~~~~~~l~h~~DGLIF~p~~spY~~G~~~~~LKWKP 331 (460)
..........+|.|+.|+|+++++++++|+.+.+.+.|++|||||||.++||.+||+..||||||
T Consensus 151 ---~~~~~~~~~~~~~i~~k~~~~~~~~~~~~~~~~~~~~~~~EGlIfk~~~~~Y~~Gr~~~~lKwKp 215 (215)
T cd07895 151 ---KKGPIDKAKEPFSVRLKDFFPLYKIEKLFEKIIPKLPHENDGLIFTPNDEPYVPGTDKNLLKWKP 215 (215)
T ss_pred ---hcChhhcCCCCeEEEecceEeHHhHHHHHHhccccCCCCCCCEEEccCCCCccCccCCcceeeCC
Confidence 11112235679999999999999999999988778999999999999999999999999999998
No 4
>KOG2386 consensus mRNA capping enzyme, guanylyltransferase (alpha) subunit [RNA processing and modification]
Probab=100.00 E-value=2.4e-36 Score=306.80 Aligned_cols=237 Identities=41% Similarity=0.633 Sum_probs=179.6
Q ss_pred CchhhhHHhcCCCHHHHHHHHHhhCCCCcchhHHHHHHHHHhccCCCCCCCCCCCCcccccccCC--CCCCCCCCCCCCc
Q 012588 1 MIVHFLMRSQSMSVAQAIKKFAEVRPPGIYKNEYIEALYTFYHEKRLDSTPCPSTPEWKRELDLN--GEAVPDDDDDGVP 78 (460)
Q Consensus 1 ~i~~yl~~~~~~~~~~a~~~F~~~rppgi~~~~y~~~l~~~y~~~~~~~~~~p~~p~w~~~~~~~--~~~~~~~~~~~~~ 78 (460)
|||+||++.++||+++|++.||.||||||||++||++||.+|++..+..+.+|+.|+|+.+.+.+ +..+.++|+...+
T Consensus 141 LI~~yL~~~~~~s~~~aik~f~~~r~~gi~k~dyi~~L~~~~~~~~p~~vs~p~~~~~~~~~~~~~~~~~~~~~Dg~i~t 220 (393)
T KOG2386|consen 141 LICAYLADVGGYSSSEAIKRFADARPPGIEKQDYIDALYSRYHDIFPFKVSCPSMPDWKRSIKLKKPVHKLHGNDGLIFT 220 (393)
T ss_pred eeeeeeeeccCccHHHHHHHHHHhCCCccCchHHHHHHhhcccccccccccCCCCcchhhhhhhccccccccccCCCcCC
Confidence 79999999999999999999999999999999999999999999997789999999999865432 1222222221111
Q ss_pred c--ccc--ccCcc------ccccCCCCCCCccccchHHHHHHHHHHHhcccCCCCCCCCCCCCcccccccccccccccCc
Q 012588 79 A--AAL--HENNE------VTMTNDDVLGDEIPNDQQDAFRHFCYQTLKLNFGGRGNMQFPGSHPVSLNSDNLQLLRQRY 148 (460)
Q Consensus 79 ~--~~~--~~~~~------~~~~~~~v~G~~~~~~~~~~~r~~~~~l~~~~~~~~~~~~FPGsqPVSl~r~nl~~l~~~~ 148 (460)
. .+. .++.+ -++.|.-++|+.....+ ..+..|.. ....| |+|||| |.|+..+.+..
T Consensus 221 ~~~~pg~~~g~~~~~~k~k~~~~n~~~~~~~~~~~q-----~~~~~l~~------~~~~~-g~~~~~--r~~~~~~~~~~ 286 (393)
T KOG2386|consen 221 PAEIPGSKNGKQEALLKWKPFSLNTIDFGVKLEKPQ-----PELGDLQC------KRKNE-GAQPVS--RENYKLLVFEY 286 (393)
T ss_pred cccCccccccchhhhhcCCchhcCCcccceeecCCC-----CCccchhh------hhccc-ccCCcc--ccchhhhhhhh
Confidence 1 111 11212 33444445555544443 22222221 12344 999999 99999999999
Q ss_pred eEEEEcCCeeEEEEEEECCE-EEEEeCCCc-cccccCcCCcccCCCCccccCCCceeeeeEEEEecCCCCCcceeEEEEe
Q 012588 149 YYATWKADGTRYMMLITIDG-CYLIDRCFN-FRRVQMRFPCRNSNEGLGEKTHHFTLLDGEMIIDKLPDSRRQERRYLIY 226 (460)
Q Consensus 149 Y~V~~K~DG~R~Ll~i~~~~-vyLidR~~~-~~~v~~~FP~~~~~~~l~~~~~~~TlLDGElV~d~~~~~~~~~~ryliF 226 (460)
|.++||+||+||||++++++ +|++||.+. +..-+++||...+.. ..+..||+||||++|+....+ .+||++|
T Consensus 287 y~~~We~dg~~~~~L~~~~~~~~~~dR~~~~~~~~~~~~~~~~~~~----~~~~~tl~dge~~lD~l~~~~--~~r~l~Y 360 (393)
T KOG2386|consen 287 YEASWEADGTRYMMLIDGDGEYYDFDRWRFVKGRENLRKIREDSDT----KVLHQTLLDGEMILDRLKEEA--IPRYLIY 360 (393)
T ss_pred hhhhhcccCcEEEEEecCCceeEechhhhHHHhhhhhhcccccccc----hhhhhhhcccceecccccccc--chhheee
Confidence 99999999999999999876 788888765 445577777553321 235789999999999876653 7899999
Q ss_pred eeeecCCccccCCCHHHHHHHHHHHhcCccch
Q 012588 227 DMMAINQASVIERPFYERWKMLEKEVIEPRNY 258 (460)
Q Consensus 227 DiL~~~G~~l~~~pf~eRl~~L~~~i~~pr~~ 258 (460)
|++.+|++++...||. |++++.++|++|+..
T Consensus 361 d~~r~n~~~v~~~~f~-r~~~~~~evi~~r~~ 391 (393)
T KOG2386|consen 361 DMVRFNSQKVEKRPFS-RWQIIEKEVIDPREL 391 (393)
T ss_pred eeeeccCcccccCcch-HHHHHHHHhcCchhc
Confidence 9999999999999999 999999999999853
No 5
>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=99.96 E-value=3.4e-29 Score=233.93 Aligned_cols=178 Identities=22% Similarity=0.305 Sum_probs=140.0
Q ss_pred CCCcccccccccccccccCceEEEEcCCeeEEEEEEECCEEEEEeCCCccccccCcCCcccCCCCccccCCCceeeeeEE
Q 012588 129 PGSHPVSLNSDNLQLLRQRYYYATWKADGTRYMMLITIDGCYLIDRCFNFRRVQMRFPCRNSNEGLGEKTHHFTLLDGEM 208 (460)
Q Consensus 129 PGsqPVSl~r~nl~~l~~~~Y~V~~K~DG~R~Ll~i~~~~vyLidR~~~~~~v~~~FP~~~~~~~l~~~~~~~TlLDGEl 208 (460)
|+++|+|+.+.+...+...+|+|++|+||+|+++++.+++++++||++. .++..||..... .+ ...+..++|||||
T Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~e~K~DG~R~~~~~~~~~v~~~sR~g~--~~~~~~~~~~~~-~~-~~~~~~~ilDGEl 76 (182)
T cd06846 1 PQLLNPILEEALSEYDEQDEYYVQEKYDGKRALIVALNGGVFAISRTGL--EVPLPSILIPGR-EL-LTLKPGFILDGEL 76 (182)
T ss_pred CCccchhhhHHHhhccccCcEEEEEccCceEEEEEEcCCeEEEEeCCCC--EEecccccccch-HH-hccCCCeeEEEEE
Confidence 4688999999977777889999999999999999999999999999997 334556544210 01 1234689999999
Q ss_pred EEecCCCCCcceeEEEEeeeeecCCccccCCCHHHHHHHHHHHhcCccchhhccccccCCCCccCCCCCeEEEeccceec
Q 012588 209 IIDKLPDSRRQERRYLIYDMMAINQASVIERPFYERWKMLEKEVIEPRNYERHNIYQSRNPYYRYDLEPFRVRRKDFWLL 288 (460)
Q Consensus 209 V~d~~~~~~~~~~ryliFDiL~~~G~~l~~~pf~eRl~~L~~~i~~pr~~~~~~l~~~~~~~~~~~~~pf~I~~K~f~~~ 288 (460)
|....+. ....++|+|||||+++|.+++++||.+|+++|++.+..... ..++.+..+..++.
T Consensus 77 v~~~~~~-~~~~~~~~~FDil~~~~~~~~~~p~~eR~~~L~~~v~~~~~-----------------~~~~~i~~~~~~~~ 138 (182)
T cd06846 77 VVENREV-ANPKPTYYAFDVVPLSGVGLRDLPYSDRFAYLKSLLKEFEG-----------------LDPVKLVPLENAPS 138 (182)
T ss_pred EeccCCC-ccceeEEEEEEEEEECCCccccCCHHHHHHHHHHHhhhhcc-----------------CCceeEEEeecccc
Confidence 9975433 22468999999999999999999999999999997754221 13555666666655
Q ss_pred hh--HHHHHHHhccccCCCCceEEEEcCCCCC--ccCCCCCeEEEcc
Q 012588 289 ST--VNKLLKEFIPKLSHDADGLVFQGWDDPY--VPRTHEGLLKWKY 331 (460)
Q Consensus 289 ~~--~~~ll~~~~~~l~h~~DGLIF~p~~spY--~~G~~~~~LKWKP 331 (460)
+. +..+++. ...|+.|||||++.++|| .+|++..|+||||
T Consensus 139 ~~~~~~~~~~~---~~~~g~EGvi~K~~~s~Y~~~~gr~~~wlK~Kp 182 (182)
T cd06846 139 YDETLDDLLEK---LKKKGKEGLVFKHPDAPYKGRPGSSGNQLKLKP 182 (182)
T ss_pred cchHHHHHHHH---hhhcCCceEEEEcCCCCccccCCCCCceEeecC
Confidence 44 3556654 467999999999999999 9999999999998
No 6
>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=99.94 E-value=4.5e-26 Score=216.38 Aligned_cols=162 Identities=22% Similarity=0.302 Sum_probs=122.1
Q ss_pred cccCceEEEEcCCeeEEEEEEECCEEEEEeCCCccccccCcCCcccCCCCccccCCCceeeeeEEEEecCCCC-------
Q 012588 144 LRQRYYYATWKADGTRYMMLITIDGCYLIDRCFNFRRVQMRFPCRNSNEGLGEKTHHFTLLDGEMIIDKLPDS------- 216 (460)
Q Consensus 144 l~~~~Y~V~~K~DG~R~Ll~i~~~~vyLidR~~~~~~v~~~FP~~~~~~~l~~~~~~~TlLDGElV~d~~~~~------- 216 (460)
....+|++++|+||+|+++++.++++++++|++. ..+..||+..+. + ....++++||||||+-..++.
T Consensus 18 ~~~~~~~~E~K~DG~R~~~~~~~~~v~l~SR~g~--~~t~~~p~i~~~--~-~~~~~~~vLDGElv~~~~~~~~~f~~~~ 92 (201)
T cd07898 18 KKPAAAWVEDKYDGIRAQVHKDGGRVEIFSRSLE--DITDQFPELAAA--A-KALPHEFILDGEILAWDDNRGLPFSELF 92 (201)
T ss_pred hCCCeEEEEEeeceEEEEEEEeCCEEEEEcCCCh--hchhhhhhHHHH--H-HhCCCCEEEEEEEEEEeCCCCCcHHHHH
Confidence 4456899999999999999999999999999987 346678865431 1 122478999999997322211
Q ss_pred -------------CcceeEEEEeeeeecCCccccCCCHHHHHHHHHHHhcCccchhhccccccCCCCccCCCCCeEEEec
Q 012588 217 -------------RRQERRYLIYDMMAINQASVIERPFYERWKMLEKEVIEPRNYERHNIYQSRNPYYRYDLEPFRVRRK 283 (460)
Q Consensus 217 -------------~~~~~ryliFDiL~~~G~~l~~~pf~eRl~~L~~~i~~pr~~~~~~l~~~~~~~~~~~~~pf~I~~K 283 (460)
....+.|+|||+|+++|++++++||.+|+++|++.+.... + .|...
T Consensus 93 ~~~~~~~~~~~~~~~~~~~~~vFDil~~~g~~l~~~p~~eR~~~L~~~~~~~~------------~---------~i~~~ 151 (201)
T cd07898 93 KRLGRKFRDKFLDEDVPVVLMAFDLLYLNGESLLDRPLRERRQLLEELFVEIP------------G---------RIRIA 151 (201)
T ss_pred HHhcccccchhhhccCcEEEEEEeEEeECCcchhhCCHHHHHHHHHHhhcCCC------------C---------cEEEe
Confidence 0134899999999999999999999999999999763210 0 13445
Q ss_pred cceechhHHHHHHHhccccCCCCceEEEEcCCCCCccCC-CCCeEEEcc
Q 012588 284 DFWLLSTVNKLLKEFIPKLSHDADGLVFQGWDDPYVPRT-HEGLLKWKY 331 (460)
Q Consensus 284 ~f~~~~~~~~ll~~~~~~l~h~~DGLIF~p~~spY~~G~-~~~~LKWKP 331 (460)
++....+.+++.+-+...+.|+.||||+++.++||.+|+ +..||||||
T Consensus 152 ~~~~~~~~~~~~~~~~~~~~~g~EGim~K~~~s~Y~~g~Rs~~wlK~K~ 200 (201)
T cd07898 152 PALPVESAEELEAAFARARARGNEGLMLKDPDSPYEPGRRGLAWLKLKK 200 (201)
T ss_pred eeEEcCCHHHHHHHHHHHHHcCCceEEEeCCCCCcCCCCcCCCcEEeCC
Confidence 555555543333323346789999999999999999996 889999998
No 7
>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=99.92 E-value=2.9e-24 Score=207.33 Aligned_cols=167 Identities=22% Similarity=0.317 Sum_probs=123.0
Q ss_pred cccccCceEEEEcCCeeEEEEEEECCEEEEEeCCCccccccCcCCcccCCCC-------ccccCCCceeeeeEEEE-ecC
Q 012588 142 QLLRQRYYYATWKADGTRYMMLITIDGCYLIDRCFNFRRVQMRFPCRNSNEG-------LGEKTHHFTLLDGEMII-DKL 213 (460)
Q Consensus 142 ~~l~~~~Y~V~~K~DG~R~Ll~i~~~~vyLidR~~~~~~v~~~FP~~~~~~~-------l~~~~~~~TlLDGElV~-d~~ 213 (460)
..+...+|++++|+||+|++++++++++.+++|+++ .++..||+...... .......+++||||||+ +..
T Consensus 28 ~~~~~~~~~~E~K~DG~R~~i~~~~~~v~l~SR~g~--~~t~~~p~~~~~~~~~~~l~~~~~~~~~~~iLDGElv~~~~~ 105 (225)
T cd07903 28 KLLKGKPFYIETKLDGERIQLHKDGNEFKYFSRNGN--DYTYLYGASLTPGSLTPYIHLAFNPKVKSCILDGEMVVWDKE 105 (225)
T ss_pred HhhcCCeEEEEEeeCceEEEEEecCCEEEEEeCCCc--cccccccccccccccchhhhhhccccCcEEEeceEEEEEEcC
Confidence 344567899999999999999999899999999987 44677887643210 00112367999999997 321
Q ss_pred CC------------------CCcceeEEEEeeeeecCCccccCCCHHHHHHHHHHHhcCccchhhccccccCCCCccCCC
Q 012588 214 PD------------------SRRQERRYLIYDMMAINQASVIERPFYERWKMLEKEVIEPRNYERHNIYQSRNPYYRYDL 275 (460)
Q Consensus 214 ~~------------------~~~~~~ryliFDiL~~~G~~l~~~pf~eRl~~L~~~i~~pr~~~~~~l~~~~~~~~~~~~ 275 (460)
.+ .....+.|+|||||+++|++++++||.+|+++|++.+.. .. +
T Consensus 106 ~~~~~~f~~l~~~~~~~~~~~~~~~~~~~vFDiL~~~g~~l~~~pl~eR~~~L~~~~~~-~~-----------~------ 167 (225)
T cd07903 106 TKRFLPFGTLKDVAKLREVEDSDLQPCFVVFDILYLNGKSLTNLPLHERKKLLEKIITP-IP-----------G------ 167 (225)
T ss_pred cCeeccchHHHHHHhhcccccCCccEEEEEEEEEEECCeecccCcHHHHHHHHHHhcCC-CC-----------C------
Confidence 11 112357899999999999999999999999999996532 10 0
Q ss_pred CCeEEEeccceec---hhHHHHHHHhccccCCCCceEEEEcCCCCCccC-CCCCeEEEccCCC
Q 012588 276 EPFRVRRKDFWLL---STVNKLLKEFIPKLSHDADGLVFQGWDDPYVPR-THEGLLKWKYARM 334 (460)
Q Consensus 276 ~pf~I~~K~f~~~---~~~~~ll~~~~~~l~h~~DGLIF~p~~spY~~G-~~~~~LKWKP~~~ 334 (460)
.+...+.... .++.++++. .+.++.||||++..+++|.+| ++..|+||||..+
T Consensus 168 ---~i~~~~~~~~~~~~~~~~~~~~---~~~~g~EGlv~K~~~s~Y~~g~Rs~~wlK~K~~Y~ 224 (225)
T cd07903 168 ---RLEVVKRTEASTKEEIEEALNE---AIDNREEGIVVKDLDSKYKPGKRGGGWIKIKPEYL 224 (225)
T ss_pred ---eEEEEEEEeCCCHHHHHHHHHH---HHHcCCceEEEecCCCCCccCCcCCCcEEechhhc
Confidence 1223333333 344556653 567999999999999999999 6789999999754
No 8
>PRK09247 ATP-dependent DNA ligase; Validated
Probab=99.91 E-value=1.5e-23 Score=225.68 Aligned_cols=170 Identities=21% Similarity=0.274 Sum_probs=126.7
Q ss_pred cccCceEEEEcCCeeEEEEEEECCEEEEEeCCCccccccCcCCcccCCCCccccCCCceeeeeEEEEecC--CCC-----
Q 012588 144 LRQRYYYATWKADGTRYMMLITIDGCYLIDRCFNFRRVQMRFPCRNSNEGLGEKTHHFTLLDGEMIIDKL--PDS----- 216 (460)
Q Consensus 144 l~~~~Y~V~~K~DG~R~Ll~i~~~~vyLidR~~~~~~v~~~FP~~~~~~~l~~~~~~~TlLDGElV~d~~--~~~----- 216 (460)
+...+|++++|+||+|++++..++++.+++|+++ .++..||+..+. . .....+++||||||.... ++.
T Consensus 222 ~~~~~~~~E~K~DG~R~qih~~~~~v~lfSR~g~--d~t~~fPei~~~--~-~~l~~~~ILDGElv~~~~~~~~~~~F~~ 296 (539)
T PRK09247 222 GDPADWQAEWKWDGIRVQLVRRGGEVRLWSRGEE--LITERFPELAEA--A-EALPDGTVLDGELLVWRPEDGRPQPFAD 296 (539)
T ss_pred cCCCcEEEEEeEcceEEEEEEeCCEEEEEeCCCc--cchhhhHHHHHH--H-HhCCCCEEEEeEEEEEECCCCCcCCHHH
Confidence 3446899999999999999999999999999998 557889987542 0 122357999999998541 110
Q ss_pred ------C---------cceeEEEEeeeeecCCccccCCCHHHHHHHHHHHhcCccchhhccccccCCCCccCCCCCeEEE
Q 012588 217 ------R---------RQERRYLIYDMMAINQASVIERPFYERWKMLEKEVIEPRNYERHNIYQSRNPYYRYDLEPFRVR 281 (460)
Q Consensus 217 ------~---------~~~~ryliFDiL~~~G~~l~~~pf~eRl~~L~~~i~~pr~~~~~~l~~~~~~~~~~~~~pf~I~ 281 (460)
. ..+++|++||||++||++++++||.+|+++|++.+.... .+. +.
T Consensus 297 l~~R~~rk~~~~~~~~~~pv~~~vFDiL~l~g~~l~~~Pl~eRr~~L~~~~~~~~-----------~~~---------i~ 356 (539)
T PRK09247 297 LQQRIGRKTVGKKLLADYPAFLRAYDLLEDGGEDLRALPLAERRARLEALIARLP-----------DPR---------LD 356 (539)
T ss_pred HHHHhcccccchhhhhcCCeEEEEEEeeeeCCcchhhCCHHHHHHHHHHHhcccC-----------CCe---------EE
Confidence 0 124689999999999999999999999999999763210 111 22
Q ss_pred eccceec---hhHHHHHHHhccccCCCCceEEEEcCCCCCccCCC-CCeEEEccCCCceEEEEEE
Q 012588 282 RKDFWLL---STVNKLLKEFIPKLSHDADGLVFQGWDDPYVPRTH-EGLLKWKYARMNSVDFLFE 342 (460)
Q Consensus 282 ~K~f~~~---~~~~~ll~~~~~~l~h~~DGLIF~p~~spY~~G~~-~~~LKWKP~~~nTVDF~l~ 342 (460)
..+.... ..+.++++. .+.++.||||++..+++|.+|++ ..|+|||+.. .|+|+++-
T Consensus 357 ~~~~~~~~~~~e~~~~~~~---a~~~g~EGlm~K~~~s~Y~~Grr~~~WlK~K~~~-~t~DlVvi 417 (539)
T PRK09247 357 LSPLVPFSDWDELAALRAA---ARERGVEGLMLKRRDSPYLVGRKKGPWWKWKRDP-LTIDAVLM 417 (539)
T ss_pred ecCceecCCHHHHHHHHHH---HHHCCCceEEEecCCCCcCCCCCcchhhcccCCC-CcEEEEEE
Confidence 2222222 244556654 57899999999999999999974 6799999852 49999984
No 9
>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=99.91 E-value=1e-23 Score=201.38 Aligned_cols=161 Identities=22% Similarity=0.314 Sum_probs=120.3
Q ss_pred cccCceEEEEcCCeeEEEEEEECCEEEEEeCCCccccccCcCCcccCCCCccccCCCceeeeeEEEEecCCCC-------
Q 012588 144 LRQRYYYATWKADGTRYMMLITIDGCYLIDRCFNFRRVQMRFPCRNSNEGLGEKTHHFTLLDGEMIIDKLPDS------- 216 (460)
Q Consensus 144 l~~~~Y~V~~K~DG~R~Ll~i~~~~vyLidR~~~~~~v~~~FP~~~~~~~l~~~~~~~TlLDGElV~d~~~~~------- 216 (460)
+...+|++++|+||+|++++..++++.|++|+++ .++..||+.... ......+++||||||+...++.
T Consensus 21 ~~~~~~~~E~K~DG~R~~~~~~~~~v~l~SR~g~--~~t~~~p~l~~~---~~~l~~~~iLDGElv~~~~~~~~~F~~l~ 95 (207)
T cd07897 21 GDPSDWQAEWKWDGIRGQLIRRGGEVFLWSRGEE--LITGSFPELLAA---AEALPDGTVLDGELLVWRDGRPLPFNDLQ 95 (207)
T ss_pred cCcccEEEEEeEceEEEEEEEcCCEEEEEeCCCC--cccccchHHHHH---HHhCCCCeEEEeEEEEecCCCccCHHHHH
Confidence 3456899999999999999998899999999987 457789987432 1122468999999998532110
Q ss_pred -------------CcceeEEEEeeeeecCCccccCCCHHHHHHHHHHHhcCccchhhccccccCCCCccCCCCCeEEEec
Q 012588 217 -------------RRQERRYLIYDMMAINQASVIERPFYERWKMLEKEVIEPRNYERHNIYQSRNPYYRYDLEPFRVRRK 283 (460)
Q Consensus 217 -------------~~~~~ryliFDiL~~~G~~l~~~pf~eRl~~L~~~i~~pr~~~~~~l~~~~~~~~~~~~~pf~I~~K 283 (460)
....+.|++||||+++|+++++.||.+|+++|++.+.. .. .+. +...
T Consensus 96 ~r~~~~~~~~~~~~~~~~~~~vFDil~l~g~~l~~~pl~eRr~~L~~l~~~-~~----------~~~---------i~~~ 155 (207)
T cd07897 96 QRLGRKTVGKKLLAEAPAAFRAYDLLELNGEDLRALPLRERRARLEALLAR-LP----------PPR---------LDLS 155 (207)
T ss_pred HHhcccccchhhHhhCCeEEEEEeeeeECceEhhhCCHHHHHHHHHHhhhh-cC----------CCc---------eeec
Confidence 01247899999999999999999999999999996632 10 111 2222
Q ss_pred cceec---hhHHHHHHHhccccCCCCceEEEEcCCCCCccCC-CCCeEEEccC
Q 012588 284 DFWLL---STVNKLLKEFIPKLSHDADGLVFQGWDDPYVPRT-HEGLLKWKYA 332 (460)
Q Consensus 284 ~f~~~---~~~~~ll~~~~~~l~h~~DGLIF~p~~spY~~G~-~~~~LKWKP~ 332 (460)
++... ..+.++++. .+.++.||||++..+++|.+|+ +..|+|.|+.
T Consensus 156 ~~~~~~~~~~~~~~~~~---~~~~g~EGiv~K~~~s~Y~~Grr~~~W~K~K~d 205 (207)
T cd07897 156 PLIAFADWEELAALRAQ---SRERGAEGLMLKRRDSPYLVGRKKGDWWKWKID 205 (207)
T ss_pred ceEecCCHHHHHHHHHH---HHHcCCeEEEEeCCCCCcCCCCcCCCeeEeCCC
Confidence 33333 344556653 5789999999999999999996 5679999974
No 10
>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=99.90 E-value=3.7e-23 Score=194.77 Aligned_cols=157 Identities=21% Similarity=0.254 Sum_probs=118.1
Q ss_pred cCceEEEEcCCeeEEEEEEECCEEEEEeCCCccccccCcCCcccCCCCccccCCCceeeeeEEEEecCCC----------
Q 012588 146 QRYYYATWKADGTRYMMLITIDGCYLIDRCFNFRRVQMRFPCRNSNEGLGEKTHHFTLLDGEMIIDKLPD---------- 215 (460)
Q Consensus 146 ~~~Y~V~~K~DG~R~Ll~i~~~~vyLidR~~~~~~v~~~FP~~~~~~~l~~~~~~~TlLDGElV~d~~~~---------- 215 (460)
..+|++++|+||+|+++++.++++.+++|++. .++..||+.... +....+.+++||||||....++
T Consensus 15 ~~~~~~e~K~DG~R~~i~~~~~~v~~~SR~g~--~~t~~~p~l~~~--~~~~~~~~~iLDGElv~~~~~~~~~F~~l~~~ 90 (190)
T cd07906 15 GEDWLYEIKWDGYRALARVDGGRVRLYSRNGL--DWTARFPELAEA--LAALPVRDAVLDGEIVVLDEGGRPDFQALQNR 90 (190)
T ss_pred CCCeEEEEeEceEEEEEEEECCEEEEEcCCCC--cchhhhHHHHHH--HHhcCCCCEEEEeEEEEECCCCCCCHHHHHHh
Confidence 45899999999999999999999999999987 345678865321 1111357899999999843221
Q ss_pred -------CCcceeEEEEeeeeecCCccccCCCHHHHHHHHHHHhcCccchhhccccccCCCCccCCCCCeEEEeccceec
Q 012588 216 -------SRRQERRYLIYDMMAINQASVIERPFYERWKMLEKEVIEPRNYERHNIYQSRNPYYRYDLEPFRVRRKDFWLL 288 (460)
Q Consensus 216 -------~~~~~~ryliFDiL~~~G~~l~~~pf~eRl~~L~~~i~~pr~~~~~~l~~~~~~~~~~~~~pf~I~~K~f~~~ 288 (460)
.....+.|+|||||+++|+++.++||.+|+++|++.+. +.. + + +........
T Consensus 91 ~~~~~~~~~~~~~~~~vFDil~~~~~~~~~~p~~eR~~~L~~~~~-~~~-----------~-------~--i~~~~~~~~ 149 (190)
T cd07906 91 LRLRRRLARTVPVVYYAFDLLYLDGEDLRGLPLLERKELLEELLP-AGS-----------P-------R--LRVSEHFEG 149 (190)
T ss_pred hcccchhcccCceEEEEEeeeeeCCcchhhCCHHHHHHHHHHHhc-cCC-----------C-------c--EEECceEcC
Confidence 01145899999999999999999999999999999663 210 0 1 222223332
Q ss_pred hhHHHHHHHhccccCCCCceEEEEcCCCCCccCC-CCCeEEEcc
Q 012588 289 STVNKLLKEFIPKLSHDADGLVFQGWDDPYVPRT-HEGLLKWKY 331 (460)
Q Consensus 289 ~~~~~ll~~~~~~l~h~~DGLIF~p~~spY~~G~-~~~~LKWKP 331 (460)
. .+.+++. .+.++.||||++..++||.+|+ +..|||||+
T Consensus 150 ~-~~~~~~~---~~~~g~EGiv~K~~~s~Y~~g~rs~~wlK~K~ 189 (190)
T cd07906 150 G-GAALFAA---ACELGLEGIVAKRADSPYRSGRRSRDWLKIKC 189 (190)
T ss_pred C-HHHHHHH---HHHcCCcEEEEecCCCCcCCCCCCCccEEEec
Confidence 2 2456664 4678999999999999999998 889999995
No 11
>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=99.90 E-value=5e-23 Score=196.53 Aligned_cols=157 Identities=19% Similarity=0.276 Sum_probs=118.2
Q ss_pred cCceEEEEcCCeeEEEEEEECCEEEEEeCCCccccccCcCCcccCCCCccccCC-CceeeeeEEEEecC-CC--------
Q 012588 146 QRYYYATWKADGTRYMMLITIDGCYLIDRCFNFRRVQMRFPCRNSNEGLGEKTH-HFTLLDGEMIIDKL-PD-------- 215 (460)
Q Consensus 146 ~~~Y~V~~K~DG~R~Ll~i~~~~vyLidR~~~~~~v~~~FP~~~~~~~l~~~~~-~~TlLDGElV~d~~-~~-------- 215 (460)
..+|++++|+||.|+++++.++++.+++|++. .++..||+.... +..... .+++||||||+-.. +.
T Consensus 24 ~~~~~~E~K~DG~R~~~~~~~~~v~~~SR~~~--~~t~~~pel~~~--~~~~~~~~~~iLDGElv~~~~~g~~~~F~~l~ 99 (207)
T cd07901 24 GGEAAVEYKYDGIRVQIHKDGDEVRIFSRRLE--DITNALPEVVEA--VRELVKAEDAILDGEAVAYDPDGRPLPFQETL 99 (207)
T ss_pred CCcEEEEEeEcceeEEEEEeCCEEEEEeCCCc--cccchhhHHHHH--HHhcCCCCCEEEeCEEEEECCCCCccCHHHHH
Confidence 46899999999999999999999999999986 457789876431 111122 68999999998531 11
Q ss_pred -----CC-------cceeEEEEeeeeecCCccccCCCHHHHHHHHHHHhcCccchhhccccccCCCCccCCCCCeEEEec
Q 012588 216 -----SR-------RQERRYLIYDMMAINQASVIERPFYERWKMLEKEVIEPRNYERHNIYQSRNPYYRYDLEPFRVRRK 283 (460)
Q Consensus 216 -----~~-------~~~~ryliFDiL~~~G~~l~~~pf~eRl~~L~~~i~~pr~~~~~~l~~~~~~~~~~~~~pf~I~~K 283 (460)
.. ...+.|+|||||+++|++++++||.+|+++|++.+.. .. . +...
T Consensus 100 ~r~~~~~~~~~~~~~~~~~~~vFDil~~~g~~l~~~pl~eR~~~L~~~~~~-~~-------------------~--i~~~ 157 (207)
T cd07901 100 RRFRRKYDVEEAAEEIPLTLFLFDILYLDGEDLLDLPLSERRKILEEIVPE-TE-------------------A--ILLA 157 (207)
T ss_pred HHhccccchhhhhccCcEEEEEEEEEEECCcchhcCCHHHHHHHHHHhcCc-CC-------------------c--EEEE
Confidence 00 1247899999999999999999999999999986532 10 0 2222
Q ss_pred cceec---hhHHHHHHHhccccCCCCceEEEEcCCCCCccC-CCCCeEEEcc
Q 012588 284 DFWLL---STVNKLLKEFIPKLSHDADGLVFQGWDDPYVPR-THEGLLKWKY 331 (460)
Q Consensus 284 ~f~~~---~~~~~ll~~~~~~l~h~~DGLIF~p~~spY~~G-~~~~~LKWKP 331 (460)
.+... .++.++++. .+.++.||||++..+++|.+| |+..||||||
T Consensus 158 ~~~~~~~~~~~~~~~~~---~~~~g~EGiv~K~~~s~Y~~g~Rs~~wlK~K~ 206 (207)
T cd07901 158 PRIVTDDPEEAEEFFEE---ALEAGHEGVMVKSLDSPYQAGRRGKNWLKVKP 206 (207)
T ss_pred EEEecCCHHHHHHHHHH---HHHcCCceEEEeCCCCCcCCCCCCCCeEEecC
Confidence 23333 344556654 578999999999999999999 6789999998
No 12
>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=99.89 E-value=8.8e-23 Score=193.00 Aligned_cols=158 Identities=21% Similarity=0.217 Sum_probs=117.8
Q ss_pred cCceEEEEcCCeeEEEEEEECCEEEEEeCCCccccccCcCCcccCCCCccccCCCceeeeeEEEEecCCCC---------
Q 012588 146 QRYYYATWKADGTRYMMLITIDGCYLIDRCFNFRRVQMRFPCRNSNEGLGEKTHHFTLLDGEMIIDKLPDS--------- 216 (460)
Q Consensus 146 ~~~Y~V~~K~DG~R~Ll~i~~~~vyLidR~~~~~~v~~~FP~~~~~~~l~~~~~~~TlLDGElV~d~~~~~--------- 216 (460)
..+|++++|+||+|+++++.++++.|++|+++ .++..||+..+. +.....++++||||||+-..+..
T Consensus 15 ~~~~~~E~K~DG~R~~~~~~~~~v~l~SR~g~--~~t~~~p~~~~~--~~~~~~~~~iLDGElv~~~~~~~~F~~l~~r~ 90 (194)
T cd07905 15 PGGWQYEPKWDGFRCLAFRDGDEVRLQSRSGK--PLTRYFPELVAA--ARALLPPGCVLDGELVVWRGGRLDFDALQQRI 90 (194)
T ss_pred CCceEEEeeeceEEEEEEEeCCEEEEEeCCCC--chhhhhHHHHHH--HHhhCCCCEEEEeEEEEEcCCCCCHHHHHHHh
Confidence 46899999999999999999999999999987 456678876431 11112357999999998422210
Q ss_pred -----------CcceeEEEEeeeeecCCccccCCCHHHHHHHHHHHhcCccchhhccccccCCCCccCCCCCeEEEeccc
Q 012588 217 -----------RRQERRYLIYDMMAINQASVIERPFYERWKMLEKEVIEPRNYERHNIYQSRNPYYRYDLEPFRVRRKDF 285 (460)
Q Consensus 217 -----------~~~~~ryliFDiL~~~G~~l~~~pf~eRl~~L~~~i~~pr~~~~~~l~~~~~~~~~~~~~pf~I~~K~f 285 (460)
....++|++||||+++|+++++.||.+|++.|++.+.. . .+. +...+.
T Consensus 91 ~~~~~~~~~~~~~~~~~~~vFDiL~l~g~~l~~~pl~eRr~~L~~~~~~-~-----------~~~---------i~~~~~ 149 (194)
T cd07905 91 HPAASRVRRLAEETPASFVAFDLLALGGRDLRGRPLRERRAALEALLAG-W-----------GPP---------LHLSPA 149 (194)
T ss_pred cccccchhhhhccCCEEEEEEeeeeeCCcccccCCHHHHHHHHHHHhcc-c-----------CCC---------eEECCc
Confidence 01347999999999999999999999999999996632 1 011 122222
Q ss_pred e-echhHHHHHHHhccccCCCCceEEEEcCCCCCccCCCCCeEEEccC
Q 012588 286 W-LLSTVNKLLKEFIPKLSHDADGLVFQGWDDPYVPRTHEGLLKWKYA 332 (460)
Q Consensus 286 ~-~~~~~~~ll~~~~~~l~h~~DGLIF~p~~spY~~G~~~~~LKWKP~ 332 (460)
. ...++.++|+. .+.++.||||++..+++|.+|+ ..|+|+||.
T Consensus 150 ~~~~~~~~~~~~~---~~~~g~EGiv~K~~~s~Y~~Gr-~~WlK~K~~ 193 (194)
T cd07905 150 TTDRAEAREWLEE---FEGAGLEGVVAKRLDGPYRPGE-RAMLKVKHR 193 (194)
T ss_pred cCCHHHHHHHHHH---HHHCCCceEEEeCCCCCcCCCC-CcEEEEecc
Confidence 2 22244556664 5689999999999999999999 689999974
No 13
>PF03919 mRNA_cap_C: mRNA capping enzyme, C-terminal domain; InterPro: IPR013846 This domain is found at the C terminus of the mRNA capping enzyme. 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; PDB: 3S24_G 3RTX_A 3KYH_D 1CKN_B 1CKO_A 1CKM_B 1P16_B.
Probab=99.89 E-value=9.2e-24 Score=180.54 Aligned_cols=94 Identities=37% Similarity=0.561 Sum_probs=66.2
Q ss_pred CCceEEEEEEEecCC--------ceeE-EEEeCCceeeecC--ceeEecCCCCCCCCceEEEEEEeCCCCeeEEEEEecC
Q 012588 333 RMNSVDFLFEVTDDD--------RQLL-YVFERGKKKLMEG--SSVEFTDREPSFYSGKIIECTWDPDVQLWKCMRIRTD 401 (460)
Q Consensus 333 ~~nTVDF~l~~~~~~--------~~~L-~v~~~g~~~~~~~--~~~~f~~~~~~~~dg~IvEC~~d~~~~~W~f~R~R~D 401 (460)
++|||||+|++.... .+.| |+. ++.. ++.. ....+. +..++++|+||||+||++.|+|+|||+|+|
T Consensus 1 e~NTIDF~l~l~~~~~~~~l~~~~g~ldy~~-~~~~-~f~~~~~~~~~~-~~~~~ld~rIVEC~~d~~~~~W~~~R~R~D 77 (105)
T PF03919_consen 1 EENTIDFKLKLEFPKGDGMLPPKVGKLDYVQ-GGYD-PFMYEEEWERLK-KDGQPLDGRIVECSFDNEKGQWKFMRIRDD 77 (105)
T ss_dssp GC-EEEEEEEEECEEECTTSCEEEEEECCCS-CTCT-ESEEEECCCCCC-CSTCCSTTCEEEEEEETTTTEEEEEEEETT
T ss_pred CCCCEeEeEEEecCCCCCcccCCCCcEEEEc-CCcc-ccchhhHHHHHh-hcccccCCcEEEEEEeCCCCcEeEEEEcCC
Confidence 489999999997431 1222 221 1111 2100 011111 567889999999999988999999999999
Q ss_pred CCCCChHHHHHHHHHhcccCCCHHHHHH
Q 012588 402 KSTPNDINTYRKVMRSIRDNITEEVLLN 429 (460)
Q Consensus 402 K~~pN~~~tv~~v~~SI~~~Vt~e~Ll~ 429 (460)
|++||+++||.+||+||.++||+++|++
T Consensus 78 K~~pN~~~t~~~v~~sI~d~Vt~e~Ll~ 105 (105)
T PF03919_consen 78 KSTPNHISTVISVLESIEDPVTEEELLE 105 (105)
T ss_dssp SSS--BHHHHHHHHHHHHCS--HHHHHH
T ss_pred CCCCccHHHHHHHHHHHHcCCCHHHhcC
Confidence 9999999999999999999999999985
No 14
>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=99.89 E-value=1.2e-22 Score=195.63 Aligned_cols=164 Identities=16% Similarity=0.244 Sum_probs=119.7
Q ss_pred ccccCceEEEEcCCeeEEEEEEEC-CEEEEEeCCCccccccCcCCcccCC-CCccccCCCceeeeeEEEEecCC-CC---
Q 012588 143 LLRQRYYYATWKADGTRYMMLITI-DGCYLIDRCFNFRRVQMRFPCRNSN-EGLGEKTHHFTLLDGEMIIDKLP-DS--- 216 (460)
Q Consensus 143 ~l~~~~Y~V~~K~DG~R~Ll~i~~-~~vyLidR~~~~~~v~~~FP~~~~~-~~l~~~~~~~TlLDGElV~d~~~-~~--- 216 (460)
.+...+|++++|+||.|+++++.+ +.+.|++|+++ .++-.||+.... .........+++||||||+-... +.
T Consensus 27 ~~~~~~~~~E~K~DG~R~~~h~~~~~~v~l~SR~g~--~~t~~~pel~~~~~~~~~~~~~~~iLDGElv~~~~~~g~~~~ 104 (219)
T cd07900 27 RFEDKEFTCEYKYDGERAQIHLLEDGKVKIFSRNLE--NNTEKYPDIVAVLPKSLKPSVKSFILDSEIVAYDRETGKILP 104 (219)
T ss_pred HhCCCeEEEEEeecceEEEEEEcCCCeEEEECCCCc--cccchhhHHHHHHHHHhcccCccEEEeeEEEEEEcCCCCCcC
Confidence 345568999999999999999886 78999999987 457788876431 11100124679999999984321 10
Q ss_pred ----------------CcceeEEEEeeeeecCCccccCCCHHHHHHHHHHHhcCccchhhccccccCCCCccCCCCCeEE
Q 012588 217 ----------------RRQERRYLIYDMMAINQASVIERPFYERWKMLEKEVIEPRNYERHNIYQSRNPYYRYDLEPFRV 280 (460)
Q Consensus 217 ----------------~~~~~ryliFDiL~~~G~~l~~~pf~eRl~~L~~~i~~pr~~~~~~l~~~~~~~~~~~~~pf~I 280 (460)
...++.|++||||++||++++++||.+|+++|++.+. +.. + . +
T Consensus 105 F~~l~~r~~~~~~~~~~~~~~~~~vFDiL~l~g~~l~~~pl~eRr~~L~~~~~-~~~-----------~-------~--~ 163 (219)
T cd07900 105 FQVLSTRKRKDVDANDIKVQVCVFAFDLLYLNGESLLKKPLRERRELLHSLFK-EVP-----------G-------R--F 163 (219)
T ss_pred hHHHhhhcccccccccCcccEEEEEEEEEEECCchhhcCCHHHHHHHHHHhcC-CCC-----------C-------e--E
Confidence 0135789999999999999999999999999999652 210 0 1 2
Q ss_pred Eeccceec---hhHHHHHHHhccccCCCCceEEEEcCC--CCCccC-CCCCeEEEccC
Q 012588 281 RRKDFWLL---STVNKLLKEFIPKLSHDADGLVFQGWD--DPYVPR-THEGLLKWKYA 332 (460)
Q Consensus 281 ~~K~f~~~---~~~~~ll~~~~~~l~h~~DGLIF~p~~--spY~~G-~~~~~LKWKP~ 332 (460)
........ ..+.++|+. .+.++.||||++..+ ++|.+| ++..|+|+||.
T Consensus 164 ~~~~~~~~~~~~~~~~~~~~---~~~~g~EGiv~K~~~~~s~Y~~g~Rs~~W~K~K~d 218 (219)
T cd07900 164 QFATSKDSEDTEEIQEFLEE---AVKNNCEGLMVKTLDSDATYEPSKRSHNWLKLKKD 218 (219)
T ss_pred EEEEEEecCCHHHHHHHHHH---HHHcCCceEEEecCCCCCccCCCCcCCCceEeCCC
Confidence 22223333 345566664 578999999999999 999998 46789999984
No 15
>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=99.89 E-value=3.3e-22 Score=187.46 Aligned_cols=163 Identities=17% Similarity=0.221 Sum_probs=135.2
Q ss_pred cCceEEEEcCCeeEEEEEEECCEEEEEeCCCcc-ccccCcCCcccCCCCccccCCCceeeeeEEEEecCCCCCcceeEEE
Q 012588 146 QRYYYATWKADGTRYMMLITIDGCYLIDRCFNF-RRVQMRFPCRNSNEGLGEKTHHFTLLDGEMIIDKLPDSRRQERRYL 224 (460)
Q Consensus 146 ~~~Y~V~~K~DG~R~Ll~i~~~~vyLidR~~~~-~~v~~~FP~~~~~~~l~~~~~~~TlLDGElV~d~~~~~~~~~~ryl 224 (460)
..+|+|-+-.-|+||||++..+.++++||+|.. ...+..||.... .+++|||+|.|..-+. ..++|+
T Consensus 20 ~~~w~~~~~P~G~R~lvv~~~g~t~~~~r~g~~~~~f~s~lP~g~~----------~~~~~g~tILDci~~~--~~~~yy 87 (186)
T cd09232 20 SEEWLVVPCPVGKRCLVVASKGKTVARSKNGRTLHRFSSALPGGSR----------KTSNSGYTILDCIYNE--DDRTYY 87 (186)
T ss_pred CcceEEEECcCceEEEEEEeCCEEEEEeCCCCEEEecccCCCCCCc----------CCCCCCCEEEEEecCC--CCCEEE
Confidence 468999999999999999998899999999973 444566765432 1278999998876543 358999
Q ss_pred EeeeeecCCccccCCCHHHHHHHHHHHhcCccchhhccccccCCCCccCCCCCeEEEeccceechhHHHHHHHhcccc--
Q 012588 225 IYDMMAINQASVIERPFYERWKMLEKEVIEPRNYERHNIYQSRNPYYRYDLEPFRVRRKDFWLLSTVNKLLKEFIPKL-- 302 (460)
Q Consensus 225 iFDiL~~~G~~l~~~pf~eRl~~L~~~i~~pr~~~~~~l~~~~~~~~~~~~~pf~I~~K~f~~~~~~~~ll~~~~~~l-- 302 (460)
|+|||+++|.++.++++.-|+..|+..+.+++...+ ....++|+++.++||+.+. +.|-+.+...+
T Consensus 88 VlDii~w~g~~l~d~~~~~Rf~wl~skl~E~~~~~~-----------~~~~~~~~f~~~p~~~~~~-~~l~~~~~~~~~~ 155 (186)
T cd09232 88 VLDVLCWNGHPLYDCETEFRFFWLRSKLEELPELDE-----------PSEKNPFRFVPLPYFPCTK-ESLQSAYSGPLND 155 (186)
T ss_pred EEEEeeeCCcccccCCcchhHHHHHhhCCCcccccc-----------ccccCCceEEecCcccCcH-HHHHHHHhccccc
Confidence 999999999999999999999999999988764221 2356899999999999986 33445666778
Q ss_pred -CCCCceEEEEcCCCCCccCCCCCeEEEccC
Q 012588 303 -SHDADGLVFQGWDDPYVPRTHEGLLKWKYA 332 (460)
Q Consensus 303 -~h~~DGLIF~p~~spY~~G~~~~~LKWKP~ 332 (460)
+|+.|||+|+++++.|++|+|+.++||||.
T Consensus 156 ~~~e~DGLlFyhk~~~Y~~G~tPlvl~wKp~ 186 (186)
T cd09232 156 DPYELDGLLFYHKESHYTPGSTPLVLWLKDY 186 (186)
T ss_pred CCCCCceEEEEeCCCcccCcCCCcEEEecCC
Confidence 999999999999989999999999999983
No 16
>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=99.89 E-value=2.7e-22 Score=201.69 Aligned_cols=169 Identities=22% Similarity=0.299 Sum_probs=125.8
Q ss_pred cCceEEEEcCCeeEEEEEEECCEEEEEeCCCccccccCcCCcccCCCCccccCCCceeeeeEEEEecCCCC---------
Q 012588 146 QRYYYATWKADGTRYMMLITIDGCYLIDRCFNFRRVQMRFPCRNSNEGLGEKTHHFTLLDGEMIIDKLPDS--------- 216 (460)
Q Consensus 146 ~~~Y~V~~K~DG~R~Ll~i~~~~vyLidR~~~~~~v~~~FP~~~~~~~l~~~~~~~TlLDGElV~d~~~~~--------- 216 (460)
..+|++++|+||+|+++++++++|.|++|+++ .++..||+.... +.....++++||||||+....+.
T Consensus 11 ~~~~~~E~K~DG~R~~~~~~~~~v~l~SR~g~--~~t~~~p~l~~~--~~~~~~~~~iLDGElv~~d~~g~~~F~~l~~r 86 (298)
T TIGR02779 11 GDDWRYEVKYDGYRCLARIEGGKVRLISRNGH--DWTEKFPILAAA--LAALPILPAVLDGEIVVLDESGRSDFSALQNR 86 (298)
T ss_pred CCCEEEEEEEceEEEEEEEeCCEEEEEeCCCC--chHhHhHHHHHH--HHhCCCCcEEEEeEEEEECCCCCCCHHHHHhh
Confidence 45799999999999999999899999999987 456678876432 11112368999999998432211
Q ss_pred ----CcceeEEEEeeeeecCCccccCCCHHHHHHHHHHHhcCccchhhccccccCCCCccCCCCCeEEEeccceechhHH
Q 012588 217 ----RRQERRYLIYDMMAINQASVIERPFYERWKMLEKEVIEPRNYERHNIYQSRNPYYRYDLEPFRVRRKDFWLLSTVN 292 (460)
Q Consensus 217 ----~~~~~ryliFDiL~~~G~~l~~~pf~eRl~~L~~~i~~pr~~~~~~l~~~~~~~~~~~~~pf~I~~K~f~~~~~~~ 292 (460)
...++.|++||||++||++++++||.+|+++|++.+.... . +..+..........+.
T Consensus 87 ~~~~~~~~~~~~vFDiL~l~g~~l~~~pl~eRr~~L~~l~~~~~-----------~--------~~~~~~~~~~~~~~~~ 147 (298)
T TIGR02779 87 LRAGRDRPATYYAFDLLYLDGEDLRDLPLSERKKLLEELLKAIK-----------G--------PLAPDRYSVHFEGDGQ 147 (298)
T ss_pred hhcCCCCceEEEEEeeeeECceehhcCCHHHHHHHHHHHhcccC-----------C--------CceeEecccCchhHHH
Confidence 1135799999999999999999999999999999653210 0 1111110112233556
Q ss_pred HHHHHhccccCCCCceEEEEcCCCCCccCCCCCeEEEccCCCceEEEEEE
Q 012588 293 KLLKEFIPKLSHDADGLVFQGWDDPYVPRTHEGLLKWKYARMNSVDFLFE 342 (460)
Q Consensus 293 ~ll~~~~~~l~h~~DGLIF~p~~spY~~G~~~~~LKWKP~~~nTVDF~l~ 342 (460)
++|+. ...++.||||++..+++|.+|++..|+|+|+. .+.|++|.
T Consensus 148 ~~~~~---~~~~g~EGiv~K~~ds~Y~~Grs~~WlK~K~~--~~~d~vV~ 192 (298)
T TIGR02779 148 ALLEA---ACRLGLEGVVAKRRDSPYRSGRSADWLKLKCR--RRQEFVIG 192 (298)
T ss_pred HHHHH---HHHcCCceEEEeCCCCCCCCCCCCCcEEEccC--CCCEEEEE
Confidence 67764 56899999999999999999998899999974 58898873
No 17
>PRK08224 ligC ATP-dependent DNA ligase; Reviewed
Probab=99.88 E-value=3e-22 Score=204.99 Aligned_cols=164 Identities=22% Similarity=0.281 Sum_probs=125.1
Q ss_pred CceEEEEcCCeeEEEEEEECCEEEEEeCCCccccccCcCCcccCCCCccccCCCceeeeeEEEEecCCCC----------
Q 012588 147 RYYYATWKADGTRYMMLITIDGCYLIDRCFNFRRVQMRFPCRNSNEGLGEKTHHFTLLDGEMIIDKLPDS---------- 216 (460)
Q Consensus 147 ~~Y~V~~K~DG~R~Ll~i~~~~vyLidR~~~~~~v~~~FP~~~~~~~l~~~~~~~TlLDGElV~d~~~~~---------- 216 (460)
.+|++++|+||+|+++++++++|.|++|++. .++..||+..+. +.....++++||||||+...++.
T Consensus 24 ~~w~~E~K~DG~R~~~~~~~~~v~l~SRng~--d~t~~fPel~~~--~~~~~~~~~vLDGEiVv~~~~~~~F~~Lq~r~~ 99 (350)
T PRK08224 24 DGWSYEPKWDGFRCLVFRDGDEVELGSRNGK--PLTRYFPELVAA--LRAELPERCVLDGEIVVARDGGLDFEALQQRIH 99 (350)
T ss_pred CcEEEEEeECeeEEEEEEECCEEEEEeCCCC--CchhhhHHHHHH--HHhhCCCCEEEeeEEEEeCCCCCCHHHHHhhhh
Confidence 4799999999999999999999999999997 556789987432 11112468999999998542211
Q ss_pred -C---------cceeEEEEeeeeecCCccccCCCHHHHHHHHHHHhcCccchhhccccccCCCCccCCCCCeEEEeccce
Q 012588 217 -R---------RQERRYLIYDMMAINQASVIERPFYERWKMLEKEVIEPRNYERHNIYQSRNPYYRYDLEPFRVRRKDFW 286 (460)
Q Consensus 217 -~---------~~~~ryliFDiL~~~G~~l~~~pf~eRl~~L~~~i~~pr~~~~~~l~~~~~~~~~~~~~pf~I~~K~f~ 286 (460)
. ..++.|++||+|++||++++++||.+|++.|++.+.. . + + +++.+..
T Consensus 100 ~~~~~~~~~~~~~pv~~~vFDlL~l~G~dl~~~Pl~eRr~~L~~l~~~-~------------~-------~--i~~~~~~ 157 (350)
T PRK08224 100 PAASRVRKLAEETPASFVAFDLLALGDRDLTGRPFAERRAALEAAAAG-S------------G-------P--VHLTPAT 157 (350)
T ss_pred ccccchhhhhhcCCEEEEEEeeeeECCcChhhCCHHHHHHHHHHhcCC-C------------C-------c--EEEeccc
Confidence 0 1246899999999999999999999999999996521 1 1 1 2222222
Q ss_pred -echhHHHHHHHhccccCCCCceEEEEcCCCCCccCCCCCeEEEccCCCceEEEEEE
Q 012588 287 -LLSTVNKLLKEFIPKLSHDADGLVFQGWDDPYVPRTHEGLLKWKYARMNSVDFLFE 342 (460)
Q Consensus 287 -~~~~~~~ll~~~~~~l~h~~DGLIF~p~~spY~~G~~~~~LKWKP~~~nTVDF~l~ 342 (460)
.....+.+|+. .+.++.||||+|..+|+|.+|+.. |+|+|+ ..++||+|.
T Consensus 158 ~~~~~~~~~~~~---a~~~G~EGIV~Kr~dS~Y~~Grr~-WlKiK~--~~~~d~vI~ 208 (350)
T PRK08224 158 TDPATARRWFEE---FEGAGLDGVIAKPLDGPYQPGKRA-MFKVKH--ERTADCVVA 208 (350)
T ss_pred CCHHHHHHHHHH---HHhCCCcEEEEeCCCCCcCCCCcC-EEEEcc--CCcEEEEEE
Confidence 22355567764 468999999999999999999876 999997 579999983
No 18
>PRK07636 ligB ATP-dependent DNA ligase; Reviewed
Probab=99.88 E-value=6.7e-22 Score=196.59 Aligned_cols=162 Identities=22% Similarity=0.258 Sum_probs=123.8
Q ss_pred cCceEEEEcCCeeEEEEEEECCEEEEEeCCCccccccCcCCcccCCCCccccCCCceeeeeEEEEecCCCC---------
Q 012588 146 QRYYYATWKADGTRYMMLITIDGCYLIDRCFNFRRVQMRFPCRNSNEGLGEKTHHFTLLDGEMIIDKLPDS--------- 216 (460)
Q Consensus 146 ~~~Y~V~~K~DG~R~Ll~i~~~~vyLidR~~~~~~v~~~FP~~~~~~~l~~~~~~~TlLDGElV~d~~~~~--------- 216 (460)
..+|++++|+||.|+++++.+++|.|++|+++ .++..||+..+. . ...+++||||||.-...+.
T Consensus 17 ~~~~~~E~K~DG~R~~~~~~~~~v~l~SR~g~--~~t~~fPe~~~~-~----~~~~~vLDGElv~~d~~g~~~F~~l~~r 89 (275)
T PRK07636 17 SENYITEPKFDGIRLIASKNNGLIRLYTRHNN--EVTAKFPELLNL-D----IPDGTVLDGELIVLGSTGAPDFEAVMER 89 (275)
T ss_pred CCcEEEEEEEceeEEEEEEeCCEEEEEeCCCC--CchhhhhhHHhh-h----cCCCEEEEeEEEEECCCCCCCHHHHHHH
Confidence 45899999999999999999999999999987 457789987542 1 2357999999998432111
Q ss_pred ----C---cceeEEEEeeeeecCCccccCCCHHHHHHHHHHHhcCccchhhccccccCCCCccCCCCCeEEEeccceech
Q 012588 217 ----R---RQERRYLIYDMMAINQASVIERPFYERWKMLEKEVIEPRNYERHNIYQSRNPYYRYDLEPFRVRRKDFWLLS 289 (460)
Q Consensus 217 ----~---~~~~ryliFDiL~~~G~~l~~~pf~eRl~~L~~~i~~pr~~~~~~l~~~~~~~~~~~~~pf~I~~K~f~~~~ 289 (460)
. ..++.|++||+|++||++++++||.+|+++|++.+. +.. . +...+... .
T Consensus 90 ~~~~~~~~~~~~~~~vFDlL~~~g~~l~~~pl~eRr~~L~~~~~-~~~------------~---------~~~~~~~~-~ 146 (275)
T PRK07636 90 FQSKKSTKIHPVVFCVFDVLYINGVSLTALPLSERKEILASLLL-PHP------------N---------VKIIEGIE-G 146 (275)
T ss_pred hccccccccCceEEEEEEeEEECceehhhCCHHHHHHHHHHhcC-CCC------------C---------EEEccccc-c
Confidence 0 134689999999999999999999999999999763 211 0 11222212 2
Q ss_pred hHHHHHHHhccccCCCCceEEEEcCCCCCccC-CCCCeEEEccCCCceEEEEEE
Q 012588 290 TVNKLLKEFIPKLSHDADGLVFQGWDDPYVPR-THEGLLKWKYARMNSVDFLFE 342 (460)
Q Consensus 290 ~~~~ll~~~~~~l~h~~DGLIF~p~~spY~~G-~~~~~LKWKP~~~nTVDF~l~ 342 (460)
....+|+. ...++.||||++..+|+|.+| ++.+|+|.|. ..++|++|.
T Consensus 147 ~~~~~~~~---~~~~g~EGiV~K~~ds~Y~~g~Rs~~WlKiK~--~~~~e~vV~ 195 (275)
T PRK07636 147 HGTAYFEL---VEERELEGIVIKKANSPYEINKRSDNWLKVIN--YQYTDVLIT 195 (275)
T ss_pred cHHHHHHH---HHHcCCcEEEEeCCCCCCCCCCCCCCeEEEec--CCeEEEEEE
Confidence 34567764 457899999999999999999 6789999995 579999883
No 19
>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=99.88 E-value=3.6e-22 Score=194.08 Aligned_cols=182 Identities=18% Similarity=0.258 Sum_probs=124.7
Q ss_pred cccccccccc----ccccCceEEEEcCCeeEEEEEEE----CCEEEEEeCCCccccccCcCCcccCC--CCcc----c-c
Q 012588 133 PVSLNSDNLQ----LLRQRYYYATWKADGTRYMMLIT----IDGCYLIDRCFNFRRVQMRFPCRNSN--EGLG----E-K 197 (460)
Q Consensus 133 PVSl~r~nl~----~l~~~~Y~V~~K~DG~R~Ll~i~----~~~vyLidR~~~~~~v~~~FP~~~~~--~~l~----~-~ 197 (460)
|-|+.-.+++ .+...+|++++|+||.|+++++. ++.|.|++|+++ .++..||+.... ..+. . .
T Consensus 4 ~~~~~~~~~~~~~~~~~~~~~~~E~K~DG~R~qih~~~~~~~~~v~lfSR~~~--d~T~~~pel~~~~~~~~~~~~~~~~ 81 (235)
T cd08039 4 PKSLKARSIKHCCKMIGSRRMWVETKYDGEYCQIHIDLSKDSSPIRIFSKSGK--DSTADRAGVHSIIRKALRIGKPGCK 81 (235)
T ss_pred cchhcccCHHHHHHHhCCCcEEEEEeecceEEEEEEecccCCCEEEEEeCCCC--cccccchhHHHHHHHHhhccccccC
Confidence 5566555554 46678899999999999999987 678999999987 556789875321 0110 0 0
Q ss_pred CCCceeeeeEEEEecC-CCC---------------------------CcceeEEEEeeeeecCCccccCCCHHHHHHHHH
Q 012588 198 THHFTLLDGEMIIDKL-PDS---------------------------RRQERRYLIYDMMAINQASVIERPFYERWKMLE 249 (460)
Q Consensus 198 ~~~~TlLDGElV~d~~-~~~---------------------------~~~~~ryliFDiL~~~G~~l~~~pf~eRl~~L~ 249 (460)
..+++|||||||+-.. .+. ...++.|++||+|++||+++++.||.+|+++|+
T Consensus 82 ~~~~~ILDGEiVv~d~~~g~~~~F~~L~~~~~~~~~~~~~~~~~~~~~~~~v~~~vFDlL~lnG~~l~~~pl~eRr~~L~ 161 (235)
T cd08039 82 FSKNCILEGEMVVWSDRQGKIDPFHKIRKHVERSGSFIGTDNDSPPHEYEHLMIVFFDVLLLDDESLLSKPYSERRDLLE 161 (235)
T ss_pred CCccEEEEeEEEEEECCCCccCCHHHHHhhcccccchhccccccccccccceEEEEEEEEEECChhhhcCCHHHHHHHHH
Confidence 1367999999987432 110 002379999999999999999999999999999
Q ss_pred HHhcCccchhhccccccCCCCccCCCCCeEEEeccceechhHHHHHHHhccccCCCCceEEEEcCCCCCccCCC------
Q 012588 250 KEVIEPRNYERHNIYQSRNPYYRYDLEPFRVRRKDFWLLSTVNKLLKEFIPKLSHDADGLVFQGWDDPYVPRTH------ 323 (460)
Q Consensus 250 ~~i~~pr~~~~~~l~~~~~~~~~~~~~pf~I~~K~f~~~~~~~~ll~~~~~~l~h~~DGLIF~p~~spY~~G~~------ 323 (460)
+.+ .|...... +. +.+.+..........+.++|+. .+..+.||||++..+++|.+|+.
T Consensus 162 ~l~-~~~~~~~~-~~-----------~~~~i~~~~~~~~~~l~~~~~~---a~~~g~EGIv~K~~~S~Y~pgr~~~~~r~ 225 (235)
T cd08039 162 SLV-HVIPGYAG-LS-----------ERFPIDFSRSSGYERLRQIFAR---AIAERWEGLVLKGDEEPYFDLFLEQGSFS 225 (235)
T ss_pred Hhc-ccCCCcEE-EE-----------EEEeecccCCCCHHHHHHHHHH---HHHcCCceEEEecCCCCcccCcccccccC
Confidence 965 32110000 00 0011111111122344556654 57889999999999999999986
Q ss_pred CCeEEEccC
Q 012588 324 EGLLKWKYA 332 (460)
Q Consensus 324 ~~~LKWKP~ 332 (460)
..||||||.
T Consensus 226 ~~WlKlK~d 234 (235)
T cd08039 226 GCWIKLKKD 234 (235)
T ss_pred CCeEEeCCC
Confidence 699999984
No 20
>PRK09633 ligD ATP-dependent DNA ligase; Reviewed
Probab=99.88 E-value=6.3e-22 Score=214.91 Aligned_cols=277 Identities=18% Similarity=0.183 Sum_probs=173.4
Q ss_pred cCceEEEEcCCeeEEEEEEECCEEEEEeCCCccccccCcCCcccCC-CCcccc--CCCceeeeeEEEEecCCCC------
Q 012588 146 QRYYYATWKADGTRYMMLITIDGCYLIDRCFNFRRVQMRFPCRNSN-EGLGEK--THHFTLLDGEMIIDKLPDS------ 216 (460)
Q Consensus 146 ~~~Y~V~~K~DG~R~Ll~i~~~~vyLidR~~~~~~v~~~FP~~~~~-~~l~~~--~~~~TlLDGElV~d~~~~~------ 216 (460)
..+|++++|+||.|+++++.+++|.|++|+++ .++..||+..+. ..+... ....++||||||+-...+.
T Consensus 15 g~~w~~E~K~DG~R~~~h~~~~~V~L~SRng~--d~T~~fPel~~~~~~~~~~~~~~~~~ILDGEiVvld~~g~~~F~~L 92 (610)
T PRK09633 15 GDEWRYEVKYDGFRCLLIIDETGITLISRNGR--ELTNTFPEIIEFCESNFEHLKEELPLTLDGELVCLVNPYRSDFEHV 92 (610)
T ss_pred CCcEEEEEeEcceEEEEEEECCEEEEEeCCCC--cchhhhhHHHHHHHhhhhccccCCceeeeeEEEEecCCCCCCHHHH
Confidence 45799999999999999999999999999997 567889986431 111100 0136899999998431110
Q ss_pred ----------------CcceeEEEEeeeeecCCccccCCCHHHHHHHHHHHhcCccchhhccccccCCCCccCCCCCeEE
Q 012588 217 ----------------RRQERRYLIYDMMAINQASVIERPFYERWKMLEKEVIEPRNYERHNIYQSRNPYYRYDLEPFRV 280 (460)
Q Consensus 217 ----------------~~~~~ryliFDiL~~~G~~l~~~pf~eRl~~L~~~i~~pr~~~~~~l~~~~~~~~~~~~~pf~I 280 (460)
....+.|++||+|++||+++++.||.+|+++|++.+.. .... ..+.. ....+ +
T Consensus 93 q~R~~~~~~~~i~~~~~~~pv~~~vFDlL~lnG~dL~~~PL~eRr~~L~~ll~~-~~~~-------~~~~~-~~~~~--i 161 (610)
T PRK09633 93 QQRGRLKNTEVIAKSANARPCQLLAFDLLELKGESLTSLPYLERKKQLDKLMKA-AKLP-------ASPDP-YAKAR--I 161 (610)
T ss_pred HhhhhccccchhhhhhcccceEEEEEeecccCCcccccCCHHHHHHHHHHHhhh-cccc-------ccccc-ccccc--e
Confidence 01236899999999999999999999999999996632 1100 00000 00011 2
Q ss_pred EeccceechhHHHHHHHhccccCCCCceEEEEcCCCCCccC-CCCCeEEEccCCCceEEEEEEEecCCcee--EEEEeCC
Q 012588 281 RRKDFWLLSTVNKLLKEFIPKLSHDADGLVFQGWDDPYVPR-THEGLLKWKYARMNSVDFLFEVTDDDRQL--LYVFERG 357 (460)
Q Consensus 281 ~~K~f~~~~~~~~ll~~~~~~l~h~~DGLIF~p~~spY~~G-~~~~~LKWKP~~~nTVDF~l~~~~~~~~~--L~v~~~g 357 (460)
...+.+ ...+.+|+. ...++.||||+|..+|+|.+| |+.+|+|.|+ ..++||+|.--..+.+. |-++++|
T Consensus 162 ~~~~~~--~~~~~l~~~---a~~~g~EGIV~Kr~dS~Y~~G~Rs~~WlKiK~--~~~~d~vI~G~~~~~g~~llgv~~~g 234 (610)
T PRK09633 162 QYIPST--TDFDALWEA---VKRYDGEGIVAKKKTSKWLENKRSKDWLKIKN--WRYVHVIVTGYDPSNGYFTGSVYKDG 234 (610)
T ss_pred EEcCCH--HHHHHHHHH---HHHcCCceEEEeCCCCCCCCCCCCCCeEEEec--cCCceeEEEEEecCCceEEEEEecCC
Confidence 333322 255667764 467899999999999999998 6789999997 47899987322112222 2234444
Q ss_pred ceeeecCceeEecCC----------CCC---------CCCceEEEEEEeCC-CCeeE---EEEEecCCCCCChHHHHHH-
Q 012588 358 KKKLMEGSSVEFTDR----------EPS---------FYSGKIIECTWDPD-VQLWK---CMRIRTDKSTPNDINTYRK- 413 (460)
Q Consensus 358 ~~~~~~~~~~~f~~~----------~~~---------~~dg~IvEC~~d~~-~~~W~---f~R~R~DK~~pN~~~tv~~- 413 (460)
.-...+....-|++. ... -.-.-|+|+.|..- .|..+ |.|+|.||+- ...++...
T Consensus 235 ~l~~vGkvgtGft~~~~~~L~~~l~~l~~~~~~~~~wV~P~LV~EV~~~e~t~g~LR~P~f~glR~DK~~-~ev~~~~~~ 313 (610)
T PRK09633 235 QLTEVGSVKHGMEDEERQTLRAIFKQNGTKTKSGEYTLEPSICVTVACITFDGGTLREPSFVSFLFDMDP-TECTYQQLQ 313 (610)
T ss_pred eEEEEEEecCCCCHHHHHHHHHHHHHhccCCCCCcEEEeeeEEEEEEEeecCCCeEEeeEEeEEEcCCCh-HHcchhhhh
Confidence 211111000012220 000 01235788888532 23343 7899999962 33322222
Q ss_pred -----------------HHHhcccCCCHHHHHHHHHHhhc--Cccchhcc
Q 012588 414 -----------------VMRSIRDNITEEVLLNEIQEIIR--LPMYADRI 444 (460)
Q Consensus 414 -----------------v~~SI~~~Vt~e~Ll~~i~~~~~--~~~~~~~~ 444 (460)
|+-- ..++|+.+|+++-..+.- ||-..+|.
T Consensus 314 ~~~~~~~~~v~~t~~dkv~~p-~~g~tK~dl~~Yy~~va~~~lp~l~~Rp 362 (610)
T PRK09633 314 RQLAPLPPKVEITSLDKPIWP-KIHKTKADYLLYLQEVSPFLLPFLRDRA 362 (610)
T ss_pred hhhccCCcccccCCCCceecC-CCCCCHHHHHHHHHHHHHHHHHHHcCCc
Confidence 1111 258999999999988855 66666665
No 21
>PHA02587 30 DNA ligase; Provisional
Probab=99.87 E-value=4.3e-21 Score=204.53 Aligned_cols=167 Identities=17% Similarity=0.253 Sum_probs=117.7
Q ss_pred ceEEEEcCCeeEEEEEEECCEEEEEeCCCccccccCcCCcccCC-CCccc---cCCCceeeeeEEEEecCCC--------
Q 012588 148 YYYATWKADGTRYMMLITIDGCYLIDRCFNFRRVQMRFPCRNSN-EGLGE---KTHHFTLLDGEMIIDKLPD-------- 215 (460)
Q Consensus 148 ~Y~V~~K~DG~R~Ll~i~~~~vyLidR~~~~~~v~~~FP~~~~~-~~l~~---~~~~~TlLDGElV~d~~~~-------- 215 (460)
+|++++|+||.|+++++.++++.+++|+++ .++ .||+.... ..+.. ....+++||||||+-....
T Consensus 153 ~~~~E~K~DG~R~q~h~~~~~v~l~SR~g~--~~~-~~p~i~~~l~~~~~~~~~~~~~~VLDGElv~~~~~~~~~~~~~f 229 (488)
T PHA02587 153 PAYAQLKADGARCFADIDADGIEIRSRNGN--EYL-GLDLLKEELKKMTAEARQRPGGVVIDGELVYVEVETKKPNGLSF 229 (488)
T ss_pred cEEEEEccCceEEEEEEeCCEEEEEecCCc--ccc-CChhHHHHHHHHhhhhcccCCcEEEEeEEEEEecccCCCccchh
Confidence 899999999999999999999999999987 223 36655321 11100 0126799999999852100
Q ss_pred ----------------------------------CCcceeEEEEeeeeecC---CccccCCCHHHHHHHHHHHhcCccch
Q 012588 216 ----------------------------------SRRQERRYLIYDMMAIN---QASVIERPFYERWKMLEKEVIEPRNY 258 (460)
Q Consensus 216 ----------------------------------~~~~~~ryliFDiL~~~---G~~l~~~pf~eRl~~L~~~i~~pr~~ 258 (460)
....++.|++||+|.++ |..+...||.+|++.|++.+..+.
T Consensus 230 ~~~~~~~~~f~q~l~~R~~~~~i~~~~l~~~~~~~~~~pv~~~vFDiL~ld~y~~~~~~~~pl~eRr~~L~~l~~~~~-- 307 (488)
T PHA02587 230 LFDDSKAKEFVGVVADRATGNGIVNKSLKGTISKEEAQEIVFQVWDIVPLEVYYGKEKSDMPYDDRFSKLAQMFEDCG-- 307 (488)
T ss_pred hcccccccchhhhhhhhhhccchhhhhhccccchhhccceEEEEEEeechhhccCCccccCCHHHHHHHHHHHHhhcC--
Confidence 00134789999999653 455788999999999999764211
Q ss_pred hhccccccCCCCccCCCCCeEEEeccc---eechhHHHHHHHhccccCCCCceEEEEcCCCCCccCCCCCeEEEccCCCc
Q 012588 259 ERHNIYQSRNPYYRYDLEPFRVRRKDF---WLLSTVNKLLKEFIPKLSHDADGLVFQGWDDPYVPRTHEGLLKWKYARMN 335 (460)
Q Consensus 259 ~~~~l~~~~~~~~~~~~~pf~I~~K~f---~~~~~~~~ll~~~~~~l~h~~DGLIF~p~~spY~~G~~~~~LKWKP~~~n 335 (460)
.+. +...++ .....+.++++. .+..+.||||.+..+++|.+||+..|+|||+. .
T Consensus 308 ---------~~~---------i~l~~~~~~~~~ee~~~~~~~---a~~~G~EGimlK~~ds~Y~~GRs~~WlKiK~~--~ 364 (488)
T PHA02587 308 ---------YDR---------VELIENQVVNNLEEAKEIYKR---YVDQGLEGIILKNTDGLWEDGRSKDQIKFKEV--I 364 (488)
T ss_pred ---------CCc---------EEEEeeEEcCCHHHHHHHHHH---HHhCCCCeEEEECCCCCCCCCCCCCcEEecCC--C
Confidence 111 222222 223455566654 56789999999999999999998899999974 5
Q ss_pred eEEEEEE
Q 012588 336 SVDFLFE 342 (460)
Q Consensus 336 TVDF~l~ 342 (460)
++|+++-
T Consensus 365 ~~dlvVv 371 (488)
T PHA02587 365 DIDLEIV 371 (488)
T ss_pred ceEEEEE
Confidence 7998873
No 22
>PRK05972 ligD ATP-dependent DNA ligase; Reviewed
Probab=99.87 E-value=5.2e-21 Score=212.84 Aligned_cols=166 Identities=20% Similarity=0.241 Sum_probs=127.0
Q ss_pred CceEEEEcCCeeEEEEEEECCEEEEEeCCCccccccCcCCcccCCCCccccCCCceeeeeEEEEecCCCC----------
Q 012588 147 RYYYATWKADGTRYMMLITIDGCYLIDRCFNFRRVQMRFPCRNSNEGLGEKTHHFTLLDGEMIIDKLPDS---------- 216 (460)
Q Consensus 147 ~~Y~V~~K~DG~R~Ll~i~~~~vyLidR~~~~~~v~~~FP~~~~~~~l~~~~~~~TlLDGElV~d~~~~~---------- 216 (460)
.+|+++.|+||.|+++++.++++.|++|+++ ..+..||+.... +.......+|||||||+....+.
T Consensus 249 ~~W~~E~K~DG~R~~a~~~gg~vrL~SRnG~--d~T~~fPel~~~--~~~l~~~~~ILDGEIVvld~~G~~~F~~Lq~r~ 324 (860)
T PRK05972 249 DGWIYEIKFDGYRILARIEGGEVRLFTRNGL--DWTAKLPALAKA--AAALGLPDAWLDGEIVVLDEDGVPDFQALQNAF 324 (860)
T ss_pred CceEEEeeeCcEEEEEEEECCEEEEEeCCCC--ccccccHHHHHH--HHhcCCCceeEeEEEEEECCCCCCCHHHHHHHh
Confidence 5899999999999999999999999999987 457789987432 11112367899999998532211
Q ss_pred ---CcceeEEEEeeeeecCCccccCCCHHHHHHHHHHHhcCccchhhccccccCCCCccCCCCCeEEEeccceechhHHH
Q 012588 217 ---RRQERRYLIYDMMAINQASVIERPFYERWKMLEKEVIEPRNYERHNIYQSRNPYYRYDLEPFRVRRKDFWLLSTVNK 293 (460)
Q Consensus 217 ---~~~~~ryliFDiL~~~G~~l~~~pf~eRl~~L~~~i~~pr~~~~~~l~~~~~~~~~~~~~pf~I~~K~f~~~~~~~~ 293 (460)
....+.|++||||++||++++++||.+|+++|++.+.. . .++ .|+..+.+.. ....
T Consensus 325 ~~~~~~~v~f~vFDLL~l~G~dL~~~PL~eRr~~L~~ll~~-~----------~~~---------~i~~s~~~~~-~g~~ 383 (860)
T PRK05972 325 DEGRTEDLVYFAFDLPFLGGEDLRELPLEERRARLRALLEA-A----------RSD---------RIRFSEHFDA-GGDA 383 (860)
T ss_pred hccCCCceEEEEEeccccCCcccccCCHHHHHHHHHHHhhh-c----------CCC---------cEEEeceecc-hHHH
Confidence 11347899999999999999999999999999996632 1 011 1344444443 3456
Q ss_pred HHHHhccccCCCCceEEEEcCCCCCccCCCCCeEEEccCCCceEEEEEE
Q 012588 294 LLKEFIPKLSHDADGLVFQGWDDPYVPRTHEGLLKWKYARMNSVDFLFE 342 (460)
Q Consensus 294 ll~~~~~~l~h~~DGLIF~p~~spY~~G~~~~~LKWKP~~~nTVDF~l~ 342 (460)
+|+. ...++.||||++..+|+|.+|++.+|||+|+. .+.+|+|.
T Consensus 384 ll~~---a~~~GlEGIVaKr~dS~Y~~GRs~~WlKiK~~--~~~E~VIg 427 (860)
T PRK05972 384 VLAS---ACRLGLEGVIGKRADSPYVSGRSEDWIKLKCR--ARQEFVIG 427 (860)
T ss_pred HHHH---HHHcCCceEEEeCCCCCCCCCCCCCcEEEecC--CCceEEEE
Confidence 7764 57899999999999999999999999999974 56788773
No 23
>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=99.87 E-value=1.2e-21 Score=188.00 Aligned_cols=157 Identities=20% Similarity=0.332 Sum_probs=113.0
Q ss_pred CceEEEEcCCeeEEEEEEECCEEEEEeCCCcccccc-CcCCcccCC--CCccccCCCceeeeeEEEEecC--CCC-----
Q 012588 147 RYYYATWKADGTRYMMLITIDGCYLIDRCFNFRRVQ-MRFPCRNSN--EGLGEKTHHFTLLDGEMIIDKL--PDS----- 216 (460)
Q Consensus 147 ~~Y~V~~K~DG~R~Ll~i~~~~vyLidR~~~~~~v~-~~FP~~~~~--~~l~~~~~~~TlLDGElV~d~~--~~~----- 216 (460)
.+|++++|+||.|++++..++++.+++|++. ..+ ..||..... ..+ ....+++||||||+-.. +..
T Consensus 34 ~~~~~E~K~DG~R~~i~~~~~~v~l~SR~g~--~~t~~~~~~~~~~~~~~~--~~~~~~iLDGEiv~~d~~~g~~~~F~~ 109 (213)
T cd07902 34 NGMYAEIKYDGERVQVHKQGDNFKFFSRSLK--PVLPHKVAHFKDYIPKAF--PHGHSMILDSEVLLVDTKTGKPLPFGT 109 (213)
T ss_pred CceEEEeccCCEEEEEEEcCCEEEEEcCCCc--ccccchhHHHHHHHHHhc--ccccceeeeeEEEEEECCCCcccccch
Confidence 4699999999999999999899999999986 222 234433210 112 11357999999998321 111
Q ss_pred ---------CcceeEEEEeeeeecCCccccCCCHHHHHHHHHHHhcCccchhhccccccCCCCccCCCCCeEEEecccee
Q 012588 217 ---------RRQERRYLIYDMMAINQASVIERPFYERWKMLEKEVIEPRNYERHNIYQSRNPYYRYDLEPFRVRRKDFWL 287 (460)
Q Consensus 217 ---------~~~~~ryliFDiL~~~G~~l~~~pf~eRl~~L~~~i~~pr~~~~~~l~~~~~~~~~~~~~pf~I~~K~f~~ 287 (460)
....+.|++||||+++|++++++||.+|+++|++.+.. .. .+ +...++..
T Consensus 110 l~~~~~~~~~~~~v~~~vFDiL~l~g~~l~~~pl~eR~~~L~~~~~~-~~------------------~~--~~~~~~~~ 168 (213)
T cd07902 110 LGIHKKSAFKDANVCLFVFDCLYYNGESLMDKPLRERRKILEDNMVE-IP------------------NR--IMLSEMKF 168 (213)
T ss_pred hhhhhccccccCceEEEEEEEeeeCCcchhcCcHHHHHHHHHHhccC-CC------------------Ce--EEEEEEEE
Confidence 01247899999999999999999999999999986531 10 01 22233333
Q ss_pred c---hhHHHHHHHhccccCCCCceEEEEcCCCCCccCCCCCeEEEccC
Q 012588 288 L---STVNKLLKEFIPKLSHDADGLVFQGWDDPYVPRTHEGLLKWKYA 332 (460)
Q Consensus 288 ~---~~~~~ll~~~~~~l~h~~DGLIF~p~~spY~~G~~~~~LKWKP~ 332 (460)
. ..+.++++. ...++.||||++..+++|.+|+. .|+||||.
T Consensus 169 ~~~~~~l~~~~~~---~~~~g~EGvV~K~~~s~Y~~G~r-~W~K~K~d 212 (213)
T cd07902 169 VKKADDLSAMIAR---VIKEGLEGLVLKDLKSVYEPGKR-HWLKVKKD 212 (213)
T ss_pred cCCHHHHHHHHHH---HHHCCCCeEEEeCCCCCccCCCC-CceEeCCC
Confidence 3 344556654 56899999999999999999986 79999984
No 24
>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=99.87 E-value=1.2e-21 Score=210.44 Aligned_cols=167 Identities=21% Similarity=0.353 Sum_probs=124.4
Q ss_pred CceEEEEcCCeeEEEEEEECCEEEEEeCCCccccccCcCCcc-cCC--CCccccCCCceeeeeEEEEecC--CCC-----
Q 012588 147 RYYYATWKADGTRYMMLITIDGCYLIDRCFNFRRVQMRFPCR-NSN--EGLGEKTHHFTLLDGEMIIDKL--PDS----- 216 (460)
Q Consensus 147 ~~Y~V~~K~DG~R~Ll~i~~~~vyLidR~~~~~~v~~~FP~~-~~~--~~l~~~~~~~TlLDGElV~d~~--~~~----- 216 (460)
.+|++++|+||.|+++++.++++.+++|+++ .++..||+. ... ..+ .....++||||||.-.. +..
T Consensus 187 ~~~~~E~K~DG~R~qih~~~~~v~l~SR~g~--~~t~~~pei~~~~~~~~~--~~~~~~ILDGElv~~d~~~g~~~~F~~ 262 (514)
T TIGR00574 187 NKFYVEYKYDGERVQIHKDGDKFKIFSRRLE--NYTYAYPEIFTEFIKEAF--PGIKSCILDGEMVAIDPETGKILPFQT 262 (514)
T ss_pred CceEEEEeecceEEEEEEcCCEEEEEcCCCc--ccccccchhHHHHHHHhc--CccceeeecceEEEEEcCCCCCcCcHh
Confidence 3899999999999999998889999999987 556788876 321 112 11346899999997432 110
Q ss_pred --------------CcceeEEEEeeeeecCCccccCCCHHHHHHHHHHHhcCccchhhccccccCCCCccCCCCCeEEEe
Q 012588 217 --------------RRQERRYLIYDMMAINQASVIERPFYERWKMLEKEVIEPRNYERHNIYQSRNPYYRYDLEPFRVRR 282 (460)
Q Consensus 217 --------------~~~~~ryliFDiL~~~G~~l~~~pf~eRl~~L~~~i~~pr~~~~~~l~~~~~~~~~~~~~pf~I~~ 282 (460)
...++.|++||||++||++++++||.+|+++|++.+ .+.. + . +..
T Consensus 263 l~~r~~~~~~~~~~~~~~~~~~vFDiL~l~g~~l~~~pl~eRr~~L~~~~-~~~~-----------~-------~--i~~ 321 (514)
T TIGR00574 263 LLRRKRRYDIDSMEKKVPVCLFVFDILYLNGESLIDEPLIERREILESIL-KPIP-----------N-------R--IEI 321 (514)
T ss_pred HHhhhhhccccccccccceEEEEEEEEEECCcchhcCcHHHHHHHHHHhc-cCCC-----------C-------c--EEE
Confidence 012478999999999999999999999999999854 3321 0 1 222
Q ss_pred ccce---echhHHHHHHHhccccCCCCceEEEEcCCCCCccC-CCCCeEEEccCC----CceEEEEE
Q 012588 283 KDFW---LLSTVNKLLKEFIPKLSHDADGLVFQGWDDPYVPR-THEGLLKWKYAR----MNSVDFLF 341 (460)
Q Consensus 283 K~f~---~~~~~~~ll~~~~~~l~h~~DGLIF~p~~spY~~G-~~~~~LKWKP~~----~nTVDF~l 341 (460)
.+.. ....+.++|+ ..+.++.||||++..+++|.+| |+..|+||||.. ..|+|+++
T Consensus 322 ~~~~~~~~~e~~~~~~~---~~~~~g~EGlv~K~~ds~Y~~G~Rs~~WlK~K~~y~~~~~~~~D~vv 385 (514)
T TIGR00574 322 AEMKITSNVEELEKFLN---EAISEGCEGLMLKDLKSIYEPGKRGWLWLKFKPEYLEGMGDTLDLVV 385 (514)
T ss_pred EEEEecCCHHHHHHHHH---HHHHcCCceEEEecCCCcccCCCCCCcceeCchhhcccccCceeEEE
Confidence 2233 3334455555 3678999999999999999999 678999999842 45999988
No 25
>PRK03180 ligB ATP-dependent DNA ligase; Reviewed
Probab=99.85 E-value=4.3e-21 Score=205.35 Aligned_cols=164 Identities=21% Similarity=0.288 Sum_probs=124.8
Q ss_pred CceEEEEcCCeeEEEEEEECCEEEEEeCCCccccccCcCCcccCC-CCccccCCCceeeeeEEEEecCC-CC--------
Q 012588 147 RYYYATWKADGTRYMMLITIDGCYLIDRCFNFRRVQMRFPCRNSN-EGLGEKTHHFTLLDGEMIIDKLP-DS-------- 216 (460)
Q Consensus 147 ~~Y~V~~K~DG~R~Ll~i~~~~vyLidR~~~~~~v~~~FP~~~~~-~~l~~~~~~~TlLDGElV~d~~~-~~-------- 216 (460)
.+|++++|+||.|++++..++++.+++|+++ .++..||+.... ..+ ...+++||||||.-... ..
T Consensus 204 ~~~~~E~K~DG~R~qih~~~~~v~l~SR~~~--d~T~~fPei~~~~~~~---~~~~~ILDGElv~~d~~g~~~~F~~l~~ 278 (508)
T PRK03180 204 GPAAVEAKLDGARVQVHRDGDDVRVYTRTLD--DITARLPEVVEAVRAL---PVRSLVLDGEAIALRPDGRPRPFQVTAS 278 (508)
T ss_pred CCeEEEEEEceeEEEEEEECCEEEEEeCCCC--cchhhhHHHHHHHHhC---CCcceeecceEEEECCCCCcCCHHHHHH
Confidence 5899999999999999999999999999987 567789987531 111 12679999999984311 10
Q ss_pred ---C---------cceeEEEEeeeeecCCccccCCCHHHHHHHHHHHhcCccchhhccccccCCCCccCCCCCeEEEecc
Q 012588 217 ---R---------RQERRYLIYDMMAINQASVIERPFYERWKMLEKEVIEPRNYERHNIYQSRNPYYRYDLEPFRVRRKD 284 (460)
Q Consensus 217 ---~---------~~~~ryliFDiL~~~G~~l~~~pf~eRl~~L~~~i~~pr~~~~~~l~~~~~~~~~~~~~pf~I~~K~ 284 (460)
. ..++.|++||+|++||++++++||.+|++.|++.+. |.. ..+. +.
T Consensus 279 R~~~k~~~~~~~~~~pv~~~~FDlL~l~G~dl~~~pl~eRr~~L~~~~~-~~~---------~~~~---------~~--- 336 (508)
T PRK03180 279 RFGRRVDVAAARATQPLSPFFFDALHLDGRDLLDAPLSERLAALDALVP-AAH---------RVPR---------LV--- 336 (508)
T ss_pred HhccccchhhhcccCceEEEEEeehhcCCcchhcCCHHHHHHHHHHhhc-ccc---------cccc---------ee---
Confidence 0 124689999999999999999999999999999663 210 0010 11
Q ss_pred ceechhHHHHHHHhccccCCCCceEEEEcCCCCCccCC-CCCeEEEccCCCceEEEEEE
Q 012588 285 FWLLSTVNKLLKEFIPKLSHDADGLVFQGWDDPYVPRT-HEGLLKWKYARMNSVDFLFE 342 (460)
Q Consensus 285 f~~~~~~~~ll~~~~~~l~h~~DGLIF~p~~spY~~G~-~~~~LKWKP~~~nTVDF~l~ 342 (460)
......+.++++. ...++.||||+|..+++|.+|+ +.+|+|||+. .|+|++|-
T Consensus 337 ~~~~~~~~~~~~~---a~~~g~EGlm~K~~ds~Y~~GrR~~~WlK~K~~--~t~D~Vvi 390 (508)
T PRK03180 337 TADPAAAAAFLAA---ALAAGHEGVMVKSLDAPYAAGRRGAGWLKVKPV--HTLDLVVL 390 (508)
T ss_pred cCCHHHHHHHHHH---HHHcCCceEEEeCCCCCcCCCCCCCCcEEEcCC--CceEEEEE
Confidence 1123355666664 5789999999999999999996 5799999984 69999983
No 26
>PRK09632 ATP-dependent DNA ligase; Reviewed
Probab=99.84 E-value=4e-20 Score=203.96 Aligned_cols=165 Identities=19% Similarity=0.246 Sum_probs=127.0
Q ss_pred cccCceEEEEcCCeeEEEEEEECCEEEEEeCCCccccccCcCCcccCC-CCccccCCCceeeeeEEEEecCCCC------
Q 012588 144 LRQRYYYATWKADGTRYMMLITIDGCYLIDRCFNFRRVQMRFPCRNSN-EGLGEKTHHFTLLDGEMIIDKLPDS------ 216 (460)
Q Consensus 144 l~~~~Y~V~~K~DG~R~Ll~i~~~~vyLidR~~~~~~v~~~FP~~~~~-~~l~~~~~~~TlLDGElV~d~~~~~------ 216 (460)
+...+|++++|+||.|+++++.++++.|++|+++ .++..||+.... ..+ ..++++||||||+-...+.
T Consensus 474 ~~~~~w~~E~K~DG~R~~~~~~~g~vrL~SRnG~--d~T~~fPel~~~~~~l---~~~~~ILDGEiVvld~~G~~~F~~L 548 (764)
T PRK09632 474 LKASQWAFEGKWDGYRLLAEADHGALRLRSRSGR--DVTAEYPELAALAEDL---ADHHVVLDGEIVALDDSGVPSFGLL 548 (764)
T ss_pred CCCCCEEEEEEECceeEEEEEeCCEEEEEeCCCC--CccccchhHHHHHhhC---CCcceeeeeEEEEeCCCCCCCHHHH
Confidence 4556899999999999999999999999999997 557789976432 122 1358999999998432221
Q ss_pred ----CcceeEEEEeeeeecCCccccCCCHHHHHHHHHHHhcCccchhhccccccCCCCccCCCCCeEEEeccceechhHH
Q 012588 217 ----RRQERRYLIYDMMAINQASVIERPFYERWKMLEKEVIEPRNYERHNIYQSRNPYYRYDLEPFRVRRKDFWLLSTVN 292 (460)
Q Consensus 217 ----~~~~~ryliFDiL~~~G~~l~~~pf~eRl~~L~~~i~~pr~~~~~~l~~~~~~~~~~~~~pf~I~~K~f~~~~~~~ 292 (460)
....+.|++||+|++||++++++||.+|+++|++.+.. .. . ++..+.+.. ..+
T Consensus 549 q~r~~~~~v~y~vFDLL~lnG~dL~~~Pl~eRR~~L~~l~~~-~~------------~---------i~~s~~~~~-~~~ 605 (764)
T PRK09632 549 QNRGRDTRVEFWAFDLLYLDGRSLLRKPYRDRRKLLEALAPS-GG------------S---------LTVPPLLPG-DGA 605 (764)
T ss_pred hhhhhcCCeEEEEEeeeccCCcccccCCHHHHHHHHHHhhCC-CC------------c---------EEecceecc-cHH
Confidence 11358999999999999999999999999999996631 10 0 222333332 345
Q ss_pred HHHHHhccccCCCCceEEEEcCCCCCccCC-CCCeEEEccCCCceEEEEE
Q 012588 293 KLLKEFIPKLSHDADGLVFQGWDDPYVPRT-HEGLLKWKYARMNSVDFLF 341 (460)
Q Consensus 293 ~ll~~~~~~l~h~~DGLIF~p~~spY~~G~-~~~~LKWKP~~~nTVDF~l 341 (460)
.+|+. ...++.||||+|..+|+|.+|+ +.+|||+|+. .++||+|
T Consensus 606 ~~l~~---a~~~GlEGIVaKr~dS~Y~pGrRs~~WlKiK~~--~~~e~VI 650 (764)
T PRK09632 606 EALAY---SRELGWEGVVAKRRDSTYQPGRRSSSWIKDKHW--RTQEVVI 650 (764)
T ss_pred HHHHH---HHHcCCcEEEEeCCCCCCCCCCcCCCeEEEecC--CceEEEE
Confidence 67764 4679999999999999999996 7899999974 6899987
No 27
>PLN03113 DNA ligase 1; Provisional
Probab=99.84 E-value=1.9e-20 Score=206.52 Aligned_cols=174 Identities=18% Similarity=0.236 Sum_probs=127.0
Q ss_pred cccccCceEEEEcCCeeEEEEEEE-CCEEEEEeCCCccccccCcCCcccCC-CCccccCCCceeeeeEEEEecC-CCC--
Q 012588 142 QLLRQRYYYATWKADGTRYMMLIT-IDGCYLIDRCFNFRRVQMRFPCRNSN-EGLGEKTHHFTLLDGEMIIDKL-PDS-- 216 (460)
Q Consensus 142 ~~l~~~~Y~V~~K~DG~R~Ll~i~-~~~vyLidR~~~~~~v~~~FP~~~~~-~~l~~~~~~~TlLDGElV~d~~-~~~-- 216 (460)
..+...+|.+++|+||.|++++.. +++|.+++|+++ .++..||+.... ..+......++|||||||.-.. .+.
T Consensus 386 ~~~~g~~~~~E~KyDGeR~QiH~~~~g~v~lfSRn~e--d~T~~fPel~~~~~~~~~~~~~~~ILDGEiVa~d~~~~~~l 463 (744)
T PLN03113 386 NKFQDMEFTCEYKYDGERAQIHFLEDGSVEIYSRNAE--RNTGKYPDVVVAISRLKKPSVKSFILDCELVAYDREKKKIL 463 (744)
T ss_pred hccCCCCEEEEEeeccceEEEEEecCCEEEEEeCCCC--cccccchhHHHHHHHhccccCCCEEEEeEEEEEECCCCCcC
Confidence 345556899999999999999975 568999999987 567889987431 1111011367999999998432 210
Q ss_pred -----------------CcceeEEEEeeeeecCCccccCCCHHHHHHHHHHHhcCccchhhccccccCCCCccCCCCCeE
Q 012588 217 -----------------RRQERRYLIYDMMAINQASVIERPFYERWKMLEKEVIEPRNYERHNIYQSRNPYYRYDLEPFR 279 (460)
Q Consensus 217 -----------------~~~~~ryliFDiL~~~G~~l~~~pf~eRl~~L~~~i~~pr~~~~~~l~~~~~~~~~~~~~pf~ 279 (460)
.+.++.|++||||++||++++++||.+|+++|++.+.. .. + .
T Consensus 464 pFq~Lq~R~rk~~~~~~~~~pv~~~aFDlLylnG~~L~~~PL~eRR~~L~~~~~~-~~-----------~-------~-- 522 (744)
T PLN03113 464 PFQILSTRARKNVVMSDIKVDVCIFAFDMLYLNGQPLIQEQLKIRREHLYESFEE-DP-----------G-------F-- 522 (744)
T ss_pred CHHHHHhhhccccchhccccceEEEEEeccccCccChhcCCHHHHHHHHHHHhcc-CC-----------C-------c--
Confidence 01246899999999999999999999999999996632 10 0 1
Q ss_pred EEeccc---eechhHHHHHHHhccccCCCCceEEEEcC--CCCCccC-CCCCeEEEccCCC----ceEEEEE
Q 012588 280 VRRKDF---WLLSTVNKLLKEFIPKLSHDADGLVFQGW--DDPYVPR-THEGLLKWKYARM----NSVDFLF 341 (460)
Q Consensus 280 I~~K~f---~~~~~~~~ll~~~~~~l~h~~DGLIF~p~--~spY~~G-~~~~~LKWKP~~~----nTVDF~l 341 (460)
+..... -....+.++|+. .+.++.||||.+.. +++|.|| |+..|||||+..+ .|+|+++
T Consensus 523 i~~~~~~~~~~~ee~~~~~~~---ai~~g~EGlmvK~l~~dS~Y~pGkRs~~WlKlK~dy~~~~~dtlDlVv 591 (744)
T PLN03113 523 FQFATAITSNDLEEIQKFLDA---AVDASCEGLIIKTLNKDATYEPSKRSNNWLKLKKDYMESIGDSLDLVP 591 (744)
T ss_pred EEEeeeeccCCHHHHHHHHHH---HHHcCCceEEEeccCCCCCccCCCCCCCeEEEechhhccccccccEEE
Confidence 222222 233455666664 57899999999985 7899999 5779999998765 4999986
No 28
>PRK01109 ATP-dependent DNA ligase; Provisional
Probab=99.84 E-value=1.7e-20 Score=204.40 Aligned_cols=166 Identities=17% Similarity=0.297 Sum_probs=124.6
Q ss_pred CceEEEEcCCeeEEEEEEECCEEEEEeCCCccccccCcCCcccCCCCccccC-CCceeeeeEEEEec-CCCC--------
Q 012588 147 RYYYATWKADGTRYMMLITIDGCYLIDRCFNFRRVQMRFPCRNSNEGLGEKT-HHFTLLDGEMIIDK-LPDS-------- 216 (460)
Q Consensus 147 ~~Y~V~~K~DG~R~Ll~i~~~~vyLidR~~~~~~v~~~FP~~~~~~~l~~~~-~~~TlLDGElV~d~-~~~~-------- 216 (460)
.+|++++|+||.|+++++.++++.+++|+++ .++..||+.... +.... ..++|||||||.-. ..+.
T Consensus 248 ~~~~~E~K~DG~R~qih~~~~~v~l~SR~~~--d~T~~~pel~~~--~~~~~~~~~~ILDGElv~~d~~~g~~~~F~~l~ 323 (590)
T PRK01109 248 GEALVEYKYDGERAQIHKKGDKVKIFSRRLE--NITHQYPDVVEY--AKEAIKAEEAIVEGEIVAVDPETGEMRPFQELM 323 (590)
T ss_pred CCeEEEecCCceEEEEEEcCCEEEEEeCCch--hhccccchHHHH--HHHhcCccceEEeeeEEEEECCCCcccChHHHh
Confidence 4799999999999999999999999999987 567889987431 11112 36899999999843 1111
Q ss_pred ----C--------cceeEEEEeeeeecCCccccCCCHHHHHHHHHHHhcCccchhhccccccCCCCccCCCCCeEEEecc
Q 012588 217 ----R--------RQERRYLIYDMMAINQASVIERPFYERWKMLEKEVIEPRNYERHNIYQSRNPYYRYDLEPFRVRRKD 284 (460)
Q Consensus 217 ----~--------~~~~ryliFDiL~~~G~~l~~~pf~eRl~~L~~~i~~pr~~~~~~l~~~~~~~~~~~~~pf~I~~K~ 284 (460)
+ ..++.|++||||++||+++++.||.+|+++|++.+.. .. . +....
T Consensus 324 ~R~r~~~~~~~~~~~p~~~~vFDiL~l~g~~l~~~pl~eRr~~L~~~~~~-~~-------------------~--~~~~~ 381 (590)
T PRK01109 324 HRKRKYDIEEAIKEYPVNVFLFDLLYVDGEDLTDKPLPERRKKLEEIVKE-ND-------------------K--VKLAE 381 (590)
T ss_pred hcccccchhhhcccCceEEEEEEEEEECCcchhhCcHHHHHHHHHHhcCC-CC-------------------c--eEEee
Confidence 0 1246899999999999999999999999999996532 11 0 12222
Q ss_pred ceec---hhHHHHHHHhccccCCCCceEEEEcC--CCCCccC-CCCCeEEEccC----CCceEEEEE
Q 012588 285 FWLL---STVNKLLKEFIPKLSHDADGLVFQGW--DDPYVPR-THEGLLKWKYA----RMNSVDFLF 341 (460)
Q Consensus 285 f~~~---~~~~~ll~~~~~~l~h~~DGLIF~p~--~spY~~G-~~~~~LKWKP~----~~nTVDF~l 341 (460)
.... ..+.++|+. ...++.||||.|.. +++|.+| |+..|+|+|+. ...|+|+++
T Consensus 382 ~~~~~~~~~~~~~~~~---a~~~g~EGiv~K~~~~ds~Y~~g~Rs~~WlK~K~dy~~~~~~~~Dlvv 445 (590)
T PRK01109 382 RIITDDVEELEKFFHR---AIEEGCEGLMAKSLGKDSIYQAGARGWLWIKYKRDYQSEMADTVDLVV 445 (590)
T ss_pred eEecCCHHHHHHHHHH---HHHcCCceEEEecCCCCCCcCCCCCCccHHHhhHHhhcccCCceeEEE
Confidence 2222 345556653 67899999999999 9999999 57789999973 356899887
No 29
>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=99.84 E-value=1.3e-20 Score=177.91 Aligned_cols=159 Identities=25% Similarity=0.431 Sum_probs=113.4
Q ss_pred cCceEEEEcCCeeEEEEEEECCEEEEEeCCCccccccCcCCcccC-CCCccccCCCceeeeeEEEE-ecCCCC-------
Q 012588 146 QRYYYATWKADGTRYMMLITIDGCYLIDRCFNFRRVQMRFPCRNS-NEGLGEKTHHFTLLDGEMII-DKLPDS------- 216 (460)
Q Consensus 146 ~~~Y~V~~K~DG~R~Ll~i~~~~vyLidR~~~~~~v~~~FP~~~~-~~~l~~~~~~~TlLDGElV~-d~~~~~------- 216 (460)
..+|++++|+||+|+++...++++.+++|++. .++..||+... ..........+++||||||. |...+.
T Consensus 18 ~~~~~~e~K~DG~R~~i~~~~~~v~~~SR~g~--~~~~~~~~l~~~l~~~~~~~~~~~vLDGElv~~d~~~~~~~~f~~~ 95 (202)
T PF01068_consen 18 GGPWYVEPKYDGVRCQIHKDGGGVRLFSRNGK--DITSQFPELAEALRELLFPDGPDFVLDGELVVLDPNTGSPLPFQEL 95 (202)
T ss_dssp TSCEEEEEEESSEEEEEEEETTEEEEEETTSS--B-GGGHHHHHHHHHHHBCTSCTEEEEEEEEEEBETTTSSBCCHHHH
T ss_pred CCCeEEEEeEeeEEeeeeeccccceeeccccc--chhhHHHHHHHHHHHHhcCCCCceEEEEEEEEEecCCCcchhHHHH
Confidence 67899999999999999999999999999987 33445665421 00000011246999999998 221110
Q ss_pred --------C-----cceeEEEEeeeeecCCccccCCCHHHHHHHHHHHhcCccchhhccccccCCCCccCCCCCeEEEec
Q 012588 217 --------R-----RQERRYLIYDMMAINQASVIERPFYERWKMLEKEVIEPRNYERHNIYQSRNPYYRYDLEPFRVRRK 283 (460)
Q Consensus 217 --------~-----~~~~ryliFDiL~~~G~~l~~~pf~eRl~~L~~~i~~pr~~~~~~l~~~~~~~~~~~~~pf~I~~K 283 (460)
. ...+.|+|||+|+++|.+++++||.+|+++|++.+..+. +. +...
T Consensus 96 ~~~~~~~~~~~~~~~~~~~~~vFDil~l~~~~l~~~p~~eR~~~L~~~~~~~~------------~~---------i~~~ 154 (202)
T PF01068_consen 96 SGRLNRRSKKIPEQSEPLQFVVFDILYLDGKDLLDLPYEERRELLEELLEPPP------------PR---------IRIV 154 (202)
T ss_dssp HHHHBHSSSCHHHHHSCEEEEEEEEEEETTEECTTSCHHHHHHHHHHHBG-BT------------SS---------EEEE
T ss_pred hhhhhhhcccchhccCcEEEEEEEEEEeCCeEeeeccHHHHHHHHHHhhccCC------------Cc---------eeEe
Confidence 0 136899999999999999999999999999999772211 11 2233
Q ss_pred cceech---hHHHHHHHhccccCCCCceEEEEcCCCCCccCCC-CCeEEEc
Q 012588 284 DFWLLS---TVNKLLKEFIPKLSHDADGLVFQGWDDPYVPRTH-EGLLKWK 330 (460)
Q Consensus 284 ~f~~~~---~~~~ll~~~~~~l~h~~DGLIF~p~~spY~~G~~-~~~LKWK 330 (460)
..+... .+.++++. .+.++.||||++..+++|.+|+. ..|+|+|
T Consensus 155 ~~~~~~~~~~~~~~~~~---~~~~g~EG~v~K~~~~~Y~~Gkrs~~w~K~K 202 (202)
T PF01068_consen 155 ESYVVNSKEELEELFEE---AIDQGFEGLVLKDPDSPYEPGKRSSGWLKVK 202 (202)
T ss_dssp EEEEESSHHHHHHHHHH---HHHTTSSEEEEEETTSSC-TTEEEEEEEEEE
T ss_pred eeecCCCHHHHHHHHHH---HHHcCCceEEEECCCCccCCCCcCCCcEEEC
Confidence 333333 44455553 56889999999999999999975 8999998
No 30
>COG1793 CDC9 ATP-dependent DNA ligase [DNA replication, recombination, and repair]
Probab=99.82 E-value=9.6e-20 Score=191.75 Aligned_cols=166 Identities=22% Similarity=0.251 Sum_probs=125.8
Q ss_pred ceEEEEcCCeeEEEEEEECCEEEEEeCCCccccccCcCCc-ccCC-CCccccCCCceeeeeEEEEecCCCC---------
Q 012588 148 YYYATWKADGTRYMMLITIDGCYLIDRCFNFRRVQMRFPC-RNSN-EGLGEKTHHFTLLDGEMIIDKLPDS--------- 216 (460)
Q Consensus 148 ~Y~V~~K~DG~R~Ll~i~~~~vyLidR~~~~~~v~~~FP~-~~~~-~~l~~~~~~~TlLDGElV~d~~~~~--------- 216 (460)
+|.+++|+||.|+++++.+++|.|++|++. .++-.||. .... ..+ ...++|||||+|+....+.
T Consensus 134 ~w~~E~K~DG~R~q~h~~~~~vrl~SR~g~--d~T~~fP~~~~~~~~~l---~~~~~iiDGE~V~~~~~~~~~F~~Lq~r 208 (444)
T COG1793 134 DWAYEEKFDGYRVQIHIDGGKVRLYSRNGE--DWTGRFPDILEAAAEAL---PADDFILDGEIVVLDEEGRLDFQALQQR 208 (444)
T ss_pred CEEEEEeeceEEEEEEEcCCEEEEEeCCCc--cchhhChHHHHHHHhcC---CCCceEEeeeEEEECCCCCCCHHHHHHH
Confidence 699999999999999999999999999997 66788993 3211 112 2357999999999542110
Q ss_pred -----------CcceeEEEEeeeeecCCccccCCCHHHHHHHHHHHhcCccchhhccccccCCCCccCCCCCeEEEeccc
Q 012588 217 -----------RRQERRYLIYDMMAINQASVIERPFYERWKMLEKEVIEPRNYERHNIYQSRNPYYRYDLEPFRVRRKDF 285 (460)
Q Consensus 217 -----------~~~~~ryliFDiL~~~G~~l~~~pf~eRl~~L~~~i~~pr~~~~~~l~~~~~~~~~~~~~pf~I~~K~f 285 (460)
......|++||+|+++|++++.+||.+|+++|++.+....... ..+ ...+
T Consensus 209 ~~~k~~v~~~~~~~~~~~~aFDlL~~dG~dL~~~pl~eRr~~Le~lv~~~~~~~-------~~~------------~i~~ 269 (444)
T COG1793 209 LRRKYDVAKLRRETPLVLFAFDLLYLDGEDLRGLPLEERRALLEELVKSSDKIE-------IAE------------RIPF 269 (444)
T ss_pred hhhccchhhhccCCceEEEEEEEEeECCcccccCchHHHHHHHHHHhccccccc-------ccc------------ceec
Confidence 0135689999999999999999999999999999775421000 001 1122
Q ss_pred eechhHHHHHHHhccccCCCCceEEEEcCCCCCccC-CCCCeEEEccCCCceEEEEEE
Q 012588 286 WLLSTVNKLLKEFIPKLSHDADGLVFQGWDDPYVPR-THEGLLKWKYARMNSVDFLFE 342 (460)
Q Consensus 286 ~~~~~~~~ll~~~~~~l~h~~DGLIF~p~~spY~~G-~~~~~LKWKP~~~nTVDF~l~ 342 (460)
........+|+. ...++.||+|.+..++||.+| +...|+|||+. .|.||.|.
T Consensus 270 ~~~~~~~~~~~~---a~~~g~EGvv~K~~ds~Y~~g~R~~~W~K~K~~--~~~d~vv~ 322 (444)
T COG1793 270 SDAEEGEAFLEA---AIELGLEGVVAKRPDSPYRAGGRSNKWLKVKRD--ETLDLVVV 322 (444)
T ss_pred cChhhHHHHHHH---HHhcCceEEEEeCCCCCcCCCCCCCcceEeccC--CcccEEEE
Confidence 344456667764 568899999999999999965 68999999985 89999983
No 31
>PHA00454 ATP-dependent DNA ligase
Probab=99.81 E-value=4.1e-19 Score=179.91 Aligned_cols=182 Identities=15% Similarity=0.133 Sum_probs=127.2
Q ss_pred CCCc-cccccccccccccc--CceEEEEcCCeeEEEEEEECCE-EEEEeCCCccccccCcCCcccCCC-------Cccc-
Q 012588 129 PGSH-PVSLNSDNLQLLRQ--RYYYATWKADGTRYMMLITIDG-CYLIDRCFNFRRVQMRFPCRNSNE-------GLGE- 196 (460)
Q Consensus 129 PGsq-PVSl~r~nl~~l~~--~~Y~V~~K~DG~R~Ll~i~~~~-vyLidR~~~~~~v~~~FP~~~~~~-------~l~~- 196 (460)
|+++ -|+|+.+++..... ..|++++|+||+|+++++.+++ +.|++|+++ .||...... .+..
T Consensus 6 ~~~~~~~~~~~~~i~~~~~~~g~~~~E~K~DG~R~~~~~~~~~~v~l~SR~g~------~~p~l~~~~~~~~~~~~~~~~ 79 (315)
T PHA00454 6 TNPFRAVDFNESAIEKALEKAGYLIADVKYDGVRGNIVVDNTADHGWLSREGK------TIPALEHLNGFDRRWAKLLND 79 (315)
T ss_pred CCccccccCCHHHHHHHHHhCCcEEEEEccceEEEEEEEcCCCeEEEEeCCCC------cccchhhhhhhhhhhhhhhhh
Confidence 4544 68999999976443 3677777999999999998764 999999986 245432110 0000
Q ss_pred ---cCCCceeeeeEEEEecCCC----------------CCcceeEEEEeeeeecC----Cccc---cCCCHHHHHHHHHH
Q 012588 197 ---KTHHFTLLDGEMIIDKLPD----------------SRRQERRYLIYDMMAIN----QASV---IERPFYERWKMLEK 250 (460)
Q Consensus 197 ---~~~~~TlLDGElV~d~~~~----------------~~~~~~ryliFDiL~~~----G~~l---~~~pf~eRl~~L~~ 250 (460)
....+++||||+|+...+. ....++.|+|||+|++| |+++ ..+||.+|.++|++
T Consensus 80 ~~~~l~~~~vLDGElv~~~~~f~~~~~~l~~k~~~~~~~~~~~v~~~vFDll~l~~~~~g~~l~~l~~~pl~~Rr~~L~~ 159 (315)
T PHA00454 80 DRCIFPDGFMLDGELMVKGVDFNTGSGLLRRKWKVLFELHLKKLHVVVYDVTPLDVLESGEDYDVMSLLMYEHVRAMVPL 159 (315)
T ss_pred hhhcCCCCeEEEEEEEecCCCHHHHHHHhccCccchhhhccCceEEEEEEeeEeccccCCccccccccccHHHHHHHHHH
Confidence 1124789999999853211 00135799999999999 6665 78999999999987
Q ss_pred HhcCccchhhccccccCCCCccCCCCCeEEEeccceec---hhHHHHHHHhccccCCCCceEEEEcCCCCCccCCCCCeE
Q 012588 251 EVIEPRNYERHNIYQSRNPYYRYDLEPFRVRRKDFWLL---STVNKLLKEFIPKLSHDADGLVFQGWDDPYVPRTHEGLL 327 (460)
Q Consensus 251 ~i~~pr~~~~~~l~~~~~~~~~~~~~pf~I~~K~f~~~---~~~~~ll~~~~~~l~h~~DGLIF~p~~spY~~G~~~~~L 327 (460)
.+.. .. .. .++..+.+.. ....++++. ...++.||||++..+++|.+|+...|+
T Consensus 160 l~~~-~~----------~~---------~~~~~~~~~~~~~~~~~~~~~~---~~~~g~EGiv~K~~ds~Y~~Grr~~~~ 216 (315)
T PHA00454 160 LMEY-FP----------EI---------DWFLSESYEVYDMESLQELYEK---KRAEGHEGLVVKDPSLIYRRGKKSGWW 216 (315)
T ss_pred HHhh-CC----------Cc---------ceEeeceEEcCCHHHHHHHHHH---HHhCCCceEEEeCCCCCCCCCCccCcE
Confidence 5421 10 00 0333344433 345556654 578999999999999999999876788
Q ss_pred EEccCCCceEEEEE
Q 012588 328 KWKYARMNSVDFLF 341 (460)
Q Consensus 328 KWKP~~~nTVDF~l 341 (460)
|+|+. .++|++|
T Consensus 217 K~K~~--~~~d~vI 228 (315)
T PHA00454 217 KMKPE--CEADGTI 228 (315)
T ss_pred EEccc--CceeEEE
Confidence 99974 5999997
No 32
>PRK09125 DNA ligase; Provisional
Probab=99.78 E-value=1.1e-17 Score=167.07 Aligned_cols=210 Identities=23% Similarity=0.337 Sum_probs=133.9
Q ss_pred ccCceEEEEcCCeeEEEEEEECCEEEEEeCCCccccccCcCCcccCCCCccccCCCceeeeeEEEEecCC----------
Q 012588 145 RQRYYYATWKADGTRYMMLITIDGCYLIDRCFNFRRVQMRFPCRNSNEGLGEKTHHFTLLDGEMIIDKLP---------- 214 (460)
Q Consensus 145 ~~~~Y~V~~K~DG~R~Ll~i~~~~vyLidR~~~~~~v~~~FP~~~~~~~l~~~~~~~TlLDGElV~d~~~---------- 214 (460)
...+|++++|+||+|++ + +++-|++|+++ .++. |+... .. ..+++||||||.-..+
T Consensus 41 ~~~~~~~E~K~DG~R~~--~--~~v~l~SR~g~--~it~--p~~~~-~~-----~~~~vLDGElv~~~~~F~~l~~r~~~ 106 (282)
T PRK09125 41 DISGYLVSEKLDGVRAY--W--DGKQLLTRQGN--PIAA--PAWFT-AG-----FPPFPLDGELWAGRGQFEAISSIVRD 106 (282)
T ss_pred ChhhEEEEeeeeeEeEE--E--CCeEEEcCCCC--cCCC--chhHH-hc-----CCCccEeEEEEeCCCCHHHHHHHHcc
Confidence 44699999999999995 2 46889999986 2221 32211 11 2378999999973210
Q ss_pred -CCC---cceeEEEEeeeeecCCccccCCCHHHHHHHHHHHhcCccchhhccccccCCCCccCCCCCeEEEeccceec--
Q 012588 215 -DSR---RQERRYLIYDMMAINQASVIERPFYERWKMLEKEVIEPRNYERHNIYQSRNPYYRYDLEPFRVRRKDFWLL-- 288 (460)
Q Consensus 215 -~~~---~~~~ryliFDiL~~~G~~l~~~pf~eRl~~L~~~i~~pr~~~~~~l~~~~~~~~~~~~~pf~I~~K~f~~~-- 288 (460)
... ..++.|++||+++++| ||.+|++.|++.+.. . ..+. ++..+....
T Consensus 107 k~~~~~~~~~v~~~vFDll~~~g------pl~eRr~~L~~li~~-~----------~~~~---------i~~~~~~~~~~ 160 (282)
T PRK09125 107 KTPDDAAWRKVRFMVFDLPDAPG------DFEERLAVLKKLLAK-L----------PSPY---------IKIIEQIRVRS 160 (282)
T ss_pred CCcchhhhcccEEEEEEcCCCCC------CHHHHHHHHHHHHhh-C----------CCCc---------EEEEeEEEcCC
Confidence 000 1357999999999986 999999999996632 1 0111 233333333
Q ss_pred -hhHHHHHHHhccccCCCCceEEEEcCCCCCccCCCCCeEEEccCCCceEEEEEEEe-c-CCc-----eeEEEEe-CCce
Q 012588 289 -STVNKLLKEFIPKLSHDADGLVFQGWDDPYVPRTHEGLLKWKYARMNSVDFLFEVT-D-DDR-----QLLYVFE-RGKK 359 (460)
Q Consensus 289 -~~~~~ll~~~~~~l~h~~DGLIF~p~~spY~~G~~~~~LKWKP~~~nTVDF~l~~~-~-~~~-----~~L~v~~-~g~~ 359 (460)
.++.++++. .+.++.||||++..+++|.+||+..|+||||. .++|++|-=- . .++ +.|.+.. .|..
T Consensus 161 ~~~~~~~~~~---~~~~G~EGiV~K~~ds~Y~~GRs~~wlKiK~~--~~~d~vIvG~~~g~Gk~~g~~gsllv~~~~g~~ 235 (282)
T PRK09125 161 EAALQQFLDQ---IVAAGGEGLMLHRPDAPYEAGRSDDLLKLKPY--YDAEATVIGHLPGKGKFAGMLGALLVETPDGRE 235 (282)
T ss_pred HHHHHHHHHH---HHHcCCCEEEEeCCCCCCcCCCCCCcEEEEec--CCCcEEEEEEEcCCCcccCceeeEEEEeCCCCE
Confidence 344556654 57899999999999999999999999999985 5889987322 1 111 2344432 3321
Q ss_pred eeecCceeEecC--CCCCCCCceEEEEEEeC--CCC---eeEEEEEecCC
Q 012588 360 KLMEGSSVEFTD--REPSFYSGKIIECTWDP--DVQ---LWKCMRIRTDK 402 (460)
Q Consensus 360 ~~~~~~~~~f~~--~~~~~~dg~IvEC~~d~--~~~---~W~f~R~R~DK 402 (460)
+--+ .-|++ .....+-|+|+++.|-. .+| .=+|.++|.|.
T Consensus 236 -~~Vg--sG~t~~~r~~~~~~g~~~~V~y~e~t~~g~lR~P~f~g~R~D~ 282 (282)
T PRK09125 236 -FKIG--SGFSDAERENPPKIGSIITYKYRGLTKNGLPRFASFLRVREDE 282 (282)
T ss_pred -EEeC--CCCCHHHhcCCCCCCCEEEEEecccCCCCcccCCEEEEEecCC
Confidence 1101 12443 22234579999999942 223 34688888883
No 33
>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=99.75 E-value=5.9e-18 Score=157.10 Aligned_cols=143 Identities=24% Similarity=0.355 Sum_probs=98.6
Q ss_pred cCceEEEEcCCeeEEEEEEECCEEEEEeCCCccccccCcCCcccCCCCccccCCCceeeeeEEEEecCC-----------
Q 012588 146 QRYYYATWKADGTRYMMLITIDGCYLIDRCFNFRRVQMRFPCRNSNEGLGEKTHHFTLLDGEMIIDKLP----------- 214 (460)
Q Consensus 146 ~~~Y~V~~K~DG~R~Ll~i~~~~vyLidR~~~~~~v~~~FP~~~~~~~l~~~~~~~TlLDGElV~d~~~----------- 214 (460)
..+|++++|+||+|+++ .++ .+++|+++ .++. +... ..++ ..++||||||.-..+
T Consensus 15 ~~~~~~e~K~DG~R~~~--~~~--~~~SR~g~--~~t~--~~~~-~~~l-----~~~ilDGElv~~~~~f~~l~~~~~~~ 80 (174)
T cd07896 15 ISGYLVSEKLDGVRAYW--DGK--QLLSRSGK--PIAA--PAWF-TAGL-----PPFPLDGELWIGRGQFEQTSSIVRSK 80 (174)
T ss_pred hHHeeechhhceEEEEE--ecc--EEEecCCc--CCCC--CHHH-HhhC-----CCCccCceEEcCCCCHHHHHHHHhcC
Confidence 35899999999999965 333 89999986 2221 1110 0112 349999999973210
Q ss_pred CC---CcceeEEEEeeeeecCCccccCCCHHHHHHHHHHHhcCccchhhccccccCCCCccCCCCCeEEEeccceech--
Q 012588 215 DS---RRQERRYLIYDMMAINQASVIERPFYERWKMLEKEVIEPRNYERHNIYQSRNPYYRYDLEPFRVRRKDFWLLS-- 289 (460)
Q Consensus 215 ~~---~~~~~ryliFDiL~~~G~~l~~~pf~eRl~~L~~~i~~pr~~~~~~l~~~~~~~~~~~~~pf~I~~K~f~~~~-- 289 (460)
.. ....+.|+|||||. +..||.+|++.|++.+.... .+ . ++..+.+.+.
T Consensus 81 ~~~~~~~~~~~f~vFDil~------~~~p~~eR~~~L~~~i~~~~-----------~~-------~--~~~~~~~~~~~~ 134 (174)
T cd07896 81 KPDDEDWRKVKFMVFDLPS------AKGPFEERLERLKNLLEKIP-----------NP-------H--IKIVPQIPVKSN 134 (174)
T ss_pred CCChhhcccceEEEEeCCC------CCCCHHHHHHHHHHHHHhCC-----------CC-------c--EEEEeeeeeCCH
Confidence 10 11358999999998 77899999999999764210 00 0 2333333333
Q ss_pred -hHHHHHHHhccccCCCCceEEEEcCCCCCccCCCCCeEEEcc
Q 012588 290 -TVNKLLKEFIPKLSHDADGLVFQGWDDPYVPRTHEGLLKWKY 331 (460)
Q Consensus 290 -~~~~ll~~~~~~l~h~~DGLIF~p~~spY~~G~~~~~LKWKP 331 (460)
.+..+++. .+.++.||||++..+++|.+||+..|+||||
T Consensus 135 ~~i~~~~~~---~~~~g~EGlv~K~~ds~Y~~gR~~~wlK~Kp 174 (174)
T cd07896 135 EALDQYLDE---VVAAGGEGLMLRRPDAPYETGRSDNLLKLKP 174 (174)
T ss_pred HHHHHHHHH---HHhcCCCeEEEecCCCcccCCcCCCceeeCC
Confidence 44455553 5789999999999999999999999999998
No 34
>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=99.68 E-value=1.8e-16 Score=170.77 Aligned_cols=140 Identities=21% Similarity=0.304 Sum_probs=99.6
Q ss_pred eCCCccccccCcCCcccCCCCccccCCCceeeeeEEEEecCCCC-------------CcceeEEEEeeeeecCCccccCC
Q 012588 173 DRCFNFRRVQMRFPCRNSNEGLGEKTHHFTLLDGEMIIDKLPDS-------------RRQERRYLIYDMMAINQASVIER 239 (460)
Q Consensus 173 dR~~~~~~v~~~FP~~~~~~~l~~~~~~~TlLDGElV~d~~~~~-------------~~~~~ryliFDiL~~~G~~l~~~ 239 (460)
+|++. ..+-.||+.... +......+++||||||+-...+. ....++|++||+|++||++++++
T Consensus 1 SRng~--d~T~~fPel~~~--~~~l~~~~~ILDGElVvld~~G~~~F~~Lq~~~~~~~~~pv~~~vFDlL~l~G~dL~~~ 76 (552)
T TIGR02776 1 TRNGH--DWTKRFPEIVKA--LALLKLLPAWIDGEIVVLDERGRADFAALQNALSAGASRPLTYYAFDLLFLSGEDLRDL 76 (552)
T ss_pred CCCcC--cchhhhHHHHHH--HhhCCCCCEEEEEEEEEECCCCCCCHHHHHHHHHhcccCceEEEEEeccccCCcccccC
Confidence 46765 557789987542 11112367999999998432211 11357999999999999999999
Q ss_pred CHHHHHHHHHHHhcCccchhhccccccCCCCccCCCCCeEEEeccceechhHHHHHHHhccccCCCCceEEEEcCCCCCc
Q 012588 240 PFYERWKMLEKEVIEPRNYERHNIYQSRNPYYRYDLEPFRVRRKDFWLLSTVNKLLKEFIPKLSHDADGLVFQGWDDPYV 319 (460)
Q Consensus 240 pf~eRl~~L~~~i~~pr~~~~~~l~~~~~~~~~~~~~pf~I~~K~f~~~~~~~~ll~~~~~~l~h~~DGLIF~p~~spY~ 319 (460)
||.+|+++|++.+.. . ..+. ++...... ...+++|+. ...++.||||+|..+++|.
T Consensus 77 Pl~eRr~~L~~ll~~-~----------~~~~---------i~~~~~~~-~~~~~~~~~---a~~~G~EGIV~K~~dS~Y~ 132 (552)
T TIGR02776 77 PLEERKKRLKQLLKA-Q----------DEPA---------IRYSDHFE-SDGDALLES---ACRLGLEGVVSKRLDSPYR 132 (552)
T ss_pred CHHHHHHHHHHHhhh-c----------CCCc---------EEEeeeec-ccHHHHHHH---HHHCCCceEEEeCCCCCCC
Confidence 999999999996632 1 0111 22222222 233467764 5689999999999999999
Q ss_pred cCCCCCeEEEccCCCceEEEEEE
Q 012588 320 PRTHEGLLKWKYARMNSVDFLFE 342 (460)
Q Consensus 320 ~G~~~~~LKWKP~~~nTVDF~l~ 342 (460)
+||+.+|||+|+ ..+.||+|.
T Consensus 133 ~GRs~~WlKlK~--~~~~e~vI~ 153 (552)
T TIGR02776 133 SGRSKDWLKLKC--RRRQEFVIT 153 (552)
T ss_pred CCCCcchhcccc--cccceEEEE
Confidence 999999999998 458888873
No 35
>KOG2386 consensus mRNA capping enzyme, guanylyltransferase (alpha) subunit [RNA processing and modification]
Probab=99.68 E-value=6.2e-18 Score=172.66 Aligned_cols=287 Identities=22% Similarity=0.213 Sum_probs=182.7
Q ss_pred CCCCCCCCcccccccccccccccCceEEEEcCCeeEEEEEEEC-----CEEEEEeCCCccccccCcCCcccCCCC---cc
Q 012588 124 GNMQFPGSHPVSLNSDNLQLLRQRYYYATWKADGTRYMMLITI-----DGCYLIDRCFNFRRVQMRFPCRNSNEG---LG 195 (460)
Q Consensus 124 ~~~~FPGsqPVSl~r~nl~~l~~~~Y~V~~K~DG~R~Ll~i~~-----~~vyLidR~~~~~~v~~~FP~~~~~~~---l~ 195 (460)
....|||+| +....+++..|...+|.||+|.||+|.++|+.. .+++-+.++...+ ..+|....... +.
T Consensus 38 ~~k~~~~~~-~f~~~dl~~~l~~~~~~vgl~iDltnt~ryy~~~~~~~~g~~Y~K~~c~g~---~~vp~~~~v~~fv~~v 113 (393)
T KOG2386|consen 38 STKTFPGSQ-RFQPKDLFELLKEHNYKVGLKIDLTNTLRYYDKPELEERGVKYLKRNCPGR---GVVPRTELVDKFVKLV 113 (393)
T ss_pred CcCCCCCcc-ccCHHHHHHHHHhcCceEEEEEeccceeeeeccccccccceeEEEeccCCc---ccCCCccchHHHHHHH
Confidence 357788888 888999999999999999999999999999953 2554444443322 12554432222 12
Q ss_pred ccCCCceeeeeEEEEecCCCCCcceeEEEEeeeeecCCccccCCCHHHHHHHHHHHhcCccchhhccccccCCCCccCCC
Q 012588 196 EKTHHFTLLDGEMIIDKLPDSRRQERRYLIYDMMAINQASVIERPFYERWKMLEKEVIEPRNYERHNIYQSRNPYYRYDL 275 (460)
Q Consensus 196 ~~~~~~TlLDGElV~d~~~~~~~~~~ryliFDiL~~~G~~l~~~pf~eRl~~L~~~i~~pr~~~~~~l~~~~~~~~~~~~ 275 (460)
+.++.+|.+|||+|...-+.+ .+...||||++|+..|. .+...-.+|++......+.+.. ....|.. .. .+.
T Consensus 114 ~~f~~~~~~~~~LI~vhcthG-~NrtgyLI~~yL~~~~~-~s~~~aik~f~~~r~~gi~k~d-yi~~L~~---~~--~~~ 185 (393)
T KOG2386|consen 114 KGFVDDTKLDDELIGVHCTHG-LNRTGYLICAYLADVGG-YSSSEAIKRFADARPPGIEKQD-YIDALYS---RY--HDI 185 (393)
T ss_pred HHHHhcccCCCCEEEEeCCCc-ccccceeeeeeeeeccC-ccHHHHHHHHHHhCCCccCchH-HHHHHhh---cc--ccc
Confidence 345678999999999765543 35789999999999887 6666666777666655554432 2222221 11 245
Q ss_pred CCeEEEeccceechhHHHHHHHhccccC-CCCceEEEEcCCCCC-ccCCCCCeEEEccCCCceEEEEEEEecCC--ceeE
Q 012588 276 EPFRVRRKDFWLLSTVNKLLKEFIPKLS-HDADGLVFQGWDDPY-VPRTHEGLLKWKYARMNSVDFLFEVTDDD--RQLL 351 (460)
Q Consensus 276 ~pf~I~~K~f~~~~~~~~ll~~~~~~l~-h~~DGLIF~p~~spY-~~G~~~~~LKWKP~~~nTVDF~l~~~~~~--~~~L 351 (460)
.||.+..+..-.-....++.. +... |..||+||++...|| ..|+...++||||..+||+||.++..... .+.|
T Consensus 186 ~p~~vs~p~~~~~~~~~~~~~---~~~~~~~~Dg~i~t~~~~pg~~~g~~~~~~k~k~~~~n~~~~~~~~~~~q~~~~~l 262 (393)
T KOG2386|consen 186 FPFKVSCPSMPDWKRSIKLKK---PVHKLHGNDGLIFTPAEIPGSKNGKQEALLKWKPFSLNTIDFGVKLEKPQPELGDL 262 (393)
T ss_pred ccccccCCCCcchhhhhhhcc---ccccccccCCCcCCcccCccccccchhhhhcCCchhcCCcccceeecCCCCCccch
Confidence 677777666544434333332 2222 999999999999999 58999999999999999999999876431 1111
Q ss_pred EEEeC--Cc-----e--eeecCceeEecCCCCCCCCce--------EEEEEEeCCCCeeEEEEEecCCCCCChHHHHHHH
Q 012588 352 YVFER--GK-----K--KLMEGSSVEFTDREPSFYSGK--------IIECTWDPDVQLWKCMRIRTDKSTPNDINTYRKV 414 (460)
Q Consensus 352 ~v~~~--g~-----~--~~~~~~~~~f~~~~~~~~dg~--------IvEC~~d~~~~~W~f~R~R~DK~~pN~~~tv~~v 414 (460)
..... |. . +.+. ...| ...+..+|. ..||..+ -+|++.+.|.+..+|++.++....
T Consensus 263 ~~~~~~~g~~~~~r~~~~~~~--~~~y--~~~We~dg~~~~~L~~~~~~~~~~---dR~~~~~~~~~~~~~~~~~~~~~~ 335 (393)
T KOG2386|consen 263 QCKRKNEGAQPVSRENYKLLV--FEYY--EASWEADGTRYMMLIDGDGEYYDF---DRWRFVKGRENLRKIREDSDTKVL 335 (393)
T ss_pred hhhhcccccCCccccchhhhh--hhhh--hhhhcccCcEEEEEecCCceeEec---hhhhHHHhhhhhhcccccccchhh
Confidence 11100 10 0 0000 0001 112223333 3344332 278888888888888888888888
Q ss_pred HHhcccCCCHHHHHHHHH
Q 012588 415 MRSIRDNITEEVLLNEIQ 432 (460)
Q Consensus 415 ~~SI~~~Vt~e~Ll~~i~ 432 (460)
++++.|+....+.+....
T Consensus 336 ~~tl~dge~~lD~l~~~~ 353 (393)
T KOG2386|consen 336 HQTLLDGEMILDRLKEEA 353 (393)
T ss_pred hhhhcccceecccccccc
Confidence 887777766655555444
No 36
>KOG0966 consensus ATP-dependent DNA ligase IV [Replication, recombination and repair]
Probab=99.64 E-value=1.5e-15 Score=163.50 Aligned_cols=210 Identities=20% Similarity=0.294 Sum_probs=141.5
Q ss_pred HHHHHHHHHHHhcccCCCCC----CCCCCCCcccccccc------cccccccCceEEEEcCCeeEEEEEEECCEEEEEeC
Q 012588 105 QDAFRHFCYQTLKLNFGGRG----NMQFPGSHPVSLNSD------NLQLLRQRYYYATWKADGTRYMMLITIDGCYLIDR 174 (460)
Q Consensus 105 ~~~~r~~~~~l~~~~~~~~~----~~~FPGsqPVSl~r~------nl~~l~~~~Y~V~~K~DG~R~Ll~i~~~~vyLidR 174 (460)
...|...|.+|..-+.+-.. -.=|--.+|--..+. +++.+...+++++.|.||.|++|+.+++..-.++|
T Consensus 198 tsDLk~Vc~~L~Dp~~~l~~~~~~i~lfsa~~PqLa~~~~~~~~~~~e~m~~~~f~lEtK~DGERiQlHk~g~~~~yfSR 277 (881)
T KOG0966|consen 198 TSDLKAVCKKLYDPSVGLKELDEDIELFSAFRPQLAQKQKLGDWAIIEKMGGQDFYLETKFDGERIQLHKDGGEYKYFSR 277 (881)
T ss_pred hhhHHHHHHHhcCCccCccccccceeehhhcCHHHHhhhccchHHHHHHhcCCceEEEeeccCceEEEEecCCEEEEEec
Confidence 45677778887743221111 122444566654443 44567788999999999999999999999989999
Q ss_pred CCc-cccccCcCCcccCC----CCccccCCCceeeeeEEEE-ecCC-------C----------CCcceeEEEEeeeeec
Q 012588 175 CFN-FRRVQMRFPCRNSN----EGLGEKTHHFTLLDGEMII-DKLP-------D----------SRRQERRYLIYDMMAI 231 (460)
Q Consensus 175 ~~~-~~~v~~~FP~~~~~----~~l~~~~~~~TlLDGElV~-d~~~-------~----------~~~~~~ryliFDiL~~ 231 (460)
++. |...=-.++..... .++.......+||||||+. |+.. . .....+.|++||+|++
T Consensus 278 Ng~dyT~~yg~s~~~g~lt~~i~~~f~~~v~~cILDGEMm~wD~~~~~f~~~G~~~dik~~~~~~~~~qp~yvvfDLLyl 357 (881)
T KOG0966|consen 278 NGNDYTYEYGASYAHGTLTQRIHGAFNKEVESCILDGEMMTWDTKTKRFCPFGSNSDIKELSSRDGSQQPCYVVFDLLYL 357 (881)
T ss_pred CCcchhhhcCcccccccccHHHHhhhhhcchheEecceEEEeecchhhhccCCchhhHHHhhccccCCCceEEEeeeeee
Confidence 975 43110111111000 1110011246899999998 4321 0 1124699999999999
Q ss_pred CCccccCCCHHHHHHHHHHHhcCccchhhccccccCCCCccCCCCCeEEEeccceechhHHHHHHHhccccCCCCceEEE
Q 012588 232 NQASVIERPFYERWKMLEKEVIEPRNYERHNIYQSRNPYYRYDLEPFRVRRKDFWLLSTVNKLLKEFIPKLSHDADGLVF 311 (460)
Q Consensus 232 ~G~~l~~~pf~eRl~~L~~~i~~pr~~~~~~l~~~~~~~~~~~~~pf~I~~K~f~~~~~~~~ll~~~~~~l~h~~DGLIF 311 (460)
||+++...|+.+|+++|++.+. |....+ +-++.+.......+++.|+. ++..+.||||.
T Consensus 358 NgksL~~~~l~qR~e~L~~v~~-p~~~~i-----------------ei~~~~~~~~~edi~~~f~~---ai~~~~EGIVl 416 (881)
T KOG0966|consen 358 NGKSLFGAPLHQRLEILKKVIV-PKSGRI-----------------EIVRSEVGSTKEDIEQFFEE---AIDNGEEGIVL 416 (881)
T ss_pred cCcccCCccHHHHHHHHHhccc-CCCCee-----------------EEeehhhcccHHHHHHHHHH---HHhcCCCceEE
Confidence 9999999999999999998543 321111 12333444555566666764 67889999999
Q ss_pred EcCCCCCccC-CCCCeEEEccCCCc
Q 012588 312 QGWDDPYVPR-THEGLLKWKYARMN 335 (460)
Q Consensus 312 ~p~~spY~~G-~~~~~LKWKP~~~n 335 (460)
+..+|.|.+| |...|+|-||..+.
T Consensus 417 K~~~S~Y~pg~R~~gW~K~KPeYlk 441 (881)
T KOG0966|consen 417 KKPDSSYVPGQRSNGWIKLKPEYLK 441 (881)
T ss_pred eccCcccCccccCCCcEeecHHHHh
Confidence 9999999999 57899999998766
No 37
>KOG0967 consensus ATP-dependent DNA ligase I [Replication, recombination and repair]
Probab=99.33 E-value=8.2e-12 Score=132.46 Aligned_cols=178 Identities=19% Similarity=0.324 Sum_probs=124.6
Q ss_pred ccccccCceEEEEcCCeeEEEEEEEC-CEEEEEeCCCccccccCcCCcccCC-CCccccCCCceeeeeEEEE-ecCCCC-
Q 012588 141 LQLLRQRYYYATWKADGTRYMMLITI-DGCYLIDRCFNFRRVQMRFPCRNSN-EGLGEKTHHFTLLDGEMII-DKLPDS- 216 (460)
Q Consensus 141 l~~l~~~~Y~V~~K~DG~R~Ll~i~~-~~vyLidR~~~~~~v~~~FP~~~~~-~~l~~~~~~~TlLDGElV~-d~~~~~- 216 (460)
|..++...|-.+||.||.|..++... +.+++++|+.+ ..+-+||..... ..+........|||||+|. |+..+.
T Consensus 359 l~rf~~~~FTCEyKYDGeRAQIH~~edG~v~IfSRN~E--~~T~kYPDi~~~~~~~~kp~v~sFIlD~EvVA~Dr~~~~I 436 (714)
T KOG0967|consen 359 LERFQDKAFTCEYKYDGERAQIHKLEDGTVEIFSRNSE--NNTGKYPDIIEVISKLKKPSVKSFILDCEVVAWDREKGKI 436 (714)
T ss_pred HHHhhCceeEEEeecCceeeeeEEccCCcEEEEecccc--cccccCccHHHHHHHhhCCccceeEEeeeEEEEeccCCcc
Confidence 34577889999999999999999875 56899999987 567899987432 1111122367899999998 433211
Q ss_pred --------C----------cceeEEEEeeeeecCCccccCCCHHHHHHHHHHHhcCccchhhccccccCCCCccCCCCCe
Q 012588 217 --------R----------RQERRYLIYDMMAINQASVIERPFYERWKMLEKEVIEPRNYERHNIYQSRNPYYRYDLEPF 278 (460)
Q Consensus 217 --------~----------~~~~ryliFDiL~~~G~~l~~~pf~eRl~~L~~~i~~pr~~~~~~l~~~~~~~~~~~~~pf 278 (460)
. +-.+..++||+|++||+++.++|+.+|.++|.+....- .+.. -|
T Consensus 437 lpFQvLSTRkRk~v~v~dikV~Vcvf~FDily~ng~~Li~~pL~eRR~~l~e~f~e~------------~g~f-----~f 499 (714)
T KOG0967|consen 437 LPFQVLSTRKRKNVDVNDIKVKVCVFVFDILYLNGESLIQEPLRERRELLHESFKEI------------PGEF-----QF 499 (714)
T ss_pred CchhhhhhhhccccchhhceEEEEEEEEeeeeeCChhhhhhhHHHHHHHHHhhcccC------------CCce-----eE
Confidence 0 12468899999999999999999999999998754221 0110 00
Q ss_pred EEEeccceechhHHHHHHHhccccCCCCceEEEEc--CCCCCccC-CCCCeEEEccCCC----ceEEEEE
Q 012588 279 RVRRKDFWLLSTVNKLLKEFIPKLSHDADGLVFQG--WDDPYVPR-THEGLLKWKYARM----NSVDFLF 341 (460)
Q Consensus 279 ~I~~K~f~~~~~~~~ll~~~~~~l~h~~DGLIF~p--~~spY~~G-~~~~~LKWKP~~~----nTVDF~l 341 (460)
....+.-++..+++.|+ ..+.+..+|||.+- .++-|.|- |+..|||-|-..+ .|+|.++
T Consensus 500 -at~~~tn~~~eiq~Fl~---~sv~~~cEGlMvKtLd~~atYep~kRs~~WlKlKkDYldgvgdslDLv~ 565 (714)
T KOG0967|consen 500 -ATSLDTNDIDEIQEFLE---ESVQNSCEGLMVKTLDTNATYEPSKRSNNWLKLKKDYLDGVGDSLDLVV 565 (714)
T ss_pred -eeeeccCCHHHHHHHHH---HhhccCcceeEEEeeccccccCchhhccchhhhhhhhhcccccceeeee
Confidence 11222234445555555 36899999999995 45678876 5789999997653 4667765
No 38
>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=99.13 E-value=5.3e-10 Score=114.47 Aligned_cols=147 Identities=17% Similarity=0.132 Sum_probs=98.2
Q ss_pred CceEEEEcCCeeEEEEEEECCEEEEEeCCCccc-cccCcCCcccCCCCccccCCCceeeeeEEEEecCC---CCC-c-ce
Q 012588 147 RYYYATWKADGTRYMMLITIDGCYLIDRCFNFR-RVQMRFPCRNSNEGLGEKTHHFTLLDGEMIIDKLP---DSR-R-QE 220 (460)
Q Consensus 147 ~~Y~V~~K~DG~R~Ll~i~~~~vyLidR~~~~~-~v~~~FP~~~~~~~l~~~~~~~TlLDGElV~d~~~---~~~-~-~~ 220 (460)
..|+|+||.||.|+.++..++++.+++|++.+. .++..+|..... .+. ..+.+.+||||+|.-..+ ... . ..
T Consensus 48 ~~~~vEEKlDG~nvri~~~~G~v~a~TR~G~i~e~~T~~~~eiv~~-~~~-~~~p~~iLdGElvg~~~p~v~~~~~~~~~ 125 (342)
T cd07894 48 GPVAVEEKMNGYNVRIVRIGGKVLAFTRGGFICPFTTDRLRDLIDP-EFF-DDHPDLVLCGEVVGPENPYVPGSYPEVED 125 (342)
T ss_pred CCEEEEEeECCcEEEEEEECCEEEEEeCCCccCccchhhHhhhchH-Hhh-ccCCCEEEEEEEEecCCccccccCccccc
Confidence 589999999999999988888999999997532 235556655221 111 123579999999975422 111 1 25
Q ss_pred eEEEEeeeeecCCccccCCCHHHHHHHHHHHhcCccchhhccccccCCCCccCCCCCeEEEeccceechhHHHHHHHhcc
Q 012588 221 RRYLIYDMMAINQASVIERPFYERWKMLEKEVIEPRNYERHNIYQSRNPYYRYDLEPFRVRRKDFWLLSTVNKLLKEFIP 300 (460)
Q Consensus 221 ~ryliFDiL~~~G~~l~~~pf~eRl~~L~~~i~~pr~~~~~~l~~~~~~~~~~~~~pf~I~~K~f~~~~~~~~ll~~~~~ 300 (460)
+.|++||++..++ ...+|+.+|.++|++... |.. + .+. .....+...+.++++.
T Consensus 126 v~F~vFDI~~~~~--~~~lp~~eR~~lLe~lg~-~~v-----------~-------~~~--~~~~~d~~~l~~~l~~--- 179 (342)
T cd07894 126 VGFFVFDIRKKNT--GRPLPVEERRELLEKYGL-PTV-----------R-------LFG--EFTADEIEELKEIIRE--- 179 (342)
T ss_pred cEEEEEeeEEcCC--CCCCCHHHHHHHHHhcCC-CCc-----------c-------eEE--EEecCCHHHHHHHHHH---
Confidence 7999999999875 667999999999988532 110 0 011 1112223445556654
Q ss_pred ccCCCCceEEEEcCCC-----CCccC
Q 012588 301 KLSHDADGLVFQGWDD-----PYVPR 321 (460)
Q Consensus 301 ~l~h~~DGLIF~p~~s-----pY~~G 321 (460)
...++.||||++..++ .|+..
T Consensus 180 ~~~~G~EGVVlK~~~~~~~~~Ky~t~ 205 (342)
T cd07894 180 LDKEGREGVVLKDPDMRVPPLKYTTS 205 (342)
T ss_pred HHHCCCceEEEeccccccCcceeecC
Confidence 4688999999999887 56654
No 39
>KOG3132 consensus m3G-cap-specific nuclear import receptor (Snurportin1) [RNA processing and modification]
Probab=97.95 E-value=0.00021 Score=68.86 Aligned_cols=155 Identities=19% Similarity=0.224 Sum_probs=106.0
Q ss_pred CceEEEEcCCeeEEEEEEECCEEEEEeCCCccccccCcCCcccCCCCcc-ccCCCceeeeeEEEEecCCCCCcceeEEEE
Q 012588 147 RYYYATWKADGTRYMMLITIDGCYLIDRCFNFRRVQMRFPCRNSNEGLG-EKTHHFTLLDGEMIIDKLPDSRRQERRYLI 225 (460)
Q Consensus 147 ~~Y~V~~K~DG~R~Ll~i~~~~vyLidR~~~~~~v~~~FP~~~~~~~l~-~~~~~~TlLDGElV~d~~~~~~~~~~ryli 225 (460)
.+|+|---.-|-|+|++...+.+....+++. .+ .+||..-...+.. .....-||||--.-- ..-+|+|
T Consensus 116 qdW~vv~~PvGKR~lvVaSrG~Tvay~k~G~--~v-~rF~S~LPGGnrr~~~a~~ytILDCIy~e--------snQTYYV 184 (325)
T KOG3132|consen 116 QDWYVVARPVGKRCLVVASRGTTVAYVKNGS--TV-HRFPSALPGGNRRKGPANSYTILDCIYHE--------SNQTYYV 184 (325)
T ss_pred cceEEEEeecCceEEEEecCCceEEEecCCe--eE-eeccccCCCCCcCCCCcccceeeeeeecc--------cCceEEE
Confidence 4899988999999999888777777788875 22 2566542110111 112356999974321 1237999
Q ss_pred eeeeecCCccccCCCHHHHHHHHHHHhcCccchhhccccccCCCCccCCCCCeEEEeccceechhHHHHHHHhccccCCC
Q 012588 226 YDMMAINQASVIERPFYERWKMLEKEVIEPRNYERHNIYQSRNPYYRYDLEPFRVRRKDFWLLSTVNKLLKEFIPKLSHD 305 (460)
Q Consensus 226 FDiL~~~G~~l~~~pf~eRl~~L~~~i~~pr~~~~~~l~~~~~~~~~~~~~pf~I~~K~f~~~~~~~~ll~~~~~~l~h~ 305 (460)
.|+++++|.++.+++..=|.-.|+.-+.+... . - ... ...+|.....+|++.+.. .|-+.+.-.++..
T Consensus 185 lD~~cWrgh~~yec~~dFRffwl~SKL~E~~~--l---~-~~t-----~~~~f~Fs~vp~~pC~q~-~l~~~~~~~~pf~ 252 (325)
T KOG3132|consen 185 LDMVCWRGHSLYECTSDFRFFWLQSKLAETGA--L---D-PPT-----VYHKFRFSVVPFYPCDQS-GLHSAYTGSLPFV 252 (325)
T ss_pred EEEEeecCcccccCchHHHHHHHhhhcccccc--C---C-CCC-----cCccceecccCCCCCCHH-HHHHHHcCCCcee
Confidence 99999999999999999999999876543211 1 0 011 124566666778887653 2334444578999
Q ss_pred CceEEEEcCCCCCccCCCC
Q 012588 306 ADGLVFQGWDDPYVPRTHE 324 (460)
Q Consensus 306 ~DGLIF~p~~spY~~G~~~ 324 (460)
.|||.|.....-|.||.++
T Consensus 253 ~DGLLFYhks~~yqpgqsp 271 (325)
T KOG3132|consen 253 RDGLLFYHKSVVYQPGQSP 271 (325)
T ss_pred eeeEEEeecceeeCCCCCc
Confidence 9999999999999999874
No 40
>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=97.64 E-value=0.00057 Score=70.60 Aligned_cols=180 Identities=18% Similarity=0.182 Sum_probs=101.2
Q ss_pred CCCCCCccccccccccc-ccccCceEEEEcCCeeEEEEEEECCEEEEEeCCCccccc-cCcCCcccCCCCccccCCCcee
Q 012588 126 MQFPGSHPVSLNSDNLQ-LLRQRYYYATWKADGTRYMMLITIDGCYLIDRCFNFRRV-QMRFPCRNSNEGLGEKTHHFTL 203 (460)
Q Consensus 126 ~~FPGsqPVSl~r~nl~-~l~~~~Y~V~~K~DG~R~Ll~i~~~~vyLidR~~~~~~v-~~~FP~~~~~~~l~~~~~~~Tl 203 (460)
.+||--+-+-+-..-|. .+.....+|+||.||..+-++..++.+++++|.+-+..- +..++...+.+-+ ..+.+.+
T Consensus 57 ~GyP~I~R~~~L~~gi~~~f~~~~v~vEEKlDG~Nvri~~~~g~l~a~tRGgyicp~tt~r~~~~~~~~~~--~d~p~l~ 134 (374)
T TIGR01209 57 RGFPHIKRILLLRPGIKRHFKDPEVVVEEKMNGYNVRIVKYGGNVYALTRGGFICPFTTERLPDLIDLEFF--DDNPDLV 134 (374)
T ss_pred cCCCCcceeeccchhhHHhcCCCcEEEEEeecCceEEEEeECCEEEEEccCcccCCCcHHHHHHHhhHHhh--ccCCCeE
Confidence 67774333222222232 244445999999999999887778899999999853210 1112221111111 1246789
Q ss_pred eeeEEEEecCCCCC------cceeEEEEeeeeecCCccccCCCHHHHHHHHHHHhcCccchhhccccccCCCCccCCCCC
Q 012588 204 LDGEMIIDKLPDSR------RQERRYLIYDMMAINQASVIERPFYERWKMLEKEVIEPRNYERHNIYQSRNPYYRYDLEP 277 (460)
Q Consensus 204 LDGElV~d~~~~~~------~~~~ryliFDiL~~~G~~l~~~pf~eRl~~L~~~i~~pr~~~~~~l~~~~~~~~~~~~~p 277 (460)
|=|||+--..+-.. .....|++|||. +...-.-+|..+|.+++++.-+.+- ..
T Consensus 135 LcGE~iGpenpY~~hs~~y~~l~~~FfvFDI~--d~~t~~~L~~~er~~l~e~yglp~V-------------------pv 193 (374)
T TIGR01209 135 LCGEMAGPENPYTPEYYPEVKEDLGFFLFDIR--EGKTNRSLPVEERLELAEKYGLPHV-------------------EI 193 (374)
T ss_pred EEEEEcCCCCCCcccCccccCCCceEEEEEEE--ECCCCccCCHHHHHHHHHHCCCCcc-------------------ce
Confidence 99999953222111 113479999997 4445677899999999887432110 01
Q ss_pred eEEEeccceechhHHHHHHHhcccc-CCCCceEEEEcCCCCCccCCCCCeEEEccCCCceEEE
Q 012588 278 FRVRRKDFWLLSTVNKLLKEFIPKL-SHDADGLVFQGWDDPYVPRTHEGLLKWKYARMNSVDF 339 (460)
Q Consensus 278 f~I~~K~f~~~~~~~~ll~~~~~~l-~h~~DGLIF~p~~spY~~G~~~~~LKWKP~~~nTVDF 339 (460)
|.. ++...+..-+.+++..| .++-||+|+|+.+.- ...+|.--++.|--|.
T Consensus 194 lg~-----~~~~~~~~~~~eii~~L~~~gREGVVlK~~~~~------~~~~KYtT~~~n~~Di 245 (374)
T TIGR01209 194 LGV-----YTADEAVEEIYEIIERLNKEGREGVVMKDPEMR------VKPLKYTTSYANINDI 245 (374)
T ss_pred eeE-----EcHHHHHHHHHHHHHHhhhcCcceEEEcCcccc------CCcceeecCccChHHH
Confidence 111 33333331122333444 478999999975431 2455555555444444
No 41
>COG1423 ATP-dependent DNA ligase, homolog of eukaryotic ligase III [DNA replication, recombination, and repair]
Probab=96.56 E-value=0.038 Score=56.35 Aligned_cols=142 Identities=18% Similarity=0.178 Sum_probs=88.3
Q ss_pred cCceEEEEcCCeeEEEEEEECCEEEEEeCCCccccc-cCcCCcccCCCCccccCCCceeeeeEEEEecCCCC-----Ccc
Q 012588 146 QRYYYATWKADGTRYMMLITIDGCYLIDRCFNFRRV-QMRFPCRNSNEGLGEKTHHFTLLDGEMIIDKLPDS-----RRQ 219 (460)
Q Consensus 146 ~~~Y~V~~K~DG~R~Ll~i~~~~vyLidR~~~~~~v-~~~FP~~~~~~~l~~~~~~~TlLDGElV~d~~~~~-----~~~ 219 (460)
....+|+||.||.-.=++..++.+|.++|.+-+..- +-+-|..-+.+=+ ..+.+++|=||||--..|=. ...
T Consensus 87 ~~~v~VEEKmnGYNVRV~k~~g~vyAiTRgG~ICPfTT~r~~~l~~~eff--~d~p~lvlcgEmvG~enPYv~~~~y~~e 164 (382)
T COG1423 87 RGKVVVEEKMNGYNVRVVKLGGEVYAITRGGLICPFTTERLRDLIDLEFF--DDYPDLVLCGEMVGPENPYVPGPYYEKE 164 (382)
T ss_pred CCcEEEEEeccCceEEEEEECCEEEEEecCceecCchhHHHHhhcchhhH--hhCCCcEEEEEeccCCCCCCCCCCCccC
Confidence 568999999999988888888999999999864311 1111211111111 22578999999997433211 123
Q ss_pred eeEEEEeeeeecCCccccCCCHHHHHHHHHHHhcCccchhhccccccCCCCccCCCCCeEEEeccceechhH-HHHHHHh
Q 012588 220 ERRYLIYDMMAINQASVIERPFYERWKMLEKEVIEPRNYERHNIYQSRNPYYRYDLEPFRVRRKDFWLLSTV-NKLLKEF 298 (460)
Q Consensus 220 ~~ryliFDiL~~~G~~l~~~pf~eRl~~L~~~i~~pr~~~~~~l~~~~~~~~~~~~~pf~I~~K~f~~~~~~-~~ll~~~ 298 (460)
.+-|.+||+--.+. =..+|..+|++++++.-+. . -+.|. -++++.+ +++. .+
T Consensus 165 ~v~fFvFDire~~t--gr~Lp~eer~~l~ekYgl~-~------------------V~~fg-----~~~~~e~~eei~-eI 217 (382)
T COG1423 165 DVGFFVFDIREKNT--GRPLPVEERLELAEKYGLP-H------------------VEIFG-----EFPADEAGEEIY-EI 217 (382)
T ss_pred CceEEEEEEEecCC--CCCCCHHHHHHHHHHcCCC-c------------------eEEee-----eechhHhHHHHH-HH
Confidence 46899999987552 3567889999999885432 1 01222 2234333 2222 23
Q ss_pred cccc-CCCCceEEEEcCCC
Q 012588 299 IPKL-SHDADGLVFQGWDD 316 (460)
Q Consensus 299 ~~~l-~h~~DGLIF~p~~s 316 (460)
+..| ..+-+|+|++..+.
T Consensus 218 ve~L~keGREGVV~Kdpdm 236 (382)
T COG1423 218 VERLNKEGREGVVMKDPDM 236 (382)
T ss_pred HHHHhhcCCcceEecCccc
Confidence 3344 46899999997553
No 42
>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=95.41 E-value=0.3 Score=49.97 Aligned_cols=159 Identities=16% Similarity=0.144 Sum_probs=84.3
Q ss_pred ceEEEEcCCeeEEEEEEECCE-EEEEeCCCccc--cccCcCCcccC-CCCccccC-CCceeeeeEEEEecC---------
Q 012588 148 YYYATWKADGTRYMMLITIDG-CYLIDRCFNFR--RVQMRFPCRNS-NEGLGEKT-HHFTLLDGEMIIDKL--------- 213 (460)
Q Consensus 148 ~Y~V~~K~DG~R~Ll~i~~~~-vyLidR~~~~~--~v~~~FP~~~~-~~~l~~~~-~~~TlLDGElV~d~~--------- 213 (460)
.|+|++|.||.-+-|...++. +..++|.+-.. .++.......+ +..+ .. .....+=||+++.+.
T Consensus 108 ~~~~e~KiDGlsi~L~Y~~G~L~~a~TRGdG~~GeDvT~n~~~i~~iP~~i--~~~p~~~eVRGEv~m~~~~F~~ln~~~ 185 (315)
T PF01653_consen 108 EFVVEPKIDGLSISLIYENGKLVRAATRGDGEVGEDVTHNVRTIKSIPLRI--PEKPGRLEVRGEVYMSKSDFEKLNEER 185 (315)
T ss_dssp EEEEEEEESSEEEEEEEETTEEEEEEEETTSSEEEB-HHHHCTSTTS-SB---SSSSSEEEEEEEEE--HHHHHHHHHHH
T ss_pred ceeEeeccceeEEEEEEeCCEEEEEEEcCCCccchhHHHHHHHHhcCchhh--ccCCcceEEEEEEEEehhhHHHHHHHH
Confidence 799999999999988777665 57899975421 22211111111 0111 11 245678899997531
Q ss_pred ---CCC---------------------CcceeEEEEeeeeecCCccccCCCHHHHHHHHHHHhcCccchhhccccccCCC
Q 012588 214 ---PDS---------------------RRQERRYLIYDMMAINQASVIERPFYERWKMLEKEVIEPRNYERHNIYQSRNP 269 (460)
Q Consensus 214 ---~~~---------------------~~~~~ryliFDiL~~~G~~l~~~pf~eRl~~L~~~i~~pr~~~~~~l~~~~~~ 269 (460)
+.. ....+.|++|++...+| +..-....++++.|+++-+.. .+
T Consensus 186 ~~~~~~~faNpRN~aAGsLr~~d~~~~~~r~L~f~~y~~~~~~~-~~~~~t~~e~l~~L~~~GF~v------------~~ 252 (315)
T PF01653_consen 186 EEEGEKPFANPRNAAAGSLRQKDPSITAERKLSFFAYGIGEPEG-DLGFNTQSERLQFLKEWGFPV------------NP 252 (315)
T ss_dssp HHTTS---SSHHHHHHHHHTSSSHHHHHTS--EEEEEEEEEETT-STT-SBHHHHHHHHHHTT--B-------------T
T ss_pred HHhccchhhhhhHHHHHhhhhccchhhhcCeeEEEEEEeccccc-ccChHHHHHHHHHHHHcCCCC------------Cc
Confidence 000 02468999999999988 333345678888888743321 01
Q ss_pred CccCCCCCeEEEeccceechhHHHHHHHh---ccccCCCCceEEEEcCCCCCcc--C----CCCCeEEEccC
Q 012588 270 YYRYDLEPFRVRRKDFWLLSTVNKLLKEF---IPKLSHDADGLVFQGWDDPYVP--R----THEGLLKWKYA 332 (460)
Q Consensus 270 ~~~~~~~pf~I~~K~f~~~~~~~~ll~~~---~~~l~h~~DGLIF~p~~spY~~--G----~~~~~LKWKP~ 332 (460)
. +.. +-....+..+.+.+ ...+.++.||||++-.+..+.- | ....-+=||+|
T Consensus 253 ~---------~~~--~~~~~~v~~~~~~~~~~R~~l~y~iDGiVikvn~~~~~~~LG~t~~~PrwAiAyKfp 313 (315)
T PF01653_consen 253 Y---------IRF--CKSIEEVEEYIEEWEERREELPYPIDGIVIKVNDLALQERLGYTSKHPRWAIAYKFP 313 (315)
T ss_dssp T---------EEE--ESSHHHHHHHHHHHHHHGCCSSS-EEEEEEEESBHHHHHHH-BESSSBSSEEEEE--
T ss_pred c---------eEe--cCCHHHHHHHHHHHHhhhhccccccCcEEEEecCHHHHHhcCCcCCCCCeEEEECcC
Confidence 0 111 11222333344333 3578999999999976544332 3 23345555554
No 43
>KOG3673 consensus FtsJ-like RNA methyltransferase [RNA processing and modification]
Probab=93.69 E-value=0.25 Score=53.19 Aligned_cols=96 Identities=22% Similarity=0.267 Sum_probs=59.7
Q ss_pred CCceeeeeEEEEecCCCCCc--ceeEEEEeeeeecCCccccCCCHHHHHHHHHHHhcCccchhhccccccCCCCccCCCC
Q 012588 199 HHFTLLDGEMIIDKLPDSRR--QERRYLIYDMMAINQASVIERPFYERWKMLEKEVIEPRNYERHNIYQSRNPYYRYDLE 276 (460)
Q Consensus 199 ~~~TlLDGElV~d~~~~~~~--~~~ryliFDiL~~~G~~l~~~pf~eRl~~L~~~i~~pr~~~~~~l~~~~~~~~~~~~~ 276 (460)
+.+|+|=-++|-.-.+.++. ..-...|.|.++++|.+|.++||.+|..+.++.+..-. .|. +..+.
T Consensus 634 Pr~t~l~v~iv~E~~GeGk~~~~~~avhIiD~~vL~G~Dvr~~py~eR~~~aeKFv~al~-----------kp~-Rkd~~ 701 (845)
T KOG3673|consen 634 PRNTILLVDIVEEVVGEGKISSEPQAVHIIDAAVLFGDDVRNLPYEERMKAAEKFVAALK-----------KPN-RKDKK 701 (845)
T ss_pred ccceeehHHHHHHHhcCccccccchheeeeeeeeecCchhhcccHHHHHHHHHHHHHHhc-----------CCC-Ccccc
Confidence 45677754555433332221 23467899999999999999999999999999774210 110 11111
Q ss_pred CeEEEeccceechhHHHHHHHhc-cccCCCC
Q 012588 277 PFRVRRKDFWLLSTVNKLLKEFI-PKLSHDA 306 (460)
Q Consensus 277 pf~I~~K~f~~~~~~~~ll~~~~-~~l~h~~ 306 (460)
.=.++.|+-|.+....++|.++. ..++|..
T Consensus 702 ~~a~r~Kp~yrL~em~~ff~nlehy~lk~ns 732 (845)
T KOG3673|consen 702 HRAERIKPTYRLAEMDEFFSNLEHYKLKHNS 732 (845)
T ss_pred ccceecccceeHHHHHHHHHhhhhhhhcCCc
Confidence 12378888888888777775432 1344443
No 44
>smart00532 LIGANc Ligase N family.
Probab=93.48 E-value=3 Score=44.70 Aligned_cols=165 Identities=16% Similarity=0.114 Sum_probs=89.9
Q ss_pred CceEEEEcCCeeEEEEEEECCE-EEEEeCCCccc--cccCcCCcccC-CCCccccCCCceeeeeEEEEecCC--------
Q 012588 147 RYYYATWKADGTRYMMLITIDG-CYLIDRCFNFR--RVQMRFPCRNS-NEGLGEKTHHFTLLDGEMIIDKLP-------- 214 (460)
Q Consensus 147 ~~Y~V~~K~DG~R~Ll~i~~~~-vyLidR~~~~~--~v~~~FP~~~~-~~~l~~~~~~~TlLDGElV~d~~~-------- 214 (460)
-.|+|++|.||.=+-|...++. +..++|.+-.. .++..-....+ +..+.........+=||+++.+..
T Consensus 103 ~~~~~epKiDGlsisL~Ye~G~l~~a~TRGDG~~GeDVT~nv~~i~~iP~~i~~~~p~~leiRGEv~~~~~~F~~ln~~~ 182 (441)
T smart00532 103 FAYVVEPKIDGLSVSLLYENGKLVQAATRGDGTVGEDVTQNVKTIRSIPLRLSGDVPERLEVRGEVFMPKEDFLALNEEL 182 (441)
T ss_pred ceEEEEEecccEEEEEEEECCEEEEEEecCCCCcceehhhhhhhhcCcChhhcccCCCeEEEEceEEEEHHHHHHHHHHH
Confidence 3699999999999877777655 68899965321 22211000000 001100011236788999985421
Q ss_pred ---------CC----------------CcceeEEEEeeeeecCCccccCCCHHHHHHHHHHHhcCccchhhccccccCCC
Q 012588 215 ---------DS----------------RRQERRYLIYDMMAINQASVIERPFYERWKMLEKEVIEPRNYERHNIYQSRNP 269 (460)
Q Consensus 215 ---------~~----------------~~~~~ryliFDiL~~~G~~l~~~pf~eRl~~L~~~i~~pr~~~~~~l~~~~~~ 269 (460)
++ ....+.|++|++...++... .....+++..|+++-+.. +
T Consensus 183 ~~~g~~~faNpRN~aAG~lr~ld~~~~~~r~L~~~~y~~~~~~~~~~-~~t~~e~l~~L~~~GF~v------------~- 248 (441)
T smart00532 183 EEEGEKPFANPRNAAAGSLRQLDPRITAKRKLRAFFYGLGTGEELFL-PKTQSEALKWLKELGFPV------------S- 248 (441)
T ss_pred HhcCCCcccChHHHHHHHHHhcCchhhhhccceEEEEEcccCCCCCC-ccCHHHHHHHHHHCCCCC------------C-
Confidence 00 01358999999864433211 235678888888743321 1
Q ss_pred CccCCCCCeEEEeccceechhHHHHHHHh---ccccCCCCceEEEEcCCCCCcc--CC----CCCeEEEccCCCc
Q 012588 270 YYRYDLEPFRVRRKDFWLLSTVNKLLKEF---IPKLSHDADGLVFQGWDDPYVP--RT----HEGLLKWKYARMN 335 (460)
Q Consensus 270 ~~~~~~~pf~I~~K~f~~~~~~~~ll~~~---~~~l~h~~DGLIF~p~~spY~~--G~----~~~~LKWKP~~~n 335 (460)
++....+. +..+....+.+ ...+.+..||||++-.+..+.- |. ...-+=||++...
T Consensus 249 -------~~~~~~~~---~~ei~~~~~~~~~~r~~l~y~iDGiViKvn~~~~~~~lG~ts~~PrwaiA~Kf~~~~ 313 (441)
T smart00532 249 -------PHTRLCKN---ADEVIEYYEEWEEKRAELPYEIDGVVVKVDDLALQRELGFTSKAPRWAIAYKFPAEE 313 (441)
T ss_pred -------CCeEeeCC---HHHHHHHHHHHHHhcccCCCCcCcEEEEecCHHHHHHhCccCCCCCeeEEECCCCce
Confidence 11111121 22333333322 3578899999999986665543 42 3456777877643
No 45
>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=93.47 E-value=2.7 Score=42.88 Aligned_cols=160 Identities=16% Similarity=0.106 Sum_probs=87.4
Q ss_pred CceEEEEcCCeeEEEEEEECCE-EEEEeCCCccc--cccCcCCcccC-CCCccccCCCceeeeeEEEEecCC--------
Q 012588 147 RYYYATWKADGTRYMMLITIDG-CYLIDRCFNFR--RVQMRFPCRNS-NEGLGEKTHHFTLLDGEMIIDKLP-------- 214 (460)
Q Consensus 147 ~~Y~V~~K~DG~R~Ll~i~~~~-vyLidR~~~~~--~v~~~FP~~~~-~~~l~~~~~~~TlLDGElV~d~~~-------- 214 (460)
..|+|++|.||.=+-|...++. +..++|.+-.. .|+..-....+ +..+.. ......+=||+++.+..
T Consensus 101 ~~~~vepKiDGlsisL~Y~~G~L~~a~TRGdG~~GeDVT~nv~~I~~IP~~i~~-~~~~levRGEv~m~~~~F~~~n~~~ 179 (307)
T cd00114 101 PAYVVEPKIDGLSISLRYENGVLVQAATRGDGTTGEDVTENVRTIRSIPLTLAG-APETLEVRGEVFMPKADFEALNKER 179 (307)
T ss_pred CcEEEEEeccceEEEEEEECCEEEEEEecCCCcchhhHHhhHhhhcccChhhcC-CCCeEEEEEEEEEEHHHHHHHHHHH
Confidence 3799999999999877776554 57899965321 22211100000 011100 02346788999985310
Q ss_pred ---------CC----------------CcceeEEEEeeeeecCCccccCCCHHHHHHHHHHHhcCccchhhccccccCCC
Q 012588 215 ---------DS----------------RRQERRYLIYDMMAINQASVIERPFYERWKMLEKEVIEPRNYERHNIYQSRNP 269 (460)
Q Consensus 215 ---------~~----------------~~~~~ryliFDiL~~~G~~l~~~pf~eRl~~L~~~i~~pr~~~~~~l~~~~~~ 269 (460)
++ ....+.|++|++...++. ......+++..|+++-+.. ++
T Consensus 180 ~~~~~~~faNpRNaaAGsLr~ld~~~~~~r~L~f~~y~~~~~~~~--~~~t~~e~l~~L~~~GF~v------------~~ 245 (307)
T cd00114 180 EERGEKPFANPRNAAAGSLRQLDPKITAKRPLRFFIYGLGEAEGL--GPKTQSEALAFLKEWGFPV------------SP 245 (307)
T ss_pred HHcCCCCccChHHHHHHHHHhcCcchhhcCcceEEEEecccccCC--CCCCHHHHHHHHHHCCCCC------------CC
Confidence 00 024578999998644321 2246788888888744321 11
Q ss_pred CccCCCCCeEEEeccceechhHHHHHHHh---ccccCCCCceEEEEcCCCCCc--cC----CCCCeEEEccC
Q 012588 270 YYRYDLEPFRVRRKDFWLLSTVNKLLKEF---IPKLSHDADGLVFQGWDDPYV--PR----THEGLLKWKYA 332 (460)
Q Consensus 270 ~~~~~~~pf~I~~K~f~~~~~~~~ll~~~---~~~l~h~~DGLIF~p~~spY~--~G----~~~~~LKWKP~ 332 (460)
. ....+ .+..+.+..+.+ ...+.+..||||++-.+.++. -| ....-+=||+|
T Consensus 246 ~--------~~~~~---~~~ev~~~~~~~~~~R~~l~y~iDGiViKvn~~~~~~~lG~tsk~PrWaiA~Kf~ 306 (307)
T cd00114 246 E--------TRLCK---NIEEVLAFYDEIEAKRDSLPYEIDGVVVKVDDLALQRELGFTSKAPRWAIAYKFP 306 (307)
T ss_pred C--------eEEeC---CHHHHHHHHHHHHHhhhcCCCCCCcEEEEEeCHHHHHHhCccCCCCCceEEeCCC
Confidence 1 11111 233334443333 457889999999997655442 22 22345666654
No 46
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=92.53 E-value=5.7 Score=44.79 Aligned_cols=164 Identities=15% Similarity=0.178 Sum_probs=89.1
Q ss_pred ceEEEEcCCeeEEEEEEECCE-EEEEeCCCccc--cccC---cCCcccCCCCccccCCCceeeeeEEEEecCC-------
Q 012588 148 YYYATWKADGTRYMMLITIDG-CYLIDRCFNFR--RVQM---RFPCRNSNEGLGEKTHHFTLLDGEMIIDKLP------- 214 (460)
Q Consensus 148 ~Y~V~~K~DG~R~Ll~i~~~~-vyLidR~~~~~--~v~~---~FP~~~~~~~l~~~~~~~TlLDGElV~d~~~------- 214 (460)
.|+|++|.||.=+-|...++. +..++|.+-.. .++. ..+.. +..+.........+=||+++.+..
T Consensus 109 ~~~~epKiDGlsisL~Y~~G~L~~a~TRGDG~~GeDvT~n~~~I~~I--P~~l~~~~p~~levRGEv~m~~~~F~~lN~~ 186 (665)
T PRK07956 109 TYLCELKIDGLAVSLLYENGVLVRAATRGDGTTGEDITANVRTIRSI--PLRLHGNEPERLEVRGEVFMPKADFEALNEE 186 (665)
T ss_pred ceEEEEecccEEEEEEEECCEEEEEEecCCCccchhHhhhhhhhccC--ChhhcccCCCeEEEEEEEEEEHHHHHHHHHH
Confidence 599999999999877776554 57899965321 1211 11110 001100012236789999985321
Q ss_pred -----C-----C----------------CcceeEEEEeeeeecCCccccCCCHHHHHHHHHHHhcCccchhhccccccCC
Q 012588 215 -----D-----S----------------RRQERRYLIYDMMAINQASVIERPFYERWKMLEKEVIEPRNYERHNIYQSRN 268 (460)
Q Consensus 215 -----~-----~----------------~~~~~ryliFDiL~~~G~~l~~~pf~eRl~~L~~~i~~pr~~~~~~l~~~~~ 268 (460)
+ + ....+.|++|++...++ ........+++..|+++-+.. +
T Consensus 187 ~~~~g~~~faNpRNaaAGslr~ld~~~~~~r~L~f~~y~~~~~~~-~~~~~t~~e~l~~L~~~GF~v------------~ 253 (665)
T PRK07956 187 RREEGEKPFANPRNAAAGSLRQLDPKITAKRPLSFFAYGVGEVEG-GELPDSQSEALEFLKAWGFPV------------N 253 (665)
T ss_pred HHhcCCCcccChHHHHhhhhhccChHHHhcCCCEEEEEecccccC-CCCCCCHHHHHHHHHHCCCCc------------C
Confidence 0 0 02358899999864331 111235678888887743321 1
Q ss_pred CCccCCCCCeEEEeccceechhHHHHHHHh---ccccCCCCceEEEEcCCCC------CccCCCCCeEEEccCCCceE
Q 012588 269 PYYRYDLEPFRVRRKDFWLLSTVNKLLKEF---IPKLSHDADGLVFQGWDDP------YVPRTHEGLLKWKYARMNSV 337 (460)
Q Consensus 269 ~~~~~~~~pf~I~~K~f~~~~~~~~ll~~~---~~~l~h~~DGLIF~p~~sp------Y~~G~~~~~LKWKP~~~nTV 337 (460)
++..... .+..+.+.++.+ ...++++.||||++-.+.. |..+....-+=||+|...-.
T Consensus 254 --------~~~~~~~---~~~ei~~~~~~~~~~R~~l~y~iDGiViKvn~~~~~~~lG~t~~~PrWaiA~Kf~~~~~~ 320 (665)
T PRK07956 254 --------PYRKLCT---SIEEVLAFYEEIEEERHDLPYDIDGVVIKVDDLALQEELGFTAKAPRWAIAYKFPAEEAT 320 (665)
T ss_pred --------CceEeeC---CHHHHHHHHHHHHHhhccCCCCCCcEEEEecCHHHHHhcCccCCCCCceeEecCCCceeE
Confidence 1111111 223333333333 3678899999999875532 33333456677777765433
No 47
>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=92.32 E-value=0.082 Score=49.28 Aligned_cols=103 Identities=17% Similarity=0.226 Sum_probs=54.3
Q ss_pred CceEEEEcCCeeEEEEEEECC-EEEEEeCCCccccccCcCCccc-----------CC------CCcc-ccCCCceeeeeE
Q 012588 147 RYYYATWKADGTRYMMLITID-GCYLIDRCFNFRRVQMRFPCRN-----------SN------EGLG-EKTHHFTLLDGE 207 (460)
Q Consensus 147 ~~Y~V~~K~DG~R~Ll~i~~~-~vyLidR~~~~~~v~~~FP~~~-----------~~------~~l~-~~~~~~TlLDGE 207 (460)
++|+|+||.||+-+-+++..+ .+.+-.|+..+. ....|.... .. ..+. .....+.+|=||
T Consensus 1 ~e~vvtEKldGtn~~i~~~~~~~~~~~~R~~~l~-~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~GE 79 (186)
T PF09414_consen 1 REVVVTEKLDGTNFSIYFDNDGRVRFQSRSHILD-PNEDFFGYQSGDNRYWAQARWLFELLKLAELASELLPENIIIYGE 79 (186)
T ss_dssp SEEEEEEE-SSEEEEEEEEECTCEEEEETTEE---TT---TTCHHHHHHCHHHHHHHHHHHHHHCCEC----SEEEEEEE
T ss_pred CeEEEEEEeCCccEEEEEeCCCceeEeccccccC-ccccccccccchHHHHHHHHHHHhhhhhhhhcccccceEEEEEEE
Confidence 368999999999998888655 477777876321 111111000 00 0000 012245566699
Q ss_pred EEE--ecCCCCCc--c-eeEEEEeeeeecCCc-cccCCCHHHHHHHHHH
Q 012588 208 MII--DKLPDSRR--Q-ERRYLIYDMMAINQA-SVIERPFYERWKMLEK 250 (460)
Q Consensus 208 lV~--d~~~~~~~--~-~~ryliFDiL~~~G~-~l~~~pf~eRl~~L~~ 250 (460)
++- ........ . ...|++|||...+.. ...-+++.+...+++.
T Consensus 80 ~~G~~~~Iq~~~~~~~~~~~F~~Fdi~~~~~~~~~~~l~~~~~~~~~~~ 128 (186)
T PF09414_consen 80 LVGAKPSIQKNRYQLDPPKDFYVFDIYDIDEQGEIRYLSWDEVREFAEE 128 (186)
T ss_dssp EECEECTTCSS----ECCCEEEEEEEEEEETCCGEEE-HHHHHHHHHCC
T ss_pred eeeecccccccccccCCCceEEEEEEEEcCCCCeeEECCHHHHHHHHHH
Confidence 997 33222211 1 578999999999533 3344556666655544
No 48
>PF05098 LEF-4: Late expression factor 4 (LEF-4); InterPro: IPR007790 The baculovirus Autographa californica nuclear polyhedrosis virus (AcMNPV) virus encodes a DNA-dependent RNA polymerase that is required for transcription of viral late genes. This polymerase is composed of four equimolar subunits, LEF-8, LEF-4, LEF-9, and p47. LEF-4 carries out all the enzymatic functions related to mRNA capping []. ; GO: 0006355 regulation of transcription, DNA-dependent
Probab=92.31 E-value=4.8 Score=42.91 Aligned_cols=207 Identities=16% Similarity=0.223 Sum_probs=109.9
Q ss_pred ccCceEEEEcCCeeEEEEEEECCEEEEEeCCCccccccCcCCcccCCCCccccCCCceeeeeEEEEecCCCCCcceeEEE
Q 012588 145 RQRYYYATWKADGTRYMMLITIDGCYLIDRCFNFRRVQMRFPCRNSNEGLGEKTHHFTLLDGEMIIDKLPDSRRQERRYL 224 (460)
Q Consensus 145 ~~~~Y~V~~K~DG~R~Ll~i~~~~vyLidR~~~~~~v~~~FP~~~~~~~l~~~~~~~TlLDGElV~d~~~~~~~~~~ryl 224 (460)
...-++..-|.||+|.=-++..+.+|+.-=++.++...+. |.+ + ....-+-|=-|+|-+ -+|+
T Consensus 232 ~~dv~~WAlKLDGvRGkG~~~~~~~~i~~DDMq~fsg~l~-~~~-----f--~~Nnvv~fQcE~i~~---------~~~Y 294 (450)
T PF05098_consen 232 NSDVKKWALKLDGVRGKGYFTNGFIIIQMDDMQMFSGKLD-PSP-----F--SLNNVVAFQCELIDD---------ETFY 294 (450)
T ss_pred ccceeEEEEeecccceeeEEeccEEEEEEchhhhhhcccc-cch-----h--hcccEEEEEEEEecC---------ceEE
Confidence 3456789999999999888887877776656654433220 111 0 001224556666643 2577
Q ss_pred Eeeeeec-----CCccccCC---CH----HHHHHHHHHHhcCccchhhccccccCCCCccCCCCCeEEEeccceechhHH
Q 012588 225 IYDMMAI-----NQASVIER---PF----YERWKMLEKEVIEPRNYERHNIYQSRNPYYRYDLEPFRVRRKDFWLLSTVN 292 (460)
Q Consensus 225 iFDiL~~-----~G~~l~~~---pf----~eRl~~L~~~i~~pr~~~~~~l~~~~~~~~~~~~~pf~I~~K~f~~~~~~~ 292 (460)
|=|+|.+ |.+..-++ |+ ..=+.+|... -. ....+ .-+ ......+.|+.-.|++..-..
T Consensus 295 ITDlL~VfkY~YnNrtQYe~s~~~Y~id~~~Ai~~ln~l-~~-~~~~~------~l~--~~~~~~~~vkFQ~F~~~p~~~ 364 (450)
T PF05098_consen 295 ITDLLHVFKYKYNNRTQYECSLDPYNIDPLDAIECLNYL-NN-ANKKI------TLK--TNTNKTISVKFQQFFDPPLNV 364 (450)
T ss_pred EeeeeeeEEEeccCcceeEeccCccccCHHHHHHHHHHh-hc-cccce------EEe--ccCCceEEEEEEeecCCcccc
Confidence 7787765 22221111 22 2333444421 00 00000 000 112345778877777642110
Q ss_pred HHHHHhccccCCCCceEEEEcCCCCCccCCCCCeEEEccCCCceEEEEEEEecCCceeEEEEeCCceeeecCceeEecCC
Q 012588 293 KLLKEFIPKLSHDADGLVFQGWDDPYVPRTHEGLLKWKYARMNSVDFLFEVTDDDRQLLYVFERGKKKLMEGSSVEFTDR 372 (460)
Q Consensus 293 ~ll~~~~~~l~h~~DGLIF~p~~spY~~G~~~~~LKWKP~~~nTVDF~l~~~~~~~~~L~v~~~g~~~~~~~~~~~f~~~ 372 (460)
. -.-.-++||.|.--.+. ...|.|. .-|+...-.. ....|....|. +....+. .
T Consensus 365 ---~---~y~t~ptDGfVvld~~~--------~yvKyK~--~kT~EleYd~----~~~~F~~~~G~---~~~~~i~---~ 418 (450)
T PF05098_consen 365 ---N---GYSTVPTDGFVVLDSNG--------RYVKYKY--VKTVELEYDA----GNNTFKSLFGP---LKNYEIV---S 418 (450)
T ss_pred ---C---CcccCCcCCEEEECCCC--------CEEEEee--cceEEEEEEc----CCCeEEcCCCc---cccceec---c
Confidence 0 01234799998765443 4556663 4576665522 11233332232 1111111 2
Q ss_pred CCCCCCceEEEEEEeCCCCeeEEEEEecCCCCCC
Q 012588 373 EPSFYSGKIIECTWDPDVQLWKCMRIRTDKSTPN 406 (460)
Q Consensus 373 ~~~~~dg~IvEC~~d~~~~~W~f~R~R~DK~~pN 406 (460)
+.....|+|-||.... ..=..++.|.|+-.||
T Consensus 419 ~~~l~~~~IYE~vi~d--~~i~ViK~RpDRlvpn 450 (450)
T PF05098_consen 419 DVQLEHGSIYECVITD--NVINVIKERPDRLVPN 450 (450)
T ss_pred ccCccCCCEEEEEEEC--CEEEEEeeCCccCCCC
Confidence 3335789999999974 6679999999999998
No 49
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=90.98 E-value=13 Score=42.16 Aligned_cols=167 Identities=14% Similarity=0.108 Sum_probs=89.1
Q ss_pred CceEEEEcCCeeEEEEEEECCE-EEEEeCCCccc--cccCcCCcccC-CCCccccCCCceeeeeEEEEecC---------
Q 012588 147 RYYYATWKADGTRYMMLITIDG-CYLIDRCFNFR--RVQMRFPCRNS-NEGLGEKTHHFTLLDGEMIIDKL--------- 213 (460)
Q Consensus 147 ~~Y~V~~K~DG~R~Ll~i~~~~-vyLidR~~~~~--~v~~~FP~~~~-~~~l~~~~~~~TlLDGElV~d~~--------- 213 (460)
..|++++|.||+=+.|.+.++. +..++|.+-.. .++..-....+ +..+.........+=||+++.+.
T Consensus 132 ~~~~~epKiDGlaisL~Ye~G~L~~a~TRGDG~~GeDVT~nv~~I~~IP~~l~~~~p~~levRGEv~m~~~~F~~lN~~~ 211 (689)
T PRK14351 132 VEYVCEPKFDGLSVEVVYEDGEYQRAATRGDGREGDDVTANVRTIRSVPQKLRGDYPDFLAVRGEVYMPKDAFQAYNRER 211 (689)
T ss_pred ceEEEEEecccEEEEEEEECCEEEEEEecCCCCcceeHhhhhhhhcccchhhcccCCCeEEEEEEEEEEHHHHHHHHHHH
Confidence 3699999999999887777554 57899965321 12210000000 00010001122457799998532
Q ss_pred ---CC-----C----------------CcceeEEEEeeeeecCCccccCCCHHHHHHHHHHHhcCccchhhccccccCCC
Q 012588 214 ---PD-----S----------------RRQERRYLIYDMMAINQASVIERPFYERWKMLEKEVIEPRNYERHNIYQSRNP 269 (460)
Q Consensus 214 ---~~-----~----------------~~~~~ryliFDiL~~~G~~l~~~pf~eRl~~L~~~i~~pr~~~~~~l~~~~~~ 269 (460)
+. + ....+.|++|++...++. .....++++.|.++-+.- .+
T Consensus 212 ~~~g~~~faNpRN~aAGslR~ldp~~~~~r~L~f~~y~~~~~~~~---~~t~~e~l~~L~~~GF~v------------~~ 276 (689)
T PRK14351 212 IERGEEPFANPRNAAAGTLRQLDPSVVAERPLDIFFFDVLDASEL---FDSHWEELERFPEWGLRV------------TD 276 (689)
T ss_pred HHcCCCCcCCHHHHHhhHhhccChHHHhcCCceEEEEecccCCCC---CCCHHHHHHHHHHCCCCc------------CC
Confidence 10 0 013589999998654431 235677888887643321 11
Q ss_pred CccCCCCCeEEEeccceechhHHHHHHHh---ccccCCCCceEEEEcCCCCC------ccCCCCCeEEEccCCCceEEE
Q 012588 270 YYRYDLEPFRVRRKDFWLLSTVNKLLKEF---IPKLSHDADGLVFQGWDDPY------VPRTHEGLLKWKYARMNSVDF 339 (460)
Q Consensus 270 ~~~~~~~pf~I~~K~f~~~~~~~~ll~~~---~~~l~h~~DGLIF~p~~spY------~~G~~~~~LKWKP~~~nTVDF 339 (460)
....... +..+.+..+.+ ...++++.||||++-.+..+ ..+....-+=||++...-.--
T Consensus 277 --------~~~~~~~---~~~~~~~~~~~~~~R~~l~y~iDGiViKvn~~~~q~~lG~ts~~PrWaiA~Kf~~~~~~T~ 344 (689)
T PRK14351 277 --------RTERVDD---IDDAIAYRDRLLAARDDLNYEIDGVVIKVDDRDAREELGATARAPRWAFAYKFPARAEETT 344 (689)
T ss_pred --------ceEeeCC---HHHHHHHHHHHHHhhhcCCCCCceEEEEeCCHHHHHHhCccCCCCCceEEEcCCCceeEEE
Confidence 0011111 22222222222 35789999999999765543 333344667778776543333
No 50
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=90.40 E-value=12 Score=42.38 Aligned_cols=167 Identities=14% Similarity=0.078 Sum_probs=87.3
Q ss_pred CceEEEEcCCeeEEEEEEECCE-EEEEeCCCccc--cccCcCCcccC-CCCccccCCCceeeeeEEEEecC---------
Q 012588 147 RYYYATWKADGTRYMMLITIDG-CYLIDRCFNFR--RVQMRFPCRNS-NEGLGEKTHHFTLLDGEMIIDKL--------- 213 (460)
Q Consensus 147 ~~Y~V~~K~DG~R~Ll~i~~~~-vyLidR~~~~~--~v~~~FP~~~~-~~~l~~~~~~~TlLDGElV~d~~--------- 213 (460)
..|+|++|.||.=+-|...++. +..++|.+-.. .++...-...+ +..+. ......+=||+++.+.
T Consensus 110 ~~~~~epKiDGlaisL~YenG~L~~a~TRGDG~~GEDVT~n~~~I~~IP~~l~--~~~~levRGEv~m~~~~F~~lN~~~ 187 (669)
T PRK14350 110 FGISVEPKIDGCSIVLYYKDGILEKALTRGDGRFGNDVTENVRTIRNVPLFID--EKVELVLRGEIYITKENFLKINKTL 187 (669)
T ss_pred ceEEEEEecccEEEEEEEECCEEEEEEecCCCCcchhHhhhhhhhcccchhcC--CCceEEEEEEEEeeHHHHHHHHHhh
Confidence 3699999999999877776554 57899965321 22210000000 00110 0123678899998531
Q ss_pred ------CCC--------------CcceeEEEEeeeeecCCccccCCCHHHHHHHHHHHhcCccchhhccccccCCCCccC
Q 012588 214 ------PDS--------------RRQERRYLIYDMMAINQASVIERPFYERWKMLEKEVIEPRNYERHNIYQSRNPYYRY 273 (460)
Q Consensus 214 ------~~~--------------~~~~~ryliFDiL~~~G~~l~~~pf~eRl~~L~~~i~~pr~~~~~~l~~~~~~~~~~ 273 (460)
+.+ ....+.|++|++...++ ......++++.|+++-+... +
T Consensus 188 ~~~faNpRNaaAGsLr~~d~~~~a~r~L~f~~y~~~~~~~---~~~t~~e~l~~L~~~GF~v~------------~---- 248 (669)
T PRK14350 188 EKPYTNARNLASGILRRIDSREVANFPLDIFVYDILYSSL---ELKTNHDAFDKLKKFGFKVN------------P---- 248 (669)
T ss_pred hccCCChhHHHHHHHHccCchhhhcCceEEEEEEcccCCC---CCCCHHHHHHHHHHCCCCCC------------c----
Confidence 100 01367999999843221 11356788888877443211 1
Q ss_pred CCCCeEEEeccceechhHHHHHH---HhccccCCCCceEEEEcCCCC------CccCCCCCeEEEccCCCceEE
Q 012588 274 DLEPFRVRRKDFWLLSTVNKLLK---EFIPKLSHDADGLVFQGWDDP------YVPRTHEGLLKWKYARMNSVD 338 (460)
Q Consensus 274 ~~~pf~I~~K~f~~~~~~~~ll~---~~~~~l~h~~DGLIF~p~~sp------Y~~G~~~~~LKWKP~~~nTVD 338 (460)
........-.+..+.+.++ +....++++.||||++-.+.. |..+....-+=||+|...-+-
T Consensus 249 ----~~~~~~~~~~~~e~~~~~~~~~~~R~~l~y~iDGiViKvn~~~~q~~lG~ts~~PrWaiA~Kf~~~~~~T 318 (669)
T PRK14350 249 ----FCRFFDGKNSIEEILNYVKDIEKKRNSFEYEIDGVVLKVSDFALREILGYTSHHPKWSMAYKFESLSGFS 318 (669)
T ss_pred ----ceEEEcCCCcHHHHHHHHHHHHHHHhcCCCCCCcEEEEecCHHHHHhcCCcCCCCCceEEEcCCCceeEE
Confidence 1000000000112222222 224578899999999975542 333334456777777654333
No 51
>PHA02142 putative RNA ligase
Probab=89.94 E-value=8.1 Score=40.32 Aligned_cols=103 Identities=12% Similarity=0.084 Sum_probs=56.5
Q ss_pred cCceEEEEcCCeeEEEEEEEC---------------------CEEEEEeCCCcc--ccccCcCCcccCCCCcccc---CC
Q 012588 146 QRYYYATWKADGTRYMMLITI---------------------DGCYLIDRCFNF--RRVQMRFPCRNSNEGLGEK---TH 199 (460)
Q Consensus 146 ~~~Y~V~~K~DG~R~Ll~i~~---------------------~~vyLidR~~~~--~~v~~~FP~~~~~~~l~~~---~~ 199 (460)
...|.+++|.||+=+-+|... +...+-+|++.. ..-+...- .....++.+. ..
T Consensus 168 ~~~f~~TeKLDGsS~tvy~~~~~~~~~~~~~~~~~~~~~~~~~~~gv~srn~~l~~~~~~~~W~-~a~~~~i~~~l~~~~ 246 (366)
T PHA02142 168 DVKFAKSLKLDGSSITMAWVTDPDLFLDLGTEDEPYAHDYDDAQFIVASRNQVLRYNADSKWWK-GVENYQIVDRLKELG 246 (366)
T ss_pred CceEEEEEEecceeEEEEEecCCcccccccccccccccccCCCceeEeeccccccccCCchHHH-HHHHcCcHHHHHhhC
Confidence 468999999999998888441 122333455431 10011000 0000111111 12
Q ss_pred CceeeeeEEEEecCCCCCc--ceeEEEEeeeeecCCccccCCCHHHHHHHHHHH
Q 012588 200 HFTLLDGEMIIDKLPDSRR--QERRYLIYDMMAINQASVIERPFYERWKMLEKE 251 (460)
Q Consensus 200 ~~TlLDGElV~d~~~~~~~--~~~ryliFDiL~~~G~~l~~~pf~eRl~~L~~~ 251 (460)
.+.-+=|||+--...++.- ....|++||+..++++. =+++.++..++++.
T Consensus 247 ~~iaIqGEl~Gp~IQ~N~~~~~~~~F~vF~v~~i~~~~--yl~~~e~~~~~~~~ 298 (366)
T PHA02142 247 MSVAIQGELMGPGIQKNRENFDKYRIFAFRAWFIDEQR--FATDEEFQDLCRTL 298 (366)
T ss_pred CcEEEEEEEecccccCccccCCCCceEEEEEEEeccce--eCCHHHHHHHHHHc
Confidence 4667899999643322111 23589999998777653 56677777777663
No 52
>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=89.91 E-value=21 Score=40.21 Aligned_cols=166 Identities=17% Similarity=0.184 Sum_probs=91.0
Q ss_pred ceEEEEcCCeeEEEEEEECCE-EEEEeCCCccc--cccC---c---CCcccCCCCccc-cCCCceeeeeEEEEecC----
Q 012588 148 YYYATWKADGTRYMMLITIDG-CYLIDRCFNFR--RVQM---R---FPCRNSNEGLGE-KTHHFTLLDGEMIIDKL---- 213 (460)
Q Consensus 148 ~Y~V~~K~DG~R~Ll~i~~~~-vyLidR~~~~~--~v~~---~---FP~~~~~~~l~~-~~~~~TlLDGElV~d~~---- 213 (460)
.|+|++|.||.=+-|.+.++. +..++|.+-.. .++. . -|.. +.. .......+=||+++.+.
T Consensus 97 ~~~~epKiDGlaisL~Ye~G~L~~a~TRGDG~~GeDvT~nv~~I~~iP~~-----i~~~~~p~~levRGEv~m~~~~F~~ 171 (652)
T TIGR00575 97 EYVVEPKIDGLSVSLTYENGVLVRALTRGDGTVGEDVTANVRTIRSIPLR-----LAGDNPPERLEVRGEVFMPKEDFEA 171 (652)
T ss_pred eEEEEEeccceEEEEEEECCEEEEEEecCCCccchhHhhhhhhhcccchh-----hcCCCCCceEEEEEEEEEEHHHHHH
Confidence 699999999999877776554 57899965321 1211 1 1211 100 01223678899998521
Q ss_pred --------C-----CC----------------CcceeEEEEeeeeecCCccccCCCHHHHHHHHHHHhcCccchhhcccc
Q 012588 214 --------P-----DS----------------RRQERRYLIYDMMAINQASVIERPFYERWKMLEKEVIEPRNYERHNIY 264 (460)
Q Consensus 214 --------~-----~~----------------~~~~~ryliFDiL~~~G~~l~~~pf~eRl~~L~~~i~~pr~~~~~~l~ 264 (460)
+ ++ ....+.|++|++.. +.+.......++++.|+++-+..
T Consensus 172 ~N~~~~~~g~~~faNpRN~aAGslr~ld~~~~~~r~L~~~~y~~~~--~~~~~~~t~~e~l~~L~~~GF~v--------- 240 (652)
T TIGR00575 172 LNEERREQGEKPFANPRNAAAGSLRQLDPRITAKRKLRFFAYGLGE--GLELPDATQYEALAWLKKWGFPV--------- 240 (652)
T ss_pred HHHHHHHcCCCCCCCcHHHHHHHHHcCCchhhhcCccEEEEEeccc--cCCCCCCCHHHHHHHHHHCCCCC---------
Confidence 0 00 02357899999752 22222246678888887743321
Q ss_pred ccCCCCccCCCCCeEEEeccceechhHHHHHHH---hccccCCCCceEEEEcCCCCC------ccCCCCCeEEEccCCCc
Q 012588 265 QSRNPYYRYDLEPFRVRRKDFWLLSTVNKLLKE---FIPKLSHDADGLVFQGWDDPY------VPRTHEGLLKWKYARMN 335 (460)
Q Consensus 265 ~~~~~~~~~~~~pf~I~~K~f~~~~~~~~ll~~---~~~~l~h~~DGLIF~p~~spY------~~G~~~~~LKWKP~~~n 335 (460)
++ +....+. +..+.+.++. ....+++..||+|++-.+.++ ..+....-+=||+|...
T Consensus 241 ---~~--------~~~~~~~---~~ei~~~~~~~~~~R~~l~y~iDGiViKvn~~~~~~~lG~t~~~PrwaiA~Kf~~~~ 306 (652)
T TIGR00575 241 ---SP--------HIRLCDS---IEEVLEYYREIEEKRDSLPYEIDGVVVKVDDLALQDELGFTSKAPRWAIAYKFPAEE 306 (652)
T ss_pred ---CC--------CeEeeCC---HHHHHHHHHHHHHhhhcCCCCCCcEEEEecCHHHHHHhCccCCCCCceEEEcCCCce
Confidence 11 1111111 2233333332 236789999999999765544 33333456778887654
Q ss_pred eEEEEEEE
Q 012588 336 SVDFLFEV 343 (460)
Q Consensus 336 TVDF~l~~ 343 (460)
.+--+..+
T Consensus 307 ~~T~l~~I 314 (652)
T TIGR00575 307 AQTKLLDV 314 (652)
T ss_pred eeEEEEEE
Confidence 44433333
No 53
>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=88.76 E-value=2.9 Score=42.88 Aligned_cols=107 Identities=12% Similarity=0.031 Sum_probs=60.4
Q ss_pred cccCceEEEEcCCeeEEEEEEECC-EEEEEeCCCccccccCcCC--cc-cCC----CC----ccc---cCCCceeeeeEE
Q 012588 144 LRQRYYYATWKADGTRYMMLITID-GCYLIDRCFNFRRVQMRFP--CR-NSN----EG----LGE---KTHHFTLLDGEM 208 (460)
Q Consensus 144 l~~~~Y~V~~K~DG~R~Ll~i~~~-~vyLidR~~~~~~v~~~FP--~~-~~~----~~----l~~---~~~~~TlLDGEl 208 (460)
|....|.|+||.||.-+=++++++ .+-.-+|++.+..-...|- .. ... .. +.. ......++=||+
T Consensus 22 l~~~ewvatEKlhGaNfsi~~~~~~~i~~akR~~~l~~~e~f~G~~~i~~~l~~~~~~l~~~l~~~~~~~~~~v~IyGEl 101 (325)
T TIGR02307 22 LGLTEWVAREKIHGTNFSIIIERDFKVTCAKRTGIILPNEDFFGYHILIKNYTASVKAIQDILETKAIIVVVSVQVFGEL 101 (325)
T ss_pred cCCceEEEEEEecCcceEEEEeCCceEEEeecccccCcccccccHHHHHHHHHHHHHHHHHHHhhhcccccceEEEEEEe
Confidence 566799999999999998888877 7878888855432111110 00 000 00 000 012446788999
Q ss_pred EEecCCCCCc-ceeEEEEeeeeecCCccccCCCHHHHHHHHHH
Q 012588 209 IIDKLPDSRR-QERRYLIYDMMAINQASVIERPFYERWKMLEK 250 (460)
Q Consensus 209 V~d~~~~~~~-~~~ryliFDiL~~~G~~l~~~pf~eRl~~L~~ 250 (460)
+.-....+.. ....|++|||......+..=+++.+-...+.+
T Consensus 102 ~G~~~q~~~~Y~~~~fyaFdI~~~~~~~~~~L~~d~~~e~~~~ 144 (325)
T TIGR02307 102 AGPGYQKPVVYSDKDFYAFDIKYTETSDDVTLVDDYMMESFCN 144 (325)
T ss_pred ecCcccCccccccccEEEEEEEEeccCcceEecHHHHHHHHHH
Confidence 9543222110 13689999996642212344566655555544
No 54
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=88.02 E-value=17 Score=40.11 Aligned_cols=165 Identities=16% Similarity=0.178 Sum_probs=90.0
Q ss_pred ceEEEEcCCeeEEEEEEECCE-EEEEeCCCccc--cccC---cCCcccCCCCccccCCCceeeeeEEEEecCC-------
Q 012588 148 YYYATWKADGTRYMMLITIDG-CYLIDRCFNFR--RVQM---RFPCRNSNEGLGEKTHHFTLLDGEMIIDKLP------- 214 (460)
Q Consensus 148 ~Y~V~~K~DG~R~Ll~i~~~~-vyLidR~~~~~--~v~~---~FP~~~~~~~l~~~~~~~TlLDGElV~d~~~------- 214 (460)
.|++++|.||.=+-|...++. +..++|.+-.. .++. .++.. +..+. .......+-||+++.+..
T Consensus 119 ~~~vepKiDGlsisL~Ye~G~Lv~a~TRGDG~~GEDVT~nv~~I~~I--P~~l~-~~~~~levRGEv~m~~~~F~~~~~g 195 (562)
T PRK08097 119 DLWVQPKVDGVAVTLVYRDGKLVQAISRGNGLKGEDWTAKARLIPAI--PQQLP-GALANLVLQGELFLRREGHIQQQMG 195 (562)
T ss_pred ceEEEEecccEEEEEEEECCEEEEEEecCCCccchhHHhhHhhhccc--chhhc-CCCCeEEEEEEEEEeHHHHHHHhcC
Confidence 599999999998877776554 57899965321 1221 11110 00110 001236788999985321
Q ss_pred --CC---------------CcceeEEEEeeeeecCCccccCCCHHHHHHHHHHHhcCccchhhccccccCCCCccCCCCC
Q 012588 215 --DS---------------RRQERRYLIYDMMAINQASVIERPFYERWKMLEKEVIEPRNYERHNIYQSRNPYYRYDLEP 277 (460)
Q Consensus 215 --~~---------------~~~~~ryliFDiL~~~G~~l~~~pf~eRl~~L~~~i~~pr~~~~~~l~~~~~~~~~~~~~p 277 (460)
++ ....+.|++|++. +| .....++++.|++.-+. .++ .
T Consensus 196 ~aNPRN~AAGsLr~~d~~~~~r~L~~f~y~~~--~~----~~t~~e~l~~L~~~GF~------------v~~-------~ 250 (562)
T PRK08097 196 GINARAKVAGLMMRKDPSPTLNQIGVFVWAWP--DG----PASMPERLAQLATAGFP------------LTQ-------R 250 (562)
T ss_pred cCCchHHHhHHHhhcCcHhhhccceEEEEECC--CC----CCCHHHHHHHHHHCCCC------------cCc-------c
Confidence 00 0124789999973 44 23567888888764322 011 0
Q ss_pred eEEEeccceechhHHHHHHHh-ccccCCCCceEEEEcCCCCCccC----CCCCeEEEccCCCceEEEEEEE
Q 012588 278 FRVRRKDFWLLSTVNKLLKEF-IPKLSHDADGLVFQGWDDPYVPR----THEGLLKWKYARMNSVDFLFEV 343 (460)
Q Consensus 278 f~I~~K~f~~~~~~~~ll~~~-~~~l~h~~DGLIF~p~~spY~~G----~~~~~LKWKP~~~nTVDF~l~~ 343 (460)
+..... ....+....+.+ ...+.++.||||++-.+..|.-| ....-+=||++....+--...+
T Consensus 251 ~~~~~~---~~~~i~~~~~~~~r~~l~y~iDGiViKvn~~~~~~~~ts~~PrWAiAyKf~~~~~~T~l~~I 318 (562)
T PRK08097 251 YTHPVK---NAEEVARWRERWYRAPLPFVTDGVVVRQAKEPPGRYWQPGQGEWAVAWKYPPVQQVAEVRAV 318 (562)
T ss_pred ceEeeC---CHHHHHHHHHHHhhccCCCCCCcEEEEecCHHHHhhccCCCCCceEEEcCCCcEEEEEEEEE
Confidence 111111 122333333332 35788999999999877666544 1234566777765444333333
No 55
>KOG1720 consensus Protein tyrosine phosphatase CDC14 [Defense mechanisms]
Probab=72.14 E-value=4.7 Score=38.83 Aligned_cols=35 Identities=23% Similarity=0.404 Sum_probs=30.1
Q ss_pred CchhhhHHhcCCCHHHHHHHHHhhCCCCcc--hhHHH
Q 012588 1 MIVHFLMRSQSMSVAQAIKKFAEVRPPGIY--KNEYI 35 (460)
Q Consensus 1 ~i~~yl~~~~~~~~~~a~~~F~~~rppgi~--~~~y~ 35 (460)
||+|||+...|+|..+||+..-..||..|- +|+++
T Consensus 164 liAc~lmy~~g~ta~eaI~~lR~~RpG~V~gpqQ~~l 200 (225)
T KOG1720|consen 164 LIACYLMYEYGMTAGEAIAWLRICRPGAVIGPQQHKL 200 (225)
T ss_pred HHHHHHHHHhCCCHHHHHHHHHhcCCccccCHHHHHH
Confidence 689999999999999999999999977664 55554
No 56
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=71.25 E-value=1e+02 Score=34.79 Aligned_cols=164 Identities=17% Similarity=0.209 Sum_probs=93.8
Q ss_pred cCceEEEEcCCeeEEEEEEECCE-EEEEeCCCccc--cccC------cCCcccCCCCccccCCCceeeeeEEEEecCC--
Q 012588 146 QRYYYATWKADGTRYMMLITIDG-CYLIDRCFNFR--RVQM------RFPCRNSNEGLGEKTHHFTLLDGEMIIDKLP-- 214 (460)
Q Consensus 146 ~~~Y~V~~K~DG~R~Ll~i~~~~-vyLidR~~~~~--~v~~------~FP~~~~~~~l~~~~~~~TlLDGElV~d~~~-- 214 (460)
...|++++|.||.=.-|+..++. +...+|.+-.. .++. ..|..-. + .+...-+=||+...+..
T Consensus 108 ~~~y~~EpKiDGlsisL~YenG~Lv~aaTRGdG~~GEDiT~NvrtI~~IP~~l~--~----~p~~lEVRGEvfm~k~~F~ 181 (667)
T COG0272 108 SVEYVVEPKIDGLAISLVYENGKLVRAATRGDGTTGEDITANVRTIRSIPLKLP--G----APAVLEVRGEVFMPKEDFE 181 (667)
T ss_pred CcceEEEeecceEEEEEEEECCEEEEeeccCCCccccchhhhhhhHhhhhhhcc--C----CCceEEEEeEEEEeHHHHH
Confidence 45899999999999877766553 56778865322 1111 1122210 0 13345678999886421
Q ss_pred -----------------CC--------------CcceeEEEEeeeeecCCccccCCCHHHHHHHHHHHhcCccchhhccc
Q 012588 215 -----------------DS--------------RRQERRYLIYDMMAINQASVIERPFYERWKMLEKEVIEPRNYERHNI 263 (460)
Q Consensus 215 -----------------~~--------------~~~~~ryliFDiL~~~G~~l~~~pf~eRl~~L~~~i~~pr~~~~~~l 263 (460)
.+ .+..+.+++|.+-...+. ..-....+++..|+.+-+.-
T Consensus 182 ~lN~~~~~~g~~~faNpRNaAAGsLRqlD~~ita~R~L~~f~y~~~~~~~~-~~~~t~~e~l~~L~~~GF~v-------- 252 (667)
T COG0272 182 ALNEEREEEGEKPFANPRNAAAGSLRQLDPKITAKRKLGFFIYAVGDGEEG-LLADTQSERLAFLKAWGFPV-------- 252 (667)
T ss_pred HHHHHHHHhCCCCcCChhhhhhhhhhccCHHHHhcCCceEEEEeCCccCCC-CCccCHHHHHHHHHHcCCCC--------
Confidence 00 124688999988765544 33445678998888754320
Q ss_pred cccCCCCccCCCCCeEEEeccceechhHHHHHHHh---ccccCCCCceEEEEcCCCC------CccCCCCCeEEEccCCC
Q 012588 264 YQSRNPYYRYDLEPFRVRRKDFWLLSTVNKLLKEF---IPKLSHDADGLVFQGWDDP------YVPRTHEGLLKWKYARM 334 (460)
Q Consensus 264 ~~~~~~~~~~~~~pf~I~~K~f~~~~~~~~ll~~~---~~~l~h~~DGLIF~p~~sp------Y~~G~~~~~LKWKP~~~ 334 (460)
++. .+-+-.+..+....+.+ -+.|++..||+|.+-.+-+ |+++....-+=||+|-.
T Consensus 253 ----~~~-----------~~~~~~~~ev~~~~~~~~~~R~~L~y~IDGvViKvn~l~~q~~lG~tsk~PrWAiAyKFpa~ 317 (667)
T COG0272 253 ----NPY-----------TRLCKNADEVLAFYEEWEKKRASLPYDIDGVVIKVNDLALQRELGFTSKAPRWAIAYKFPAE 317 (667)
T ss_pred ----CcH-----------hhhcCCHHHHHHHHHHHHhhcccCCCccceEEEEeccHHHHHHhCCccCCCceeeeecCCch
Confidence 110 11122222333333332 3679999999999875433 55555556677887754
Q ss_pred ceEEE
Q 012588 335 NSVDF 339 (460)
Q Consensus 335 nTVDF 339 (460)
..+--
T Consensus 318 e~~T~ 322 (667)
T COG0272 318 EAVTK 322 (667)
T ss_pred heeeE
Confidence 43333
No 57
>PF14671 DSPn: Dual specificity protein phosphatase, N-terminal half; PDB: 1OHD_A 1OHE_A 1OHC_A.
Probab=64.20 E-value=3.5 Score=37.29 Aligned_cols=27 Identities=30% Similarity=0.468 Sum_probs=20.6
Q ss_pred CchhhhHHhcCCCHHHHHHHHHhhCCC
Q 012588 1 MIVHFLMRSQSMSVAQAIKKFAEVRPP 27 (460)
Q Consensus 1 ~i~~yl~~~~~~~~~~a~~~F~~~rpp 27 (460)
||++|+|=.++||.++|.+.|+..-||
T Consensus 87 Lig~y~Vi~l~~spe~A~~~l~~~~p~ 113 (141)
T PF14671_consen 87 LIGAYAVIYLGMSPEEAYKPLASIQPP 113 (141)
T ss_dssp HHHHHHHHTS---HHHHHHHHTTTT--
T ss_pred HHHHHHHHhcCCCHHHHHHHHHhcCCC
Confidence 689999999999999999999988755
No 58
>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=58.41 E-value=95 Score=32.26 Aligned_cols=103 Identities=10% Similarity=0.019 Sum_probs=50.7
Q ss_pred CceEEEEcCCeeEEEEEEEC-CEEEEE------eCCCccccc--cCcCCc--ccCC-CCccccC-CCceeeeeEEEEecC
Q 012588 147 RYYYATWKADGTRYMMLITI-DGCYLI------DRCFNFRRV--QMRFPC--RNSN-EGLGEKT-HHFTLLDGEMIIDKL 213 (460)
Q Consensus 147 ~~Y~V~~K~DG~R~Ll~i~~-~~vyLi------dR~~~~~~v--~~~FP~--~~~~-~~l~~~~-~~~TlLDGElV~d~~ 213 (460)
..|.+++|.||+=+.+|... ++-|+. +|+..+..- +...-. .... ..+.... ..+.-+=||++--..
T Consensus 159 ~~~~~TeKldGss~tv~~~~~~~~~~~~~~Gvcsr~~~l~~~~~~~~W~~a~~~~i~~~l~~~~~~~~vaiqGEl~G~gI 238 (341)
T TIGR02306 159 EKVAKTEKLHGTSITVAWVTDEERFLVLSKGVASRNLVLRENADNKYWKAVENYQIVDRAKAAELRMSVAIFGEVMGPGI 238 (341)
T ss_pred ceEEEEEEecceeEEEEEecCCcccccccceeecCCcccccCCCchhHHHHHhcChHHHHhhcccCceEEEEEEEeCccc
Confidence 68999999999998777643 222222 344432110 110000 0000 0011001 134568899996433
Q ss_pred CCC--CcceeE-EEEeeeeecCCccccCCCHHHHHHHHHHH
Q 012588 214 PDS--RRQERR-YLIYDMMAINQASVIERPFYERWKMLEKE 251 (460)
Q Consensus 214 ~~~--~~~~~r-yliFDiL~~~G~~l~~~pf~eRl~~L~~~ 251 (460)
.++ ...... |.+|++ ..+|.. +=++..++..++.+.
T Consensus 239 Q~n~Yg~~~~~~~f~F~v-~~~~~~-ryld~~~~~~~~~~~ 277 (341)
T TIGR02306 239 QKNRYGFDKYRTVFAFRA-FFDGEQ-RFLTDEDFQDLCLTL 277 (341)
T ss_pred cCCcCCCCCCceEEEEEE-EEcCcc-eecCHHHHHHHHHhc
Confidence 211 111234 667776 334442 345778888877763
No 59
>PF10640 Pox_ATPase-GT: mRNA capping enzyme N-terminal, ATPase and guanylyltransferase; InterPro: IPR019602 Viral mRNA capping enzymes catalyse the first two reactions in the mRNA cap formation pathway. They are a heterodimer consisting of a large and small subunit. This domain is the N terminus of the large subunit viral mRNA capping enzyme, and carries both the ATPase and the guanylyltransferase activities of the enzyme. The guanylyltransferase enzymatic region runs from residues 242 (leucine)-273(arginine) [], the core of the active site being the lysine residue at 260 []. The ATPase activity is at the very N-terminal part of the domain []. ; GO: 0004484 mRNA guanylyltransferase activity, 0004651 polynucleotide 5'-phosphatase activity
Probab=53.51 E-value=61 Score=32.89 Aligned_cols=93 Identities=22% Similarity=0.337 Sum_probs=58.4
Q ss_pred HHHHHHHHHHHhcccCCCCCCCCC--CCC-ccc---ccccccccccccCceEEEEcCCeeEEEEEEECCEEEEEeCCCcc
Q 012588 105 QDAFRHFCYQTLKLNFGGRGNMQF--PGS-HPV---SLNSDNLQLLRQRYYYATWKADGTRYMMLITIDGCYLIDRCFNF 178 (460)
Q Consensus 105 ~~~~r~~~~~l~~~~~~~~~~~~F--PGs-qPV---Sl~r~nl~~l~~~~Y~V~~K~DG~R~Ll~i~~~~vyLidR~~~~ 178 (460)
..+|...|+-+. .+. ..+-.. |+. -|| -|-++.|..|.-.+|+++-|+||+=..+.+...++|+.=-...|
T Consensus 184 ~~eL~~~~~~iF-m~~--~~ni~L~~~~~k~pvkT~MLkkqdi~~ldl~~ly~tsKtDGv~~~V~i~~~~i~C~f~hl~y 260 (313)
T PF10640_consen 184 LNELTTLFRAIF-MAN--PDNIFLVTPNIKPPVKTHMLKKQDIPGLDLENLYITSKTDGVGTVVKITVKGIYCYFSHLGY 260 (313)
T ss_pred HHHHHHHHHHHh-ccC--cccEEEeCCCCCCCceeeeeccccccccchhheEEEEeecCceEEEEEecCceEEEEEEeeE
Confidence 567777777766 221 122222 332 244 35677888899999999999999999888888876653222221
Q ss_pred ccccCcCCcccCCCCccccCCCceeeeeEEEE
Q 012588 179 RRVQMRFPCRNSNEGLGEKTHHFTLLDGEMII 210 (460)
Q Consensus 179 ~~v~~~FP~~~~~~~l~~~~~~~TlLDGElV~ 210 (460)
..+||.... ......|=||++.
T Consensus 261 ---~irY~~~~~-------i~~~i~l~gEa~K 282 (313)
T PF10640_consen 261 ---IIRYNANRN-------IDNPIVLYGEAIK 282 (313)
T ss_pred ---EEEcccccC-------CCCceEEEeeeee
Confidence 134443322 2356778999997
No 60
>KOG1716 consensus Dual specificity phosphatase [Defense mechanisms]
Probab=39.64 E-value=37 Score=34.04 Aligned_cols=39 Identities=18% Similarity=0.345 Sum_probs=33.0
Q ss_pred CchhhhHHhcCCCHHHHHHHHHhhCCCCcchhHHHHHHH
Q 012588 1 MIVHFLMRSQSMSVAQAIKKFAEVRPPGIYKNEYIEALY 39 (460)
Q Consensus 1 ~i~~yl~~~~~~~~~~a~~~F~~~rppgi~~~~y~~~l~ 39 (460)
+++|||+..++|++++|.+.-...||=.=...-++..|.
T Consensus 172 ~viAYlM~~~~~~l~~A~~~vk~~R~~i~PN~gf~~QL~ 210 (285)
T KOG1716|consen 172 LVIAYLMKYEGLSLEDAYELVKSRRPIISPNFGFLRQLL 210 (285)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHhCCccCCCHHHHHHHH
Confidence 478999999999999999999888876646888877773
No 61
>PF14555 UBA_4: UBA-like domain; PDB: 2DAL_A 3BQ3_A 2L4E_A 2L4F_A 2DZL_A 2L2D_A 2DAM_A 1V92_A 3E21_A.
Probab=38.71 E-value=27 Score=24.64 Aligned_cols=22 Identities=5% Similarity=0.166 Sum_probs=17.3
Q ss_pred hhhhHHhcCCCHHHHHHHHHhh
Q 012588 3 VHFLMRSQSMSVAQAIKKFAEV 24 (460)
Q Consensus 3 ~~yl~~~~~~~~~~a~~~F~~~ 24 (460)
+..+.+..+|.++.||..|=..
T Consensus 18 A~~~L~~~~wdle~Av~~y~~~ 39 (43)
T PF14555_consen 18 AIQYLEANNWDLEAAVNAYFDD 39 (43)
T ss_dssp HHHHHHHTTT-HHHHHHHHHHS
T ss_pred HHHHHHHcCCCHHHHHHHHHhC
Confidence 4567889999999999998654
No 62
>PRK12361 hypothetical protein; Provisional
Probab=36.02 E-value=45 Score=36.59 Aligned_cols=46 Identities=11% Similarity=0.359 Sum_probs=35.3
Q ss_pred CchhhhHHh-cCCCHHHHHHHHHhhCCCCcchhHHHHHHHHHhccCC
Q 012588 1 MIVHFLMRS-QSMSVAQAIKKFAEVRPPGIYKNEYIEALYTFYHEKR 46 (460)
Q Consensus 1 ~i~~yl~~~-~~~~~~~a~~~F~~~rppgi~~~~y~~~l~~~y~~~~ 46 (460)
++++||+.+ .+|++++|++...++||--.=....++.|=..|....
T Consensus 192 vv~ayLm~~~~~~~~~eA~~~vr~~Rp~v~~n~~q~~~l~~~~~~~~ 238 (547)
T PRK12361 192 VLAAYLLCKDPDLTVEEVLQQIKQIRKTARLNKRQLRALEKMLEQGK 238 (547)
T ss_pred HHHHHHHHhccCCCHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHcCC
Confidence 368999977 5899999999999999966666666666655554433
No 63
>KOG2283 consensus Clathrin coat dissociation kinase GAK/PTEN/Auxilin and related tyrosine phosphatases [Signal transduction mechanisms; General function prediction only]
Probab=33.67 E-value=25 Score=37.70 Aligned_cols=25 Identities=32% Similarity=0.469 Sum_probs=23.5
Q ss_pred CchhhhHHhcCCC-HHHHHHHHHhhC
Q 012588 1 MIVHFLMRSQSMS-VAQAIKKFAEVR 25 (460)
Q Consensus 1 ~i~~yl~~~~~~~-~~~a~~~F~~~r 25 (460)
||||||+...-++ .++|+..|++.|
T Consensus 124 ~icA~L~~~~~~~ta~eald~~~~kR 149 (434)
T KOG2283|consen 124 MICAYLIYSGISATAEEALDYFNEKR 149 (434)
T ss_pred EEeHHHHhhhhcCCHHHHHHHHhhhh
Confidence 7999999998886 999999999999
No 64
>PF03162 Y_phosphatase2: Tyrosine phosphatase family; InterPro: IPR004861 Protein tyrosine (pTyr) phosphorylation is a common post-translational modification which can create novel recognition motifs for protein interactions and cellular localisation, affect protein stability, and regulate enzyme activity. Consequently, maintaining an appropriate level of protein tyrosine phosphorylation is essential for many cellular functions. Tyrosine-specific protein phosphatases (PTPase; 3.1.3.48 from EC) catalyse the removal of a phosphate group attached to a tyrosine residue, using a cysteinyl-phosphate enzyme intermediate. These enzymes are key regulatory components in signal transduction pathways (such as the MAP kinase pathway) and cell cycle control, and are important in the control of cell growth, proliferation, differentiation and transformation [, ]. The PTP superfamily can be divided into four subfamilies []: (1) pTyr-specific phosphatases (2) dual specificity phosphatases (dTyr and dSer/dThr) (3) Cdc25 phosphatases (dTyr and/or dThr) (4) LMW (low molecular weight) phosphatases Based on their cellular localisation, PTPases are also classified as: Receptor-like, which are transmembrane receptors that contain PTPase domains [] Non-receptor (intracellular) PTPases [] All PTPases carry the highly conserved active site motif C(X)5R (PTP signature motif), employ a common catalytic mechanism, and share a similar core structure made of a central parallel beta-sheet with flanking alpha-helices containing a beta-loop-alpha-loop that encompasses the PTP signature motif []. Functional diversity between PTPases is endowed by regulatory domains and subunits. This entry represents protein-tyrosine phosphatases predominantly from fungi, plants and bacteria, several of which are putative enzymes. These proteins are closely related to the Y-phosphatase and DSPc families. This entry includes the PTPase SIW14 from Saccharomyces cerevisiae (Baker's yeast), which plays a role in actin filament organisation and endocytosis.; PDB: 2Q47_A 1XRI_A.
Probab=27.55 E-value=43 Score=30.85 Aligned_cols=53 Identities=19% Similarity=0.317 Sum_probs=23.7
Q ss_pred hhhhHHhcCCCHHHHHHHHHhhCCCCcchhHHHHHHHHHhccCCCCCCCCCCCCcc
Q 012588 3 VHFLMRSQSMSVAQAIKKFAEVRPPGIYKNEYIEALYTFYHEKRLDSTPCPSTPEW 58 (460)
Q Consensus 3 ~~yl~~~~~~~~~~a~~~F~~~rppgi~~~~y~~~l~~~y~~~~~~~~~~p~~p~w 58 (460)
|+=|-.-.||++++|+++|..--.+ |..|.++.|-..-+.+...+..-+.|.|
T Consensus 109 vg~lRk~Q~W~~~~i~~Ey~~f~~~---~~~~~~~~fIe~f~~~~~~~~~~~~~~w 161 (164)
T PF03162_consen 109 VGCLRKLQGWSLSSIFDEYRRFAGP---KIRYLDEQFIELFDVELVVPPNNPKWLW 161 (164)
T ss_dssp HHHHHHHTTB-HHHHHHHHHHHHGG---G--HHHHHHHHT----------------
T ss_pred HHHHHHHcCCCHHHHHHHHHHhcCC---CCcHHHHHHHHhcCcceecccccccccc
Confidence 4445577899999999998764333 5566777665555544323344444555
No 65
>PF11396 DUF2874: Protein of unknown function (DUF2874); InterPro: IPR021533 This bacterial family of proteins are probable periplasmic proteins with unknown function. There are between one and four copies of this domain per sequence. ; PDB: 3DUE_A 3U1W_B 3DB7_A 4DSD_A 3ELG_A.
Probab=24.37 E-value=66 Score=23.88 Aligned_cols=43 Identities=19% Similarity=0.414 Sum_probs=32.2
Q ss_pred CCCCCCcccccccccccccccCceEEEEcCCeeEEEEEEECCEEE
Q 012588 126 MQFPGSHPVSLNSDNLQLLRQRYYYATWKADGTRYMMLITIDGCY 170 (460)
Q Consensus 126 ~~FPGsqPVSl~r~nl~~l~~~~Y~V~~K~DG~R~Ll~i~~~~vy 170 (460)
..|||++-.+..+..-..- ..|-|.-+-+|..+-++++.+|-+
T Consensus 18 ~~yp~~~i~~v~~~~~~~~--~~Y~v~l~~~~~~~~v~fd~~G~~ 60 (61)
T PF11396_consen 18 KNYPGAKIKEVEKETDPGG--KYYEVELKKGGNEYEVYFDANGNW 60 (61)
T ss_dssp HHSTTSEEEEEEEEEETTE--EEEEEEETETTTSEEEEEETTS-E
T ss_pred HHCCCCeEEEEEEEEcCCC--CEEEEEEEEeCCeEEEEEcCCCCC
Confidence 4599999888777665432 578899999998888888766543
No 66
>COG3640 CooC CO dehydrogenase maturation factor [Cell division and chromosome partitioning]
Probab=22.92 E-value=58 Score=32.23 Aligned_cols=67 Identities=19% Similarity=0.196 Sum_probs=46.9
Q ss_pred CCCCccccchHHHHHHHHHHHhcccCCCCCCCCCCCCcccccccccccccccCceEEEEcCCeeEEEEEEE----CCEEE
Q 012588 95 VLGDEIPNDQQDAFRHFCYQTLKLNFGGRGNMQFPGSHPVSLNSDNLQLLRQRYYYATWKADGTRYMMLIT----IDGCY 170 (460)
Q Consensus 95 v~G~~~~~~~~~~~r~~~~~l~~~~~~~~~~~~FPGsqPVSl~r~nl~~l~~~~Y~V~~K~DG~R~Ll~i~----~~~vy 170 (460)
.+|++.+.+.+...|...++.. ...||..|.+|.+.|...=.-.+=+++|.-| +|.|++-. +.|||
T Consensus 46 ~LGve~~~~~lg~~~e~~~k~~---------~a~~~~~~~~~fk~~~~~~di~~e~~~e~~~-~~LLvmGkie~~GeGC~ 115 (255)
T COG3640 46 ALGVEEPMKYLGGKRELLKKRT---------GAEPGGPPGEMFKENPLVSDLPDEYLVENGD-IDLLVMGKIEEGGEGCA 115 (255)
T ss_pred hcCCCCCCcccccHHHHHHHHh---------ccCCCCCcccccccCcchhhhhHHHhhhcCC-ccEEEeccccCCCCccc
Confidence 5788888888888888888876 5667778888999988642222235666666 88776633 34676
Q ss_pred E
Q 012588 171 L 171 (460)
Q Consensus 171 L 171 (460)
+
T Consensus 116 C 116 (255)
T COG3640 116 C 116 (255)
T ss_pred c
Confidence 4
Done!