Query 014751
Match_columns 419
No_of_seqs 125 out of 133
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 08:10:09 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/014751.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/014751hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3132 m3G-cap-specific nucle 100.0 1.1E-96 2E-101 702.6 17.9 259 2-285 22-282 (325)
2 cd09232 Snurportin-1_C C-termi 100.0 2E-69 4.4E-74 502.8 18.5 182 97-282 2-186 (186)
3 cd06846 Adenylation_DNA_ligase 99.7 5.4E-16 1.2E-20 141.7 14.3 170 101-281 2-182 (182)
4 PF01331 mRNA_cap_enzyme: mRNA 99.5 3.2E-13 7E-18 125.0 11.3 159 116-280 16-192 (192)
5 PF11538 Snurportin1: Snurport 99.3 1.9E-12 4E-17 93.5 4.0 39 4-42 1-40 (40)
6 cd07895 Adenylation_mRNA_cappi 98.7 4.5E-07 9.7E-12 85.5 14.1 162 116-281 41-215 (215)
7 cd07906 Adenylation_DNA_ligase 98.6 3E-07 6.5E-12 85.1 12.0 156 101-277 3-185 (190)
8 cd07897 Adenylation_DNA_ligase 98.2 2.3E-05 5.1E-10 74.0 12.3 163 101-280 7-201 (207)
9 cd07905 Adenylation_DNA_ligase 98.1 4.9E-05 1.1E-09 71.0 13.1 160 101-282 3-191 (194)
10 cd07903 Adenylation_DNA_ligase 98.0 6E-05 1.3E-09 71.5 10.8 156 116-281 33-221 (225)
11 TIGR02779 NHEJ_ligase_lig DNA 97.9 0.00038 8.2E-09 69.4 16.5 164 109-290 6-192 (298)
12 PRK08224 ligC ATP-dependent DN 97.9 0.00037 8.1E-09 71.4 16.4 168 101-289 11-207 (350)
13 cd07902 Adenylation_DNA_ligase 97.9 7.8E-05 1.7E-09 70.7 10.4 145 116-280 34-208 (213)
14 PRK05972 ligD ATP-dependent DN 97.8 0.00069 1.5E-08 76.6 17.6 194 100-313 235-452 (860)
15 PF01068 DNA_ligase_A_M: ATP d 97.8 7.7E-05 1.7E-09 68.6 7.5 145 115-280 18-200 (202)
16 PRK07636 ligB ATP-dependent DN 97.7 0.00091 2E-08 66.2 15.1 154 102-280 6-185 (275)
17 TIGR00574 dnl1 DNA ligase I, A 97.5 0.00055 1.2E-08 73.1 11.2 161 100-281 168-371 (514)
18 PRK09632 ATP-dependent DNA lig 97.5 0.0026 5.6E-08 71.3 16.5 149 115-289 476-650 (764)
19 cd07901 Adenylation_DNA_ligase 97.5 0.0011 2.4E-08 62.4 11.6 150 115-280 24-205 (207)
20 cd07898 Adenylation_DNA_ligase 97.5 0.0011 2.4E-08 61.9 11.0 149 116-281 21-200 (201)
21 PLN03113 DNA ligase 1; Provisi 97.3 0.0019 4.2E-08 72.2 11.5 168 100-280 371-576 (744)
22 PRK09633 ligD ATP-dependent DN 97.2 0.0099 2.2E-07 65.3 16.0 175 101-288 3-215 (610)
23 cd07900 Adenylation_DNA_ligase 97.2 0.0026 5.6E-08 60.9 10.1 149 117-280 32-214 (219)
24 cd08039 Adenylation_DNA_ligase 97.2 0.005 1.1E-07 59.9 12.2 143 117-273 23-219 (235)
25 PRK09247 ATP-dependent DNA lig 97.2 0.0032 7E-08 67.9 11.5 166 100-282 207-406 (539)
26 PRK01109 ATP-dependent DNA lig 97.1 0.0033 7.1E-08 68.5 10.8 165 100-280 229-430 (590)
27 PRK03180 ligB ATP-dependent DN 96.9 0.0067 1.4E-07 65.1 11.2 162 100-281 185-381 (508)
28 PHA00454 ATP-dependent DNA lig 96.6 0.012 2.5E-07 59.4 10.0 149 125-282 36-219 (315)
29 PHA02587 30 DNA ligase; Provis 96.6 0.017 3.6E-07 61.8 11.1 157 117-282 153-363 (488)
30 cd07896 Adenylation_kDNA_ligas 96.1 0.023 4.9E-07 51.8 7.8 133 116-280 16-171 (174)
31 COG1793 CDC9 ATP-dependent DNA 96.0 0.15 3.3E-06 54.1 14.4 159 109-289 126-321 (444)
32 PRK09125 DNA ligase; Provision 95.1 0.17 3.7E-06 50.5 10.2 136 116-281 43-201 (282)
33 KOG0966 ATP-dependent DNA liga 86.0 3.3 7.1E-05 47.1 8.8 168 97-282 232-436 (881)
34 TIGR02776 NHEJ_ligase_prk DNA 85.9 2.8 6.1E-05 45.9 8.2 90 182-283 57-146 (552)
35 KOG3132 m3G-cap-specific nucle 80.2 0.78 1.7E-05 45.8 1.1 163 3-192 1-175 (325)
36 COG5226 CEG1 mRNA capping enzy 78.1 5.2 0.00011 41.4 6.2 173 114-289 60-255 (404)
37 TIGR02609 doc_partner putative 69.7 5.3 0.00011 32.3 3.2 54 325-387 13-66 (74)
38 COG5064 SRP1 Karyopherin (impo 64.2 5.6 0.00012 41.9 2.9 44 3-46 7-54 (526)
39 PF14766 RPA_interact_N: Repli 52.8 29 0.00063 25.5 4.2 38 5-42 2-40 (42)
40 PRK04337 50S ribosomal protein 51.6 24 0.00051 30.1 4.1 35 125-159 39-79 (87)
41 PF06257 DUF1021: Protein of u 47.6 9.4 0.0002 31.6 1.1 30 125-154 16-45 (76)
42 PF01247 Ribosomal_L35Ae: Ribo 46.1 26 0.00056 30.3 3.5 35 125-159 39-87 (95)
43 cd07289 PX_PI3K_C2_alpha The p 42.8 43 0.00093 29.4 4.5 44 171-217 2-51 (109)
44 KOG0275 Conserved WD40 repeat- 41.8 42 0.00092 35.3 4.9 54 124-190 358-422 (508)
45 PF01749 IBB: Importin beta bi 40.7 4.4 9.5E-05 34.4 -1.9 44 3-46 6-52 (97)
46 PRK08097 ligB NAD-dependent DN 40.7 1.3E+02 0.0029 33.4 8.8 97 249-355 270-379 (562)
47 PF04014 Antitoxin-MazE: Antid 40.3 34 0.00074 24.9 3.0 29 325-353 10-39 (47)
48 PTZ00041 60S ribosomal protein 40.3 34 0.00075 30.7 3.5 35 125-159 58-106 (120)
49 smart00532 LIGANc Ligase N fam 39.4 1.5E+02 0.0033 31.8 8.9 96 250-355 272-382 (441)
50 PF09866 DUF2093: Uncharacteri 37.1 22 0.00048 26.5 1.5 18 336-353 2-19 (42)
51 KOG0296 Angio-associated migra 33.4 1E+02 0.0022 32.8 6.1 49 123-177 199-252 (399)
52 PRK11347 antitoxin ChpS; Provi 32.7 49 0.0011 27.6 3.1 29 325-353 15-43 (83)
53 COG3698 Predicted periplasmic 31.7 89 0.0019 31.1 5.1 96 258-355 79-202 (250)
54 KOG1136 Predicted cleavage and 28.4 85 0.0018 33.3 4.6 53 124-180 14-67 (501)
55 PRK09798 antitoxin MazE; Provi 28.4 66 0.0014 26.8 3.2 29 325-353 16-44 (82)
56 KOG0887 60S ribosomal protein 28.0 66 0.0014 28.5 3.2 39 116-159 45-97 (111)
57 KOG2618 Uncharacterized conser 27.8 1.3E+02 0.0029 31.4 5.8 83 115-217 110-194 (366)
58 PF07250 Glyoxal_oxid_N: Glyox 27.7 1.5E+02 0.0033 29.4 6.1 45 112-159 165-212 (243)
59 PHA02651 IL-1 receptor antagon 25.8 1.4E+02 0.0029 28.4 5.1 56 255-321 102-157 (165)
60 cd07894 Adenylation_RNA_ligase 25.3 2.6E+02 0.0056 29.1 7.5 141 113-274 45-208 (342)
61 KOG0166 Karyopherin (importin) 24.7 44 0.00095 36.7 1.9 38 4-42 6-47 (514)
62 PRK09974 putative regulator Pr 24.5 83 0.0018 27.9 3.2 69 325-395 21-100 (111)
63 PF05970 PIF1: PIF1-like helic 24.3 25 0.00055 36.1 0.0 82 125-218 49-130 (364)
64 PF03427 CBM_19: Carbohydrate 23.1 64 0.0014 25.8 2.1 16 116-131 43-58 (61)
65 cd04663 Nudix_Hydrolase_6 Memb 22.9 2.1E+02 0.0045 25.5 5.5 19 192-210 90-108 (126)
66 PRK14350 ligA NAD-dependent DN 22.8 3.5E+02 0.0076 30.8 8.4 96 249-356 273-385 (669)
67 COG1430 Uncharacterized conser 21.2 2.6E+02 0.0056 25.3 5.8 84 256-348 40-123 (126)
68 PHA02979 hypothetical protein; 21.1 1.1E+02 0.0024 27.6 3.3 18 336-353 102-120 (140)
69 TIGR00575 dnlj DNA ligase, NAD 20.3 5.9E+02 0.013 28.8 9.6 95 250-354 265-374 (652)
No 1
>KOG3132 consensus m3G-cap-specific nuclear import receptor (Snurportin1) [RNA processing and modification]
Probab=100.00 E-value=1.1e-96 Score=702.62 Aligned_cols=259 Identities=56% Similarity=0.973 Sum_probs=238.8
Q ss_pred CCCCCCCcCCCCC-CchHHH-HHHHHHHHHHHhHHHHHHHHhhhhhhhccccCCCCCCCCCCCCCCCCCccccCCCCccc
Q 014751 2 APPDLRRPFKRTA-ISDQQR-RRELSLQRQSQNRRDAQQQARCLASSVLSLQSQYPDPVPELEIEPESQPQQEAGPLTKD 79 (419)
Q Consensus 2 aph~~~~~~k~~~-~~~Q~~-RR~~~Le~Qk~~R~d~~~~aR~La~~~~~~~~~~~~~~~e~~~~~~~~e~~~~~~~~~~ 79 (419)
+||||.+|||.+. ..+|++ ||+.+|++||.+|.|+++|+|+||.++|+ + + |++| + .
T Consensus 22 ~~hpR~sQykn~~s~aeQ~arrr~~llelQks~r~D~~~~~r~lA~dd~t----g--------~--Esee------~--k 79 (325)
T KOG3132|consen 22 LSHPRQSQYKNLTSDAEQRARRRASLLELQKSSRPDVDPEIRSLAVDDLT----G--------T--ESEE------S--K 79 (325)
T ss_pred ccCchhhhhhhhhhHHHHHHHHHHHHHHhhhcCCCCccHHHHhhcccccc----c--------c--cchh------h--h
Confidence 7999999999986 445554 55569999999999999999999999886 2 1 1101 1 3
Q ss_pred hhhhhhhhccCCcchhhhhhhcccccccccCCCCCCCceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEEeeccCCCCCC
Q 014751 80 LDIRQASKLRGPEVRKWFASQLMLPEWMIDVPDRLSHDWYVFARPAGKRCIVVSSNGTTVSRERNGSILHHFPSALPSGA 159 (419)
Q Consensus 80 ~d~~~~~k~~gk~~rk~ya~qLMlsEWl~dvP~dL~~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~~F~S~LPgG~ 159 (419)
.|++++++.+||+.+||||+||||||||+|||++|+++|+||+||+|||||||||+|+|++|+|+|+++++|+|+||||+
T Consensus 80 ~d~~~a~~~tgk~~~K~yA~qlMLsEWliDvP~~LsqdW~vv~~PvGKR~lvVaSrG~Tvay~k~G~~v~rF~S~LPGGn 159 (325)
T KOG3132|consen 80 FDVRQASRLTGKEARKWYAKQLMLSEWLIDVPDNLSQDWYVVARPVGKRCLVVASRGTTVAYVKNGSTVHRFPSALPGGN 159 (325)
T ss_pred hhhhHHhhhcchhHHHHHHHHhhhHHHhccCccccCcceEEEEeecCceEEEEecCCceEEEecCCeeEeeccccCCCCC
Confidence 56678888999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCCCCCCcEEEeeeEecCCcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCCCCCceeccccccC
Q 014751 160 RTKDPSGSAQSYCILDCIFHELDQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVYNC 239 (419)
Q Consensus 160 ~~~~~~~~~~~ytILDCIy~e~~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~n~~~F~~lp~~~c 239 (419)
++ .+.+++||||||||+|.|+|||||||||||||++|+|++|||||||+|||+|.+++++++.+|+|+|+++|+|||
T Consensus 160 rr---~~~a~~ytILDCIy~esnQTYYVlD~~cWrgh~~yec~~dFRffwl~SKL~E~~~l~~~t~~~~f~Fs~vp~~pC 236 (325)
T KOG3132|consen 160 RR---KGPANSYTILDCIYHESNQTYYVLDMVCWRGHSLYECTSDFRFFWLQSKLAETGALDPPTVYHKFRFSVVPFYPC 236 (325)
T ss_pred cC---CCCcccceeeeeeecccCceEEEEEEEeecCcccccCchHHHHHHHhhhccccccCCCCCcCccceecccCCCCC
Confidence 85 467899999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ChHhHHHHHhcCCCCCcccEEeEeccccccCCCCcCeeeeccCCCc
Q 014751 240 DQRGLYSAYIESVPYAKDGLLFYNKHAHYQTGNTPLALVWKDEKCS 285 (419)
Q Consensus 240 ~~~~L~~~~~~~~p~~~DGLLFYHKea~Y~~G~TPLv~~wkD~~~s 285 (419)
++++|..+|++++||.+||||||||..+|+||.||||||+|....+
T Consensus 237 ~q~~l~~~~~~~~pf~~DGLLFYhks~~yqpgqsplvgwlkp~ml~ 282 (325)
T KOG3132|consen 237 DQSGLHSAYTGSLPFVRDGLLFYHKSVVYQPGQSPLVGWLKPWMLP 282 (325)
T ss_pred CHHHHHHHHcCCCceeeeeEEEeecceeeCCCCCccccccchhhhH
Confidence 9999999999999999999999999999999999999999965544
No 2
>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=100.00 E-value=2e-69 Score=502.82 Aligned_cols=182 Identities=55% Similarity=1.061 Sum_probs=175.6
Q ss_pred hhhhcccccccccCCCCCCCceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEEeeccCCCCCCCCCCCCCCCCCcEEEee
Q 014751 97 FASQLMLPEWMIDVPDRLSHDWYVFARPAGKRCIVVSSNGTTVSRERNGSILHHFPSALPSGARTKDPSGSAQSYCILDC 176 (419)
Q Consensus 97 ya~qLMlsEWl~dvP~dL~~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~~F~S~LPgG~~~~~~~~~~~~ytILDC 176 (419)
||||||+||||+++|+||+++|+|+|||+||||||||++|.|++|+|+|++++.|+|.||||+..+ ..+++|||||
T Consensus 2 ~~~~lml~Ewm~~~p~~l~~~w~~~~~P~G~R~lvv~~~g~t~~~~r~g~~~~~f~s~lP~g~~~~----~~~g~tILDc 77 (186)
T cd09232 2 YANQLMLSEWMVEVPDDLSEEWLVVPCPVGKRCLVVASKGKTVARSKNGRTLHRFSSALPGGSRKT----SNSGYTILDC 77 (186)
T ss_pred cccceechhhcccCCCccCcceEEEECcCceEEEEEEeCCEEEEEeCCCCEEEecccCCCCCCcCC----CCCCCEEEEE
Confidence 899999999999999999999999999999999999999999999999999999999999998642 5689999999
Q ss_pred eEecCCcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCCCCCceeccccccCChHhHHHHHhcCC---C
Q 014751 177 IFHELDQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVYNCDQRGLYSAYIESV---P 253 (419)
Q Consensus 177 Iy~e~~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~n~~~F~~lp~~~c~~~~L~~~~~~~~---p 253 (419)
||++.+.||||||||||||++++||+||||||||+|||+|.+.....+..|+|+|+.+|+|+|+.++|.++|+... +
T Consensus 78 i~~~~~~~yyVlDii~w~g~~l~d~~~~~Rf~wl~skl~E~~~~~~~~~~~~~~f~~~p~~~~~~~~l~~~~~~~~~~~~ 157 (186)
T cd09232 78 IYNEDDRTYYVLDVLCWNGHPLYDCETEFRFFWLRSKLEELPELDEPSEKNPFRFVPLPYFPCTKESLQSAYSGPLNDDP 157 (186)
T ss_pred ecCCCCCEEEEEEEeeeCCcccccCCcchhHHHHHhhCCCccccccccccCCceEEecCcccCcHHHHHHHHhcccccCC
Confidence 9999999999999999999999999999999999999999887777788999999999999999999999999998 9
Q ss_pred CCcccEEeEeccccccCCCCcCeeeeccC
Q 014751 254 YAKDGLLFYNKHAHYQTGNTPLALVWKDE 282 (419)
Q Consensus 254 ~~~DGLLFYHKea~Y~~G~TPLv~~wkD~ 282 (419)
+++||||||||+++|++|.||||+||||+
T Consensus 158 ~e~DGLlFyhk~~~Y~~G~tPlvl~wKp~ 186 (186)
T cd09232 158 YELDGLLFYHKESHYTPGSTPLVLWLKDY 186 (186)
T ss_pred CCCceEEEEeCCCcccCcCCCcEEEecCC
Confidence 99999999999999999999999999985
No 3
>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=99.68 E-value=5.4e-16 Score=141.71 Aligned_cols=170 Identities=23% Similarity=0.264 Sum_probs=141.2
Q ss_pred cccccccccCCC--CCCCceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEEeeccCCCCCCCCCCCCCCCCCcEEEeeeE
Q 014751 101 LMLPEWMIDVPD--RLSHDWYVFARPAGKRCIVVSSNGTTVSRERNGSILHHFPSALPSGARTKDPSGSAQSYCILDCIF 178 (419)
Q Consensus 101 LMlsEWl~dvP~--dL~~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~~F~S~LPgG~~~~~~~~~~~~ytILDCIy 178 (419)
.|++.|+...+. ....+|++-+..-|.||+++..+|.+.+++|+|..+..+...+|.... ......|||||-+
T Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~e~K~DG~R~~~~~~~~~v~~~sR~g~~~~~~~~~~~~~~~-----~~~~~~~ilDGEl 76 (182)
T cd06846 2 QLLNPILEEALSEYDEQDEYYVQEKYDGKRALIVALNGGVFAISRTGLEVPLPSILIPGREL-----LTLKPGFILDGEL 76 (182)
T ss_pred CccchhhhHHHhhccccCcEEEEEccCceEEEEEEcCCeEEEEeCCCCEEecccccccchHH-----hccCCCeeEEEEE
Confidence 378888887654 457899999999999999999999999999999988876666764110 1123469999998
Q ss_pred ecCC-------cEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCCCCCceeccccccCChHhHHHHHhcC
Q 014751 179 HELD-------QTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVYNCDQRGLYSAYIES 251 (419)
Q Consensus 179 ~e~~-------~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~n~~~F~~lp~~~c~~~~L~~~~~~~ 251 (419)
.-.+ -+|||.|||+|+|..+.+++..-|+-+|++.+.+.... .++.+..++.++|+.+.+.+++...
T Consensus 77 v~~~~~~~~~~~~~~~FDil~~~~~~~~~~p~~eR~~~L~~~v~~~~~~------~~~~i~~~~~~~~~~~~~~~~~~~~ 150 (182)
T cd06846 77 VVENREVANPKPTYYAFDVVPLSGVGLRDLPYSDRFAYLKSLLKEFEGL------DPVKLVPLENAPSYDETLDDLLEKL 150 (182)
T ss_pred EeccCCCccceeEEEEEEEEEECCCccccCCHHHHHHHHHHHhhhhccC------CceeEEEeecccccchHHHHHHHHh
Confidence 7654 38999999999999999999999999999999775321 3577788888898877788888777
Q ss_pred CCCCcccEEeEeccccc--cCCCCcCeeeecc
Q 014751 252 VPYAKDGLLFYNKHAHY--QTGNTPLALVWKD 281 (419)
Q Consensus 252 ~p~~~DGLLFYHKea~Y--~~G~TPLv~~wkD 281 (419)
...-.||++|-+.++.| .+|.++.++.||.
T Consensus 151 ~~~g~EGvi~K~~~s~Y~~~~gr~~~wlK~Kp 182 (182)
T cd06846 151 KKKGKEGLVFKHPDAPYKGRPGSSGNQLKLKP 182 (182)
T ss_pred hhcCCceEEEEcCCCCccccCCCCCceEeecC
Confidence 77889999999999999 9999999999984
No 4
>PF01331 mRNA_cap_enzyme: mRNA capping enzyme, catalytic domain; InterPro: IPR001339 The mRNA capping enzyme in yeasts is composed of two separate chains, alpha a mRNA guanyltransferase and beta an RNA 5'-triphosphate. X-ray crystallography reveals a large conformational change during guanyl transfer by mRNA capping enzymes []. Binding of the enzyme to nucleotides is specific to the GMP moiety of GTP. The viral mRNA capping enzyme is a monomer that transfers a GMP cap onto the end of mRNA that terminates with a 5'-diphosphate tail.; GO: 0004484 mRNA guanylyltransferase activity, 0006370 mRNA capping, 0006397 mRNA processing; PDB: 3RTX_A 3KYH_D 3S24_G 1CKN_B 1CKO_A 1CKM_B 1P16_B.
Probab=99.47 E-value=3.2e-13 Score=124.95 Aligned_cols=159 Identities=21% Similarity=0.397 Sum_probs=109.3
Q ss_pred CceEEEEecCCcEEEEEeeCCeEEEEcCCCcE--EE--eeccCCCCCCCCCCCCCCCCCcEEEeeeEecC------CcEE
Q 014751 116 HDWYVFARPAGKRCIVVSSNGTTVSRERNGSI--LH--HFPSALPSGARTKDPSGSAQSYCILDCIFHEL------DQTY 185 (419)
Q Consensus 116 ~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~--l~--~F~S~LPgG~~~~~~~~~~~~ytILDCIy~e~------~~ty 185 (419)
.+++|..=.-|.|+|+...++.+-..+++-.. +. .|+....+. .+.....||||+.+..+ .-+|
T Consensus 16 ~~Y~V~eKaDG~Ryll~i~~~~~ylidr~~~~~~v~~~~~p~~~~~~------~~~~~~~TLLDGElV~d~~~~~~~~~f 89 (192)
T PF01331_consen 16 KDYFVCEKADGTRYLLLITDNGVYLIDRKNNVFKVDNLHFPSKKDSS------DGRHHQDTLLDGELVLDKDPGEKKPRF 89 (192)
T ss_dssp S-EEEEEEESSEEEEEEEEEEEEEEEETTS-EEEESSST-ECTTC--------TTCEGCSEEEEEEEEEEECTTCEEEEE
T ss_pred CCcEEEECCCCcEEEEEEecceEEEEeCCCcEEEecCcccccccccc------cccccCCEEEEEEEEcccCCCCCceEE
Confidence 47788888999999999999877666666543 22 455544321 12235579999966533 4699
Q ss_pred EEEEEEeeCCcccccccchhhHHHhhhhccccCCC-----C-CCCCCCCCceeccccccCChHhH--HHHHhcCCCCCcc
Q 014751 186 YVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGAC-----D-APSHYYKFRFSTVPVYNCDQRGL--YSAYIESVPYAKD 257 (419)
Q Consensus 186 YVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~-----~-~~s~~n~~~F~~lp~~~c~~~~L--~~~~~~~~p~~~D 257 (419)
||.|+|+|+|..+.+++...|+.||+..+.+.... . ...+..||.+..-+.++...... ...+....+++.|
T Consensus 90 lifD~l~~~G~~v~~~~~~~Rl~~l~~~i~~p~~~~~~~~~~~~~~~~pf~i~~K~~~~~~~~~~~~~~~~~~~l~h~~D 169 (192)
T PF01331_consen 90 LIFDILAINGQNVTDKPLDERLAYLQEEIIEPRKNAELKSGIIKKKKEPFSIRIKDFFPIYQIEKLLFEEFIPKLPHETD 169 (192)
T ss_dssp EEEEEEEETTEEGCCSBHHHHHHHHHHHTHHHHHHHHCHTTSCTCTTSSSEEEE---EEGGGHHHHCHHCCCCCTTSTEE
T ss_pred EEEeeehhCCcEeccCCHHHHHHHHHHHHHHHHHhhccccccccccccceeeeccccHHHHhhHHHHHHHhhccCCCCCC
Confidence 99999999999999999999999999887763211 1 11223566666667776643322 3344567889999
Q ss_pred cEEeEeccccccCCCCcCeeeec
Q 014751 258 GLLFYNKHAHYQTGNTPLALVWK 280 (419)
Q Consensus 258 GLLFYHKea~Y~~G~TPLv~~wk 280 (419)
||+|.+.+..|.+|..+-++=||
T Consensus 170 GLIFtp~~~pY~~Gt~~~llKWK 192 (192)
T PF01331_consen 170 GLIFTPVNTPYVPGTCPNLLKWK 192 (192)
T ss_dssp EEEEEESSSB--SEEEEEEEEE-
T ss_pred EEEEecCCCCccCCCCCccEeeC
Confidence 99999999999999999999997
No 5
>PF11538 Snurportin1: Snurportin1; InterPro: IPR024721 Snurportin-1 is a nuclear import receptor that contains an N-terminal importin beta binding domain which is essential for its function as an snRNP-specific nuclear import receptor []. Snurportin-1 interacts with m3G-cap where it enhances the m3G-cap dependent nuclear import of U snRNPs in Xenopus laevis oocytes and digitonin-permeabilized HeLa cells []. This entry represents the snurportin-1 N-terminal importin beta binding domain (IBB). The essential role of the IBB domain for snurportin-1 function suggests that snurportin-1 cooperates with importin beta in mediating nuclear import of snRNPs.; GO: 0005515 protein binding; PDB: 3LWW_D 3NC0_E 3NBZ_E 2Q5D_C 3NBY_B 3GB8_B 3GJX_B 2QNA_B 2P8Q_B.
Probab=99.30 E-value=1.9e-12 Score=93.51 Aligned_cols=39 Identities=31% Similarity=0.330 Sum_probs=35.3
Q ss_pred CCCCCcCCCCC-CchHHHHHHHHHHHHHHhHHHHHHHHhh
Q 014751 4 PDLRRPFKRTA-ISDQQRRRELSLQRQSQNRRDAQQQARC 42 (419)
Q Consensus 4 h~~~~~~k~~~-~~~Q~~RR~~~Le~Qk~~R~d~~~~aR~ 42 (419)
|||+++||.+. +.+|++||+++|++||++|+|++||||+
T Consensus 1 HPR~sqYK~~~~~~~Q~eRR~~~Le~QK~kR~d~~~~aR~ 40 (40)
T PF11538_consen 1 HPRLSQYKNKGSALDQEERRREFLERQKNKRLDYVNHARR 40 (40)
T ss_dssp -TTCSCTT-TTTSCSHHHHHHHHHHHHHSHHSHHHHHHHH
T ss_pred CccHHHhhcccchHhHHHHHHHHHHHHHHHhHHHHHhccC
Confidence 89999999996 7799999999999999999999999995
No 6
>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=98.67 E-value=4.5e-07 Score=85.52 Aligned_cols=162 Identities=17% Similarity=0.293 Sum_probs=113.4
Q ss_pred CceEEEEecCCcEEEEEeeC-CeEEEEcCCCcEEEeeccCCCCCCCCCCCCCCCCCcEEEeeeEecCCc------EEEEE
Q 014751 116 HDWYVFARPAGKRCIVVSSN-GTTVSRERNGSILHHFPSALPSGARTKDPSGSAQSYCILDCIFHELDQ------TYYVI 188 (419)
Q Consensus 116 ~~Wl~vpcPvGkRcLVVas~-G~T~ay~k~G~~l~~F~S~LPgG~~~~~~~~~~~~ytILDCIy~e~~~------tyYVL 188 (419)
.+|++-.=--|-||+++..+ |.+..++++|..+....-.+|..... .....-||||+=+..... +|||.
T Consensus 41 ~~y~ve~K~DG~R~~l~~~~~~~v~l~sR~~~~~~~~~~~~~~~~~~----~~~~~~~ilDGElv~~~~~~~~~~~~~vF 116 (215)
T cd07895 41 NDYFVCEKSDGVRYLLLITGRGEVYLIDRKNDVFKVPGLFFPRRKNL----EPHHQGTLLDGELVIDKVPGKKRPRYLIF 116 (215)
T ss_pred CCeEEEEeEcCeEEEEEEecCCcEEEEeCCCCeEEeccccCCCcccc----cccccCeeeEEEEEEEcCCCceEEEEEEE
Confidence 57777777789999999998 99999999998766433344421110 111345999997775443 69999
Q ss_pred EEEeeCCcccccccchhhHHHhhhhccccCCCC----C-CCCCCCCceeccccccCC-hHhHHHHHhcCCCCCcccEEeE
Q 014751 189 DMVCWRGYSLYDCTAEFRFFWLNSKLAETGACD----A-PSHYYKFRFSTVPVYNCD-QRGLYSAYIESVPYAKDGLLFY 262 (419)
Q Consensus 189 Dvl~W~g~~l~dceteFRffWl~SKl~E~~~~~----~-~s~~n~~~F~~lp~~~c~-~~~L~~~~~~~~p~~~DGLLFY 262 (419)
|+|+++|.++.+.+..=|.-.|+.-+.+...-. . .....++.+..-++++++ .+.+...+....+...|||+|-
T Consensus 117 DiL~~~g~~l~~~pl~~R~~~L~~~i~~~~~~~~~~~~~~~~~~~~~i~~k~~~~~~~~~~~~~~~~~~~~~~~EGlIfk 196 (215)
T cd07895 117 DILAFNGQSVTEKPLSERLKYIKKEVIEPRNELLKKGPIDKAKEPFSVRLKDFFPLYKIEKLFEKIIPKLPHENDGLIFT 196 (215)
T ss_pred EEEEECCcCccCCCHHHHHHHHHHhchhHHHHhhhcChhhcCCCCeEEEecceEeHHhHHHHHHhccccCCCCCCCEEEc
Confidence 999999999999999999988888776532100 0 011223455556677763 2333333322357889999999
Q ss_pred eccccccCCCCcCeeeecc
Q 014751 263 NKHAHYQTGNTPLALVWKD 281 (419)
Q Consensus 263 HKea~Y~~G~TPLv~~wkD 281 (419)
..++.|.+|.++.++=||.
T Consensus 197 ~~~~~Y~~Gr~~~~lKwKp 215 (215)
T cd07895 197 PNDEPYVPGTDKNLLKWKP 215 (215)
T ss_pred cCCCCccCccCCcceeeCC
Confidence 9999999999998888873
No 7
>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=98.65 E-value=3e-07 Score=85.14 Aligned_cols=156 Identities=20% Similarity=0.245 Sum_probs=110.5
Q ss_pred cccccccccCCCCCCCceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEEe-eccCCCCCCCCCCCCCCCCCcEEEeeeEe
Q 014751 101 LMLPEWMIDVPDRLSHDWYVFARPAGKRCIVVSSNGTTVSRERNGSILHH-FPSALPSGARTKDPSGSAQSYCILDCIFH 179 (419)
Q Consensus 101 LMlsEWl~dvP~dL~~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~~-F~S~LPgG~~~~~~~~~~~~ytILDCIy~ 179 (419)
-||+.=.-.+|+ +++|++=+---|-||+|+...|...++||+|..+.. |+....-... ....-|||||-+.
T Consensus 3 pmLa~~~~~~~~--~~~~~~e~K~DG~R~~i~~~~~~v~~~SR~g~~~t~~~p~l~~~~~~------~~~~~~iLDGElv 74 (190)
T cd07906 3 PMLATLVDEPPD--GEDWLYEIKWDGYRALARVDGGRVRLYSRNGLDWTARFPELAEALAA------LPVRDAVLDGEIV 74 (190)
T ss_pred CeECCcCCCCCC--CCCeEEEEeEceEEEEEEEECCEEEEEcCCCCcchhhhHHHHHHHHh------cCCCCEEEEeEEE
Confidence 366666655555 469999999999999999999999999999987642 4321100000 0122399999554
Q ss_pred c-------------------------CCcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCCCCCceecc
Q 014751 180 E-------------------------LDQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTV 234 (419)
Q Consensus 180 e-------------------------~~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~n~~~F~~l 234 (419)
- ..-+|||.|||..+|.++.+=+..=|+-.|.+-+... +-++...
T Consensus 75 ~~~~~~~~~F~~l~~~~~~~~~~~~~~~~~~~vFDil~~~~~~~~~~p~~eR~~~L~~~~~~~----------~~~i~~~ 144 (190)
T cd07906 75 VLDEGGRPDFQALQNRLRLRRRLARTVPVVYYAFDLLYLDGEDLRGLPLLERKELLEELLPAG----------SPRLRVS 144 (190)
T ss_pred EECCCCCCCHHHHHHhhcccchhcccCceEEEEEeeeeeCCcchhhCCHHHHHHHHHHHhccC----------CCcEEEC
Confidence 2 1246999999999999988888888999888877653 2245667
Q ss_pred ccccCChHhHHHHHhcCCCCCcccEEeEeccccccCCC-CcCee
Q 014751 235 PVYNCDQRGLYSAYIESVPYAKDGLLFYNKHAHYQTGN-TPLAL 277 (419)
Q Consensus 235 p~~~c~~~~L~~~~~~~~p~~~DGLLFYHKea~Y~~G~-TPLv~ 277 (419)
|++....+.+ +.....--.+|+++-+.++.|.+|. |+.++
T Consensus 145 ~~~~~~~~~~---~~~~~~~g~EGiv~K~~~s~Y~~g~rs~~wl 185 (190)
T cd07906 145 EHFEGGGAAL---FAAACELGLEGIVAKRADSPYRSGRRSRDWL 185 (190)
T ss_pred ceEcCCHHHH---HHHHHHcCCcEEEEecCCCCcCCCCCCCccE
Confidence 7777664332 3222233579999999999999999 87543
No 8
>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=98.18 E-value=2.3e-05 Score=73.97 Aligned_cols=163 Identities=20% Similarity=0.275 Sum_probs=113.9
Q ss_pred cccccccccCCCCC--CCceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEE-eeccCCCCCCCCCCCCCCCCCcEEEeee
Q 014751 101 LMLPEWMIDVPDRL--SHDWYVFARPAGKRCIVVSSNGTTVSRERNGSILH-HFPSALPSGARTKDPSGSAQSYCILDCI 177 (419)
Q Consensus 101 LMlsEWl~dvP~dL--~~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~-~F~S~LPgG~~~~~~~~~~~~ytILDCI 177 (419)
-||++=.-.+|+.+ ..+|++=+==-|-||++....|....+||+|..+. .|+....--. .-..-||||+=
T Consensus 7 pmLA~~~~~~~~~~~~~~~~~~E~K~DG~R~~~~~~~~~v~l~SR~g~~~t~~~p~l~~~~~-------~l~~~~iLDGE 79 (207)
T cd07897 7 FMLAHPLEDDPEDLGDPSDWQAEWKWDGIRGQLIRRGGEVFLWSRGEELITGSFPELLAAAE-------ALPDGTVLDGE 79 (207)
T ss_pred ceeCCcCCCchhhhcCcccEEEEEeEceEEEEEEEcCCEEEEEeCCCCcccccchHHHHHHH-------hCCCCeEEEeE
Confidence 35666555555532 34788888788999999999999999999998765 3543211000 00124999984
Q ss_pred Ee---cC-------------------------CcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCCCCC
Q 014751 178 FH---EL-------------------------DQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKF 229 (419)
Q Consensus 178 y~---e~-------------------------~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~n~~ 229 (419)
.. .. .-+|+|.|||..+|.++.+.+..=|.--|.+-+.+.+ .-
T Consensus 80 lv~~~~~~~~~F~~l~~r~~~~~~~~~~~~~~~~~~~vFDil~l~g~~l~~~pl~eRr~~L~~l~~~~~---------~~ 150 (207)
T cd07897 80 LLVWRDGRPLPFNDLQQRLGRKTVGKKLLAEAPAAFRAYDLLELNGEDLRALPLRERRARLEALLARLP---------PP 150 (207)
T ss_pred EEEecCCCccCHHHHHHHhcccccchhhHhhCCeEEEEEeeeeECceEhhhCCHHHHHHHHHHhhhhcC---------CC
Confidence 32 10 1279999999999999999998888888888665421 13
Q ss_pred ceeccccccCC-hHhHHHHHhcCCCCCcccEEeEeccccccCCCCcCeeeec
Q 014751 230 RFSTVPVYNCD-QRGLYSAYIESVPYAKDGLLFYNKHAHYQTGNTPLALVWK 280 (419)
Q Consensus 230 ~F~~lp~~~c~-~~~L~~~~~~~~p~~~DGLLFYHKea~Y~~G~TPLv~~wk 280 (419)
.+.+.|+..|+ .+.+.++|......-..|+++-..++.|.+|..- -.|||
T Consensus 151 ~i~~~~~~~~~~~~~~~~~~~~~~~~g~EGiv~K~~~s~Y~~Grr~-~~W~K 201 (207)
T cd07897 151 RLDLSPLIAFADWEELAALRAQSRERGAEGLMLKRRDSPYLVGRKK-GDWWK 201 (207)
T ss_pred ceeecceEecCCHHHHHHHHHHHHHcCCeEEEEeCCCCCcCCCCcC-CCeeE
Confidence 55667777774 4667777765555568999999999999999643 23565
No 9
>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=98.12 E-value=4.9e-05 Score=70.96 Aligned_cols=160 Identities=19% Similarity=0.229 Sum_probs=111.7
Q ss_pred cccccccccCCCCCCCceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEE-eeccCCCCCCCCCCCCCCCCCcEEEeeeEe
Q 014751 101 LMLPEWMIDVPDRLSHDWYVFARPAGKRCIVVSSNGTTVSRERNGSILH-HFPSALPSGARTKDPSGSAQSYCILDCIFH 179 (419)
Q Consensus 101 LMlsEWl~dvP~dL~~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~-~F~S~LPgG~~~~~~~~~~~~ytILDCIy~ 179 (419)
-||+.-...+|+ ..+|++=+==-|-||+++...|.+..+|++|..+. .||....-- .. ....-+||||=.-
T Consensus 3 PmLa~~~~~~~~--~~~~~~E~K~DG~R~~~~~~~~~v~l~SR~g~~~t~~~p~~~~~~-~~-----~~~~~~iLDGElv 74 (194)
T cd07905 3 PMLARAVDALPE--PGGWQYEPKWDGFRCLAFRDGDEVRLQSRSGKPLTRYFPELVAAA-RA-----LLPPGCVLDGELV 74 (194)
T ss_pred ceeCCccCCCCC--CCceEEEeeeceEEEEEEEeCCEEEEEeCCCCchhhhhHHHHHHH-Hh-----hCCCCEEEEeEEE
Confidence 367666666665 56899988889999999999999999999998765 344321100 00 0011389998543
Q ss_pred c----------------------------CCcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCCCCCce
Q 014751 180 E----------------------------LDQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRF 231 (419)
Q Consensus 180 e----------------------------~~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~n~~~F 231 (419)
- ..-+|+|.|||..+|.++.+.+..=|.--|.+-+.+. .-.+
T Consensus 75 ~~~~~~~~F~~l~~r~~~~~~~~~~~~~~~~~~~~vFDiL~l~g~~l~~~pl~eRr~~L~~~~~~~----------~~~i 144 (194)
T cd07905 75 VWRGGRLDFDALQQRIHPAASRVRRLAEETPASFVAFDLLALGGRDLRGRPLRERRAALEALLAGW----------GPPL 144 (194)
T ss_pred EEcCCCCCHHHHHHHhcccccchhhhhccCCEEEEEEeeeeeCCcccccCCHHHHHHHHHHHhccc----------CCCe
Confidence 1 1137999999999999999999998888888777543 1234
Q ss_pred eccccccCChHhHHHHHhcCCCCCcccEEeEeccccccCCCCcCeeeeccC
Q 014751 232 STVPVYNCDQRGLYSAYIESVPYAKDGLLFYNKHAHYQTGNTPLALVWKDE 282 (419)
Q Consensus 232 ~~lp~~~c~~~~L~~~~~~~~p~~~DGLLFYHKea~Y~~G~TPLv~~wkD~ 282 (419)
..+|... +.+.+.+++.....--..|+++-..++.|++|. . .|||=.
T Consensus 145 ~~~~~~~-~~~~~~~~~~~~~~~g~EGiv~K~~~s~Y~~Gr-~--~WlK~K 191 (194)
T cd07905 145 HLSPATT-DRAEAREWLEEFEGAGLEGVVAKRLDGPYRPGE-R--AMLKVK 191 (194)
T ss_pred EECCccC-CHHHHHHHHHHHHHCCCceEEEeCCCCCcCCCC-C--cEEEEe
Confidence 5556432 334455555544445578999999999999998 3 688743
No 10
>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=97.97 E-value=6e-05 Score=71.49 Aligned_cols=156 Identities=17% Similarity=0.231 Sum_probs=106.7
Q ss_pred CceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEE-eeccCCCCCC-CC--CCCCCCCCCcEEEeee---EecC-------
Q 014751 116 HDWYVFARPAGKRCIVVSSNGTTVSRERNGSILH-HFPSALPSGA-RT--KDPSGSAQSYCILDCI---FHEL------- 181 (419)
Q Consensus 116 ~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~-~F~S~LPgG~-~~--~~~~~~~~~ytILDCI---y~e~------- 181 (419)
.+|++=.==-|-||+|...+|....+||+|..+. .|+-..=... .. ...-.....-+||||= ++..
T Consensus 33 ~~~~~E~K~DG~R~~i~~~~~~v~l~SR~g~~~t~~~p~~~~~~~~~~~l~~~~~~~~~~~iLDGElv~~~~~~~~~~~f 112 (225)
T cd07903 33 KPFYIETKLDGERIQLHKDGNEFKYFSRNGNDYTYLYGASLTPGSLTPYIHLAFNPKVKSCILDGEMVVWDKETKRFLPF 112 (225)
T ss_pred CeEEEEEeeCceEEEEEecCCEEEEEeCCCccccccccccccccccchhhhhhccccCcEEEeceEEEEEEcCcCeeccc
Confidence 4666666667999999999999999999998765 3442210000 00 0000011234899973 3221
Q ss_pred -----------------CcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCCCCCceeccccccCCh-Hh
Q 014751 182 -----------------DQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVYNCDQ-RG 243 (419)
Q Consensus 182 -----------------~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~n~~~F~~lp~~~c~~-~~ 243 (419)
.-+|+|.|||..+|.++.+.+..=|.-=|.+-+.+. +.++..+|.+.++. +.
T Consensus 113 ~~l~~~~~~~~~~~~~~~~~~~vFDiL~~~g~~l~~~pl~eR~~~L~~~~~~~----------~~~i~~~~~~~~~~~~~ 182 (225)
T cd07903 113 GTLKDVAKLREVEDSDLQPCFVVFDILYLNGKSLTNLPLHERKKLLEKIITPI----------PGRLEVVKRTEASTKEE 182 (225)
T ss_pred hHHHHHHhhcccccCCccEEEEEEEEEEECCeecccCcHHHHHHHHHHhcCCC----------CCeEEEEEEEeCCCHHH
Confidence 136999999999999999988888877777665432 13566778887754 66
Q ss_pred HHHHHhcCCCCCcccEEeEeccccccCC-CCcCeeeecc
Q 014751 244 LYSAYIESVPYAKDGLLFYNKHAHYQTG-NTPLALVWKD 281 (419)
Q Consensus 244 L~~~~~~~~p~~~DGLLFYHKea~Y~~G-~TPLv~~wkD 281 (419)
+.+++.....--..|+++-..++.|.+| .|..++=||.
T Consensus 183 ~~~~~~~~~~~g~EGlv~K~~~s~Y~~g~Rs~~wlK~K~ 221 (225)
T cd07903 183 IEEALNEAIDNREEGIVVKDLDSKYKPGKRGGGWIKIKP 221 (225)
T ss_pred HHHHHHHHHHcCCceEEEecCCCCCccCCcCCCcEEech
Confidence 7777665555568999999999999999 6777766663
No 11
>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=97.95 E-value=0.00038 Score=69.39 Aligned_cols=164 Identities=19% Similarity=0.229 Sum_probs=109.3
Q ss_pred cCCCCCCCceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEE-eeccCCCCCCCCCCCCCCCCCcEEEeeeEec---C---
Q 014751 109 DVPDRLSHDWYVFARPAGKRCIVVSSNGTTVSRERNGSILH-HFPSALPSGARTKDPSGSAQSYCILDCIFHE---L--- 181 (419)
Q Consensus 109 dvP~dL~~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~-~F~S~LPgG~~~~~~~~~~~~ytILDCIy~e---~--- 181 (419)
+.|.+ +.+|++=+==-|-||++....|....+||+|..+. .|+... .... .....-+||||=+.- .
T Consensus 6 ~~~~~-~~~~~~E~K~DG~R~~~~~~~~~v~l~SR~g~~~t~~~p~l~-~~~~-----~~~~~~~iLDGElv~~d~~g~~ 78 (298)
T TIGR02779 6 TTPPT-GDDWRYEVKYDGYRCLARIEGGKVRLISRNGHDWTEKFPILA-AALA-----ALPILPAVLDGEIVVLDESGRS 78 (298)
T ss_pred CCCCC-CCCEEEEEEEceEEEEEEEeCCEEEEEeCCCCchHhHhHHHH-HHHH-----hCCCCcEEEEeEEEEECCCCCC
Confidence 44433 46899888888999999999999999999998764 453211 0000 000123999984432 1
Q ss_pred ---------------CcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCCCCCceeccccccC-ChHhHH
Q 014751 182 ---------------DQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVYNC-DQRGLY 245 (419)
Q Consensus 182 ---------------~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~n~~~F~~lp~~~c-~~~~L~ 245 (419)
.-+|+|.|||..+|.++.+-+..=|.--|.+-+.+.+. +..+. +. .+ +.+.+.
T Consensus 79 ~F~~l~~r~~~~~~~~~~~~vFDiL~l~g~~l~~~pl~eRr~~L~~l~~~~~~--------~~~~~--~~-~~~~~~~~~ 147 (298)
T TIGR02779 79 DFSALQNRLRAGRDRPATYYAFDLLYLDGEDLRDLPLSERKKLLEELLKAIKG--------PLAPD--RY-SVHFEGDGQ 147 (298)
T ss_pred CHHHHHhhhhcCCCCceEEEEEeeeeECceehhcCCHHHHHHHHHHHhcccCC--------CceeE--ec-ccCchhHHH
Confidence 12799999999999999888888888777776654321 11111 11 22 234455
Q ss_pred HHHhcCCCCCcccEEeEeccccccCCCCcCeeeeccCCCccceee
Q 014751 246 SAYIESVPYAKDGLLFYNKHAHYQTGNTPLALVWKDEKCSQYVID 290 (419)
Q Consensus 246 ~~~~~~~p~~~DGLLFYHKea~Y~~G~TPLv~~wkD~~~s~y~~d 290 (419)
+++......-..|+++-+.++.|++|.|.-++=+|.....-++|-
T Consensus 148 ~~~~~~~~~g~EGiv~K~~ds~Y~~Grs~~WlK~K~~~~~d~vV~ 192 (298)
T TIGR02779 148 ALLEAACRLGLEGVVAKRRDSPYRSGRSADWLKLKCRRRQEFVIG 192 (298)
T ss_pred HHHHHHHHcCCceEEEeCCCCCCCCCCCCCcEEEccCCCCEEEEE
Confidence 555544455689999999999999999888777776555444443
No 12
>PRK08224 ligC ATP-dependent DNA ligase; Reviewed
Probab=97.93 E-value=0.00037 Score=71.40 Aligned_cols=168 Identities=19% Similarity=0.213 Sum_probs=110.4
Q ss_pred cccccccccCCCCCCCceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEE-eeccCCCCCCCCCCCCCCCCCcEEEeeeEe
Q 014751 101 LMLPEWMIDVPDRLSHDWYVFARPAGKRCIVVSSNGTTVSRERNGSILH-HFPSALPSGARTKDPSGSAQSYCILDCIFH 179 (419)
Q Consensus 101 LMlsEWl~dvP~dL~~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~-~F~S~LPgG~~~~~~~~~~~~ytILDCIy~ 179 (419)
-||+.....+|+. .+|++=+==-|-||++....|.+..+|+||.-+. +||-...-... ....-+|||+=..
T Consensus 11 PMLA~~~~~~~~~--~~w~~E~K~DG~R~~~~~~~~~v~l~SRng~d~t~~fPel~~~~~~------~~~~~~vLDGEiV 82 (350)
T PRK08224 11 PMLAKSVDAIPPG--DGWSYEPKWDGFRCLVFRDGDEVELGSRNGKPLTRYFPELVAALRA------ELPERCVLDGEIV 82 (350)
T ss_pred CccCCccCCCCCC--CcEEEEEeECeeEEEEEEECCEEEEEeCCCCCchhhhHHHHHHHHh------hCCCCEEEeeEEE
Confidence 5777766555553 5799988889999999999999999999998875 57652111000 0011389997432
Q ss_pred c--C--------------------------CcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCCCCCce
Q 014751 180 E--L--------------------------DQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRF 231 (419)
Q Consensus 180 e--~--------------------------~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~n~~~F 231 (419)
- . .-+|||.|+|.++|.++.+-+..=|.=.|.+-+... . .+
T Consensus 83 v~~~~~~~F~~Lq~r~~~~~~~~~~~~~~~pv~~~vFDlL~l~G~dl~~~Pl~eRr~~L~~l~~~~---------~--~i 151 (350)
T PRK08224 83 VARDGGLDFEALQQRIHPAASRVRKLAEETPASFVAFDLLALGDRDLTGRPFAERRAALEAAAAGS---------G--PV 151 (350)
T ss_pred EeCCCCCCHHHHHhhhhccccchhhhhhcCCEEEEEEeeeeECCcChhhCCHHHHHHHHHHhcCCC---------C--cE
Confidence 1 1 127999999999999999888777777777766321 1 24
Q ss_pred eccccccCChHhHHHHHhcCCCCCcccEEeEeccccccCCCCcCeeeeccCCCcccee
Q 014751 232 STVPVYNCDQRGLYSAYIESVPYAKDGLLFYNKHAHYQTGNTPLALVWKDEKCSQYVI 289 (419)
Q Consensus 232 ~~lp~~~c~~~~L~~~~~~~~p~~~DGLLFYHKea~Y~~G~TPLv~~wkD~~~s~y~~ 289 (419)
.+.|.+.. .+...+++......-..|++.-..++.|.+|..- ++=+|-.....++|
T Consensus 152 ~~~~~~~~-~~~~~~~~~~a~~~G~EGIV~Kr~dS~Y~~Grr~-WlKiK~~~~~d~vI 207 (350)
T PRK08224 152 HLTPATTD-PATARRWFEEFEGAGLDGVIAKPLDGPYQPGKRA-MFKVKHERTADCVV 207 (350)
T ss_pred EEecccCC-HHHHHHHHHHHHhCCCcEEEEeCCCCCcCCCCcC-EEEEccCCcEEEEE
Confidence 44554432 2344444543344568999999999999999765 44444433333433
No 13
>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=97.91 E-value=7.8e-05 Score=70.71 Aligned_cols=145 Identities=17% Similarity=0.166 Sum_probs=99.1
Q ss_pred CceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEEe--ec---cCCCCCCCCCCCCCCCCCcEEEeee---Eec-------
Q 014751 116 HDWYVFARPAGKRCIVVSSNGTTVSRERNGSILHH--FP---SALPSGARTKDPSGSAQSYCILDCI---FHE------- 180 (419)
Q Consensus 116 ~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~~--F~---S~LPgG~~~~~~~~~~~~ytILDCI---y~e------- 180 (419)
.+|++=+==-|-||+|+-..|....+||+|.-+.. |+ ..++..-+ ...-|||||= +..
T Consensus 34 ~~~~~E~K~DG~R~~i~~~~~~v~l~SR~g~~~t~~~~~~~~~~~~~~~~-------~~~~~iLDGEiv~~d~~~g~~~~ 106 (213)
T cd07902 34 NGMYAEIKYDGERVQVHKQGDNFKFFSRSLKPVLPHKVAHFKDYIPKAFP-------HGHSMILDSEVLLVDTKTGKPLP 106 (213)
T ss_pred CceEEEeccCCEEEEEEEcCCEEEEEcCCCcccccchhHHHHHHHHHhcc-------cccceeeeeEEEEEECCCCcccc
Confidence 35766666679999999888999999999976432 22 21221110 0123888863 322
Q ss_pred --------------CCcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCCCCCceeccccccCC-hHhHH
Q 014751 181 --------------LDQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVYNCD-QRGLY 245 (419)
Q Consensus 181 --------------~~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~n~~~F~~lp~~~c~-~~~L~ 245 (419)
..-+|||.|||.++|.++.+.+..=|.-=|.+-+.+.. -++.+.|...++ .+.+.
T Consensus 107 F~~l~~~~~~~~~~~~v~~~vFDiL~l~g~~l~~~pl~eR~~~L~~~~~~~~----------~~~~~~~~~~~~~~~~l~ 176 (213)
T cd07902 107 FGTLGIHKKSAFKDANVCLFVFDCLYYNGESLMDKPLRERRKILEDNMVEIP----------NRIMLSEMKFVKKADDLS 176 (213)
T ss_pred cchhhhhhccccccCceEEEEEEEeeeCCcchhcCcHHHHHHHHHHhccCCC----------CeEEEEEEEEcCCHHHHH
Confidence 12479999999999999999888877766666553321 135666766663 45666
Q ss_pred HHHhcCCCCCcccEEeEeccccccCCCCcCeeeec
Q 014751 246 SAYIESVPYAKDGLLFYNKHAHYQTGNTPLALVWK 280 (419)
Q Consensus 246 ~~~~~~~p~~~DGLLFYHKea~Y~~G~TPLv~~wk 280 (419)
+++.....--..|+++-+.++.|.+|.. .|||
T Consensus 177 ~~~~~~~~~g~EGvV~K~~~s~Y~~G~r---~W~K 208 (213)
T cd07902 177 AMIARVIKEGLEGLVLKDLKSVYEPGKR---HWLK 208 (213)
T ss_pred HHHHHHHHCCCCeEEEeCCCCCccCCCC---CceE
Confidence 6665544556899999999999999986 4777
No 14
>PRK05972 ligD ATP-dependent DNA ligase; Reviewed
Probab=97.82 E-value=0.00069 Score=76.62 Aligned_cols=194 Identities=19% Similarity=0.221 Sum_probs=128.5
Q ss_pred hcccccccccCCCCCCCceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEE-eeccCCCCCCCCCCCCCCCCCcEEEeeeE
Q 014751 100 QLMLPEWMIDVPDRLSHDWYVFARPAGKRCIVVSSNGTTVSRERNGSILH-HFPSALPSGARTKDPSGSAQSYCILDCIF 178 (419)
Q Consensus 100 qLMlsEWl~dvP~dL~~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~-~F~S~LPgG~~~~~~~~~~~~ytILDCIy 178 (419)
.-||+.-....|++ .+|++=.==-|-||++...+|....+|+||.-+. +|+...-.-. . ..-.-+|||+=.
T Consensus 235 ~PMLAt~~~~~p~g--~~W~~E~K~DG~R~~a~~~gg~vrL~SRnG~d~T~~fPel~~~~~-~-----l~~~~~ILDGEI 306 (860)
T PRK05972 235 APQLATLVDRPPSG--DGWIYEIKFDGYRILARIEGGEVRLFTRNGLDWTAKLPALAKAAA-A-----LGLPDAWLDGEI 306 (860)
T ss_pred CcccCccCCCCCCc--CceEEEeeeCcEEEEEEEECCEEEEEeCCCCccccccHHHHHHHH-h-----cCCCceeEeEEE
Confidence 35777755566654 7999988889999999999999999999998754 4553211000 0 001137999844
Q ss_pred ec---------------------CCcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCCCCCceeccccc
Q 014751 179 HE---------------------LDQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVY 237 (419)
Q Consensus 179 ~e---------------------~~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~n~~~F~~lp~~ 237 (419)
.- ..-+|||.|||..+|.++.+.+..=|.--|++-+.+.. ++ .+...+++
T Consensus 307 Vvld~~G~~~F~~Lq~r~~~~~~~~v~f~vFDLL~l~G~dL~~~PL~eRr~~L~~ll~~~~--------~~-~i~~s~~~ 377 (860)
T PRK05972 307 VVLDEDGVPDFQALQNAFDEGRTEDLVYFAFDLPFLGGEDLRELPLEERRARLRALLEAAR--------SD-RIRFSEHF 377 (860)
T ss_pred EEECCCCCCCHHHHHHHhhccCCCceEEEEEeccccCCcccccCCHHHHHHHHHHHhhhcC--------CC-cEEEecee
Confidence 31 11379999999999999999988888888877665421 11 45667777
Q ss_pred cCChHhHHHHHhcCCCCCcccEEeEeccccccCCCCcCeeeeccCCCccceee--cCCCCCccccceEEEEEecCCce
Q 014751 238 NCDQRGLYSAYIESVPYAKDGLLFYNKHAHYQTGNTPLALVWKDEKCSQYVID--TDSKGQVLSQQQVVLELQEDGKL 313 (419)
Q Consensus 238 ~c~~~~L~~~~~~~~p~~~DGLLFYHKea~Y~~G~TPLv~~wkD~~~s~y~~d--~d~~g~~~~~q~vvL~~~~~g~l 313 (419)
.++.+.+.+ .....-..|++.-..++.|.+|.|.-|+=+|-....-++|- +..+|....--++.|-+.++|+|
T Consensus 378 ~~~g~~ll~---~a~~~GlEGIVaKr~dS~Y~~GRs~~WlKiK~~~~~E~VIgGy~~~~Gkr~g~gSLLlGvyd~~~L 452 (860)
T PRK05972 378 DAGGDAVLA---SACRLGLEGVIGKRADSPYVSGRSEDWIKLKCRARQEFVIGGYTDPKGSRSGFGSLLLGVHDDDHL 452 (860)
T ss_pred cchHHHHHH---HHHHcCCceEEEeCCCCCCCCCCCCCcEEEecCCCceEEEEEEeCCCCccccceeEEEEEecCCEE
Confidence 776544333 22334588999999999999999988777776666666664 33334311112345554444443
No 15
>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=97.76 E-value=7.7e-05 Score=68.62 Aligned_cols=145 Identities=23% Similarity=0.310 Sum_probs=104.5
Q ss_pred CCceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEEe-eccC-------CCCCCCCCCCCCCCCCcEEEeeeEec------
Q 014751 115 SHDWYVFARPAGKRCIVVSSNGTTVSRERNGSILHH-FPSA-------LPSGARTKDPSGSAQSYCILDCIFHE------ 180 (419)
Q Consensus 115 ~~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~~-F~S~-------LPgG~~~~~~~~~~~~ytILDCIy~e------ 180 (419)
...|++=+==-|-||+|+...|....+||+|..+.. |+.. +..+. .-+||||=..-
T Consensus 18 ~~~~~~e~K~DG~R~~i~~~~~~v~~~SR~g~~~~~~~~~l~~~l~~~~~~~~----------~~~vLDGElv~~d~~~~ 87 (202)
T PF01068_consen 18 GGPWYVEPKYDGVRCQIHKDGGGVRLFSRNGKDITSQFPELAEALRELLFPDG----------PDFVLDGELVVLDPNTG 87 (202)
T ss_dssp TSCEEEEEEESSEEEEEEEETTEEEEEETTSSB-GGGHHHHHHHHHHHBCTSC----------TEEEEEEEEEEBETTTS
T ss_pred CCCeEEEEeEeeEEeeeeeccccceeecccccchhhHHHHHHHHHHHHhcCCC----------CceEEEEEEEEEecCCC
Confidence 567888888889999999999999999999998765 4422 22211 12899983331
Q ss_pred -----------------------CCcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCCCCCceeccccc
Q 014751 181 -----------------------LDQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVY 237 (419)
Q Consensus 181 -----------------------~~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~n~~~F~~lp~~ 237 (419)
..-+|||.|||..+|.++.+.+.+=|.--|..-+.. ..-.+..++++
T Consensus 88 ~~~~f~~~~~~~~~~~~~~~~~~~~~~~~vFDil~l~~~~l~~~p~~eR~~~L~~~~~~----------~~~~i~~~~~~ 157 (202)
T PF01068_consen 88 SPLPFQELSGRLNRRSKKIPEQSEPLQFVVFDILYLDGKDLLDLPYEERRELLEELLEP----------PPPRIRIVESY 157 (202)
T ss_dssp SBCCHHHHHHHHBHSSSCHHHHHSCEEEEEEEEEEETTEECTTSCHHHHHHHHHHHBG-----------BTSSEEEEEEE
T ss_pred cchhHHHHhhhhhhhcccchhccCcEEEEEEEEEEeCCeEeeeccHHHHHHHHHHhhcc----------CCCceeEeeee
Confidence 245899999999999999888888888888777721 12456777888
Q ss_pred cCCh-HhHHHHHhcCCCCCcccEEeEeccccccCCCCcCeeeec
Q 014751 238 NCDQ-RGLYSAYIESVPYAKDGLLFYNKHAHYQTGNTPLALVWK 280 (419)
Q Consensus 238 ~c~~-~~L~~~~~~~~p~~~DGLLFYHKea~Y~~G~TPLv~~wk 280 (419)
.|+. +.+.+++.....--..|+++-..++.|++|.. --.|||
T Consensus 158 ~~~~~~~~~~~~~~~~~~g~EG~v~K~~~~~Y~~Gkr-s~~w~K 200 (202)
T PF01068_consen 158 VVNSKEELEELFEEAIDQGFEGLVLKDPDSPYEPGKR-SSGWLK 200 (202)
T ss_dssp EESSHHHHHHHHHHHHHTTSSEEEEEETTSSC-TTEE-EEEEEE
T ss_pred cCCCHHHHHHHHHHHHHcCCceEEEECCCCccCCCCc-CCCcEE
Confidence 8854 55666554433344789999999999999965 234665
No 16
>PRK07636 ligB ATP-dependent DNA ligase; Reviewed
Probab=97.74 E-value=0.00091 Score=66.24 Aligned_cols=154 Identities=17% Similarity=0.140 Sum_probs=104.4
Q ss_pred ccccccccCCCCCCCceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEE-eeccCCCCCCCCCCCCCCCCCcEEEeeeEec
Q 014751 102 MLPEWMIDVPDRLSHDWYVFARPAGKRCIVVSSNGTTVSRERNGSILH-HFPSALPSGARTKDPSGSAQSYCILDCIFHE 180 (419)
Q Consensus 102 MlsEWl~dvP~dL~~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~-~F~S~LPgG~~~~~~~~~~~~ytILDCIy~e 180 (419)
||+.-....|++ .+|++=+==-|-||++....|....+|++|..++ +||..+.-.- ..-+|||+=..-
T Consensus 6 mLa~~~~~~~~~--~~~~~E~K~DG~R~~~~~~~~~v~l~SR~g~~~t~~fPe~~~~~~---------~~~~vLDGElv~ 74 (275)
T PRK07636 6 MLLESAKEPFNS--ENYITEPKFDGIRLIASKNNGLIRLYTRHNNEVTAKFPELLNLDI---------PDGTVLDGELIV 74 (275)
T ss_pred ccCCcCCCCCCC--CcEEEEEEEceeEEEEEEeCCEEEEEeCCCCCchhhhhhHHhhhc---------CCCEEEEeEEEE
Confidence 666654444443 5898888889999999999999999999998765 5665432211 112899985431
Q ss_pred ------------------------CCcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCCCCCceecccc
Q 014751 181 ------------------------LDQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPV 236 (419)
Q Consensus 181 ------------------------~~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~n~~~F~~lp~ 236 (419)
..-+|||.|+|.++|.++.+-+..=|.=.|.+-+... + .+..+|.
T Consensus 75 ~d~~g~~~F~~l~~r~~~~~~~~~~~~~~~vFDlL~~~g~~l~~~pl~eRr~~L~~~~~~~----------~-~~~~~~~ 143 (275)
T PRK07636 75 LGSTGAPDFEAVMERFQSKKSTKIHPVVFCVFDVLYINGVSLTALPLSERKEILASLLLPH----------P-NVKIIEG 143 (275)
T ss_pred ECCCCCCCHHHHHHHhccccccccCceEEEEEEeEEECceehhhCCHHHHHHHHHHhcCCC----------C-CEEEccc
Confidence 1237999999999999998888777766665554321 1 2345555
Q ss_pred ccCChHhHHHHHhcCCCCCcccEEeEeccccccCC-CCcCeeeec
Q 014751 237 YNCDQRGLYSAYIESVPYAKDGLLFYNKHAHYQTG-NTPLALVWK 280 (419)
Q Consensus 237 ~~c~~~~L~~~~~~~~p~~~DGLLFYHKea~Y~~G-~TPLv~~wk 280 (419)
...+.+.+.+.. ..--..|+++-..++.|.+| .|.-++=.|
T Consensus 144 ~~~~~~~~~~~~---~~~g~EGiV~K~~ds~Y~~g~Rs~~WlKiK 185 (275)
T PRK07636 144 IEGHGTAYFELV---EERELEGIVIKKANSPYEINKRSDNWLKVI 185 (275)
T ss_pred ccccHHHHHHHH---HHcCCcEEEEeCCCCCCCCCCCCCCeEEEe
Confidence 554444433322 22347799999999999998 677654444
No 17
>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=97.55 E-value=0.00055 Score=73.11 Aligned_cols=161 Identities=21% Similarity=0.224 Sum_probs=117.0
Q ss_pred hcccccccccCCCC---CCCceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEE-eeccC--------CCCCCCCCCCCCC
Q 014751 100 QLMLPEWMIDVPDR---LSHDWYVFARPAGKRCIVVSSNGTTVSRERNGSILH-HFPSA--------LPSGARTKDPSGS 167 (419)
Q Consensus 100 qLMlsEWl~dvP~d---L~~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~-~F~S~--------LPgG~~~~~~~~~ 167 (419)
+-||++....+|+. +..+|++=.==-|-||+|...+|....+||+|.-+. .|+.. +|.+
T Consensus 168 ~PMLA~~~~~~~~~~~~~~~~~~~E~K~DG~R~qih~~~~~v~l~SR~g~~~t~~~pei~~~~~~~~~~~~--------- 238 (514)
T TIGR00574 168 KPMLAERAKSIEEALKKKGNKFYVEYKYDGERVQIHKDGDKFKIFSRRLENYTYAYPEIFTEFIKEAFPGI--------- 238 (514)
T ss_pred ccccCCccCCHHHHHHHhCCceEEEEeecceEEEEEEcCCEEEEEcCCCcccccccchhHHHHHHHhcCcc---------
Confidence 45777766555532 234788888888999999998899999999998765 56543 3321
Q ss_pred CCCcEEEeee---EecC--------------------------CcEEEEEEEEeeCCcccccccchhhHHHhhhhccccC
Q 014751 168 AQSYCILDCI---FHEL--------------------------DQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETG 218 (419)
Q Consensus 168 ~~~ytILDCI---y~e~--------------------------~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~ 218 (419)
.-||||+= ++.. .-+|||.|||..+|.++.+-+..=|.=-|++-+.+.+
T Consensus 239 --~~~ILDGElv~~d~~~g~~~~F~~l~~r~~~~~~~~~~~~~~~~~~vFDiL~l~g~~l~~~pl~eRr~~L~~~~~~~~ 316 (514)
T TIGR00574 239 --KSCILDGEMVAIDPETGKILPFQTLLRRKRRYDIDSMEKKVPVCLFVFDILYLNGESLIDEPLIERREILESILKPIP 316 (514)
T ss_pred --ceeeecceEEEEEcCCCCCcCcHhHHhhhhhccccccccccceEEEEEEEEEECCcchhcCcHHHHHHHHHHhccCCC
Confidence 13788863 3221 1389999999999999999888888888877664421
Q ss_pred CCCCCCCCCCCceeccccccC-ChHhHHHHHhcCCCCCcccEEeEeccccccCC-CCcCeeeecc
Q 014751 219 ACDAPSHYYKFRFSTVPVYNC-DQRGLYSAYIESVPYAKDGLLFYNKHAHYQTG-NTPLALVWKD 281 (419)
Q Consensus 219 ~~~~~s~~n~~~F~~lp~~~c-~~~~L~~~~~~~~p~~~DGLLFYHKea~Y~~G-~TPLv~~wkD 281 (419)
-.+..+|...+ +.+.+.+++.....--..|+++-..++.|++| .++-|+=||.
T Consensus 317 ----------~~i~~~~~~~~~~~e~~~~~~~~~~~~g~EGlv~K~~ds~Y~~G~Rs~~WlK~K~ 371 (514)
T TIGR00574 317 ----------NRIEIAEMKITSNVEELEKFLNEAISEGCEGLMLKDLKSIYEPGKRGWLWLKFKP 371 (514)
T ss_pred ----------CcEEEEEEEecCCHHHHHHHHHHHHHcCCceEEEecCCCcccCCCCCCcceeCch
Confidence 24667788777 45667776665555568999999999999999 7877666664
No 18
>PRK09632 ATP-dependent DNA ligase; Reviewed
Probab=97.53 E-value=0.0026 Score=71.32 Aligned_cols=149 Identities=18% Similarity=0.237 Sum_probs=107.1
Q ss_pred CCceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEE-eecc------CCCCCCCCCCCCCCCCCcEEEeeeEe---c----
Q 014751 115 SHDWYVFARPAGKRCIVVSSNGTTVSRERNGSILH-HFPS------ALPSGARTKDPSGSAQSYCILDCIFH---E---- 180 (419)
Q Consensus 115 ~~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~-~F~S------~LPgG~~~~~~~~~~~~ytILDCIy~---e---- 180 (419)
+.+|++=+==-|-||++...+|....+|+||.-+. +|+. .||+ .-+|||+=.. +
T Consensus 476 ~~~w~~E~K~DG~R~~~~~~~g~vrL~SRnG~d~T~~fPel~~~~~~l~~------------~~~ILDGEiVvld~~G~~ 543 (764)
T PRK09632 476 ASQWAFEGKWDGYRLLAEADHGALRLRSRSGRDVTAEYPELAALAEDLAD------------HHVVLDGEIVALDDSGVP 543 (764)
T ss_pred CCCEEEEEEECceeEEEEEeCCEEEEEeCCCCCccccchhHHHHHhhCCC------------cceeeeeEEEEeCCCCCC
Confidence 35798888788999999999999999999998655 5663 3332 1389997543 2
Q ss_pred -----------CCcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCCCCCceeccccccCChHhHHHHHh
Q 014751 181 -----------LDQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVYNCDQRGLYSAYI 249 (419)
Q Consensus 181 -----------~~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~n~~~F~~lp~~~c~~~~L~~~~~ 249 (419)
..-+|||.|||..+|.++.+.+..=|.=.|.+-+.+. -.+...+.+..+.+.+ +.
T Consensus 544 ~F~~Lq~r~~~~~v~y~vFDLL~lnG~dL~~~Pl~eRR~~L~~l~~~~-----------~~i~~s~~~~~~~~~~---l~ 609 (764)
T PRK09632 544 SFGLLQNRGRDTRVEFWAFDLLYLDGRSLLRKPYRDRRKLLEALAPSG-----------GSLTVPPLLPGDGAEA---LA 609 (764)
T ss_pred CHHHHhhhhhcCCeEEEEEeeeccCCcccccCCHHHHHHHHHHhhCCC-----------CcEEecceecccHHHH---HH
Confidence 1248999999999999999988888887777766421 1234455566554443 33
Q ss_pred cCCCCCcccEEeEeccccccCCC-CcCeeeeccCCCcccee
Q 014751 250 ESVPYAKDGLLFYNKHAHYQTGN-TPLALVWKDEKCSQYVI 289 (419)
Q Consensus 250 ~~~p~~~DGLLFYHKea~Y~~G~-TPLv~~wkD~~~s~y~~ 289 (419)
.....-..|++.-..++.|.+|. |.-++=+|-.....++|
T Consensus 610 ~a~~~GlEGIVaKr~dS~Y~pGrRs~~WlKiK~~~~~e~VI 650 (764)
T PRK09632 610 YSRELGWEGVVAKRRDSTYQPGRRSSSWIKDKHWRTQEVVI 650 (764)
T ss_pred HHHHcCCcEEEEeCCCCCCCCCCcCCCeEEEecCCceEEEE
Confidence 22334588999999999999996 88766666555555555
No 19
>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=97.52 E-value=0.0011 Score=62.44 Aligned_cols=150 Identities=17% Similarity=0.137 Sum_probs=102.9
Q ss_pred CCceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEE-eeccCCCCCCCCCCCCCCCCCcEEEeeeE---ec----------
Q 014751 115 SHDWYVFARPAGKRCIVVSSNGTTVSRERNGSILH-HFPSALPSGARTKDPSGSAQSYCILDCIF---HE---------- 180 (419)
Q Consensus 115 ~~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~-~F~S~LPgG~~~~~~~~~~~~ytILDCIy---~e---------- 180 (419)
...|++=+==-|-||+|....+....+||+|.-+. .|+...+-.... ....-+|||+=. .+
T Consensus 24 ~~~~~~E~K~DG~R~~~~~~~~~v~~~SR~~~~~t~~~pel~~~~~~~-----~~~~~~iLDGElv~~~~~g~~~~F~~l 98 (207)
T cd07901 24 GGEAAVEYKYDGIRVQIHKDGDEVRIFSRRLEDITNALPEVVEAVREL-----VKAEDAILDGEAVAYDPDGRPLPFQET 98 (207)
T ss_pred CCcEEEEEeEcceeEEEEEeCCEEEEEeCCCccccchhhHHHHHHHhc-----CCCCCEEEeCEEEEECCCCCccCHHHH
Confidence 56777777778999999999999999999997653 554321110000 000128888633 21
Q ss_pred ----------------CCcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCCCCCceeccccccCC-hHh
Q 014751 181 ----------------LDQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVYNCD-QRG 243 (419)
Q Consensus 181 ----------------~~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~n~~~F~~lp~~~c~-~~~ 243 (419)
..-+|||.|||..+|.++.+-+..-|.--|.+-+... -.+.++|...|+ .+.
T Consensus 99 ~~r~~~~~~~~~~~~~~~~~~~vFDil~~~g~~l~~~pl~eR~~~L~~~~~~~-----------~~i~~~~~~~~~~~~~ 167 (207)
T cd07901 99 LRRFRRKYDVEEAAEEIPLTLFLFDILYLDGEDLLDLPLSERRKILEEIVPET-----------EAILLAPRIVTDDPEE 167 (207)
T ss_pred HHHhccccchhhhhccCcEEEEEEEEEEECCcchhcCCHHHHHHHHHHhcCcC-----------CcEEEEEEEecCCHHH
Confidence 0136999999999999988888887877777666432 135566777774 456
Q ss_pred HHHHHhcCCCCCcccEEeEeccccccCC-CCcCeeeec
Q 014751 244 LYSAYIESVPYAKDGLLFYNKHAHYQTG-NTPLALVWK 280 (419)
Q Consensus 244 L~~~~~~~~p~~~DGLLFYHKea~Y~~G-~TPLv~~wk 280 (419)
+.+++......-..|+++-+.++.|.+| .|.-++=||
T Consensus 168 ~~~~~~~~~~~g~EGiv~K~~~s~Y~~g~Rs~~wlK~K 205 (207)
T cd07901 168 AEEFFEEALEAGHEGVMVKSLDSPYQAGRRGKNWLKVK 205 (207)
T ss_pred HHHHHHHHHHcCCceEEEeCCCCCcCCCCCCCCeEEec
Confidence 6666655555568999999999999999 676554444
No 20
>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=97.48 E-value=0.0011 Score=61.92 Aligned_cols=149 Identities=19% Similarity=0.222 Sum_probs=99.8
Q ss_pred CceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEE-eeccCCCCCCCCCCCCCCCCCcEEEeeeE---ecCC---------
Q 014751 116 HDWYVFARPAGKRCIVVSSNGTTVSRERNGSILH-HFPSALPSGARTKDPSGSAQSYCILDCIF---HELD--------- 182 (419)
Q Consensus 116 ~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~-~F~S~LPgG~~~~~~~~~~~~ytILDCIy---~e~~--------- 182 (419)
..|++=.==-|-||+++...|....+||+|..+. .|+-...-.. ....-|||||=+ +...
T Consensus 21 ~~~~~E~K~DG~R~~~~~~~~~v~l~SR~g~~~t~~~p~i~~~~~-------~~~~~~vLDGElv~~~~~~~~~f~~~~~ 93 (201)
T cd07898 21 AAAWVEDKYDGIRAQVHKDGGRVEIFSRSLEDITDQFPELAAAAK-------ALPHEFILDGEILAWDDNRGLPFSELFK 93 (201)
T ss_pred CeEEEEEeeceEEEEEEEeCCEEEEEcCCChhchhhhhhHHHHHH-------hCCCCEEEEEEEEEEeCCCCCcHHHHHH
Confidence 3566655556999999999999999999998753 3332111000 012359999743 2211
Q ss_pred ----------------cEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCCCCCceeccccccCCh-HhHH
Q 014751 183 ----------------QTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVYNCDQ-RGLY 245 (419)
Q Consensus 183 ----------------~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~n~~~F~~lp~~~c~~-~~L~ 245 (419)
-+|||.|||..+|.++.+=+..=|.==|..-+... +-++..+|...++. +.+.
T Consensus 94 ~~~~~~~~~~~~~~~~~~~~vFDil~~~g~~l~~~p~~eR~~~L~~~~~~~----------~~~i~~~~~~~~~~~~~~~ 163 (201)
T cd07898 94 RLGRKFRDKFLDEDVPVVLMAFDLLYLNGESLLDRPLRERRQLLEELFVEI----------PGRIRIAPALPVESAEELE 163 (201)
T ss_pred HhcccccchhhhccCcEEEEEEeEEeECCcchhhCCHHHHHHHHHHhhcCC----------CCcEEEeeeEEcCCHHHHH
Confidence 36999999999999888766555554444433221 23456677777764 4466
Q ss_pred HHHhcCCCCCcccEEeEeccccccCCC-CcCeeeecc
Q 014751 246 SAYIESVPYAKDGLLFYNKHAHYQTGN-TPLALVWKD 281 (419)
Q Consensus 246 ~~~~~~~p~~~DGLLFYHKea~Y~~G~-TPLv~~wkD 281 (419)
.++.....--.+|+++-..++.|.+|. |.-|+=||.
T Consensus 164 ~~~~~~~~~g~EGim~K~~~s~Y~~g~Rs~~wlK~K~ 200 (201)
T cd07898 164 AAFARARARGNEGLMLKDPDSPYEPGRRGLAWLKLKK 200 (201)
T ss_pred HHHHHHHHcCCceEEEeCCCCCcCCCCcCCCcEEeCC
Confidence 666555555689999999999999996 877766664
No 21
>PLN03113 DNA ligase 1; Provisional
Probab=97.26 E-value=0.0019 Score=72.16 Aligned_cols=168 Identities=18% Similarity=0.222 Sum_probs=114.7
Q ss_pred hcccccccccCCC---CC-CCceEEEEecCCcEEEEEe-eCCeEEEEcCCCcEE-EeeccCCCCCCCCCCCCCCCCCcEE
Q 014751 100 QLMLPEWMIDVPD---RL-SHDWYVFARPAGKRCIVVS-SNGTTVSRERNGSIL-HHFPSALPSGARTKDPSGSAQSYCI 173 (419)
Q Consensus 100 qLMlsEWl~dvP~---dL-~~~Wl~vpcPvGkRcLVVa-s~G~T~ay~k~G~~l-~~F~S~LPgG~~~~~~~~~~~~ytI 173 (419)
.-||++..-.+++ .+ +.+|++=.==-|-||.|+. .+|....|+|||.-+ .+||-.+--.... ...+-.-||
T Consensus 371 ~PMLA~~~~~~~eil~~~~g~~~~~E~KyDGeR~QiH~~~~g~v~lfSRn~ed~T~~fPel~~~~~~~---~~~~~~~~I 447 (744)
T PLN03113 371 GPMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHFLEDGSVEIYSRNAERNTGKYPDVVVAISRL---KKPSVKSFI 447 (744)
T ss_pred CCccCCCCCChHHHhhccCCCCEEEEEeeccceEEEEEecCCEEEEEeCCCCcccccchhHHHHHHHh---ccccCCCEE
Confidence 3688886655533 23 3468777666799999985 688999999999764 4676443111000 000112399
Q ss_pred Eeee---EecCC-------------------------cEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCC
Q 014751 174 LDCI---FHELD-------------------------QTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSH 225 (419)
Q Consensus 174 LDCI---y~e~~-------------------------~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~ 225 (419)
|||= |+..+ -+|||.|+|.+||.++.+.+..-|---|++-|.+.
T Consensus 448 LDGEiVa~d~~~~~~lpFq~Lq~R~rk~~~~~~~~~pv~~~aFDlLylnG~~L~~~PL~eRR~~L~~~~~~~-------- 519 (744)
T PLN03113 448 LDCELVAYDREKKKILPFQILSTRARKNVVMSDIKVDVCIFAFDMLYLNGQPLIQEQLKIRREHLYESFEED-------- 519 (744)
T ss_pred EEeEEEEEECCCCCcCCHHHHHhhhccccchhccccceEEEEEeccccCccChhcCCHHHHHHHHHHHhccC--------
Confidence 9984 33221 26999999999999999999888888888777552
Q ss_pred CCCCceeccccccC-ChHhHHHHHhcCCCCCcccEEeEe--ccccccCC-CCcCeeeec
Q 014751 226 YYKFRFSTVPVYNC-DQRGLYSAYIESVPYAKDGLLFYN--KHAHYQTG-NTPLALVWK 280 (419)
Q Consensus 226 ~n~~~F~~lp~~~c-~~~~L~~~~~~~~p~~~DGLLFYH--Kea~Y~~G-~TPLv~~wk 280 (419)
+-+|...+...+ +.+.+...+......-..||+.-. .++.|++| .+.-|+=||
T Consensus 520 --~~~i~~~~~~~~~~~ee~~~~~~~ai~~g~EGlmvK~l~~dS~Y~pGkRs~~WlKlK 576 (744)
T PLN03113 520 --PGFFQFATAITSNDLEEIQKFLDAAVDASCEGLIIKTLNKDATYEPSKRSNNWLKLK 576 (744)
T ss_pred --CCcEEEeeeeccCCHHHHHHHHHHHHHcCCceEEEeccCCCCCccCCCCCCCeEEEe
Confidence 124666777665 466777777666666789999996 58899999 566655555
No 22
>PRK09633 ligD ATP-dependent DNA ligase; Reviewed
Probab=97.21 E-value=0.0099 Score=65.28 Aligned_cols=175 Identities=18% Similarity=0.214 Sum_probs=112.1
Q ss_pred cccccccccCCCCCCCceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEE-eeccC------CCCCCCCCCCCCCCCCcEE
Q 014751 101 LMLPEWMIDVPDRLSHDWYVFARPAGKRCIVVSSNGTTVSRERNGSILH-HFPSA------LPSGARTKDPSGSAQSYCI 173 (419)
Q Consensus 101 LMlsEWl~dvP~dL~~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~-~F~S~------LPgG~~~~~~~~~~~~ytI 173 (419)
-||+..-...|++ .+|++=.==-|-||++...+|....||+||.-+. +|+.. +++..+ +..-+|
T Consensus 3 PMLa~~~~~~p~g--~~w~~E~K~DG~R~~~h~~~~~V~L~SRng~d~T~~fPel~~~~~~~~~~~~-------~~~~~I 73 (610)
T PRK09633 3 PMQPTLTTSIPIG--DEWRYEVKYDGFRCLLIIDETGITLISRNGRELTNTFPEIIEFCESNFEHLK-------EELPLT 73 (610)
T ss_pred CCcCCcCCCCCCC--CcEEEEEeEcceEEEEEEECCEEEEEeCCCCcchhhhhHHHHHHHhhhhccc-------cCCcee
Confidence 3676666666654 7899888888999999999999999999998765 56652 111110 011279
Q ss_pred EeeeE---ecC---------------------------CcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCC
Q 014751 174 LDCIF---HEL---------------------------DQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAP 223 (419)
Q Consensus 174 LDCIy---~e~---------------------------~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~ 223 (419)
||+=. .+. .-+|||.|||..+|.++.+-+..=|.=-|.+=+.+.+.-.+.
T Consensus 74 LDGEiVvld~~g~~~F~~Lq~R~~~~~~~~i~~~~~~~pv~~~vFDlL~lnG~dL~~~PL~eRr~~L~~ll~~~~~~~~~ 153 (610)
T PRK09633 74 LDGELVCLVNPYRSDFEHVQQRGRLKNTEVIAKSANARPCQLLAFDLLELKGESLTSLPYLERKKQLDKLMKAAKLPASP 153 (610)
T ss_pred eeeEEEEecCCCCCCHHHHHhhhhccccchhhhhhcccceEEEEEeecccCCcccccCCHHHHHHHHHHHhhhccccccc
Confidence 99743 211 026999999999999999988888877777766543210000
Q ss_pred CCCCCCceeccccccCChHhHHHHHhcCCCCCcccEEeEeccccccCC-CCcCeeeeccCCCccce
Q 014751 224 SHYYKFRFSTVPVYNCDQRGLYSAYIESVPYAKDGLLFYNKHAHYQTG-NTPLALVWKDEKCSQYV 288 (419)
Q Consensus 224 s~~n~~~F~~lp~~~c~~~~L~~~~~~~~p~~~DGLLFYHKea~Y~~G-~TPLv~~wkD~~~s~y~ 288 (419)
.....-.+..++++. ...+++......-..|++.-..++.|.+| .|.-|+=+|-.....++
T Consensus 154 ~~~~~~~i~~~~~~~----~~~~l~~~a~~~g~EGIV~Kr~dS~Y~~G~Rs~~WlKiK~~~~~d~v 215 (610)
T PRK09633 154 DPYAKARIQYIPSTT----DFDALWEAVKRYDGEGIVAKKKTSKWLENKRSKDWLKIKNWRYVHVI 215 (610)
T ss_pred ccccccceEEcCCHH----HHHHHHHHHHHcCCceEEEeCCCCCCCCCCCCCCeEEEeccCCceeE
Confidence 000111334444433 34444433333457999999999999988 78876666643333333
No 23
>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=97.19 E-value=0.0026 Score=60.91 Aligned_cols=149 Identities=15% Similarity=0.137 Sum_probs=94.2
Q ss_pred ceEEEEecCCcEEEEEeeC-CeEEEEcCCCcEEE-eeccCCCCCCCCCCCCCCCCCcEEEeee---EecC----------
Q 014751 117 DWYVFARPAGKRCIVVSSN-GTTVSRERNGSILH-HFPSALPSGARTKDPSGSAQSYCILDCI---FHEL---------- 181 (419)
Q Consensus 117 ~Wl~vpcPvGkRcLVVas~-G~T~ay~k~G~~l~-~F~S~LPgG~~~~~~~~~~~~ytILDCI---y~e~---------- 181 (419)
.|++=+==-|-||++.... |....+||+|.-++ +|+....-.... . .....-|||||= +...
T Consensus 32 ~~~~E~K~DG~R~~~h~~~~~~v~l~SR~g~~~t~~~pel~~~~~~~--~-~~~~~~~iLDGElv~~~~~~g~~~~F~~l 108 (219)
T cd07900 32 EFTCEYKYDGERAQIHLLEDGKVKIFSRNLENNTEKYPDIVAVLPKS--L-KPSVKSFILDSEIVAYDRETGKILPFQVL 108 (219)
T ss_pred eEEEEEeecceEEEEEEcCCCeEEEECCCCccccchhhHHHHHHHHH--h-cccCccEEEeeEEEEEEcCCCCCcChHHH
Confidence 5666555669999998765 89999999998653 554322110000 0 000123899974 3321
Q ss_pred ---------------CcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCCCCCceeccccccCC-hHhHH
Q 014751 182 ---------------DQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVYNCD-QRGLY 245 (419)
Q Consensus 182 ---------------~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~n~~~F~~lp~~~c~-~~~L~ 245 (419)
.-+|+|.|||..+|.++.+=+ |.-.+..|++.-. + .+-++.++++..++ .+.+.
T Consensus 109 ~~r~~~~~~~~~~~~~~~~~vFDiL~l~g~~l~~~p----l~eRr~~L~~~~~--~----~~~~~~~~~~~~~~~~~~~~ 178 (219)
T cd07900 109 STRKRKDVDANDIKVQVCVFAFDLLYLNGESLLKKP----LRERRELLHSLFK--E----VPGRFQFATSKDSEDTEEIQ 178 (219)
T ss_pred hhhcccccccccCcccEEEEEEEEEEECCchhhcCC----HHHHHHHHHHhcC--C----CCCeEEEEEEEecCCHHHHH
Confidence 125999999999998776644 4444444544311 1 12346677777764 55676
Q ss_pred HHHhcCCCCCcccEEeEecc--ccccCC-CCcCeeeec
Q 014751 246 SAYIESVPYAKDGLLFYNKH--AHYQTG-NTPLALVWK 280 (419)
Q Consensus 246 ~~~~~~~p~~~DGLLFYHKe--a~Y~~G-~TPLv~~wk 280 (419)
+++......-..|++.-..+ +.|.+| .|. .|||
T Consensus 179 ~~~~~~~~~g~EGiv~K~~~~~s~Y~~g~Rs~--~W~K 214 (219)
T cd07900 179 EFLEEAVKNNCEGLMVKTLDSDATYEPSKRSH--NWLK 214 (219)
T ss_pred HHHHHHHHcCCceEEEecCCCCCccCCCCcCC--CceE
Confidence 77665555678999999999 999998 565 3555
No 24
>cd08039 Adenylation_DNA_ligase_Fungal Adenylation domain of uncharacterized fungal ATP-dependent DNA ligase-like proteins. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. This group is composed of uncharacterized fungal proteins with similarity to ATP-dependent DNA ligases. ATP dependent DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains including a DNA-binding domain, an adenylation (nucleotidyltransferase (NTase)) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The adenylation domain binds ATP and contains many of the active-site res
Probab=97.18 E-value=0.005 Score=59.85 Aligned_cols=143 Identities=13% Similarity=0.088 Sum_probs=91.0
Q ss_pred ceEEEEecCCcEEEEEee----CCeEEEEcCCCcEE-EeeccC-------CCCCCCCCCCCCCCCCcEEEeeeE---ecC
Q 014751 117 DWYVFARPAGKRCIVVSS----NGTTVSRERNGSIL-HHFPSA-------LPSGARTKDPSGSAQSYCILDCIF---HEL 181 (419)
Q Consensus 117 ~Wl~vpcPvGkRcLVVas----~G~T~ay~k~G~~l-~~F~S~-------LPgG~~~~~~~~~~~~ytILDCIy---~e~ 181 (419)
+|++=.==-|-||+|... .|.+..+|++|.-+ +.|+-. |..+.. ......-+||||=+ +..
T Consensus 23 ~~~~E~K~DG~R~qih~~~~~~~~~v~lfSR~~~d~T~~~pel~~~~~~~~~~~~~----~~~~~~~~ILDGEiVv~d~~ 98 (235)
T cd08039 23 RMWVETKYDGEYCQIHIDLSKDSSPIRIFSKSGKDSTADRAGVHSIIRKALRIGKP----GCKFSKNCILEGEMVVWSDR 98 (235)
T ss_pred cEEEEEeecceEEEEEEecccCCCEEEEEeCCCCcccccchhHHHHHHHHhhcccc----ccCCCccEEEEeEEEEEECC
Confidence 344444445999999876 78899999999875 456631 111100 00112348999844 431
Q ss_pred C---------------------------------cEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCCCC
Q 014751 182 D---------------------------------QTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYK 228 (419)
Q Consensus 182 ~---------------------------------~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~n~ 228 (419)
+ -+|||.|||.+||.++.+-+..-|---|.+=+...+ +
T Consensus 99 ~g~~~~F~~L~~~~~~~~~~~~~~~~~~~~~~~~v~~~vFDlL~lnG~~l~~~pl~eRr~~L~~l~~~~~--------~- 169 (235)
T cd08039 99 QGKIDPFHKIRKHVERSGSFIGTDNDSPPHEYEHLMIVFFDVLLLDDESLLSKPYSERRDLLESLVHVIP--------G- 169 (235)
T ss_pred CCccCCHHHHHhhcccccchhccccccccccccceEEEEEEEEEECChhhhcCCHHHHHHHHHHhcccCC--------C-
Confidence 1 289999999999999998887776665555443211 1
Q ss_pred Cceecccccc------CChHhHHHHHhcCCCCCcccEEeEeccccccCCCC
Q 014751 229 FRFSTVPVYN------CDQRGLYSAYIESVPYAKDGLLFYNKHAHYQTGNT 273 (419)
Q Consensus 229 ~~F~~lp~~~------c~~~~L~~~~~~~~p~~~DGLLFYHKea~Y~~G~T 273 (419)
.+.+++... .+.+.+.+++.....--..|++.-..++.|.+|.+
T Consensus 170 -~~~~~~~~~i~~~~~~~~~~l~~~~~~a~~~g~EGIv~K~~~S~Y~pgr~ 219 (235)
T cd08039 170 -YAGLSERFPIDFSRSSGYERLRQIFARAIAERWEGLVLKGDEEPYFDLFL 219 (235)
T ss_pred -cEEEEEEEeecccCCCCHHHHHHHHHHHHHcCCceEEEecCCCCcccCcc
Confidence 122222222 24566777776555556889999999999999975
No 25
>PRK09247 ATP-dependent DNA ligase; Validated
Probab=97.15 E-value=0.0032 Score=67.93 Aligned_cols=166 Identities=17% Similarity=0.170 Sum_probs=115.1
Q ss_pred hcccccccccCCCCCC--CceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEE-eeccCCCCCCCCCCCCCCCCCcEEEee
Q 014751 100 QLMLPEWMIDVPDRLS--HDWYVFARPAGKRCIVVSSNGTTVSRERNGSILH-HFPSALPSGARTKDPSGSAQSYCILDC 176 (419)
Q Consensus 100 qLMlsEWl~dvP~dL~--~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~-~F~S~LPgG~~~~~~~~~~~~ytILDC 176 (419)
..||++...++.+.+. .+|++=.==-|-||+++..+|....+||+|.-+. +||-..--... . ..-|||||
T Consensus 207 ~pMLA~~~~~~~~~~~~~~~~~~E~K~DG~R~qih~~~~~v~lfSR~g~d~t~~fPei~~~~~~------l-~~~~ILDG 279 (539)
T PRK09247 207 PFFLAHPLEDEDLTLGDPADWQAEWKWDGIRVQLVRRGGEVRLWSRGEELITERFPELAEAAEA------L-PDGTVLDG 279 (539)
T ss_pred CCeeCCcCCCchhhhcCCCcEEEEEeEcceEEEEEEeCCEEEEEeCCCccchhhhHHHHHHHHh------C-CCCEEEEe
Confidence 3688888776554321 3688777778999999999999999999998754 45532211000 0 11389997
Q ss_pred e---Eec-C--------------------------CcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCC
Q 014751 177 I---FHE-L--------------------------DQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHY 226 (419)
Q Consensus 177 I---y~e-~--------------------------~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~ 226 (419)
= +.. . .-+|+|.|||..+|.++.+-+..=|.=-|++-+.+.+
T Consensus 280 Elv~~~~~~~~~~~F~~l~~R~~rk~~~~~~~~~~pv~~~vFDiL~l~g~~l~~~Pl~eRr~~L~~~~~~~~-------- 351 (539)
T PRK09247 280 ELLVWRPEDGRPQPFADLQQRIGRKTVGKKLLADYPAFLRAYDLLEDGGEDLRALPLAERRARLEALIARLP-------- 351 (539)
T ss_pred EEEEEECCCCCcCCHHHHHHHhcccccchhhhhcCCeEEEEEEeeeeCCcchhhCCHHHHHHHHHHHhcccC--------
Confidence 3 331 0 1279999999999999999988888877777765432
Q ss_pred CCCceeccccccCC-hHhHHHHHhcCCCCCcccEEeEeccccccCCCCcCeeeeccC
Q 014751 227 YKFRFSTVPVYNCD-QRGLYSAYIESVPYAKDGLLFYNKHAHYQTGNTPLALVWKDE 282 (419)
Q Consensus 227 n~~~F~~lp~~~c~-~~~L~~~~~~~~p~~~DGLLFYHKea~Y~~G~TPLv~~wkD~ 282 (419)
.-+|...|...++ .+.+...+.....--..|+++-..++.|++|..-- .|||=.
T Consensus 352 -~~~i~~~~~~~~~~~~e~~~~~~~a~~~g~EGlm~K~~~s~Y~~Grr~~-~WlK~K 406 (539)
T PRK09247 352 -DPRLDLSPLVPFSDWDELAALRAAARERGVEGLMLKRRDSPYLVGRKKG-PWWKWK 406 (539)
T ss_pred -CCeEEecCceecCCHHHHHHHHHHHHHCCCceEEEecCCCCcCCCCCcc-hhhccc
Confidence 1256677776663 45566666655556689999999999999996532 355533
No 26
>PRK01109 ATP-dependent DNA ligase; Provisional
Probab=97.08 E-value=0.0033 Score=68.51 Aligned_cols=165 Identities=16% Similarity=0.179 Sum_probs=111.8
Q ss_pred hcccccccccCCC---CCCCceEEEEecCCcEEEEEeeCCeEEEEcCCCcEE-EeeccCCCCCCCCCCCCCCCCCcEEEe
Q 014751 100 QLMLPEWMIDVPD---RLSHDWYVFARPAGKRCIVVSSNGTTVSRERNGSIL-HHFPSALPSGARTKDPSGSAQSYCILD 175 (419)
Q Consensus 100 qLMlsEWl~dvP~---dL~~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l-~~F~S~LPgG~~~~~~~~~~~~ytILD 175 (419)
+-||++....+|+ .++.+|++=.==-|-||+|....|....+||||.-+ +.||...+--... -...-||||
T Consensus 229 ~PmLA~~~~~~~~~~~~~~~~~~~E~K~DG~R~qih~~~~~v~l~SR~~~d~T~~~pel~~~~~~~-----~~~~~~ILD 303 (590)
T PRK01109 229 RPMLAERLSSPKEILKKMGGEALVEYKYDGERAQIHKKGDKVKIFSRRLENITHQYPDVVEYAKEA-----IKAEEAIVE 303 (590)
T ss_pred CcccCCccCCHHHHHHHcCCCeEEEecCCceEEEEEEcCCEEEEEeCCchhhccccchHHHHHHHh-----cCccceEEe
Confidence 4577776655442 245678766666899999999999999999999754 3565432211000 001238999
Q ss_pred e---eEec-CC-------------------------cEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCC
Q 014751 176 C---IFHE-LD-------------------------QTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHY 226 (419)
Q Consensus 176 C---Iy~e-~~-------------------------~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~ 226 (419)
| +|+. .. -+|||.|||.++|.++.+-+..-|.=-|++-+.+.+
T Consensus 304 GElv~~d~~~g~~~~F~~l~~R~r~~~~~~~~~~~p~~~~vFDiL~l~g~~l~~~pl~eRr~~L~~~~~~~~-------- 375 (590)
T PRK01109 304 GEIVAVDPETGEMRPFQELMHRKRKYDIEEAIKEYPVNVFLFDLLYVDGEDLTDKPLPERRKKLEEIVKEND-------- 375 (590)
T ss_pred eeEEEEECCCCcccChHHHhhcccccchhhhcccCceEEEEEEEEEECCcchhhCcHHHHHHHHHHhcCCCC--------
Confidence 7 3441 11 158999999999999999888888777777664421
Q ss_pred CCCceeccccccCC-hHhHHHHHhcCCCCCcccEEeEec--cccccCC-CCcCeeeec
Q 014751 227 YKFRFSTVPVYNCD-QRGLYSAYIESVPYAKDGLLFYNK--HAHYQTG-NTPLALVWK 280 (419)
Q Consensus 227 n~~~F~~lp~~~c~-~~~L~~~~~~~~p~~~DGLLFYHK--ea~Y~~G-~TPLv~~wk 280 (419)
.+...++..++ .+.+.+++.....--..|++.-.. ++.|.+| .+.-|+=+|
T Consensus 376 ---~~~~~~~~~~~~~~~~~~~~~~a~~~g~EGiv~K~~~~ds~Y~~g~Rs~~WlK~K 430 (590)
T PRK01109 376 ---KVKLAERIITDDVEELEKFFHRAIEEGCEGLMAKSLGKDSIYQAGARGWLWIKYK 430 (590)
T ss_pred ---ceEEeeeEecCCHHHHHHHHHHHHHcCCceEEEecCCCCCCcCCCCCCccHHHhh
Confidence 25566666653 456777776656566889999999 9999999 565443344
No 27
>PRK03180 ligB ATP-dependent DNA ligase; Reviewed
Probab=96.91 E-value=0.0067 Score=65.14 Aligned_cols=162 Identities=18% Similarity=0.159 Sum_probs=111.8
Q ss_pred hcccccccccCCCC---CCCceEEEEecCCcEEEEEeeCCeEEEEcCCCcEE-EeeccCCCCCCCCCCCCCCCCCcEEEe
Q 014751 100 QLMLPEWMIDVPDR---LSHDWYVFARPAGKRCIVVSSNGTTVSRERNGSIL-HHFPSALPSGARTKDPSGSAQSYCILD 175 (419)
Q Consensus 100 qLMlsEWl~dvP~d---L~~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l-~~F~S~LPgG~~~~~~~~~~~~ytILD 175 (419)
+.||+....++|+. ++.+|++=.==-|-||+|+..+|....|||+|.-+ ++||..+-.- .. ....-+|||
T Consensus 185 ~PMLA~~~~~~~~~~~~~~~~~~~E~K~DG~R~qih~~~~~v~l~SR~~~d~T~~fPei~~~~-~~-----~~~~~~ILD 258 (508)
T PRK03180 185 RPMLAQTATSVAEALARLGGPAAVEAKLDGARVQVHRDGDDVRVYTRTLDDITARLPEVVEAV-RA-----LPVRSLVLD 258 (508)
T ss_pred CCccCCcCCChHHHHHHhCCCeEEEEEEceeEEEEEEECCEEEEEeCCCCcchhhhHHHHHHH-Hh-----CCCcceeec
Confidence 56888887766653 44678888878899999999999999999999865 4565332100 00 001238888
Q ss_pred eeE---ecC--------------------------CcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCC
Q 014751 176 CIF---HEL--------------------------DQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHY 226 (419)
Q Consensus 176 CIy---~e~--------------------------~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~ 226 (419)
|=. ++. .-+||+.|+|.++|.++.+-+..=|.--|++-+.+.
T Consensus 259 GElv~~d~~g~~~~F~~l~~R~~~k~~~~~~~~~~pv~~~~FDlL~l~G~dl~~~pl~eRr~~L~~~~~~~--------- 329 (508)
T PRK03180 259 GEAIALRPDGRPRPFQVTASRFGRRVDVAAARATQPLSPFFFDALHLDGRDLLDAPLSERLAALDALVPAA--------- 329 (508)
T ss_pred ceEEEECCCCCcCCHHHHHHHhccccchhhhcccCceEEEEEeehhcCCcchhcCCHHHHHHHHHHhhccc---------
Confidence 733 211 137999999999999998888777766666655320
Q ss_pred CCCceeccccccC-ChHhHHHHHhcCCCCCcccEEeEeccccccCCC-CcCeeeecc
Q 014751 227 YKFRFSTVPVYNC-DQRGLYSAYIESVPYAKDGLLFYNKHAHYQTGN-TPLALVWKD 281 (419)
Q Consensus 227 n~~~F~~lp~~~c-~~~~L~~~~~~~~p~~~DGLLFYHKea~Y~~G~-TPLv~~wkD 281 (419)
..+|...+ +.+.+.+.+.....--..|++.-+.++.|.+|. +..|+=||-
T Consensus 330 -----~~~~~~~~~~~~~~~~~~~~a~~~g~EGlm~K~~ds~Y~~GrR~~~WlK~K~ 381 (508)
T PRK03180 330 -----HRVPRLVTADPAAAAAFLAAALAAGHEGVMVKSLDAPYAAGRRGAGWLKVKP 381 (508)
T ss_pred -----ccccceecCCHHHHHHHHHHHHHcCCceEEEeCCCCCcCCCCCCCCcEEEcC
Confidence 11233333 466777777665666789999999999999995 666655663
No 28
>PHA00454 ATP-dependent DNA ligase
Probab=96.64 E-value=0.012 Score=59.42 Aligned_cols=149 Identities=14% Similarity=0.108 Sum_probs=91.8
Q ss_pred CCcEEEEEeeCCe-EEEEcCCCcEEEeeccCC------CCCCCCCCCCCCCCCcEEEeeeEecC----------------
Q 014751 125 AGKRCIVVSSNGT-TVSRERNGSILHHFPSAL------PSGARTKDPSGSAQSYCILDCIFHEL---------------- 181 (419)
Q Consensus 125 vGkRcLVVas~G~-T~ay~k~G~~l~~F~S~L------PgG~~~~~~~~~~~~ytILDCIy~e~---------------- 181 (419)
-|-||++....|. ...+|++|..+....... +.--+. ....-..-.|||+=..-.
T Consensus 36 DG~R~~~~~~~~~~v~l~SR~g~~~p~l~~~~~~~~~~~~~~~~--~~~~l~~~~vLDGElv~~~~~f~~~~~~l~~k~~ 113 (315)
T PHA00454 36 DGVRGNIVVDNTADHGWLSREGKTIPALEHLNGFDRRWAKLLND--DRCIFPDGFMLDGELMVKGVDFNTGSGLLRRKWK 113 (315)
T ss_pred ceEEEEEEEcCCCeEEEEeCCCCcccchhhhhhhhhhhhhhhhh--hhhcCCCCeEEEEEEEecCCCHHHHHHHhccCcc
Confidence 3899999887775 999999997432211110 000000 000001136888643211
Q ss_pred --------CcEEEEEEEEeeCCccc-c--cccchhhHHHhhhhccccCCCCCCCCCCCCceeccccccC-ChHhHHHHHh
Q 014751 182 --------DQTYYVIDMVCWRGYSL-Y--DCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVYNC-DQRGLYSAYI 249 (419)
Q Consensus 182 --------~~tyYVLDvl~W~g~~l-~--dceteFRffWl~SKl~E~~~~~~~s~~n~~~F~~lp~~~c-~~~~L~~~~~ 249 (419)
.-+|||.|+|.++|..- . ++....++-+.+..|++.-. . ...-.+...|++.| +.+.+.+++.
T Consensus 114 ~~~~~~~~~v~~~vFDll~l~~~~~g~~l~~l~~~pl~~Rr~~L~~l~~--~---~~~~~~~~~~~~~~~~~~~~~~~~~ 188 (315)
T PHA00454 114 VLFELHLKKLHVVVYDVTPLDVLESGEDYDVMSLLMYEHVRAMVPLLME--Y---FPEIDWFLSESYEVYDMESLQELYE 188 (315)
T ss_pred chhhhccCceEEEEEEeeEeccccCCccccccccccHHHHHHHHHHHHh--h---CCCcceEeeceEEcCCHHHHHHHHH
Confidence 13799999999995421 1 22355677777777765421 0 11123778899988 4567777776
Q ss_pred cCCCCCcccEEeEeccccccCCCCcCeeeeccC
Q 014751 250 ESVPYAKDGLLFYNKHAHYQTGNTPLALVWKDE 282 (419)
Q Consensus 250 ~~~p~~~DGLLFYHKea~Y~~G~TPLv~~wkD~ 282 (419)
....--..|++.-..++.|++|.+. .|||=.
T Consensus 189 ~~~~~g~EGiv~K~~ds~Y~~Grr~--~~~K~K 219 (315)
T PHA00454 189 KKRAEGHEGLVVKDPSLIYRRGKKS--GWWKMK 219 (315)
T ss_pred HHHhCCCceEEEeCCCCCCCCCCcc--CcEEEc
Confidence 6555668999999999999999764 367754
No 29
>PHA02587 30 DNA ligase; Provisional
Probab=96.57 E-value=0.017 Score=61.82 Aligned_cols=157 Identities=16% Similarity=0.174 Sum_probs=101.2
Q ss_pred ceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEEeeccCCCCCCCCCCCCCCCCCcEEEeeeEe---c-------------
Q 014751 117 DWYVFARPAGKRCIVVSSNGTTVSRERNGSILHHFPSALPSGARTKDPSGSAQSYCILDCIFH---E------------- 180 (419)
Q Consensus 117 ~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~~F~S~LPgG~~~~~~~~~~~~ytILDCIy~---e------------- 180 (419)
.|++=.==-|-||.++..+|....|||+|.-++.|+-..+.-......-.....-+|||+=.. .
T Consensus 153 ~~~~E~K~DG~R~q~h~~~~~v~l~SR~g~~~~~~p~i~~~l~~~~~~~~~~~~~~VLDGElv~~~~~~~~~~~~~f~~~ 232 (488)
T PHA02587 153 PAYAQLKADGARCFADIDADGIEIRSRNGNEYLGLDLLKEELKKMTAEARQRPGGVVIDGELVYVEVETKKPNGLSFLFD 232 (488)
T ss_pred cEEEEEccCceEEEEEEeCCEEEEEecCCccccCChhHHHHHHHHhhhhcccCCcEEEEeEEEEEecccCCCccchhhcc
Confidence 566555567999999999999999999999876553221110000000000012378887331 1
Q ss_pred ----------------------------------CCcEEEEEEEEee---CCcccccccchhhHHHhhhhccccCCCCCC
Q 014751 181 ----------------------------------LDQTYYVIDMVCW---RGYSLYDCTAEFRFFWLNSKLAETGACDAP 223 (419)
Q Consensus 181 ----------------------------------~~~tyYVLDvl~W---~g~~l~dceteFRffWl~SKl~E~~~~~~~ 223 (419)
..-+|||.|+|-+ .|..+.+-+..=|.=.|++-+...+
T Consensus 233 ~~~~~~f~q~l~~R~~~~~i~~~~l~~~~~~~~~~pv~~~vFDiL~ld~y~~~~~~~~pl~eRr~~L~~l~~~~~----- 307 (488)
T PHA02587 233 DSKAKEFVGVVADRATGNGIVNKSLKGTISKEEAQEIVFQVWDIVPLEVYYGKEKSDMPYDDRFSKLAQMFEDCG----- 307 (488)
T ss_pred cccccchhhhhhhhhhccchhhhhhccccchhhccceEEEEEEeechhhccCCccccCCHHHHHHHHHHHHhhcC-----
Confidence 1126999999953 2333556666667666666553111
Q ss_pred CCCCCCceeccccccC-ChHhHHHHHhcCCCCCcccEEeEeccccccCCCCcCeeeeccC
Q 014751 224 SHYYKFRFSTVPVYNC-DQRGLYSAYIESVPYAKDGLLFYNKHAHYQTGNTPLALVWKDE 282 (419)
Q Consensus 224 s~~n~~~F~~lp~~~c-~~~~L~~~~~~~~p~~~DGLLFYHKea~Y~~G~TPLv~~wkD~ 282 (419)
.-++.++|...| +.+.+.+.+.....--..|++.-+.++.|++|.+.-+++||..
T Consensus 308 ----~~~i~l~~~~~~~~~ee~~~~~~~a~~~G~EGimlK~~ds~Y~~GRs~~WlKiK~~ 363 (488)
T PHA02587 308 ----YDRVELIENQVVNNLEEAKEIYKRYVDQGLEGIILKNTDGLWEDGRSKDQIKFKEV 363 (488)
T ss_pred ----CCcEEEEeeEEcCCHHHHHHHHHHHHhCCCCeEEEECCCCCCCCCCCCCcEEecCC
Confidence 125566777666 4567777776666667899999999999999999988899854
No 30
>cd07896 Adenylation_kDNA_ligase_like Adenylation domain of kDNA ligases and similar proteins. The mitochondrial DNA of parasitic protozoans is highly unusual. It is termed the kinetoplast DNA (kDNA) and consists of circular DNA molecules (maxicircles) and several thousand smaller circular molecules (minicircles). This group is composed of kDNA ligase, Chlorella virus DNA ligase, and similar proteins. kDNA ligase and Chlorella virus DNA ligase are the smallest known ATP-dependent ligases. They are involved in DNA replication or repair. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. They have a highly modular architecture consisting of a unique arrangement of two or more discrete domains. The adenylation and the C-terminal oligonucleotide/oligosaccharide binding (OB)-fold domains comprise a catalytic core unit that is common to most me
Probab=96.11 E-value=0.023 Score=51.84 Aligned_cols=133 Identities=20% Similarity=0.201 Sum_probs=81.9
Q ss_pred CceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEEeeccCCCCCCCCCCCCCCCCCcEEEeeeEec---------------
Q 014751 116 HDWYVFARPAGKRCIVVSSNGTTVSRERNGSILHHFPSALPSGARTKDPSGSAQSYCILDCIFHE--------------- 180 (419)
Q Consensus 116 ~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~~F~S~LPgG~~~~~~~~~~~~ytILDCIy~e--------------- 180 (419)
..|++=+==-|-||++. |. .++||+|..+..- ..+.-+- .. +|||+=+.-
T Consensus 16 ~~~~~e~K~DG~R~~~~---~~-~~~SR~g~~~t~~-~~~~~~l---------~~-~ilDGElv~~~~~f~~l~~~~~~~ 80 (174)
T cd07896 16 SGYLVSEKLDGVRAYWD---GK-QLLSRSGKPIAAP-AWFTAGL---------PP-FPLDGELWIGRGQFEQTSSIVRSK 80 (174)
T ss_pred HHeeechhhceEEEEEe---cc-EEEecCCcCCCCC-HHHHhhC---------CC-CccCceEEcCCCCHHHHHHHHhcC
Confidence 46666555569999763 33 8899999875421 1111010 11 788874432
Q ss_pred -------CCcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCCCCCceeccccccCC-hHhHHHHHhcCC
Q 014751 181 -------LDQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVYNCD-QRGLYSAYIESV 252 (419)
Q Consensus 181 -------~~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~n~~~F~~lp~~~c~-~~~L~~~~~~~~ 252 (419)
..-.|||.|+|. .+. +..=|.=-|.+-+.+.+ .-.|.++|++.|. .+.+..++....
T Consensus 81 ~~~~~~~~~~~f~vFDil~-~~~-----p~~eR~~~L~~~i~~~~---------~~~~~~~~~~~~~~~~~i~~~~~~~~ 145 (174)
T cd07896 81 KPDDEDWRKVKFMVFDLPS-AKG-----PFEERLERLKNLLEKIP---------NPHIKIVPQIPVKSNEALDQYLDEVV 145 (174)
T ss_pred CCChhhcccceEEEEeCCC-CCC-----CHHHHHHHHHHHHHhCC---------CCcEEEEeeeeeCCHHHHHHHHHHHH
Confidence 124899999998 222 33334444444443321 2357788888884 455666665444
Q ss_pred CCCcccEEeEeccccccCCCCcCeeeec
Q 014751 253 PYAKDGLLFYNKHAHYQTGNTPLALVWK 280 (419)
Q Consensus 253 p~~~DGLLFYHKea~Y~~G~TPLv~~wk 280 (419)
.--.+|+++-..++.|++|.+. .|||
T Consensus 146 ~~g~EGlv~K~~ds~Y~~gR~~--~wlK 171 (174)
T cd07896 146 AAGGEGLMLRRPDAPYETGRSD--NLLK 171 (174)
T ss_pred hcCCCeEEEecCCCcccCCcCC--Ccee
Confidence 4458999999999999999886 4555
No 31
>COG1793 CDC9 ATP-dependent DNA ligase [DNA replication, recombination, and repair]
Probab=96.01 E-value=0.15 Score=54.14 Aligned_cols=159 Identities=19% Similarity=0.260 Sum_probs=112.5
Q ss_pred cCCCCCCCceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEE-eecc-------CCCCCCCCCCCCCCCCCcEEEee---e
Q 014751 109 DVPDRLSHDWYVFARPAGKRCIVVSSNGTTVSRERNGSILH-HFPS-------ALPSGARTKDPSGSAQSYCILDC---I 177 (419)
Q Consensus 109 dvP~dL~~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~-~F~S-------~LPgG~~~~~~~~~~~~ytILDC---I 177 (419)
+.|.....+|.+=.==-|-||.+....|....|||+|.-+. +||. .||.. -+|||+ +
T Consensus 126 ~~~~~~~~~w~~E~K~DG~R~q~h~~~~~vrl~SR~g~d~T~~fP~~~~~~~~~l~~~------------~~iiDGE~V~ 193 (444)
T COG1793 126 EALPRDGGDWAYEEKFDGYRVQIHIDGGKVRLYSRNGEDWTGRFPDILEAAAEALPAD------------DFILDGEIVV 193 (444)
T ss_pred ccCCCCCCCEEEEEeeceEEEEEEEcCCEEEEEeCCCccchhhChHHHHHHHhcCCCC------------ceEEeeeEEE
Confidence 33444455699888889999999999999999999997654 5662 23321 389996 3
Q ss_pred Eec-------------------------CCcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCCCCCcee
Q 014751 178 FHE-------------------------LDQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFS 232 (419)
Q Consensus 178 y~e-------------------------~~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~n~~~F~ 232 (419)
+++ ..-+||+.|+|.-+|+++.+.+..=|--=|.+-+...+. +...
T Consensus 194 ~~~~~~~~F~~Lq~r~~~k~~v~~~~~~~~~~~~aFDlL~~dG~dL~~~pl~eRr~~Le~lv~~~~~---------~~~~ 264 (444)
T COG1793 194 LDEEGRLDFQALQQRLRRKYDVAKLRRETPLVLFAFDLLYLDGEDLRGLPLEERRALLEELVKSSDK---------IEIA 264 (444)
T ss_pred ECCCCCCCHHHHHHHhhhccchhhhccCCceEEEEEEEEeECCcccccCchHHHHHHHHHHhccccc---------cccc
Confidence 332 135799999999999999999999998888888876411 1111
Q ss_pred ccccccCChHhHHHHHhcCCCCCcccEEeEeccccccCC-CCcCeeeeccCCCcccee
Q 014751 233 TVPVYNCDQRGLYSAYIESVPYAKDGLLFYNKHAHYQTG-NTPLALVWKDEKCSQYVI 289 (419)
Q Consensus 233 ~lp~~~c~~~~L~~~~~~~~p~~~DGLLFYHKea~Y~~G-~TPLv~~wkD~~~s~y~~ 289 (419)
..-.+ -+.+.....+.....--..|++=-++++.|++| .+-.|+=||-...-.++|
T Consensus 265 ~~i~~-~~~~~~~~~~~~a~~~g~EGvv~K~~ds~Y~~g~R~~~W~K~K~~~~~d~vv 321 (444)
T COG1793 265 ERIPF-SDAEEGEAFLEAAIELGLEGVVAKRPDSPYRAGGRSNKWLKVKRDETLDLVV 321 (444)
T ss_pred cceec-cChhhHHHHHHHHHhcCceEEEEeCCCCCcCCCCCCCcceEeccCCcccEEE
Confidence 11112 334556666655555568999999999999954 698888888654444433
No 32
>PRK09125 DNA ligase; Provisional
Probab=95.06 E-value=0.17 Score=50.52 Aligned_cols=136 Identities=20% Similarity=0.199 Sum_probs=87.8
Q ss_pred CceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEEeeccCCCCCCCCCCCCCCCCCcEEEeeeEec---------------
Q 014751 116 HDWYVFARPAGKRCIVVSSNGTTVSRERNGSILHHFPSALPSGARTKDPSGSAQSYCILDCIFHE--------------- 180 (419)
Q Consensus 116 ~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~~F~S~LPgG~~~~~~~~~~~~ytILDCIy~e--------------- 180 (419)
.+|++=+==-|-||.+ .| +..+||+|..+.. +..+-.+- . -+|||+=..-
T Consensus 43 ~~~~~E~K~DG~R~~~---~~-v~l~SR~g~~it~-p~~~~~~~---------~-~~vLDGElv~~~~~F~~l~~r~~~k 107 (282)
T PRK09125 43 SGYLVSEKLDGVRAYW---DG-KQLLTRQGNPIAA-PAWFTAGF---------P-PFPLDGELWAGRGQFEAISSIVRDK 107 (282)
T ss_pred hhEEEEeeeeeEeEEE---CC-eEEEcCCCCcCCC-chhHHhcC---------C-CccEeEEEEeCCCCHHHHHHHHccC
Confidence 4787777667999963 34 6799999998643 11110000 0 2688875421
Q ss_pred -------CCcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCCCCCceeccccccCC-hHhHHHHHhcCC
Q 014751 181 -------LDQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVYNCD-QRGLYSAYIESV 252 (419)
Q Consensus 181 -------~~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~n~~~F~~lp~~~c~-~~~L~~~~~~~~ 252 (419)
..-+|||.|++..+| +..-|.=-|.+-+.+.+ + -.+..+|+..|+ .+.+.+++....
T Consensus 108 ~~~~~~~~~v~~~vFDll~~~g------pl~eRr~~L~~li~~~~--------~-~~i~~~~~~~~~~~~~~~~~~~~~~ 172 (282)
T PRK09125 108 TPDDAAWRKVRFMVFDLPDAPG------DFEERLAVLKKLLAKLP--------S-PYIKIIEQIRVRSEAALQQFLDQIV 172 (282)
T ss_pred CcchhhhcccEEEEEEcCCCCC------CHHHHHHHHHHHHhhCC--------C-CcEEEEeEEEcCCHHHHHHHHHHHH
Confidence 123899999997765 44445555666554321 1 146778888884 455666665555
Q ss_pred CCCcccEEeEeccccccCCCCcCeeeecc
Q 014751 253 PYAKDGLLFYNKHAHYQTGNTPLALVWKD 281 (419)
Q Consensus 253 p~~~DGLLFYHKea~Y~~G~TPLv~~wkD 281 (419)
.--..|+++-+.++.|++|.|.-++=+|.
T Consensus 173 ~~G~EGiV~K~~ds~Y~~GRs~~wlKiK~ 201 (282)
T PRK09125 173 AAGGEGLMLHRPDAPYEAGRSDDLLKLKP 201 (282)
T ss_pred HcCCCEEEEeCCCCCCcCCCCCCcEEEEe
Confidence 55689999999999999999875444443
No 33
>KOG0966 consensus ATP-dependent DNA ligase IV [Replication, recombination and repair]
Probab=86.00 E-value=3.3 Score=47.15 Aligned_cols=168 Identities=18% Similarity=0.308 Sum_probs=113.2
Q ss_pred hhhhcccccccccCCCCC-CCceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEE-eeccCCCCCCCCCCCCCC-------
Q 014751 97 FASQLMLPEWMIDVPDRL-SHDWYVFARPAGKRCIVVSSNGTTVSRERNGSILH-HFPSALPSGARTKDPSGS------- 167 (419)
Q Consensus 97 ya~qLMlsEWl~dvP~dL-~~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~-~F~S~LPgG~~~~~~~~~------- 167 (419)
.|+.-|+.+| ++=+.+ +++.++=-==-|-|..+.-..|.-.-+++||.-.. .| |.+..++...+
T Consensus 232 La~~~~~~~~--~~~e~m~~~~f~lEtK~DGERiQlHk~g~~~~yfSRNg~dyT~~y-----g~s~~~g~lt~~i~~~f~ 304 (881)
T KOG0966|consen 232 LAQKQKLGDW--AIIEKMGGQDFYLETKFDGERIQLHKDGGEYKYFSRNGNDYTYEY-----GASYAHGTLTQRIHGAFN 304 (881)
T ss_pred HHhhhccchH--HHHHHhcCCceEEEeeccCceEEEEecCCEEEEEecCCcchhhhc-----CcccccccccHHHHhhhh
Confidence 4555677777 332333 33333333456999999999888888899997533 33 22221111110
Q ss_pred -CCCcEEEeeeE---ecC-----------------------CcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCC
Q 014751 168 -AQSYCILDCIF---HEL-----------------------DQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGAC 220 (419)
Q Consensus 168 -~~~ytILDCIy---~e~-----------------------~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~ 220 (419)
.=.-|||||=+ +.. +-+|-|.|+|..||.++..-+-.-|.+-|++=+.+.+.
T Consensus 305 ~~v~~cILDGEMm~wD~~~~~f~~~G~~~dik~~~~~~~~~qp~yvvfDLLylNgksL~~~~l~qR~e~L~~v~~p~~~- 383 (881)
T KOG0966|consen 305 KEVESCILDGEMMTWDTKTKRFCPFGSNSDIKELSSRDGSQQPCYVVFDLLYLNGKSLFGAPLHQRLEILKKVIVPKSG- 383 (881)
T ss_pred hcchheEecceEEEeecchhhhccCCchhhHHHhhccccCCCceEEEeeeeeecCcccCCccHHHHHHHHHhcccCCCC-
Confidence 12358999843 211 25677889999999999999999999999887766432
Q ss_pred CCCCCCCCCceeccccccCC-hHhHHHHHhcCCCCCcccEEeEeccccccCCCCcCeeeeccC
Q 014751 221 DAPSHYYKFRFSTVPVYNCD-QRGLYSAYIESVPYAKDGLLFYNKHAHYQTGNTPLALVWKDE 282 (419)
Q Consensus 221 ~~~s~~n~~~F~~lp~~~c~-~~~L~~~~~~~~p~~~DGLLFYHKea~Y~~G~TPLv~~wkD~ 282 (419)
++.++++-.|. .+.+.+.+...+.---.|++----++.|.+|.- -=+|.|..
T Consensus 384 ---------~iei~~~~~~~~~edi~~~f~~ai~~~~EGIVlK~~~S~Y~pg~R-~~gW~K~K 436 (881)
T KOG0966|consen 384 ---------RIEIVRSEVGSTKEDIEQFFEEAIDNGEEGIVLKKPDSSYVPGQR-SNGWIKLK 436 (881)
T ss_pred ---------eeEEeehhhcccHHHHHHHHHHHHhcCCCceEEeccCcccCcccc-CCCcEeec
Confidence 36778887774 677777776655555679999999999999976 45677654
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=85.89 E-value=2.8 Score=45.94 Aligned_cols=90 Identities=19% Similarity=0.216 Sum_probs=62.0
Q ss_pred CcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCCCCCceeccccccCChHhHHHHHhcCCCCCcccEEe
Q 014751 182 DQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVYNCDQRGLYSAYIESVPYAKDGLLF 261 (419)
Q Consensus 182 ~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~n~~~F~~lp~~~c~~~~L~~~~~~~~p~~~DGLLF 261 (419)
.-+|||.|+|..+|.++.+.+..-|.=-|++-|.+... + .+...+.+..+.+ +++.....--..|++.
T Consensus 57 pv~~~vFDlL~l~G~dL~~~Pl~eRr~~L~~ll~~~~~--------~-~i~~~~~~~~~~~---~~~~~a~~~G~EGIV~ 124 (552)
T TIGR02776 57 PLTYYAFDLLFLSGEDLRDLPLEERKKRLKQLLKAQDE--------P-AIRYSDHFESDGD---ALLESACRLGLEGVVS 124 (552)
T ss_pred ceEEEEEeccccCCcccccCCHHHHHHHHHHHhhhcCC--------C-cEEEeeeecccHH---HHHHHHHHCCCceEEE
Confidence 45899999999999999998888888888777654211 1 1233333444444 3333333345789999
Q ss_pred EeccccccCCCCcCeeeeccCC
Q 014751 262 YNKHAHYQTGNTPLALVWKDEK 283 (419)
Q Consensus 262 YHKea~Y~~G~TPLv~~wkD~~ 283 (419)
-+.++.|.+|.|.-|+=+|-..
T Consensus 125 K~~dS~Y~~GRs~~WlKlK~~~ 146 (552)
T TIGR02776 125 KRLDSPYRSGRSKDWLKLKCRR 146 (552)
T ss_pred eCCCCCCCCCCCcchhcccccc
Confidence 9999999999988765555433
No 35
>KOG3132 consensus m3G-cap-specific nuclear import receptor (Snurportin1) [RNA processing and modification]
Probab=80.25 E-value=0.78 Score=45.80 Aligned_cols=163 Identities=29% Similarity=0.419 Sum_probs=91.2
Q ss_pred CCCCCCcCCCCCCchHHHHHHHHHHHHHHhH---HHHHHHHhhhhhhhccccC-CCCCCCCCCCCCCCCCccccCCCCcc
Q 014751 3 PPDLRRPFKRTAISDQQRRRELSLQRQSQNR---RDAQQQARCLASSVLSLQS-QYPDPVPELEIEPESQPQQEAGPLTK 78 (419)
Q Consensus 3 ph~~~~~~k~~~~~~Q~~RR~~~Le~Qk~~R---~d~~~~aR~La~~~~~~~~-~~~~~~~e~~~~~~~~e~~~~~~~~~ 78 (419)
||..++|+|+..+.+|.+||+..+-||.|-| .++...||++++. +.++. ..+|.++ + -.+.-.+++-.++.
T Consensus 1 ~~el~~~l~s~f~vdql~~~~~~hpR~sQykn~~s~aeQ~arrr~~l-lelQks~r~D~~~--~--~r~lA~dd~tg~Es 75 (325)
T KOG3132|consen 1 PHELRRPLKSRFIVDQLKRRELSHPRQSQYKNLTSDAEQRARRRASL-LELQKSSRPDVDP--E--IRSLAVDDLTGTES 75 (325)
T ss_pred ChhHhhhhhcccccchhhhhhccCchhhhhhhhhhHHHHHHHHHHHH-HHhhhcCCCCccH--H--HHhhcccccccccc
Confidence 7889999999999999999999999999988 8999999999973 33332 2233222 1 11222334433311
Q ss_pred chhhhhhhhccCCcchhhhhhhcccccccccCCCCCCCceEE-EEecCCcEEEEEe-eCCe-EEEEcCCCcEEEeecc--
Q 014751 79 DLDIRQASKLRGPEVRKWFASQLMLPEWMIDVPDRLSHDWYV-FARPAGKRCIVVS-SNGT-TVSRERNGSILHHFPS-- 153 (419)
Q Consensus 79 ~~d~~~~~k~~gk~~rk~ya~qLMlsEWl~dvP~dL~~~Wl~-vpcPvGkRcLVVa-s~G~-T~ay~k~G~~l~~F~S-- 153 (419)
+ .+|...+...+.--+. +..|..+- -.| .+|++ ||=-.|+--.||+ .-|+ |-+-.-.|..+..-.+
T Consensus 76 ----e-e~k~d~~~a~~~tgk~--~~K~yA~q-lML-sEWliDvP~~LsqdW~vv~~PvGKR~lvVaSrG~Tvay~k~G~ 146 (325)
T KOG3132|consen 76 ----E-ESKFDVRQASRLTGKE--ARKWYAKQ-LML-SEWLIDVPDNLSQDWYVVARPVGKRCLVVASRGTTVAYVKNGS 146 (325)
T ss_pred ----h-hhhhhhhHHhhhcchh--HHHHHHHH-hhh-HHHhccCccccCcceEEEEeecCceEEEEecCCceEEEecCCe
Confidence 1 1222221111111111 23343321 123 57875 5667777766665 4443 4455667887765542
Q ss_pred ---CCCCCCCCCCCCCCCCCcEEEeeeEecCCcEEEEEEEEe
Q 014751 154 ---ALPSGARTKDPSGSAQSYCILDCIFHELDQTYYVIDMVC 192 (419)
Q Consensus 154 ---~LPgG~~~~~~~~~~~~ytILDCIy~e~~~tyYVLDvl~ 192 (419)
..|.--+ .|+.+. ..++.|-|||+|.
T Consensus 147 ~v~rF~S~LP----GGnrr~---------~~a~~ytILDCIy 175 (325)
T KOG3132|consen 147 TVHRFPSALP----GGNRRK---------GPANSYTILDCIY 175 (325)
T ss_pred eEeeccccCC----CCCcCC---------CCcccceeeeeee
Confidence 1222111 111111 3578999999986
No 36
>COG5226 CEG1 mRNA capping enzyme, guanylyltransferase (alpha) subunit [RNA processing and modification]
Probab=78.14 E-value=5.2 Score=41.36 Aligned_cols=173 Identities=20% Similarity=0.304 Sum_probs=98.4
Q ss_pred CCCceEEEEecCCcEEEEEee--------CCeEEEEcCCCcEEEee-ccCCCCCCCCC--CCCCCCCCcEEEeeeEecC-
Q 014751 114 LSHDWYVFARPAGKRCIVVSS--------NGTTVSRERNGSILHHF-PSALPSGARTK--DPSGSAQSYCILDCIFHEL- 181 (419)
Q Consensus 114 L~~~Wl~vpcPvGkRcLVVas--------~G~T~ay~k~G~~l~~F-~S~LPgG~~~~--~~~~~~~~ytILDCIy~e~- 181 (419)
|..|+++.--.-|-|||+... +|.-.-|-.|=+.++.| +-.+|.-..+. .-.+.-.++-|+||.-.+.
T Consensus 60 l~~dy~VCEKsDGvR~Ll~vte~p~tg~~~~y~~DR~nnfY~v~~~f~p~~~~~k~ge~l~~dtlldgelV~d~~p~~k~ 139 (404)
T COG5226 60 LNNDYLVCEKSDGVRALLLVTEEPVTGAFRGYFYDRRNNFYEVHTSFPPCSTVLKDGEVLLEDTLLDGELVFDCLPYEKV 139 (404)
T ss_pred HhCCeEEEEccCCeEEEEEEEecccCCCcceEEEeccCceEEeccccCCcccccccCcEEeccceecceEEEEeccccch
Confidence 477899888899999998653 23333333344445533 32344322110 0112235667777765543
Q ss_pred -CcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCC------CCCCCCCCCceeccccccCChHhHHHHHh--cCC
Q 014751 182 -DQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGAC------DAPSHYYKFRFSTVPVYNCDQRGLYSAYI--ESV 252 (419)
Q Consensus 182 -~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~------~~~s~~n~~~F~~lp~~~c~~~~L~~~~~--~~~ 252 (419)
+-.|-+.|.|..+|+-+...+++=|+=-++--++. +.. ...+...||.|. ++.+.-+ -++..++. ...
T Consensus 140 ~qlryl~fdcLa~~g~~~~~~~~s~Rl~~l~Ke~~k-p~~~~r~s~~~~~~~fpf~~s-~K~M~~s-yg~~ki~k~ip~L 216 (404)
T COG5226 140 PQLRYLLFDCLAYAGMFVERMEKSERLKTLQKEDEK-PRERKRVSIEIDSGSFPFHFS-VKQMLKS-YGFWKIYKKIPEL 216 (404)
T ss_pred HHHHHHHHHHhhhcceeEeecchhhHHHHhhhhhcc-cHhhhhheeeccccccceeee-HHHHHhh-hhHHHHHhhcccc
Confidence 33566778888888877777777776555433332 110 011222333332 2222111 12334452 233
Q ss_pred CCCcccEEeEeccccccCCCCcCeeeeccC--CCcccee
Q 014751 253 PYAKDGLLFYNKHAHYQTGNTPLALVWKDE--KCSQYVI 289 (419)
Q Consensus 253 p~~~DGLLFYHKea~Y~~G~TPLv~~wkD~--~~s~y~~ 289 (419)
+.--|||+|---++.|+.|.--+.+-||.+ |+..|.+
T Consensus 217 ~HgnDGLIFTp~~~PY~~Gkd~~lLKWKP~~~NTiDF~l 255 (404)
T COG5226 217 KHGNDGLIFTPADEPYSVGKDGALLKWKPASLNTIDFRL 255 (404)
T ss_pred cCCCCceEeccCCCCcccCccceeeecCccccCceeeee
Confidence 456899999999999999998999999998 4445543
No 37
>TIGR02609 doc_partner putative addiction module antidote. Members of this protein family are putative addiction module antidote proteins that appear recurringly in two-gene operons with members of the Doc (death-on-curing) family TIGR01550. Members of this family contain a SpoVT/AbrB-like domain (pfam04014). Note that the gene pairs with a member of this family tend to be found on bacterial chromosomes, not on plasmids.
Probab=69.72 E-value=5.3 Score=32.30 Aligned_cols=54 Identities=19% Similarity=0.257 Sum_probs=37.4
Q ss_pred cccchhhhhcCCCCCCeeeEEEcCCceeeccCceeeeceEEeecCCccccCCchhhHHHHHHh
Q 014751 325 CLDGEFIQKSGLQSGSLLKFAIGNGGLSFVDGKLEKSDLNYLGKSNRARMFADSYSKVIFQYM 387 (419)
Q Consensus 325 ~~~~~~i~~~~l~~g~L~Rf~i~~~~~~~~~~~~~~~~l~~~~~~~~~R~~aDs~sKIlfq~~ 387 (419)
++|.+++.+.||.+|+-+-+.+.++++.+.--+. .....+.+.++..++|-+|.
T Consensus 13 tIPk~i~~~lgl~~Gd~v~v~~~~~~iii~~~~~---------~~~~~~~~~~~~~~~~~~y~ 66 (74)
T TIGR02609 13 TLPKEVLESLGLKEGDTLYVDEEEGGLKLKRFDE---------GKELEKKMQMAVERAMSKYD 66 (74)
T ss_pred EECHHHHHHcCcCCCCEEEEEEECCEEEEEECCC---------CccHHHHHHHHHHHHHHHHH
Confidence 6899999999999999999888888877721110 11223345556777776663
No 38
>COG5064 SRP1 Karyopherin (importin) alpha [Intracellular trafficking and secretion]
Probab=64.17 E-value=5.6 Score=41.88 Aligned_cols=44 Identities=32% Similarity=0.411 Sum_probs=32.4
Q ss_pred CCCCCCcCCCCCCc--hHHHHH--HHHHHHHHHhHHHHHHHHhhhhhh
Q 014751 3 PPDLRRPFKRTAIS--DQQRRR--ELSLQRQSQNRRDAQQQARCLASS 46 (419)
Q Consensus 3 ph~~~~~~k~~~~~--~Q~~RR--~~~Le~Qk~~R~d~~~~aR~La~~ 46 (419)
|.-||.-||.|... |.-+|| +...|..|+||.+.+|+-|+|++.
T Consensus 7 p~~Rr~~fk~Kg~f~adelRr~ReeQQvElRkqKreE~LnKrRNl~dv 54 (526)
T COG5064 7 PEARRYNFKGKGRFSADELRRRREEQQVELRKQKREELLNKRRNLADV 54 (526)
T ss_pred hHHHHhcccCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccc
Confidence 44478889999732 222222 367888999999999999999764
No 39
>PF14766 RPA_interact_N: Replication protein A interacting N-terminal
Probab=52.77 E-value=29 Score=25.52 Aligned_cols=38 Identities=21% Similarity=0.205 Sum_probs=31.6
Q ss_pred CCCCcCCC-CCCchHHHHHHHHHHHHHHhHHHHHHHHhh
Q 014751 5 DLRRPFKR-TAISDQQRRRELSLQRQSQNRRDAQQQARC 42 (419)
Q Consensus 5 ~~~~~~k~-~~~~~Q~~RR~~~Le~Qk~~R~d~~~~aR~ 42 (419)
|++++||. +...=.++=|+.-+++-|+.|.++++..|.
T Consensus 2 ~~r~~~k~~~~p~WKe~lR~rC~~R~r~~R~~lL~k~R~ 40 (42)
T PF14766_consen 2 RRRSLYKQRKSPPWKETLRERCLERVRESRTQLLWKYRQ 40 (42)
T ss_pred cchhhhccCCCccHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 56788887 444448888999999999999999999985
No 40
>PRK04337 50S ribosomal protein L35Ae; Validated
Probab=51.61 E-value=24 Score=30.07 Aligned_cols=35 Identities=23% Similarity=0.430 Sum_probs=26.0
Q ss_pred CCcEEEEEeeCCe------EEEEcCCCcEEEeeccCCCCCC
Q 014751 125 AGKRCIVVSSNGT------TVSRERNGSILHHFPSALPSGA 159 (419)
Q Consensus 125 vGkRcLVVas~G~------T~ay~k~G~~l~~F~S~LPgG~ 159 (419)
+||||.-|...|. |...-.+|-...+|.++||+-+
T Consensus 39 lGKrv~yvyk~grviwGKItR~HGnsGvVrAkF~~nLP~~a 79 (87)
T PRK04337 39 IGRKVIWKDPTGNKYVGKIVRVHGNRGEVRARFKPGLPGQA 79 (87)
T ss_pred cCceEEEEeCCCCEEEEEEEeeeCCCceEEEEECCCCChHH
Confidence 4777777765443 4556678999999999999844
No 41
>PF06257 DUF1021: Protein of unknown function (DUF1021); InterPro: IPR009366 This entry consists of several hypothetical bacterial proteins of unknown function.; PDB: 3FB9_A.
Probab=47.56 E-value=9.4 Score=31.61 Aligned_cols=30 Identities=30% Similarity=0.511 Sum_probs=22.3
Q ss_pred CCcEEEEEeeCCeEEEEcCCCcEEEeeccC
Q 014751 125 AGKRCIVVSSNGTTVSRERNGSILHHFPSA 154 (419)
Q Consensus 125 vGkRcLVVas~G~T~ay~k~G~~l~~F~S~ 154 (419)
+|+|+.|.|++|.-+...+.|-+...|||.
T Consensus 16 vG~~V~l~a~~GRkK~~~r~GvL~~tYPsv 45 (76)
T PF06257_consen 16 VGKRVKLKANKGRKKIIEREGVLEETYPSV 45 (76)
T ss_dssp TTSEEEEEE--SSS--S-EEEEEEEE-SSE
T ss_pred CCCEEEEEEcCCceEEEEEEEEEEeecCcE
Confidence 799999999999999999999999999875
No 42
>PF01247 Ribosomal_L35Ae: Ribosomal protein L35Ae; InterPro: IPR001780 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The ribosomal L35A eukaryotic and archaebacterial ribosomal proteins can be grouped on the basis of sequence similarities. One of these families consists of: Vertebrate L35A. Caenorhabditis elegans L35A (F10E7.7). Saccharomyces cerevisiae L37A/L37B (Rp47). Plant L35A. Pyrococcus woesei L35A homologue []. These proteins have 87 to 110 amino-acid residues.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZR_j 2LP6_A 1SQR_A 4A18_H 4A1D_H 4A19_H 4A1B_H 3IZS_j.
Probab=46.15 E-value=26 Score=30.26 Aligned_cols=35 Identities=31% Similarity=0.458 Sum_probs=23.5
Q ss_pred CCcEEEEEee--------CCe------EEEEcCCCcEEEeeccCCCCCC
Q 014751 125 AGKRCIVVSS--------NGT------TVSRERNGSILHHFPSALPSGA 159 (419)
Q Consensus 125 vGkRcLVVas--------~G~------T~ay~k~G~~l~~F~S~LPgG~ 159 (419)
.||||.-|.. ++. |.+.-.+|-...+|.++||+-.
T Consensus 39 lGKrv~yvyk~~~~~~~~k~r~iwGkV~r~HGnsGvVrAkF~~nLP~~a 87 (95)
T PF01247_consen 39 LGKRVAYVYKAKNKKNGSKGRVIWGKVTRPHGNSGVVRAKFKKNLPPQA 87 (95)
T ss_dssp TT-EEEEEECE-SSSTTECSEEEEEEEEEESTTTTEEEEEESS--STTG
T ss_pred cCcEEEEEEecccccCCCcEeEEEEEEEeEEcCCCEEEEEeCCCCChHH
Confidence 5888888764 332 4455779999999999999854
No 43
>cd07289 PX_PI3K_C2_alpha The phosphoinositide binding Phox Homology Domain of the Alpha Isoform of Class II Phosphoinositide 3-Kinases. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. The Phosphoinositide 3-Kinase (PI3K) family of enzymes catalyzes the phosphorylation of the 3-hydroxyl group of the inositol ring of phosphatidylinositol. PI3Ks play an important role in a variety of fundamental cellular processes, including cell motility, the Ras pathway, vesicle trafficking and secretion, immune cell activation and apoptosis. PI3Ks are divided into three main classes (I, II, and III) based on their substrate specificity, regulation, and domain structure. Class II PI3Ks preferentially use PI as a substrate to produce PI3P, but can also phosphorylate PI4P to produce PI(3,4)P2. They function as monomers and do not associate with any regulatory subunits. Class II enzymes contain an N-terminal Ras binding domain, a lipid binding C2 dom
Probab=42.82 E-value=43 Score=29.41 Aligned_cols=44 Identities=18% Similarity=0.305 Sum_probs=31.1
Q ss_pred cEEEee--eEecCCcEEEEEEEEeeCCcc----cccccchhhHHHhhhhcccc
Q 014751 171 YCILDC--IFHELDQTYYVIDMVCWRGYS----LYDCTAEFRFFWLNSKLAET 217 (419)
Q Consensus 171 ytILDC--Iy~e~~~tyYVLDvl~W~g~~----l~dceteFRffWl~SKl~E~ 217 (419)
-||+++ .++..+...|++.|. |+|.. +|-.-.| |+=||.||.|.
T Consensus 2 ~~V~~f~Kr~~p~k~yvY~i~V~-~~~~~~~~~I~Rry~e--F~~Lh~kL~~~ 51 (109)
T cd07289 2 VSVFTYHKRYNPDKHYIYVVRIL-REGQIEPSFVFRTFDE--FQELHNKLSIL 51 (109)
T ss_pred cEEeeEEEEEcCCCeEEEEEEEE-ECCCceeEEEEeeHHH--HHHHHHHHHHH
Confidence 378888 776666778999998 87763 3333333 57789999885
No 44
>KOG0275 consensus Conserved WD40 repeat-containing protein [General function prediction only]
Probab=41.75 E-value=42 Score=35.26 Aligned_cols=54 Identities=28% Similarity=0.458 Sum_probs=0.0
Q ss_pred cCCcEEEEEeeCCeEEEE-cCCCcEEEeeccCCCCCCCCCCCCCCCCCcEEEeeeEecCC----------cEEEEEEE
Q 014751 124 PAGKRCIVVSSNGTTVSR-ERNGSILHHFPSALPSGARTKDPSGSAQSYCILDCIFHELD----------QTYYVIDM 190 (419)
Q Consensus 124 PvGkRcLVVas~G~T~ay-~k~G~~l~~F~S~LPgG~~~~~~~~~~~~ytILDCIy~e~~----------~tyYVLDv 190 (419)
+.|.+.+--++.|+.+++ .|.+-|+.+|. |+| .+|+|+-.|.-..| +|.||+.+
T Consensus 358 ~dG~~iisaSsDgtvkvW~~KtteC~~Tfk---~~~----------~d~~vnsv~~~PKnpeh~iVCNrsntv~imn~ 422 (508)
T KOG0275|consen 358 DDGHHIISASSDGTVKVWHGKTTECLSTFK---PLG----------TDYPVNSVILLPKNPEHFIVCNRSNTVYIMNM 422 (508)
T ss_pred CCCCeEEEecCCccEEEecCcchhhhhhcc---CCC----------CcccceeEEEcCCCCceEEEEcCCCeEEEEec
No 45
>PF01749 IBB: Importin beta binding domain; InterPro: IPR002652 The exchange of macromolecules between the nucleus and cytoplasm takes place through nuclear pore complexes within the nuclear membrane. Active transport of large molecules through these pore complexes require carrier proteins, called karyopherins (importins and exportins), which shuttle between the two compartments. Members of the importin-alpha (karyopherin-alpha) family can form heterodimers with importin-beta. As part of a heterodimer, importin-beta mediates interactions with the pore complex, while importin-alpha acts as an adaptor protein to bind the nuclear localisation signal (NLS) on the cargo through the classical NLS import of proteins. Proteins can contain one (monopartite) or two (bipartite) NLS motifs. Importin-alpha contains several armadillo (ARM) repeats, which produce a curving structure with two NLS-binding sites, a major one close to the N terminus and a minor one close to the C terminus. Ran GTPase helps to control the unidirectional transfer of cargo. The cytoplasm contains primarily RanGDP and the nucleus RanGTP through the actions of RanGAP and RanGEF, respectively. In the nucleus, RanGTP binds to importin-beta within the importin/cargo complex, causing a conformational change in importin-beta that releases it from importin-alpha-bound cargo. The N-terminal importin-beta-binding (IBB) domain of importin-alpha contains an auto-regulatory region that mimics the NLS motif []. The release of importin-beta frees the auto-regulatory region on importin-alpha to loop back and bind to the major NLS-binding site, causing the cargo to be released []. This entry represents the N-terminal IBB domain of importin-alpha that contains the auto-regulatory region. More information about these proteins can be found at Protein of the Month: Importins [].; GO: 0008565 protein transporter activity, 0006606 protein import into nucleus, 0006886 intracellular protein transport, 0005634 nucleus, 0005737 cytoplasm; PDB: 1BK5_B 1UN0_A 1WA5_B 2C1T_A 1EE4_A 1BK6_A 1EE5_A 3TJ3_A 2JDQ_A 3FEY_C ....
Probab=40.74 E-value=4.4 Score=34.38 Aligned_cols=44 Identities=23% Similarity=0.421 Sum_probs=30.9
Q ss_pred CCCCCCcCCCCCCchHHHHH---HHHHHHHHHhHHHHHHHHhhhhhh
Q 014751 3 PPDLRRPFKRTAISDQQRRR---ELSLQRQSQNRRDAQQQARCLASS 46 (419)
Q Consensus 3 ph~~~~~~k~~~~~~Q~~RR---~~~Le~Qk~~R~d~~~~aR~La~~ 46 (419)
+..|+..||.++....+-|| +..++..|++|.+.+..-|++...
T Consensus 6 ~~~R~~~yK~~g~d~~e~RrrRee~~veLRK~KReE~l~KRRn~~~~ 52 (97)
T PF01749_consen 6 PENRRKSYKNKGKDAEEMRRRREEEQVELRKQKREEQLQKRRNINMA 52 (97)
T ss_dssp -GGGGGGSTTTT-SHHHHHHHCCCCHHHHCHHHHHCCHSCCHT----
T ss_pred HHHHHHHHccCCCChHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCC
Confidence 34688999999854344333 479999999999999999999754
No 46
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=40.66 E-value=1.3e+02 Score=33.42 Aligned_cols=97 Identities=19% Similarity=0.260 Sum_probs=60.0
Q ss_pred hcCCCCCcccEEeEeccccccCCCC---cCe-eeeccCCCccceeecCCCCCccccceEEEEEecCCcee--------cc
Q 014751 249 IESVPYAKDGLLFYNKHAHYQTGNT---PLA-LVWKDEKCSQYVIDTDSKGQVLSQQQVVLELQEDGKLS--------TS 316 (419)
Q Consensus 249 ~~~~p~~~DGLLFYHKea~Y~~G~T---PLv-~~wkD~~~s~y~~d~d~~g~~~~~q~vvL~~~~~g~l~--------T~ 316 (419)
....||++||++....+..|..|.| |-+ ..|| | ... . ....-..|+.++-..|.+. +.
T Consensus 270 r~~l~y~iDGiViKvn~~~~~~~~ts~~PrWAiAyK------f--~~~-~-~~T~l~~I~~qVGRTG~iTPVA~lePV~l 339 (562)
T PRK08097 270 RAPLPFVTDGVVVRQAKEPPGRYWQPGQGEWAVAWK------Y--PPV-Q-QVAEVRAVQFAVGRTGKITVVLELEPVML 339 (562)
T ss_pred hccCCCCCCcEEEEecCHHHHhhccCCCCCceEEEc------C--CCc-E-EEEEEEEEEEecCCCceeeEEEEEEEEEe
Confidence 4678999999999999988877644 433 2333 1 111 0 0011123444444456543 55
Q ss_pred CCCceEEecc-cchhhhhcCCCCCCeeeEEEcCCceeecc
Q 014751 317 DDPPVIFGCL-DGEFIQKSGLQSGSLLKFAIGNGGLSFVD 355 (419)
Q Consensus 317 D~~pv~~~~~-~~~~i~~~~l~~g~L~Rf~i~~~~~~~~~ 355 (419)
+|.-|-=++| |.+.|...+++.|+-+...=.++.|.-+.
T Consensus 340 ~GttVsrATLhN~~~i~~~~I~iGD~V~V~raGdVIP~I~ 379 (562)
T PRK08097 340 DDKRVSRVNIGSVRRWQQWDIAPGDQVLVSLAGQGIPRLD 379 (562)
T ss_pred CCEEEEEeecCCHHHHHHcCCCCCCEEEEEecCCCCccee
Confidence 5533333344 66889999999999999887777776543
No 47
>PF04014 Antitoxin-MazE: Antidote-toxin recognition MazE; InterPro: IPR007159 This domain is found in AbrB from Bacillus subtilis. The product of the abrB gene is an ambiactive repressor and activator of the transcription of genes expressed during the transition state between vegetative growth and the onset of stationary phase and sporulation []. AbrB is thought to interact directly with the transcription initiation regions of genes under its control []. AbrB contains a helix-turn-helix structure, but this domain ends before the helix-turn-helix begins []. The product of the B. subtilis gene spoVT is another member of this family and is also a transcriptional regulator []. DNA-binding activity in this AbrB homologue requires hexamerisation []. Another family member has been isolated from the Sulfolobus solfataricus and has been identified as a homologue of bacterial repressor-like proteins. The Escherichia coli family member SohA or Prl1F appears to be bifunctional and is able to regulate its own expression as well as relieve the export block imposed by high-level synthesis of beta-galactosidase hybrid proteins [].; PDB: 2L66_A 2GLW_A 3TND_D 2W1T_B 2RO5_B 2FY9_A 2RO3_B 1UB4_C 3ZVK_G 1YFB_B ....
Probab=40.34 E-value=34 Score=24.92 Aligned_cols=29 Identities=21% Similarity=0.444 Sum_probs=24.5
Q ss_pred cccchhhhhcCCCCCCeeeEEEcCCc-eee
Q 014751 325 CLDGEFIQKSGLQSGSLLKFAIGNGG-LSF 353 (419)
Q Consensus 325 ~~~~~~i~~~~l~~g~L~Rf~i~~~~-~~~ 353 (419)
++|.++..+.++++|+-+.+.+.++| +.+
T Consensus 10 ~iPk~~~~~l~l~~Gd~v~i~~~~~g~i~i 39 (47)
T PF04014_consen 10 TIPKEIREKLGLKPGDEVEIEVEGDGKIVI 39 (47)
T ss_dssp EE-HHHHHHTTSSTTTEEEEEEETTSEEEE
T ss_pred ECCHHHHHHcCCCCCCEEEEEEeCCCEEEE
Confidence 57999999999999999999999885 544
No 48
>PTZ00041 60S ribosomal protein L35a; Provisional
Probab=40.26 E-value=34 Score=30.73 Aligned_cols=35 Identities=31% Similarity=0.440 Sum_probs=26.4
Q ss_pred CCcEEEEEeeC-------------C-eEEEEcCCCcEEEeeccCCCCCC
Q 014751 125 AGKRCIVVSSN-------------G-TTVSRERNGSILHHFPSALPSGA 159 (419)
Q Consensus 125 vGkRcLVVas~-------------G-~T~ay~k~G~~l~~F~S~LPgG~ 159 (419)
+||||.-|..- | .|...-.+|-+..+|.++||+-+
T Consensus 58 lGKrvayvyka~~~~~~~k~RviwGKVtR~HGnsGvVrAkF~~nLPp~A 106 (120)
T PTZ00041 58 LGKRVAYVYKAKKLKNGTKFRAIWGKITRPHGNSGVVRARFNKNLPPKA 106 (120)
T ss_pred ccceEEEEEcCccccCCcceeEEEEEEEcccCCCcEEEEEeCCCCChHH
Confidence 59999888632 3 24455678999999999999954
No 49
>smart00532 LIGANc Ligase N family.
Probab=39.37 E-value=1.5e+02 Score=31.83 Aligned_cols=96 Identities=17% Similarity=0.232 Sum_probs=60.6
Q ss_pred cCCCCCcccEEeEeccccccC--CCC---cCe-eeeccCCCccceeecCCCCCccccceEEEEEecCCcee--------c
Q 014751 250 ESVPYAKDGLLFYNKHAHYQT--GNT---PLA-LVWKDEKCSQYVIDTDSKGQVLSQQQVVLELQEDGKLS--------T 315 (419)
Q Consensus 250 ~~~p~~~DGLLFYHKea~Y~~--G~T---PLv-~~wkD~~~s~y~~d~d~~g~~~~~q~vvL~~~~~g~l~--------T 315 (419)
...||++||+++...+-.++. |.| |-| ..||=+.-. ....=..|+.++-..|.+. +
T Consensus 272 ~~l~y~iDGiViKvn~~~~~~~lG~ts~~PrwaiA~Kf~~~~----------~~T~l~~I~~qVGRTG~iTPvA~lePV~ 341 (441)
T smart00532 272 AELPYEIDGVVVKVDDLALQRELGFTSKAPRWAIAYKFPAEE----------AETKLLDIIVQVGRTGKITPVAELEPVF 341 (441)
T ss_pred ccCCCCcCcEEEEecCHHHHHHhCccCCCCCeeEEECCCCce----------eEEEEEEEEEecCCCceeeEEEEEEeEE
Confidence 568999999999999998877 766 543 456522211 0011123555554456542 4
Q ss_pred cCCCceEEecc-cchhhhhcCCCCCCeeeEEEcCCceeecc
Q 014751 316 SDDPPVIFGCL-DGEFIQKSGLQSGSLLKFAIGNGGLSFVD 355 (419)
Q Consensus 316 ~D~~pv~~~~~-~~~~i~~~~l~~g~L~Rf~i~~~~~~~~~ 355 (419)
.+|.-|-=++| |.+.|...++++|+-+...-+++.|.-+.
T Consensus 342 l~G~tVsrATLhN~~~i~~~~i~iGd~V~V~raGdVIP~I~ 382 (441)
T smart00532 342 LAGSTVSRATLHNEDEIEEKDIRIGDTVVVRKAGDVIPKVV 382 (441)
T ss_pred ECCEEEEecccCCHHHHHHcCCCCCCEEEEEECCCcCccee
Confidence 55522222233 45889999999999999888888776643
No 50
>PF09866 DUF2093: Uncharacterized protein conserved in bacteria (DUF2093); InterPro: IPR018661 This family of various hypothetical prokaryotic proteins has no known function.
Probab=37.13 E-value=22 Score=26.47 Aligned_cols=18 Identities=22% Similarity=0.492 Sum_probs=16.0
Q ss_pred CCCCCeeeEEEcCCceee
Q 014751 336 LQSGSLLKFAIGNGGLSF 353 (419)
Q Consensus 336 l~~g~L~Rf~i~~~~~~~ 353 (419)
++||+-++|||++..|.+
T Consensus 2 l~pG~~V~CAVTg~~IpL 19 (42)
T PF09866_consen 2 LSPGSFVRCAVTGQPIPL 19 (42)
T ss_pred ccCCCEEEEEeeCCcccH
Confidence 689999999999887776
No 51
>KOG0296 consensus Angio-associated migratory cell protein (contains WD40 repeats) [Function unknown]
Probab=33.36 E-value=1e+02 Score=32.77 Aligned_cols=49 Identities=27% Similarity=0.344 Sum_probs=37.3
Q ss_pred ecCCcEEEEEeeCCeEEEE-cCCCcEEEeeccC----CCCCCCCCCCCCCCCCcEEEeee
Q 014751 123 RPAGKRCIVVSSNGTTVSR-ERNGSILHHFPSA----LPSGARTKDPSGSAQSYCILDCI 177 (419)
Q Consensus 123 cPvGkRcLVVas~G~T~ay-~k~G~~l~~F~S~----LPgG~~~~~~~~~~~~ytILDCI 177 (419)
.|-|||.+....+|+.++. .|.|..+++..+. +|+ .+-+..+.|+++|-
T Consensus 199 ~pdGKr~~tgy~dgti~~Wn~ktg~p~~~~~~~e~~~~~~------~~~~~~~~~~~~g~ 252 (399)
T KOG0296|consen 199 IPDGKRILTGYDDGTIIVWNPKTGQPLHKITQAEGLELPC------ISLNLAGSTLTKGN 252 (399)
T ss_pred cCCCceEEEEecCceEEEEecCCCceeEEecccccCcCCc------cccccccceeEecc
Confidence 4789999999999999999 7899999988754 333 22234556888874
No 52
>PRK11347 antitoxin ChpS; Provisional
Probab=32.67 E-value=49 Score=27.59 Aligned_cols=29 Identities=17% Similarity=0.307 Sum_probs=26.8
Q ss_pred cccchhhhhcCCCCCCeeeEEEcCCceee
Q 014751 325 CLDGEFIQKSGLQSGSLLKFAIGNGGLSF 353 (419)
Q Consensus 325 ~~~~~~i~~~~l~~g~L~Rf~i~~~~~~~ 353 (419)
++|++++.+.+|..|+-+-+.+.++++.+
T Consensus 15 riPk~il~~l~l~~G~~v~i~v~~~~iii 43 (83)
T PRK11347 15 VIPNIVMKELNLQPGQSVEAQVSNNQLIL 43 (83)
T ss_pred EeCHHHHHHcCCCCCCEEEEEEECCEEEE
Confidence 68999999999999999999999988877
No 53
>COG3698 Predicted periplasmic protein [Function unknown]
Probab=31.67 E-value=89 Score=31.13 Aligned_cols=96 Identities=26% Similarity=0.449 Sum_probs=60.8
Q ss_pred cEEeEeccccccCCCCcCeeeeccCCC------------------ccceeecCCCCCccccceEEEEEecCCceeccCCC
Q 014751 258 GLLFYNKHAHYQTGNTPLALVWKDEKC------------------SQYVIDTDSKGQVLSQQQVVLELQEDGKLSTSDDP 319 (419)
Q Consensus 258 GLLFYHKea~Y~~G~TPLv~~wkD~~~------------------s~y~~d~d~~g~~~~~q~vvL~~~~~g~l~T~D~~ 319 (419)
.++|-.+.+.|.++.+||-+.--+-.- --|++..+-.|. .+.+..+.. ...=.++|--||
T Consensus 79 ~l~fAmN~GmY~~d~~PlGL~VE~G~e~~~ln~a~G~GNF~l~PnGVFyl~g~kaGv-~~teaf~~~-~~~~~fAtQSGP 156 (250)
T COG3698 79 SLLFAMNGGMYHPDYAPLGLYVENGKEQVPLNTAGGEGNFFLLPNGVFYLGGDKAGV-LRTEAFVKS-RPEPDFATQSGP 156 (250)
T ss_pred eEEEEecCcccCCCCCcceEEecCCeeecccccCCCCCceeEcCCeeEEEcCCccee-eeHHHHHhc-CCCCceeccCCC
Confidence 489999999999999999754333210 112333222222 112221111 123457899997
Q ss_pred ceEE-ecccchhhhhc---------CCCCCCeeeEEEcCCceeecc
Q 014751 320 PVIF-GCLDGEFIQKS---------GLQSGSLLKFAIGNGGLSFVD 355 (419)
Q Consensus 320 pv~~-~~~~~~~i~~~---------~l~~g~L~Rf~i~~~~~~~~~ 355 (419)
=+|| |.+...|+..+ |++.+-.++|+|+++-+++.|
T Consensus 157 MLvi~G~LhPrf~~~~~S~K~RnGVGV~k~G~~~FaiS~~~vnFyd 202 (250)
T COG3698 157 MLVINGKLHPRFHPDSASRKRRNGVGVCKDGVAVFAISQGAVNFYD 202 (250)
T ss_pred EEEEcCccCccccCCcccceeecCccCCCCCeEEEEEecCcchhhh
Confidence 6555 47888776522 488889999999999998875
No 54
>KOG1136 consensus Predicted cleavage and polyadenylation specificity factor (CPSF subunit) [RNA processing and modification]
Probab=28.44 E-value=85 Score=33.31 Aligned_cols=53 Identities=19% Similarity=0.351 Sum_probs=30.8
Q ss_pred cCCcEEEEEeeCCeEEEEcCCCcEEEeeccCCCCCCCCCCCCCCCCCcE-EEeeeEec
Q 014751 124 PAGKRCIVVSSNGTTVSRERNGSILHHFPSALPSGARTKDPSGSAQSYC-ILDCIFHE 180 (419)
Q Consensus 124 PvGkRcLVVas~G~T~ay~k~G~~l~~F~S~LPgG~~~~~~~~~~~~yt-ILDCIy~e 180 (419)
-+|+-|++|+-+|+++...-.=..=.+=.-+.|..+.- +. +..+| .||||...
T Consensus 14 dvGrSCilvsi~Gk~iM~DCGMHMG~nD~rRfPdFSyI---~~-~g~~~~~idCvIIs 67 (501)
T KOG1136|consen 14 DVGRSCILVSIGGKNIMFDCGMHMGFNDDRRFPDFSYI---SK-SGRFTDAIDCVIIS 67 (501)
T ss_pred ccCceEEEEEECCcEEEEecccccccCccccCCCceee---cC-CCCcccceeEEEEe
Confidence 37899999999999998764322111111123444331 11 22344 89999863
No 55
>PRK09798 antitoxin MazE; Provisional
Probab=28.41 E-value=66 Score=26.76 Aligned_cols=29 Identities=17% Similarity=0.257 Sum_probs=26.7
Q ss_pred cccchhhhhcCCCCCCeeeEEEcCCceee
Q 014751 325 CLDGEFIQKSGLQSGSLLKFAIGNGGLSF 353 (419)
Q Consensus 325 ~~~~~~i~~~~l~~g~L~Rf~i~~~~~~~ 353 (419)
++|..++.+.||..|+-+-+.|.++++.+
T Consensus 16 RIPk~~l~~l~l~~g~~vei~v~~~~iiI 44 (82)
T PRK09798 16 RIPATLMQALNLNIDDEVKIDLVDGKLII 44 (82)
T ss_pred EcCHHHHHHcCCCCCCEEEEEEECCEEEE
Confidence 68999999999999999999999888877
No 56
>KOG0887 consensus 60S ribosomal protein L35A/L37 [Translation, ribosomal structure and biogenesis]
Probab=28.01 E-value=66 Score=28.46 Aligned_cols=39 Identities=36% Similarity=0.658 Sum_probs=28.0
Q ss_pred CceEEEEecCCcEEEEEee-----C--------C-eEEEEcCCCcEEEeeccCCCCCC
Q 014751 116 HDWYVFARPAGKRCIVVSS-----N--------G-TTVSRERNGSILHHFPSALPSGA 159 (419)
Q Consensus 116 ~~Wl~vpcPvGkRcLVVas-----~--------G-~T~ay~k~G~~l~~F~S~LPgG~ 159 (419)
.+|| .||||..|.. + | .|.+--.+|-+-.+|.|+||.-.
T Consensus 45 a~fY-----lGkR~~yvYKa~~~~~~~k~RvIWGkVTr~HGNsG~VrAkF~~Nlp~Ka 97 (111)
T KOG0887|consen 45 ASFY-----LGKRCVYVYKAKPEVRGSKTRVIWGKVTRPHGNSGVVRAKFTSNLPPKA 97 (111)
T ss_pred hhee-----ecCcEEEEEecCCCCCCceEEEEEEEEecccCCcceEEEEeccCCChhH
Confidence 4665 4999888873 1 2 24445678888999999999843
No 57
>KOG2618 consensus Uncharacterized conserved protein [Function unknown]
Probab=27.75 E-value=1.3e+02 Score=31.36 Aligned_cols=83 Identities=13% Similarity=0.233 Sum_probs=48.5
Q ss_pred CCceEEEEecCCcEEEEEeeCCeE--EEEcCCCcEEEeeccCCCCCCCCCCCCCCCCCcEEEeeeEecCCcEEEEEEEEe
Q 014751 115 SHDWYVFARPAGKRCIVVSSNGTT--VSRERNGSILHHFPSALPSGARTKDPSGSAQSYCILDCIFHELDQTYYVIDMVC 192 (419)
Q Consensus 115 ~~~Wl~vpcPvGkRcLVVas~G~T--~ay~k~G~~l~~F~S~LPgG~~~~~~~~~~~~ytILDCIy~e~~~tyYVLDvl~ 192 (419)
+..-+.+|||.| ||+|++..-.- ++-++.--.+..|. .|-.- ----|.||.=.|.-.+.|-.-||-
T Consensus 110 Esksfrrpl~Kg-RCvVl~dGfyEWkt~gskkqpYfI~f~----dgRlL-------~mAglfD~wE~egGD~LYtfTIIT 177 (366)
T KOG2618|consen 110 ESKSFRRPLEKG-RCVVLMDGFYEWKTVGSKKQPYFISFR----DGRLL-------FMAGLFDYWEKEGGDDLYTFTIIT 177 (366)
T ss_pred hhhhhhccCCCC-cEEEEecceeeeeeccccCCceEEEEe----cCcee-------EeeeehheecccCCceeEEEEEEE
Confidence 345568899999 99999864321 11111111122221 00000 001378888877778899888887
Q ss_pred eCCcccccccchhhHHHhhhhcccc
Q 014751 193 WRGYSLYDCTAEFRFFWLNSKLAET 217 (419)
Q Consensus 193 W~g~~l~dceteFRffWl~SKl~E~ 217 (419)
-.+-. -+-|||-|+.-.
T Consensus 178 ~qssk--------~LswlH~RMPaI 194 (366)
T KOG2618|consen 178 AQSSK--------ELSWLHERMPAI 194 (366)
T ss_pred ecCch--------HhHHHHhhCcee
Confidence 65543 267999998754
No 58
>PF07250 Glyoxal_oxid_N: Glyoxal oxidase N-terminus; InterPro: IPR009880 This entry represents the N terminus (approximately 300 residues) of a number of plant and fungal glyoxal oxidase enzymes. Glyoxal oxidase catalyses the oxidation of aldehydes to carboxylic acids, coupled with reduction of dioxygen to hydrogen peroxide. It is an essential component of the extracellular lignin degradation pathways of the wood-rot fungus Phanerochaete chrysosporium [].
Probab=27.69 E-value=1.5e+02 Score=29.41 Aligned_cols=45 Identities=24% Similarity=0.605 Sum_probs=30.3
Q ss_pred CCCCCceE--EEEecCCcEEEEEeeCCeEEEEcCCC-cEEEeeccCCCCCC
Q 014751 112 DRLSHDWY--VFARPAGKRCIVVSSNGTTVSRERNG-SILHHFPSALPSGA 159 (419)
Q Consensus 112 ~dL~~~Wl--~vpcPvGkRcLVVas~G~T~ay~k~G-~~l~~F~S~LPgG~ 159 (419)
..+..+|| +...|-| +.+|.+.++ +++++..+ .++..|| .||||.
T Consensus 165 ~~~~~nlYP~~~llPdG-~lFi~an~~-s~i~d~~~n~v~~~lP-~lPg~~ 212 (243)
T PF07250_consen 165 DTLPNNLYPFVHLLPDG-NLFIFANRG-SIIYDYKTNTVVRTLP-DLPGGP 212 (243)
T ss_pred ccCccccCceEEEcCCC-CEEEEEcCC-cEEEeCCCCeEEeeCC-CCCCCc
Confidence 34456776 4568998 556666665 66665554 4668999 689984
No 59
>PHA02651 IL-1 receptor antagonist; Provisional
Probab=25.77 E-value=1.4e+02 Score=28.38 Aligned_cols=56 Identities=14% Similarity=0.156 Sum_probs=37.3
Q ss_pred CcccEEeEeccccccCCCCcCeeeeccCCCccceeecCCCCCccccceEEEEEecCCceeccCCCce
Q 014751 255 AKDGLLFYNKHAHYQTGNTPLALVWKDEKCSQYVIDTDSKGQVLSQQQVVLELQEDGKLSTSDDPPV 321 (419)
Q Consensus 255 ~~DGLLFYHKea~Y~~G~TPLv~~wkD~~~s~y~~d~d~~g~~~~~q~vvL~~~~~g~l~T~D~~pv 321 (419)
+..-|||||++.- . ...+--+.+.-.+|+|...+. +|.|.|.- .-|+..+.|+.||
T Consensus 102 ~~kRFlFyr~~sG----~---tstFESaafPgWfIsTs~~e~---~~PV~Lt~-~~~~~~~~~~~~~ 157 (165)
T PHA02651 102 QDKRFAFIRSDNG----H---TSTFESVAFPGWFLCTSSGDG---IEPVGLTY-KGDKDDNDDDENN 157 (165)
T ss_pred cceeEEEEEccCC----C---ceEEEecCCCCcEEEeccccC---CcceEeec-ccCCcccccccce
Confidence 5789999999953 1 335556778888999965443 47899985 5554444444444
No 60
>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=25.29 E-value=2.6e+02 Score=29.07 Aligned_cols=141 Identities=13% Similarity=0.105 Sum_probs=75.3
Q ss_pred CCCCceEEEEecCCcEEEEEeeCCeEEEEcCCCcEE----EeeccCCCCCCCCCCCCCCCCCcEEEeeeEe---------
Q 014751 113 RLSHDWYVFARPAGKRCIVVSSNGTTVSRERNGSIL----HHFPSALPSGARTKDPSGSAQSYCILDCIFH--------- 179 (419)
Q Consensus 113 dL~~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l----~~F~S~LPgG~~~~~~~~~~~~ytILDCIy~--------- 179 (419)
.+...|++-.==-|-|+-|...+|...++|++|.+. .+++..+|...-. . ..+ .|||+=+.
T Consensus 45 ~f~~~~~vEEKlDG~nvri~~~~G~v~a~TR~G~i~e~~T~~~~eiv~~~~~~---~--~p~-~iLdGElvg~~~p~v~~ 118 (342)
T cd07894 45 HFKGPVAVEEKMNGYNVRIVRIGGKVLAFTRGGFICPFTTDRLRDLIDPEFFD---D--HPD-LVLCGEVVGPENPYVPG 118 (342)
T ss_pred cCCCCEEEEEeECCcEEEEEEECCEEEEEeCCCccCccchhhHhhhchHHhhc---c--CCC-EEEEEEEEecCCccccc
Confidence 334578877666799999988899999999999865 2333333331100 0 011 66774211
Q ss_pred ----cCCcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCCCCCceeccccccCC-hHhHHHHHhcCCCC
Q 014751 180 ----ELDQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVYNCD-QRGLYSAYIESVPY 254 (419)
Q Consensus 180 ----e~~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~n~~~F~~lp~~~c~-~~~L~~~~~~~~p~ 254 (419)
...-+|||.||+..++. ..+-+--++..|++.+. +..+. +..+.++ .+.+.+.+.....-
T Consensus 119 ~~~~~~~v~F~vFDI~~~~~~------~~lp~~eR~~lLe~lg~-----~~v~~----~~~~~~~d~~~l~~~l~~~~~~ 183 (342)
T cd07894 119 SYPEVEDVGFFVFDIRKKNTG------RPLPVEERRELLEKYGL-----PTVRL----FGEFTADEIEELKEIIRELDKE 183 (342)
T ss_pred cCccccccEEEEEeeEEcCCC------CCCCHHHHHHHHHhcCC-----CCcce----EEEEecCCHHHHHHHHHHHHHC
Confidence 12569999999987741 11222222333333321 01111 1123333 33444444433333
Q ss_pred CcccEEeEeccc-----cccCCCCc
Q 014751 255 AKDGLLFYNKHA-----HYQTGNTP 274 (419)
Q Consensus 255 ~~DGLLFYHKea-----~Y~~G~TP 274 (419)
-..|+.+-..++ .|+...+-
T Consensus 184 G~EGVVlK~~~~~~~~~Ky~t~~~~ 208 (342)
T cd07894 184 GREGVVLKDPDMRVPPLKYTTSYSN 208 (342)
T ss_pred CCceEEEeccccccCcceeecCCCC
Confidence 477888877776 56555443
No 61
>KOG0166 consensus Karyopherin (importin) alpha [Intracellular trafficking, secretion, and vesicular transport]
Probab=24.67 E-value=44 Score=36.71 Aligned_cols=38 Identities=21% Similarity=0.353 Sum_probs=30.3
Q ss_pred CCCCCcCCCCCCchHHHHH----HHHHHHHHHhHHHHHHHHhh
Q 014751 4 PDLRRPFKRTAISDQQRRR----ELSLQRQSQNRRDAQQQARC 42 (419)
Q Consensus 4 h~~~~~~k~~~~~~Q~~RR----~~~Le~Qk~~R~d~~~~aR~ 42 (419)
|.+++.||.+. -+|+++| +...|..|+||.+.+.+-|+
T Consensus 6 ~~~~~~~k~~~-~~~~e~Rrrr~e~~veiRk~kree~l~k~R~ 47 (514)
T KOG0166|consen 6 NNRRRRYKNKG-VDAEEMRRRREEQVVEIRKNKREESLLKRRN 47 (514)
T ss_pred HHHHHHHhhcc-ccHHHHHHhcchhHHHHHHHHHHHHHHHHhh
Confidence 55788899998 4555422 46889999999999999999
No 62
>PRK09974 putative regulator PrlF; Provisional
Probab=24.45 E-value=83 Score=27.93 Aligned_cols=69 Identities=14% Similarity=0.176 Sum_probs=40.1
Q ss_pred cccchhhhhcCCCCCCeeeEEEcC-CceeeccCcee------eeceEEee---cCCccccCCchhhHHHHHHhhh-cCCC
Q 014751 325 CLDGEFIQKSGLQSGSLLKFAIGN-GGLSFVDGKLE------KSDLNYLG---KSNRARMFADSYSKVIFQYMVR-HTPL 393 (419)
Q Consensus 325 ~~~~~~i~~~~l~~g~L~Rf~i~~-~~~~~~~~~~~------~~~l~~~~---~~~~~R~~aDs~sKIlfq~~~r-~~p~ 393 (419)
|+|.++....||+||+-++|.+.+ |++.+.....+ ++=|.|+. ..++.|.. ++++-|.|.+.- ++++
T Consensus 21 TIPk~IR~~Lgl~~GdkI~f~i~~dG~V~i~~~~~~~~Dp~ig~FL~fLa~Di~~~p~~l~--~l~~~l~~r~~~Lv~gv 98 (111)
T PRK09974 21 TVPAPVRKALKLKKRDSIHYEILPGGQVFICRLGDEEEDPVLGAFLDFLAADIQNNPQRIR--PFDKSLIQRGKKLVAGV 98 (111)
T ss_pred eccHHHHHHcCCCCCCEEEEEEeCCCEEEEEECCCCCCCchHHHHHHHHHHHHHhCchhcc--CCCHHHHHHHHHHhCCC
Confidence 468888899999999999999874 44555322211 12233322 22233333 455666666655 5555
Q ss_pred ch
Q 014751 394 KF 395 (419)
Q Consensus 394 ~i 395 (419)
.+
T Consensus 99 ~V 100 (111)
T PRK09974 99 DV 100 (111)
T ss_pred cc
Confidence 44
No 63
>PF05970 PIF1: PIF1-like helicase; InterPro: IPR010285 This entry represents PIF1 helicase and related proteins. The PIF1 helicase inhibits telomerase activity and is cell cycle regulated [, ].
Probab=24.33 E-value=25 Score=36.07 Aligned_cols=82 Identities=17% Similarity=0.293 Sum_probs=57.4
Q ss_pred CCcEEEEEeeCCeEEEEcCCCcEEEeeccCCCCCCCCCCCCCCCCCcEEEeeeEecCCcEEEEEEEEeeCCcccccccch
Q 014751 125 AGKRCIVVSSNGTTVSRERNGSILHHFPSALPSGARTKDPSGSAQSYCILDCIFHELDQTYYVIDMVCWRGYSLYDCTAE 204 (419)
Q Consensus 125 vGkRcLVVas~G~T~ay~k~G~~l~~F~S~LPgG~~~~~~~~~~~~ytILDCIy~e~~~tyYVLDvl~W~g~~l~dcete 204 (419)
.|+.|+++|+-|.+..--.+|..+|+|- .||-+... ...+=+ ..-......+.-+|+|.|...+|..+.+
T Consensus 49 ~~~~~~~~a~tg~AA~~i~~G~T~hs~f-~i~~~~~~-------~~~~~~-~~~~~~~~~l~~~~~lIiDEism~~~~~- 118 (364)
T PF05970_consen 49 RGKKVLVTAPTGIAAFNIPGGRTIHSFF-GIPINNNE-------KSQCKI-SKNSRLRERLRKADVLIIDEISMVSADM- 118 (364)
T ss_pred ccceEEEecchHHHHHhccCCcchHHhc-Cccccccc-------cccccc-cccchhhhhhhhheeeecccccchhHHH-
Confidence 6889999999998776666999999887 46665321 001100 0011224677888999999999998876
Q ss_pred hhHHHhhhhccccC
Q 014751 205 FRFFWLNSKLAETG 218 (419)
Q Consensus 205 FRffWl~SKl~E~~ 218 (419)
|.|++.+|...-
T Consensus 119 --l~~i~~~lr~i~ 130 (364)
T PF05970_consen 119 --LDAIDRRLRDIR 130 (364)
T ss_pred --HHHHHHhhhhhh
Confidence 788888887753
No 64
>PF03427 CBM_19: Carbohydrate binding domain (family 19); InterPro: IPR005089 A carbohydrate-binding module (CBM) is defined as a contiguous amino acid sequence within a carbohydrate-active enzyme with a discreet fold having carbohydrate-binding activity. A few exceptions are CBMs in cellulosomal scaffolding proteins and rare instances of independent putative CBMs. The requirement of CBMs existing as modules within larger enzymes sets this class of carbohydrate-binding protein apart from other non-catalytic sugar binding proteins such as lectins and sugar transport proteins. CBMs were previously classified as cellulose-binding domains (CBDs) based on the initial discovery of several modules that bound cellulose [, ]. However, additional modules in carbohydrate-active enzymes are continually being found that bind carbohydrates other than cellulose yet otherwise meet the CBM criteria, hence the need to reclassify these polypeptides using more inclusive terminology. Previous classification of cellulose-binding domains were based on amino acid similarity. Groupings of CBDs were called "Types" and numbered with roman numerals (e.g. Type I or Type II CBDs). In keeping with the glycoside hydrolase classification, these groupings are now called families and numbered with Arabic numerals. Families 1 to 13 are the same as Types I to XIII. For a detailed review on the structure and binding modes of CBMs see []. This entry represents CBM19 from CAZY which consists of 60-70 residues with chitin-binding function.; GO: 0004568 chitinase activity, 0006032 chitin catabolic process
Probab=23.13 E-value=64 Score=25.82 Aligned_cols=16 Identities=31% Similarity=0.829 Sum_probs=14.2
Q ss_pred CceEEEEecCCcEEEE
Q 014751 116 HDWYVFARPAGKRCIV 131 (419)
Q Consensus 116 ~~Wl~vpcPvGkRcLV 131 (419)
..|++.+||.|--|+-
T Consensus 43 G~Wv~~~C~~Gt~C~~ 58 (61)
T PF03427_consen 43 GTWVITPCPAGTTCFA 58 (61)
T ss_pred CcEEEeeCCCCCEEee
Confidence 6999999999988874
No 65
>cd04663 Nudix_Hydrolase_6 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belong to this superfamily requires a divalent cation, such as Mg2+ or Mn2+ for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, U=I, L or V) which functions as metal binding and catalytic site. Substrates of nudix hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate specificity are
Probab=22.91 E-value=2.1e+02 Score=25.49 Aligned_cols=19 Identities=42% Similarity=0.994 Sum_probs=14.4
Q ss_pred eeCCcccccccchhhHHHh
Q 014751 192 CWRGYSLYDCTAEFRFFWL 210 (419)
Q Consensus 192 ~W~g~~l~dceteFRffWl 210 (419)
.|++.+..+...+|+|+|+
T Consensus 90 ~~~~~~~~~E~~~i~~~Wv 108 (126)
T cd04663 90 SWVHFVQDDGGHEFRFFWV 108 (126)
T ss_pred cccCcccCCCCceEEEEEE
Confidence 5777777777777888887
No 66
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=22.77 E-value=3.5e+02 Score=30.82 Aligned_cols=96 Identities=20% Similarity=0.317 Sum_probs=58.9
Q ss_pred hcCCCCCcccEEeEeccccccC--CCC---cCe-eeeccCCCccceeecCCCCCccccceEEEEEecCCcee--------
Q 014751 249 IESVPYAKDGLLFYNKHAHYQT--GNT---PLA-LVWKDEKCSQYVIDTDSKGQVLSQQQVVLELQEDGKLS-------- 314 (419)
Q Consensus 249 ~~~~p~~~DGLLFYHKea~Y~~--G~T---PLv-~~wkD~~~s~y~~d~d~~g~~~~~q~vvL~~~~~g~l~-------- 314 (419)
....||++||+++...+-.++. |.| |-| ..||=+.-. ....=..|+.++-..|.+.
T Consensus 273 R~~l~y~iDGiViKvn~~~~q~~lG~ts~~PrWaiA~Kf~~~~----------~~T~l~~I~~qVGRTG~iTPVA~l~PV 342 (669)
T PRK14350 273 RNSFEYEIDGVVLKVSDFALREILGYTSHHPKWSMAYKFESLS----------GFSKVNDIVVQVGRSGKITPVANIEKV 342 (669)
T ss_pred HhcCCCCCCcEEEEecCHHHHHhcCCcCCCCCceEEEcCCCce----------eEEEEEEEEEecCCceeeeEEEEEEeE
Confidence 3568999999999999887654 544 644 445521111 0001122444444456542
Q ss_pred ccCCCceEEe--c-ccchhhhhcCCCCCCeeeEEEcCCceeeccC
Q 014751 315 TSDDPPVIFG--C-LDGEFIQKSGLQSGSLLKFAIGNGGLSFVDG 356 (419)
Q Consensus 315 T~D~~pv~~~--~-~~~~~i~~~~l~~g~L~Rf~i~~~~~~~~~~ 356 (419)
+.+| +.|. + =|.+.|...++++|+-+...=.+++|.-+.+
T Consensus 343 ~l~G--~tVsrATLhN~~~I~~~di~iGD~V~V~raGdVIP~I~~ 385 (669)
T PRK14350 343 FVAG--AFITNASLHNQDYIDSIGLNVGDVVKISRRGDVIPAVEL 385 (669)
T ss_pred EECC--EEEEEeccCCHHHHHHcCCCCCCEEEEEecCCCCCceee
Confidence 4444 3333 2 2457889999999999998888888776543
No 67
>COG1430 Uncharacterized conserved protein [Function unknown]
Probab=21.16 E-value=2.6e+02 Score=25.28 Aligned_cols=84 Identities=19% Similarity=0.201 Sum_probs=43.9
Q ss_pred cccEEeEeccccccCCCCcCeeeeccCCCccceeecCCCCCccccceEEEEEecCCceeccCCCceEEecccchhhhhcC
Q 014751 256 KDGLLFYNKHAHYQTGNTPLALVWKDEKCSQYVIDTDSKGQVLSQQQVVLELQEDGKLSTSDDPPVIFGCLDGEFIQKSG 335 (419)
Q Consensus 256 ~DGLLFYHKea~Y~~G~TPLv~~wkD~~~s~y~~d~d~~g~~~~~q~vvL~~~~~g~l~T~D~~pv~~~~~~~~~i~~~~ 335 (419)
=-|+||.+++.. +.+.|=|.-..-==.+.-|++|.|-+-+. |.=...+.+.-.. ++-.+=.++...++++|
T Consensus 40 d~GMLFv~~~~~------~~~~wMknt~lpLDiiFid~dg~i~~i~~--~~P~~~~~~~~~~-~~~yvLEl~~G~~~~~~ 110 (126)
T COG1430 40 DHGMLFVFPETR------RVAFWMKNTMLPLDIIFIDSDGRVVDIVE--LVPWSTYPCKSYG-PVRYVLELPAGWAARLG 110 (126)
T ss_pred CceEEEecCCCc------eeEEeeecCCcceEEEEEcCCCCEEEEEe--ccccccCCCCCCC-CccEEEEecCCchhhcC
Confidence 459999998543 33344443222111122355566332111 2212223332222 22233367888889999
Q ss_pred CCCCCeeeEEEcC
Q 014751 336 LQSGSLLKFAIGN 348 (419)
Q Consensus 336 l~~g~L~Rf~i~~ 348 (419)
+++|+-++|-..+
T Consensus 111 i~vGd~v~~~~~~ 123 (126)
T COG1430 111 IKVGDRVEFRPLG 123 (126)
T ss_pred CccCCEEEecccC
Confidence 9999999986544
No 68
>PHA02979 hypothetical protein; Provisional
Probab=21.14 E-value=1.1e+02 Score=27.58 Aligned_cols=18 Identities=28% Similarity=0.604 Sum_probs=14.7
Q ss_pred CCCCCeeeEEEcC-Cceee
Q 014751 336 LQSGSLLKFAIGN-GGLSF 353 (419)
Q Consensus 336 l~~g~L~Rf~i~~-~~~~~ 353 (419)
|+|.+++||+.-+ |.+.+
T Consensus 102 L~~NNiVkF~S~~y~kidI 120 (140)
T PHA02979 102 LRKNNIVKFSSCNYGKIDI 120 (140)
T ss_pred eecCCEEEEEecCCCcEEe
Confidence 8999999998766 66665
No 69
>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=20.34 E-value=5.9e+02 Score=28.84 Aligned_cols=95 Identities=18% Similarity=0.241 Sum_probs=56.6
Q ss_pred cCCCCCcccEEeEecccccc-----CCCCcCe-eeeccCCCccceeecCCCCCccccceEEEEEecCCcee--------c
Q 014751 250 ESVPYAKDGLLFYNKHAHYQ-----TGNTPLA-LVWKDEKCSQYVIDTDSKGQVLSQQQVVLELQEDGKLS--------T 315 (419)
Q Consensus 250 ~~~p~~~DGLLFYHKea~Y~-----~G~TPLv-~~wkD~~~s~y~~d~d~~g~~~~~q~vvL~~~~~g~l~--------T 315 (419)
...||++||+++-..+-.++ .+..|-| ..||=+.-. ....=..|+.++--.|.+. +
T Consensus 265 ~~l~y~iDGiViKvn~~~~~~~lG~t~~~PrwaiA~Kf~~~~----------~~T~l~~I~~qVGRTG~iTPvA~lePV~ 334 (652)
T TIGR00575 265 DSLPYEIDGVVVKVDDLALQDELGFTSKAPRWAIAYKFPAEE----------AQTKLLDVVVQVGRTGAITPVAKLEPVF 334 (652)
T ss_pred hcCCCCCCcEEEEecCHHHHHHhCccCCCCCceEEEcCCCce----------eeEEEEEEEEecCCCceeeeEEEEeeEE
Confidence 57899999999999887774 2334644 445522111 0000122444443345532 4
Q ss_pred cCCCceEEecc-cchhhhhcCCCCCCeeeEEEcCCceeec
Q 014751 316 SDDPPVIFGCL-DGEFIQKSGLQSGSLLKFAIGNGGLSFV 354 (419)
Q Consensus 316 ~D~~pv~~~~~-~~~~i~~~~l~~g~L~Rf~i~~~~~~~~ 354 (419)
.+|.-|-=++| |.+.|...+++.|+-+...=.++.|.-+
T Consensus 335 l~G~~VsrAtLhN~~~i~~~~i~iGD~V~V~raGdVIP~i 374 (652)
T TIGR00575 335 VAGTTVSRATLHNEDEIEELDIRIGDTVVVRKAGDVIPKV 374 (652)
T ss_pred ECCEEEEEeecCCHHHHHHcCCCCCCEEEEEecCCcCcee
Confidence 44421222232 4578999999999999998887777664
Done!