Query 016089
Match_columns 395
No_of_seqs 123 out of 133
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 03:41:32 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/016089.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/016089hhsearch_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 2.1E-97 5E-102 703.2 17.9 256 2-282 22-279 (325)
2 cd09232 Snurportin-1_C C-termi 100.0 5.2E-70 1.1E-74 502.9 18.4 183 96-282 1-186 (186)
3 cd06846 Adenylation_DNA_ligase 99.7 3.6E-16 7.8E-21 141.6 14.2 170 101-281 2-182 (182)
4 PF01331 mRNA_cap_enzyme: mRNA 99.5 2E-13 4.3E-18 125.3 11.1 159 116-280 16-192 (192)
5 PF11538 Snurportin1: Snurport 99.3 1.4E-12 3.1E-17 93.5 4.0 39 4-42 1-40 (40)
6 cd07895 Adenylation_mRNA_cappi 98.7 2.4E-07 5.3E-12 86.6 13.6 159 116-280 41-214 (215)
7 cd07906 Adenylation_DNA_ligase 98.7 2.1E-07 4.5E-12 85.5 12.0 158 101-279 3-187 (190)
8 cd07897 Adenylation_DNA_ligase 98.3 1.2E-05 2.7E-10 75.2 12.3 163 101-280 7-201 (207)
9 cd07905 Adenylation_DNA_ligase 98.2 3E-05 6.4E-10 71.8 13.1 159 101-281 3-190 (194)
10 cd07903 Adenylation_DNA_ligase 98.0 5.1E-05 1.1E-09 71.4 11.1 156 116-281 33-221 (225)
11 TIGR02779 NHEJ_ligase_lig DNA 98.0 0.00033 7.2E-09 69.2 16.4 151 109-283 6-185 (298)
12 cd07902 Adenylation_DNA_ligase 98.0 6.2E-05 1.3E-09 70.8 10.4 145 116-280 34-208 (213)
13 PRK05972 ligD ATP-dependent DN 97.9 0.00039 8.5E-09 77.9 18.1 170 101-290 236-427 (860)
14 PRK08224 ligC ATP-dependent DN 97.9 0.0004 8.7E-09 70.6 16.5 159 101-282 11-198 (350)
15 PRK07636 ligB ATP-dependent DN 97.9 0.00045 9.7E-09 67.8 15.0 154 102-280 6-185 (275)
16 PF01068 DNA_ligase_A_M: ATP d 97.8 5.8E-05 1.3E-09 68.8 7.7 145 115-280 18-200 (202)
17 PRK09632 ATP-dependent DNA lig 97.6 0.0018 3.9E-08 72.0 16.9 140 115-280 476-641 (764)
18 TIGR00574 dnl1 DNA ligase I, A 97.6 0.00031 6.7E-09 74.4 10.5 161 100-281 168-371 (514)
19 cd07898 Adenylation_DNA_ligase 97.6 0.0014 2.9E-08 60.8 13.4 149 116-281 21-200 (201)
20 cd07901 Adenylation_DNA_ligase 97.6 0.00093 2E-08 62.4 11.8 150 115-280 24-205 (207)
21 PRK09633 ligD ATP-dependent DN 97.5 0.003 6.4E-08 68.8 16.1 168 101-281 3-208 (610)
22 PLN03113 DNA ligase 1; Provisi 97.3 0.0015 3.1E-08 72.6 11.6 168 100-280 371-576 (744)
23 cd07900 Adenylation_DNA_ligase 97.3 0.0019 4.1E-08 61.3 10.1 149 117-280 32-214 (219)
24 cd08039 Adenylation_DNA_ligase 97.3 0.0037 8E-08 60.3 12.2 143 117-273 23-219 (235)
25 PRK09247 ATP-dependent DNA lig 97.2 0.0023 5.1E-08 68.4 11.5 164 100-280 207-404 (539)
26 PRK01109 ATP-dependent DNA lig 97.1 0.003 6.6E-08 68.2 10.9 165 100-280 229-430 (590)
27 PRK03180 ligB ATP-dependent DN 96.9 0.006 1.3E-07 64.9 11.1 161 100-280 185-380 (508)
28 PHA00454 ATP-dependent DNA lig 96.8 0.0075 1.6E-07 60.3 10.0 149 125-282 36-219 (315)
29 PHA02587 30 DNA ligase; Provis 96.7 0.011 2.4E-07 62.6 11.2 158 117-283 153-364 (488)
30 cd07896 Adenylation_kDNA_ligas 96.2 0.019 4.1E-07 51.9 7.9 133 116-280 16-171 (174)
31 COG1793 CDC9 ATP-dependent DNA 96.1 0.13 2.8E-06 54.2 14.3 158 109-288 126-320 (444)
32 PRK09125 DNA ligase; Provision 95.2 0.15 3.3E-06 50.5 10.3 134 116-283 43-203 (282)
33 KOG0966 ATP-dependent DNA liga 87.5 2.5 5.5E-05 47.7 8.9 168 97-282 232-436 (881)
34 TIGR02776 NHEJ_ligase_prk DNA 86.1 2.8 6.1E-05 45.6 8.3 88 182-281 57-144 (552)
35 KOG3132 m3G-cap-specific nucle 81.3 0.68 1.5E-05 45.9 1.1 163 3-192 1-175 (325)
36 COG5226 CEG1 mRNA capping enzy 78.3 4.5 9.7E-05 41.5 5.8 169 114-285 60-249 (404)
37 COG5064 SRP1 Karyopherin (impo 65.7 5 0.00011 41.9 2.9 44 3-46 7-54 (526)
38 PRK04337 50S ribosomal protein 55.1 20 0.00043 30.3 4.1 36 125-160 39-80 (87)
39 PF14766 RPA_interact_N: Repli 53.8 28 0.0006 25.4 4.2 38 5-42 2-40 (42)
40 PF06257 DUF1021: Protein of u 50.9 7.9 0.00017 31.8 1.1 30 125-154 16-45 (76)
41 PF01247 Ribosomal_L35Ae: Ribo 50.0 21 0.00045 30.6 3.5 36 125-160 39-88 (95)
42 KOG0275 Conserved WD40 repeat- 45.5 34 0.00074 35.7 4.9 54 124-190 358-422 (508)
43 PTZ00041 60S ribosomal protein 44.1 28 0.00061 31.0 3.5 36 125-160 58-107 (120)
44 PF01749 IBB: Importin beta bi 42.8 3.9 8.4E-05 34.4 -1.9 44 3-46 6-52 (97)
45 cd07289 PX_PI3K_C2_alpha The p 41.4 46 0.001 29.0 4.4 44 171-217 2-51 (109)
46 KOG2618 Uncharacterized conser 40.2 69 0.0015 33.1 6.0 82 115-217 110-194 (366)
47 KOG0296 Angio-associated migra 36.5 85 0.0018 33.1 6.1 53 123-177 199-252 (399)
48 KOG0887 60S ribosomal protein 30.7 57 0.0012 28.7 3.2 39 116-159 45-97 (111)
49 KOG1136 Predicted cleavage and 30.1 77 0.0017 33.4 4.6 53 124-180 14-67 (501)
50 PF07250 Glyoxal_oxid_N: Glyox 29.3 1.4E+02 0.003 29.4 6.1 45 112-159 165-212 (243)
51 PF05970 PIF1: PIF1-like helic 27.1 21 0.00045 36.4 0.0 82 125-218 49-130 (364)
52 cd07894 Adenylation_RNA_ligase 27.0 2.4E+02 0.0051 29.1 7.5 77 113-195 45-138 (342)
53 PF03427 CBM_19: Carbohydrate 26.2 52 0.0011 26.1 2.1 16 116-131 43-58 (61)
54 KOG0166 Karyopherin (importin) 25.8 41 0.00089 36.7 1.9 38 4-42 6-47 (514)
55 cd04663 Nudix_Hydrolase_6 Memb 25.6 1.8E+02 0.0038 25.8 5.5 19 192-210 90-108 (126)
56 PF02210 Laminin_G_2: Laminin 20.9 4.4E+02 0.0095 21.0 7.7 91 254-346 4-102 (128)
57 KOG2923 Uncharacterized conser 20.5 1.6E+02 0.0034 23.9 3.7 19 114-133 16-34 (67)
58 KOG3390 General control of ami 20.4 1.3E+02 0.0027 26.5 3.5 28 16-47 11-38 (120)
59 KOG1274 WD40 repeat protein [G 20.2 1.8E+02 0.004 33.8 5.6 50 104-156 515-564 (933)
No 1
>KOG3132 consensus m3G-cap-specific nuclear import receptor (Snurportin1) [RNA processing and modification]
Probab=100.00 E-value=2.1e-97 Score=703.23 Aligned_cols=256 Identities=57% Similarity=0.987 Sum_probs=237.1
Q ss_pred CCCCCCCcCCCCC-CchHHH-HHHHHHHHHHHhHHHHHHHHhhhhhhhccccCCCCCCCCCCCCCCCCCccccCCCCccc
Q 016089 2 APPDLRRPFKRTA-ISDQQR-RRELSLQRQSQNRRDAQQQARCLASSVLSLQSQYPDPVPELEIEPESQPQQEAGPLTKD 79 (395)
Q Consensus 2 aph~~~~~~k~~~-~~~Q~~-RR~~~Le~Qk~~R~d~~~~aR~La~~~~~~~~~~~~~~~e~~~~~~~~e~~~~~~~~~~ 79 (395)
+||||.+|||.+. ..+|.+ ||+.+|++||.+|.|+++|+|+||.++|+ + + |++| + .
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 445555 55569999999999999999999999887 2 1 1101 1 3
Q ss_pred hhhhhhhhccCCCchhhhhhhhccccccccCCCCCCCceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEEeeccCCCCCC
Q 016089 80 LDIRQASKLRGPEVRKWFASQLMLPEWMIDVPDRLSHDWYVFARPAGKRCIVVSSNGTTVSRERNGSILHHFPSALPSGA 159 (395)
Q Consensus 80 ~d~~~~~k~~gk~~rk~ya~qLMlsEWl~dvP~dL~~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~~F~S~LPgG~ 159 (395)
.|++++++.+||+++||||+||||||||+|||++|+++|+||+||+|||||||||+|+|++|+|+|+++++|+|+||||+
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 016089 160 RTKDPSGSAQSYCILDCIFHELDQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVYNC 239 (395)
Q Consensus 160 ~~~~~~~~~~~ytILDCIy~e~~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~n~~~F~~lp~~~c 239 (395)
++ .+.+++||||||||+|.|+|||||||||||||++|+|++|||||||+|||+|.+++++++.+|+|+|+++|+|||
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 86 367899999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ChHhHHHHHhcCCCCccccEEeEeccccccCCCCCCeeeeccC
Q 016089 240 DQRGLYSAYIESVPYAKDGLLFYNKHAHYQTGNTPLALVWKDE 282 (395)
Q Consensus 240 ~~~~L~~~~s~~~p~~~DGLLFYHKea~Y~~G~TPLv~~wKD~ 282 (395)
++++|..+|++++||.+||||||||+.+|+||.||||||+|..
T Consensus 237 ~q~~l~~~~~~~~pf~~DGLLFYhks~~yqpgqsplvgwlkp~ 279 (325)
T KOG3132|consen 237 DQSGLHSAYTGSLPFVRDGLLFYHKSVVYQPGQSPLVGWLKPW 279 (325)
T ss_pred CHHHHHHHHcCCCceeeeeEEEeecceeeCCCCCccccccchh
Confidence 9999999999999999999999999999999999999999943
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=5.2e-70 Score=502.93 Aligned_cols=183 Identities=55% Similarity=1.054 Sum_probs=175.9
Q ss_pred hhhhhhccccccccCCCCCCCceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEEeeccCCCCCCCCCCCCCCCCCcEEee
Q 016089 96 WFASQLMLPEWMIDVPDRLSHDWYVFARPAGKRCIVVSSNGTTVSRERNGSILHHFPSALPSGARTKDPSGSAQSYCILD 175 (395)
Q Consensus 96 ~ya~qLMlsEWl~dvP~dL~~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~~F~S~LPgG~~~~~~~~~~~~ytILD 175 (395)
.||||||+||||+++|+||+++|+|+|||+||||||||++|.|++|+|+|++++.|+|.||||+..+ ..+++||||
T Consensus 1 ~~~~~lml~Ewm~~~p~~l~~~w~~~~~P~G~R~lvv~~~g~t~~~~r~g~~~~~f~s~lP~g~~~~----~~~g~tILD 76 (186)
T cd09232 1 LYANQLMLSEWMVEVPDDLSEEWLVVPCPVGKRCLVVASKGKTVARSKNGRTLHRFSSALPGGSRKT----SNSGYTILD 76 (186)
T ss_pred CcccceechhhcccCCCccCcceEEEECcCceEEEEEEeCCEEEEEeCCCCEEEecccCCCCCCcCC----CCCCCEEEE
Confidence 3899999999999999999999999999999999999999999999999999999999999998652 578999999
Q ss_pred eeeecCCcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCCCCCceeccccccCChHhHHHHHhcCC---
Q 016089 176 CIFHELDQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVYNCDQRGLYSAYIESV--- 252 (395)
Q Consensus 176 CIy~e~~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~n~~~F~~lp~~~c~~~~L~~~~s~~~--- 252 (395)
|||++.+.||||||||||||++++||+||||||||+|||+|.+.....+..|+|+|+.+|+|+|+.++|.++|+...
T Consensus 77 ci~~~~~~~yyVlDii~w~g~~l~d~~~~~Rf~wl~skl~E~~~~~~~~~~~~~~f~~~p~~~~~~~~l~~~~~~~~~~~ 156 (186)
T cd09232 77 CIYNEDDRTYYVLDVLCWNGHPLYDCETEFRFFWLRSKLEELPELDEPSEKNPFRFVPLPYFPCTKESLQSAYSGPLNDD 156 (186)
T ss_pred EecCCCCCEEEEEEEeeeCCcccccCCcchhHHHHHhhCCCccccccccccCCceEEecCcccCcHHHHHHHHhcccccC
Confidence 99999999999999999999999999999999999999999887777788999999999999999999999999999
Q ss_pred CCccccEEeEeccccccCCCCCCeeeeccC
Q 016089 253 PYAKDGLLFYNKHAHYQTGNTPLALVWKDE 282 (395)
Q Consensus 253 p~~~DGLLFYHKea~Y~~G~TPLv~~wKD~ 282 (395)
++++||||||||++||++|.||||+||||+
T Consensus 157 ~~e~DGLlFyhk~~~Y~~G~tPlvl~wKp~ 186 (186)
T cd09232 157 PYELDGLLFYHKESHYTPGSTPLVLWLKDY 186 (186)
T ss_pred CCCCceEEEEeCCCcccCcCCCcEEEecCC
Confidence 999999999999999999999999999985
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=99.69 E-value=3.6e-16 Score=141.65 Aligned_cols=170 Identities=23% Similarity=0.264 Sum_probs=141.3
Q ss_pred hccccccccCCC--CCCCceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEEeeccCCCCCCCCCCCCCCCCCcEEeeeee
Q 016089 101 LMLPEWMIDVPD--RLSHDWYVFARPAGKRCIVVSSNGTTVSRERNGSILHHFPSALPSGARTKDPSGSAQSYCILDCIF 178 (395)
Q Consensus 101 LMlsEWl~dvP~--dL~~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~~F~S~LPgG~~~~~~~~~~~~ytILDCIy 178 (395)
.|++.|+...++ ....+|++-+..-|.||+++..+|.+.+++|+|..+..+...+|.... ......|||||-+
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 378888887754 457899999999999999999999999999999988876666765111 1123459999998
Q ss_pred ecCC-------cEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCCCCCceeccccccCChHhHHHHHhcC
Q 016089 179 HELD-------QTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVYNCDQRGLYSAYIES 251 (395)
Q Consensus 179 ~e~~-------~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~n~~~F~~lp~~~c~~~~L~~~~s~~ 251 (395)
.-.+ -+|||.|||+|+|..+.+++..-|+-+|++.+.+.... .++.+..++.++|..+.+.+++...
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 3577888888898877788888777
Q ss_pred CCCccccEEeEeccccc--cCCCCCCeeeecc
Q 016089 252 VPYAKDGLLFYNKHAHY--QTGNTPLALVWKD 281 (395)
Q Consensus 252 ~p~~~DGLLFYHKea~Y--~~G~TPLv~~wKD 281 (395)
...-.+|++|-+.++.| .+|.++.++.||.
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 9999999999983
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=99.48 E-value=2e-13 Score=125.28 Aligned_cols=159 Identities=21% Similarity=0.409 Sum_probs=109.5
Q ss_pred CceEEEEecCCcEEEEEeeCCeEEEEcCCCcE--EE--eeccCCCCCCCCCCCCCCCCCcEEeeeeeecC------CcEE
Q 016089 116 HDWYVFARPAGKRCIVVSSNGTTVSRERNGSI--LH--HFPSALPSGARTKDPSGSAQSYCILDCIFHEL------DQTY 185 (395)
Q Consensus 116 ~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~--l~--~F~S~LPgG~~~~~~~~~~~~ytILDCIy~e~------~~ty 185 (395)
.+++|..=.-|.|+|+...++.+-..+++-.. +. .|+....+. .+.....||||+.+..+ .-+|
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 12235679999966533 4699
Q ss_pred EEEEEEeeCCcccccccchhhHHHhhhhccccCCCC------CCCCCCCCceeccccccCChHh--HHHHHhcCCCCccc
Q 016089 186 YVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACD------APSHYYKFRFSTVPVYNCDQRG--LYSAYIESVPYAKD 257 (395)
Q Consensus 186 YVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~------~~s~~n~~~F~~lp~~~c~~~~--L~~~~s~~~p~~~D 257 (395)
||.|+|+|+|..+.+++...|+.||+..+.+..... ......||.+..-+.++..... +........+++.|
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 999999999999999999999999998887632111 1122356666667777664322 23344567889999
Q ss_pred cEEeEeccccccCCCCCCeeeec
Q 016089 258 GLLFYNKHAHYQTGNTPLALVWK 280 (395)
Q Consensus 258 GLLFYHKea~Y~~G~TPLv~~wK 280 (395)
||+|.+.+..|.+|..+-++=||
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=99.32 E-value=1.4e-12 Score=93.49 Aligned_cols=39 Identities=31% Similarity=0.330 Sum_probs=35.3
Q ss_pred CCCCCcCCCCC-CchHHHHHHHHHHHHHHhHHHHHHHHhh
Q 016089 4 PDLRRPFKRTA-ISDQQRRRELSLQRQSQNRRDAQQQARC 42 (395)
Q Consensus 4 h~~~~~~k~~~-~~~Q~~RR~~~Le~Qk~~R~d~~~~aR~ 42 (395)
|||+++||.+. +.+|++||+++|++||++|+|++||||+
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 7799999999999999999999999996
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=98.72 E-value=2.4e-07 Score=86.55 Aligned_cols=159 Identities=16% Similarity=0.284 Sum_probs=113.3
Q ss_pred CceEEEEecCCcEEEEEeeC-CeEEEEcCCCcEEEeeccCCCCCCCCCCCCCCCCCcEEeeeeeecCCc------EEEEE
Q 016089 116 HDWYVFARPAGKRCIVVSSN-GTTVSRERNGSILHHFPSALPSGARTKDPSGSAQSYCILDCIFHELDQ------TYYVI 188 (395)
Q Consensus 116 ~~Wl~vpcPvGkRcLVVas~-G~T~ay~k~G~~l~~F~S~LPgG~~~~~~~~~~~~ytILDCIy~e~~~------tyYVL 188 (395)
.+|++-.=--|-||+++..+ |.+..++++|..+....-.+|..... .....-||||+=+..... +|||.
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 112345999997775443 69999
Q ss_pred EEEeeCCcccccccchhhHHHhhhhccccCCCC----C-CCCCCCCceeccccccCChHhHHHHHhc---CCCCccccEE
Q 016089 189 DMVCWRGYSLYDCTAEFRFFWLNSKLAETGACD----A-PSHYYKFRFSTVPVYNCDQRGLYSAYIE---SVPYAKDGLL 260 (395)
Q Consensus 189 Dvl~W~g~~l~dceteFRffWl~SKl~E~~~~~----~-~s~~n~~~F~~lp~~~c~~~~L~~~~s~---~~p~~~DGLL 260 (395)
|+|+++|.++.+.+..=|.-.|+.-+.+...-. . .....++.+..-++++++ .+..++.. ..+...|||+
T Consensus 117 DiL~~~g~~l~~~pl~~R~~~L~~~i~~~~~~~~~~~~~~~~~~~~~i~~k~~~~~~--~~~~~~~~~~~~~~~~~EGlI 194 (215)
T cd07895 117 DILAFNGQSVTEKPLSERLKYIKKEVIEPRNELLKKGPIDKAKEPFSVRLKDFFPLY--KIEKLFEKIIPKLPHENDGLI 194 (215)
T ss_pred EEEEECCcCccCCCHHHHHHHHHHhchhHHHHhhhcChhhcCCCCeEEEecceEeHH--hHHHHHHhccccCCCCCCCEE
Confidence 999999999999999999988888776532110 0 011233455566677763 34444433 3577899999
Q ss_pred eEeccccccCCCCCCeeeec
Q 016089 261 FYNKHAHYQTGNTPLALVWK 280 (395)
Q Consensus 261 FYHKea~Y~~G~TPLv~~wK 280 (395)
|-..++.|.+|.+..++=||
T Consensus 195 fk~~~~~Y~~Gr~~~~lKwK 214 (215)
T cd07895 195 FTPNDEPYVPGTDKNLLKWK 214 (215)
T ss_pred EccCCCCccCccCCcceeeC
Confidence 99999999999999888887
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=98.69 E-value=2.1e-07 Score=85.45 Aligned_cols=158 Identities=20% Similarity=0.234 Sum_probs=111.2
Q ss_pred hccccccccCCCCCCCceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEEe-eccCCCCCCCCCCCCCCCCCcEEeeeeee
Q 016089 101 LMLPEWMIDVPDRLSHDWYVFARPAGKRCIVVSSNGTTVSRERNGSILHH-FPSALPSGARTKDPSGSAQSYCILDCIFH 179 (395)
Q Consensus 101 LMlsEWl~dvP~dL~~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~~-F~S~LPgG~~~~~~~~~~~~ytILDCIy~ 179 (395)
-||+.=.-.+|+ +++|++=+---|-||+|+...|...++||+|..+.. |+..+.-... ....-|||||-+.
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 366666665655 469999999999999999999999999999987642 4321100000 0112399999554
Q ss_pred c-------------------------CCcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCCCCCceecc
Q 016089 180 E-------------------------LDQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTV 234 (395)
Q Consensus 180 e-------------------------~~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~n~~~F~~l 234 (395)
- ..-+|||.|||..+|.++.+=+..=|+-.|.+-+... .-++.+.
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-CCCeeee
Q 016089 235 PVYNCDQRGLYSAYIESVPYAKDGLLFYNKHAHYQTGN-TPLALVW 279 (395)
Q Consensus 235 p~~~c~~~~L~~~~s~~~p~~~DGLLFYHKea~Y~~G~-TPLv~~w 279 (395)
|++....+.+. .....--.+|+++-+.++.|.+|. |+.++=|
T Consensus 145 ~~~~~~~~~~~---~~~~~~g~EGiv~K~~~s~Y~~g~rs~~wlK~ 187 (190)
T cd07906 145 EHFEGGGAALF---AAACELGLEGIVAKRADSPYRSGRRSRDWLKI 187 (190)
T ss_pred ceEcCCHHHHH---HHHHHcCCcEEEEecCCCCcCCCCCCCccEEE
Confidence 77776643333 222233479999999999999999 8754333
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=98.26 E-value=1.2e-05 Score=75.16 Aligned_cols=163 Identities=20% Similarity=0.275 Sum_probs=113.9
Q ss_pred hccccccccCCCCC--CCceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEE-eeccCCCCCCCCCCCCCCCCCcEEeeee
Q 016089 101 LMLPEWMIDVPDRL--SHDWYVFARPAGKRCIVVSSNGTTVSRERNGSILH-HFPSALPSGARTKDPSGSAQSYCILDCI 177 (395)
Q Consensus 101 LMlsEWl~dvP~dL--~~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~-~F~S~LPgG~~~~~~~~~~~~ytILDCI 177 (395)
-||++=.-.+|+.+ ..+|++=+==-|-||++....|....+||+|..+. .|+....--. .-..-||||+=
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 34788888778999999999999999999998765 3543311000 00123999984
Q ss_pred ee---cC-------------------------CcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCCCCC
Q 016089 178 FH---EL-------------------------DQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKF 229 (395)
Q Consensus 178 y~---e~-------------------------~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~n~~ 229 (395)
.. .. .-+|+|.|||..+|.++.+.+..=|.--|.+-+.+.+ .-
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 016089 230 RFSTVPVYNCD-QRGLYSAYIESVPYAKDGLLFYNKHAHYQTGNTPLALVWK 280 (395)
Q Consensus 230 ~F~~lp~~~c~-~~~L~~~~s~~~p~~~DGLLFYHKea~Y~~G~TPLv~~wK 280 (395)
.+.+.|+..|+ .+.+.+++......-..|+++-..++.|.+|..- -.|||
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 4667777765555568999999999999999653 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=98.19 E-value=3e-05 Score=71.78 Aligned_cols=159 Identities=18% Similarity=0.214 Sum_probs=111.1
Q ss_pred hccccccccCCCCCCCceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEE-eeccCCCCCCCCCCCCCCCCCcEEeeeeee
Q 016089 101 LMLPEWMIDVPDRLSHDWYVFARPAGKRCIVVSSNGTTVSRERNGSILH-HFPSALPSGARTKDPSGSAQSYCILDCIFH 179 (395)
Q Consensus 101 LMlsEWl~dvP~dL~~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~-~F~S~LPgG~~~~~~~~~~~~ytILDCIy~ 179 (395)
-||+.-...+|+ ..+|++=+==-|-||+++...|.+..+|++|..+. .||....--.. ....-+||||=..
T Consensus 3 PmLa~~~~~~~~--~~~~~~E~K~DG~R~~~~~~~~~v~l~SR~g~~~t~~~p~~~~~~~~------~~~~~~iLDGElv 74 (194)
T cd07905 3 PMLARAVDALPE--PGGWQYEPKWDGFRCLAFRDGDEVRLQSRSGKPLTRYFPELVAAARA------LLPPGCVLDGELV 74 (194)
T ss_pred ceeCCccCCCCC--CCceEEEeeeceEEEEEEEeCCEEEEEeCCCCchhhhhHHHHHHHHh------hCCCCEEEEeEEE
Confidence 367666666665 56899988888999999999999999999998765 34432100000 0011289998543
Q ss_pred c----------------------------CCcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCCCCCce
Q 016089 180 E----------------------------LDQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRF 231 (395)
Q Consensus 180 e----------------------------~~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~n~~~F 231 (395)
- ..-+|+|.|||..+|.++.+.+..=|.--|.+-+.+. .-.+
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 eccccccCChHhHHHHHhcCCCCccccEEeEeccccccCCCCCCeeeecc
Q 016089 232 STVPVYNCDQRGLYSAYIESVPYAKDGLLFYNKHAHYQTGNTPLALVWKD 281 (395)
Q Consensus 232 ~~lp~~~c~~~~L~~~~s~~~p~~~DGLLFYHKea~Y~~G~TPLv~~wKD 281 (395)
.++|... +.+.+.+++.....--..|+++-..++.|++|. . .|||=
T Consensus 145 ~~~~~~~-~~~~~~~~~~~~~~~g~EGiv~K~~~s~Y~~Gr-~--~WlK~ 190 (194)
T cd07905 145 HLSPATT-DRAEAREWLEEFEGAGLEGVVAKRLDGPYRPGE-R--AMLKV 190 (194)
T ss_pred EECCccC-CHHHHHHHHHHHHHCCCceEEEeCCCCCcCCCC-C--cEEEE
Confidence 4555432 334455555544445578999999999999998 3 68873
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=98.02 E-value=5.1e-05 Score=71.39 Aligned_cols=156 Identities=17% Similarity=0.227 Sum_probs=106.4
Q ss_pred CceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEE-eeccCCCCCC-CC--CCCCCCCCCcEEeeeee---ecC-------
Q 016089 116 HDWYVFARPAGKRCIVVSSNGTTVSRERNGSILH-HFPSALPSGA-RT--KDPSGSAQSYCILDCIF---HEL------- 181 (395)
Q Consensus 116 ~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~-~F~S~LPgG~-~~--~~~~~~~~~ytILDCIy---~e~------- 181 (395)
.+|++=.==-|-||+|...+|....+||+|..+. .|+-..=... .. ...-.....-+||||=. ...
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 00000112338999743 221
Q ss_pred -----------------CcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCCCCCceeccccccCCh-Hh
Q 016089 182 -----------------DQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVYNCDQ-RG 243 (395)
Q Consensus 182 -----------------~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~n~~~F~~lp~~~c~~-~~ 243 (395)
.-+|+|.|||..+|.++.+.+..=|.-=|.+-+.+. +-++..+|...++. +.
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 13567778887754 66
Q ss_pred HHHHHhcCCCCccccEEeEeccccccCC-CCCCeeeecc
Q 016089 244 LYSAYIESVPYAKDGLLFYNKHAHYQTG-NTPLALVWKD 281 (395)
Q Consensus 244 L~~~~s~~~p~~~DGLLFYHKea~Y~~G-~TPLv~~wKD 281 (395)
+.+++.....--..|+++-..++.|.+| .|..++=||.
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=97.97 E-value=0.00033 Score=69.22 Aligned_cols=151 Identities=21% Similarity=0.261 Sum_probs=105.0
Q ss_pred cCCCCCCCceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEE-eecc------CCCCCCCCCCCCCCCCCcEEeeeeeec-
Q 016089 109 DVPDRLSHDWYVFARPAGKRCIVVSSNGTTVSRERNGSILH-HFPS------ALPSGARTKDPSGSAQSYCILDCIFHE- 180 (395)
Q Consensus 109 dvP~dL~~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~-~F~S------~LPgG~~~~~~~~~~~~ytILDCIy~e- 180 (395)
+.|.+ +.+|++=+==-|-||++....|....+||+|..+. .|+. .+|. .-+||||=+.-
T Consensus 6 ~~~~~-~~~~~~E~K~DG~R~~~~~~~~~v~l~SR~g~~~t~~~p~l~~~~~~~~~------------~~~iLDGElv~~ 72 (298)
T TIGR02779 6 TTPPT-GDDWRYEVKYDGYRCLARIEGGKVRLISRNGHDWTEKFPILAAALAALPI------------LPAVLDGEIVVL 72 (298)
T ss_pred CCCCC-CCCEEEEEEEceEEEEEEEeCCEEEEEeCCCCchHhHhHHHHHHHHhCCC------------CcEEEEeEEEEE
Confidence 44433 46898888888999999999999999999998764 4532 2222 13999984432
Q ss_pred --C------------------CcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCCCCCceeccccccC-
Q 016089 181 --L------------------DQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVYNC- 239 (395)
Q Consensus 181 --~------------------~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~n~~~F~~lp~~~c- 239 (395)
. .-+|+|.|||..+|.++.+-+..=|.--|.+-+.+.+. +..+. +. .+
T Consensus 73 d~~g~~~F~~l~~r~~~~~~~~~~~~vFDiL~l~g~~l~~~pl~eRr~~L~~l~~~~~~--------~~~~~--~~-~~~ 141 (298)
T TIGR02779 73 DESGRSDFSALQNRLRAGRDRPATYYAFDLLYLDGEDLRDLPLSERKKLLEELLKAIKG--------PLAPD--RY-SVH 141 (298)
T ss_pred CCCCCCCHHHHHhhhhcCCCCceEEEEEeeeeECceehhcCCHHHHHHHHHHHhcccCC--------CceeE--ec-ccC
Confidence 1 12799999999999999888888888777776654321 11111 11 12
Q ss_pred ChHhHHHHHhcCCCCccccEEeEeccccccCCCCCCeeeeccCC
Q 016089 240 DQRGLYSAYIESVPYAKDGLLFYNKHAHYQTGNTPLALVWKDEK 283 (395)
Q Consensus 240 ~~~~L~~~~s~~~p~~~DGLLFYHKea~Y~~G~TPLv~~wKD~~ 283 (395)
+.+.+.+++......-..|+++-+.++.|++|.|.-++=+|...
T Consensus 142 ~~~~~~~~~~~~~~~g~EGiv~K~~ds~Y~~Grs~~WlK~K~~~ 185 (298)
T TIGR02779 142 FEGDGQALLEAACRLGLEGVVAKRRDSPYRSGRSADWLKLKCRR 185 (298)
T ss_pred chhHHHHHHHHHHHcCCceEEEeCCCCCCCCCCCCCcEEEccCC
Confidence 23445555554445568999999999999999987776666443
No 12
>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=97.95 E-value=6.2e-05 Score=70.82 Aligned_cols=145 Identities=17% Similarity=0.162 Sum_probs=98.8
Q ss_pred CceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEEe--ec---cCCCCCCCCCCCCCCCCCcEEeeee---eec-------
Q 016089 116 HDWYVFARPAGKRCIVVSSNGTTVSRERNGSILHH--FP---SALPSGARTKDPSGSAQSYCILDCI---FHE------- 180 (395)
Q Consensus 116 ~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~~--F~---S~LPgG~~~~~~~~~~~~ytILDCI---y~e------- 180 (395)
.+|++=+==-|-||+|+-..|....+||+|.-+.. |+ ..++..-+ ...-|||||= +..
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 35666666679999999888999999999976432 22 21221100 0112788863 322
Q ss_pred --------------CCcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCCCCCceeccccccCC-hHhHH
Q 016089 181 --------------LDQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVYNCD-QRGLY 245 (395)
Q Consensus 181 --------------~~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~n~~~F~~lp~~~c~-~~~L~ 245 (395)
..-+|||.|||.++|.++.+.+..=|.-=|.+-+.+. + -++.+.|...++ .+.+.
T Consensus 107 F~~l~~~~~~~~~~~~v~~~vFDiL~l~g~~l~~~pl~eR~~~L~~~~~~~---------~-~~~~~~~~~~~~~~~~l~ 176 (213)
T cd07902 107 FGTLGIHKKSAFKDANVCLFVFDCLYYNGESLMDKPLRERRKILEDNMVEI---------P-NRIMLSEMKFVKKADDLS 176 (213)
T ss_pred cchhhhhhccccccCceEEEEEEEeeeCCcchhcCcHHHHHHHHHHhccCC---------C-CeEEEEEEEEcCCHHHHH
Confidence 1247999999999999999988877766666655332 1 135666766663 45666
Q ss_pred HHHhcCCCCccccEEeEeccccccCCCCCCeeeec
Q 016089 246 SAYIESVPYAKDGLLFYNKHAHYQTGNTPLALVWK 280 (395)
Q Consensus 246 ~~~s~~~p~~~DGLLFYHKea~Y~~G~TPLv~~wK 280 (395)
+++.....--..|+++-+.++.|.+|.. .|||
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 13
>PRK05972 ligD ATP-dependent DNA ligase; Reviewed
Probab=97.94 E-value=0.00039 Score=77.95 Aligned_cols=170 Identities=17% Similarity=0.177 Sum_probs=118.5
Q ss_pred hccccccccCCCCCCCceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEE-eeccCCCCCCCCCCCCCCCCCcEEeeeeee
Q 016089 101 LMLPEWMIDVPDRLSHDWYVFARPAGKRCIVVSSNGTTVSRERNGSILH-HFPSALPSGARTKDPSGSAQSYCILDCIFH 179 (395)
Q Consensus 101 LMlsEWl~dvP~dL~~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~-~F~S~LPgG~~~~~~~~~~~~ytILDCIy~ 179 (395)
-||+.-....|++ .+|++=.==-|-||++...+|....+|+||.-+. +|+...-.-.. ..-.-+|||+=..
T Consensus 236 PMLAt~~~~~p~g--~~W~~E~K~DG~R~~a~~~gg~vrL~SRnG~d~T~~fPel~~~~~~------l~~~~~ILDGEIV 307 (860)
T PRK05972 236 PQLATLVDRPPSG--DGWIYEIKFDGYRILARIEGGEVRLFTRNGLDWTAKLPALAKAAAA------LGLPDAWLDGEIV 307 (860)
T ss_pred cccCccCCCCCCc--CceEEEeeeCcEEEEEEEECCEEEEEeCCCCccccccHHHHHHHHh------cCCCceeEeEEEE
Confidence 4777755566654 7999988889999999999999999999998754 45532110000 0001279998443
Q ss_pred c---------------------CCcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCCCCCceecccccc
Q 016089 180 E---------------------LDQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVYN 238 (395)
Q Consensus 180 e---------------------~~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~n~~~F~~lp~~~ 238 (395)
- ..-+|||.|||..+|.++.+.+..=|.--|++-+.+.. + -.+...+++.
T Consensus 308 vld~~G~~~F~~Lq~r~~~~~~~~v~f~vFDLL~l~G~dL~~~PL~eRr~~L~~ll~~~~--------~-~~i~~s~~~~ 378 (860)
T PRK05972 308 VLDEDGVPDFQALQNAFDEGRTEDLVYFAFDLPFLGGEDLRELPLEERRARLRALLEAAR--------S-DRIRFSEHFD 378 (860)
T ss_pred EECCCCCCCHHHHHHHhhccCCCceEEEEEeccccCCcccccCCHHHHHHHHHHHhhhcC--------C-CcEEEeceec
Confidence 1 11379999999999999999988888888877665421 1 1456677777
Q ss_pred CChHhHHHHHhcCCCCccccEEeEeccccccCCCCCCeeeeccCCCccceee
Q 016089 239 CDQRGLYSAYIESVPYAKDGLLFYNKHAHYQTGNTPLALVWKDEKCSQYVID 290 (395)
Q Consensus 239 c~~~~L~~~~s~~~p~~~DGLLFYHKea~Y~~G~TPLv~~wKD~~~s~y~~d 290 (395)
++.+.+.+ .....-..|++.-..++.|.+|.|.-|+=+|-....-++|-
T Consensus 379 ~~g~~ll~---~a~~~GlEGIVaKr~dS~Y~~GRs~~WlKiK~~~~~E~VIg 427 (860)
T PRK05972 379 AGGDAVLA---SACRLGLEGVIGKRADSPYVSGRSEDWIKLKCRARQEFVIG 427 (860)
T ss_pred chHHHHHH---HHHHcCCceEEEeCCCCCCCCCCCCCcEEEecCCCceEEEE
Confidence 76544333 22334588999999999999999988777775555555553
No 14
>PRK08224 ligC ATP-dependent DNA ligase; Reviewed
Probab=97.93 E-value=0.0004 Score=70.59 Aligned_cols=159 Identities=19% Similarity=0.209 Sum_probs=106.8
Q ss_pred hccccccccCCCCCCCceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEE-eeccCCCCCCCCCCCCCCCCCcEEeeeeee
Q 016089 101 LMLPEWMIDVPDRLSHDWYVFARPAGKRCIVVSSNGTTVSRERNGSILH-HFPSALPSGARTKDPSGSAQSYCILDCIFH 179 (395)
Q Consensus 101 LMlsEWl~dvP~dL~~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~-~F~S~LPgG~~~~~~~~~~~~ytILDCIy~ 179 (395)
-||+.....+|+. .+|++=+==-|-||++....|.+..+|+||.-+. +|+....-... ....-+|||+=..
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 5799888889999999999999999999998875 57652110000 0011289997432
Q ss_pred c--C--------------------------CcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCCCCCce
Q 016089 180 E--L--------------------------DQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRF 231 (395)
Q Consensus 180 e--~--------------------------~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~n~~~F 231 (395)
- . .-+|||.|+|.++|.++.+-+..=|.=.|.+-+... . .+
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 eccccccCChHhHHHHHhcCCCCccccEEeEeccccccCCCCCCeeeeccC
Q 016089 232 STVPVYNCDQRGLYSAYIESVPYAKDGLLFYNKHAHYQTGNTPLALVWKDE 282 (395)
Q Consensus 232 ~~lp~~~c~~~~L~~~~s~~~p~~~DGLLFYHKea~Y~~G~TPLv~~wKD~ 282 (395)
.+.|.+.. .+...+++......-..|++.-..++.|.+|..- |+|-.
T Consensus 152 ~~~~~~~~-~~~~~~~~~~a~~~G~EGIV~Kr~dS~Y~~Grr~---WlKiK 198 (350)
T PRK08224 152 HLTPATTD-PATARRWFEEFEGAGLDGVIAKPLDGPYQPGKRA---MFKVK 198 (350)
T ss_pred EEecccCC-HHHHHHHHHHHHhCCCcEEEEeCCCCCcCCCCcC---EEEEc
Confidence 44554432 2344444543344558999999999999999765 55533
No 15
>PRK07636 ligB ATP-dependent DNA ligase; Reviewed
Probab=97.86 E-value=0.00045 Score=67.82 Aligned_cols=154 Identities=17% Similarity=0.140 Sum_probs=104.0
Q ss_pred ccccccccCCCCCCCceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEE-eeccCCCCCCCCCCCCCCCCCcEEeeeeeec
Q 016089 102 MLPEWMIDVPDRLSHDWYVFARPAGKRCIVVSSNGTTVSRERNGSILH-HFPSALPSGARTKDPSGSAQSYCILDCIFHE 180 (395)
Q Consensus 102 MlsEWl~dvP~dL~~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~-~F~S~LPgG~~~~~~~~~~~~ytILDCIy~e 180 (395)
||+.-....|++ .+|++=+==-|-||++....|....+|++|..+. +||..+.-.- ..-+|||+=..-
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 5665432111 012899985531
Q ss_pred ------------------------CCcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCCCCCceecccc
Q 016089 181 ------------------------LDQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPV 236 (395)
Q Consensus 181 ------------------------~~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~n~~~F~~lp~ 236 (395)
..-+|||.|+|.++|.++.+-+..=|.=.|.+-+... + .+..+|.
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 016089 237 YNCDQRGLYSAYIESVPYAKDGLLFYNKHAHYQTG-NTPLALVWK 280 (395)
Q Consensus 237 ~~c~~~~L~~~~s~~~p~~~DGLLFYHKea~Y~~G-~TPLv~~wK 280 (395)
...+.+.+.+.. ..--..|+++-..++.|.+| .|.-++=.|
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 22347799999999999988 677554444
No 16
>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=97.82 E-value=5.8e-05 Score=68.79 Aligned_cols=145 Identities=23% Similarity=0.307 Sum_probs=104.5
Q ss_pred CCceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEEe-eccC-------CCCCCCCCCCCCCCCCcEEeeeeeec------
Q 016089 115 SHDWYVFARPAGKRCIVVSSNGTTVSRERNGSILHH-FPSA-------LPSGARTKDPSGSAQSYCILDCIFHE------ 180 (395)
Q Consensus 115 ~~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~~-F~S~-------LPgG~~~~~~~~~~~~ytILDCIy~e------ 180 (395)
...|++=+==-|-||+|+...|....+||+|..+.. |+.. +..+.+ -+||||=..-
T Consensus 18 ~~~~~~e~K~DG~R~~i~~~~~~v~~~SR~g~~~~~~~~~l~~~l~~~~~~~~~----------~~vLDGElv~~d~~~~ 87 (202)
T PF01068_consen 18 GGPWYVEPKYDGVRCQIHKDGGGVRLFSRNGKDITSQFPELAEALRELLFPDGP----------DFVLDGELVVLDPNTG 87 (202)
T ss_dssp TSCEEEEEEESSEEEEEEEETTEEEEEETTSSB-GGGHHHHHHHHHHHBCTSCT----------EEEEEEEEEEBETTTS
T ss_pred CCCeEEEEeEeeEEeeeeeccccceeecccccchhhHHHHHHHHHHHHhcCCCC----------ceEEEEEEEEEecCCC
Confidence 567888888889999999999999999999998765 4422 222111 2899983331
Q ss_pred -----------------------CCcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCCCCCceeccccc
Q 016089 181 -----------------------LDQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVY 237 (395)
Q Consensus 181 -----------------------~~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~n~~~F~~lp~~ 237 (395)
..-+|+|.|||..+|.++.+.+.+=|.--|..-+.. ..-.+..++++
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 016089 238 NCDQ-RGLYSAYIESVPYAKDGLLFYNKHAHYQTGNTPLALVWK 280 (395)
Q Consensus 238 ~c~~-~~L~~~~s~~~p~~~DGLLFYHKea~Y~~G~TPLv~~wK 280 (395)
.|+. +.+.+++.....--..|+++-..++.|++|.. --.|||
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 55666554443344789999999999999966 234665
No 17
>PRK09632 ATP-dependent DNA ligase; Reviewed
Probab=97.63 E-value=0.0018 Score=72.03 Aligned_cols=140 Identities=18% Similarity=0.239 Sum_probs=101.5
Q ss_pred CCceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEE-eecc------CCCCCCCCCCCCCCCCCcEEeeeeee---c----
Q 016089 115 SHDWYVFARPAGKRCIVVSSNGTTVSRERNGSILH-HFPS------ALPSGARTKDPSGSAQSYCILDCIFH---E---- 180 (395)
Q Consensus 115 ~~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~-~F~S------~LPgG~~~~~~~~~~~~ytILDCIy~---e---- 180 (395)
+.+|++=+==-|-||++...+|....+|+||.-+. +|+. .||+. -+|||+=.. +
T Consensus 476 ~~~w~~E~K~DG~R~~~~~~~g~vrL~SRnG~d~T~~fPel~~~~~~l~~~------------~~ILDGEiVvld~~G~~ 543 (764)
T PRK09632 476 ASQWAFEGKWDGYRLLAEADHGALRLRSRSGRDVTAEYPELAALAEDLADH------------HVVLDGEIVALDDSGVP 543 (764)
T ss_pred CCCEEEEEEECceeEEEEEeCCEEEEEeCCCCCccccchhHHHHHhhCCCc------------ceeeeeEEEEeCCCCCC
Confidence 35798888788999999999999999999998655 5663 34331 289997543 2
Q ss_pred -----------CCcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCCCCCceeccccccCChHhHHHHHh
Q 016089 181 -----------LDQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVYNCDQRGLYSAYI 249 (395)
Q Consensus 181 -----------~~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~n~~~F~~lp~~~c~~~~L~~~~s 249 (395)
..-+|||.|||..+|.++.+.+..=|.=.|.+-+.+. -.+...+.+..+.+.+.+
T Consensus 544 ~F~~Lq~r~~~~~v~y~vFDLL~lnG~dL~~~Pl~eRR~~L~~l~~~~-----------~~i~~s~~~~~~~~~~l~--- 609 (764)
T PRK09632 544 SFGLLQNRGRDTRVEFWAFDLLYLDGRSLLRKPYRDRRKLLEALAPSG-----------GSLTVPPLLPGDGAEALA--- 609 (764)
T ss_pred CHHHHhhhhhcCCeEEEEEeeeccCCcccccCCHHHHHHHHHHhhCCC-----------CcEEecceecccHHHHHH---
Confidence 1248999999999999999988888887777766421 123445556655444333
Q ss_pred cCCCCccccEEeEeccccccCCC-CCCeeeec
Q 016089 250 ESVPYAKDGLLFYNKHAHYQTGN-TPLALVWK 280 (395)
Q Consensus 250 ~~~p~~~DGLLFYHKea~Y~~G~-TPLv~~wK 280 (395)
....--..|++.-..++.|.+|. |.-++=+|
T Consensus 610 ~a~~~GlEGIVaKr~dS~Y~pGrRs~~WlKiK 641 (764)
T PRK09632 610 YSRELGWEGVVAKRRDSTYQPGRRSSSWIKDK 641 (764)
T ss_pred HHHHcCCcEEEEeCCCCCCCCCCcCCCeEEEe
Confidence 22334588999999999999996 88655555
No 18
>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=97.62 E-value=0.00031 Score=74.36 Aligned_cols=161 Identities=21% Similarity=0.224 Sum_probs=116.7
Q ss_pred hhccccccccCCCC---CCCceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEE-eeccC--------CCCCCCCCCCCCC
Q 016089 100 QLMLPEWMIDVPDR---LSHDWYVFARPAGKRCIVVSSNGTTVSRERNGSILH-HFPSA--------LPSGARTKDPSGS 167 (395)
Q Consensus 100 qLMlsEWl~dvP~d---L~~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~-~F~S~--------LPgG~~~~~~~~~ 167 (395)
+-||++....+|+. +..+|++=.==-|-||+|...+|....+||+|.-+. .|+.. +|.+
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 016089 168 AQSYCILDCI---FHEL--------------------------DQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETG 218 (395)
Q Consensus 168 ~~~ytILDCI---y~e~--------------------------~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~ 218 (395)
.-||||+= ++.. .-+|||.|||..+|.++.+-+..=|.=-|.+-+.+.+
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 12788863 3221 1389999999999999999888888888877664421
Q ss_pred CCCCCCCCCCCceeccccccC-ChHhHHHHHhcCCCCccccEEeEeccccccCC-CCCCeeeecc
Q 016089 219 ACDAPSHYYKFRFSTVPVYNC-DQRGLYSAYIESVPYAKDGLLFYNKHAHYQTG-NTPLALVWKD 281 (395)
Q Consensus 219 ~~~~~s~~n~~~F~~lp~~~c-~~~~L~~~~s~~~p~~~DGLLFYHKea~Y~~G-~TPLv~~wKD 281 (395)
-.+..++...+ +.+.+.+++.....--..|+++-..++.|++| .+.-|+=||.
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 24667778777 45667776665555568999999999999999 7776666664
No 19
>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=97.61 E-value=0.0014 Score=60.85 Aligned_cols=149 Identities=19% Similarity=0.221 Sum_probs=99.6
Q ss_pred CceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEE-eeccCCCCCCCCCCCCCCCCCcEEeeeee---ecC----------
Q 016089 116 HDWYVFARPAGKRCIVVSSNGTTVSRERNGSILH-HFPSALPSGARTKDPSGSAQSYCILDCIF---HEL---------- 181 (395)
Q Consensus 116 ~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~-~F~S~LPgG~~~~~~~~~~~~ytILDCIy---~e~---------- 181 (395)
..|++=.==-|-||+++...|....+||+|..+. .|+-...-.. ....-|||||=+ +..
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 3566555556999999999999999999998753 3432111000 012349999743 221
Q ss_pred ---------------CcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCCCCCceeccccccCCh-HhHH
Q 016089 182 ---------------DQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVYNCDQ-RGLY 245 (395)
Q Consensus 182 ---------------~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~n~~~F~~lp~~~c~~-~~L~ 245 (395)
.-+|||.|||..+|.++.+=+..=|.==|..-+... +-++..+|...++. +.+.
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 136999999999999888766555554444433221 23456677777764 4466
Q ss_pred HHHhcCCCCccccEEeEeccccccCCC-CCCeeeecc
Q 016089 246 SAYIESVPYAKDGLLFYNKHAHYQTGN-TPLALVWKD 281 (395)
Q Consensus 246 ~~~s~~~p~~~DGLLFYHKea~Y~~G~-TPLv~~wKD 281 (395)
.++.....--.+|+++-..++.|.+|. |.-|+=||.
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 777766664
No 20
>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=97.57 E-value=0.00093 Score=62.38 Aligned_cols=150 Identities=17% Similarity=0.137 Sum_probs=102.6
Q ss_pred CCceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEE-eeccCCCCCCCCCCCCCCCCCcEEeeeee---ec----------
Q 016089 115 SHDWYVFARPAGKRCIVVSSNGTTVSRERNGSILH-HFPSALPSGARTKDPSGSAQSYCILDCIF---HE---------- 180 (395)
Q Consensus 115 ~~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~-~F~S~LPgG~~~~~~~~~~~~ytILDCIy---~e---------- 180 (395)
...|++=+==-|-||+|....|....+||+|.-+. .|+...+-.... ....-+|||+=. .+
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 46777777778999999999999999999997653 554321110000 000128888733 21
Q ss_pred ----------------CCcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCCCCCceeccccccCC-hHh
Q 016089 181 ----------------LDQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVYNCD-QRG 243 (395)
Q Consensus 181 ----------------~~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~n~~~F~~lp~~~c~-~~~ 243 (395)
..-+|||.|||..+|.++.+-+..-|.--|.+-+... -.+.++|...++ .+.
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 134566777764 456
Q ss_pred HHHHHhcCCCCccccEEeEeccccccCC-CCCCeeeec
Q 016089 244 LYSAYIESVPYAKDGLLFYNKHAHYQTG-NTPLALVWK 280 (395)
Q Consensus 244 L~~~~s~~~p~~~DGLLFYHKea~Y~~G-~TPLv~~wK 280 (395)
+.+++......-..|+++-+.++.|.+| .|.-++=||
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 21
>PRK09633 ligD ATP-dependent DNA ligase; Reviewed
Probab=97.50 E-value=0.003 Score=68.75 Aligned_cols=168 Identities=18% Similarity=0.222 Sum_probs=109.2
Q ss_pred hccccccccCCCCCCCceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEE-eeccC------CCCCCCCCCCCCCCCCcEE
Q 016089 101 LMLPEWMIDVPDRLSHDWYVFARPAGKRCIVVSSNGTTVSRERNGSILH-HFPSA------LPSGARTKDPSGSAQSYCI 173 (395)
Q Consensus 101 LMlsEWl~dvP~dL~~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~-~F~S~------LPgG~~~~~~~~~~~~ytI 173 (395)
-||+..-...|++ .+|++=.==-|-||++...+|....+|+||.-+. +|+.. +++..+ +..-+|
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 6899888788999999999999999999998765 56652 111110 011279
Q ss_pred eeeeee---cC---------------------------CcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCC
Q 016089 174 LDCIFH---EL---------------------------DQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAP 223 (395)
Q Consensus 174 LDCIy~---e~---------------------------~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~ 223 (395)
||+=.. +. .-+|||.|||..+|.++.+-+..=|.=-|.+=+.+.+.-.+.
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 997432 11 026999999999999999988888877777766543210000
Q ss_pred CCCCCCceeccccccCChHhHHHHHhcCCCCccccEEeEeccccccCC-CCCCeeeecc
Q 016089 224 SHYYKFRFSTVPVYNCDQRGLYSAYIESVPYAKDGLLFYNKHAHYQTG-NTPLALVWKD 281 (395)
Q Consensus 224 s~~n~~~F~~lp~~~c~~~~L~~~~s~~~p~~~DGLLFYHKea~Y~~G-~TPLv~~wKD 281 (395)
.....-.+..++++. ...+++......-..|++.-..++.|.+| .|.-|+=+|-
T Consensus 154 ~~~~~~~i~~~~~~~----~~~~l~~~a~~~g~EGIV~Kr~dS~Y~~G~Rs~~WlKiK~ 208 (610)
T PRK09633 154 DPYAKARIQYIPSTT----DFDALWEAVKRYDGEGIVAKKKTSKWLENKRSKDWLKIKN 208 (610)
T ss_pred ccccccceEEcCCHH----HHHHHHHHHHHcCCceEEEeCCCCCCCCCCCCCCeEEEec
Confidence 000111334444433 34444433333457999999999999988 7887666663
No 22
>PLN03113 DNA ligase 1; Provisional
Probab=97.34 E-value=0.0015 Score=72.56 Aligned_cols=168 Identities=18% Similarity=0.222 Sum_probs=114.2
Q ss_pred hhccccccccCCC---CC-CCceEEEEecCCcEEEEEe-eCCeEEEEcCCCcEE-EeeccCCCCCCCCCCCCCCCCCcEE
Q 016089 100 QLMLPEWMIDVPD---RL-SHDWYVFARPAGKRCIVVS-SNGTTVSRERNGSIL-HHFPSALPSGARTKDPSGSAQSYCI 173 (395)
Q Consensus 100 qLMlsEWl~dvP~---dL-~~~Wl~vpcPvGkRcLVVa-s~G~T~ay~k~G~~l-~~F~S~LPgG~~~~~~~~~~~~ytI 173 (395)
.-||++..-.+++ .+ +.+|++=.==-|-||.|+. .+|....|+|||.-+ .+||-.+--.... ...+-.-+|
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 3588886655543 23 3468776666799999985 688999999999764 4676443111000 000012399
Q ss_pred eeee---eecCC-------------------------cEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCC
Q 016089 174 LDCI---FHELD-------------------------QTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSH 225 (395)
Q Consensus 174 LDCI---y~e~~-------------------------~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~ 225 (395)
|||= |+..+ -+|||.|||.+||.++.+.+..-|-=-|++-|.+.
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 26999999999999999999888888888777553
Q ss_pred CCCCceeccccccC-ChHhHHHHHhcCCCCccccEEeEe--ccccccCC-CCCCeeeec
Q 016089 226 YYKFRFSTVPVYNC-DQRGLYSAYIESVPYAKDGLLFYN--KHAHYQTG-NTPLALVWK 280 (395)
Q Consensus 226 ~n~~~F~~lp~~~c-~~~~L~~~~s~~~p~~~DGLLFYH--Kea~Y~~G-~TPLv~~wK 280 (395)
+-+|...+...+ +.+.+...+......-..||+.-. .++.|++| .+.-|+=||
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 58899998 565555555
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=97.28 E-value=0.0019 Score=61.31 Aligned_cols=149 Identities=15% Similarity=0.137 Sum_probs=93.8
Q ss_pred ceEEEEecCCcEEEEEeeC-CeEEEEcCCCcEEE-eeccCCCCCCCCCCCCCCCCCcEEeeee---eecC----------
Q 016089 117 DWYVFARPAGKRCIVVSSN-GTTVSRERNGSILH-HFPSALPSGARTKDPSGSAQSYCILDCI---FHEL---------- 181 (395)
Q Consensus 117 ~Wl~vpcPvGkRcLVVas~-G~T~ay~k~G~~l~-~F~S~LPgG~~~~~~~~~~~~ytILDCI---y~e~---------- 181 (395)
.|++=+==-|-||++.... |....+||+|.-+. +|+....-.... . .....-+||||= +...
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 5666555569999998765 89999999998653 453322110000 0 000112899974 3321
Q ss_pred ---------------CcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCCCCCceeccccccCC-hHhHH
Q 016089 182 ---------------DQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVYNCD-QRGLY 245 (395)
Q Consensus 182 ---------------~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~n~~~F~~lp~~~c~-~~~L~ 245 (395)
.-+|+|.|||..+|.++.+=+ |.-.+..|++.-. + .+-++.++++..++ .+.+.
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 12356677777764 55676
Q ss_pred HHHhcCCCCccccEEeEecc--ccccCC-CCCCeeeec
Q 016089 246 SAYIESVPYAKDGLLFYNKH--AHYQTG-NTPLALVWK 280 (395)
Q Consensus 246 ~~~s~~~p~~~DGLLFYHKe--a~Y~~G-~TPLv~~wK 280 (395)
+++......-..|++.-..+ +.|.+| .|. .|||
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=97.28 E-value=0.0037 Score=60.29 Aligned_cols=143 Identities=13% Similarity=0.088 Sum_probs=90.9
Q ss_pred ceEEEEecCCcEEEEEee----CCeEEEEcCCCcEE-EeeccC-------CCCCCCCCCCCCCCCCcEEeeeee---ecC
Q 016089 117 DWYVFARPAGKRCIVVSS----NGTTVSRERNGSIL-HHFPSA-------LPSGARTKDPSGSAQSYCILDCIF---HEL 181 (395)
Q Consensus 117 ~Wl~vpcPvGkRcLVVas----~G~T~ay~k~G~~l-~~F~S~-------LPgG~~~~~~~~~~~~ytILDCIy---~e~ 181 (395)
+|++=.==-|-||+|... .|.+..+|++|.-+ +.|+-. |..+.. ......-+||||=. +..
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 00011238999844 431
Q ss_pred C---------------------------------cEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCCCC
Q 016089 182 D---------------------------------QTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYK 228 (395)
Q Consensus 182 ~---------------------------------~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~n~ 228 (395)
+ -+|||.|||.+||.++.+=+..-|---|.+=+...+ +
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 016089 229 FRFSTVPVYN------CDQRGLYSAYIESVPYAKDGLLFYNKHAHYQTGNT 273 (395)
Q Consensus 229 ~~F~~lp~~~------c~~~~L~~~~s~~~p~~~DGLLFYHKea~Y~~G~T 273 (395)
.+.+++... .+.+.+.+++.....--..|++.-..++.|.+|.+
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 23566777776555556889999999999999975
No 25
>PRK09247 ATP-dependent DNA ligase; Validated
Probab=97.24 E-value=0.0023 Score=68.43 Aligned_cols=164 Identities=18% Similarity=0.180 Sum_probs=114.2
Q ss_pred hhccccccccCCCCCC--CceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEE-eeccCCCCCCCCCCCCCCCCCcEEeee
Q 016089 100 QLMLPEWMIDVPDRLS--HDWYVFARPAGKRCIVVSSNGTTVSRERNGSILH-HFPSALPSGARTKDPSGSAQSYCILDC 176 (395)
Q Consensus 100 qLMlsEWl~dvP~dL~--~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~-~F~S~LPgG~~~~~~~~~~~~ytILDC 176 (395)
..||++...++.+.+. .+|++=.==-|-||+++..+|....+||+|.-+. +||-..--... - ..-|||||
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 3588888776554321 3688777778999999999999999999998754 45532210000 0 11289997
Q ss_pred e---eec-C--------------------------CcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCC
Q 016089 177 I---FHE-L--------------------------DQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHY 226 (395)
Q Consensus 177 I---y~e-~--------------------------~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~ 226 (395)
= +.. . .-+|+|.|||..+|.++.+-+..=|.=-|++-+.+.+
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-hHhHHHHHhcCCCCccccEEeEeccccccCCCCCCeeeec
Q 016089 227 YKFRFSTVPVYNCD-QRGLYSAYIESVPYAKDGLLFYNKHAHYQTGNTPLALVWK 280 (395)
Q Consensus 227 n~~~F~~lp~~~c~-~~~L~~~~s~~~p~~~DGLLFYHKea~Y~~G~TPLv~~wK 280 (395)
.-+|...|...++ .+.+..++.....--..|+++-..++.|++|..-- .|||
T Consensus 352 -~~~i~~~~~~~~~~~~e~~~~~~~a~~~g~EGlm~K~~~s~Y~~Grr~~-~WlK 404 (539)
T PRK09247 352 -DPRLDLSPLVPFSDWDELAALRAAARERGVEGLMLKRRDSPYLVGRKKG-PWWK 404 (539)
T ss_pred -CCeEEecCceecCCHHHHHHHHHHHHHCCCceEEEecCCCCcCCCCCcc-hhhc
Confidence 1256677776663 45566666655556689999999999999996532 3555
No 26
>PRK01109 ATP-dependent DNA ligase; Provisional
Probab=97.12 E-value=0.003 Score=68.20 Aligned_cols=165 Identities=16% Similarity=0.179 Sum_probs=111.2
Q ss_pred hhccccccccCCC---CCCCceEEEEecCCcEEEEEeeCCeEEEEcCCCcEE-EeeccCCCCCCCCCCCCCCCCCcEEee
Q 016089 100 QLMLPEWMIDVPD---RLSHDWYVFARPAGKRCIVVSSNGTTVSRERNGSIL-HHFPSALPSGARTKDPSGSAQSYCILD 175 (395)
Q Consensus 100 qLMlsEWl~dvP~---dL~~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l-~~F~S~LPgG~~~~~~~~~~~~ytILD 175 (395)
+-||++....+|+ .++.+|++=.==-|-||+|....|....+||+|.-+ +.||...+--... -...-||||
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 4577776555442 245678765666899999999999999999999754 3565432211000 001238999
Q ss_pred e---eeec-CC-------------------------cEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCC
Q 016089 176 C---IFHE-LD-------------------------QTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHY 226 (395)
Q Consensus 176 C---Iy~e-~~-------------------------~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~ 226 (395)
| +|+. .. -+|||.|||.++|.++.+-+..-|.=-|++-+.+.+
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 3431 11 158999999999999999888888777777664421
Q ss_pred CCCceeccccccCC-hHhHHHHHhcCCCCccccEEeEec--cccccCC-CCCCeeeec
Q 016089 227 YKFRFSTVPVYNCD-QRGLYSAYIESVPYAKDGLLFYNK--HAHYQTG-NTPLALVWK 280 (395)
Q Consensus 227 n~~~F~~lp~~~c~-~~~L~~~~s~~~p~~~DGLLFYHK--ea~Y~~G-~TPLv~~wK 280 (395)
.+...++..++ .+.+.+++.....--..|++.-.. ++.|.+| .+.-|+=+|
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 24556666653 456777776655566889999999 9999999 565443333
No 27
>PRK03180 ligB ATP-dependent DNA ligase; Reviewed
Probab=96.95 E-value=0.006 Score=64.94 Aligned_cols=161 Identities=18% Similarity=0.161 Sum_probs=111.0
Q ss_pred hhccccccccCCCC---CCCceEEEEecCCcEEEEEeeCCeEEEEcCCCcEE-EeeccCCCCCCCCCCCCCCCCCcEEee
Q 016089 100 QLMLPEWMIDVPDR---LSHDWYVFARPAGKRCIVVSSNGTTVSRERNGSIL-HHFPSALPSGARTKDPSGSAQSYCILD 175 (395)
Q Consensus 100 qLMlsEWl~dvP~d---L~~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l-~~F~S~LPgG~~~~~~~~~~~~ytILD 175 (395)
+.||+....++|+. ++.+|++=.==-|-||+|+..+|....+||+|.-+ ++||..+-.- .. ....-+|||
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 4665332100 00 001128888
Q ss_pred eee---ecC--------------------------CcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCC
Q 016089 176 CIF---HEL--------------------------DQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHY 226 (395)
Q Consensus 176 CIy---~e~--------------------------~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~ 226 (395)
|=. .+. .-+||+.|+|.++|.++.+-+..=|.--|.+-+.+.
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-CCCeeeec
Q 016089 227 YKFRFSTVPVYNC-DQRGLYSAYIESVPYAKDGLLFYNKHAHYQTGN-TPLALVWK 280 (395)
Q Consensus 227 n~~~F~~lp~~~c-~~~~L~~~~s~~~p~~~DGLLFYHKea~Y~~G~-TPLv~~wK 280 (395)
..+|...+ +.+.+.+.+.....--..|+..-+.++.|.+|. +..|+=||
T Consensus 330 -----~~~~~~~~~~~~~~~~~~~~a~~~g~EGlm~K~~ds~Y~~GrR~~~WlK~K 380 (508)
T PRK03180 330 -----HRVPRLVTADPAAAAAFLAAALAAGHEGVMVKSLDAPYAAGRRGAGWLKVK 380 (508)
T ss_pred -----ccccceecCCHHHHHHHHHHHHHcCCceEEEeCCCCCcCCCCCCCCcEEEc
Confidence 11233333 466777777666666689999999999999995 56655555
No 28
>PHA00454 ATP-dependent DNA ligase
Probab=96.82 E-value=0.0075 Score=60.27 Aligned_cols=149 Identities=14% Similarity=0.108 Sum_probs=91.6
Q ss_pred CCcEEEEEeeCCe-EEEEcCCCcEEEeeccCC------CCCCCCCCCCCCCCCcEEeeeeeecC----------------
Q 016089 125 AGKRCIVVSSNGT-TVSRERNGSILHHFPSAL------PSGARTKDPSGSAQSYCILDCIFHEL---------------- 181 (395)
Q Consensus 125 vGkRcLVVas~G~-T~ay~k~G~~l~~F~S~L------PgG~~~~~~~~~~~~ytILDCIy~e~---------------- 181 (395)
-|-||++....|. ...+|++|..+....... +.--+. .......=.|||+=..-.
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 000001126788643211
Q ss_pred --------CcEEEEEEEEeeCCccc-c--cccchhhHHHhhhhccccCCCCCCCCCCCCceeccccccC-ChHhHHHHHh
Q 016089 182 --------DQTYYVIDMVCWRGYSL-Y--DCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVYNC-DQRGLYSAYI 249 (395)
Q Consensus 182 --------~~tyYVLDvl~W~g~~l-~--dceteFRffWl~SKl~E~~~~~~~s~~n~~~F~~lp~~~c-~~~~L~~~~s 249 (395)
.-+|||.|+|..+|..- . ++....++-+.+..|++.-. . .....+...|++.| +.+.+.+++.
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 11124778899988 4567777776
Q ss_pred cCCCCccccEEeEeccccccCCCCCCeeeeccC
Q 016089 250 ESVPYAKDGLLFYNKHAHYQTGNTPLALVWKDE 282 (395)
Q Consensus 250 ~~~p~~~DGLLFYHKea~Y~~G~TPLv~~wKD~ 282 (395)
....--..|++.-..++.|.+|.+. .|||=.
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 367644
No 29
>PHA02587 30 DNA ligase; Provisional
Probab=96.75 E-value=0.011 Score=62.62 Aligned_cols=158 Identities=16% Similarity=0.168 Sum_probs=101.4
Q ss_pred ceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEEeeccCCCCCCCCCCCCCCCCCcEEeeeeee---c-------------
Q 016089 117 DWYVFARPAGKRCIVVSSNGTTVSRERNGSILHHFPSALPSGARTKDPSGSAQSYCILDCIFH---E------------- 180 (395)
Q Consensus 117 ~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~~F~S~LPgG~~~~~~~~~~~~ytILDCIy~---e------------- 180 (395)
.|++=.==-|-||+++..+|....|||+|.-++.|+-..+.-......-.....=+|||+=.. .
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 566555567999999999999999999999876553221110000000000001278887331 1
Q ss_pred ----------------------------------CCcEEEEEEEEee---CCcccccccchhhHHHhhhhccccCCCCCC
Q 016089 181 ----------------------------------LDQTYYVIDMVCW---RGYSLYDCTAEFRFFWLNSKLAETGACDAP 223 (395)
Q Consensus 181 ----------------------------------~~~tyYVLDvl~W---~g~~l~dceteFRffWl~SKl~E~~~~~~~ 223 (395)
..-+|||.|+|-+ .|..+.+-+..=|.=.|++-+...+
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 2333556666667666666554111
Q ss_pred CCCCCCceeccccccC-ChHhHHHHHhcCCCCccccEEeEeccccccCCCCCCeeeeccCC
Q 016089 224 SHYYKFRFSTVPVYNC-DQRGLYSAYIESVPYAKDGLLFYNKHAHYQTGNTPLALVWKDEK 283 (395)
Q Consensus 224 s~~n~~~F~~lp~~~c-~~~~L~~~~s~~~p~~~DGLLFYHKea~Y~~G~TPLv~~wKD~~ 283 (395)
.-++.++|...| +.+.+.+++.....--..|++.-+.++.|++|.+.-+++||...
T Consensus 308 ----~~~i~l~~~~~~~~~ee~~~~~~~a~~~G~EGimlK~~ds~Y~~GRs~~WlKiK~~~ 364 (488)
T PHA02587 308 ----YDRVELIENQVVNNLEEAKEIYKRYVDQGLEGIILKNTDGLWEDGRSKDQIKFKEVI 364 (488)
T ss_pred ----CCcEEEEeeEEcCCHHHHHHHHHHHHhCCCCeEEEECCCCCCCCCCCCCcEEecCCC
Confidence 125566777666 45677777766666678999999999999999999888998543
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=96.23 E-value=0.019 Score=51.87 Aligned_cols=133 Identities=20% Similarity=0.199 Sum_probs=81.9
Q ss_pred CceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEEeeccCCCCCCCCCCCCCCCCCcEEeeeeeec---------------
Q 016089 116 HDWYVFARPAGKRCIVVSSNGTTVSRERNGSILHHFPSALPSGARTKDPSGSAQSYCILDCIFHE--------------- 180 (395)
Q Consensus 116 ~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~~F~S~LPgG~~~~~~~~~~~~ytILDCIy~e--------------- 180 (395)
..|++=+==-|-||++. |. .++||+|..+..- ..+.-+ - .. +|||+=..-
T Consensus 16 ~~~~~e~K~DG~R~~~~---~~-~~~SR~g~~~t~~-~~~~~~--------l-~~-~ilDGElv~~~~~f~~l~~~~~~~ 80 (174)
T cd07896 16 SGYLVSEKLDGVRAYWD---GK-QLLSRSGKPIAAP-AWFTAG--------L-PP-FPLDGELWIGRGQFEQTSSIVRSK 80 (174)
T ss_pred HHeeechhhceEEEEEe---cc-EEEecCCcCCCCC-HHHHhh--------C-CC-CccCceEEcCCCCHHHHHHHHhcC
Confidence 46666555569999763 33 8899999875421 111100 0 11 788874432
Q ss_pred -------CCcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCCCCCceeccccccCC-hHhHHHHHhcCC
Q 016089 181 -------LDQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVYNCD-QRGLYSAYIESV 252 (395)
Q Consensus 181 -------~~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~n~~~F~~lp~~~c~-~~~L~~~~s~~~ 252 (395)
..-.|||.|+|. .+. +..=|.=-|.+-+.+.+ .-.|.++|.+.|. .+.+..++....
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 016089 253 PYAKDGLLFYNKHAHYQTGNTPLALVWK 280 (395)
Q Consensus 253 p~~~DGLLFYHKea~Y~~G~TPLv~~wK 280 (395)
.--.+|+++-..++.|++|.+. .|||
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=96.11 E-value=0.13 Score=54.24 Aligned_cols=158 Identities=20% Similarity=0.252 Sum_probs=111.9
Q ss_pred cCCCCCCCceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEE-eecc-------CCCCCCCCCCCCCCCCCcEEeee---e
Q 016089 109 DVPDRLSHDWYVFARPAGKRCIVVSSNGTTVSRERNGSILH-HFPS-------ALPSGARTKDPSGSAQSYCILDC---I 177 (395)
Q Consensus 109 dvP~dL~~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~-~F~S-------~LPgG~~~~~~~~~~~~ytILDC---I 177 (395)
+.|.....+|.+=.==-|-||.+....|....|||+|.-+. +||. .||.. -+|||+ +
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 33444455799888889999999999999999999997654 5662 23322 289996 3
Q ss_pred eec-------------------------CCcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCCCCCcee
Q 016089 178 FHE-------------------------LDQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFS 232 (395)
Q Consensus 178 y~e-------------------------~~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~n~~~F~ 232 (395)
+++ ..-+||+.|+|.-+|+++.+.+..=|--=|.+-+...+. +...
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 ccccccCChHhHHHHHhcCCCCccccEEeEecccccc-CCCCCCeeeeccCCCccce
Q 016089 233 TVPVYNCDQRGLYSAYIESVPYAKDGLLFYNKHAHYQ-TGNTPLALVWKDEKCSQYV 288 (395)
Q Consensus 233 ~lp~~~c~~~~L~~~~s~~~p~~~DGLLFYHKea~Y~-~G~TPLv~~wKD~~~s~y~ 288 (395)
..-.+ -+.+.....+.....--..|++=-++++.|+ .|.+-.|+=||-...-.++
T Consensus 265 ~~i~~-~~~~~~~~~~~~a~~~g~EGvv~K~~ds~Y~~g~R~~~W~K~K~~~~~d~v 320 (444)
T COG1793 265 ERIPF-SDAEEGEAFLEAAIELGLEGVVAKRPDSPYRAGGRSNKWLKVKRDETLDLV 320 (444)
T ss_pred cceec-cChhhHHHHHHHHHhcCceEEEEeCCCCCcCCCCCCCcceEeccCCcccEE
Confidence 11111 3345566666555555689999999999999 5568888888855433333
No 32
>PRK09125 DNA ligase; Provisional
Probab=95.21 E-value=0.15 Score=50.47 Aligned_cols=134 Identities=20% Similarity=0.211 Sum_probs=88.9
Q ss_pred CceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEEeecc----CCCCCCCCCCCCCCCCCcEEeeeeeec-----------
Q 016089 116 HDWYVFARPAGKRCIVVSSNGTTVSRERNGSILHHFPS----ALPSGARTKDPSGSAQSYCILDCIFHE----------- 180 (395)
Q Consensus 116 ~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~~F~S----~LPgG~~~~~~~~~~~~ytILDCIy~e----------- 180 (395)
.+|++=+==-|-||.+ .| +..+||+|..+.. +. .+| -+|||+=..-
T Consensus 43 ~~~~~E~K~DG~R~~~---~~-v~l~SR~g~~it~-p~~~~~~~~--------------~~vLDGElv~~~~~F~~l~~r 103 (282)
T PRK09125 43 SGYLVSEKLDGVRAYW---DG-KQLLTRQGNPIAA-PAWFTAGFP--------------PFPLDGELWAGRGQFEAISSI 103 (282)
T ss_pred hhEEEEeeeeeEeEEE---CC-eEEEcCCCCcCCC-chhHHhcCC--------------CccEeEEEEeCCCCHHHHHHH
Confidence 4777777667999963 34 6789999998643 11 122 1688875431
Q ss_pred -----------CCcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCCCCCceeccccccCC-hHhHHHHH
Q 016089 181 -----------LDQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVYNCD-QRGLYSAY 248 (395)
Q Consensus 181 -----------~~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~n~~~F~~lp~~~c~-~~~L~~~~ 248 (395)
..-+|||.|++..+| +..-|.=-|.+-+.+.+ .-.+..+|+..|+ .+.+.+++
T Consensus 104 ~~~k~~~~~~~~~v~~~vFDll~~~g------pl~eRr~~L~~li~~~~---------~~~i~~~~~~~~~~~~~~~~~~ 168 (282)
T PRK09125 104 VRDKTPDDAAWRKVRFMVFDLPDAPG------DFEERLAVLKKLLAKLP---------SPYIKIIEQIRVRSEAALQQFL 168 (282)
T ss_pred HccCCcchhhhcccEEEEEEcCCCCC------CHHHHHHHHHHHHhhCC---------CCcEEEEeEEEcCCHHHHHHHH
Confidence 123899999997765 44445555666554321 1146778888884 45566666
Q ss_pred hcCCCCccccEEeEeccccccCCCCCCeeeeccCC
Q 016089 249 IESVPYAKDGLLFYNKHAHYQTGNTPLALVWKDEK 283 (395)
Q Consensus 249 s~~~p~~~DGLLFYHKea~Y~~G~TPLv~~wKD~~ 283 (395)
.....--..|+++-+.++.|++|.|.-++=+|...
T Consensus 169 ~~~~~~G~EGiV~K~~ds~Y~~GRs~~wlKiK~~~ 203 (282)
T PRK09125 169 DQIVAAGGEGLMLHRPDAPYEAGRSDDLLKLKPYY 203 (282)
T ss_pred HHHHHcCCCEEEEeCCCCCCcCCCCCCcEEEEecC
Confidence 55555568999999999999999987555555433
No 33
>KOG0966 consensus ATP-dependent DNA ligase IV [Replication, recombination and repair]
Probab=87.51 E-value=2.5 Score=47.70 Aligned_cols=168 Identities=18% Similarity=0.308 Sum_probs=113.5
Q ss_pred hhhhhccccccccCCCCC-CCceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEE-eeccCCCCCCCCCCCCC--------
Q 016089 97 FASQLMLPEWMIDVPDRL-SHDWYVFARPAGKRCIVVSSNGTTVSRERNGSILH-HFPSALPSGARTKDPSG-------- 166 (395)
Q Consensus 97 ya~qLMlsEWl~dvP~dL-~~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~-~F~S~LPgG~~~~~~~~-------- 166 (395)
.|+.-|+.+| ++=+.+ +.+.++=-==-|-|..+.-..|.-.-+++||.=.. .| |-+...+...
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 4555567777 333333 23333333456999999999888888899997533 33 2222111111
Q ss_pred CCCCcEEeeeee---ecC-----------------------CcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCC
Q 016089 167 SAQSYCILDCIF---HEL-----------------------DQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGAC 220 (395)
Q Consensus 167 ~~~~ytILDCIy---~e~-----------------------~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~ 220 (395)
..=.-|||||=+ +.. +-+|-|.|+|..||.++..-+-.-|.+-|++=+.+.+.
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 012348999843 211 25677889999999999999999999999887766432
Q ss_pred CCCCCCCCCceeccccccCC-hHhHHHHHhcCCCCccccEEeEeccccccCCCCCCeeeeccC
Q 016089 221 DAPSHYYKFRFSTVPVYNCD-QRGLYSAYIESVPYAKDGLLFYNKHAHYQTGNTPLALVWKDE 282 (395)
Q Consensus 221 ~~~s~~n~~~F~~lp~~~c~-~~~L~~~~s~~~p~~~DGLLFYHKea~Y~~G~TPLv~~wKD~ 282 (395)
++.++++-.|. .+.+.+.+...+.---.|++.---++.|.+|.- -=+|.|..
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 677777776655555679999999999999987 55677754
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=86.08 E-value=2.8 Score=45.55 Aligned_cols=88 Identities=19% Similarity=0.209 Sum_probs=61.1
Q ss_pred CcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCCCCCceeccccccCChHhHHHHHhcCCCCccccEEe
Q 016089 182 DQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVYNCDQRGLYSAYIESVPYAKDGLLF 261 (395)
Q Consensus 182 ~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~n~~~F~~lp~~~c~~~~L~~~~s~~~p~~~DGLLF 261 (395)
.-+|||.|+|..+|.++.+.+..-|.=-|++-|.+... + .+...+.+..+.+ +++.....--..|++.
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 45899999999999999998888888878777654211 1 1233333444444 3333333344789999
Q ss_pred EeccccccCCCCCCeeeecc
Q 016089 262 YNKHAHYQTGNTPLALVWKD 281 (395)
Q Consensus 262 YHKea~Y~~G~TPLv~~wKD 281 (395)
-+.++.|.+|.|.-|+=+|-
T Consensus 125 K~~dS~Y~~GRs~~WlKlK~ 144 (552)
T TIGR02776 125 KRLDSPYRSGRSKDWLKLKC 144 (552)
T ss_pred eCCCCCCCCCCCcchhcccc
Confidence 99999999999887655553
No 35
>KOG3132 consensus m3G-cap-specific nuclear import receptor (Snurportin1) [RNA processing and modification]
Probab=81.34 E-value=0.68 Score=45.88 Aligned_cols=163 Identities=29% Similarity=0.416 Sum_probs=90.7
Q ss_pred CCCCCCcCCCCCCchHHHHHHHHHHHHHHhH---HHHHHHHhhhhhhhccccC-CCCCCCCCCCCCCCCCccccCCCCcc
Q 016089 3 PPDLRRPFKRTAISDQQRRRELSLQRQSQNR---RDAQQQARCLASSVLSLQS-QYPDPVPELEIEPESQPQQEAGPLTK 78 (395)
Q Consensus 3 ph~~~~~~k~~~~~~Q~~RR~~~Le~Qk~~R---~d~~~~aR~La~~~~~~~~-~~~~~~~e~~~~~~~~e~~~~~~~~~ 78 (395)
||..++|+|+..+.+|.+||+..+-||.|-| .++...||++++. +.++. ..+|.++ + -.+.-.+++-.++.
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 chhhhhhhhccCCCchhhhhhhhccccccccCCCCCCCceEE-EEecCCcEEEEEe-eCCe-EEEEcCCCcEEEeecc--
Q 016089 79 DLDIRQASKLRGPEVRKWFASQLMLPEWMIDVPDRLSHDWYV-FARPAGKRCIVVS-SNGT-TVSRERNGSILHHFPS-- 153 (395)
Q Consensus 79 ~~d~~~~~k~~gk~~rk~ya~qLMlsEWl~dvP~dL~~~Wl~-vpcPvGkRcLVVa-s~G~-T~ay~k~G~~l~~F~S-- 153 (395)
+ .+|...+...+.--+. +..|..+- --| .+|++ ||=-.|.--.||+ .-|+ |-+-.-.|..+..-.+
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 1222222211111111 23343221 123 57875 5666777666665 4443 4455567887765542
Q ss_pred ---CCCCCCCCCCCCCCCCCcEEeeeeeecCCcEEEEEEEEe
Q 016089 154 ---ALPSGARTKDPSGSAQSYCILDCIFHELDQTYYVIDMVC 192 (395)
Q Consensus 154 ---~LPgG~~~~~~~~~~~~ytILDCIy~e~~~tyYVLDvl~ 192 (395)
+.|.-=++ |+.+. ..++.|-|||+|.
T Consensus 147 ~v~rF~S~LPG----Gnrr~---------~~a~~ytILDCIy 175 (325)
T KOG3132|consen 147 TVHRFPSALPG----GNRRK---------GPANSYTILDCIY 175 (325)
T ss_pred eEeeccccCCC----CCcCC---------CCcccceeeeeee
Confidence 12211110 11111 3578999999986
No 36
>COG5226 CEG1 mRNA capping enzyme, guanylyltransferase (alpha) subunit [RNA processing and modification]
Probab=78.33 E-value=4.5 Score=41.51 Aligned_cols=169 Identities=20% Similarity=0.299 Sum_probs=97.3
Q ss_pred CCCceEEEEecCCcEEEEEee--------CCeEEEEcCCCcEEEee-ccCCCCCCCCC--CCCCCCCCcEEeeeeeecC-
Q 016089 114 LSHDWYVFARPAGKRCIVVSS--------NGTTVSRERNGSILHHF-PSALPSGARTK--DPSGSAQSYCILDCIFHEL- 181 (395)
Q Consensus 114 L~~~Wl~vpcPvGkRcLVVas--------~G~T~ay~k~G~~l~~F-~S~LPgG~~~~--~~~~~~~~ytILDCIy~e~- 181 (395)
|..|+++.--.-|-|||+... +|.-.-|-.|=+.++.| +-.+|.-..+- .-.+.-.++-|+||.-.+.
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 477899988899999998653 23333333344445533 32344332110 0112235677788865543
Q ss_pred -CcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCC------CCCCCCCCCceeccccccCChHhHHHHHh--cCC
Q 016089 182 -DQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGAC------DAPSHYYKFRFSTVPVYNCDQRGLYSAYI--ESV 252 (395)
Q Consensus 182 -~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~------~~~s~~n~~~F~~lp~~~c~~~~L~~~~s--~~~ 252 (395)
+-.|-+.|.|..+|+-+...+++=|+=-++--++. +.. ...+...||.|. ++.+.-+ -++..++. ...
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 12344552 133
Q ss_pred CCccccEEeEeccccccCCCCCCeeeeccCCCc
Q 016089 253 PYAKDGLLFYNKHAHYQTGNTPLALVWKDEKCS 285 (395)
Q Consensus 253 p~~~DGLLFYHKea~Y~~G~TPLv~~wKD~~~s 285 (395)
+.--|||+|---++-|+.|.--+.+-||.++-.
T Consensus 217 ~HgnDGLIFTp~~~PY~~Gkd~~lLKWKP~~~N 249 (404)
T COG5226 217 KHGNDGLIFTPADEPYSVGKDGALLKWKPASLN 249 (404)
T ss_pred cCCCCceEeccCCCCcccCccceeeecCccccC
Confidence 456899999999999999999999999998544
No 37
>COG5064 SRP1 Karyopherin (importin) alpha [Intracellular trafficking and secretion]
Probab=65.75 E-value=5 Score=41.95 Aligned_cols=44 Identities=32% Similarity=0.411 Sum_probs=32.4
Q ss_pred CCCCCCcCCCCCCc--hHHHHH--HHHHHHHHHhHHHHHHHHhhhhhh
Q 016089 3 PPDLRRPFKRTAIS--DQQRRR--ELSLQRQSQNRRDAQQQARCLASS 46 (395)
Q Consensus 3 ph~~~~~~k~~~~~--~Q~~RR--~~~Le~Qk~~R~d~~~~aR~La~~ 46 (395)
|.-||.-||.|... +.-+|| +...|..|+||.+.+|+-|+|++.
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 44478899999732 222222 367888999999999999999754
No 38
>PRK04337 50S ribosomal protein L35Ae; Validated
Probab=55.07 E-value=20 Score=30.33 Aligned_cols=36 Identities=22% Similarity=0.398 Sum_probs=26.6
Q ss_pred CCcEEEEEeeCCe------EEEEcCCCcEEEeeccCCCCCCC
Q 016089 125 AGKRCIVVSSNGT------TVSRERNGSILHHFPSALPSGAR 160 (395)
Q Consensus 125 vGkRcLVVas~G~------T~ay~k~G~~l~~F~S~LPgG~~ 160 (395)
+||||.-|...|. |...-.+|-...+|.++||+-+-
T Consensus 39 lGKrv~yvyk~grviwGKItR~HGnsGvVrAkF~~nLP~~a~ 80 (87)
T PRK04337 39 IGRKVIWKDPTGNKYVGKIVRVHGNRGEVRARFKPGLPGQAL 80 (87)
T ss_pred cCceEEEEeCCCCEEEEEEEeeeCCCceEEEEECCCCChHHc
Confidence 4777777765443 45566789999999999998543
No 39
>PF14766 RPA_interact_N: Replication protein A interacting N-terminal
Probab=53.83 E-value=28 Score=25.43 Aligned_cols=38 Identities=21% Similarity=0.205 Sum_probs=31.5
Q ss_pred CCCCcCCC-CCCchHHHHHHHHHHHHHHhHHHHHHHHhh
Q 016089 5 DLRRPFKR-TAISDQQRRRELSLQRQSQNRRDAQQQARC 42 (395)
Q Consensus 5 ~~~~~~k~-~~~~~Q~~RR~~~Le~Qk~~R~d~~~~aR~ 42 (395)
|++++||. +...=.++=|+.-+++-|+.|.++++..|.
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
>PF06257 DUF1021: Protein of unknown function (DUF1021); InterPro: IPR009366 This entry consists of several hypothetical bacterial proteins of unknown function.; PDB: 3FB9_A.
Probab=50.87 E-value=7.9 Score=31.82 Aligned_cols=30 Identities=30% Similarity=0.511 Sum_probs=22.3
Q ss_pred CCcEEEEEeeCCeEEEEcCCCcEEEeeccC
Q 016089 125 AGKRCIVVSSNGTTVSRERNGSILHHFPSA 154 (395)
Q Consensus 125 vGkRcLVVas~G~T~ay~k~G~~l~~F~S~ 154 (395)
+|+|+.|.|++|.-+...+.|-+...|||.
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 799999999999999999999999999874
No 41
>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=49.99 E-value=21 Score=30.56 Aligned_cols=36 Identities=31% Similarity=0.423 Sum_probs=24.1
Q ss_pred CCcEEEEEee--------CCe------EEEEcCCCcEEEeeccCCCCCCC
Q 016089 125 AGKRCIVVSS--------NGT------TVSRERNGSILHHFPSALPSGAR 160 (395)
Q Consensus 125 vGkRcLVVas--------~G~------T~ay~k~G~~l~~F~S~LPgG~~ 160 (395)
.||||.-|.. ++. |.+.-.+|-...+|.++||+-.-
T Consensus 39 lGKrv~yvyk~~~~~~~~k~r~iwGkV~r~HGnsGvVrAkF~~nLP~~a~ 88 (95)
T PF01247_consen 39 LGKRVAYVYKAKNKKNGSKGRVIWGKVTRPHGNSGVVRAKFKKNLPPQAI 88 (95)
T ss_dssp TT-EEEEEECE-SSSTTECSEEEEEEEEEESTTTTEEEEEESS--STTGC
T ss_pred cCcEEEEEEecccccCCCcEeEEEEEEEeEEcCCCEEEEEeCCCCChHHc
Confidence 5888888764 332 44557799999999999998643
No 42
>KOG0275 consensus Conserved WD40 repeat-containing protein [General function prediction only]
Probab=45.46 E-value=34 Score=35.66 Aligned_cols=54 Identities=28% Similarity=0.458 Sum_probs=0.0
Q ss_pred cCCcEEEEEeeCCeEEEE-cCCCcEEEeeccCCCCCCCCCCCCCCCCCcEEeeeeeecCC----------cEEEEEEE
Q 016089 124 PAGKRCIVVSSNGTTVSR-ERNGSILHHFPSALPSGARTKDPSGSAQSYCILDCIFHELD----------QTYYVIDM 190 (395)
Q Consensus 124 PvGkRcLVVas~G~T~ay-~k~G~~l~~F~S~LPgG~~~~~~~~~~~~ytILDCIy~e~~----------~tyYVLDv 190 (395)
+.|.+.+--++.|+.+++ .|.+-|+.+|. |+| .+|+|+-.|.-..+ +|.||+.+
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 43
>PTZ00041 60S ribosomal protein L35a; Provisional
Probab=44.08 E-value=28 Score=31.05 Aligned_cols=36 Identities=31% Similarity=0.406 Sum_probs=27.0
Q ss_pred CCcEEEEEeeC-------------C-eEEEEcCCCcEEEeeccCCCCCCC
Q 016089 125 AGKRCIVVSSN-------------G-TTVSRERNGSILHHFPSALPSGAR 160 (395)
Q Consensus 125 vGkRcLVVas~-------------G-~T~ay~k~G~~l~~F~S~LPgG~~ 160 (395)
+||||.-|..- | .|...-.+|-+..+|.++||+-+-
T Consensus 58 lGKrvayvyka~~~~~~~k~RviwGKVtR~HGnsGvVrAkF~~nLPp~A~ 107 (120)
T PTZ00041 58 LGKRVAYVYKAKKLKNGTKFRAIWGKITRPHGNSGVVRARFNKNLPPKAI 107 (120)
T ss_pred ccceEEEEEcCccccCCcceeEEEEEEEcccCCCcEEEEEeCCCCChHHc
Confidence 59999888632 3 244556789999999999999643
No 44
>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=42.80 E-value=3.9 Score=34.42 Aligned_cols=44 Identities=23% Similarity=0.421 Sum_probs=30.9
Q ss_pred CCCCCCcCCCCCCchHHHHH---HHHHHHHHHhHHHHHHHHhhhhhh
Q 016089 3 PPDLRRPFKRTAISDQQRRR---ELSLQRQSQNRRDAQQQARCLASS 46 (395)
Q Consensus 3 ph~~~~~~k~~~~~~Q~~RR---~~~Le~Qk~~R~d~~~~aR~La~~ 46 (395)
+..|+..||.++....+-|| +..++..|++|.+.+..-|++...
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 45
>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=41.40 E-value=46 Score=29.01 Aligned_cols=44 Identities=18% Similarity=0.305 Sum_probs=31.0
Q ss_pred cEEeee--eeecCCcEEEEEEEEeeCCcc----cccccchhhHHHhhhhcccc
Q 016089 171 YCILDC--IFHELDQTYYVIDMVCWRGYS----LYDCTAEFRFFWLNSKLAET 217 (395)
Q Consensus 171 ytILDC--Iy~e~~~tyYVLDvl~W~g~~----l~dceteFRffWl~SKl~E~ 217 (395)
-||+++ .+...+...|++.|. |+|.. +|-.-.| |+=||.||.|.
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 46
>KOG2618 consensus Uncharacterized conserved protein [Function unknown]
Probab=40.20 E-value=69 Score=33.14 Aligned_cols=82 Identities=16% Similarity=0.264 Sum_probs=48.7
Q ss_pred CCceEEEEecCCcEEEEEeeCCe---EEEEcCCCcEEEeeccCCCCCCCCCCCCCCCCCcEEeeeeeecCCcEEEEEEEE
Q 016089 115 SHDWYVFARPAGKRCIVVSSNGT---TVSRERNGSILHHFPSALPSGARTKDPSGSAQSYCILDCIFHELDQTYYVIDMV 191 (395)
Q Consensus 115 ~~~Wl~vpcPvGkRcLVVas~G~---T~ay~k~G~~l~~F~S~LPgG~~~~~~~~~~~~ytILDCIy~e~~~tyYVLDvl 191 (395)
+..-+.+|||.| ||+|++..-. |+ -++.--.+..|. .|-. -----|.||.=.|.-.+.|-.-||
T Consensus 110 Esksfrrpl~Kg-RCvVl~dGfyEWkt~-gskkqpYfI~f~----dgRl-------L~mAglfD~wE~egGD~LYtfTII 176 (366)
T KOG2618|consen 110 ESKSFRRPLEKG-RCVVLMDGFYEWKTV-GSKKQPYFISFR----DGRL-------LFMAGLFDYWEKEGGDDLYTFTII 176 (366)
T ss_pred hhhhhhccCCCC-cEEEEecceeeeeec-cccCCceEEEEe----cCce-------eEeeeehheecccCCceeEEEEEE
Confidence 345568899999 9999986432 11 111111122221 0000 000137888887777899988888
Q ss_pred eeCCcccccccchhhHHHhhhhcccc
Q 016089 192 CWRGYSLYDCTAEFRFFWLNSKLAET 217 (395)
Q Consensus 192 ~W~g~~l~dceteFRffWl~SKl~E~ 217 (395)
--.+-. -+-|||-|+.-.
T Consensus 177 T~qssk--------~LswlH~RMPaI 194 (366)
T KOG2618|consen 177 TAQSSK--------ELSWLHERMPAI 194 (366)
T ss_pred EecCch--------HhHHHHhhCcee
Confidence 766543 267999998754
No 47
>KOG0296 consensus Angio-associated migratory cell protein (contains WD40 repeats) [Function unknown]
Probab=36.50 E-value=85 Score=33.06 Aligned_cols=53 Identities=21% Similarity=0.165 Sum_probs=37.6
Q ss_pred ecCCcEEEEEeeCCeEEEE-cCCCcEEEeeccCCCCCCCCCCCCCCCCCcEEeeee
Q 016089 123 RPAGKRCIVVSSNGTTVSR-ERNGSILHHFPSALPSGARTKDPSGSAQSYCILDCI 177 (395)
Q Consensus 123 cPvGkRcLVVas~G~T~ay-~k~G~~l~~F~S~LPgG~~~~~~~~~~~~ytILDCI 177 (395)
.|-|||.+....+|+.++. .|.|..+++..+.= ++.. .-.+-+..+.|+++|-
T Consensus 199 ~pdGKr~~tgy~dgti~~Wn~ktg~p~~~~~~~e-~~~~-~~~~~~~~~~~~~~g~ 252 (399)
T KOG0296|consen 199 IPDGKRILTGYDDGTIIVWNPKTGQPLHKITQAE-GLEL-PCISLNLAGSTLTKGN 252 (399)
T ss_pred cCCCceEEEEecCceEEEEecCCCceeEEecccc-cCcC-CccccccccceeEecc
Confidence 4789999999999999999 78999999887553 1110 0122234566888874
No 48
>KOG0887 consensus 60S ribosomal protein L35A/L37 [Translation, ribosomal structure and biogenesis]
Probab=30.65 E-value=57 Score=28.68 Aligned_cols=39 Identities=36% Similarity=0.658 Sum_probs=28.0
Q ss_pred CceEEEEecCCcEEEEEee-----C--------C-eEEEEcCCCcEEEeeccCCCCCC
Q 016089 116 HDWYVFARPAGKRCIVVSS-----N--------G-TTVSRERNGSILHHFPSALPSGA 159 (395)
Q Consensus 116 ~~Wl~vpcPvGkRcLVVas-----~--------G-~T~ay~k~G~~l~~F~S~LPgG~ 159 (395)
.+|| .||||..|.. + | .|.+--.+|-+-.+|.|+||.-.
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 4999888863 1 2 24445678888999999999853
No 49
>KOG1136 consensus Predicted cleavage and polyadenylation specificity factor (CPSF subunit) [RNA processing and modification]
Probab=30.06 E-value=77 Score=33.40 Aligned_cols=53 Identities=19% Similarity=0.358 Sum_probs=30.9
Q ss_pred cCCcEEEEEeeCCeEEEEcCCCcEEEeeccCCCCCCCCCCCCCCCCCcE-Eeeeeeec
Q 016089 124 PAGKRCIVVSSNGTTVSRERNGSILHHFPSALPSGARTKDPSGSAQSYC-ILDCIFHE 180 (395)
Q Consensus 124 PvGkRcLVVas~G~T~ay~k~G~~l~~F~S~LPgG~~~~~~~~~~~~yt-ILDCIy~e 180 (395)
-+|+-|++|+-+|+++...-.=..=.+=.-+.|..|.- + ++..+| .||||...
T Consensus 14 dvGrSCilvsi~Gk~iM~DCGMHMG~nD~rRfPdFSyI---~-~~g~~~~~idCvIIs 67 (501)
T KOG1136|consen 14 DVGRSCILVSIGGKNIMFDCGMHMGFNDDRRFPDFSYI---S-KSGRFTDAIDCVIIS 67 (501)
T ss_pred ccCceEEEEEECCcEEEEecccccccCccccCCCceee---c-CCCCcccceeEEEEe
Confidence 37899999999999998764322111111123444331 1 123344 89999863
No 50
>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=29.26 E-value=1.4e+02 Score=29.41 Aligned_cols=45 Identities=24% Similarity=0.605 Sum_probs=30.3
Q ss_pred CCCCCceE--EEEecCCcEEEEEeeCCeEEEEcCCC-cEEEeeccCCCCCC
Q 016089 112 DRLSHDWY--VFARPAGKRCIVVSSNGTTVSRERNG-SILHHFPSALPSGA 159 (395)
Q Consensus 112 ~dL~~~Wl--~vpcPvGkRcLVVas~G~T~ay~k~G-~~l~~F~S~LPgG~ 159 (395)
..+..+|| +...|-| +.+|.+.++ +++++..+ .++..|| .||||.
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 699984
No 51
>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=27.13 E-value=21 Score=36.35 Aligned_cols=82 Identities=17% Similarity=0.293 Sum_probs=57.2
Q ss_pred CCcEEEEEeeCCeEEEEcCCCcEEEeeccCCCCCCCCCCCCCCCCCcEEeeeeeecCCcEEEEEEEEeeCCcccccccch
Q 016089 125 AGKRCIVVSSNGTTVSRERNGSILHHFPSALPSGARTKDPSGSAQSYCILDCIFHELDQTYYVIDMVCWRGYSLYDCTAE 204 (395)
Q Consensus 125 vGkRcLVVas~G~T~ay~k~G~~l~~F~S~LPgG~~~~~~~~~~~~ytILDCIy~e~~~tyYVLDvl~W~g~~l~dcete 204 (395)
.|+.|+++|+-|.+..--.+|..+|+|- .||-+... ...+=+ ..-......+.-+|+|.|...+|..+.+
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 6899999999998776666999999887 46655321 000100 0011224677788999999999998876
Q ss_pred hhHHHhhhhccccC
Q 016089 205 FRFFWLNSKLAETG 218 (395)
Q Consensus 205 FRffWl~SKl~E~~ 218 (395)
|.|++.+|...-
T Consensus 119 --l~~i~~~lr~i~ 130 (364)
T PF05970_consen 119 --LDAIDRRLRDIR 130 (364)
T ss_pred --HHHHHHhhhhhh
Confidence 778888887653
No 52
>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=26.98 E-value=2.4e+02 Score=29.14 Aligned_cols=77 Identities=14% Similarity=0.105 Sum_probs=49.1
Q ss_pred CCCCceEEEEecCCcEEEEEeeCCeEEEEcCCCcEE----EeeccCCCCCCCCCCCCCCCCCcEEeeeeee---------
Q 016089 113 RLSHDWYVFARPAGKRCIVVSSNGTTVSRERNGSIL----HHFPSALPSGARTKDPSGSAQSYCILDCIFH--------- 179 (395)
Q Consensus 113 dL~~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l----~~F~S~LPgG~~~~~~~~~~~~ytILDCIy~--------- 179 (395)
.+...|++-.==-|-|+-|...+|...++|++|.+. .+++..+|..--. ...+ .|||+=+.
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-----DHPD-LVLCGEVVGPENPYVPG 118 (342)
T ss_pred cCCCCEEEEEeECCcEEEEEEECCEEEEEeCCCccCccchhhHhhhchHHhhc-----cCCC-EEEEEEEEecCCccccc
Confidence 334578876666799999988899999999999865 2333333322100 0011 66774311
Q ss_pred ----cCCcEEEEEEEEeeCC
Q 016089 180 ----ELDQTYYVIDMVCWRG 195 (395)
Q Consensus 180 ----e~~~tyYVLDvl~W~g 195 (395)
...-+|||.||+..++
T Consensus 119 ~~~~~~~v~F~vFDI~~~~~ 138 (342)
T cd07894 119 SYPEVEDVGFFVFDIRKKNT 138 (342)
T ss_pred cCccccccEEEEEeeEEcCC
Confidence 1256999999998764
No 53
>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=26.19 E-value=52 Score=26.12 Aligned_cols=16 Identities=31% Similarity=0.829 Sum_probs=14.3
Q ss_pred CceEEEEecCCcEEEE
Q 016089 116 HDWYVFARPAGKRCIV 131 (395)
Q Consensus 116 ~~Wl~vpcPvGkRcLV 131 (395)
..|++.+||.|--||-
T Consensus 43 G~Wv~~~C~~Gt~C~~ 58 (61)
T PF03427_consen 43 GTWVITPCPAGTTCFA 58 (61)
T ss_pred CcEEEeeCCCCCEEee
Confidence 6999999999998874
No 54
>KOG0166 consensus Karyopherin (importin) alpha [Intracellular trafficking, secretion, and vesicular transport]
Probab=25.77 E-value=41 Score=36.65 Aligned_cols=38 Identities=21% Similarity=0.353 Sum_probs=30.3
Q ss_pred CCCCCcCCCCCCchHHHHH----HHHHHHHHHhHHHHHHHHhh
Q 016089 4 PDLRRPFKRTAISDQQRRR----ELSLQRQSQNRRDAQQQARC 42 (395)
Q Consensus 4 h~~~~~~k~~~~~~Q~~RR----~~~Le~Qk~~R~d~~~~aR~ 42 (395)
|.+++.||.+. -+|+++| +...|..|+||.+.+.+-|+
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 55
>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=25.61 E-value=1.8e+02 Score=25.75 Aligned_cols=19 Identities=42% Similarity=0.994 Sum_probs=14.2
Q ss_pred eeCCcccccccchhhHHHh
Q 016089 192 CWRGYSLYDCTAEFRFFWL 210 (395)
Q Consensus 192 ~W~g~~l~dceteFRffWl 210 (395)
.|++.+..+...+|+|+|+
T Consensus 90 ~~~~~~~~~E~~~i~~~Wv 108 (126)
T cd04663 90 SWVHFVQDDGGHEFRFFWV 108 (126)
T ss_pred cccCcccCCCCceEEEEEE
Confidence 5777777777777888887
No 56
>PF02210 Laminin_G_2: Laminin G domain; InterPro: IPR012680 Laminins are large heterotrimeric glycoproteins involved in basement membrane function []. The laminin globular (G) domain can be found in one to several copies in various laminin family members, including a large number of extracellular proteins. The C terminus of the laminin alpha chain contains a tandem repeat of five laminin G domains, which are critical for heparin-binding and cell attachment activity []. Laminin alpha4 is distributed in a variety of tissues including peripheral nerves, dorsal root ganglion, skeletal muscle and capillaries; in the neuromuscular junction, it is required for synaptic specialisation []. The structure of the laminin-G domain has been predicted to resemble that of pentraxin []. Laminin G domains can vary in their function, and a variety of binding functions have been ascribed to different LamG modules. For example, the laminin alpha1 and alpha2 chains each have five C-teminal laminin G domains, where only domains LG4 and LG5 contain binding sites for heparin, sulphatides and the cell surface receptor dystroglycan []. Laminin G-containing proteins appear to have a wide variety of roles in cell adhesion, signalling, migration, assembly and differentiation. This entry represents one subtype of laminin G domains, which is sometimes found in association with thrombospondin-type laminin G domains (IPR012679 from INTERPRO).; PDB: 3POY_A 3QCW_B 3R05_B 3ASI_A 3MW4_B 3MW3_A 1QU0_D 1DYK_A 1OKQ_A 3SH4_A ....
Probab=20.88 E-value=4.4e+02 Score=21.04 Aligned_cols=91 Identities=16% Similarity=0.133 Sum_probs=45.8
Q ss_pred CccccEEeEeccccc--------cCCCCCCeeeeccCCCccceeecCCCCCccccceEEEEEccCCceeccCCCCeEEee
Q 016089 254 YAKDGLLFYNKHAHY--------QTGNTPLALVWKDEKCSQYVIDTDSKGQVLSQQQVVLELQEDGKLSTSDDPPVIFGC 325 (395)
Q Consensus 254 ~~~DGLLFYHKea~Y--------~~G~TPLv~~wKD~~~s~y~~d~d~~g~~~~~q~vvL~~~~~g~l~T~D~~pv~~~~ 325 (395)
...||+|||....+. ..|. |+..|+........+.....=.-..+..|.+......--.+-|+.++....
T Consensus 4 ~~~~g~Ll~~~~~~~~~~l~l~l~~g~--l~~~~~~g~~~~~~~~~~~~~~dg~wh~v~i~~~~~~~~l~Vd~~~~~~~~ 81 (128)
T PF02210_consen 4 RSPNGLLLYIGSEDNGDFLSLELVDGR--LVVRYNLGGSEIVTTFSNSNLNDGQWHKVSISRDGNRVTLTVDGQSVSSES 81 (128)
T ss_dssp SSSSEEEEEEEESTTSEEEEEEEETTE--EEEEEESSSSEEEEEECSSSSTSSSEEEEEEEEETTEEEEEETTSEEEEEE
T ss_pred CCCCEeEEEEcCCCCCEEEEEEEECCE--EEEEEEccccceeeeccCccccccceeEEEEEEeeeeEEEEecCccceEEe
Confidence 357999999998887 2222 445555442222222211110111245566666555545667776666655
Q ss_pred cchhhhhhccccCeEEeccCC
Q 016089 326 LDGEFIQKLEKSDLNYLGKSN 346 (395)
Q Consensus 326 ~~~~~~~~~~~~dl~~~~~~~ 346 (395)
.+......+...+--|+|-.+
T Consensus 82 ~~~~~~~~~~~~~~l~iGg~~ 102 (128)
T PF02210_consen 82 LPSSSSDSLDPDGSLYIGGLP 102 (128)
T ss_dssp SSSTTHHCBESEEEEEESSTT
T ss_pred ccccceecccCCCCEEEeccc
Confidence 544332233333446666444
No 57
>KOG2923 consensus Uncharacterized conserved protein [Function unknown]
Probab=20.46 E-value=1.6e+02 Score=23.86 Aligned_cols=19 Identities=21% Similarity=0.525 Sum_probs=14.7
Q ss_pred CCCceEEEEecCCcEEEEEe
Q 016089 114 LSHDWYVFARPAGKRCIVVS 133 (395)
Q Consensus 114 L~~~Wl~vpcPvGkRcLVVa 133 (395)
.+.+-+-.|||-|-| +.|+
T Consensus 16 ~e~~~y~yPCpCGDr-f~It 34 (67)
T KOG2923|consen 16 EENQTYYYPCPCGDR-FQIT 34 (67)
T ss_pred cCCCeEEcCCCCCCe-eeec
Confidence 356778899999999 5555
No 58
>KOG3390 consensus General control of amino-acid synthesis 5-like 1 [Transcription]
Probab=20.44 E-value=1.3e+02 Score=26.55 Aligned_cols=28 Identities=32% Similarity=0.466 Sum_probs=22.8
Q ss_pred chHHHHHHHHHHHHHHhHHHHHHHHhhhhhhh
Q 016089 16 SDQQRRRELSLQRQSQNRRDAQQQARCLASSV 47 (395)
Q Consensus 16 ~~Q~~RR~~~Le~Qk~~R~d~~~~aR~La~~~ 47 (395)
..|.+|| |.|.+.|.+.+-+|-+|++..
T Consensus 11 ~kq~eRr----elqEK~r~EAI~aA~~l~~al 38 (120)
T KOG3390|consen 11 EKQSERR----ELQEKTRKEAIRAAARLADAL 38 (120)
T ss_pred HHHHHHH----HHHHHHHHHHHHHHHHHHHHH
Confidence 3588888 667778999999999999754
No 59
>KOG1274 consensus WD40 repeat protein [General function prediction only]
Probab=20.18 E-value=1.8e+02 Score=33.84 Aligned_cols=50 Identities=22% Similarity=0.232 Sum_probs=40.0
Q ss_pred ccccccCCCCCCCceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEEeeccCCC
Q 016089 104 PEWMIDVPDRLSHDWYVFARPAGKRCIVVSSNGTTVSRERNGSILHHFPSALP 156 (395)
Q Consensus 104 sEWl~dvP~dL~~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~~F~S~LP 156 (395)
+||-..+|.. ++=..|.|--| +++|.++.|..++.+..|....-|....|
T Consensus 515 seWtm~lP~~--E~~~~V~~t~~-~Vav~TS~~~lRvFt~gGvq~~I~t~~gP 564 (933)
T KOG1274|consen 515 SEWTMILPLQ--ESIEAVAATSG-WVAVATSLGYLRVFTIGGVQREIFTLPGP 564 (933)
T ss_pred cceeeecCCC--CceeEEEccCc-EEEEEeccceEEEEEecceeeeEeecccc
Confidence 6999999987 45555556555 88999999999999999999999954444
Done!