Query psy1520
Match_columns 107
No_of_seqs 177 out of 1019
Neff 4.1
Searched_HMMs 46136
Date Fri Aug 16 23:14:27 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy1520.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/1520hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0435|consensus 100.0 1.9E-38 4.2E-43 279.2 5.5 92 14-105 506-597 (876)
2 COG0495 LeuS Leucyl-tRNA synth 100.0 2.9E-36 6.3E-41 267.9 3.2 92 12-103 502-596 (814)
3 PLN02563 aminoacyl-tRNA ligase 100.0 6.3E-33 1.4E-37 249.4 4.1 70 14-83 595-664 (963)
4 TIGR00396 leuS_bact leucyl-tRN 100.0 5.3E-31 1.1E-35 233.4 4.3 90 14-103 499-621 (842)
5 PRK00390 leuS leucyl-tRNA synt 99.9 8.4E-27 1.8E-31 205.5 4.5 85 14-103 502-587 (805)
6 PF00133 tRNA-synt_1: tRNA syn 99.5 9.7E-15 2.1E-19 125.3 1.4 72 26-103 505-578 (601)
7 cd00812 LeuRS_core catalytic c 99.4 2.3E-13 4.9E-18 108.3 3.1 77 26-103 215-292 (314)
8 PRK12300 leuS leucyl-tRNA synt 99.3 3.1E-13 6.8E-18 121.1 2.2 71 27-103 522-594 (897)
9 PLN02959 aminoacyl-tRNA ligase 99.3 7.4E-13 1.6E-17 121.1 3.2 70 28-103 664-735 (1084)
10 PTZ00419 valyl-tRNA synthetase 99.3 4E-12 8.7E-17 114.8 4.6 70 27-102 530-601 (995)
11 PLN02381 valyl-tRNA synthetase 99.3 3.4E-12 7.4E-17 116.7 3.9 73 24-102 597-671 (1066)
12 PRK13208 valS valyl-tRNA synth 99.2 6E-12 1.3E-16 111.0 3.6 74 24-103 475-550 (800)
13 TIGR00392 ileS isoleucyl-tRNA 99.2 5.3E-12 1.2E-16 111.9 3.3 72 26-103 555-628 (861)
14 PRK05743 ileS isoleucyl-tRNA s 99.2 3.2E-12 7E-17 114.8 1.5 66 32-103 542-609 (912)
15 PRK14900 valS valyl-tRNA synth 99.1 3.2E-11 7E-16 110.1 2.6 70 28-103 484-555 (1052)
16 TIGR00395 leuS_arch leucyl-tRN 99.1 4.7E-11 1E-15 107.7 1.9 70 28-103 566-637 (938)
17 PRK06039 ileS isoleucyl-tRNA s 99.1 5E-11 1.1E-15 107.7 1.7 70 27-103 537-609 (975)
18 PTZ00427 isoleucine-tRNA ligas 98.8 2.3E-09 4.9E-14 99.7 3.3 72 26-103 664-737 (1205)
19 PRK13804 ileS isoleucyl-tRNA s 98.8 1.9E-09 4.1E-14 97.8 2.0 65 33-103 581-647 (961)
20 cd00817 ValRS_core catalytic c 98.7 4.6E-09 9.9E-14 86.0 2.3 70 28-103 289-360 (382)
21 TIGR00422 valS valyl-tRNA synt 98.7 6E-09 1.3E-13 92.8 2.9 69 28-102 471-541 (861)
22 PRK05729 valS valyl-tRNA synth 98.7 5.5E-09 1.2E-13 93.4 2.3 71 27-103 465-537 (874)
23 cd00668 Ile_Leu_Val_MetRS_core 98.7 1.5E-08 3.2E-13 80.0 3.3 69 29-103 220-290 (312)
24 PLN02943 aminoacyl-tRNA ligase 98.6 2.2E-08 4.7E-13 91.0 2.8 70 27-103 528-600 (958)
25 COG0060 IleS Isoleucyl-tRNA sy 98.6 1.5E-08 3.3E-13 92.6 0.6 66 32-103 549-619 (933)
26 PLN02882 aminoacyl-tRNA ligase 98.5 6.7E-08 1.4E-12 89.6 3.5 70 28-103 560-631 (1159)
27 PLN02843 isoleucyl-tRNA synthe 98.5 3.4E-08 7.4E-13 90.0 1.3 66 31-102 560-627 (974)
28 cd00818 IleRS_core catalytic c 98.4 8.8E-08 1.9E-12 77.3 2.1 69 29-103 246-316 (338)
29 KOG0433|consensus 98.3 2.2E-07 4.9E-12 84.3 1.3 64 34-103 565-630 (937)
30 PRK11893 methionyl-tRNA synthe 98.3 3.7E-07 8.1E-12 75.7 2.1 68 29-103 248-316 (511)
31 PRK12267 methionyl-tRNA synthe 98.0 2.4E-06 5.2E-11 74.1 2.3 66 31-103 250-316 (648)
32 TIGR00398 metG methionyl-tRNA 98.0 4.2E-06 9.1E-11 70.5 2.9 68 29-103 271-344 (530)
33 cd00814 MetRS_core catalytic c 97.8 1.9E-05 4.1E-10 63.0 3.4 64 33-103 233-297 (319)
34 cd00672 CysRS_core catalytic c 97.7 1.4E-05 2.9E-10 61.7 1.8 62 35-103 128-191 (213)
35 TIGR00435 cysS cysteinyl-tRNA 97.5 4.1E-05 8.9E-10 64.9 1.7 63 35-103 219-282 (465)
36 PRK12268 methionyl-tRNA synthe 97.5 8E-05 1.7E-09 63.2 2.7 64 35-103 287-351 (556)
37 PRK00260 cysS cysteinyl-tRNA s 97.4 5.2E-05 1.1E-09 64.0 0.8 62 35-103 220-283 (463)
38 COG0525 ValS Valyl-tRNA synthe 97.3 0.00014 3E-09 66.9 2.9 70 28-103 471-542 (877)
39 PRK12418 cysteinyl-tRNA synthe 97.3 9.7E-05 2.1E-09 62.0 1.2 64 35-104 214-279 (384)
40 PRK00133 metG methionyl-tRNA s 97.0 0.00042 9.2E-09 60.8 2.6 59 38-103 287-346 (673)
41 TIGR03447 mycothiol_MshC cyste 97.0 0.00031 6.8E-09 59.6 1.4 62 36-103 242-305 (411)
42 PLN02224 methionine-tRNA ligas 96.9 0.00047 1E-08 60.9 2.3 66 31-103 317-383 (616)
43 KOG0432|consensus 96.3 0.0021 4.6E-08 59.7 2.2 67 30-102 541-609 (995)
44 PRK00750 lysK lysyl-tRNA synth 96.2 0.0035 7.5E-08 54.0 2.7 72 23-102 220-296 (510)
45 PTZ00399 cysteinyl-tRNA-synthe 96.1 0.0017 3.8E-08 57.6 0.6 63 35-103 268-332 (651)
46 PF09334 tRNA-synt_1g: tRNA sy 94.9 0.011 2.3E-07 49.3 1.1 58 38-102 285-343 (391)
47 cd00674 LysRS_core_class_I cat 94.9 0.012 2.7E-07 49.0 1.4 74 22-103 212-292 (353)
48 PRK01611 argS arginyl-tRNA syn 94.9 0.013 2.8E-07 50.0 1.5 59 38-103 276-339 (507)
49 TIGR00456 argS arginyl-tRNA sy 94.3 0.042 9.1E-07 47.6 3.2 56 38-102 331-388 (566)
50 KOG0437|consensus 94.2 0.0068 1.5E-07 56.3 -1.8 69 28-101 656-725 (1080)
51 PF01406 tRNA-synt_1e: tRNA sy 94.0 0.036 7.8E-07 45.7 2.3 61 35-102 206-268 (300)
52 PRK14536 cysS cysteinyl-tRNA s 93.8 0.035 7.6E-07 48.2 1.9 61 36-103 234-296 (490)
53 COG0143 MetG Methionyl-tRNA sy 93.2 0.063 1.4E-06 47.5 2.5 69 28-103 277-350 (558)
54 PRK14534 cysS cysteinyl-tRNA s 93.1 0.052 1.1E-06 47.1 1.9 64 33-103 231-296 (481)
55 PLN02946 cysteine-tRNA ligase 92.7 0.04 8.6E-07 48.7 0.5 62 35-103 277-340 (557)
56 KOG0436|consensus 90.1 0.21 4.6E-06 44.2 2.3 68 28-102 292-360 (578)
57 KOG0434|consensus 90.0 0.066 1.4E-06 49.8 -0.8 73 25-103 544-618 (1070)
58 PLN02610 probable methionyl-tR 89.7 0.29 6.3E-06 44.7 3.0 60 38-102 304-364 (801)
59 PF00750 tRNA-synt_1d: tRNA sy 86.7 0.15 3.2E-06 41.8 -0.8 60 38-102 242-304 (354)
60 PRK14535 cysS cysteinyl-tRNA s 86.6 0.26 5.6E-06 45.0 0.6 69 35-103 446-525 (699)
61 cd00802 class_I_aaRS_core cata 83.2 2.5 5.4E-05 29.6 4.3 45 36-88 94-139 (143)
62 PRK12451 arginyl-tRNA syntheta 81.9 0.78 1.7E-05 40.0 1.5 59 38-102 328-387 (562)
63 PF10910 DUF2744: Protein of u 81.8 1.3 2.8E-05 32.7 2.5 81 10-99 2-88 (125)
64 PLN02286 arginine-tRNA ligase 76.3 1.5 3.3E-05 38.5 1.6 60 38-102 331-394 (576)
65 PF01479 S4: S4 domain; Inter 73.3 3.3 7.1E-05 24.0 2.1 45 57-101 4-48 (48)
66 COG0018 ArgS Arginyl-tRNA synt 67.8 5.4 0.00012 35.5 3.1 58 38-102 338-399 (577)
67 TIGR00467 lysS_arch lysyl-tRNA 57.3 6.1 0.00013 34.7 1.5 76 22-103 210-291 (515)
68 PF00579 tRNA-synt_1b: tRNA sy 51.7 31 0.00067 27.1 4.5 59 34-97 148-210 (292)
69 COG0215 CysS Cysteinyl-tRNA sy 50.2 4.4 9.5E-05 35.6 -0.5 63 35-103 221-285 (464)
70 PF08199 E2: Bacteriophage E2- 43.1 13 0.00029 22.1 1.0 19 48-67 3-21 (37)
71 cd00805 TyrRS_core catalytic c 42.4 46 0.001 26.3 4.2 52 35-95 151-204 (269)
72 PF02844 GARS_N: Phosphoribosy 39.1 14 0.0003 26.0 0.7 9 41-49 9-17 (100)
73 cd06603 GH31_GANC_GANAB_alpha 37.5 44 0.00096 27.0 3.5 32 31-62 170-202 (339)
74 PF12496 BNIP2: Bcl2-/adenovir 36.2 13 0.00029 27.3 0.3 12 68-79 110-121 (127)
75 PF01837 DUF39: Domain of unkn 35.8 18 0.00038 30.8 0.9 12 36-47 71-82 (340)
76 COG0377 NuoB NADH:ubiquinone o 31.6 19 0.00041 28.5 0.5 16 28-43 127-142 (194)
77 PF07218 RAP1: Rhoptry-associa 31.3 26 0.00056 32.4 1.3 48 10-68 25-72 (782)
78 PF01560 HCV_NS1: Hepatitis C 30.5 17 0.00036 30.9 0.0 12 35-46 243-254 (344)
79 PF09318 DUF1975: Domain of un 29.9 41 0.0009 24.3 2.0 27 40-66 13-55 (203)
80 PF13275 S4_2: S4 domain; PDB: 26.2 35 0.00077 22.3 1.0 47 56-102 10-56 (65)
81 COG0522 RpsD Ribosomal protein 25.5 1E+02 0.0022 24.2 3.5 54 47-101 88-141 (205)
82 PRK08560 tyrosyl-tRNA syntheta 25.4 1E+02 0.0022 25.1 3.7 57 34-99 167-228 (329)
83 KOG1687|consensus 24.9 46 0.001 25.6 1.5 25 29-53 124-148 (168)
84 TIGR03287 methan_mark_16 putat 24.9 34 0.00074 29.5 0.9 13 35-47 75-87 (391)
85 PF02980 FokI_C: Restriction e 24.5 52 0.0011 24.9 1.7 35 34-68 52-100 (142)
86 PF01921 tRNA-synt_1f: tRNA sy 22.8 37 0.0008 28.9 0.7 67 28-102 225-298 (360)
87 PF04522 DUF585: Protein of un 21.8 45 0.00097 27.3 1.0 26 14-41 108-133 (248)
88 PRK13354 tyrosyl-tRNA syntheta 20.9 1.7E+02 0.0036 24.9 4.3 57 35-99 186-243 (410)
No 1
>KOG0435|consensus
Probab=100.00 E-value=1.9e-38 Score=279.20 Aligned_cols=92 Identities=52% Similarity=0.859 Sum_probs=89.0
Q ss_pred cccCCCCCCCCCChhhhcccccceEEeecchhHHHHHHHHHHHHHHHHhcCCCCCCCccccccccceeecCeeeecCCCc
Q psy1520 14 TKSRDINAEVSFNTDKAQDWLPVDIYIGGKEHAVLHLYYARFIAHFLHAQGKTPAREPFKRLLVQGMIMGQTYREKTSGK 93 (107)
Q Consensus 14 ~~~dp~n~~~~fd~~~~~~WmPVD~YIGGiEHAilHLLYaRF~~K~L~D~G~v~~~EPF~~Ll~QGMV~~~~~k~ks~Gn 93 (107)
.|+||+|...|||++.+.+|||||+||||+|||||||||||||+|||+|+|++++.|||++|++||||+|++|+.++.|+
T Consensus 506 RylDpkN~e~~~d~a~a~k~MPVDvYIGG~EHAvlHLlYaRF~~kFl~di~~~~t~EPF~~Li~QGmV~G~tf~~~~sG~ 585 (876)
T KOG0435|consen 506 RYLDPKNPEEPFDKAKAKKNMPVDVYIGGKEHAVLHLLYARFIAKFLKDIGVVSTAEPFTKLITQGMVRGKTFRTKESGK 585 (876)
T ss_pred eecCCCCcccccchhhhhccCceeEEeccHHHHHHHHHHHHHHHHHHhhcCCCcCCCcHHHHHhhhcccceEEecCCCCc
Confidence 47899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeCCCceeecCC
Q psy1520 94 YLKPDEVFTKGS 105 (107)
Q Consensus 94 ~v~p~ev~~~~~ 105 (107)
||.|+||...|+
T Consensus 586 yl~~~ev~~~nd 597 (876)
T KOG0435|consen 586 YLGPEEVQQVND 597 (876)
T ss_pred cCCHHHhhhhcC
Confidence 999999987765
No 2
>COG0495 LeuS Leucyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.9e-36 Score=267.92 Aligned_cols=92 Identities=41% Similarity=0.747 Sum_probs=86.6
Q ss_pred cccccCCCCC-CCCCChhhhcccccceEEeecchhHHHHHHHHHHHHHHHHhcCCCCCCCccccccccceeec-Ceeee-
Q psy1520 12 TKTKSRDINA-EVSFNTDKAQDWLPVDIYIGGKEHAVLHLYYARFIAHFLHAQGKTPAREPFKRLLVQGMIMG-QTYRE- 88 (107)
Q Consensus 12 ~~~~~dp~n~-~~~fd~~~~~~WmPVD~YIGGiEHAilHLLYaRF~~K~L~D~G~v~~~EPF~~Ll~QGMV~~-~~~k~- 88 (107)
+..|+||.|. +.++++++++||||||+||||+|||++||||+|||||+|+|.|+|+.+|||++|++||||++ ++-||
T Consensus 502 ~~r~~d~~~~~~~~~~~e~~~yW~PVD~yigG~ehavlHLly~rF~Hkal~d~g~~p~~epf~~L~~qGmVl~~~g~KMS 581 (814)
T COG0495 502 YLRFFDPIFLGELPFDREEFNYWYPVDLYIGGIEHAVLHLLYFRFFHKALFDEGLVPKDEPFKKLITQGMVLGEEGEKMS 581 (814)
T ss_pred cHhhcChhcCccchhcHHHHhcccChheeecchhHHHHHHHHHHHHHHHhcccCcCCCccchhhhhccceEEecCCCccc
Confidence 4578999998 79999999999999999999999999999999999999999999999999999999999999 57775
Q ss_pred cCCCceeCCCceeec
Q psy1520 89 KTSGKYLKPDEVFTK 103 (107)
Q Consensus 89 ks~Gn~v~p~ev~~~ 103 (107)
||+||+|+|+|++.+
T Consensus 582 KSKgN~v~p~~~i~~ 596 (814)
T COG0495 582 KSKGNVVDPEEAVEK 596 (814)
T ss_pred cccCCCCCHHHHHHH
Confidence 999999999998764
No 3
>PLN02563 aminoacyl-tRNA ligase
Probab=99.97 E-value=6.3e-33 Score=249.37 Aligned_cols=70 Identities=44% Similarity=0.798 Sum_probs=67.8
Q ss_pred cccCCCCCCCCCChhhhcccccceEEeecchhHHHHHHHHHHHHHHHHhcCCCCCCCccccccccceeec
Q psy1520 14 TKSRDINAEVSFNTDKAQDWLPVDIYIGGKEHAVLHLYYARFIAHFLHAQGKTPAREPFKRLLVQGMIMG 83 (107)
Q Consensus 14 ~~~dp~n~~~~fd~~~~~~WmPVD~YIGGiEHAilHLLYaRF~~K~L~D~G~v~~~EPF~~Ll~QGMV~~ 83 (107)
.|+||+|++++||++.+++|||||+||||+|||||||||+|||+++|+|+|++..+|||++|++||||++
T Consensus 595 r~~~p~~~~~~~~~~~~~~w~PvD~yigG~dhailHLlY~Rfw~~~l~~~g~~~~~ePfk~ll~qGmVl~ 664 (963)
T PLN02563 595 RFMDPKNSNALVDKEKEKYWMPVDLYVGGAEHAVLHLLYARFWHKVLYDIGVVSTKEPFQCLVNQGMILG 664 (963)
T ss_pred HHhCCCccccccCHHHHhCcCCCcEeeccHHHHhhHhHHHHHHHHHHHHhhccCCcccHHHHhccceeec
Confidence 3789999999999999999999999999999999999999999999999999999999999999999996
No 4
>TIGR00396 leuS_bact leucyl-tRNA synthetase, eubacterial and mitochondrial family. The leucyl-tRNA synthetases belong to two families so broadly different that they are represented by separate models. This model includes both eubacterial and mitochondrial leucyl-tRNA synthetases. It generates higher scores for some valyl-tRNA synthetases than for any archaeal or eukaryotic cytosolic leucyl-tRNA synthetase. Note that the enzyme from Aquifex aeolicus is split into alpha and beta chains; neither chain is long enough to score above the trusted cutoff, but the alpha chain scores well above the noise cutoff. The beta chain must be found by a model and search designed for partial length matches.
Probab=99.96 E-value=5.3e-31 Score=233.37 Aligned_cols=90 Identities=44% Similarity=0.826 Sum_probs=83.1
Q ss_pred cccCCCCCCCCCChhhhcccccceEEeecchhHHHHHHHHHHHHHHHHhcCCCCCCCccccccccceeec-----Cee--
Q psy1520 14 TKSRDINAEVSFNTDKAQDWLPVDIYIGGKEHAVLHLYYARFIAHFLHAQGKTPAREPFKRLLVQGMIMG-----QTY-- 86 (107)
Q Consensus 14 ~~~dp~n~~~~fd~~~~~~WmPVD~YIGGiEHAilHLLYaRF~~K~L~D~G~v~~~EPF~~Ll~QGMV~~-----~~~-- 86 (107)
.|+||+|...||+++.+++|+|||+||||+||||+||||||||+++|+++|+++.+|||++|++||||++ .+.
T Consensus 499 r~~~p~~~~~~~~~~~~~~~~PvD~yi~G~dhailHLlyaRf~~~~l~~~~~~~~~~Pfk~l~~~G~Vl~~~~~~~G~~~ 578 (842)
T TIGR00396 499 RYLDPKNTDQPFDKEKAEYWLPVDLYIGGAEHAILHLLYARFWHKFLYDIGYVSTKEPFKKLINQGMVLGFYYPPNGKSP 578 (842)
T ss_pred HhhCCCCcCCCcChHHHhccCCCcEeeccHHHHHHHHHHHHHHHHHHHhccccCCCccHHHHhccceEEeeeecCCCCcc
Confidence 3689999889999999999999999999999999999999999999999999999999999999999998 233
Q ss_pred -------------------------ee-cCCCceeCCCceeec
Q psy1520 87 -------------------------RE-KTSGKYLKPDEVFTK 103 (107)
Q Consensus 87 -------------------------k~-ks~Gn~v~p~ev~~~ 103 (107)
|| ||+||+|+|++++.+
T Consensus 579 ~~~~~~~~~~~~~~~~~~~~~~~~~KMSKS~GN~v~p~~ii~~ 621 (842)
T TIGR00396 579 PDELTERDEKAKDKSGGELVVVGYEKMSKSKGNGIDPQEIVKK 621 (842)
T ss_pred ChhhhccccccccccCCcccccchhhhhhcCCCcCCHHHHHHH
Confidence 65 999999999998754
No 5
>PRK00390 leuS leucyl-tRNA synthetase; Validated
Probab=99.93 E-value=8.4e-27 Score=205.54 Aligned_cols=85 Identities=47% Similarity=0.853 Sum_probs=80.0
Q ss_pred cccCCCCCCCCCChhhhcccccceEEeecchhHHHHHHHHHHHHHHHHhcCCCCCCCccccccccceeecCeeee-cCCC
Q psy1520 14 TKSRDINAEVSFNTDKAQDWLPVDIYIGGKEHAVLHLYYARFIAHFLHAQGKTPAREPFKRLLVQGMIMGQTYRE-KTSG 92 (107)
Q Consensus 14 ~~~dp~n~~~~fd~~~~~~WmPVD~YIGGiEHAilHLLYaRF~~K~L~D~G~v~~~EPF~~Ll~QGMV~~~~~k~-ks~G 92 (107)
.|++|+|+..+||++.+++|+|||+|+||+|||++||+|+|||+++|.++|+++.+|||++|++|||| || ||+|
T Consensus 502 ~~~~p~~~~~~~~~~~~~~~~P~Dly~~G~D~~i~hL~y~Rf~~~~l~~~~~~~~~~Pfk~v~~~G~v-----KMSKS~G 576 (805)
T PRK00390 502 RYTDPHNDEAPFDKEAANYWLPVDQYIGGIEHAVLHLLYARFFTKVLRDLGLVSSDEPFKKLLTQGMV-----KMSKSKG 576 (805)
T ss_pred HhcCcccccCcCChHHhhCcCCCcEEeccHHHHHHHHHHHHHHHHHHHHhhcccCCcchhhheecCcE-----EeCCCCC
Confidence 46789988889999999999999999999999999999999999999999999999999999999999 65 9999
Q ss_pred ceeCCCceeec
Q psy1520 93 KYLKPDEVFTK 103 (107)
Q Consensus 93 n~v~p~ev~~~ 103 (107)
|+|+|.+++.+
T Consensus 577 N~i~p~~~i~~ 587 (805)
T PRK00390 577 NVVDPDDIIEK 587 (805)
T ss_pred CCCCHHHHHHH
Confidence 99999998754
No 6
>PF00133 tRNA-synt_1: tRNA synthetases class I (I, L, M and V); InterPro: IPR002300 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. The class Ia aminoacyl-tRNA synthetases consist of the isoleucyl, methionyl, valyl, leucyl, cysteinyl, and arginyl-tRNA synthetases; the class Ib include the glutamyl and glutaminyl-tRNA synthetases, and the class Ic are the tyrosyl and tryptophanyl-tRNA synthetases [].; GO: 0000166 nucleotide binding, 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0006418 tRNA aminoacylation for protein translation, 0005737 cytoplasm; PDB: 1OBC_A 2AJH_B 4ARI_A 2AJG_B 4AQ7_D 2AJI_B 4ARC_A 4AS1_A 1QU3_A 1QU2_A ....
Probab=99.47 E-value=9.7e-15 Score=125.26 Aligned_cols=72 Identities=26% Similarity=0.654 Sum_probs=58.8
Q ss_pred ChhhhcccccceEEeecchhHHHHHHHHHHHHHHHHhcCCCCCCCccccccccceeecC-eeee-cCCCceeCCCceeec
Q psy1520 26 NTDKAQDWLPVDIYIGGKEHAVLHLYYARFIAHFLHAQGKTPAREPFKRLLVQGMIMGQ-TYRE-KTSGKYLKPDEVFTK 103 (107)
Q Consensus 26 d~~~~~~WmPVD~YIGGiEHAilHLLYaRF~~K~L~D~G~v~~~EPF~~Ll~QGMV~~~-~~k~-ks~Gn~v~p~ev~~~ 103 (107)
+++..++|.|||+|++|.||...|+.++.|.+-+|.+ ++||+++++||||++. +.|| ||+||+|+|++++.+
T Consensus 505 ~~~~~~~~~P~D~~~~G~D~~~~W~~~~l~~~~~l~~------~~pfk~v~~hG~vld~~G~KMSKS~GNvi~p~~ii~~ 578 (601)
T PF00133_consen 505 DREEFEYWYPVDLYIEGKDQIRGWFQSSLFLSVALFG------KEPFKKVITHGFVLDEDGRKMSKSKGNVIDPEDIIEK 578 (601)
T ss_dssp SCHHHHHHSSBSEEEEEGGGTTTHHHHHHHHHHHHSS------STSBSEEEEE--EEETTSSB-BTTTTB--BHHHHHHH
T ss_pred cchhccccCCcccccCCccchhhHHHHhHhhcccccc------CCchheeeecccccccceeecccCCCcccCHHHHHHH
Confidence 4677899999999999999999999999999988754 4499999999999974 5665 999999999998753
No 7
>cd00812 LeuRS_core catalytic core domain of leucyl-tRNA synthetases. Leucyl tRNA synthetase (LeuRS) catalytic core domain. This class I enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. In Aquifex aeolicus, the gene encoding LeuRS is split in two, just before the KMSKS motif. Consequently, LeuRS is a heterodimer, which likely superimposes with the LeuRS monomer found in most other organisms. LeuRS has an insertion in the core domain, which is subject to both deletions and rearrangements and thus differs between prokaryotic LeuRS and archaeal/eukaryotic LeuRS. This editing region hydrolyzes mischarged cognate tRNAs and thus prevents the incorporation of chemically similar amino acids.
Probab=99.37 E-value=2.3e-13 Score=108.28 Aligned_cols=77 Identities=44% Similarity=0.753 Sum_probs=69.9
Q ss_pred ChhhhcccccceEEeecchhHHHHHHHHHHHHHHHHhcCCCCCCCccccccccceeecCeeee-cCCCceeCCCceeec
Q psy1520 26 NTDKAQDWLPVDIYIGGKEHAVLHLYYARFIAHFLHAQGKTPAREPFKRLLVQGMIMGQTYRE-KTSGKYLKPDEVFTK 103 (107)
Q Consensus 26 d~~~~~~WmPVD~YIGGiEHAilHLLYaRF~~K~L~D~G~v~~~EPF~~Ll~QGMV~~~~~k~-ks~Gn~v~p~ev~~~ 103 (107)
+++..++|.|+|+|++|.||..-|++|.+||..+|...|++ ..+|+++++.+|||+.++.|| ||+||+|+|+|++.+
T Consensus 215 ~~~~~~~w~p~di~v~G~D~i~~h~~~~~~~~~~l~~~g~~-~~~~~~~~~~~g~v~~~g~KmSkS~Gn~v~~~dll~~ 292 (314)
T cd00812 215 DREEFEYWYPVDIYIGGKEHAPNHLLYSRFNHKALFDEGLV-TDEPPKGLIVQGMVLLEGEKMSKSKGNVVTPDEAIKK 292 (314)
T ss_pred hHHHHHHhCCCeeeecchhHHHHHHHHHHHHHHHHcCcccc-cccCcHHheecceEecCccccCCcCCCCCCHHHHHHH
Confidence 34567899999999999999999999999999999999987 678999999999999888775 999999999998754
No 8
>PRK12300 leuS leucyl-tRNA synthetase; Reviewed
Probab=99.34 E-value=3.1e-13 Score=121.10 Aligned_cols=71 Identities=18% Similarity=0.351 Sum_probs=63.4
Q ss_pred hhhhcccccceEEeecchhHHHHHHHHHHHHHHHHhcCCCCCCCcc-ccccccceeecCeeee-cCCCceeCCCceeec
Q psy1520 27 TDKAQDWLPVDIYIGGKEHAVLHLYYARFIAHFLHAQGKTPAREPF-KRLLVQGMIMGQTYRE-KTSGKYLKPDEVFTK 103 (107)
Q Consensus 27 ~~~~~~WmPVD~YIGGiEHAilHLLYaRF~~K~L~D~G~v~~~EPF-~~Ll~QGMV~~~~~k~-ks~Gn~v~p~ev~~~ 103 (107)
++..++|.|+|+|++|.||+..||.|.+|.+.++.+.. |+ ++++.||||+.++.|| ||+||+|+|.|++.+
T Consensus 522 ~~~f~~~~P~D~~~~GkDii~~Hl~~~~~~~~a~~~~~------~~Pk~v~~hG~vl~~G~KMSKS~GNvVdp~eii~~ 594 (897)
T PRK12300 522 REEFLYWYPVDWRHSGKDLIPNHLTFFIFNHVAIFPEE------KWPRGIVVNGFVLLEGKKMSKSKGNVIPLRKAIEE 594 (897)
T ss_pred HHHHhccCCceEEEeeeccCccHHHHHHHHHHHhcCCC------ccCcEEEEcceEEECCccccCcCCCCCCHHHHHHH
Confidence 35678999999999999999999999999999887654 67 8999999999988885 999999999998754
No 9
>PLN02959 aminoacyl-tRNA ligase
Probab=99.32 E-value=7.4e-13 Score=121.07 Aligned_cols=70 Identities=21% Similarity=0.442 Sum_probs=63.2
Q ss_pred hhhcccccceEEeecchhHHHHHHHHHHHHHHHHhcCCCCCCCcc-ccccccceeecCeeee-cCCCceeCCCceeec
Q psy1520 28 DKAQDWLPVDIYIGGKEHAVLHLYYARFIAHFLHAQGKTPAREPF-KRLLVQGMIMGQTYRE-KTSGKYLKPDEVFTK 103 (107)
Q Consensus 28 ~~~~~WmPVD~YIGGiEHAilHLLYaRF~~K~L~D~G~v~~~EPF-~~Ll~QGMV~~~~~k~-ks~Gn~v~p~ev~~~ 103 (107)
+..++|.|+|+|++|.||+..||.|++|.+.++.+ ++|| ++++.+|||+.++.|| ||+||+|+|.|++.+
T Consensus 664 ~ef~~~yP~Dl~~sG~Dii~~wl~~~l~~~~al~~------~~P~p~~v~v~G~V~~~G~KMSKSkGNvI~p~diI~k 735 (1084)
T PLN02959 664 QEFEYWYPFDLRVSGKDLIQNHLTFAIYNHTAIWA------EEHWPRGFRCNGHLMLNSEKMSKSTGNFLTLRQAIEE 735 (1084)
T ss_pred HHHHhhCCCeEEEecccHHHHHHHHHHHHHHHhcC------CCCCCceEEEccEEecCCcCccccCCCcCCHHHHHHH
Confidence 45789999999999999999999999999999876 5899 5699999999888875 999999999998754
No 10
>PTZ00419 valyl-tRNA synthetase-like protein; Provisional
Probab=99.26 E-value=4e-12 Score=114.76 Aligned_cols=70 Identities=29% Similarity=0.533 Sum_probs=59.5
Q ss_pred hhhhcccccceEEeecchhHHHHHHHHHHHHHHHHhcCCCCCCCccccccccceeec-Ceeee-cCCCceeCCCceee
Q psy1520 27 TDKAQDWLPVDIYIGGKEHAVLHLYYARFIAHFLHAQGKTPAREPFKRLLVQGMIMG-QTYRE-KTSGKYLKPDEVFT 102 (107)
Q Consensus 27 ~~~~~~WmPVD~YIGGiEHAilHLLYaRF~~K~L~D~G~v~~~EPF~~Ll~QGMV~~-~~~k~-ks~Gn~v~p~ev~~ 102 (107)
.+..++|.|+|+|++| |.|+++.++|++...+.-.| .+||++++.||||++ ++.|| ||+||+|+|.+++.
T Consensus 530 ~~~~~~~~P~d~~~~G--~Dii~~W~arm~~~~~~~~~----~~Pfk~v~~HG~v~d~~G~KMSKSlGNvIdP~~ii~ 601 (995)
T PTZ00419 530 TDDLQRFFPTSLLETG--SDILFFWVARMVMMSLHLTD----KLPFKTVFLHAMVRDSQGEKMSKSKGNVIDPLEVIE 601 (995)
T ss_pred hHHHhhcCCCcEEEec--hhHHhHHHHHHHHHHHHhcC----CCChHHHhccceEECCCCCCcccCCCCcCChHHHhc
Confidence 3557899999999999 66889999999666665444 799999999999998 55665 99999999999976
No 11
>PLN02381 valyl-tRNA synthetase
Probab=99.25 E-value=3.4e-12 Score=116.71 Aligned_cols=73 Identities=23% Similarity=0.450 Sum_probs=60.4
Q ss_pred CCChhhhcccccceEEeecchhHHHHHHHHHHHHHHHHhcCCCCCCCccccccccceeec-Ceeee-cCCCceeCCCcee
Q psy1520 24 SFNTDKAQDWLPVDIYIGGKEHAVLHLYYARFIAHFLHAQGKTPAREPFKRLLVQGMIMG-QTYRE-KTSGKYLKPDEVF 101 (107)
Q Consensus 24 ~fd~~~~~~WmPVD~YIGGiEHAilHLLYaRF~~K~L~D~G~v~~~EPF~~Ll~QGMV~~-~~~k~-ks~Gn~v~p~ev~ 101 (107)
|++.+..++|+|+|+|+-| |.++|+.++|++-..+. +...+||++++.||||++ .+.|| ||+||+|+|.+++
T Consensus 597 P~~~~~~~~~~P~d~~~~G--~Dii~~W~~rmi~~~~~----~~~~~PFk~v~~hG~V~D~~G~KMSKS~GNvIdP~~vi 670 (1066)
T PLN02381 597 PDDTDDLKAFYPTSVLETG--HDILFFWVARMVMMGMQ----LGGDVPFRKVYLHPMIRDAHGRKMSKSLGNVIDPLEVI 670 (1066)
T ss_pred CCCHHHHhccCCCeeeeec--chhhhhHHHHHHHHHHH----hCCCCchHHheecceEECCCCCCCCCCCCCCCCHHHHH
Confidence 5566778999999999988 77788888888844333 567899999999999998 44565 9999999999997
Q ss_pred e
Q psy1520 102 T 102 (107)
Q Consensus 102 ~ 102 (107)
.
T Consensus 671 ~ 671 (1066)
T PLN02381 671 N 671 (1066)
T ss_pred h
Confidence 6
No 12
>PRK13208 valS valyl-tRNA synthetase; Reviewed
Probab=99.22 E-value=6e-12 Score=110.98 Aligned_cols=74 Identities=23% Similarity=0.493 Sum_probs=60.9
Q ss_pred CCChhhhcccccceEEeecchhHHHHHHHHHHHHHHHHhcCCCCCCCccccccccceeec-Ceeee-cCCCceeCCCcee
Q psy1520 24 SFNTDKAQDWLPVDIYIGGKEHAVLHLYYARFIAHFLHAQGKTPAREPFKRLLVQGMIMG-QTYRE-KTSGKYLKPDEVF 101 (107)
Q Consensus 24 ~fd~~~~~~WmPVD~YIGGiEHAilHLLYaRF~~K~L~D~G~v~~~EPF~~Ll~QGMV~~-~~~k~-ks~Gn~v~p~ev~ 101 (107)
|.+++..++|.|+|+|++|.++...|+.|..+++..+ ...+||++++.||||+. ++.|| ||+||+|+|.|++
T Consensus 475 ~~~~~~~~~~~P~d~~~~G~Di~~~w~~~~l~~~~~~------~~~~Pf~~v~~hg~v~~~~G~KMSKS~GN~i~p~~~i 548 (800)
T PRK13208 475 ERDEDLFEKVFPMDLRPQGHDIIRTWLFYTILRAYLL------TGKLPWKNIMISGMVLDPDGKKMSKSKGNVVTPEELL 548 (800)
T ss_pred CCChhhhhhcCCceEEEeecchhhhHHHHHHHHHHHh------cCCCCcceEEEeeEEECCCCCCCCCCCCCCCCHHHHH
Confidence 3456678899999999999999988877777665554 23589999999999996 66675 9999999999987
Q ss_pred ec
Q psy1520 102 TK 103 (107)
Q Consensus 102 ~~ 103 (107)
.+
T Consensus 549 ~~ 550 (800)
T PRK13208 549 EK 550 (800)
T ss_pred HH
Confidence 54
No 13
>TIGR00392 ileS isoleucyl-tRNA synthetase. The isoleucyl tRNA synthetase (IleS) is a class I amino acyl-tRNA ligase and is particularly closely related to the valyl tRNA synthetase. This model may recognize IleS from every species, including eukaryotic cytosolic and mitochondrial forms.
Probab=99.22 E-value=5.3e-12 Score=111.93 Aligned_cols=72 Identities=21% Similarity=0.426 Sum_probs=56.7
Q ss_pred ChhhhcccccceEEeecchhHHHHHHHHHHHHHHHHhcCCCCCCCccccccccceeec-Ceeee-cCCCceeCCCceeec
Q psy1520 26 NTDKAQDWLPVDIYIGGKEHAVLHLYYARFIAHFLHAQGKTPAREPFKRLLVQGMIMG-QTYRE-KTSGKYLKPDEVFTK 103 (107)
Q Consensus 26 d~~~~~~WmPVD~YIGGiEHAilHLLYaRF~~K~L~D~G~v~~~EPF~~Ll~QGMV~~-~~~k~-ks~Gn~v~p~ev~~~ 103 (107)
+.+..++|.|+|+|++|.||+..|+-.+.+.+-.+ ...+||+++++||||+. ++.|| ||+||+|+|.|++.+
T Consensus 555 ~~~~f~~~~P~d~~i~G~Di~r~Wf~~~~~~~~~~------~~~~P~k~v~~hG~vl~~~G~KMSKSkGNvI~p~d~i~~ 628 (861)
T TIGR00392 555 ENEKFKEVFPADFILEGSDQTRGWFYSSLAIGTAL------FGQAPYKNVITHGFTLDEKGRKMSKSLGNVVDPLKVINK 628 (861)
T ss_pred CcchhhccCCceEEEEecchhccHHHHHHHHHHHH------cCCCChHhhEecceEECCCCCCcCCCCCCCCCHHHHHHH
Confidence 33457899999999999999887755555544332 24799999999999996 56665 999999999998753
No 14
>PRK05743 ileS isoleucyl-tRNA synthetase; Reviewed
Probab=99.21 E-value=3.2e-12 Score=114.80 Aligned_cols=66 Identities=23% Similarity=0.495 Sum_probs=53.2
Q ss_pred ccccceEEeecchhHHHHHHHHHHHHHHHHhcCCCCCCCccccccccceeec-Ceeee-cCCCceeCCCceeec
Q psy1520 32 DWLPVDIYIGGKEHAVLHLYYARFIAHFLHAQGKTPAREPFKRLLVQGMIMG-QTYRE-KTSGKYLKPDEVFTK 103 (107)
Q Consensus 32 ~WmPVD~YIGGiEHAilHLLYaRF~~K~L~D~G~v~~~EPF~~Ll~QGMV~~-~~~k~-ks~Gn~v~p~ev~~~ 103 (107)
+|.|+|+|++|.||+.+| |.+..+....+ ...+||+++++||||++ ++.|| ||+||+|+|.+++.+
T Consensus 542 ~~~P~Dl~~~G~Di~r~W-----f~~~l~~~~~~-~g~~P~k~vl~HG~vld~~G~KMSKSlGNvIdP~~ii~~ 609 (912)
T PRK05743 542 LGYPADLYLEGSDQHRGW-----FQSSLLTSVAT-RGKAPYKQVLTHGFTVDGKGRKMSKSLGNVIDPQDVIKK 609 (912)
T ss_pred cCCCceEEEecccccchH-----HHHHHHHHHHh-cCCCccceeEEeeeEECCCCCCCCCCCCCcCCHHHHHHh
Confidence 789999999999999776 22333444444 45799999999999997 67775 999999999998754
No 15
>PRK14900 valS valyl-tRNA synthetase; Provisional
Probab=99.10 E-value=3.2e-11 Score=110.11 Aligned_cols=70 Identities=23% Similarity=0.479 Sum_probs=60.9
Q ss_pred hhhcccccceEEeecchhHHHHHHHHHHHHHHHHhcCCCCCCCccccccccceeec-Ceeee-cCCCceeCCCceeec
Q psy1520 28 DKAQDWLPVDIYIGGKEHAVLHLYYARFIAHFLHAQGKTPAREPFKRLLVQGMIMG-QTYRE-KTSGKYLKPDEVFTK 103 (107)
Q Consensus 28 ~~~~~WmPVD~YIGGiEHAilHLLYaRF~~K~L~D~G~v~~~EPF~~Ll~QGMV~~-~~~k~-ks~Gn~v~p~ev~~~ 103 (107)
+..++|.|+|+|++| |.++++.++|++...+...|. .||++++.||||+. ++.|| ||+||+|+|.|++.+
T Consensus 484 ~~~~~~~P~d~~~~G--~Dii~~W~a~~l~~~~~~~~~----~Pfk~V~~hG~v~d~~G~KMSKSkGNvIdP~dvIe~ 555 (1052)
T PRK14900 484 DTLRTFYPTSVMETG--HDIIFFWVARMMMMGLHFMGE----VPFRTVYLHPMVRDEKGQKMSKTKGNVIDPLVITEQ 555 (1052)
T ss_pred HHHHhhCCchhhccc--ccHHhHHHHHHHHHHHHhcCC----CccceeEecccEECCCCCCccCCCCCCCCHHHHHHH
Confidence 357889999999999 667788899999999988775 68999999999998 66775 999999999998753
No 16
>TIGR00395 leuS_arch leucyl-tRNA synthetase, archaeal and cytosolic family. The leucyl-tRNA synthetases belong to two families so broadly different that they are represented by separate models. This model includes both archaeal and cytosolic eukaryotic leucyl-tRNA synthetases; the eubacterial and mitochondrial forms differ so substantially that some other tRNA ligases score higher by this model than does any eubacterial LeuS.
Probab=99.06 E-value=4.7e-11 Score=107.69 Aligned_cols=70 Identities=23% Similarity=0.407 Sum_probs=61.3
Q ss_pred hhhcccccceEEeecchhHHHHHHHHHHHHHHHHhcCCCCCCCcc-ccccccceeecCeeee-cCCCceeCCCceeec
Q psy1520 28 DKAQDWLPVDIYIGGKEHAVLHLYYARFIAHFLHAQGKTPAREPF-KRLLVQGMIMGQTYRE-KTSGKYLKPDEVFTK 103 (107)
Q Consensus 28 ~~~~~WmPVD~YIGGiEHAilHLLYaRF~~K~L~D~G~v~~~EPF-~~Ll~QGMV~~~~~k~-ks~Gn~v~p~ev~~~ 103 (107)
+..++|.|+|++++|.|+...|+.|.+|.+.++... +|| ++++.||||+.++.|| ||+||+|+|.+++.+
T Consensus 566 ~ef~~~yP~D~~~~GkDii~~H~~~~i~~~~a~~~~------~~~Pk~i~~~G~vl~~G~KMSKSlGNvI~p~d~i~~ 637 (938)
T TIGR00395 566 REFEYWYPLDWRISGKDLIPNHLTFYIFHHVAIFPE------KFWPRGIVVNGYVMLEGKKMSKSKGNVLTLEQAVEK 637 (938)
T ss_pred HHHhhcCCceEEEEeeccccchHHHHHHHHHHcCCc------cccCcEEEEeceEEeCCccccCcCCCCCCHHHHHHH
Confidence 467899999999999999999999999988876543 355 8999999999988885 999999999998754
No 17
>PRK06039 ileS isoleucyl-tRNA synthetase; Reviewed
Probab=99.05 E-value=5e-11 Score=107.74 Aligned_cols=70 Identities=29% Similarity=0.459 Sum_probs=56.3
Q ss_pred hhhhcccccceEEeecchhHHHHHHHHHHHHHHHHhcCCCCC-CCccccccccceeec-Ceeee-cCCCceeCCCceeec
Q psy1520 27 TDKAQDWLPVDIYIGGKEHAVLHLYYARFIAHFLHAQGKTPA-REPFKRLLVQGMIMG-QTYRE-KTSGKYLKPDEVFTK 103 (107)
Q Consensus 27 ~~~~~~WmPVD~YIGGiEHAilHLLYaRF~~K~L~D~G~v~~-~EPF~~Ll~QGMV~~-~~~k~-ks~Gn~v~p~ev~~~ 103 (107)
++..++|.|+|+|++|.||. |||-..|..+|..-. .+||++++.||||+. ++.|| ||+||+|+|.|++.+
T Consensus 537 ~~~f~~~~Pad~~~~G~Di~-------r~Wf~~l~~~~~~~~~~~pfk~v~~hG~Vld~~G~KMSKSlGNvIdP~dli~~ 609 (975)
T PRK06039 537 KEWFEKHFPADFIVEGIDQT-------RGWFYTLLALSTALFDRPPYKNVLVHGHVLDEDGQKMSKSLGNYVDPFEVFDK 609 (975)
T ss_pred hhhhhccCCceEEEechhhH-------hhHHHHHHHHHHHhcCCCcccEEEEeeeEECCCCCCcCCCCCCcCCHHHHHHH
Confidence 34457899999999999995 556666666665544 689999999999997 56675 999999999998754
No 18
>PTZ00427 isoleucine-tRNA ligase, putative; Provisional
Probab=98.81 E-value=2.3e-09 Score=99.75 Aligned_cols=72 Identities=21% Similarity=0.418 Sum_probs=59.8
Q ss_pred ChhhhcccccceEEeecchhHHHHHHHHHHHHHHHHhcCCCCCCCccccccccceeec-Ceeee-cCCCceeCCCceeec
Q psy1520 26 NTDKAQDWLPVDIYIGGKEHAVLHLYYARFIAHFLHAQGKTPAREPFKRLLVQGMIMG-QTYRE-KTSGKYLKPDEVFTK 103 (107)
Q Consensus 26 d~~~~~~WmPVD~YIGGiEHAilHLLYaRF~~K~L~D~G~v~~~EPF~~Ll~QGMV~~-~~~k~-ks~Gn~v~p~ev~~~ 103 (107)
+++..++|.|.|+++-|.++-.+|+.++=+.+-.|.+ .-||++++.||+|++ ++.|| ||+||+|+|.+++.+
T Consensus 664 ~~~~f~~~fPaD~i~eG~Dq~rgWf~s~l~~s~~l~~------~~PfK~VlvHG~Vld~dG~KMSKSlGNvIDP~evI~k 737 (1205)
T PTZ00427 664 EKEDFHKIFPADFIAEGLDQTRGWFYTLLVISTLLFD------KAPFKNLICNGLVLASDGKKMSKRLKNYPDPLYILDK 737 (1205)
T ss_pred chhhHhccCCceEEEEecchhccHHHHHHHHHHHhcC------CCCcceeEEccEEEcCCCCCcccCCCCCCCHHHHHHh
Confidence 3566778999999999999999996666666655543 489999999999997 66775 999999999998754
No 19
>PRK13804 ileS isoleucyl-tRNA synthetase; Provisional
Probab=98.79 E-value=1.9e-09 Score=97.79 Aligned_cols=65 Identities=23% Similarity=0.440 Sum_probs=52.6
Q ss_pred cccceEEeecchhHHHHHHHHHHHHHHHHhcCCCCCCCccccccccceeec-Ceeee-cCCCceeCCCceeec
Q psy1520 33 WLPVDIYIGGKEHAVLHLYYARFIAHFLHAQGKTPAREPFKRLLVQGMIMG-QTYRE-KTSGKYLKPDEVFTK 103 (107)
Q Consensus 33 WmPVD~YIGGiEHAilHLLYaRF~~K~L~D~G~v~~~EPF~~Ll~QGMV~~-~~~k~-ks~Gn~v~p~ev~~~ 103 (107)
+.|+|+|+.|.|+..++ |+..|-....+....||+++++||||+. ++.|| ||+||+|+|.+++.+
T Consensus 581 ~~PaD~~~eG~Di~rgW------F~s~ll~s~~~~~~~P~k~V~~HG~vld~~G~KMSKSlGNvIdP~~ii~~ 647 (961)
T PRK13804 581 KWPADLYLEGSDQHRGW------FNSSLLESCGTRGRAPYKAVLTHGFTLDEKGEKMSKSLGNTVSPQDVIKQ 647 (961)
T ss_pred CCCceEEEEEcccccHH------HHHHHHHHHHhcCCCChhhEEEeccEECCCCCCccCCCCCcCCHHHHHHh
Confidence 35999999999998776 4444444444566799999999999997 77775 999999999998753
No 20
>cd00817 ValRS_core catalytic core domain of valyl-tRNA synthetases. Valine amino-acyl tRNA synthetase (ValRS) catalytic core domain. This enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. ValRS has an insertion in the core domain, which is subject to both deletions and rearrangements. This editing region hydrolyzes mischarged cognate tRNAs and thus prevents the incorporation of chemically similar amino acids.
Probab=98.73 E-value=4.6e-09 Score=86.00 Aligned_cols=70 Identities=17% Similarity=0.385 Sum_probs=55.5
Q ss_pred hhhcccccceEEeecchhHHHHHHHHHHHHHHHHhcCCCCCCCccccccccceeec-Ceeee-cCCCceeCCCceeec
Q psy1520 28 DKAQDWLPVDIYIGGKEHAVLHLYYARFIAHFLHAQGKTPAREPFKRLLVQGMIMG-QTYRE-KTSGKYLKPDEVFTK 103 (107)
Q Consensus 28 ~~~~~WmPVD~YIGGiEHAilHLLYaRF~~K~L~D~G~v~~~EPF~~Ll~QGMV~~-~~~k~-ks~Gn~v~p~ev~~~ 103 (107)
+..++|.|+|+++||.++...|..+.-+....+ .| ..||++++.+|||++ ++.|| ||+||+|+|+|++.+
T Consensus 289 ~~~~~~~p~d~~~~G~D~~~~h~~~~l~~~~~~--~g----~~p~~~v~~hg~v~~~~g~KMSKS~Gn~v~~~dll~~ 360 (382)
T cd00817 289 KDLKKFYPTSLLVTGHDIIFFWVARMIMRGLKL--TG----KLPFKEVYLHGLVRDEDGRKMSKSLGNVIDPLDVIDG 360 (382)
T ss_pred hhHhhcCCCCeeeeecCcCchHHHHHHHHHHHh--hC----CCchHHeEeeeeEECCCCCCccccCCCCCCHHHHHHh
Confidence 456789999999999999999988854443333 23 368999999999994 56664 999999999998753
No 21
>TIGR00422 valS valyl-tRNA synthetase. The valyl-tRNA synthetase (ValS) is a class I amino acyl-tRNA ligase and is particularly closely related to the isoleucyl tRNA synthetase.
Probab=98.72 E-value=6e-09 Score=92.82 Aligned_cols=69 Identities=20% Similarity=0.420 Sum_probs=55.3
Q ss_pred hhhcccccceEEeecchhHHHHHHHHHHHHHHHHhcCCCCCCCccccccccceeec-Ceeee-cCCCceeCCCceee
Q psy1520 28 DKAQDWLPVDIYIGGKEHAVLHLYYARFIAHFLHAQGKTPAREPFKRLLVQGMIMG-QTYRE-KTSGKYLKPDEVFT 102 (107)
Q Consensus 28 ~~~~~WmPVD~YIGGiEHAilHLLYaRF~~K~L~D~G~v~~~EPF~~Ll~QGMV~~-~~~k~-ks~Gn~v~p~ev~~ 102 (107)
+..++|.|+|+++.|.+....|+.|.=+.+..+ . ...||++++.||||+. ++.|| ||+||+|+|.+++.
T Consensus 471 ~~~~~~~P~d~~~~G~Dii~fw~~~~~~~~~~~--~----~~~Pfk~v~~hG~v~d~~G~KMSKS~GN~i~p~~~i~ 541 (861)
T TIGR00422 471 KDLKKFYPTDLLVTGYDIIFFWVARMIFRSLAL--T----GQVPFKEVYIHGLVRDEQGRKMSKSLGNVIDPLDVIE 541 (861)
T ss_pred HHHhhcCCcceeecchhhhhHHHHHHHHHHHHh--c----CCCchheEEEeeEEECCCCCCCCcCCCCCCCHHHHHH
Confidence 457889999999999998888866544433333 2 3789999999999997 66775 99999999999875
No 22
>PRK05729 valS valyl-tRNA synthetase; Reviewed
Probab=98.71 E-value=5.5e-09 Score=93.44 Aligned_cols=71 Identities=24% Similarity=0.497 Sum_probs=55.9
Q ss_pred hhhhcccccceEEeecchhHHHHHHHHHHHHHHHHhcCCCCCCCccccccccceeec-Ceeee-cCCCceeCCCceeec
Q psy1520 27 TDKAQDWLPVDIYIGGKEHAVLHLYYARFIAHFLHAQGKTPAREPFKRLLVQGMIMG-QTYRE-KTSGKYLKPDEVFTK 103 (107)
Q Consensus 27 ~~~~~~WmPVD~YIGGiEHAilHLLYaRF~~K~L~D~G~v~~~EPF~~Ll~QGMV~~-~~~k~-ks~Gn~v~p~ev~~~ 103 (107)
.+..++|.|+|+++.|.+.... -.+|++...+... ...||++++.||||++ ++.|| ||+||+|+|.|++.+
T Consensus 465 ~~~~~~~~P~d~~~~G~Dii~~--W~a~~~~~~~~~~----~~~Pfk~v~~hG~v~d~~G~KMSKSlGNvIdP~dvi~~ 537 (874)
T PRK05729 465 TEDLKRFYPTSVLVTGFDIIFF--WVARMIMMGLHFT----GQVPFKDVYIHGLVRDEQGRKMSKSKGNVIDPLDLIDK 537 (874)
T ss_pred cHHHHhcCCcccccccccccch--HHHHHHHHHHHhc----CCCchhheEEeeeEECCCCCCcccCCCCCCCHHHHHHH
Confidence 4557889999999999996544 4566665555543 3689999999999996 66675 999999999998753
No 23
>cd00668 Ile_Leu_Val_MetRS_core catalytic core domain of isoleucyl, leucyl, valyl and methioninyl tRNA synthetases. Catalytic core domain of isoleucyl, leucyl, valyl and methioninyl tRNA synthetases. These class I enzymes are all monomers. However, in some species, MetRS functions as a homodimer, as a result of an additional C-terminal domain. These enzymes aminoacylate the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. Enzymes in this subfamily share an insertion in the core domain, which is subject to both deletions and rearrangements. This editing region hydrolyzes mischarged cognate tRNAs and thus prevents the incorporation of chemically similar amino acids. MetRS has a significantly shorter insertion, which lacks the editing function.
Probab=98.67 E-value=1.5e-08 Score=80.03 Aligned_cols=69 Identities=25% Similarity=0.314 Sum_probs=57.2
Q ss_pred hhcccccceEEeecchhHHHHHHHHHHHHHHHHhcCCCCCCCccccccccceeecCe-eee-cCCCceeCCCceeec
Q psy1520 29 KAQDWLPVDIYIGGKEHAVLHLYYARFIAHFLHAQGKTPAREPFKRLLVQGMIMGQT-YRE-KTSGKYLKPDEVFTK 103 (107)
Q Consensus 29 ~~~~WmPVD~YIGGiEHAilHLLYaRF~~K~L~D~G~v~~~EPF~~Ll~QGMV~~~~-~k~-ks~Gn~v~p~ev~~~ 103 (107)
..++|.|+|+++||.++...|..+.......+. ...||++++.+|||+.+. .|| ||+||+|+|+|++..
T Consensus 220 ~~~~~~~~di~~~G~D~~~~h~~~~~~~~~~~~------~~~~~~~~~~~g~~~~~~g~KmSKS~gn~v~~~d~~~~ 290 (312)
T cd00668 220 WFKDSYPADWHLIGKDILRGWANFWITMLVALF------GEIPPKNLLVHGFVLDEGGQKMSKSKGNVIDPSDVVEK 290 (312)
T ss_pred hhhhcCCceEEEEecchhhhHHHHHHHHHHHhc------CCCCcceeEECcEEEcCCCccccccCCCcCCHHHHHHH
Confidence 456778999999999999999888877666542 124899999999999888 775 999999999998753
No 24
>PLN02943 aminoacyl-tRNA ligase
Probab=98.60 E-value=2.2e-08 Score=91.01 Aligned_cols=70 Identities=19% Similarity=0.346 Sum_probs=54.0
Q ss_pred hhhhcccccceEEeecchhHHHHHHHHHHHHHHHHhcCCC-CCCCccccccccceeec-Ceeee-cCCCceeCCCceeec
Q psy1520 27 TDKAQDWLPVDIYIGGKEHAVLHLYYARFIAHFLHAQGKT-PAREPFKRLLVQGMIMG-QTYRE-KTSGKYLKPDEVFTK 103 (107)
Q Consensus 27 ~~~~~~WmPVD~YIGGiEHAilHLLYaRF~~K~L~D~G~v-~~~EPF~~Ll~QGMV~~-~~~k~-ks~Gn~v~p~ev~~~ 103 (107)
.+..++|.|+|+|+.|.+.. |||--.|.-+|+- ....||++++.||+|++ ++.|| ||+||+|+|.|++.+
T Consensus 528 ~~~~~~~yP~dl~~~G~Dii-------~fW~a~m~~~~~~~~~~~Pf~~v~~hg~v~~~~G~KMSKS~GN~i~p~~~i~~ 600 (958)
T PLN02943 528 AEDFKKFYPTTVLETGHDIL-------FFWVARMVMMGIEFTGTVPFSYVYLHGLIRDSQGRKMSKTLGNVIDPLDTIKE 600 (958)
T ss_pred hHHHhccCCCeEEEEeehHH-------HHHHHHHHHhhhhhcCCCChheEEEeccEECCCCCcccCcCCCCCCHHHHHHh
Confidence 45678999999999998876 3444443334553 34679999999999986 66675 999999999998754
No 25
>COG0060 IleS Isoleucyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=98.56 E-value=1.5e-08 Score=92.62 Aligned_cols=66 Identities=23% Similarity=0.441 Sum_probs=55.0
Q ss_pred ccccc---eEEeecchhHHHHHHHHHHHHHHHHhcCCCCCCCccccccccceeecCe-eee-cCCCceeCCCceeec
Q psy1520 32 DWLPV---DIYIGGKEHAVLHLYYARFIAHFLHAQGKTPAREPFKRLLVQGMIMGQT-YRE-KTSGKYLKPDEVFTK 103 (107)
Q Consensus 32 ~WmPV---D~YIGGiEHAilHLLYaRF~~K~L~D~G~v~~~EPF~~Ll~QGMV~~~~-~k~-ks~Gn~v~p~ev~~~ 103 (107)
.|.|- |+|..|+++.++| |+..|--.-.+...-||+++|+||+|+++. .|| ||.||+|+|.||+++
T Consensus 549 ~~~~~~~aD~~lEGsDQ~RGW------F~Ssl~~s~a~~~~aPYk~vltHGfvlDe~GrKMSKSlGN~v~P~~V~~~ 619 (933)
T COG0060 549 LKFPALFADFYLEGSDQTRGW------FYSSLLTSTALFGRAPYKNVLTHGFVLDEKGRKMSKSLGNVVDPQDVIDK 619 (933)
T ss_pred ccCccccCcEEEEeccccchh------HHHHHHHHHHHcCCchHHHHhhcccEECCCCCCccccCCCcCCHHHHHHh
Confidence 44454 9999999999998 666666666667799999999999999855 565 999999999999864
No 26
>PLN02882 aminoacyl-tRNA ligase
Probab=98.51 E-value=6.7e-08 Score=89.64 Aligned_cols=70 Identities=20% Similarity=0.365 Sum_probs=52.9
Q ss_pred hhhcccccceEEeecchhHHHHHHHHHHHHHHHHhcCCCCCCCccccccccceeec-Ceeee-cCCCceeCCCceeec
Q psy1520 28 DKAQDWLPVDIYIGGKEHAVLHLYYARFIAHFLHAQGKTPAREPFKRLLVQGMIMG-QTYRE-KTSGKYLKPDEVFTK 103 (107)
Q Consensus 28 ~~~~~WmPVD~YIGGiEHAilHLLYaRF~~K~L~D~G~v~~~EPF~~Ll~QGMV~~-~~~k~-ks~Gn~v~p~ev~~~ 103 (107)
+..+.+.|+|+++-|.++..+|..++=+.+-+ +-...||++++.||+|+. ++.|| ||+||+|+|.+++.+
T Consensus 560 ~~f~~~~PaD~i~eG~Dq~RgWf~~ll~~s~~------l~~~~pfk~VivhG~vlde~G~KMSKSlGNvIdP~evi~~ 631 (1159)
T PLN02882 560 ELFEKNFPADFVAEGLDQTRGWFYTLMVLSTA------LFDKPAFKNLICNGLVLAEDGKKMSKSLKNYPDPNEVIDK 631 (1159)
T ss_pred hHhhccCCceEEEEecchhhhHHHHHHHHHHH------hcCCCCcceeEEccEEECCCCCCcccCCCCCCCHHHHHHH
Confidence 33455689999999999999983222222222 234589999999999998 56775 999999999998753
No 27
>PLN02843 isoleucyl-tRNA synthetase
Probab=98.50 E-value=3.4e-08 Score=89.96 Aligned_cols=66 Identities=20% Similarity=0.420 Sum_probs=52.2
Q ss_pred cccccceEEeecchhHHHHHHHHHHHHHHHHhcCCCCCCCccccccccceeec-Ceeee-cCCCceeCCCceee
Q psy1520 31 QDWLPVDIYIGGKEHAVLHLYYARFIAHFLHAQGKTPAREPFKRLLVQGMIMG-QTYRE-KTSGKYLKPDEVFT 102 (107)
Q Consensus 31 ~~WmPVD~YIGGiEHAilHLLYaRF~~K~L~D~G~v~~~EPF~~Ll~QGMV~~-~~~k~-ks~Gn~v~p~ev~~ 102 (107)
+.+.|.|+|+.|.++..+|+-.+=+.+-. .....||+++++||+|+. ++.|| ||+||+|+|.+++.
T Consensus 560 ~~~~PaDl~~eG~Di~rgWf~s~l~~~~~------~~g~~Pfk~v~~HG~vld~~G~KMSKSlGNvI~p~~vi~ 627 (974)
T PLN02843 560 GLSYPADLYLEGSDQHRGWFQSSLLTSVA------TKGKAPYKSVLTHGFVLDEKGFKMSKSLGNVVDPRLVIE 627 (974)
T ss_pred ccCCCceeeeeeccccchHHHHHHHHHHH------hcCCCccceEEEeccEECCCCCCcCCCCCCcCCHHHHHh
Confidence 35679999999999999984443333322 244679999999999998 46775 99999999999876
No 28
>cd00818 IleRS_core catalytic core domain of isoleucyl-tRNA synthetases. Isoleucine amino-acyl tRNA synthetases (IleRS) catalytic core domain . This class I enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. IleRS has an insertion in the core domain, which is subject to both deletions and rearrangements. This editing region hydrolyzes mischarged cognate tRNAs and thus prevents the incorporation of chemically similar amino acids.
Probab=98.44 E-value=8.8e-08 Score=77.34 Aligned_cols=69 Identities=22% Similarity=0.482 Sum_probs=52.3
Q ss_pred hhcccccceEEeecchhHHHHHHHHHHHHHHHHhcCCCCCCCccccccccceeec-Ceeee-cCCCceeCCCceeec
Q psy1520 29 KAQDWLPVDIYIGGKEHAVLHLYYARFIAHFLHAQGKTPAREPFKRLLVQGMIMG-QTYRE-KTSGKYLKPDEVFTK 103 (107)
Q Consensus 29 ~~~~WmPVD~YIGGiEHAilHLLYaRF~~K~L~D~G~v~~~EPF~~Ll~QGMV~~-~~~k~-ks~Gn~v~p~ev~~~ 103 (107)
..++|.|+|+++-|.++...|+-+.=| ...+ +....||++++.+|+++. ++.|| ||+||+|.|+|++..
T Consensus 246 ~~~~~~p~d~~~~GkDii~~wf~~~~~-~~~~-----~~~~~p~~~~~~hg~~~~~~g~KmSKS~gn~i~~~~~~~~ 316 (338)
T cd00818 246 DFEELFPADFILEGSDQTRGWFYSLLL-LSTA-----LFGKAPYKNVIVHGFVLDEDGRKMSKSLGNYVDPQEVVDK 316 (338)
T ss_pred hhhccCCCeEEeecchHHhHHHHHHHH-HHHH-----hcCCCccceEEEEeeEECCCCCCCCCCCCCcCCHHHHHHH
Confidence 467889999999999999876333322 2222 233689999999999986 46664 999999999998653
No 29
>KOG0433|consensus
Probab=98.29 E-value=2.2e-07 Score=84.30 Aligned_cols=64 Identities=19% Similarity=0.362 Sum_probs=55.8
Q ss_pred ccceEEeecchhHHHHHHHHHHHHHHHHhcCCCCCCCccccccccceeecCe-eee-cCCCceeCCCceeec
Q psy1520 34 LPVDIYIGGKEHAVLHLYYARFIAHFLHAQGKTPAREPFKRLLVQGMIMGQT-YRE-KTSGKYLKPDEVFTK 103 (107)
Q Consensus 34 mPVD~YIGGiEHAilHLLYaRF~~K~L~D~G~v~~~EPF~~Ll~QGMV~~~~-~k~-ks~Gn~v~p~ev~~~ 103 (107)
-+.|+|..|.++.++| |...|-..-.+....||+.+++||+++++. +|| ||.||||+|+.|++.
T Consensus 565 ~~aDv~LEG~DQ~rGW------FQSsLLTsvA~q~kAPYk~vivHGFtlDE~G~KMSKSlGNVidP~~v~~G 630 (937)
T KOG0433|consen 565 HVADVYLEGVDQFRGW------FQSSLLTSVAVQNKAPYKKVIVHGFTLDENGNKMSKSLGNVVDPTMVTDG 630 (937)
T ss_pred cceeeEEecchhcchH------HHHHHHHHHHHhccCCchheeeeeeEecCCccchhhcccCcCCHHHHhCC
Confidence 3799999999999998 777777777777889999999999999965 675 999999999998764
No 30
>PRK11893 methionyl-tRNA synthetase; Reviewed
Probab=98.27 E-value=3.7e-07 Score=75.73 Aligned_cols=68 Identities=21% Similarity=0.334 Sum_probs=54.9
Q ss_pred hhcccccceEEeecchhHHHHHHHHHHHHHHHHhcCCCCCCCccccccccceeecCeeee-cCCCceeCCCceeec
Q psy1520 29 KAQDWLPVDIYIGGKEHAVLHLYYARFIAHFLHAQGKTPAREPFKRLLVQGMIMGQTYRE-KTSGKYLKPDEVFTK 103 (107)
Q Consensus 29 ~~~~WmPVD~YIGGiEHAilHLLYaRF~~K~L~D~G~v~~~EPF~~Ll~QGMV~~~~~k~-ks~Gn~v~p~ev~~~ 103 (107)
..++|.|.|++++|.++..-|..+---+...+ | ...| +..+.+|||+.++.|| ||+||+|+|.|++..
T Consensus 248 ~~~~~~~~D~~~~G~D~~~~h~~~~~a~~~a~---~---~~~p-~~~~~~g~v~~~G~KMSKS~GN~i~~~dll~~ 316 (511)
T PRK11893 248 LFNKYWPADVHLIGKDILRFHAVYWPAFLMAA---G---LPLP-KRVFAHGFLTLDGEKMSKSLGNVIDPFDLVDE 316 (511)
T ss_pred HHHhcCCCcceEecccccccchhHHHHHHHhC---C---CCCC-CEEEeeccEEECCeeecccCCcEEcHHHHHHH
Confidence 35677799999999999999988854333332 3 3677 9999999999988885 999999999998754
No 31
>PRK12267 methionyl-tRNA synthetase; Reviewed
Probab=98.03 E-value=2.4e-06 Score=74.12 Aligned_cols=66 Identities=23% Similarity=0.416 Sum_probs=55.2
Q ss_pred cccccceEEeecchhHHHHHHHHHHHHHHHHhcCCCCCCCccccccccceeecCeeee-cCCCceeCCCceeec
Q psy1520 31 QDWLPVDIYIGGKEHAVLHLYYARFIAHFLHAQGKTPAREPFKRLLVQGMIMGQTYRE-KTSGKYLKPDEVFTK 103 (107)
Q Consensus 31 ~~WmPVD~YIGGiEHAilHLLYaRF~~K~L~D~G~v~~~EPF~~Ll~QGMV~~~~~k~-ks~Gn~v~p~ev~~~ 103 (107)
+.|-|.|+++-|.+...-|.+| |.-+|.-.|+ .|+++++.+|+++.++.|| ||+||+|+|.|++..
T Consensus 250 ~~~wp~~~~~~GkDii~fH~i~---wpa~l~~~~~----~~p~~v~~hg~l~~eg~KMSKS~GN~i~p~d~l~~ 316 (648)
T PRK12267 250 KKFWPADVHLVGKDILRFHAIY---WPIMLMALGL----PLPKKVFAHGWWLMKDGKMSKSKGNVVDPEELVDR 316 (648)
T ss_pred HhhcccceEEEeeeecchhHHH---HHHHHHhCCC----CCCcEEEecceEEECCceecccCCcccCHHHHHHH
Confidence 3344999999999999989875 6666666663 5999999999999988875 999999999998653
No 32
>TIGR00398 metG methionyl-tRNA synthetase. The methionyl-tRNA synthetase (metG) is a class I amino acyl-tRNA ligase. This model appears to recognize the methionyl-tRNA synthetase of every species, including eukaryotic cytosolic and mitochondrial forms. The UPGMA difference tree calculated after search and alignment according to this model shows an unusual deep split between two families of MetG. One family contains forms from the Archaea, yeast cytosol, spirochetes, and E. coli, among others. The other family includes forms from yeast mitochondrion, Synechocystis sp., Bacillus subtilis, the Mycoplasmas, Aquifex aeolicus, and Helicobacter pylori. The E. coli enzyme is homodimeric, although monomeric forms can be prepared that are fully active. Activity of this enzyme in bacteria includes aminoacylation of fMet-tRNA with Met; subsequent formylation of the Met to fMet is catalyzed by a separate enzyme. Note that the protein from Aquifex aeolicus is split into an alpha (large) and beta (sma
Probab=97.99 E-value=4.2e-06 Score=70.48 Aligned_cols=68 Identities=19% Similarity=0.333 Sum_probs=55.1
Q ss_pred hhcccccce-----EEeecchhHHHHHHHHHHHHHHHHhcCCCCCCCccccccccceeecCeeee-cCCCceeCCCceee
Q psy1520 29 KAQDWLPVD-----IYIGGKEHAVLHLYYARFIAHFLHAQGKTPAREPFKRLLVQGMIMGQTYRE-KTSGKYLKPDEVFT 102 (107)
Q Consensus 29 ~~~~WmPVD-----~YIGGiEHAilHLLYaRF~~K~L~D~G~v~~~EPF~~Ll~QGMV~~~~~k~-ks~Gn~v~p~ev~~ 102 (107)
..+.|.|-| +++-|.+-..-|.+|-. -+|..+|+ .|+++++.+|||+.++.|| ||+||+|+|+|++.
T Consensus 271 ~~~~~w~~~~~~~~v~~~G~Di~~~h~~~~~---a~l~~~~~----~~~~~~~~~g~v~~~g~KmSKS~Gn~i~~~d~i~ 343 (530)
T TIGR00398 271 DWKKWWNNDEDAELIHFIGKDIVRFHTIYWP---AMLMGLGL----PLPTQVFSHGYLTVEGGKMSKSLGNVVDPSDLLA 343 (530)
T ss_pred hHHHhCCCCCCceEEEEEecccchhHHHHHH---HHHHhCCC----CCCCEEEeeccEEECCceecccCCceecHHHHHH
Confidence 345677888 99999999999977643 34555563 5899999999999998885 99999999999865
Q ss_pred c
Q psy1520 103 K 103 (107)
Q Consensus 103 ~ 103 (107)
.
T Consensus 344 ~ 344 (530)
T TIGR00398 344 R 344 (530)
T ss_pred H
Confidence 3
No 33
>cd00814 MetRS_core catalytic core domain of methioninyl-tRNA synthetases. Methionine tRNA synthetase (MetRS) catalytic core domain. This class I enzyme aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. MetRS, which consists of the core domain and an anti-codon binding domain, functions as a monomer. However, in some species the anti-codon binding domain is followed by an EMAP domain. In this case, MetRS functions as a homodimer. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. As a result of a deletion event, MetRS has a significantly shorter core domain insertion than IleRS, ValRS, and LeuR. Consequently, the MetRS insertion lacks the editing function.
Probab=97.79 E-value=1.9e-05 Score=62.96 Aligned_cols=64 Identities=19% Similarity=0.326 Sum_probs=53.6
Q ss_pred cccceEEeecchhHHHHHHHHHHHHHHHHhcCCCCCCCccccccccceeecCeeee-cCCCceeCCCceeec
Q psy1520 33 WLPVDIYIGGKEHAVLHLYYARFIAHFLHAQGKTPAREPFKRLLVQGMIMGQTYRE-KTSGKYLKPDEVFTK 103 (107)
Q Consensus 33 WmPVD~YIGGiEHAilHLLYaRF~~K~L~D~G~v~~~EPF~~Ll~QGMV~~~~~k~-ks~Gn~v~p~ev~~~ 103 (107)
+-|.|+++.|.+...-|.+ ||--.|...| -.|+++++.+|+++.++.|| ||+||+|+|.|++..
T Consensus 233 ~~~~~v~~~G~D~~~fh~~---~~pa~l~~~~----~~~~~~~~~~~~~~~~g~kmSkS~gn~i~~~~~l~~ 297 (319)
T cd00814 233 GWPELVHFIGKDIIRFHAI---YWPAMLLGAG----LPLPTRIVAHGYLTVEGKKMSKSRGNVVDPDDLLER 297 (319)
T ss_pred CCCceEEEEeechhhhhHH---HHHHHHHhCC----CCCCcEeeeeeeEEECCeeecccCCcccCHHHHHHH
Confidence 3489999999999998876 5555676677 36899999999999988875 999999999998654
No 34
>cd00672 CysRS_core catalytic core domain of cysteinyl tRNA synthetase. Cysteinyl tRNA synthetase (CysRS) catalytic core domain. This class I enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding.
Probab=97.74 E-value=1.4e-05 Score=61.67 Aligned_cols=62 Identities=19% Similarity=0.272 Sum_probs=50.4
Q ss_pred cceEEeecchhHHHHHHHHHHHHHHHHhcCCCCCCCcccccccc-ceeecCeeee-cCCCceeCCCceeec
Q psy1520 35 PVDIYIGGKEHAVLHLYYARFIAHFLHAQGKTPAREPFKRLLVQ-GMIMGQTYRE-KTSGKYLKPDEVFTK 103 (107)
Q Consensus 35 PVD~YIGGiEHAilHLLYaRF~~K~L~D~G~v~~~EPF~~Ll~Q-GMV~~~~~k~-ks~Gn~v~p~ev~~~ 103 (107)
|+|+..||++|.--|+-+.++.+.++.+ +||.+-+.+ |||.-++-|| ||+||+|+|+|++..
T Consensus 128 ~~dih~~G~Dl~fpH~~~~~a~~~a~~g-------~~~~~~~~h~~~v~~~g~KMSKs~Gn~v~~~dll~~ 191 (213)
T cd00672 128 TFDIHGGGVDLIFPHHENEIAQSEAATG-------KPFARYWLHTGHLTIDGEKMSKSLGNFITVRDALKK 191 (213)
T ss_pred CccEEeecCCCCcChHHHHHHHHHHHhC-------CCCCcEEEEEEEEeccCcchhhcCCCccCHHHHHHH
Confidence 7999999999999999999999988763 277765555 6666666664 999999999998653
No 35
>TIGR00435 cysS cysteinyl-tRNA synthetase. This model finds the cysteinyl-tRNA synthetase from most but not from all species. The enzyme from one archaeal species, Archaeoglobus fulgidus, is found but the equivalent enzymes from some other Archaea, including Methanococcus jannaschii, are not found, although biochemical evidence suggests that tRNA(Cys) in these species are charged directly with Cys rather than through a misacylation and correction pathway as for tRNA(Gln).
Probab=97.51 E-value=4.1e-05 Score=64.90 Aligned_cols=63 Identities=17% Similarity=0.226 Sum_probs=51.9
Q ss_pred cceEEeecchhHHHHHHHHHHHHHHHHhcCCCCCCCccccccccceeecCeeee-cCCCceeCCCceeec
Q psy1520 35 PVDIYIGGKEHAVLHLYYARFIAHFLHAQGKTPAREPFKRLLVQGMIMGQTYRE-KTSGKYLKPDEVFTK 103 (107)
Q Consensus 35 PVD~YIGGiEHAilHLLYaRF~~K~L~D~G~v~~~EPF~~Ll~QGMV~~~~~k~-ks~Gn~v~p~ev~~~ 103 (107)
|+|+..||++|.--|+-+-+..+.++.. ..|.+.++..|||.-++.|| ||+||+|.|.|++..
T Consensus 219 ~~Dih~gG~Dl~fpHhene~aqs~a~~g------~~~~~~~~h~g~v~~~g~KMSKS~GN~i~~~dll~~ 282 (465)
T TIGR00435 219 QIDIHGGGVDLIFPHHENEIAQSEAAFG------KQLAKYWMHNGFLMIDNEKMSKSLGNFFTVRDVLKN 282 (465)
T ss_pred CceeeccccccccchHHHHHHHHHHhcC------CCCCcEEEEeeEEEecCccccccCCCcCCHHHHHHH
Confidence 6999999999999999999999988653 23444457789998877775 999999999998653
No 36
>PRK12268 methionyl-tRNA synthetase; Reviewed
Probab=97.45 E-value=8e-05 Score=63.17 Aligned_cols=64 Identities=17% Similarity=0.289 Sum_probs=50.4
Q ss_pred cceEEeecchhHHHHHHHHHHHHHHHHhcCCCCCCCccccccccceeecCeeee-cCCCceeCCCceeec
Q psy1520 35 PVDIYIGGKEHAVLHLYYARFIAHFLHAQGKTPAREPFKRLLVQGMIMGQTYRE-KTSGKYLKPDEVFTK 103 (107)
Q Consensus 35 PVD~YIGGiEHAilHLLYaRF~~K~L~D~G~v~~~EPF~~Ll~QGMV~~~~~k~-ks~Gn~v~p~ev~~~ 103 (107)
|-++.+=|.|...-| +.+|.-.|...|. +..-| ++++++|||+.++.|| ||+||+|+|.|++.+
T Consensus 287 ~~~~~~~G~D~~~Fh---~~~~p~~l~~~~~-~~~~P-~~v~~~G~v~~~G~KMSKS~GN~I~p~dli~~ 351 (556)
T PRK12268 287 TKSYYFIGKDNIPFH---SIIWPAMLLGSGE-PLKLP-DEIVSSEYLTLEGGKFSKSRGWGIWVDDALER 351 (556)
T ss_pred CeEEEEEeeccCcch---HHHHHHHHHhcCC-CCCCC-CEeeccCCEEECCeeeccCCCcccCHHHHHHH
Confidence 556888899987755 4556677878876 45556 5999999999888775 999999999998754
No 37
>PRK00260 cysS cysteinyl-tRNA synthetase; Validated
Probab=97.39 E-value=5.2e-05 Score=63.99 Aligned_cols=62 Identities=19% Similarity=0.307 Sum_probs=49.0
Q ss_pred cceEEeecchhHHHHHHHHHHHHHHHHhcCCCCCCCccccccc-cceeecCeeee-cCCCceeCCCceeec
Q psy1520 35 PVDIYIGGKEHAVLHLYYARFIAHFLHAQGKTPAREPFKRLLV-QGMIMGQTYRE-KTSGKYLKPDEVFTK 103 (107)
Q Consensus 35 PVD~YIGGiEHAilHLLYaRF~~K~L~D~G~v~~~EPF~~Ll~-QGMV~~~~~k~-ks~Gn~v~p~ev~~~ 103 (107)
|+|+..||++|.--|+=.-.+-+..+. | .||.+... .|||..++.|| ||+||+|+|.|++..
T Consensus 220 ~~Dih~gG~DlifpHh~neiaqs~a~~--g-----~p~~~~w~H~g~v~~~G~KMSKS~GN~i~~~dll~~ 283 (463)
T PRK00260 220 TFDIHGGGADLIFPHHENEIAQSEAAT--G-----KPFANYWMHNGFVTVNGEKMSKSLGNFFTIRDLLKK 283 (463)
T ss_pred CcceecCccccCCCchHhHHHHHHHhc--C-----CCcceEEEEccEEccCCCcccCcCCCCCCHHHHHHH
Confidence 799999999999999866655555543 2 79988666 58888777775 999999999998753
No 38
>COG0525 ValS Valyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=97.34 E-value=0.00014 Score=66.92 Aligned_cols=70 Identities=24% Similarity=0.561 Sum_probs=52.0
Q ss_pred hhhcccccceEEeecchhHHHHHHHHHHHHHHHHhcCCCCCCCccccccccceeecCe-eee-cCCCceeCCCceeec
Q psy1520 28 DKAQDWLPVDIYIGGKEHAVLHLYYARFIAHFLHAQGKTPAREPFKRLLVQGMIMGQT-YRE-KTSGKYLKPDEVFTK 103 (107)
Q Consensus 28 ~~~~~WmPVD~YIGGiEHAilHLLYaRF~~K~L~D~G~v~~~EPF~~Ll~QGMV~~~~-~k~-ks~Gn~v~p~ev~~~ 103 (107)
+..++..|.|+-+=|- =|++.-=||++-..++=. .+.||+.++-||||.++. .|| ||+||+|+|.|++.+
T Consensus 471 ~~l~~fyPt~llvtG~--DIIffWvarmi~~~~~~~----~~~PFk~V~ihGLVrDe~G~KMSKS~GNvIDP~d~I~~ 542 (877)
T COG0525 471 PDLKKFYPTDLLVTGH--DIIFFWVARMIMRGLHLT----GEVPFKDVYIHGLVRDEQGRKMSKSKGNVIDPLDVIDK 542 (877)
T ss_pred hHHHhcCCCccccccc--hhhHHHHHHHHHHHHHhc----CCCCccEEEEeeeEEcCCCCCCcccCCCcCCHHHHHHH
Confidence 3455666999999994 466554555555554433 358999999999999865 565 999999999998753
No 39
>PRK12418 cysteinyl-tRNA synthetase; Provisional
Probab=97.28 E-value=9.7e-05 Score=62.02 Aligned_cols=64 Identities=23% Similarity=0.250 Sum_probs=52.3
Q ss_pred cceEEeecchhHHHHHHHHHHHHHHHHhcCCCCCCCcccccccc-ceeecCeeee-cCCCceeCCCceeecC
Q psy1520 35 PVDIYIGGKEHAVLHLYYARFIAHFLHAQGKTPAREPFKRLLVQ-GMIMGQTYRE-KTSGKYLKPDEVFTKG 104 (107)
Q Consensus 35 PVD~YIGGiEHAilHLLYaRF~~K~L~D~G~v~~~EPF~~Ll~Q-GMV~~~~~k~-ks~Gn~v~p~ev~~~~ 104 (107)
|+|+-.||+++.--|+=+-++-+.++.+ ..||.+.+.| |||..++.|| ||+||+|+|.|+++.|
T Consensus 214 ~~DIH~GG~DL~FPHHeneiaq~~a~~g------~~~~~~~w~H~g~l~~~G~KMSKSlGN~i~~~ell~~G 279 (384)
T PRK12418 214 GFDIQGGGSDLIFPHHEFSAAHAEAATG------ERRFARHYVHAGMIGLDGEKMSKSRGNLVFVSRLRAAG 279 (384)
T ss_pred CcccccCccccccchhHhHHHHHHHhcC------CCCcceEEEECCEECCCCCcccCcCCCcCCHHHHHhcc
Confidence 4999999999999999999988887643 3599998887 5555566775 9999999999986543
No 40
>PRK00133 metG methionyl-tRNA synthetase; Reviewed
Probab=97.02 E-value=0.00042 Score=60.84 Aligned_cols=59 Identities=15% Similarity=0.267 Sum_probs=47.4
Q ss_pred EEeecchhHHHHHHHHHHHHHHHHhcCCCCCCCccccccccceeecCeeee-cCCCceeCCCceeec
Q psy1520 38 IYIGGKEHAVLHLYYARFIAHFLHAQGKTPAREPFKRLLVQGMIMGQTYRE-KTSGKYLKPDEVFTK 103 (107)
Q Consensus 38 ~YIGGiEHAilHLLYaRF~~K~L~D~G~v~~~EPF~~Ll~QGMV~~~~~k~-ks~Gn~v~p~ev~~~ 103 (107)
+.+=|.+-..-| +.||--+|.-.|+ .+.++++.+|||+.++.|| ||+||+|+|.|++.+
T Consensus 287 v~~iGkDi~~fH---~i~wpa~l~a~g~----~lP~~v~~hg~v~~~G~KMSKS~GNvV~p~dlie~ 346 (673)
T PRK00133 287 YHFIGKDIIYFH---TLFWPAMLEGAGY----RLPTNVFAHGFLTVEGAKMSKSRGTFIWARTYLDH 346 (673)
T ss_pred EEEEeecchhHH---HHHHHHHHHhCCC----CCCCEEeeeccEEecCCcccccCCcccCHHHHHHH
Confidence 677778887766 5567777777775 3459999999999988875 999999999998754
No 41
>TIGR03447 mycothiol_MshC cysteine--1-D-myo-inosityl 2-amino-2-deoxy-alpha-D-glucopyranoside ligase. Members of this protein family are MshC, l-cysteine:1-D-myo-inosityl 2-amino-2-deoxy-alpha-D-glucopyranoside ligase, an enzyme that uses ATP to ligate a Cys residue to a mycothiol precursor molecule, in the second to last step in mycothiol biosynthesis. This enzyme shows considerable homology to Cys--tRNA ligases, and many instances are misannotated as such. Mycothiol is found in Mycobacterium tuberculosis, Corynebacterium glutamicum, Streptomyces coelicolor, and various other members of the Actinobacteria. Mycothiol is an analog to glutathione.
Probab=96.97 E-value=0.00031 Score=59.62 Aligned_cols=62 Identities=21% Similarity=0.184 Sum_probs=52.5
Q ss_pred ceEEeecchhHHHHHHHHHHHHHHHHhcCCCCCCCcccccccc-ceeecCeeee-cCCCceeCCCceeec
Q psy1520 36 VDIYIGGKEHAVLHLYYARFIAHFLHAQGKTPAREPFKRLLVQ-GMIMGQTYRE-KTSGKYLKPDEVFTK 103 (107)
Q Consensus 36 VD~YIGGiEHAilHLLYaRF~~K~L~D~G~v~~~EPF~~Ll~Q-GMV~~~~~k~-ks~Gn~v~p~ev~~~ 103 (107)
+|+-.||+++.-=|+-+-++-+.++. ...||.+...| |||..++.|| ||+||+|++.|+++.
T Consensus 242 ~Dih~GG~DLifpHheneiaq~~A~~------g~~~~~~~w~H~g~l~~~G~KMSKSlGN~i~~~dl~~~ 305 (411)
T TIGR03447 242 FDIQGGGSDLIFPHHEFSAAHAEAAT------GVRRMARHYVHAGMIGLDGEKMSKSLGNLVFVSKLRAA 305 (411)
T ss_pred eecccCcccccccchHhHHHHHHHhc------CCCCcceEEEECCEECcCCCCccCcCCCCCCHHHHHhc
Confidence 99999999999999999999988753 23599998877 6777677775 999999999998754
No 42
>PLN02224 methionine-tRNA ligase
Probab=96.95 E-value=0.00047 Score=60.85 Aligned_cols=66 Identities=24% Similarity=0.312 Sum_probs=52.8
Q ss_pred cccccceEEeecchhHHHHHHHHHHHHHHHHhcCCCCCCCccccccccceeecCeeee-cCCCceeCCCceeec
Q psy1520 31 QDWLPVDIYIGGKEHAVLHLYYARFIAHFLHAQGKTPAREPFKRLLVQGMIMGQTYRE-KTSGKYLKPDEVFTK 103 (107)
Q Consensus 31 ~~WmPVD~YIGGiEHAilHLLYaRF~~K~L~D~G~v~~~EPF~~Ll~QGMV~~~~~k~-ks~Gn~v~p~ev~~~ 103 (107)
.+|-|.|+.+.|.+-..-|.+| |--+|...|+ .+-++++.+|+++-++-|| ||+||+|+|.|++..
T Consensus 317 ~~~w~~~v~~iGKDii~fH~i~---wpa~l~~~g~----~~P~~i~~~g~l~~eG~KMSKS~GN~i~p~e~l~~ 383 (616)
T PLN02224 317 SFGWPASLHLIGKDILRFHAVY---WPAMLMSAGL----ELPKMVFGHGFLTKDGMKMGKSLGNTLEPFELVQK 383 (616)
T ss_pred ccCCCcceEEEeecccccHHHH---HHHHHHHCCC----CCCcEEEecccEecCCccccccCCccCCHHHHHHH
Confidence 3445999999999988877655 5666777774 3559999999999888875 999999999997653
No 43
>KOG0432|consensus
Probab=96.32 E-value=0.0021 Score=59.71 Aligned_cols=67 Identities=24% Similarity=0.509 Sum_probs=46.2
Q ss_pred hcccccceEEeecchhHHHHHHHHHHHHHHHHhcCCCCCCCccccccccceeecC-eeee-cCCCceeCCCceee
Q psy1520 30 AQDWLPVDIYIGGKEHAVLHLYYARFIAHFLHAQGKTPAREPFKRLLVQGMIMGQ-TYRE-KTSGKYLKPDEVFT 102 (107)
Q Consensus 30 ~~~WmPVD~YIGGiEHAilHLLYaRF~~K~L~D~G~v~~~EPF~~Ll~QGMV~~~-~~k~-ks~Gn~v~p~ev~~ 102 (107)
.+...|.++-==| |=||-.--||+.---|. +...-||++.+-||||.+. +.|| ||.||||+|-||+.
T Consensus 541 ~~~fyP~sllETG--~DILfFWVaRMvmLg~k----LtG~lPF~~V~LH~mVRDa~GRKMSKSLGNVIDPlDVI~ 609 (995)
T KOG0432|consen 541 FKNFYPLSLLETG--HDILFFWVARMVMLGLK----LTGELPFKEVLLHGLVRDAHGRKMSKSLGNVIDPLDVID 609 (995)
T ss_pred HHhcCCchhhhcC--chHHHHHHHHHHHhhhh----hcCCCCchheeechhhccccccccchhhccccCHHHHhc
Confidence 3444566655444 55666445555433332 2367799999999999974 4665 99999999999875
No 44
>PRK00750 lysK lysyl-tRNA synthetase; Reviewed
Probab=96.19 E-value=0.0035 Score=54.03 Aligned_cols=72 Identities=21% Similarity=0.333 Sum_probs=51.0
Q ss_pred CCCChhhhccc--ccceEEeecchhHH-HHHHHHHHHHHHHHhcCCCCCCCccccccccceeecC-eee-ecCCCceeCC
Q psy1520 23 VSFNTDKAQDW--LPVDIYIGGKEHAV-LHLYYARFIAHFLHAQGKTPAREPFKRLLVQGMIMGQ-TYR-EKTSGKYLKP 97 (107)
Q Consensus 23 ~~fd~~~~~~W--mPVD~YIGGiEHAi-lHLLYaRF~~K~L~D~G~v~~~EPF~~Ll~QGMV~~~-~~k-~ks~Gn~v~p 97 (107)
-++-.+=+-+| +-||+.++|.+|+. .+.++.+.-..+| |. .-|+. +..|||+.+ +-| |||+||+|+|
T Consensus 220 L~Wr~dW~~rW~~l~Vd~e~~GkDh~~~s~~~~~~i~~~il---g~---~~P~~--~~y~~v~~~~G~KMSKSkGN~i~~ 291 (510)
T PRK00750 220 LQWKVDWPMRWAALGVDFEPFGKDHASASYDTSKKIAREIL---GG---EPPEP--FVYELFLDKKGEKISKSKGNVITI 291 (510)
T ss_pred cCCCCCcHHHHHHcCCCEEeeCcccCcchHHHHHHHHHHHc---CC---CCCee--eeeeeEEeCCCCcccccCCCccCH
Confidence 34444556677 68999999999998 6655554333233 32 34655 678999987 556 4999999999
Q ss_pred Cceee
Q psy1520 98 DEVFT 102 (107)
Q Consensus 98 ~ev~~ 102 (107)
+|++.
T Consensus 292 ~d~l~ 296 (510)
T PRK00750 292 EDWLE 296 (510)
T ss_pred HHHHH
Confidence 98754
No 45
>PTZ00399 cysteinyl-tRNA-synthetase; Provisional
Probab=96.14 E-value=0.0017 Score=57.59 Aligned_cols=63 Identities=14% Similarity=0.247 Sum_probs=46.3
Q ss_pred cceEEeecchhHHHHHHHHHHHHHHHHhcCCCCCCCcccccccc-ceeecCeeee-cCCCceeCCCceeec
Q psy1520 35 PVDIYIGGKEHAVLHLYYARFIAHFLHAQGKTPAREPFKRLLVQ-GMIMGQTYRE-KTSGKYLKPDEVFTK 103 (107)
Q Consensus 35 PVD~YIGGiEHAilHLLYaRF~~K~L~D~G~v~~~EPF~~Ll~Q-GMV~~~~~k~-ks~Gn~v~p~ev~~~ 103 (107)
|+|+--||+++.-=|.=.-+.-+.++. ...||.+.+.| |+|+-++.|| ||+||+|+|.|++..
T Consensus 268 ~~DIh~gG~DL~FPHHeNEiAQseA~~------~~~~~v~y~~H~G~L~i~G~KMSKSLGNfItp~dlLek 332 (651)
T PTZ00399 268 PIDIHSGGIDLKFPHHDNELAQSEAYF------DKHQWVNYFLHSGHLHIKGLKMSKSLKNFITIRQALSK 332 (651)
T ss_pred cceeeccCCCCCCCcchhHHHHHHHhh------CCCCCCcEEEEEEEEEeccchhhhcCCCcccHHHHHHH
Confidence 689999999886556333333333333 23589888888 9999888875 999999999998753
No 46
>PF09334 tRNA-synt_1g: tRNA synthetases class I (M); InterPro: IPR015413 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This domain is found in methionyl and leucyl tRNA synthetases. ; GO: 0000166 nucleotide binding, 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0006418 tRNA aminoacylation for protein translation, 0005737 cytoplasm; PDB: 2D5B_A 1A8H_A 1WOY_A 2D54_A 4DLP_A 2CT8_B 2CSX_A 1MED_A 1PFU_A 1PFW_A ....
Probab=94.95 E-value=0.011 Score=49.30 Aligned_cols=58 Identities=24% Similarity=0.378 Sum_probs=43.0
Q ss_pred EEeecchhHHHHHHHHHHHHHHHHhcCCCCCCCccccccccceeecCeeee-cCCCceeCCCceee
Q psy1520 38 IYIGGKEHAVLHLYYARFIAHFLHAQGKTPAREPFKRLLVQGMIMGQTYRE-KTSGKYLKPDEVFT 102 (107)
Q Consensus 38 ~YIGGiEHAilHLLYaRF~~K~L~D~G~v~~~EPF~~Ll~QGMV~~~~~k~-ks~Gn~v~p~ev~~ 102 (107)
+++=|.+-+.-|.+|-=. +|.-.|+- +.++++++|+++-++.|+ ||+||+|.|+|++.
T Consensus 285 v~~iGkDi~~fH~i~~pa---~l~a~~~~----lP~~i~~~~~~~~~g~K~SkS~gn~i~~~~~~~ 343 (391)
T PF09334_consen 285 VHFIGKDIIRFHAIYWPA---MLLAAGLP----LPRRIVVHGFLTLDGEKMSKSRGNVIWPDDLLE 343 (391)
T ss_dssp EEEEEGGGHHHHHTHHHH---HHHHCTB-------SEEEEE--EEETTCCEETTTTESSBHHHHHH
T ss_pred EEEEccchhHHHHHHhHH---HHhcccCC----CCCEEEeeeeEEECCeeccccCCcccCHHHHHH
Confidence 788899999999988443 44444443 448999999999988874 99999999998764
No 47
>cd00674 LysRS_core_class_I catalytic core domain of class I lysyl tRNA synthetase. Class I lysyl tRNA synthetase (LysRS) catalytic core domain. This class I enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. The class I LysRS is found only in archaea and some bacteria and has evolved separately from class II LysRS, as the two do not share structural or sequence similarity.
Probab=94.92 E-value=0.012 Score=48.97 Aligned_cols=74 Identities=19% Similarity=0.271 Sum_probs=49.6
Q ss_pred CCCCChhhhccc--ccceEEeecchhHHH--HHHHHHHHHHHHH-hcCCCCCCCccccccccceeecCee-e-ecCCCce
Q psy1520 22 EVSFNTDKAQDW--LPVDIYIGGKEHAVL--HLYYARFIAHFLH-AQGKTPAREPFKRLLVQGMIMGQTY-R-EKTSGKY 94 (107)
Q Consensus 22 ~~~fd~~~~~~W--mPVD~YIGGiEHAil--HLLYaRF~~K~L~-D~G~v~~~EPF~~Ll~QGMV~~~~~-k-~ks~Gn~ 94 (107)
.-++-.+=+-+| +-||+=++|.+|+-- .--- ...+++ -+|. ..|+. +..|||+.+.- | |||+||+
T Consensus 212 KL~Wr~dW~~rW~~l~Vd~E~~GkDh~~~ggs~~~---~~~i~~~ilg~---~~P~~--~~ye~V~l~gg~KMSKSkGnv 283 (353)
T cd00674 212 KLTWRVDWPMRWAILGVDFEPFGKDHASAGGSYDT---GKEIAREIFGG---EPPVP--VMYEFIGLKGGGKMSSSKGNV 283 (353)
T ss_pred ccCCCCCchhhhhhcCCCEEeeCccccccccHHHH---HHHHHHHHhCC---CCCeE--EEeeeEEeCCCCccCCCCCCc
Confidence 445555666777 689999999999832 1222 233333 3444 33644 66799987665 5 5999999
Q ss_pred eCCCceeec
Q psy1520 95 LKPDEVFTK 103 (107)
Q Consensus 95 v~p~ev~~~ 103 (107)
|+|+|++..
T Consensus 284 I~~~dll~~ 292 (353)
T cd00674 284 ITPSDWLEV 292 (353)
T ss_pred CCHHHHHHH
Confidence 999998653
No 48
>PRK01611 argS arginyl-tRNA synthetase; Reviewed
Probab=94.90 E-value=0.013 Score=49.98 Aligned_cols=59 Identities=25% Similarity=0.497 Sum_probs=40.3
Q ss_pred EEeecchhHHHHHHHHHHHHHHHHhcCCCCCCCc-cccccc--cceeecCe-ee-ecCCCceeCCCceeec
Q psy1520 38 IYIGGKEHAVLHLYYARFIAHFLHAQGKTPAREP-FKRLLV--QGMIMGQT-YR-EKTSGKYLKPDEVFTK 103 (107)
Q Consensus 38 ~YIGGiEHAilHLLYaRF~~K~L~D~G~v~~~EP-F~~Ll~--QGMV~~~~-~k-~ks~Gn~v~p~ev~~~ 103 (107)
+||-|.+|. +| ..| ...+++-+|.. ++ ...++. .|||+++. .| ||++||+|+|+|++.+
T Consensus 276 i~V~g~~q~-~h--f~~-~~~~~~~lg~~---~~~~~~~~h~~~glv~~~~g~KMSkR~Gn~i~l~dll~~ 339 (507)
T PRK01611 276 IYVVGADHH-GH--FKR-LKAALKALGYD---PDALEVLLHQMVGLVRGGEGVKMSTRAGNVVTLDDLLDE 339 (507)
T ss_pred EEEECCChH-HH--HHH-HHHHHHHcCCC---cccceEEEEEEEEeeECCCCCcccCCCCceeEHHHHHHH
Confidence 899999998 56 223 33667777753 22 233433 48998854 45 4999999999998764
No 49
>TIGR00456 argS arginyl-tRNA synthetase. This model recognizes arginyl-tRNA synthetase in every completed genome to date. An interesting feature of the alignment of all arginyl-tRNA synthetases is a fairly deep split between two families. One family includes archaeal, eukaryotic and organellar, spirochete, E. coli, and Synechocystis sp. The second, sharing a deletion of about 25 residues in the central region relative to the first, includes Bacillus subtilis, Aquifex aeolicus, the Mycoplasmas and Mycobacteria, and the Gram-negative bacterium Helicobacter pylori.
Probab=94.26 E-value=0.042 Score=47.62 Aligned_cols=56 Identities=30% Similarity=0.474 Sum_probs=40.0
Q ss_pred EEeecchhHHHHHHHHHHHHHHHHhcCCCCCCCccccc--cccceeecCeeeecCCCceeCCCceee
Q psy1520 38 IYIGGKEHAVLHLYYARFIAHFLHAQGKTPAREPFKRL--LVQGMIMGQTYREKTSGKYLKPDEVFT 102 (107)
Q Consensus 38 ~YIGGiEHAilHLLYaRF~~K~L~D~G~v~~~EPF~~L--l~QGMV~~~~~k~ks~Gn~v~p~ev~~ 102 (107)
+||-|.+|. +| ..|.| .+|..+|+-. | .+| +..|||.+.. .+|++||+|+|+|++.
T Consensus 331 I~V~g~~q~-~h--~~~v~-~~l~~lG~~~---~-~~l~h~~~~~V~~~k-mSkr~Gn~V~~~dll~ 388 (566)
T TIGR00456 331 IYVWGSDHH-LH--IAQFF-AILEKLGFYK---K-KELIHLNFGMVPLGS-MKTRRGNVISLDNLLD 388 (566)
T ss_pred EEEecCcHH-HH--HHHHH-HHHHHcCCCC---C-CceEEEEEEEEECCC-CCccCCceeeHHHHHH
Confidence 699999997 55 45544 7888899742 2 345 4566787743 2589999999997654
No 50
>KOG0437|consensus
Probab=94.21 E-value=0.0068 Score=56.26 Aligned_cols=69 Identities=20% Similarity=0.391 Sum_probs=57.5
Q ss_pred hhhcccccceEEeecchhHHHHHHHHHHHHHHHHhcCCCCCCCccccccccceeecCeeee-cCCCceeCCCcee
Q psy1520 28 DKAQDWLPVDIYIGGKEHAVLHLYYARFIAHFLHAQGKTPAREPFKRLLVQGMIMGQTYRE-KTSGKYLKPDEVF 101 (107)
Q Consensus 28 ~~~~~WmPVD~YIGGiEHAilHLLYaRF~~K~L~D~G~v~~~EPF~~Ll~QGMV~~~~~k~-ks~Gn~v~p~ev~ 101 (107)
+..+||.|+|+-++|.+=.=-||.|.=|-|-+|...-.+| +...+.|-++-.+.|| ||+||+..-++-+
T Consensus 656 ~eF~Y~YPiDlrvsGKDLi~NHLtfflynHvAl~~~k~WP-----kgiraNGHLmLNsEKMSKSTGNfmTL~qai 725 (1080)
T KOG0437|consen 656 REFEYFYPIDLRVSGKDLIPNHLTFFLYNHVALFPEKKWP-----KGIRANGHLMLNSEKMSKSTGNFMTLEQAI 725 (1080)
T ss_pred HhhhcccceeeeeccccccccceeEeeeehhhhcccccCc-----cceeeCceEEecchhhccccCCeeeHHHHH
Confidence 5578999999999999999999999888888888866666 4678888888777775 9999998876643
No 51
>PF01406 tRNA-synt_1e: tRNA synthetases class I (C) catalytic domain; InterPro: IPR015803 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. Cysteinyl-tRNA synthetase (6.1.1.16 from EC) is an alpha monomer and belongs to class Ia.; GO: 0000166 nucleotide binding, 0004817 cysteine-tRNA ligase activity, 0005524 ATP binding, 0006423 cysteinyl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 3SP1_B 3TQO_A 3C8Z_B 1LI5_B 1LI7_B 1U0B_B.
Probab=94.04 E-value=0.036 Score=45.73 Aligned_cols=61 Identities=16% Similarity=0.212 Sum_probs=43.9
Q ss_pred cceEEeecchhHHHHHHHHHHHHHHHHhcCCCCCCCcccccc-ccceeecCeeee-cCCCceeCCCceee
Q psy1520 35 PVDIYIGGKEHAVLHLYYARFIAHFLHAQGKTPAREPFKRLL-VQGMIMGQTYRE-KTSGKYLKPDEVFT 102 (107)
Q Consensus 35 PVD~YIGGiEHAilHLLYaRF~~K~L~D~G~v~~~EPF~~Ll-~QGMV~~~~~k~-ks~Gn~v~p~ev~~ 102 (107)
++|+--||+++.-=|.=.-+--+.++.+ +||.+.. -.|||.-++.|| ||.||++...|+.+
T Consensus 206 ~~DIH~GG~DL~FPHHENEiAqs~a~~g-------~~~a~~W~H~g~l~~~g~KMSKSlgN~~~i~dll~ 268 (300)
T PF01406_consen 206 TFDIHGGGIDLIFPHHENEIAQSEAATG-------KPFANYWMHNGHLNVDGEKMSKSLGNFITIRDLLK 268 (300)
T ss_dssp SEEEEEEEGGGTTTHHHHHHHHHHHHHS-------S-SEEEEEEE--EEETTCE--TTTT---BHHHHHT
T ss_pred CceEEccccccCCCCccchHHHHHHhhC-------chHHHHHHHHHHHhhcCccccccCCCEEEHHHHhh
Confidence 6999999999999998777777777763 6777665 459999888886 99999999888764
No 52
>PRK14536 cysS cysteinyl-tRNA synthetase; Provisional
Probab=93.81 E-value=0.035 Score=48.21 Aligned_cols=61 Identities=25% Similarity=0.382 Sum_probs=47.3
Q ss_pred ceEEeecchhHHHHHHHHHHHHHHHHhcCCCCCCCcccc-ccccceeecCeeee-cCCCceeCCCceeec
Q psy1520 36 VDIYIGGKEHAVLHLYYARFIAHFLHAQGKTPAREPFKR-LLVQGMIMGQTYRE-KTSGKYLKPDEVFTK 103 (107)
Q Consensus 36 VD~YIGGiEHAilHLLYaRF~~K~L~D~G~v~~~EPF~~-Ll~QGMV~~~~~k~-ks~Gn~v~p~ev~~~ 103 (107)
+|+..||+++.-=|.-.-+--+.++. | .||.+ .+.+||++-++.|| ||+||+|...|++..
T Consensus 234 ~DIH~GG~DliFPHHeneiAqs~a~~--g-----~~~~~~w~h~g~l~~~g~KMSKSlGN~itl~dll~~ 296 (490)
T PRK14536 234 CDIHIGGVDHIRVHHTNEIAQCEAAT--G-----KPWVRYWLHHEFLLMNKGKMSKSAGQFLTLSSLQEK 296 (490)
T ss_pred eeEEeccccCCCcchhhHHHHHHHhc--C-----CCcceEEEEcCEEeecCccccccCCCcccHHHHHhc
Confidence 89999999999999877776666553 2 46655 55667777666665 999999999998765
No 53
>COG0143 MetG Methionyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=93.22 E-value=0.063 Score=47.47 Aligned_cols=69 Identities=22% Similarity=0.423 Sum_probs=53.3
Q ss_pred hhhcccccce----EEeecchhHHHHHHHHHHHHHHHHhcCCCCCCCccccccccceeecCeeee-cCCCceeCCCceee
Q psy1520 28 DKAQDWLPVD----IYIGGKEHAVLHLYYARFIAHFLHAQGKTPAREPFKRLLVQGMIMGQTYRE-KTSGKYLKPDEVFT 102 (107)
Q Consensus 28 ~~~~~WmPVD----~YIGGiEHAilHLLYaRF~~K~L~D~G~v~~~EPF~~Ll~QGMV~~~~~k~-ks~Gn~v~p~ev~~ 102 (107)
+..+.|-|-| +++=|.|=..=|-+ ||--+|...|+= ..++++++|+++-++-|| ||+||+|.|.+++.
T Consensus 277 ~~~~~~W~~~~~e~vhfIGKDii~FHav---~wPamL~~~~~~----lP~~i~ahg~l~~~G~KmSKSrG~~V~~~~~~~ 349 (558)
T COG0143 277 EDFKKFWPADDTELVHFIGKDIIRFHAV---YWPAMLMAAGLP----LPTRIFAHGFLTLEGQKMSKSRGNVVDPDELLE 349 (558)
T ss_pred HHHHhhCCCCCceEEEEeccccCcchhh---HHHHHHHhCCCC----CCCEEEeeeeEEECCccccccCCcEEeHHHHHH
Confidence 4556666777 56666775555533 488899888876 779999999999988885 99999999999764
Q ss_pred c
Q psy1520 103 K 103 (107)
Q Consensus 103 ~ 103 (107)
.
T Consensus 350 ~ 350 (558)
T COG0143 350 Q 350 (558)
T ss_pred H
Confidence 3
No 54
>PRK14534 cysS cysteinyl-tRNA synthetase; Provisional
Probab=93.15 E-value=0.052 Score=47.14 Aligned_cols=64 Identities=14% Similarity=0.232 Sum_probs=47.9
Q ss_pred cccceEEeecchhHHHHHHHHHHHHHHHHhcCCCCCCCcc-ccccccceeecCeeee-cCCCceeCCCceeec
Q psy1520 33 WLPVDIYIGGKEHAVLHLYYARFIAHFLHAQGKTPAREPF-KRLLVQGMIMGQTYRE-KTSGKYLKPDEVFTK 103 (107)
Q Consensus 33 WmPVD~YIGGiEHAilHLLYaRF~~K~L~D~G~v~~~EPF-~~Ll~QGMV~~~~~k~-ks~Gn~v~p~ev~~~ 103 (107)
|-.+|+..||+++.-=|.-.-+-.+.++. .+|| .-.+.+|||+-++.|| ||.||+|..+|++..
T Consensus 231 g~~~DIH~GG~DliFPHHene~Aqs~a~~-------g~~~~~~W~H~g~l~~~g~KMSKSlGN~i~l~dll~~ 296 (481)
T PRK14534 231 KSTLDIHLGGVDHIGVHHINEIAIAECYL-------NKKWCDMFVHGEFLIMEYEKMSKSNNNFITIKDLEDQ 296 (481)
T ss_pred CCcceEEecccccCCCcchhHHHHHhhhc-------CCCcceEEEEecEEEecCceecccCCCcccHHHHHhc
Confidence 44589999999999888666555554432 2355 5567788999877775 999999999998754
No 55
>PLN02946 cysteine-tRNA ligase
Probab=92.71 E-value=0.04 Score=48.69 Aligned_cols=62 Identities=15% Similarity=0.136 Sum_probs=46.6
Q ss_pred cceEEeecchhHHHHHHHHHHHHHHHHhcCCCCCCCccc-cccccceeecCeeee-cCCCceeCCCceeec
Q psy1520 35 PVDIYIGGKEHAVLHLYYARFIAHFLHAQGKTPAREPFK-RLLVQGMIMGQTYRE-KTSGKYLKPDEVFTK 103 (107)
Q Consensus 35 PVD~YIGGiEHAilHLLYaRF~~K~L~D~G~v~~~EPF~-~Ll~QGMV~~~~~k~-ks~Gn~v~p~ev~~~ 103 (107)
++|+-.||+++.-=|.=.-+.-+.+... .||. --+..|||+-++.|| ||+||+|.+.|++..
T Consensus 277 ~~DIH~GG~DL~FPHHENEiAQsea~~g-------~~~a~yW~H~G~v~~~G~KMSKSlGN~itl~dll~~ 340 (557)
T PLN02946 277 SFDIHGGGMDLVFPHHENEIAQSCAACC-------DSNISYWIHNGFVTVDSEKMSKSLGNFFTIRQVIDL 340 (557)
T ss_pred CeeEeccccccCCCcccchHHHHHHHhC-------CCCCceeeEeeEEEeCCCCcCCcCCCcCCHHHHHHh
Confidence 3999999999988886666655555432 3443 336689999888776 999999999988753
No 56
>KOG0436|consensus
Probab=90.05 E-value=0.21 Score=44.19 Aligned_cols=68 Identities=24% Similarity=0.284 Sum_probs=54.9
Q ss_pred hhhcccccceEEeecchhHHHHHHHHHHHHHHHHhcCCCCCCCccccccccceeecCeeee-cCCCceeCCCceee
Q psy1520 28 DKAQDWLPVDIYIGGKEHAVLHLYYARFIAHFLHAQGKTPAREPFKRLLVQGMIMGQTYRE-KTSGKYLKPDEVFT 102 (107)
Q Consensus 28 ~~~~~WmPVD~YIGGiEHAilHLLYaRF~~K~L~D~G~v~~~EPF~~Ll~QGMV~~~~~k~-ks~Gn~v~p~ev~~ 102 (107)
..+..|-|..+-|=|.+=+.-|-.| |-.||-..|+- |=++.+-||.-+-.+-|| ||.||+|+|-+++.
T Consensus 292 ~~ls~~wPat~HvIGKDIlrFHavY---WPafLmaAGlp----lP~~I~vHghwt~ngmKMsKSLGNvvdP~~l~~ 360 (578)
T KOG0436|consen 292 TALSFGWPATLHVIGKDILRFHAVY---WPAFLMAAGLP----LPKMIFVHGHWTKNGMKMSKSLGNVVDPFELVQ 360 (578)
T ss_pred ceeecCCCceeeehhhhhhhhhhhh---hHHHHHhcCCC----CccEEEEeeeeeecceecchhhccccCHHHHHH
Confidence 3467788999999999988888776 88999888874 446777888887777776 99999999987654
No 57
>KOG0434|consensus
Probab=90.05 E-value=0.066 Score=49.78 Aligned_cols=73 Identities=19% Similarity=0.382 Sum_probs=56.3
Q ss_pred CChhhhcccccceEEeecchhHHHHHHHHHHHHHHHHhcCCCCCCCccccccccceeecCee-ee-cCCCceeCCCceee
Q psy1520 25 FNTDKAQDWLPVDIYIGGKEHAVLHLYYARFIAHFLHAQGKTPAREPFKRLLVQGMIMGQTY-RE-KTSGKYLKPDEVFT 102 (107)
Q Consensus 25 fd~~~~~~WmPVD~YIGGiEHAilHLLYaRF~~K~L~D~G~v~~~EPF~~Ll~QGMV~~~~~-k~-ks~Gn~v~p~ev~~ 102 (107)
-+++..+.=.|.|.--.|+++.++|..=.-...- ++-.+-||++++..|+|+.+.- || |++-||=+|..+++
T Consensus 544 enk~~fe~~fPadFIaEGlDQTRGWFYTL~VlsT------~LF~kppfkNvIvnGlVLAeDG~KMSKrlkNYPdP~~iin 617 (1070)
T KOG0434|consen 544 ENKEEFEENFPADFIAEGLDQTRGWFYTLLVLST------ALFGKPPFKNVIVNGLVLAEDGKKMSKRLKNYPDPSLIIN 617 (1070)
T ss_pred cchHHHhhcCchHhhhhccccccchhhHHHHHHH------HHcCCCcchheeEeeeEEecccHHHhhhhhcCCCHHHHHH
Confidence 3567778889999999999999998333333333 3345789999999999998664 44 89999999988875
Q ss_pred c
Q psy1520 103 K 103 (107)
Q Consensus 103 ~ 103 (107)
+
T Consensus 618 k 618 (1070)
T KOG0434|consen 618 K 618 (1070)
T ss_pred h
Confidence 4
No 58
>PLN02610 probable methionyl-tRNA synthetase
Probab=89.73 E-value=0.29 Score=44.72 Aligned_cols=60 Identities=15% Similarity=0.125 Sum_probs=43.5
Q ss_pred EEeecchhHHHHHHHHHHHHHHHHhcCCCCCCCccccccccceeecCeeee-cCCCceeCCCceee
Q psy1520 38 IYIGGKEHAVLHLYYARFIAHFLHAQGKTPAREPFKRLLVQGMIMGQTYRE-KTSGKYLKPDEVFT 102 (107)
Q Consensus 38 ~YIGGiEHAilHLLYaRF~~K~L~D~G~v~~~EPF~~Ll~QGMV~~~~~k~-ks~Gn~v~p~ev~~ 102 (107)
+.+=|.+=+.-|-+| |--+|.-.|.- --+.++++.+|+++-++-|| ||+||+|+|.+++.
T Consensus 304 ~hfiGKDi~~fH~i~---wPa~L~a~g~~--~~~p~~i~~~g~l~~eG~KMSKS~GNvV~p~~~i~ 364 (801)
T PLN02610 304 YQFMGKDNVPFHTVM---FPSTLLGTGEN--WTMMKTISVTEYLNYEGGKFSKSKGVGVFGNDAKD 364 (801)
T ss_pred EEEEeeecchhHHHH---HHHHHHhCCCC--cCCCCEEEeccCEecCCceecCcCCcccCHHHHHh
Confidence 466666766666443 66666666640 01457999999999888875 99999999999875
No 59
>PF00750 tRNA-synt_1d: tRNA synthetases class I (R); InterPro: IPR015945 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This entry represents the core region of arginyl-tRNA synthetase (6.1.1.19 from EC), which has been crystallized and preliminary X-ray crystallographic analysis of yeast arginyl-tRNA synthetase-yeast tRNAArg complexes is available []. ; GO: 0000166 nucleotide binding, 0004814 arginine-tRNA ligase activity, 0005524 ATP binding, 0006420 arginyl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 2ZUE_A 2ZUF_A 3FNR_A 1IQ0_A 1F7V_A 1F7U_A 1BS2_A 3GDZ_B.
Probab=86.68 E-value=0.15 Score=41.77 Aligned_cols=60 Identities=18% Similarity=0.342 Sum_probs=40.5
Q ss_pred EEeecchhHHHHHHHHHHHHHHHHhcCCCCCCCccccccccceeecCeee--e-cCCCceeCCCceee
Q psy1520 38 IYIGGKEHAVLHLYYARFIAHFLHAQGKTPAREPFKRLLVQGMIMGQTYR--E-KTSGKYLKPDEVFT 102 (107)
Q Consensus 38 ~YIGGiEHAilHLLYaRF~~K~L~D~G~v~~~EPF~~Ll~QGMV~~~~~k--~-ks~Gn~v~p~ev~~ 102 (107)
+||-|.+|. +| ..=...+|..+|.-+....+. -+.+|||+...-+ | +.+|++|..+|++.
T Consensus 242 iyV~~~~q~-~h---f~~l~~~l~~lg~~~~~~~~~-H~~~g~vl~~~gk~~mstR~G~~i~l~dlld 304 (354)
T PF00750_consen 242 IYVVGADQK-GH---FKQLFAILEALGYDPEAVKLQ-HVSFGVVLLKDGKVKMSTRKGNVITLDDLLD 304 (354)
T ss_dssp EEEEEGGGH-HH---HHHHHHHHHHTT-HHHHCTEE-EEEE-EEEETTBEESS-TTTTSSTBHHHHHH
T ss_pred EEEecCchh-hH---HHHHHHHHHHhCCCCCCCEEE-EEEEEEEEcCCCCccccCCCCCceEHHHHHH
Confidence 899999998 66 333456777778544444433 2589999765433 4 77899999988865
No 60
>PRK14535 cysS cysteinyl-tRNA synthetase; Provisional
Probab=86.56 E-value=0.26 Score=44.99 Aligned_cols=69 Identities=19% Similarity=0.208 Sum_probs=47.8
Q ss_pred cceEEeecchhHHHHHHHHHHHHHHHHhc--CCC----C-CC--Cccccc-cccceeecCeeee-cCCCceeCCCceeec
Q psy1520 35 PVDIYIGGKEHAVLHLYYARFIAHFLHAQ--GKT----P-AR--EPFKRL-LVQGMIMGQTYRE-KTSGKYLKPDEVFTK 103 (107)
Q Consensus 35 PVD~YIGGiEHAilHLLYaRF~~K~L~D~--G~v----~-~~--EPF~~L-l~QGMV~~~~~k~-ks~Gn~v~p~ev~~~ 103 (107)
++|+--||+++.-=|.=.-+--+.++... +.- . .. +||.+- +..|||+-++.|| ||.||+|+|.|++..
T Consensus 446 ~~DIHgGG~DLiFPHHENEiAQseA~~g~~~~~~~~~~~~~~~~~~~aryWmHnG~V~vdGeKMSKSLGN~it~~dlLe~ 525 (699)
T PRK14535 446 TFDIHGGGADLQFPHHENEIAQSVGATGHTCGHHHAQTHHGQSIASHVKYWLHNGFIRVDGEKMSKSLGNFFTIREVLKQ 525 (699)
T ss_pred cceeECCccccCCCCCccHHHHHHHhhCCCcccccccccccccccccccEEEECCeEeeCCCccCCCCCCcCCHHHHHHh
Confidence 39999999999887766665555554321 010 1 11 256664 5669999777775 999999999988653
No 61
>cd00802 class_I_aaRS_core catalytic core domain of class I amino acyl-tRNA synthetase. Class I amino acyl-tRNA synthetase (aaRS) catalytic core domain. These enzymes are mostly monomers which aminoacylate the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding.
Probab=83.20 E-value=2.5 Score=29.59 Aligned_cols=45 Identities=24% Similarity=0.333 Sum_probs=29.1
Q ss_pred ceEEeecchhHHHHHHHHHHHHHHHHhcCCCCCCCccccccccceeecCe-eee
Q psy1520 36 VDIYIGGKEHAVLHLYYARFIAHFLHAQGKTPAREPFKRLLVQGMIMGQT-YRE 88 (107)
Q Consensus 36 VD~YIGGiEHAilHLLYaRF~~K~L~D~G~v~~~EPF~~Ll~QGMV~~~~-~k~ 88 (107)
.|+|+||.||.- |.-..+-+.+.+ |. ...| .-+..|||++.. -||
T Consensus 94 ~~i~~~G~Dq~~-h~~~~~~i~~~~---~~--~~~p--~~~~~~~l~~~~g~Km 139 (143)
T cd00802 94 CDIHLGGSDQLG-HIELGLELLKKA---GG--PARP--FGLTFGRVMGADGTKM 139 (143)
T ss_pred cEEEEechhHHH-HHHHHHHHHHHh---CC--CCCc--eEEEeCCeECCCCCcC
Confidence 599999999996 765555555544 41 1223 456678998755 444
No 62
>PRK12451 arginyl-tRNA synthetase; Reviewed
Probab=81.90 E-value=0.78 Score=40.03 Aligned_cols=59 Identities=22% Similarity=0.386 Sum_probs=41.8
Q ss_pred EEeecchhHHHHHHHHHHHHHHHHhcCCCCCCCccccccccceeecCeeee-cCCCceeCCCceee
Q psy1520 38 IYIGGKEHAVLHLYYARFIAHFLHAQGKTPAREPFKRLLVQGMIMGQTYRE-KTSGKYLKPDEVFT 102 (107)
Q Consensus 38 ~YIGGiEHAilHLLYaRF~~K~L~D~G~v~~~EPF~~Ll~QGMV~~~~~k~-ks~Gn~v~p~ev~~ 102 (107)
+||-|.+|. +| ..| ...+|..+|+.+. +- -.-+.-|||...+-+| +-+|++|.-+|++.
T Consensus 328 IyV~g~dq~-~h--~~~-l~~~~~~lg~~~~-~~-l~h~~~g~V~~~g~kmStR~G~~v~l~dLld 387 (562)
T PRK12451 328 LYVVGPEQS-LH--FNQ-FFTVLKKLGYTWV-DG-MEHVPFGLILKDGKKMSTRKGRVVLLEEVLE 387 (562)
T ss_pred EEEeCCcHH-HH--HHH-HHHHHHHcCCCcc-cC-eEEEeeeeEecCCCCCcCCCCCeeEHHHHHH
Confidence 899999997 55 333 4478888887532 21 2236677998765554 77899999999865
No 63
>PF10910 DUF2744: Protein of unknown function (DUF2744); InterPro: IPR021226 This entry is represented by Mycobacteriophage D29, Gp29. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=81.82 E-value=1.3 Score=32.74 Aligned_cols=81 Identities=16% Similarity=0.135 Sum_probs=50.7
Q ss_pred cccccccCCCCCCCCCChhhhcccccceEE-eecchhHHHHHHHHHHHHHHHHhcCCCCCC-----Cccccccccceeec
Q psy1520 10 IKTKTKSRDINAEVSFNTDKAQDWLPVDIY-IGGKEHAVLHLYYARFIAHFLHAQGKTPAR-----EPFKRLLVQGMIMG 83 (107)
Q Consensus 10 ~~~~~~~dp~n~~~~fd~~~~~~WmPVD~Y-IGGiEHAilHLLYaRF~~K~L~D~G~v~~~-----EPF~~Ll~QGMV~~ 83 (107)
|.|..-|||+|.++. --|+=+.+= ++| ..+|.|--|.|=|++-|.++|+...+ +.-.++..=.+ |
T Consensus 2 iptQe~~D~~dPeEh------flWaL~~lP~~~G-~~~it~~~~lr~wS~hLw~cGfrh~ds~lP~q~~iK~~pP~r--g 72 (125)
T PF10910_consen 2 IPTQEECDPNDPEEH------FLWALRNLPGPAG-AGLITPPGYLRDWSEHLWECGFRHHDSQLPQQQIIKYQPPFR--G 72 (125)
T ss_pred CcchhhcCCCCHHHH------HHHHHccCCCCCC-CCccCCHHHHHHHHHHHHHcCCCCCccccchhhhhhccCCCC--C
Confidence 556666777765444 445433322 334 78899999999999999999999887 33323322111 1
Q ss_pred CeeeecCCCceeCCCc
Q psy1520 84 QTYREKTSGKYLKPDE 99 (107)
Q Consensus 84 ~~~k~ks~Gn~v~p~e 99 (107)
..--..+.|.||+.|+
T Consensus 73 ~~h~~n~agrWV~~d~ 88 (125)
T PF10910_consen 73 PRHWYNNAGRWVPIDE 88 (125)
T ss_pred CccccCCcceeecCCC
Confidence 1111356788998766
No 64
>PLN02286 arginine-tRNA ligase
Probab=76.34 E-value=1.5 Score=38.47 Aligned_cols=60 Identities=17% Similarity=0.336 Sum_probs=41.0
Q ss_pred EEeecchhHHHHHHHHHHHHHHHHhcCCCCC--CCccccccccceeecCee-e-ecCCCceeCCCceee
Q psy1520 38 IYIGGKEHAVLHLYYARFIAHFLHAQGKTPA--REPFKRLLVQGMIMGQTY-R-EKTSGKYLKPDEVFT 102 (107)
Q Consensus 38 ~YIGGiEHAilHLLYaRF~~K~L~D~G~v~~--~EPF~~Ll~QGMV~~~~~-k-~ks~Gn~v~p~ev~~ 102 (107)
+||-|.+|. +| ..| +..+|+-+|+.+. .+-+. -+.-|||++..- + ++-+|++|.-+|++.
T Consensus 331 IyVvg~~q~-~h--f~~-v~~~l~~lG~~~~~~~~~l~-h~~~g~V~~~~g~kmStR~G~~v~L~dlld 394 (576)
T PLN02286 331 IYVTDVGQQ-QH--FDM-VFKAAKRAGWLPEDTYPRLE-HVGFGLVLGEDGKRFRTRSGEVVRLVDLLD 394 (576)
T ss_pred EEEEeCcHH-HH--HHH-HHHHHHHcCCCccccCCceE-EEeeccEECCCCCcccCCCCCeeEHHHHHH
Confidence 899999997 66 333 3478888887633 22232 266789974332 3 577999999999875
No 65
>PF01479 S4: S4 domain; InterPro: IPR002942 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 S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterised, small proteins that may be involved in translation regulation []. The S4 domain probably mediates binding to RNA.; GO: 0003723 RNA binding; PDB: 3BBU_A 1DM9_B 2K6P_A 3U5G_E 3U5C_E 3IZB_D 2XZM_D 2XZN_D 3O30_E 3O2Z_E ....
Probab=73.28 E-value=3.3 Score=24.04 Aligned_cols=45 Identities=27% Similarity=0.377 Sum_probs=34.4
Q ss_pred HHHHHhcCCCCCCCccccccccceeecCeeeecCCCceeCCCcee
Q psy1520 57 AHFLHAQGKTPAREPFKRLLVQGMIMGQTYREKTSGKYLKPDEVF 101 (107)
Q Consensus 57 ~K~L~D~G~v~~~EPF~~Ll~QGMV~~~~~k~ks~Gn~v~p~ev~ 101 (107)
-++|...|+.++..=.++|+.||-|.-++-..+..+--|.|.|++
T Consensus 4 d~~L~~~~~~~sr~~a~~~I~~g~V~VNg~~v~~~~~~v~~~d~I 48 (48)
T PF01479_consen 4 DKFLSRLGLASSRSEARRLIKQGRVKVNGKVVKDPSYIVKPGDVI 48 (48)
T ss_dssp HHHHHHTTSSSSHHHHHHHHHTTTEEETTEEESSTTSBESTTEEE
T ss_pred HHHHHHcCCcCCHHHHHHhcCCCEEEECCEEEcCCCCCCCCcCCC
Confidence 578888999999999999999999986555445455566666653
No 66
>COG0018 ArgS Arginyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=67.83 E-value=5.4 Score=35.53 Aligned_cols=58 Identities=24% Similarity=0.504 Sum_probs=40.7
Q ss_pred EEeecchhHHHHHHHHHHHHHHHHhcCCCCCCCcccccccc--ceeec-Ceee-ecCCCceeCCCceee
Q psy1520 38 IYIGGKEHAVLHLYYARFIAHFLHAQGKTPAREPFKRLLVQ--GMIMG-QTYR-EKTSGKYLKPDEVFT 102 (107)
Q Consensus 38 ~YIGGiEHAilHLLYaRF~~K~L~D~G~v~~~EPF~~Ll~Q--GMV~~-~~~k-~ks~Gn~v~p~ev~~ 102 (107)
+||-|.||. +| ..|++ .+|.-+|+.+.. ..|+.| |||.+ +..| |+..|++|.-+|+..
T Consensus 338 IyV~gadq~-~~--~~ql~-~~l~~~g~~~~~---~~~~h~~~~l~~~~~g~kmStR~G~~vtl~dlld 399 (577)
T COG0018 338 IYVLGADQH-GH--FKQLK-AVLELLGYGPDK---EVLLHQGVGLVRGGEGVKMSTRAGNVVTLDDLLD 399 (577)
T ss_pred EEEeCCcch-hH--HHHHH-HHHHHhcCCCcc---ceEEEEEEeeeECCCCccccccCCceEEHHHHHH
Confidence 899999997 56 45544 466778888776 445554 56776 3344 478999999888753
No 67
>TIGR00467 lysS_arch lysyl-tRNA synthetase, archaeal and spirochete. This model represents the lysyl-tRNA synthetases that are class I amino-acyl tRNA synthetases. It includes archaeal and spirochete examples of the enzyme. All other known examples are class IIc amino-acyl tRNA synthetases and seem to form a separate orthologous set.
Probab=57.29 E-value=6.1 Score=34.66 Aligned_cols=76 Identities=13% Similarity=0.168 Sum_probs=43.8
Q ss_pred CCCCChhhhccc--ccceEEeecchhHH-H--HHHHHHHHHHHHHhcCCCCCCCccccccccceeecCeee-ecCCCcee
Q psy1520 22 EVSFNTDKAQDW--LPVDIYIGGKEHAV-L--HLYYARFIAHFLHAQGKTPAREPFKRLLVQGMIMGQTYR-EKTSGKYL 95 (107)
Q Consensus 22 ~~~fd~~~~~~W--mPVD~YIGGiEHAi-l--HLLYaRF~~K~L~D~G~v~~~EPF~~Ll~QGMV~~~~~k-~ks~Gn~v 95 (107)
.-++-.+=+-+| +-||.=-.|.+|+. + +-...+--.. -+|. ...++|.--+-| +.+++.| |||+||+|
T Consensus 210 KL~WkvdW~~RW~~lgV~~Ep~GkDH~~~ggsy~~~~~ia~~---~l~~-~~P~~~~ye~v~--L~~~g~KMSKS~Gn~i 283 (515)
T TIGR00467 210 KLPWRVDWPARWKIEKVTFEPAGKDHAAAGGSYDTGVNIAKE---IFQY-SPPVTVQYEWIS--LKGKGGKMSSSKGDVI 283 (515)
T ss_pred ccCCCCCcHhhHhhhCcccccCCCCccCccCCchhHHHHHHH---HhCC-CCCcCcEEEEEE--EcCCCccccCCCCCCc
Confidence 444555666677 68999999999975 1 2222222222 2332 222334433333 2234445 59999999
Q ss_pred CCCceeec
Q psy1520 96 KPDEVFTK 103 (107)
Q Consensus 96 ~p~ev~~~ 103 (107)
+++|++..
T Consensus 284 tl~dll~~ 291 (515)
T TIGR00467 284 SVKDVLEV 291 (515)
T ss_pred cHHHHHHH
Confidence 99988653
No 68
>PF00579 tRNA-synt_1b: tRNA synthetases class I (W and Y); InterPro: IPR002305 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. The class Ia aminoacyl-tRNA synthetases consist of the isoleucyl, methionyl, valyl, leucyl, cysteinyl, and arginyl-tRNA synthetases; the class Ib include the glutamyl and glutaminyl-tRNA synthetases, and the class Ic are the tyrosyl and tryptophanyl-tRNA synthetases [].; GO: 0000166 nucleotide binding, 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0006418 tRNA aminoacylation for protein translation, 0005737 cytoplasm; PDB: 2JAN_A 3P0J_B 3P0I_B 3P0H_B 1YID_C 2A4M_C 1YIA_C 1YI8_C 2EL7_A 3PRH_A ....
Probab=51.69 E-value=31 Score=27.07 Aligned_cols=59 Identities=19% Similarity=0.172 Sum_probs=38.7
Q ss_pred ccceEEeecchhHHHHHHHHHHHHHHHHhcCCCCCCCccccccccceeecC-ee-ee-cCCCc-eeCC
Q psy1520 34 LPVDIYIGGKEHAVLHLYYARFIAHFLHAQGKTPAREPFKRLLVQGMIMGQ-TY-RE-KTSGK-YLKP 97 (107)
Q Consensus 34 mPVD~YIGGiEHAilHLLYaRF~~K~L~D~G~v~~~EPF~~Ll~QGMV~~~-~~-k~-ks~Gn-~v~p 97 (107)
+-.|+-+||+++. .|+..+|=+.+-+... ....+|+.=+. . |+.+- +. || ||.+| .|..
T Consensus 148 l~~~~~~~G~DQ~-~~~~l~rd~a~k~~~~--~~~~~p~~l~~-~-~l~~l~G~~KMSKS~~ns~I~L 210 (292)
T PF00579_consen 148 LKADLVPGGIDQR-GHIELARDLARKFNYK--EIFPKPAGLTS-P-LLPGLDGQKKMSKSDPNSAIFL 210 (292)
T ss_dssp TTHSEEEEEGGGH-HHHHHHHHHHHHHTHH--STSSS-EEEEE-T-CBBSTTSSSBTTTTTTGGS-BT
T ss_pred eccccccccchHH-HHHHHHHHHHhhhccc--ccccCchheee-c-cccccCCccccCccCCccEEEE
Confidence 4578999999998 8999999888877776 33445533222 2 55543 23 54 99999 4443
No 69
>COG0215 CysS Cysteinyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=50.15 E-value=4.4 Score=35.57 Aligned_cols=63 Identities=17% Similarity=0.289 Sum_probs=41.1
Q ss_pred cceEEeecchhHHHHHHHHHHHHHHHHhcCCCCCCCccccc-cccceeecCeeee-cCCCceeCCCceeec
Q psy1520 35 PVDIYIGGKEHAVLHLYYARFIAHFLHAQGKTPAREPFKRL-LVQGMIMGQTYRE-KTSGKYLKPDEVFTK 103 (107)
Q Consensus 35 PVD~YIGGiEHAilHLLYaRF~~K~L~D~G~v~~~EPF~~L-l~QGMV~~~~~k~-ks~Gn~v~p~ev~~~ 103 (107)
..|+=-||++..-=|-=--+--+. -....+||.+- +-.|||.-++.|| ||.||++...|+.++
T Consensus 221 ~~DIHgGG~DLiFPHHENEiAQse------a~~g~~~~a~yWmH~G~l~i~geKMSKSLGNfiti~d~l~~ 285 (464)
T COG0215 221 TFDIHGGGSDLIFPHHENEIAQSE------AATGVKPFAKYWMHNGFLNIDGEKMSKSLGNFITVRDLLKK 285 (464)
T ss_pred CcceecCcccccCCCcccHHHHHH------hhhCCCcceeEeEEcceeeecCcCcccccCCeeEHHHHHhh
Confidence 489999999987555110000111 11223787665 4569999888886 999999988777653
No 70
>PF08199 E2: Bacteriophage E2-like protein; InterPro: IPR013184 This is a family of short conserved proteins of 37 amino acids, described in Lactococcus phage c2 and in related phage. The function of these proteins is unknown.
Probab=43.14 E-value=13 Score=22.06 Aligned_cols=19 Identities=26% Similarity=0.485 Sum_probs=12.8
Q ss_pred HHHHHHHHHHHHHHhcCCCC
Q psy1520 48 LHLYYARFIAHFLHAQGKTP 67 (107)
Q Consensus 48 lHLLYaRF~~K~L~D~G~v~ 67 (107)
.-|||+|| -|+.+..-+++
T Consensus 3 ~rlly~rf-gk~ikrrilid 21 (37)
T PF08199_consen 3 SRLLYSRF-GKFIKRRILID 21 (37)
T ss_pred HHHHHHHH-HHHHHHHHhhh
Confidence 56999997 56665554544
No 71
>cd00805 TyrRS_core catalytic core domain of tyrosinyl-tRNA synthetase. Tyrosinyl-tRNA synthetase (TyrRS) catalytic core domain. TyrRS is a homodimer which attaches Tyr to the appropriate tRNA. TyrRS is a class I tRNA synthetases, so it aminoacylates the 2'-OH of the nucleotide at the 3' end of the tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formationof the enzyme bound aminoacyl-adenylate. It contains the class I characteristic HIGH and KMSKS motifs, which are involved in ATP binding.
Probab=42.41 E-value=46 Score=26.31 Aligned_cols=52 Identities=21% Similarity=0.367 Sum_probs=35.6
Q ss_pred cceEEeecchhHHHHHHHHHHHHHHHHhcCCCCCCCccccccccceeecCe-eee-cCCCcee
Q psy1520 35 PVDIYIGGKEHAVLHLYYARFIAHFLHAQGKTPAREPFKRLLVQGMIMGQT-YRE-KTSGKYL 95 (107)
Q Consensus 35 PVD~YIGGiEHAilHLLYaRF~~K~L~D~G~v~~~EPF~~Ll~QGMV~~~~-~k~-ks~Gn~v 95 (107)
-.|+.+||+++- .|+.-+|=+.+-+ + ..+||. ++.-++.+.. -|| ||.+|.+
T Consensus 151 ~~~l~~~G~DQ~-~~i~~~rd~a~r~---~---~~~~~~--l~~~ll~~l~G~KMSKS~~~~~ 204 (269)
T cd00805 151 DVDLQLGGSDQR-GNITLGRDLIRKL---G---YKKVVG--LTTPLLTGLDGGKMSKSEGNAI 204 (269)
T ss_pred hCCeeEecHHHH-HHHHHHHHHHHHh---C---CCCcEE--EeeccccCCCCCcccCCCCCcc
Confidence 359999999998 7888887666554 2 345555 4556665433 364 8999877
No 72
>PF02844 GARS_N: Phosphoribosylglycinamide synthetase, N domain; InterPro: IPR020562 Phosphoribosylglycinamide synthetase (6.3.4.13 from EC) (GARS) (phosphoribosylamine glycine ligase) [] catalyses the second step in the de novo biosynthesis of purine. The reaction catalysed by phosphoribosylglycinamide synthetase is the ATP-dependent addition of 5-phosphoribosylamine to glycine to form 5'phosphoribosylglycinamide: ATP + 5-phosphoribosylamine + glycine = ADP + Pi + 5'-phosphoribosylglycinamide In bacteria, GARS is a monofunctional enzyme (encoded by the purD gene). In yeast, GARS is part of a bifunctional enzyme (encoded by the ADE5/7 gene) in conjunction with phosphoribosylformylglycinamidine cyclo-ligase (AIRS) (IPR000728 from INTERPRO). In higher eukaryotes, GARS is part of a trifunctional enzyme in conjunction with AIRS (IPR000728 from INTERPRO) and with phosphoribosylglycinamide formyltransferase (GART) (), forming GARS-AIRS-GART. This entry represents the N-domain, which is related to the N-terminal domain of biotin carboxylase/carbamoyl phosphate synthetase (IPR005481 from INTERPRO).; GO: 0004637 phosphoribosylamine-glycine ligase activity, 0009113 purine base biosynthetic process; PDB: 3MJF_A 2XD4_A 2XCL_A 2IP4_A 2YW2_B 2YYA_A 3LP8_A 1VKZ_A 2YS6_A 2YRX_A ....
Probab=39.08 E-value=14 Score=26.01 Aligned_cols=9 Identities=56% Similarity=1.073 Sum_probs=7.8
Q ss_pred ecchhHHHH
Q psy1520 41 GGKEHAVLH 49 (107)
Q Consensus 41 GGiEHAilH 49 (107)
||-|||+.|
T Consensus 9 GgREHAia~ 17 (100)
T PF02844_consen 9 GGREHAIAW 17 (100)
T ss_dssp SHHHHHHHH
T ss_pred CHHHHHHHH
Confidence 789999876
No 73
>cd06603 GH31_GANC_GANAB_alpha This family includes the closely related glycosyl hydrolase family 31 (GH31) isozymes, neutral alpha-glucosidase C (GANC) and the alpha subunit of heterodimeric neutral alpha-glucosidase AB (GANAB). Initially distinguished on the basis of differences in electrophoretic mobility in starch gel, GANC and GANAB have been shown to have other differences, including those of substrate specificity. GANC and GANAB are key enzymes in glycogen metabolism that hydrolyze terminal, non-reducing 1,4-linked alpha-D-glucose residues from glycogen in the endoplasmic reticulum. The GANC/GANAB family includes the alpha-glucosidase II (ModA) from Dictyostelium discoideum as well as the alpha-glucosidase II (GLS2, or ROT2 - Reversal of TOR2 lethality protein 2) from Saccharomyces cerevisiae.
Probab=37.48 E-value=44 Score=27.02 Aligned_cols=32 Identities=25% Similarity=0.353 Sum_probs=25.6
Q ss_pred cccccceE-EeecchhHHHHHHHHHHHHHHHHh
Q psy1520 31 QDWLPVDI-YIGGKEHAVLHLYYARFIAHFLHA 62 (107)
Q Consensus 31 ~~WmPVD~-YIGGiEHAilHLLYaRF~~K~L~D 62 (107)
+..+|.|. +.||.+|..+|=+|.-+++++.++
T Consensus 170 ~~~~p~d~~~~~~~~~~~~hN~y~~~~~~a~~e 202 (339)
T cd06603 170 ELTMPKDAIHYGGIEHREVHNIYGLYMHMATFD 202 (339)
T ss_pred CCcCCCcceecCCCcHHHHhhHhHHHHHHHHHH
Confidence 44578875 557799999999999999987765
No 74
>PF12496 BNIP2: Bcl2-/adenovirus E1B nineteen kDa-interacting protein 2; InterPro: IPR022181 This domain family is found in eukaryotes, and is typically between 119 and 133 amino acids in length. There is a conserved HGGY sequence motif. This family is Bcl2-/adenovirus E1B nineteen kDa-interacting protein 2. It interacts with pro- and anti- apoptotic molecules in the cell.
Probab=36.20 E-value=13 Score=27.29 Aligned_cols=12 Identities=42% Similarity=0.924 Sum_probs=10.7
Q ss_pred CCCccccccccc
Q psy1520 68 AREPFKRLLVQG 79 (107)
Q Consensus 68 ~~EPF~~Ll~QG 79 (107)
.-|||+|.|+||
T Consensus 110 vIEPYkrViSHG 121 (127)
T PF12496_consen 110 VIEPYKRVISHG 121 (127)
T ss_pred ecccceeeeccC
Confidence 459999999998
No 75
>PF01837 DUF39: Domain of unknown function DUF39; InterPro: IPR002708 This domain, whose function is not known, is about 320 residues long and is found in proteins that have two C-terminal CBS domains, IPR000644 from INTERPRO. The protein O26943 from SWISSPROT is described as inosine-5'-monophosphate dehydrogenase related protein VIII, based on the sequence simarity it shares to the CBS domains.
Probab=35.78 E-value=18 Score=30.83 Aligned_cols=12 Identities=42% Similarity=0.988 Sum_probs=11.6
Q ss_pred ceEEeecchhHH
Q psy1520 36 VDIYIGGKEHAV 47 (107)
Q Consensus 36 VD~YIGGiEHAi 47 (107)
||+||||-+|.-
T Consensus 71 VD~~lgaT~~s~ 82 (340)
T PF01837_consen 71 VDLYLGATQHSE 82 (340)
T ss_pred EEEEEeccccCC
Confidence 999999999998
No 76
>COG0377 NuoB NADH:ubiquinone oxidoreductase 20 kD subunit and related Fe-S oxidoreductases [Energy production and conversion]
Probab=31.63 E-value=19 Score=28.52 Aligned_cols=16 Identities=38% Similarity=0.677 Sum_probs=13.1
Q ss_pred hhhcccccceEEeecc
Q psy1520 28 DKAQDWLPVDIYIGGK 43 (107)
Q Consensus 28 ~~~~~WmPVD~YIGGi 43 (107)
..+++-.|||+||=|-
T Consensus 127 ~g~D~~vPVDvyIPGC 142 (194)
T COG0377 127 QGVDRVVPVDVYIPGC 142 (194)
T ss_pred eccceeEeeeeecCCC
Confidence 4567779999999984
No 77
>PF07218 RAP1: Rhoptry-associated protein 1 (RAP-1); InterPro: IPR009864 This family consists of several rhoptry-associated protein 1 (RAP-1) sequences which appear to be specific to Plasmodium falciparum [].
Probab=31.32 E-value=26 Score=32.45 Aligned_cols=48 Identities=17% Similarity=0.263 Sum_probs=33.3
Q ss_pred cccccccCCCCCCCCCChhhhcccccceEEeecchhHHHHHHHHHHHHHHHHhcCCCCC
Q psy1520 10 IKTKTKSRDINAEVSFNTDKAQDWLPVDIYIGGKEHAVLHLYYARFIAHFLHAQGKTPA 68 (107)
Q Consensus 10 ~~~~~~~dp~n~~~~fd~~~~~~WmPVD~YIGGiEHAilHLLYaRF~~K~L~D~G~v~~ 68 (107)
|.....+|-+.+.+-|+.+..++|||.|- | - +..-|++-..|+-++..
T Consensus 25 inge~~i~nh~e~eefn~dd~n~wm~ldd-------~--n--flntwtknvsdisf~e~ 72 (782)
T PF07218_consen 25 INGERKIDNHREAEEFNVDDINSWMKLDD-------A--N--FLNTWTKNVSDISFLES 72 (782)
T ss_pred ecccccccccccccccCcccchhcccccH-------H--H--HHHHHhhcccchhhhhc
Confidence 44556677787788899999999999983 1 1 22337776666666554
No 78
>PF01560 HCV_NS1: Hepatitis C virus non-structural protein E2/NS1; InterPro: IPR002531 The hypervariable region of the E2/NS1 region of Hepatitis C virus varies greatly between viral isolates. E2 is thought to encode a structurally unconstrained envelope protein [].; PDB: 2KZQ_A 4DGV_A 4DGY_A.
Probab=30.48 E-value=17 Score=30.94 Aligned_cols=12 Identities=50% Similarity=1.010 Sum_probs=0.0
Q ss_pred cceEEeecchhH
Q psy1520 35 PVDIYIGGKEHA 46 (107)
Q Consensus 35 PVD~YIGGiEHA 46 (107)
.|-+|+||+||-
T Consensus 243 kvrm~vgg~ehr 254 (344)
T PF01560_consen 243 KVRMYVGGVEHR 254 (344)
T ss_dssp ------------
T ss_pred EEEEEeeccccc
Confidence 588999999994
No 79
>PF09318 DUF1975: Domain of unknown function (DUF1975); InterPro: IPR015397 This domain is functionally uncharacterised and found predominantly in the N-terminal region of various prokaryotic alpha-glucosyltransferases.
Probab=29.88 E-value=41 Score=24.34 Aligned_cols=27 Identities=30% Similarity=0.375 Sum_probs=17.8
Q ss_pred eecchhHHHHHH----------------HHHHHHHHHHhcCCC
Q psy1520 40 IGGKEHAVLHLY----------------YARFIAHFLHAQGKT 66 (107)
Q Consensus 40 IGGiEHAilHLL----------------YaRF~~K~L~D~G~v 66 (107)
=||+|||.++=+ |.+-.+..|+.+|+-
T Consensus 13 ~sGie~A~~~R~~lF~~~~~~~~ivt~~y~~~l~~~l~~~~~~ 55 (203)
T PF09318_consen 13 NSGIEHAQLKRLKLFKENGIPAKIVTRDYNPNLHQILKELGIP 55 (203)
T ss_pred cchhHHHHHHHHHHHHHCCCCeEEEEeeCChhHHHHHHHcCCC
Confidence 389999987632 445566666666663
No 80
>PF13275 S4_2: S4 domain; PDB: 1P9K_A.
Probab=26.16 E-value=35 Score=22.26 Aligned_cols=47 Identities=23% Similarity=0.357 Sum_probs=30.7
Q ss_pred HHHHHHhcCCCCCCCccccccccceeecCeeeecCCCceeCCCceee
Q psy1520 56 IAHFLHAQGKTPAREPFKRLLVQGMIMGQTYREKTSGKYLKPDEVFT 102 (107)
Q Consensus 56 ~~K~L~D~G~v~~~EPF~~Ll~QGMV~~~~~k~ks~Gn~v~p~ev~~ 102 (107)
...+|+-.|++++.-=-+.++.+|+|.-++.....+|.=+.|.|++.
T Consensus 10 L~qlLK~~glv~sGGeAK~~I~~g~V~VNGe~e~rrg~Kl~~GD~V~ 56 (65)
T PF13275_consen 10 LGQLLKLAGLVSSGGEAKALIQEGEVKVNGEVETRRGKKLRPGDVVE 56 (65)
T ss_dssp HHHHHHHHTS-SSSSTTSHHHHHHHHEETTB----SS----SSEEEE
T ss_pred HHHHHhHcCCcccHHHHHHHHHcCceEECCEEccccCCcCCCCCEEE
Confidence 46899999999998888999999999866654445566666666554
No 81
>COG0522 RpsD Ribosomal protein S4 and related proteins [Translation, ribosomal structure and biogenesis]
Probab=25.50 E-value=1e+02 Score=24.18 Aligned_cols=54 Identities=19% Similarity=0.296 Sum_probs=38.3
Q ss_pred HHHHHHHHHHHHHHHhcCCCCCCCccccccccceeecCeeeecCCCceeCCCcee
Q psy1520 47 VLHLYYARFIAHFLHAQGKTPAREPFKRLLVQGMIMGQTYREKTSGKYLKPDEVF 101 (107)
Q Consensus 47 ilHLLYaRF~~K~L~D~G~v~~~EPF~~Ll~QGMV~~~~~k~ks~Gn~v~p~ev~ 101 (107)
++.+|=.| .--+.+.+|+.++.-=-..|++||-|+-.+-+...-+-.|+|.|++
T Consensus 88 ~~~~LErR-Ld~vVyR~GfA~T~~qARQlV~HGHI~VnGk~V~iPSy~V~~gdei 141 (205)
T COG0522 88 LLALLERR-LDNVVYRLGFAKTRRQARQLVSHGHILVNGKRVNIPSYLVSPGDEI 141 (205)
T ss_pred HHHHHHHH-HHHHHHHhcccccHHHHHHHhhcceEEECCEEeccCcEEecCCCEE
Confidence 45666666 4567788999999888899999999986654433334456666554
No 82
>PRK08560 tyrosyl-tRNA synthetase; Validated
Probab=25.37 E-value=1e+02 Score=25.14 Aligned_cols=57 Identities=25% Similarity=0.335 Sum_probs=36.5
Q ss_pred ccceEEeecchhHHHHHHHHHHHHHHHHhcCCCCCCCccccccccceeecCe---eee-cCC-CceeCCCc
Q psy1520 34 LPVDIYIGGKEHAVLHLYYARFIAHFLHAQGKTPAREPFKRLLVQGMIMGQT---YRE-KTS-GKYLKPDE 99 (107)
Q Consensus 34 mPVD~YIGGiEHAilHLLYaRF~~K~L~D~G~v~~~EPF~~Ll~QGMV~~~~---~k~-ks~-Gn~v~p~e 99 (107)
+.+|+-+||+++. -|+..+|=+.+-+ + ..+|+.- ..-||.+-. -|| ||. ||.|.-+|
T Consensus 167 ~~ad~vpvG~DQ~-~h~~l~Rdia~~~---n---~~~p~~l--~~~~l~~L~g~~~KMSKS~p~~~I~L~D 228 (329)
T PRK08560 167 LDVDIAVGGMDQR-KIHMLAREVLPKL---G---YKKPVCI--HTPLLTGLDGGGIKMSKSKPGSAIFVHD 228 (329)
T ss_pred hCCCEEEechhHH-HHHHHHHHhhHhc---C---CCCceEE--EcCccCCCCCCCCCCcCCCCCCeecccC
Confidence 4689999999998 7888777665533 3 2356542 244665522 254 888 77765433
No 83
>KOG1687|consensus
Probab=24.87 E-value=46 Score=25.63 Aligned_cols=25 Identities=32% Similarity=0.555 Sum_probs=18.6
Q ss_pred hhcccccceEEeecchhHHHHHHHH
Q psy1520 29 KAQDWLPVDIYIGGKEHAVLHLYYA 53 (107)
Q Consensus 29 ~~~~WmPVD~YIGGiEHAilHLLYa 53 (107)
..++-.|||+|+-|-------|||.
T Consensus 124 GcDriiPVDiYvPGCPPtaEAllyg 148 (168)
T KOG1687|consen 124 GCDRIIPVDIYVPGCPPTAEALLYG 148 (168)
T ss_pred cccceeeeeeecCCCCCCHHHHHHH
Confidence 4567789999999976555556664
No 84
>TIGR03287 methan_mark_16 putative methanogenesis marker 16 metalloprotein. Members of this protein family, to date, are found in a completed prokaryotic genome if and only if the species is one of the archaeal methanogens. The exact function is unknown, but likely is linked to methanogenesis or a process closely connected to it. This protein is a predicted to bind FeS clusters, based on the presence of two copies of the Fer4 domain (pfam00037), with each copy having four Cys residues invariant across all members.
Probab=24.87 E-value=34 Score=29.46 Aligned_cols=13 Identities=31% Similarity=0.460 Sum_probs=11.4
Q ss_pred cceEEeecchhHH
Q psy1520 35 PVDIYIGGKEHAV 47 (107)
Q Consensus 35 PVD~YIGGiEHAi 47 (107)
-||+|+||-+|+-
T Consensus 75 ~vd~~~~~t~~~~ 87 (391)
T TIGR03287 75 LVDLIVYGTAHSD 87 (391)
T ss_pred EEEEEeeccccCC
Confidence 4999999999964
No 85
>PF02980 FokI_C: Restriction endonuclease FokI, catalytic domain; InterPro: IPR004233 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. Thie entry represents the type IIS restriction endonuclease FokI (3.1.21.4 from EC), which is a member of an unusual class of bipartite restriction enzymes that recognise a specific DNA sequence and cleave DNA nonspecifically a short distance away from that sequence []. FokI contains amino- and carboxy-terminal domains corresponding to the DNA-recognition (IPR004234 from INTERPRO) and cleavage functions, respectively. The catalytic domain contains only a single catalytic centre, raising the question of how monomeric FokI manages to cleave both DNA strands. The catalytic domain is sequestered in a 'piggyback' fashion by the recognition domain [].; GO: 0003677 DNA binding, 0009036 Type II site-specific deoxyribonuclease activity, 0009307 DNA restriction-modification system; PDB: 1FOK_A 2FOK_B.
Probab=24.55 E-value=52 Score=24.91 Aligned_cols=35 Identities=31% Similarity=0.391 Sum_probs=26.0
Q ss_pred ccceEEeecchhHH--------------HHHHHHHHHHHHHHhcCCCCC
Q psy1520 34 LPVDIYIGGKEHAV--------------LHLYYARFIAHFLHAQGKTPA 68 (107)
Q Consensus 34 mPVD~YIGGiEHAi--------------lHLLYaRF~~K~L~D~G~v~~ 68 (107)
+|.|+||-|..-|- .-==|||++...|..+|+|..
T Consensus 52 ~pe~l~i~~l~~a~~~~ek~kIksd~EgTSDKYaR~I~~wL~k~glv~~ 100 (142)
T PF02980_consen 52 YPEDLYIQWLAEAEEDKEKKKIKSDWEGTSDKYARMICGWLKKVGLVEQ 100 (142)
T ss_dssp --HHHHHHHHHTS--CCCHHHHHHH---HHHHHHHHHHHHHHHTTSEEE
T ss_pred CcHHHHHHHHHHhhchhHHHHHhcccccchHHHHHHHHHHHHHhchhee
Confidence 58888888877765 223599999999999999974
No 86
>PF01921 tRNA-synt_1f: tRNA synthetases class I (K); InterPro: IPR002904 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. Lysyl-tRNA synthetase (6.1.1.6 from EC) is an alpha 2 homodimer that belong to both class I and class II. In eubacteria and eukaryota lysyl-tRNA synthetases belong to class II in the same family as aspartyl tRNA synthetase. The class Ic lysyl-tRNA synthetase family is present in archaea and in a number of bacterial groups that include the alphaproteobacteria and spirochaetes[]. A refined crystal structures shows that the active site of LysU is shaped to position the substrates for the nucleophilic attack of the lysine carboxylate on the ATP alpha-phosphate. No residues are directly involved in catalysis, but a number of highly conserved amino acids and three metal ions coordinate the substrates and stabilise the pentavalent transition state. A loop close to the catalytic pocket, disordered in the lysine-bound structure, becomes ordered upon adenine binding [].; GO: 0000166 nucleotide binding, 0004824 lysine-tRNA ligase activity, 0005524 ATP binding, 0006430 lysyl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 1IRX_A.
Probab=22.83 E-value=37 Score=28.90 Aligned_cols=67 Identities=21% Similarity=0.255 Sum_probs=27.5
Q ss_pred hhhccc--ccceEEeecchhHH---HHHHHHHHHHHHHHhcCCCCCCCccccccccceeecCee-e-ecCCCceeCCCce
Q psy1520 28 DKAQDW--LPVDIYIGGKEHAV---LHLYYARFIAHFLHAQGKTPAREPFKRLLVQGMIMGQTY-R-EKTSGKYLKPDEV 100 (107)
Q Consensus 28 ~~~~~W--mPVD~YIGGiEHAi---lHLLYaRF~~K~L~D~G~v~~~EPF~~Ll~QGMV~~~~~-k-~ks~Gn~v~p~ev 100 (107)
+=+-+| +-||.=-+|.+|+. .-=...+.-.+ ++...-|+. +.=.+|+.++- | |+|+||+++|+|.
T Consensus 225 DW~mRW~~lgVdfEp~GKDH~~~GGS~d~~~~I~~~------i~g~~pP~~--~~YE~~~~~g~~kmSsSkG~~~t~~e~ 296 (360)
T PF01921_consen 225 DWPMRWAALGVDFEPFGKDHASPGGSYDTSKRIARE------ILGYEPPVP--FPYEFFLDKGGGKMSSSKGNGITPEEW 296 (360)
T ss_dssp HHHHHHHHTT-SEEEEEHHHHCTTSHHHHHHHHHHH------CC-----EE--EEE--EEES--------------HHHH
T ss_pred cChhhhhhcCceeccCCCccCCCCCChhhHHHHHHH------HhCCCCCCC--CCeeEEEeCCCcccccCCCCccCHHHH
Confidence 334566 68999999999998 54333332223 333333322 22344554443 4 5999999999886
Q ss_pred ee
Q psy1520 101 FT 102 (107)
Q Consensus 101 ~~ 102 (107)
..
T Consensus 297 L~ 298 (360)
T PF01921_consen 297 LE 298 (360)
T ss_dssp HT
T ss_pred HH
Confidence 53
No 87
>PF04522 DUF585: Protein of unknown function (DUF585); InterPro: IPR007610 This region represents the N-termini of Broad bean mottle virus, Gp1 (2a protein), and is always found N-terminal to a predicted RNA dependent RNA polymerase region (IPR001788 from INTERPRO).; GO: 0003723 RNA binding, 0003968 RNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=21.78 E-value=45 Score=27.32 Aligned_cols=26 Identities=19% Similarity=0.228 Sum_probs=19.1
Q ss_pred cccCCCCCCCCCChhhhcccccceEEee
Q psy1520 14 TKSRDINAEVSFNTDKAQDWLPVDIYIG 41 (107)
Q Consensus 14 ~~~dp~n~~~~fd~~~~~~WmPVD~YIG 41 (107)
-|+|-. ...+|.+.++.|+|+|--=|
T Consensus 108 LYLDi~--gSFVdEsE~DDW~P~DTsDG 133 (248)
T PF04522_consen 108 LYLDIE--GSFVDESEVDDWYPEDTSDG 133 (248)
T ss_pred heecCC--CCccCHhhcccceeccCcCC
Confidence 366643 35789999999999986444
No 88
>PRK13354 tyrosyl-tRNA synthetase; Provisional
Probab=20.95 E-value=1.7e+02 Score=24.95 Aligned_cols=57 Identities=21% Similarity=0.214 Sum_probs=0.0
Q ss_pred cceEEeecchhHHHHHHHHHHHHHHHHhcCCCCCCCccccccccceeecCeeee-cCCCceeCCCc
Q psy1520 35 PVDIYIGGKEHAVLHLYYARFIAHFLHAQGKTPAREPFKRLLVQGMIMGQTYRE-KTSGKYLKPDE 99 (107)
Q Consensus 35 PVD~YIGGiEHAilHLLYaRF~~K~L~D~G~v~~~EPF~~Ll~QGMV~~~~~k~-ks~Gn~v~p~e 99 (107)
.+|+-+||+++- .|+.-+|=+.+-+. ...| -.+.+.-+.-.++-|| ||.||.|.-++
T Consensus 186 ~~~iq~gG~DQ~-~ni~~grdl~~r~~------~~~~-~~lt~PlL~g~dG~KMsKS~~naI~L~d 243 (410)
T PRK13354 186 DVDLQIGGTDQW-GNILMGRDLQRKLE------GEEQ-FGLTMPLLEGADGTKMGKSAGGAIWLDP 243 (410)
T ss_pred CCCEEEecHHHH-HHHHHHHHHHHHhC------CCCc-eEeccCCccCCCCCccCCCCCCceeccC
Done!