Align Aspartate--tRNA(Asp/Asn) ligase; EC 6.1.1.23; Aspartyl-tRNA synthetase; AspRS; Non-discriminating aspartyl-tRNA synthetase; ND-AspRS (uncharacterized)
to candidate WP_011602405.1 FRAAL_RS05245 aspartate--tRNA ligase
Query= curated2:B0K978 (592 letters) >NCBI__GCF_000058485.1:WP_011602405.1 Length = 618 Score = 541 bits (1394), Expect = e-158 Identities = 292/586 (49%), Positives = 393/586 (67%), Gaps = 21/586 (3%) Query: 10 RTHMCGELTVEDVDKSVVVMGWVQRRRDHG-GLVFIDLRDRTGIVQVVFSNEVSSEAFEK 68 RTH+C +L + V ++V V GWV RR HG L F+DLRD +G++QVV V Sbjct: 29 RTHLCADLRADHVGRTVSVCGWVAHRRQHGQSLTFVDLRDHSGLLQVVVDGSVD------ 82 Query: 69 VQSVRSEYVLAIEGKVVKRAPENVNPKISTGEIEIYANTLKILSKSETPPFPIEDRSN-V 127 VRSEYVL + G V R NP ++TGE+E+ ++ILS + PPFP++DR++ V Sbjct: 83 ---VRSEYVLRVTGTVAIRPEGTANPALATGEVELRDCAVEILSVATPPPFPLDDRADAV 139 Query: 128 SEAIRLKYRYLDLRRPSMQQNLMTRFKITKVVRDFLNRNGFIEIETPLLIKSTPEGARDY 187 E+ RL YRYLDLRR MQ+NL TR + +R L F+E+ETPLL+ STPEGAR++ Sbjct: 140 DESTRLAYRYLDLRRERMQRNLRTRSAVLGAMRAALAPLDFVEVETPLLMPSTPEGAREF 199 Query: 188 LVPSRIYPGKFYALPQSPQIFKQLLMISGFDKYYQIAKCLRDEDLRADRQPEFTQIDIEM 247 +VPSR +PG FYALPQSPQ+FKQLLM+ G D+Y+Q A+CLRDEDLRADRQ EFTQ+D+EM Sbjct: 200 IVPSRQFPGSFYALPQSPQLFKQLLMVGGTDRYFQFARCLRDEDLRADRQYEFTQLDLEM 259 Query: 248 SFVEVEDVLKINEKMIAEIFKETLGIDVPIPFKRLSYQESMERFGTDKPDLRFGMELKDL 307 SFV+ +DVL + + + VP P +R+++ ESM RFG DKPDLRFGMEL +L Sbjct: 260 SFVDQDDVLDVISAAVLAAARAVRTDTVP-PIERITWHESMNRFGVDKPDLRFGMELVEL 318 Query: 308 SDIVAQSEFNVFKTALKNNGSVRGINVK-GAASMPRRQLDELVEFAKTYGAKGLLWIQV- 365 + I A S F F A +++GI V G+A+ RR+LD+L AK GAKGL+W++V Sbjct: 319 TAIFAGSGFKAFAGA----EAIKGIRVPGGSAAHNRRRLDDLTTRAKALGAKGLVWMRVG 374 Query: 366 FEKEVKSPATKFLSEEEMKKILERLEAEAGDLLLIVADKDEIVFDTLAHLRLELGKRFNL 425 E++SP KFLS +E+ I+ +A GDLLL+VAD + L LR +LG+ Sbjct: 375 AGGELESPVAKFLSADELAGIVAATDAVEGDLLLLVADAWATTCEVLGQLRNDLGR--PP 432 Query: 426 IDENKYEFVWIVDFPL-LEYDEGEKRYVAKHHPFTAPKDEDIELLEKEPLKVRAKAYDIV 484 + FVW+VDFPL + D R HHPFT P +DI LE EPL VR++AYD+V Sbjct: 433 AGQGPLRFVWVVDFPLFVGVDPATGRPKPGHHPFTRPHPDDIAKLESEPLAVRSRAYDLV 492 Query: 485 LNGTEIGGGSIRIHDTELQKRMFKVLGFSEEKAWERFGFLMEAFKYGAPPHGGIAYGLDR 544 LNG E+G GSIRIH++ LQ+R+F +LG + ++A RFGF + F YGAPPHGG A G+DR Sbjct: 493 LNGWELGSGSIRIHESALQQRIFGLLGITPDEANARFGFFLTPFGYGAPPHGGFAVGIDR 552 Query: 545 LAMIITGSDTIRDVIAFPKTQNAVCLMTDAPSEVSEEQLKELHIKV 590 L I+ G + IR+VIAFPKTQ+ + +T AP++V++ QL+EL ++V Sbjct: 553 LVAILAGEENIREVIAFPKTQSGLDPLTGAPTQVTDRQLRELGVRV 598 Lambda K H 0.319 0.138 0.393 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 910 Number of extensions: 41 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 592 Length of database: 618 Length adjustment: 37 Effective length of query: 555 Effective length of database: 581 Effective search space: 322455 Effective search space used: 322455 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory