Align Aspartate--tRNA(Asp/Asn) ligase; EC 6.1.1.23 (characterized, see rationale)
to candidate WP_005455618.1 SACCYDRAFT_RS09205 aspartate--tRNA ligase
Query= uniprot:SYDND_DESVH (610 letters) >NCBI__GCF_000244975.1:WP_005455618.1 Length = 590 Score = 567 bits (1462), Expect = e-166 Identities = 298/593 (50%), Positives = 397/593 (66%), Gaps = 13/593 (2%) Query: 24 RTHSCCELTAADVGNDVCIMGWVQYRRDHGGLIFVDLRDRKGLTQVVFSPDFAPEAHKDA 83 RTH L A VG V + GWV RRDHGG+IF+DLRD G+ QVVF E + A Sbjct: 3 RTHDAGTLRAEHVGQTVTLTGWVARRRDHGGVIFIDLRDASGVAQVVFREG---EMAERA 59 Query: 84 HIVRSEYVLAIRGRVRPRPEGMTNPGMKTGEIEVVVSEWKLLNTSKTPPFLIEDRTEASE 143 H +RSEY L + G V RPEG NP + TG+IEV+V+E ++L+ S PF I++R + E Sbjct: 60 HALRSEYCLKVTGEVSRRPEGNENPDIPTGDIEVLVTELEVLSESAVLPFPIDERLDVGE 119 Query: 144 NLRLAWRYLDLRRPRMARNFMLRHRAAQSARRYLDELDFLEIETPYLTKATPEGARDFLV 203 RL +RYLDLRR AR LR + AR L + FLEIETP +T++TPEGARDFLV Sbjct: 120 ETRLRYRYLDLRRNGPARIMRLRSEVNRVAREVLHQHGFLEIETPTMTRSTPEGARDFLV 179 Query: 204 PSRLNHGMFYALPQSPQIFKQLLMVSGMDRYYQIVRCFRDEDMRADRQLEFTQIDIEMSF 263 P+RL G +YALPQSPQ+FKQLLMV G++RYYQI RC+RDED RADRQ EFTQ+DIEMSF Sbjct: 180 PARLKPGSWYALPQSPQLFKQLLMVGGLERYYQIARCYRDEDFRADRQPEFTQLDIEMSF 239 Query: 264 VDEERVMSMAEGLMSRVMKDTLGVDVTVPFPRMTYDQAMGEYGVDKPDTRFDLRLKDVTD 323 V+++ V+++AE ++S + K G +VT PF RM+Y +AM +YG DKPD RF L L ++TD Sbjct: 240 VEQDDVIALAENVLSALWK-LAGAEVTTPFRRMSYAEAMSKYGTDKPDLRFGLELVELTD 298 Query: 324 AVRGSEFKLFAKAPLVKAMRVPGGETMTRKEIDEFTEFVKIYGAQGLAWIKIRE-GEWQS 382 + F++F +AP V A+ +PGG R+ +D + E+ K G +GLA++ + E G Sbjct: 299 FFADTPFRVF-QAPYVGAVVMPGGADQPRRTLDAWQEWAKQRGHRGLAYVLVGEDGTLGG 357 Query: 383 PIAKFLSEAERAALVAALGLEVGDIVFFQAGEPGMVNAALGNLRVKLGQHLGLIPEDTYN 442 P+AK LSE ER LV A G + GD +FF AG+P LG RV++ L +I E+ ++ Sbjct: 358 PVAKNLSETERENLVEAAGAKPGDCIFFAAGKPKDARQLLGMARVEIAHRLDMIDENAWS 417 Query: 443 FLWVTDFPLFEYDEEEK-------RYVACHHPFTSPKDGHFDLMTSDPAAARARAYDMVL 495 F+WV DFP+FE E+ ++ A HH FTSP D SDPA A A AYD+V Sbjct: 418 FVWVVDFPMFEAAEDSDDVSVGGGKWTALHHAFTSPTPEWIDKFESDPAGALAYAYDIVC 477 Query: 496 NGYELGGGSIRIHSAEVQRRMFAALGLDPQEAEEKFGFLIQALEHGAPPHGGIAFGMDRL 555 NG E+GGGSIRIH A+VQ+R+F +GL +EA+EKFGFL+ A ++G PPHGGIAFG DR+ Sbjct: 478 NGNEIGGGSIRIHRADVQKRVFEIMGLSEEEAQEKFGFLLDAFQYGPPPHGGIAFGWDRI 537 Query: 556 VMLLTGSPSIRDVIAFPKTQKATCLMTQAPDAVSARQLRDLGIRLRETPQEQK 608 VMLL G+ S+R+VIAFPKT +T AP ++A+Q ++ G+ + +Q+ Sbjct: 538 VMLLAGAESLREVIAFPKTGGGYDPLTGAPAPITAQQRKEAGVDAKPVTTQQR 590 Lambda K H 0.322 0.138 0.415 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: 1009 Number of extensions: 45 Number of successful extensions: 7 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: 610 Length of database: 590 Length adjustment: 37 Effective length of query: 573 Effective length of database: 553 Effective search space: 316869 Effective search space used: 316869 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 (21.9 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