Align Aspartate--tRNA(Asp/Asn) ligase; EC 6.1.1.23 (characterized, see rationale)
to candidate WP_028315299.1 G491_RS0115860 aspartate--tRNA ligase
Query= uniprot:SYDND_DESVH (610 letters) >NCBI__GCF_000429905.1:WP_028315299.1 Length = 597 Score = 744 bits (1922), Expect = 0.0 Identities = 361/591 (61%), Positives = 453/591 (76%), Gaps = 5/591 (0%) Query: 19 LGDWQRTHSCCELTAADVGNDVCIMGWVQYRRDHGGLIFVDLRDRKGLTQVVFSPDFAPE 78 LG +RTH+C L D G V +MGW Q RDHGG+IF+DLRDR G+TQVVF+P+ + Sbjct: 5 LGSMRRTHNCGVLRKEDTGKTVTLMGWAQRWRDHGGVIFIDLRDRYGVTQVVFNPEHNAD 64 Query: 79 AHKDAHIVRSEYVLAIRGRVRPRPEGMTNPGMKTGEIEVVVSEWKLLNTSKTPPFLIEDR 138 HK A +RSE+V+A++G V RP+GM NP M+TGEIE++VSE K+LN SKTPPF++ED Sbjct: 65 VHKLADTIRSEWVIAVQGEVLERPDGMVNPKMETGEIEIMVSELKILNKSKTPPFMVEDN 124 Query: 139 TEASENLRLAWRYLDLRRPRMARNFMLRHRAAQSARRYLDELDFLEIETPYLTKATPEGA 198 E SENLRL +RYLDLRRPR+A+N MLRH R +L+E +FL+IETP LTK+TPEGA Sbjct: 125 VEVSENLRLEYRYLDLRRPRIAKNIMLRHHVGACVRAFLNENEFLDIETPVLTKSTPEGA 184 Query: 199 RDFLVPSRLNHGMFYALPQSPQIFKQLLMVSGMDRYYQIVRCFRDEDMRADRQLEFTQID 258 RD+LVPSR+N G+FYALPQSPQ+FKQLLMV+G DRYYQIVRCFRDED+RADRQ EFTQID Sbjct: 185 RDYLVPSRVNTGLFYALPQSPQLFKQLLMVAGYDRYYQIVRCFRDEDLRADRQPEFTQID 244 Query: 259 IEMSFVDEERVMSMAEGLMSRVMKDTLGVDVTVPFPRMTYDQAMGEYGVDKPDTRFDLRL 318 +EMSFV EE VM +AE +++RV KD +G DV PF R+TY AM YG+DKPD RFDL L Sbjct: 245 LEMSFVGEEDVMGIAEQMIARVFKDVMGKDVKTPFDRLTYKDAMDRYGLDKPDLRFDLEL 304 Query: 319 KDVTDAVRGSEFKLFA----KAPLVKAMRVPGGETMTRKEIDEFTEFVKIYGAQGLAWIK 374 K+V+ V GS+FK+FA K +VKAM G +RK ID+ T FV +YGA+GLAWIK Sbjct: 305 KEVSSIVEGSDFKVFASVVKKGGMVKAMNAKGCAHFSRKVIDDLTAFVAVYGAKGLAWIK 364 Query: 375 IRE-GEWQSPIAKFLSEAERAALVAALGLEVGDIVFFQAGEPGMVNAALGNLRVKLGQHL 433 ++E G WQSPIAKF ++ E+AA+ L + GD++FF A + N ALG+LR ++ + L Sbjct: 365 VKEDGSWQSPIAKFFTDDEKAAMAQTLDMAPGDLIFFVADNVKVTNDALGHLRNRVAKEL 424 Query: 434 GLIPEDTYNFLWVTDFPLFEYDEEEKRYVACHHPFTSPKDGHFDLMTSDPAAARARAYDM 493 GLI E+ + F+WVT+FPL EYDE EKRYVA HHPFT+P + DL+ +DP A R+RAYDM Sbjct: 425 GLIDENEFRFVWVTEFPLVEYDETEKRYVALHHPFTAPMEEDLDLLETDPGAVRSRAYDM 484 Query: 494 VLNGYELGGGSIRIHSAEVQRRMFAALGLDPQEAEEKFGFLIQALEHGAPPHGGIAFGMD 553 VLNG ELGGGSIRIH E+Q ++F LGL +EAEEKFGFL++AL GAPPHGG+AFG D Sbjct: 485 VLNGTELGGGSIRIHQPEMQEKVFNMLGLGQEEAEEKFGFLLKALAFGAPPHGGLAFGFD 544 Query: 554 RLVMLLTGSPSIRDVIAFPKTQKATCLMTQAPDAVSARQLRDLGIRLRETP 604 RL+MLL+G SIRD+I FPKTQKA CL+T AP V+ QL +L +R+++ P Sbjct: 545 RLIMLLSGENSIRDIIPFPKTQKAACLLTDAPSEVAFEQLAELALRIKKDP 595 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: 1072 Number of extensions: 35 Number of successful extensions: 3 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: 597 Length adjustment: 37 Effective length of query: 573 Effective length of database: 560 Effective search space: 320880 Effective search space used: 320880 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