Align aspartate-tRNAAsn ligase (EC 6.1.1.23) (characterized)
to candidate WP_041315154.1 HM1_RS08320 aspartate--tRNA ligase
Query= BRENDA::O32038 (592 letters) >NCBI__GCF_000019165.1:WP_041315154.1 Length = 604 Score = 703 bits (1814), Expect = 0.0 Identities = 348/588 (59%), Positives = 450/588 (76%), Gaps = 2/588 (0%) Query: 4 RTYYCGDITEKAIGESVTLKGWVQKRRDLGGLIFIDLRDRTGIVQVVFNPDVSKEALAIA 63 R++ GD+ G++VTL GWVQ+RRD GGLIF+DLRDR+G+VQVVF+P+V KEA A Sbjct: 10 RSHRGGDLRIDHAGQTVTLMGWVQRRRDHGGLIFVDLRDRSGLVQVVFSPEVGKEAFTKA 69 Query: 64 EGIRNEYVLDIQGKVVAREEGTVNPNLKTGAIEIHADGVNVLNAAKTPPFAISDQAEEVS 123 E +RNEYVL + G V R EGTVN NL +G I+++A + VLN+AKTPPF I D + V Sbjct: 70 EDVRNEYVLAVTGDVRPRPEGTVNANLPSGQIDVYARQLWVLNSAKTPPFYIEDGVD-VD 128 Query: 124 EDVRLKHRYLDLRRPAMFQTMQLRHNVTKAVRSFLDENGFLDIETPILTGSTPEGARDYL 183 E VRLK+RYLDLRRP M + + +RH KA+R FLD NGFL+IETP+LT STPEGAR+++ Sbjct: 129 ETVRLKYRYLDLRRPEMQRNLIIRHKTAKAMRDFLDRNGFLEIETPMLTKSTPEGAREFM 188 Query: 184 VPSRVHEGEFYALPQSPQLFKQLLMVSGIERYYQIARCFRDEDLRADRQPEFTQIDIEMS 243 VPSR+H GEF+ LPQSPQL+KQ+LMV+G+ERY+QI RCFRDEDLRADRQPEFTQ+DIEMS Sbjct: 189 VPSRIHPGEFFVLPQSPQLYKQILMVAGMERYFQIVRCFRDEDLRADRQPEFTQLDIEMS 248 Query: 244 FMSQEDIMSLAEEMMAKVMRETKGEELQLPLPRMTYDEAMNKYGSDKPDTRFDMLLTDVS 303 F +D+++L EEM+A + +E G+E+ P R+ Y EAM ++GSDKPD RF + L D++ Sbjct: 249 FTQMDDLLTLMEEMVAHIFKEALGKEISTPFRRIPYAEAMGRFGSDKPDLRFGLELIDLT 308 Query: 304 DIVKDTEFKVFSSAVANGGVVKAINVKGGAGDYSRKDIDALGAFAANYGAKGLAWVKVEA 363 + VKD EFKVF+S V GG VKAIN KG A +SRK+ID L A YGAKGLA++++ Sbjct: 309 ETVKDVEFKVFASVVKGGGEVKAINAKGCA-HFSRKEIDDLTKGVAVYGAKGLAYIQMTE 367 Query: 364 DGVKGPIAKFFDEEKQSKLIEALDAAEGDLLLFGADQFEVVAASLGALRLKLGKERGLID 423 +G K PIAKFF +E+ + +++ L A +GDLLLF AD+ VVAASLG LR +L + LID Sbjct: 368 EGPKSPIAKFFTDEQLNAVLDRLGAEKGDLLLFVADKPSVVAASLGFLRQELARRLNLID 427 Query: 424 EKLFNFLWVIDWPLLEHDPEEGRFYAAHHPFTMPVREDLELIETAPEDMKAQAYDLVLNG 483 + F WV+D+PL+E+DPEE R+ A HHPFT P EDL+L++ P ++A+AYDLVLNG Sbjct: 428 SEKLEFAWVVDFPLVEYDPEEKRYNAIHHPFTAPKDEDLDLLDKEPGKVRAKAYDLVLNG 487 Query: 484 YELGGGSIRIFEKDIQEKMFALLGFSPEEAAEQFGFLLEAFEYGAPPHGGIALGLDRLVM 543 ELGGGS+RI+ +DIQEKMFA+LG + EEA ++FGFLL+AF+YG PPHGGIA GLDR++M Sbjct: 488 VELGGGSLRIYRRDIQEKMFAILGLTAEEAYQKFGFLLDAFDYGTPPHGGIAFGLDRMIM 547 Query: 544 LLAGRTNLRDTIAFPKTASASCLMTEAPGEVSDAQLDELHLSIKKKVK 591 L+ GR +RD IAFPKT SAS +M +AP V+ QL ELH+ + VK Sbjct: 548 LMTGRDTIRDVIAFPKTQSASDMMVDAPSAVTPRQLKELHIKLDLPVK 595 Lambda K H 0.319 0.137 0.394 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: 1055 Number of extensions: 37 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: 592 Length of database: 604 Length adjustment: 37 Effective length of query: 555 Effective length of database: 567 Effective search space: 314685 Effective search space used: 314685 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