Align aspartate-tRNAAsn ligase (EC 6.1.1.23) (characterized)
to candidate WP_013075119.1 BTUS_RS05485 aspartate--tRNA ligase
Query= BRENDA::O32038 (592 letters) >NCBI__GCF_000092905.1:WP_013075119.1 Length = 598 Score = 704 bits (1817), Expect = 0.0 Identities = 352/581 (60%), Positives = 438/581 (75%), Gaps = 2/581 (0%) Query: 4 RTYYCGDITEKAIGESVTLKGWVQKRRDLGGLIFIDLRDRTGIVQVVFNPDVSKEALAIA 63 RT CG +TE IG V L GWVQ+RRDLGG+IF+DLRDR+GIVQVV + + + A A+A Sbjct: 11 RTAMCGRLTESDIGREVVLSGWVQRRRDLGGVIFLDLRDRSGIVQVVSSQEFGEAAFAVA 70 Query: 64 EGIRNEYVLDIQGKVVAREEGTVNPNLKTGAIEIHADGVNVLNAAKTPPFAISDQAEEVS 123 + +RNEYV+ ++G VVAR+ TVNPNL+TG IE+ A V +LN +K PF I D + V Sbjct: 71 DLVRNEYVISVRGDVVARDPETVNPNLETGTIEVRAREVELLNRSKPTPFPIEDGID-VD 129 Query: 124 EDVRLKHRYLDLRRPAMFQTMQLRHNVTKAVRSFLDENGFLDIETPILTGSTPEGARDYL 183 E VRL+ RYLDLRRP M +T LRH + VR FLD +GF++IETP+LT TPEGARDYL Sbjct: 130 ESVRLRFRYLDLRRPEMQRTFLLRHRAMQQVRRFLDLHGFMEIETPMLTRRTPEGARDYL 189 Query: 184 VPSRVHEGEFYALPQSPQLFKQLLMVSGIERYYQIARCFRDEDLRADRQPEFTQIDIEMS 243 VPSRVH G+FYALPQSPQLFKQLLMVSG ERY+QI RCFRDEDLRADRQPEFTQIDIEMS Sbjct: 190 VPSRVHPGQFYALPQSPQLFKQLLMVSGFERYFQIVRCFRDEDLRADRQPEFTQIDIEMS 249 Query: 244 FMSQEDIMSLAEEMMAKVMRETKGEELQLPLPRMTYDEAMNKYGSDKPDTRFDMLLTDVS 303 FM + L E MMA++ +E G + LP R+ YDEAM +YGSDKPD RF + + DV+ Sbjct: 250 FMPLTEFQELMERMMAELFQELLGVTVPLPFRRIPYDEAMLRYGSDKPDLRFGLEIRDVT 309 Query: 304 DIVKDTEFKVFSSAVANGGVVKAINVKGGAGDYSRKDIDALGAFAANYGAKGLAWVKVEA 363 ++VK F+VF SAV +GG V+ +N KG G +SRK+ID LGA A GAKGLAW+ + Sbjct: 310 EMVKTCGFRVFQSAVNSGGAVRGLNAKG-CGGFSRKEIDDLGALAGQLGAKGLAWMVITE 368 Query: 364 DGVKGPIAKFFDEEKQSKLIEALDAAEGDLLLFGADQFEVVAASLGALRLKLGKERGLID 423 +GVK PIAKFF +E+ + L A GDLLLF AD+ E+ A LG LRL LG+ GLID Sbjct: 369 EGVKSPIAKFFTDEELGAIRRELGAEVGDLLLFVADRPEICAEVLGQLRLHLGRRLGLID 428 Query: 424 EKLFNFLWVIDWPLLEHDPEEGRFYAAHHPFTMPVREDLELIETAPEDMKAQAYDLVLNG 483 + F F W+ D+PL +D EE R+ A HHPFTMP ED++L+E P ++AQAYD+VLNG Sbjct: 429 DASFAFAWITDFPLFSYDEEEKRWVAEHHPFTMPRWEDVDLMERDPARVRAQAYDMVLNG 488 Query: 484 YELGGGSIRIFEKDIQEKMFALLGFSPEEAAEQFGFLLEAFEYGAPPHGGIALGLDRLVM 543 YE+GGGS+RI+ +DIQE MF LGFS +EA E+FGFLLEAFEYGAPPHGG+A G DR++M Sbjct: 489 YEIGGGSLRIYRRDIQEAMFRTLGFSMDEAREKFGFLLEAFEYGAPPHGGMAFGFDRVIM 548 Query: 544 LLAGRTNLRDTIAFPKTASASCLMTEAPGEVSDAQLDELHL 584 L+AG++++R+ IAFPKTASASCL+T AP ++SD Q ELH+ Sbjct: 549 LMAGKSSIRECIAFPKTASASCLLTGAPSQISDEQWRELHI 589 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: 1027 Number of extensions: 51 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: 598 Length adjustment: 37 Effective length of query: 555 Effective length of database: 561 Effective search space: 311355 Effective search space used: 311355 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