Align Acyl-coenzyme A synthetase ACSM3, mitochondrial; Acyl-CoA synthetase medium-chain family member 3; Butyrate--CoA ligase 3; Butyryl-coenzyme A synthetase 3; Middle-chain acyl-CoA synthetase 3; Propionate--CoA ligase; Protein SA homolog; EC 6.2.1.2; EC 6.2.1.17 (characterized)
to candidate GFF3565 PS417_18255 AMP-binding protein
Query= SwissProt::Q3UNX5 (580 letters) >FitnessBrowser__WCS417:GFF3565 Length = 546 Score = 248 bits (632), Expect = 6e-70 Identities = 169/500 (33%), Positives = 261/500 (52%), Gaps = 20/500 (4%) Query: 83 NGEELRWSFEELGLLSRKFANILTEACSLQRGDRVMVILPKIPEWWLANVACLRTGTVLI 142 +G +F EL + +F N L E ++ G+RV ++P+ E +A + R G V Sbjct: 52 DGRATHHTFSELQAHAARFGNFLREQ-GVKPGERVAGLMPRTVELLIAILGTWRIGAVYQ 110 Query: 143 PGTTQLTQKDILYRLQSSKAKCIITDDTLAPAVDAVAAKCENLHSKLIVSQHSREGWGNL 202 P T K I RL S+A+ I+TD P +D V C ++IV+ + Sbjct: 111 PLFTAFGPKAIEQRLGCSEARWIVTDAHNRPKLDDVI-DCP----RIIVTGAGPRNPDDY 165 Query: 203 KEMMKYASDSHTCVDTKHDEM--MAIYFTSGTTGPPKMIGHTHSSFGLGLSVNGRFWLDL 260 CV D + TSGTTGP K + S+ L R +DL Sbjct: 166 DFWTVLDRQQADCVPELLDASAPFLLMCTSGTTGPAKPLEVPLSAI-LAFKGYMRDSIDL 224 Query: 261 IASDVMWNTSDTGWAKSAWSSVFSPWTQGACVFAHYLPRFESTSILQTLSKFPITVFCSA 320 D WN +D GWA + +V P G + P F S + ++K+ IT + Sbjct: 225 REDDHFWNLADPGWAYGLYYAVTGPLACGRATLFYDGP-FAVDSTCRIIAKYAITNLAGS 283 Query: 321 PTAYRMLVQND--MSSYKFNSLKHCVSAGEPINPEVMEQWRKKTGLDIYEGYGQTETVLI 378 PTAYR+L+ + L+ SAGEP+NP+V+ + + G+ I++ YGQTE ++ Sbjct: 284 PTAYRLLIAAGAAFADTVRGRLRVISSAGEPLNPQVIRWFADELGVVIHDHYGQTEIGMV 343 Query: 379 CGNFKGMK--IKPGSMGKPSPAFDVKILDENGATLPPGQEGDIALQVLPERPFGLFTHYV 436 N G++ ++ GS G P + + +LD+ LPPG+ G +A+ P F Y Sbjct: 344 LCNHHGLRHPVREGSAGYAVPGYRIVVLDDAHRELPPGRPGVLAVD-RERSPLCWFEGYF 402 Query: 437 DNPSKTASTLRGSFYITGDRGYMDEDGYFWFVARSDDIILSSGYRIGPFEVESALIEHPS 496 P++ +Y++GD +++DG FV R+DD+I +SGYR+GPF+VESALIEHP+ Sbjct: 403 GMPTQA---FVDRYYLSGDIVELNDDGSISFVGRNDDVITTSGYRVGPFDVESALIEHPA 459 Query: 497 IAESAVVSSPDPIRGEVVKAFIVLNPDYKSHDQEQLKKEIQEHVKKTTAPYKYPRKVEFI 556 + E+AV+ PDP R E++KAF+VLN +S +L + ++ HV++ A + YPR++EF+ Sbjct: 460 VVEAAVIGKPDPQRTELIKAFVVLNS--QSLPSTELAEVLRLHVRQRLAAHAYPREIEFV 517 Query: 557 EELPKTVSGKVKRNELRKKE 576 E LPKT SGK++R LR +E Sbjct: 518 EHLPKTPSGKLQRFILRNQE 537 Lambda K H 0.319 0.134 0.416 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: 774 Number of extensions: 40 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 580 Length of database: 546 Length adjustment: 36 Effective length of query: 544 Effective length of database: 510 Effective search space: 277440 Effective search space used: 277440 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 Sep 17 2021. The underlying query database was built on Sep 17 2021.
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