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 PP_2213 PP_2213 putative acyl-CoA synthetase
Query= SwissProt::Q3UNX5 (580 letters) >FitnessBrowser__Putida:PP_2213 Length = 561 Score = 277 bits (709), Expect = 7e-79 Identities = 175/500 (35%), Positives = 276/500 (55%), Gaps = 19/500 (3%) Query: 81 DGNGEELRWSFEELGLLSRKFANILTEACSLQRGDRVMVILPKIPEWWLANVACLRTGTV 140 D +G +SF++L + + +FAN+L +A + GDRV ++P+ PE + +A R G V Sbjct: 63 DRDGNSACYSFDQLQVQAARFANVL-KAQGVGAGDRVAGLMPRTPELLVTILATWRLGAV 121 Query: 141 LIPGTTQLTQKDILYRLQSSKAKCIITDDTLAPAVDAVAAKCENLHSKLIVSQHSREGWG 200 P T K I +RL+ S A+ ++TD +D V A I++ +R G Sbjct: 122 YQPLFTAFGPKAIEHRLEQSHARVVVTDSHNRAKLDDVHA------CPTIITVKARSGEL 175 Query: 201 NLKEMMKYASDSHTCVDTKHDEMMAIYFTSGTTGPPKMIGHTHSSFGLGLSVNGRFWLDL 260 + ++ ++ A+D V ++ + FTSGTTGP K + + + R ++L Sbjct: 176 DFQQCLERAADVCEPVMRSGNDPFLLMFTSGTTGPAKPLEVPLRAI-VAFQGYMRDAIEL 234 Query: 261 IASDVMWNTSDTGWAKSAWSSVFSPWTQGACVFAHYLPRFESTSILQTLSKFPITVFCSA 320 + D WN +D GWA + +V P + G + P F S + + K IT + Sbjct: 235 LPEDNFWNLADPGWAYGLYYAVTGPLSLGHATTFYDGP-FSVESCARVIDKLGITNLAGS 293 Query: 321 PTAYRMLVQ--NDMSSYKFNSLKHCVSAGEPINPEVMEQWRKKTGLDIYEGYGQTETVLI 378 PTAYR+L+ D S+ L+ SAGEP+NPEV+ + + G+ I++ YGQTE ++ Sbjct: 294 PTAYRLLIAAGKDFSAPIKGRLRVVSSAGEPLNPEVIRWFADELGVTIHDHYGQTELGMV 353 Query: 379 CGNFKGMK--IKPGSMGKPSPAFDVKILDENGATLPPGQEGDIALQVLPERPFGLFTHYV 436 N G++ + GS G P + ++DE G LP GQ G +A+ + P F Y Sbjct: 354 LCNHHGLQHPVHLGSAGYAIPGHRIVVVDEQGNELPAGQPGILAVD-REQSPLCWFGGYH 412 Query: 437 DNPSKTASTLRGSFYITGDRGYMDEDGYFWFVARSDDIILSSGYRIGPFEVESALIEHPS 496 P+K G +Y++GD ++ DG FV RSDD+I +SGYR+GPF+VESALIEHP+ Sbjct: 413 GLPTKA---FVGKYYLSGDTVELNPDGSISFVGRSDDVITTSGYRVGPFDVESALIEHPA 469 Query: 497 IAESAVVSSPDPIRGEVVKAFIVLNPDYKSHDQEQLKKEIQEHVKKTTAPYKYPRKVEFI 556 + E+AV+ PDP R E++KAF+VL Y +L++ +++HV++ + YPR++EF+ Sbjct: 470 VIEAAVIGKPDPERTELIKAFVVLASGYAG--SVELEETLRQHVRQRLYAHAYPREIEFV 527 Query: 557 EELPKTVSGKVKRNELRKKE 576 ELPKT SGK++R LR +E Sbjct: 528 SELPKTPSGKLQRFILRNQE 547 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: 740 Number of extensions: 41 Number of successful extensions: 9 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: 580 Length of database: 561 Length adjustment: 36 Effective length of query: 544 Effective length of database: 525 Effective search space: 285600 Effective search space used: 285600 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