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 GFF944 HP15_923 acetyl-coA synthetase/AMP-(fatty) acid ligase
Query= SwissProt::Q3UNX5 (580 letters) >FitnessBrowser__Marino:GFF944 Length = 549 Score = 262 bits (669), Expect = 3e-74 Identities = 174/531 (32%), Positives = 267/531 (50%), Gaps = 28/531 (5%) Query: 53 NFAKDVLDQWTNMEKAGKRLSNPAFWWIDGNGEELRWSFEELGLLSRKFANILTEACSLQ 112 N ++ D+W + S A ++ +G + +F EL S +FAN L ++ + Sbjct: 32 NVCHEICDKWADDP------SRVALYYETEDGGDGTLTFAELKEASARFANYL-KSQGIG 84 Query: 113 RGDRVMVILPKIPEWWLANVACLRTGTVLIPGTTQLTQKDILYRLQSSKAKCIITDDTLA 172 +GDRV +LP+ PE + LR G V P T I YR + + K ++T+ Sbjct: 85 KGDRVAALLPRTPELLIVIAGTLRAGAVYQPLFTAFGSGAIEYRFERASTKLVVTNPENY 144 Query: 173 PAVDAVAAKCENLHSKLIVSQHSREGWGNL---KEMMKYASDSHTCVDTKHDEMMAIYFT 229 P ++ V +V ++ E ++ +E + S V K D+ FT Sbjct: 145 PKLNDVKV------CPPVVGVNASEIGADIPDFEETLAAQSSDFEPVMIKGDDPFLQMFT 198 Query: 230 SGTTGPPKMIGHTHSSFGLGLSVNGRFWLDLIASDVMWNTSDTGWAKSAWSSVFSPWTQG 289 SGT G K + + L V ++ +DL D WN +D GWA + +V P G Sbjct: 199 SGTVGKSKGVAVPAKAL-LAFYVYMKYAIDLQDGDRFWNVADPGWAYGLYYAVVGPLLMG 257 Query: 290 ACVFAHYLPR-FESTSILQTLSKFPITVFCSAPTAYRMLVQND--MSSYKFNSLKHCVSA 346 H+ P F S + K+ IT +APTAYR+L ND + + L+ SA Sbjct: 258 HAT--HFNPGGFTPESTYDMIRKYKITNLAAAPTAYRLLKANDHVLPEGENLGLRVASSA 315 Query: 347 GEPINPEVMEQWRKKTGLDIYEGYGQTETVLICGNFKGMK--IKPGSMGKPSPAFDVKIL 404 GEP+NPEV+ R + + + YGQTET + C NF G+ ++ GSMG SP V L Sbjct: 316 GEPLNPEVVNWIRNRHYCPVKDHYGQTETGMTCCNFHGLAHPVREGSMGYASPGHKVVAL 375 Query: 405 DENGATLPPGQEGDIALQVLPERPFGLFTHYVDNPSKTASTLRGSFYITGDRGYMDEDGY 464 +E + G+ G +A+ V F H+ +Y+TGD +G Sbjct: 376 NEKNEVVGEGEVGQLAVDVKASPLF----HFDGYTWGEKDPFVNGYYLTGDMVINHGNGN 431 Query: 465 FWFVARSDDIILSSGYRIGPFEVESALIEHPSIAESAVVSSPDPIRGEVVKAFIVLNPDY 524 F F R DDII ++GYR+GP +VES L+EH ++AES VV PD RG ++KA++V+ DY Sbjct: 432 FSFSGRDDDIITTAGYRVGPADVESTLLEHAAVAESGVVGKPDEKRGSIIKAYVVIKGDY 491 Query: 525 KSHDQEQLKKEIQEHVKKTTAPYKYPRKVEFIEELPKTVSGKVKRNELRKK 575 D++ LK E+QE V++ + + +PR++EF++ELPKT SGK++R LR + Sbjct: 492 ALGDEQALKDELQELVRRRLSTHAFPREIEFVDELPKTPSGKIQRFVLRNQ 542 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: 810 Number of extensions: 42 Number of successful extensions: 7 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: 549 Length adjustment: 36 Effective length of query: 544 Effective length of database: 513 Effective search space: 279072 Effective search space used: 279072 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