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 Ac3H11_4478 Acetyl-coenzyme A synthetase (EC 6.2.1.1)
Query= SwissProt::Q3UNX5 (580 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4478 Length = 536 Score = 165 bits (418), Expect = 4e-45 Identities = 147/532 (27%), Positives = 244/532 (45%), Gaps = 58/532 (10%) Query: 76 AFWWIDGNGEELRWSFEELGLLSRKFANILTEACSLQRGDRVMVILPKIPEWWLANVACL 135 A+ W G+ L W+ +L S FA L +A + +G+ V + + P++ +A+ Sbjct: 26 AYLWY---GQPLTWA--QLDAASDAFAARL-QALGVAKGEPVALFMNNCPQYVMAHYGIQ 79 Query: 136 RTGTVLIPGTTQLTQKDILYRLQSSKAKCIITDDTLAPAVDAVAAKCENLHSKLI-VSQH 194 + G ++ P + ++ Y+L + + I+ D L P VD V AK H ++ ++ Sbjct: 80 KIGAIVCPCGPLNKEHELEYQLTDLQTRVIVAADVLLPVVDKVRAKTALQHVFVVRYAEL 139 Query: 195 SREGWGNLK---EMMKYASDSHT----CVD---------------TKHDEMMAIYFTSGT 232 +G ++ E++ + + C D D++ + +TSGT Sbjct: 140 LPDGTPSIDVPAELLNMRTAMGSVPAGCEDFLAATRTGARPAPVALSMDDISLMTYTSGT 199 Query: 233 TGPPK--MIGHTHSSFGLGLSVNGRFWLDLIASDVMWNTSDTGWAKSAWSSVFSPWTQGA 290 TG PK M+ + +++F S + + + + + V P GA Sbjct: 200 TGLPKGAMLSYGNATFKTAASADCN---GMTPHETLLAVAPLYHIAGMVMGVNLPVYTGA 256 Query: 291 CVFAHYLPRFESTSILQTLSKFPITVFCSAPTAYRMLVQ------NDMSSYKFNSLKHCV 344 Y RF+ + Q L + +T + S L+Q D S+ + N + Sbjct: 257 TAVLLY--RFDPLGVAQALERHRVTWWYSIAPMNGALMQVPGARDMDWSALRRNPV---T 311 Query: 345 SAGEPINPEVMEQWRKKTGLDIYE--GYGQTETVLICGNFKGMKIKPGSMGKPSPAFDVK 402 S G + +QW++ I YG +ET + I+ G+ G+P P ++ Sbjct: 312 SFGITFTEALAQQWQQFAPNCIAHEAAYGLSETHTVDTAMPVDAIRWGTQGQPVPGNTIR 371 Query: 403 ILD-ENGATLPPGQEGDIALQVLPERPFGLFTHYVDNPSKTASTLRGSFYITGDRGYMDE 461 I+D + GA LP G+ G+I + G F Y + P TA TLR + TGD G +D Sbjct: 372 IVDPDTGAPLPTGEVGEITIHGP-----GNFKGYWNKPEATAKTLRDGWVYTGDMGKIDA 426 Query: 462 DGYFWFVARSDDIILSSGYRIGPFEVESALIEHPSIAESAVVSSPDPIRGEVVKAFIVLN 521 DGY F+ R ++I SGY + P EVE+ LI+HP++A++AV+ PD +GEV +AFIV Sbjct: 427 DGYLTFIGRFKEMIKVSGYSVFPEEVETLLIKHPAVAQAAVIGVPDAEKGEVARAFIVKK 486 Query: 522 PDYKSHDQEQLKKEIQEHVKKTTAPYKYPRKVEFIEELPKTVSGKVKRNELR 573 P Q+ + ++ APYK PR+V FI+ LP T +GKV R LR Sbjct: 487 P-----GQDLDAAALVAWCRENMAPYKAPREVRFIDALPATGAGKVLRRLLR 533 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: 729 Number of extensions: 39 Number of successful extensions: 6 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: 536 Length adjustment: 36 Effective length of query: 544 Effective length of database: 500 Effective search space: 272000 Effective search space used: 272000 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