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 WP_086509453.1 BZY95_RS08185 benzoate-CoA ligase family protein
Query= SwissProt::Q3UNX5 (580 letters) >NCBI__GCF_002151265.1:WP_086509453.1 Length = 543 Score = 227 bits (579), Expect = 8e-64 Identities = 168/536 (31%), Positives = 273/536 (50%), Gaps = 31/536 (5%) Query: 47 EIPEYFNFAKDVLDQWTNMEKA-GKRLSNPAFWWIDGNGEELRWSFEELGLLSRKFANIL 105 + P N A ++ D+W +E+ G+R++ + GNG R S+ EL S + A+ L Sbjct: 31 DYPARLNAAVELCDRW--LERGHGERVA------LIGNGR--RRSYRELAEWSNRLAHAL 80 Query: 106 TEACSLQRGDRVMVILPKIPEWWLANVACLRTGTVLIPGTTQLTQKDILYRLQSSKAKCI 165 E ++ G+RV++ P +A + G V++ L ++ + ++ Sbjct: 81 VEELGVRPGNRVLIRSANNPAMVACWLAATKAGAVVVNTMPMLRASELAQIVDKAEIALA 140 Query: 166 ITDDTLAPAVDAVAAKCENLHSKLIVSQHSREGWGNLK-EMMKYASDSHT---CVDTKHD 221 + D L ++ AA+ S L+ +G N E+ + A D T V T D Sbjct: 141 LCDTRLLEELETCAAE-----SALLKRVVGFDGTANHDAELDRLALDKPTEFKAVATAAD 195 Query: 222 EMMAIYFTSGTTGPPKMIGHTHSSFGLGLSVNGRFWLDLIASDVMWNTSDTGWAKSAWSS 281 ++ + FTSGTTG PK H H + R L + A DV + + Sbjct: 196 DVALLGFTSGTTGQPKATMHFHRDLLIIADGYAREVLQVSADDVFVGSPPLAFTFGLGGL 255 Query: 282 VFSPWTQGACVFAHYLPRFESTSILQTLSKFPITVFCSAPTAYRMLVQNDMSSYKFNSLK 341 P GA A L + ++++ + + TV +APTAYR ++ + + + +SL+ Sbjct: 256 AIFPLRFGAS--AVLLEKATPPNMMEIIREHRATVVFTAPTAYRTMLASLENGEELDSLR 313 Query: 342 HCVSAGEPINPEVMEQWRKKTGLDIYEGYGQTETVLICGNFKGMKIKPGSMGKPSPAFDV 401 VSAGE + + +W +KTG I +G G TE + I + +P GKP ++ Sbjct: 314 LAVSAGETLPAPIYHEWIEKTGKPILDGIGATEMLHIFISNHLDDHRPACTGKPVAGYEA 373 Query: 402 KILDENGATLPPGQEGDIALQVLPERPFGLFTHYVDNPSKTASTLRGSFYITGDRGYMDE 461 K++D LP G+ G +A++ P G Y+ N + +R + ITGD Y DE Sbjct: 374 KVVDAEMNELPRGEVGRLAVR----GPTGC--RYL-NDVRQLKYVRDGWNITGDAFYQDE 426 Query: 462 DGYFWFVARSDDIILSSGYRIGPFEVESALIEHPSIAESAVVSSPDPIRGEVVKAFIVLN 521 + YF F AR+DD+I+S+GY I EVE+AL+ H ++AE AV+ +P+ RG++V+AF+VL+ Sbjct: 427 EDYFHFAARNDDMIVSAGYNIAGPEVEAALLAHEAVAECAVIGAPNGERGQIVEAFVVLS 486 Query: 522 PDYKSHDQEQLKKEIQEHVKKTTAPYKYPRKVEFIEELPKTVSGKVKRNELRKKEW 577 P + D E +K+ +Q VK+ APYKYPR V F+E LPKT +GKV+R LR++ + Sbjct: 487 PGVEP-DAECVKR-LQTFVKQRIAPYKYPRSVRFVEALPKTATGKVQRFRLRQEHY 540 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: 735 Number of extensions: 30 Number of successful extensions: 5 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: 543 Length adjustment: 36 Effective length of query: 544 Effective length of database: 507 Effective search space: 275808 Effective search space used: 275808 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 24 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