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_010529673.1 ON01_RS03745 acyl--CoA ligase
Query= SwissProt::Q3UNX5 (580 letters) >NCBI__GCF_000224785.1:WP_010529673.1 Length = 526 Score = 388 bits (997), Expect = e-112 Identities = 216/518 (41%), Positives = 306/518 (59%), Gaps = 11/518 (2%) Query: 63 TNMEK-AGKRLSNPAFWWIDGNGEELRWSFEELGLLSRKFANILTEACSLQRGDRVMVIL 121 T ME A K A W GE ++E+L K N E L++GDRV++++ Sbjct: 16 TEMEYFAAKSPERNAVVWCSEKGESKEITYEQLMKNVNKIGNAFKEK-GLEKGDRVLIMI 74 Query: 122 PKIPEWWLANVACLRTGTVLIPGTTQLTQKDILYRLQSSKAKCIITDDTLAPAVDAVAAK 181 P++ E + +A L++G ++IPG+ L KD+ YR+ + I++ P V Sbjct: 75 PRLIEAYETYLAALKSGIIVIPGSEMLKTKDLQYRISHGEVSAIVS---YYPYVGQFTDV 131 Query: 182 CENLHSKLIVSQHSREGWGNLKEMMKYASDSHTCVDTKHDEMMAIYFTSGTTGPPKMIGH 241 E L +S +GW N+ ++ + ASD DT D++ +TSGTTG PK + H Sbjct: 132 KEFEQLTLFSVGNSVDGWHNMDKLKENASDKLDMADTTKDDVAFFSYTSGTTGNPKAVVH 191 Query: 242 THSSFGLGLSVNGRFWLDLIASDVMWNTSDTGWAKSAWSSVFSPWTQGACVFAHYLPRFE 301 TH L+ WL + D +W T+ GW K WS S GA F YL +F+ Sbjct: 192 THGWGYAHLNTAPENWLCINEGDKVWATAGPGWQKWIWSPFLSVLGSGATGFV-YLGKFD 250 Query: 302 STSILQTLSKFPITVFCSAPTAYRMLVQND-MSSYKFNSLKHCVSAGEPINPEVMEQWRK 360 + L L I V C PT YR++ + D + Y+ +L VSAGEP+N EV++ +RK Sbjct: 251 PKTYLGLLQDEDINVLCCTPTEYRLMAKVDNLDDYQLPALHSAVSAGEPLNREVIDTFRK 310 Query: 361 KTGLDIYEGYGQTETVLICGNFKGMKIKPGSMGKPSPAFDVKILDENGATLPPGQEGDIA 420 + + +GYGQTE L+ G K K+KPGSMGKP+P +V+I++E+G +P + GDIA Sbjct: 311 YFNVTVRDGYGQTENTLLLGFMKDTKVKPGSMGKPTPGNEVEIINEDGQPVPANKIGDIA 370 Query: 421 LQVLPERPFGLFTHYVDNPSKTASTLRGSFYITGDRGYMDEDGYFWFVARSDDIILSSGY 480 +++ + P LF Y + +T + RG +Y+TGD+ DEDGYFWF RSDDII+SSGY Sbjct: 371 VKL--DSP-ALFREYYKDAERTRMSQRGEYYVTGDQASKDEDGYFWFEGRSDDIIISSGY 427 Query: 481 RIGPFEVESALIEHPSIAESAVVSSPDPIRGEVVKAFIVLNPDYKSHDQEQLKKEIQEHV 540 IGPFEVE AL++HP + E AVV+SPD +RG VVKAFIVL D + L +++Q+HV Sbjct: 428 TIGPFEVEDALVKHPFVQECAVVASPDEVRGNVVKAFIVLQQGVNPDDPD-LVRDLQKHV 486 Query: 541 KKTTAPYKYPRKVEFIEELPKTVSGKVKRNELRKKEWV 578 K+ TAPYKYPRK+EFI+ELPKT SGK++R ELR+ E V Sbjct: 487 KELTAPYKYPRKIEFIDELPKTTSGKIRRVELRQNEKV 524 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: 816 Number of extensions: 45 Number of successful extensions: 6 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: 526 Length adjustment: 36 Effective length of query: 544 Effective length of database: 490 Effective search space: 266560 Effective search space used: 266560 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