Align medium-chain acyl-CoA ligase (EC 6.2.1.2); phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate WP_028309904.1 H566_RS0100560 long-chain fatty acid--CoA ligase
Query= BRENDA::O74725 (578 letters) >NCBI__GCF_000482785.1:WP_028309904.1 Length = 594 Score = 182 bits (462), Expect = 3e-50 Identities = 170/583 (29%), Positives = 254/583 (43%), Gaps = 74/583 (12%) Query: 34 RHASSRDPYTCGITGKSYSSKEVANRVDSLARSLSKEFGWAPNEGSEWDKTLAVFALNTI 93 RHA R +TC SY+ R+D+L+R+ + W G +AV N + Sbjct: 37 RHAR-RTAFTCLGARMSYA------RLDALSRAFA---AWLQARGMAPGGRVAVMLPNLM 86 Query: 94 DSLPLFWAVHRLGGVLTPANASYSAAELTHQLLDSKAKALVTCVPLLSISLEAAAKAGLP 153 V R G VL N Y+A EL HQL DS A+A+V + EA LP Sbjct: 87 SWPVAAAGVIRAGSVLVNVNPLYTARELAHQLADSGAEAIVVLDKVTPSLAEA-----LP 141 Query: 154 KNRIYLLDVPE--QLLGGVKPPAGYKSVSELTQA--GKSLPPVDELRWSAGEGARR---- 205 RI ++ V LLG ++ A + + + +LP L + EG R Sbjct: 142 ATRIRVIVVASAGDLLGPLRGAATDFVLRHVRKEVPAMTLPGAVRLPRALAEGRRLQSRA 201 Query: 206 -------TAFVCYSSGTSGLPKGVMISHRNVIANTLQIKAF------EQNYRDGGGTKPA 252 A + Y+ GT+G KG M+SHRN++AN Q +A+ E + G A Sbjct: 202 PDPAPDDVAVLQYTGGTTGTAKGAMLSHRNLLANLAQSRAWLAPAWTEDGQKAVGADHGA 261 Query: 253 STEVALGL--------------------------LPQSHIYALVVIGHAGAYRGDQTIVL 286 G LP H++A V G +++ Sbjct: 262 DRNTGAGADRNANVASATSVDAGANAEPLTVLIALPLYHVFAFTVGALLFMELGGHAVLV 321 Query: 287 PKFELKSYLNAIQQYKISALFLVPPIIIHMLGTQDVCSKYDLSSVTSLFTGAAPLGMETA 346 P L A+ + +F + L + D S++ G + A Sbjct: 322 PDPRRIDGLVALLKRHRIHVFPAVNTLFRELTRHPRIGEVDFSALRLSIGGGMAVQPSVA 381 Query: 347 ADFLKLYPNILIRQGYGLTETCTVVSSTH-PHDIWLGSSGALLPGVEARIVTPENKEITT 405 AD+ ++ + ++ +GYGL+ET +V+ + + GS G LP I + Sbjct: 382 ADWRRVTGSNIV-EGYGLSETSPIVACNPVTTEGFTGSIGLPLPSTAISIRDDDGLTELA 440 Query: 406 YDSPGELVVRSPSVVLGYLNNEKATAETFV-DGWMRTGDEAVIRRSPKGIEHVFIVDRIK 464 + PGE+ VR P V+ GY N TA+ F DGW+RTGD V+ G IVDR K Sbjct: 441 HGVPGEICVRGPQVMAGYWNRPAETAQAFTPDGWLRTGDIGVM----DGEGRTVIVDRKK 496 Query: 465 ELIKVKGLQVAPAELEAHILAHPDVSDCAVIAIPDDRAGEVPKAIVVKSASAGSDESVSQ 524 +++ V G V P E+EA + AHP V++CAVI +PD+ +GE K +VV+ +A + Sbjct: 497 DMVLVSGFNVYPNEIEALVAAHPGVAECAVIGVPDEHSGEAVKLVVVRRNAALD----TA 552 Query: 525 ALVKYVEDHKARHKWLKGGIRFVDAIPKSPSGKILRRLIRDQE 567 L + D A +K K I F D +PKS GK+LRR +R++E Sbjct: 553 TLTAFCRDRLAGYKRPK-IIEFRDVLPKSQVGKVLRRSLRERE 594 Lambda K H 0.316 0.134 0.392 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: 772 Number of extensions: 47 Number of successful extensions: 7 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: 578 Length of database: 594 Length adjustment: 37 Effective length of query: 541 Effective length of database: 557 Effective search space: 301337 Effective search space used: 301337 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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