Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate WP_012041256.1 BBTA_RS04490 long-chain-fatty-acid--CoA ligase
Query= BRENDA::A7KUK6 (562 letters) >NCBI__GCF_000015165.1:WP_012041256.1 Length = 563 Score = 205 bits (521), Expect = 4e-57 Identities = 166/536 (30%), Positives = 257/536 (47%), Gaps = 47/536 (8%) Query: 46 TYKSLRDASLDFGKGLKALYEWRKGDVLALFTPNSIDTPVVMWGTLWAGGTISPANPGYT 105 +Y+ L D S+ G L+ L KG +AL PN + P+ + G L AG + NP YT Sbjct: 50 SYRELDDMSVAMGAYLQGL-GLAKGARVALMMPNVLQYPIAISGVLRAGYAVVNVNPLYT 108 Query: 106 VDELAFQLKNSHAKGLVTQASVLPVAREAAKKVGMPEDRIILIGDQRD-----------P 154 EL QLK+S A+ ++ + A + VG + + I+I D Sbjct: 109 PRELEHQLKDSGAEAIIVLENF---AHTVQQVVGQTKVKHIIIASMGDLLGFKGVIVNLV 165 Query: 155 DARVKHFTSVRNISGAT------------RYRKQKITPAKDVAFLVYSSGTTGVPKGVMI 202 R+K ++ GA R++K I P DVAFL Y+ GTTGV KG + Sbjct: 166 VRRLKKMVPAFSLPGAVPFNDALAAGRSKRFQKPVIGP-DDVAFLQYTGGTTGVSKGATL 224 Query: 203 SHRNIVANIRQQFIAEGEMLSWNGGPDGKGDRVLAFLPFYHIYGLTCLITQALYKG-YHL 261 HRN+VAN+ Q ++ P ++ LP YHI+ LTC A+ G +L Sbjct: 225 LHRNVVANVLQNDAWLQPVME--RPPHVDQLLIVCALPLYHIFALTCCFLLAVRAGGANL 282 Query: 262 IVMSKFDIEKWCAHVQNYRCSFSYIVPPVVLLLGKHPVVDKYDLSSLRMMNSGAAPLTQE 321 ++ + DI + + Y+ + V + L HP K D S L++ N G + + Sbjct: 283 LIPNPRDIPSFIKELMKYQVNNFPAVNTLYNGLLHHPDFRKLDFSKLKVSNGGGMAVQRP 342 Query: 322 LVEAVYSRIKVGIKQGYGLSETSPTTHSQRWEDWREAMGSVGRLMPNMQAKYMTMPEDGS 381 + E I +GYGLSET+P + E G++G +P+ ++++ +D Sbjct: 343 VAEQWKQVTGCSIAEGYGLSETAPVL-TCNLPTSTEFTGTIGLPLPST---WLSIRDD-- 396 Query: 382 EPKEVGEGEVGELYLKGPNVFLGYHENPEATKGCLSEDGWFQTGDVGYQDAKGNFYITDR 441 + EV G+ GE+ KGP V GY P+ T ++ DG+F+TGD+G A G+ I DR Sbjct: 397 DGNEVPLGQAGEICAKGPQVMAGYWNRPDETAKVMTADGFFRTGDIGIMAADGSIKIVDR 456 Query: 442 VKELIKYKGFQVPPAELEGYLVDNDAIDDVAVIGIESETHGSEVPMACVVRSAKSKSSGT 501 K++I GF V P E+E + + + + AVIG+ E G EV A VV+ K Sbjct: 457 KKDMILVSGFNVYPNEVEEVIATHPGVLETAVIGLPDEKTG-EVVKAFVVK----KDPAL 511 Query: 502 SEKDEAARIIKWLDSKVASHKRLRGGVHFVDEIPKNPSGKILRRILKQKFKGAAEA 557 + +D I+K +++ ++K + + F E+PK GKILRR L+ + K A A Sbjct: 512 TAED----IVKHCHAQLTNYK-VPKQIEFRTELPKTNVGKILRRELRDEKKNPAAA 562 Lambda K H 0.317 0.136 0.410 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: 747 Number of extensions: 31 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: 562 Length of database: 563 Length adjustment: 36 Effective length of query: 526 Effective length of database: 527 Effective search space: 277202 Effective search space used: 277202 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 (21.7 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