Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate Ac3H11_964 Acetoacetyl-CoA synthetase [leucine] (EC 6.2.1.16)
Query= BRENDA::A7KUK6 (562 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_964 Length = 517 Score = 179 bits (453), Expect = 3e-49 Identities = 154/517 (29%), Positives = 245/517 (47%), Gaps = 45/517 (8%) Query: 45 YTYKSLRDASLDFGKGLKALYEWRKGDVLALFTPNSIDTPVVMWGTLWAGGTISPANPGY 104 YT+ L AS L +L + +G +A+ S++ V+ TL AG P N Y Sbjct: 35 YTWGDLDRASARMANLLASL-KLPEGSRVAVQVEKSVEAMVLYLATLRAGYVFLPLNTAY 93 Query: 105 TVDELAFQLKNSHAKGLVTQASVLPVAREAAKKVGMPEDRIILIGDQRDPDA--RVKHFT 162 E+ + + N+ +V + A G + +GD R R H + Sbjct: 94 QSAEIEYFIGNAEPGVVVCTPGNFGWVSKIAFTQGT--GHVFTLGDDRTGSLLERAAHHS 151 Query: 163 SVRNISGATRYRKQKITPAKDVAFLVYSSGTTGVPKGVMISHRNIVANIRQQFIAEGEML 222 V T +K A D+A ++Y+SGTTG KG M++H N+++N + + Sbjct: 152 DVH-----TPVQKS----ADDLAAILYTSGTTGRSKGAMLTHGNLLSNA----VTLKDYW 198 Query: 223 SWNGGPDGKGDRVLAFLPFYHIYGLTCLITQALYKGYHLIVMSKFDIEKWCAHVQNYRCS 282 W G D ++ LP +H++GL I AL G +I +KFD + A + R + Sbjct: 199 GWKAG-----DVLIHALPIFHVHGLFVAIHGALINGSKMIWFAKFDPKAVLAAMP--RAT 251 Query: 283 FSYIVPPVVLLLGKHPVVDKYDLSSLRMMNSGAAPLTQELVEAVYSRIKVGIKQGYGLSE 342 VP + + L + K ++R+ +G+APL E R I + YG+SE Sbjct: 252 VFMGVPTLYVRLLAEAGLTKEAAKNMRLFIAGSAPLLIETFTEWQQRTGHTILERYGMSE 311 Query: 343 TSPTTHSQRWEDWREAM------GSVGRLMPNMQAKYMTMPEDGSEPKEVGEGEVGELYL 396 T T + D R A +VG +P + + + +D ++P VGE +G + + Sbjct: 312 TIMLTSNPYAADKRHAGQTERRGATVGFPLPGVGLRVV---DDANKPLPVGE--IGSIQV 366 Query: 397 KGPNVFLGYHENPEATKGCLSEDGWFQTGDVGYQDAKGNFYITDRVKELIKYKGFQVPPA 456 KGPNVF GY PE T ++DGWF+TGDVG DA+ I R K+LI G+ V PA Sbjct: 367 KGPNVFKGYWRMPEKTAEEFTQDGWFKTGDVGKVDARDYVSIVGRSKDLIISGGYNVYPA 426 Query: 457 ELEGYLVDNDAIDDVAVIGIESETHGSEVPMACVVRSAKSKSSGTSEKDEAARIIKWLDS 516 E+EGY+ D + + A++G+ G EV +A V+ G S +A I+ L S Sbjct: 427 EIEGYINDMPGVAESALVGVPHPDFG-EVGVAVVI-----AKPGASLNPDA--IVAQLKS 478 Query: 517 KVASHKRLRGGVHFVDEIPKNPSGKILRRILKQKFKG 553 ++A+ K + V E+P+N GK+ + +L+++ KG Sbjct: 479 QLANFK-IPKKCFVVPELPRNTMGKVQKNLLREQHKG 514 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: 643 Number of extensions: 35 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: 562 Length of database: 517 Length adjustment: 35 Effective length of query: 527 Effective length of database: 482 Effective search space: 254014 Effective search space used: 254014 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: 52 (24.6 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