Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate 201721 SO2581 long-chain-fatty-acid--CoA ligase (NCBI ptt file)
Query= BRENDA::A7KUK6 (562 letters) >FitnessBrowser__MR1:201721 Length = 557 Score = 207 bits (528), Expect = 7e-58 Identities = 166/533 (31%), Positives = 252/533 (47%), Gaps = 49/533 (9%) Query: 46 TYKSLRDASLDFGKGLKALYEWRKGDVLALFTPNSIDTPVVMWGTLWAGGTISPANPGYT 105 TY+ L + S F L+ + +KGD +AL PN + P+ ++G L AG + NP YT Sbjct: 50 TYRKLEERSRAFAAYLQNELKLQKGDRVALMMPNLLQYPIALFGILRAGMVVVNVNPLYT 109 Query: 106 VDELAFQLKNSHAKGLVTQASVLPVAREAAKKVGMPEDRIILIGDQRDPDAR-------- 157 EL QL +S AK +V ++ E + + I +GD R Sbjct: 110 PRELKHQLIDSGAKAIVVVSNFARTLEEVVDQTPVKSVIITGLGDLLSAPKRTLVNFVVK 169 Query: 158 ----------VKHFTSVRNISGATRYRKQKITPA---KDVAFLVYSSGTTGVPKGVMISH 204 + H S+R R R Q + P D+AFL Y+ GTTGV KG M++H Sbjct: 170 YIKKLVPKYDLPHALSMRETLSRGR-RMQYVKPVITGDDLAFLQYTGGTTGVSKGAMLTH 228 Query: 205 RNIVANIRQQFIAEGEMLSWNGGPDGKGDRVLAFLPFYHIYGLTCLITQALYKG-YHLIV 263 N+VAN+ Q A L DG + V+ LP YHI+ LT L+KG +L++ Sbjct: 229 SNVVANVLQANGAYSPALR-----DGS-EFVVTALPLYHIFALTVNCLLFLHKGSQNLLI 282 Query: 264 MSKFDIEKWCAHVQNYRCSFSYIVPPVVLLLGKHPVVDKYDLSSLRMMNSGAAPLTQELV 323 + DI + A ++ Y + V + L + D S L++ G + + + Sbjct: 283 TNPRDIPGFVAELKKYPFTALTGVNTLFNALVNSSDFSELDFSRLKLSIGGGMAVQKAVA 342 Query: 324 EAVYSRIKVGIKQGYGLSETSP--TTHSQRWEDWREAMGSVGRLMPNMQAKYMTMPEDGS 381 + + K + +GYGL+E SP T + + GS+G P+ + + +D Sbjct: 343 DKWQNITKTRLLEGYGLTEASPLLTCCPYNLDGYN---GSIGFPAPST---LIQVRDDAG 396 Query: 382 EPKEVGEGEVGELYLKGPNVFLGYHENPEATKGCLSEDGWFQTGDVGYQDAKGNFYITDR 441 + +GE GEL+ KGP + GY + PE T + DGW TGD+GY D +G FYI DR Sbjct: 397 NV--LPQGETGELFGKGPQIMKGYWQRPEETAKVIDNDGWLATGDIGYMDEQGFFYIVDR 454 Query: 442 VKELIKYKGFQVPPAELEGYLVDNDAIDDVAVIGIESETHGSEVPMACVVRSAKSKSSGT 501 K++I GF V P E+E + + + +VA +G+ ++ G E+ VV+ KS + Sbjct: 455 KKDMILVSGFNVFPNEVEEVVALHPKVIEVAAVGVPNDASG-ELVKVFVVKKDKSLT--- 510 Query: 502 SEKDEAARIIKWLDSKVASHKRLRGGVHFVDEIPKNPSGKILRRILKQKFKGA 554 A IIK + +K + V F DE+PK GKILRR L+ + K A Sbjct: 511 -----AEDIIKHCRVHLTGYK-VPKLVEFRDELPKTNVGKILRRELRDEVKRA 557 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: 695 Number of extensions: 38 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: 557 Length adjustment: 36 Effective length of query: 526 Effective length of database: 521 Effective search space: 274046 Effective search space used: 274046 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 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