Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate BWI76_RS17800 BWI76_RS17800 long-chain-fatty-acid--CoA ligase
Query= BRENDA::A7KUK6 (562 letters) >FitnessBrowser__Koxy:BWI76_RS17800 Length = 572 Score = 213 bits (542), Expect = 2e-59 Identities = 173/559 (30%), Positives = 262/559 (46%), Gaps = 51/559 (9%) Query: 21 LFERKDRAYPDDKIIYQDADTQRHYTYKSLRDASLDFGKGLKALYEWRKGDVLALFTPNS 80 LFE R Y D + TY+ L + S F L+ +KGD +AL PN Sbjct: 39 LFEHAVRRYADQPAFINMGEVM---TYRKLEERSRAFAAYLQEGLGLQKGDRVALMMPNL 95 Query: 81 IDTPVVMWGTLWAGGTISPANPGYTVDELAFQLKNSHAKGLVTQASVLPVAREAAKKVGM 140 + PV ++G L AG + NP YT EL QL +S A +V ++ + K + Sbjct: 96 LQYPVALFGILRAGMIVVNVNPLYTPRELEHQLNDSGAAAIVIVSNFAHTLEKVVDKTQV 155 Query: 141 PEDRIILIGDQRDP------DARVKH---------------FTSVRNISGATRYRKQKIT 179 + +GDQ P + VK+ F S +Y K +I Sbjct: 156 KHVILTRMGDQLSPAKGTVVNFVVKYIKRLVPKYHLPDAISFRSALQHGYRMQYIKPEIV 215 Query: 180 PAKDVAFLVYSSGTTGVPKGVMISHRNIVANIRQQFIAEGEMLSWNGGPDGKGDRVLAFL 239 P +D+AFL Y+ GTTGV KG M++HRN++AN+ Q G +L GK + V+ L Sbjct: 216 P-QDLAFLQYTGGTTGVAKGAMLTHRNMLANLEQVNGTYGPLLH-----RGK-ELVVTAL 268 Query: 240 PFYHIYGLT--CLITQALYKGYHLIVMSKFDIEKWCAHVQNYRCSFSYIVPPVVLLLGKH 297 P YHI+ LT CL+ L G +L++ + DI + Y + V + L + Sbjct: 269 PLYHIFALTMNCLLFIEL-GGQNLLITNPRDIPGLVKELAKYPFTAMTGVNTLFNALLNN 327 Query: 298 PVVDKYDLSSLRMMNSGAAPLTQELVEAVYSRIKVGIKQGYGLSETSPTTHSQRWEDWRE 357 + D SSL + G P+ Q + E + +GYGL+E +P S D Sbjct: 328 KEFQQLDFSSLHLSAGGGMPVQQVVAERWVKLTGQYLLEGYGLTECAPLV-SVNPHDIDY 386 Query: 358 AMGSVGRLMPNMQAKYMTMPEDGSEPKEVGEGEVGELYLKGPNVFLGYHENPEATKGCLS 417 GS+G +P+ +AK + + EV GE GEL +KGP V LGY + P+AT + Sbjct: 387 HSGSIGLPVPSTEAKLVD-----DDDNEVPPGEPGELCVKGPQVMLGYWQRPDATAEII- 440 Query: 418 EDGWFQTGDVGYQDAKGNFYITDRVKELIKYKGFQVPPAELEGYLVDNDAIDDVAVIGIE 477 +DGW TGD+ D +G I DR K++I GF V P E+E ++ + + +VA +G+ Sbjct: 441 KDGWLHTGDIAVMDEEGFLRIVDRKKDMILVSGFNVYPNEIEDVVMQHAGVQEVAAVGVP 500 Query: 478 SETHGSEVPMACVVRSAKSKSSGTSEKDEAARIIKWLDSKVASHKRLRGGVHFVDEIPKN 537 S + G V + V K + T E +I + ++ +K + V F DE+PK+ Sbjct: 501 SGSSGEAVKIFVV----KKDPTLTEE-----MLITFCRRQLTGYK-VPKHVEFRDELPKS 550 Query: 538 PSGKILRRILKQKFKGAAE 556 GKILRR L+ + + + Sbjct: 551 NVGKILRRELRDEARAKVD 569 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: 761 Number of extensions: 39 Number of successful extensions: 8 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: 572 Length adjustment: 36 Effective length of query: 526 Effective length of database: 536 Effective search space: 281936 Effective search space used: 281936 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