Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate 5209735 Shew_2188 long-chain-fatty-acid--CoA ligase (RefSeq)
Query= BRENDA::A7KUK6 (562 letters) >FitnessBrowser__PV4:5209735 Length = 557 Score = 210 bits (534), Expect = 1e-58 Identities = 169/570 (29%), Positives = 265/570 (46%), Gaps = 52/570 (9%) Query: 9 LVDIPEVDLWTFLFERKDRAYPDDKIIYQDADTQRHYTYKSLRDASLDFGKGLKALYEWR 68 ++D + LFE Y D T TY+ L + S F L+ + + Sbjct: 16 IIDAKQYSSLIDLFESSVAKYADQPAFVNMGAT---LTYRKLEERSRAFAAYLQNELKLQ 72 Query: 69 KGDVLALFTPNSIDTPVVMWGTLWAGGTISPANPGYTVDELAFQLKNSHAKGLVTQASVL 128 KGD +A+ PN + P+ ++G L AG + NP YT EL QL +S AK +V ++ Sbjct: 73 KGDRVAIMMPNLLQYPIALFGILRAGMVVVNVNPLYTPRELKHQLNDSGAKAIVVVSNFA 132 Query: 129 PVAREAAKKVGMPEDRIILIGD------------------QRDPDARVKHFTSVRNISGA 170 + ++ + + +GD + P + H S+R Sbjct: 133 NTLEQVVEQTPVKSVILTGLGDLLSAPKRTLVNFVVKYIKKMVPKYHLPHAISMRQSLSK 192 Query: 171 TRYRKQKITPA---KDVAFLVYSSGTTGVPKGVMISHRNIVANIRQQFIAEGEMLSWNGG 227 R R Q + P D+AFL Y+ GTTGV KG M++H NIV+N+ Q A +L+ Sbjct: 193 GR-RLQYVKPTIKGDDIAFLQYTGGTTGVSKGAMLTHGNIVSNLLQADAAYSPLLA---- 247 Query: 228 PDGKGDRVLAFLPFYHIYGLTCLITQALYKGYH-LIVMSKFDIEKWCAHVQNYRCSFSYI 286 DGK + V+ LP YHI+ LT L+KG + L++ + DI + + ++ + + Sbjct: 248 -DGK-EFVVTALPLYHIFALTVNCLLFLHKGANNLLITNPRDIPAFVSELKKHPFTALTG 305 Query: 287 VPPVVLLLGKHPVVDKYDLSSLRMMNSGAAPLTQELVEAVYSRIKVGIKQGYGLSETSP- 345 V + L D S+L++ G + + + + K + +GYGL+E SP Sbjct: 306 VNTLFNALVSSEEFKTLDFSNLKLSIGGGMAVQRAVADKWQGITKTRLLEGYGLTEASPL 365 Query: 346 -TTHSQRWEDWREAMGSVGRLMPNMQAKYMTMPEDGSEPKEVGEGEVGELYLKGPNVFLG 404 T E + GS+G P E+G+ + +GE GEL+ KGP V G Sbjct: 366 LTCCPYNLEGYN---GSIG--FPVANTDMQVRDEEGNV---LPQGETGELFAKGPQVMKG 417 Query: 405 YHENPEATKGCLSEDGWFQTGDVGYQDAKGNFYITDRVKELIKYKGFQVPPAELEGYLVD 464 Y + PE T + +DG+ TGD+GY D +G F+I DR K++I GF V P E+E + Sbjct: 418 YWQRPEETAKVIDKDGYLATGDIGYMDEQGFFFIVDRKKDMILVSGFNVFPNEVEEVVAL 477 Query: 465 NDAIDDVAVIGIESETHGSEVPMACVVRSAKSKSSGTSEKDEAARIIKWLDSKVASHKRL 524 + + +VA +G+ E G E+ VV KS + ++IK + +K + Sbjct: 478 HPKVLEVAAVGVPHEVSG-ELVKVFVVPKDKSLTE--------EQVIKHCRHHLTGYK-I 527 Query: 525 RGGVHFVDEIPKNPSGKILRRILKQKFKGA 554 V F DE+PK+ GKILRR L+ + K A Sbjct: 528 PKLVEFRDELPKSNVGKILRRELRDEAKSA 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: 685 Number of extensions: 33 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