Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate 6938794 Sama_2897 long-chain-fatty-acid--CoA ligase (RefSeq)
Query= BRENDA::D3GE78 (556 letters) >FitnessBrowser__SB2B:6938794 Length = 531 Score = 177 bits (448), Expect = 1e-48 Identities = 145/483 (30%), Positives = 228/483 (47%), Gaps = 21/483 (4%) Query: 67 LQRGDRVLLFSGNDLFFPVVFLGVIMAGGIFTGANPTFVARELAYQLQDSGATYLLCASN 126 LQ GD+V + N F + GV+ AG + NP + REL +Q +DSGA L+ S+ Sbjct: 63 LQPGDKVAIQLPNLTQFVIAAYGVLKAGMVLVNTNPLYTERELIHQFKDSGAKVLVVLSD 122 Query: 127 SLETGLEAAKQAKLPQSHIFAYDTSIYDGVTNPQKGCAYWSDLLASEEEGAAFTWDELST 186 L T + + + + I + + P+ G + L + G+ +W ++ Sbjct: 123 LLPTLAKVVAETPI-ELVISTHALDLVSPQIQPKTGLKN-IEFLKALNLGSQESWQPVA- 179 Query: 187 PALSSTTLALNYSSGTTGRPKGVEISHRNYVANMLQYCHTASLHPDYKARLERSRWLCFL 246 A ST AL Y+ GTTG KG +SH N +AN LQ C + ++ L Sbjct: 180 -ANHSTLAALQYTGGTTGLSKGAMLSHGNLIANALQ-CRDRLANVITPGE---DIFVAPL 234 Query: 247 PMYHAMAQNIFIAAALYR-ATPVYIMSKFDFVKMLEYTQRFRITDFILVPPVVVALAKHP 305 P+YH A + + + + A V I + D +++ ++ T F + + VAL Sbjct: 235 PIYHIYAFLVNLVLFVEQGACSVLIPNPRDIPSLIKTLAKYPFTGFAGLNTLFVALCHQE 294 Query: 306 AVGQYDLSSVELVGSGAAPLGREVCEEVEKLWPPGK-INIKQGWGMTEATCSVTGWNPAE 364 D S ++L SG G + E LW I +G+G++E + +T N Sbjct: 295 EFRALDFSHLKLTISG----GTALTEAAAGLWQQTTGCTISEGYGLSETSPVIT-LNQPG 349 Query: 365 ISTSASVGELNANCEAKIMFDGVEVKERNSRGELWVRAPNVMKGYWRNEKATKETKTEDG 424 ++G E +I+ + GEL VR P VM GYW+ T+ ++DG Sbjct: 350 AERLGTIGRPVLATEVQILDEDETPVPMGQAGELAVRGPQVMSGYWQQAGETERVFSKDG 409 Query: 425 WLLTGDIAFVDDDGKFHVVDRMKELIKVKGNQVAPAELEALLLEHPAISDVAVIGVV-IN 483 + TGDIA + DG + +VDR K++I V G V P E+E +L HPA+ + AVIGV Sbjct: 410 FFKTGDIAIAEPDGCYRIVDRKKDMIIVSGFNVYPNEVENVLASHPAVLECAVIGVADER 469 Query: 484 NDERPRAYVVLRP---GQSATANEIAHYLDNKVSAFKRITGGVVFLEAIPKNPSGKILRM 540 + E +A +VL+P A A AH N ++ +K+ + F+ ++PK+ GKILR Sbjct: 470 SGEAVKAVIVLKPSVEADDARAAITAHCQAN-LAGYKQ-PRHIEFVASLPKSTVGKILRR 527 Query: 541 KLR 543 LR Sbjct: 528 ALR 530 Lambda K H 0.319 0.134 0.403 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: 577 Number of extensions: 29 Number of successful extensions: 4 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: 556 Length of database: 531 Length adjustment: 35 Effective length of query: 521 Effective length of database: 496 Effective search space: 258416 Effective search space used: 258416 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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