Align medium-chain acyl-CoA ligase (EC 6.2.1.2); phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate GFF4309 PS417_22070 long-chain fatty acid--CoA ligase
Query= BRENDA::O74725 (578 letters) >FitnessBrowser__WCS417:GFF4309 Length = 562 Score = 173 bits (439), Expect = 1e-47 Identities = 149/484 (30%), Positives = 229/484 (47%), Gaps = 42/484 (8%) Query: 104 RLGGVLTPANASYSAAELTHQLLDSKAKALVTCVPLLSISLEAAAKAGLPKNRIYLLDVP 163 R G ++ N Y+ E+ HQ D+ +ALV S E + + YL+ Sbjct: 97 RAGLIVVNTNPLYTPREMRHQFKDAGVRALVYLNLFGSRVQEVCSDTEID----YLI--- 149 Query: 164 EQLLGGVKPPAGYKSVSELTQAGKSLPPVDEL----------RWSAGEGARR-------T 206 E +G P A V+ L K + P L AG G R Sbjct: 150 EARMGDFMPTAKGWLVNTLVDKVKKMVPAYSLPRAVAFKRALHMGAGLGVTRHPVTLDDI 209 Query: 207 AFVCYSSGTSGLPKGVMISHRNVIANTLQIKA-FEQNYRDGGGTKPASTEVALGLLPQSH 265 A + Y+ GT+GL KG M++H N++AN Q++A Q DG EV + LP H Sbjct: 210 AVLQYTGGTTGLAKGAMLTHGNLVANMQQVRACMSQTGDDGHPLIKEGQEVMIAPLPLYH 269 Query: 266 IYALVVIGHAGAYRGDQTIVLPK-FELKSYLNAIQQYKISALFLVPPIIIHMLGTQDVCS 324 IYA G+ +++ ++ ++ +++++ + L + + + ++ D S Sbjct: 270 IYAFTANCMCMMVSGNHNVLITNPRDIGGFIKELKKWRFTGLLGLNTLFVALMDHPDFKS 329 Query: 325 KYDLSSVTSLFTGAAPLGMETAADFLKLYPNILIRQGYGLTETCTVVSSTHPHD--IWLG 382 D S + +G L TA + ++ I +GYGLTET + V+ST+P+ LG Sbjct: 330 -LDFSHLKLTNSGGTALIKATAERWQQI-TGCAIGEGYGLTET-SPVASTNPYGNKSRLG 386 Query: 383 SSGALLPGVEARIVTPENKEITTYDSPGELVVRSPSVVLGYLNNEKATAETF-VDGWMRT 441 + G +P +++ E+ + GEL ++ P V+ GY +ATAE +GW++T Sbjct: 387 TVGIPVPATAMKVIDDHGVELPLGER-GELCIKGPQVMKGYWQQPEATAEALDAEGWLKT 445 Query: 442 GDEAVIRRSPKGIEHVFIVDRIKELIKVKGLQVAPAELEAHILAHPDVSDCAVIAIPDDR 501 GD AVI V IVDR K+LI V G V P E+E ++AHP V++CAVI +PD+R Sbjct: 446 GDIAVIDEEG----FVSIVDRKKDLIIVSGFNVYPNEIEDVVMAHPAVANCAVIGVPDER 501 Query: 502 AGEVPKAIVVKSASAGSDESVSQALVKYVEDHKARHKWLKGGIRFVDAIPKSPSGKILRR 561 GE K VV A S E L Y + + +K K I D++P +P GKILRR Sbjct: 502 TGEAVKLFVVARAEGVSLEE----LKAYCKTNFTGYKVPK-HIVLRDSLPMTPVGKILRR 556 Query: 562 LIRD 565 +RD Sbjct: 557 ELRD 560 Lambda K H 0.316 0.134 0.392 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: 712 Number of extensions: 36 Number of successful extensions: 7 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: 578 Length of database: 562 Length adjustment: 36 Effective length of query: 542 Effective length of database: 526 Effective search space: 285092 Effective search space used: 285092 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 (21.6 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