Align medium-chain acyl-CoA ligase (EC 6.2.1.2); phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate CCNA_02483 CCNA_02483 4-coumarate--CoA ligase
Query= BRENDA::O74725 (578 letters) >FitnessBrowser__Caulo:CCNA_02483 Length = 496 Score = 146 bits (369), Expect = 2e-39 Identities = 146/491 (29%), Positives = 217/491 (44%), Gaps = 67/491 (13%) Query: 85 LAVFALNTIDSLPLFWAVHRLGGVLTPANASYSAAELTHQLLDSKAKALVTCVPLLSISL 144 LAV A N + + L A RLG + P N SA+EL H L++ A++ + Sbjct: 56 LAVLAKNQVLLVILHLACARLGAMFAPLNWRLSASEL-HALIEDADPAMI-------VGD 107 Query: 145 EAAAKAGLPKNRIYLLDVPEQLLGGVKPPAGYKSVSELTQAGKSLPPVDELRWSAGEGAR 204 + A AGL LDV + P ++ E Sbjct: 108 DQLAAAGLDGVD---LDVLRAEIDCADPDTRARADRE----------------------- 141 Query: 205 RTAFVCYSSGTSGLPKGVMISHRNVIANTLQIKAFEQNYRDGGGTKPASTEVALGLLPQS 264 R + + Y+SGTSG PKG ++S RN+ + G K V L P Sbjct: 142 RPSLILYTSGTSGRPKGALLSERNLDQTAINF---------GRLGKVTHESVFLVDAPMF 192 Query: 265 HIYALVVIGHAGAYRGDQTIVLPKFELKSYLNAIQQ--YKISALFLVPPIIIHMLGTQDV 322 HI L+ G +V FE L + I+ F VP + ML Q Sbjct: 193 HIIGLITSIRPVLMHGGAILVSDGFEPARTLGRLGDPTLGITHYFCVPQMAA-MLRRQPA 251 Query: 323 CSKYDLSSVTSLFTGAAPLGMETAADFLK-LYPNILIRQGYGLTETCTVVSSTHPHDIWL 381 L +T++FTG AP A D L I + GYG++E TV P D L Sbjct: 252 FDASALRRLTAIFTGGAP---HPAPDIRAWLAEGIPMVDGYGMSEAGTVFGM--PADATL 306 Query: 382 -----GSSGALLPGVEARIVTPENKEITTYDSPGELVVRSPSVVLGYLNNEKATAETFV- 435 GS+G +P V RIV ++++ PGEL+++ +V GY + TA F Sbjct: 307 IDARAGSAGLCMPPVFTRIVDEQDRDCPP-GVPGELLLKGDNVFRGYWRRPEDTARAFTE 365 Query: 436 DGWMRTGDEAVIRRSPKGIEHVFIVDRIKELIKVKGLQVAPAELEAHILAHPDVSDCAVI 495 DGW RTGD A+ + ++VDR K++ G V PAE+EA + HP + +CAV+ Sbjct: 366 DGWFRTGDIALADAEG----YHWLVDRKKDMFISGGENVYPAEIEAALADHPAILECAVV 421 Query: 496 AIPDDRAGEVPKAIVVKSASAGSDESVSQALVKYVEDHKARHKWLKGGIRFVDAIPKSPS 555 +PD R GEV +V A D ++ ++ ++ED AR+K L + V A+P++ S Sbjct: 422 GVPDPRWGEVGHLVVTCREGAVLDLAL---ILSHLEDRLARYK-LPKALTLVAALPRTAS 477 Query: 556 GKILRRLIRDQ 566 GKI + ++R++ Sbjct: 478 GKIQKTVLRER 488 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: 687 Number of extensions: 49 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 578 Length of database: 496 Length adjustment: 35 Effective length of query: 543 Effective length of database: 461 Effective search space: 250323 Effective search space used: 250323 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: 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