Align Phenylacetyl-CoA:acceptor oxidoreductase small subunit PadC (characterized, see rationale)
to candidate Echvi_2097 Echvi_2097 Fe-S-cluster-containing hydrogenase components 1
Query= uniprot:A0A2R4BLY8 (215 letters) >FitnessBrowser__Cola:Echvi_2097 Length = 1029 Score = 120 bits (300), Expect = 1e-31 Identities = 79/256 (30%), Positives = 109/256 (42%), Gaps = 49/256 (19%) Query: 4 YAMVADLRRCVGCQTCTAACK-HTNATPPGVQ-------WRWVL-------DVEAGEFPD 48 + + D+ CVGC CT AC+ N G + W+ D EAG+ Sbjct: 762 WGLAIDMNSCVGCGACTVACQVENNVAVVGKEEVLNRREMAWIRIDRYYSSDAEAGDLEG 821 Query: 49 VSR-------TFVPVGCQHCDEPPCETVCPTTATKKRADGLVTIDYDLCIGCAYCSVACP 101 + + TF P+ CQHC+ PCETVCP AT ++GL + Y+ CIG YC+ CP Sbjct: 822 LEKASDNPEVTFQPMMCQHCNNAPCETVCPVAATTHSSEGLNQMTYNRCIGTRYCANNCP 881 Query: 102 YNARYKVNFAEPAYGDRLMANEKQRADPARV-----------GVATKCTFCSDRIDYGVA 150 Y R F D N Q D ++ GV KC+ C RI G Sbjct: 882 YKVRRFNWFKYHDNKDFSKVNVAQNDDLGKMVLNPDVTVRARGVMEKCSMCVQRIQAGKL 941 Query: 151 HGLTPG---VDPDATPACANACIANALTFGDIDDPNSKASRLLR-------------ENE 194 D + ACA AC +AL FGD++DP SK S++L+ E Sbjct: 942 AAKRENRKVKDGEINVACAVACSTDALVFGDLNDPKSKVSQMLKIEENTTSAVKEVNEER 1001 Query: 195 HFRMHEELGTGPGFFY 210 + + EE+ P +Y Sbjct: 1002 AYHVLEEINVSPNIWY 1017 Lambda K H 0.323 0.137 0.461 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: 525 Number of extensions: 22 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: 215 Length of database: 1029 Length adjustment: 33 Effective length of query: 182 Effective length of database: 996 Effective search space: 181272 Effective search space used: 181272 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 (21.9 bits) S2: 51 (24.3 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