Align Phenylacetyl-CoA:acceptor oxidoreductase small subunit PadC (characterized, see rationale)
to candidate 15019 b0895 dimethyl sulfoxide reductase, anaerobic, subunit B (NCBI)
Query= uniprot:A0A2R4BLY8 (215 letters) >FitnessBrowser__Keio:15019 Length = 205 Score = 117 bits (292), Expect = 2e-31 Identities = 66/192 (34%), Positives = 87/192 (45%), Gaps = 41/192 (21%) Query: 2 TRYAMVADLRRCVGCQTCTAACKHTNATPPGVQWRWVLDVEAGEFPD--------VSRTF 53 T+Y D RC GC+TC ACK P V +R + + G++ + V + Sbjct: 3 TQYGFFIDSSRCTGCKTCELACKDYKDLTPEVSFRRIYEYAGGDWQEDNGVWHQNVFAYY 62 Query: 54 VPVGCQHCDEPPCETVCPTTATKKRADGLVTIDYDLCIGCAYCSVACPYNARYKVNFAEP 113 + + C HC++P C VCP+ A KR DG V +D D+CIGC YC +ACPY A P Sbjct: 63 LSISCNHCEDPACTKVCPSGAMHKREDGFVVVDEDVCIGCRYCHMACPYGA--------P 114 Query: 114 AYGDRLMANEKQRADPARVGVATKCTFCSDRIDYGVAHGLTPGVDPDATPACANACIANA 173 Y NE + G TKC C DR+ G P C +C A Sbjct: 115 QY------NETK-------GHMTKCDGCYDRVAEG------------KKPICVESCPLRA 149 Query: 174 LTFGDIDDPNSK 185 L FG ID+ K Sbjct: 150 LDFGPIDELRKK 161 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: 243 Number of extensions: 24 Number of successful extensions: 5 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: 205 Length adjustment: 21 Effective length of query: 194 Effective length of database: 184 Effective search space: 35696 Effective search space used: 35696 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: 45 (21.9 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