Align Phenylacetyl-CoA:acceptor oxidoreductase small subunit PadC (characterized, see rationale)
to candidate CA265_RS17845 CA265_RS17845 molybdopterin oxidoreductase
Query= uniprot:A0A2R4BLY8 (215 letters) >FitnessBrowser__Pedo557:CA265_RS17845 Length = 1010 Score = 122 bits (307), Expect = 2e-32 Identities = 79/246 (32%), Positives = 104/246 (42%), Gaps = 38/246 (15%) Query: 4 YAMVADLRRCVGCQTCTAACKHTNATPP--------GVQWRWVL---------------- 39 + M DL C GC +C AC N P + W+ Sbjct: 753 WVMAIDLNACTGCGSCIVACNVENNIPVVGRDEVRRRREMHWIRIDRYYSYETKDGDVTR 812 Query: 40 DVEAGEFPDVSRTFV---PVGCQHCDEPPCETVCPTTATKKRADGLVTIDYDLCIGCAYC 96 + E + D+ V P+ CQHCD PCETVCP AT +DGL + Y+ C+G YC Sbjct: 813 EKEIAKLEDLDHVSVVHQPMLCQHCDHAPCETVCPVLATVHSSDGLNHMAYNRCVGTRYC 872 Query: 97 SVACPYNAR--YKVNFAEPAYGDRLMANE------KQRADPARVGVATKCTFCSDRIDYG 148 + CPY R N+ + D + NE GV KC+ C RI G Sbjct: 873 ANNCPYKVRRFNWFNYWNDSRFDNYLNNEFTQLVLNPDVTTRSRGVMEKCSMCIQRIQGG 932 Query: 149 VAHG---LTPGVDPDATPACANACIANALTFGDIDDPNSKASRLLRENEHFRMHEELGTG 205 P D D AC AC ANA+ FGD +DPNS+ S+ LR + + EE+ Sbjct: 933 KLQAKLEKRPLKDGDIKMACQEACSANAIVFGDANDPNSEVSKALRSERIYYVLEEINVK 992 Query: 206 PGFFYL 211 PG Y+ Sbjct: 993 PGIGYM 998 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: 533 Number of extensions: 19 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 215 Length of database: 1010 Length adjustment: 33 Effective length of query: 182 Effective length of database: 977 Effective search space: 177814 Effective search space used: 177814 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