Align Phenylacetyl-CoA:acceptor oxidoreductase small subunit PadC (characterized, see rationale)
to candidate 6938800 Sama_2903 NrfC, Fe-S-cluster-containing hydrogenase component 1 (RefSeq)
Query= uniprot:A0A2R4BLY8 (215 letters) >FitnessBrowser__SB2B:6938800 Length = 230 Score = 137 bits (345), Expect = 2e-37 Identities = 80/213 (37%), Positives = 105/213 (49%), Gaps = 36/213 (16%) Query: 2 TRYAMVADLRRCVGCQTCTAACKHTNATPPGVQWRWVLDVEA--GEFPDVSRTFVPVGCQ 59 T+YAMV D C+GC C AC+ TN P GV R ++ GE+P+ S F V CQ Sbjct: 42 TKYAMVHDENACIGCNACVQACRETNQIPEGVT-RVKIERRGPFGEYPNQSYRFSRVSCQ 100 Query: 60 HCDEPPCETVCPTTATK-KRADGLVTIDYDLCIGCAYCSVACPYNARYKVNFAEPAYGDR 118 HC+ PC VCPT A + G+V ++ D C+GC YC ACPY RY Sbjct: 101 HCEAAPCVRVCPTGAAYIDKETGIVAVNSDRCVGCQYCIAACPYQVRY------------ 148 Query: 119 LMANEKQRADPARVGVATKCTFCSDRIDYGVAHGLTPGVDPDATPACANACIANALTFGD 178 + E + AD KC FC +A GL P AC AC ALTFG+ Sbjct: 149 -IHPETRTAD--------KCDFCQKS---RLAQGLQP--------ACVEACPTKALTFGN 188 Query: 179 IDDPNSKASRLLRENEHFRMHEELGTGPGFFYL 211 + DP S+ +LL+ +R +LGT P F++ Sbjct: 189 LKDPESELVKLLKAKPSYRAKVDLGTRPKLFHI 221 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: 244 Number of extensions: 15 Number of successful extensions: 6 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: 230 Length adjustment: 22 Effective length of query: 193 Effective length of database: 208 Effective search space: 40144 Effective search space used: 40144 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