Align Phenylacetyl-CoA:acceptor oxidoreductase small subunit PadC (characterized, see rationale)
to candidate GFF2722 PGA1_c27640 formate dehydrogenase iron-sulfur subunit
Query= uniprot:A0A2R4BLY8 (215 letters) >FitnessBrowser__Phaeo:GFF2722 Length = 197 Score = 95.1 bits (235), Expect = 8e-25 Identities = 59/185 (31%), Positives = 79/185 (42%), Gaps = 24/185 (12%) Query: 1 MTRYAMVADLRRCVGCQTCTAACKHTNATPPGVQWRWVLDVEAGEFPDVSRTFVPVGCQH 60 M R + D RC+ C C ACK+ + P G+ R V+ + G+ + S + V C H Sbjct: 1 MARAKFLCDAERCIECNACVTACKNEHEVPWGINRRRVVTINDGKPGERS---ISVACMH 57 Query: 61 CDEPPCETVCPTTATKKRADGLVTIDYDLCIGCAYCSVACPYNARYKVNFAEPAYGDRLM 120 C + PC VCP + +G+V DLCIGC YC ACP+ A P Y Sbjct: 58 CSDAPCMAVCPVDCFYQNEEGVVLHSKDLCIGCGYCFYACPFGA--------PQY----- 104 Query: 121 ANEKQRADPARVGVATKCTFCSDRID--YGVAHGLTPG---VDPDATPACANACIANALT 175 Q + G KCTFC+ + + A G + P CA C AL Sbjct: 105 ---PQAGNFGSRGKMDKCTFCAGGPEETHSNAEFSKYGRNRIAEGKLPICAEMCSTKALL 161 Query: 176 FGDID 180 GD D Sbjct: 162 AGDGD 166 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: 216 Number of extensions: 19 Number of successful extensions: 3 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: 197 Length adjustment: 21 Effective length of query: 194 Effective length of database: 176 Effective search space: 34144 Effective search space used: 34144 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