Align Phenylacetyl-CoA:acceptor oxidoreductase small subunit PadC (characterized, see rationale)
to candidate 18100 b4072 formate-dependent nitrite reductase, 4Fe4S subunit (NCBI)
Query= uniprot:A0A2R4BLY8 (215 letters) >FitnessBrowser__Keio:18100 Length = 223 Score = 145 bits (366), Expect = 6e-40 Identities = 81/209 (38%), Positives = 100/209 (47%), Gaps = 34/209 (16%) Query: 3 RYAMVADLRRCVGCQTCTAACKHTNATPPGVQWRWVLDVEA-GEFPDVSRTFVPVGCQHC 61 RY MV D C+GC C AC+ N P GV ++ E GEFPDV F CQHC Sbjct: 36 RYGMVHDESLCIGCTACMDACREVNKVPEGVSRLTIIRSEPQGEFPDVKYRFFRKSCQHC 95 Query: 62 DEPPCETVCPTTAT-KKRADGLVTIDYDLCIGCAYCSVACPYNARYKVNFAEPAYGDRLM 120 D PC VCPT A+ + A G+V ++ DLC+GC YC ACPY +V F P Sbjct: 96 DHAPCVDVCPTGASFRDAASGIVDVNPDLCVGCQYCIAACPY----RVRFIHPV------ 145 Query: 121 ANEKQRADPARVGVATKCTFCSDRIDYGVAHGLTPGVDPDATPACANACIANALTFGDID 180 A KC FC + PAC AC ALTFG++D Sbjct: 146 -----------TKTADKCDFCRKT-----------NLQAGKLPACVEACPTKALTFGNLD 183 Query: 181 DPNSKASRLLRENEHFRMHEELGTGPGFF 209 DPNS+ S+LLR+ +R LGT P + Sbjct: 184 DPNSEISQLLRQKPTYRYKLALGTKPKLY 212 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: 234 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: 223 Length adjustment: 22 Effective length of query: 193 Effective length of database: 201 Effective search space: 38793 Effective search space used: 38793 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