Align Phenylacetyl-CoA:acceptor oxidoreductase small subunit PadC (characterized, see rationale)
to candidate WP_086508321.1 BZY95_RS01920 4Fe-4S dicluster domain-containing protein
Query= uniprot:A0A2R4BLY8 (215 letters) >NCBI__GCF_002151265.1:WP_086508321.1 Length = 259 Score = 142 bits (359), Expect = 4e-39 Identities = 79/214 (36%), Positives = 111/214 (51%), Gaps = 39/214 (18%) Query: 3 RYAMVADLRRCVGCQTCTAACKHTNATPPGVQWRWVL---DVEAGEFPDVSRTFVPVGCQ 59 RY M+ DLR+C+GCQ CT +C N P G ++R + +VE E +++ +P C Sbjct: 46 RYGMLIDLRQCIGCQACTVSCHIENDAPLG-KFRTTVSQYEVEHQETGELATFMLPRLCN 104 Query: 60 HCDEPPCETVCPTTATKKRADGLVTIDYDLCIGCAYCSVACPYNARYKVNFAEPAYGDRL 119 HC+ PPC VCP AT ++ DG+V +D D C+GCAYC ACPY+AR+ +N Sbjct: 105 HCENPPCVPVCPVQATYQQQDGIVVVDSDRCVGCAYCVNACPYDARF-IN---------- 153 Query: 120 MANEKQRADPARVGVATKCTFCSDRIDYGVAHGLTPGVDPDATPACANACIANALTFGDI 179 R A KCTFC+ R++ G+ PAC +C+ A GD+ Sbjct: 154 ----------DRTQTADKCTFCAHRLEAGL------------LPACVESCVGGARIIGDM 191 Query: 180 DDPNSKASRLLRENEHFRM--HEELGTGPGFFYL 211 DP S+ SR++ E+ M E T P FYL Sbjct: 192 RDPESQISRMIAEHRDALMVLQPEKNTLPQVFYL 225 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: 251 Number of extensions: 20 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: 259 Length adjustment: 23 Effective length of query: 192 Effective length of database: 236 Effective search space: 45312 Effective search space used: 45312 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: 46 (22.3 bits)
This GapMind analysis is from Sep 24 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