Align Phenylacetyl-CoA:acceptor oxidoreductase small subunit PadC (characterized, see rationale)
to candidate 6939078 Sama_3176 polysulfide reductase, subunit B (RefSeq)
Query= uniprot:A0A2R4BLY8 (215 letters) >FitnessBrowser__SB2B:6939078 Length = 188 Score = 129 bits (324), Expect = 4e-35 Identities = 76/214 (35%), Positives = 100/214 (46%), Gaps = 33/214 (15%) Query: 3 RYAMVADLRRCVGCQTCTAACKHTNATPPGVQWRWV-LDVEAGEFPDVSRTFVPVGCQHC 61 RY MV D +C+GCQ C+ AC+ N P GV V ++ GE P + + V CQ C Sbjct: 4 RYVMVHDENKCIGCQACSVACRSINQVPDGVSRLQVRIEGPFGEAPHLHFKYNRVSCQQC 63 Query: 62 DEPPCETVCPTTATKKRADGLVTIDYDLCIGCAYCSVACPYNARYKVNFAEPAYGDRLMA 121 ++ PC VCPT A DG+V+I + C+GC YC ACP YKV F P Sbjct: 64 EDAPCVKVCPTGAAYVGDDGIVSIKAEKCVGCMYCVAACP----YKVRFMNP-------- 111 Query: 122 NEKQRADPARVGVATKCTFCSDRIDYGVAHGLTPGVDPDATPACANACIANALTFGDIDD 181 VA KC FC + +A G PAC C +AL FGD D Sbjct: 112 ---------ETRVADKCNFCKET---RLARG--------EQPACVTVCPTDALCFGDAAD 151 Query: 182 PNSKASRLLRENEHFRMHEELGTGPGFFYLWEKK 215 P S+ S+LL ++ LGT P + + K+ Sbjct: 152 PASEVSKLLATKVSYQDKTHLGTKPRLYRIPAKR 185 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: 19 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: 188 Length adjustment: 21 Effective length of query: 194 Effective length of database: 167 Effective search space: 32398 Effective search space used: 32398 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