Align Iron-sulfur cluster-binding oxidoreductase, putative benzoyl-CoA reductase electron transfer protein (characterized, see rationale)
to candidate WP_004512043.1 GMET_RS09080 hypothetical protein
Query= uniprot:Q39TV9 (179 letters) >NCBI__GCF_000012925.1:WP_004512043.1 Length = 178 Score = 264 bits (674), Expect = 7e-76 Identities = 120/174 (68%), Positives = 147/174 (84%), Gaps = 2/174 (1%) Query: 7 KRIVKTINIDADKCNGCRACEVICSAFHAMPPYSSNNPARSRVRVVRDPLRDIYVPLYAG 66 KR V+TI +DADKCNGCR CE++CSAFHA+PPYSSNNPARSR++V+ + L DI++P++AG Sbjct: 5 KRKVRTITVDADKCNGCRTCEIMCSAFHAVPPYSSNNPARSRIQVITNRLEDIWMPVFAG 64 Query: 67 EYTESECIGRDKFIIDGKEYDECGFCRASCPSRDLFREPDSGLPLKCDLCDGEPEPLCVK 126 EYTESEC+GR+K+IIDGKEY+EC CRA+CPSRDLF+EPDSGLPLKCD+CDGE EP+CVK Sbjct: 65 EYTESECMGRNKYIIDGKEYNECDSCRAACPSRDLFKEPDSGLPLKCDMCDGEDEPVCVK 124 Query: 127 WCLVGALSVTER--EVEEPDESVKRTEMEIGLESLISRFGADVVADTVEQLTKK 178 WCLV AL ER EVEE D TEME+GLESL+ + G D V DTV +++KK Sbjct: 125 WCLVDALVYEEREEEVEEKDIQTTVTEMEVGLESLVRKHGFDKVMDTVARMSKK 178 Lambda K H 0.319 0.137 0.424 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: 196 Number of extensions: 9 Number of successful extensions: 2 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: 179 Length of database: 178 Length adjustment: 19 Effective length of query: 160 Effective length of database: 159 Effective search space: 25440 Effective search space used: 25440 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 (21.8 bits) S2: 44 (21.6 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