Align Benzoyl-CoA reductase electron transfer protein, putative (characterized, see rationale)
to candidate 349651 BT0123 NADH-ubiquinone oxidoreductase subunit (NCBI ptt file)
Query= uniprot:Q39TW4 (150 letters) >FitnessBrowser__Btheta:349651 Length = 158 Score = 130 bits (328), Expect = 7e-36 Identities = 54/148 (36%), Positives = 94/148 (63%) Query: 3 ISRIDQIIDKHDGEASSLIQILLDIQSEHNWLPKEALKRVCERLQVPMSRITHIATFYKA 62 + ++ I DKH A LI IL + Q H +LP+E + + +L++P+S++ + TFY Sbjct: 11 VEQVKTICDKHGNNAGELINILHEAQHLHGYLPEEMQRIIASKLRIPVSKVYGVVTFYTF 70 Query: 63 FSLVPKGRHQVHVCMGTACHVRGAQRVLDTVQEVTGVKSGETDSDLKFSVETVNCLGCCA 122 F++ PKG+H + VCMGTAC+VRG++++L+ + V G++ GET D K+S++ + C+G C Sbjct: 71 FTMTPKGKHPISVCMGTACYVRGSEKLLEEFKRVLGIEVGETTPDGKYSLDCLRCVGACG 130 Query: 123 LGPVMEVDGKHHGNIAPSQIASVLNNCE 150 L PV+ + K +G + P + ++ E Sbjct: 131 LAPVVMIGEKVYGRLQPVDVKKIIEELE 158 Lambda K H 0.321 0.135 0.408 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: 90 Number of extensions: 3 Number of successful extensions: 1 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: 150 Length of database: 158 Length adjustment: 17 Effective length of query: 133 Effective length of database: 141 Effective search space: 18753 Effective search space used: 18753 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: 43 (21.2 bits)
This GapMind analysis is from Apr 09 2024. 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