Align Benzoyl-CoA reductase electron transfer protein, putative (characterized, see rationale)
to candidate Synpcc7942_0278 Synpcc7942_0278 bidirectional hydrogenase complex protein HoxE
Query= uniprot:Q39TW4 (150 letters) >FitnessBrowser__SynE:Synpcc7942_0278 Length = 165 Score = 117 bits (292), Expect = 1e-31 Identities = 54/131 (41%), Positives = 85/131 (64%) Query: 5 RIDQIIDKHDGEASSLIQILLDIQSEHNWLPKEALKRVCERLQVPMSRITHIATFYKAFS 64 R++ I + +A +LI+IL + QS + +L +E L+ V E+L +P S++ +A+FY F Sbjct: 16 RLELAIKRQAAQADALIEILHEAQSLYGYLDRELLQWVAEQLALPRSKVYGVASFYHLFQ 75 Query: 65 LVPKGRHQVHVCMGTACHVRGAQRVLDTVQEVTGVKSGETDSDLKFSVETVNCLGCCALG 124 L P GRH+ HVC+GTAC+V+G+Q +LD + G++ GET +D S+ TV C+G C + Sbjct: 76 LNPSGRHRCHVCLGTACYVKGSQAILDCLIAELGIREGETTNDGSVSLGTVRCVGACGIA 135 Query: 125 PVMEVDGKHHG 135 PV+ DG G Sbjct: 136 PVVVYDGDIQG 146 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: 76 Number of extensions: 1 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: 165 Length adjustment: 17 Effective length of query: 133 Effective length of database: 148 Effective search space: 19684 Effective search space used: 19684 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 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