Align 2-deoxy-D-ribose dehydrogenase α subunit (characterized)
to candidate 202168 SO3049 isoquinoline 1-oxidoreductase, alpha subunit, putative (NCBI ptt file)
Query= metacyc::MONOMER-20832 (151 letters) >FitnessBrowser__MR1:202168 Length = 164 Score = 164 bits (415), Expect = 6e-46 Identities = 79/151 (52%), Positives = 105/151 (69%), Gaps = 5/151 (3%) Query: 1 MELRINQKAYQVDADADTPLLWVIRDDLGLTGTKYGCGLAQCGACSVLVDGNVVRSCVTP 60 + L IN +++ ++AD + P+LW +RD LGLTGTKYGCG CGAC+V VDG VR+C+T Sbjct: 18 LNLTINGRSFTLNADPNMPILWALRDILGLTGTKYGCGAGLCGACTVHVDGQPVRACLTS 77 Query: 61 VAGVVGREITTIEAIETDEVGKRVVATWVEHQVAQCGYCQSGQVMAATALLKHTPAPSKA 120 V+ G+++TTIE ++ +++ W EH V QCGYCQ+GQ+M+A AL+ P PS Sbjct: 78 VSQAQGKQLTTIEGLD----NQKLKNAWAEHNVPQCGYCQAGQLMSAAALVTQHPKPSAE 133 Query: 121 QIDAAMI-NLCRCGTYNAIHAAVDDLAKQGG 150 QIDAAM NLCRCGTY I AA+ AKQ G Sbjct: 134 QIDAAMSGNLCRCGTYPRIKAALQSYAKQEG 164 Lambda K H 0.320 0.134 0.410 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: 111 Number of extensions: 5 Number of successful extensions: 3 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: 151 Length of database: 164 Length adjustment: 17 Effective length of query: 134 Effective length of database: 147 Effective search space: 19698 Effective search space used: 19698 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: 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