Align glycolaldehyde oxidoreductase small subunit (characterized)
to candidate 6939345 Sama_3438 isoquinoline 1-oxidoreductase, alpha subunit, putative (RefSeq)
Query= metacyc::MONOMER-18073 (163 letters) >FitnessBrowser__SB2B:6939345 Length = 151 Score = 112 bits (281), Expect = 2e-30 Identities = 53/143 (37%), Positives = 88/143 (61%), Gaps = 4/143 (2%) Query: 14 VKVNGVLYERYVSPRILLVDFLREELGLTGTKIGCDTTTCGACTVLLNGKSVKSCTLFAV 73 +K+NG L+ P++ L+ LR+ +GLTGTK GC CGACTV ++G+ +++C Sbjct: 4 LKINGRLFTLDADPKMPLLWALRDLMGLTGTKYGCGAGLCGACTVHVDGEPMRACLTSIK 63 Query: 74 QADGAEITTIEGLSVDSKLHPIQEAFKENFALQCGFCTPGMIMQAYFLLKENPNPSEEEV 133 +G +TTIEGL+ + ++++++ + QCGFC G +M A L+ ++P PS+ ++ Sbjct: 64 SLEGKSVTTIEGLADEQ----LKDSWRRHKVPQCGFCQAGQLMSAAALVSKHPRPSDSQI 119 Query: 134 RDGLHGNICRCTGYQNIVKAVLD 156 + + GNICRC Y I A+ D Sbjct: 120 DEAMAGNICRCGTYTRIRAAIKD 142 Lambda K H 0.322 0.138 0.409 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: 99 Number of extensions: 3 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: 163 Length of database: 151 Length adjustment: 17 Effective length of query: 146 Effective length of database: 134 Effective search space: 19564 Effective search space used: 19564 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