Align 2-deoxy-D-ribonate 3-dehydrogenase (characterized)
to candidate WP_084936983.1 HA51_RS22390 SDR family oxidoreductase
Query= reanno::BFirm:BPHYT_RS04775 (263 letters) >NCBI__GCF_002095475.1:WP_084936983.1 Length = 246 Score = 113 bits (282), Expect = 4e-30 Identities = 77/249 (30%), Positives = 138/249 (55%), Gaps = 13/249 (5%) Query: 12 GLRVLISGAAAGIGAAIAQAFLDVGANVYICDVDPAAIDRARTAHPQLHAGVADVSDCAQ 71 G RVLI+ A GIG A A+ F + GANV D++ A+ + P DV+D A Sbjct: 5 GKRVLITAAGQGIGLASARYFAEQGANVVGSDINITALQDLQNVTPYR----LDVTDRAA 60 Query: 72 VDRIIDDARSKLGGLDLLINNAGIAGPTGAVEDLDPAEWERTIGTNLNSQFYFLRKAVP- 130 + +++ LG +D+L N AG+ +G + EW+ + N+++ F+ ++ +P Sbjct: 61 IRAAVEE----LGPVDVLFNCAGVVH-SGNLLACTEQEWQFALDLNVSAMFHMIQAFLPG 115 Query: 131 LLKETSANPGIIAMASVAGRL-GYAFRTPYAASKWAIVGMVKSLAIELGPNNVRVNAILP 189 +L + + II M+SVA + G A R Y+A+K A++G+ +S+A + + +R NAI P Sbjct: 116 MLAQKKGS--IINMSSVASSVKGVANRFAYSATKAAVIGLTRSVAADFIADGIRCNAICP 173 Query: 190 GVVEGERMDRVISARAESLGIGFDQMKGEYLQKISLRRMVTVHDVAAMALFLASPAGQNI 249 G V+ + + I+ +A++ G D++ ++ + + R+ TV ++A +A +LAS A Sbjct: 174 GTVDSPSLRQRIATQAQAEGKSEDEVYAAFVARQPIGRIGTVEEIAYLAAYLASDASNYT 233 Query: 250 SGQAISVDG 258 +G A +DG Sbjct: 234 TGTAQVIDG 242 Lambda K H 0.320 0.136 0.391 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: 140 Number of extensions: 6 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: 263 Length of database: 246 Length adjustment: 24 Effective length of query: 239 Effective length of database: 222 Effective search space: 53058 Effective search space used: 53058 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: 47 (22.7 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