Align 2-deoxy-D-ribonate 3-dehydrogenase (characterized)
to candidate WP_017867501.1 LACPOB_RS0103790 SDR family oxidoreductase
Query= reanno::BFirm:BPHYT_RS04775 (263 letters) >NCBI__GCF_000349725.1:WP_017867501.1 Length = 253 Score = 102 bits (253), Expect = 1e-26 Identities = 71/254 (27%), Positives = 119/254 (46%), Gaps = 20/254 (7%) Query: 12 GLRVLISGAAAGIGAAIAQAFLDVGANVYICDVDPAAIDRARTAHPQLHAGV---ADVSD 68 G +++GA+ GIGAA A+ F GANV I D++P+ A+ + DV+D Sbjct: 8 GKTAIVTGASGGIGAATAKLFAQNGANVVIGDINPSGQKVAQEIKDAGGKAIFVKTDVAD 67 Query: 69 CAQVDRIIDDARSKLGGLDLLINNAGIAGPTGAVEDLDPAEWERTIGTNLNSQFYFLRKA 128 V +ID A G +D+ NNAG+A D+ E+++ + + F ++ Sbjct: 68 STSVKNLIDQAIQAYGKIDVAFNNAGMANLPDKASDMPEEEYDKAMNVDAKCVFLCMKYE 127 Query: 129 VPLLKETSANPGIIAMASVAGRLGYAFRT-PYAASKWAIVGMVKSLAIELGPNNVRVNAI 187 + +++ + I+ +S++G PY A+K A++GM +S A + +RVN I Sbjct: 128 LDNMRKHNGG-AIVNTSSISGLSAKPDNMLPYIAAKHAVIGMTRSAAFDHAKEGIRVNTI 186 Query: 188 LPGVVEGERMDRVISARAESLGIGFDQMKGEYLQKISLRRMVTVH---DVAAMALFLASP 244 PG++E E + G+ ++ + L M D+A M LFL S Sbjct: 187 APGLIETEMTE------------GYKDTPEKWAEMTGLNPMNAAGKPIDIANMVLFLCSD 234 Query: 245 AGQNISGQAISVDG 258 A + + ISVDG Sbjct: 235 ASRFTTASVISVDG 248 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: 143 Number of extensions: 8 Number of successful extensions: 4 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: 253 Length adjustment: 24 Effective length of query: 239 Effective length of database: 229 Effective search space: 54731 Effective search space used: 54731 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