Align L-arabinose 1-dehydrogenase (EC 1.1.1.46) (characterized)
to candidate N515DRAFT_1253 N515DRAFT_1253 2-dehydro-3-deoxy-L-fuconate dehydrogenase (EC 1.1.1.-)
Query= reanno::pseudo5_N2C3_1:AO356_20240 (272 letters) >FitnessBrowser__Dyella79:N515DRAFT_1253 Length = 248 Score = 145 bits (365), Expect = 1e-39 Identities = 91/252 (36%), Positives = 138/252 (54%), Gaps = 10/252 (3%) Query: 18 RLKDKVVLLTGAAQGIGEAIVAAFASQQARLVISDIQAQKVEAVAAHWRERGADVHALQA 77 RL K L+T A GIG A AFA + AR++ +DI Q + A++A ++ + Sbjct: 4 RLAGKHALVTAAGAGIGRATALAFAREGARVLATDIDEQALAALSAE----APELRTERL 59 Query: 78 DVSKQQDLQAMARRAVELHGRIDVLVNCAGVNVFRDPLEMTEEDWRRCFAIDLDGAWYGC 137 DV+ + R V H DVL NCAG L+ + W+R FAI++D ++ C Sbjct: 60 DVTDPVQID----RLVASHPPFDVLFNCAGYVHAGTILDTDDAAWKRSFAINVDSMFHLC 115 Query: 138 KAVLPQMIEQGVGSIINIASVHSS-HIIPGCFPYPVAKHGLLGLTRALGIEYAPKGVRVN 196 + VLP M+E+G GSI+N++SV SS +P F Y K ++GLT+++ ++ +G+R N Sbjct: 116 QRVLPAMLERGGGSIVNMSSVASSIKGVPNRFAYSTTKAAVIGLTKSVAADFVGRGIRCN 175 Query: 197 AIAPGYIETQLNVDYWNGF-ADPHAERQRALDLHPPRRVGQPIEVAMTAVFLASDEAPFI 255 AI PG ++T D D A + ++ P R+G P E+AM A++LASDEA F Sbjct: 176 AICPGTVKTPSLGDRVRALGGDEDAVWRGFVERQPMGRLGNPEEIAMLALYLASDEAAFT 235 Query: 256 NASCITIDGGRS 267 + +DGG S Sbjct: 236 TGTVHIVDGGWS 247 Lambda K H 0.321 0.137 0.419 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: 163 Number of extensions: 7 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: 272 Length of database: 248 Length adjustment: 24 Effective length of query: 248 Effective length of database: 224 Effective search space: 55552 Effective search space used: 55552 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: 47 (22.7 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