Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate YP_002827509.1 NGR_c30130 short chain dehydrogenase/reductase family oxidoreductase
Query= reanno::pseudo1_N1B4:Pf1N1B4_412 (272 letters) >NCBI__GCF_000018545.1:YP_002827509.1 Length = 251 Score = 167 bits (422), Expect = 3e-46 Identities = 97/252 (38%), Positives = 138/252 (54%), Gaps = 3/252 (1%) Query: 17 ERLKNKVVLLTGAAQGIGEAIVATFASQQARLVISDIQGEKVEKVAAHWREQGADVVAIK 76 +R + KV ++TG GIG AI A + A +V+SD+ GE VAA QG +A+ Sbjct: 2 KRFEGKVAVVTGGGGGIGSAISRRLADEGALVVVSDVNGEAAGAVAAEIVSQGGSAIAVA 61 Query: 77 ADVSRQQDLHAMARLAIELHGRIDVLVNCAGVNVFRDPLQMTEEDWHRCFAIDLDGAWYG 136 AD+S+++ + + GRID+LVN AG+N + L +T++DWH FA++LD +Y Sbjct: 62 ADISQREPCFGLIAEVFDQKGRIDILVNNAGINRRGNLLALTDDDWHTSFAVNLDSMFYL 121 Query: 137 CKAVLPQMIEQGIGSIINIASTHSTHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGIRVN 196 C+A +P MIE G G I+N AS + P Y K + T+ L +YAP IRVN Sbjct: 122 CRAAIPHMIEAGGGVIVNTASQWGLYPAPNHIAYNTTKAAVAAFTQNLARDYAPHKIRVN 181 Query: 197 AIAPGYIETQLNVDYWNGFADPHAERQRAFDLHPPRRIGQPIEVAMTAVFLASDEAPFIN 256 A+ PG I T + A+ + L P RIG+P EVA FLASDEA F+ Sbjct: 182 AVCPGEIHTPMLEAGVKRAGRTIADLGK---LVPFGRIGRPEEVAALVAFLASDEAAFMC 238 Query: 257 ASCITIDGGRSV 268 S + I G ++V Sbjct: 239 GSLVEITGAQAV 250 Lambda K H 0.321 0.138 0.424 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: 154 Number of extensions: 7 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: 272 Length of database: 251 Length adjustment: 25 Effective length of query: 247 Effective length of database: 226 Effective search space: 55822 Effective search space used: 55822 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 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