Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate WP_086509102.1 BZY95_RS06205 2-deoxy-D-gluconate 3-dehydrogenase
Query= reanno::pseudo1_N1B4:Pf1N1B4_412 (272 letters) >NCBI__GCF_002151265.1:WP_086509102.1 Length = 250 Score = 123 bits (309), Expect = 3e-33 Identities = 87/253 (34%), Positives = 126/253 (49%), Gaps = 18/253 (7%) Query: 19 LKNKVVLLTGAAQGIGEAIVATFASQQARLV-----ISDIQGEKVEKVAAHWREQGADVV 73 L +V ++TG +G+G+ + A A +V SD EKVE + G V Sbjct: 6 LHGRVAMVTGCNKGLGQGLALALAEAGADIVGVNRSNSDETREKVEAL-------GRRYV 58 Query: 74 AIKADVSRQQDLHAMARLAIELHGRIDVLVNCAGVNVFRDPLQMTEEDWHRCFAIDLDGA 133 A++A++ R +AR A+E GR+D+L+N AG L TEEDW ++L A Sbjct: 59 AVEAELGRDTPEAIVAR-ALESTGRLDMLINNAGAIRRAPALTFTEEDWEAVVDVNLKAA 117 Query: 134 WYGCKAVLPQMIEQGI-GSIINIASTHSTHIIPGCFPYPVAKHGLLGLTRALGIEYAPKG 192 ++ +AV ++E+G G I+N+AS S Y +K GLLGLTR L E+A G Sbjct: 118 FFLAQAVARHLVERGAPGRIVNVASVLSFQGGIRVPAYTASKSGLLGLTRLLANEWAAHG 177 Query: 193 IRVNAIAPGYIETQLNVDYWNGFADPHAERQRAFDLHPPRRIGQPIEVAMTAVFLASDEA 252 I VNAIAPGY+ T D + P R G P ++A +FL SD A Sbjct: 178 ITVNAIAPGYMAT----DNTQALREDATRSAEILGRIPAGRWGTPEDLAGAVIFLCSDAA 233 Query: 253 PFINASCITIDGG 265 ++N + +DGG Sbjct: 234 AYVNGHALAVDGG 246 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: 159 Number of extensions: 10 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: 250 Length adjustment: 25 Effective length of query: 247 Effective length of database: 225 Effective search space: 55575 Effective search space used: 55575 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