Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate WP_012405999.1 BPHY_RS33955 short chain dehydrogenase
Query= reanno::pseudo6_N2E2:Pf6N2E2_5967 (272 letters) >NCBI__GCF_000020045.1:WP_012405999.1 Length = 258 Score = 153 bits (386), Expect = 4e-42 Identities = 88/249 (35%), Positives = 139/249 (55%), Gaps = 4/249 (1%) Query: 20 KNKVVLLTGAAQGIGEAIVAAFASQQARLVISDIQAEKVETVAAHWRERGADVHALKADV 79 + KV +TGAA GIG+A AFA + A +V+ D+ E + A E+G +K DV Sbjct: 10 EGKVAFVTGAANGIGQATALAFAQEGADVVVVDLSEEGAKATARMIEEQGVRALPVKCDV 69 Query: 80 SNQQDLHAMARHAVERHGRIDVLVNCAGVN-VFRDPLEMTEEDWRRCFAIDLDGAWYGCK 138 SN +D+ A ++ GR+D N AG+ ++++E + R ++L G +Y K Sbjct: 70 SNPKDVQAALAATMDTFGRLDFAFNNAGIEQALAYTADISDELFERNLRVNLGGVFYCMK 129 Query: 139 AVLPQMIEQGVGSIINIASTHSSHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGVRVNAI 198 +P M++ G GSI+N +S I G Y AKHG+LGLT++ +EYA +GVR+NA+ Sbjct: 130 YQIPLMLKNGGGSIVNTSSGAGVVGIRGQGAYCAAKHGVLGLTKSAALEYAKEGVRINAV 189 Query: 199 APGYIETQLNVDYWNGFADPYAERQRALDLHPPRRIGQPIEVAMTAVFLASDEAPFINAS 258 PG I+T + + G + R+R + P R+G+P E+A T ++L SD A F Sbjct: 190 CPGIIDTPMIGRFTQGTEE---NRKRMIAQEPIGRLGRPEEIANTVLWLCSDVAGFAIGH 246 Query: 259 CITIDGGRS 267 + +DGG++ Sbjct: 247 AVVVDGGQT 255 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: 159 Number of extensions: 9 Number of successful extensions: 3 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: 258 Length adjustment: 25 Effective length of query: 247 Effective length of database: 233 Effective search space: 57551 Effective search space used: 57551 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