Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate WP_037569004.1 BS73_RS03225 SDR family oxidoreductase
Query= reanno::pseudo6_N2E2:Pf6N2E2_5967 (272 letters) >NCBI__GCF_000744815.1:WP_037569004.1 Length = 252 Score = 137 bits (345), Expect = 2e-37 Identities = 83/255 (32%), Positives = 128/255 (50%), Gaps = 11/255 (4%) Query: 16 GERLKNKVVLLTGAAQGIGEAIVAAFASQQARLVISDIQAEKVETVAAHWRERGADVHAL 75 G + L+TGA GIG A FA A + + DI A+ A RE G + A+ Sbjct: 3 GAAAPRRAGLVTGAGSGIGRATALRFARDGAAVAVLDIDADAAAETAESIREDGGEALAV 62 Query: 76 KADVSNQQDLHAMARHAVERHGRIDVLVNCAGVNVFRDPL-EMTEEDWRRCFAIDLDGAW 134 D+++++ + A V G +D VN AG+ L EM E++ R ++L G + Sbjct: 63 TVDIADERAVAAAVERTVASFGGLDFAVNNAGLASHHRRLDEMAPEEFERVVRVNLTGTF 122 Query: 135 YGCKAVLPQMIEQGVGSIINIASTHSSHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGVR 194 + + LP + +G G+I+N+AS + IP Y AKHG++GLT+ ++YAP+G+R Sbjct: 123 HCMRYELPALRARGGGAIVNVASNGGLYAIPTAPAYVAAKHGIVGLTKVAAVDYAPQGIR 182 Query: 195 VNAIAPGYIETQLNVDYWNGFADPYAERQ---RALDLHPPRRIGQPIEVAMTAVFLASDE 251 VNA+ PG T GF A + P R+ P E A AV+L SD+ Sbjct: 183 VNAVCPGPTRTP-------GFEAVAAGTDMIAMQASITPLGRLATPEEAAAAAVWLCSDD 235 Query: 252 APFINASCITIDGGR 266 A ++ +++DGGR Sbjct: 236 ASYVTGIALSVDGGR 250 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: 160 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: 252 Length adjustment: 25 Effective length of query: 247 Effective length of database: 227 Effective search space: 56069 Effective search space used: 56069 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