Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate GFF3147 PGA1_c31980 short chain dehydrogenase
Query= reanno::pseudo6_N2E2:Pf6N2E2_5967 (272 letters) >FitnessBrowser__Phaeo:GFF3147 Length = 253 Score = 135 bits (339), Expect = 1e-36 Identities = 87/254 (34%), Positives = 133/254 (52%), Gaps = 5/254 (1%) Query: 18 RLKNKVVLLTGAAQGIGEAIVAAFASQQARLVISDIQAEKVETVAAHWRERGADVHALK- 76 RL K ++TG A G G IV F ++ AR++I+DI A+ A+ E A+ Sbjct: 2 RLAGKCAIVTGGASGFGAGIVTKFLTEGARVMIADINADAAAAAASDVCETYGPDRAIAQ 61 Query: 77 -ADVSNQQDLHAMARHAVERHGRIDVLVNCAGVNVFRDPLE-MTEEDWRRCFAIDLDGAW 134 DVS++ + MA+ A+ G+ID+LVN AGV+ PLE ++EED+ R A+++ + Sbjct: 62 TVDVSDRASVDQMAQAALNHFGQIDILVNNAGVSHLPTPLEDVSEEDFDRVVAVNMKSVY 121 Query: 135 YGCKAVLPQMIEQGVGSIINIASTHSSHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGVR 194 +A++P M + G+I+N+AST P Y +K ++ TR + +E AP GVR Sbjct: 122 LTARALVPHMKSRQSGAILNVASTAGVSPRPNLNWYNASKGWMITATRTMAVELAPAGVR 181 Query: 195 VNAIAPGYIETQLNVDYWNGFADPYAERQRALDLHPPRRIGQPIEVAMTAVFLASDEAPF 254 VNAI P ET L + D R + L P R P ++ A +L SDEA Sbjct: 182 VNAINPVAGETPLLKTFMG--EDTPEVRAKFLSTIPIGRFSTPEDMGNAACYLCSDEASM 239 Query: 255 INASCITIDGGRSV 268 + + +DGGR + Sbjct: 240 VTGVALEVDGGRCI 253 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: 132 Number of extensions: 4 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: 253 Length adjustment: 25 Effective length of query: 247 Effective length of database: 228 Effective search space: 56316 Effective search space used: 56316 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 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