Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate GFF1678 Psest_1716 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases)
Query= reanno::pseudo1_N1B4:Pf1N1B4_412 (272 letters) >FitnessBrowser__psRCH2:GFF1678 Length = 253 Score = 144 bits (364), Expect = 1e-39 Identities = 83/249 (33%), Positives = 133/249 (53%), Gaps = 4/249 (1%) Query: 22 KVVLLTGAAQGIGEAIVATFASQQARLVISDIQGEKVEKVAAHWREQGADVVAIKADVSR 81 +V L+TGAA GIG A FA Q ++V++DI + A R G + +A++ DV+R Sbjct: 8 QVALVTGAAAGIGRATAQAFAEQGLKVVLADIDEAGIRDGAESIRAAGGEAIAVRCDVTR 67 Query: 82 QQDLHAMARLAIELHGRIDVLVNCAGVNVFRDPL-QMTEEDWHRCFAIDLDGAWYGCKAV 140 ++ A+ + GR+D N AG+ + + L + +E ++ +++ G W K Sbjct: 68 DAEVKALIEQVLAQFGRLDYAFNNAGIEIEQGRLAEGSEAEFDAIMGVNVKGVWLCMKHQ 127 Query: 141 LPQMIEQGIGSIINIASTHSTHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGIRVNAIAP 200 LP M+ QG G+I+N AS P Y +KH ++GLT++ IEYA K IRVNA+ P Sbjct: 128 LPVMLAQGGGAIVNTASVAGLGAAPKMSIYAASKHAVIGLTKSAAIEYAKKKIRVNAVCP 187 Query: 201 GYIETQLNVDYWNGFADPHAERQRAFDLHPPRRIGQPIEVAMTAVFLASDEAPFINASCI 260 I+T + + ADP + + A +HP RIG+ E+A ++L D A F + Sbjct: 188 AVIDTDMFRRAYE--ADPR-KAEFAAAMHPVGRIGKVEEIAAAVLYLCCDGAAFTTGQAL 244 Query: 261 TIDGGRSVM 269 +DGG + + Sbjct: 245 AVDGGATAI 253 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: 153 Number of extensions: 8 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: 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 (21.9 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