Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate 8502147 DvMF_2858 short-chain dehydrogenase/reductase SDR (RefSeq)
Query= reanno::pseudo6_N2E2:Pf6N2E2_5967 (272 letters) >FitnessBrowser__Miya:8502147 Length = 245 Score = 81.6 bits (200), Expect = 1e-20 Identities = 71/245 (28%), Positives = 111/245 (45%), Gaps = 14/245 (5%) Query: 25 LLTGAAQGIGEAIVAAFASQQARLVISDIQ--AEKVETVAAHWRERGADVHALKADVSNQ 82 ++TG ++GIG AI A +V++ +E V A R G V A+ ADV Sbjct: 9 IVTGGSRGIGRAIALRLAQDGFCVVVNYASNAPAALEVVDAIARTGGQAV-AVPADVGET 67 Query: 83 QDLHAMARHAVERHGRIDVLVNCAGVNVFRDPLEMTEEDWRRCFAIDLDGAWYGCKAVLP 142 D+ + A + G++ V+VN AG+ + + +L G + + Sbjct: 68 GDVEGLFAAAHDAFGQVGVVVNSAGIMPMLPIAGGDTAAFEKVLRTNLTGT-FNVLSRAA 126 Query: 143 QMIEQGVGSIINIASTHSSHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGVRVNAIAPGY 202 + G G II ++++ + PG PY +K G+ GL R L E + + VNA+APG Sbjct: 127 NALTAG-GRIIALSTSVIAKPFPGYGPYIASKAGVEGLVRVLANELRGRSITVNAVAPGP 185 Query: 203 IETQLNVDYWNGFADPYAERQRAL--DLHPPRRIGQPIEVAMTAVFLASDEAPFINASCI 260 + T L F + E Q A L P R+G P E+A FL E +INA + Sbjct: 186 VATDL-------FLNGKTEEQIAAIGKLAPLERLGTPEEIAGVVSFLVGPEGGWINAQVV 238 Query: 261 TIDGG 265 ++GG Sbjct: 239 RVNGG 243 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: 144 Number of extensions: 6 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: 245 Length adjustment: 24 Effective length of query: 248 Effective length of database: 221 Effective search space: 54808 Effective search space used: 54808 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