Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate PP_1946 PP_1946 Oxidoreductase, short chain dehydrogenase/reductase family
Query= reanno::pseudo6_N2E2:Pf6N2E2_5967 (272 letters) >FitnessBrowser__Putida:PP_1946 Length = 262 Score = 134 bits (336), Expect = 3e-36 Identities = 80/250 (32%), Positives = 132/250 (52%), Gaps = 11/250 (4%) Query: 22 KVVLLTGAAQGIGEAIVAAFASQQARLVISDIQAEKVETVAAHWRERGADVHALKADVSN 81 KVVL+TGA GIG A AFA A + ++DI + + G + DV + Sbjct: 10 KVVLVTGAGSGIGRATALAFAQSGASVAVADISTDHGLKTVELVKAEGGEATFFHVDVGS 69 Query: 82 QQDLHAMARHAVERHGRIDVLVNCAGVNVFRDPL-EMTEEDWRRCFAIDLDGAWYGCKAV 140 + + +M V +G +D+ N AG+ PL E+ ++WRR ++L +Y K Sbjct: 70 EPSVQSMLAGVVAHYGGLDIAHNNAGIEANIVPLAELDSDNWRRVIDVNLSSVFYCLKGE 129 Query: 141 LPQMIEQGVGSIINIASTHSSHIIPG--CFPYPVAKHGLLGLTRALGIEYAPKGVRVNAI 198 +P M+++G G+I+N AS +S +I G Y KHG++GLT+A I+YA + +R+NA+ Sbjct: 130 IPLMLKRGGGAIVNTAS--ASGLIGGYRLSGYTATKHGVVGLTKAAAIDYANQNIRINAV 187 Query: 199 APGYIETQLNVDYWNGFADPYAERQRALDLHPPRRIGQPIEVAMTAVFLASDEAPFINAS 258 PG +++ D P R R L P R+ E+A + ++L SD+A ++ Sbjct: 188 CPGPVDSPFLADM------PQPMRDRLLFGTPIGRLATAEEIARSVLWLCSDDAKYVVGH 241 Query: 259 CITIDGGRSV 268 +++DGG +V Sbjct: 242 SMSVDGGVAV 251 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: 147 Number of extensions: 9 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: 262 Length adjustment: 25 Effective length of query: 247 Effective length of database: 237 Effective search space: 58539 Effective search space used: 58539 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