Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate Ac3H11_493 toluenesulfonate zinc-independent alcohol dehydrogenase
Query= reanno::pseudo6_N2E2:Pf6N2E2_5967 (272 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_493 Length = 253 Score = 143 bits (361), Expect = 3e-39 Identities = 89/253 (35%), Positives = 139/253 (54%), Gaps = 3/253 (1%) Query: 18 RLKNKVVLLTGAAQGIGEAIVAAFASQQARLVISDIQAEKVETVAAHWRERGADVHALKA 77 R+ NK +++TGA GIGE I A++ +++++DI + V A G KA Sbjct: 2 RVSNKSIIVTGAGNGIGEGIAKRLAAEGGKVIVNDINEAGGQRVVAEITAAGGTAAFFKA 61 Query: 78 DVSNQQDLHAMARHAVERHGRIDVLVNCAG-VNVFRDPLEMTEEDWRRCFAIDLDGAWYG 136 DV+N + AM AV +GR+DV+VN AG + R LE++EE++ + +AI++ + Sbjct: 62 DVTNSAQVKAMVDEAVRLYGRLDVVVNNAGWTHRNRPMLEVSEEEFDKVYAINMKSIYLS 121 Query: 137 CKAVLPQMIEQGVGSIINIASTHSSHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGVRVN 196 +P + + G GSIINIAST PG Y +K ++ ++++ E P +RVN Sbjct: 122 AIHAVPALRQAGGGSIINIASTAGLRPRPGLTWYNGSKGAVIITSKSMAAELGPDNIRVN 181 Query: 197 AIAPGY-IETQLNVDYWNGFADPYAERQRALDLHPPRRIGQPIEVAMTAVFLASDEAPFI 255 I P + +T L ++ G D A R + L P R ++VA A++LAS+EA FI Sbjct: 182 CINPVFNPDTGLAAEFAGGPVDD-ARRAKFLATIPLGRFSTALDVANAALYLASEEASFI 240 Query: 256 NASCITIDGGRSV 268 + CI +DGGR V Sbjct: 241 SGVCIEVDGGRCV 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: 130 Number of extensions: 5 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 (21.8 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