Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate Echvi_2940 Echvi_2940 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases)
Query= reanno::pseudo1_N1B4:Pf1N1B4_412 (272 letters) >FitnessBrowser__Cola:Echvi_2940 Length = 251 Score = 138 bits (348), Expect = 1e-37 Identities = 92/251 (36%), Positives = 137/251 (54%), Gaps = 10/251 (3%) Query: 19 LKNKVVLLTGAAQGIGEAIVATFASQQARLVISDIQGEKVEKVAAHWREQGADVVAIKAD 78 +KNK +L+TG A GIG A+ FA + + D + EKVA +G V ++ D Sbjct: 1 MKNKTILITGGASGIGLAMTKRFAEEGGNVYFIDYDQKTGEKVAEELTSKGHRVTFLQGD 60 Query: 79 VSRQQDLHAMARLAIELHGRIDVLVNCAGVNVFRDPLQMTEEDWHRCFAIDLDGAWYGCK 138 VS+ ++ M + + G IDVLVN AG++ + EED+ R + +++ G + Sbjct: 61 VSQTEE---MKQTISSISGSIDVLVNNAGISHVGNLENTAEEDFDRLYQVNVKGIYNCSL 117 Query: 139 AVLPQMIEQGIGSIINIASTHSTHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGIRVNAI 198 A LP+M E+G GSIIN+AS ST +P F Y + K + +T ++ +Y IRVN+I Sbjct: 118 ASLPKMKEKG-GSIINMASVASTMGLPDRFAYSMTKGAVFSMTLSMARDYVEYNIRVNSI 176 Query: 199 APGYIETQLNVDYWNGFADPHAERQRAFD----LHPPRRIGQPIEVAMTAVFLASDEAPF 254 APG + T VD + P E++ FD P R+G+P E+A AV+L+SDEA F Sbjct: 177 APGRVHTPF-VDGFLAKNYPGKEKE-MFDKLAATQPIGRMGKPEEIAAMAVYLSSDEASF 234 Query: 255 INASCITIDGG 265 + IDGG Sbjct: 235 LTGGNYPIDGG 245 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: 154 Number of extensions: 7 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: 251 Length adjustment: 25 Effective length of query: 247 Effective length of database: 226 Effective search space: 55822 Effective search space used: 55822 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