Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate Echvi_3364 Echvi_3364 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases)
Query= reanno::pseudo1_N1B4:Pf1N1B4_412 (272 letters) >FitnessBrowser__Cola:Echvi_3364 Length = 255 Score = 133 bits (334), Expect = 4e-36 Identities = 85/248 (34%), Positives = 133/248 (53%), Gaps = 5/248 (2%) Query: 19 LKNKVVLLTGAAQGIGEAIVATFASQQARLVISDIQGEKVEKVAAHWREQGADVVAIKAD 78 L NKV L+TGA++GIG +I FA+ A++VI E ++++A E+G D++ I + Sbjct: 9 LNNKVALITGASKGIGLSIAEFFAAAGAKVVICSRHQEHLDEIAKKLYEKGYDIMGIACN 68 Query: 79 VSRQQDLHAMARLAIELHGRIDVLVNCAGVNVFRDPL-QMTEEDWHRCFAIDLDGAWYGC 137 V R +L + IE +G+ID+LVN AG N + P+ + T E + + +++ + Sbjct: 69 VGRPNELVQLVEKTIEAYGQIDILVNNAGTNPYMGPVHETTLELFDKIMDVNVKAPFELS 128 Query: 138 KAVLPQMIEQGIGSIINIASTHSTHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGIRVNA 197 K LP + + SIINI+S + P Y V+K L LT+ E+ + IRVNA Sbjct: 129 KLCLPHLRKSSQASIINISSIGALSPEPQLGIYSVSKSALHSLTKVCAKEWGQQKIRVNA 188 Query: 198 IAPGYIETQLNVDYWNGFADPHAERQRAFDLHPPRRIGQPIEVAMTAVFLASDEAPFINA 257 I PG I+T + W +R +R+G+ E+A A+FLAS A +I+ Sbjct: 189 ICPGIIKTNFSKALWGNDQIMDVIMKRL----AIKRLGKTEEIAALALFLASPAASYISG 244 Query: 258 SCITIDGG 265 S T+DGG Sbjct: 245 SIFTVDGG 252 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: 132 Number of extensions: 6 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: 255 Length adjustment: 25 Effective length of query: 247 Effective length of database: 230 Effective search space: 56810 Effective search space used: 56810 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