Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate 5209125 Shew_1603 3-oxoacyl-(acyl-carrier-protein) reductase (RefSeq)
Query= reanno::pseudo6_N2E2:Pf6N2E2_5967 (272 letters) >FitnessBrowser__PV4:5209125 Length = 248 Score = 120 bits (301), Expect = 3e-32 Identities = 83/249 (33%), Positives = 125/249 (50%), Gaps = 13/249 (5%) Query: 19 LKNKVVLLTGAAQGIGEAIVAAFASQQARLVISDIQAEKVETVAAHWRERGADVHALKAD 78 L KV L+TGA++GIG A+ A LVI +E+ AA G H L + Sbjct: 7 LTGKVALVTGASRGIGRAVAETLVEAGA-LVIGTATSER--GAAAIQEYLGDKGHGLVLN 63 Query: 79 VSNQQDLHAMARHAVERHGRIDVLVNCAGVNVFRDPLEMTEEDWRRCFAIDLDGAWYGCK 138 V++ + + + E+ G +D+LVN AG+ + M E++W +L + K Sbjct: 64 VTDSESIDHLFASIKEKVGEVDILVNNAGITRDNLLMRMKEDEWTDIIDTNLTSLYRTSK 123 Query: 139 AVLPQMIEQGVGSIINIASTHSSHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGVRVNAI 198 VL M+++ G IINI S + G Y AK GL+G T++L E A + + VNAI Sbjct: 124 QVLRAMMKKRSGRIINIGSVVGTMGNAGQTNYCAAKAGLIGFTKSLAREVASRQITVNAI 183 Query: 199 APGYIETQLNVDYWNGFADPYAERQR--ALDLHPPRRIGQPIEVAMTAVFLASDEAPFIN 256 APG+I+T + D E Q+ + P R+GQP E+A +FLASD A +I Sbjct: 184 APGFIQTDM--------TDELTEEQQKGIMSQVPMERLGQPQEIANAVLFLASDSAAYIT 235 Query: 257 ASCITIDGG 265 + ++GG Sbjct: 236 GETLHVNGG 244 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: 136 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: 248 Length adjustment: 24 Effective length of query: 248 Effective length of database: 224 Effective search space: 55552 Effective search space used: 55552 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