Align L-arabinose 1-dehydrogenase (EC 1.1.1.46) (characterized)
to candidate Synpcc7942_1573 Synpcc7942_1573 3-oxoacyl-(acyl-carrier protein) reductase
Query= reanno::pseudo5_N2C3_1:AO356_20240 (272 letters) >FitnessBrowser__SynE:Synpcc7942_1573 Length = 266 Score = 132 bits (331), Expect = 1e-35 Identities = 82/267 (30%), Positives = 145/267 (54%), Gaps = 16/267 (5%) Query: 18 RLKDKVVLLTGAAQGIGEAIVAAFASQQARLVI--------SDIQAQKVEAVAAHW---R 66 +L +++ L+TG++QGIG+ I AS+ A +VI ++ ++VEA A + Sbjct: 3 KLDNQIALVTGSSQGIGQEIAIRLASEGASVVIDYRSHPEGAEETRKQVEAAGAQCHLAK 62 Query: 67 ERGADVHALQADVSKQQDLQAMARRAVELHGRIDVLVNCAGVNVFRDPLEMTEEDWRRCF 126 + + + +QAD+ ++ + +++ G++D+LVN AG+ E+TE D+ Sbjct: 63 DHAPEGYVVQADLGDVTQVRNLVAESIKHFGKLDILVNNAGMERRAPFWEVTEADYDMVL 122 Query: 127 AIDLDGAWYGCKAVLPQMIE-QGVGSIINIASVHSSHIIPGCFPYPVAKHGLLGLTRALG 185 ++L GA++ +A++ ++E + G IINI+SVH P Y ++K G+ +TR L Sbjct: 123 NVNLKGAFFAAQALVQHLLETKRPGKIINISSVHEELPFPNFASYCLSKGGIKMMTRDLA 182 Query: 186 IEYAPKGVRVNAIAPGYIETQLNVDYWNGFADPHAERQRALDLHPPRRVGQPIEVAMTAV 245 +E G+ +N +APG IET +N + N E L P +R+G+P ++A + Sbjct: 183 VELGEYGITINNVAPGAIETPINTNLLNN----PTELNALLGNIPLKRLGKPKDIASLVL 238 Query: 246 FLASDEAPFINASCITIDGGRSVMYHD 272 FLAS +A +I + I DGG YH+ Sbjct: 239 FLASPDADYITGTTIFADGGLLWNYHE 265 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: 160 Number of extensions: 6 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: 266 Length adjustment: 25 Effective length of query: 247 Effective length of database: 241 Effective search space: 59527 Effective search space used: 59527 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