Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate CA265_RS09980 CA265_RS09980 NAD(P)-dependent oxidoreductase
Query= reanno::pseudo1_N1B4:Pf1N1B4_412 (272 letters) >FitnessBrowser__Pedo557:CA265_RS09980 Length = 284 Score = 112 bits (280), Expect = 9e-30 Identities = 84/256 (32%), Positives = 124/256 (48%), Gaps = 15/256 (5%) Query: 18 RLKNKVVLLTGAAQGIGEAIVATFASQQARLVI----SDIQGEKVEKVAAHWREQGADVV 73 +L N+V L+TG GIG ++ FA + A + I DI ++ +K+ +G + Sbjct: 37 KLNNQVALITGGDSGIGRSVAVHFAREGADVAIVYLNEDIDAKETQKMV---EAEGKKCL 93 Query: 74 AIKADVSRQQDLHAMARLAIELHGRIDVLVNCAGVNV-FRDPLQMTEEDWHRCFAIDLDG 132 IK DV + I+ G+I++LVN AG+ V +DP ++ + F ++ G Sbjct: 94 LIKGDVKKPAFCKKAVENTIKQFGKINILVNNAGMQVPQKDPKKIDNKQLEDTFRTNIFG 153 Query: 133 AWYGCKAVLPQMIEQGIGSIINIASTHSTHIIPGCFPYPVAKHGLLGLTRALGIEYAPKG 192 +Y VL + + G SIIN S + P Y K + TR+L A KG Sbjct: 154 YFYFAHEVL-EHFKPG-DSIINTTSVTAYRSSPNLIDYSSTKGAITSFTRSLATNLATKG 211 Query: 193 IRVNAIAPGYIETQLNVDYWNGFADPHAERQRAFDLHPPRRIGQPIEVAMTAVFLASDEA 252 IRVNA+APG + T L V ++ Q A + R GQP E+A VFLASD+A Sbjct: 212 IRVNAVAPGPVWTPLIVSTFDEKKIKSFGSQTAME-----RAGQPSEIAPAYVFLASDDA 266 Query: 253 PFINASCITIDGGRSV 268 FI I ++GG V Sbjct: 267 SFITGQVIHVNGGEVV 282 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: 122 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: 284 Length adjustment: 25 Effective length of query: 247 Effective length of database: 259 Effective search space: 63973 Effective search space used: 63973 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