Align L-arabinose 1-dehydrogenase; D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate CA265_RS00310 CA265_RS00310 oxidoreductase
Query= reanno::BFirm:BPHYT_RS16920 (266 letters) >FitnessBrowser__Pedo557:CA265_RS00310 Length = 246 Score = 110 bits (275), Expect = 3e-29 Identities = 86/247 (34%), Positives = 124/247 (50%), Gaps = 11/247 (4%) Query: 22 LVDRTVLITGGATGIGASFVEHFAAQGARVAF-FDIDASAGEALADELGDSKHKPLFLSC 80 L D+ L+TGG+ GIGA+ V+ AA+GA+V F + A A+ E+ + + L Sbjct: 4 LTDKIALVTGGSRGIGAAIVKRLAAEGAKVIFTYAHSAEKALAVVAEVEAAGGVAVALKA 63 Query: 81 DLTDIDALQKAIADVKAALGPIQVLVNNAANDKRHTIGEVTRESFDAGIAVNIRHQFFAA 140 T + A+A A G I VLVNNA E T E ++ +AVN++ F AA Sbjct: 64 SSTIAGEVTGAVAKTIADFGRIDVLVNNAGIYIGKAFEEHTLEDYNEIMAVNVQAVFVAA 123 Query: 141 QAVMEDMKAANSGSIINLGSISWMLKNGGYP---VYVMSKSAVQGLTRGLARDLGHFNIR 197 A ++ M G II +GS M N P +Y MSKSA+QG TRGLARDLG I Sbjct: 124 LAAVKAMP--EGGRIITIGSN--MGDNAVGPETTLYTMSKSALQGFTRGLARDLGARKIT 179 Query: 198 VNTLVPGWVMTEKQKRLWLDDAGRRSIKEGQCIDAELEPADLARMALFLAADDSRMITAQ 257 VN + PG + T+ D ++ + D+A F+A++++R IT Sbjct: 180 VNLVQPGPINTDMNP---ADAPLADFLRTRMALPDYGTVEDIASFVSFIASEEARYITGS 236 Query: 258 DIVVDGG 264 + +DGG Sbjct: 237 FLTIDGG 243 Lambda K H 0.320 0.134 0.388 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: 167 Number of extensions: 11 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: 266 Length of database: 246 Length adjustment: 24 Effective length of query: 242 Effective length of database: 222 Effective search space: 53724 Effective search space used: 53724 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