Align L-arabinose 1-dehydrogenase; D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate 18291 b4266 gluconate 5-dehydrogenase (NCBI)
Query= reanno::BFirm:BPHYT_RS16920 (266 letters) >FitnessBrowser__Keio:18291 Length = 254 Score = 117 bits (294), Expect = 2e-31 Identities = 77/244 (31%), Positives = 117/244 (47%) Query: 21 SLVDRTVLITGGATGIGASFVEHFAAQGARVAFFDIDASAGEALADELGDSKHKPLFLSC 80 SL + +LITG A GIG GA++ DI A E ++L + + Sbjct: 6 SLAGKNILITGSAQGIGFLLATGLGKYGAQIIINDITAERAELAVEKLHQEGIQAVAAPF 65 Query: 81 DLTDIDALQKAIADVKAALGPIQVLVNNAANDKRHTIGEVTRESFDAGIAVNIRHQFFAA 140 ++T + A+ ++ +GPI VLVNNA +RH E + ++ IAVN F + Sbjct: 66 NVTHKHEIDAAVEHIEKDIGPIDVLVNNAGIQRRHPFTEFPEQEWNDVIAVNQTAVFLVS 125 Query: 141 QAVMEDMKAANSGSIINLGSISWMLKNGGYPVYVMSKSAVQGLTRGLARDLGHFNIRVNT 200 QAV M +G +IN+ S+ L Y SK AV+ LTRG+ +L NI+VN Sbjct: 126 QAVTRHMVERKAGKVINICSMQSELGRDTITPYAASKGAVKMLTRGMCVELARHNIQVNG 185 Query: 201 LVPGWVMTEKQKRLWLDDAGRRSIKEGQCIDAELEPADLARMALFLAADDSRMITAQDIV 260 + PG+ TE K L D+A + + +P +L A+FL++ S + + Sbjct: 186 IAPGYFKTEMTKALVEDEAFTAWLCKRTPAARWGDPQELIGAAVFLSSKASDFVNGHLLF 245 Query: 261 VDGG 264 VDGG Sbjct: 246 VDGG 249 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: 171 Number of extensions: 9 Number of successful extensions: 2 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: 254 Length adjustment: 24 Effective length of query: 242 Effective length of database: 230 Effective search space: 55660 Effective search space used: 55660 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