Align L-arabinose 1-dehydrogenase; D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate CCNA_01885 CCNA_01885 short chain dehydrogenase
Query= reanno::BFirm:BPHYT_RS16920 (266 letters) >FitnessBrowser__Caulo:CCNA_01885 Length = 258 Score = 129 bits (324), Expect = 6e-35 Identities = 86/246 (34%), Positives = 126/246 (51%), Gaps = 3/246 (1%) Query: 22 LVDRTVLITGGATGIGASFVEHFAAQGARVAFFDIDASAGEALADELGDSKHKPLFLSCD 81 L R +TG + G+G + AA+GA VA D+ A +A ADE+ + K + L CD Sbjct: 11 LEGRVAAVTGASRGLGRATAALLAAEGAMVALLDLKAHWAQAAADEIIAAGGKAVGLGCD 70 Query: 82 LTDIDALQKAIADVKAALGPIQVLVNNAANDKRHTIGEVTRESFDAGIAVNIRHQFFAAQ 141 ++D +AL + V A G VLVNNA + + + ES D ++V + Q Sbjct: 71 VSDREALTATLGAVNDAHGRFDVLVNNAMWNVYEPLAAIRPESLDRMVSVGFSGVIWGMQ 130 Query: 142 AVMEDMKAANSGSIINLGSISWMLKNGGYPVYVMSKSAVQGLTRGLARDLGHFNIRVNTL 201 A M A+ GSI+N+ S+S L Y K+ V G+TR A +LG NIRVN + Sbjct: 131 AAAPLMAASGGGSIVNIASVSAQLGIPNGIAYCGVKAGVAGMTRAAAAELGAMNIRVNAV 190 Query: 202 VPGWVMTEKQKRLWLDDAGRRSIKEGQCIDAEL-EPADLARMALFLAADDSRMITAQDIV 260 P V TE +R+ ++ R +++ GQ L D+A+ +LA DDS +T Q + Sbjct: 191 APSTVDTEGVRRVVSEE--RIAMRIGQTPLGRLGTTEDIAKAVRYLACDDSDFVTGQMLT 248 Query: 261 VDGGWA 266 VDGG A Sbjct: 249 VDGGLA 254 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: 138 Number of extensions: 6 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: 258 Length adjustment: 25 Effective length of query: 241 Effective length of database: 233 Effective search space: 56153 Effective search space used: 56153 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