Align L-arabinose 1-dehydrogenase; D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate GFF2165 PS417_11045 3-oxoacyl-ACP reductase
Query= reanno::BFirm:BPHYT_RS16920 (266 letters) >FitnessBrowser__WCS417:GFF2165 Length = 255 Score = 274 bits (700), Expect = 2e-78 Identities = 140/249 (56%), Positives = 173/249 (69%) Query: 17 ARYPSLVDRTVLITGGATGIGASFVEHFAAQGARVAFFDIDASAGEALADELGDSKHKPL 76 A YP L +TVLI+GGA+GIG V FAAQGA+V F D S GE LA L H Sbjct: 6 AVYPDLEGKTVLISGGASGIGEFMVRAFAAQGAKVGFVDRAQSQGERLAALLSSRGHTVE 65 Query: 77 FLSCDLTDIDALQKAIADVKAALGPIQVLVNNAANDKRHTIGEVTRESFDAGIAVNIRHQ 136 F++CD+TD A + AI + +LGPI VLVNNAAND RHT+ EV E FD IAVN++H Sbjct: 66 FVNCDITDEIAYKAAIGRFEHSLGPISVLVNNAANDARHTLEEVDSEMFDRLIAVNLKHA 125 Query: 137 FFAAQAVMEDMKAANSGSIINLGSISWMLKNGGYPVYVMSKSAVQGLTRGLARDLGHFNI 196 FFAA+AV+ MK+A G+IINLGS+ WM+ + GYPVY SK+A G+TR LAR+LG I Sbjct: 126 FFAAKAVVPMMKSAGGGAIINLGSVGWMMASAGYPVYAASKAAAHGMTRALARELGPSRI 185 Query: 197 RVNTLVPGWVMTEKQKRLWLDDAGRRSIKEGQCIDAELEPADLARMALFLAADDSRMITA 256 RVNTLVPGWVMTEKQ +W+DDA + I QC+ + P +A MALFLA+D S M +A Sbjct: 186 RVNTLVPGWVMTEKQLAMWVDDAAKELISRSQCLPGSVLPEHIANMALFLASDASAMCSA 245 Query: 257 QDIVVDGGW 265 Q+ +VDGGW Sbjct: 246 QNFIVDGGW 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: 214 Number of extensions: 4 Number of successful extensions: 1 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: 255 Length adjustment: 24 Effective length of query: 242 Effective length of database: 231 Effective search space: 55902 Effective search space used: 55902 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