Align sorbitol dehydrogenase, D-fructose forming (EC 1.1.1.14) (characterized)
to candidate GFF2280 PGA1_c23120 putative sorbitol dehydrogenase
Query= reanno::BFirm:BPHYT_RS16120 (260 letters) >FitnessBrowser__Phaeo:GFF2280 Length = 269 Score = 157 bits (398), Expect = 2e-43 Identities = 97/261 (37%), Positives = 145/261 (55%), Gaps = 8/261 (3%) Query: 4 RLQDKVAILTGAASGIGEAVARRYLDEGARCVLVDVK--PADSFGDSLRATYGDRVLTVS 61 RL+ K ++TGAA G+G+A A + +GA L D+ A D++ A + V Sbjct: 5 RLKGKNILITGAARGMGQANAESFAAQGANVCLGDLDGDEAQKVADAINAAGNGMAIAVK 64 Query: 62 ADVTRRDDIQRIVASTLERFGQIDILFNNAALFDMRPILEESWDVFDRLFAVNVKGMFFL 121 DVT R D VA+T+E FG I++ NA L R ++ D +D + VN K M+ Sbjct: 65 MDVTSRADNAAAVAATVEAFGSINVGLFNAGLNKPRFFMDIDEDNWDMIMNVNTKAMWLG 124 Query: 122 MQAVAQKMVEQGCGG----KIINMSSQAGRRGEALVSHYCATKAAVLSYTQSAALALAPH 177 MQ VA++M+ QG K+IN+ S A ++ V+ YC +K L+ T+ AL LA H Sbjct: 125 MQEVARQMIAQGPMEDHPYKLINVGSIASKKPLVDVTVYCTSKYGCLALTECGALGLAEH 184 Query: 178 KINVNGIAPGVVDTPMWNEV--DALFARYENRPLGEKKRLVGEAVPLGRMGVPDDLTGAA 235 I VNG APGVV TP+W ++ D + ++ R + +V A+ + R+ P D+ G A Sbjct: 185 NITVNGYAPGVVVTPLWEQLDKDLVDIGFKEREGQAYEDIVDSALVIKRLSYPKDIVGTA 244 Query: 236 LFLASADADYITAQTLNVDGG 256 FLAS D+DY+T Q +++DGG Sbjct: 245 SFLASDDSDYMTGQMISIDGG 265 Lambda K H 0.321 0.135 0.393 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: 188 Number of extensions: 14 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: 260 Length of database: 269 Length adjustment: 25 Effective length of query: 235 Effective length of database: 244 Effective search space: 57340 Effective search space used: 57340 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