Align D-sorbitol 2-dehydrogenase (EC 1.1.1.14) (characterized)
to candidate 3607132 Dshi_0554 short-chain dehydrogenase/reductase SDR (RefSeq)
Query= reanno::acidovorax_3H11:Ac3H11_2940 (244 letters) >FitnessBrowser__Dino:3607132 Length = 241 Score = 267 bits (683), Expect = 1e-76 Identities = 128/239 (53%), Positives = 173/239 (72%) Query: 6 NLQGQVAAITGAASGIGFASAQTMADAGARVVLIDRDEAALAKACATIGPNALPLVLDLL 65 +L G+V AITG ASGIG A A+ DAGA+V +IDR+ AL + A +G A+P+V DL+ Sbjct: 3 DLSGKVVAITGGASGIGLACARACIDAGAKVAIIDRNATALEEVRAELGAQAVPIVTDLM 62 Query: 66 DARQCASLLQRTLALAGQLDIFHANAGLYVGGDLVDADPDAIDRMLNLNVNVVMKNVHNV 125 D A +L R L AG+LD FHANAG YVGGD++ DPD D +LNLN+N ++VH V Sbjct: 63 DKASVAQMLSRILDKAGRLDAFHANAGAYVGGDVLAGDPDEWDHVLNLNINAAFRSVHAV 122 Query: 126 LPHMIERGTGDIIVTSSLAAHFPTPWEPVYASSKWAVNCFVQTVRRQVFKHGIRVGSISP 185 LPH+ ++G+GD+I+TSS+A P WEP+Y +SK AV F +VRRQ+ KHG+RVG+I P Sbjct: 123 LPHLAKQGSGDVILTSSVAGVIPVVWEPIYTASKHAVQAFTHSVRRQMSKHGVRVGAILP 182 Query: 186 GPVITSLLADWPAEKLAEAKASGSLIEAAEVAEVVLFMLTRPRGMTIRDVVMMPTNFDL 244 GPV+T+LL DWP K+ +A A GSL++ +VA+ V+FMLTRP +TIRD+V++P DL Sbjct: 183 GPVVTALLDDWPKPKMEQALAEGSLMQPKDVADCVVFMLTRPSNVTIRDLVLLPNAVDL 241 Lambda K H 0.321 0.134 0.391 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: 183 Number of extensions: 9 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: 244 Length of database: 241 Length adjustment: 23 Effective length of query: 221 Effective length of database: 218 Effective search space: 48178 Effective search space used: 48178 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: 46 (22.3 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