Align Probable NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; Short chain dehydrogenase/reductase; YlSDR; EC 1.1.1.138 (characterized)
to candidate Ac3H11_2257 Short-chain dehydrogenase/reductase SDR
Query= SwissProt::Q6CEE9 (278 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2257 Length = 267 Score = 109 bits (273), Expect = 6e-29 Identities = 82/263 (31%), Positives = 134/263 (50%), Gaps = 15/263 (5%) Query: 16 TPVPKVSKNIMERFSLKGKVASITGSSSGIGFAVAEAFAQAGADVAIWYNSKPSDEKAEY 75 +P P + +I F G+V +TG + GIG A FA GA I D + + Sbjct: 5 SPAPSLPSSIY--FGHTGRVCIVTGGAQGIGEACVRRFAAEGAKPVI---VDVDDARGQA 59 Query: 76 LSKTYGVRSKAYKCAVTNAKQVETTIQTIEKDFGKIDIFIANAGIPWTAGPMIDVPNNEE 135 L+ G + +C V + QV+ + + G+ID+ + NAGI + A ++V + Sbjct: 60 LAAELG--ALYVRCDVGDKAQVDALVAQVLAAHGRIDVLVNNAGI-FRAADFLEV-TEAD 115 Query: 136 WDKVVDLDLNGAYYCAKYAGQIFKKQGYGSFIFTASMSGHIVNIPQMQACYNAAKCAVLH 195 +D V+ ++L G++ + + G G+ + +S++G ++ IP + A YN +K V Sbjct: 116 FDAVLRVNLKGSFLVGQAVARAMVTSGGGAIVNMSSVNG-VLAIPNI-ASYNVSKGGVNQ 173 Query: 196 LSRSLAVEWAGF-ARCNTVSPGYMATEISD---FIPRDTKEKWWQLIPMGREGDPSELAG 251 L+R +A+ A R N V+PG +ATE++ + K K PM R G PSE+A Sbjct: 174 LTRVMALALADKNIRVNAVAPGTIATELAAKAVLTSDEAKRKIMSRTPMKRLGQPSEIAD 233 Query: 252 AYIYLASDASTYTTGADILVDGG 274 +LASDA++Y TG + VDGG Sbjct: 234 VVAWLASDAASYVTGEIVTVDGG 256 Lambda K H 0.317 0.132 0.409 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: 165 Number of extensions: 11 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: 278 Length of database: 267 Length adjustment: 25 Effective length of query: 253 Effective length of database: 242 Effective search space: 61226 Effective search space used: 61226 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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