Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate Pf6N2E2_1375 Multiple polyol-specific dehydrogenase (EC 1.1.1.-)
Query= metacyc::MONOMER-16231 (254 letters) >lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1375 Multiple polyol-specific dehydrogenase (EC 1.1.1.-) Length = 257 Score = 154 bits (390), Expect = 1e-42 Identities = 97/261 (37%), Positives = 135/261 (51%), Gaps = 13/261 (4%) Query: 1 MKLLEGKTVLVTGASTGIGRAAAIGAAQHGADVAINYAHSDGPAQSCVAEIEALGQRAIA 60 MK LEGK+ LVTGA+ GIGR A GA VAI +D + A LG A A Sbjct: 1 MKRLEGKSALVTGAARGIGRTFAQAYINEGATVAI----ADIDLERAQATAAELGDSAYA 56 Query: 61 VKGDVADPQTAQDFVAKAVETFGKVDVMVSNAGICPFHAFLDMPVDVVERTFKVNLHGAY 120 VK DV D + + V GK+D++++NA + +++ ER F +N+ G Sbjct: 57 VKMDVTDQASIDQAIEAVVARVGKLDILINNAALFDLAPIVEITRQSYERLFSINVAGTL 116 Query: 121 FMVQAAAQQMVRQGHGGSIVAVSSISALVGGEYQTHYTPTKAGVHSLMQSTAIALGKHGI 180 F +QAAA+QM+RQGHGG I+ ++S + G Y TKA V SL QS + L KH I Sbjct: 117 FTLQAAARQMIRQGHGGRIINMASQAGRRGEALVGVYCATKAAVISLTQSAGLDLIKHRI 176 Query: 181 RCNSVLPGTILTE---------INKDDLADQEKREYMEARTPLGRLGAPEDLAGPIVFLA 231 N++ PG + E ++L EK+ + P GR+G EDL G +FLA Sbjct: 177 NVNAIAPGVVDGEHWDGVDALFARHENLPLGEKKRQAGQQVPYGRMGTAEDLTGMAIFLA 236 Query: 232 SDMAAYVTGAALLVDGGMYVN 252 S + YV VDGG +++ Sbjct: 237 STESEYVVAQTYNVDGGNWMS 257 Lambda K H 0.318 0.133 0.379 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: 120 Number of extensions: 5 Number of successful extensions: 3 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: 254 Length of database: 257 Length adjustment: 24 Effective length of query: 230 Effective length of database: 233 Effective search space: 53590 Effective search space used: 53590 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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