Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate Echvi_1862 Echvi_1862 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases)
Query= metacyc::MONOMER-16230 (256 letters) >FitnessBrowser__Cola:Echvi_1862 Length = 246 Score = 127 bits (318), Expect = 3e-34 Identities = 79/244 (32%), Positives = 132/244 (54%), Gaps = 11/244 (4%) Query: 9 IVTGASRGIGRAAARE-CARQGARVVIGHSGSDEGRAGALSLAEEIAAFGGTAIAVGADA 67 +VTG + G+G A A++ C ++IG + S LA+ G D Sbjct: 7 LVTGGASGLGLATAKKFCDHDITTIIIGRNES--------KLAKAQEELGPNCHYYAFDL 58 Query: 68 ADLDSGEKLVAAAVEAFGSVDVLVNNAGICPFHSFLDMPRELYLKTVGTNLNGAYFTVQA 127 DL + L+ G +D+LVNNAGI F+++ E + + + TN+ + + Sbjct: 59 NDLPNIPDLINTITTEHGKIDILVNNAGINMKKPFIEVTDEEFQQIITTNVFAVFSLSRE 118 Query: 128 AARRMKEQGRGGAIIAVSSISALVGGAMQTHYTPTKAGLLSLMQSCAIALGPYGIRCNAV 187 A+ M Q + GAI+ +SS+++ G YT +K+ + + ++ A+ L P GIR N V Sbjct: 119 IAKTMASQ-KHGAIVNISSMASQYGIPKVIAYTASKSAIEGMTKAMAVELSPLGIRVNCV 177 Query: 188 LPGTIATDINKEDLS-DLEKRERMTSRVPLGRLGEPDDLAGPIVFLASDMARYVTGASLL 246 PG IAT+++ + L+ D E+++++ SR P+G LG P ++A + +LAS+ A Y+TG L Sbjct: 178 APGFIATEMSAKALNGDPERKQKVLSRTPMGALGTPANIADAVYYLASESASYITGTILP 237 Query: 247 VDGG 250 VDGG Sbjct: 238 VDGG 241 Lambda K H 0.319 0.136 0.383 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: 125 Number of extensions: 6 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: 256 Length of database: 246 Length adjustment: 24 Effective length of query: 232 Effective length of database: 222 Effective search space: 51504 Effective search space used: 51504 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: 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