Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate Ac3H11_1292 Enoyl-[acyl-carrier-protein] reductase [NADPH] (EC 1.3.1.10)
Query= metacyc::MONOMER-16231 (254 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1292 Length = 259 Score = 135 bits (340), Expect = 8e-37 Identities = 86/246 (34%), Positives = 126/246 (51%), Gaps = 4/246 (1%) Query: 4 LEGKTVLVTGASTGIGRAAAIGAAQHGADVAINYAHSDGPAQSCVAEIEALGQRAIAVKG 63 L GK LVTG + GIG A A+ GA VA Y+ S PAQ+ VA IE+ G +A+A++ Sbjct: 14 LAGKVALVTGGARGIGAAIVRRLARDGAAVAFTYSSSAAPAQALVAAIESAGGKALALRA 73 Query: 64 DVADPQTAQDFVAKAVETFGKVDVMVSNAGICPFHAFLDMPVDVVERTFKVNLHGAYFMV 123 D AD V A T G++D++V+NAG+ + + T VN+ + Sbjct: 74 DSADAAALTQAVDHAARTLGRLDILVNNAGVAVAGVLDSFSLADFDHTLNVNVRAVFVAT 133 Query: 124 QAAAQQMVRQGHGGSIVAVSSI-SALVGGEYQTHYTPTKAGVHSLMQSTAIALGKHGIRC 182 QAA + M + G G ++ + S S V + Y +KA + L + A LG GI Sbjct: 134 QAAVRHMGQGGAYGRVITIGSTNSDRVPWPGFSVYGMSKAAIVGLTKGLARDLGPRGITV 193 Query: 183 NSVLPGTILTEINKDDLADQEKREYMEARTPLGRLGAPEDLAGPIVFLASDMAAYVTGAA 242 N+V PG + T++N AD M L R P+++AG + +LA + VTGA+ Sbjct: 194 NNVQPGPVNTDMNP---ADGPMAGDMHGLMALNRHAHPDEIAGMVAYLAGPESGMVTGAS 250 Query: 243 LLVDGG 248 LL+DGG Sbjct: 251 LLIDGG 256 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: 156 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: 254 Length of database: 259 Length adjustment: 24 Effective length of query: 230 Effective length of database: 235 Effective search space: 54050 Effective search space used: 54050 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