Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate WP_108358580.1 B9Z44_RS13785 3-oxoacyl-ACP reductase FabG
Query= reanno::pseudo13_GW456_L13:PfGW456L13_2119 (272 letters) >NCBI__GCF_003063475.1:WP_108358580.1 Length = 255 Score = 151 bits (381), Expect = 2e-41 Identities = 90/251 (35%), Positives = 136/251 (54%), Gaps = 6/251 (2%) Query: 15 RGERLKNKVVLLTGAAQGIGEAIVATFASQQARLIISDIQGEKVEKVAAHWRDQGADVVA 74 + +RL+ KV L+TGAAQGIG A FA + A +I+ D++ V++ + GA + Sbjct: 8 QAQRLQGKVSLITGAAQGIGLATALKFAREGAIVIVCDVKQAAVDEAVKQCQALGAQALG 67 Query: 75 IKADVSRQQDLHAMARLAIDLHGRIDVLVNCAGVNVFRDPLEMTEEDWRRCFAIDLDGAW 134 DV+++ + A + +D GRIDVLVN AG+ +MT E + R ++L G + Sbjct: 68 FVVDVTQRDMVDATVKAVLDKFGRIDVLVNNAGITQDARLQKMTLEQFDRVIDVNLRGVF 127 Query: 135 YGCKAVLPQMIEQGIGSIINIASTHSTHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGVR 194 + +AV M+ QG G I+N +S + G Y K G++G T+ E PKG+R Sbjct: 128 HCAQAVTEAMVAQGSGVILNASSVVGIYGNFGQTNYAATKFGVIGFTKTWSRELGPKGIR 187 Query: 195 VNAIAPGYIETQLNVDYWNGFADPHAERQRAFDLHPPRRIGQPIEVAMTAVFLASDEAPF 254 VNA+APG+I+T + P D P +R+GQP ++A FLASDEA + Sbjct: 188 VNAVAPGFIQTPILSTI------PEKVIHEMTDRVPLKRLGQPEDIANVYAFLASDEAAY 241 Query: 255 INASCITIDGG 265 IN + I + GG Sbjct: 242 INGTVIEVAGG 252 Lambda K H 0.322 0.138 0.426 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: 130 Number of extensions: 5 Number of successful extensions: 2 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: 272 Length of database: 255 Length adjustment: 25 Effective length of query: 247 Effective length of database: 230 Effective search space: 56810 Effective search space used: 56810 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: 47 (22.7 bits)
This GapMind analysis is from Sep 24 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