Align L-2-keto-3-deoxyrhamnonate 4-dehydrogenase subunit (EC 1.1.1.401) (characterized)
to candidate 3609150 Dshi_2538 fumarylacetoacetate (FAA) hydrolase (RefSeq)
Query= metacyc::MONOMER-16233 (285 letters) >FitnessBrowser__Dino:3609150 Length = 228 Score = 116 bits (290), Expect = 5e-31 Identities = 75/232 (32%), Positives = 117/232 (50%), Gaps = 18/232 (7%) Query: 51 LVEGEPRYGVPVKG------IGKIVAIGLNYEDHAIESNLPIPTEPMMFMKALSSLNGPN 104 +++ P +P+ G + ++ IG NY HAIE EP F + + P+ Sbjct: 5 VIDTPPLVALPIAGMDALFPVRRVYCIGRNYAAHAIEMGHNPDREPPFFFQKNPNNLDPS 64 Query: 105 DEVVLPKNSTHGDWEVELGVVIGETCRFVSEDEALSKVAGYVLVNDVSERF---NQKQRG 161 E P +++ E E+ V++ + DEA S + GY L D++ R QK+ G Sbjct: 65 GEFPYPPHTSDVHHEAEVAVMLKSGGTNIPIDEAESHIYGYALSLDMTRRDLQGEQKKMG 124 Query: 162 TQWSKGKGHDTFCPVGPWLVTPDEVGDPQDLDMHLNVNGTRMQTGNTKTMIFNVAQLISY 221 W GK + PVGP + +E G + + L VNG Q G+ MI+ VA++ISY Sbjct: 125 RPWEIGKAFERSAPVGP-IHRIEETGPLNEGALRLTVNGETRQEGDLNQMIWKVAEMISY 183 Query: 222 VSEYITLYPGDLMITGTPPGVGEGKKPQAIYLKAGDVMELGIEKLGTQRQQV 273 +SEY L PGD++++GTP GV ++ GDVME+ +E LG+ +V Sbjct: 184 LSEYFELAPGDVILSGTPSGVAA--------VERGDVMEISVEGLGSMSVKV 227 Lambda K H 0.316 0.137 0.411 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: 191 Number of extensions: 15 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: 285 Length of database: 228 Length adjustment: 24 Effective length of query: 261 Effective length of database: 204 Effective search space: 53244 Effective search space used: 53244 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: 42 (22.0 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