Align 2,4-diketo-3-deoxy-L-rhamnonate hydrolase (EC 3.7.1.-) (characterized)
to candidate WP_013707421.1 DESAC_RS12405 DUF2437 domain-containing protein
Query= reanno::BFirm:BPHYT_RS34210 (282 letters) >NCBI__GCF_000195295.1:WP_013707421.1 Length = 252 Score = 190 bits (482), Expect = 3e-53 Identities = 110/272 (40%), Positives = 163/272 (59%), Gaps = 28/272 (10%) Query: 1 MKLLRYGPKGQEKPGLLDAQGKIRDLSKVVADIDGAALTDEGLAKLRALDPASLPLVEGN 60 M+L+R+ +G+ G+LD VV + G + D L K SL V+ Sbjct: 1 MRLIRFAYQGRSHYGVLD--------DDVVFPLTGPPVGDFALLKYCF----SLSEVQ-- 46 Query: 61 PRMGPCVGKIGKFICIGLNYADHAAESNLPVPAEPVIFNKWTSAISGPNDDVEIPRGSKK 120 + PC + K I +GLNY DHAAE + +P EP+IF K ++A+ GP+ + P S + Sbjct: 47 -LLAPC--EPSKIIALGLNYRDHAAEMRMALPTEPLIFLKPSTAVIGPSTPIVYPPQSCR 103 Query: 121 TDWEVELGVVIGKPAKYIDEANALDYVAGYCVINDVSEREWQIEKGGTWDKGKGFDTFGP 180 D+E ELGVVIG+P + EA A +Y+ GY +NDV+ R+ Q +K G + + K FDTF P Sbjct: 104 VDYEAELGVVIGRPVSKVSEAKAKNYILGYTCVNDVTARDLQ-KKDGQFTRSKSFDTFCP 162 Query: 181 IGPWVVTRDEVADPQNLSLWLEVDGHRYQNGSTKTMVFGVAKLVSYVSQCMSLQPGDVIS 240 +GPW+ T ++ADP NL + ++G R Q+ +T+ +VFGVA L+S++S M+L PGDVI+ Sbjct: 163 LGPWIET--DIADPDNLVVEAILNGERRQHSTTQNLVFGVAALISFISHIMTLLPGDVIA 220 Query: 241 TGTPPGVGMGVKPNPVFLKPGQTIRLGIEGLG 272 TGTP GVG ++PG I + +EG+G Sbjct: 221 TGTPSGVGP--------MQPGDHIEIRVEGVG 244 Lambda K H 0.315 0.138 0.422 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: 249 Number of extensions: 13 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: 282 Length of database: 252 Length adjustment: 25 Effective length of query: 257 Effective length of database: 227 Effective search space: 58339 Effective search space used: 58339 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 (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