Align 2,4-diketo-3-deoxy-L-rhamnonate hydrolase (EC 3.7.1.-) (characterized)
to candidate GFF3802 Psest_3871 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase (catechol pathway)
Query= reanno::BFirm:BPHYT_RS34210 (282 letters) >FitnessBrowser__psRCH2:GFF3802 Length = 221 Score = 119 bits (298), Expect = 6e-32 Identities = 74/206 (35%), Positives = 112/206 (54%), Gaps = 13/206 (6%) Query: 70 IGKFICIGLNYADHAAESNLPVPAEPVIFNKWTSAISGPNDDVEIPRGSKKTDWEVELGV 129 +GK +CIG NYA+HA E N PVP EP++F K S +D IP +E E+ V Sbjct: 17 LGKVVCIGRNYAEHAKELNNPVPTEPLLFIKAGSCSVPLDDGFSIPSDRGAVHYEAEIAV 76 Query: 130 VIGKP-AKYIDEANALDYVAGYCVINDVSEREWQI---EKGGTWDKGKGFDTFGPIGPWV 185 +IGKP ++ +E D ++G+ D++ R+ Q EKG W+ K FD + P+ Sbjct: 77 LIGKPLSRKPNEEEVRDAISGFAPALDLTLRDVQAKLKEKGHPWEIAKSFDGACVLAPF- 135 Query: 186 VTRDEVADPQNLSLWLEVDGHRYQNGSTKTMVFGVAKLVSYVSQCMSLQPGDVISTGTPP 245 V D V D ++ + L ++G Q+G++ M+ + L+ +++ SLQPGDV+ TGTP Sbjct: 136 VPGDAVEDLGDIGIRLTINGEVRQDGNSSQMLNAILPLLQHIAGHFSLQPGDVVLTGTPA 195 Query: 246 GVGMGVKPNPVFLKPGQTIRLGIEGL 271 GVG LK G + L + GL Sbjct: 196 GVGP--------LKQGDQLVLELVGL 213 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: 221 Number of extensions: 11 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: 221 Length adjustment: 24 Effective length of query: 258 Effective length of database: 197 Effective search space: 50826 Effective search space used: 50826 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: 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