Align 2,4-diketo-3-deoxy-L-rhamnonate hydrolase (EC 3.7.1.-) (characterized)
to candidate CA265_RS15165 CA265_RS15165 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase
Query= reanno::BFirm:BPHYT_RS34210 (282 letters) >FitnessBrowser__Pedo557:CA265_RS15165 Length = 203 Score = 114 bits (286), Expect = 1e-30 Identities = 71/180 (39%), Positives = 101/180 (56%), Gaps = 4/180 (2%) Query: 72 KFICIGLNYADHAAESNLPVPAEPVIFNKWTSAISGPNDDVEIPRGSKKTDWEVELGVVI 131 K I IG NYA+HA E N PVP PVIF K +A+ N +P S +E+E+ + I Sbjct: 2 KIIAIGRNYAEHAKELNNPVPTTPVIFLKPDTAVLKDNKPFYLPDFSDDVHYELEVVLKI 61 Query: 132 GKPAKYIDEANALDYVAGYCVINDVSEREWQI---EKGGTWDKGKGFDTFGPIGPWVVTR 188 K K+I E A +Y + D + R+ Q EKG W+ K FD PI + + Sbjct: 62 CKEGKHIAEKFAANYYDEVGLGIDFTARDIQSKHKEKGLPWELAKAFDNSAPISIFH-PK 120 Query: 189 DEVADPQNLSLWLEVDGHRYQNGSTKTMVFGVAKLVSYVSQCMSLQPGDVISTGTPPGVG 248 + D NL+ L+++G R Q G TK ++F K++S+VSQ ++L+ GD+I TGTP GVG Sbjct: 121 SDFEDLYNLNFELKINGERRQVGHTKDLLFSFEKIISFVSQYITLKKGDLIFTGTPQGVG 180 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: 170 Number of extensions: 8 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: 203 Length adjustment: 23 Effective length of query: 259 Effective length of database: 180 Effective search space: 46620 Effective search space used: 46620 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