Align 2,4-diketo-3-deoxy-L-rhamnonate hydrolase (EC 3.7.1.-) (characterized)
to candidate YP_428778.1 Rru_A3697 fumarylacetoacetate (FAA) hydrolase
Query= reanno::BFirm:BPHYT_RS34210 (282 letters) >NCBI__GCF_000013085.1:YP_428778.1 Length = 233 Score = 105 bits (263), Expect = 7e-28 Identities = 74/210 (35%), Positives = 104/210 (49%), Gaps = 13/210 (6%) Query: 70 IGKFICIGLNYADHAAE-SNLPVPAEPVIFNKWTSAISGPNDDVEIPRGSKKTDWEVELG 128 +G+ C+G NYADHA E P P F+K A+ V P+ + EVEL Sbjct: 24 VGRVFCVGRNYADHAREMGGDPHKEPPFFFSKPGDAVVPLGGAVPYPQATSNLHHEVELV 83 Query: 129 VVIGKPAKYIDEANALDYVAGYCVINDVSEREWQIEK---GGTWDKGKGFDTFGPIGPWV 185 V +G I ALD V GY V D++ R+ Q G WD KGF+ GP+G + Sbjct: 84 VALGGGGHDIAPDKALDLVWGYAVGIDLTRRDLQDSAKRAGRPWDMAKGFEASGPVGA-I 142 Query: 186 VTRDEVADPQNLSLWLEVDGHRYQNGSTKTMVFGVAKLVSYVSQCMSLQPGDVISTGTPP 245 + ++ L V+G Q G K M++ V+ ++S++S+ M L+PGD+I TGTP Sbjct: 143 TPAATTGALTSGAISLSVNGVPRQTGDLKDMIWPVSDVISFLSRLMVLRPGDLIFTGTPA 202 Query: 246 GVGMGVKPNPVFLKPGQTIRLGIEGLGEQT 275 GVG PV + G +R I GL T Sbjct: 203 GVG------PV--EEGDELRAEIAGLDPLT 224 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: 231 Number of extensions: 13 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: 282 Length of database: 233 Length adjustment: 24 Effective length of query: 258 Effective length of database: 209 Effective search space: 53922 Effective search space used: 53922 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