Align 2,4-diketo-3-deoxy-L-rhamnonate hydrolase (EC 3.7.1.-) (characterized)
to candidate WP_043529939.1 JH15_RS10280 fumarylacetoacetate hydrolase family protein
Query= reanno::BFirm:BPHYT_RS34210 (282 letters) >NCBI__GCF_000759345.1:WP_043529939.1 Length = 285 Score = 411 bits (1056), Expect = e-119 Identities = 195/277 (70%), Positives = 233/277 (84%), Gaps = 1/277 (0%) Query: 1 MKLLRYGPKGQEKPGLLDAQGKIRDLSKVVADIDGAALTDEGLAKLRALDPASLPLVEGN 60 MKLLR+GP GQEKPG+LDA G +RDLS + D+ G AL+ E LA+L +DPASLP V Sbjct: 1 MKLLRFGPVGQEKPGMLDANGTLRDLSAHIDDLRGEALSQERLAELARIDPASLPEVPAG 60 Query: 61 PRMGPCVGKIGKFICIGLNYADHAAESNLPVPAEPVIFNKWTSAISGPNDDVEIPRGSKK 120 R+GPCV +GKFICIGLNY+DHAAE+ VPAEPVIFNKWTSAI GPNDDV IPRGS+K Sbjct: 61 ARIGPCVAGVGKFICIGLNYSDHAAETGAEVPAEPVIFNKWTSAICGPNDDVIIPRGSQK 120 Query: 121 TDWEVELGVVIGKPAKYIDEANALDYVAGYCVINDVSEREWQIEKGGTWDKGKGFDTFGP 180 TDWEVELGV+IGK +YIDE+NA+ +VAG+CV+NDVSERE+Q+E+ G+WDKGKG DTFGP Sbjct: 121 TDWEVELGVIIGKGGRYIDESNAMAHVAGFCVVNDVSEREYQLERCGSWDKGKGCDTFGP 180 Query: 181 IGPWVVTRDEVADPQNLSLWLEVDGHRYQNGSTKTMVFGVAKLVSYVSQCMSLQPGDVIS 240 +GPW+VT DE+ DP +L +WLEVDG RYQ+GST TMV+ V L+SY+S+ MSLQPGDVIS Sbjct: 181 LGPWLVTPDEIDDPHSLGMWLEVDGKRYQDGSTDTMVYQVPFLISYLSRFMSLQPGDVIS 240 Query: 241 TGTPPGVGMGVKPNPVFLKPGQTIRLGIEGLGEQTQK 277 TGTPPGVGMG KP V+LKPGQ +RLGI+GLGEQ Q+ Sbjct: 241 TGTPPGVGMGQKPQ-VYLKPGQRMRLGIDGLGEQEQR 276 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: 419 Number of extensions: 14 Number of successful extensions: 2 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: 285 Length adjustment: 26 Effective length of query: 256 Effective length of database: 259 Effective search space: 66304 Effective search space used: 66304 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