Align 2,4-diketo-3-deoxy-L-rhamnonate hydrolase (EC 3.7.1.-) (characterized)
to candidate HSERO_RS06355 HSERO_RS06355 ureidoglycolate lyase
Query= reanno::BFirm:BPHYT_RS34210 (282 letters) >FitnessBrowser__HerbieS:HSERO_RS06355 Length = 281 Score = 458 bits (1178), Expect = e-134 Identities = 215/281 (76%), Positives = 245/281 (87%) Query: 1 MKLLRYGPKGQEKPGLLDAQGKIRDLSKVVADIDGAALTDEGLAKLRALDPASLPLVEGN 60 MKLLRYGP GQEKPG+LD GKIRDLS + D++GA L D L K+R LD +LP+VEGN Sbjct: 1 MKLLRYGPVGQEKPGILDQAGKIRDLSAHIKDVNGAVLDDASLEKIRKLDLNTLPVVEGN 60 Query: 61 PRMGPCVGKIGKFICIGLNYADHAAESNLPVPAEPVIFNKWTSAISGPNDDVEIPRGSKK 120 PR+G CVG IGKFICIGLNYADHAAESNLP+PAEPV+FNKWTSA+ GPND+V+IPRGSKK Sbjct: 61 PRIGACVGNIGKFICIGLNYADHAAESNLPIPAEPVVFNKWTSAVVGPNDNVKIPRGSKK 120 Query: 121 TDWEVELGVVIGKPAKYIDEANALDYVAGYCVINDVSEREWQIEKGGTWDKGKGFDTFGP 180 TDWEVELGV+IGK YIDE +A+ +VAGYCV+NDVSERE+QIE+GGTWDKGKG DTFGP Sbjct: 121 TDWEVELGVIIGKGGSYIDEKDAMSHVAGYCVVNDVSEREYQIERGGTWDKGKGCDTFGP 180 Query: 181 IGPWVVTRDEVADPQNLSLWLEVDGHRYQNGSTKTMVFGVAKLVSYVSQCMSLQPGDVIS 240 IGPW+VTRDEVADPQ L +WLEVDG RYQNG+T TM+F VA +VSY+S+ MSLQPGDVIS Sbjct: 181 IGPWLVTRDEVADPQKLGMWLEVDGKRYQNGNTSTMIFNVAHIVSYLSRFMSLQPGDVIS 240 Query: 241 TGTPPGVGMGVKPNPVFLKPGQTIRLGIEGLGEQTQKTYAA 281 TGTPPGVGMGVKP V+L+ GQTIRLGI+GLGEQ QKT A Sbjct: 241 TGTPPGVGMGVKPEAVYLRAGQTIRLGIDGLGEQEQKTIDA 281 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: 406 Number of extensions: 7 Number of successful extensions: 1 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: 281 Length adjustment: 26 Effective length of query: 256 Effective length of database: 255 Effective search space: 65280 Effective search space used: 65280 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 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