Align 2,4-diketo-3-deoxy-L-rhamnonate hydrolase (EC 3.7.1.-) (characterized)
to candidate RR42_RS00385 RR42_RS00385 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase
Query= reanno::BFirm:BPHYT_RS34210 (282 letters) >FitnessBrowser__Cup4G11:RR42_RS00385 Length = 280 Score = 361 bits (926), Expect = e-104 Identities = 180/280 (64%), Positives = 220/280 (78%), Gaps = 2/280 (0%) Query: 1 MKLLRYGPKGQEKPGLLDAQGKIRDLSKVVADIDGAALTDEGLAKLRALDPASLPLVEGN 60 MKL+R G G E+PGL+DA+G++RDLS V+ + AL+ E LA+L LDPA+LP+V+ Sbjct: 1 MKLVRVGKPGAERPGLIDAEGRVRDLSGVLDGLGPQALSAEALARLARLDPATLPVVQAE 60 Query: 61 PRMGPCVGKIGKFICIGLNYADHAAESNLPVPAEPVIFNKWTSAISGPNDDVEIPRGSKK 120 P G IGK + IGLNYADHAAE+ + +PAEP++F K S+++GPND V +PRGS+K Sbjct: 61 RFGVPWTG-IGKIVAIGLNYADHAAEAGMALPAEPIVFLKANSSLNGPNDPVMLPRGSEK 119 Query: 121 TDWEVELGVVIGKPAKYIDEANALDYVAGYCVINDVSEREWQIEKGGTWDKGKGFDTFGP 180 TDWEVELGVVIGK A+ + A+AL +VAGYCV+NDVSERE+QIE+GGTWDKGKG DTF P Sbjct: 120 TDWEVELGVVIGKVARDVSLADALSHVAGYCVVNDVSEREFQIERGGTWDKGKGCDTFCP 179 Query: 181 IGPWVVTRDEVADPQNLSLWLEVDGHRYQNGSTKTMVFGVAKLVSYVSQCMSLQPGDVIS 240 +GPW+VTRDEV DPQ L LWL+V+G R Q GST TMVF VA LVSYVS+ M+L PGD+I Sbjct: 180 VGPWLVTRDEVPDPQALGLWLDVNGQRVQKGSTATMVFDVATLVSYVSRFMTLHPGDLIC 239 Query: 241 TGTPPGVGMGVKPNPVFLKPGQTIRLGIEGLGEQTQKTYA 280 TGTPPGVGMG KP P FLK G T+RLGI+GLGEQ Q A Sbjct: 240 TGTPPGVGMGFKP-PRFLKAGDTMRLGIDGLGEQGQTVVA 278 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: 388 Number of extensions: 6 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: 280 Length adjustment: 26 Effective length of query: 256 Effective length of database: 254 Effective search space: 65024 Effective search space used: 65024 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