Align 2-keto-3-deoxy-L-rhamnonate aldolase (EC 4.1.2.53) (characterized)
to candidate RR42_RS29120 RR42_RS29120 alpha-dehydro-beta-deoxy-D-glucarate aldolase
Query= BRENDA::P76469 (267 letters) >FitnessBrowser__Cup4G11:RR42_RS29120 Length = 255 Score = 210 bits (534), Expect = 3e-59 Identities = 113/246 (45%), Positives = 152/246 (61%), Gaps = 1/246 (0%) Query: 1 MNALLSNPFKERLRKGEVQIGLWLSSTTAYMAEIAATSGYDWLLIDGEHAPNTIQDLYHQ 60 M + L N F+ + + IG W S A EI +G+DWLL+DGEH+PN + Q Sbjct: 1 MPSPLPNRFRADVLAHKRVIGCWCSLGNATTTEILGLAGFDWLLLDGEHSPNDVLTFIPQ 60 Query: 61 LQAVAPYASQPVIRPVEGSKPLIKQVLDIGAQTLLIPMVDTAEQARQVVSATRYPPYGER 120 L A+ S PV+RP LIK++LDIG LIP V++AEQA + VSATRYPP G R Sbjct: 61 LMALQGSVSAPVVRPPANDPVLIKRLLDIGFYNFLIPFVESAEQAGRAVSATRYPPAGVR 120 Query: 121 GVGASVARAARWGRIENYMAQVNDSLCLLVQVESKTALDNLDEILDVEGIDGVFIGPADL 180 GV +S R+ R+G + Y +Q+ND++C+LVQ+ES+ +D DEI V+G+DG+FIGP DL Sbjct: 121 GV-SSAQRSNRYGTVPEYFSQINDNICVLVQIESRKGVDAADEICAVDGVDGIFIGPNDL 179 Query: 181 SASLGYPDNAGHPEVQRIIETSIRRIRAAGKAAGFLAVAPDMAQQCLAWGANFVAVGVDT 240 +A+ G+ N HPEVQ + R AGKA G L A++ L GA+FVAVGVD Sbjct: 180 AAAYGHLGNPNHPEVQAQVARIFAAARRAGKAVGTLTPVEADARRYLDMGASFVAVGVDQ 239 Query: 241 MLYSDA 246 L+ A Sbjct: 240 GLFRTA 245 Lambda K H 0.318 0.134 0.393 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: 177 Number of extensions: 9 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: 267 Length of database: 255 Length adjustment: 25 Effective length of query: 242 Effective length of database: 230 Effective search space: 55660 Effective search space used: 55660 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: 41 (21.7 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