Align 2-keto-3-deoxy-L-rhamnonate aldolase (EC 4.1.2.53) (characterized)
to candidate WP_086509089.1 BZY95_RS06135 2-dehydro-3-deoxyglucarate aldolase
Query= BRENDA::P76469 (267 letters) >NCBI__GCF_002151265.1:WP_086509089.1 Length = 256 Score = 281 bits (718), Expect = 1e-80 Identities = 132/241 (54%), Positives = 179/241 (74%) Query: 7 NPFKERLRKGEVQIGLWLSSTTAYMAEIAATSGYDWLLIDGEHAPNTIQDLYHQLQAVAP 66 N FK RL GE G+WL + Y+AE+AAT+G+DWLL+DGEHAPN + L QLQA+AP Sbjct: 6 NDFKRRLLSGEPLTGIWLGLASPYVAELAATAGFDWLLLDGEHAPNDLASLLGQLQAIAP 65 Query: 67 YASQPVIRPVEGSKPLIKQVLDIGAQTLLIPMVDTAEQARQVVSATRYPPYGERGVGASV 126 YASQPV+RP G L+KQ LDIGA LLIPMV+TA+QA ++V+ATRYPP+G RG+G+ + Sbjct: 66 YASQPVVRPPHGDAALLKQYLDIGAHNLLIPMVETADQAAELVAATRYPPHGVRGMGSML 125 Query: 127 ARAARWGRIENYMAQVNDSLCLLVQVESKTALDNLDEILDVEGIDGVFIGPADLSASLGY 186 ARA+RWG++E+Y+A+ +D +CL++Q+ES AL NL+ I VEG+D +F+GPADL A++G+ Sbjct: 126 ARASRWGQVEDYVARADDEICLILQLESPRALANLEAIAAVEGVDALFVGPADLCAAMGH 185 Query: 187 PDNAGHPEVQRIIETSIRRIRAAGKAAGFLAVAPDMAQQCLAWGANFVAVGVDTMLYSDA 246 N GHP+V+ I+ ++ RIRAAG AG L + A LA G FV VG+D +L + A Sbjct: 186 RGNPGHPQVRATIDDALDRIRAAGSVAGILTLDEQQAHDYLAAGCGFVGVGIDALLLAQA 245 Query: 247 L 247 L Sbjct: 246 L 246 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: 198 Number of extensions: 6 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: 267 Length of database: 256 Length adjustment: 25 Effective length of query: 242 Effective length of database: 231 Effective search space: 55902 Effective search space used: 55902 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 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