Align 2-keto-3-deoxy-L-rhamnonate aldolase (EC 4.1.2.53) (characterized)
to candidate WP_012049283.1 SWIT_RS15600 4-hydroxy-2-oxoheptanedioate aldolase
Query= BRENDA::P76469 (267 letters) >NCBI__GCF_000016765.1:WP_012049283.1 Length = 263 Score = 253 bits (646), Expect = 3e-72 Identities = 126/253 (49%), Positives = 169/253 (66%) Query: 7 NPFKERLRKGEVQIGLWLSSTTAYMAEIAATSGYDWLLIDGEHAPNTIQDLYHQLQAVAP 66 N FK L + VQIGLW + Y AEI A +G+DWLL+DGEHAPN + L QLQAVA Sbjct: 2 NDFKTALLQDRVQIGLWQALANPYTAEICAGAGFDWLLLDGEHAPNDLPLLLAQLQAVAA 61 Query: 67 YASQPVIRPVEGSKPLIKQVLDIGAQTLLIPMVDTAEQARQVVSATRYPPYGERGVGASV 126 Y +PV+R G L+KQ+LDIGA++LL+PMV++A QA +V ATRYPP G RGVG+++ Sbjct: 62 YPVEPVVRLPTGDAVLVKQMLDIGARSLLVPMVESAAQAEAMVRATRYPPQGTRGVGSAI 121 Query: 127 ARAARWGRIENYMAQVNDSLCLLVQVESKTALDNLDEILDVEGIDGVFIGPADLSASLGY 186 RA+RW R NY+ + D +CL+VQ+ES AL L I ++ G+DG+FIGP+DL+ASLG+ Sbjct: 122 GRASRWNRTHNYLNEAEDEICLMVQIESAAALAALPSIAELPGVDGIFIGPSDLAASLGH 181 Query: 187 PDNAGHPEVQRIIETSIRRIRAAGKAAGFLAVAPDMAQQCLAWGANFVAVGVDTMLYSDA 246 + GH VQR IE +I +R + KA G LA +A++ L GA FVAVG D L + Sbjct: 182 LGDPGHAAVQRAIERAIATVRTSAKAVGILAADEGLARRYLELGATFVAVGTDVTLLARG 241 Query: 247 LDQRLAMFKSGKN 259 + FK G++ Sbjct: 242 AEALARRFKGGRD 254 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: 159 Number of extensions: 3 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: 263 Length adjustment: 25 Effective length of query: 242 Effective length of database: 238 Effective search space: 57596 Effective search space used: 57596 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