Align 2-keto-3-deoxy-L-rhamnonate aldolase (EC 4.1.2.53) (characterized)
to candidate 3609200 Dshi_2586 HpcH/HpaI aldolase (RefSeq)
Query= BRENDA::P76469 (267 letters) >FitnessBrowser__Dino:3609200 Length = 251 Score = 100 bits (248), Expect = 4e-26 Identities = 70/230 (30%), Positives = 111/230 (48%), Gaps = 9/230 (3%) Query: 9 FKERLRKGEVQIGLWLSSTTAYMAEIAATSGYDWLLIDGEHAPNTIQDLYHQLQAVAPYA 68 F+ R+ GE+ G ++ + M E+ A SG D+ +D EHAP + L Sbjct: 4 FRTRMLAGEMLAGTFVKTPAIEMVEVLALSGLDFACLDAEHAPFDRGRIDACLALGLALG 63 Query: 69 SQPVIRPVEGSKPLIKQVLDIGAQTLLIPMVDTAEQARQVVSATRYPPYGERGVGASVAR 128 ++R E + P + Q LD GA +++P VD+A A ++ A RY +G RG S Sbjct: 64 FPLLVRVAEATPPALMQALDAGAAGVVVPHVDSAAAAARIAKACRYG-HGGRGFAGSTRS 122 Query: 129 AARWGRIENYMAQVNDSLCLLVQVESKTALDNLDEILDVEGIDGVFIGPADLSASLGYPD 188 A R + ++ Q+E +D + I G+DG+F+GPADLS S G D Sbjct: 123 AGYGTRGMGDVLSDGPKPLVIAQIEDPEGVDACEGIAATPGVDGIFLGPADLSVSHGKMD 182 Query: 189 NAGHPEVQRIIETSIRRIRAAGKAAG--FLAVAPDMAQQCLAWGANFVAV 236 PE+ I+ R+ AA A+G ++ PD+ ++ AW A+ +V Sbjct: 183 QTS-PELMAAID----RVGAACAASGKPYMTFTPDV-EKAAAWRAHGFSV 226 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: 146 Number of extensions: 7 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: 267 Length of database: 251 Length adjustment: 24 Effective length of query: 243 Effective length of database: 227 Effective search space: 55161 Effective search space used: 55161 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