Align 2-keto-3-deoxy-L-rhamnonate aldolase (EC 4.1.2.53) (characterized)
to candidate BPHYT_RS24135 BPHYT_RS24135 alpha-dehydro-beta-deoxy-D-glucarate aldolase
Query= BRENDA::P76469 (267 letters) >FitnessBrowser__BFirm:BPHYT_RS24135 Length = 266 Score = 193 bits (490), Expect = 4e-54 Identities = 100/242 (41%), Positives = 144/242 (59%), Gaps = 1/242 (0%) Query: 5 LSNPFKERLRKGEVQIGLWLSSTTAYMAEIAATSGYDWLLIDGEHAPNTIQDLYHQLQAV 64 L N F+ + GE IG W S + + E+ G+DW+L+D EHAPN + L QL A+ Sbjct: 10 LPNSFRRAVCGGETLIGCWASLASPIVTELLGIVGFDWMLLDAEHAPNDVLTLIPQLMAL 69 Query: 65 APYASQPVIRPVEGSKPLIKQVLDIGAQTLLIPMVDTAEQARQVVSATRYPPYGERGVGA 124 AS PV+RP IK++LD G L+P V++A+ A + V+ATRYPP G RGV Sbjct: 70 KDSASAPVVRPPANDSVFIKRLLDSGFSNFLVPFVESADDAARAVAATRYPPQGIRGVSV 129 Query: 125 SVARAARWGRIENYMAQVNDSLCLLVQVESKTALDNLDEILDVEGIDGVFIGPADLSASL 184 S R + + +Y + ND++C++VQ+ES+ A+D +DEIL V+G+D VF+GP+DL+A+ Sbjct: 130 S-HRGNHYATVPDYFSVANDNVCVIVQIESRKAVDAIDEILAVDGVDAVFVGPSDLAAAY 188 Query: 185 GYPDNAGHPEVQRIIETSIRRIRAAGKAAGFLAVAPDMAQQCLAWGANFVAVGVDTMLYS 244 G NA H +VQ I R +AAGK +G LA A++ ++ G VAV D L Sbjct: 189 GQLGNANHSDVQAAIAHVFERAQAAGKPSGILAPVQADAERYISMGCRVVAVCADMGLLK 248 Query: 245 DA 246 A Sbjct: 249 GA 250 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: 174 Number of extensions: 6 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: 266 Length adjustment: 25 Effective length of query: 242 Effective length of database: 241 Effective search space: 58322 Effective search space used: 58322 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