Align 2-keto-3-deoxy-L-rhamnonate aldolase (EC 4.1.2.53) (characterized)
to candidate BWI76_RS19980 BWI76_RS19980 2-keto-3-deoxy-L-rhamnonate aldolase
Query= BRENDA::P76469 (267 letters) >FitnessBrowser__Koxy:BWI76_RS19980 Length = 267 Score = 446 bits (1146), Expect = e-130 Identities = 223/267 (83%), Positives = 241/267 (90%) Query: 1 MNALLSNPFKERLRKGEVQIGLWLSSTTAYMAEIAATSGYDWLLIDGEHAPNTIQDLYHQ 60 MNA+LSNPFK L +GE QIGLWLSST++YMAEIAATSGYDWLLIDGEHAPNTIQDLYHQ Sbjct: 1 MNAILSNPFKAGLLQGEAQIGLWLSSTSSYMAEIAATSGYDWLLIDGEHAPNTIQDLYHQ 60 Query: 61 LQAVAPYASQPVIRPVEGSKPLIKQVLDIGAQTLLIPMVDTAEQARQVVSATRYPPYGER 120 LQA+APY SQPVIRPVEG++ LIKQVLDIGA+TLLIPMVDTAEQAR++VSATRYPP G R Sbjct: 61 LQAIAPYVSQPVIRPVEGNRSLIKQVLDIGARTLLIPMVDTAEQAREIVSATRYPPVGTR 120 Query: 121 GVGASVARAARWGRIENYMAQVNDSLCLLVQVESKTALDNLDEILDVEGIDGVFIGPADL 180 GVGA VARAARWGR+ENYMAQ ND LCLL+QVESKTALDNLD IL+VEGIDGVFIGPADL Sbjct: 121 GVGAGVARAARWGRVENYMAQANDELCLLIQVESKTALDNLDAILEVEGIDGVFIGPADL 180 Query: 181 SASLGYPDNAGHPEVQRIIETSIRRIRAAGKAAGFLAVAPDMAQQCLAWGANFVAVGVDT 240 SASLGYPDNAGHP+VQRIIE SIRRIRAAGKAAGFLAV P+MA + LAWGANFVAVGVDT Sbjct: 181 SASLGYPDNAGHPDVQRIIEQSIRRIRAAGKAAGFLAVDPEMAHKALAWGANFVAVGVDT 240 Query: 241 MLYSDALDQRLAMFKSGKNGPRIKGSY 267 LY+ ALD+RLAMFK KGSY Sbjct: 241 NLYTRALDKRLAMFKPIAEQAEGKGSY 267 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: 300 Number of extensions: 9 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: 267 Length adjustment: 25 Effective length of query: 242 Effective length of database: 242 Effective search space: 58564 Effective search space used: 58564 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