Align 2-keto-3-deoxy-L-rhamnonate aldolase (EC 4.1.2.53) (characterized)
to candidate RR42_RS26640 RR42_RS26640 2-keto-3-deoxy-L-rhamnonate aldolase
Query= BRENDA::P76469 (267 letters) >FitnessBrowser__Cup4G11:RR42_RS26640 Length = 267 Score = 281 bits (719), Expect = 1e-80 Identities = 141/248 (56%), Positives = 180/248 (72%) Query: 7 NPFKERLRKGEVQIGLWLSSTTAYMAEIAATSGYDWLLIDGEHAPNTIQDLYHQLQAVAP 66 N FK L + QIGLWLS + Y+AE++AT+G+DWLLIDGEHAPN ++ + LQA+AP Sbjct: 5 NAFKAALAASQPQIGLWLSMASPYLAEVSATAGFDWLLIDGEHAPNDLRGTLNALQAIAP 64 Query: 67 YASQPVIRPVEGSKPLIKQVLDIGAQTLLIPMVDTAEQARQVVSATRYPPYGERGVGASV 126 Y SQPV+R V G PLIKQ+LDIGA+ LL+PMVDTAEQA +V ATRYPP G RGVG++V Sbjct: 65 YRSQPVVRCVAGEVPLIKQLLDIGAKNLLVPMVDTAEQAAALVCATRYPPQGIRGVGSAV 124 Query: 127 ARAARWGRIENYMAQVNDSLCLLVQVESKTALDNLDEILDVEGIDGVFIGPADLSASLGY 186 RA++W +Y+ +D +CLLVQ E+ AL NLD I V+G+DGVFIGPADL+AS+G+ Sbjct: 125 GRASQWSARADYLDVADDEICLLVQAETVKALANLDAICAVDGVDGVFIGPADLAASMGH 184 Query: 187 PDNAGHPEVQRIIETSIRRIRAAGKAAGFLAVAPDMAQQCLAWGANFVAVGVDTMLYSDA 246 N GHPEVQ IE ++R I A+GKAAG L P +A++ L G FVA GVD +LY+ A Sbjct: 185 RGNPGHPEVQAAIEGAMRTIAASGKAAGTLTSDPKLARRYLDLGCTFVATGVDVLLYASA 244 Query: 247 LDQRLAMF 254 + A F Sbjct: 245 ARRLAADF 252 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: 216 Number of extensions: 4 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