Align 2-keto-3-deoxy-L-rhamnonate aldolase; KDR aldolase; EC 4.1.2.53; 2-dehydro-3-deoxyrhamnonate aldolase (uncharacterized)
to candidate H281DRAFT_03252 H281DRAFT_03252 2,4-dihydroxyhept-2-enedioate aldolase (EC 4.1.2.-)
Query= curated2:B5R262 (267 letters) >FitnessBrowser__Burk376:H281DRAFT_03252 Length = 267 Score = 274 bits (700), Expect = 2e-78 Identities = 140/263 (53%), Positives = 179/263 (68%) Query: 3 ALLSNPFKEGLRKGDTQIGLWLSSTTSYMAEIAATSGYDWLLIDGEHAPNTVQDLYHQLQ 62 +L N FK LR+G Q GLW + +Y+ E+ AT+G+DWLLID EHAPN V+ QLQ Sbjct: 2 SLPQNTFKRALREGTPQFGLWAALADAYVTELLATAGFDWLLIDNEHAPNDVRSTLAQLQ 61 Query: 63 AIAPYASQPVIRPIEGSKALIKQVLDIGAQTLLIPMVDTAEQARQVVSATRYPPLGQRGV 122 A+A YAS PV+RP+ ALIKQ+LDIGAQTLL+PM+DTA QA V+ATRYPP G RGV Sbjct: 62 AVAAYASHPVVRPVRSDSALIKQLLDIGAQTLLLPMIDTASQAADAVAATRYPPQGIRGV 121 Query: 123 GASVARAARWGRIDNYMAQANESLCLLVQVESKVALENLDAILEVEGIDGVFIGPADLSA 182 G+++ARA+RW RI +Y+ +A + LC+LVQVE+ + NL AI V+G+DGVF GPADLSA Sbjct: 122 GSALARASRWNRIPDYLTRAADELCVLVQVETVEGMNNLAAIAAVDGVDGVFFGPADLSA 181 Query: 183 SLGYPDNAGHPEVQRIIESCIYRIRAAGKAAGFLAVDPAMAQKCLAWGANFVAVGVDTML 242 S+G G V+ I I +R AGKAAG LA D A+A++ LA GA FVAVG DT L Sbjct: 182 SMGLLGQPGEASVREAIRGGIESVRRAGKAAGVLAPDRAIAEEYLAAGATFVAVGTDTGL 241 Query: 243 YTEALDSRLAMFKSVQSVSTAKR 265 + A A +K+ + R Sbjct: 242 LSRAAADLAASYKNTAGSRVSAR 264 Lambda K H 0.318 0.132 0.384 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: 199 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