Align 2-keto-3-deoxy-L-rhamnonate aldolase; KDR aldolase; EC 4.1.2.53; 2-dehydro-3-deoxyrhamnonate aldolase (uncharacterized)
to candidate Ac3H11_1482 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase (EC 4.1.2.n4)
Query= curated2:B5R262 (267 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1482 Length = 274 Score = 264 bits (675), Expect = 1e-75 Identities = 132/242 (54%), Positives = 170/242 (70%) Query: 1 MNALLSNPFKEGLRKGDTQIGLWLSSTTSYMAEIAATSGYDWLLIDGEHAPNTVQDLYHQ 60 M + +N F+ LR+G QIGLW+ + AE A G+DWLL+DGEHAPN V+ + Q Sbjct: 1 MMQIPNNRFRNALREGQPQIGLWVGLADANAAEALAGCGFDWLLLDGEHAPNDVRSVLDQ 60 Query: 61 LQAIAPYASQPVIRPIEGSKALIKQVLDIGAQTLLIPMVDTAEQARQVVSATRYPPLGQR 120 L+A+APY + PV+RP++ AL+KQ LD+GAQTLLIPMVDT EQA +V A RY P G R Sbjct: 61 LRAVAPYPAHPVVRPVQADVALVKQYLDVGAQTLLIPMVDTPEQAALMVRAMRYAPEGIR 120 Query: 121 GVGASVARAARWGRIDNYMAQANESLCLLVQVESKVALENLDAILEVEGIDGVFIGPADL 180 G+GA++ARA+RW ++++Y+ AN +CLLVQ E+ +A++NL AI +G+DGVF GPADL Sbjct: 121 GMGAALARASRWNQVEDYLNCANGEMCLLVQAETPLAMQNLQAIAATDGVDGVFFGPADL 180 Query: 181 SASLGYPDNAGHPEVQRIIESCIYRIRAAGKAAGFLAVDPAMAQKCLAWGANFVAVGVDT 240 SAS+GY A HP VQR I I +RA GKA G L D +AQ L GA FVAVGVDT Sbjct: 181 SASMGYRGQASHPAVQRAILEGIATVRAVGKAPGILMADRQLAQSYLDAGALFVAVGVDT 240 Query: 241 ML 242 L Sbjct: 241 TL 242 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: 207 Number of extensions: 8 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: 274 Length adjustment: 25 Effective length of query: 242 Effective length of database: 249 Effective search space: 60258 Effective search space used: 60258 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