Align 2-keto-3-deoxy-L-rhamnonate aldolase; KDR aldolase; EC 4.1.2.53; 2-dehydro-3-deoxyrhamnonate aldolase (uncharacterized)
to candidate Ac3H11_3372 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase (EC 4.1.2.n4)
Query= curated2:B5R262 (267 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3372 Length = 277 Score = 278 bits (712), Expect = 7e-80 Identities = 148/269 (55%), Positives = 185/269 (68%), Gaps = 9/269 (3%) Query: 6 SNPFKEGLRKGDTQIGLWLSSTTSYMAEIAATSGYDWLLIDGEHAPNTVQDLYHQLQAIA 65 +N FK+ L +G+ QIGLWL +Y AEI A +GYDWLL+DGEHAPN ++ + HQLQAIA Sbjct: 5 TNSFKQALAQGEAQIGLWLGLADAYTAEILAGTGYDWLLVDGEHAPNDLRSILHQLQAIA 64 Query: 66 PY---------ASQPVIRPIEGSKALIKQVLDIGAQTLLIPMVDTAEQARQVVSATRYPP 116 AS V R G ALIKQ LDIGAQTLL+PMVDT EQA+Q+V ATRY P Sbjct: 65 SASSALPPGARASHAVARVPVGDTALIKQYLDIGAQTLLVPMVDTPEQAQQLVRATRYAP 124 Query: 117 LGQRGVGASVARAARWGRIDNYMAQANESLCLLVQVESKVALENLDAILEVEGIDGVFIG 176 G RG+G+++AR++RW Y+ +AN+ +CLLVQ E+ A+ +LDAI G+DGVFIG Sbjct: 125 EGVRGMGSALARSSRWQAYPRYVHEANQQICLLVQAETVEAMAHLDAIAATPGVDGVFIG 184 Query: 177 PADLSASLGYPDNAGHPEVQRIIESCIYRIRAAGKAAGFLAVDPAMAQKCLAWGANFVAV 236 PADLSAS+G+P N GHP+VQ I I RI AGKA G LA + A A++ LA GA FVAV Sbjct: 185 PADLSASMGHPGNPGHPDVQAAIHDGIARILRAGKAPGILATNEAQARQWLAAGALFVAV 244 Query: 237 GVDTMLYTEALDSRLAMFKSVQSVSTAKR 265 GVDTML T A + LA F++ + A R Sbjct: 245 GVDTMLLTSAAQNLLARFRTGPDAAAAPR 273 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: 214 Number of extensions: 13 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: 277 Length adjustment: 25 Effective length of query: 242 Effective length of database: 252 Effective search space: 60984 Effective search space used: 60984 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