Align 2-keto-3-deoxy-L-rhamnonate aldolase; KDR aldolase; EC 4.1.2.53; 2-dehydro-3-deoxyrhamnonate aldolase (uncharacterized)
to candidate N515DRAFT_2292 N515DRAFT_2292 4-hydroxy-2-oxoheptanedioate aldolase
Query= curated2:B5R262 (267 letters) >FitnessBrowser__Dyella79:N515DRAFT_2292 Length = 242 Score = 102 bits (254), Expect = 8e-27 Identities = 72/240 (30%), Positives = 115/240 (47%), Gaps = 6/240 (2%) Query: 20 IGLWLSSTTSYMAEIAATSGYDWLLIDGEHAPNTVQDLYHQLQAIAPYASQPVIRPIEGS 79 IGL S + + E+ +GYD++L+D EH + L H ++A P +R E Sbjct: 5 IGLLQSVPSPLLCEMLGHAGYDFVLLDLEHVLLSPDQLQHAIRACELGGCAPWVRVPEVD 64 Query: 80 KALIKQVLDIGAQTLLIPMVDTAEQARQVVSATRYPPLGQRGVGASVARAARWGRIDNYM 139 + LI +VLD GA+ ++I ++T EQA + V+A R+PPLG+RG+ + +Y+ Sbjct: 65 EKLIGRVLDAGARGVVISRLETVEQAERAVAAARFPPLGRRGITGGRVTGFGKTALPDYI 124 Query: 140 AQANESLCLLVQVESKVALENLDAILEVEGIDGVFIGPADLSASLGYPDNAGHPEVQRII 199 QAN + ++ +ES+ + L IL V GI V G DL+ LG H +V + + Sbjct: 125 EQANREIHVVPMIESEAGVRALPQILAVPGISLVMEGALDLALDLGLGPQPLHADVWQRL 184 Query: 200 ESCIYRIRAAGKAAGFLAVDPAMAQKCLAWGA---NFVAVGVDTMLYTEALDSRLAMFKS 256 + AG +P Q+ W A ++ G D L AL R A ++ Sbjct: 185 QDIADCCDTAGIP---FCPNPRNEQQLRYWAAREVRWMLAGEDRGLLLAALRDRAAALRA 241 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: 114 Number of extensions: 4 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: 242 Length adjustment: 24 Effective length of query: 243 Effective length of database: 218 Effective search space: 52974 Effective search space used: 52974 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