GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LRA4 in Cupriavidus basilensis 4G11

Align 2-keto-3-deoxy-L-rhamnonate aldolase; KDR aldolase; EC 4.1.2.53; 2-dehydro-3-deoxyrhamnonate aldolase (uncharacterized)
to candidate RR42_RS27855 RR42_RS27855 4-hydroxy-2-oxo-heptane-1,7-dioate aldolase

Query= curated2:B5R262
         (267 letters)



>FitnessBrowser__Cup4G11:RR42_RS27855
          Length = 267

 Score =  271 bits (692), Expect = 1e-77
 Identities = 135/257 (52%), Positives = 173/257 (67%)

Query: 7   NPFKEGLRKGDTQIGLWLSSTTSYMAEIAATSGYDWLLIDGEHAPNTVQDLYHQLQAIAP 66
           N FK  L   + QIGLWL   + Y AE+ A +G+DWLLIDGEHAPNTV  +  QLQA+A 
Sbjct: 6   NTFKRALAANEQQIGLWLGLASPYTAEVLAGAGFDWLLIDGEHAPNTVPTILAQLQALAA 65

Query: 67  YASQPVIRPIEGSKALIKQVLDIGAQTLLIPMVDTAEQARQVVSATRYPPLGQRGVGASV 126
           Y  +PV+R        IKQ+LD+G QTLL+PMV  A +A   V+ATRYPP G RGVG+++
Sbjct: 66  YPVRPVVRASWNDTVQIKQLLDLGVQTLLVPMVQDATEAAAAVAATRYPPQGVRGVGSAM 125

Query: 127 ARAARWGRIDNYMAQANESLCLLVQVESKVALENLDAILEVEGIDGVFIGPADLSASLGY 186
           ARA+RW R+  Y+AQAN  +C+LVQVE++  L +LDAI   EG+DGVFIGPADL+A +G+
Sbjct: 126 ARASRWNRVGGYLAQANGEMCVLVQVETRAGLAHLDAIAATEGVDGVFIGPADLAADMGH 185

Query: 187 PDNAGHPEVQRIIESCIYRIRAAGKAAGFLAVDPAMAQKCLAWGANFVAVGVDTMLYTEA 246
             N GHPEV+  I   I RIR AGK AG L+ D A +++ +A G  F AVGVD  +   A
Sbjct: 186 LGNPGHPEVRSAIADAIVRIRRAGKGAGILSADVAQSRQYVALGTTFTAVGVDATMLARA 245

Query: 247 LDSRLAMFKSVQSVSTA 263
            +S  A FK   S  T+
Sbjct: 246 AESLAAQFKGHGSAGTS 262


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: 10
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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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