GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LRA4 in Rhizobium leguminosarum bv. trifolii WSM1325

Align 2-keto-3-deoxy-L-rhamnonate aldolase; KDR aldolase; EC 4.1.2.53; 2-dehydro-3-deoxyrhamnonate aldolase (uncharacterized)
to candidate WP_012763251.1 RLEG_RS27370 aldolase/citrate lyase family protein

Query= curated2:B5R262
         (267 letters)



>NCBI__GCF_000023185.1:WP_012763251.1
          Length = 263

 Score =  120 bits (300), Expect = 4e-32
 Identities = 76/226 (33%), Positives = 118/226 (52%), Gaps = 8/226 (3%)

Query: 20  IGLWLSSTTSYMAEIAATSGYDWLLIDGEHAPNTVQDLYHQLQAIAPY--ASQPVIRPIE 77
           I  W+    + +A   A   +D +++D +H    + D+     A+A    A +P +  I 
Sbjct: 21  ISAWIGIPDATLANHLAQEAFDAIVLDMQHG---MWDMPSAANAVAQVRLAGKPALARIP 77

Query: 78  -GSKALIKQVLDIGAQTLLIPMVDTAEQARQVVSATRYPPLGQRGVGASVARAARWGRID 136
            G  A   ++LD GA  ++ PM+++AE A+  V AT+YPPLG+R  G S+A        D
Sbjct: 78  VGDFASASRLLDAGASGIIAPMINSAEDAQAFVKATKYPPLGERSWGPSLALNHTGLSAD 137

Query: 137 NYMAQANESLCLLVQVESKVALENLDAILEVEGIDGVFIGPADLSASLGYPDNA--GHPE 194
           +Y+  AN     +  +E++ ALE +D IL V GIDG+FIGP+DLS +L   D       E
Sbjct: 138 DYLKNANALTVAIAMIETRAALEAIDDILGVAGIDGIFIGPSDLSIALSNGDQVAPNAAE 197

Query: 195 VQRIIESCIYRIRAAGKAAGFLAVDPAMAQKCLAWGANFVAVGVDT 240
           +   ++  + R RA GK A   A D   A + L +G + V  G +T
Sbjct: 198 IDSAMQHAVSRCRAHGKVACAFAGDGERAGELLKFGFDLVIAGAET 243


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: 141
Number of extensions: 3
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: 263
Length adjustment: 25
Effective length of query: 242
Effective length of database: 238
Effective search space:    57596
Effective search space used:    57596
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 Apr 09 2024. 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