GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LRA4 in Burkholderia phytofirmans PsJN

Align 2-keto-3-deoxy-L-rhamnonate aldolase (EC 4.1.2.53) (characterized)
to candidate BPHYT_RS24135 BPHYT_RS24135 alpha-dehydro-beta-deoxy-D-glucarate aldolase

Query= BRENDA::P76469
         (267 letters)



>FitnessBrowser__BFirm:BPHYT_RS24135
          Length = 266

 Score =  193 bits (490), Expect = 4e-54
 Identities = 100/242 (41%), Positives = 144/242 (59%), Gaps = 1/242 (0%)

Query: 5   LSNPFKERLRKGEVQIGLWLSSTTAYMAEIAATSGYDWLLIDGEHAPNTIQDLYHQLQAV 64
           L N F+  +  GE  IG W S  +  + E+    G+DW+L+D EHAPN +  L  QL A+
Sbjct: 10  LPNSFRRAVCGGETLIGCWASLASPIVTELLGIVGFDWMLLDAEHAPNDVLTLIPQLMAL 69

Query: 65  APYASQPVIRPVEGSKPLIKQVLDIGAQTLLIPMVDTAEQARQVVSATRYPPYGERGVGA 124
              AS PV+RP       IK++LD G    L+P V++A+ A + V+ATRYPP G RGV  
Sbjct: 70  KDSASAPVVRPPANDSVFIKRLLDSGFSNFLVPFVESADDAARAVAATRYPPQGIRGVSV 129

Query: 125 SVARAARWGRIENYMAQVNDSLCLLVQVESKTALDNLDEILDVEGIDGVFIGPADLSASL 184
           S  R   +  + +Y +  ND++C++VQ+ES+ A+D +DEIL V+G+D VF+GP+DL+A+ 
Sbjct: 130 S-HRGNHYATVPDYFSVANDNVCVIVQIESRKAVDAIDEILAVDGVDAVFVGPSDLAAAY 188

Query: 185 GYPDNAGHPEVQRIIETSIRRIRAAGKAAGFLAVAPDMAQQCLAWGANFVAVGVDTMLYS 244
           G   NA H +VQ  I     R +AAGK +G LA     A++ ++ G   VAV  D  L  
Sbjct: 189 GQLGNANHSDVQAAIAHVFERAQAAGKPSGILAPVQADAERYISMGCRVVAVCADMGLLK 248

Query: 245 DA 246
            A
Sbjct: 249 GA 250


Lambda     K      H
   0.318    0.134    0.393 

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: 174
Number of extensions: 6
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: 266
Length adjustment: 25
Effective length of query: 242
Effective length of database: 241
Effective search space:    58322
Effective search space used:    58322
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