GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LRA4 in Pseudomonas fluorescens FW300-N2C3

Align 2-keto-3-deoxy-L-rhamnonate aldolase; KDR aldolase; EC 4.1.2.53; 2-dehydro-3-deoxyrhamnonate aldolase (uncharacterized)
to candidate AO356_25560 AO356_25560 2-keto-3-deoxy-L-rhamnonate aldolase

Query= curated2:B5R262
         (267 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_25560
          Length = 265

 Score =  306 bits (783), Expect = 4e-88
 Identities = 151/249 (60%), Positives = 187/249 (75%)

Query: 7   NPFKEGLRKGDTQIGLWLSSTTSYMAEIAATSGYDWLLIDGEHAPNTVQDLYHQLQAIAP 66
           N FK+ LR G+ QIGLWL    +Y AE+AA +G+DWLLIDGEHAPN ++ L  QLQA+AP
Sbjct: 6   NTFKQRLRSGEAQIGLWLGLADAYCAELAANAGFDWLLIDGEHAPNDLRTLLGQLQAVAP 65

Query: 67  YASQPVIRPIEGSKALIKQVLDIGAQTLLIPMVDTAEQARQVVSATRYPPLGQRGVGASV 126
           Y  QPVIRP+ G  ALIKQVLDIG QTLL+PMV++AEQAR++V A  YPP G RGVG+++
Sbjct: 66  YPGQPVIRPVVGDTALIKQVLDIGVQTLLVPMVESAEQARELVRAIHYPPQGVRGVGSAL 125

Query: 127 ARAARWGRIDNYMAQANESLCLLVQVESKVALENLDAILEVEGIDGVFIGPADLSASLGY 186
           ARA+RW  I  Y+ +A+E +CLLVQ+ES+  L NLDAI  VEG+DGVFIGPADLSAS+G+
Sbjct: 126 ARASRWNSIPGYLDKADEQMCLLVQIESREGLANLDAIAAVEGVDGVFIGPADLSASMGF 185

Query: 187 PDNAGHPEVQRIIESCIYRIRAAGKAAGFLAVDPAMAQKCLAWGANFVAVGVDTMLYTEA 246
             N GHP+VQ  IE  I RIR AGKAAG L+ D  +A++ +  GA FVAVGVDT +    
Sbjct: 186 RGNPGHPQVQAAIEDAIARIRQAGKAAGILSADEKLARRYIELGAAFVAVGVDTTVLMRG 245

Query: 247 LDSRLAMFK 255
           L +  A FK
Sbjct: 246 LQTLAATFK 254


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: 225
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: 265
Length adjustment: 25
Effective length of query: 242
Effective length of database: 240
Effective search space:    58080
Effective search space used:    58080
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