GapMind for catabolism of small carbon sources

 

Alignments for a candidate for garR in Pseudomonas fluorescens FW300-N1B4

Align 2-hydroxy-3-oxopropionate reductase; EC 1.1.1.60; Tartronate semialdehyde reductase; TSAR (uncharacterized)
to candidate Pf1N1B4_1220 2-hydroxy-3-oxopropionate reductase (EC 1.1.1.60)

Query= curated2:P77161
         (292 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1220
          Length = 291

 Score =  118 bits (295), Expect = 2e-31
 Identities = 85/282 (30%), Positives = 139/282 (49%), Gaps = 5/282 (1%)

Query: 1   MKLGFIGLGIMGTPMAINLARAGHQLHVTTIGPVA-DELLSLGAVSVETARQVTEASDII 59
           M+LGFIGLG MG PM +NL +AGH++ V        DEL   GA  V++     +A +++
Sbjct: 1   MELGFIGLGTMGVPMVLNLLKAGHRVKVWNRSSAPLDELARAGAQPVDSPALAAQA-EVL 59

Query: 60  FIMVPDTPQVEEVLFGENGCTKASLKGKTIVDMSSISPIETKRFARQVNELGGDYLDAPV 119
             M+ D   +  V     G    +  G   V+MS++S    K FA    E    Y+ APV
Sbjct: 60  ISMLGDDVAIRSVFIDGKGLDGLAA-GSVHVNMSTVSVALAKEFAALHTERDVAYVSAPV 118

Query: 120 SGGEIGAREGTLSIMVGGDEAVFERVKPLFELLGKNITLVGGNGD-GQTCKVANQIIVAL 178
            G    A  G L+I+  G      RV+PLF++LG+     G   +     K++  +++A 
Sbjct: 119 LGRVDVAAAGNLNILASGPAQALARVQPLFDVLGRKTWPFGECAELACVAKLSANLMIAS 178

Query: 179 NIEAVSEALLFASKAGADPVRVRQALMGGFASSRILEVHGERMIKRTFNP-GFKIALHQK 237
            IE++++A   AS  G       + +        + + +G+ MI + F P GFK++L  K
Sbjct: 179 AIESMAQASTLASSYGISRATFIEMITSTLFPVPVYQGYGQLMIDKHFEPAGFKLSLGLK 238

Query: 238 DLNLALQSAKALALNLPNTATCQELFNTCAANGGSQLDHSAL 279
           D+ LAL++ +A  + LP  +  ++      A+G    D ++L
Sbjct: 239 DIRLALEAGEAAQVPLPFASVLKDNLLDGMAHGQGDQDWASL 280


Lambda     K      H
   0.318    0.135    0.376 

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: 171
Number of extensions: 10
Number of successful extensions: 3
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: 292
Length of database: 291
Length adjustment: 26
Effective length of query: 266
Effective length of database: 265
Effective search space:    70490
Effective search space used:    70490
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: 48 (23.1 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