GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gyaR in Synechococcus elongatus PCC 7942

Align Glyoxylate reductase; EC 1.1.1.26 (uncharacterized)
to candidate Synpcc7942_1501 Synpcc7942_1501 D-3-phosphoglycerate dehydrogenase

Query= curated2:B1L765
         (332 letters)



>FitnessBrowser__SynE:Synpcc7942_1501
          Length = 546

 Score =  200 bits (508), Expect = 8e-56
 Identities = 111/305 (36%), Positives = 184/305 (60%), Gaps = 8/305 (2%)

Query: 3   PRVFVTREIPERGLSKIEEHFELDLWKDEAPPSKKVIIERVKDCDALVSLLTDPIDAEVF 62
           P+V V+  I + GL  + +  ++D+ K    PS+  + + + + DAL+      + AEV 
Sbjct: 19  PKVLVSDPIDQVGLDILSQVAQVDV-KTGLSPSE--LAQIIGEYDALMLRSGTRVTAEVI 75

Query: 63  EAAPKLRIVAQYAVGYDNIDVKEATKRGIYVTNTPGVLTETTADFAFALLMAAARRVVEA 122
           EA  KLRI+ +  VG DN+DV  AT+RGI V N+P   T   A+   A++++ +R + +A
Sbjct: 76  EAGQKLRIIGRAGVGVDNVDVPAATRRGIVVVNSPEGNTIAAAEHTLAMMLSLSRHIPDA 135

Query: 123 DRYVREGKWKVAWHPMMMLGYDVYGRTLGIVGMGRIGAAVARRAKGFGMRILYYDSIRRE 182
           +   + G     W     +G +VY +TLG+VG+G+IG+ VA  AK  GM++L YD     
Sbjct: 136 NASTKSG----GWDRKSFVGTEVYKKTLGVVGLGKIGSHVATVAKAMGMKLLAYDPFISA 191

Query: 183 DFEKELGVEYVPLEKLLEESDFVSLHVPLTEETYHMIGEEQLRRMKRTAILVNTSRGKVV 242
           +  +++G   V L+ L +E+D+++LH+P T ET ++I  E L +MK T  ++N +RG V+
Sbjct: 192 ERAEQIGARLVELDILFQEADYITLHIPKTPETANLINAETLAKMKPTTRIINCARGGVI 251

Query: 243 DQKALYKALKEGWIAGAGLDVFEQEPIPPDDPLLKL-ENVVLAPHAASASHETRSRMAEM 301
           +++AL  A+  G I GA LDV++QEP+  D PL  L +N++L PH  +++ E +  +A  
Sbjct: 252 NEQALADAIAAGKIGGAALDVYDQEPLQADSPLRALGKNLILTPHLGASTTEAQVNVAVD 311

Query: 302 VAENL 306
           VAE +
Sbjct: 312 VAEQI 316


Lambda     K      H
   0.319    0.137    0.398 

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: 412
Number of extensions: 19
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: 332
Length of database: 546
Length adjustment: 32
Effective length of query: 300
Effective length of database: 514
Effective search space:   154200
Effective search space used:   154200
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (24.3 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