GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gyaR in Shewanella oneidensis MR-1

Align Glyoxylate reductase; EC 1.1.1.26 (characterized)
to candidate 200048 SO0862 D-3-phosphoglycerate dehydrogenase (NCBI ptt file)

Query= SwissProt::Q9C4M5
         (331 letters)



>FitnessBrowser__MR1:200048
          Length = 409

 Score =  156 bits (395), Expect = 7e-43
 Identities = 103/328 (31%), Positives = 164/328 (50%), Gaps = 18/328 (5%)

Query: 2   KPKVFITRQIPENGIKMIEK--FYEIELWKDPKAPPRGVLLEKVREVDALVTLVTDKVDK 59
           K K+ +   + ++ + + E+  +  IE  K         L E +++   +      ++  
Sbjct: 10  KIKILLLEGVHQSAVDVFERAGYTNIEYHKASLGDE--ALHESIKDAHFIGIRSRTQLSA 67

Query: 60  ELLENAPKLKIIAQYAVGYDNIDIEEATKRGIYVTNTPGVLTDATADLAFALLLAVARRI 119
           ++L+ A KL  I  + +G + +D+  A   GI V N P   T + A+L    ++ + R I
Sbjct: 68  DVLKRAEKLIAIGCFCIGTNQVDLATAESLGIPVFNAPFSNTRSVAELVLGEIIMLMRGI 127

Query: 120 VEADAFVRSGEWKKSEVGWHPLMFLGYGLKGKTLGIVGFGRIGQALAKRAKGFGMKIIYY 179
            E +A    G W K+  G        Y ++GKTLG++G+G IG  L   A+  GM+++++
Sbjct: 128 PERNAIAHRGGWMKTAAG-------SYEVRGKTLGVIGYGHIGTQLGILAETLGMRVVFF 180

Query: 180 SRTRKPEAEEEIGAEYVDFETLLKESDFISLHVPLTKETYHMIGEKELKLMKPNAILINT 239
               K         +    E LL ++D +SLHVP T +T  MI   E   M+  +I IN 
Sbjct: 181 DIEDKLPLGN--AQQIHSMEQLLAQADVVSLHVPETPQTKDMISTAEFAAMRKGSIFINA 238

Query: 240 SRGAVVDTNALIKALKEGWIAGAGLDVFEEEPYYNEELF-----KLKNVVLAPHIGSATH 294
           SRG VVD +AL  ALKE  +AGA +DVF  EP  N++ F      L NV+L PH+G +T 
Sbjct: 239 SRGTVVDIDALTVALKERHLAGAAIDVFPVEPQSNDDEFISPLRGLDNVLLTPHVGGSTA 298

Query: 295 EAREGMAELVAKNLIAFAKGEIPPNLVN 322
           EA+E +   VA  L  ++      + VN
Sbjct: 299 EAQENIGIEVAGKLAKYSDNGSTVSAVN 326


Lambda     K      H
   0.317    0.137    0.392 

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: 280
Number of extensions: 18
Number of successful extensions: 4
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: 331
Length of database: 409
Length adjustment: 30
Effective length of query: 301
Effective length of database: 379
Effective search space:   114079
Effective search space used:   114079
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 (21.6 bits)
S2: 49 (23.5 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