GapMind for catabolism of small carbon sources

 

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

Align Glyoxylate reductase; EC 1.1.1.26 (characterized)
to candidate Pf1N1B4_2272 D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95)

Query= SwissProt::Q9C4M5
         (331 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2272
          Length = 409

 Score =  167 bits (423), Expect = 4e-46
 Identities = 102/293 (34%), Positives = 156/293 (53%), Gaps = 14/293 (4%)

Query: 35  PRGVLLEKVREVDALVTLVTDKVDKELLENAPKLKIIAQYAVGYDNIDIEEATKRGIYVT 94
           P   L EK+ +   +      ++ +E+ ++A KL  +  + +G + +D+  A +RGI V 
Sbjct: 43  PEAQLKEKIADAHFIGIRSRTQLTEEIFDHAKKLVAVGCFCIGTNQVDLNAARERGIAVF 102

Query: 95  NTPGVLTDATADLAFALLLAVARRIVEADAFVRSGEWKKSEVGWHPLMFLGYGLKGKTLG 154
           N P   T + A+L  A  + + R I E +A    G W KS           + ++GK LG
Sbjct: 103 NAPYSNTRSVAELVLAEAILLLRGIPEKNASCHRGGWIKSAAN-------SFEIRGKKLG 155

Query: 155 IVGFGRIGQALAKRAKGFGMKIIYYSRTRKPEAEEEIGAEYVDFETLLKESDFISLHVPL 214
           IVG+G IG  L+  A+G GM++ +Y    K         +  +   LL  SD ++LHVP 
Sbjct: 156 IVGYGSIGTQLSVLAEGLGMQVYFYDTVTKLPLGN--ATQVGNLHELLGMSDIVTLHVPE 213

Query: 215 TKETYHMIGEKELKLMKPNAILINTSRGAVVDTNALIKALKEGWIAGAGLDVFEEEPYYN 274
           T  T  MIGEKE++ +K   ILIN +RG VV+ +AL  A+K+  + GA +DVF  EP  N
Sbjct: 214 TAATQWMIGEKEIRAIKKGGILINAARGTVVELDALADAIKDKHLIGAAIDVFPVEPRSN 273

Query: 275 EELFK-----LKNVVLAPHIGSATHEAREGMAELVAKNLIAFAKGEIPPNLVN 322
           EE F+     L NV+L PHIG +T EA+  +   VA+ L+ ++      + VN
Sbjct: 274 EEEFESPLRGLDNVILTPHIGGSTAEAQANIGLEVAEKLVKYSDNGTSVSSVN 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: 308
Number of extensions: 16
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