GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gyaR in Pseudomonas fluorescens FW300-N2E3

Align Glyoxylate reductase; EC 1.1.1.26 (characterized)
to candidate AO353_21585 AO353_21585 hydroxyacid dehydrogenase

Query= SwissProt::Q9C4M5
         (331 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_21585
          Length = 316

 Score =  167 bits (424), Expect = 2e-46
 Identities = 102/269 (37%), Positives = 152/269 (56%), Gaps = 15/269 (5%)

Query: 45  EVDALVTLVTDKVDKELLENAPKLKIIAQYAVGYDNIDIEEATKRGIYVTNTPGVLTDAT 104
           ++DA++T     +  + +     LKII     GY+ +D++ A+ RGI VTN  GV   + 
Sbjct: 45  QIDAVLTRGPLGLYADEIAALANLKIICVIGAGYEQVDLQAASDRGITVTNGAGVNASSV 104

Query: 105 ADLAFALLLAVARRIVEADAFVRSGEWKKSEVGWHPLMFLGYGLKGKTLGIVGFGRIGQA 164
           AD A ALLL++ R I   DA VR GEW K          +   L GK LG++G G +G A
Sbjct: 105 ADHAMALLLSLVRDIPRCDAAVRRGEWPK---------IMRPSLAGKRLGVLGLGAVGMA 155

Query: 165 LAKRA-KGFGMKIIYYSRTRKPEAEEEIGAEYVDFET-LLKESDFISLHVPLTKETYHMI 222
           +AKRA  GF M + Y+SR    +   +I  ++    T L + SDF+ +  P    T H++
Sbjct: 156 IAKRAANGFDMTVSYHSR----QLLSDIPYDFCSTPTELARVSDFLIVCTPGGIGTQHLV 211

Query: 223 GEKELKLMKPNAILINTSRGAVVDTNALIKALKEGWIAGAGLDVFEEEPYYNEELFKLKN 282
            ++ L  + P   ++N +R +VV T+ L+ AL++  IAGA LDVF+EEP   + L  L N
Sbjct: 212 NKQVLDALGPQGFIVNIARASVVATSDLVSALEQRRIAGAALDVFDEEPQVPDALKVLSN 271

Query: 283 VVLAPHIGSATHEAREGMAELVAKNLIAF 311
           V+L PH+   + EA +G  ELV +NL+AF
Sbjct: 272 VILTPHVAGLSPEATKGTVELVGQNLMAF 300


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: 214
Number of extensions: 9
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: 331
Length of database: 316
Length adjustment: 28
Effective length of query: 303
Effective length of database: 288
Effective search space:    87264
Effective search space used:    87264
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: 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