GapMind for catabolism of small carbon sources

 

Alignments for a candidate for garR in Pseudomonas fluorescens FW300-N2C3

Align 2-hydroxy-3-oxopropionate reductase (EC 1.1.1.60) (characterized)
to candidate AO356_07865 AO356_07865 3-hydroxyisobutyrate dehydrogenase

Query= BRENDA::Q8ZLV8
         (296 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_07865
          Length = 295

 Score =  181 bits (458), Expect = 2e-50
 Identities = 99/293 (33%), Positives = 157/293 (53%), Gaps = 7/293 (2%)

Query: 3   MKVGFIGLGIMGKPMSKNLLKAGYSLVVSDRNPEAIADVIAAGAETASTAKAIAEQCDVI 62
           M + FIGLG MG PM++NLLKAG+SL + D N   +A++ A G   +++ +  A+   ++
Sbjct: 1   MNIAFIGLGNMGAPMARNLLKAGHSLNLFDLNQTVLAELAALGGTVSASPRDAAQGAALV 60

Query: 63  ITMLPNSPHVKEVALGENGIIEGAKPGTVLIDMSSIAPLASREISDALKAKGVEMLDAPV 122
           ITMLP + HV+ V LGE+G++ G   GT  +D S+I P  +R+++ A   +GV M DAPV
Sbjct: 61  ITMLPAAAHVRSVWLGEDGVLAGIAAGTPAVDCSTIDPQTARDVAAAAAKQGVAMADAPV 120

Query: 123 SGGEPKAIDGTLSVMVGGDKAIFDKYYDLMKAMAGSVVHTGDIGAGNVTKLANQVIVALN 182
           SGG   A  GTL+ MVG    +F     ++  M  ++VH G++G G + K+ N +++ ++
Sbjct: 121 SGGTGGAAAGTLTFMVGATAELFATLQPVLAQMGRNIVHCGEVGTGQIAKICNNLLLGIS 180

Query: 183 IAAMSEALTLATKAGVNPDLVYQAIRGGLAGSTVLDAKAP-------MVMDRNFKPGFRI 235
           +  +SEA+ L    G++  ++   I          D   P           R +  GF  
Sbjct: 181 MVGVSEAMALGDALGIDTQVLAGIINSSTGRCWSSDTYNPWPGVIETAPASRGYTGGFGA 240

Query: 236 DLHIKDLANALDTSHGVGAQLPLTAAVMEMMQALRADGHGNDDHSALACYYEK 288
           DL +KDL  A + +      + L A   ++ QA+   G G  D SA+   Y K
Sbjct: 241 DLMLKDLGLATEAARQAHQPVVLGAVAQQLYQAMSQRGEGGKDFSAIVNSYRK 293


Lambda     K      H
   0.316    0.132    0.367 

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: 227
Number of extensions: 7
Number of successful extensions: 2
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: 296
Length of database: 295
Length adjustment: 26
Effective length of query: 270
Effective length of database: 269
Effective search space:    72630
Effective search space used:    72630
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