GapMind for catabolism of small carbon sources

 

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

Align 2-hydroxy-3-oxopropionate reductase (EC 1.1.1.60) (characterized)
to candidate Pf1N1B4_5077 D-beta-hydroxybutyrate dehydrogenase (EC 1.1.1.30)

Query= BRENDA::Q8ZLV8
         (296 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5077
          Length = 301

 Score =  168 bits (426), Expect = 1e-46
 Identities = 88/279 (31%), Positives = 153/279 (54%), Gaps = 1/279 (0%)

Query: 5   VGFIGLGIMGKPMSKNLLKAGYSLVVSDRNPEAIADVIAAGAETASTAKAIAEQCDVIIT 64
           VG +GLG MG  ++++LL++G+++   D            G    S+   +A +CDVIIT
Sbjct: 6   VGVVGLGAMGLGIARSLLRSGFNVHACDVRAAVTEQFAGEGGVACSSPAHMAAECDVIIT 65

Query: 65  MLPNSPHVKEVALGENGIIEGAKPGTVLIDMSSIAPLASREISDALKAKGVEMLDAPVSG 124
           ++ N+   + V  GE G +   +PG+++I  +++AP  + ++   L A+G+  LDAP+SG
Sbjct: 66  VVVNAEQTETVLFGEGGAVAALRPGSLVIGCATVAPTYAVDLGQRLTAQGLLYLDAPISG 125

Query: 125 GEPKAIDGTLSVMVGGDKAIFDKYYDLMKAMAGSVVHTGDI-GAGNVTKLANQVIVALNI 183
           G  KA  G +++M  G    + K   ++  MAG V   GD  G G+  K+ NQ++  ++I
Sbjct: 126 GAAKAAAGEMTMMTSGPADAYAKAEAVLAGMAGKVYRLGDTHGLGSKVKIINQLLAGVHI 185

Query: 184 AAMSEALTLATKAGVNPDLVYQAIRGGLAGSTVLDAKAPMVMDRNFKPGFRIDLHIKDLA 243
           AA +EA+ L  + GV+ D +Y+ I      S + + + P ++  ++ P   +D+ +KDL 
Sbjct: 186 AASAEAMALGLREGVDADALYEVITHSAGNSWMFENRVPHILKADYTPLSAVDIFVKDLG 245

Query: 244 NALDTSHGVGAQLPLTAAVMEMMQALRADGHGNDDHSAL 282
             LDT+      LPL+A   +M     + G G +D SA+
Sbjct: 246 LVLDTARASKFPLPLSATAHQMFMQASSAGFGREDDSAV 284


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: 217
Number of extensions: 9
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: 301
Length adjustment: 27
Effective length of query: 269
Effective length of database: 274
Effective search space:    73706
Effective search space used:    73706
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