GapMind for catabolism of small carbon sources

 

Aligments for a candidate for fadB in Burkholderia phytofirmans PsJN

Align 3-hydroxyacyl-CoA dehydrogenase type-2; 17-beta-hydroxysteroid dehydrogenase 10; 17-beta-HSD 10; 3-hydroxy-2-methylbutyryl-CoA dehydrogenase; 3-hydroxyacyl-CoA dehydrogenase type II; Mitochondrial ribonuclease P protein 2; Mitochondrial RNase P protein 2; Scully protein; Type II HADH; EC 1.1.1.35; EC 1.1.1.51; EC 1.1.1.178 (characterized)
to candidate BPHYT_RS15890 BPHYT_RS15890 3-hydroxy-2-methylbutyryl-CoA dehydrogenase

Query= SwissProt::O18404
         (255 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS15890 BPHYT_RS15890
           3-hydroxy-2-methylbutyryl-CoA dehydrogenase
          Length = 252

 Score =  279 bits (713), Expect = 5e-80
 Identities = 148/254 (58%), Positives = 183/254 (72%), Gaps = 5/254 (1%)

Query: 2   IKNAVSLVTGGASGLGRATAERLAKQGASVILADLPSSKGNEVAKELGDKVVFVPVDVTS 61
           I++ V L+TGGASGLG ATA    + G  V+LADL    G  +AKELG   VFV  DV+ 
Sbjct: 3   IRDNVFLITGGASGLGAATARLFVENGGKVVLADLNVDAGEALAKELGG--VFVRCDVSR 60

Query: 62  EKDVSAALQTAKDKFGRLDLTVNCAGTATAVKTFNFNKNVAHRLEDFQRVININTVGTFN 121
           E D + A++ A  K G L   VNCAG A AVKT    K+  H L+ F R I+IN +GTFN
Sbjct: 61  EDDATQAVEAAT-KLGTLRGLVNCAGVAPAVKTVG--KDGPHPLDAFARTISINLIGTFN 117

Query: 122 VIRLSAGLMGANEPNQDGQRGVIVNTASVAAFDGQIGQAAYSASKAAVVGMTLPIARDLS 181
           ++RL+A  M  NEPN +G+RGVI+NTASVAAFDGQIGQAAY+ASKA V GMTLPIARDLS
Sbjct: 118 MVRLAAAAMSKNEPNANGERGVIINTASVAAFDGQIGQAAYAASKAGVAGMTLPIARDLS 177

Query: 182 TQGIRICTIAPGLFNTPMLAALPEKVRTFLAKSIPFPQRLGEPSEYAHLVQAIYENPLLN 241
              IR+ TIAPG+F TPML  +P++V+  L   +PFP RLG+P EYA L + I++NP+LN
Sbjct: 178 RNAIRVMTIAPGIFETPMLLGMPQEVQDALGAMVPFPPRLGKPVEYAMLAKQIFDNPMLN 237

Query: 242 GEVIRIDGALRMMP 255
           GEVIR+DGA+RM P
Sbjct: 238 GEVIRLDGAIRMQP 251


Lambda     K      H
   0.317    0.133    0.369 

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: 247
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: 255
Length of database: 252
Length adjustment: 24
Effective length of query: 231
Effective length of database: 228
Effective search space:    52668
Effective search space used:    52668
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 (21.7 bits)
S2: 47 (22.7 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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