GapMind for catabolism of small carbon sources

 

Aligments for a candidate for mmsB in Pseudomonas fluorescens FW300-N1B4

Align 3-hydroxyisobutyrate dehydrogenase (EC 1.1.1.31) (characterized)
to candidate Pf1N1B4_1220 2-hydroxy-3-oxopropionate reductase (EC 1.1.1.60)

Query= reanno::psRCH2:GFF2390
         (296 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1220
           2-hydroxy-3-oxopropionate reductase (EC 1.1.1.60)
          Length = 291

 Score =  124 bits (312), Expect = 2e-33
 Identities = 94/299 (31%), Positives = 145/299 (48%), Gaps = 30/299 (10%)

Query: 1   MHIGFIGLGNMGAPMAHNLLKAGHQLSVFDLNAAAVENLVGAGALPVDSPTAIAQGNAEL 60
           M +GFIGLG MG PM  NLLKAGH++ V++ ++A ++ L  AGA PVDSP   AQ  AE+
Sbjct: 1   MELGFIGLGTMGVPMVLNLLKAGHRVKVWNRSSAPLDELARAGAQPVDSPALAAQ--AEV 58

Query: 61  IITMLPAAAHVKGVYLGVNGLIAHSRAGVMLIDCSTIDPHSAREVAKAAAEHGNPMLDAP 120
           +I+ML     ++ V++   GL   + AG + ++ ST+    A+E A    E     + AP
Sbjct: 59  LISMLGDDVAIRSVFIDGKGLDGLA-AGSVHVNMSTVSVALAKEFAALHTERDVAYVSAP 117

Query: 121 VSGGTGGAAAGTLTFMVGGSDPDFDHAQPILAAMGKNIVHCG-AAGNGQVAKVANNMLLG 179
           V G    AAAG L  +  G        QP+   +G+     G  A    VAK++ N+++ 
Sbjct: 118 VLGRVDVAAAGNLNILASGPAQALARVQPLFDVLGRKTWPFGECAELACVAKLSANLMIA 177

Query: 180 ISMIGVAEAMALGVALGMDAKTLAGVINTSSGRCWSSDTYNPFPGVLDNVPSSRGYS--- 236
            ++  +A+A  L  + G+   T   +I           T   FP     VP  +GY    
Sbjct: 178 SAIESMAQASTLASSYGISRATFIEMI-----------TSTLFP-----VPVYQGYGQLM 221

Query: 237 -------GGFGSDLMLKDLGLATEAAKQVRQPVILGALAQQLYQSFSAQGHGGLDFSAI 288
                   GF   L LKD+ LA EA +  + P+   ++ +       A G G  D++++
Sbjct: 222 IDKHFEPAGFKLSLGLKDIRLALEAGEAAQVPLPFASVLKDNLLDGMAHGQGDQDWASL 280


Lambda     K      H
   0.318    0.134    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: 239
Number of extensions: 11
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: 296
Length of database: 291
Length adjustment: 26
Effective length of query: 270
Effective length of database: 265
Effective search space:    71550
Effective search space used:    71550
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: 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 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, the preprint on GapMind for carbon sources, 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