GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bkdA in Pseudomonas stutzeri RCH2

Align 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) (EC 1.2.4.4) (characterized)
to candidate GFF2176 Psest_2219 pyruvate dehydrogenase E1 component, alpha subunit

Query= BRENDA::Q72GU1
         (367 letters)



>FitnessBrowser__psRCH2:GFF2176
          Length = 330

 Score =  166 bits (419), Expect = 1e-45
 Identities = 101/310 (32%), Positives = 157/310 (50%), Gaps = 3/310 (0%)

Query: 41  LYRDMLAARMLDERYTILIRTGKT-SFIAPAAGHEAAQVAIAHAIRPGFDWVFPYYRDHG 99
           L RDML  R+++ER   L   GK   F+    G EA  V   HA+    D +   YR+HG
Sbjct: 17  LLRDMLRVRIMEERAAELYGEGKIRGFLHLYIGEEAVAVGALHALAAD-DAIVATYREHG 75

Query: 100 LALALGIPLKELFGQMLATKADPNKGRQMPEHPGSKALNFFTVASPIASHVPPAAGAAIS 159
            AL  G+ ++ +  +M   +   + GR    H       FF   + +   +P A G A++
Sbjct: 76  HALIQGVSMRAIMAEMYGRQQGCSGGRGGSMHLFDAGTRFFGGNAIVGGGLPLAVGLALA 135

Query: 160 MKLLRTGQVAVCTFGDGATSEGDWYAGINFAAVQGAPAVFVCENNFYAISVDYRHQTHSP 219
            ++ +  +V+ C FG+GA +EG ++  +N AA+   P +F CENN YA+           
Sbjct: 136 EQMRQGTRVSACFFGEGAMAEGAFHESMNLAALWQLPVLFCCENNLYAMGTALARSQSQT 195

Query: 220 TIADKAHAFGIPGYLVDGMDVLASYYVVKEAVERARRGEGPSLVELRVYRYGPHSSADDD 279
            +  KA A+ +    VDGMDV+A +   + AVE  R G+GP  +EL+ YR+  HS  D +
Sbjct: 196 DLCAKAAAYRVAARAVDGMDVVAVHDATRAAVEHVRSGQGPYFLELQTYRFRAHSMFDPE 255

Query: 280 SRYRPKEEVAFWRKKDPIPRFRRFLEARGLWNEEWEEDVREEIRAELERGLKEAEEAGPV 339
             YR K EV  W+++DPI  +   L+A+GL +      +   +R E+E  +  AE     
Sbjct: 256 -LYRDKAEVELWKQRDPIHSYSVRLQAQGLLDAAGLLAIEAAVREEVEDAVAYAEAGTLE 314

Query: 340 PPEWMFADVF 349
           P E +  DV+
Sbjct: 315 PVEQLCNDVY 324


Lambda     K      H
   0.320    0.138    0.426 

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: 295
Number of extensions: 14
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: 367
Length of database: 330
Length adjustment: 29
Effective length of query: 338
Effective length of database: 301
Effective search space:   101738
Effective search space used:   101738
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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