GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mhpD in Paraburkholderia bryophila 376MFSha3.1

Align 2-oxopent-4-enoate hydratase (EC 4.2.1.80) (characterized)
to candidate H281DRAFT_01664 H281DRAFT_01664 2-oxo-3-hexenedioate decarboxylase

Query= BRENDA::P77608
         (269 letters)



>FitnessBrowser__Burk376:H281DRAFT_01664
          Length = 255

 Score =  112 bits (280), Expect = 8e-30
 Identities = 71/220 (32%), Positives = 110/220 (50%), Gaps = 3/220 (1%)

Query: 36  EAAYAIQHINVQHDVAQGRRVVGRKVGLTHPKVQQQLGVDQPDFGTLFADMCYGDNEIIP 95
           + AY IQ  +++  + +G R VG K+G T      Q+G+    +G L   M   +   I 
Sbjct: 33  DEAYRIQAESIRRRLDRGERRVGVKMGFTSRAKMVQMGLSDVIWGRLTDAMQIEEGTAID 92

Query: 96  FSRVLQPRIEAEIALVLNRDLPATDITFDELYNAIEWVLPALEVVGSRIRDWSIQFVDTV 155
            SR +  R E EIA +L R L   ++T  +   A+E + PA+E++ SR +D+     + +
Sbjct: 93  LSRFIHARCEPEIAFILKRPLEG-NVTGPQALAAVEAIAPAIEIIDSRYKDFKFSLPEVI 151

Query: 156 ADNASCGVYVIGGPAQRPAGLDLKNCAMKMTRNNEEVSSGRGSECLGHPLNAAVWLARKM 215
           ADNAS   +VIG  A     +D  N  + ++ +   V  G  +  LGHPL + V  AR  
Sbjct: 152 ADNASSSGFVIG--AWCDPKIDFSNLGLTVSIDGRVVQVGSTAALLGHPLRSLVAAARLS 209

Query: 216 ASLGEPLRTGDIILTGALGPMVAVNAGDRFEAHIEGIGSV 255
           A  GEPL+ G I++ G   P   +  G      +E +GSV
Sbjct: 210 AEAGEPLQAGWIVMAGGATPAEWIKLGQYTSVDMEQLGSV 249


Lambda     K      H
   0.319    0.135    0.399 

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: 184
Number of extensions: 8
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: 269
Length of database: 255
Length adjustment: 25
Effective length of query: 244
Effective length of database: 230
Effective search space:    56120
Effective search space used:    56120
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 (21.7 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 (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