GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mhpD in Pseudomonas fluorescens GW456-L13

Align 2-oxopent-4-enoate hydratase subunit (EC 4.2.1.80) (characterized)
to candidate PfGW456L13_2504 4-oxalocrotonate decarboxylase (EC 4.1.1.77)

Query= metacyc::MONOMER-3403
         (222 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2504
          Length = 263

 Score =  278 bits (710), Expect = 9e-80
 Identities = 140/222 (63%), Positives = 170/222 (76%), Gaps = 1/222 (0%)

Query: 1   MDKTLINELGDELYQAMVQRETVTPLTSRGFDISVEDAYHISLRMLERRLAAGERVIGKK 60
           M   L  E G+ELYQA++   T+ PLT R   IS+EDAYHISL  +ERR+AAG++++GKK
Sbjct: 1   MSVQLRREFGEELYQALLSGSTLAPLTERWPSISIEDAYHISLYAIERRVAAGDQIVGKK 60

Query: 61  IGVTSKAVQNMLGVHQPDFGYLTDAMVYNSGEAMPIS-EKLIQPRAEGEIAFILKKDLMG 119
           IGVTS AVQ ML VHQPDFG++T  M ++    + +S  KLIQPRAEGEIAF LK DL+G
Sbjct: 61  IGVTSAAVQQMLNVHQPDFGFITRQMSFDDDAQISLSANKLIQPRAEGEIAFKLKHDLVG 120

Query: 120 PGVTNADVLAATECVIPCFEVVDSRIQDWKIKIQDTVADNASCGLFVLGDQAVSPRQVDL 179
           PG+T ADVLAATE V+PCFE+VDSRI DW+I+IQDTVADNASCG+FVLGD  V PR++DL
Sbjct: 121 PGITEADVLAATEYVMPCFEIVDSRIHDWRIRIQDTVADNASCGVFVLGDSKVDPRELDL 180

Query: 180 VTCGMLVEKNGQLLSTGAGAAALGSPVNCVAWLANTLGHFGI 221
               M V KN + LS G G+A  G+P+  VAWLANTLG FGI
Sbjct: 181 PNLRMRVFKNAEPLSEGLGSAVQGNPLTAVAWLANTLGAFGI 222


Lambda     K      H
   0.319    0.136    0.395 

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: 182
Number of extensions: 3
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: 222
Length of database: 263
Length adjustment: 23
Effective length of query: 199
Effective length of database: 240
Effective search space:    47760
Effective search space used:    47760
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: 46 (22.3 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