GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Pseudomonas putida KT2440

Align Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17) (characterized)
to candidate PP_2217 PP_2217 enoyl-CoA hydratase

Query= reanno::psRCH2:GFF2389
         (257 letters)



>FitnessBrowser__Putida:PP_2217
          Length = 257

 Score =  395 bits (1015), Expect = e-115
 Identities = 193/257 (75%), Positives = 223/257 (86%)

Query: 1   MTFETLLVDIQERVALITLNRPQALNALNGQLISELNQALGQLEADPQIGCIVLTGSAKA 60
           M FET+L+DI  +V LITLNRPQALNALN Q++ E+NQAL QLE DP IGC+VLTGSAKA
Sbjct: 1   MAFETILLDIHGKVGLITLNRPQALNALNAQIVGEINQALDQLERDPNIGCVVLTGSAKA 60

Query: 61  FAAGADIKEMAELTYPQIYLDDFFADADRIATRRKPLIAAVAGYALGGGCELALLCDMIF 120
           FAAGADIKEMAEL YPQIY+DD F+DADRIA RRKP+IAAV+G+ALGGGCELA++CD I 
Sbjct: 61  FAAGADIKEMAELQYPQIYVDDLFSDADRIANRRKPIIAAVSGFALGGGCELAMMCDFIL 120

Query: 121 AADNARFGQPEVNLGVLPGIGGTQRLTRAVGKAKAMDMCLTGRQMDAAEAERAGLVARVF 180
           AADNA+FGQPE+NLGVLPG+GGTQRLTRAVGKAKAM++CLTGR M A EAERAGLVAR+ 
Sbjct: 121 AADNAKFGQPEINLGVLPGMGGTQRLTRAVGKAKAMELCLTGRLMGAEEAERAGLVARIV 180

Query: 181 PAESLLEETLKAARVIAEKSLPATMMIKESVNRAFETTLAEGIRFERRVFHAVFATADQK 240
           P   L+EE LK A  IA KS+P +MM+KESVNRAFE TL+EG+RFERRVFHA F+T DQK
Sbjct: 181 PQAELVEEALKVAATIASKSIPVSMMVKESVNRAFEVTLSEGVRFERRVFHAAFSTEDQK 240

Query: 241 EGMAAFSEKRKPEFTNR 257
           EGMAAF  KR+ +F +R
Sbjct: 241 EGMAAFIAKREAQFKDR 257


Lambda     K      H
   0.321    0.135    0.375 

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: 273
Number of extensions: 4
Number of successful extensions: 1
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: 257
Length of database: 257
Length adjustment: 24
Effective length of query: 233
Effective length of database: 233
Effective search space:    54289
Effective search space used:    54289
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 (21.9 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