GapMind for catabolism of small carbon sources

 

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

Align Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17) (characterized)
to candidate PfGW456L13_2984 Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17)

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



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2984
          Length = 257

 Score =  388 bits (997), Expect = e-113
 Identities = 190/257 (73%), Positives = 222/257 (86%)

Query: 1   MTFETLLVDIQERVALITLNRPQALNALNGQLISELNQALGQLEADPQIGCIVLTGSAKA 60
           +++ET+L++   RV LITLNRPQALNALN Q++SELNQAL   EAD  IGCIVLTGS KA
Sbjct: 1   VSYETILLETHGRVGLITLNRPQALNALNAQIVSELNQALDGFEADSNIGCIVLTGSKKA 60

Query: 61  FAAGADIKEMAELTYPQIYLDDFFADADRIATRRKPLIAAVAGYALGGGCELALLCDMIF 120
           FAAGADIKEMAELTYPQIY+DD F+D+DR+A RRKP+IAAV G+ALGGGCELAL+CD I 
Sbjct: 61  FAAGADIKEMAELTYPQIYIDDLFSDSDRVANRRKPIIAAVNGFALGGGCELALMCDFIL 120

Query: 121 AADNARFGQPEVNLGVLPGIGGTQRLTRAVGKAKAMDMCLTGRQMDAAEAERAGLVARVF 180
           A DNARFGQPE+NLGVLPG+GGTQRLTRAVGKAKAM+MCL+GR +DA EAER G+VAR+ 
Sbjct: 121 AGDNARFGQPEINLGVLPGMGGTQRLTRAVGKAKAMEMCLSGRLIDAVEAERCGIVARIV 180

Query: 181 PAESLLEETLKAARVIAEKSLPATMMIKESVNRAFETTLAEGIRFERRVFHAVFATADQK 240
           P++ LL+E LK A +IA+KSLP  MM+KESVNRAFE +LAEG+RFERRVFHA FAT DQK
Sbjct: 181 PSDELLDEALKVAALIAKKSLPIAMMVKESVNRAFEVSLAEGVRFERRVFHAAFATQDQK 240

Query: 241 EGMAAFSEKRKPEFTNR 257
           EGMAAF  KR+ EF  +
Sbjct: 241 EGMAAFIAKREAEFQGK 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: 262
Number of extensions: 5
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