GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Phaeobacter inhibens BS107

Align Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17) (characterized)
to candidate GFF3595 PGA1_c36500 enoyl-CoA hydratase/isomerase

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



>FitnessBrowser__Phaeo:GFF3595
          Length = 258

 Score =  320 bits (819), Expect = 2e-92
 Identities = 162/258 (62%), Positives = 206/258 (79%), Gaps = 1/258 (0%)

Query: 1   MTFETLLVDIQERVALITLNRPQALNALNGQLISELNQALGQLEADPQIGCIVLTGSAKA 60
           M +ET+ V++Q+ V  I LNRP+ALNALN +L+SEL  AL + +A  ++ CI+LTGS KA
Sbjct: 1   MAYETINVEVQDHVCQIKLNRPEALNALNSELLSELCTALEEADASDKVRCIILTGSEKA 60

Query: 61  FAAGADIKEMAELTYPQIYLDDFFADA-DRIATRRKPLIAAVAGYALGGGCELALLCDMI 119
           FAAGADIKEM++ ++ +++  + FA   DRI+  RKP+IAAVAGYALGGGCELA+LCD I
Sbjct: 61  FAAGADIKEMSDKSFTEVFSTNLFAGVNDRISAIRKPIIAAVAGYALGGGCELAMLCDFI 120

Query: 120 FAADNARFGQPEVNLGVLPGIGGTQRLTRAVGKAKAMDMCLTGRQMDAAEAERAGLVARV 179
            AAD A+FGQPE+NLGV+ GIGGTQRLTR VGK+K+MDM LTGR M A EAERAGLV+RV
Sbjct: 121 IAADTAKFGQPEINLGVIAGIGGTQRLTRFVGKSKSMDMNLTGRFMTAEEAERAGLVSRV 180

Query: 180 FPAESLLEETLKAARVIAEKSLPATMMIKESVNRAFETTLAEGIRFERRVFHAVFATADQ 239
            PA+ LL+E   AA  IAEKSL   M +KE+VNR++E  L+EG+ FERRVFH++FAT DQ
Sbjct: 181 VPAKKLLDEATAAAHKIAEKSLLTAMAVKETVNRSYELPLSEGLLFERRVFHSMFATEDQ 240

Query: 240 KEGMAAFSEKRKPEFTNR 257
           KEGMAAF EKR+ +F ++
Sbjct: 241 KEGMAAFLEKREAQFRDK 258


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: 213
Number of extensions: 8
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: 257
Length of database: 258
Length adjustment: 24
Effective length of query: 233
Effective length of database: 234
Effective search space:    54522
Effective search space used:    54522
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