GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaF in Pseudomonas stutzeri RCH2

Align Enoyl-CoA hydratase (characterized, see rationale)
to candidate GFF2389 Psest_2437 Enoyl-CoA hydratase/carnithine racemase

Query= uniprot:A0A2Z5MEB0
         (258 letters)



>FitnessBrowser__psRCH2:GFF2389
          Length = 257

 Score =  331 bits (849), Expect = 8e-96
 Identities = 167/258 (64%), Positives = 206/258 (79%), Gaps = 1/258 (0%)

Query: 1   MVYENILVETRGRVGLVTLSRPKALNALNDALMDELGVALREFDADDAIGAIVLTGSEKA 60
           M +E +LV+ + RV L+TL+RP+ALNALN  L+ EL  AL + +AD  IG IVLTGS KA
Sbjct: 1   MTFETLLVDIQERVALITLNRPQALNALNGQLISELNQALGQLEADPQIGCIVLTGSAKA 60

Query: 61  FAAGADIGMMSTYSYMDVYKGDYITRNWETVRSIRKPIIAAVAGFALGGGCELAMMCDMI 120
           FAAGADI  M+  +Y  +Y  D+   + + + + RKP+IAAVAG+ALGGGCELA++CDMI
Sbjct: 61  FAAGADIKEMAELTYPQIYLDDFFA-DADRIATRRKPLIAAVAGYALGGGCELALLCDMI 119

Query: 121 FAADTAKFGQPEIKLGIMPGAGGTQRLPRAVSKAKAMDLCLTARFMDAAEAERAGLVSRV 180
           FAAD A+FGQPE+ LG++PG GGTQRL RAV KAKAMD+CLT R MDAAEAERAGLV+RV
Sbjct: 120 FAADNARFGQPEVNLGVLPGIGGTQRLTRAVGKAKAMDMCLTGRQMDAAEAERAGLVARV 179

Query: 181 IPAASLIDESIAAGATIAEFPLPAVMMVKESVNRAYETTLAEGVHFERRLFHSLFATEDQ 240
            PA SL++E++ A   IAE  LPA MM+KESVNRA+ETTLAEG+ FERR+FH++FAT DQ
Sbjct: 180 FPAESLLEETLKAARVIAEKSLPATMMIKESVNRAFETTLAEGIRFERRVFHAVFATADQ 239

Query: 241 KEGMAAFVEKRKPVFKHR 258
           KEGMAAF EKRKP F +R
Sbjct: 240 KEGMAAFSEKRKPEFTNR 257


Lambda     K      H
   0.322    0.135    0.383 

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: 227
Number of extensions: 5
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: 258
Length of database: 257
Length adjustment: 24
Effective length of query: 234
Effective length of database: 233
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