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_3284 PP_3284 enoyl-CoA hydratase-isomerase

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



>FitnessBrowser__Putida:PP_3284
          Length = 257

 Score =  231 bits (588), Expect = 1e-65
 Identities = 129/253 (50%), Positives = 166/253 (65%), Gaps = 3/253 (1%)

Query: 8   VDIQ---ERVALITLNRPQALNALNGQLISELNQALGQLEADPQIGCIVLTGSAKAFAAG 64
           +D+Q     V LITL RP+ALNAL  +L++EL  AL     D  +   V+TGSAKAFAAG
Sbjct: 5   IDVQAPEHGVQLITLQRPEALNALCTELLAELAAALQAAGNDEHVRATVITGSAKAFAAG 64

Query: 65  ADIKEMAELTYPQIYLDDFFADADRIATRRKPLIAAVAGYALGGGCELALLCDMIFAADN 124
           ADI+EMA+     I  D   A    IA   KPLIAAV GYALGGGCELA+  D++ A+ +
Sbjct: 65  ADIREMADRDLVGILNDPRVAHWQSIAAFAKPLIAAVNGYALGGGCELAMCADIVIASTD 124

Query: 125 ARFGQPEVNLGVLPGIGGTQRLTRAVGKAKAMDMCLTGRQMDAAEAERAGLVARVFPAES 184
           ARFGQPE+NLG++PG GGTQRL RAVGK  AM M LTG  + A  A++AGLV+ +   E 
Sbjct: 125 ARFGQPEINLGIIPGAGGTQRLLRAVGKPLAMQMVLTGEAITALRAQQAGLVSEITQPEL 184

Query: 185 LLEETLKAARVIAEKSLPATMMIKESVNRAFETTLAEGIRFERRVFHAVFATADQKEGMA 244
            +E  ++ AR IA K+  A  + KE++ +A +T LA G+RFER  F  +  TAD+ EG+ 
Sbjct: 185 TVERAMQVARSIAAKAPLAVRLAKEALLKAGDTDLASGLRFERHAFTLLAGTADRDEGIR 244

Query: 245 AFSEKRKPEFTNR 257
           AF EKR+  F  R
Sbjct: 245 AFQEKRQARFQGR 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: 194
Number of extensions: 9
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