GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuC in Pseudomonas putida KT2440

Align methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized)
to candidate PP_3284 PP_3284 enoyl-CoA hydratase-isomerase

Query= BRENDA::F4JML5
         (301 letters)



>FitnessBrowser__Putida:PP_3284
          Length = 257

 Score =  159 bits (402), Expect = 6e-44
 Identities = 95/250 (38%), Positives = 142/250 (56%), Gaps = 5/250 (2%)

Query: 52  DSGIIEVNLDRPVTKNAINKEMLKSLQNAFESIHQDNSARVVMIRSLVPGVFCAGADLKE 111
           + G+  + L RP   NA+  E+L  L  A ++   D   R  +I       F AGAD++E
Sbjct: 11  EHGVQLITLQRPEALNALCTELLAELAAALQAAGNDEHVRATVITGSAKA-FAAGADIRE 69

Query: 112 RRTMSPSEVHTYVNSLRYM-FSFIEALSIPTIAAIEGAALGGGLEMALACDLRICGENAV 170
              M+  ++   +N  R   +  I A + P IAA+ G ALGGG E+A+  D+ I   +A 
Sbjct: 70  ---MADRDLVGILNDPRVAHWQSIAAFAKPLIAAVNGYALGGGCELAMCADIVIASTDAR 126

Query: 171 FGLPETGLAIIPGAGGTQRLSRLVGRSVSKELIFTGRKIDAIEAANKGLVNICVTAGEAH 230
           FG PE  L IIPGAGGTQRL R VG+ ++ +++ TG  I A+ A   GLV+         
Sbjct: 127 FGQPEINLGIIPGAGGTQRLLRAVGKPLAMQMVLTGEAITALRAQQAGLVSEITQPELTV 186

Query: 231 EKAIEMAQQINEKGPLAIKMAKKAIDEGIETNMASGLEVEEMCYQKLLNTQDRLEGLAAF 290
           E+A+++A+ I  K PLA+++AK+A+ +  +T++ASGL  E   +  L  T DR EG+ AF
Sbjct: 187 ERAMQVARSIAAKAPLAVRLAKEALLKAGDTDLASGLRFERHAFTLLAGTADRDEGIRAF 246

Query: 291 AEKRKPLYTG 300
            EKR+  + G
Sbjct: 247 QEKRQARFQG 256


Lambda     K      H
   0.318    0.134    0.373 

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: 145
Number of extensions: 7
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: 301
Length of database: 257
Length adjustment: 25
Effective length of query: 276
Effective length of database: 232
Effective search space:    64032
Effective search space used:    64032
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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