GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuC in Sphingomonas koreensis DSMZ 15582

Align methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized)
to candidate Ga0059261_2908 Ga0059261_2908 Enoyl-CoA hydratase/carnithine racemase

Query= BRENDA::F4JML5
         (301 letters)



>FitnessBrowser__Korea:Ga0059261_2908
          Length = 275

 Score =  130 bits (327), Expect = 3e-35
 Identities = 88/258 (34%), Positives = 126/258 (48%), Gaps = 11/258 (4%)

Query: 50  GSDSGIIEVNLDRPVTKNAINKEMLKSLQNAFESIHQDNSARVVMIRSLVPGVFCAGADL 109
           G    + ++ L RP   NA++  M  +L  A ES+  D + R V++ S     FCAG DL
Sbjct: 16  GRAGAVADIRLRRPFKMNALDGPMFDALIAAAESVAVDPTIRAVVL-SGEGKAFCAGIDL 74

Query: 110 K--------ERRTMSPSEVHTYVNSLRYMFSFIEALSIPTIAAIEGAALGGGLEMALACD 161
           +        E +    S  H   N  +        + +P IAA+ G A GGGL++ L  D
Sbjct: 75  ESLQALMSDEGKQAMQSRSHGLANRYQQAALAWREVPVPVIAALHGVAFGGGLQIPLGAD 134

Query: 162 LRICGENAVFGLPETGLAIIPGAGGTQRLSRLVGRSVSKELIFTGRKIDAIEAANKGLVN 221
           +RI   +  F L E    I+P   GT  L  +V   V +ELI+T R    IEAA+ G+V 
Sbjct: 135 IRISAPDTKFSLMEVRWGIVPDMAGTVLLRSIVREDVLRELIYTARVFTGIEAASMGIVT 194

Query: 222 ICVTAGEAHEKAIEMAQQINEKGPLAIKMAKKAIDEGIETNMASGLEVEEMCYQKLLNTQ 281
               A   H  A+E+A  I E+GP A++ AK+ ++E    +    L  E      LL   
Sbjct: 195 --QLAANPHVAALELASSIAEQGPRAVRAAKQLLNETQSVSPQVALLSESEAQVGLLAGP 252

Query: 282 DRLEGLAAFAEKRKPLYT 299
           D++E L A AE+RKP YT
Sbjct: 253 DQIEALNAHAEQRKPYYT 270


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: 144
Number of extensions: 4
Number of successful extensions: 3
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: 275
Length adjustment: 26
Effective length of query: 275
Effective length of database: 249
Effective search space:    68475
Effective search space used:    68475
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