GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaI in Cupriavidus basilensis 4G11

Align 3-oxoadipate CoA-transferase subunit A; EC 2.8.3.6 (characterized)
to candidate RR42_RS22970 RR42_RS22970 3-oxoadipate CoA-transferase

Query= CharProtDB::CH_021928
         (231 letters)



>FitnessBrowser__Cup4G11:RR42_RS22970
          Length = 230

 Score =  249 bits (635), Expect = 4e-71
 Identities = 120/220 (54%), Positives = 162/220 (73%)

Query: 1   MINKTYESIASAVEGITDGSTIMVGGFGTAGMPSELIDGLIATGARDLTIISNNAGNGEI 60
           M+NK   S A A+  + DG+T+MVGGFG+AG+P  LI  ++A GARDLT+ISNNAG    
Sbjct: 1   MVNKRVASCAEAIADLRDGATVMVGGFGSAGLPDGLIAAVLAHGARDLTVISNNAGYDGE 60

Query: 61  GLAALLMAGSVRKVVCSFPRQSDSYVFDELYRAGKIELEVVPQGNLAERIAAAGSGIGAF 120
           G+A+L+ AG +RK+VCS+P  + +  F + YR G++ELE+V QG L ERI  AG+G+G F
Sbjct: 61  GVASLIEAGRMRKLVCSYPLTAGATAFRDAYRRGEVELELVAQGTLVERIRCAGAGLGGF 120

Query: 121 FSPTGYGTLLAEGKETREIDGRMYVLEMPLHADFALIKAHKGDRWGNLTYRKAARNFGPI 180
           + P   GT+LA+GK+TREI+G ++VLE+PLHADFALI+    DR GNL Y  A RNF PI
Sbjct: 121 YCPITAGTILAQGKDTREINGVLHVLELPLHADFALIRGRHADRLGNLDYHLAGRNFNPI 180

Query: 181 MAMAAKTAIAQVDQVVELGELDPEHIITPGIFVQRVVAVS 220
           MA AA+  +A+V+ +VE G ++PE I+TPGIFV RVV  +
Sbjct: 181 MATAARVVVAEVEAMVEAGAMNPEQIVTPGIFVHRVVTAN 220


Lambda     K      H
   0.318    0.135    0.381 

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: 159
Number of extensions: 6
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: 231
Length of database: 230
Length adjustment: 23
Effective length of query: 208
Effective length of database: 207
Effective search space:    43056
Effective search space used:    43056
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: 46 (22.3 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