GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dch in Cupriavidus basilensis 4G11

Align cyclohexa-1,5-dienecarbonyl-CoA hydratase monomer (EC 4.2.1.100) (characterized)
to candidate RR42_RS23710 RR42_RS23710 enoyl-CoA hydratase

Query= metacyc::MONOMER-18320
         (256 letters)



>FitnessBrowser__Cup4G11:RR42_RS23710
          Length = 249

 Score =  100 bits (250), Expect = 2e-26
 Identities = 78/251 (31%), Positives = 116/251 (46%), Gaps = 12/251 (4%)

Query: 13  KVATITLNVPNS-NWLTIPMMKEINEALMDVKKDPTIQLLVFDHAGDKAFCDGVDVA--- 68
           +VA I LN P   N L   +M  +  AL+  ++D  +  +V     DKAF  G D+A   
Sbjct: 4   RVAVIRLNRPRQMNALNDALMDALGLALLACEQDDGVGAIVIT-GNDKAFAAGADIAAMR 62

Query: 69  --DHVPEKVDEMIDLFHGMFRNMAAMDVTSVCLVNGRSLGGGCELMAFCDIVIASEKAKI 126
             D++       I       RN+    + +V    G +LGGGCEL   CDI+IA++ A  
Sbjct: 63  GWDYMDVFKSNYITRNWETLRNVRKPVIAAVA---GYALGGGCELAMACDILIAADNAVF 119

Query: 127 GQPEINLAVFPPVAAAW-FPKIMGLKKAMELILTGKIISAKEAEAIGLVNVVLPVEGFRE 185
           G PE+ LAV P        P+ +   KAM++ +T + + A EAE  GLV+ V+      +
Sbjct: 120 GLPELKLAVIPGAGGTQRLPRAISKAKAMDMCMTARNMDADEAERSGLVSRVVAAGRLMD 179

Query: 186 AAQKFMADFTSKSRPVAMWARRAIMAGLNLDFLQALKASEIIYMQGCMATEDANEGLASF 245
            A          S P  M  + AI         + +   E   +    ATED  EG+ +F
Sbjct: 180 EAMAVAQTIAGFSLPSMMAVKEAINRACESSLSEGM-LFERRQLHALFATEDLKEGMNAF 238

Query: 246 LEKRKPVFKDK 256
           LE+R  VF+ +
Sbjct: 239 LERRAAVFRHR 249


Lambda     K      H
   0.322    0.136    0.401 

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: 152
Number of extensions: 10
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: 256
Length of database: 249
Length adjustment: 24
Effective length of query: 232
Effective length of database: 225
Effective search space:    52200
Effective search space used:    52200
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: 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