GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Acidovorax caeni R-24608

Align Enoyl-CoA-hydratase; EC 4.2.1.17 (characterized)
to candidate WP_054254926.1 BN2503_RS01750 enoyl-CoA hydratase

Query= SwissProt::G4V4T7
         (265 letters)



>NCBI__GCF_001298675.1:WP_054254926.1
          Length = 261

 Score =  133 bits (334), Expect = 4e-36
 Identities = 94/249 (37%), Positives = 121/249 (48%), Gaps = 6/249 (2%)

Query: 14  VAYVTMDRPAVLNAMDRRMHEELAGIWDDVEADDDVRAVVLTGAGDRAFSVGQDLKERAR 73
           V  +T++ PA  NA+   M   L    D+V  D+  R VVL   G RAF  G +LKE A+
Sbjct: 17  VVTLTLNDPARFNALGADMLAALQQALDNVARDEGARVVVLAANG-RAFCAGHNLKEMAQ 75

Query: 74  LNESGVAPTTFGSGGQAGHPRLTDRFTLSKPVVARVRGYALGGGFELVLACDIVIAAEDA 133
             E       F    +     +     L  PV+ARV G A   G +LV  CD+ +A+EDA
Sbjct: 76  HPELAYYQQLFAQCSRM----MLSIHKLPVPVIARVHGMATAAGCQLVAQCDLAVASEDA 131

Query: 134 VFALPEVRLGLIAGAGGVFRLPRQLPQKVAMGYLLTGRRMDAATALRHGLVNEVVPAAEL 193
            FA   +  GL      V  L R +P K AM  LLTG  +DA TAL  GLVN VVPA  L
Sbjct: 132 SFATSGIHYGLFCATPSV-PLVRNVPAKRAMEMLLTGDFIDARTALEQGLVNRVVPAEAL 190

Query: 194 DQCVADWTDSLVRAAPLSVRAIKEAALRSVDLPLEEAFTTSYHWEERRRRSADAIEGVRA 253
           D  V     S++    ++V   K    +  +L L+ A+  +          ADA EG RA
Sbjct: 191 DAEVEKLVQSILGKPRVAVAMGKAVVYQHRELGLDAAYQLAGQTMAANMMDADAQEGARA 250

Query: 254 FAEKRDPIW 262
           FAEKR P W
Sbjct: 251 FAEKRQPAW 259


Lambda     K      H
   0.320    0.136    0.399 

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: 147
Number of extensions: 6
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: 265
Length of database: 261
Length adjustment: 25
Effective length of query: 240
Effective length of database: 236
Effective search space:    56640
Effective search space used:    56640
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 (21.8 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 24 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