GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Algoriphagus aquaeductus T4

Align Probable enoyl-CoA hydratase; EC 4.2.1.17 (uncharacterized)
to candidate WP_111392290.1 CLV31_RS07705 enoyl-CoA hydratase/isomerase family protein

Query= curated2:Q52995
         (257 letters)



>NCBI__GCF_003253485.1:WP_111392290.1
          Length = 260

 Score =  112 bits (280), Expect = 8e-30
 Identities = 84/260 (32%), Positives = 131/260 (50%), Gaps = 12/260 (4%)

Query: 1   MSYETLLVETQGRVGLITLNRPQALNALNAVLMRELDAALKAFDADRAVGAIVLAGSEKA 60
           M  +T+L   + ++G ITLNRP+  NAL+  L+ EL  A     AD++V  ++L    KA
Sbjct: 1   MMEKTVLTHVENQLGFITLNRPEKRNALSPQLIGELSEAFAQMKADKSVKLVILQAKGKA 60

Query: 61  FAAGADIKEMQGL-------DFVDGYLADFLGGWEHVANARKPMIAAVSGFALGGGCELA 113
           F AGAD++ +Q L       +  D +    L  +  +    K +IA V G AL GGC L 
Sbjct: 61  FCAGADLEYLQELQQFSYEENLEDSHRLKRL--FSQIYEFPKVVIAKVQGHALAGGCGLV 118

Query: 114 MMCDFIIASETAKFGQPEITLGVIPGMGGSQRLTRAVGKAKAMDLILTGRMMDAAEAERS 173
            +CDF  A   A FG  E  +G +P +  S  L   +G  +A +L+++G M+ A +A+  
Sbjct: 119 TVCDFAFADSEALFGYTEAKIGFVPAL-VSVFLAEQIGHYRAGELLISGEMISAKKADEF 177

Query: 174 GLVSRVVAPDRLLEEALGA-AEKIASFSLPAAMMAKEAVNRSL-ELTLAEGLRFERRLFQ 231
           GL++  +    L    L   A K+   +   +M   + + RSL ++T  + L        
Sbjct: 178 GLITGYMDGASLDHWVLNEFALKLIRDNSAFSMGETKRLLRSLGKVTRDQALDAAAEANA 237

Query: 232 SLFATEDQKEGMAAFVAKRK 251
              A ED K+G+AAF+ K K
Sbjct: 238 RARAHEDCKKGIAAFLQKTK 257


Lambda     K      H
   0.321    0.134    0.371 

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: 10
Number of successful extensions: 4
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: 257
Length of database: 260
Length adjustment: 24
Effective length of query: 233
Effective length of database: 236
Effective search space:    54988
Effective search space used:    54988
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: 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