GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PGA1_c12640 in Escherichia coli BW25113

Align D-lactate transporter, ATP-binding component (characterized)
to candidate 16258 b2149 fused methyl-galactoside transporter subunits of ABC superfamily: ATP-binding components (NCBI)

Query= reanno::Phaeo:GFF1248
         (251 letters)



>FitnessBrowser__Keio:16258
          Length = 506

 Score =  123 bits (309), Expect = 6e-33
 Identities = 69/223 (30%), Positives = 121/223 (54%), Gaps = 10/223 (4%)

Query: 3   ILEVKNVGKRFGGLQALSDVNLSVRENTVHAIIGPNGAGKSTLLNCLVGKLIPDTGSVMF 62
           +LE+  + K F G++AL +VNL VR +++HA++G NGAGKSTLL CL G    D+G+++F
Sbjct: 13  LLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGTILF 72

Query: 63  DGKSVLGRAPYEINQMGISRVFQTPEIFGDLSVLENMMIPCFAKRDGAFEMNAISAVSGQ 122
            GK +   +  E  + GIS V Q   +    SV++NM +  +  + G F          Q
Sbjct: 73  QGKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTK-GMF--------VDQ 123

Query: 123 RDILEKAEHMLEEMNMADKRHMNAASMSRGDKRRLEIGMCLSQEPRLLLLDEPTAGMARA 182
             +  + + + +E+++         ++S    + +EI    S   +++++DEPT+ +   
Sbjct: 124 DKMYRETKAIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEK 183

Query: 183 DTNNTIDLLKQIKSERDITIAIIEHDMHVVFSLADRITVLAQG 225
           + N+   +++++K ER   I  I H M  +F L D +TVL  G
Sbjct: 184 EVNHLFTIIRKLK-ERGCGIVYISHKMEEIFQLCDEVTVLRDG 225



 Score = 54.3 bits (129), Expect = 5e-12
 Identities = 51/227 (22%), Positives = 101/227 (44%), Gaps = 13/227 (5%)

Query: 3   ILEVKNVGKRFGGLQALSDVNLSVRENTVHAIIGPNGAGKSTLLNCLVGKLIPDTGSVMF 62
           ILEV+N+        ++ DV+  + +  +  I G  GA ++ ++  L G      G++  
Sbjct: 265 ILEVRNLTSL--RQPSIRDVSFDLHKGEILGIAGLVGAKRTDIVETLFGIREKSAGTITL 322

Query: 63  DGKSVLGRAPYEINQMGISRVFQ---TPEIFGDLSVLENMMIPCFAKRDGAFEMNAISAV 119
            GK +      E    G + V +   +  I+  L +  N +I            N +  +
Sbjct: 323 HGKQINNHNANEAINHGFALVTEERRSTGIYAYLDIGFNSLISNIRNYK-----NKVGLL 377

Query: 120 SGQRDILEKAEHMLEEMNMADKRHMNA-ASMSRGDKRRLEIGMCLSQEPRLLLLDEPTAG 178
              R +    + +++ M +    H     S+S G+++++ IG  L  +P +L+LDEPT G
Sbjct: 378 DNSR-MKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQPEILMLDEPTRG 436

Query: 179 MARADTNNTIDLLKQIKSERDITIAIIEHDMHVVFSLADRITVLAQG 225
           +          L+ ++ +++   I II  +M  +  + DRI V++ G
Sbjct: 437 IDVGAKFEIYQLIAEL-AKKGKGIIIISSEMPELLGITDRILVMSNG 482


Lambda     K      H
   0.318    0.135    0.379 

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: 271
Number of extensions: 14
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 251
Length of database: 506
Length adjustment: 29
Effective length of query: 222
Effective length of database: 477
Effective search space:   105894
Effective search space used:   105894
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: 49 (23.5 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