GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisM in Cupriavidus basilensis 4G11

Align ABC transporter for L-Lysine, permease component 2 (characterized)
to candidate RR42_RS31740 RR42_RS31740 ABC transporter permease

Query= reanno::pseudo5_N2C3_1:AO356_09910
         (229 letters)



>FitnessBrowser__Cup4G11:RR42_RS31740
          Length = 222

 Score =  139 bits (351), Expect = 3e-38
 Identities = 79/214 (36%), Positives = 132/214 (61%), Gaps = 10/214 (4%)

Query: 11  PKLAQGATLTLELVAIAVIAGLLLAIPLGIAR-SSRLWQVRALPYAYIFFFRGTPLLVQL 69
           P L +GA +T+E+ A A++ G ++ + +GI R   R   V  L  AY+   RGTPLLVQL
Sbjct: 13  PDLVRGAGVTVEVTACALVLGCVMGLLVGIGRLDPRRRVVYGLCTAYVTAIRGTPLLVQL 72

Query: 70  FLVYYGLAQFDAVRSSALWPYLRDPFWCATVTMTLHTAAYIAEILRGAIQAIPKGEIEAA 129
           FL+++GL QFD          L   F C  + + +++ AY++EI+RGAIQ++ KG++EAA
Sbjct: 73  FLLFFGLPQFDI---------LLPAFVCGVIGLGIYSGAYVSEIVRGAIQSVDKGQMEAA 123

Query: 130 RALGMSRPKALFYIMLPRAARIGLPAYSNEVILMLKASALASTVTLLELTGMARTIIART 189
           R++GMS  +A+  ++LP+A    +P   NE I ++K SAL S +T+ ++    + II+ +
Sbjct: 124 RSIGMSSGQAMRAVILPQAIVRMIPPLGNEFIALIKNSALVSLLTIHDVMHEGQKIISVS 183

Query: 190 YLPVEIFFAAGMFYLLMSFLLVQGFKQLERWLRV 223
           Y  +E++ A  + YLL++       + +E+ LR+
Sbjct: 184 YRSLEVYLAIALVYLLLTSAAGLFLRHMEQRLRM 217


Lambda     K      H
   0.331    0.141    0.434 

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: 138
Number of extensions: 5
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: 229
Length of database: 222
Length adjustment: 22
Effective length of query: 207
Effective length of database: 200
Effective search space:    41400
Effective search space used:    41400
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (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