GapMind for catabolism of small carbon sources

 

Aligments for a candidate for mglA in Klebsiella michiganensis M5al

Align Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate BWI76_RS19640 BWI76_RS19640 galactose/methyl galactoside ABC transporter ATP-binding protein MglA

Query= TCDB::P0AAG8
         (506 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS19640 BWI76_RS19640
           galactose/methyl galactoside ABC transporter ATP-binding
           protein MglA
          Length = 506

 Score =  941 bits (2431), Expect = 0.0
 Identities = 475/506 (93%), Positives = 493/506 (97%)

Query: 1   MVSSTTPSSGEYLLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLF 60
           MVS+ +  SGEYLLEM+ INKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLF
Sbjct: 1   MVSNNSERSGEYLLEMTNINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLF 60

Query: 61  GIYQKDSGTILFQGKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGMF 120
           GIYQKDSG+ILFQG+EIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKG+F
Sbjct: 61  GIYQKDSGSILFQGQEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGVF 120

Query: 121 VDQDKMYRETKAIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSL 180
           VDQDKMYR+TKAIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSL
Sbjct: 121 VDQDKMYRDTKAIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSL 180

Query: 181 TEKEVNHLFTIIRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDK 240
           TEKEVNHLF IIRKLKERGCGIVYISHKMEEIFQLCDE+T+LRDGQWIAT+PL GL MDK
Sbjct: 181 TEKEVNHLFKIIRKLKERGCGIVYISHKMEEIFQLCDEITILRDGQWIATQPLEGLDMDK 240

Query: 241 IIAMMVGRSLNQRFPDKENKPGEVILEVRNLTSLRQPSIRDVSFDLHKGEILGIAGLVGA 300
           IIAMMVGRSLNQRFP+KENKPGEVILEVRNLTSLRQPSIRD+SFDLHKGEILGIAGLVGA
Sbjct: 241 IIAMMVGRSLNQRFPNKENKPGEVILEVRNLTSLRQPSIRDISFDLHKGEILGIAGLVGA 300

Query: 301 KRTDIVETLFGIREKSAGTITLHGKQINNHNANEAINHGFALVTEERRSTGIYAYLDIGF 360
           KRTDIVETLFGIREK+ GTI LHGK+INNH+ANEAINHGFALVTEERRSTGIYAYLDIGF
Sbjct: 301 KRTDIVETLFGIREKAGGTIRLHGKKINNHSANEAINHGFALVTEERRSTGIYAYLDIGF 360

Query: 361 NSLISNIRNYKNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRW 420
           NSLISNI+ YKNKVGLLDNSRMKSDTQWVIDSMRVKTPG  TQIGSLSGGNQQKVIIGRW
Sbjct: 361 NSLISNIKKYKNKVGLLDNSRMKSDTQWVIDSMRVKTPGQHTQIGSLSGGNQQKVIIGRW 420

Query: 421 LLTQPEILMLDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMS 480
           LLTQPEILMLDEPTRGIDVGAKFEIYQLIAELAKK KGIIIISSEMPELLGITDRILVMS
Sbjct: 421 LLTQPEILMLDEPTRGIDVGAKFEIYQLIAELAKKDKGIIIISSEMPELLGITDRILVMS 480

Query: 481 NGLVSGIVDTKTTTQNEILRLASLHL 506
           NGLV+GIV+TKTTTQNEILRLASLHL
Sbjct: 481 NGLVAGIVETKTTTQNEILRLASLHL 506


Lambda     K      H
   0.318    0.136    0.384 

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: 923
Number of extensions: 25
Number of successful extensions: 5
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: 506
Length of database: 506
Length adjustment: 34
Effective length of query: 472
Effective length of database: 472
Effective search space:   222784
Effective search space used:   222784
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: 52 (24.6 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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