Align Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate WP_007675905.1 BN137_RS06860 galactose/methyl galactoside ABC transporter ATP-binding protein MglA
Query= TCDB::P0AAG8 (506 letters) >NCBI__GCF_000319285.1:WP_007675905.1 Length = 506 Score = 944 bits (2441), Expect = 0.0 Identities = 477/506 (94%), Positives = 496/506 (98%) Query: 1 MVSSTTPSSGEYLLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLF 60 MVS+ T S GEYLLEM+ INKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLF Sbjct: 1 MVSNNTQSPGEYLLEMTNINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLF 60 Query: 61 GIYQKDSGTILFQGKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGMF 120 GIYQKDSG+ILFQGKE+DFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGMF Sbjct: 61 GIYQKDSGSILFQGKEVDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGMF 120 Query: 121 VDQDKMYRETKAIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSL 180 VDQ+KMY +TKAIFDELDIDIDP+ARVGTLSVSQMQMIEIAKAFSY+AKIVIMDEPTSSL Sbjct: 121 VDQEKMYLDTKAIFDELDIDIDPKARVGTLSVSQMQMIEIAKAFSYDAKIVIMDEPTSSL 180 Query: 181 TEKEVNHLFTIIRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDK 240 TEKEVNHLF IIRKLKERGCGIVYISHKMEEIFQLCDE+T+LRDGQWIAT+ L GL MDK Sbjct: 181 TEKEVNHLFKIIRKLKERGCGIVYISHKMEEIFQLCDEITILRDGQWIATQSLDGLDMDK 240 Query: 241 IIAMMVGRSLNQRFPDKENKPGEVILEVRNLTSLRQPSIRDVSFDLHKGEILGIAGLVGA 300 IIAMMVGRSLNQRFPD+EN+PGEVILEVRNLTSLRQPSIRDVSFDLHKGEILGIAGLVGA Sbjct: 241 IIAMMVGRSLNQRFPDRENQPGEVILEVRNLTSLRQPSIRDVSFDLHKGEILGIAGLVGA 300 Query: 301 KRTDIVETLFGIREKSAGTITLHGKQINNHNANEAINHGFALVTEERRSTGIYAYLDIGF 360 KRTDIVETLFGIREKS GTI+LHGK+INNH+ANEAIN+GFALVTEERRSTGIYAYLDIGF Sbjct: 301 KRTDIVETLFGIREKSGGTISLHGKKINNHSANEAINNGFALVTEERRSTGIYAYLDIGF 360 Query: 361 NSLISNIRNYKNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRW 420 NSLISNIRNYK+K+GLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRW Sbjct: 361 NSLISNIRNYKSKIGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRW 420 Query: 421 LLTQPEILMLDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMS 480 LLTQPEILMLDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMS Sbjct: 421 LLTQPEILMLDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMS 480 Query: 481 NGLVSGIVDTKTTTQNEILRLASLHL 506 NGLVSGIVDTKTTTQNEILRLASLHL Sbjct: 481 NGLVSGIVDTKTTTQNEILRLASLHL 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: 927 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 24 2021. The underlying query database was built on Sep 17 2021.
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:
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