Alignments for a candidate for mglA in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for mglA in Burkholderia phytofirmans PsJN

Align Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate BPHYT_RS27185 BPHYT_RS27185 D-ribose transporter ATP-binding protein

Query= TCDB::P0AAG8
         (506 letters)



>FitnessBrowser__BFirm:BPHYT_RS27185
          Length = 516

 Score =  414 bits (1063), Expect = e-120
 Identities = 213/498 (42%), Positives = 321/498 (64%), Gaps = 4/498 (0%)

Query: 7   PSSGEYLLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKD 66
           P     +L++ G++K FPGV ALD ++L +    +HA+ GENGAGKSTL+K + G Y+ D
Sbjct: 17  PPVSREILQLKGVSKRFPGVVALDGIDLDLCAGEVHAVCGENGAGKSTLMKIISGQYRAD 76

Query: 67  SGTILFQGKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGMFVDQDKM 126
            G + ++G  + F S  +A   GI+++HQELNLV   SV +N++L R P +G FVD   +
Sbjct: 77  EGVVRYRGAPVQFSSTSDAQAAGIAIIHQELNLVPHLSVAENIYLAREPKRGPFVDYRTL 136

Query: 127 YRETKAIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVN 186
               +     + +++ P   VG LS++Q QM+EIAKA S +A+++IMDEPTSSLTE E  
Sbjct: 137 NSNAQRCLQRIGLNVSPSTLVGALSLAQQQMVEIAKALSLDARVLIMDEPTSSLTESETV 196

Query: 187 HLFTIIRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIAMMV 246
            LF IIR+L+  G  I+YISH+++E+ ++ D VTVLRDG+ IAT   A  T+++I+A MV
Sbjct: 197 QLFRIIRELRAGGVAILYISHRLDEMAEIVDRVTVLRDGRHIATSDFASTTVNEIVARMV 256

Query: 247 GRSLNQRFPDKENKP-GEVILEVRNLTSLRQPSIRDVSFDLHKGEILGIAGLVGAKRTDI 305
           GR L+  +P +++ P  +++L VR+L   R      +SF+L KGEILG AGL+GA RT+ 
Sbjct: 257 GRPLDDAYPPRQSTPSNQILLRVRDLQ--RTGVFGPLSFELRKGEILGFAGLMGAGRTET 314

Query: 306 VETLFGIREKSAGTITLHGKQINNHNANEAINHGFALVTEERRSTGIYAYLDIGFNSLIS 365
              +FG     +G+ITL  + +   +  EAI HG A ++E+R+  G+   + +  N  ++
Sbjct: 315 ARAIFGAERPDSGSITLGDEPVTIGSPREAIRHGIAYLSEDRKKDGLALSMPVSANITLA 374

Query: 366 NIRNYKNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQP 425
           N+R   ++ G L  S   +  +  +  + ++TP  +    +LSGGNQQK++I +WL    
Sbjct: 375 NVRAISSR-GFLRFSEETAIAERYVRELGIRTPTVKQIARNLSGGNQQKIVISKWLYRGS 433

Query: 426 EILMLDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGLVS 485
            IL  DEPTRGIDVGAK+ IY L+  LA  G G+++ISSE+PELLG+TDRI V   G ++
Sbjct: 434 RILFFDEPTRGIDVGAKYAIYGLMDRLAADGVGVVLISSELPELLGMTDRIAVFHEGRIT 493

Query: 486 GIVDTKTTTQNEILRLAS 503
            +++T+ T+Q EIL  AS
Sbjct: 494 AVLETRQTSQEEILHHAS 511



 Score = 64.7 bits (156), Expect = 8e-15
 Identities = 55/229 (24%), Positives = 103/229 (44%), Gaps = 16/229 (6%)

Query: 32  VNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGTILFQGKEIDFHSAKEALENGIS 91
           ++ ++R   I    G  GAG++   + +FG  + DSG+I    + +   S +EA+ +GI+
Sbjct: 291 LSFELRKGEILGFAGLMGAGRTETARAIFGAERPDSGSITLGDEPVTIGSPREAIRHGIA 350

Query: 92  MVHQELN---LVLQRSVMDNMWLGRY---PTKGMFVDQDKMYRETKAIFD----ELDIDI 141
            + ++     L L   V  N+ L       ++G        + E  AI +    EL I  
Sbjct: 351 YLSEDRKKDGLALSMPVSANITLANVRAISSRGFL-----RFSEETAIAERYVRELGIRT 405

Query: 142 DPRARVG-TLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFTIIRKLKERGC 200
               ++   LS    Q I I+K     ++I+  DEPT  +       ++ ++ +L   G 
Sbjct: 406 PTVKQIARNLSGGNQQKIVISKWLYRGSRILFFDEPTRGIDVGAKYAIYGLMDRLAADGV 465

Query: 201 GIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIAMMVGRS 249
           G+V IS ++ E+  + D + V  +G+  A       + ++I+    GRS
Sbjct: 466 GVVLISSELPELLGMTDRIAVFHEGRITAVLETRQTSQEEILHHASGRS 514


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: 587
Number of extensions: 24
Number of successful extensions: 6
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: 506
Length of database: 516
Length adjustment: 35
Effective length of query: 471
Effective length of database: 481
Effective search space:   226551
Effective search space used:   226551
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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Protein sequences (fasta format)
Organisms (tab-delimited)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources