Alignments for a candidate for mglA in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for mglA in Paraburkholderia bryophila 376MFSha3.1

Align Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate H281DRAFT_03380 H281DRAFT_03380 monosaccharide ABC transporter ATP-binding protein, CUT2 family

Query= TCDB::P0AAG8
         (506 letters)



>FitnessBrowser__Burk376:H281DRAFT_03380
          Length = 515

 Score =  429 bits (1102), Expect = e-124
 Identities = 219/492 (44%), Positives = 324/492 (65%), Gaps = 4/492 (0%)

Query: 13  LLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGTILF 72
           +L++ G++K FPGV ALD ++L +R   +HA+ GENGAGKSTL+K + G Y  D G I +
Sbjct: 22  ILQLKGVSKRFPGVVALDGIDLDLRSGEVHAVCGENGAGKSTLMKIISGQYHADDGVICY 81

Query: 73  QGKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGMFVDQDKMYRETKA 132
           +GK + F S  +A   GI+++HQELNLV   SV +N++L R P +G FVD   +    + 
Sbjct: 82  EGKPVQFASTSDAQAAGIAIIHQELNLVPHLSVAENIYLAREPKRGPFVDYRTLNANAQR 141

Query: 133 IFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFTII 192
               + +++ P   VG LS++Q QM+EIAKA S +A+++IMDEPTSSLTE E   LF II
Sbjct: 142 CLQRIGLNVSPTTLVGALSIAQQQMVEIAKALSLDARVLIMDEPTSSLTESETVQLFRII 201

Query: 193 RKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIAMMVGRSLNQ 252
           R+L+  G  I+YISH+++E+ ++ D VTVLRDG+ IAT   A  T+++I+A MVGR+L+ 
Sbjct: 202 RELRADGVAILYISHRLDEMAEIVDRVTVLRDGRHIATSDFASTTINEIVARMVGRALDD 261

Query: 253 RFPDKENKPGE-VILEVRNLTSLRQPSIRDVSFDLHKGEILGIAGLVGAKRTDIVETLFG 311
            +P +E+ P E V++ VR+L   R  +   +SFDL KGEILG AGL+GA RT++   +FG
Sbjct: 262 AYPPRESVPTEQVLMRVRDLQ--RTDTFGPLSFDLRKGEILGFAGLMGAGRTEVARAIFG 319

Query: 312 IREKSAGTITLHGKQINNHNANEAINHGFALVTEERRSTGIYAYLDIGFNSLISNIRNYK 371
                +G+I L    +   +  EAI HG A ++E+R+  G+   + +  N  +SN+R   
Sbjct: 320 AERLDSGSIQLGDTPVTIRSPREAIRHGIAYLSEDRKKDGLALSMPVAANITLSNVRAIS 379

Query: 372 NKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQPEILMLD 431
           ++ G L  S   +  +  +  + ++TP  +    +LSGGNQQK++I +WL     IL  D
Sbjct: 380 SR-GFLRFSEETAIAERYVRELAIRTPTVKQIARNLSGGNQQKIVISKWLYRGSRILFFD 438

Query: 432 EPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGLVSGIVDTK 491
           EPTRGIDVGAK+ IY+L+  LA  G G+++ISSE+PELLG+TDRI V   GL++ +++T+
Sbjct: 439 EPTRGIDVGAKYAIYKLMDRLAADGVGVVLISSELPELLGMTDRIAVFHEGLITAVLETR 498

Query: 492 TTTQNEILRLAS 503
            T+Q EIL  AS
Sbjct: 499 QTSQEEILHYAS 510



 Score = 63.2 bits (152), Expect = 2e-14
 Identities = 55/229 (24%), Positives = 101/229 (44%), Gaps = 16/229 (6%)

Query: 32  VNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGTILFQGKEIDFHSAKEALENGIS 91
           ++  +R   I    G  GAG++ + + +FG  + DSG+I      +   S +EA+ +GI+
Sbjct: 290 LSFDLRKGEILGFAGLMGAGRTEVARAIFGAERLDSGSIQLGDTPVTIRSPREAIRHGIA 349

Query: 92  MVHQELN---LVLQRSVMDNMWLGRY---PTKGMFVDQDKMYRETKAIFD----ELDIDI 141
            + ++     L L   V  N+ L       ++G        + E  AI +    EL I  
Sbjct: 350 YLSEDRKKDGLALSMPVAANITLSNVRAISSRGFL-----RFSEETAIAERYVRELAIRT 404

Query: 142 DPRARVG-TLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFTIIRKLKERGC 200
               ++   LS    Q I I+K     ++I+  DEPT  +       ++ ++ +L   G 
Sbjct: 405 PTVKQIARNLSGGNQQKIVISKWLYRGSRILFFDEPTRGIDVGAKYAIYKLMDRLAADGV 464

Query: 201 GIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIAMMVGRS 249
           G+V IS ++ E+  + D + V  +G   A       + ++I+    GRS
Sbjct: 465 GVVLISSELPELLGMTDRIAVFHEGLITAVLETRQTSQEEILHYASGRS 513


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: 20
Number of successful extensions: 7
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: 515
Length adjustment: 35
Effective length of query: 471
Effective length of database: 480
Effective search space:   226080
Effective search space used:   226080
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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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, 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

GapMind for catabolism of small carbon sources