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_RS20740 BPHYT_RS20740 D-ribose transporter ATP binding protein

Query= TCDB::P0AAG8
         (506 letters)



>FitnessBrowser__BFirm:BPHYT_RS20740
          Length = 503

 Score =  424 bits (1089), Expect = e-123
 Identities = 215/494 (43%), Positives = 329/494 (66%), Gaps = 5/494 (1%)

Query: 13  LLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGTILF 72
           L+ +  ++K FPGV+AL  V  ++    +HALMGENGAGKSTL+K L G+Y +D+G IL+
Sbjct: 4   LISVKRLSKRFPGVRALHEVQFELVAGEVHALMGENGAGKSTLMKILAGVYTRDTGEILY 63

Query: 73  QGKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTK--GMFVDQDKMYRET 130
           +G+ +DF S +EA   G+ ++HQEL L+   ++  NM++GR P    G+F+D+DK+  + 
Sbjct: 64  EGQPVDFQSPREAQAVGVGIIHQELQLMNHLTIAQNMFIGREPRGRLGLFLDEDKLNAQA 123

Query: 131 KAIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFT 190
             I   + + +DPRA V +L+V++ QM+EIAKA S++++++IMDEPTS+L + E+  LF 
Sbjct: 124 HDILARMHVTLDPRALVSSLTVARQQMVEIAKALSFDSRVLIMDEPTSALNDAEIAELFR 183

Query: 191 IIRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIAMMVGRSL 250
           IIR LK+RG GI+YISHKM+E+ Q+ D VTVLRDG+++AT  +   T+  II MMVGR+L
Sbjct: 184 IIRDLKKRGVGIIYISHKMDELKQIADRVTVLRDGEYVATVAVKDTTVQAIIGMMVGRTL 243

Query: 251 NQRFPDKE-NKPGEVILEVRNLTSLRQPSIRDVSFDLHKGEILGIAGLVGAKRTDIVETL 309
               P +     GEV LEV  L +   P +RDVSF L KGEILG AGL+GA RT++   +
Sbjct: 244 TDAAPSQHIANQGEVALEVTRLNA--GPLVRDVSFALRKGEILGFAGLMGAGRTEVARAV 301

Query: 310 FGIREKSAGTITLHGKQINNHNANEAINHGFALVTEERRSTGIYAYLDIGFNSLISNIRN 369
           FG     +G I + G +    N ++A+  G   ++E+R+  G+   + +  N ++SN+R 
Sbjct: 302 FGADPIESGEIVVKGVKATIRNPSDAVARGIGYLSEDRKRFGLATGMSVESNIVMSNLRK 361

Query: 370 YKNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQPEILM 429
           + +    L  ++++      I+ + ++TP    ++  LSGGNQQK++I +WL    ++L 
Sbjct: 362 FLSLNFFLRRTQIRKTAAHFINLLAIRTPSATQEVRLLSGGNQQKIVIAKWLERDCDVLF 421

Query: 430 LDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGLVSGIVD 489
            DEPTRGIDVGAK EIY+L+  LA +GK I++ISSE+PE+L ++DRI+VM  G ++G + 
Sbjct: 422 FDEPTRGIDVGAKSEIYKLLRSLADQGKAIVMISSELPEILRMSDRIVVMCEGRITGELA 481

Query: 490 TKTTTQNEILRLAS 503
               TQ  I++LA+
Sbjct: 482 AAGATQERIMQLAT 495



 Score = 78.2 bits (191), Expect = 6e-19
 Identities = 64/249 (25%), Positives = 120/249 (48%), Gaps = 13/249 (5%)

Query: 8   SSGEYLLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDS 67
           + GE  LE++ +N   P V+   +V+  +R   I    G  GAG++ + + +FG    +S
Sbjct: 254 NQGEVALEVTRLNAG-PLVR---DVSFALRKGEILGFAGLMGAGRTEVARAVFGADPIES 309

Query: 68  GTILFQGKEIDFHSAKEALENGISMVHQE---LNLVLQRSVMDNMWLG---RYPTKGMFV 121
           G I+ +G +    +  +A+  GI  + ++     L    SV  N+ +    ++ +   F+
Sbjct: 310 GEIVVKGVKATIRNPSDAVARGIGYLSEDRKRFGLATGMSVESNIVMSNLRKFLSLNFFL 369

Query: 122 DQDKMYRETKAIFDELDIDIDPRA--RVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSS 179
            + ++ R+T A F  L     P A   V  LS    Q I IAK    +  ++  DEPT  
Sbjct: 370 RRTQI-RKTAAHFINLLAIRTPSATQEVRLLSGGNQQKIVIAKWLERDCDVLFFDEPTRG 428

Query: 180 LTEKEVNHLFTIIRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMD 239
           +     + ++ ++R L ++G  IV IS ++ EI ++ D + V+ +G+       AG T +
Sbjct: 429 IDVGAKSEIYKLLRSLADQGKAIVMISSELPEILRMSDRIVVMCEGRITGELAAAGATQE 488

Query: 240 KIIAMMVGR 248
           +I+ +   R
Sbjct: 489 RIMQLATQR 497


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: 558
Number of extensions: 22
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: 503
Length adjustment: 34
Effective length of query: 472
Effective length of database: 469
Effective search space:   221368
Effective search space used:   221368
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:

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