Alignments for a candidate for BPHYT_RS34245 in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for BPHYT_RS34245 in Burkholderia phytofirmans PsJN

Align ABC transporter related; Flags: Precursor (characterized, see rationale)
to candidate BPHYT_RS01820 BPHYT_RS01820 sugar ABC transporter ATP-binding protein

Query= uniprot:B2T9V9
         (510 letters)



>FitnessBrowser__BFirm:BPHYT_RS01820
          Length = 544

 Score =  293 bits (750), Expect = 1e-83
 Identities = 173/487 (35%), Positives = 271/487 (55%), Gaps = 5/487 (1%)

Query: 6   SELTSSVPVVEALEVTKRFGSTAALNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLRK 65
           S LT S P++E  ++   FG   AL   ++ V  GE HAL+G+NGAGKST++ ILTG  +
Sbjct: 11  SPLTRS-PLLEMQDIGISFGGVPALRSANLSVAAGEVHALIGQNGAGKSTMIKILTGAYR 69

Query: 66  PDTGEVRFSGAAAPSIADRDAWRERVACVYQHSTIIRDLSVAENLFINRQPLRGGVIDWQ 125
             +G VRF G        + A    ++ +YQ   ++   SVAEN+F+ R+P R G+IDW 
Sbjct: 70  RGSGSVRFEGREVDFRTPKQAREAGISTIYQEINLVPFRSVAENIFLGREPRRFGLIDWH 129

Query: 126 AMRRDARALLDHWKIDVREDARAGDLSVEARQLVEIARALSYGARFIILDEPTAQLDGDE 185
           A+++ A ALL+ + + +      G  S   +Q+V +ARA+S  A+ +I+DE T+ LD  E
Sbjct: 130 AVQQRAAALLESFGLQIDVKKPVGRYSTAIQQMVALARAVSSDAKMVIMDESTSSLDERE 189

Query: 186 IKRLFRRISELQREGVTFLFISHHLQEVYEICQAVTVLRDARHIVSAPVSALPREQLIEA 245
           ++ LF  + +L+ +G   +F+SH L E+Y +C  VTV+RD + +  + ++ + + QL+  
Sbjct: 190 VELLFTVVRKLRDDGRAVIFVSHRLDELYALCDRVTVMRDGQTVAQSTMADMDKLQLVTT 249

Query: 246 MTGERGGLAVA-DAAARGALPADTAVALELKELTGA--DYEGVSFTVKRGEVVGLTGATS 302
           M G      V  DA AR A  A     +       A      VS  V  GE VGL G   
Sbjct: 250 MLGRTLAAVVQDDAEAREANLARRGKQMIAATQLSAHPKVSDVSLEVHAGEAVGLAGLLG 309

Query: 303 SGRTSVAEAIAGLRAAKRGTISVDGAILPPGDVPASLAHGIGCVPKDRHHEGLVLTQSVA 362
           SGRT     + G    +RG++S+ G  +       +++ G+  + +DR  EG+V   SV 
Sbjct: 310 SGRTETMRLMFGADPLERGSLSIGGETVALKSPQDAISRGLAYLTEDRKAEGIVPELSVR 369

Query: 363 ENASMTIARVLGKFGIAAPAKKNAFGQKMIDALGIVAQGPEHVVSGLSGGNQQKVVMARA 422
           +N ++   R L K G+    K+ A   + I +LGI  +  +  +  LSGGNQQKV++AR 
Sbjct: 370 DNLTLVCLRTLAKNGVVDVKKQQAIVDRFIASLGIKLRSADQPIRELSGGNQQKVLLARW 429

Query: 423 LATNPNVLVLIDPTAGVDVKSKEALLSVVDRVREEGKAVLVVSGELDDL-RTCDRVLVMF 481
           LA  P++L+L +PT G+DV +K  +  +V  +R+ G AVL+ + EL++L    DR +V+ 
Sbjct: 430 LAAEPSLLLLDEPTRGIDVGAKAEVAKIVRELRDAGLAVLLSASELEELTAVADRAVVIR 489

Query: 482 RGRVAAE 488
            GR  AE
Sbjct: 490 DGRTVAE 496



 Score = 68.9 bits (167), Expect = 4e-16
 Identities = 63/262 (24%), Positives = 119/262 (45%), Gaps = 14/262 (5%)

Query: 30  LNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDTGEVRFSGAAAPSIADRDAWRE 89
           ++DVS+ V  GE+  L G  G+G++  + ++ G    + G +   G      + +DA   
Sbjct: 289 VSDVSLEVHAGEAVGLAGLLGSGRTETMRLMFGADPLERGSLSIGGETVALKSPQDAISR 348

Query: 90  RVACVYQHST---IIRDLSVAENLFIN--RQPLRGGVIDWQAMRRDARALLDHWKIDVRE 144
            +A + +      I+ +LSV +NL +   R   + GV+D +  +      +    I +R 
Sbjct: 349 GLAYLTEDRKAEGIVPELSVRDNLTLVCLRTLAKNGVVDVKKQQAIVDRFIASLGIKLRS 408

Query: 145 -DARAGDLSVEARQLVEIARALSYGARFIILDEPTAQLDGDEIKRLFRRISELQREGVTF 203
            D    +LS   +Q V +AR L+     ++LDEPT  +D      + + + EL+  G+  
Sbjct: 409 ADQPIRELSGGNQQKVLLARWLAAEPSLLLLDEPTRGIDVGAKAEVAKIVRELRDAGLAV 468

Query: 204 LFISHHLQEVYEICQAVTVLRDARHIVSAPVSALPREQLIEAMT-GERGGLAVADAAARG 262
           L  +  L+E+  +     V+RD R +     + +    +++A+  G  G   +A+A    
Sbjct: 469 LLSASELEELTAVADRAVVIRDGRTVAELNGADMSETAIMDAIAYGSDGHSQLAEA---- 524

Query: 263 ALPADTAVALELKELTGADYEG 284
              A TA A  +++    D  G
Sbjct: 525 ---AQTANAAHIEDALEGDRHG 543


Lambda     K      H
   0.318    0.134    0.377 

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: 639
Number of extensions: 28
Number of successful extensions: 5
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: 510
Length of database: 544
Length adjustment: 35
Effective length of query: 475
Effective length of database: 509
Effective search space:   241775
Effective search space used:   241775
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)
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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