Alignments for a candidate for ytfR in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for ytfR in Burkholderia phytofirmans PsJN

Align galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized)
to candidate BPHYT_RS27185 BPHYT_RS27185 D-ribose transporter ATP-binding protein

Query= ecocyc::YTFR-MONOMER
         (500 letters)



>FitnessBrowser__BFirm:BPHYT_RS27185
          Length = 516

 Score =  372 bits (956), Expect = e-107
 Identities = 201/493 (40%), Positives = 307/493 (62%), Gaps = 8/493 (1%)

Query: 7   QEILRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTI 66
           +EIL+ +G+SK FPGV ALD +D  L  GE+ A+ GENGAGKSTL+K ++G Y AD G +
Sbjct: 21  REILQLKGVSKRFPGVVALDGIDLDLCAGEVHAVCGENGAGKSTLMKIISGQYRADEGVV 80

Query: 67  WLEGQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGREPKRFGLLRRKEMEKRA 126
              G  +   +T+ AQ  GI  ++QE+NL+P++SVA+N+++ REPKR   +  + +   A
Sbjct: 81  RYRGAPVQFSSTSDAQAAGIAIIHQELNLVPHLSVAENIYLAREPKRGPFVDYRTLNSNA 140

Query: 127 TELMASYGFSLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFD 186
              +   G ++     +   S+A QQ+V I +A+ L A+VLI+DEPT+SL   E   LF 
Sbjct: 141 QRCLQRIGLNVSPSTLVGALSLAQQQMVEIAKALSLDARVLIMDEPTSSLTESETVQLFR 200

Query: 187 LMRQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMMLGREL 246
           ++R+LR  GV++++++H LD++ ++ DR+TVLR+G  +   +       E+V  M+GR L
Sbjct: 201 IIRELRAGGVAILYISHRLDEMAEIVDRVTVLRDGRHIATSDFASTTVNEIVARMVGRPL 260

Query: 247 DTHALQRAGRTLLSDKPVAAFKNYGKKGTIAPFDLEVRPGEIVGLAGLLGSGRTETAEVI 306
           D     R  ++  S++ +   ++  + G   P   E+R GEI+G AGL+G+GRTETA  I
Sbjct: 261 DDAYPPR--QSTPSNQILLRVRDLQRTGVFGPLSFELRKGEILGFAGLMGAGRTETARAI 318

Query: 307 FGIKPADSGTALIKGKPQNLRSPHQASVLGIGFCPEDRKTDGIIAAASVRENIILA---L 363
           FG +  DSG+  +  +P  + SP +A   GI +  EDRK DG+  +  V  NI LA    
Sbjct: 319 FGAERPDSGSITLGDEPVTIGSPREAIRHGIAYLSEDRKKDGLALSMPVSANITLANVRA 378

Query: 364 QAQRGWLRPISRKEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTRPQF 423
            + RG+LR     E+  IAER++R+LGIRTP+ +Q    LSGGNQQK+++S+WL    + 
Sbjct: 379 ISSRGFLR---FSEETAIAERYVRELGIRTPTVKQIARNLSGGNQQKIVISKWLYRGSRI 435

Query: 424 LILDEPTRGIDVGAHAEIIRLIETLCADGLALLVISSELEELVGYADRVIIMRDRKQVAE 483
           L  DEPTRGIDVGA   I  L++ L ADG+ +++ISSEL EL+G  DR+ +  + +  A 
Sbjct: 436 LFFDEPTRGIDVGAKYAIYGLMDRLAADGVGVVLISSELPELLGMTDRIAVFHEGRITAV 495

Query: 484 IPLAELSVPAIMN 496
           +   + S   I++
Sbjct: 496 LETRQTSQEEILH 508



 Score = 77.8 bits (190), Expect = 9e-19
 Identities = 63/249 (25%), Positives = 111/249 (44%), Gaps = 10/249 (4%)

Query: 2   TTDQHQEILRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHA 61
           +T  +Q +LR   L +          + F LR+GEI+   G  GAG++   +A+ G    
Sbjct: 269 STPSNQILLRVRDLQR----TGVFGPLSFELRKGEILGFAGLMGAGRTETARAIFGAERP 324

Query: 62  DRGTIWLEGQAISPKNTAHAQQLGIGTVYQEVN---LLPNMSVADNLFIG--REPKRFGL 116
           D G+I L  + ++  +   A + GI  + ++     L  +M V+ N+ +   R     G 
Sbjct: 325 DSGSITLGDEPVTIGSPREAIRHGIAYLSEDRKKDGLALSMPVSANITLANVRAISSRGF 384

Query: 117 LRRKEMEKRATELMASYGFSLD-VREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTAS 175
           LR  E    A   +   G     V++     S   QQ + I + +   +++L  DEPT  
Sbjct: 385 LRFSEETAIAERYVRELGIRTPTVKQIARNLSGGNQQKIVISKWLYRGSRILFFDEPTRG 444

Query: 176 LDTQEVELLFDLMRQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQI 235
           +D      ++ LM +L   GV ++ ++  L ++  ++DRI V   G      ET +  Q 
Sbjct: 445 IDVGAKYAIYGLMDRLAADGVGVVLISSELPELLGMTDRIAVFHEGRITAVLETRQTSQE 504

Query: 236 ELVKMMLGR 244
           E++    GR
Sbjct: 505 EILHHASGR 513


Lambda     K      H
   0.321    0.138    0.391 

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: 615
Number of extensions: 22
Number of successful extensions: 8
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: 500
Length of database: 516
Length adjustment: 34
Effective length of query: 466
Effective length of database: 482
Effective search space:   224612
Effective search space used:   224612
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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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Candidates (tab-delimited)
Steps (tab-delimited)
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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