Alignments for a candidate for PS417_12065 in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for PS417_12065 in Burkholderia phytofirmans PsJN

Align D-ribose transporter ATP-binding protein; SubName: Full=Putative xylitol transport system ATP-binding protein; SubName: Full=Sugar ABC transporter ATP-binding protein (characterized, see rationale)
to candidate BPHYT_RS28215 BPHYT_RS28215 D-ribose transporter ATP binding protein

Query= uniprot:A0A1N7TX47
         (495 letters)



>FitnessBrowser__BFirm:BPHYT_RS28215
          Length = 509

 Score =  355 bits (910), Expect = e-102
 Identities = 204/478 (42%), Positives = 288/478 (60%), Gaps = 4/478 (0%)

Query: 7   LQAEHVAKAYAGVPALRDGRLSLRAGSVHALCGGNGAGKSTFLSILMGITQRDAGSILLN 66
           L+  H +K++  V AL DG L+L  G VHAL G NGAGKST + IL G+ Q D G ++++
Sbjct: 11  LELRHASKSFGRVRALSDGDLALWPGEVHALLGENGAGKSTVVKILAGVHQPDTGELVVD 70

Query: 67  GAPVQFNRPSEALAAGIAMITQELEPIPYMTVAENIWLGREPRRAGCIVDNKALNRRTRE 126
           G   +F  P+EA  AG+A+I QE      +++AENI++GR+P      +   A+ R    
Sbjct: 71  GEARRFATPAEARDAGLAVIYQEPTLFFDLSIAENIFMGRQPVDRIGRIQYDAMRREVDG 130

Query: 127 LLDSLEFDVDATSPMHRLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEHEAQTLFKAI 186
           LL SL  D+ A   +  LS+A  Q++EIAKA S +  V+IMDEPT+A+   E + LF  +
Sbjct: 131 LLASLGVDLRADQLVRGLSIADQQVIEIAKALSLNANVLIMDEPTAALSLPEVERLFTIV 190

Query: 187 RRLTAQGAGIVYVSHRLSELAQIADDYSIFRDGAFVESGRMADIDRDHLVRGIVGQELTR 246
           R+L  +   I++++HRL E+  +    +I RDGA V  G   D++ + +V  +VG++L  
Sbjct: 191 RKLRERDVAILFITHRLDEVFALTQRVTIMRDGAKVFDGLTTDLNTEAIVAKMVGRDLET 250

Query: 247 IDHKVGRECAANTCLQVDNLSRAGEFHDISLQLRQGEILGIYGLMGSGRSEFLNCIYGLT 306
              K  R       L V  L+R G F DIS  +R GEI+ + GL+G+GRSE    I+G+ 
Sbjct: 251 FYPKAERP-PGEVRLSVRGLTRVGVFKDISFDVRAGEIVALAGLVGAGRSEVARAIFGID 309

Query: 307 VADSGSVTLQGKPMPIGLPKATINAGMSLVTEDRKDSGLVLTGSILSNIALSAYKRLSSW 366
             DSG + + GK +  G P A + AG++LV EDR+  GL L  SI  N +++   RL   
Sbjct: 310 PLDSGEIWIAGKRLTAGRPAAAVRAGLALVPEDRRQQGLALELSIARNASMTVLGRLVKH 369

Query: 367 SLINARKETQLAEDMVKRLQIKTTSLELPVASMSGGNQQKVVLAKCLSTEPVCLLCDEPT 426
            LI+AR ETQLA     RL++K      PV ++SGGNQQKVVL K L+T P  L+ DEPT
Sbjct: 370 GLISARSETQLANQWGTRLRLKAGDPNAPVGTLSGGNQQKVVLGKWLATGPKVLIIDEPT 429

Query: 427 RGIDEGAKQEIYHLLDQFVRGGGAAIVVSSEAPELLHLSDRIAVFKGGRLVTISTDTA 484
           RGID GAK E+Y  L + VR G A +++SSE PE+L ++DR+ V   GR   IS D A
Sbjct: 430 RGIDVGAKAEVYSALAELVRDGMAVLMISSELPEVLGMADRVLVMHEGR---ISADIA 484



 Score = 78.6 bits (192), Expect = 5e-19
 Identities = 60/239 (25%), Positives = 107/239 (44%), Gaps = 11/239 (4%)

Query: 19  VPALRDGRLSLRAGSVHALCGGNGAGKSTFLSILMGITQRDAGSILLNGAPVQFNRPSEA 78
           V   +D    +RAG + AL G  GAG+S     + GI   D+G I + G  +   RP+ A
Sbjct: 272 VGVFKDISFDVRAGEIVALAGLVGAGRSEVARAIFGIDPLDSGEIWIAGKRLTAGRPAAA 331

Query: 79  LAAGIAMITQELEPIPYMTVAENIWLGREPRRA--GCIVDNKALNRRTRELLDS-----L 131
           + AG+A++ ++        +A  + + R       G +V +  ++ R+   L +     L
Sbjct: 332 VRAGLALVPEDRRQ---QGLALELSIARNASMTVLGRLVKHGLISARSETQLANQWGTRL 388

Query: 132 EFDV-DATSPMHRLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEHEAQTLFKAIRRLT 190
                D  +P+  LS    Q V + K  +   +V+I+DEPT  I       ++ A+  L 
Sbjct: 389 RLKAGDPNAPVGTLSGGNQQKVVLGKWLATGPKVLIIDEPTRGIDVGAKAEVYSALAELV 448

Query: 191 AQGAGIVYVSHRLSELAQIADDYSIFRDGAFVESGRMADIDRDHLVRGIVGQELTRIDH 249
             G  ++ +S  L E+  +AD   +  +G        AD D + ++   +GQ +  + H
Sbjct: 449 RDGMAVLMISSELPEVLGMADRVLVMHEGRISADIARADADEERIMGAALGQPMPPLGH 507



 Score = 58.9 bits (141), Expect = 4e-13
 Identities = 50/229 (21%), Positives = 101/229 (44%), Gaps = 9/229 (3%)

Query: 265 NLSRAGEFHDISLQLRQGEILGIYGLMGSGRSEFLNCIYGLTVADSGSVTLQGKPMPIGL 324
           +  R     D  L L  GE+  + G  G+G+S  +  + G+   D+G + + G+      
Sbjct: 19  SFGRVRALSDGDLALWPGEVHALLGENGAGKSTVVKILAGVHQPDTGELVVDGEARRFAT 78

Query: 325 PKATINAGMSLVTEDRKDSGLVLTGSILSNIALSAYK--RLSSWSLINARKETQLAEDMV 382
           P    +AG++++ ++     L    SI  NI +      R+        R+E    + ++
Sbjct: 79  PAEARDAGLAVIYQEPT---LFFDLSIAENIFMGRQPVDRIGRIQYDAMRREV---DGLL 132

Query: 383 KRLQIKTTSLELPVASMSGGNQQKVVLAKCLSTEPVCLLCDEPTRGIDEGAKQEIYHLLD 442
             L +   + +L V  +S  +QQ + +AK LS     L+ DEPT  +     + ++ ++ 
Sbjct: 133 ASLGVDLRADQL-VRGLSIADQQVIEIAKALSLNANVLIMDEPTAALSLPEVERLFTIVR 191

Query: 443 QFVRGGGAAIVVSSEAPELLHLSDRIAVFKGGRLVTISTDTALSQEALL 491
           +      A + ++    E+  L+ R+ + + G  V     T L+ EA++
Sbjct: 192 KLRERDVAILFITHRLDEVFALTQRVTIMRDGAKVFDGLTTDLNTEAIV 240


Lambda     K      H
   0.319    0.135    0.381 

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: 597
Number of extensions: 33
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 495
Length of database: 509
Length adjustment: 34
Effective length of query: 461
Effective length of database: 475
Effective search space:   218975
Effective search space used:   218975
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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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