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_RS19720 BPHYT_RS19720 arabinose ABC transporter ATP-binding protein

Query= uniprot:A0A1N7TX47
         (495 letters)



>FitnessBrowser__BFirm:BPHYT_RS19720
          Length = 515

 Score =  351 bits (900), Expect = e-101
 Identities = 192/489 (39%), Positives = 292/489 (59%), Gaps = 3/489 (0%)

Query: 7   LQAEHVAKAYAGVPALRDGRLSLRAGSVHALCGGNGAGKSTFLSILMGITQRDAGSILLN 66
           L+ + +   + GV AL    L +R G VH L G NGAGKST L +L G+ Q  AG++ L+
Sbjct: 26  LRLDGITVRFPGVLALDQVSLEVRRGEVHGLMGENGAGKSTLLKVLSGVNQPAAGTLSLD 85

Query: 67  GAPVQFNRPSEALAAGIAMITQELEPIPYMTVAENIWLGREPRRAGCIVDNKALNRRTRE 126
           G   QF     A+AAG+A+I QEL  +P +TVAEN+ LG  P R G I+D KAL  R   
Sbjct: 86  GVEQQFITTKAAIAAGVAIIYQELHLVPELTVAENLMLGALPNRFG-ILDEKALVARAVR 144

Query: 127 LLDSLEFDVDATSPMHRLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEHEAQTLFKAI 186
            L+ L   +D +  +  LS+ Q Q++EI KA   D +V+  DEPTS++   E   LF+ I
Sbjct: 145 ELERLGEKIDPSQQVKNLSIGQRQMIEIGKALMRDARVIAFDEPTSSLSSRETTQLFRII 204

Query: 187 RRLTAQGAGIVYVSHRLSELAQIADDYSIFRDGAFVESGRMAD-IDRDHLVRGIVGQELT 245
           R L A+G  I+YV+HR+ E+ ++ D  ++FRDG  +++    + +DRD L+  +VG+ + 
Sbjct: 205 RALKAEGRAIIYVTHRMDEVYELCDRVTVFRDGRRIDTFEAGEGLDRDRLISCMVGRSIA 264

Query: 246 RIDHKVGRECAANTCLQVDNLSRAGEFHDISLQLRQGEILGIYGLMGSGRSEFLNCIYGL 305
            +     R+   +  L V  +   G     S   R+GEI+G +GL+G+GRSE +  IYG 
Sbjct: 265 DVYGYRSRDLG-DVQLDVKEMMGRGLREPASFTARKGEIVGFFGLVGAGRSELMKLIYGA 323

Query: 306 TVADSGSVTLQGKPMPIGLPKATINAGMSLVTEDRKDSGLVLTGSILSNIALSAYKRLSS 365
              D+G + L+GK +    P+  + AG++L  EDRK  G+V   S+  N+ +S  +  S 
Sbjct: 324 VKPDAGEIALKGKRVRFATPRDAVRAGVALCPEDRKQEGIVSIASVSDNLNISCRRHFSR 383

Query: 366 WSLINARKETQLAEDMVKRLQIKTTSLELPVASMSGGNQQKVVLAKCLSTEPVCLLCDEP 425
           ++++N RKE Q A++ + +L IKT + + P+ ++SGGNQQKV+L++ L+ +    L DEP
Sbjct: 384 FNVLNGRKEAQTAKEFIGKLAIKTRNGDTPIGTLSGGNQQKVILSRWLAEDIDVFLMDEP 443

Query: 426 TRGIDEGAKQEIYHLLDQFVRGGGAAIVVSSEAPELLHLSDRIAVFKGGRLVTISTDTAL 485
           TRGID GA+ EIY LL      G   IVVSS+  E++ ++DR+ V K GR+V        
Sbjct: 444 TRGIDVGARSEIYGLLYGLAEAGRTVIVVSSDLAEVIGVADRVIVMKEGRIVGDLPKAQA 503

Query: 486 SQEALLRLA 494
           + +AL++LA
Sbjct: 504 TPDALIKLA 512


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: 569
Number of extensions: 26
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 495
Length of database: 515
Length adjustment: 34
Effective length of query: 461
Effective length of database: 481
Effective search space:   221741
Effective search space used:   221741
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.

Links

Downloads

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:

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:

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:

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:

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