Alignments for a candidate for rhaT' in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for rhaT' in Burkholderia phytofirmans PsJN

Align RhaT, component of Rhamnose porter (Richardson et al., 2004) (Transport activity is dependent on rhamnokinase (RhaK; AAQ92412) activity (Richardson and Oresnik, 2007) This could be an example of group translocation!) (characterized)
to candidate BPHYT_RS28215 BPHYT_RS28215 D-ribose transporter ATP binding protein

Query= TCDB::Q7BSH4
         (512 letters)



>FitnessBrowser__BFirm:BPHYT_RS28215
          Length = 509

 Score =  420 bits (1079), Expect = e-122
 Identities = 222/490 (45%), Positives = 326/490 (66%), Gaps = 1/490 (0%)

Query: 21  LEMRGISQIFPGVKALDNVSIALHPGTVTALIGENGAGKSTLVKILTGIYRPNEGEILVD 80
           LE+R  S+ F  V+AL +  +AL PG V AL+GENGAGKST+VKIL G+++P+ GE++VD
Sbjct: 11  LELRHASKSFGRVRALSDGDLALWPGEVHALLGENGAGKSTVVKILAGVHQPDTGELVVD 70

Query: 81  GRPTTFASAQAAIDAGVTAIHQETVLFDELTVAENIFLGHAPRTRFRTIDWQTMNSRSKA 140
           G    FA+   A DAG+  I+QE  LF +L++AENIF+G  P  R   I +  M      
Sbjct: 71  GEARRFATPAEARDAGLAVIYQEPTLFFDLSIAENIFMGRQPVDRIGRIQYDAMRREVDG 130

Query: 141 LLTALESNIDPTIRLKDLSIAQRHLVAIARALSIEARIVIMDEPTAALSRKEIDDLFRIV 200
           LL +L  ++     ++ LSIA + ++ IA+ALS+ A ++IMDEPTAALS  E++ LF IV
Sbjct: 131 LLASLGVDLRADQLVRGLSIADQQVIEIAKALSLNANVLIMDEPTAALSLPEVERLFTIV 190

Query: 201 RGLKEQGKAILFISHKFDELYEIADDFVVFPRRSRRPVRGVSRKTPQDEIVRMMVGRDVE 260
           R L+E+  AILFI+H+ DE++ +     +  R   +   G++     + IV  MVGRD+E
Sbjct: 191 RKLRERDVAILFITHRLDEVFALTQRVTIM-RDGAKVFDGLTTDLNTEAIVAKMVGRDLE 249

Query: 261 NVFPKIDVAIGGPVLEIRNYSHRTEFRDISFTLRKGEILGVYGLIGAGRSELSQSLFGIT 320
             +PK +   G   L +R  +    F+DISF +R GEI+ + GL+GAGRSE+++++FGI 
Sbjct: 250 TFYPKAERPPGEVRLSVRGLTRVGVFKDISFDVRAGEIVALAGLVGAGRSEVARAIFGID 309

Query: 321 KPLSGKMVLEGQEITIHSPQDAIRAGIVYVPEERGRHGLALPMPIFQNMTLPSLARTSRR 380
              SG++ + G+ +T   P  A+RAG+  VPE+R + GLAL + I +N ++  L R  + 
Sbjct: 310 PLDSGEIWIAGKRLTAGRPAAAVRAGLALVPEDRRQQGLALELSIARNASMTVLGRLVKH 369

Query: 381 GFLRAANEFALARKYAERLDLRAAALSVPVGTLSGGNQQKVVIGKWLATAPKVIILDEPT 440
           G + A +E  LA ++  RL L+A   + PVGTLSGGNQQKVV+GKWLAT PKV+I+DEPT
Sbjct: 370 GLISARSETQLANQWGTRLRLKAGDPNAPVGTLSGGNQQKVVLGKWLATGPKVLIIDEPT 429

Query: 441 KGIDIGSKAAVHGFISELAAEGLSIIMVSSELPEIIGMSDRVLVMKEGLSAGIFERAELS 500
           +GID+G+KA V+  ++EL  +G++++M+SSELPE++GM+DRVLVM EG  +    RA+  
Sbjct: 430 RGIDVGAKAEVYSALAELVRDGMAVLMISSELPEVLGMADRVLVMHEGRISADIARADAD 489

Query: 501 PEALVRAATG 510
            E ++ AA G
Sbjct: 490 EERIMGAALG 499


Lambda     K      H
   0.320    0.137    0.382 

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: 688
Number of extensions: 26
Number of successful extensions: 6
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: 512
Length of database: 509
Length adjustment: 35
Effective length of query: 477
Effective length of database: 474
Effective search space:   226098
Effective search space used:   226098
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)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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, or view the source code.

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