GapMind for catabolism of small carbon sources

 

Aligments for a candidate for rhaT' in Pseudomonas fluorescens GW456-L13

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 PfGW456L13_7 ABC transporter ATP-binding protein

Query= TCDB::Q7BSH4
         (512 letters)



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_7 ABC transporter
           ATP-binding protein
          Length = 521

 Score =  222 bits (565), Expect = 3e-62
 Identities = 146/474 (30%), Positives = 241/474 (50%), Gaps = 19/474 (4%)

Query: 21  LEMRGISQIFPGVKALDNVSIALHPGTVTALIGENGAGKSTLVKILTGIYRPNEGEILVD 80
           L++R I++ +PG  A D + + + PG + AL+GENGAGKSTL+KI+ G+   + GE++  
Sbjct: 14  LQLRRITKRYPGCLANDAIDLTIAPGEIHALLGENGAGKSTLMKIIYGVTHADSGEVIWQ 73

Query: 81  GRPTTFASAQAAIDAGVTAIHQETVLFDELTVAENIFL--GHAPRTRFRTIDWQTMNSRS 138
           G+  +  +   A   G+  + Q   LF+ L+VA+NI L  G A  T       + +  + 
Sbjct: 74  GQRVSLRNPAQARGLGIGMVFQHFSLFETLSVAQNIALAMGAAAGTP------KQLEPKI 127

Query: 139 KALLTALESNIDPTIRLKDLSIAQRHLVAIARALSIEARIVIMDEPTAALSRKEIDDLFR 198
           + +       ++P   +  LSI +R  V I R L  + R++I+DEPT+ L+ +E DDLF 
Sbjct: 128 REVSRRYGMTLEPERLVHSLSIGERQRVEIIRCLMQDIRLLILDEPTSVLTPQEADDLFV 187

Query: 199 IVRGLKEQGKAILFISHKFDELYEIADDFVVFPRRSRRPVRGVSRKTPQDEIVRMMVGRD 258
            +R L  +G +ILFISHK  E+  +     V  R  R     V  +    ++ R+MVG  
Sbjct: 188 TLRRLAAEGCSILFISHKLGEVRALCHSATVL-RGGRVAGHCVPAECSDQQLARLMVGEA 246

Query: 259 VENVFPKIDVAIGGPVLEIRNYSHRT------EFRDISFTLRKGEILGVYGLIGAGRSEL 312
            E +     V  G   L++R  S            +I   +R+GEI+G+ G+ G G+ EL
Sbjct: 247 AELIADYPKVTGGDACLDVRGLSWHNPDPFGCSLANIDLEVRRGEIVGIAGVAGNGQDEL 306

Query: 313 SQSLFG--ITKPLSGKMVLEGQEITIHSPQDAIR-AGIVYVPEERGRHGLALPMPIFQNM 369
              L G  +    +   +  G+E   H   DA R  G+ +VP ER  HG    + +  N 
Sbjct: 307 LALLSGEALLPRNASATIRFGKEPVAHLRPDARRQLGLAFVPAERLGHGAVPELSLADNA 366

Query: 370 TLPSLAR-TSRRGFLRAANEFALARKYAERLDLRAAALSVPVGTLSGGNQQKVVIGKWLA 428
            L +        G ++     ALA +   R  ++      P  +LSGGN QK ++G+ + 
Sbjct: 367 LLTAFQHGLVSNGLIQRGKVEALAEEIIRRFGVKTPDSQAPARSLSGGNLQKFILGREIL 426

Query: 429 TAPKVIILDEPTKGIDIGSKAAVHGFISELAAEGLSIIMVSSELPEIIGMSDRV 482
             P++++   PT G+D+G+ A +H  +  L   G +I+++S +L E+  +SDR+
Sbjct: 427 QQPRLLVAAHPTWGVDVGAAATIHRALIALRDAGAAILVISEDLDELFQISDRL 480


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: 638
Number of extensions: 38
Number of successful extensions: 8
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: 521
Length adjustment: 35
Effective length of query: 477
Effective length of database: 486
Effective search space:   231822
Effective search space used:   231822
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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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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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