GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rhaT' in Pseudomonas fluorescens FW300-N1B4

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 Pf1N1B4_1243 ABC transporter ATP-binding protein

Query= TCDB::Q7BSH4
         (512 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1243
          Length = 521

 Score =  216 bits (550), Expect = 2e-60
 Identities = 146/474 (30%), Positives = 242/474 (51%), Gaps = 19/474 (4%)

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

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

Query: 139 KALLTALESNIDPTIRLKDLSIAQRHLVAIARALSIEARIVIMDEPTAALSRKEIDDLFR 198
           + +       ++P   +  LSI +R  V I R L  + R++I+DEPT+ L+ +E D+LF 
Sbjct: 128 REVSQRYGMALEPERLVHSLSIGERQRVEIIRCLMQDIRLLILDEPTSVLTPQEADELFV 187

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

Query: 259 VENV--FPKI---DVAIGGPVLEIRNYS-HRTEFRDISFTLRKGEILGVYGLIGAGRSEL 312
            E +  +PK+   D  +    L   N        ++I F +R GEI+GV G+ G G+ EL
Sbjct: 247 AELITDYPKVMGADAFLSVTGLSWHNPDPFGCSLKNIDFDVRSGEIVGVAGVAGNGQDEL 306

Query: 313 SQSLFG---ITKPLSGKMVLEGQEITIHSPQDAIRAGIVYVPEERGRHGLALPMPIFQNM 369
              L G   + +  S  +   GQ +    P    + G+ +VP ER  HG    + +  N 
Sbjct: 307 LALLSGEERLPRDDSATISFGGQPVAHLRPDARRKLGLAFVPAERLGHGAVPELSLADNA 366

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

Query: 429 TAPKVIILDEPTKGIDIGSKAAVHGFISELAAEGLSIIMVSSELPEIIGMSDRV 482
             PK+++   PT G+D+G+ A +H  +  L   G +I+++S +L E+  + DR+
Sbjct: 427 QQPKLLVAAHPTWGVDVGAAATIHRALIALRDAGAAILVISEDLDELFQICDRL 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: 621
Number of extensions: 32
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 (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