GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rhaT' in Pseudomonas simiae WCS417

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 GFF4164 PS417_21330 L-arabinose transporter ATP-binding protein

Query= TCDB::Q7BSH4
         (512 letters)



>FitnessBrowser__WCS417:GFF4164
          Length = 499

 Score =  355 bits (912), Expect = e-102
 Identities = 198/493 (40%), Positives = 298/493 (60%), Gaps = 6/493 (1%)

Query: 19  AILEMRGISQIFPGVKALDNVSIALHPGTVTALIGENGAGKSTLVKILTGIYRPNEGEIL 78
           A L   GI + FPGVKAL  +S    P  V AL+GENGAGKSTL+KIL G Y P+ G + 
Sbjct: 4   AALRFNGIGKEFPGVKALSQISFEARPREVHALMGENGAGKSTLLKILGGAYLPSSGTLQ 63

Query: 79  VDGRPTTFASAQAAIDAGVTAIHQETVLFDELTVAENIFLGHAPRTRFRTIDWQTMNSRS 138
           +  +   F SA  +I  GV  IHQE  L  E+TVAEN+FLGH P TRF  ++   +  ++
Sbjct: 64  IGEQTMDFKSAADSIACGVAVIHQELHLVPEMTVAENLFLGHLP-TRFGVVNRSQLRKQA 122

Query: 139 KALLTALESNIDPTIRLKDLSIAQRHLVAIARALSIEARIVIMDEPTAALSRKEIDDLFR 198
            A L  L   IDP  +L  LS+ QR LV IA+ALS  A ++  DEPT++LS +EID L  
Sbjct: 123 LACLKGLADEIDPDEKLGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLMA 182

Query: 199 IVRGLKEQGKAILFISHKFDELYEIADDFVVFPRRSRRPVRGVS--RKTPQDEIVRMMVG 256
           I+  L+++GK +L++SH+ +E++ I +   VF  +  R VR          D++V  MVG
Sbjct: 183 IITRLRDEGKVVLYVSHRMEEVFRICNAVTVF--KDGRYVRTFDDMNALSHDQLVTCMVG 240

Query: 257 RDVENVFPKIDVAIGGPVLEIRNYSHRTEFRDISFTLRKGEILGVYGLIGAGRSELSQSL 316
           RD+++++       G   L++           +S  + KGEILG++GL+GAGR+EL + L
Sbjct: 241 RDIQDIYDYRQREQGEVALKVEGLLGPGLREPVSLNVHKGEILGLFGLVGAGRTELFRLL 300

Query: 317 FGITKPLSGKMVLEGQEITIHSPQDAIRAGIVYVPEERGRHGLALPMPIFQNMTLPSLAR 376
            G+T+  +G + L GQ + + SP+DAI AG++  PE+R + G+     + +N+ + +   
Sbjct: 301 SGLTRSTAGSLALCGQTLQLRSPRDAIAAGVLLCPEDRKKEGIIPLSSVAENINISARGA 360

Query: 377 TSRRGF-LRAANEFALARKYAERLDLRAAALSVPVGTLSGGNQQKVVIGKWLATAPKVII 435
            S  G+ LR   E   A +  + + ++       +  LSGGNQQK ++G+WL+   KV++
Sbjct: 361 HSTFGWLLRDGWETTNADRQIKAMKVKTPNAEQKIMYLSGGNQQKAILGRWLSMPMKVLL 420

Query: 436 LDEPTKGIDIGSKAAVHGFISELAAEGLSIIMVSSELPEIIGMSDRVLVMKEGLSAGIFE 495
           LDEPT+GIDIG+K+ ++  I  LAA G+++I+VSS+L E++G+SDR+LVM EG   G   
Sbjct: 421 LDEPTRGIDIGAKSEIYQIIHNLAASGIAVIVVSSDLMEVMGISDRILVMSEGALTGELT 480

Query: 496 RAELSPEALVRAA 508
           R +     L++ A
Sbjct: 481 RDQADEARLLQLA 493


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: 576
Number of extensions: 26
Number of successful extensions: 9
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: 499
Length adjustment: 34
Effective length of query: 478
Effective length of database: 465
Effective search space:   222270
Effective search space used:   222270
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