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 GFF2162 PS417_11030 L-arabinose transporter ATP-binding protein

Query= TCDB::Q7BSH4
         (512 letters)



>FitnessBrowser__WCS417:GFF2162
          Length = 500

 Score =  358 bits (919), Expect = e-103
 Identities = 200/492 (40%), Positives = 307/492 (62%), Gaps = 4/492 (0%)

Query: 19  AILEMRGISQIFPGVKALDNVSIALHPGTVTALIGENGAGKSTLVKILTGIYRPNEGEIL 78
           A L   GI + FPGVKALD +S + HPG V AL+GENGAGKSTL+KIL G Y PN G + 
Sbjct: 4   AALRFDGIGKTFPGVKALDGISFSAHPGQVHALMGENGAGKSTLLKILGGAYIPNSGTLH 63

Query: 79  VDGRPTTFASAQAAIDAGVTAIHQETVLFDELTVAENIFLGHAPRTRFRTIDWQTMNSRS 138
           +  +   F SA  +I +GV  IHQE  L  E++VAEN+FLGH P +RF  ++   +  ++
Sbjct: 64  IGEQVMAFKSAADSIASGVAVIHQELHLVPEMSVAENLFLGHLP-SRFGVVNRGLLRKQA 122

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

Query: 199 IVRGLKEQGKAILFISHKFDELYEIADDFVVF-PRRSRRPVRGVSRKTPQDEIVRMMVGR 257
           I+  L+++GK +L++SH+ +E++ I +   VF   R  R    +S  T  D++V  MVGR
Sbjct: 183 IIARLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFEDMSALT-HDQLVTCMVGR 241

Query: 258 DVENVFPKIDVAIGGPVLEIRNYSHRTEFRDISFTLRKGEILGVYGLIGAGRSELSQSLF 317
           D+++++       G   L++           +SF +RKGEILG++GL+GAGR+EL + L 
Sbjct: 242 DIQDIYDYRPREHGEVALKVDGLLGPGLREPVSFNVRKGEILGLFGLVGAGRTELFRLLS 301

Query: 318 GITKPLSGKMVLEGQEITIHSPQDAIRAGIVYVPEERGRHGLALPMPIFQNMTLPSLART 377
           G+ +  +G++ L G+ + + SP+DAI AG++  PE+R + G+     + +N+ + +    
Sbjct: 302 GLERASAGQLELCGEPLHLQSPRDAIAAGVLLCPEDRKKEGIIPLSSVAENINISARGAH 361

Query: 378 SRRGF-LRAANEFALARKYAERLDLRAAALSVPVGTLSGGNQQKVVIGKWLATAPKVIIL 436
           S  G+ LR   E   A +    + ++    +  +  LSGGNQQK ++G+WL+   KV++L
Sbjct: 362 STFGWLLREGWEKGNADQQINAMKVKTPNAAQKIMYLSGGNQQKSILGRWLSMPMKVLLL 421

Query: 437 DEPTKGIDIGSKAAVHGFISELAAEGLSIIMVSSELPEIIGMSDRVLVMKEGLSAGIFER 496
           DEPT+GIDIG+KA ++  I  LAA+G+++I+VSS+L E++G++DR+LV+ EG   G   R
Sbjct: 422 DEPTRGIDIGAKAEIYQIIHNLAAQGIAVIVVSSDLMEVMGIADRILVLCEGALRGEQTR 481

Query: 497 AELSPEALVRAA 508
              +   L++ A
Sbjct: 482 EHATESNLLQLA 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: 581
Number of extensions: 29
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: 500
Length adjustment: 34
Effective length of query: 478
Effective length of database: 466
Effective search space:   222748
Effective search space used:   222748
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