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 GFF2332 PS417_11890 D-ribose transporter ATP-binding protein

Query= TCDB::Q7BSH4
         (512 letters)



>FitnessBrowser__WCS417:GFF2332
          Length = 517

 Score =  404 bits (1039), Expect = e-117
 Identities = 212/507 (41%), Positives = 332/507 (65%), Gaps = 5/507 (0%)

Query: 6   QQPVTDSKTGDAPAILEMRGISQIFPGVKALDNVSIALHPGTVTALIGENGAGKSTLVKI 65
           Q P    +T + P +LE+  IS+ FPGV AL +V + + PGTV AL+GENGAGKSTL+KI
Sbjct: 9   QPPSLQPQTLEEPYLLEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKI 68

Query: 66  LTGIYRPNEGEILVDGRPTTFASAQAAIDAGVTAIHQETVLFDELTVAENIFLGHAPRTR 125
           + GIY+P+ GEI + G+P  F +  AA  AG+  IHQE  L   +++AENI++G      
Sbjct: 69  IAGIYQPDAGEIRLRGKPIVFETPLAAQKAGIAMIHQELNLMPHMSIAENIWIGREQLNS 128

Query: 126 FRTIDWQTMNSRSKALLTALESNIDPTIRLKDLSIAQRHLVAIARALSIEARIVIMDEPT 185
              ++ + M+  +  LL  L  N+DP  ++ +LSIA+R +V IA+A+S ++ I+IMDEPT
Sbjct: 129 LHMVNHREMHRCTAELLARLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPT 188

Query: 186 AALSRKEIDDLFRIVRGLKEQGKAILFISHKFDELYEIADDFVVFPRRSRRPVRGVSRKT 245
           +A++ KE+  LF I+  LK QGK I++I+HK +E++ IAD+  VF  R    + G+ R  
Sbjct: 189 SAITEKEVAHLFSIIADLKSQGKGIVYITHKMNEVFAIADEVAVF--RDGHYI-GLQRAD 245

Query: 246 PQ--DEIVRMMVGRDVENVFPKIDVAIGGPVLEIRNYSHRTEFRDISFTLRKGEILGVYG 303
               D ++ MMVGR++  +FP  +  IG  +L +R+ +    F+D+SF L  GEILG+ G
Sbjct: 246 SMNSDSLISMMVGRELSQLFPLRETPIGDLLLTVRDLTLDGVFKDVSFDLHAGEILGIAG 305

Query: 304 LIGAGRSELSQSLFGITKPLSGKMVLEGQEITIHSPQDAIRAGIVYVPEERGRHGLALPM 363
           L+G+GR+ +++++FGIT   SG++ L+G+ + I  P  AI  G   + E+R   GL   +
Sbjct: 306 LMGSGRTNVAETIFGITPSSSGQITLDGKAVRISDPHMAIEKGFALLTEDRKLSGLFPCL 365

Query: 364 PIFQNMTLPSLARTSRRGFLRAANEFALARKYAERLDLRAAALSVPVGTLSGGNQQKVVI 423
            + +NM +  L   +  GF++     AL     ++L ++  +L   + TLSGGNQQK ++
Sbjct: 366 SVLENMEMAVLPHYTGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALL 425

Query: 424 GKWLATAPKVIILDEPTKGIDIGSKAAVHGFISELAAEGLSIIMVSSELPEIIGMSDRVL 483
            +WL T P+++ILDEPT+GID+G+KA ++  I+ LA+EG+++IM+SSELPE++GMSDRV+
Sbjct: 426 ARWLMTNPRLLILDEPTRGIDVGAKAEIYRLIAFLASEGMAVIMISSELPEVLGMSDRVM 485

Query: 484 VMKEGLSAGIFERAELSPEALVRAATG 510
           VM EG   G  +R+E + E +++ A+G
Sbjct: 486 VMHEGELMGTLDRSEATQEKVMQLASG 512


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: 578
Number of extensions: 32
Number of successful extensions: 7
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: 517
Length adjustment: 35
Effective length of query: 477
Effective length of database: 482
Effective search space:   229914
Effective search space used:   229914
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