GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rhaT' in Pseudomonas fluorescens FW300-N2C3

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 AO356_20250 AO356_20250 L-arabinose transporter ATP-binding protein

Query= TCDB::Q7BSH4
         (512 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_20250
          Length = 514

 Score =  367 bits (942), Expect = e-106
 Identities = 203/504 (40%), Positives = 311/504 (61%), Gaps = 4/504 (0%)

Query: 7   QPVTDSKTGDAPAILEMRGISQIFPGVKALDNVSIALHPGTVTALIGENGAGKSTLVKIL 66
           Q  T ++  +    L   GI + FPGV+AL N+S   HPG V AL+GENGAGKSTL+KIL
Sbjct: 2   QAQTATRQHNIGGSLRFNGIGKSFPGVQALANISFVAHPGQVHALMGENGAGKSTLLKIL 61

Query: 67  TGIYRPNEGEILVDGRPTTFASAQAAIDAGVTAIHQETVLFDELTVAENIFLGHAPRTRF 126
            G Y P+ G++ +  +   F     +I +GV  IHQE  L  E+TVAEN+FLGH P  RF
Sbjct: 62  GGAYIPSSGDLQIGEQTMAFKGTADSIASGVAVIHQELHLVPEMTVAENLFLGHLP-ARF 120

Query: 127 RTIDWQTMNSRSKALLTALESNIDPTIRLKDLSIAQRHLVAIARALSIEARIVIMDEPTA 186
             ++   +  ++  LL  L   IDP  ++  LS+ QR LV IA+ALS  A ++  DEPT+
Sbjct: 121 GLVNRGVLRQQALTLLKGLADEIDPQEKVGRLSLGQRQLVEIAKALSRGAHVIAFDEPTS 180

Query: 187 ALSRKEIDDLFRIVRGLKEQGKAILFISHKFDELYEIADDFVVF-PRRSRRPVRGVSRKT 245
           +LS +EID L  I+  L+++GK +L++SH+ +E++ I +   VF   R  R    +S  T
Sbjct: 181 SLSAREIDRLMAIIARLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFENMSELT 240

Query: 246 PQDEIVRMMVGRDVENVFPKIDVAIGGPVLEIRNYSHRTEFRDISFTLRKGEILGVYGLI 305
             D++V  MVGRD+++++       G   L++++         +SF + KGEILG++GL+
Sbjct: 241 -HDQLVTCMVGRDIQDIYDYRPRERGDVALQVKSLLGPGLREPVSFQVHKGEILGLFGLV 299

Query: 306 GAGRSELSQSLFGITKPLSGKMVLEGQEITIHSPQDAIRAGIVYVPEERGRHGLALPMPI 365
           GAGR+EL + L G+ +   G +VL G+E+ + SP+DAI AG++  PE+R + G+     +
Sbjct: 300 GAGRTELFRLLSGLERQSEGSLVLHGKELKLRSPRDAIAAGVLLCPEDRKKEGIIPLGSV 359

Query: 366 FQNMTLPSLARTSRRG-FLRAANEFALARKYAERLDLRAAALSVPVGTLSGGNQQKVVIG 424
            +N+ + +    S  G  LR   E   A K  + L ++  A S  +  LSGGNQQK ++G
Sbjct: 360 GENINISARPAHSALGCLLRGDWERGNADKQIKSLKVKTPAASQKIMYLSGGNQQKAILG 419

Query: 425 KWLATAPKVIILDEPTKGIDIGSKAAVHGFISELAAEGLSIIMVSSELPEIIGMSDRVLV 484
           +WL+   KV++LDEPT+GIDIG+KA ++  I  LAA+G+++I+VSS+L E++G+SDR+LV
Sbjct: 420 RWLSMPMKVLLLDEPTRGIDIGAKAEIYQIIHNLAADGIAVIVVSSDLMEVMGISDRILV 479

Query: 485 MKEGLSAGIFERAELSPEALVRAA 508
           + EG   G   R + +   L++ A
Sbjct: 480 LCEGAMRGELSRDQANESNLLQLA 503


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: 579
Number of extensions: 33
Number of successful extensions: 10
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: 514
Length adjustment: 35
Effective length of query: 477
Effective length of database: 479
Effective search space:   228483
Effective search space used:   228483
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