Alignments for a candidate for rhaT' in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for rhaT' in Escherichia coli BW25113

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 16258 b2149 fused methyl-galactoside transporter subunits of ABC superfamily: ATP-binding components (NCBI)

Query= TCDB::Q7BSH4
         (512 letters)



>FitnessBrowser__Keio:16258
          Length = 506

 Score =  375 bits (963), Expect = e-108
 Identities = 200/507 (39%), Positives = 323/507 (63%), Gaps = 11/507 (2%)

Query: 9   VTDSKTGDAPAILEMRGISQIFPGVKALDNVSIALHPGTVTALIGENGAGKSTLVKILTG 68
           V+ +       +LEM GI++ FPGVKALDNV++ + P ++ AL+GENGAGKSTL+K L G
Sbjct: 2   VSSTTPSSGEYLLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFG 61

Query: 69  IYRPNEGEILVDGRPTTFASAQAAIDAGVTAIHQETVLFDELTVAENIFLGHAPRTRFRT 128
           IY+ + G IL  G+   F SA+ A++ G++ +HQE  L  + +V +N++LG  P T+   
Sbjct: 62  IYQKDSGTILFQGKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYP-TKGMF 120

Query: 129 IDWQTMNSRSKALLTALESNIDPTIRLKDLSIAQRHLVAIARALSIEARIVIMDEPTAAL 188
           +D   M   +KA+   L+ +IDP  R+  LS++Q  ++ IA+A S  A+IVIMDEPT++L
Sbjct: 121 VDQDKMYRETKAIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSL 180

Query: 189 SRKEIDDLFRIVRGLKEQGKAILFISHKFDELYEIADDFVVFPRR---SRRPVRGVSRKT 245
           + KE++ LF I+R LKE+G  I++ISHK +E++++ D+  V       +  P+ G++   
Sbjct: 181 TEKEVNHLFTIIRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLT--- 237

Query: 246 PQDEIVRMMVGRDVENVFPKIDVAIGGPVLEIRNYS--HRTEFRDISFTLRKGEILGVYG 303
             D+I+ MMVGR +   FP  +   G  +LE+RN +   +   RD+SF L KGEILG+ G
Sbjct: 238 -MDKIIAMMVGRSLNQRFPDKENKPGEVILEVRNLTSLRQPSIRDVSFDLHKGEILGIAG 296

Query: 304 LIGAGRSELSQSLFGITKPLSGKMVLEGQEITIHSPQDAIRAGIVYVPEERGRHGLALPM 363
           L+GA R+++ ++LFGI +  +G + L G++I  H+  +AI  G   V EER   G+   +
Sbjct: 297 LVGAKRTDIVETLFGIREKSAGTITLHGKQINNHNANEAINHGFALVTEERRSTGIYAYL 356

Query: 364 PIFQNMTLPSLARTSRR-GFLRAANEFALARKYAERLDLRAAALSVPVGTLSGGNQQKVV 422
            I  N  + ++     + G L  +   +  +   + + ++       +G+LSGGNQQKV+
Sbjct: 357 DIGFNSLISNIRNYKNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVI 416

Query: 423 IGKWLATAPKVIILDEPTKGIDIGSKAAVHGFISELAAEGLSIIMVSSELPEIIGMSDRV 482
           IG+WL T P++++LDEPT+GID+G+K  ++  I+ELA +G  II++SSE+PE++G++DR+
Sbjct: 417 IGRWLLTQPEILMLDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRI 476

Query: 483 LVMKEGLSAGIFERAELSPEALVRAAT 509
           LVM  GL +GI +    +   ++R A+
Sbjct: 477 LVMSNGLVSGIVDTKTTTQNEILRLAS 503



 Score = 81.6 bits (200), Expect = 6e-20
 Identities = 62/226 (27%), Positives = 107/226 (47%), Gaps = 8/226 (3%)

Query: 288 DISFTLRKGEILGVYGLIGAGRSELSQSLFGITKPLSGKMVLEGQEITIHSPQDAIRAGI 347
           +++  +R   I  + G  GAG+S L + LFGI +  SG ++ +G+EI  HS ++A+  GI
Sbjct: 31  NVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGTILFQGKEIDFHSAKEALENGI 90

Query: 348 VYVPEERGRHGLALPMPIFQNMTLPSLARTSRRG-FLRAANEFALARKYAERLDLRAAAL 406
             V +E     L L   +  NM L    R   +G F+     +   +   + LD+     
Sbjct: 91  SMVHQELN---LVLQRSVMDNMWL---GRYPTKGMFVDQDKMYRETKAIFDELDIDIDPR 144

Query: 407 SVPVGTLSGGNQQKVVIGKWLATAPKVIILDEPTKGIDIGSKAAVHGFISELAAEGLSII 466
           +  VGTLS    Q + I K  +   K++I+DEPT  +       +   I +L   G  I+
Sbjct: 145 A-RVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFTIIRKLKERGCGIV 203

Query: 467 MVSSELPEIIGMSDRVLVMKEGLSAGIFERAELSPEALVRAATGNA 512
            +S ++ EI  + D V V+++G        A L+ + ++    G +
Sbjct: 204 YISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIAMMVGRS 249


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: 605
Number of extensions: 32
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 512
Length of database: 506
Length adjustment: 34
Effective length of query: 478
Effective length of database: 472
Effective search space:   225616
Effective search space used:   225616
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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources