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

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_00965 AO356_00965 sugar ABC transporter ATP-binding protein

Query= TCDB::Q7BSH4
         (512 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_00965
          Length = 517

 Score =  287 bits (735), Expect = 6e-82
 Identities = 175/499 (35%), Positives = 279/499 (55%), Gaps = 12/499 (2%)

Query: 16  DAPAILEMRGISQIFPGVKALDNVSIALHPGTVTALIGENGAGKSTLVKILTGIYRPNEG 75
           D  A+L + GI + +     L ++++ L  G V AL GENGAGKSTL KI+ G+  P  G
Sbjct: 5   DPNAVLCVSGIGKTY-AQPVLTDINLTLMRGEVLALTGENGAGKSTLSKIIGGLVTPTTG 63

Query: 76  EILVDGRPTTFASAQAAIDAGVTAIHQETVLFDELTVAENIFLGHAPRTRFRTIDWQTMN 135
           ++   G+     S   A + GV  + QE  L   L+VAEN+FL + P        W +  
Sbjct: 64  QMQFQGQDYRPGSRTQAEELGVRMVMQELNLLPTLSVAENLFLDNLPSHG----GWISRK 119

Query: 136 SRSKALLTALES----NIDPTIRLKDLSIAQRHLVAIARALSIEARIVIMDEPTAALSRK 191
              KA + A+       IDP   + +L I  + +V IAR L  +  ++I+DEPTA L+ +
Sbjct: 120 QLRKAAIEAMAQVGLDAIDPDTLVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAR 179

Query: 192 EIDDLFRIVRGLKEQGKAILFISHKFDELYEIADDFVVFPRRSRRPVRGVSRKTPQDEIV 251
           E++ LF  +  L+ +G AI++ISH+ +EL  +A    V    +   V  ++     +++V
Sbjct: 180 EVEMLFEQITRLQARGVAIIYISHRLEELARVAQRIAVLRDGNLVCVEPMANYD-SEQLV 238

Query: 252 RMMVGRDVENVFPKIDVAIGGPVLEIRNYSHRTEFRDISFTLRKGEILGVYGLIGAGRSE 311
            +MVGR++          IG P L ++  +   + RD+SF +R GEI G+ GLIGAGR+E
Sbjct: 239 TLMVGRELGEHIDLGPRQIGAPALTVKGLTRSDKVRDVSFEVRSGEIFGISGLIGAGRTE 298

Query: 312 LSQSLFGITKPLSGKMVL--EGQEITIHSPQDAIRAGIVYVPEERGRHGLALPMPIFQNM 369
           L + +FG     SG + L    + ++I SP DA+  GI  + E+R   GL L   I  N+
Sbjct: 299 LLRLIFGADPADSGTVALGSPARVVSIRSPSDAVAHGIALITEDRKGEGLLLTQSIAANI 358

Query: 370 TLPSLARTSRRGFLRAANEFALARKYAERLDLRAAALSVPVGTLSGGNQQKVVIGKWLAT 429
            L ++   S  G +  + E ALA++  + + +R+++ +  V  LSGGNQQKVVIG+WL  
Sbjct: 359 ALGNMPEISSAGLVNGSAELALAQRQVDAMRIRSSSPTQLVSELSGGNQQKVVIGRWLER 418

Query: 430 APKVIILDEPTKGIDIGSKAAVHGFISELAAEGLSIIMVSSELPEIIGMSDRVLVMKEGL 489
              V++ DEPT+GID+G+K  ++  + EL  +G ++++VSS+L E++ + DR+ V+  G 
Sbjct: 419 DCAVMLFDEPTRGIDVGAKFDIYALLGELTRQGKALVVVSSDLRELMLICDRIGVLSAGR 478

Query: 490 SAGIFERAELSPEALVRAA 508
               FER   + + L+ AA
Sbjct: 479 LIDTFERDSWTQDDLLAAA 497



 Score = 86.7 bits (213), Expect = 2e-21
 Identities = 67/223 (30%), Positives = 108/223 (48%), Gaps = 5/223 (2%)

Query: 288 DISFTLRKGEILGVYGLIGAGRSELSQSLFGITKPLSGKMVLEGQEITIHSPQDAIRAGI 347
           DI+ TL +GE+L + G  GAG+S LS+ + G+  P +G+M  +GQ+    S   A   G+
Sbjct: 26  DINLTLMRGEVLALTGENGAGKSTLSKIIGGLVTPTTGQMQFQGQDYRPGSRTQAEELGV 85

Query: 348 VYVPEERGRHGLALPMPIFQNMTLPSLARTSRRGFLRAANEFALARKYAERLDLRAAALS 407
             V +E     L   + + +N+ L +L   S  G++        A +   ++ L A    
Sbjct: 86  RMVMQELN---LLPTLSVAENLFLDNLP--SHGGWISRKQLRKAAIEAMAQVGLDAIDPD 140

Query: 408 VPVGTLSGGNQQKVVIGKWLATAPKVIILDEPTKGIDIGSKAAVHGFISELAAEGLSIIM 467
             VG L  G+QQ V I + L     V+ILDEPT  +       +   I+ L A G++II 
Sbjct: 141 TLVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVEMLFEQITRLQARGVAIIY 200

Query: 468 VSSELPEIIGMSDRVLVMKEGLSAGIFERAELSPEALVRAATG 510
           +S  L E+  ++ R+ V+++G    +   A    E LV    G
Sbjct: 201 ISHRLEELARVAQRIAVLRDGNLVCVEPMANYDSEQLVTLMVG 243


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: 616
Number of extensions: 29
Number of successful extensions: 7
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: 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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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