Alignments for a candidate for betS in Pseudomonas stutzeri RCH2

GapMind for catabolism of small carbon sources

Alignments for a candidate for betS in Pseudomonas stutzeri RCH2

Align Glycine betaine/proline betaine transporter BetS (characterized)
to candidate GFF2585 Psest_2635 choline/carnitine/betaine transport

Query= SwissProt::G3XCN6
         (706 letters)



>FitnessBrowser__psRCH2:GFF2585
          Length = 688

 Score =  511 bits (1316), Expect = e-149
 Identities = 262/654 (40%), Positives = 392/654 (59%), Gaps = 18/654 (2%)

Query: 52  KVNLPVFVGSVAVIALFVGIGVIAPKRAESIFSGMQTAILSGFGWLYLLSVAVFLFSMLF 111
           ++N  VF GS   I LF    +    R+ ++ + +   I + FGW Y L+V ++L  ++ 
Sbjct: 17  RINPVVFYGSAIAIVLFAVWTMFFTDRSLAVINTVLGWISNTFGWFYFLAVLLYLLFVVV 76

Query: 112 LAFSRYGELKLGPDDSEPEFRYLSWIAMLFAAGMGIGLMYFAVGEPMTHFASPPEAEPLT 171
           +A SRYG+++LGPD S+PEF  ++W AMLF+AG+GI L++F + EP+T F  PP  E  +
Sbjct: 77  VATSRYGKIRLGPDHSKPEFNVVTWAAMLFSAGIGIDLLFFCIAEPITQFLEPPVGEGGS 136

Query: 172 IAAQREAMSVTFFHWGVHAWAIYSVVGLSLAYFGYRYNLPLTVRSGLYPLLKEGIHGPIG 231
             A R AM +TF HWG+  W +Y++VG+SLAYF +R  LPL++RS LYP+  + I+GPIG
Sbjct: 137 TQAARHAMELTFLHWGLSGWGVYTLVGMSLAYFSFRQGLPLSIRSSLYPIFGKRIYGPIG 196

Query: 232 HVVDIFAICGTMFGLATSLGFGILQINSGLNYLLGIPQSIYVQLLLVTVVTAIATISVVT 291
           H VD  A+ GT+FG+ATSLG GI+Q+N GLNY+ GIP+    Q +LV ++   + IS  T
Sbjct: 197 HTVDTAAVLGTIFGIATSLGIGIIQLNFGLNYIFGIPEGTLTQAVLVVLIVVFSAISAAT 256

Query: 292 GVEKGVRILSETNLFLAVLLMLFVLVVGPTGTLMRDFVQNIGLYLDSLVLRTFNIYAY-E 350
           GVE+G+R LSE N+ LAVLL+LFVLVVG T  L+   V N+G Y  + +  + + YAY  
Sbjct: 257 GVERGIRRLSEFNMLLAVLLLLFVLVVGDTVFLLNALVMNVGDYFSNFISLSLDTYAYRR 316

Query: 351 PRPWIDSWTLFYWAWWISWSPFVGMFIARISRGRTVREFVTAVLFVPAMFTFLWMTVFGN 410
           P  W+++WT+F+WAWWI+W PFVG+F+ARISRGRT+REFV   L +P  F   WM++ GN
Sbjct: 317 PTDWLNAWTVFFWAWWIAWGPFVGLFLARISRGRTIREFVIGTLLLPLAFMMAWMSIMGN 376

Query: 411 TAIYVDTTIANG--ELARDVKADLSVALFQFFEYLPWPAVTSTLAVLLVSIFFVTSSDSG 468
           +AI +   +  G  E  +   ++   +++ F + LPW  +T+ +  +L  +FFVTS DSG
Sbjct: 377 SAIEM---VMGGALEFGQQAVSNPGSSIYLFLQSLPWAGLTTIVVTILAIVFFVTSGDSG 433

Query: 469 SLVID---TIASGGETATPALQRIFWCSLSGIVAAVLLSTGGLTALQSATISTALPFSLV 525
           SLV+    +I     +  P   RI W ++ G++   LL  GGLTALQ   +   LPFS+V
Sbjct: 434 SLVLSNFTSILKDVNSDAPVWMRILWAAIIGVLTLALLIAGGLTALQGTVVIMGLPFSIV 493

Query: 526 MLILVWSLF-----VGMRADLARTQSPGSLGPRA-YPASGVPWQRRLAMTLSTPDRRAVE 579
           +L +++ LF      G+ AD  +    G L  RA    + + W +RL+  +S P R  + 
Sbjct: 494 LLFMMYGLFKALHVEGVMADSYQKSLSGYLSGRATLEHTQMNWSQRLSRAMSFPSRSQIR 553

Query: 580 KFLQASVLPALEAVARELTRRSRPASVGRDAETG--ALTLTVPAEGHRDFVYGVQMSEHK 637
           ++L+    PA+E + + L  +  P  +  + E G   L L V     +DF Y +      
Sbjct: 554 RYLKDVCKPAMEEIQKALGEKGVPVDI-VEGEPGNEHLALHVNLGSEQDFTYQIWPVRGT 612

Query: 638 LPAFTAYDATVADVRYEARTFFSDGSRGYDIMGMADNQIINDVLFQFERYTGFV 691
           +P+F     +     Y        GS GYD+MG +  Q+I D+L  +E +  F+
Sbjct: 613 MPSFALRTQSGNADYYRLEVHLRQGSLGYDLMGYSRRQLIEDILDHYEHHMHFL 666


Lambda     K      H
   0.326    0.139    0.422 

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: 1290
Number of extensions: 66
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: 706
Length of database: 688
Length adjustment: 39
Effective length of query: 667
Effective length of database: 649
Effective search space:   432883
Effective search space used:   432883
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 54 (25.4 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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