Alignments for a candidate for betS in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for betS in Pseudomonas simiae WCS417

Align Glycine betaine/proline betaine transporter BetS (characterized)
to candidate GFF221 PS417_01120 choline transporter

Query= SwissProt::G3XCN6
         (706 letters)



>FitnessBrowser__WCS417:GFF221
          Length = 666

 Score =  533 bits (1373), Expect = e-155
 Identities = 272/655 (41%), Positives = 407/655 (62%), Gaps = 20/655 (3%)

Query: 52  KVNLPVFVGSVAVIALFVGIGVIA-PKRAESIFSGMQTAILSGFGWLYLLSVAVFLFSML 110
           ++N PVF  +   I LF GI VIA P++A +     Q    +  GW Y+L++ ++L  ++
Sbjct: 13  RMNAPVFYFAATFILLF-GITVIAIPQQAGAWLLAAQNWAANTVGWYYMLAMTLYLVFVV 71

Query: 111 FLAFSRYGELKLGPDDSEPEFRYLSWIAMLFAAGMGIGLMYFAVGEPMTHFASPPEAEPL 170
             A S YG++KLG D  EPEF YLSW  MLFAAG+ I L +F V EP+TH   PP+  P+
Sbjct: 72  VTALSGYGKIKLGADHDEPEFSYLSWAGMLFAAGISITLFFFCVSEPLTHLVQPPQGAPM 131

Query: 171 TIAAQREAMSVTFFHWGVHAWAIYSVVGLSLAYFGYRYNLPLTVRSGLYPLLKEGIHGPI 230
              A R+AM + F HWG+H W +++ VG++LAYF YR+NLPL +RS LYPL+ + I+GPI
Sbjct: 132 NADAARQAMQILFLHWGLHGWGVFAFVGMALAYFAYRHNLPLALRSALYPLIGKRINGPI 191

Query: 231 GHVVDIFAICGTMFGLATSLGFGILQINSGLNYLLGIPQSIYVQLLLVTVVTAIATISVV 290
           G+ VD F I  T+FGL   +GFG+L +NSGL+YL GI  + ++Q+ L+T++   A I  V
Sbjct: 192 GYAVDGFGIIATVFGLGADMGFGVLHLNSGLDYLFGIAHTQWIQVGLITLMMGAAIIVAV 251

Query: 291 TGVEKGVRILSETNLFLAVLLMLFVLVVGPTGTLMRDFVQNIGLYLDSLVLRTFNIYAYE 350
            GV+KGVR++S+ N+ LA  L+LFVL  GPT  L+   +QNIG YL +L  ++F++YAY+
Sbjct: 252 AGVDKGVRVMSDINMLLACALLLFVLFAGPTQHLLNTLIQNIGDYLGALPTKSFDVYAYD 311

Query: 351 -PRPWIDSWTLFYWAWWISWSPFVGMFIARISRGRTVREFVTAVLFVPAMFTFLWMTVFG 409
            P  W+  WT+FYWAWWI+WSPFVG+FIARISRGRT+REFV  VL +P  FT  WM++FG
Sbjct: 312 KPSDWLGGWTVFYWAWWIAWSPFVGLFIARISRGRTIREFVFGVLLIPLGFTLAWMSIFG 371

Query: 410 NTAIYVDTTIANGELARDVKA--DLSVALFQFFEYLPWPAVTSTLAVLLVSIFFVTSSDS 467
           N+AI  D  + +G +A    A  D S++L+   E  PW      + V +  +FFVTS+DS
Sbjct: 372 NSAI--DQVLNHGLVALGQSAIDDPSMSLYLLLETYPWSKTVIAVTVFISFVFFVTSADS 429

Query: 468 GSLVIDTIASGGETAT---PALQRIFWCSLSGIVAAVLLSTGGLTALQSATISTALPFSL 524
           G++V+ T++S G  A    P   R+FW +++ +V + LL  G + +L+SA + T+LPFS+
Sbjct: 430 GTVVLSTLSSKGGNADEDGPKWLRVFWGAMTALVTSALLFAGSIDSLKSAVVLTSLPFSM 489

Query: 525 VMLILVWSL----FVGMRADLARTQSPGSLGPRAYPASGVPWQRRLAMTLSTPDRRAVEK 580
           ++L+++W L    ++  +  +A+  S   +        G  W++RL+  +  P R  V +
Sbjct: 490 ILLLMMWGLHKAFYLESQKQIAQLHSLAPVSAARKGRGG--WRQRLSQAVHFPSRDEVYR 547

Query: 581 FLQASVLPALEAVARELTRRSRPASVGRDAETGALTLTVPAEGHRDFVYGVQMSEHKLPA 640
           FL+++V PA+E V      +        D    +++L +     R FVY VQM  +  P+
Sbjct: 548 FLESTVRPAIEEVTAVFVEKGLNVVTQPDPSNDSVSLEIGHGEERPFVYQVQMRGYFTPS 607

Query: 641 FTAYDATVADVR----YEARTFFSDGSRGYDIMGMADNQIINDVLFQFERYTGFV 691
           F        ++     Y A    ++GS+ YD++G    QIIND+L Q+ER+  F+
Sbjct: 608 FARGGMGSKEINNRRYYRAEVHLAEGSQDYDLVGYTKEQIINDILDQYERHLQFL 662


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: 1226
Number of extensions: 68
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: 666
Length adjustment: 39
Effective length of query: 667
Effective length of database: 627
Effective search space:   418209
Effective search space used:   418209
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.

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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