Alignments for a candidate for betS in Dietzia timorensis ID05-A0528

GapMind for catabolism of small carbon sources

Alignments for a candidate for betS in Dietzia timorensis ID05-A0528

Align Glycine betaine/proline betaine transporter BetS (characterized)
to candidate WP_075844956.1 BJL86_RS10330 BCCT family transporter

Query= SwissProt::G3XCN6
         (706 letters)



>NCBI__GCF_001659785.1:WP_075844956.1
          Length = 725

 Score =  434 bits (1116), Expect = e-126
 Identities = 245/694 (35%), Positives = 367/694 (52%), Gaps = 27/694 (3%)

Query: 32  FLVPLSRAESVGR----LHQVQRFKVNLPVFVGSVAVIALFVGIGVIAPKRAESIFSGMQ 87
           F  P S   + GR      Q     VN PVF G+  +I  FV    I P  A +   G  
Sbjct: 7   FAAPESNDTTDGRPDTATTQATHSAVNWPVFAGTSVIIVAFVLWAAIWPDAASTAIFGAM 66

Query: 88  TAILSGFGWLYLLSVAVFLFSMLFLAFSRYGELKLGPDDSEPEFRYLSWIAMLFAAGMGI 147
             + + FGW Y+L+  + +  ++ +AFSR G  K+GPD S P+F   +W AMLFAAG+G+
Sbjct: 67  DWVATNFGWYYILTATIVVVFVIVVAFSRVGRTKMGPDHSRPKFNLFTWAAMLFAAGIGV 126

Query: 148 GLMYFAVGEPMTHFASPPEAEPLTIAAQREAMSVTFFHWGVHAWAIYSVVGLSLAYFGYR 207
            LM+F +  P T++ +PP+   ++  A R A   T FH+G+  WA+Y+++G++   F YR
Sbjct: 127 DLMFFGISGPATNYLTPPDVGAMSDEAARMAPIWTIFHYGIPGWAMYALMGMAFGLFAYR 186

Query: 208 YNLPLTVRSGLYPLLKEGIHGPIGHVVDIFAICGTMFGLATSLGFGILQINSGLNYLLGI 267
           Y+LPL++RS L P+  + IHG  GH V+I A  GT+FG++ SLG G++ +N GL+ L G+
Sbjct: 187 YHLPLSIRSALAPIFGKRIHGAAGHTVEIAATIGTIFGISVSLGIGVVFLNYGLSELFGV 246

Query: 268 PQSIYVQLLLVTVVTAIATISVVTGVEKGVRILSETNLFLAVLLMLFVLVVGPTGTLMRD 327
           P S+ VQ+ L+ +   I   S V+GV+KG+R LSE N+ LA++L L+VL  G T  ++  
Sbjct: 247 PNSLSVQIALMALAVFITIASTVSGVDKGIRRLSELNVILAIVLALWVLFSGQTAHMLDA 306

Query: 328 FVQNIGLYLDSLVLRTFNIYAYE-------PRPWIDSWTLFYWAWWISWSPFVGMFIARI 380
            VQNIG +         N +AY           W   WTLF+WAWWI+W+PFV +F+ARI
Sbjct: 307 LVQNIGDFFSRFPSMMMNTFAYSTGTADYPAEQWKADWTLFFWAWWIAWAPFVSLFLARI 366

Query: 381 SRGRTVREFVTAVLFVPAMFTFLWMTVFGNTAIYVDTTIANGELARDVKADLSVALFQFF 440
           SRGRT+R+FV  VL +P  F  +W+++FGN A+   +   + E             F   
Sbjct: 367 SRGRTLRQFVIGVLLIPFSFILMWVSIFGNAAL---SFFDDQEFLNQAVELPESGFFTLL 423

Query: 441 EYLPWPAVTSTLAVLLVSIFFVTSSDSGSLVIDTIASG---GETATPALQRIFWCSLSGI 497
           E  P    T ++AVL    F+VTS+DSGSLV+  + S     ++  P   RI W  ++G 
Sbjct: 424 EQYPGSTFTISIAVLTGMFFYVTSADSGSLVMANMTSKPTMNDSDGPPWLRIVWAVITGA 483

Query: 498 VAAVLLSTGGLTALQSATISTALPFSLVMLILVWSLFVGMRA-----DLARTQSPGSLGP 552
           +  V+L   G+  LQ+AT+   LP S+++ ++++SL+  ++      D  +   P  L  
Sbjct: 484 LTLVMLFIDGVYTLQAATVMVGLPLSILIYLVMFSLWKVLKTEQLGIDSRQATLPTLLTS 543

Query: 553 RAY-PASGVPWQRRLAMTLSTPDRRAVEKFLQASVLPALEAVARELTRRSRPASVGR--- 608
           R         W++RL   +S         F+     PA+E VA E+       S  R   
Sbjct: 544 RVRDQGERGNWRQRLKHRMSYASETEAADFVSNVASPAIEEVAAEIKSMGFEVSCHRGSH 603

Query: 609 -DAETGALTLTVPAEGHRDFVYGVQMSEHKLPAFTAYDATVADVRYEARTFFSDGSRGYD 667
            D+    + L V      DF Y      + +P+F    A V D  Y    F   GSRG D
Sbjct: 604 PDSNIPYIDLVVSFPNSEDFKYQAYPVAYSVPSFATNLAAVRDTYYRVEIFSIHGSRGRD 663

Query: 668 IMGMADNQIINDVLFQFERYTGFVRSPESSLLAT 701
           IMG   +Q+I DVL  ++ +  ++       LAT
Sbjct: 664 IMGYTQDQVITDVLDAYDAHIAYLNLSGDGSLAT 697


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: 1383
Number of extensions: 76
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: 725
Length adjustment: 39
Effective length of query: 667
Effective length of database: 686
Effective search space:   457562
Effective search space used:   457562
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: 55 (25.8 bits)

This GapMind analysis is from Sep 24 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 2024 update 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