Alignments for a candidate for betS in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for betS in Escherichia coli BW25113

Align Glycine betaine/proline betaine transporter BetS (characterized)
to candidate 14452 b0314 choline transporter of high affinity (NCBI)

Query= SwissProt::G3XCN6
         (706 letters)



>FitnessBrowser__Keio:14452
          Length = 677

 Score =  489 bits (1260), Expect = e-142
 Identities = 258/660 (39%), Positives = 400/660 (60%), Gaps = 18/660 (2%)

Query: 46  HQVQRFKVNLPVFVGSVAVIALFVGIGVIAPKRAESIFSGMQTAILSG-FGWLYLLSVAV 104
           H  ++ K+N  VF  S  +I LF  +  I  +   +++ G     +S  FGW YLL+  +
Sbjct: 6   HSREKDKINPVVFYTSAGLILLF-SLTTILFRDFSALWIGRTLDWVSKTFGWYYLLAATL 64

Query: 105 FLFSMLFLAFSRYGELKLGPDDSEPEFRYLSWIAMLFAAGMGIGLMYFAVGEPMTHFASP 164
           ++  ++ +A SR+G +KLGP+ S+PEF  LSW AMLFAAG+GI LM+F+V EP+T +  P
Sbjct: 65  YIVFVVCIACSRFGSVKLGPEQSKPEFSLLSWAAMLFAAGIGIDLMFFSVAEPVTQYMQP 124

Query: 165 PEAEPLTIAAQREAMSVTFFHWGVHAWAIYSVVGLSLAYFGYRYNLPLTVRSGLYPLLKE 224
           PE    TI A R+AM  T FH+G+  W++Y+++G++L YF YRYNLPLT+RS LYP+  +
Sbjct: 125 PEGAGQTIEAARQAMVWTLFHYGLTGWSMYALMGMALGYFSYRYNLPLTIRSALYPIFGK 184

Query: 225 GIHGPIGHVVDIFAICGTMFGLATSLGFGILQINSGLNYLLGIPQSIYVQLLLVTVVTAI 284
            I+GPIGH VDI A+ GT+FG+AT+LG G++Q+N GL+ L  IP S+  +  L+ +   I
Sbjct: 185 RINGPIGHSVDIAAVIGTIFGIATTLGIGVVQLNYGLSVLFDIPDSMAAKAALIALSVII 244

Query: 285 ATISVVTGVEKGVRILSETNLFLAVLLMLFVLVVGPTGTLMRDFVQNIGLYLDSLVLRTF 344
           ATISV +GV+KG+R+LSE N+ LA+ L+LFVL +G T  L+   V N+G Y++  +  T 
Sbjct: 245 ATISVTSGVDKGIRVLSELNVALALGLILFVLFMGDTSFLLNALVLNVGDYVNRFMGMTL 304

Query: 345 NIYAYE-PRPWIDSWTLFYWAWWISWSPFVGMFIARISRGRTVREFVTAVLFVPAMFTFL 403
           N +A++ P  W+++WTLF+WAWW++WSPFVG+F+ARISRGRT+R+FV   L +P  FT L
Sbjct: 305 NSFAFDRPVEWMNNWTLFFWAWWVAWSPFVGLFLARISRGRTIRQFVLGTLIIPFTFTLL 364

Query: 404 WMTVFGNTAIYVDTTIANGELARDVKADLSVALFQFFEYLPWPAVTSTLAVLLVSIFFVT 463
           W++VFGN+A+Y +        A +         +      P    ++++A +   +F+VT
Sbjct: 365 WLSVFGNSALY-EIIHGGAAFAEEAMVHPERGFYSLLAQYPAFTFSASVATITGLLFYVT 423

Query: 464 SSDSGSLVIDTIAS---GGETATPALQRIFWCSLSGIVAAVLLSTGGLTALQSATISTAL 520
           S+DSG+LV+    S      +  P   R+FW    G++   +L T G++ALQ+ T+   L
Sbjct: 424 SADSGALVLGNFTSQLKDINSDAPGWLRVFWSVAIGLLTLGMLMTNGISALQNTTVIMGL 483

Query: 521 PFSLVMLILVWSLFVGMRA-DLARTQSPGSLGPRAYPASG-VPWQRRLAMTLSTPDRRAV 578
           PFS V+  ++  L+  ++  D  R  +     PR       + W++RL+  ++ P  R  
Sbjct: 484 PFSFVIFFVMAGLYKSLKVEDYRRESANRDTAPRPLGLQDRLSWKKRLSRLMNYPGTRYT 543

Query: 579 EKFLQASVLPALEAVARELTRR-------SRPASVGRDAETGALTLTVPAEGHRDFVYGV 631
           ++ ++    PA+E VA+EL  R       S P   G+  + G L L V     ++FVY +
Sbjct: 544 KQMMETVCYPAMEEVAQELRLRGAYVELKSLPPEEGQ--QLGHLDLLVHMGEEQNFVYQI 601

Query: 632 QMSEHKLPAFTAYDATVADVRYEARTFFSDGSRGYDIMGMADNQIINDVLFQFERYTGFV 691
              ++ +P FT    +     Y   TF  +GS+G D+M  +  Q+I D+L Q+ER+  F+
Sbjct: 602 WPQQYSVPGFTYRARSGKSTYYRLETFLLEGSQGNDLMDYSKEQVITDILDQYERHLNFI 661


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: 1262
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: 677
Length adjustment: 39
Effective length of query: 667
Effective length of database: 638
Effective search space:   425546
Effective search space used:   425546
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