Alignments for a candidate for betS in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for betS in Klebsiella michiganensis M5al

Align Glycine betaine/proline betaine transporter BetS (characterized)
to candidate BWI76_RS07630 BWI76_RS07630 high-affinity choline transporter BetT

Query= SwissProt::G3XCN6
         (706 letters)



>FitnessBrowser__Koxy:BWI76_RS07630
          Length = 677

 Score =  490 bits (1262), Expect = e-143
 Identities = 257/656 (39%), Positives = 396/656 (60%), Gaps = 16/656 (2%)

Query: 49  QRFKVNLPVFVGSVAVIALFVGIGVIAPKRAESIFSGMQTAILSGFGWLYLLSVAVFLFS 108
           ++ K+N  VF  S  +I LF  + +     + +        +   FGW YLL+  +++  
Sbjct: 9   EKDKINPVVFYTSAGLILLFSLMTLFFSDFSAAWIGRTLNWVSRTFGWYYLLAATLYIVF 68

Query: 109 MLFLAFSRYGELKLGPDDSEPEFRYLSWIAMLFAAGMGIGLMYFAVGEPMTHFASPPEAE 168
           ++ +A SR+G +KLGP+ S+PEF  LSW AMLFAAG+GI LM+F+V EP+T +  PPE  
Sbjct: 69  VVCIACSRFGSVKLGPEHSKPEFSVLSWAAMLFAAGIGIDLMFFSVAEPVTQYMQPPEGA 128

Query: 169 PLTIAAQREAMSVTFFHWGVHAWAIYSVVGLSLAYFGYRYNLPLTVRSGLYPLLKEGIHG 228
             T+ A R+AM  T FH+G+  W++Y+++G++L YF YRYNLPLT+RS LYP+  + I+G
Sbjct: 129 GQTMEAARQAMVWTLFHYGLTGWSMYALMGMALGYFSYRYNLPLTIRSALYPIFGKKING 188

Query: 229 PIGHVVDIFAICGTMFGLATSLGFGILQINSGLNYLLGIPQSIYVQLLLVTVVTAIATIS 288
           PIGH VDI A+ GT+FG+AT+LG G++Q+N GL+ L  IP S+  +  L+ +   IATIS
Sbjct: 189 PIGHSVDIAAVIGTIFGIATTLGIGVVQLNYGLSVLFNIPDSLGAKAALIVLSVIIATIS 248

Query: 289 VVTGVEKGVRILSETNLFLAVLLMLFVLVVGPTGTLMRDFVQNIGLYLDSLVLRTFNIYA 348
           V +GV+KG+RILSE N+ LA+ L+LF+L +G T  L+   V N+G Y++  +  T N +A
Sbjct: 249 VTSGVDKGIRILSELNVVLALGLILFILFMGDTEFLLNALVLNVGDYVNRFMGMTLNSFA 308

Query: 349 YE-PRPWIDSWTLFYWAWWISWSPFVGMFIARISRGRTVREFVTAVLFVPAMFTFLWMTV 407
           ++ P  W+++WTLF+WAWW++WSPFVG+F+ARISRGRT+R+FV   L +P  FT LW++V
Sbjct: 309 FDRPVEWMNNWTLFFWAWWVAWSPFVGLFLARISRGRTIRQFVVGTLIIPFTFTLLWLSV 368

Query: 408 FGNTAIYVDTTIANGELARDVKADLSVALFQFFEYLPWPAVTSTLAVLLVSIFFVTSSDS 467
           FGN+A+Y +    N   A +  A      +      P    ++++A +   +F+VTS+DS
Sbjct: 369 FGNSALY-EIIHGNAAFAAEAVAHPERGFYNLLAQYPAFTFSASVATITGLLFYVTSADS 427

Query: 468 GSLVIDTIAS---GGETATPALQRIFWCSLSGIVAAVLLSTGGLTALQSATISTALPFSL 524
           G+LV+    S      +  P   RIFW  + G++   +L T G++ALQ+AT+   LPFS 
Sbjct: 428 GALVLGNFTSKLKDINSDAPNWLRIFWSVVIGLLTLGMLMTNGISALQNATVIMGLPFSF 487

Query: 525 VMLILVWSLFVGMRA-DLARTQSPGSLGPRAYPASG-VPWQRRLAMTLSTPDRRAVEKFL 582
           V+  ++  L+  ++  D  R  +     PR       + W++RL+  ++ P  R   + +
Sbjct: 488 VIFFVMAGLYKSLKVEDYRRESANRDTAPRPLGVQDRLSWKKRLSRLMNYPGTRYTRQMM 547

Query: 583 QASVLPALEAVARELTRR-------SRPASVGRDAETGALTLTVPAEGHRDFVYGVQMSE 635
           +    PA+E VA+EL  R       S P   G     G L L V     ++FVY +   +
Sbjct: 548 ETVCFPAMEEVAQELKLRGAYVELKSLPPEEG--DSLGHLDLLVHMGDEQNFVYQIWPQQ 605

Query: 636 HKLPAFTAYDATVADVRYEARTFFSDGSRGYDIMGMADNQIINDVLFQFERYTGFV 691
           + +P FT    +     Y   TF  +GS+G D+M  +  Q+I D+L Q+ER+  F+
Sbjct: 606 YSIPGFTYRARSGKSTYYRLETFLLEGSQGNDLMDYSKEQVITDILDQYERHLNFI 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: 1285
Number of extensions: 73
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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Protein sequences (fasta format)
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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