Alignments for a candidate for betS in Shewanella amazonensis SB2B

GapMind for catabolism of small carbon sources

Alignments for a candidate for betS in Shewanella amazonensis SB2B

Align Glycine betaine/proline betaine transporter BetS (characterized)
to candidate 6937001 Sama_1175 choline/carnitine/betaine transport (RefSeq)

Query= SwissProt::G3XCN6
         (706 letters)



>FitnessBrowser__SB2B:6937001
          Length = 658

 Score =  629 bits (1621), Expect = 0.0
 Identities = 318/646 (49%), Positives = 436/646 (67%), Gaps = 7/646 (1%)

Query: 50  RFKVNLPVFVGSVAVIALFVGIGVIAPKRAESIFSGMQTAILSGFGWLYLLSVAVFLFSM 109
           ++ +N PVF GS+ +I L V +G I P++A+  F  +Q  +    GWLY+L VAVFL  +
Sbjct: 4   KYSINRPVFFGSLFLITLLVALGAIWPQQAQQWFGAVQHWLEVKAGWLYVLGVAVFLVFI 63

Query: 110 LFLAFSRYGELKLGPDDSEPEFRYLSWIAMLFAAGMGIGLMYFAVGEPMTHFASPPEAEP 169
           +F+  SR+G++KLGPD +EP++ Y SWIAMLF+AGMGIGLM+F V EP+ H  +PP+A P
Sbjct: 64  VFVMVSRFGDIKLGPDHAEPDYSYKSWIAMLFSAGMGIGLMFFGVAEPVMHLIAPPDATP 123

Query: 170 LTIAAQREAMSVTFFHWGVHAWAIYSVVGLSLAYFGYRYNLPLTVRSGLYPLLKEGIHGP 229
            +I A R+AM +TFFHWG+HAWAIY+VV LSLAYF YR+ LPL  RS LYPL+ E IHGP
Sbjct: 124 ESIEAARQAMKITFFHWGIHAWAIYAVVALSLAYFAYRHKLPLLPRSALYPLIGERIHGP 183

Query: 230 IGHVVDIFAICGTMFGLATSLGFGILQINSGLNYLLG--IPQSIYVQLLLVTVVTAIATI 287
           IGH VD FA+ GTMFG+ATSLGFG+LQ+N+GLN+L G   P S  +Q+ L+ V+T IAT+
Sbjct: 184 IGHAVDAFAVLGTMFGVATSLGFGVLQVNAGLNFLFGDQFPVSTPLQVGLIAVITLIATV 243

Query: 288 SVVTGVEKGVRILSETNLFLAVLLMLFVLVVGPTGTLMRDFVQNIGLYLDSLVLRTFNIY 347
           SV +G++KGV+ LSE NL LAV+LML VL+VGPT  L++  VQN G Y   +V +TFN+Y
Sbjct: 244 SVFSGLDKGVKRLSELNLLLAVVLMLVVLLVGPTVALLQAIVQNTGAYFSDIVGKTFNLY 303

Query: 348 AYEPR-PWIDSWTLFYWAWWISWSPFVGMFIARISRGRTVREFVTAVLFVPAMFTFLWMT 406
           AY+ +  W+  WTL YW WWISWSPFVG FIAR+SRGRT+REF+  VLFVP+ FTFLWMT
Sbjct: 304 AYQQKNDWLGGWTLLYWGWWISWSPFVGTFIARVSRGRTIREFLLGVLFVPSGFTFLWMT 363

Query: 407 VFGNTAIYVDTTIANGELARDVKADLSVALFQFFEYLPWPAVTSTLAVLLVSIFFVTSSD 466
           VFGN+AI       N  LA  V +D+SVALF FF+ LP  ++ S +A+ LV  FFVTSSD
Sbjct: 364 VFGNSAIDQILHQGNTVLADAVSSDVSVALFVFFQQLPLTSLLSAVALCLVVTFFVTSSD 423

Query: 467 SGSLVIDTIASGGETATPALQRIFWCSLSGIVAAVLLSTGGLTALQSATISTALPFSLVM 526
           SGSLVID + SGG+ ++P  QR+FW  + G+VA+VLL  GGL ALQ+A I++A+PF LVM
Sbjct: 424 SGSLVIDNLTSGGDMSSPVWQRVFWALMQGVVASVLLLAGGLQALQTAAIASAMPFLLVM 483

Query: 527 LILVWSLFVGMRADLARTQSPGSLGPRA-YPASGVPWQRRLAMTLSTPDRRAVEKFLQAS 585
           L++   LF  ++ D  +  S         Y ++ V W+ RL + ++ P  +    F++  
Sbjct: 484 LLICLGLFKALQDDWLKLSSVQLHHTSVQYASANVEWRERLKVLVNQPSAKDARAFIRGP 543

Query: 586 VLPALEAVARELTRRSRPASVGRDAETGALTLTVPAEGHRDFVYGVQMSEHKLPAFTAYD 645
              AL+ VA         A V +  +   + L + ++ H DFVYG+++ ++        +
Sbjct: 544 ARQALKQVASAFVNEGIDARVVQQED--RVRLLIASDNHPDFVYGLRLRQYSKVPVHGVE 601

Query: 646 ATVADVRYEARTFFSDGSRGYDIMGMADNQIINDVLFQFERYTGFV 691
            T  D  Y    F   G + YD++G    Q+  D + Q+E+Y  ++
Sbjct: 602 ETDDDF-YRVEVFLEHGGQHYDVLGYTVEQLQADAVTQYEKYLHYL 646


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: 1191
Number of extensions: 57
Number of successful extensions: 5
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: 658
Length adjustment: 39
Effective length of query: 667
Effective length of database: 619
Effective search space:   412873
Effective search space used:   412873
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