Alignments for a candidate for betS in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Alignments for a candidate for betS in Sinorhizobium meliloti 1021

Align Glycine betaine/proline betaine transporter BetS (characterized)
to candidate SM_b20333 SM_b20333 transporter protein

Query= SwissProt::G3XCN6
         (706 letters)



>FitnessBrowser__Smeli:SM_b20333
          Length = 706

 Score = 1389 bits (3595), Expect = 0.0
 Identities = 706/706 (100%), Positives = 706/706 (100%)

Query: 1   MQNRVVSCRFTGSTARRATMPEGIRGRSHILFLVPLSRAESVGRLHQVQRFKVNLPVFVG 60
           MQNRVVSCRFTGSTARRATMPEGIRGRSHILFLVPLSRAESVGRLHQVQRFKVNLPVFVG
Sbjct: 1   MQNRVVSCRFTGSTARRATMPEGIRGRSHILFLVPLSRAESVGRLHQVQRFKVNLPVFVG 60

Query: 61  SVAVIALFVGIGVIAPKRAESIFSGMQTAILSGFGWLYLLSVAVFLFSMLFLAFSRYGEL 120
           SVAVIALFVGIGVIAPKRAESIFSGMQTAILSGFGWLYLLSVAVFLFSMLFLAFSRYGEL
Sbjct: 61  SVAVIALFVGIGVIAPKRAESIFSGMQTAILSGFGWLYLLSVAVFLFSMLFLAFSRYGEL 120

Query: 121 KLGPDDSEPEFRYLSWIAMLFAAGMGIGLMYFAVGEPMTHFASPPEAEPLTIAAQREAMS 180
           KLGPDDSEPEFRYLSWIAMLFAAGMGIGLMYFAVGEPMTHFASPPEAEPLTIAAQREAMS
Sbjct: 121 KLGPDDSEPEFRYLSWIAMLFAAGMGIGLMYFAVGEPMTHFASPPEAEPLTIAAQREAMS 180

Query: 181 VTFFHWGVHAWAIYSVVGLSLAYFGYRYNLPLTVRSGLYPLLKEGIHGPIGHVVDIFAIC 240
           VTFFHWGVHAWAIYSVVGLSLAYFGYRYNLPLTVRSGLYPLLKEGIHGPIGHVVDIFAIC
Sbjct: 181 VTFFHWGVHAWAIYSVVGLSLAYFGYRYNLPLTVRSGLYPLLKEGIHGPIGHVVDIFAIC 240

Query: 241 GTMFGLATSLGFGILQINSGLNYLLGIPQSIYVQLLLVTVVTAIATISVVTGVEKGVRIL 300
           GTMFGLATSLGFGILQINSGLNYLLGIPQSIYVQLLLVTVVTAIATISVVTGVEKGVRIL
Sbjct: 241 GTMFGLATSLGFGILQINSGLNYLLGIPQSIYVQLLLVTVVTAIATISVVTGVEKGVRIL 300

Query: 301 SETNLFLAVLLMLFVLVVGPTGTLMRDFVQNIGLYLDSLVLRTFNIYAYEPRPWIDSWTL 360
           SETNLFLAVLLMLFVLVVGPTGTLMRDFVQNIGLYLDSLVLRTFNIYAYEPRPWIDSWTL
Sbjct: 301 SETNLFLAVLLMLFVLVVGPTGTLMRDFVQNIGLYLDSLVLRTFNIYAYEPRPWIDSWTL 360

Query: 361 FYWAWWISWSPFVGMFIARISRGRTVREFVTAVLFVPAMFTFLWMTVFGNTAIYVDTTIA 420
           FYWAWWISWSPFVGMFIARISRGRTVREFVTAVLFVPAMFTFLWMTVFGNTAIYVDTTIA
Sbjct: 361 FYWAWWISWSPFVGMFIARISRGRTVREFVTAVLFVPAMFTFLWMTVFGNTAIYVDTTIA 420

Query: 421 NGELARDVKADLSVALFQFFEYLPWPAVTSTLAVLLVSIFFVTSSDSGSLVIDTIASGGE 480
           NGELARDVKADLSVALFQFFEYLPWPAVTSTLAVLLVSIFFVTSSDSGSLVIDTIASGGE
Sbjct: 421 NGELARDVKADLSVALFQFFEYLPWPAVTSTLAVLLVSIFFVTSSDSGSLVIDTIASGGE 480

Query: 481 TATPALQRIFWCSLSGIVAAVLLSTGGLTALQSATISTALPFSLVMLILVWSLFVGMRAD 540
           TATPALQRIFWCSLSGIVAAVLLSTGGLTALQSATISTALPFSLVMLILVWSLFVGMRAD
Sbjct: 481 TATPALQRIFWCSLSGIVAAVLLSTGGLTALQSATISTALPFSLVMLILVWSLFVGMRAD 540

Query: 541 LARTQSPGSLGPRAYPASGVPWQRRLAMTLSTPDRRAVEKFLQASVLPALEAVARELTRR 600
           LARTQSPGSLGPRAYPASGVPWQRRLAMTLSTPDRRAVEKFLQASVLPALEAVARELTRR
Sbjct: 541 LARTQSPGSLGPRAYPASGVPWQRRLAMTLSTPDRRAVEKFLQASVLPALEAVARELTRR 600

Query: 601 SRPASVGRDAETGALTLTVPAEGHRDFVYGVQMSEHKLPAFTAYDATVADVRYEARTFFS 660
           SRPASVGRDAETGALTLTVPAEGHRDFVYGVQMSEHKLPAFTAYDATVADVRYEARTFFS
Sbjct: 601 SRPASVGRDAETGALTLTVPAEGHRDFVYGVQMSEHKLPAFTAYDATVADVRYEARTFFS 660

Query: 661 DGSRGYDIMGMADNQIINDVLFQFERYTGFVRSPESSLLATSPEER 706
           DGSRGYDIMGMADNQIINDVLFQFERYTGFVRSPESSLLATSPEER
Sbjct: 661 DGSRGYDIMGMADNQIINDVLFQFERYTGFVRSPESSLLATSPEER 706


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: 1876
Number of extensions: 80
Number of successful extensions: 1
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: 706
Length adjustment: 39
Effective length of query: 667
Effective length of database: 667
Effective search space:   444889
Effective search space used:   444889
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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