Alignments for a candidate for braE in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Alignments for a candidate for braE in Sinorhizobium meliloti 1021

Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate SMc01950 SMc01950 high-affinity branched-chain amino acid ABC transporter permease

Query= uniprot:Q1MCU1
         (463 letters)



>FitnessBrowser__Smeli:SMc01950
          Length = 461

 Score =  722 bits (1863), Expect = 0.0
 Identities = 363/463 (78%), Positives = 411/463 (88%), Gaps = 2/463 (0%)

Query: 1   MANIENSAGKPDAGLVRKGLTEALFAAVLSFGMFVLYVGLKTDQNISNELIIVQRWGLLA 60
           MAN+ ++     + L  + L EA+FA +++ GMFVL+VGLKTDQNI NELI+ QRWGLLA
Sbjct: 1   MANVASTTASAGSELTARALREAVFAGLITLGMFVLFVGLKTDQNIRNELILTQRWGLLA 60

Query: 61  IFVAVAAIGRFAMVVFIRPNIDRRKLSKAREGELDISTEKSFFHRHFLKIALIALLLYPM 120
            FVA+A +GRF MV +++P + +RK +KA     D+  E++FF R++ KIA+I LL+YP 
Sbjct: 61  TFVAIAMVGRFLMVAYVQPRLAQRKAAKAAAP--DVVKEETFFSRNWSKIAVILLLIYPP 118

Query: 121 VVVAIKGPQGSLTYVDNFGIQILIYVMLAWGLNIVVGLAGLLDLGYVAFYAVGAYSYALL 180
           V+VA+ G QGSL +VDNFGIQILIYVMLAWGLNIVVGLAGLLDLGYVAFYAVGAYSYALL
Sbjct: 119 VIVALVGVQGSLKWVDNFGIQILIYVMLAWGLNIVVGLAGLLDLGYVAFYAVGAYSYALL 178

Query: 181 SSYFGLSFWVLLPLSGIFAALWGVILGFPVLRLRGDYLAIVTLAFGEIIRLVLINWTDVT 240
           SSYFGLSFWVLLP++G+ AA WGV+LGFPVLRLRGDYLAIVTLAFGEIIRLVLINWT+VT
Sbjct: 179 SSYFGLSFWVLLPIAGLLAACWGVVLGFPVLRLRGDYLAIVTLAFGEIIRLVLINWTEVT 238

Query: 241 KGTFGISSIPKATLFGIPFDATAGGFAKLFHLPISSAYYKIFLFYLILALCMLTAYVTIR 300
           KGTFG+S I KATLFGI FDAT  GFA +  LP+SSAYYKIFLFYLIL L +LTA+VTIR
Sbjct: 239 KGTFGVSGIAKATLFGIKFDATKDGFAAMMGLPMSSAYYKIFLFYLILGLALLTAFVTIR 298

Query: 301 LRRMPIGRAWEALREDEIACRSLGINTVTTKLTAFATGAMFAGFAGSFFAARQGFVSPES 360
           LRRMPIGRAWEALREDEIACRSLGINTVTTKLTAFATGAMF GFAGSFFA RQGFVSPES
Sbjct: 299 LRRMPIGRAWEALREDEIACRSLGINTVTTKLTAFATGAMFGGFAGSFFAVRQGFVSPES 358

Query: 361 FVFLESAVILAIVVLGGMGSLTGIAIAAIVMVGGTELLREMSFLKLIFGPDFTPELYRML 420
           FVFLESAVILAIVVLGGMGSLTGIAIAA+VM+GGTE+LRE++FLK+IFGP FTPELYRML
Sbjct: 359 FVFLESAVILAIVVLGGMGSLTGIAIAAVVMIGGTEILRELTFLKMIFGPTFTPELYRML 418

Query: 421 IFGLAMVVVMLFKPRGFVGSREPTAFLRERKAISGSFIKEGHG 463
           IFGLAMVVVM++KPRGFVGSREPTAFLRER+AISGSF KEGHG
Sbjct: 419 IFGLAMVVVMVWKPRGFVGSREPTAFLRERRAISGSFTKEGHG 461


Lambda     K      H
   0.330    0.145    0.432 

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: 846
Number of extensions: 32
Number of successful extensions: 2
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: 463
Length of database: 461
Length adjustment: 33
Effective length of query: 430
Effective length of database: 428
Effective search space:   184040
Effective search space used:   184040
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 (21.8 bits)
S2: 51 (24.3 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, or view the source code.

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