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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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:

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:

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:

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:

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