GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlE in Burkholderia phytofirmans PsJN

Align ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, periplasmic substrate-binding protein (characterized)
to candidate BPHYT_RS16115 BPHYT_RS16115 sugar ABC transporter substrate-binding protein

Query= reanno::WCS417:GFF2493
         (440 letters)



>FitnessBrowser__BFirm:BPHYT_RS16115
          Length = 440

 Score =  549 bits (1414), Expect = e-161
 Identities = 269/441 (60%), Positives = 325/441 (73%), Gaps = 6/441 (1%)

Query: 1   MKFTAKALLASTCMMTCMTLSAVSFGAQTLTIATVNNSDMIRMQKLSKTFEAEHPEIKLN 60
           +K T KA+ A    + C  LSA    A T+TIAT+NN DMI ++KLS  FE  +P+IKLN
Sbjct: 5   LKSTLKAVSAGA--VACFALSA---SAATVTIATLNNPDMIELKKLSPEFEKANPDIKLN 59

Query: 61  WVVLEENVLRQRLTTDIATQGGQFDVLTIGMYEAALWGAKGWLEPMKDLPASYDLDDVFP 120
           WV+LEENVLRQR TTDI T  GQFDV+TIG YE   WG +GWL P+ +LPA YDL+DV  
Sbjct: 60  WVILEENVLRQRATTDITTGSGQFDVMTIGAYETPQWGKRGWLTPLTNLPADYDLNDVVK 119

Query: 121 SVRDGLSVKGSLYALPFYAESSITYYRTDLFKDAGLTMPEHPTWTQIGEFASKLTDKTKE 180
           + RDGLS  G LYALPFY ESS+TYYR DLF+ AGL MP+ PT+ QI +FA KLTDK   
Sbjct: 120 TARDGLSSGGQLYALPFYVESSMTYYRKDLFEKAGLKMPDQPTYDQIKQFADKLTDKANG 179

Query: 181 QYGLCLRGKAGWGENMALITTLANGYGARWFDEKWQPEFNGPEWKDALNFYVDNMKKSGP 240
            YG+CLRGKAGWGENMA  TT+ N +G RWFDEKW  +   PEWK A+ FYVD +KK GP
Sbjct: 180 IYGICLRGKAGWGENMAYGTTVVNTFGGRWFDEKWNAQLTSPEWKKAMTFYVDLLKKDGP 239

Query: 241 PGASSNGFNENLALFNSGKCAIWVDASVAGSFVTDKTQSKVADHVGFTFAPHEKTDKGTS 300
           PGASSNGFNENL L +SGKCA+W+DA+VA   + +K QS++AD VGF  AP   T KG+ 
Sbjct: 240 PGASSNGFNENLTLMSSGKCAMWIDATVAAGMLYNKQQSQIADKVGFAAAPVAVTPKGSH 299

Query: 301 WLYSWSLAIPTSSKAKDAAKVFTSWATSKEYGELVAKTDGIANVPPGTRKSTY-NDEYMK 359
           WL++W+LAIP SSK  DAAK F +WATSK+Y ELVAK +G A+VPPGTRKSTY   EY +
Sbjct: 300 WLWAWALAIPKSSKQADAAKKFITWATSKQYIELVAKDEGWASVPPGTRKSTYARAEYKQ 359

Query: 360 AAPFAKVTLESLKVADPTKPTLKPVPYIGIQLVTIPEFQAIGTQVGKFFSGALTGQQTVD 419
           AAPF    L++++ ADP  PTLKPVPY G+Q V IPEFQ+ GT VG+  SGA+ GQ T+D
Sbjct: 360 AAPFGDFVLKAIETADPEHPTLKPVPYTGVQFVGIPEFQSFGTVVGQSISGAIAGQMTID 419

Query: 420 AALTAAQTTTEREMKRAGYPK 440
            AL A   T +R +K+AGY K
Sbjct: 420 QALAAGNATADRAVKQAGYQK 440


Lambda     K      H
   0.315    0.130    0.394 

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: 627
Number of extensions: 20
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: 440
Length of database: 440
Length adjustment: 32
Effective length of query: 408
Effective length of database: 408
Effective search space:   166464
Effective search space used:   166464
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 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