GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylH in Burkholderia phytofirmans PsJN

Align Monosaccharide-transporting ATPase, component of Xylose transporter, XylFGH (XylF (R), 359 aas; XylG (C), 525 aas; XylH (M), 389 aas (characterized)
to candidate BPHYT_RS32810 BPHYT_RS32810 xylose ABC transporter permease

Query= TCDB::A6LW12
         (389 letters)



>FitnessBrowser__BFirm:BPHYT_RS32810
          Length = 399

 Score =  391 bits (1005), Expect = e-113
 Identities = 194/366 (53%), Positives = 267/366 (72%)

Query: 24  KMAAILIATAAIWVLFTFLTDGNFLTTRNLSNLFRQMSITGVLAIGMVFVIILGEIDLSA 83
           K+ A+LIA AAIW+ F+ LT G F+T RNLSNL RQMSITG+LA GMVFVII GEIDLS 
Sbjct: 33  KILALLIAVAAIWIFFSALTHGAFVTPRNLSNLLRQMSITGMLACGMVFVIIAGEIDLSV 92

Query: 84  GSTLGLLGGIAAILNVWFGFSAIPTVVITLILGVIMGAWNGYWIAFRNVPSFIVTLASML 143
           GS LGLLGG+AAIL+V   +    T+ + ++LGV++G +NG+W  +R VPSFIV L  ML
Sbjct: 93  GSLLGLLGGVAAILDVNRHWPIGVTLPVVMLLGVLVGMFNGWWSTYRRVPSFIVGLGGML 152

Query: 144 VFRGVLIGITGGNTVAPLTADFKAIGQAYLPTVVGYILVVLAIVGSAYLILGNRKNKIKY 203
            +RG+L+G+TGG+T+AP++  F  +GQ YLP + G  L V+  +  A+L +  R+N+ +Y
Sbjct: 153 AYRGILLGVTGGSTIAPVSDSFVFVGQGYLPRLAGDTLAVVLFLLLAFLTIRQRRNRERY 212

Query: 204 NIEVRPMALDVLTIVGIGVISLVLVLILNDYQGFPIPVFIMLLLALILAFVGTKTIFGRR 263
            + V P+  DV+ +VG GVI    V  L+ Y G P+PV ++L L  I  ++ T+T+FGRR
Sbjct: 213 QLRVVPVWQDVVKVVGAGVILAGFVATLDRYGGIPVPVLLLLALLGIFTWIATQTVFGRR 272

Query: 264 IYGIGGNRDAARLSGINVKKHIIVIYSVLGLLCAVAGILLTSRLNAGSVSAGQNAEMDAI 323
           IY +G N +A RLSG+N  +  + I++++GL+CA  GI+ T+RL AGS SAG   E+DAI
Sbjct: 273 IYAVGSNLEATRLSGVNTNRVKLAIFALMGLMCAFGGIVNTARLAAGSPSAGSMGELDAI 332

Query: 324 ASCVIGGASLAGGSGTVAGALVGALVMASIDNGMSMMNTPTFWQYIVKGLILLIAVWMDI 383
           A+C IGG S+ GGSGTV GAL+GALVMAS+DNGMSM++   +WQ IVKG IL++AVW+D+
Sbjct: 333 AACFIGGTSMRGGSGTVYGALIGALVMASLDNGMSMLDVDAYWQMIVKGSILVLAVWIDV 392

Query: 384 SSKNKK 389
            S + +
Sbjct: 393 VSGSNR 398


Lambda     K      H
   0.326    0.142    0.410 

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: 449
Number of extensions: 21
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: 389
Length of database: 399
Length adjustment: 31
Effective length of query: 358
Effective length of database: 368
Effective search space:   131744
Effective search space used:   131744
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 (21.6 bits)
S2: 50 (23.9 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