GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gguB in Paraburkholderia bryophila 376MFSha3.1

Align GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate H281DRAFT_03879 H281DRAFT_03879 xylose ABC transporter membrane protein

Query= TCDB::O05177
         (398 letters)



>FitnessBrowser__Burk376:H281DRAFT_03879
          Length = 399

 Score =  262 bits (670), Expect = 1e-74
 Identities = 141/366 (38%), Positives = 221/366 (60%), Gaps = 12/366 (3%)

Query: 29  MLIALVAIMVFFQFYTGGILFRPVNLTNLILQNSFIVIMALGMLLVIVAGHIDLSVGSIV 88
           +LIA+ AI +FF   T G    P NL+NL+ Q S   ++A GM+ VI+AG IDLSVGS++
Sbjct: 37  LLIAVAAIWIFFSVLTHGAFVTPRNLSNLLRQMSITGMLACGMVFVIIAGEIDLSVGSLL 96

Query: 89  AFVGAIAAILTVQWGMNPFLAALICLVIGGIIGAAQGYWIAYHRIPSFIVTLAGMLVFRG 148
             +G +AAIL V       +   + +++G ++G   G+W  Y R+PSFIV L GML +RG
Sbjct: 97  GLLGGVAAILDVNRHWPIGVTLPVVMLLGVLVGVFNGWWSTYRRVPSFIVGLGGMLAYRG 156

Query: 149 LTLFVLGGKNIGPFPTDFQVISTGFLPDIGGIEGLNTTSMILTVLITVALFYLAWRRRVV 208
           + L V GG  I P    F  +  G+LP + G    +T +++L VL+     +L  R+R  
Sbjct: 157 ILLGVTGGSTIAPVSDGFVFVGQGYLPTLAG----DTLAVVLFVLLA----FLTLRQRRN 208

Query: 209 NVKHGIDVEPFGFFIVQNLLISGAILFLGY--QLSTYRGLPNVLIVMLVLIALYSFVTRR 266
             ++ + V P    + +  +I   ++  G+   L  Y G+P  ++++L L+ +++++  +
Sbjct: 209 RERYQLSVVPVWQDVAK--VIGAGVILAGFVATLDRYGGIPVPVLLLLALLGIFTWIATQ 266

Query: 267 TTIGRRVYAMGGNEKATKLSGINTERLSFLTFVNMGVLAGLAGMIIATRLNSATPKAGVG 326
           T  GRR+YA+G N +AT+LSG+NT R+    F  MG++   AG++   RL + +P AG  
Sbjct: 267 TVFGRRIYAVGSNLEATRLSGVNTNRVKLAIFALMGLMCAFAGIVNTARLAAGSPSAGSM 326

Query: 327 FELDVIAACFIGGASASGGVGKITGAVIGAFIMGVMNNGMSIVGLGIDFQQMVKGLVLLA 386
            ELD IAACFIGG S  GG G + GA+IGA +M  ++NGMS++ +   +Q +VKG +L+ 
Sbjct: 327 GELDAIAACFIGGTSMRGGSGTVYGALIGALVMASLDNGMSMLDVDAYWQMIVKGSILVL 386

Query: 387 AVFFDV 392
           AV+ DV
Sbjct: 387 AVWIDV 392


Lambda     K      H
   0.329    0.145    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: 560
Number of extensions: 39
Number of successful extensions: 3
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: 398
Length of database: 399
Length adjustment: 31
Effective length of query: 367
Effective length of database: 368
Effective search space:   135056
Effective search space used:   135056
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: 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