GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gguB in Klebsiella michiganensis M5al

Align GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate BWI76_RS27040 BWI76_RS27040 xylose ABC transporter permease

Query= TCDB::O05177
         (398 letters)



>FitnessBrowser__Koxy:BWI76_RS27040
          Length = 393

 Score =  267 bits (682), Expect = 5e-76
 Identities = 143/375 (38%), Positives = 222/375 (59%), Gaps = 8/375 (2%)

Query: 23  NIREYGMLIALVAIMVFFQFYTGGILFRPVNLTNLILQNSFIVIMALGMLLVIVAGHIDL 82
           N++ + M+ A+VAIM+FF + T G      N++NL+ Q +   I+A+GM+ VI++  IDL
Sbjct: 26  NLQVFVMIAAIVAIMLFFTWTTEGAYLSARNISNLLRQTAITGILAVGMVFVIISAEIDL 85

Query: 83  SVGSIVAFVGAIAAILTVQWGMNPFLAALICLVIGGIIGAAQGYWIAYHRIPSFIVTLAG 142
           SVGS++  +G  AAI  V  G    L  ++ LV+G ++GA  G+W+AY ++PSFIVTLAG
Sbjct: 86  SVGSMMGLLGGAAAIFDVWLGWPLPLTIVVTLVLGLLLGAWNGWWVAYRKVPSFIVTLAG 145

Query: 143 MLVFRGLTLFVLGGKNIGPFPTDFQVISTGFLPDIGGIEGLNTTSMILTVLITVALFYLA 202
           ML FRG+ + +  G  + P       I   +LPD  G          + VL   A     
Sbjct: 146 MLAFRGILIGITNGTTVSPTSPAMSQIGQSYLPDGIGFG--------IGVLGMAAFIIWQ 197

Query: 203 WRRRVVNVKHGIDVEPFGFFIVQNLLISGAILFLGYQLSTYRGLPNVLIVMLVLIALYSF 262
           WR R+     G+        + +  + +  +L   + L+ YRG+P  ++++  L+    F
Sbjct: 198 WRGRMRRQALGLSTPASASTVGRQTITAVIVLGAIWLLNDYRGVPTPVLILTALLLAGMF 257

Query: 263 VTRRTTIGRRVYAMGGNEKATKLSGINTERLSFLTFVNMGVLAGLAGMIIATRLNSATPK 322
           +  RT  GRR+YA+GGN +A +LSGI+ ER     F   G++  +AG+I+++RL + +P 
Sbjct: 258 MATRTAFGRRIYAIGGNLEAARLSGISVERTKLAVFAINGLMVAIAGLILSSRLGAGSPS 317

Query: 323 AGVGFELDVIAACFIGGASASGGVGKITGAVIGAFIMGVMNNGMSIVGLGIDFQQMVKGL 382
           AG   ELD IAAC IGG S +GG+G + GAV+GAFIM  ++NGMS++ +   +Q +VKG+
Sbjct: 318 AGNIAELDAIAACVIGGTSLAGGIGSVAGAVMGAFIMSALDNGMSMMDVATFWQYIVKGV 377

Query: 383 VLLAAVFFDVYNKNK 397
           +LL AV+ D   K +
Sbjct: 378 ILLLAVWMDSATKRR 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: 576
Number of extensions: 40
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 398
Length of database: 393
Length adjustment: 31
Effective length of query: 367
Effective length of database: 362
Effective search space:   132854
Effective search space used:   132854
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