GapMind for catabolism of small carbon sources

 

Aligments for a candidate for mglC 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)



>lcl|FitnessBrowser__Koxy:BWI76_RS27040 BWI76_RS27040 xylose ABC
           transporter permease
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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