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_RS14865 BWI76_RS14865 ribose ABC transporter permease

Query= TCDB::O05177
         (398 letters)



>FitnessBrowser__Koxy:BWI76_RS14865
          Length = 339

 Score =  146 bits (368), Expect = 1e-39
 Identities = 110/364 (30%), Positives = 174/364 (47%), Gaps = 71/364 (19%)

Query: 28  GMLIALVAIMVFFQFYTGGILFRPVNLTNLILQNSFIVIMALGMLLVIVAGHIDLSVGSI 87
           G+LI L+ +++    +      R  NL N+    S   I+A GM  VI+   IDLSVGSI
Sbjct: 26  GILIVLLVLLILMSTFAPNFN-RVDNLLNIARSISVNAILAAGMTFVILTSGIDLSVGSI 84

Query: 88  VAFVGAIAAILTVQWGMNPFLAALICLVIGGIIGAAQGYWIAYHRIPSFIVTLAGMLVFR 147
           VA  G ++                       ++ A  G       IP+ +  LAG+ V  
Sbjct: 85  VAVSGVVS-----------------------VVAAMAG-------IPAPLAILAGVGV-- 112

Query: 148 GLTLFVLGGKNIGPFPTDFQVISTGFLPDIGGIEGLNTTSMILTVLITVALFYLAWRRRV 207
           G    +L G            + T +L     I  L T + +  +  T+           
Sbjct: 113 GALCGLLNG------------VLTAYLALAPFIVTLGTMTFLRGMAYTIT---------- 150

Query: 208 VNVKHGIDVEPFGFFIVQNLLISGAILFLGYQLSTYRGLPNVLIVMLVLIALYSFVTRRT 267
                  + +P         ++S ++ F         G+P  +I+MLV+  L  F+  RT
Sbjct: 151 -------EGQP---------IVSSSLSFRELGNGYLIGIPIPVIIMLVVYLLAWFILERT 194

Query: 268 TIGRRVYAMGGNEKATKLSGINTERLSFLTFVNMGVLAGLAGMIIATRLNSATPKAGVGF 327
             GR +YA+GGN +A +L+G+  +R+    ++  GV AGLAG+I A R+ SA P AG G+
Sbjct: 195 RFGRHIYAVGGNAQAARLAGVRVKRVLAAVYMIAGVCAGLAGIIFAARVISAQPTAGTGY 254

Query: 328 ELDVIAACFIGGASASGGVGKITGAVIGAFIMGVMNNGMSIVGLGIDFQQMVKGLVLLAA 387
           ELD IAA  +GG S +GG G+I G +IG+ I+GV++ G+ ++ +    Q ++KG+V++ A
Sbjct: 255 ELDAIAAVVLGGTSLAGGRGRIIGTLIGSIILGVLSTGLILLSVPFFTQLLIKGIVIILA 314

Query: 388 VFFD 391
           V  D
Sbjct: 315 VAID 318


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: 452
Number of extensions: 35
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: 2
Length of query: 398
Length of database: 339
Length adjustment: 30
Effective length of query: 368
Effective length of database: 309
Effective search space:   113712
Effective search space used:   113712
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: 49 (23.5 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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