GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Koxy:BWI76_RS14865 BWI76_RS14865 ribose ABC
           transporter permease
          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.

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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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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