GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gguB in Sinorhizobium meliloti 1021

Align GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate SMc02031 SMc02031 permease

Query= TCDB::O05177
         (398 letters)



>FitnessBrowser__Smeli:SMc02031
          Length = 349

 Score =  151 bits (382), Expect = 2e-41
 Identities = 117/379 (30%), Positives = 187/379 (49%), Gaps = 61/379 (16%)

Query: 20  IRSNIREYGMLIALVAIMVFFQFYTGGILFRPVNLTNLILQNSFIVIMALGMLLVIVAGH 79
           +++ + + G LIALV +M +  F T   L    NL+N+  Q++F+ I+A+G   VI+ G 
Sbjct: 23  LKAVVFQAGPLIALVLLMAYLAFATSNFLTLD-NLSNVARQSAFVAILAVGQTFVILTGG 81

Query: 80  IDLSVGSIVAFVGAIAAILTVQWGMNPFLAALICLVIGGIIGAAQGYWIAYHRIPSFIVT 139
           IDLSV +I A   +I A+L  Q            LV+ GI          +  +P  +  
Sbjct: 82  IDLSVAAIAALSASITAVLLTQ-----------PLVLFGI---------DFGFVPPPVAI 121

Query: 140 LAGMLVFRGLTLFVLGGKNIGPFPTDFQVISTGFLPDIGGIEGLNTTSMILTVLITVALF 199
           L G+L+  G+    L G  I  F           +PD     G  T              
Sbjct: 122 LIGILI--GMAAGALNGWLISKFK----------IPDFIATLGTMT-------------- 155

Query: 200 YLAWRRRVVNVKHGIDVEPF--GFFIVQNLL-ISGAILFLGYQLSTYRGLPNVLIVMLVL 256
             A+R   + V  G+ V  F  G  + ++L+ + G  LF         G+P   ++ L+ 
Sbjct: 156 --AFRGAALLVTDGLPVPSFNAGRQLPESLIWVGGGQLF---------GVPVSALIALLC 204

Query: 257 IALYSFVTRRTTIGRRVYAMGGNEKATKLSGINTERLSFLTFVNMGVLAGLAGMIIATRL 316
            A   +V R T +GR +YA+GGN  A   SGI+  R   +T+   G+LA +AG+I+  RL
Sbjct: 205 AAAGWYVLRYTALGRAIYAVGGNRAAAHSSGISISRTKIMTYAISGLLAAIAGIILVGRL 264

Query: 317 NSATPKAGVGFELDVIAACFIGGASASGGVGKITGAVIGAFIMGVMNNGMSIVGLGIDFQ 376
           NSA      G EL  IA+  IGG +  GG G + G++IGA I+GV+ NG++++ +   +Q
Sbjct: 265 NSANALMADGEELRSIASVVIGGTNLFGGEGGVWGSIIGAAIIGVLGNGLNLLDVSPFWQ 324

Query: 377 QMVKGLVLLAAVFFDVYNK 395
           ++ +G+V++  V FD + +
Sbjct: 325 RIAQGVVIVVVVIFDQWRR 343


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: 454
Number of extensions: 33
Number of successful extensions: 4
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: 349
Length adjustment: 30
Effective length of query: 368
Effective length of database: 319
Effective search space:   117392
Effective search space used:   117392
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