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 SM_b20893 SM_b20893 sugar uptake ABC transporter permease

Query= TCDB::O05177
         (398 letters)



>FitnessBrowser__Smeli:SM_b20893
          Length = 404

 Score =  564 bits (1453), Expect = e-165
 Identities = 285/398 (71%), Positives = 334/398 (83%), Gaps = 6/398 (1%)

Query: 7   TNEESNVISVGSYIRSNIREYGMLIALVAIMVFFQFYTGGILFRPVNLTNLILQNSFIVI 66
           T+ E+   S+G Y+R+NIREYG+L+ALV IM+FFQF T G+LFRPVN+TNL+LQNSFIVI
Sbjct: 5   TSTETTKPSIGDYLRNNIREYGLLVALVIIMLFFQFVTNGVLFRPVNITNLVLQNSFIVI 64

Query: 67  MALGMLLVIVAGHIDLSVGSIVAFVGAIAAILTVQWGMNPFLAALICLVIGGIIGAAQGY 126
           MALGMLL+IVAGHIDLSVGSIVAF+GAI+AI+ V+WG+  F+    CL++GGI+GAAQGY
Sbjct: 65  MALGMLLIIVAGHIDLSVGSIVAFIGAISAIMLVKWGLPAFVVIPACLIVGGIMGAAQGY 124

Query: 127 WIAYHRIPSFIVTLAGMLVFRGLTLFVLGGKNIGPFPTDFQVISTGFLPDI-----GGIE 181
           W+AY +IPSFIVTLAGMLVFRG+T  VLGG+ IGPFP DFQ++STGF+PD         E
Sbjct: 125 WVAYQKIPSFIVTLAGMLVFRGMTYVVLGGRPIGPFPKDFQILSTGFVPDFLYFLSPSPE 184

Query: 182 GLNTTSMILTVLITVALFYLAW-RRRVVNVKHGIDVEPFGFFIVQNLLISGAILFLGYQL 240
            +     ++ VL+ V     A  R R +N +HG + EPF FF +Q  +IS   LFLG+QL
Sbjct: 185 TIKNMVALVAVLLLVGYAIFAGVRNRRINEQHGTENEPFVFFAIQMAVISLVALFLGFQL 244

Query: 241 STYRGLPNVLIVMLVLIALYSFVTRRTTIGRRVYAMGGNEKATKLSGINTERLSFLTFVN 300
           STYRGLPNVL+VM VLIA+Y+FVT R+TIGRR+YAMGGNEKATKLSGINTERL+F  FVN
Sbjct: 245 STYRGLPNVLVVMGVLIAVYTFVTTRSTIGRRIYAMGGNEKATKLSGINTERLTFYAFVN 304

Query: 301 MGVLAGLAGMIIATRLNSATPKAGVGFELDVIAACFIGGASASGGVGKITGAVIGAFIMG 360
           MG LA LAGMII  RLNSATPKAGVGFELDVIAACFIGGASASGGVGKITGAVIGAFIMG
Sbjct: 305 MGALAALAGMIITARLNSATPKAGVGFELDVIAACFIGGASASGGVGKITGAVIGAFIMG 364

Query: 361 VMNNGMSIVGLGIDFQQMVKGLVLLAAVFFDVYNKNKG 398
           VMNNGMSI+G+GID+QQ++KGLVLLAAVFFDVYNKNKG
Sbjct: 365 VMNNGMSIMGIGIDYQQLIKGLVLLAAVFFDVYNKNKG 402


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: 747
Number of extensions: 40
Number of successful extensions: 2
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: 404
Length adjustment: 31
Effective length of query: 367
Effective length of database: 373
Effective search space:   136891
Effective search space used:   136891
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