GapMind for catabolism of small carbon sources

 

Aligments for a candidate for xylH 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)



>lcl|FitnessBrowser__Smeli:SM_b20893 SM_b20893 sugar uptake ABC
           transporter permease
          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 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