GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglC in Collimonas pratensis Ter91

Align GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate WP_099047307.1 CPter91_RS17205 sugar ABC transporter permease

Query= TCDB::O05177
         (398 letters)



>NCBI__GCF_001584185.1:WP_099047307.1
          Length = 403

 Score =  516 bits (1330), Expect = e-151
 Identities = 244/379 (64%), Positives = 319/379 (84%)

Query: 19  YIRSNIREYGMLIALVAIMVFFQFYTGGILFRPVNLTNLILQNSFIVIMALGMLLVIVAG 78
           ++++N+REYGML++L+AIM FFQ+ T G L  P+NLTNL+LQNS+IVIMALGML+VIVAG
Sbjct: 25  FLKNNMREYGMLMSLIAIMAFFQYMTNGTLMEPLNLTNLVLQNSYIVIMALGMLMVIVAG 84

Query: 79  HIDLSVGSIVAFVGAIAAILTVQWGMNPFLAALICLVIGGIIGAAQGYWIAYHRIPSFIV 138
           HIDLSVGS+V F+GA+AA+L V   +N  LA+++C++ GG+IGAAQGYW+A+ +IPSFIV
Sbjct: 85  HIDLSVGSVVGFIGALAAVLIVNLHVNFVLASILCILAGGVIGAAQGYWVAFFKIPSFIV 144

Query: 139 TLAGMLVFRGLTLFVLGGKNIGPFPTDFQVISTGFLPDIGGIEGLNTTSMILTVLITVAL 198
           TLAGMLVF+GLTL +L G++IGPFP DFQ++S+GF+PD+     +  TS+++ V++   +
Sbjct: 145 TLAGMLVFKGLTLALLQGQSIGPFPDDFQMLSSGFIPDLFNATDMRITSLLVGVVVAAIM 204

Query: 199 FYLAWRRRVVNVKHGIDVEPFGFFIVQNLLISGAILFLGYQLSTYRGLPNVLIVMLVLIA 258
             +  R R    KHG++ EP+ FFI++N + +G I+F  Y L++Y+G+PNVLI+M +L+ 
Sbjct: 205 IVVKVRARAKQSKHGMEDEPYLFFILKNAIFAGVIIFFSYLLASYKGMPNVLIIMFLLMV 264

Query: 259 LYSFVTRRTTIGRRVYAMGGNEKATKLSGINTERLSFLTFVNMGVLAGLAGMIIATRLNS 318
           +Y+FV  RTTIGRR+YA+GGNEKA KLSGI T R+SF TF+NMG+LA LAG+I A RLN+
Sbjct: 265 VYTFVANRTTIGRRIYAVGGNEKAAKLSGIKTSRVSFYTFINMGMLAALAGLIFAARLNT 324

Query: 319 ATPKAGVGFELDVIAACFIGGASASGGVGKITGAVIGAFIMGVMNNGMSIVGLGIDFQQM 378
           ATPKAG GFELDVIAACFIGGASASGGVGK+ GAVIGAF+MGVMNNGMSI+G+GID+QQ+
Sbjct: 325 ATPKAGTGFELDVIAACFIGGASASGGVGKVMGAVIGAFVMGVMNNGMSIMGIGIDYQQV 384

Query: 379 VKGLVLLAAVFFDVYNKNK 397
           +KGLVLLAAVF DVYNKNK
Sbjct: 385 IKGLVLLAAVFVDVYNKNK 403


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: 643
Number of extensions: 26
Number of successful extensions: 1
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: 403
Length adjustment: 31
Effective length of query: 367
Effective length of database: 372
Effective search space:   136524
Effective search space used:   136524
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 24 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