GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglC in Gracilibacillus halophilus YIM-C55.5

Align GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate WP_003463745.1 J416_RS02050 sugar ABC transporter permease

Query= TCDB::O05177
         (398 letters)



>NCBI__GCF_000359605.1:WP_003463745.1
          Length = 386

 Score =  414 bits (1064), Expect = e-120
 Identities = 201/378 (53%), Positives = 279/378 (73%)

Query: 21  RSNIREYGMLIALVAIMVFFQFYTGGILFRPVNLTNLILQNSFIVIMALGMLLVIVAGHI 80
           R+N+REYGM+IALV I   F   T G+ F P+NLTNLILQN FI+++A+GM+LVI+ G+I
Sbjct: 9   RNNLREYGMIIALVLITGLFWILTDGVTFTPLNLTNLILQNGFILVLAVGMVLVIITGNI 68

Query: 81  DLSVGSIVAFVGAIAAILTVQWGMNPFLAALICLVIGGIIGAAQGYWIAYHRIPSFIVTL 140
           DLSVGS+VAF+GAIA +L +   +  +LA ++ ++ G +IG  QG+WIAY  IPSFIVTL
Sbjct: 69  DLSVGSVVAFIGAIAGVLMINHDVPVWLAVVLSILAGAVIGVWQGFWIAYIGIPSFIVTL 128

Query: 141 AGMLVFRGLTLFVLGGKNIGPFPTDFQVISTGFLPDIGGIEGLNTTSMILTVLITVALFY 200
           AGML+FRGLTL++L G+++ PFP  FQ IS GFLPD+ G   ++  +++ + +I++ L Y
Sbjct: 129 AGMLIFRGLTLYLLNGQSLAPFPESFQNISGGFLPDLFGGSDIHILTLVFSAVISLVLIY 188

Query: 201 LAWRRRVVNVKHGIDVEPFGFFIVQNLLISGAILFLGYQLSTYRGLPNVLIVMLVLIALY 260
           L + RR   +++  +V P    + +  ++   I +  YQL+   G+P VL+++L LI +Y
Sbjct: 189 LEFNRRKTQLQYKFEVVPVWITLAKLAILVFVINWFAYQLALNEGMPMVLVIVLFLIVIY 248

Query: 261 SFVTRRTTIGRRVYAMGGNEKATKLSGINTERLSFLTFVNMGVLAGLAGMIIATRLNSAT 320
           +F+ + T +GR +YA GGN+KA  LSGI T+R+ F  FVN G+LA LAG++ A RLNSAT
Sbjct: 249 TFIMKNTVMGRHIYATGGNKKAADLSGIKTKRVVFGVFVNNGILAALAGLMFAARLNSAT 308

Query: 321 PKAGVGFELDVIAACFIGGASASGGVGKITGAVIGAFIMGVMNNGMSIVGLGIDFQQMVK 380
           P AG   ELD IAA FIGGAS +GGVG + GA++G  +MGVMNNGMS++G+GID+QQ +K
Sbjct: 309 PAAGEMLELDAIAAVFIGGASMAGGVGTVIGAIVGGLVMGVMNNGMSLIGIGIDWQQFIK 368

Query: 381 GLVLLAAVFFDVYNKNKG 398
           G+VLL AV FDVYNKNKG
Sbjct: 369 GMVLLIAVGFDVYNKNKG 386


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: 619
Number of extensions: 34
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: 386
Length adjustment: 31
Effective length of query: 367
Effective length of database: 355
Effective search space:   130285
Effective search space used:   130285
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