GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglC in Pseudomonas simiae WCS417

Align GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate GFF2143 PS417_10930 D-xylose ABC transporter permease

Query= TCDB::O05177
         (398 letters)



>FitnessBrowser__WCS417:GFF2143
          Length = 378

 Score =  266 bits (679), Expect = 1e-75
 Identities = 154/365 (42%), Positives = 222/365 (60%), Gaps = 10/365 (2%)

Query: 29  MLIALVAIMVFFQFYTGGILFRPVNLTNLILQNSFIVIMALGMLLVIVAGHIDLSVGSIV 88
           ++IA+  I VFF + T G    P NL+NL+ Q S   I+A GM+LVI++G IDLSVGS++
Sbjct: 16  LVIAVAVIWVFFSWQTEGGFLTPRNLSNLLRQMSITGILACGMVLVIISGEIDLSVGSLL 75

Query: 89  AFVGAIAAILTVQWGMNPFLAALICLVIGGI-IGAAQGYWIAYHRIPSFIVTLAGMLVFR 147
             +G +AAIL V + + P LA L  + + G+ IG A GY  AY RIPSFIV L GML FR
Sbjct: 76  GLLGGLAAILDVVYHI-PLLANLSLVALCGLMIGLANGYMTAYLRIPSFIVGLGGMLAFR 134

Query: 148 GLTLFVLGGKNIGPFPTDFQVISTGFLPDIGGIEGLNTTSMILTVLITVALFYLAWRRRV 207
           G+ L + GG  I P       +  G+LP   GI GL      LTV +T       W++R 
Sbjct: 135 GILLGITGGTTIAPVSPSLVYVGQGYLPHSVGI-GLGVLLFSLTVFLT-------WKQRR 186

Query: 208 VNVKHGIDVEPFGFFIVQNLLISGAILFLGYQLSTYRGLPNVLIVMLVLIALYSFVTRRT 267
               HG+        +V+  +I   +      L++Y G+P  ++++LVL+ ++S+VT +T
Sbjct: 187 NRALHGLAAHSLVRDLVRVAVIGAVLAGFVTTLNSYDGIPVPVLLLLVLLGVFSYVTSQT 246

Query: 268 TIGRRVYAMGGNEKATKLSGINTERLSFLTFVNMGVLAGLAGMIIATRLNSATPKAGVGF 327
             GRRVYA+G N +AT+LSGIN + +    F  MGV+  LAG++   RL + +P AG   
Sbjct: 247 VFGRRVYAVGSNMEATRLSGINVQAVKLWIFGIMGVMCALAGLVNTARLAAGSPSAGNMG 306

Query: 328 ELDVIAACFIGGASASGGVGKITGAVIGAFIMGVMNNGMSIVGLGIDFQQMVKGLVLLAA 387
           ELD IAACFIGG S  GG G + GA++GA ++  ++NGMS++ +   +Q +VKG +L+ A
Sbjct: 307 ELDAIAACFIGGTSMRGGSGTVYGALLGALVITSLDNGMSMLDVDSYWQMIVKGSILVLA 366

Query: 388 VFFDV 392
           V+ DV
Sbjct: 367 VWVDV 371


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: 527
Number of extensions: 37
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: 378
Length adjustment: 30
Effective length of query: 368
Effective length of database: 348
Effective search space:   128064
Effective search space used:   128064
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