GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglC in Pseudomonas simiae WCS417

Align Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized)
to candidate GFF2365 PS417_12060 sugar ABC transporter permease

Query= TCDB::G4FGN4
         (313 letters)



>FitnessBrowser__WCS417:GFF2365
          Length = 325

 Score =  249 bits (637), Expect = 5e-71
 Identities = 124/300 (41%), Positives = 192/300 (64%), Gaps = 1/300 (0%)

Query: 12  GIFLILIAIVVFLGVTTREFLTVENIFTVILNVSFIAIMSFGMTMVIITSGIDLSVGSIL 71
           G+ L+ I + V +  ++  F+T  N   ++   S   I++ GMT VI+T GIDLSVGSIL
Sbjct: 26  GLPLVFILLCVVMAFSSEYFMTWRNWMDILRQTSINGILAVGMTYVILTKGIDLSVGSIL 85

Query: 72  GAASVVMGLLMDEKGLSPFLSVVIGLAVGVGFGLANGLLITKARLAPFISTLGMLSVGRG 131
             A +   ++  + G     +V  G+  G   G+ NG ++    + PF++TLGMLS+ RG
Sbjct: 86  AFAGLCSAMVATQ-GYGLLAAVSAGMFAGAMLGVVNGFMVANLSIPPFVATLGMLSIARG 144

Query: 132 LAYVMSGGWPISPFPESFTVHGQGMVGPVPVPVIYMAVIGVIAHIFLKYTVTGRRIYAIG 191
           + ++++ G PI+  P+++   G G +GP+ VP+I  AV+ +I  + L+YT  GR +YA+G
Sbjct: 145 MTFILNDGSPITDLPDAYLALGIGKIGPIGVPIIIFAVVALIFWMVLRYTTYGRYVYAVG 204

Query: 192 GNMEASKLVGIKTDRILILVYTINGFLAAFAGFLLTAWLGVAQPNAGQGYELDVIAATVI 251
           GN ++++  GI   +++  VY ++G LA  AG +L+A    A P AG  YELD IAA VI
Sbjct: 205 GNEKSARTSGIGVRKVMFSVYVVSGLLAGLAGVVLSARTTSALPQAGVSYELDAIAAVVI 264

Query: 252 GGTSLSGGEGTILGAFLGAVIMGVLRNGMILLGVSSFWQQVVIGIVIIIAIAIDQIRRAK 311
           GGTSLSGG G+I+G   GA+++GV+ NG+ LLGVSS++QQV  G++I+ A+ ID  R+ K
Sbjct: 265 GGTSLSGGTGSIVGTLFGALLIGVINNGLNLLGVSSYYQQVAKGLIIVFAVLIDVWRKKK 324


Lambda     K      H
   0.328    0.145    0.421 

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: 320
Number of extensions: 19
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: 313
Length of database: 325
Length adjustment: 28
Effective length of query: 285
Effective length of database: 297
Effective search space:    84645
Effective search space used:    84645
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 (21.7 bits)
S2: 48 (23.1 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