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 GFF3462 PS417_17725 ribose ABC transporter permease

Query= TCDB::G4FGN4
         (313 letters)



>FitnessBrowser__WCS417:GFF3462
          Length = 330

 Score =  236 bits (603), Expect = 4e-67
 Identities = 125/294 (42%), Positives = 187/294 (63%), Gaps = 3/294 (1%)

Query: 15  LILIAIVVFLGVTTREFLTVENIFTVILNVSFIAIMSFGMTMVIITSGIDLSVGSILGAA 74
           L+++ +V+ L   T  FLT  N+  +   VS  AI++ GMT VI+T GIDLSVG ++  +
Sbjct: 38  LVVVTLVMILASDT--FLTASNLSNIARQVSINAIIAVGMTCVILTGGIDLSVGPVMALS 95

Query: 75  SVVMGLLMDEKGLSPFLSVVIGLAVGVGFGLANGLLITKARLAPFISTLGMLSVGRGLAY 134
             +   LM   GL P L++  G+ +GV FG+ NGL +    + P I TL  + + RGL  
Sbjct: 96  GTLTAGLM-VAGLPPGLAIGAGMLIGVAFGIGNGLFVAYLHMPPIIVTLATMGIARGLGL 154

Query: 135 VMSGGWPISPFPESFTVHGQGMVGPVPVPVIYMAVIGVIAHIFLKYTVTGRRIYAIGGNM 194
           + + G+PIS  P+ F   G+  +  + VP++ M +  ++A++ L++T  GR IYAIGGN 
Sbjct: 155 MYTDGYPISGLPDWFAFFGRESLFGIQVPILIMLLTYLVAYVLLQHTRIGRYIYAIGGNE 214

Query: 195 EASKLVGIKTDRILILVYTINGFLAAFAGFLLTAWLGVAQPNAGQGYELDVIAATVIGGT 254
           EA +L G++  R  +LVY I+G  AA AG +LT+ L   QPNAG  +ELD IAA V+GG 
Sbjct: 215 EAVRLSGVRAARFKLLVYGISGLTAAIAGLVLTSRLMSGQPNAGVSFELDAIAAVVLGGA 274

Query: 255 SLSGGEGTILGAFLGAVIMGVLRNGMILLGVSSFWQQVVIGIVIIIAIAIDQIR 308
           S++GG G I+G  LGA+++GVL NG+ +LGVS + Q V+ G +I++AI I + R
Sbjct: 275 SIAGGRGVIVGTLLGAMLLGVLNNGLNMLGVSPYVQSVIKGGIILLAIFISRQR 328


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: 332
Number of extensions: 30
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 313
Length of database: 330
Length adjustment: 28
Effective length of query: 285
Effective length of database: 302
Effective search space:    86070
Effective search space used:    86070
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