GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__WCS417:GFF3462 PS417_17725 ribose ABC
           transporter permease
          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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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