GapMind for catabolism of small carbon sources

 

Aligments for a candidate for thuF in Phaeobacter inhibens BS107

Align Maltose transport system permease protein malF aka TT_C1628, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized)
to candidate GFF726 PGA1_c07410 binding protein dependent transport system permease

Query= TCDB::Q72H67
         (291 letters)



>lcl|FitnessBrowser__Phaeo:GFF726 PGA1_c07410 binding protein
           dependent transport system permease
          Length = 315

 Score =  142 bits (357), Expect = 1e-38
 Identities = 85/282 (30%), Positives = 147/282 (52%), Gaps = 9/282 (3%)

Query: 5   RQVRLAWILVLPTLLVVVLVAGYPLAQVFYWSFFKADIAFVEPPEFVGLENYAYLFQDPD 64
           RQ    W+ + P ++  +    +P+ Q F  SF++ D   +  P+F+G+ENY  L  D  
Sbjct: 28  RQALAPWLFLAPGVIFFLFYVIFPILQSFNLSFYRWD--GLGDPQFIGMENYRELMDDRA 85

Query: 65  FRQALWNTLKFTVVSVSLETVLGLAIALIIHSNFRGRGLVRTAILIPWAIPTVVSAKMWQ 124
           F  +LWN LK+ ++ + L    GL IAL ++    G  L ++    P+ I  VV   ++ 
Sbjct: 86  FEVSLWNNLKWLLLYL-LAIPAGLFIALFLNQTVTGIRLYKSLFFFPFVISQVVVGLVFS 144

Query: 125 WMLNDVYGVINVLGVKLGLLSQKVAFLARPELLLPSIIAVDVWKTTPFMALLLLAGLQMI 184
           W  +  +G++N +   +GL    +  L  P L+   II   +W  T +  +L L GL  +
Sbjct: 145 WFYDPTFGLLNQVLAWVGL--GPINVLGDPTLVTYGIIIAGLWPQTAYCMILYLTGLNAV 202

Query: 185 PEELYEAASIDGASRWQQFWSITLPLLTPALVVALIFRTLDALRVFDVVFVMSGVNP--A 242
             E  EAA +DGA   +  W + +P L PA  VA +   + ALR FD++ +M+   P  +
Sbjct: 203 DPEQVEAARLDGAKGAKMLWYVIIPQLRPATFVAFVVTIIGALRSFDLISIMTNGGPFGS 262

Query: 243 TRTLAVYN-RQTLVDFQ-DLGYGSAISVAILVIIFAFVLLYM 282
           +R L+ Y   + L ++   +GYG+AI+V + +I+  F+  ++
Sbjct: 263 SRVLSFYMFEKALSEYGFRMGYGAAIAVVLFLIMLCFIAYFL 304


Lambda     K      H
   0.329    0.142    0.433 

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: 277
Number of extensions: 16
Number of successful extensions: 5
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: 291
Length of database: 315
Length adjustment: 27
Effective length of query: 264
Effective length of database: 288
Effective search space:    76032
Effective search space used:    76032
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: 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