GapMind for catabolism of small carbon sources

 

Aligments for a candidate for thuG in Pseudomonas fluorescens FW300-N1B4

Align Maltose transport system permease protein malG aka TT_C1629, 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 Pf1N1B4_4848 Various polyols ABC transporter, permease component 2

Query= TCDB::Q72H66
         (280 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4848 Various polyols ABC
           transporter, permease component 2
          Length = 276

 Score =  159 bits (402), Expect = 6e-44
 Identities = 90/275 (32%), Positives = 153/275 (55%), Gaps = 4/275 (1%)

Query: 5   SRLLGRLFFYLLVVFVVVYSVFPFYWAVISSFKPSDALFSPDPSFLPVPFTLEHYENVFL 64
           SR L  L    L   + +   FP +W V++SFK     F+  P F+  P TLE+Y ++  
Sbjct: 6   SRRLQSLLLGTLAWAIAILIFFPIFWMVLTSFKTEIDAFATPPQFIFTP-TLENYLHINE 64

Query: 65  QANFGRNLLNSLIVAGGATLLSLVLGVLAAYALGRLPFPPKNAVMYIVLSMTMFPQIAVL 124
           ++++     NS++++  AT L L++ V AAY++           +  +LS  M P + VL
Sbjct: 65  RSDYFSFAWNSVVISFSATALCLLIAVPAAYSMAFYETQRTKGTLLWMLSTKMLPPVGVL 124

Query: 125 GGLFLLLRQTGLFNTHLGLILTYLLFTLPFTVWVLVGYFRGLPRELEEAAYVDGATPLQT 184
             ++LL +  GL +T + LI+ Y L  LP  VW++  YF+ +P+++ EAA +DGAT  Q 
Sbjct: 125 MPIYLLAKSFGLLDTRIALIVIYTLINLPIVVWMIYTYFKDIPKDILEAARLDGATLWQE 184

Query: 185 LLKVMLPLTGPGLVTTGLLAFIAAWNEYLFALTFTVGDSVKTVPPAIASFGGATPFEIPW 244
           +++V+LP+   GL +T LL+ I  WNE  ++L  T       +   IAS+  ++P  + W
Sbjct: 185 MVRVLLPIAKGGLASTVLLSLILCWNEAFWSLNLT-SSQAAPLTALIASY--SSPEGLFW 241

Query: 245 GSIMAASVVVTVPLVVLVLVFQQRIVAGLTAGAVK 279
             + A S +   P+++   + Q+++V GL+ GAVK
Sbjct: 242 AKLSAVSTLACAPILIFGWISQKQLVRGLSFGAVK 276


Lambda     K      H
   0.329    0.145    0.439 

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: 137
Number of extensions: 7
Number of successful extensions: 3
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: 280
Length of database: 276
Length adjustment: 25
Effective length of query: 255
Effective length of database: 251
Effective search space:    64005
Effective search space used:    64005
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: 47 (22.7 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