GapMind for catabolism of small carbon sources

 

Aligments for a candidate for SMc02871 in Escherichia coli BW25113

Align N-Acetyl-D-glucosamine ABC transport system, permease component 2 (characterized)
to candidate 15432 b1312 predicted sugar transporter subunit: membrane component of ABC superfamily (NCBI)

Query= reanno::Phaeo:GFF2752
         (280 letters)



>lcl|FitnessBrowser__Keio:15432 b1312 predicted sugar transporter
           subunit: membrane component of ABC superfamily (NCBI)
          Length = 280

 Score =  137 bits (345), Expect = 3e-37
 Identities = 84/270 (31%), Positives = 141/270 (52%), Gaps = 15/270 (5%)

Query: 19  LITYTLIALFPVFVILVNSFK-TRKAIFRDPLGLPTSDTFSLVGYQTVLKQG--DFFLYF 75
           L  + +I LFP FV+L+ SFK  ++AI   P  LP    ++L  Y  +       F  YF
Sbjct: 17  LALFLIITLFPFFVMLMTSFKGAKEAISLHPTLLPQQ--WTLEHYVDIFNPMIFPFVDYF 74

Query: 76  QNSMIVTVVSLALVLLFGAMAAFALAEYRFKGNMLLG-----LYLALGIMIPIRIGTVAI 130
           +NS++V+VVS  + +  G + A+AL+  RFKG M +      +Y+  GI++      V +
Sbjct: 75  RNSLVVSVVSSVVAVFLGILGAYALSRLRFKGRMTINASFYTVYMFSGILL-----VVPL 129

Query: 131 LELMVDTGLVNTLTALILVYTAQGLPLAVFILSEFMKQVSDDLKNAGRIDGLSEYTIFFR 190
            +++   G+ +T  ALI+    Q LP AVF+L  +   + D+++ A  +DGL+   I FR
Sbjct: 130 FKIITALGIYDTEMALIITMVTQTLPTAVFMLKSYFDTIPDEIEEAAMMDGLNRLQIIFR 189

Query: 191 LVLPLVRPAMATVAVFNMIPIWNDLWFPLILAPAEETKTLTLGSQVFIGQFVTDWNAVLS 250
           + +PL    + +V V+  +  WND  F  I   +    TL +G           W  +++
Sbjct: 190 ITVPLAMSGLISVFVYCFMVAWNDYLFASIFLSSASNFTLPVGLNALFSTPDYIWGRMMA 249

Query: 251 ALSMAILPVMVLYVIFSRQLIRGITSGAVK 280
           A  +  LPV+++Y +  R +  G+T+G VK
Sbjct: 250 ASLVTALPVVIMYALSERFIKSGLTAGGVK 279


Lambda     K      H
   0.330    0.143    0.414 

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: 233
Number of extensions: 18
Number of successful extensions: 4
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: 280
Length adjustment: 26
Effective length of query: 254
Effective length of database: 254
Effective search space:    64516
Effective search space used:    64516
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 (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 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