GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Keio:15432
          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:

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