GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuG in Escherichia coli BW25113

Align Trehalose/maltose transport system permease protein MalG (characterized)
to candidate 15432 b1312 predicted sugar transporter subunit: membrane component of ABC superfamily (NCBI)

Query= SwissProt::Q7LYX6
         (278 letters)



>FitnessBrowser__Keio:15432
          Length = 280

 Score =  180 bits (457), Expect = 3e-50
 Identities = 106/278 (38%), Positives = 166/278 (59%), Gaps = 5/278 (1%)

Query: 3   EEVLKRILLIIGAILMAIICLFPFIWMIVVSF--AEDPTFLGSPLVEYKSTLENYVRVLS 60
           +  L RI    G  L  II LFPF  M++ SF  A++   L   L+  + TLE+YV + +
Sbjct: 5   KRTLSRIGFYCGLALFLIITLFPFFVMLMTSFKGAKEAISLHPTLLPQQWTLEHYVDIFN 64

Query: 61  DPTLHFPAYLKNSIIIASLVTLTTVSISSLAAYAVSRIEFKGRLLIPIFVLGLSMFPQIS 120
                F  Y +NS++++ + ++  V +  L AYA+SR+ FKGR+ I      + MF  I 
Sbjct: 65  PMIFPFVDYFRNSLVVSVVSSVVAVFLGILGAYALSRLRFKGRMTINASFYTVYMFSGIL 124

Query: 121 LVGYLFKFIEKLGWVNTYQALYFPYVAWTLPLSLWILLSYFSQLPKDLDEAAMIDGASRI 180
           LV  LFK I  LG  +T  AL    V  TLP ++++L SYF  +P +++EAAM+DG +R+
Sbjct: 125 LVVPLFKIITALGIYDTEMALIITMVTQTLPTAVFMLKSYFDTIPDEIEEAAMMDGLNRL 184

Query: 181 KTLTTIILPLSAPALFSTALLVFIAAFNEFMFALLFTTDHRARTVPVGI-ALFQGVHGEI 239
           + +  I +PL+   L S  +  F+ A+N+++FA +F +     T+PVG+ ALF     + 
Sbjct: 185 QIIFRITVPLAMSGLISVFVYCFMVAWNDYLFASIFLSSASNFTLPVGLNALFS--TPDY 242

Query: 240 PWGSVMAASVISTIPLVIMALLFQKYIVSGLTAGALKG 277
            WG +MAAS+++ +P+VIM  L +++I SGLTAG +KG
Sbjct: 243 IWGRMMAASLVTALPVVIMYALSERFIKSGLTAGGVKG 280


Lambda     K      H
   0.329    0.142    0.422 

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: 245
Number of extensions: 8
Number of successful extensions: 2
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: 278
Length of database: 280
Length adjustment: 26
Effective length of query: 252
Effective length of database: 254
Effective search space:    64008
Effective search space used:    64008
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