GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsC in Escherichia coli BW25113

Align Sugar ABC transporter permease (characterized, see rationale)
to candidate 15432 b1312 predicted sugar transporter subunit: membrane component of ABC superfamily (NCBI)

Query= uniprot:A0A165KQ00
         (289 letters)



>FitnessBrowser__Keio:15432
          Length = 280

 Score =  120 bits (302), Expect = 3e-32
 Identities = 83/282 (29%), Positives = 139/282 (49%), Gaps = 10/282 (3%)

Query: 10  SVGRFLVYAVLALATAFFLLPLYAMLVTSFKYAEEIRSTSLLALPGSLNWSAWGTAWQSA 69
           ++ R   Y  LAL     L P + ML+TSFK A+E  S     LP       W       
Sbjct: 7   TLSRIGFYCGLALFLIITLFPFFVMLMTSFKGAKEAISLHPTLLP-----QQWTLEHYVD 61

Query: 70  CTGVDCNGLRPFFMNSVAMAVPAVLISTVWGALNGYVLSLWKFRGSDALFGMLLFGVFMP 129
                      +F NS+ ++V + +++   G L  Y LS  +F+G   +     + V+M 
Sbjct: 62  IFNPMIFPFVDYFRNSLVVSVVSSVVAVFLGILGAYALSRLRFKGRMTI-NASFYTVYMF 120

Query: 130 FQVVLL-PMSQVLGWLGLSSSITGLVLVHCLAGLAGTTLFFRNYYAAIPKELVNAARMDG 188
             ++L+ P+ +++  LG+  +   L++      L       ++Y+  IP E+  AA MDG
Sbjct: 121 SGILLVVPLFKIITALGIYDTEMALIITMVTQTLPTAVFMLKSYFDTIPDEIEEAAMMDG 180

Query: 189 ASFFQIFWRIVLPLSTPIVMVTLIWQFTNIWNDFLFGVVF-SGTDSKPVTVGLNNLANTS 247
            +  QI +RI +PL+   ++   ++ F   WND+LF  +F S   +  + VGLN L +T 
Sbjct: 181 LNRLQIIFRITVPLAMSGLISVFVYCFMVAWNDYLFASIFLSSASNFTLPVGLNALFSTP 240

Query: 248 SSVKAYNVDMAAAIIAGLPTMVIYVLAGKFFVRGLTAGAVKG 289
             +  +   MAA+++  LP +++Y L+ +F   GLTAG VKG
Sbjct: 241 DYI--WGRMMAASLVTALPVVIMYALSERFIKSGLTAGGVKG 280


Lambda     K      H
   0.327    0.139    0.436 

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: 201
Number of extensions: 10
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: 289
Length of database: 280
Length adjustment: 26
Effective length of query: 263
Effective length of database: 254
Effective search space:    66802
Effective search space used:    66802
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 (21.7 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