GapMind for catabolism of small carbon sources

 

Aligments for a candidate for TM1747 in Escherichia coli BW25113

Align TM1747, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized)
to candidate 15364 b1244 oligopeptide permease ABC transporter membrane protein (NCBI)

Query= TCDB::Q9X269
         (341 letters)



>lcl|FitnessBrowser__Keio:15364 b1244 oligopeptide permease ABC
           transporter membrane protein (NCBI)
          Length = 306

 Score =  251 bits (642), Expect = 1e-71
 Identities = 127/317 (40%), Positives = 205/317 (64%), Gaps = 15/317 (4%)

Query: 25  LKFLLKRLLTIAISMVVVIVITYVLMWLAPGNFFELQRVRDAIARVTTPDDPAYQATLKG 84
           LKF+L+R L    ++ ++I I++ +M LAPG+ F  +R        T P +      +  
Sbjct: 2   LKFILRRCLEAIPTLFILITISFFMMRLAPGSPFTGER--------TLPPE-----VMAN 48

Query: 85  FEERYGLNNPLWKQILMYLKGAVVFKFGPSFSDPARNIEDLIKEKFPITFTLALSSILFA 144
            E +Y LN+P+  Q   YLK      FGPSF     ++ DL+   FP++  L  ++   A
Sbjct: 49  IEAKYHLNDPIMTQYFSYLKQLAHGDFGPSFKYKDYSVNDLVASSFPVSAKLGAAAFFLA 108

Query: 145 LVVGVPLGILAALKKNTWIDYTAMTVSVIGVAIPSYVVAVFLILIFSIYLGWLPTSGWEG 204
           +++GV  G++AALK+NT  DYT M +++ GV IPS+VVA  L++IF+I L WLP  GW G
Sbjct: 109 VILGVSAGVIAALKQNTKWDYTVMGLAMTGVVIPSFVVAPLLVMIFAIILHWLPGGGWNG 168

Query: 205 --IRTKILPTIALALGPLASVARFTRVSLLDTLNQDFIRTAYAKGGDDRTVIMKHALRPS 262
             ++  ILP +AL+L  +AS+AR TR S+++ L+ +FIRTA AKG   R +I++HAL+P+
Sbjct: 169 GALKFMILPMVALSLAYIASIARITRGSMIEVLHSNFIRTARAKGLPMRRIILRHALKPA 228

Query: 263 MIPLVTIVGPQMAYLMVGTVWVENIFRIPGLGQLFANAAVTRDYPLLVTSTFILALTVMI 322
           ++P+++ +GP    ++ G++ +E I+ +PG+GQLF N A+ RDY L+++ T ++    ++
Sbjct: 229 LLPVLSYMGPAFVGIITGSMVIETIYGLPGIGQLFVNGALNRDYSLVLSLTILVGALTIL 288

Query: 323 MNLIVDVLYAILDPRIK 339
            N IVDVLYA++DP+I+
Sbjct: 289 FNAIVDVLYAVIDPKIR 305


Lambda     K      H
   0.328    0.143    0.429 

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: 275
Number of extensions: 12
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: 341
Length of database: 306
Length adjustment: 28
Effective length of query: 313
Effective length of database: 278
Effective search space:    87014
Effective search space used:    87014
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: 48 (23.1 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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