GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Keio:15364
          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.

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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