GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc02872 in Escherichia coli BW25113

Align ABC transporter for N-Acetyl-D-glucosamine, permease protein 1 (characterized)
to candidate 18061 b4033 maltose transporter subunit (NCBI)

Query= reanno::Smeli:SMc02872
         (315 letters)



>FitnessBrowser__Keio:18061
          Length = 514

 Score = 87.4 bits (215), Expect = 7e-22
 Identities = 75/256 (29%), Positives = 114/256 (44%), Gaps = 25/256 (9%)

Query: 54  GQLTFVGLGNFKVLFGDPRWAADFWNALKNNFVFFLIHMAVQNPIGIALAAMLSVPKLRF 113
           G     G  NF  +F D      F        VF LI + +   +G+ LA ++    LR 
Sbjct: 254 GYTVTTGWKNFTRVFTDEGIQKPFLAIFVWTVVFSLITVFLTVAVGMVLACLVQWEALRG 313

Query: 114 GAFYRTAIFLPTLLSFVIVGFIWKLILSPIWGVAPYLLDTVGLRSLFG---PWLGKPDTA 170
            A YR  + LP  +   I   I+K + +  +G    +L      +LFG    W   P TA
Sbjct: 314 KAVYRVLLILPYAVPSFISILIFKGLFNQSFGEINMMLS-----ALFGVKPAWFSDPTTA 368

Query: 171 LIAVSLISVWQYIGIPMMLIYAALLNIPDEVTEAAELDGVTGWSQFWKIKLPLILPAIGI 230
              + +++ W      M+L    L  IPD++ EA+ +DG   +  F+KI LPL++  +  
Sbjct: 369 RTMLIIVNTWLGYPYMMILCMGLLKAIPDDLYEASAMDGAGPFQNFFKITLPLLIKPLTP 428

Query: 231 VSILTFVGNFNAFDLIYTVQGALAGPDK--------STDILGTLLYRTFF---GFQLQLG 279
           + I +F  NFN F LI  +     GPD+         TD+L    YR  F   G Q    
Sbjct: 429 LMIASFAFNFNNFVLIQLLTN--GGPDRLGTTTPAGYTDLLVNYTYRIAFEGGGGQ---- 482

Query: 280 DRSMGATIAAIMFLII 295
           D  + A IA ++FL++
Sbjct: 483 DFGLAAAIATLIFLLV 498


Lambda     K      H
   0.331    0.146    0.461 

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: 445
Number of extensions: 26
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: 315
Length of database: 514
Length adjustment: 31
Effective length of query: 284
Effective length of database: 483
Effective search space:   137172
Effective search space used:   137172
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 50 (23.9 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