GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TT_C0326 in Escherichia coli BW25113

Align Sugar transport system permease protein aka TT_C0326, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized)
to candidate 18060 b4032 maltose transporter subunit (NCBI)

Query= TCDB::Q72KX4
         (268 letters)



>FitnessBrowser__Keio:18060
          Length = 296

 Score = 89.7 bits (221), Expect = 6e-23
 Identities = 81/281 (28%), Positives = 122/281 (43%), Gaps = 26/281 (9%)

Query: 10  LLLMAGFFLLPVYLVVLTALKEPARITLETVWQWPHPPYWESFRTAW---------EAFR 60
           LLL     + P+ +VV  +L++    T   +   P    W+ ++ A              
Sbjct: 20  LLLFIAAIMFPLLMVVAISLRQGNFATGSLI---PEQISWDHWKLALGFSVEQADGRITP 76

Query: 61  PKFQ------NSVVLAVSATLLSALVGSLNGYVLAKWPFRGSG-LLFALILFGMFIPYQS 113
           P F       NSV +A  + +    + +   Y  A+  F G   LL  +++F MF P   
Sbjct: 77  PPFPVLLWLWNSVKVAGISAIGIVALSTTCAYAFARMRFPGKATLLKGMLIFQMF-PAVL 135

Query: 114 ILIPLFQFMKSIGLYGSLFGL-----VLVHVIYGIPIVTLIFRNYYSEIPDELVEAARID 168
            L+ L+     +G Y    GL     V+   + GI +     + Y+  I   L EAA +D
Sbjct: 136 SLVALYALFDRLGEYIPFIGLNTHGGVIFAYLGGIALHVWTIKGYFETIDSSLEEAAALD 195

Query: 169 GAGFFGIFRHVILPLSVPAFVVVAIWQFTQIWNEFLFAVTLTRP-ESQPITVALAQLAGG 227
           GA  +  FR V+LPLSVP   VV I  F     E   A  L R   S  + V + Q    
Sbjct: 196 GATPWQAFRLVLLPLSVPILAVVFILSFIAAITEVPVASLLLRDVNSYTLAVGMQQYLNP 255

Query: 228 EAVKWNLPMAGAILAALPTLLVYILLGRYFLRGLLAGSVKG 268
           +   W    A A+++ALP  +V++L  R+ + GL AG VKG
Sbjct: 256 QNYLWGDFAAAAVMSALPITIVFLLAQRWLVNGLTAGGVKG 296


Lambda     K      H
   0.330    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: 216
Number of extensions: 17
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: 268
Length of database: 296
Length adjustment: 26
Effective length of query: 242
Effective length of database: 270
Effective search space:    65340
Effective search space used:    65340
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