GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlG in Escherichia coli BW25113

Align MtlG, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized)
to candidate 18060 b4032 maltose transporter subunit (NCBI)

Query= TCDB::O30493
         (276 letters)



>FitnessBrowser__Keio:18060
          Length = 296

 Score = 93.2 bits (230), Expect = 6e-24
 Identities = 78/254 (30%), Positives = 112/254 (44%), Gaps = 25/254 (9%)

Query: 31  WMVLTSFKTE-IDAFATPPQFIFTPTLENYLHINERSNYFSYAWNSVLISFSATALCLLI 89
           W +   F  E  D   TPP F   P L              + WNSV ++  +    + +
Sbjct: 59  WKLALGFSVEQADGRITPPPF---PVL-------------LWLWNSVKVAGISAIGIVAL 102

Query: 90  SVPAAYSMAFYETKRTKSTLLWMLSTKMLPPVGVLMPIYLLAKSFGL------LDTRIAL 143
           S   AY+ A        + L  ML  +M P V  L+ +Y L    G       L+T   +
Sbjct: 103 STTCAYAFARMRFPGKATLLKGMLIFQMFPAVLSLVALYALFDRLGEYIPFIGLNTHGGV 162

Query: 144 IIIYTLINLPIVVWMVYTYFKDIPKDILEAARLDGATLWQEMVRVLLPIAKGGLASTVLL 203
           I  Y L  + + VW +  YF+ I   + EAA LDGAT WQ    VLLP++   LA   +L
Sbjct: 163 IFAY-LGGIALHVWTIKGYFETIDSSLEEAAALDGATPWQAFRLVLLPLSVPILAVVFIL 221

Query: 204 SLILCWNEA-FWSLNLTSSNAAPLTALIASYSSPEGLFWAKLSAVSTLACAPILIFGWIS 262
           S I    E    SL L   N+  L   +  Y +P+   W   +A + ++  PI I   ++
Sbjct: 222 SFIAAITEVPVASLLLRDVNSYTLAVGMQQYLNPQNYLWGDFAAAAVMSALPITIVFLLA 281

Query: 263 QKQLVRGLSFGAVK 276
           Q+ LV GL+ G VK
Sbjct: 282 QRWLVNGLTAGGVK 295


Lambda     K      H
   0.327    0.137    0.426 

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: 245
Number of extensions: 13
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: 276
Length of database: 296
Length adjustment: 26
Effective length of query: 250
Effective length of database: 270
Effective search space:    67500
Effective search space used:    67500
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