GapMind for catabolism of small carbon sources

 

Aligments for a candidate for PS417_11885 in Escherichia coli BW25113

Align Rhizopine-binding protein (characterized, see rationale)
to candidate 16259 b2150 methyl-galactoside transporter subunit (NCBI)

Query= uniprot:A0A0N9WNI6
         (308 letters)



>lcl|FitnessBrowser__Keio:16259 b2150 methyl-galactoside transporter
           subunit (NCBI)
          Length = 332

 Score =  135 bits (339), Expect = 2e-36
 Identities = 99/332 (29%), Positives = 169/332 (50%), Gaps = 31/332 (9%)

Query: 2   KTKIRFASLALSLMLASGAALADLRIGVSMSQFDDTWLTYLRESMDKQAKSMPDGVKLQF 61
           K  +  +++  S++  + A  AD RIGV++ ++DD +++ +R+++++ AK+ PD V+L  
Sbjct: 3   KKVLTLSAVMASMLFGAAAHAADTRIGVTIYKYDDNFMSVVRKAIEQDAKAAPD-VQLLM 61

Query: 62  EDARSDVVKQLSQVESFISQKVDAIVVNPVDTAATRKITEAAVKAGIPLVYVNRRPDDLK 121
            D+++D  KQ  Q++  +++ V A+ +N VD AA   + E A    +P+V+ N+ P    
Sbjct: 62  NDSQNDQSKQNDQIDVLLAKGVKALAINLVDPAAAGTVIEKARGQNVPVVFFNKEPSRKA 121

Query: 122 LPK--GVITVASNDLEAGQMQMQYLAE----------KMKGKGDIVILLGDLANNSTTNR 169
           L        V ++  E+G +Q   +A+             G+   V+L G+  +     R
Sbjct: 122 LDSYDKAYYVGTDSKESGIIQGDLIAKHWAANQGWDLNKDGQIQFVLLKGEPGHPDAEAR 181

Query: 170 TKGV-KEVLAKYPGIKIDQEQ--TGTWSRDKGMTLVNDWLT--QGRKFDAIVSNNDEMAI 224
           T  V KE+  K  GIK +Q Q  T  W   +    ++ WL+     K + +++NND MA+
Sbjct: 182 TTYVIKELNDK--GIKTEQLQLDTAMWDTAQAKDKMDAWLSGPNANKIEVVIANNDAMAM 239

Query: 225 GAAMALKQAGVEKGSVLIAGVDGTPDGLRAVKKGDLAVSVFQDANGQAVDSIDAAVKMAK 284
           GA  ALK     K S+ + GVD  P+ L  VK G LA +V  DAN QA  + D A  +A 
Sbjct: 240 GAVEALK--AHNKSSIPVFGVDALPEALALVKSGALAGTVLNDANNQAKATFDLAKNLAD 297

Query: 285 NEPV---------EQAVWVPYRLITPENVDQF 307
            +            + V VPY  +  +N+ +F
Sbjct: 298 GKGAADGTNWKIDNKVVRVPYVGVDKDNLAEF 329


Lambda     K      H
   0.315    0.130    0.360 

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: 264
Number of extensions: 14
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: 308
Length of database: 332
Length adjustment: 28
Effective length of query: 280
Effective length of database: 304
Effective search space:    85120
Effective search space used:    85120
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.5 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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