GapMind for catabolism of small carbon sources

 

Aligments for a candidate for patA in Shewanella oneidensis MR-1

Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate 200454 SO1276 4-aminobutyrate aminotransferase (NCBI ptt file)

Query= BRENDA::P42588
         (459 letters)



>lcl|FitnessBrowser__MR1:200454 SO1276 4-aminobutyrate
           aminotransferase (NCBI ptt file)
          Length = 425

 Score =  177 bits (449), Expect = 6e-49
 Identities = 141/421 (33%), Positives = 210/421 (49%), Gaps = 44/421 (10%)

Query: 47  NPGFLEYRKSVTAGGDYGAVE--WQAGSLNTLV-DTQGQEFIDCLGGFGIFNVGHRNPVV 103
           N   +  R++  AGG  G +   + A + N  V D +G+EFID  GG  + N GH +P V
Sbjct: 5   NDSLMARRQAAVAGG-VGQIHPIFTARAENASVWDVEGREFIDFAGGIAVLNTGHLHPKV 63

Query: 104 VSAVQNQLAKQPLHSQELLDPLRAML--AKTLAALTPGKL-KYSFFCNSGTESVEAALKL 160
            +AV  QL +   H+  ++    + +   + L  L PG   K +    SG+E+VE A+K+
Sbjct: 64  KAAVAAQL-EDFSHTCFMVLGYESYIQVCEKLNQLVPGDFAKKTALFTSGSEAVENAVKV 122

Query: 161 AKAYQSPRGKFTFIATSGAFHGKSLGALSATAK-------------STFRKPFMPLLPGF 207
           A+AY    G   F  TSG +HG+++ AL+ T K             + FR  F   L G 
Sbjct: 123 ARAYTKRAGVIAF--TSG-YHGRTMAALALTGKVAPYSKGMGLMSANVFRAEFPCALHGV 179

Query: 208 RHVPFGNIEAMRTALNECKKTGD--DVAAVILEPIQGEGGVILPPPGYLTAVRKLCDEFG 265
                 + +AM +     K   +  D+AA+ILEP+QGEGG     P ++  +R LCD  G
Sbjct: 180 -----SDDDAMASIERIFKNDAEPSDIAAIILEPVQGEGGFYAVSPAFMQRLRALCDREG 234

Query: 266 ALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKALGGGVMPIGATIATEEVFSVLFDN 325
            ++I DEVQTG GRTG  FA E   V  DI   AK++ GG  P+       +V   +   
Sbjct: 235 IMLIADEVQTGAGRTGTFFAMEQMGVSADITTFAKSIAGG-FPLSGITGRAQVMDAI--G 291

Query: 326 PFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQKGDMLLDGFRQLAREYPDLVQEAR 385
           P     T+GGNPLACAAALA + V  E+ L  +A   GD +      +  E+P  + + R
Sbjct: 292 PGGLGGTYGGNPLACAAALAVLEVFEEEKLLERANAIGDRIKSALNTMQVEHPQ-IADVR 350

Query: 386 GKGMLMAIEFV-DNEIGYNFASEMFRQR------VLVAGTLNNAKTIRIEPPLTLTIEQC 438
           G G + AIE + D +    + +++  +       +L  GT  N   +RI  PLT++  Q 
Sbjct: 351 GLGAMNAIELMEDGKPAPQYCAQILAEARNRGLILLSCGTYGN--VLRILVPLTVSDTQL 408

Query: 439 E 439
           +
Sbjct: 409 D 409


Lambda     K      H
   0.320    0.135    0.393 

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: 417
Number of extensions: 17
Number of successful extensions: 4
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: 459
Length of database: 425
Length adjustment: 32
Effective length of query: 427
Effective length of database: 393
Effective search space:   167811
Effective search space used:   167811
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (24.3 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 preprint 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