GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__MR1:200454
          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:

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