GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patA in Shewanella amazonensis SB2B

Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate 6938533 Sama_2636 4-aminobutyrate aminotransferase (RefSeq)

Query= BRENDA::P42588
         (459 letters)



>FitnessBrowser__SB2B:6938533
          Length = 425

 Score =  188 bits (477), Expect = 3e-52
 Identities = 143/417 (34%), Positives = 208/417 (49%), Gaps = 36/417 (8%)

Query: 47  NPGFLEYRKSVTAGG--DYGAVEWQAGSLNTLVDTQGQEFIDCLGGFGIFNVGHRNPVVV 104
           N   +  R++  AGG      V  +     T+ D +G+E+ID  GG  + N GH +P V 
Sbjct: 5   NDSLMVRRRAAVAGGVGQIHPVFTERAENATVWDVEGREYIDFAGGIAVLNTGHLHPKVK 64

Query: 105 SAVQNQLAKQPLHSQELLDPLRAMLA--KTLAALTPGKL-KYSFFCNSGTESVEAALKLA 161
           +AV  QL K   H+  ++    + +A  + L  L PG   K S    SG+E+VE A+K+A
Sbjct: 65  AAVAEQLEKFS-HTCFMVLGYESYVAVCEKLNQLVPGDFAKKSALFTSGSEAVENAIKVA 123

Query: 162 KAYQSPRGKFTFIATSGAFHGKSLGALSATAK-------------STFRKPFMPLLPGFR 208
           +AY    G   F  TSG +HG+++ AL+ T K             + FR  F   L G  
Sbjct: 124 RAYTKRAGVIAF--TSG-YHGRTMAALALTGKVAPYSKGMGLMQANVFRAEFPCALHGVS 180

Query: 209 HVP-FGNIEAMRTALNECKKTGDDVAAVILEPIQGEGGVILPPPGYLTAVRKLCDEFGAL 267
                 +IE  R   N+ + +  D+AA+ILEP+QGEGG     PG++  +R+LCD  G +
Sbjct: 181 EDDAMASIE--RIFKNDAEPS--DIAAIILEPVQGEGGFYAATPGFMKRLRELCDREGIM 236

Query: 268 MILDEVQTGMGRTGKMFACEHENVQPDILCLAKALGGGVMPIGATIATEEVFSVLFDNPF 327
           +I DEVQTG GRTG  FA E   V  DI   AK++ GG  P+       EV   +   P 
Sbjct: 237 LIADEVQTGAGRTGTFFAMEQMGVAADITTFAKSIAGG-FPLSGITGRAEVMDAI--GPG 293

Query: 328 LHTTTFGGNPLACAAALATINVLLEQNLPAQAEQKGDMLLDGFRQLAREYPDLVQEARGK 387
               T+GG+PLACAAALA I V  E+ L  ++   G  +     +LA  YP  + E RG 
Sbjct: 294 GLGGTYGGSPLACAAALAVIEVFEEEKLLERSNAIGQTIKSAIGELASRYPQ-IAEVRGL 352

Query: 388 GMLMAIEFVDN-----EIGYNFASEMFRQRVLVAGTLNNAKTIRIEPPLTLTIEQCE 439
           G ++AIE ++N     E      +E   + +++         +RI  P+T   EQ +
Sbjct: 353 GSMIAIELMENGKPAPEYCPQVLTEARNRGLILLSCGTYGNVLRILVPITAPDEQIQ 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: 418
Number of extensions: 27
Number of successful extensions: 5
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