GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabT in Sphingobium czechense LL01

Align 4-aminobutyrate aminotransferase; EC 2.6.1.19 (characterized, see rationale)
to candidate WP_066608605.1 V473_RS18720 diaminobutyrate--2-oxoglutarate transaminase

Query= uniprot:A1S8Y2
         (425 letters)



>NCBI__GCF_001046645.1:WP_066608605.1
          Length = 436

 Score =  182 bits (463), Expect = 1e-50
 Identities = 132/425 (31%), Positives = 215/425 (50%), Gaps = 19/425 (4%)

Query: 6   DSLMVRRRAAVAGGVGQIHPVFTERAENATVWDVEGREYIDFAGGIAVLNTGHLHPKVKA 65
           D+ +  RR +      +  P    +A+   + D +G  Y+DF  G + LN GH HP +K 
Sbjct: 15  DTAIYERRESAVRSYARAMPRQFNQAQGVWMHDNQGGRYLDFLSGCSTLNYGHNHPVLKN 74

Query: 66  AVAEQLEKFSHTCFMVLGYESYVAVCEKLNQLV--PGDFAKKSALFT--SGSEAVENAIK 121
           A+ + +     T  + L  ++       L  ++  P D   + A+FT  +G+ AVE AIK
Sbjct: 75  ALVDYIVNDGITHGLDLHTDAKADFLAALEDVILTPRDLDYR-AMFTGPTGTNAVEAAIK 133

Query: 122 VARAYTKRAGVIAFTSGYHGRTMAALALTGKVAPYSKGMGLMQANVFRAEFPCALHGVSE 181
           +AR  T R  VIAFT+G+HG T+ ALA TG  A    G G+   +V    +    HG   
Sbjct: 134 LARKITGRELVIAFTNGFHGMTLGALACTGNAAKRG-GAGVPLNHVSHEPYD-GYHGPGV 191

Query: 182 DDAMASIERIFKNDAEPSDI-AAIILEPVQGEGGFYAATPGFMKRLRELCDREGIMLIAD 240
           D A   +ER   + +   D  AAI++E VQGEGG  AA+P +++++ ++  R G ++I D
Sbjct: 192 DTA-EQLERRLSDPSSGLDAPAAILVETVQGEGGLNAASPRWLRQIADIAKRHGALMIID 250

Query: 241 EVQTGAGRTGTFFAMEQMGVAADITTFAKSIAG-GFPLSGITGRAEVMDAIGPGGLGGTY 299
           ++Q G GRTG FF+ E MG   DI T AKS++G G P +    R E +D   PG   GT+
Sbjct: 251 DIQAGCGRTGNFFSFEGMGFTPDIVTMAKSLSGMGLPFALTLFRPE-LDQWSPGEHNGTF 309

Query: 300 GGSPLACAAALAVIEVFEEEKLLERSNA-IGQTIKSAIGELASRYPQIAEVRGLGSMIAI 358
            G+  A   A A +  F  +   ++  A  G  ++  +  +A+ +     +RG G M  I
Sbjct: 310 RGNNHAFVTATATLRHFWSDGNFQQDIARRGALLERRLAAMATEHG--LSIRGRGMMRGI 367

Query: 359 ELMENGKPAPEYCPQVLTEARNRGLILLSCGTYGNVLRILVPITAPDEQIQRGLEIMAEC 418
           ++      + E    +      +GLI+ + G +  ++++L P+   D  +  GL+I+ + 
Sbjct: 368 DV-----GSGEIAQTITAACFAQGLIIETSGAHDEIVKVLAPLVIDDSVLSAGLDILEQS 422

Query: 419 FEAVL 423
             + L
Sbjct: 423 VRSAL 427


Lambda     K      H
   0.319    0.136    0.391 

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: 441
Number of extensions: 28
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: 425
Length of database: 436
Length adjustment: 32
Effective length of query: 393
Effective length of database: 404
Effective search space:   158772
Effective search space used:   158772
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 24 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