GapMind for catabolism of small carbon sources

 

Aligments for a candidate for davT in Shewanella sp. ANA-3

Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate 7025922 Shewana3_3071 glutamate-1-semialdehyde aminotransferase (RefSeq)

Query= BRENDA::Q9I6M4
         (426 letters)



>lcl|FitnessBrowser__ANA3:7025922 Shewana3_3071
           glutamate-1-semialdehyde aminotransferase (RefSeq)
          Length = 430

 Score =  169 bits (428), Expect = 2e-46
 Identities = 121/367 (32%), Positives = 182/367 (49%), Gaps = 32/367 (8%)

Query: 5   NESLLKRRQAAVPRGVGQI---------HPVVAERAENSTVWDVEGREYIDFAGGIAVLN 55
           +E+L ++ +  +P GV             P+  E+A+ + ++D +G+ YID+ G    + 
Sbjct: 4   SEALFEQAKKTIPGGVNSPVRAFNGVGGSPLFIEKADGAYIYDADGKAYIDYVGSWGPMI 63

Query: 56  TGHLHPK----VIAAVQEQLGKLSHTCFQVLAYEPYIELAEEIAKRVPGDFPKKTLLVTS 111
            GH HPK    V+AAV   L   + T       E  +++AE++   VP    ++  +V+S
Sbjct: 64  LGHNHPKIREAVLAAVHNGLSFGAPT-------ELEVQMAEKVIAMVPSI--EQVRMVSS 114

Query: 112 GSEAVENAVKIARAATGRAGVIAFTGAYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRAL 171
           G+EA  +A+++AR  T R  ++ F G YHG     L   G     + G    PG I    
Sbjct: 115 GTEATMSAIRLARGFTNRDKILKFEGCYHGHADCLLVKAGSGA-LTLGQPSSPG-IPEDF 172

Query: 172 APCELHGVSEDDSIASIERIFKNDAQPQDIAAIIIEPVQGEGGFYVNSKSFMQRLRALCD 231
           A   L  V  D  + S+  +F+    P +I+ IIIEPV G          F++ LRA+CD
Sbjct: 173 AKHTLTAVYND--LDSVRSLFEQ--YPTEISCIIIEPVAGNMNCIPPIPGFLEGLRAMCD 228

Query: 232 QHGILLIADEVQTGAGRTGTFFATEQLGIVPDLTTFAKSVGGGFPISGVAGKAEIMDAIA 291
           + G LLI DEV TG  R     A    G+ PDLTT  K +GGG P+    G+ E+M  IA
Sbjct: 229 EFGALLIIDEVMTGF-RVSRSGAQGHYGVTPDLTTLGKVIGGGMPVGAFGGRKEVMQFIA 287

Query: 292 PGG---LGGTYAGSPIACAAALAVLKVFEEEKLLERSQAVGERLKAGLREIQAKHKVIGD 348
           P G     GT +G+PIA +A LA ++   EE L E   A  +R+  G +    KH +   
Sbjct: 288 PTGPVYQAGTLSGNPIAMSAGLAQMEALCEEGLYEALSAKTKRIAEGFKAAADKHGIPMA 347

Query: 349 VRGLGSM 355
           +  +G M
Sbjct: 348 INYVGGM 354


Lambda     K      H
   0.319    0.137    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: 458
Number of extensions: 28
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: 426
Length of database: 430
Length adjustment: 32
Effective length of query: 394
Effective length of database: 398
Effective search space:   156812
Effective search space used:   156812
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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