GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davT in Shewanella oneidensis MR-1

Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate 200475 SO1300 glutamate-1-semialdehyde-2,1-aminomutase (NCBI ptt file)

Query= BRENDA::Q9I6M4
         (426 letters)



>FitnessBrowser__MR1:200475
          Length = 430

 Score =  167 bits (424), Expect = 4e-46
 Identities = 120/367 (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++ LR+LCD
Sbjct: 173 AKHTLTAVYND--LDSVRSLFEQ--YPTEISCIIIEPVAGNMNCIPPIPGFLEGLRSLCD 228

Query: 232 QHGILLIADEVQTGAGRTGTFFATEQLGIVPDLTTFAKSVGGGFPISGVAGKAEIMDAIA 291
           + G LLI DEV TG  R     A    G+ PDLTT  K +GGG P+    G+ ++M  IA
Sbjct: 229 EFGALLIIDEVMTGF-RVSKSGAQGHYGVTPDLTTLGKVIGGGMPVGAFGGRKDVMQFIA 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: 452
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: 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.

Links

Downloads

Related tools

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