GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pta in Dechlorosoma suillum PS

Align Phosphate acetyltransferase; EC 2.3.1.8; Phosphotransacetylase (uncharacterized)
to candidate Dsui_0543 Dsui_0543 malic enzyme

Query= curated2:Q726S7
         (704 letters)



>FitnessBrowser__PS:Dsui_0543
          Length = 758

 Score =  192 bits (487), Expect = 7e-53
 Identities = 103/315 (32%), Positives = 182/315 (57%), Gaps = 5/315 (1%)

Query: 392 RIVLPEGAEERILRAADILVRREVADIILLGDANTVGSRIGDLGLDM---DGVQIVQPNL 448
           R++  EG +ER+LRA  +++   +A  IL+G    + +R+  +G  +   +  ++V PN 
Sbjct: 444 RVIYAEGEDERVLRAIQVILEERLAKPILVGRPEVIEARLQKIGSKLKAGEHFEVVNPNY 503

Query: 449 SPKFDEYVAAYHECRKKKGISMEQAR-DMMNDPTYFGTMMVHKGDADGMVSGAINTTAHT 507
             ++ E  +AYH+  K++G++++ A+  + +D T  G M+V  G AD ++ G     AH 
Sbjct: 504 DERYKECWSAYHQLMKRRGVTIDIAKMRLRSDNTIIGAMLVKLGYADALICGMSGRFAHH 563

Query: 508 IRPAFEFIKTKPGVSIVSSVFLMCLKDRVLVFGDCAVNPNPTAEQLAEIAISASHTARIF 567
           +R   E I    G + ++++  + L +R L   D  VN NP A+QLA+IA+ A+ T R F
Sbjct: 564 LRQVEEVIGKAAGHNTLAAMNHLLLPNRALFLCDTHVNENPDAQQLADIAVMAAETVRSF 623

Query: 568 GVDPRVAMLSYSTGSSGKGADVEKVIEATRIAKERAPELLLEGPLQYDAAIDMDVARTKL 627
           G+ P+VA+LS+S   S + A   K+ EA  IA+ +AP+L ++G +  D+A+  ++     
Sbjct: 624 GITPKVALLSHSNFGSSQSASARKMSEAADIARAKAPDLEIDGEMHGDSALSEEIRLQSD 683

Query: 628 PGSTVAGQATVFIFPDLNTGNNTYKAVQRAAG-AVAIGPVLQGLNKPVNDLSRGCTVADI 686
           P S + G+A V + P+L+  N +Y  ++   G  V IGP+L G+ KPV+ L+   TV  +
Sbjct: 684 PESPLKGEANVLVMPNLDAANISYNLLKMTGGEGVTIGPILMGVAKPVHVLTATATVRRL 743

Query: 687 VNTVAITAIQAQAEK 701
           VN  A+  + A+ ++
Sbjct: 744 VNMTALAVVDAKKQR 758


Lambda     K      H
   0.319    0.135    0.383 

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: 1059
Number of extensions: 43
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: 704
Length of database: 758
Length adjustment: 40
Effective length of query: 664
Effective length of database: 718
Effective search space:   476752
Effective search space used:   476752
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 (21.7 bits)
S2: 55 (25.8 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