GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pta in Dinoroseobacter shibae DFL-12

Align phosphotransacetylase (EC 2.3.1.8) (characterized)
to candidate 3610086 Dshi_3467 Malate dehydrogenase (oxaloacetate-decarboxylating) (NADP(+))., Phosphate acetyltransferase (RefSeq)

Query= metacyc::PTACLOS-MONOMER
         (333 letters)



>FitnessBrowser__Dino:3610086
          Length = 752

 Score =  137 bits (345), Expect = 9e-37
 Identities = 99/325 (30%), Positives = 164/325 (50%), Gaps = 12/325 (3%)

Query: 3   LIESIWECAKQDKKRIILAEGEEKRNLIAADKIIKEGLAELVLVGDENKIKEK--ASELN 60
           +++ ++  AK  + R+I AEG++ R L AA    + GL + ++VG ++ +K +  A+ + 
Sbjct: 431 MLQGMFARAKGTQARMIFAEGDDIRVLRAAVTYQRSGLGKALVVGRQDDVKTRLEAAGIG 490

Query: 61  LDISKAEIMDPETSLKTETYARDFYELRKHKGMTIEKSEKMV-RDPLYFATMALKDGYVD 119
               + EI++   +   ETY    Y   + KG       ++  RD   F+ + L  G+ D
Sbjct: 491 DAFRELEIVNAGNTRHLETYKEFLYGRLQRKGYDTSDIHRLAARDRHAFSALMLAHGHGD 550

Query: 120 GMVSGAVHTTGDLLRPGLQIIKTAPGVKIVSGFFVMIIPDCDYGEEGLLLFADCAVNPNP 179
           G+V+GA   +  +L   +  +  A       G   +++      +  ++L AD  V+  P
Sbjct: 551 GLVTGATRKSAHVLGL-INTVFDAGAEDGAVGVTALLV------KGRIVLIADTLVHEWP 603

Query: 180 TSDELADIAITTAETARKLCNVEPKVAMLSFSTMGSAKGEMVDKVKNAVEITKKFRPDLA 239
             ++LADIA   A TAR L  +EP+VA +SFST G    E   K+  A  +      D  
Sbjct: 604 DEEDLADIATRAAGTARSL-GLEPRVAFVSFSTFGYPVSERATKMHRAPRVLDARGVDFE 662

Query: 240 IDGELQLDAAIDSEVAALKAPSSNVAGNANVLVFPDLQTGNIGYKLVQRFAKAKAIGPIC 299
            DGE+ +D A+D E+ A + P   ++G ANVLV P   + +I  KL+Q+   A  IGPI 
Sbjct: 663 YDGEMTVDVALDPEIMA-QYPFCRLSGPANVLVVPARHSASISVKLMQQLGDATVIGPIL 721

Query: 300 QGFAKPINDLSRGCSSEDIVNVVAI 324
            G  KPI   S   ++ DI+N+  +
Sbjct: 722 SGVGKPIQLCSATSTANDILNMAVL 746


Lambda     K      H
   0.316    0.134    0.374 

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: 494
Number of extensions: 19
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: 333
Length of database: 752
Length adjustment: 34
Effective length of query: 299
Effective length of database: 718
Effective search space:   214682
Effective search space used:   214682
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 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