GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ1 in Dechlorosoma suillum PS

Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate Dsui_3239 Dsui_3239 acetyl-CoA acetyltransferase

Query= uniprot:A0A2Z5MFE9
         (400 letters)



>FitnessBrowser__PS:Dsui_3239
          Length = 392

 Score =  296 bits (758), Expect = 7e-85
 Identities = 168/395 (42%), Positives = 244/395 (61%), Gaps = 9/395 (2%)

Query: 6   ICDAIRTPIGRYGGALKDVRADDLGAVPIKALIQRNPGVDWRAVDDVIYGCANQAGEDNR 65
           +  A+R+ +G +GG+L  +   +LG + +K  I R  GVD +AV     G          
Sbjct: 7   VLSAVRSAVGGFGGSLAGMEPAELGGLVVKEAIAR-AGVDPKAVTFATVGNCIPTETRYA 65

Query: 66  NVARMSALLAGLPADAPGATINRLCGSGMDAVGTAARAIKAGEAQLMIAGGVESMTRAPF 125
            VAR++ +  G+  D+    +NRLCGS M A+ ++A+AI  G+A   I GGVE M+R  +
Sbjct: 66  YVARLATIQGGMSMDSVAFAVNRLCGSAMQAIVSSAQAIMLGDADYAIGGGVEVMSRGAY 125

Query: 126 VMGKAASAFTRQAEIHDTTIGWRFVNPLMKRQYGVDSMPETAENVAEQFGISRADQDAFA 185
           ++    S     A + DT      V+ L    +GV  M  TAEN+  ++G++R +QDAFA
Sbjct: 126 LLPALRSG----ARMGDTKAIDAMVSVLTD-PFGVGHMGITAENLVTKWGLTREEQDAFA 180

Query: 186 LASQQKAARAQRDGTLAQEIVGVEIAQKKGDAIRVTLDEHPRETSLESLARLKGVVRPDG 245
           L SQ +AA+A  +G    +IV +    KKGD +  T DEHPR T++E+LA++K   + DG
Sbjct: 181 LESQNRAAKAIAEGRFKSQIVPITFQTKKGDVVFDT-DEHPRATTMEALAKMKAAFKKDG 239

Query: 246 TVTAGNASGVNDGACALLIASQQAAEQYGLRRRARVVGMATAGVEPRIMGIGPAPATQKL 305
           +VTAGNASG+ND A  L++A    A   G +  AR+V  A AGV   IMG GP P+++  
Sbjct: 240 SVTAGNASGINDAAAFLVLADAAKAAAAGHKPIARLVSYAIAGVPNEIMGEGPIPSSKLA 299

Query: 306 LRQLGMTLDQLDVIELNEAFASQGLAVLRMLGLRDDDPRVNPNGGAIALGHPLGASGARL 365
           L++ G+TLDQ+D++E NEAFA+Q LAV + LGL  D  + N NGGAIALGHP+GA+G  +
Sbjct: 300 LQKAGLTLDQIDLVESNEAFAAQSLAVAKGLGL--DPAKTNVNGGAIALGHPVGATGGVI 357

Query: 366 VTTALHQLERSNGRFALCTMCIGVGQGIALVIERL 400
           VT  LH+++R+  R+ + TMCIG GQGI  + ER+
Sbjct: 358 VTKLLHEMQRTGARYGMATMCIGGGQGITTIYERI 392


Lambda     K      H
   0.319    0.134    0.386 

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: 396
Number of extensions: 20
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: 400
Length of database: 392
Length adjustment: 31
Effective length of query: 369
Effective length of database: 361
Effective search space:   133209
Effective search space used:   133209
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: 50 (23.9 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