GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patA in Dechlorosoma suillum PS

Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate Dsui_0023 Dsui_0023 acetylornithine/succinylornithine aminotransferase

Query= BRENDA::P42588
         (459 letters)



>FitnessBrowser__PS:Dsui_0023
          Length = 396

 Score =  188 bits (477), Expect = 3e-52
 Identities = 130/386 (33%), Positives = 204/386 (52%), Gaps = 32/386 (8%)

Query: 76  LVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLDPLRAMLAKTLAA 135
           LVD QG+ ++D + G+ +  +GH +P +V A+ +Q  K       L++P  A   +    
Sbjct: 33  LVDQQGKRYLDFVQGWAVNCLGHGHPAIVEALASQAGK-------LINPSPAFYNEPSLK 85

Query: 136 LTPGKLKYS-----FFCNSGTESVEAALKLAKAYQSPR--GKFTFIATSGAFHGKSLGAL 188
           L  G   +S     FF ++G E+ E A+KLA+ +      G    I  +G FHG++L  +
Sbjct: 86  LAAGLAAHSCFDRVFFASTGAEANEGAIKLARKWGQKHKGGAHEIITFAGGFHGRTLATM 145

Query: 189 SATAKSTFRKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPIQGEGGVIL 248
           SA+ K  +   F P +PGF      +++++   +NE         A++LEPIQGEGGV+ 
Sbjct: 146 SASGKPGWDTLFAPQVPGFPKAQLNDLDSVAALINE------RTVAIMLEPIQGEGGVVP 199

Query: 249 PPPGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKALGGGVMP 308
               +L  +R++CD+ G L+I+DEVQTGMGRTGK+FA +H  ++PDI+ L K +GGGV P
Sbjct: 200 ASAEFLQLLRQICDDRGLLLIVDEVQTGMGRTGKLFAHQHAGIEPDIMTLGKGIGGGV-P 258

Query: 309 IGATIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQKGDMLLD 368
           + A +A E V      +      T+ GNPL  A   A + VL      A+   KG+ L  
Sbjct: 259 LSALLAKESVCCFEAGD---QGGTYNGNPLMTAVGAAVLEVLTAPGFLAEVAAKGEYLGA 315

Query: 369 GFRQLAREYPDLVQEARGKGMLMAIEFVDNEIGYNFASEMFRQRVLVAGTLNNA---KTI 425
           G ++L+      ++  RG+G+L A+   D E G     E  R+R    G L NA     +
Sbjct: 316 GLQRLSDRLG--LRGERGQGLLRALLLAD-ERGPAIV-EAARERG-PEGLLLNAPRPHLL 370

Query: 426 RIEPPLTLTIEQCELVIKAARKALAA 451
           R  P LT++ E+ + ++    + L A
Sbjct: 371 RFMPSLTVSREEIDQMLAWLEELLRA 396


Lambda     K      H
   0.320    0.135    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: 400
Number of extensions: 16
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: 459
Length of database: 396
Length adjustment: 32
Effective length of query: 427
Effective length of database: 364
Effective search space:   155428
Effective search space used:   155428
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 (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