GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pta in Burkholderia phytofirmans PsJN

Align Phosphate acetyltransferase; Phosphotransacetylase; EC 2.3.1.8 (characterized)
to candidate BPHYT_RS18310 BPHYT_RS18310 malic enzyme

Query= SwissProt::P77844
         (329 letters)



>FitnessBrowser__BFirm:BPHYT_RS18310
          Length = 760

 Score =  159 bits (403), Expect = 2e-43
 Identities = 107/321 (33%), Positives = 170/321 (52%), Gaps = 13/321 (4%)

Query: 14  ARAEHSHIVLPEGDDDRILMAAHQLLDQDICDITILGDPVKIKERATELGLHLNTA---Y 70
           A++E + IV  EG+D+R+L AA  +L + I    ++G P  I+ R  ++G  L       
Sbjct: 437 AKSEPARIVFAEGEDERVLRAAQFVLLEKIAKPILVGRPSVIEMRLKKMGSKLKCGDDFE 496

Query: 71  LVNPLTDPRLEEFAEQFAELRKSKSVTIDEAREIMKDIS-YFGTMMVHNGDADGMVSGAA 129
           +V+P  DPR ++  + + EL   + VT D A+  M+  +   G ++V  G+ADGM+ G  
Sbjct: 497 IVDPEDDPRYQQSWQAYHELGAREGVTPDVAKAAMRKFNTLIGAILVRLGEADGMICGMI 556

Query: 130 NTTAHTIKPSFQIIKTVPEASVVSSIFLMVLRGRLWAFGDCAVNPNPTAEQLGEIAVVSA 189
                 +K   Q++         +++ L++L GR     D  VN  PTAEQL ++ +++A
Sbjct: 557 GQYHAHLKFIEQVLGKADNVQNFAAMNLLMLPGRNLFICDTYVNETPTAEQLADMTMLAA 616

Query: 190 KTAAQFGIDPRVAILSYSTGNSGGGSDVDRAIDALAEARRL----NPELCVDGPLQFDAA 245
               +FGI P+VA+LS    NS  GS    +   +A AR+L     P L +DG +  DAA
Sbjct: 617 GEIEKFGITPKVALLS----NSNFGSAPSSSSQRMAAARKLIVERAPSLEIDGEMHGDAA 672

Query: 246 VDPGVARKKMPDSDVAGQANVFIFPDLEAGNIGYKTAQRT-GHALAVGPILQGLNKPVND 304
           +   V +   P + + G+AN+ I P++EA NI Y   +   G  + VGP L G  KPV+ 
Sbjct: 673 LSEVVRKAAFPGTTLTGEANLLIMPNVEAANITYNLLKMIGGEGVTVGPFLLGAEKPVHI 732

Query: 305 LSRGATVPDIVNTVAITAIQA 325
           L+  ATV  I+N  A+ +  A
Sbjct: 733 LTPAATVRRIINMTAVASANA 753


Lambda     K      H
   0.318    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: 531
Number of extensions: 33
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 329
Length of database: 760
Length adjustment: 34
Effective length of query: 295
Effective length of database: 726
Effective search space:   214170
Effective search space used:   214170
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 (21.7 bits)
S2: 52 (24.6 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