GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gnl in Burkholderia phytofirmans PsJN

Align Periplasmic gluconolactonase, PpgL (characterized, see rationale)
to candidate BPHYT_RS06110 BPHYT_RS06110 3-carboxymuconate cyclase

Query= uniprot:Q9HWH7
         (388 letters)



>FitnessBrowser__BFirm:BPHYT_RS06110
          Length = 385

 Score =  307 bits (787), Expect = 3e-88
 Identities = 176/380 (46%), Positives = 231/380 (60%), Gaps = 9/380 (2%)

Query: 11  ALAPLTGVAPQAQAASLYNLLVGTYTEGSSEGIQVYRFDGADGSVKGPLRVAHTSNPSYL 70
           A A  +G AP   A  +Y++LVGTYT   SEG+ VYRFD   G     +  A T NPSYL
Sbjct: 9   AFAQDSGPAP---ADGVYDMLVGTYTGPKSEGLYVYRFDTKTGEATR-VSAAQTVNPSYL 64

Query: 71  TFAPDQRTLFVVNEN-GRGGKGDTVGRATSYRFDPISGRLQQISQVQTLADHPTYSSLSH 129
             + D+R ++ VNE  G  G     G  +++RFD  SG+L  +++V +  + P Y SLS 
Sbjct: 65  VVSRDRRFVYAVNEMPGDNGPATQRGGISAFRFDAASGQLTFLNKVSSDGNDPCYLSLSP 124

Query: 130 DGRYLFVANYSV--QPEGSVAVLPVRADGSL-APVVQVESHQASKVHPRQVSGHVHSVVS 186
           DG+YL  ANYSV   P GS AV P++ADG + A V+ V       V  RQ + HVHS V 
Sbjct: 125 DGKYLLTANYSVAADPGGSFAVFPLQADGQVGASVLTVHHEGGGPVKGRQDNSHVHSTVF 184

Query: 187 SPDGQYLFAPDLGADKVFVYRYAPEQAERPLQAADPAFVPTPPGSGPRHLIFSADGRFAY 246
           SPDG YLFA DLGADK++ YRY P+ +       D  +     GSGPRHL+F ADG+ AY
Sbjct: 185 SPDGHYLFAQDLGADKLYSYRYTPDGSRGLFGPTDWRYNQEKAGSGPRHLVFGADGKHAY 244

Query: 247 LTLELSGQVMVFAHEGNGRLRQLQTHDLAPAGFQGKVGAGALHLSADGRFLGVLNRGDDN 306
           LT E++  V  F +  +G+L Q+QT  L   GF+G VGA A+HLS DGRFL   NRGD N
Sbjct: 245 LTSEMAATVSTFDYN-DGKLTQVQTLPLTEPGFKGAVGAAAIHLSPDGRFLYATNRGDAN 303

Query: 307 QLVTFAVDPASGQLRFVERRSVEGTEPREFAFSPGGRFVLVANQNSDQLRVFARDPQSGQ 366
            +V F+VDP +G L+ V  +S  G  PREFA  P G +++V NQNSD + VF RD QSG 
Sbjct: 304 DIVIFSVDPTNGHLKKVGHQSSMGKSPREFAIDPTGNWLIVGNQNSDTVYVFKRDQQSGL 363

Query: 367 VGKTLQSVEVGSPSDLRFVA 386
           +    +  E+G+P D + V+
Sbjct: 364 LEANPKHFELGAPVDFKLVS 383


Lambda     K      H
   0.318    0.135    0.395 

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: 627
Number of extensions: 40
Number of successful extensions: 10
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: 388
Length of database: 385
Length adjustment: 30
Effective length of query: 358
Effective length of database: 355
Effective search space:   127090
Effective search space used:   127090
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: 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