GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gnl in Paraburkholderia bryophila 376MFSha3.1

Align Periplasmic gluconolactonase, PpgL (characterized, see rationale)
to candidate H281DRAFT_00300 H281DRAFT_00300 6-phosphogluconolactonase

Query= uniprot:Q9HWH7
         (388 letters)



>FitnessBrowser__Burk376:H281DRAFT_00300
          Length = 434

 Score =  327 bits (837), Expect = 5e-94
 Identities = 178/372 (47%), Positives = 235/372 (63%), Gaps = 6/372 (1%)

Query: 19  APQAQAASLYNLLVGTYTEGSSEGIQVYRFDGADGSVKGPLRVAHTSNPSYLTFAPDQRT 78
           A  A A  +Y++LVGTYT G SEG+ VYRFD   G     + VA T NPSYL  + D+R 
Sbjct: 63  AGPAPADGVYDMLVGTYTGGKSEGLYVYRFDTKTGDATR-VSVAQTVNPSYLVVSRDRRF 121

Query: 79  LFVVNE-NGRGGKGDTVGRATSYRFDPISGRLQQISQVQTLADHPTYSSLSHDGRYLFVA 137
           ++ VNE  G  G     G  +++RFD  SG+L  +++V    + P Y SLS DG+YL  A
Sbjct: 122 VYAVNELPGDNGPASQRGGISAFRFDAASGQLSFLNKVSADGNDPCYLSLSPDGKYLLTA 181

Query: 138 NYSV--QPEGSVAVLPVRADGSL-APVVQVESHQASKVHPRQVSGHVHSVVSSPDGQYLF 194
           NYSV   P GS AV PV+ADG L A V+ V       V  RQ + HVHS V SPDG+YLF
Sbjct: 182 NYSVAADPGGSFAVFPVQADGQLGASVLTVHHEGGGPVKGRQDNSHVHSTVFSPDGRYLF 241

Query: 195 APDLGADKVFVYRYAPEQAERPLQAADPAFVPTPPGSGPRHLIFSADGRFAYLTLELSGQ 254
           A DLGADK++ YRY P+ +       D  +    PG+GPRHL+F  DG+ AYLT EL+  
Sbjct: 242 AQDLGADKLYSYRYTPDGSRGLFGPTDWRYTQEKPGTGPRHLVFGVDGKHAYLTSELAAT 301

Query: 255 VMVFAHEGNGRLRQLQTHDLAPAGFQGKVGAGALHLSADGRFLGVLNRGDDNQLVTFAVD 314
           V +F ++ +G+L Q+QT  L   GF+G VGA A+HLS DGRFL   NRGD N++V F+VD
Sbjct: 302 VSIFNYD-DGKLTQVQTVSLTEPGFKGAVGAAAIHLSPDGRFLYATNRGDANEIVIFSVD 360

Query: 315 PASGQLRFVERRSVEGTEPREFAFSPGGRFVLVANQNSDQLRVFARDPQSGQVGKTLQSV 374
           P +G L+ +  +S  G  PREFA  P G++++V NQNSD + VF RDPQSG +    + +
Sbjct: 361 PTNGHLKKIGHQSSLGKSPREFAIDPTGKWLIVGNQNSDTVYVFRRDPQSGLLEANPKRI 420

Query: 375 EVGSPSDLRFVA 386
           E+GSP D + V+
Sbjct: 421 EIGSPVDFKLVS 432


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: 691
Number of extensions: 47
Number of successful extensions: 12
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: 434
Length adjustment: 31
Effective length of query: 357
Effective length of database: 403
Effective search space:   143871
Effective search space used:   143871
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