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

GapMind for catabolism of small carbon sources

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

Align D-galactono-lactonase (EC 3.1.1.-) (characterized)
to candidate H281DRAFT_00300 H281DRAFT_00300 6-phosphogluconolactonase

Query= reanno::pseudo13_GW456_L13:PfGW456L13_3314
         (389 letters)



>FitnessBrowser__Burk376:H281DRAFT_00300
          Length = 434

 Score =  323 bits (827), Expect = 8e-93
 Identities = 162/364 (44%), Positives = 241/364 (66%), Gaps = 7/364 (1%)

Query: 26  YQLLVGSYTAGQSQGIYRLAFDSRTGQIDASPLQVIKSANPSWLTLSKDQRHLFVVNENG 85
           Y +LVG+YT G+S+G+Y   FD++TG  DA+ + V ++ NPS+L +S+D+R ++ VNE  
Sbjct: 72  YDMLVGTYTGGKSEGLYVYRFDTKTG--DATRVSVAQTVNPSYLVVSRDRRFVYAVNEL- 128

Query: 86  PGQTDPV---GRVSSFAIDPKTHALSLISQVQSLGNEPTHSSLSIDGSHLFVSNYSVAED 142
           PG   P    G +S+F  D  +  LS +++V + GN+P + SLS DG +L  +NYSVA D
Sbjct: 129 PGDNGPASQRGGISAFRFDAASGQLSFLNKVSADGNDPCYLSLSPDGKYLLTANYSVAAD 188

Query: 143 PGGTLAVLPVAADGKLKAVVQMSSHPASRVNPERQASAHVHSTIPSPDGRYVFANDLGAD 202
           PGG+ AV PV ADG+L A V    H        RQ ++HVHST+ SPDGRY+FA DLGAD
Sbjct: 189 PGGSFAVFPVQADGQLGASVLTVHHEGGGPVKGRQDNSHVHSTVFSPDGRYLFAQDLGAD 248

Query: 203 KVFAYRFDPKANPELPLTPATPAFVQLPPGSGPRHLLFSADGKHAWLTMEMSAQVAVFDY 262
           K+++YR+ P  +  L   P    + Q  PG+GPRHL+F  DGKHA+LT E++A V++F+Y
Sbjct: 249 KLYSYRYTPDGSRGL-FGPTDWRYTQEKPGTGPRHLVFGVDGKHAYLTSELAATVSIFNY 307

Query: 263 HDGQLEQTQMVDLAAGQPVSDKAAAALHASADGKFLYVSNRGTANQLLVFAIDPATGHLS 322
            DG+L Q Q V L          AAA+H S DG+FLY +NRG AN++++F++DP  GHL 
Sbjct: 308 DDGKLTQVQTVSLTEPGFKGAVGAAAIHLSPDGRFLYATNRGDANEIVIFSVDPTNGHLK 367

Query: 323 ELQRRAVEGDHPREFSLDPSGKFLLIANQKSNQIVVVERDARTGLLGKTVQKLPMDAPSD 382
           ++  ++  G  PREF++DP+GK+L++ NQ S+ + V  RD ++GLL    +++ + +P D
Sbjct: 368 KIGHQSSLGKSPREFAIDPTGKWLIVGNQNSDTVYVFRRDPQSGLLEANPKRIEIGSPVD 427

Query: 383 LRFL 386
            + +
Sbjct: 428 FKLV 431


Lambda     K      H
   0.316    0.132    0.382 

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: 658
Number of extensions: 53
Number of successful extensions: 9
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: 389
Length of database: 434
Length adjustment: 31
Effective length of query: 358
Effective length of database: 403
Effective search space:   144274
Effective search space used:   144274
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 (21.6 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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Protein sequences (fasta format)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources