Alignments for a candidate for dgoD in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for dgoD in Burkholderia phytofirmans PsJN

Align L-arabinonate dehydratase; ArDHT; D-fuconate dehydratase; Galactonate dehydratase; L-arabonate dehydratase; EC 4.2.1.25; EC 4.2.1.67; EC 4.2.1.6 (characterized)
to candidate BPHYT_RS19730 BPHYT_RS19730 dihydroxy-acid dehydratase

Query= SwissProt::B5ZZ34
         (579 letters)



>FitnessBrowser__BFirm:BPHYT_RS19730
          Length = 577

 Score =  773 bits (1996), Expect = 0.0
 Identities = 381/571 (66%), Positives = 456/571 (79%), Gaps = 2/571 (0%)

Query: 9   RKLRSQEWYGGTSRDVIYHRGWLKNQGYPHDLFDGRPVIGILNTWSDMTPCNGHLRELAE 68
           + LRSQ W+G   RD   HR W+KNQG PHD FDGRPVIGI NTWS++TPCN H RELAE
Sbjct: 9   KPLRSQAWFGLKDRDGFLHRSWMKNQGIPHDEFDGRPVIGICNTWSELTPCNAHFRELAE 68

Query: 69  KVKAGVWEAGGFPLEVPVFSASENTFRPTAMMYRNLAALAVEEAIRGQPMDGCVLLVGCD 128
            VK GV EAGG PLE PV S  E   RPTAM++RNLA++ VEE+IRG PMDG +LLVGCD
Sbjct: 69  YVKKGVHEAGGLPLEFPVMSLGETNLRPTAMLFRNLASMDVEESIRGNPMDGVILLVGCD 128

Query: 129 KTTPSLLMGAASCDLPSIVVTGGPMLNGYFRGERVGSGTHLWKFSEMVKAGEMTQAEFLE 188
           KTTP+LLMGAASC+LP++ V+GGPMLNG FRG+ +GSGT +W+ SE V+AG MTQ EF E
Sbjct: 129 KTTPALLMGAASCNLPALAVSGGPMLNGRFRGKNIGSGTGVWQMSEEVRAGTMTQEEFTE 188

Query: 189 AEASMSRSSGTCNTMGTASTMASMAEALGMALSGNAAIPGVDSRRKVMAQLTGRRIVQMV 248
           AE+ M+RS G C TMGTASTMASM E+LGM L  NAAIP VD+RR+V+A L GRRIV MV
Sbjct: 189 AESCMNRSRGHCMTMGTASTMASMVESLGMGLPHNAAIPAVDARRQVLAHLAGRRIVDMV 248

Query: 249 KDDLKPSEIMTKQAFENAIRTNAAIGGSTNAVIHLLAIAGRVGIDLSLDDWDRCGRDVPT 308
           ++DL   +I+T+QAFENAIRTNAAIGGSTNAV+HL+A+A R+G++LSL+DW+  G +VP 
Sbjct: 249 REDLTMDKILTRQAFENAIRTNAAIGGSTNAVVHLIALAKRIGVELSLEDWE-LGSNVPC 307

Query: 309 IVNLMPSGKYLMEEFFYAGGLPVVLKRLGEAGLLHKDALTVSGETVWDEVKDVVNWNEDV 368
           +VNL PSG+YLME+F+YAGGLP VLK+LGE GLLHK+ALTV+G+T+WD V++  N++E V
Sbjct: 308 LVNLQPSGEYLMEDFYYAGGLPAVLKQLGEQGLLHKEALTVNGKTLWDNVRNAANYDEKV 367

Query: 369 ILPAEKALTSSGGIVVLRGNLAPKGAVLKPSAASPHLLVHKGRAVVFEDIDDYKAKINDD 428
           I    +      GI VL+GNLAP GAV+KPSAA+  LL H+GRAVVFE+I++  AKI+D+
Sbjct: 368 ITTFAEPFKPKAGIAVLKGNLAPNGAVIKPSAATASLLKHRGRAVVFENIEELHAKIDDE 427

Query: 429 NLDIDENCIMVMKNCGPKGYPGMAEVGNMGLPPKVLKKGILDMVRISDARMSGTAYGTVV 488
           +LDIDE+CIMV+K  GPKGYPG AEVGNM LP KVL+KGI DMVRISD RMSGTAYG VV
Sbjct: 428 SLDIDEHCIMVLKGAGPKGYPGFAEVGNMPLPKKVLQKGITDMVRISDGRMSGTAYGAVV 487

Query: 489 LHTSPEAAVGGPLAVVKNGDMIELDVPNRRLHLDISDEELARRLAEWQPNHDLPTSGYAF 548
           LH SPEAA GGPLA V+ GDMIELDV  RRLHLD++DEELARR A WQ   + P  GY  
Sbjct: 488 LHVSPEAAAGGPLAFVQTGDMIELDVEERRLHLDVTDEELARRRAAWQA-PEAPKRGYYK 546

Query: 549 LHQQHVEGADTGADLDFLKGCRGNAVGKDSH 579
           L+ +HV  AD GADLDFL G  G  V +DSH
Sbjct: 547 LYVEHVLQADQGADLDFLVGSSGAPVPRDSH 577


Lambda     K      H
   0.318    0.135    0.408 

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: 1133
Number of extensions: 57
Number of successful extensions: 3
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: 579
Length of database: 577
Length adjustment: 36
Effective length of query: 543
Effective length of database: 541
Effective search space:   293763
Effective search space used:   293763
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: 53 (25.0 bits)

This GapMind analysis is from Apr 09 2024. 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 2024 update 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