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_RS31695 BPHYT_RS31695 dihydroxy-acid dehydratase

Query= SwissProt::B5ZZ34
         (579 letters)



>FitnessBrowser__BFirm:BPHYT_RS31695
          Length = 595

 Score =  470 bits (1210), Expect = e-137
 Identities = 256/571 (44%), Positives = 352/571 (61%), Gaps = 15/571 (2%)

Query: 9   RKLRSQEWYGGTSRDV---IYHRGWLKNQGYPHDLFDGRPVIGILNTWSDMTPCNGHLRE 65
           + LRS+ W+  +       +Y   ++       +L   RPVIGI  T SD++PCN H  E
Sbjct: 8   KSLRSRAWFNNSDNPAMTALYLERFMNYGLTLEELKSERPVIGIAQTGSDLSPCNRHHVE 67

Query: 66  LAEKVKAGVWEAGGFPLEVPVFSASENTFRPTAMMYRNLAALAVEEAIRGQPMDGCVLLV 125
           LA++VK G+ +AGG P+E PV    E   RPTA + RNLA L + EA+ G P DG VL  
Sbjct: 68  LAQRVKDGIRDAGGIPIEFPVHPIQETVRRPTASLDRNLAYLGLVEALYGYPFDGVVLTT 127

Query: 126 GCDKTTPSLLMGAASCDLPSIVVTGGPMLNGYFRGERVGSGTHLWKFSEMVKAGEMTQAE 185
           GCDKTTP++LMGAA+ D+PSIV++GGPMLN +++GER GSGT +W     + AG M   E
Sbjct: 128 GCDKTTPAMLMGAATVDIPSIVLSGGPMLNAWYKGERAGSGTIIWHARSELAAGRMDYDE 187

Query: 186 FLEAEASMSRSSGTCNTMGTASTMASMAEALGMALSGNAAIPGVDSRRKVMAQLTGRRIV 245
           FL   A+ + S G CN+MGTA +M S+AE LGM+L G   IP     R  MA  TGR+IV
Sbjct: 188 FLSCVANSAPSIGHCNSMGTALSMNSLAEVLGMSLPGCGTIPAPYRERGQMAYQTGRQIV 247

Query: 246 QMVKDDLKPSEIMTKQAFENAIRTNAAIGGSTNAVIHLLAIAGRVGIDLSLDDWDRCGRD 305
           Q+V DD++PS ++T++AFENAI   +AIG STN   H+ AIA  +G+DL + DWDR G D
Sbjct: 248 QLVHDDVRPSSLLTREAFENAIVVASAIGASTNCPPHINAIARHIGVDLDIRDWDRLGYD 307

Query: 306 VPTIVNLMPSGKYLMEEFFYAGGLPVVLKRLGEAGLLHKDALTVSGETVWDEVKDVVNWN 365
           +P +VN MP+GKYL EEF  AGG+  V+  L +AG LH D  TVSG+T+     D    +
Sbjct: 308 IPLLVNCMPAGKYLGEEFHRAGGVAAVVHELLKAGKLHGDVQTVSGKTLAQCYGDSPATD 367

Query: 366 EDVILPAEKALTSSGGIVVLRGNLAPKGAVLKPSAASPHLL-----------VHKGRAVV 414
            DVI P    L S  G  VL GNL    AV+K S  S                 +GRA+V
Sbjct: 368 ADVIRPYASPLKSEAGFAVLGGNLF-DSAVMKTSVISDDFRHKYLENPADPGAFEGRAIV 426

Query: 415 FEDIDDYKAKINDDNLDIDENCIMVMKNCGPKGYPGMAEVGNMGLPPKVLKKGILDMVRI 474
           FE  +DY  +I+D  L+IDENCI+ ++  GP GYPG AEV NM  P +++K+G+  +  +
Sbjct: 427 FEGPEDYHDRIDDPALEIDENCILFIRGTGPVGYPGAAEVVNMIPPSELIKRGVTLLPCV 486

Query: 475 SDARMSGTAYGTVVLHTSPEAAVGGPLAVVKNGDMIELDVPNRRLHLDISDEELARRLAE 534
            D R SGT+    +L+ SPE+A+GG LA+++ GD +  D+  RR  + + ++EL RR  E
Sbjct: 487 GDGRQSGTSASPSILNASPESAIGGGLAILQTGDRVRFDLTRRRADMLVPEDELDRRRRE 546

Query: 535 WQPNHDLPTSGYAFLHQQHVEGADTGADLDF 565
           W+    +  + +  LH+++V   + GA LDF
Sbjct: 547 WKAYEFVNQTPWQELHRRYVGQLEDGACLDF 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: 975
Number of extensions: 60
Number of successful extensions: 2
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: 595
Length adjustment: 37
Effective length of query: 542
Effective length of database: 558
Effective search space:   302436
Effective search space used:   302436
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 Sep 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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, or view the source code.

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