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.

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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