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

GapMind for catabolism of small carbon sources

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

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 H281DRAFT_03422 H281DRAFT_03422 dihydroxyacid dehydratase (EC 4.2.1.9)

Query= SwissProt::B5ZZ34
         (579 letters)



>FitnessBrowser__Burk376:H281DRAFT_03422
          Length = 592

 Score =  564 bits (1453), Expect = e-165
 Identities = 281/558 (50%), Positives = 385/558 (68%), Gaps = 2/558 (0%)

Query: 10  KLRSQEWYGGTSRDVIYHRGWLKNQGYPHDLFDGRPVIGILNTWSDMTPCNGHLRELAEK 69
           +LRS  WYG        HR      GY    + G+PVI ++NTWS++  C+ H ++  E+
Sbjct: 9   QLRSYRWYGVNDLRSFGHRSRTAQMGYHASDYMGKPVIAVVNTWSEINSCHTHFKQRVEE 68

Query: 70  VKAGVWEAGGFPLEVPVFSASENTFRPTAMMYRNLAALAVEEAIRGQPMDGCVLLVGCDK 129
           VK G+W+AGGFP+E+PV + +E   +PT M+YRN  A+  EE ++  P DGCVL+ GCDK
Sbjct: 69  VKRGIWQAGGFPVEMPVMTLAEPFQKPTTMLYRNFLAMETEEILKSYPFDGCVLMGGCDK 128

Query: 130 TTPSLLMGAASCDLPSIVVTGGPMLNGYFRGERVGSGTHLWKFSEMVKAGEMTQAEFLEA 189
           TTP LLMGA S +LPSI +  GPML G + G  +GSG+  WK+   ++AG++T+ E+   
Sbjct: 129 TTPGLLMGAISMNLPSIFLPAGPMLRGNWNGRTLGSGSDTWKYWAELRAGKITEDEWKGI 188

Query: 190 EASMSRSSGTCNTMGTASTMASMAEALGMALSGNAAIPGVDSRRKVMAQLTGRRIVQMVK 249
           E+ ++RS G C TMGTASTM S AEALG+ L G ++IP VDSR    A LTG+RIV+MV 
Sbjct: 189 ESGIARSPGHCMTMGTASTMTSAAEALGLTLPGFSSIPAVDSRHAQFASLTGQRIVEMVW 248

Query: 250 DDLKPSEIMTKQAFENAIRTNAAIGGSTNAVIHLLAIAGRVGIDLSLDDWDRCGRDVPTI 309
            D+KPS+I+T ++F+NA+ T  A+ GSTNA++HL+A+A R GIDL+   +D   R  P I
Sbjct: 249 TDVKPSDILTAKSFDNAVTTVLAMSGSTNAIVHLVAVARRAGIDLTTARFDELSRITPVI 308

Query: 310 VNLMPSGKYLMEEFFYAGGLPVVLKRLGEAGLLHKDALTVSGETVWDEVKDVVNWNEDVI 369
            NL PSG+YLME+FFYAGGL  +L  LG+  L+    +TV+G T+ + +     +N+DVI
Sbjct: 309 GNLRPSGQYLMEDFFYAGGLRALLLELGD--LIDGSQMTVNGSTLGENIAGAEIFNDDVI 366

Query: 370 LPAEKALTSSGGIVVLRGNLAPKGAVLKPSAASPHLLVHKGRAVVFEDIDDYKAKINDDN 429
                 + +S G+ VL GNLAP GAV+KP+A   HLL H+GRAVVF+D  D  A+I+ ++
Sbjct: 367 RKRGNPVVASDGLAVLTGNLAPDGAVIKPAAMEAHLLNHRGRAVVFKDYADMAARIDMED 426

Query: 430 LDIDENCIMVMKNCGPKGYPGMAEVGNMGLPPKVLKKGILDMVRISDARMSGTAYGTVVL 489
           LDI  + ++V+++ GP G PGM E G + +P K+LK+G+ DMVRISDARMSGT+YG  VL
Sbjct: 427 LDITADSVIVLQHAGPVGAPGMPEWGQLPIPQKLLKQGVRDMVRISDARMSGTSYGACVL 486

Query: 490 HTSPEAAVGGPLAVVKNGDMIELDVPNRRLHLDISDEELARRLAEWQPNHDLPTSGYAFL 549
           H +PE+ VGGPLA+VK+GDMI+LDV  RRLHL++SDEEL+ R A WQP       G+  +
Sbjct: 487 HVAPESFVGGPLALVKDGDMIQLDVAARRLHLEVSDEELSARKAAWQPPKLPFERGFGVM 546

Query: 550 HQQHVEGADTGADLDFLK 567
           HQ HV  A+ G D DFL+
Sbjct: 547 HQLHVLQANKGCDFDFLE 564


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: 1024
Number of extensions: 45
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: 592
Length adjustment: 37
Effective length of query: 542
Effective length of database: 555
Effective search space:   300810
Effective search space used:   300810
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:

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