Alignments for a candidate for dgoD in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Alignments for a candidate for dgoD in Dinoroseobacter shibae DFL-12

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 3607836 Dshi_1244 Dihydroxy-acid dehydratase (RefSeq)

Query= SwissProt::B5ZZ34
         (579 letters)



>FitnessBrowser__Dino:3607836
          Length = 569

 Score =  659 bits (1701), Expect = 0.0
 Identities = 334/568 (58%), Positives = 420/568 (73%), Gaps = 4/568 (0%)

Query: 12  RSQEWYGGTSRDVIYHRGWLKNQGYPHDLFDGRPVIGILNTWSDMTPCNGHLRELAEKVK 71
           R++ WYG   +D   HR W+KNQG+P  +FDGRPVIGI NTWS++TPCN  LR LAE VK
Sbjct: 6   RNRAWYGKLDKDGFIHRSWMKNQGFPDHVFDGRPVIGICNTWSELTPCNHGLRTLAEGVK 65

Query: 72  AGVWEAGGFPLEVPVFSASENTFRPTAMMYRNLAALAVEEAIRGQPMDGCVLLVGCDKTT 131
            GVWEAGGFP+E PV S  E   +PTAM++RNL A+ VEE+IR   MDG VLL GCDKTT
Sbjct: 66  RGVWEAGGFPVEFPVMSLGETQMKPTAMLFRNLLAMDVEESIRAYGMDGVVLLGGCDKTT 125

Query: 132 PSLLMGAASCDLPSIVVTGGPMLNGYFRGERVGSGTHLWKFSEMVKAGEMTQAEFLEAEA 191
           P  LMGAAS DLPSIVV+ GPMLNG +RG+ +GSGT +WKFSE V+AGEMT A+F+ AEA
Sbjct: 126 PGQLMGAASVDLPSIVVSAGPMLNGKYRGQDIGSGTDVWKFSEAVRAGEMTLADFMNAEA 185

Query: 192 SMSRSSGTCNTMGTASTMASMAEALGMALSGNAAIPGVDSRRKVMAQLTGRRIVQMVKDD 251
            MSRS+G C TMGTASTMAS+ EA+GM+L  NAA+P VD+RR  +A LTG+RIV+MV++D
Sbjct: 186 GMSRSAGVCMTMGTASTMASLVEAMGMSLPLNAALPAVDARRMALAHLTGKRIVEMVEED 245

Query: 252 LKPSEIMTKQAFENAIRTNAAIGGSTNAVIHLLAIAGRVGIDLSLDDWDRCGRDVPTIVN 311
           L+PS I+TK AFENAI  NAA+GGSTNAV+HLLA+AGR G+DL+L D++  G ++P +VN
Sbjct: 246 LRPSAILTKPAFENAILANAAVGGSTNAVMHLLALAGRAGVDLTLKDFE-IGGEIPLLVN 304

Query: 312 LMPSGKYLMEEFFYAGGLPVVLKRLGEAGLLHKDALTVSGETVWDEVKDVVNWNEDVILP 371
            MPSGKYLME+F YAGG+PVVL  L +     + A TV G+ +    +    +N DVI  
Sbjct: 305 CMPSGKYLMEDFAYAGGMPVVLSELRDH---LRPATTVLGKDIAAYTEGAECFNRDVIHA 361

Query: 372 AEKALTSSGGIVVLRGNLAPKGAVLKPSAASPHLLVHKGRAVVFEDIDDYKAKINDDNLD 431
            +  +  + G+ VLRG+LAP GA++KPSAA+  LL H+G A VFE+I+D KA I+ D+L 
Sbjct: 362 YDAPVKPAAGLRVLRGSLAPDGAIVKPSAATDALLEHEGPAFVFENIEDMKANIDRDDLP 421

Query: 432 IDENCIMVMKNCGPKGYPGMAEVGNMGLPPKVLKKGILDMVRISDARMSGTAYGTVVLHT 491
           I  + I+V+K CGPKGYPGM EVGNM +P K++++G+ DM+R+SDARMSGTAYGTV+LH 
Sbjct: 422 ITPDTILVLKGCGPKGYPGMPEVGNMPIPAKLVREGVRDMIRVSDARMSGTAYGTVILHV 481

Query: 492 SPEAAVGGPLAVVKNGDMIELDVPNRRLHLDISDEELARRLAEWQPNHDLPTSGYAFLHQ 551
           +PEA  GGPLA+VK GD I +      L L +   ELA R A WQP+    T GYA L+ 
Sbjct: 482 APEAQAGGPLALVKTGDRIRVSAREGVLDLLVDATELAARRAAWQPDPPHYTRGYAKLYI 541

Query: 552 QHVEGADTGADLDFLKGCRGNAVGKDSH 579
            HV  AD GADLDFL G     V ++SH
Sbjct: 542 DHVLQADRGADLDFLVGKDTRPVTRESH 569


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: 1036
Number of extensions: 49
Number of successful extensions: 4
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: 569
Length adjustment: 36
Effective length of query: 543
Effective length of database: 533
Effective search space:   289419
Effective search space used:   289419
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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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