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

GapMind for Amino acid biosynthesis

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

Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate 3607836 Dshi_1244 Dihydroxy-acid dehydratase (RefSeq)

Query= curated2:A8AB39
         (552 letters)



>FitnessBrowser__Dino:3607836
          Length = 569

 Score =  347 bits (891), Expect = e-100
 Identities = 216/546 (39%), Positives = 314/546 (57%), Gaps = 19/546 (3%)

Query: 15  HRALWRASGLIDEELR-RPLIGVANSWNEIVPGHVHLDKVAEAVKAGIRMAGGTPLEFGT 73
           HR+  +  G  D     RP+IG+ N+W+E+ P +  L  +AE VK G+  AGG P+EF  
Sbjct: 21  HRSWMKNQGFPDHVFDGRPVIGICNTWSELTPCNHGLRTLAEGVKRGVWEAGGFPVEFPV 80

Query: 74  IAVCDGIAMGHEGMR-YSLPSREVIADTVEIMVEAHRLDAVVMVTNCDKITPGFLLAAAR 132
           ++      +G   M+  ++  R ++A  VE  + A+ +D VV++  CDK TPG L+ AA 
Sbjct: 81  MS------LGETQMKPTAMLFRNLLAMDVEESIRAYGMDGVVLLGGCDKTTPGQLMGAAS 134

Query: 133 LEVPVILINGGPMMPGVYGKERIDFKDLMERMNVLIKEGRTE--ELRKLEESALPGPGSC 190
           +++P I+++ GPM+ G Y  + I     + + +  ++ G     +    E       G C
Sbjct: 135 VDLPSIVVSAGPMLNGKYRGQDIGSGTDVWKFSEAVRAGEMTLADFMNAEAGMSRSAGVC 194

Query: 191 AGLFTANTMNMLSEAMGLMLPGASTVPAVEARRLWYAKLTGMRIVKMVEEGLTPDKILTR 250
             + TA+TM  L EAMG+ LP  + +PAV+ARR+  A LTG RIV+MVEE L P  ILT+
Sbjct: 195 MTMGTASTMASLVEAMGMSLPLNAALPAVDARRMALAHLTGKRIVEMVEEDLRPSAILTK 254

Query: 251 KALENAIAVDMALGGSTNSVLHLEALAYELGIDLPLEVFDEISRKVPHIASISPSGRHFV 310
            A ENAI  + A+GGSTN+V+HL ALA   G+DL L+ F EI  ++P + +  PSG++ +
Sbjct: 255 PAFENAILANAAVGGSTNAVMHLLALAGRAGVDLTLKDF-EIGGEIPLLVNCMPSGKYLM 313

Query: 311 VDLDRAGGIPAVLKELGEAGLIHKDALTVTGKTVWENVKDAAVLDREVIRPLDNPYSPFG 370
            D   AGG+P VL EL +     + A TV GK +    + A   +R+VI   D P  P  
Sbjct: 314 EDFAYAGGMPVVLSELRDH---LRPATTVLGKDIAAYTEGAECFNRDVIHAYDAPVKPAA 370

Query: 371 GLAILKGSLAPNGAVVKASAVKRELWKFKGVARVFDREEDAVKAIRGGE--IEPGTVIVI 428
           GL +L+GSLAP+GA+VK SA    L + +G A VF+  ED    I   +  I P T++V+
Sbjct: 371 GLRVLRGSLAPDGAIVKPSAATDALLEHEGPAFVFENIEDMKANIDRDDLPITPDTILVL 430

Query: 429 RYEGPRGGPGMREM--LTATAAVMALGLGDKVALVTDGRFSGATRGPAIGHVSPEAAAGG 486
           +  GP+G PGM E+  +   A ++  G+ D +  V+D R SG   G  I HV+PEA AGG
Sbjct: 431 KGCGPKGYPGMPEVGNMPIPAKLVREGVRDMIR-VSDARMSGTAYGTVILHVAPEAQAGG 489

Query: 487 PIALVQDGDEIVIDIEKRRLDLLVDEKELEERRARWKPKVKPLRRGILRRYAKMALSADK 546
           P+ALV+ GD I +   +  LDLLVD  EL  RRA W+P      RG  + Y    L AD+
Sbjct: 490 PLALVKTGDRIRVSAREGVLDLLVDATELAARRAAWQPDPPHYTRGYAKLYIDHVLQADR 549

Query: 547 GGALEY 552
           G  L++
Sbjct: 550 GADLDF 555


Lambda     K      H
   0.319    0.138    0.401 

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: 850
Number of extensions: 48
Number of successful extensions: 7
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: 552
Length of database: 569
Length adjustment: 36
Effective length of query: 516
Effective length of database: 533
Effective search space:   275028
Effective search space used:   275028
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 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 Aug 03 2021. The underlying query database was built on Aug 03 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, or see changes to Amino acid biosynthesis since the publication.

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 Amino acid biosynthesis