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.

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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