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 3608367 Dshi_1769 6-phosphogluconate dehydratase (RefSeq)

Query= curated2:Q5SIY0
         (555 letters)



>FitnessBrowser__Dino:3608367
          Length = 601

 Score =  249 bits (637), Expect = 2e-70
 Identities = 182/539 (33%), Positives = 267/539 (49%), Gaps = 33/539 (6%)

Query: 34  VGVVNTFTDGMPCNFHLRELAQHLKAGLKEAGLFP-FEFGAPAISDGISMGTPGMRASLV 92
           +G+V  + D +  +   ++    +K   + AG       G PA+ DG++ G  GM  SL 
Sbjct: 69  IGIVTAYNDMLSAHQPFKDYPDKIKEAARRAGATAQVAGGVPAMCDGVTQGQVGMELSLF 128

Query: 93  SREVIADSVELIAQGYLYDGMVGLSACDKTIPGTAMGVIRSG-VPGMILYGGTIAPGEWQ 151
           SR+VIA +  +      +D    L  CDK +PG  +     G +PG+ +  G +  G   
Sbjct: 129 SRDVIALATGVALSHNTFDAAAYLGVCDKIVPGLVIAAATFGYLPGVFVPAGPMVSGLPN 188

Query: 152 GRKLTIVEVFEAVGQRAAGKISEEELLEIERRAIPGPGACGGQYTANTMAMALEALGLSP 211
            +K  + + F      AAG+I  ++L+E E  +  GPG C    TAN+  M +E +GL  
Sbjct: 189 DQKAKVRQQF------AAGEIGRDKLMEAEMASYHGPGTCTFYGTANSNQMLMEFMGLHL 242

Query: 212 VGYNAIPAVHPEKERATKEAGKILA--WAIAHDWKPK-DFLTRKSFLNAIAAVAATGGST 268
            G + +    P +E  T  A + LA    + ++++P  D L  K+F+N I  + ATGGST
Sbjct: 243 PGASFVNPGTPLREALTAAAAERLAAITQLGNEYRPVCDILDAKAFVNGIVGLMATGGST 302

Query: 269 NAVLHLLALAKEAGVELSLDDFDQISRKTPVIADLRPWGTYTAWELYEAGGTALVFKRLL 328
           N V+HL A+A+ AGV L L DF  IS  TP++A + P G       + AGG A +   LL
Sbjct: 303 NLVIHLPAMARAAGVILDLQDFADISEATPLMARVYPNGLADVNHFHAAGGLAYMIGELL 362

Query: 329 EAGLLFGEEKTLTGRTLAEE------VERAYREQEG------QKVVFPVEKALKPHGGLV 376
             GLL  + KT+ G  LA+       ++   R ++G       K++ P      P GGL 
Sbjct: 363 SEGLLHPDTKTIAGDGLADYAREPKLIDGVLRWEDGPRRSLNAKILRPASDGFAPSGGLK 422

Query: 377 VLKGNLAPKGAVLKLAGTERTYFEGPARVFDSEEAAMEKVLKGEIRPGDVVVIRYVGPKG 436
            LKGNL      +     ER   E  ARVF+ + A  +    GE     VV++R+ GPK 
Sbjct: 423 ELKGNLGRGVMKVSAVAPERHVIEARARVFEDQGAVKDAFKAGEFTEDTVVIVRFQGPK- 481

Query: 437 APGMPEMLSVTSAI-VGEGLGPEVALLTDGRFSGGTRGLMIG-HIAPEAFVGGPIALLEE 494
           A GMPE+ ++T  + V +  G +VAL+TDGR SG +  +    H+APEA  GG +A +  
Sbjct: 482 ANGMPELHALTPVLAVLQDRGLKVALVTDGRMSGASGKVPAAIHVAPEALDGGLMAKVRT 541

Query: 495 GDRIRIDVEGRRLEVLLPEEELERRRARWRPRPPAFTHG----LFARYAALVRQADEGA 549
           GD +R+D     LEVL P  E    RA   P     +HG    LF  +   V  A  GA
Sbjct: 542 GDLVRVDAVAGVLEVLEPGVE---DRAPAMPDLSGNSHGIGRELFDVFRTTVGPASTGA 597


Lambda     K      H
   0.318    0.138    0.405 

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: 950
Number of extensions: 50
Number of successful extensions: 6
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: 555
Length of database: 601
Length adjustment: 36
Effective length of query: 519
Effective length of database: 565
Effective search space:   293235
Effective search space used:   293235
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 Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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
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