Alignments for a candidate for ilvD in Shewanella sp. ANA-3

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Shewanella sp. ANA-3

Align dihydroxy-acid dehydratase subunit (EC 4.2.1.9) (characterized)
to candidate 7024896 Shewana3_2070 dihydroxy-acid dehydratase (RefSeq)

Query= metacyc::MONOMER-11919
         (549 letters)



>FitnessBrowser__ANA3:7024896
          Length = 586

 Score =  334 bits (857), Expect = 5e-96
 Identities = 204/541 (37%), Positives = 319/541 (58%), Gaps = 17/541 (3%)

Query: 15  HRSLLARCGLTDDDFE-KPFIGIANSYTDIVPGHIHLRELAEAVKEGVNAAGGVAFEFNT 73
           +RS +   G+ +  F+ KP IGI N+++++ P + HLRELA+ VK G+  AGG+  EF  
Sbjct: 34  YRSWMKNQGIPEHHFQNKPVIGICNTWSELTPCNGHLRELAQRVKNGIREAGGIPVEFPV 93

Query: 74  MAICDGIAMNHDGMKYSLASREIVADTVESMAMAHALDGLVLLPTCDKIVPGMLMAAARL 133
            +  +      +    ++ +R + A   E     + +DG+VLL  CDK  P +LM AA  
Sbjct: 94  FSNGES-----NLRPSAMLTRNLAAMDTEEAIRGNPIDGVVLLVGCDKTTPALLMGAASC 148

Query: 134 DIPAIVVTGGPMLPGEFKGRKVDLIN-VYEGVGTVSAGEMSEDELEELERCACPGPRSCA 192
           D+P IVVTGGPML G+ KG+ V     V+E      AG +S       E        +C 
Sbjct: 149 DLPTIVVTGGPMLNGKHKGKDVGSGTLVWELHQEYKAGNISLAAFMNAEADMSRSTGTCN 208

Query: 193 GLFTANTMACLTEALGMSLPGCATAHAVSSRKRQIARLSGKRIVEMVQENLKPTMIMSQE 252
            + TA+TMAC+ E LG+SLP  AT  AV SR++ +A +SG RIV+MV+E+L  + I+S++
Sbjct: 209 TMGTASTMACMVETLGVSLPHNATIPAVDSRRQVLAHMSGMRIVDMVKEDLTLSKILSRD 268

Query: 253 AFENAVMVDLALGGSTNTTLHIPAIAAEIDGLNINLDLFDELSRVIPHIASISPAGEHMM 312
           AF NA+ V+ A+GGSTN  +H+ AIA  I G+ ++LD +      +P I ++ P+G+++M
Sbjct: 269 AFINAIKVNAAIGGSTNAVIHLKAIAGRI-GVELSLDDWRH-GYTVPTIVNLKPSGQYLM 326

Query: 313 LDLDRAGGIPAVLKTLEDH--INRECVTCTGRTVQENIENVKVGHRDVIRPLDSPVHSEG 370
            D   AGG+PAVL+ L +H  +++  +T    ++ +N++     +++VI  L++P+   G
Sbjct: 327 EDFYYAGGLPAVLRQLFEHDLLSKNTLTVNAASLWDNVKEAPCYNQEVIMSLENPLVENG 386

Query: 371 GLAILRGNLAPRGSVVKQGAVAEDMMVHEGPAKVFNSEDECMEAIFGGR--IDEGDVIVI 428
           G+ +LRGNLAPRG+V+K  A +  +M H G A VF S D+    I      IDE  ++V+
Sbjct: 387 GIRVLRGNLAPRGAVIKPSAASAHLMQHRGKAVVFESFDDYNARIGDPELDIDENSIMVL 446

Query: 429 RYEGPKGGPGMREMLNP--TSAIAGMGLERVALITDGRFSGGTRGPCVGHVSPEAMEDGP 486
           +  GPKG PGM E+ N      +   G++ +  I+D R SG   G  V HV+PEA   GP
Sbjct: 447 KNCGPKGYPGMAEVGNMGLPPKLLKKGIKDMVRISDARMSGTAFGTVVLHVAPEAQALGP 506

Query: 487 LAAVNDGDIIRIDIPSRKLEVDLSPREIEERLQ--SAVKPRRSVKGWLARYRKLAGSADT 544
           LAAV +GD+I +D  +  L++++S +E++ RL   + VK      G+L+ +++    AD 
Sbjct: 507 LAAVQNGDMIALDTYAGTLQLEISDQELQARLAKLATVKSIPVNGGYLSLFKEHVLQADE 566

Query: 545 G 545
           G
Sbjct: 567 G 567


Lambda     K      H
   0.319    0.136    0.397 

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: 793
Number of extensions: 35
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: 549
Length of database: 586
Length adjustment: 36
Effective length of query: 513
Effective length of database: 550
Effective search space:   282150
Effective search space used:   282150
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 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