Alignments for a candidate for ilvD in Dyella japonica UNC79MFTsu3.2

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Dyella japonica UNC79MFTsu3.2

Align dihydroxy-acid dehydratase subunit (EC 4.2.1.9) (characterized)
to candidate N515DRAFT_2409 N515DRAFT_2409 dihydroxy-acid dehydratase

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



>FitnessBrowser__Dyella79:N515DRAFT_2409
          Length = 574

 Score =  361 bits (926), Expect = e-104
 Identities = 213/548 (38%), Positives = 318/548 (58%), Gaps = 12/548 (2%)

Query: 7   KRGIQRAPHRSLLARCGLTDDDFE-KPFIGIANSYTDIVPGHIHLRELAEAVKEGVNAAG 65
           + G Q   +RS L   GL +D F+ +P IGI N+++++ P +   RELAE VK GV  AG
Sbjct: 17  REGKQGFYYRSWLKGLGLPNDMFDGRPVIGICNTWSELTPCNSSFRELAEHVKRGVYEAG 76

Query: 66  GVAFEFNTMAICDGIAMNHDGMKYSLASREIVADTVESMAMAHALDGLVLLPTCDKIVPG 125
           G   EF  M++ +   M    M +    R + +  VE    A+ +DG+VLL  CDK  P 
Sbjct: 77  GFPLEFPVMSLGE-TQMRPTAMLF----RNLASMDVEESIRANPIDGVVLLMGCDKTTPA 131

Query: 126 MLMAAARLDIPAIVVTGGPMLPGEFKGRKVDL-INVYEGVGTVSAGEMSEDELEELERCA 184
           ++M AA +++P I ++GGP L G ++G+ +     V      V AGE++++E  E E C 
Sbjct: 132 LMMGAASVNLPTIGLSGGPSLSGNWRGQPIGSGTGVIRMSEMVRAGELAQEEFVEAEACM 191

Query: 185 CPGPRSCAGLFTANTMACLTEALGMSLPGCATAHAVSSRKRQIARLSGKRIVEMVQENLK 244
                SC  + TA+TMA + EALG+SLP  A   AV SR+ ++A LSG+RIVEMV E+L+
Sbjct: 192 QRSKGSCMTMGTASTMASMVEALGLSLPENAAIPAVDSRRFRLAHLSGRRIVEMVHEDLR 251

Query: 245 PTMIMSQEAFENAVMVDLALGGSTNTTLHIPAIAAEIDGLNINLDLFDELSRVIPHIASI 304
            + I+++ AFENA+  + A+GGSTN  +H+ A+A  + G+ + LD +D L   +P + ++
Sbjct: 252 MSKILTRAAFENAIRANAAIGGSTNAVIHLLALAGRL-GVELALDDWDRLGSHLPCLVNL 310

Query: 305 SPAGEHMMLDLDRAGGIPAVLKTLEDHINRECVTCTGRTVQENIENVKVGHRDVIRPLDS 364
            P+G+++M D   AGG+PAVL+ +  H++   +T  GRT+ +NI      +RDVIRP++ 
Sbjct: 311 KPSGDYLMEDFYYAGGLPAVLREIAPHLHLGALTANGRTLGDNIATAPCWNRDVIRPIEE 370

Query: 365 PVHSEGGLAILRGNLAPRGSVVKQGAVAEDMMVHEGPAKVFNSEDECMEAIFGGR--IDE 422
           P+  E G+A+LRGNLAP G+V+K  A +  ++ H G A VF + D+    I      IDE
Sbjct: 371 PLKREAGIAVLRGNLAPDGAVIKPSAASAHLLQHRGRAVVFENIDDFKARIDDEALDIDE 430

Query: 423 GDVIVIRYEGPKGGPGMREMLNP--TSAIAGMGLERVALITDGRFSGGTRGPCVGHVSPE 480
             V+V++  GP+G PGM E+ N      +   G+  +  I+D R SG   G  V H SPE
Sbjct: 431 TCVMVLKNCGPRGYPGMAEVGNMPLPPKLLRRGITDIVRISDARMSGTAYGTVVLHASPE 490

Query: 481 AMEDGPLAAVNDGDIIRIDIPSRKLEVDLSPREIEERLQSAVKPRRSVKGWLARYRKLAG 540
           A   G LA V DGD I +D+P R+L +DL+  E+  R  +   P    +GW   Y     
Sbjct: 491 AAAGGNLALVRDGDFIELDVPGRRLHLDLADDELARRRAAWKAPPPPERGWAKLYVDHVQ 550

Query: 541 SADTGAVL 548
            A  GA L
Sbjct: 551 QAHLGADL 558


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: 845
Number of extensions: 37
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: 549
Length of database: 574
Length adjustment: 36
Effective length of query: 513
Effective length of database: 538
Effective search space:   275994
Effective search space used:   275994
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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Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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