Alignments for a candidate for ilvD in Burkholderia phytofirmans PsJN

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Burkholderia phytofirmans PsJN

Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate BPHYT_RS25650 BPHYT_RS25650 dihydroxy-acid dehydratase

Query= SwissProt::P9WKJ5
         (575 letters)



>FitnessBrowser__BFirm:BPHYT_RS25650
          Length = 588

 Score =  496 bits (1277), Expect = e-144
 Identities = 267/563 (47%), Positives = 355/563 (63%), Gaps = 9/563 (1%)

Query: 18  KPRSRDVTDGLEKAAARGMLRAVGMDDEDFAKPQIGVASSWNEITPCNLSLDRLANAVKE 77
           K RSR VTDG+ +A  R  LRA G+DDE   KP + +  ++ E TPC++SL+++++ V+ 
Sbjct: 6   KHRSRRVTDGVTRAPHRAFLRATGLDDESMQKPFVAIVDTFGENTPCSMSLNQVSDNVRL 65

Query: 78  GVFSAGGYPLEFGTISVSDGISMGHEGMHFSLVSREVIADSVEVVMQAERLDGSVLLAGC 137
           G+ + GG P+    ISVSDG SM H GM  SLVSREV+ADSVE+ ++A   D  + +AGC
Sbjct: 66  GIAAGGGVPIRGSAISVSDGTSMNHSGMRMSLVSREVVADSVELFVRAHNYDALIGVAGC 125

Query: 138 DKSLPGMLMAAARLDLAAVFLYAGSILPGRAK------LSDGSERDVTIIDAFEAVGACS 191
           DK+LPG+LM   R+++  VFL+ G++LPG A          G +R  TI+   EAVG   
Sbjct: 126 DKTLPGILMGMVRVNVPGVFLFGGAMLPGVAPGQLPGGAGTGLQRQSTILTTIEAVGTTQ 185

Query: 192 RGLMSRADVDAIERAICPGEGACGGMYTANTMASAAEALGMSLPGSAAPPATDRRRDGFA 251
           RG MSRA +DAIE+   P  G+C G +TANTMA  AE LG++  GSA  PA    R   A
Sbjct: 186 RGDMSRAQLDAIEKQCTPTAGSCPGQFTANTMAMVAETLGLAPLGSAMVPAVYSERIAIA 245

Query: 252 RRSGQAVVELLRRG-ITARDILTKEAFENAIAVVMAFGGSTNAVLHLLAIAHEANVALSL 310
           RR+G+ V+ +L +G    RD++T E+ ENA A V A GGSTNA LH+ AIA+EA +  +L
Sbjct: 246 RRAGETVMRILTQGGPLPRDLVTMESLENACAAVAATGGSTNAALHIPAIANEAGIRFAL 305

Query: 311 QDFSRIGSGVPHLADVKPFGRHVMSDVDHIGGVPVVMKALLDAGLLHGDCLTVTGHTMAE 370
            D  R+ + +P + D++P GR++  D+ H GGVP V+ ALL  G LHGD     G T+AE
Sbjct: 306 DDVQRVFAKIPLIGDLQPGGRYLAQDLHHAGGVPAVLNALLAGGFLHGDVPAFGGGTLAE 365

Query: 371 NLAAITPPDPDGKVLRALANPIHPSGGITILHGSLAPEGAVVKTAGFDSDVFEGTARVFD 430
            L+A +   PDG V+R    P+  +GG+ IL G+LAP+GA +K AG  S  F G  RVF+
Sbjct: 366 ALSAFS--GPDGIVVRPCDEPLGENGGLVILRGNLAPDGACLKIAGLKSLSFTGAVRVFE 423

Query: 431 GERAALDALEDGTITVGDAVVIRYEGPKGGPGMREMLAITGAIKGAGLGKDVLLLTDGRF 490
            E   +  +       GD +VIR EGPKGGPGMREML +T AI G G+G+ V LLTDGRF
Sbjct: 424 CEEDCMAVVAARDYREGDVLVIRNEGPKGGPGMREMLGVTAAIYGQGMGEKVALLTDGRF 483

Query: 491 SGGTTGLCVGHIAPEAVDGGPIALLRNGDRIRLDVAGRVLDVLADPAEFASRQQDFSPPP 550
           SG T G+C+G++ PEA  GGPI LLRN DR+ +D    +L V     E A R+ D     
Sbjct: 484 SGATRGMCIGYVGPEAAAGGPIGLLRNDDRVHIDARAGILRVDLSDDELARRRADAPARA 543

Query: 551 PRYTTGVLSKYVKLVSSAAVGAV 573
            R   GVL KY  LV  A +GAV
Sbjct: 544 SRRLAGVLEKYEALVRPAHLGAV 566


Lambda     K      H
   0.318    0.136    0.393 

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: 1015
Number of extensions: 56
Number of successful extensions: 4
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: 575
Length of database: 588
Length adjustment: 36
Effective length of query: 539
Effective length of database: 552
Effective search space:   297528
Effective search space used:   297528
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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Protein sequences (fasta format)
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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