Alignments for a candidate for ilvD in Xenophilus azovorans DSM 13620

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Xenophilus azovorans DSM 13620

Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate WP_038213205.1 Q392_RS23315 dihydroxy-acid dehydratase

Query= SwissProt::P9WKJ5
         (575 letters)



>NCBI__GCF_000745855.1:WP_038213205.1
          Length = 582

 Score =  468 bits (1205), Expect = e-136
 Identities = 253/567 (44%), Positives = 347/567 (61%), Gaps = 17/567 (2%)

Query: 17  IKPRSRDVTDGLEKAAARGMLRAVGMDDEDFAKPQIGVASSWNEITPCNLSLDRLANAVK 76
           + PRS  +  G  +A  R  LRA+G DDED A+P +GV  +  E++PCNL+L   A   K
Sbjct: 10  LPPRSATIHTGTIRATTRAFLRALGQDDEDIARPHVGVFHTGGEMSPCNLNLREQAQHAK 69

Query: 77  EGVFSAGGYPLEFGTISVSDGISMGHEGMHFSLVSREVIADSVEVVMQAERLDGSVLLAG 136
            G+++AGG P E   +SVSDG++M H GM FSL+SRE+IADSVE  ++  + DG   +  
Sbjct: 70  TGIYAAGGTPHECPVVSVSDGLTMAHSGMRFSLISRELIADSVEASVRGHQWDGVFAIGA 129

Query: 137 CDKSLPGMLMAAARLDLAAVFLYAGSILPGRAKLSDGSERDVTIIDAFEAVGACSRGLMS 196
           CDK+LPG++M   R ++  VF++ G+ LPGR        RD+ ++D +E +G    G  +
Sbjct: 130 CDKNLPGLMMGIVRCNVPGVFVHGGAALPGRI---GPHGRDLNVVDTYETIGKLLAGEAT 186

Query: 197 RADVDAIERAICPGEGACGGMYTANTMASAAEALGMSLPGSAAPPATDRRRDGFARRSGQ 256
             +++ + RA  P  G+C G +TANTM   +EALG++  GS+  PA    R    RR+ +
Sbjct: 187 AEELETMSRACLPTAGSCAGQFTANTMGMVSEALGLAPIGSSMVPAVYSERAPLMRRAAK 246

Query: 257 AVVELLRRGITA-----RDILTKEAFENAIAVVMAFGGSTNAVLHLLAIAHEANVALSLQ 311
            ++  +   +       RDI+T++A ENA AVV A GGSTNA LH+ AIAHEA +   L 
Sbjct: 247 QLMRAVSASLEGGGPLPRDIVTRQALENACAVVCATGGSTNAALHIPAIAHEAGIRFHLD 306

Query: 312 DFSRIGSGVPHLADVKPFGRHVMSDVDHIGGVPVVMKALLDAGLLHGDCLTVTGHTMAEN 371
           D + + +  P +A++ P G+++  DV  IGG  VV++ALLD G LHGD LT TG T+AE 
Sbjct: 307 DVAEVFARTPLIANLSPGGKYLARDVYSIGGAGVVLRALLDQGHLHGDALTWTGRTLAEE 366

Query: 372 LAAITPPDPDGKVLRALANPIHPSGGITILHGSLAPEGAVVKTAGFDSDVFEGTARVFDG 431
           LA     +PDG+V+R    PI P GG+T+L G+L P+GA++KTAG  + V EG ARVF+ 
Sbjct: 367 LAGCA--EPDGEVVRRAGEPISPDGGLTVLKGNLCPDGALLKTAGLKTLVHEGPARVFEN 424

Query: 432 ERAALDALEDGTITVGDAVVIRYEGPKGGPGMREMLAITGAIKGAGLGKDVLLLTDGRFS 491
           E  A  A+++     GD +VIR EGPKG PGMREML IT  + G G+G  V LLTDGRFS
Sbjct: 425 EEEAQAAVQNRRYQAGDVIVIRNEGPKGSPGMREMLGITALLYGQGMGDKVALLTDGRFS 484

Query: 492 GGTTGLCVGHIAPEAVDGGPIALLRNGDRIRLDV--AGRVLDVLADPAEFASR---QQDF 546
           G T GLC+G+  PEA  GGPIA LR+GDRI +D     R + V     E   R   +   
Sbjct: 485 GATRGLCIGYAGPEAAAGGPIAALRDGDRIAIDARPGARSITVALPAEEIVMRLNQKAGV 544

Query: 547 SPPPPRYTTGVLSKYVKLVSSAAVGAV 573
           +   PR   G+L KY   V  A  GAV
Sbjct: 545 NEGAPR--GGLLEKYALTVRPAHQGAV 569


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: 1050
Number of extensions: 55
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: 582
Length adjustment: 36
Effective length of query: 539
Effective length of database: 546
Effective search space:   294294
Effective search space used:   294294
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 10 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