Alignments for a candidate for ilvD in Nitriliruptor alkaliphilus DSM 45188

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Nitriliruptor alkaliphilus DSM 45188

Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate WP_052668147.1 NITAL_RS20450 dihydroxy-acid dehydratase

Query= SwissProt::P9WKJ5
         (575 letters)



>NCBI__GCF_000969705.1:WP_052668147.1
          Length = 565

 Score =  737 bits (1902), Expect = 0.0
 Identities = 374/561 (66%), Positives = 438/561 (78%), Gaps = 7/561 (1%)

Query: 14  VADIKPRSRDVTDGLEKAAARGMLRAVGMDDEDFAKPQIGVASSWNEITPCNLSLDRLAN 73
           VAD+KP SRDVTDG E+A AR MLRA+GM D+D++KPQIGVASSWNE+TPCNL LDRLA 
Sbjct: 6   VADLKPVSRDVTDGYERAPARAMLRAIGMGDDDWSKPQIGVASSWNEVTPCNLPLDRLAK 65

Query: 74  AVKEGVFSAGGYPLEFGTISVSDGISMGHEGMHFSLVSREVIADSVEVVMQAERLDGSVL 133
             K G+  AGG+P+EF TI+VSDGISMGHEGM  SLVSREVIADSVE VM AER DG V 
Sbjct: 66  QAKLGIRDAGGFPIEFNTIAVSDGISMGHEGMRASLVSREVIADSVETVMHAERFDGMVT 125

Query: 134 LAGCDKSLPGMLMAAARLDLAAVFLYAGSILPGRAKLSDGSERDVTIIDAFEAVGACSRG 193
            AGCDKSLPGM+MAA RLD+A+ FLY GSILPG+    DG   D++I D FEAVGA  R 
Sbjct: 126 FAGCDKSLPGMVMAAVRLDVASTFLYGGSILPGQ---HDG--HDISIQDVFEAVGARGRD 180

Query: 194 LMSRADVDAIERAICPGEGACGGMYTANTMASAAEALGMSLPGSAAPPATDRRRDGFARR 253
            +  A++D IERA CP EGAC GM+TANTMASA EALG++LPGS+  PA D RRD FARR
Sbjct: 181 QIDDAELDRIERAACPSEGACAGMFTANTMASAVEALGLALPGSSTAPAPDPRRDEFARR 240

Query: 254 SGQAVVELLRRGITARDILTKEAFENAIAVVMAFGGSTNAVLHLLAIAHEANVALSLQDF 313
           SG AV+ LL  GITAR I+T+EA ENA +VVMA GGSTNAVLHL+AIA EA V  SL DF
Sbjct: 241 SGAAVLHLLEEGITARRIVTREALENATSVVMALGGSTNAVLHLIAIAREAEVEFSLDDF 300

Query: 314 SRIGSGVPHLADVKPFGRHVMSDVDHIGGVPVVMKALLDAGLLHGDCLTVTGHTMAENLA 373
            RIG  VPH+AD KP GR+ M+D+D IGGVPVV+K LLDAGLLHGDCLTVTG ++ + + 
Sbjct: 301 DRIGRRVPHIADTKPGGRYFMTDLDRIGGVPVVLKELLDAGLLHGDCLTVTGRSLGDEIE 360

Query: 374 AITPPDPDGKVLRALANPIHPSGGITILHGSLAPEGAVVKTAGF--DSDVFEGTARVFDG 431
           A+  P PDG+V+  L  PIH  GG+ IL GSLAPEGAVVK AG   D+  FEG ARVFDG
Sbjct: 361 AMDVPAPDGEVVHPLDRPIHADGGLAILRGSLAPEGAVVKIAGIPEDNHQFEGPARVFDG 420

Query: 432 ERAALDALEDGTITVGDAVVIRYEGPKGGPGMREMLAITGAIKGAGLGKDVLLLTDGRFS 491
           E+ A++A+  G I  GD +VIRYEGPKGGPGMREMLA+T A+KGAGLG  V LLTDGRFS
Sbjct: 421 EQDAMEAVLTGRIVDGDVIVIRYEGPKGGPGMREMLAVTSAVKGAGLGASVALLTDGRFS 480

Query: 492 GGTTGLCVGHIAPEAVDGGPIALLRNGDRIRLDVAGRVLDVLADPAEFASRQQDFSPPPP 551
           G T G  +GH+APEA DGGPIA +R GDRIR+DV  R +D+L D  E A+R++ + P PP
Sbjct: 481 GATHGFSIGHVAPEATDGGPIAFVREGDRIRIDVPSRTMDLLVDEGELATRREGWQPLPP 540

Query: 552 RYTTGVLSKYVKLVSSAAVGA 572
           RYT GVL+KY + VSSA++GA
Sbjct: 541 RYTRGVLAKYARTVSSASLGA 561


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: 1131
Number of extensions: 51
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: 565
Length adjustment: 36
Effective length of query: 539
Effective length of database: 529
Effective search space:   285131
Effective search space used:   285131
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)

Align candidate WP_052668147.1 NITAL_RS20450 (dihydroxy-acid dehydratase)
to HMM TIGR00110 (ilvD: dihydroxy-acid dehydratase (EC 4.2.1.9))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.aa/TIGR00110.hmm
# target sequence database:        /tmp/gapView.3901.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00110  [M=543]
Accession:   TIGR00110
Description: ilvD: dihydroxy-acid dehydratase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                                 Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.3e-233  760.7   0.2   4.9e-233  760.5   0.2    1.0  1  lcl|NCBI__GCF_000969705.1:WP_052668147.1  NITAL_RS20450 dihydroxy-acid deh


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000969705.1:WP_052668147.1  NITAL_RS20450 dihydroxy-acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  760.5   0.2  4.9e-233  4.9e-233       1     541 [.      24     563 ..      24     565 .] 0.99

  Alignments for each domain:
  == domain 1  score: 760.5 bits;  conditional E-value: 4.9e-233
                                 TIGR00110   1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiam 69 
                                               +ara+l+a+G+ d+d +kP+i+v++s++e++P+++ l+ lak++k +i++aGg + efntiavsDGi+m
  lcl|NCBI__GCF_000969705.1:WP_052668147.1  24 PARAMLRAIGMGDDDWSKPQIGVASSWNEVTPCNLPLDRLAKQAKLGIRDAGGFPIEFNTIAVSDGISM 92 
                                               579****************************************************************** PP

                                 TIGR00110  70 gheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktk 138
                                               gheGm+ sL+sre+iaDsvetv++a+++D++v+ + CDk +PGm+maa+rl++ + + +GG++ +g+  
  lcl|NCBI__GCF_000969705.1:WP_052668147.1  93 GHEGMRASLVSREVIADSVETVMHAERFDGMVTFAGCDKSLPGMVMAAVRLDVASTFLYGGSILPGQHD 161
                                               ********************************************************************* PP

                                 TIGR00110 139 lsekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstlla 207
                                                +++i++ dvfeavg+   ++++++el++ier acP+ g+C+G+ftan+ma++ ealGl+lPgsst++a
  lcl|NCBI__GCF_000969705.1:WP_052668147.1 162 -GHDISIQDVFEAVGARGRDQIDDAELDRIERAACPSEGACAGMFTANTMASAVEALGLALPGSSTAPA 229
                                               .9******************************************************************* PP

                                 TIGR00110 208 tsaekkelakksgkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklsld 276
                                                + ++ e+a++sg+ + +l+++ i+ r+i+t+ea+ena ++++alGGstn+vLhl+aia+ea+v++sld
  lcl|NCBI__GCF_000969705.1:WP_052668147.1 230 PDPRRDEFARRSGAAVLHLLEEGITARRIVTREALENATSVVMALGGSTNAVLHLIAIAREAEVEFSLD 298
                                               ********************************************************************* PP

                                 TIGR00110 277 dfdrlsrkvPllaklkPsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlrv 345
                                               dfdr+ r+vP++a+ kP+g+++++dl+r GGv+ vlkel  +gllh d+ltvtG++l++++e ++v   
  lcl|NCBI__GCF_000969705.1:WP_052668147.1 299 DFDRIGRRVPHIADTKPGGRYFMTDLDRIGGVPVVLKELLDAGLLHGDCLTVTGRSLGDEIEAMDVPAP 367
                                               ********************************************************************* PP

                                 TIGR00110 346 dqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeG 414
                                               d +v+++ld p++++ggla+L+G+la+eGavvkiag+ ed  +feGpa+vf+ e++a+ea+l+g++ +G
  lcl|NCBI__GCF_000969705.1:WP_052668147.1 368 DGEVVHPLDRPIHADGGLAILRGSLAPEGAVVKIAGIPEDNHQFEGPARVFDGEQDAMEAVLTGRIVDG 436
                                               ********************************************************************* PP

                                 TIGR00110 415 dvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialve 483
                                               dv+viryeGPkGgPGmremLa tsa++g+GLg +vaL+tDGrfsG+t+G+siGhv+Pea+ gG+ia+v+
  lcl|NCBI__GCF_000969705.1:WP_052668147.1 437 DVIVIRYEGPKGGPGMREMLAVTSAVKGAGLGASVALLTDGRFSGATHGFSIGHVAPEATDGGPIAFVR 505
                                               ********************************************************************* PP

                                 TIGR00110 484 dGDkikiDienrkldlevseeelaerrakakkkearevkgaLakyaklvssadkGavl 541
                                               +GD+i+iD+++r++dl v+e ela+rr+ +++  +r+++g+Lakya+ vssa+ Ga +
  lcl|NCBI__GCF_000969705.1:WP_052668147.1 506 EGDRIRIDVPSRTMDLLVDEGELATRREGWQPLPPRYTRGVLAKYARTVSSASLGATT 563
                                               *******************************************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (565 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 10.11
//
[ok]

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