Alignments for a candidate for ilvD in Sphingomonas wittichii RW1

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Sphingomonas wittichii RW1

Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate WP_012049461.1 SWIT_RS16515 dihydroxy-acid dehydratase

Query= SwissProt::P9WKJ5
         (575 letters)



>NCBI__GCF_000016765.1:WP_012049461.1
          Length = 561

 Score =  526 bits (1356), Expect = e-154
 Identities = 275/554 (49%), Positives = 364/554 (65%), Gaps = 8/554 (1%)

Query: 21  SRDVTDGLEKAAARGMLRAVGMDDEDFAKPQIGVASSWNEITPCNLSLDRLANAVKEGVF 80
           SR +TDGL++A  R  LRA+G DD    +P  G+ S+   +TPC++SL   A A K G+ 
Sbjct: 13  SRTITDGLDRAPHRAFLRAMGHDDVAIGQPFAGIVSTGASVTPCSMSLAPQAEAAKAGLQ 72

Query: 81  SAGGYPLEFGTISVSDGISMGHEGMHFSLVSREVIADSVEVVMQAERLDGSVLLAGCDKS 140
           +AG  P EF TI+V+D +SM H GM FSLVSRE+IADS+E V +A   DG +  A CDK+
Sbjct: 73  AAGVTPFEFSTITVADSMSMNHAGMRFSLVSREIIADSIEAVTRAHGYDGLIGFAACDKT 132

Query: 141 LPGMLMAAARLDLAAVFLYAGSILPGRAKLSDGSERDVTIIDAFEAVGACSRGLMSRADV 200
           LPG +M   R++  +VF+Y G+ LPGR +      RD+ I+D +E VG    G M  A++
Sbjct: 133 LPGTMMGMIRVNRPSVFVYGGAALPGRWQ-----GRDIGIVDVYEGVGRVYAGEMDEAEL 187

Query: 201 DAIERAICPGEGACGGMYTANTMASAAEALGMSLPGSAAPPATDRRRDGFARRSGQAVVE 260
             +E+A  P  G+C G +TANTMA  AE LG++LP SA  PA    R   A  SG+ +  
Sbjct: 188 TRLEKAGVPTVGSCAGQFTANTMAMVAETLGLALPRSAMMPAVASERRALAEESGRVLGR 247

Query: 261 LLRRG-ITARDILTKEAFENAIAVVMAFGGSTNAVLHLLAIAHEANVALSLQDFSRIGSG 319
           L+R G    RD++T+ + ENA A V A GGSTNA LHL AIAHEA ++ +++D + I   
Sbjct: 248 LIREGGPRPRDLVTRRSLENAAATVAATGGSTNAALHLPAIAHEAGISFTMEDIAAIFDR 307

Query: 320 VPHLADVKPFGRHVMSDVDHIGGVPVVMKALLDAGLLHGDCLTVTGHTMAENLAAITPPD 379
            P LAD+KP GR    D+  +GGVP V++A+L+AG+LHGDC T+TG T+ E  AA   P 
Sbjct: 308 TPLLADLKPGGRFWARDLHEVGGVPTVLRAMLEAGVLHGDCPTITGRTIGEIAAAA--PA 365

Query: 380 PDGKVLRALANPIHPSGGITILHGSLAPEGAVVKTAGFDSDVFEGTARVFDGERAALDAL 439
           PDG+V+R    PI P+GG+ +L GSLAP+GA++K AG      EG ARVFDGE AA+DA+
Sbjct: 366 PDGEVVRPADRPIAPTGGVIVLRGSLAPDGAMLKVAGLKRLSHEGPARVFDGEEAAVDAV 425

Query: 440 EDGTITVGDAVVIRYEGPKGGPGMREMLAITGAIKGAGLGKDVLLLTDGRFSGGTTGLCV 499
                  GD +VIR EGPKGGPGMREML +T  I G G+G+ V LLTDGRFSG T G+C+
Sbjct: 426 RRQDYQPGDVIVIRGEGPKGGPGMREMLGVTALIYGQGMGEQVALLTDGRFSGATRGMCI 485

Query: 500 GHIAPEAVDGGPIALLRNGDRIRLDVAGRVLDVLADPAEFASRQQDFSPPPPRYTTGVLS 559
           GH+ PEA  GGP+AL+R+GDRIR+D   R LD+L D AE   R+  ++ P    T+  L 
Sbjct: 486 GHVGPEASAGGPLALVRDGDRIRIDAGQRTLDLLVDAAELERRRAAWTAPEATVTSPTLR 545

Query: 560 KYVKLVSSAAVGAV 573
           KY +LV  A +GAV
Sbjct: 546 KYARLVGPAHLGAV 559


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: 1014
Number of extensions: 51
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: 575
Length of database: 561
Length adjustment: 36
Effective length of query: 539
Effective length of database: 525
Effective search space:   282975
Effective search space used:   282975
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_012049461.1 SWIT_RS16515 (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.26218.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.1e-198  647.1   0.8   1.2e-198  646.9   0.8    1.0  1  lcl|NCBI__GCF_000016765.1:WP_012049461.1  SWIT_RS16515 dihydroxy-acid dehy


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000016765.1:WP_012049461.1  SWIT_RS16515 dihydroxy-acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  646.9   0.8  1.2e-198  1.2e-198       1     541 [.      24     560 ..      24     561 .] 0.99

  Alignments for each domain:
  == domain 1  score: 646.9 bits;  conditional E-value: 1.2e-198
                                 TIGR00110   1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiam 69 
                                               ++ra+l+a+G  d  +++P+ ++v++  +++P+ ++l   a+++k++++aaG +++ef ti+v+D ++m
  lcl|NCBI__GCF_000016765.1:WP_012049461.1  24 PHRAFLRAMGHDDVAIGQPFAGIVSTGASVTPCSMSLAPQAEAAKAGLQAAGVTPFEFSTITVADSMSM 92 
                                               69******************************************************************* PP

                                 TIGR00110  70 gheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktk 138
                                               +h Gm++sL+sreiiaDs+e+v +ah +D+l+  ++CDk +PG +m+++r+n+P+++v+GG+  +g+ +
  lcl|NCBI__GCF_000016765.1:WP_012049461.1  93 NHAGMRFSLVSREIIADSIEAVTRAHGYDGLIGFAACDKTLPGTMMGMIRVNRPSVFVYGGAALPGRWQ 161
                                               ********************************************************************* PP

                                 TIGR00110 139 lsekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstlla 207
                                                +++i +vdv+e+vg++ ag+++e+el+++e+ ++Pt gsC+G ftan+ma+++e+lGl+lP s+ ++a
  lcl|NCBI__GCF_000016765.1:WP_012049461.1 162 -GRDIGIVDVYEGVGRVYAGEMDEAELTRLEKAGVPTVGSCAGQFTANTMAMVAETLGLALPRSAMMPA 229
                                               .9******************************************************************* PP

                                 TIGR00110 208 tsaekkelakksgkrivelvkkn.ikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklsl 275
                                               + +e+++la++sg+ +  l+++   +Prd++t++++ena + + a+GGstn+ Lhl+aia+eag+++++
  lcl|NCBI__GCF_000016765.1:WP_012049461.1 230 VASERRALAEESGRVLGRLIREGgPRPRDLVTRRSLENAAATVAATGGSTNAALHLPAIAHEAGISFTM 298
                                               ********************997257******************************************* PP

                                 TIGR00110 276 ddfdrlsrkvPllaklkPsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlr 344
                                               +d+  + +++Plla+lkP+g+    dlh++GGv++vl+ + ++g+lh d+ t+tG+t++e+++ ++   
  lcl|NCBI__GCF_000016765.1:WP_012049461.1 299 EDIAAIFDRTPLLADLKPGGRFWARDLHEVGGVPTVLRAMLEAGVLHGDCPTITGRTIGEIAAAAPAP- 366
                                               ******************************************************************99. PP

                                 TIGR00110 345 vdqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvke 413
                                                d +v+r+ d p+  +gg+ vL+G+la++Ga+ k+ag +   l +eGpa+vf+ ee+a++a+ + + + 
  lcl|NCBI__GCF_000016765.1:WP_012049461.1 367 -DGEVVRPADRPIAPTGGVIVLRGSLAPDGAMLKVAGLKR--LSHEGPARVFDGEEAAVDAVRRQDYQP 432
                                               .***************************************..9************************** PP

                                 TIGR00110 414 GdvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialv 482
                                               Gdv+vir eGPkGgPGmremL  t+ + g G+g++vaL+tDGrfsG+trG++iGhv Pea +gG++alv
  lcl|NCBI__GCF_000016765.1:WP_012049461.1 433 GDVIVIRGEGPKGGPGMREMLGVTALIYGQGMGEQVALLTDGRFSGATRGMCIGHVGPEASAGGPLALV 501
                                               ********************************************************************* PP

                                 TIGR00110 483 edGDkikiDienrkldlevseeelaerrakakkkearevkgaLakyaklvssadkGavl 541
                                               +dGD+i+iD+ +r+ldl v+ +el++rra+++++ea  ++ +L+kya+lv  a+ Gav+
  lcl|NCBI__GCF_000016765.1:WP_012049461.1 502 RDGDRIRIDAGQRTLDLLVDAAELERRRAAWTAPEATVTSPTLRKYARLVGPAHLGAVT 560
                                               *********************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (561 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 0.00s 00:00:00.02 Elapsed: 00:00:00.03
# Mc/sec: 9.85
//
[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