Alignments for a candidate for ilvD in Sphingomonas koreensis DSMZ 15582

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Sphingomonas koreensis DSMZ 15582

Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate Ga0059261_4216 Ga0059261_4216 Dihydroxyacid dehydratase/phosphogluconate dehydratase

Query= SwissProt::P9WKJ5
         (575 letters)



>FitnessBrowser__Korea:Ga0059261_4216
          Length = 573

 Score =  520 bits (1339), Expect = e-152
 Identities = 273/553 (49%), Positives = 363/553 (65%), Gaps = 6/553 (1%)

Query: 21  SRDVTDGLEKAAARGMLRAVGMDDEDFAKPQIGVASSWNEITPCNLSLDRLANAVKEGVF 80
           SR V+ G E+A  R    A+G+ +E+ A+P + +AS+ N+  PCN +LD  A+A ++GV 
Sbjct: 12  SRHVSVGPERAPHRSYYYAMGISEEEIARPFVALASAGNDSAPCNTTLDAQADAARKGVA 71

Query: 81  SAGGYPLEFGTISVSDGISMGHEGMHFSLVSREVIADSVEVVMQAERLDGSVLLAGCDKS 140
             GG P  F TI+V+DGI+MGH+GM  SLVSREVIADSVE+ ++    D  V  AGCDKS
Sbjct: 72  DNGGLPRRFNTITVTDGIAMGHQGMKSSLVSREVIADSVELSVRGHCYDALVGFAGCDKS 131

Query: 141 LPGMLMAAARLDLAAVFLYAGSILPGRAKLSDGSERDVTIIDAFEAVGACSRGLMSRADV 200
           LPGM+MA  RL++ ++F+Y GSILPGR +     +RDVT++D FE VG  + G    ++V
Sbjct: 132 LPGMMMAMLRLNIPSIFVYGGSILPGRYQ-----DRDVTVVDVFEVVGKFAAGTCPISEV 186

Query: 201 DAIERAICPGEGACGGMYTANTMASAAEALGMSLPGSAAPPATDRRRDGFARRSGQAVVE 260
            A+E+  CPG GACGG YTANTMA   EA+G+SLP S   PA    R+  A  +G  V+E
Sbjct: 187 HALEKVACPGHGACGGQYTANTMACVGEAIGLSLPNSNMVPAPYTSREQIAVAAGYQVME 246

Query: 261 LLRRGITARDILTKEAFENAIAVVMAFGGSTNAVLHLLAIAHEANVALSLQDFSRIGSGV 320
           LL R I  RDI T+EAF NA  +V A GGSTN  LHL A+A EA +   L D + +    
Sbjct: 247 LLERNIRPRDICTREAFINAARIVAATGGSTNGALHLPAMASEAGIDFDLFDVAEVFKST 306

Query: 321 PHLADVKPFGRHVMSDVDHIGGVPVVMKALLDAGLLHGDCLTVTGHTMAENLAAITPPDP 380
           P+ AD+KP G++V  D+   GGV ++MK++L+ GLL+GDC+TVTG T+ EN+  +T  +P
Sbjct: 307 PYAADLKPGGKYVAKDMYEAGGVYMLMKSMLENGLLYGDCMTVTGKTLGENIDQVT-WNP 365

Query: 381 DGKVLRALANPIHPSGGITILHGSLAPEGAVVKTAGFDSDVFEGTARVFDGERAALDALE 440
           D KV+  +  PI P+GG+  L G+LAP GA+VK AG    VFEG AR FD E  A  A+E
Sbjct: 366 DQKVIYDVRTPITPTGGVVGLRGTLAPNGAIVKVAGMSRLVFEGPARCFDCEEDAFAAVE 425

Query: 441 DGTITVGDAVVIRYEGPKGGPGMREMLAITGAIKGAGLGKDVLLLTDGRFSGGTTGLCVG 500
              I  G+ VVIRYEGPKGGPGMREML+ T A+ G G+G+ V L+TDGRFSG T G C+G
Sbjct: 426 KREIREGEVVVIRYEGPKGGPGMREMLSTTAALYGLGMGEKVALITDGRFSGATRGFCIG 485

Query: 501 HIAPEAVDGGPIALLRNGDRIRLDVAGRVLDVLADPAEFASRQQDFSPPPPRYTTGVLSK 560
           H+ PEA + GPIAL+ +GD IR+D     +D+       A R+  + P    Y +G L +
Sbjct: 486 HVGPEAAECGPIALVEDGDTIRIDAEAGTIDLHVAEDVLAERRARWQPRENAYQSGALWR 545

Query: 561 YVKLVSSAAVGAV 573
           Y + V  A  GAV
Sbjct: 546 YAQNVGPAYKGAV 558


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: 974
Number of extensions: 45
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: 573
Length adjustment: 36
Effective length of query: 539
Effective length of database: 537
Effective search space:   289443
Effective search space used:   289443
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 Ga0059261_4216 Ga0059261_4216 (Dihydroxyacid dehydratase/phosphogluconate 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.13959.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.2e-204  664.7   0.6     6e-204  664.5   0.6    1.0  1  lcl|FitnessBrowser__Korea:Ga0059261_4216  Ga0059261_4216 Dihydroxyacid deh


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Korea:Ga0059261_4216  Ga0059261_4216 Dihydroxyacid dehydratase/phosphogluconate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  664.5   0.6    6e-204    6e-204       1     541 [.      23     559 ..      23     561 .. 0.99

  Alignments for each domain:
  == domain 1  score: 664.5 bits;  conditional E-value: 6e-204
                                 TIGR00110   1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiam 69 
                                               ++r+ ++a+G+++e++ +P++a++++ ++ +P++ +l+  a+++++++ ++Gg + +fnti+v+DGiam
  lcl|FitnessBrowser__Korea:Ga0059261_4216  23 PHRSYYYAMGISEEEIARPFVALASAGNDSAPCNTTLDAQADAARKGVADNGGLPRRFNTITVTDGIAM 91 
                                               689****************************************************************** PP

                                 TIGR00110  70 gheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktk 138
                                               gh+Gmk sL+sre+iaDsve  v++h++Dalv  + CDk +PGm+ma+lrlniP+i+v+GG++ +g+++
  lcl|FitnessBrowser__Korea:Ga0059261_4216  92 GHQGMKSSLVSREVIADSVELSVRGHCYDALVGFAGCDKSLPGMMMAMLRLNIPSIFVYGGSILPGRYQ 160
                                               ********************************************************************* PP

                                 TIGR00110 139 lsekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstlla 207
                                                 +++++vdvfe vg+ aag    +e++++e++acP+ g+C+G +tan+mac+ ea+GlslP+s  ++a
  lcl|FitnessBrowser__Korea:Ga0059261_4216 161 -DRDVTVVDVFEVVGKFAAGTCPISEVHALEKVACPGHGACGGQYTANTMACVGEAIGLSLPNSNMVPA 228
                                               .8******************************************************************* PP

                                 TIGR00110 208 tsaekkelakksgkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklsld 276
                                                 + ++++a  +g +++el+++ni+Prdi t+eaf na  ++ a+GGstn  Lhl+a+a+eag++++l 
  lcl|FitnessBrowser__Korea:Ga0059261_4216 229 PYTSREQIAVAAGYQVMELLERNIRPRDICTREAFINAARIVAATGGSTNGALHLPAMASEAGIDFDLF 297
                                               ********************************************************************* PP

                                 TIGR00110 277 dfdrlsrkvPllaklkPsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlrv 345
                                               d+ ++ + +P  a+lkP+gk+v +d+ +aGGv +++k++ ++gll  d++tvtGktl+e++++v+ +  
  lcl|FitnessBrowser__Korea:Ga0059261_4216 298 DVAEVFKSTPYAADLKPGGKYVAKDMYEAGGVYMLMKSMLENGLLYGDCMTVTGKTLGENIDQVTWN-P 365
                                               *****************************************************************99.8 PP

                                 TIGR00110 346 dqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeG 414
                                               dq+vi  +  p++ +gg+  L+G la++Ga+vk+ag++   l+feGpa+ f+ ee+a +a+ +++++eG
  lcl|FitnessBrowser__Korea:Ga0059261_4216 366 DQKVIYDVRTPITPTGGVVGLRGTLAPNGAIVKVAGMSR--LVFEGPARCFDCEEDAFAAVEKREIREG 432
                                               9*************************************9..9*************************** PP

                                 TIGR00110 415 dvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialve 483
                                               +vvviryeGPkGgPGmremL  t+al glG+g+kvaLitDGrfsG+trG++iGhv Peaae G+ialve
  lcl|FitnessBrowser__Korea:Ga0059261_4216 433 EVVVIRYEGPKGGPGMREMLSTTAALYGLGMGEKVALITDGRFSGATRGFCIGHVGPEAAECGPIALVE 501
                                               ********************************************************************* PP

                                 TIGR00110 484 dGDkikiDienrkldlevseeelaerrakakkkearevkgaLakyaklvssadkGavl 541
                                               dGD+i+iD+e+ ++dl+v e+ laerra+++++e+ +++gaL +ya+ v  a kGav+
  lcl|FitnessBrowser__Korea:Ga0059261_4216 502 DGDTIRIDAEAGTIDLHVAEDVLAERRARWQPRENAYQSGALWRYAQNVGPAYKGAVT 559
                                               ********************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (573 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 0.02s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 9.29
//
[ok]

This GapMind analysis is from Apr 09 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