Alignments for a candidate for ilvD in Dinoroseobacter shibae DFL-12

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Dinoroseobacter shibae DFL-12

Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate 3606698 Dshi_0129 dihydroxy-acid dehydratase (RefSeq)

Query= SwissProt::P9WKJ5
         (575 letters)



>FitnessBrowser__Dino:3606698
          Length = 577

 Score =  538 bits (1385), Expect = e-157
 Identities = 283/556 (50%), Positives = 369/556 (66%), Gaps = 9/556 (1%)

Query: 21  SRDVTDGLEKAAARGMLRAVGMDDEDFAKPQIGVASSWNEITPCNLSLDRLANAVKEGVF 80
           SR VT+G  +A  R    A+GM +E+  +P +GVA+ WNE  PCN++L R A AVK GV 
Sbjct: 13  SRHVTEGPSRAPHRSYYYAMGMTEEEIHQPLVGVATCWNEAAPCNIALSRQAQAVKMGVK 72

Query: 81  SAGGYPLEFGTISVSDGISMGHEGMHFSLVSREVIADSVEVVMQAERLDGSVLLAGCDKS 140
            A G P EF TI+V+DGI+MGHEGM  SL SRE IAD+VE+ M+    D  V LAGCDKS
Sbjct: 73  QASGTPREFTTITVTDGIAMGHEGMRSSLASREAIADTVELTMRGHCYDAIVGLAGCDKS 132

Query: 141 LPGMLMAAARLDLAAVFLYAGSILPGRAKLSDGSERDVTIIDAFEAVGACSRGLMSRADV 200
           LPGM+MA  RL++ +VF+Y GSILPGR      +  DVT+ D FEAVG    G  + A++
Sbjct: 133 LPGMMMAMVRLNVPSVFIYGGSILPGRL-----NGEDVTVQDVFEAVGKHQAGNYTDAEL 187

Query: 201 DAIERAICPGEGACGGMYTANTMASAAEALGMSLPGSAAPPATDRRRDGFARRSGQAVVE 260
           + +ER  CP  GACGG +TANTMA  +EA+G++LP SA  PA    RD +   SG+AV++
Sbjct: 188 EVLERVACPSAGACGGQFTANTMACVSEAIGLALPNSAGAPAPYESRDQYGEASGRAVMD 247

Query: 261 LLRRGITARDILTKEAFENAIAVVMAFGGSTNAVLHLLAIAHEANVALSLQDFSRIGSGV 320
           L+ +GI ARDI+T+++ ENA  +V   GGSTNA LHL AIAHEA +  +LQD   I    
Sbjct: 248 LIEKGIRARDIVTRKSLENAARIVACTGGSTNAGLHLPAIAHEAGIEFTLQDVCDIFRDT 307

Query: 321 PHLADVKPFGRHVMSDVDHIGGVPVVMKALLDAGLLHGDCLTVTGHTMAENLAAITPPDP 380
           P+  D+KP G++V  D+   GGVPVVM+ L  AGL+H DC+TVTG+++ E L  +T  + 
Sbjct: 308 PYFVDLKPGGKYVAKDMYEAGGVPVVMRELRRAGLIHEDCMTVTGYSIGEELDKVT-LEA 366

Query: 381 DGKVLRALANPIHPSGGITILHGSLAPEGAVVKTAGFDSD--VFEGTARVFDGERAALDA 438
           DG+V+  +  P+  +GG+  L G+LAPEGA+VK AG   D  VF G ARVF+ E  A +A
Sbjct: 367 DGRVIYPVDTPLSTTGGVVGLEGNLAPEGAIVKIAGMSDDQLVFTGPARVFECEEDAFEA 426

Query: 439 LEDGTITVGDAVVIRYEGPKGGPGMREMLAITGAIKGAGLGKDVLLLTDGRFSGGTTGLC 498
           +++     GD  VIR EGP GGPGMREMLA T A+ G G+GK V L+TDGRFSG T G C
Sbjct: 427 VQNRAYAEGDVFVIRNEGPAGGPGMREMLATTAALSGQGMGKKVALITDGRFSGATRGFC 486

Query: 499 VGHIAPEAVDGGPIALLRNGDRIRLDVAGRVLDVLADPAEFASRQQDFSPPPPR-YTTGV 557
           VGH+ PEA  GGPIA+L++GD I +D     L V     E A+R+  +S P    Y +G 
Sbjct: 487 VGHVGPEAAHGGPIAMLKDGDMITIDALKGELSVALSEDELAARKDAWSGPRETIYASGA 546

Query: 558 LSKYVKLVSSAAVGAV 573
           L KY +LV  A +GAV
Sbjct: 547 LWKYAQLVGGARLGAV 562


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: 956
Number of extensions: 48
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: 577
Length adjustment: 36
Effective length of query: 539
Effective length of database: 541
Effective search space:   291599
Effective search space used:   291599
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 3606698 Dshi_0129 (dihydroxy-acid dehydratase (RefSeq))
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.24388.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
     6e-208  677.7   3.8   6.9e-208  677.5   3.8    1.0  1  lcl|FitnessBrowser__Dino:3606698  Dshi_0129 dihydroxy-acid dehydra


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3606698  Dshi_0129 dihydroxy-acid dehydratase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  677.5   3.8  6.9e-208  6.9e-208       1     541 [.      24     563 ..      24     565 .. 0.99

  Alignments for each domain:
  == domain 1  score: 677.5 bits;  conditional E-value: 6.9e-208
                         TIGR00110   1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamgheGmkys 77 
                                       ++r+ ++a+G+++e++++P+++v+ +++e +P+++ l+  a++vk ++++a g++ ef ti+v+DGiamgheGm+ s
  lcl|FitnessBrowser__Dino:3606698  24 PHRSYYYAMGMTEEEIHQPLVGVATCWNEAAPCNIALSRQAQAVKMGVKQASGTPREFTTITVTDGIAMGHEGMRSS 100
                                       689************************************************************************** PP

                         TIGR00110  78 LpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktklsekidlvdvfeavge 154
                                       L+sre iaD+ve  +++h++Da+v ++ CDk +PGm+ma++rln+P+++++GG++ +g+++ +e++++ dvfeavg+
  lcl|FitnessBrowser__Dino:3606698 101 LASREAIADTVELTMRGHCYDAIVGLAGCDKSLPGMMMAMVRLNVPSVFIYGGSILPGRLN-GEDVTVQDVFEAVGK 176
                                       *************************************************************.9************** PP

                         TIGR00110 155 yaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllatsaekkelakksgkrivelvkkni 231
                                        +ag+ +++ele +er+acP+ag+C+G ftan+mac++ea+Gl+lP+s+ ++a  + + +  + sg+ +++l++k i
  lcl|FitnessBrowser__Dino:3606698 177 HQAGNYTDAELEVLERVACPSAGACGGQFTANTMACVSEAIGLALPNSAGAPAPYESRDQYGEASGRAVMDLIEKGI 253
                                       ***************************************************************************** PP

                         TIGR00110 232 kPrdiltkeafenaitldlalGGstntvLhllaiakeagvklslddfdrlsrkvPllaklkPsgkkviedlhraGGv 308
                                       + rdi+t++++ena  ++  +GGstn+ Lhl+aia+eag++++l+d+  + r +P  ++lkP+gk+v +d+ +aGGv
  lcl|FitnessBrowser__Dino:3606698 254 RARDIVTRKSLENAARIVACTGGSTNAGLHLPAIAHEAGIEFTLQDVCDIFRDTPYFVDLKPGGKYVAKDMYEAGGV 330
                                       ***************************************************************************** PP

                         TIGR00110 309 savlkeldkegllhkdaltvtGktlaetlekvkvlrvdqdvirsldnpvkkegglavLkGnlaeeGavvkiagveed 385
                                       + v++el ++gl+h+d++tvtG +++e+l+kv++  +d  vi ++d p++ +gg+  L Gnla+eGa+vkiag+++d
  lcl|FitnessBrowser__Dino:3606698 331 PVVMRELRRAGLIHEDCMTVTGYSIGEELDKVTLE-ADGRVIYPVDTPLSTTGGVVGLEGNLAPEGAIVKIAGMSDD 406
                                       *********************************99.8999************************************* PP

                         TIGR00110 386 ilkfeGpakvfeseeealeailggkvkeGdvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtr 462
                                        l+f+Gpa+vfe ee+a ea+ ++   eGdv vir eGP GgPGmremLa t+al+g G+gkkvaLitDGrfsG+tr
  lcl|FitnessBrowser__Dino:3606698 407 QLVFTGPARVFECEEDAFEAVQNRAYAEGDVFVIRNEGPAGGPGMREMLATTAALSGQGMGKKVALITDGRFSGATR 483
                                       ***************************************************************************** PP

                         TIGR00110 463 GlsiGhvsPeaaegGaialvedGDkikiDienrkldlevseeelaerrakakkkea.revkgaLakyaklvssadkG 538
                                       G+++Ghv Peaa+gG+ia+++dGD+i+iD+ + +l +++se+ela+r+++++ +++  + +gaL kya+lv +a  G
  lcl|FitnessBrowser__Dino:3606698 484 GFCVGHVGPEAAHGGPIAMLKDGDMITIDALKGELSVALSEDELAARKDAWSGPREtIYASGALWKYAQLVGGARLG 560
                                       ***************************************************977653799***************** PP

                         TIGR00110 539 avl 541
                                       av+
  lcl|FitnessBrowser__Dino:3606698 561 AVT 563
                                       *97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (577 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: 00:00:00.02
# Mc/sec: 11.69
//
[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