Alignments for a candidate for ilvD in Haloferax volcanii DS2

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Haloferax volcanii DS2

Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate WP_004042767.1 C498_RS08250 dihydroxy-acid dehydratase

Query= SwissProt::P9WKJ5
         (575 letters)



>NCBI__GCF_000337315.1:WP_004042767.1
          Length = 584

 Score =  561 bits (1446), Expect = e-164
 Identities = 295/575 (51%), Positives = 391/575 (68%), Gaps = 8/575 (1%)

Query: 2   PQTTDEAASVSTVADIKPRSRDVTDGLEKAAARGMLRAVGMDDEDFAKPQIGVASSWNEI 61
           P+  D     S+  D   RS +VT+G +KA  R M RA+G DDEDF+ P +GV +   +I
Sbjct: 6   PREEDPDDVFSSGKDPNLRSTEVTEGPDKAPHRAMFRAMGFDDEDFSSPMVGVPNPAADI 65

Query: 62  TPCNLSLDRLANAVKEGVFSAGGYPLEFGTISVSDGISMGHEGMHFSLVSREVIADSVEV 121
           TPCN+ LD +A+A  EG+ +AGG P+EFGT+++SD ISMG EGM  SL+SREVIADSVE+
Sbjct: 66  TPCNVHLDDVADAAIEGIDAAGGMPIEFGTVTISDAISMGTEGMKASLISREVIADSVEL 125

Query: 122 VMQAERLDGSVLLAGCDKSLPGMLMAAARLDLAAVFLYAGSILPGRAKLSDGSERDVTII 181
           V   ER+D  V +AGCDK+LPGM+MAA R DL +VFLY GSI+PG+ +      R+VT+ 
Sbjct: 126 VSFGERMDALVTVAGCDKNLPGMMMAAIRTDLPSVFLYGGSIMPGQHE-----GREVTVQ 180

Query: 182 DAFEAVGACSRGLMSRADVDAIERAICPGEGACGGMYTANTMASAAEALGMSLPGSAAPP 241
           + FE VG  + G MS  ++D +ER  CPG G+CGGM+TANTMAS +EALGM+  GSA+ P
Sbjct: 181 NVFEGVGTYAEGDMSADELDDLERHACPGAGSCGGMFTANTMASISEALGMAPLGSASAP 240

Query: 242 ATDRRRDGFARRSGQAVVELLRRGITARDILTKEAFENAIAVVMAFGGSTNAVLHLLAIA 301
           A    R   ARR+G+ V++ +       DILTK++FENAI + +A GGSTNAVLHLLA+A
Sbjct: 241 AESDERYENARRAGEVVLDCVENDRRPSDILTKKSFENAITLQVATGGSTNAVLHLLALA 300

Query: 302 HEANVALSLQDFSRIGSGVPHLADVKPFGRHVMSDVDHIGGVPVVMKALLDAGLLHGDCL 361
            EA V L +++F+ I    P +A+++P G  VM+D+  IGG+PVV++ L++AGL HGD +
Sbjct: 301 AEAGVDLDIEEFNEISRRTPKIANLQPGGTRVMNDLHEIGGIPVVIRRLVEAGLFHGDAM 360

Query: 362 TVTGHTMAENLAAITPPDPDG---KVLRALANPIHPSGGITILHGSLAPEGAVVKTAGFD 418
           TVTG T+AE L  +  PD DG     L  +  P    G I IL G+LAP+GAV+K  G D
Sbjct: 361 TVTGRTIAEELDHLDLPDDDGLEADFLYTVDEPYQDEGAIKILTGNLAPDGAVLKVTGDD 420

Query: 419 SDVFEGTARVFDGERAALDALEDGTITVGDAVVIRYEGPKGGPGMREMLAITGAIKGAGL 478
           +    G ARVF+ E  A+  +++G I  GD + IR EGP+GGPGMREML +T A+ G G 
Sbjct: 421 AFHHTGPARVFENEEDAMRYVQEGHIEEGDVIAIRNEGPRGGPGMREMLGVTAAVVGQGH 480

Query: 479 GKDVLLLTDGRFSGGTTGLCVGHIAPEAVDGGPIALLRNGDRIRLDVAGRVLDVLADPAE 538
             DV LLTDGRFSG T G  VGH+APEA +GGPI LL +GD + +D+  R L V     E
Sbjct: 481 EDDVALLTDGRFSGATRGPMVGHVAPEAAEGGPIGLLEDGDEVTVDIPNRELSVDLSDEE 540

Query: 539 FASRQQDFSPPPPRYTTGVLSKYVKLVSSAAVGAV 573
             +R++D+ P PP YT+GVL+KY +   SAA GAV
Sbjct: 541 LEARKEDWEPKPPAYTSGVLAKYARDFGSAANGAV 575


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: 1066
Number of extensions: 54
Number of successful extensions: 5
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: 584
Length adjustment: 36
Effective length of query: 539
Effective length of database: 548
Effective search space:   295372
Effective search space used:   295372
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_004042767.1 C498_RS08250 (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.2144531.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.2e-217  707.9   2.4   4.9e-217  707.7   2.4    1.0  1  NCBI__GCF_000337315.1:WP_004042767.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000337315.1:WP_004042767.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  707.7   2.4  4.9e-217  4.9e-217       1     541 [.      36     576 ..      36     578 .. 0.99

  Alignments for each domain:
  == domain 1  score: 707.7 bits;  conditional E-value: 4.9e-217
                             TIGR00110   1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamgheG 73 
                                           ++ra+++a+G+ ded++ P+++v n   +i+P++vhl+d+a+++ e+i+aaGg++ ef+t+++sD i+mg+eG
  NCBI__GCF_000337315.1:WP_004042767.1  36 PHRAMFRAMGFDDEDFSSPMVGVPNPAADITPCNVHLDDVADAAIEGIDAAGGMPIEFGTVTISDAISMGTEG 108
                                           69*********************************************************************** PP

                             TIGR00110  74 mkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktklsekidlv 146
                                           mk sL sre+iaDsve v  ++++Dalv+++ CDk++PGm+maa+r+++P+++ +GG++++g+ + ++++++ 
  NCBI__GCF_000337315.1:WP_004042767.1 109 MKASLISREVIADSVELVSFGERMDALVTVAGCDKNLPGMMMAAIRTDLPSVFLYGGSIMPGQHE-GREVTVQ 180
                                           *****************************************************************.9****** PP

                             TIGR00110 147 dvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllatsaekkelakks 219
                                           +vfe+vg+ya+g++s +el+++er+acP+agsC+G+ftan+ma+++ealG++  gs++++a s e+ e a+++
  NCBI__GCF_000337315.1:WP_004042767.1 181 NVFEGVGTYAEGDMSADELDDLERHACPGAGSCGGMFTANTMASISEALGMAPLGSASAPAESDERYENARRA 253
                                           ************************************************************************* PP

                             TIGR00110 220 gkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklslddfdrlsrkvPllaklk 292
                                           g+ + + v+++ +P+diltk++fenaitl++a+GGstn+vLhlla+a+eagv+l++++f+++sr++P++a+l+
  NCBI__GCF_000337315.1:WP_004042767.1 254 GEVVLDCVENDRRPSDILTKKSFENAITLQVATGGSTNAVLHLLALAAEAGVDLDIEEFNEISRRTPKIANLQ 326
                                           ************************************************************************* PP

                             TIGR00110 293 PsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlr...vdqdvirsldnpvkkegg 362
                                           P+g +v++dlh+ GG++ v++ l ++gl+h da+tvtG+t+ae+l++ ++     ++ d + ++d+p+++eg 
  NCBI__GCF_000337315.1:WP_004042767.1 327 PGGTRVMNDLHEIGGIPVVIRRLVEAGLFHGDAMTVTGRTIAEELDHLDLPDddgLEADFLYTVDEPYQDEGA 399
                                           ***********************************************998754446678************** PP

                             TIGR00110 363 lavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeGdvvviryeGPkGgPGmremLa 435
                                           +++L+Gnla++Gav k++g +    +++Gpa+vfe+ee+a+  + +g+++eGdv+ ir eGP+GgPGmremL 
  NCBI__GCF_000337315.1:WP_004042767.1 400 IKILTGNLAPDGAVLKVTGDDA--FHHTGPARVFENEEDAMRYVQEGHIEEGDVIAIRNEGPRGGPGMREMLG 470
                                           *******************988..************************************************* PP

                             TIGR00110 436 PtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDienrkldlevseeelae 508
                                            t+a+vg G +++vaL+tDGrfsG+trG+++Ghv+PeaaegG+i+l+edGD++++Di+nr+l +++s+eel++
  NCBI__GCF_000337315.1:WP_004042767.1 471 VTAAVVGQGHEDDVALLTDGRFSGATRGPMVGHVAPEAAEGGPIGLLEDGDEVTVDIPNRELSVDLSDEELEA 543
                                           ************************************************************************* PP

                             TIGR00110 509 rrakakkkearevkgaLakyaklvssadkGavl 541
                                           r++++++k + +++g+Lakya+   sa +Gav+
  NCBI__GCF_000337315.1:WP_004042767.1 544 RKEDWEPKPPAYTSGVLAKYARDFGSAANGAVT 576
                                           *******************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (584 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 23.23
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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