Alignments for a candidate for ilvD in Pseudarthrobacter sulfonivorans Ar51

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Pseudarthrobacter sulfonivorans Ar51

Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate WP_058932073.1 AU252_RS19105 dihydroxy-acid dehydratase

Query= SwissProt::P9WKJ5
         (575 letters)



>NCBI__GCF_001484605.1:WP_058932073.1
          Length = 573

 Score =  885 bits (2286), Expect = 0.0
 Identities = 439/570 (77%), Positives = 496/570 (87%)

Query: 6   DEAASVSTVADIKPRSRDVTDGLEKAAARGMLRAVGMDDEDFAKPQIGVASSWNEITPCN 65
           D   +     DIKPRSR VTDG+  A ARGM RAVGM D+DFAKPQIGVASSWNEITPCN
Sbjct: 4   DTQTATENKIDIKPRSRVVTDGIHAAPARGMFRAVGMGDDDFAKPQIGVASSWNEITPCN 63

Query: 66  LSLDRLANAVKEGVFSAGGYPLEFGTISVSDGISMGHEGMHFSLVSREVIADSVEVVMQA 125
           LSL+RLA   KEGV + GG+P++FGTISVSDGISMGHEGMHFSLVSREVIADSVE VMQA
Sbjct: 64  LSLNRLAQGAKEGVHAGGGFPMQFGTISVSDGISMGHEGMHFSLVSREVIADSVETVMQA 123

Query: 126 ERLDGSVLLAGCDKSLPGMLMAAARLDLAAVFLYAGSILPGRAKLSDGSERDVTIIDAFE 185
           ER+DGSVLLAGCDKSLPGMLMAAARLDLA+VFLYAGSI+PG  KL DGSE++VT+IDAFE
Sbjct: 124 ERIDGSVLLAGCDKSLPGMLMAAARLDLASVFLYAGSIMPGWVKLEDGSEKEVTLIDAFE 183

Query: 186 AVGACSRGLMSRADVDAIERAICPGEGACGGMYTANTMASAAEALGMSLPGSAAPPATDR 245
           AVGAC+ G MS  D+  IE+AICPGEGACGGMYTANTMA   EALGMSLPGSAAPP+ DR
Sbjct: 184 AVGACAAGKMSLEDLTRIEKAICPGEGACGGMYTANTMACIGEALGMSLPGSAAPPSADR 243

Query: 246 RRDGFARRSGQAVVELLRRGITARDILTKEAFENAIAVVMAFGGSTNAVLHLLAIAHEAN 305
           RRD FAR+SG+AVV LLR GITARDI+TK+AFENAIAV MAFGGSTNAVLHLLAIA EA 
Sbjct: 244 RRDEFARKSGEAVVNLLRLGITARDIMTKKAFENAIAVTMAFGGSTNAVLHLLAIAREAE 303

Query: 306 VALSLQDFSRIGSGVPHLADVKPFGRHVMSDVDHIGGVPVVMKALLDAGLLHGDCLTVTG 365
           V L+L+DF+RIG  +PHL D+KPFGR+VM+DVD IGGVPV+M+ALLDAGLLHGDCLTVTG
Sbjct: 304 VELNLEDFNRIGDKIPHLGDLKPFGRYVMTDVDKIGGVPVIMRALLDAGLLHGDCLTVTG 363

Query: 366 HTMAENLAAITPPDPDGKVLRALANPIHPSGGITILHGSLAPEGAVVKTAGFDSDVFEGT 425
            T+AENLAAI PPD DGK+LRA+ NPIH +GGITILHG++APEGAVVK+AGFD+DVFEGT
Sbjct: 364 KTVAENLAAINPPDLDGKILRAMDNPIHKTGGITILHGTMAPEGAVVKSAGFDADVFEGT 423

Query: 426 ARVFDGERAALDALEDGTITVGDAVVIRYEGPKGGPGMREMLAITGAIKGAGLGKDVLLL 485
           ARVF+ E+ AL AL++G I  GD VVIRYEGPKGGPGMREMLAITGAIKGAGLGKDVLLL
Sbjct: 424 ARVFEREQGALAALDEGLIKAGDVVVIRYEGPKGGPGMREMLAITGAIKGAGLGKDVLLL 483

Query: 486 TDGRFSGGTTGLCVGHIAPEAVDGGPIALLRNGDRIRLDVAGRVLDVLADPAEFASRQQD 545
           TDGRFSGGTTGLC+GH+APEAVDGGPIA +++GDRIR+D+A R  D+L D AE  SR+  
Sbjct: 484 TDGRFSGGTTGLCIGHVAPEAVDGGPIAFVKDGDRIRVDIAARSFDLLVDEAELESRKIG 543

Query: 546 FSPPPPRYTTGVLSKYVKLVSSAAVGAVCG 575
           + P P ++T GVL+KY KLV SA+ GA CG
Sbjct: 544 WEPLPAKFTKGVLAKYAKLVHSASTGAYCG 573


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: 1194
Number of extensions: 40
Number of successful extensions: 2
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 WP_058932073.1 AU252_RS19105 (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.22051.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-222  724.3   4.1   5.4e-222  724.0   4.1    1.0  1  lcl|NCBI__GCF_001484605.1:WP_058932073.1  AU252_RS19105 dihydroxy-acid deh


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001484605.1:WP_058932073.1  AU252_RS19105 dihydroxy-acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  724.0   4.1  5.4e-222  5.4e-222       2     539 ..      31     570 ..      30     572 .. 0.99

  Alignments for each domain:
  == domain 1  score: 724.0 bits;  conditional E-value: 5.4e-222
                                 TIGR00110   2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamg 70 
                                               ar +++a+G+ d+d+ kP+i+v++s++ei+P++++l+ la+ +ke+++a Gg +++f+ti+vsDGi+mg
  lcl|NCBI__GCF_001484605.1:WP_058932073.1  31 ARGMFRAVGMGDDDFAKPQIGVASSWNEITPCNLSLNRLAQGAKEGVHAGGGFPMQFGTISVSDGISMG 99 
                                               799****************************************************************** PP

                                 TIGR00110  71 heGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktkl 139
                                               heGm++sL+sre+iaDsvetv++a+++D+ v+++ CDk +PGmlmaa+rl++ +++ + G++++g +kl
  lcl|NCBI__GCF_001484605.1:WP_058932073.1 100 HEGMHFSLVSREVIADSVETVMQAERIDGSVLLAGCDKSLPGMLMAAARLDLASVFLYAGSIMPGWVKL 168
                                               ******************************************************************999 PP

                                 TIGR00110 140 ....sekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsst 204
                                                    ++++l+d+feavg++aagk+s e+l++ie+  cP+ g+C+G++tan+mac+ ealG+slPgs++
  lcl|NCBI__GCF_001484605.1:WP_058932073.1 169 edgsEKEVTLIDAFEAVGACAAGKMSLEDLTRIEKAICPGEGACGGMYTANTMACIGEALGMSLPGSAA 237
                                               8876789************************************************************** PP

                                 TIGR00110 205 llatsaekkelakksgkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvkl 273
                                                ++++ ++ e+a+ksg+ +v+l++  i+ rdi+tk+afenai++ +a GGstn+vLhllaia+ea+v+l
  lcl|NCBI__GCF_001484605.1:WP_058932073.1 238 PPSADRRRDEFARKSGEAVVNLLRLGITARDIMTKKAFENAIAVTMAFGGSTNAVLHLLAIAREAEVEL 306
                                               ********************************************************************* PP

                                 TIGR00110 274 slddfdrlsrkvPllaklkPsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkv 342
                                               +l+df+r+ +k+P+l++lkP g++v++d+++ GGv+ +++ l  +gllh d+ltvtGkt+ae+l+ ++ 
  lcl|NCBI__GCF_001484605.1:WP_058932073.1 307 NLEDFNRIGDKIPHLGDLKPFGRYVMTDVDKIGGVPVIMRALLDAGLLHGDCLTVTGKTVAENLAAINP 375
                                               ********************************************************************* PP

                                 TIGR00110 343 lrvdqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkv 411
                                                 +d +++r++dnp++k+gg+ +L+G +a+eGavvk ag +    +feG+a+vfe e+ al+a+ +g +
  lcl|NCBI__GCF_001484605.1:WP_058932073.1 376 PDLDGKILRAMDNPIHKTGGITILHGTMAPEGAVVKSAGFDA--DVFEGTARVFEREQGALAALDEGLI 442
                                               *99**************************************9..679********************** PP

                                 TIGR00110 412 keGdvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaia 480
                                               k+GdvvviryeGPkGgPGmremLa t a++g+GLgk+v L+tDGrfsGgt+Gl+iGhv+Pea+ gG+ia
  lcl|NCBI__GCF_001484605.1:WP_058932073.1 443 KAGDVVVIRYEGPKGGPGMREMLAITGAIKGAGLGKDVLLLTDGRFSGGTTGLCIGHVAPEAVDGGPIA 511
                                               ********************************************************************* PP

                                 TIGR00110 481 lvedGDkikiDienrkldlevseeelaerrakakkkearevkgaLakyaklvssadkGa 539
                                               +v+dGD+i++Di +r +dl v+e+el++r+  +++  a+ +kg+Lakyaklv sa++Ga
  lcl|NCBI__GCF_001484605.1:WP_058932073.1 512 FVKDGDRIRVDIAARSFDLLVDEAELESRKIGWEPLPAKFTKGVLAKYAKLVHSASTGA 570
                                               **********************************************************9 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 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 10.98
//
[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