Alignments for a candidate for ilvD in Desulfatiglans anilini DSM 4660

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Desulfatiglans anilini DSM 4660

Align dihydroxy-acid dehydratase subunit (EC 4.2.1.9) (characterized)
to candidate WP_028320187.1 H567_RS0102530 dihydroxy-acid dehydratase

Query= metacyc::MONOMER-11919
         (549 letters)



>NCBI__GCF_000422285.1:WP_028320187.1
          Length = 558

 Score =  599 bits (1545), Expect = e-176
 Identities = 308/552 (55%), Positives = 403/552 (73%), Gaps = 7/552 (1%)

Query: 2   KSDTIKRGIQRAPHRSLLARCGLTDDDFEKPFIGIANSYTDIVPGHIHLRELAEAVKEGV 61
           +SD + +G +RAPHRSLL   G  D + E+P IGIANS+ +I+PGHIHL  L +AVK G+
Sbjct: 5   RSDLMLQGAERAPHRSLLRADGFCDWEMERPIIGIANSFNEIIPGHIHLDRLVDAVKAGI 64

Query: 62  NAAGGVAFEFNTMAICDGIAMNHDGMKYSLASREIVADTVESMAMAHALDGLVLLPTCDK 121
            AAGG    FNT+ +CDGIAMNH+GMKYSL SRE++AD+VE MAMAH  DGLVLL +CDK
Sbjct: 65  YAAGGTPMVFNTIGVCDGIAMNHEGMKYSLPSRELIADSVEIMAMAHPFDGLVLLASCDK 124

Query: 122 IVPGMLMAAARLDIPAIVVTGGPMLPGEFKGRKVDLINVYEGVGTVSAGEMSEDELEELE 181
           I+PGML+AAARL+IPAI ++GGPMLPG   GR++ L  V+E VG + +G ++ ++L   E
Sbjct: 125 IIPGMLIAAARLNIPAIFLSGGPMLPGRVAGREMGLDKVFEAVGALKSGRITSEDLHSYE 184

Query: 182 RCACPGPRSCAGLFTANTMACLTEALGMSLPGCATAHAVSSRKRQIARLSGKRIVEMVQE 241
             ACPG  SC+G+FTANTM+ L+EALGMSLP   +A AV S +  +A+ +G + VE+V+ 
Sbjct: 185 CGACPGAGSCSGMFTANTMSNLSEALGMSLPYNGSAPAVYSDRVHLAKETGMKAVELVRS 244

Query: 242 NLKPTMIMSQEAFENAVMVDLALGGSTNTTLHIPAIAAEIDGLNINLDLFDELSRVIPHI 301
           NL+P  IM++EAF NA+  D+ALGGSTNT LH+PAIA   D +++ L  FD  +  IPH+
Sbjct: 245 NLRPRDIMTREAFGNAIAADMALGGSTNTALHLPAIAYYAD-VDLTLKDFDPYTARIPHL 303

Query: 302 ASISPAGEHMMLDLDRAGGIPAVLKTLEDH--INRECVTCTGRTVQENIENVKVGHRD-- 357
            S++PAG H ++DL  AGG+PA+L  L     I+ E  T  G  + E +E +  G RD  
Sbjct: 304 TSMAPAGPHHIIDLYHAGGVPAILAELGQAGLIDLETRTVYGTRLGEMLERIGAGIRDTK 363

Query: 358 VIRPLDSPVHSEGGLAILRGNLAPRGSVVKQGAVAEDMMVHEGPAKVFNSEDECMEAIFG 417
           VIRP+  PVHS GGLA+L GNLAP G++VKQ AVA +M+ H GPA++F+SE++ + AI G
Sbjct: 364 VIRPVKDPVHSTGGLAVLTGNLAPEGAIVKQAAVAPEMLQHRGPARIFSSEEDAVAAITG 423

Query: 418 GRIDEGDVIVIRYEGPKGGPGMREMLNPTSAIAGMGLER-VALITDGRFSGGTRGPCVGH 476
           GRI +GDV+VIRYEGP+GGPGMREML+PTS +AGMG+++ VALITDGRFSG TRG  +GH
Sbjct: 424 GRIQKGDVLVIRYEGPRGGPGMREMLSPTSVLAGMGMDKDVALITDGRFSGATRGSSIGH 483

Query: 477 VSPEAMEDGPLAAVNDGDIIRIDIPSRKLEVDLSPREIEERLQSAVKPRRSVK-GWLARY 535
           VSPEA   GP+AAV +GD I IDIP + L ++LS   I ERL         V+ G+L RY
Sbjct: 484 VSPEAAAGGPIAAVEEGDTIEIDIPGKSLRLNLSDEAIAERLSRLPAFEPKVRHGYLGRY 543

Query: 536 RKLAGSADTGAV 547
            ++  SAD GAV
Sbjct: 544 ARMVSSADKGAV 555


Lambda     K      H
   0.319    0.136    0.397 

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: 1046
Number of extensions: 46
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: 549
Length of database: 558
Length adjustment: 36
Effective length of query: 513
Effective length of database: 522
Effective search space:   267786
Effective search space used:   267786
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)

Align candidate WP_028320187.1 H567_RS0102530 (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.24241.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.4e-237  775.4   0.6   1.6e-237  775.3   0.6    1.0  1  lcl|NCBI__GCF_000422285.1:WP_028320187.1  H567_RS0102530 dihydroxy-acid de


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000422285.1:WP_028320187.1  H567_RS0102530 dihydroxy-acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  775.3   0.6  1.6e-237  1.6e-237       1     542 [.      17     557 ..      17     558 .] 1.00

  Alignments for each domain:
  == domain 1  score: 775.3 bits;  conditional E-value: 1.6e-237
                                 TIGR00110   1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiam 69 
                                               ++r+ll+a G+ d ++e+Pii+++ns++ei+Pgh+hl+ l ++vk++i+aaGg+++ fnti+v+DGiam
  lcl|NCBI__GCF_000422285.1:WP_028320187.1  17 PHRSLLRADGFCDWEMERPIIGIANSFNEIIPGHIHLDRLVDAVKAGIYAAGGTPMVFNTIGVCDGIAM 85 
                                               69******************************************************************* PP

                                 TIGR00110  70 gheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktk 138
                                               +heGmkysLpsre+iaDsve +++ah +D+lv+++sCDki+PGml+aa+rlniPai+ sGGpm +g+++
  lcl|NCBI__GCF_000422285.1:WP_028320187.1  86 NHEGMKYSLPSRELIADSVEIMAMAHPFDGLVLLASCDKIIPGMLIAAARLNIPAIFLSGGPMLPGRVA 154
                                               ********************************************************************* PP

                                 TIGR00110 139 lsekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstlla 207
                                                ++++ l +vfeavg+ ++g+++ e+l+++e  acP+agsCsG+ftan+m+ l+ealG+slP++++++a
  lcl|NCBI__GCF_000422285.1:WP_028320187.1 155 -GREMGLDKVFEAVGALKSGRITSEDLHSYECGACPGAGSCSGMFTANTMSNLSEALGMSLPYNGSAPA 222
                                               .9******************************************************************* PP

                                 TIGR00110 208 tsaekkelakksgkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklsld 276
                                               + +++ +lak++g++ velv+ n++Prdi+t+eaf nai+ d+alGGstnt Lhl+aia  a+v+l+l+
  lcl|NCBI__GCF_000422285.1:WP_028320187.1 223 VYSDRVHLAKETGMKAVELVRSNLRPRDIMTREAFGNAIAADMALGGSTNTALHLPAIAYYADVDLTLK 291
                                               ********************************************************************* PP

                                 TIGR00110 277 dfdrlsrkvPllaklkPsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlrv 345
                                               dfd  + ++P+l++++P+g + i+dl +aGGv+a+l el ++gl++ ++ tv G+ l+e+le++     
  lcl|NCBI__GCF_000422285.1:WP_028320187.1 292 DFDPYTARIPHLTSMAPAGPHHIIDLYHAGGVPAILAELGQAGLIDLETRTVYGTRLGEMLERIGAGIR 360
                                               *******************************************************************9* PP

                                 TIGR00110 346 dqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeG 414
                                               d++vir++++pv+++gglavL+Gnla+eGa+vk+a+v+ ++l+++Gpa++f see+a++ai gg++++G
  lcl|NCBI__GCF_000422285.1:WP_028320187.1 361 DTKVIRPVKDPVHSTGGLAVLTGNLAPEGAIVKQAAVAPEMLQHRGPARIFSSEEDAVAAITGGRIQKG 429
                                               ********************************************************************* PP

                                 TIGR00110 415 dvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialve 483
                                               dv+viryeGP+GgPGmremL Pts+l+g+G++k+vaLitDGrfsG+trG siGhvsPeaa+gG+ia ve
  lcl|NCBI__GCF_000422285.1:WP_028320187.1 430 DVLVIRYEGPRGGPGMREMLSPTSVLAGMGMDKDVALITDGRFSGATRGSSIGHVSPEAAAGGPIAAVE 498
                                               ********************************************************************* PP

                                 TIGR00110 484 dGDkikiDienrkldlevseeelaerrakakkkearevkgaLakyaklvssadkGavld 542
                                               +GD+i+iDi+ + l l++s+e +aer  +  + e++  +g+L +ya++vssadkGav +
  lcl|NCBI__GCF_000422285.1:WP_028320187.1 499 EGDTIEIDIPGKSLRLNLSDEAIAERLSRLPAFEPKVRHGYLGRYARMVSSADKGAVFE 557
                                               ********************************************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (558 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: 12.20
//
[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