Alignments for a candidate for ilvD in Methanothermobacter thermautotrophicus Delta H

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Methanothermobacter thermautotrophicus Delta H

Align dihydroxy-acid dehydratase subunit (EC 4.2.1.9) (characterized)
to candidate WP_048061057.1 MTH_RS06930 dihydroxy-acid dehydratase

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



>NCBI__GCF_000008645.1:WP_048061057.1
          Length = 549

 Score = 1083 bits (2802), Expect = 0.0
 Identities = 547/549 (99%), Positives = 547/549 (99%)

Query: 1   MKSDTIKRGIQRAPHRSLLARCGLTDDDFEKPFIGIANSYTDIVPGHIHLRELAEAVKEG 60
           MKSDTIKRGIQRAPHRSLL  CGLTDDDFEKPFIGIANSYTDIVPGHIHLRELAEAVKEG
Sbjct: 1   MKSDTIKRGIQRAPHRSLLRACGLTDDDFEKPFIGIANSYTDIVPGHIHLRELAEAVKEG 60

Query: 61  VNAAGGVAFEFNTMAICDGIAMNHDGMKYSLASREIVADTVESMAMAHALDGLVLLPTCD 120
           VNAAGGVAFEFNTMAICDGIAMNHDGMKYSLASREIVADTVESMAMAHALDGLVLLPTCD
Sbjct: 61  VNAAGGVAFEFNTMAICDGIAMNHDGMKYSLASREIVADTVESMAMAHALDGLVLLPTCD 120

Query: 121 KIVPGMLMAAARLDIPAIVVTGGPMLPGEFKGRKVDLINVYEGVGTVSAGEMSEDELEEL 180
           KIVPGMLMAAARLDIPAIVVTGGPMLPGEFKGRKVDLINVYEGVGTVSAGEMSEDELEEL
Sbjct: 121 KIVPGMLMAAARLDIPAIVVTGGPMLPGEFKGRKVDLINVYEGVGTVSAGEMSEDELEEL 180

Query: 181 ERCACPGPRSCAGLFTANTMACLTEALGMSLPGCATAHAVSSRKRQIARLSGKRIVEMVQ 240
           ERCACPGPRSCAGLFTANTMACLTEALGMSLPGCATAHAVSSRKRQIARLSGKRIVEMVQ
Sbjct: 181 ERCACPGPRSCAGLFTANTMACLTEALGMSLPGCATAHAVSSRKRQIARLSGKRIVEMVQ 240

Query: 241 ENLKPTMIMSQEAFENAVMVDLALGGSTNTTLHIPAIAAEIDGLNINLDLFDELSRVIPH 300
           ENLKPTMIMSQEAFENAVMVDLALGGSTNTTLHIPAIAAEIDGLNINLDLFDELSRVIPH
Sbjct: 241 ENLKPTMIMSQEAFENAVMVDLALGGSTNTTLHIPAIAAEIDGLNINLDLFDELSRVIPH 300

Query: 301 IASISPAGEHMMLDLDRAGGIPAVLKTLEDHINRECVTCTGRTVQENIENVKVGHRDVIR 360
           IASISPAGEHMMLDLDRAGGIPAVLKTLEDHINRECVTCTGRTVQENIENVKVGHRDVIR
Sbjct: 301 IASISPAGEHMMLDLDRAGGIPAVLKTLEDHINRECVTCTGRTVQENIENVKVGHRDVIR 360

Query: 361 PLDSPVHSEGGLAILRGNLAPRGSVVKQGAVAEDMMVHEGPAKVFNSEDECMEAIFGGRI 420
           PLDSPVHSEGGLAILRGNLAPRGSVVKQGAVAEDMMVHEGPAKVFNSEDECMEAIFGGRI
Sbjct: 361 PLDSPVHSEGGLAILRGNLAPRGSVVKQGAVAEDMMVHEGPAKVFNSEDECMEAIFGGRI 420

Query: 421 DEGDVIVIRYEGPKGGPGMREMLNPTSAIAGMGLERVALITDGRFSGGTRGPCVGHVSPE 480
           DEGDVIVIRYEGPKGGPGMREMLNPTSAIAGMGLERVALITDGRFSGGTRGPCVGHVSPE
Sbjct: 421 DEGDVIVIRYEGPKGGPGMREMLNPTSAIAGMGLERVALITDGRFSGGTRGPCVGHVSPE 480

Query: 481 AMEDGPLAAVNDGDIIRIDIPSRKLEVDLSPREIEERLQSAVKPRRSVKGWLARYRKLAG 540
           AMEDGPLAAVNDGDIIRIDIPSRKLEVDLSPREIEERLQSAVKPRRSVKGWLARYRKLAG
Sbjct: 481 AMEDGPLAAVNDGDIIRIDIPSRKLEVDLSPREIEERLQSAVKPRRSVKGWLARYRKLAG 540

Query: 541 SADTGAVLR 549
           SADTGAVLR
Sbjct: 541 SADTGAVLR 549


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: 1318
Number of extensions: 31
Number of successful extensions: 1
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: 549
Length adjustment: 36
Effective length of query: 513
Effective length of database: 513
Effective search space:   263169
Effective search space used:   263169
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_048061057.1 MTH_RS06930 (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.19849.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     2e-271  887.2   4.8   2.3e-271  887.0   4.8    1.0  1  lcl|NCBI__GCF_000008645.1:WP_048061057.1  MTH_RS06930 dihydroxy-acid dehyd


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000008645.1:WP_048061057.1  MTH_RS06930 dihydroxy-acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  887.0   4.8  2.3e-271  2.3e-271       1     542 [.      14     549 .]      14     549 .] 1.00

  Alignments for each domain:
  == domain 1  score: 887.0 bits;  conditional E-value: 2.3e-271
                                 TIGR00110   1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiam 69 
                                               ++r+ll+a+Gl+d+d+ekP+i+++nsyt+ivPgh+hl++la++vke+++aaGgva+efnt+a++DGiam
  lcl|NCBI__GCF_000008645.1:WP_048061057.1  14 PHRSLLRACGLTDDDFEKPFIGIANSYTDIVPGHIHLRELAEAVKEGVNAAGGVAFEFNTMAICDGIAM 82 
                                               69******************************************************************* PP

                                 TIGR00110  70 gheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktk 138
                                               +h+GmkysL+srei+aD+ve++++ahalD+lv++++CDkivPGmlmaa+rl+iPaivv+GGpm +g++k
  lcl|NCBI__GCF_000008645.1:WP_048061057.1  83 NHDGMKYSLASREIVADTVESMAMAHALDGLVLLPTCDKIVPGMLMAAARLDIPAIVVTGGPMLPGEFK 151
                                               ********************************************************************* PP

                                 TIGR00110 139 lsekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstlla 207
                                                ++k+dl++v+e+vg+++ag++se+elee+er+acP+++sC+Glftan+macltealG+slPg++t++a
  lcl|NCBI__GCF_000008645.1:WP_048061057.1 152 -GRKVDLINVYEGVGTVSAGEMSEDELEELERCACPGPRSCAGLFTANTMACLTEALGMSLPGCATAHA 219
                                               .9******************************************************************* PP

                                 TIGR00110 208 tsaekkelakksgkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeag.vklsl 275
                                               +s++k+++a+ sgkrive+v++n+kP++i+++eafena+++dlalGGstnt+Lh++aia+e++ ++++l
  lcl|NCBI__GCF_000008645.1:WP_048061057.1 220 VSSRKRQIARLSGKRIVEMVQENLKPTMIMSQEAFENAVMVDLALGGSTNTTLHIPAIAAEIDgLNINL 288
                                               **************************************************************99***** PP

                                 TIGR00110 276 ddfdrlsrkvPllaklkPsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlr 344
                                               d fd+lsr +P++a+++P+g++++ dl+raGG++avlk+l  e++++++++t+tG+t++e++e+vkv  
  lcl|NCBI__GCF_000008645.1:WP_048061057.1 289 DLFDELSRVIPHIASISPAGEHMMLDLDRAGGIPAVLKTL--EDHINRECVTCTGRTVQENIENVKVG- 354
                                               ****************************************..**************************. PP

                                 TIGR00110 345 vdqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvke 413
                                                ++dvir+ld+pv++eggla+L+Gnla++G+vvk+++v+ed++++eGpakvf+se+e++eai+gg+++e
  lcl|NCBI__GCF_000008645.1:WP_048061057.1 355 -HRDVIRPLDSPVHSEGGLAILRGNLAPRGSVVKQGAVAEDMMVHEGPAKVFNSEDECMEAIFGGRIDE 422
                                               .******************************************************************** PP

                                 TIGR00110 414 GdvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialv 482
                                               Gdv+viryeGPkGgPGmremL+Ptsa++g+GL++ vaLitDGrfsGgtrG+++GhvsPea+e+G++a v
  lcl|NCBI__GCF_000008645.1:WP_048061057.1 423 GDVIVIRYEGPKGGPGMREMLNPTSAIAGMGLER-VALITDGRFSGGTRGPCVGHVSPEAMEDGPLAAV 490
                                               *********************************9.********************************** PP

                                 TIGR00110 483 edGDkikiDienrkldlevseeelaerrakakkkearevkgaLakyaklvssadkGavld 542
                                               +dGD+i+iDi++rkl++++s +e++er ++a+k++ r+vkg+La+y+kl+ sad+Gavl+
  lcl|NCBI__GCF_000008645.1:WP_048061057.1 491 NDGDIIRIDIPSRKLEVDLSPREIEERLQSAVKPR-RSVKGWLARYRKLAGSADTGAVLR 549
                                               ********************************999.9*********************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (549 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: 00:00:00.03
# Mc/sec: 7.91
//
[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