Alignments for a candidate for ilvD in Methanobacterium lacus AL-21

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Methanobacterium lacus AL-21

Align dihydroxy-acid dehydratase subunit (EC 4.2.1.9) (characterized)
to candidate WP_013643691.1 METBO_RS00425 dihydroxy-acid dehydratase

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



>NCBI__GCF_000191585.1:WP_013643691.1
          Length = 551

 Score =  825 bits (2131), Expect = 0.0
 Identities = 396/551 (71%), Positives = 480/551 (87%), Gaps = 2/551 (0%)

Query: 1   MKSDTIKRGIQRAPHRSLLARCGLTDDDFEKPFIGIANSYTDIVPGHIHLRELAEAVKEG 60
           M+SDTIK+G+ RAPHRSLL  CGL D D +KPFIGIANSYTDIVPGH+HL  +A+ VK+ 
Sbjct: 1   MRSDTIKKGLHRAPHRSLLRACGLNDADMKKPFIGIANSYTDIVPGHVHLNSIADTVKQS 60

Query: 61  VNAAGGVAFEFNTMAICDGIAMNHDGMKYSLASREIVADTVESMAMAHALDGLVLLPTCD 120
           +  AGG+ FEFNTMAICDGIAMNH+GMKYSLASREIVADTVESMAMAH  DGLVL+PTCD
Sbjct: 61  IAEAGGLGFEFNTMAICDGIAMNHEGMKYSLASREIVADTVESMAMAHQFDGLVLIPTCD 120

Query: 121 KIVPGMLMAAARLDIPAIVVTGGPMLPGEFKGRKVDLINVYEGVGTVSAGEMSEDELEEL 180
           KIVPGMLMAAARLDIPAIVVTGGPMLPG++KG+ VDLI+VYE VG VS+G+M+E+E++EL
Sbjct: 121 KIVPGMLMAAARLDIPAIVVTGGPMLPGKYKGKNVDLISVYEAVGAVSSGKMTEEEIDEL 180

Query: 181 ERCACPGPRSCAGLFTANTMACLTEALGMSLPGCATAHAVSSRKRQIARLSGKRIVEMVQ 240
           ERCACPGP SC+GLFTANTMAC+TEA+GMSLP CATAHAV  +K  IA  SGK+I+E+V+
Sbjct: 181 ERCACPGPGSCSGLFTANTMACITEAIGMSLPYCATAHAVDKKKLSIASDSGKKILELVE 240

Query: 241 ENLKPTMIMSQEAFENAVMVDLALGGSTNTTLHIPAIAAEID--GLNINLDLFDELSRVI 298
           +N+ P+ IM+Q+AF+NA+ VD+ALGGS+NT LH+PAIA E++  G+ ++LDLF+++S+ I
Sbjct: 241 KNITPSKIMTQQAFKNAIAVDMALGGSSNTALHVPAIAFELEEQGVKVDLDLFNDMSKEI 300

Query: 299 PHIASISPAGEHMMLDLDRAGGIPAVLKTLEDHINRECVTCTGRTVQENIENVKVGHRDV 358
           PHI  +SPAGEH MLDLD+AGGIPAVLK +E+ ++   +TCTG+++ ENI   +V   +V
Sbjct: 301 PHITHLSPAGEHTMLDLDKAGGIPAVLKVIEEKLDITTITCTGKSLGENIAEARVLDGNV 360

Query: 359 IRPLDSPVHSEGGLAILRGNLAPRGSVVKQGAVAEDMMVHEGPAKVFNSEDECMEAIFGG 418
           I  L+ P+H EGG+A+L+GNLAP GSVVKQGAV EDMMVHEGPAKVF+SE+EC+EAIF G
Sbjct: 361 IHTLEDPIHVEGGIAVLKGNLAPNGSVVKQGAVKEDMMVHEGPAKVFDSEEECVEAIFDG 420

Query: 419 RIDEGDVIVIRYEGPKGGPGMREMLNPTSAIAGMGLERVALITDGRFSGGTRGPCVGHVS 478
           +IDEGDVIVIRYEGPKGGPGMREMLNPTSAI+GM ++ VALITDGRFSGGTRGP +GH+S
Sbjct: 421 KIDEGDVIVIRYEGPKGGPGMREMLNPTSAISGMEIKSVALITDGRFSGGTRGPSIGHIS 480

Query: 479 PEAMEDGPLAAVNDGDIIRIDIPSRKLEVDLSPREIEERLQSAVKPRRSVKGWLARYRKL 538
           PEAM DGPLAAVN+GDII+IDIP+RKLE+ +   EI+ER++ A KP R VKGWLARYRKL
Sbjct: 481 PEAMADGPLAAVNNGDIIKIDIPNRKLELKVPESEIKERIKVADKPERPVKGWLARYRKL 540

Query: 539 AGSADTGAVLR 549
           A SAD GA+LR
Sbjct: 541 ATSADEGAILR 551


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: 1161
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: 549
Length of database: 551
Length adjustment: 36
Effective length of query: 513
Effective length of database: 515
Effective search space:   264195
Effective search space used:   264195
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_013643691.1 METBO_RS00425 (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.21043.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.3e-255  833.0  10.5     6e-255  832.8  10.5    1.0  1  lcl|NCBI__GCF_000191585.1:WP_013643691.1  METBO_RS00425 dihydroxy-acid deh


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000191585.1:WP_013643691.1  METBO_RS00425 dihydroxy-acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  832.8  10.5    6e-255    6e-255       1     542 [.      14     551 .]      14     551 .] 0.99

  Alignments for each domain:
  == domain 1  score: 832.8 bits;  conditional E-value: 6e-255
                                 TIGR00110   1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiam 69 
                                               ++r+ll+a+Gl+d+d++kP+i+++nsyt+ivPghvhl+ +a++vk++i +aGg  +efnt+a++DGiam
  lcl|NCBI__GCF_000191585.1:WP_013643691.1  14 PHRSLLRACGLNDADMKKPFIGIANSYTDIVPGHVHLNSIADTVKQSIAEAGGLGFEFNTMAICDGIAM 82 
                                               69******************************************************************* PP

                                 TIGR00110  70 gheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktk 138
                                               +heGmkysL+srei+aD+ve++++ah++D+lv+i++CDkivPGmlmaa+rl+iPaivv+GGpm +gk+k
  lcl|NCBI__GCF_000191585.1:WP_013643691.1  83 NHEGMKYSLASREIVADTVESMAMAHQFDGLVLIPTCDKIVPGMLMAAARLDIPAIVVTGGPMLPGKYK 151
                                               ********************************************************************* PP

                                 TIGR00110 139 lsekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstlla 207
                                                ++++dl++v+eavg++++gk++eee++e+er+acP++gsCsGlftan+mac+tea+G+slP+++t++a
  lcl|NCBI__GCF_000191585.1:WP_013643691.1 152 -GKNVDLISVYEAVGAVSSGKMTEEEIDELERCACPGPGSCSGLFTANTMACITEAIGMSLPYCATAHA 219
                                               .9******************************************************************* PP

                                 TIGR00110 208 tsaekkelakksgkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeag...vkl 273
                                               ++++k+++a+ sgk+i elv+kni+P++i+t++af+nai++d+alGGs+nt Lh++aia e +   vk+
  lcl|NCBI__GCF_000191585.1:WP_013643691.1 220 VDKKKLSIASDSGKKILELVEKNITPSKIMTQQAFKNAIAVDMALGGSSNTALHVPAIAFELEeqgVKV 288
                                               ***********************************************************7654444*** PP

                                 TIGR00110 274 slddfdrlsrkvPllaklkPsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkv 342
                                               +ld f+ +s+++P++++l+P+g++ + dl++aGG++avlk++  e++l+  ++t+tGk+l+e++++++v
  lcl|NCBI__GCF_000191585.1:WP_013643691.1 289 DLDLFNDMSKEIPHITHLSPAGEHTMLDLDKAGGIPAVLKVI--EEKLDITTITCTGKSLGENIAEARV 355
                                               ******************************************..999********************** PP

                                 TIGR00110 343 lrvdqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkv 411
                                               l  d +vi++l++p++ egg+avLkGnla++G+vvk+++v+ed++++eGpakvf+seee++eai++gk+
  lcl|NCBI__GCF_000191585.1:WP_013643691.1 356 L--DGNVIHTLEDPIHVEGGIAVLKGNLAPNGSVVKQGAVKEDMMVHEGPAKVFDSEEECVEAIFDGKI 422
                                               9..****************************************************************** PP

                                 TIGR00110 412 keGdvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaia 480
                                               +eGdv+viryeGPkGgPGmremL+Ptsa++g+ +++ vaLitDGrfsGgtrG+siGh+sPea+++G++a
  lcl|NCBI__GCF_000191585.1:WP_013643691.1 423 DEGDVIVIRYEGPKGGPGMREMLNPTSAISGMEIKS-VALITDGRFSGGTRGPSIGHISPEAMADGPLA 490
                                               *********************************987.******************************** PP

                                 TIGR00110 481 lvedGDkikiDienrkldlevseeelaerrakakkkearevkgaLakyaklvssadkGavld 542
                                                v++GD+ikiDi+nrkl+l+v e e++er + a+k+e r vkg+La+y+kl++sad+Ga+l+
  lcl|NCBI__GCF_000191585.1:WP_013643691.1 491 AVNNGDIIKIDIPNRKLELKVPESEIKERIKVADKPE-RPVKGWLARYRKLATSADEGAILR 551
                                               *****************************99999988.99*******************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (551 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 8.84
//
[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