Alignments for a candidate for ilvD in Anaerobutyricum hallii DSM 3353

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Anaerobutyricum hallii DSM 3353

Align dihydroxy-acid dehydratase subunit (EC 4.2.1.9) (characterized)
to candidate WP_005351052.1 EUBHAL_RS13305 dihydroxy-acid dehydratase

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



>NCBI__GCF_000173975.1:WP_005351052.1
          Length = 557

 Score =  562 bits (1449), Expect = e-164
 Identities = 283/553 (51%), Positives = 399/553 (72%), Gaps = 7/553 (1%)

Query: 1   MKSDTIKRGIQRAPHRSLLARCGLTDDDFEKPFIGIANSYTDIVPGHIHLRELAEAVKEG 60
           M SD +K+G+Q+APHRSL    G T ++ E+P +GI +SY +IVPGH++L ++ +AVK G
Sbjct: 1   MNSDHVKKGMQQAPHRSLFNALGYTKEEMERPLVGIVSSYNEIVPGHMNLDKITQAVKMG 60

Query: 61  VNAAGGVAFEFNTMAICDGIAMNHDGMKYSLASREIVADTVESMAMAHALDGLVLLPTCD 120
           V  AGG    F  +A+CDGIAM H GMKYSL +RE++AD+ E MA AH  D LV++P CD
Sbjct: 61  VAMAGGTPVVFPAIAVCDGIAMGHTGMKYSLVTRELIADSTECMAKAHQFDALVMIPNCD 120

Query: 121 KIVPGMLMAAARLDIPAIVVTGGPMLPGEFKGRKVDLINVYEGVGTVSAGEMSEDELEEL 180
           K VPG+LMAAAR+++P + V+GGPML G   GRK  L +++E VG   AG+M+ +++EE 
Sbjct: 121 KNVPGLLMAAARINVPTVFVSGGPMLAGHVDGRKRSLSSMFEAVGAYEAGKMTAEKVEEY 180

Query: 181 ERCACPGPRSCAGLFTANTMACLTEALGMSLPGCATAHAVSSRKRQIARLSGKRIVEMVQ 240
               CP   SC+G++TAN+M C+TE LGM L G  T  AV S + ++A+ +G +++E+++
Sbjct: 181 VNKVCPTCGSCSGMYTANSMNCMTEVLGMGLRGNGTIPAVYSERIRLAKHAGMKVMELLK 240

Query: 241 ENLKPTMIMSQEAFENAVMVDLALGGSTNTTLHIPAIAAEIDGLNINLDLFDELSRVIPH 300
            N++P+ IM+++AF N + VD+ALG STNT LH+PAIA E  G+ +N+D+ +E+S   P+
Sbjct: 241 NNVRPSDIMTKKAFLNCLTVDMALGCSTNTMLHLPAIAHEA-GVELNMDIANEISAKTPN 299

Query: 301 IASISPAGEHMMLDLDRAGGIPAVLKTLEDH--INRECVTCTGRTVQENIENVKVGHRDV 358
           +  ++PAG   M DL+ AGG+ AV+  L     +  + +T TG+TV ENI++V   + +V
Sbjct: 300 LCHLAPAGPTYMEDLNEAGGVYAVMNELSKKGLLYEDQITVTGKTVGENIKDVHNLNPEV 359

Query: 359 IRPLDSPVHSEGGLAILRGNLAPRGSVVKQGAVAEDMMVHEGPAKVFNSEDECMEAIFGG 418
           IRP+D+P  ++GG+A+L+GN+AP   +VKQ AV  +MMVHEGPA+VF+ E++ ++AI GG
Sbjct: 360 IRPIDNPYMAQGGIAVLKGNIAPDTGIVKQSAVVPEMMVHEGPARVFDCEEDAIKAIKGG 419

Query: 419 RIDEGDVIVIRYEGPKGGPGMREMLNPTSAIAGMGL-ERVALITDGRFSGGTRGPCVGHV 477
            I  GDV+VIRYEGPKGGPGMREMLNPTSAIAGMGL + VALITDGRFSG +RG  +GHV
Sbjct: 420 DIVPGDVVVIRYEGPKGGPGMREMLNPTSAIAGMGLGDSVALITDGRFSGASRGASIGHV 479

Query: 478 SPEAMEDGPLAAVNDGDIIRIDIPSRKLEVDLSPREIEERLQSAVKPR--RSVKGWLARY 535
           SPEA   GP+A + +GDII+IDIP+  L VD+S  E+ +R +   +PR  +   G+L RY
Sbjct: 480 SPEAAVGGPIALIEEGDIIKIDIPNNSLNVDVSDEELAKR-KEKWQPREPKITDGYLRRY 538

Query: 536 RKLAGSADTGAVL 548
             L  S + GAVL
Sbjct: 539 AALVTSGNRGAVL 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: 959
Number of extensions: 57
Number of successful extensions: 6
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: 557
Length adjustment: 36
Effective length of query: 513
Effective length of database: 521
Effective search space:   267273
Effective search space used:   267273
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_005351052.1 EUBHAL_RS13305 (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.1352383.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   7.6e-242  789.6  10.7   8.7e-242  789.4  10.7    1.0  1  NCBI__GCF_000173975.1:WP_005351052.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000173975.1:WP_005351052.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  789.4  10.7  8.7e-242  8.7e-242       1     542 [.      14     552 ..      14     553 .. 1.00

  Alignments for each domain:
  == domain 1  score: 789.4 bits;  conditional E-value: 8.7e-242
                             TIGR00110   1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamgheG 73 
                                           ++r+l++a+G+++e++e+P++++v+sy+eivPgh++l++++++vk ++  aGg+++ f  iav+DGiamgh+G
  NCBI__GCF_000173975.1:WP_005351052.1  14 PHRSLFNALGYTKEEMERPLVGIVSSYNEIVPGHMNLDKITQAVKMGVAMAGGTPVVFPAIAVCDGIAMGHTG 86 
                                           69*********************************************************************** PP

                             TIGR00110  74 mkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktklsekidlv 146
                                           mkysL++re+iaDs e ++kah++Dalv+i++CDk+vPG+lmaa+r+n+P+++vsGGpm ag++  ++k +l+
  NCBI__GCF_000173975.1:WP_005351052.1  87 MKYSLVTRELIADSTECMAKAHQFDALVMIPNCDKNVPGLLMAAARINVPTVFVSGGPMLAGHVD-GRKRSLS 158
                                           *****************************************************************.9****** PP

                             TIGR00110 147 dvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllatsaekkelakks 219
                                           ++feavg+y+agk++ e++ee+++  cPt+gsCsG++tansm+c+te+lG+ l g++t++a+ +e+ +lak++
  NCBI__GCF_000173975.1:WP_005351052.1 159 SMFEAVGAYEAGKMTAEKVEEYVNKVCPTCGSCSGMYTANSMNCMTEVLGMGLRGNGTIPAVYSERIRLAKHA 231
                                           ************************************************************************* PP

                             TIGR00110 220 gkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklslddfdrlsrkvPllaklk 292
                                           g++++el+k+n++P+di+tk+af n +t+d+alG stnt+Lhl+aia+eagv+l++d  +++s k+P l++l+
  NCBI__GCF_000173975.1:WP_005351052.1 232 GMKVMELLKNNVRPSDIMTKKAFLNCLTVDMALGCSTNTMLHLPAIAHEAGVELNMDIANEISAKTPNLCHLA 304
                                           ************************************************************************* PP

                             TIGR00110 293 PsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlrvdqdvirsldnpvkkegglav 365
                                           P+g +++edl++aGGv av++el+k+gll +d +tvtGkt++e++++v+ l  + +vir++dnp+ ++gg+av
  NCBI__GCF_000173975.1:WP_005351052.1 305 PAGPTYMEDLNEAGGVYAVMNELSKKGLLYEDQITVTGKTVGENIKDVHNL--NPEVIRPIDNPYMAQGGIAV 375
                                           ***********************************************9999..9******************* PP

                             TIGR00110 366 LkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeGdvvviryeGPkGgPGmremLaPts 438
                                           LkGn+a++  +vk+++v  +++++eGpa+vf+ ee+a++ai gg++  GdvvviryeGPkGgPGmremL+Pts
  NCBI__GCF_000173975.1:WP_005351052.1 376 LKGNIAPDTGIVKQSAVVPEMMVHEGPARVFDCEEDAIKAIKGGDIVPGDVVVIRYEGPKGGPGMREMLNPTS 448
                                           ************************************************************************* PP

                             TIGR00110 439 alvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDienrkldlevseeelaerra 511
                                           a++g+GLg++vaLitDGrfsG++rG siGhvsPeaa+gG+ial+e+GD+ikiDi+n+ l+++vs+eela+r++
  NCBI__GCF_000173975.1:WP_005351052.1 449 AIAGMGLGDSVALITDGRFSGASRGASIGHVSPEAAVGGPIALIEEGDIIKIDIPNNSLNVDVSDEELAKRKE 521
                                           ************************************************************************* PP

                             TIGR00110 512 kakkkearevkgaLakyaklvssadkGavld 542
                                           k++++e++ + g+L++ya lv+s ++Gavld
  NCBI__GCF_000173975.1:WP_005351052.1 522 KWQPREPKITDGYLRRYAALVTSGNRGAVLD 552
                                           *****************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (557 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 30.43
//
[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