Alignments for a candidate for ilvD in Bacillus alkalinitrilicus DSM 22532

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Bacillus alkalinitrilicus DSM 22532

Align dihydroxyacid dehydratase (EC 4.2.1.9) (characterized)
to candidate WP_078427776.1 BK574_RS05060 dihydroxy-acid dehydratase

Query= metacyc::MONOMER-18815
         (557 letters)



>NCBI__GCF_002019605.1:WP_078427776.1
          Length = 556

 Score =  588 bits (1516), Expect = e-172
 Identities = 293/553 (52%), Positives = 395/553 (71%), Gaps = 3/553 (0%)

Query: 5   KRSQNITQGVARSPNRSMYYALGYKKEDFDKPMVGIANGHSTITPCNAGLQRLADAAIDA 64
           K   ++   + ++PNR+M  A+G   EDF+KP VGIA+  S +TPCN  +  LA  A + 
Sbjct: 7   KSRSSVFNDINKAPNRAMIRAMGITDEDFNKPFVGIASTWSEVTPCNMHIDELARKAKEG 66

Query: 65  IKASDANPQVFGTPTISDGMSMGTEGMKYSLISREVIADCIETAAQGQWMDGVVVIGGCD 124
                  P +F T T+SDG+SMGTEG+++SL SREVIAD IET    Q  DGVV IGGCD
Sbjct: 67  TLNGGGTPFIFNTITVSDGISMGTEGIRFSLPSREVIADSIETVMGAQSYDGVVAIGGCD 126

Query: 125 KNMPGGMIALARTNVPGIYVYGGTIKPGNWKGKDLTIVSSFEAVGEFTAGRMSQEDFEGV 184
           KNMPG MIA+ R N+P ++VYGGTI+ G   GKD+ IVS+FEAVG++  G + +E    V
Sbjct: 127 KNMPGCMIAIGRLNLPAVFVYGGTIRAGKVDGKDIDIVSAFEAVGKYNNGDIDREQLHKV 186

Query: 185 EKNACPSTGSCGGMYTANTMSSSFEALGMSLLYSSTMANPDQEKVDSAAESARVLVEAIK 244
           E +ACP  GSCGGMYTANTM+S+ EA+GMSL  SS+     +EK+    ++ + ++  + 
Sbjct: 187 ECHACPGAGSCGGMYTANTMASAIEAMGMSLPGSSSNPAETKEKLQDCIDAGKAVMNLLS 246

Query: 245 QDIKPRDIITRKSIENAVALIMATGGSTNAVLHYLAIAHAAEVEWTIDDFERIRRKVPVI 304
           + I P+DI+T+K+ ENA+ ++MA GGSTNAVLH LA+AH  +VE  +DDFERIR+KVP I
Sbjct: 247 KGITPKDIMTKKAFENAITVVMALGGSTNAVLHLLALAHTIDVELELDDFERIRKKVPHI 306

Query: 305 CNLKPSGQYVATDLHKAGGIPQVMKILLKAGMLHGDCLTITGRTLAEELENVPDTPRADQ 364
            +LKPSG+YV  DL   GG+P VMK+LL  G+LHGDCLT+TG+T+ E L+ +   P  + 
Sbjct: 307 ADLKPSGKYVMEDLSLIGGVPGVMKLLLDKGLLHGDCLTVTGQTIEENLKEI--VPLKEG 364

Query: 365 DVILPIEKALYAEGHLAILKGNLAEEGAVAKITGLKNPVITGPARVFEDEQSAMEAILAD 424
             I+  E      G L +L+GNLA EGA+AK++GLK   ITGPARVF+ E+ A +A+L +
Sbjct: 365 QEIISFENPKRETGPLVVLRGNLAPEGALAKMSGLKIKEITGPARVFDTEKDATDAVLNN 424

Query: 425 KINAGDILVLRYLGPKGGPGMPEMLAPTSAIIGKGLGESVGFITDGRFSGGTWGMVVGHV 484
           KIN GD++V+RY+GPKGGPGM EML+ T+ ++GKGLGE VG ITDGRFSGGT G+VVGH+
Sbjct: 425 KINPGDVIVIRYVGPKGGPGMAEMLSITAIVVGKGLGEKVGLITDGRFSGGTHGLVVGHI 484

Query: 485 APEAYVGGTIALVQEGDSITIDAHKLLLQLNVADEELARRRANWKQPAPRYTRGVLAKFS 544
           +PEA VGG I L+QEGD ITI++    L +NV+ E+ A R  +W  P  +  +G L+K++
Sbjct: 485 SPEAQVGGPIGLIQEGDLITINSETQELTVNVSPEKFAERAKDW-TPPEQNLKGYLSKYA 543

Query: 545 KLASTASKGAVTD 557
           +L S+ASKGA+TD
Sbjct: 544 RLVSSASKGAITD 556


Lambda     K      H
   0.316    0.133    0.386 

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: 951
Number of extensions: 43
Number of successful extensions: 3
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: 557
Length of database: 556
Length adjustment: 36
Effective length of query: 521
Effective length of database: 520
Effective search space:   270920
Effective search space used:   270920
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 (21.6 bits)
S2: 53 (25.0 bits)

Align candidate WP_078427776.1 BK574_RS05060 (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.17329.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.1e-228  744.6   7.4   3.6e-228  744.4   7.4    1.0  1  lcl|NCBI__GCF_002019605.1:WP_078427776.1  BK574_RS05060 dihydroxy-acid deh


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002019605.1:WP_078427776.1  BK574_RS05060 dihydroxy-acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  744.4   7.4  3.6e-228  3.6e-228       1     542 [.      20     556 .]      20     556 .] 0.99

  Alignments for each domain:
  == domain 1  score: 744.4 bits;  conditional E-value: 3.6e-228
                                 TIGR00110   1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiam 69 
                                               ++ra+++a+G++ded++kP+++++++++e++P+++h+++la+++ke+  + Gg+++ fnti+vsDGi+m
  lcl|NCBI__GCF_002019605.1:WP_078427776.1  20 PNRAMIRAMGITDEDFNKPFVGIASTWSEVTPCNMHIDELARKAKEGTLNGGGTPFIFNTITVSDGISM 88 
                                               68******************************************************************* PP

                                 TIGR00110  70 gheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktk 138
                                               g+eG+++sLpsre+iaDs+etv+ a+ +D++v+i+ CDk++PG ++a  rln+Pa++v+GG++ agk+ 
  lcl|NCBI__GCF_002019605.1:WP_078427776.1  89 GTEGIRFSLPSREVIADSIETVMGAQSYDGVVAIGGCDKNMPGCMIAIGRLNLPAVFVYGGTIRAGKVD 157
                                               ********************************************************************* PP

                                 TIGR00110 139 lsekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstlla 207
                                                +++id+v++feavg+y++g+++ e+l+++e +acP+agsC+G++tan+ma++ ea+G+slPgss+ +a
  lcl|NCBI__GCF_002019605.1:WP_078427776.1 158 -GKDIDIVSAFEAVGKYNNGDIDREQLHKVECHACPGAGSCGGMYTANTMASAIEAMGMSLPGSSSNPA 225
                                               .9******************************************************************* PP

                                 TIGR00110 208 tsaekkelakksgkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklsld 276
                                                ++ek++ +  +gk +++l+ k i+P+di+tk+afenait+++alGGstn+vLhlla+a++++v+l+ld
  lcl|NCBI__GCF_002019605.1:WP_078427776.1 226 ETKEKLQDCIDAGKAVMNLLSKGITPKDIMTKKAFENAITVVMALGGSTNAVLHLLALAHTIDVELELD 294
                                               ********************************************************************* PP

                                 TIGR00110 277 dfdrlsrkvPllaklkPsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlrv 345
                                               df+r+++kvP++a+lkPsgk+v+edl   GGv++v+k l  +gllh d+ltvtG+t++e+l+++  l++
  lcl|NCBI__GCF_002019605.1:WP_078427776.1 295 DFERIRKKVPHIADLKPSGKYVMEDLSLIGGVPGVMKLLLDKGLLHGDCLTVTGQTIEENLKEIVPLKE 363
                                               ******************************************************************999 PP

                                 TIGR00110 346 dqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeG 414
                                               +q++i s +np +++g l vL+Gnla+eGa++k++g +  i +++Gpa+vf+ e++a +a+l+ k++ G
  lcl|NCBI__GCF_002019605.1:WP_078427776.1 364 GQEII-SFENPKRETGPLVVLRGNLAPEGALAKMSGLK--IKEITGPARVFDTEKDATDAVLNNKINPG 429
                                               99998.79****************************96..59*************************** PP

                                 TIGR00110 415 dvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialve 483
                                               dv+viry GPkGgPGm emL  t+ +vg GLg+kv+LitDGrfsGgt+Gl++Gh+sPea +gG+i+l++
  lcl|NCBI__GCF_002019605.1:WP_078427776.1 430 DVIVIRYVGPKGGPGMAEMLSITAIVVGKGLGEKVGLITDGRFSGGTHGLVVGHISPEAQVGGPIGLIQ 498
                                               ********************************************************************* PP

                                 TIGR00110 484 dGDkikiDienrkldlevseeelaerrakakkkearevkgaLakyaklvssadkGavld 542
                                               +GD i+i+ e ++l ++vs e +aer ++++++e ++ kg+L+kya+lvssa+kGa++d
  lcl|NCBI__GCF_002019605.1:WP_078427776.1 499 EGDLITINSETQELTVNVSPEKFAERAKDWTPPE-QNLKGYLSKYARLVSSASKGAITD 556
                                               ********************************99.88*******************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (556 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: 00:00:00.02
# Mc/sec: 10.74
//
[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