Alignments for a candidate for ilvD in Clostridium acetobutylicum ATCC 824

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Clostridium acetobutylicum ATCC 824

Align dihydroxy-acid dehydratase subunit (EC 4.2.1.9) (characterized)
to candidate NP_349767.1 CA_C3170 dihydroxy-acid dehydratase

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



>NCBI__GCF_000008765.1:NP_349767.1
          Length = 552

 Score =  606 bits (1562), Expect = e-178
 Identities = 301/550 (54%), Positives = 416/550 (75%), Gaps = 7/550 (1%)

Query: 1   MKSDTIKRGIQRAPHRSLLARCGLTDDDFEKPFIGIANSYTDIVPGHIHLRELAEAVKEG 60
           M SD   +G++RAPHRSL    G  D++ ++P IGIANSY++++PGH++L ++ +AVK+G
Sbjct: 1   MNSDKAMKGVERAPHRSLFKALGFIDEEMDRPLIGIANSYSELIPGHMNLDKIVKAVKDG 60

Query: 61  VNAAGGVAFEFNTMAICDGIAMNHDGMKYSLASREIVADTVESMAMAHALDGLVLLPTCD 120
           +  AGGV  EF T+ +CDGI+MNH GM YSL SR+I+AD+VE +A AHALDGLVL+P CD
Sbjct: 61  IRMAGGVPVEFGTIGVCDGISMNHKGMSYSLPSRQIIADSVEIVAKAHALDGLVLVPNCD 120

Query: 121 KIVPGMLMAAARLDIPAIVVTGGPMLPGEFKGRKVDLINVYEGVGTVSAGEMSEDELEEL 180
           K+VPGMLMAA R++IP+IV++GGPML G   GR  DL +V+E VG VSAG+MS +EL EL
Sbjct: 121 KVVPGMLMAAGRVNIPSIVISGGPMLSGRTNGRVTDLNSVFEAVGAVSAGKMSLEELAEL 180

Query: 181 ERCACPGPRSCAGLFTANTMACLTEALGMSLPGCATAHAVSSRKRQIARLSGKRIVEMVQ 240
           E  ACP   SC+G+FTAN+M CL+E LG++LP   T  AV S + ++A+ +G +IVE+VQ
Sbjct: 181 ENTACPTCGSCSGMFTANSMNCLSEVLGLALPYNGTIPAVFSERLRLAKKAGMKIVELVQ 240

Query: 241 ENLKPTMIMSQEAFENAVMVDLALGGSTNTTLHIPAIAAEIDGLNINLDLFDELSRVIPH 300
           ++++P+ I+++ AF NAV +D+ALGGSTN+ LH+PAIA E D ++IN D  +E+S  IPH
Sbjct: 241 KDIRPSDILTEAAFMNAVAMDMALGGSTNSLLHLPAIAYECD-VDINFDKINEISEKIPH 299

Query: 301 IASISPAGEHMMLDLDRAGGIPAVLKTL--EDHINRECVTCTGRTVQENIENVKVGHRDV 358
           +  +SPAG H + DL  AGGIPAV+  +  +  +N EC+T TG+T+ EN+++ K+ + DV
Sbjct: 300 VCKLSPAGFHHIEDLHMAGGIPAVVNGIIKKGLLNGECMTVTGKTLYENVKDAKIKNIDV 359

Query: 359 IRPLDSPVHSEGGLAILRGNLAPRGSVVKQGAVAEDMMVHEGPAKVFNSEDECMEAIFGG 418
           IR +D+P    GGL++LRGNLAP G++VK+ AVA +MM H GPA+VFNSE+E  +AI GG
Sbjct: 360 IR-IDNPYSETGGLSVLRGNLAPDGAIVKKAAVAPEMMQHTGPARVFNSEEEVSKAILGG 418

Query: 419 RIDEGDVIVIRYEGPKGGPGMREMLNPTSAIAGMGLER-VALITDGRFSGGTRGPCVGHV 477
           +I+ GDV+VIRYEGPKGGPGM+EML+PT+++AGMGL++ VALITDGRFSG TRG  +GHV
Sbjct: 419 KINPGDVVVIRYEGPKGGPGMKEMLSPTASLAGMGLDKSVALITDGRFSGATRGASIGHV 478

Query: 478 SPEAMEDGPLAAVNDGDIIRIDIPSRKLEVDLSPREIEERLQSAVKPRRSVKGWLARYRK 537
           SPEA E GP+  V +GD I IDI  + + + +   +++ R    V+  + VKG+L  YR+
Sbjct: 479 SPEAAEGGPIGLVEEGDTIEIDIEKKTINLLVPEEKLKNRKPEKVE--KPVKGYLNTYRQ 536

Query: 538 LAGSADTGAV 547
              SA TGAV
Sbjct: 537 GVSSACTGAV 546


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: 1014
Number of extensions: 42
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: 552
Length adjustment: 36
Effective length of query: 513
Effective length of database: 516
Effective search space:   264708
Effective search space used:   264708
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 NP_349767.1 CA_C3170 (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.13893.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                              -----------
   8.6e-243  792.7   9.0     1e-242  792.5   9.0    1.0  1  lcl|NCBI__GCF_000008765.1:NP_349767.1  CA_C3170 dihydroxy-acid dehydrat


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000008765.1:NP_349767.1  CA_C3170 dihydroxy-acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  792.5   9.0    1e-242    1e-242       1     541 [.      14     547 ..      14     549 .. 0.99

  Alignments for each domain:
  == domain 1  score: 792.5 bits;  conditional E-value: 1e-242
                              TIGR00110   1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamghe 72 
                                            ++r+l+ka+G+ de++++P+i+++nsy+e++Pgh++l+++ k+vk++i+ aGgv++ef+ti+v+DGi+m+h+
  lcl|NCBI__GCF_000008765.1:NP_349767.1  14 PHRSLFKALGFIDEEMDRPLIGIANSYSELIPGHMNLDKIVKAVKDGIRMAGGVPVEFGTIGVCDGISMNHK 85 
                                            69********************************************************************** PP

                              TIGR00110  73 GmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktklsekid 144
                                            Gm ysLpsr+iiaDsve v+kahalD+lv++++CDk+vPGmlmaa r+niP+iv+sGGpm +g+t+ ++  d
  lcl|NCBI__GCF_000008765.1:NP_349767.1  86 GMSYSLPSRQIIADSVEIVAKAHALDGLVLVPNCDKVVPGMLMAAGRVNIPSIVISGGPMLSGRTN-GRVTD 156
                                            ******************************************************************.9**** PP

                              TIGR00110 145 lvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllatsaekkela 216
                                            l +vfeavg+++agk+s eel e+e++acPt+gsCsG+ftansm+cl+e+lGl+lP+++t++a+ +e+++la
  lcl|NCBI__GCF_000008765.1:NP_349767.1 157 LNSVFEAVGAVSAGKMSLEELAELENTACPTCGSCSGMFTANSMNCLSEVLGLALPYNGTIPAVFSERLRLA 228
                                            ************************************************************************ PP

                              TIGR00110 217 kksgkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklslddfdrlsrkvPll 288
                                            kk+g++ivelv+k+i+P+dilt++af na+++d+alGGstn+ Lhl+aia e +v++++d+++++s+k+P++
  lcl|NCBI__GCF_000008765.1:NP_349767.1 229 KKAGMKIVELVQKDIRPSDILTEAAFMNAVAMDMALGGSTNSLLHLPAIAYECDVDINFDKINEISEKIPHV 300
                                            ************************************************************************ PP

                              TIGR00110 289 aklkPsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlrvdqdvirsldnpvkke 360
                                            +kl+P+g + iedlh aGG++av++ + k+gll+ +++tvtGktl+e+++++k++  + dvir +dnp++++
  lcl|NCBI__GCF_000008765.1:NP_349767.1 301 CKLSPAGFHHIEDLHMAGGIPAVVNGIIKKGLLNGECMTVTGKTLYENVKDAKIK--NIDVIR-IDNPYSET 369
                                            ******************************************************9..99***8.8******* PP

                              TIGR00110 361 gglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeGdvvviryeGPkGgPGmre 432
                                            ggl vL+Gnla++Ga+vk a+v+ ++++++Gpa+vf+seee+ +ailggk++ GdvvviryeGPkGgPGm+e
  lcl|NCBI__GCF_000008765.1:NP_349767.1 370 GGLSVLRGNLAPDGAIVKKAAVAPEMMQHTGPARVFNSEEEVSKAILGGKINPGDVVVIRYEGPKGGPGMKE 441
                                            ************************************************************************ PP

                              TIGR00110 433 mLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDienrkldlevsee 504
                                            mL Pt+ l+g+GL+k+vaLitDGrfsG+trG siGhvsPeaaegG+i+lve+GD+i+iDie+++++l v ee
  lcl|NCBI__GCF_000008765.1:NP_349767.1 442 MLSPTASLAGMGLDKSVALITDGRFSGATRGASIGHVSPEAAEGGPIGLVEEGDTIEIDIEKKTINLLVPEE 513
                                            ************************************************************************ PP

                              TIGR00110 505 elaerrakakkkearevkgaLakyaklvssadkGavl 541
                                             l++r+ ++++k    vkg+L+ y++ vssa +Gav 
  lcl|NCBI__GCF_000008765.1:NP_349767.1 514 KLKNRKPEKVEKP---VKGYLNTYRQGVSSACTGAVF 547
                                            *****99888877...89*****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (552 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: 12.62
//
[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