Alignments for a candidate for ilvD in Archaeoglobus veneficus SNP6

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Archaeoglobus veneficus SNP6

Align dihydroxy-acid dehydratase subunit (EC 4.2.1.9) (characterized)
to candidate WP_013684023.1 ARCVE_RS06770 dihydroxy-acid dehydratase

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



>NCBI__GCF_000194625.1:WP_013684023.1
          Length = 547

 Score =  595 bits (1535), Expect = e-174
 Identities = 294/547 (53%), Positives = 397/547 (72%), Gaps = 2/547 (0%)

Query: 1   MKSDTIKRGIQRAPHRSLLARCGLTDDDFEKPFIGIANSYTDIVPGHIHLRELAEAVKEG 60
           M+SD IKRGI+R  HR+LL   GLTD+D +KPFIG+AN+Y +IVPGH+ L  +++AVKEG
Sbjct: 1   MRSDEIKRGIERTAHRALLKATGLTDEDMDKPFIGVANAYNNIVPGHMLLDRISDAVKEG 60

Query: 61  VNAAGGVAFEFNTMAICDGIAMNHDGMKYSLASREIVADTVESMAMAHALDGLVLLPTCD 120
           + +AGGVAFEF  + ICDGIAM HDGM+++L SRE++AD++E+M  AH  DGLV++ +CD
Sbjct: 61  IASAGGVAFEFGVIGICDGIAMGHDGMRFALPSRELIADSIEAMVQAHCFDGLVVVGSCD 120

Query: 121 KIVPGMLMAAARLDIPAIVVTGGPMLPGEFKGRKVDLINVYEGVGTVSAGEMSEDELEEL 180
           KIVPGMLMA  RLDIPAI VTGGPML      + V +   +E  G   AG +SE+EL+  
Sbjct: 121 KIVPGMLMAMLRLDIPAIAVTGGPMLAERIGEKVVTIKTAFEAAGEYKAGRISEEELKLY 180

Query: 181 ERCACPGPRSCAGLFTANTMACLTEALGMSLPGCATAHAVSSRKRQIARLSGKRIVEMVQ 240
           E        SC GL+TANTM  LTE LG+SLP C+T+   SSRK +IA+ SGKR+VE+V+
Sbjct: 181 EDYCAAYCGSCQGLYTANTMQILTETLGLSLPYCSTSPCGSSRKLRIAKESGKRVVELVK 240

Query: 241 ENLKPTMIMSQEAFENAVMVDLALGGSTNTTLHIPAIAAEIDGLNINLDLFDELSRVIPH 300
             +KP+ I+++E+F NA+ +D+ +GGSTNT LH+PAIA E  G+ ++LD+FDE+SR  PH
Sbjct: 241 RGIKPSDIITEESFRNAITMDMLIGGSTNTVLHLPAIAREA-GIELSLDVFDEISRKTPH 299

Query: 301 IASISPAGEHMMLDLDRAGGIPAVLKTLEDHINRECVTCTGRTVQENIENVKVGHRDVIR 360
           I S+ PA E+ + DLD +GG+P +++  + + + E +T +G  + +      V  RD+IR
Sbjct: 300 IVSLDPASEYTIADLDESGGVPMLIQRAKKYFSNE-LTISGLRIYDIATKAFVRGRDIIR 358

Query: 361 PLDSPVHSEGGLAILRGNLAPRGSVVKQGAVAEDMMVHEGPAKVFNSEDECMEAIFGGRI 420
            + +P+H EGG+AIL GNLA +G VVK  AV EDM+  EG AKVF+SE E ++AI    +
Sbjct: 359 EVTNPIHKEGGIAILYGNLAEKGCVVKAAAVKEDMLRFEGEAKVFDSEQEALKAILNSEV 418

Query: 421 DEGDVIVIRYEGPKGGPGMREMLNPTSAIAGMGLERVALITDGRFSGGTRGPCVGHVSPE 480
           ++G+V+VIRY GPKG PGM EML PT+AIAGMGL RVALITDGRFSG TRGPC+GH+SPE
Sbjct: 419 EDGNVVVIRYMGPKGAPGMPEMLLPTAAIAGMGLSRVALITDGRFSGATRGPCIGHISPE 478

Query: 481 AMEDGPLAAVNDGDIIRIDIPSRKLEVDLSPREIEERLQSAVKPRRSVKGWLARYRKLAG 540
           A   G +A V DGD+I IDIP+R++E+ +    +EER +      + + G+LARY KL  
Sbjct: 479 AAVGGNIALVEDGDVISIDIPARRIELKVDNNVLEERRKKWKPKEKKLTGYLARYAKLVS 538

Query: 541 SADTGAV 547
            A+ GAV
Sbjct: 539 GAEKGAV 545


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: 878
Number of extensions: 28
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: 549
Length of database: 547
Length adjustment: 36
Effective length of query: 513
Effective length of database: 511
Effective search space:   262143
Effective search space used:   262143
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_013684023.1 ARCVE_RS06770 (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.16206.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.2e-249  814.4   4.5   2.5e-249  814.3   4.5    1.0  1  lcl|NCBI__GCF_000194625.1:WP_013684023.1  ARCVE_RS06770 dihydroxy-acid deh


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000194625.1:WP_013684023.1  ARCVE_RS06770 dihydroxy-acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  814.3   4.5  2.5e-249  2.5e-249       1     541 [.      14     546 ..      14     547 .] 0.99

  Alignments for each domain:
  == domain 1  score: 814.3 bits;  conditional E-value: 2.5e-249
                                 TIGR00110   1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiam 69 
                                               a+rallkatGl+ded++kP+i+v+n+y++ivPgh+ l+ ++++vke+i +aGgva+ef++i+++DGiam
  lcl|NCBI__GCF_000194625.1:WP_013684023.1  14 AHRALLKATGLTDEDMDKPFIGVANAYNNIVPGHMLLDRISDAVKEGIASAGGVAFEFGVIGICDGIAM 82 
                                               69******************************************************************* PP

                                 TIGR00110  70 gheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktk 138
                                               gh+Gm+++Lpsre+iaDs+e++v+ah++D+lvv++sCDkivPGmlma+lrl+iPai+v+GGpm a+++ 
  lcl|NCBI__GCF_000194625.1:WP_013684023.1  83 GHDGMRFALPSRELIADSIEAMVQAHCFDGLVVVGSCDKIVPGMLMAMLRLDIPAIAVTGGPMLAERIG 151
                                               ********************************************************************9 PP

                                 TIGR00110 139 lsekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstlla 207
                                                 + ++++ +fea+gey+ag++seeel+ +e++++ ++gsC+Gl+tan+m++lte+lGlslP++st+++
  lcl|NCBI__GCF_000194625.1:WP_013684023.1 152 -EKVVTIKTAFEAAGEYKAGRISEEELKLYEDYCAAYCGSCQGLYTANTMQILTETLGLSLPYCSTSPC 219
                                               .6899999************************************************************* PP

                                 TIGR00110 208 tsaekkelakksgkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklsld 276
                                                s++k+++ak+sgkr+velvk+ ikP+di+t+e+f nait+d+++GGstntvLhl+aia+eag++lsld
  lcl|NCBI__GCF_000194625.1:WP_013684023.1 220 GSSRKLRIAKESGKRVVELVKRGIKPSDIITEESFRNAITMDMLIGGSTNTVLHLPAIAREAGIELSLD 288
                                               ********************************************************************* PP

                                 TIGR00110 277 dfdrlsrkvPllaklkPsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlrv 345
                                                fd++srk+P++++l+P++++ i+dl+++GGv+++++ +  ++++ ++ lt++G  +++++ k+ v+  
  lcl|NCBI__GCF_000194625.1:WP_013684023.1 289 VFDEISRKTPHIVSLDPASEYTIADLDESGGVPMLIQRA--KKYFSNE-LTISGLRIYDIATKAFVR-- 352
                                               ************************************999..7778777.9*************9999.. PP

                                 TIGR00110 346 dqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeG 414
                                               ++d+ir++ np++kegg+a+L+Gnlae+G+vvk+a+v+ed+l+feG+akvf+se+eal+ail+ +v++G
  lcl|NCBI__GCF_000194625.1:WP_013684023.1 353 GRDIIREVTNPIHKEGGIAILYGNLAEKGCVVKAAAVKEDMLRFEGEAKVFDSEQEALKAILNSEVEDG 421
                                               ********************************************************************* PP

                                 TIGR00110 415 dvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialve 483
                                               +vvviry+GPkG+PGm+emL Pt+a++g+GL + vaLitDGrfsG+trG++iGh+sPeaa+gG+ialve
  lcl|NCBI__GCF_000194625.1:WP_013684023.1 422 NVVVIRYMGPKGAPGMPEMLLPTAAIAGMGLSR-VALITDGRFSGATRGPCIGHISPEAAVGGNIALVE 489
                                               ********************************9.*********************************** PP

                                 TIGR00110 484 dGDkikiDienrkldlevseeelaerrakakkkearevkgaLakyaklvssadkGavl 541
                                               dGD i+iDi++r+++l+v+++ l+err+k+k+ke ++  g+La+yaklvs+a+kGav 
  lcl|NCBI__GCF_000194625.1:WP_013684023.1 490 DGDVISIDIPARRIELKVDNNVLEERRKKWKPKE-KKLTGYLARYAKLVSGAEKGAVF 546
                                               ********************************99.789******************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (547 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 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 12.93
//
[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