Alignments for a candidate for ilvD in Desulfuromonas acetexigens

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Desulfuromonas acetexigens

Align dihydroxy-acid dehydratase subunit (EC 4.2.1.9) (characterized)
to candidate WP_092053017.1 BQ4888_RS02110 dihydroxy-acid dehydratase

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



>NCBI__GCF_900111775.1:WP_092053017.1
          Length = 556

 Score =  577 bits (1488), Expect = e-169
 Identities = 301/552 (54%), Positives = 388/552 (70%), Gaps = 6/552 (1%)

Query: 2   KSDTIKRGIQRAPHRSLLARCGLTDDDFEKPFIGIANSYTDIVPGHIHLRELAEAVKEGV 61
           +SD I +G +R PHR+LL   GL D    +PFIGIA S+TD++PGH  +REL   +++GV
Sbjct: 5   RSDAITQGFERTPHRALLKGTGLPDSSMNRPFIGIATSFTDLIPGHTGMRELERFIEKGV 64

Query: 62  NAAGGVAFEFNTMAICDGIAMNHDGMKYSLASREIVADTVESMAMAHALDGLVLLPTCDK 121
           +  GG AF F    +CDGIAM H GM YSL +RE++AD +ES+A AH LDGLVLL  CDK
Sbjct: 65  HTGGGHAFFFGIPGVCDGIAMGHKGMHYSLPTRELIADMIESVAEAHRLDGLVLLTNCDK 124

Query: 122 IVPGMLMAAARLDIPAIVVTGGPMLPGEFK-GRKVDLI-NVYEGVGTVSAGEMSEDELEE 179
           I PGMLMAAARLDIP IVVT GPM+ G  + GR+   + + +E +    AG + E EL +
Sbjct: 125 ITPGMLMAAARLDIPCIVVTAGPMMTGTGRQGRRFSFVTDTFEAMARYKAGVIDEKELMQ 184

Query: 180 LERCACPGPRSCAGLFTANTMACLTEALGMSLPGCATAHAVSSRKRQIARLSGKRIVEMV 239
            E  ACP   SC GLFTANTMA LTE LGMSL GC TA AVSS K++IA  SG+RIVE+V
Sbjct: 185 CEEHACPTAGSCQGLFTANTMAILTETLGMSLLGCGTALAVSSLKKRIAFASGERIVELV 244

Query: 240 QENLKPTMIMSQEAFENAVMVDLALGGSTNTTLHIPAIAAEIDGLNINLDLFDELSRVIP 299
           ++N+ P  I+++ AFENA+ VDLALGGS+NT LH+ +IA E  G+++ L+ FD L R  P
Sbjct: 245 RDNITPRQILTKAAFENAIRVDLALGGSSNTVLHLLSIAREA-GVDLPLEEFDRLGRTTP 303

Query: 300 HIASISPAGEHMMLDLDRAGGIPAVLKTLEDHINRECVTCTGRTVQENIENVKVGHRDVI 359
            +AS++P G+H M DLD AGG+ AVL  L D I ++  T TG + Q+ I +V     +V+
Sbjct: 304 QLASMNPGGKHFMEDLDAAGGVAAVLYQLRDLI-QDNPTLTGLSTQQIIASVADVDEEVV 362

Query: 360 RPLDSPVHSEGGLAILRGNLAPRGSVVKQGAVAEDMMVHEGPAKVFNSEDECMEAIFGGR 419
            P+  P+ +EGGLAIL GNLAP G+VVKQ  V+E MM   G A+ F SE+  M A+ GG+
Sbjct: 363 HPVSDPIRAEGGLAILSGNLAPDGAVVKQSGVSEKMMRFSGKARCFESEEAAMTALMGGQ 422

Query: 420 IDEGDVIVIRYEGPKGGPGMREMLNPTSAIAGMGL-ERVALITDGRFSGGTRGPCVGHVS 478
           +  GDV+VIRYEGPKGGPGMREML PT+ + G+GL + VALITDGRFSGGTRGPC+GHVS
Sbjct: 423 VVAGDVVVIRYEGPKGGPGMREMLAPTATLMGLGLGDSVALITDGRFSGGTRGPCIGHVS 482

Query: 479 PEAMEDGPLAAVNDGDIIRIDIPSRKLEVDLSPREIEERLQSAVKPRRSVK-GWLARYRK 537
           PEA   GP+A V DGD I +DIP+R L++ +    + ER     +P   +K GWLARY  
Sbjct: 483 PEAAVGGPIALVEDGDTIELDIPNRALKLQVDDVVLAERRARWSRPEPKIKTGWLARYAA 542

Query: 538 LAGSADTGAVLR 549
           +  SA+TGA+ +
Sbjct: 543 VVTSANTGAICK 554


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: 968
Number of extensions: 47
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: 556
Length adjustment: 36
Effective length of query: 513
Effective length of database: 520
Effective search space:   266760
Effective search space used:   266760
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_092053017.1 BQ4888_RS02110 (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.14800.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   8.8e-234  762.9   1.6     1e-233  762.8   1.6    1.0  1  lcl|NCBI__GCF_900111775.1:WP_092053017.1  BQ4888_RS02110 dihydroxy-acid de


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900111775.1:WP_092053017.1  BQ4888_RS02110 dihydroxy-acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  762.8   1.6    1e-233    1e-233       1     542 [.      17     554 ..      17     555 .. 0.99

  Alignments for each domain:
  == domain 1  score: 762.8 bits;  conditional E-value: 1e-233
                                 TIGR00110   1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiam 69 
                                               ++rallk tGl d  +++P+i+++ s+t+++Pgh  +++l + +++++++ Gg a+ f++ +v+DGiam
  lcl|NCBI__GCF_900111775.1:WP_092053017.1  17 PHRALLKGTGLPDSSMNRPFIGIATSFTDLIPGHTGMRELERFIEKGVHTGGGHAFFFGIPGVCDGIAM 85 
                                               69******************************************************************* PP

                                 TIGR00110  70 gheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktk 138
                                               gh+Gm+ysLp+re+iaD +e+v++ah+lD+lv++++CDki+PGmlmaa+rl+iP ivv+ Gpm++g  +
  lcl|NCBI__GCF_900111775.1:WP_092053017.1  86 GHKGMHYSLPTRELIADMIESVAEAHRLDGLVLLTNCDKITPGMLMAAARLDIPCIVVTAGPMMTGTGR 154
                                               ********************************************************************* PP

                                 TIGR00110 139 lsekid.lvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstll 206
                                                +++++ ++d fea+ +y+ag ++e+el + e++acPtagsC+Glftan+ma+lte+lG+sl g++t+l
  lcl|NCBI__GCF_900111775.1:WP_092053017.1 155 QGRRFSfVTDTFEAMARYKAGVIDEKELMQCEEHACPTAGSCQGLFTANTMAILTETLGMSLLGCGTAL 223
                                               ****983469*********************************************************** PP

                                 TIGR00110 207 atsaekkelakksgkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklsl 275
                                               a+s+ kk++a  sg+rivelv+ ni+Pr+iltk+afenai +dlalGGs+ntvLhll+ia+eagv+l l
  lcl|NCBI__GCF_900111775.1:WP_092053017.1 224 AVSSLKKRIAFASGERIVELVRDNITPRQILTKAAFENAIRVDLALGGSSNTVLHLLSIAREAGVDLPL 292
                                               ********************************************************************* PP

                                 TIGR00110 276 ddfdrlsrkvPllaklkPsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlr 344
                                               ++fdrl r++P+la+++P+gk+++edl++aGGv avl +l  ++l++++  t+tG + ++++++v    
  lcl|NCBI__GCF_900111775.1:WP_092053017.1 293 EEFDRLGRTTPQLASMNPGGKHFMEDLDAAGGVAAVLYQL--RDLIQDN-PTLTGLSTQQIIASVADV- 357
                                               ****************************************..8888877.9************99988. PP

                                 TIGR00110 345 vdqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvke 413
                                                d++v++++++p+++eggla+L Gnla++Gavvk++gv+e++++f G+a+ fesee+a+ a++gg+v +
  lcl|NCBI__GCF_900111775.1:WP_092053017.1 358 -DEEVVHPVSDPIRAEGGLAILSGNLAPDGAVVKQSGVSEKMMRFSGKARCFESEEAAMTALMGGQVVA 425
                                               .******************************************************************** PP

                                 TIGR00110 414 GdvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialv 482
                                               GdvvviryeGPkGgPGmremLaPt++l+glGLg++vaLitDGrfsGgtrG++iGhvsPeaa+gG+ialv
  lcl|NCBI__GCF_900111775.1:WP_092053017.1 426 GDVVVIRYEGPKGGPGMREMLAPTATLMGLGLGDSVALITDGRFSGGTRGPCIGHVSPEAAVGGPIALV 494
                                               ********************************************************************* PP

                                 TIGR00110 483 edGDkikiDienrkldlevseeelaerrakakkkearevkgaLakyaklvssadkGavld 542
                                               edGD+i++Di+nr+l+l+v++  laerra+++++e++ + g+La+ya +v+sa++Ga+ +
  lcl|NCBI__GCF_900111775.1:WP_092053017.1 495 EDGDTIELDIPNRALKLQVDDVVLAERRARWSRPEPKIKTGWLARYAAVVTSANTGAICK 554
                                               *********************************************************976 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: 0.02u 0.02s 00:00:00.04 Elapsed: 00:00:00.02
# Mc/sec: 10.19
//
[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