Alignments for a candidate for ilvD in Desulfarculus baarsii DSM 2075

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Desulfarculus baarsii DSM 2075

Align dihydroxy-acid dehydratase subunit (EC 4.2.1.9) (characterized)
to candidate WP_013257167.1 DEBA_RS01680 dihydroxy-acid dehydratase

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



>NCBI__GCF_000143965.1:WP_013257167.1
          Length = 561

 Score =  606 bits (1563), Expect = e-178
 Identities = 321/554 (57%), Positives = 396/554 (71%), Gaps = 6/554 (1%)

Query: 1   MKSDTIKRGIQRAPHRSLLARCGLTDDDFEKPFIGIANSYTDIVPGHIHLRELAEAVKEG 60
           M+SD ++ G+ RAP RSLL   G  D+   KP IGIANSY+ +VPGHIHL +LA AV EG
Sbjct: 1   MRSDKVRLGVHRAPQRSLLRAMGHDDETMVKPLIGIANSYSQVVPGHIHLNDLALAVAEG 60

Query: 61  VNAAGGVAFEFNTMAICDGIAMNHDGMKYSLASREIVADTVESMAMAHALDGLVLLPTCD 120
           V  AGG   EFNTMAICDG+ M HDGM  SL SREIVAD+VE MA AH  DGLVLL +CD
Sbjct: 61  VRQAGGQPMEFNTMAICDGLVMGHDGMHASLPSREIVADSVELMAQAHCFDGLVLLASCD 120

Query: 121 KIVPGMLMAAARLDIPAIVVTGGPMLPGEFKGRKVDLINVYEGVGTVSAGEMSEDELEEL 180
           KIVPGMLMAAARLDIP + VTGGPM  G   G++VDLI V+EGV  V++G+M+ D+L  L
Sbjct: 121 KIVPGMLMAAARLDIPVVAVTGGPMAAGRLDGKRVDLITVFEGVAKVASGQMTPDDLARL 180

Query: 181 ERCACPGPRSCAGLFTANTMACLTEALGMSLPGCATAHAVSSRKRQIARLSGKRIVEMVQ 240
           ER ACPGP SCAG+FTANTMAC+TEALG+SLPGCA A A    KR+IAR SG +IVE+  
Sbjct: 181 ERLACPGPGSCAGMFTANTMACITEALGLSLPGCACALAAGPEKRRIARDSGLKIVELAS 240

Query: 241 ENLKPTMIMSQEAFENAVMVDLALGGSTNTTLHIPAIAAEIDGLNINLDLFDELSRVIPH 300
            +L+P+ I++  AFENA  VDLALGGSTNT LH+PAI A   G++  L  FD L+R  PH
Sbjct: 241 RDLRPSAILTPAAFENACRVDLALGGSTNTALHLPAI-AHAAGVSFGLADFDRLARQTPH 299

Query: 301 IASISPAGEHMMLDLDRAGGIPAVLKTLEDHINRECVTCTGRT---VQENIENVKVGHRD 357
           + S+SP G   M +L  AGG+  VL+ L   I+  C+   G     + E   ++ V  + 
Sbjct: 300 LCSMSPGGPMHMENLGAAGGVGGVLRALAPLIDASCLAVGGSIADYMTERQPDLVVDGQL 359

Query: 358 VIRPLDSPVHSEGGLAILRGNLAPRGSVVKQGAVAEDMMVHEGPAKVFNSEDECMEAIFG 417
           VI PL +PVH +GG+A+LRGNLAP G+VVKQ AVA +MM H+GPA+VF+SED  + A   
Sbjct: 360 VIHPLSAPVHDQGGIAVLRGNLAPDGAVVKQTAVAPEMMRHQGPAQVFDSEDAAVAAYDQ 419

Query: 418 GRIDEGDVIVIRYEGPKGGPGMREMLNPTSAIAGMGLE-RVALITDGRFSGGTRGPCVGH 476
           GRI  G V+V+RYEGP GGPGMREML  T+ I+G  L  +VALITDGRFSGG+RG  +GH
Sbjct: 420 GRIRPGGVLVVRYEGPAGGPGMREMLALTALISGGPLSGKVALITDGRFSGGSRGAAIGH 479

Query: 477 VSPEAMEDGPLAAVNDGDIIRIDIPSRKLEVDLSPREIEERLQSAVKP-RRSVKGWLARY 535
           VSPEA + G +  V DGD+I IDIP R+LE+ ++  E+E R Q+  +P  +  +G LARY
Sbjct: 480 VSPEAAQGGLIGLVADGDMIEIDIPGRRLELAVAAEELERRRQAWRRPAAKFARGPLARY 539

Query: 536 RKLAGSADTGAVLR 549
             L GSA  GAVLR
Sbjct: 540 AALVGSAAGGAVLR 553


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: 1192
Number of extensions: 58
Number of successful extensions: 5
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: 561
Length adjustment: 36
Effective length of query: 513
Effective length of database: 525
Effective search space:   269325
Effective search space used:   269325
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_013257167.1 DEBA_RS01680 (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.2318008.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.7e-225  734.5   2.7   4.3e-225  734.3   2.7    1.0  1  NCBI__GCF_000143965.1:WP_013257167.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000143965.1:WP_013257167.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  734.3   2.7  4.3e-225  4.3e-225       1     542 [.      14     553 ..      14     554 .. 0.98

  Alignments for each domain:
  == domain 1  score: 734.3 bits;  conditional E-value: 4.3e-225
                             TIGR00110   1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamgheG 73 
                                           ++r+ll+a+G  de + kP+i+++nsy+++vPgh+hl+dla +v+e++++aGg ++efnt+a++DG+ mgh+G
  NCBI__GCF_000143965.1:WP_013257167.1  14 PQRSLLRAMGHDDETMVKPLIGIANSYSQVVPGHIHLNDLALAVAEGVRQAGGQPMEFNTMAICDGLVMGHDG 86 
                                           589********************************************************************** PP

                             TIGR00110  74 mkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktklsekidlv 146
                                           m+ sLpsrei+aDsve +++ah++D+lv+++sCDkivPGmlmaa+rl+iP+++v+GGpm+ag++  ++++dl+
  NCBI__GCF_000143965.1:WP_013257167.1  87 MHASLPSREIVADSVELMAQAHCFDGLVLLASCDKIVPGMLMAAARLDIPVVAVTGGPMAAGRLD-GKRVDLI 158
                                           *****************************************************************.9****** PP

                             TIGR00110 147 dvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllatsaekkelakks 219
                                            vfe+v ++a+g+++ ++l ++er acP++gsC+G+ftan+mac+tealGlslPg++ +la+  ek+++a+ s
  NCBI__GCF_000143965.1:WP_013257167.1 159 TVFEGVAKVASGQMTPDDLARLERLACPGPGSCAGMFTANTMACITEALGLSLPGCACALAAGPEKRRIARDS 231
                                           ************************************************************************* PP

                             TIGR00110 220 gkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklslddfdrlsrkvPllaklk 292
                                           g +ivel  ++++P+ ilt +afena  +dlalGGstnt Lhl+aia+ agv++ l dfdrl+r++P+l++++
  NCBI__GCF_000143965.1:WP_013257167.1 232 GLKIVELASRDLRPSAILTPAAFENACRVDLALGGSTNTALHLPAIAHAAGVSFGLADFDRLARQTPHLCSMS 304
                                           ************************************************************************* PP

                             TIGR00110 293 PsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlrvdqd.virsldnpvkkeggla 364
                                           P+g   +e+l +aGGv +vl+ l  + l++  +l+v G+    + e+ + l vd + vi++l+ pv+++gg+a
  NCBI__GCF_000143965.1:WP_013257167.1 305 PGGPMHMENLGAAGGVGGVLRAL--APLIDASCLAVGGSIADYMTERQPDLVVDGQlVIHPLSAPVHDQGGIA 375
                                           ***********************..99*********998777777777666665555**************** PP

                             TIGR00110 365 vLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeGdvvviryeGPkGgPGmremLaPt 437
                                           vL+Gnla++Gavvk+++v+ ++++++Gpa+vf+se++a++a  +g+++ G v+v+ryeGP GgPGmremLa t
  NCBI__GCF_000143965.1:WP_013257167.1 376 VLRGNLAPDGAVVKQTAVAPEMMRHQGPAQVFDSEDAAVAAYDQGRIRPGGVLVVRYEGPAGGPGMREMLALT 448
                                           ************************************************************************* PP

                             TIGR00110 438 salvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDienrkldlevseeelaerr 510
                                           + ++g  L  kvaLitDGrfsGg+rG +iGhvsPeaa+gG i+lv dGD+i+iDi+ r+l+l+v  eel++rr
  NCBI__GCF_000143965.1:WP_013257167.1 449 ALISGGPLSGKVALITDGRFSGGSRGAAIGHVSPEAAQGGLIGLVADGDMIEIDIPGRRLELAVAAEELERRR 521
                                           ************************************************************************* PP

                             TIGR00110 511 akakkkearevkgaLakyaklvssadkGavld 542
                                           ++++++ a+  +g La+ya lv sa  Gavl+
  NCBI__GCF_000143965.1:WP_013257167.1 522 QAWRRPAAKFARGPLARYAALVGSAAGGAVLR 553
                                           ******************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (561 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 37.50
//
[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 2024 update 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 original 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