Alignments for a candidate for ilvD in Geobacter metallireducens GS-15

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Geobacter metallireducens GS-15

Align dihydroxy-acid dehydratase subunit (EC 4.2.1.9) (characterized)
to candidate WP_004512108.1 GMET_RS06340 dihydroxy-acid dehydratase

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



>NCBI__GCF_000012925.1:WP_004512108.1
          Length = 553

 Score =  586 bits (1510), Expect = e-172
 Identities = 305/551 (55%), Positives = 394/551 (71%), Gaps = 6/551 (1%)

Query: 1   MKSDTIKRGIQRAPHRSLLARCGLTDDDFEKPFIGIANSYTDIVPGHIHLRELAEAVKEG 60
           M+SDTIK+GI+R PHR+L+   G+   +  KPFIG+A S+TD++PGH+ +R+L   +++G
Sbjct: 1   MRSDTIKQGIERTPHRALIKGTGVPQSEMAKPFIGVATSFTDLIPGHVGMRDLERFIEKG 60

Query: 61  VNAAGGVAFEFNTMAICDGIAMNHDGMKYSLASREIVADTVESMAMAHALDGLVLLPTCD 120
           +++ GG AF F    +CDGIAM H GM YSL +RE++AD VES+A AH LDGLVLL  CD
Sbjct: 61  IHSGGGYAFFFGIPGVCDGIAMGHKGMHYSLPTRELIADMVESVAEAHRLDGLVLLTNCD 120

Query: 121 KIVPGMLMAAARLDIPAIVVTGGPMLPGE-FKGRKVDLI-NVYEGVGTVSAGEMSEDELE 178
           KI PGMLMAAARLDIP IVVT GPM+ G   +GR+   + + +E +    AG +   EL+
Sbjct: 121 KITPGMLMAAARLDIPTIVVTAGPMMAGRGVEGRRFSFVTDTFEAMARYKAGVIDAKELQ 180

Query: 179 ELERCACPGPRSCAGLFTANTMACLTEALGMSLPGCATAHAVSSRKRQIARLSGKRIVEM 238
             E  ACPG  SC GLFTANTMA LTE LGMSLP C TA AVS+ KR+IA  SG++IV++
Sbjct: 181 VCEDNACPGMGSCQGLFTANTMAILTETLGMSLPRCGTALAVSALKRRIAFASGEKIVDL 240

Query: 239 VQENLKPTMIMSQEAFENAVMVDLALGGSTNTTLHIPAIAAEIDGLNINLDLFDELSRVI 298
           V+  + P  I+++ AFENA+ VDLALGGS+NT LH+ AIA E  G+++ L+ FD LS+  
Sbjct: 241 VRNGVTPRQILTRAAFENAIRVDLALGGSSNTVLHLLAIAREA-GVDLPLETFDILSKET 299

Query: 299 PHIASISPAGEHMMLDLDRAGGIPAVLKTLEDHINRECVTCTGRTVQENIENVKVGHRDV 358
           P IAS++PAGE+ M DLD AGG+  VLK L   I ++  T  G T +E    V+     V
Sbjct: 300 PQIASMNPAGEYFMEDLDAAGGVVGVLKQLGGTI-KDSPTVLGLTTRELASTVESVDERV 358

Query: 359 IRPLDSPVHSEGGLAILRGNLAPRGSVVKQGAVAEDMMVHEGPAKVFNSEDECMEAIFGG 418
           IRP+  PV  EGG+A+L GNLAP+G+VVKQ  V+  MM  EG A+ F+SE+  M A+ GG
Sbjct: 359 IRPVSDPVKKEGGIAVLFGNLAPKGAVVKQSGVSAPMMQFEGTARCFDSEELAMAALMGG 418

Query: 419 RIDEGDVIVIRYEGPKGGPGMREMLNPTSAIAGMGL-ERVALITDGRFSGGTRGPCVGHV 477
           +I  GDV+VIRYEGPKGGPGMREML PT+ + G+GL + VAL+TDGRFSGGTRGPC+GH+
Sbjct: 419 KITSGDVVVIRYEGPKGGPGMREMLAPTATLMGLGLGDSVALVTDGRFSGGTRGPCIGHI 478

Query: 478 SPEAMEDGPLAAVNDGDIIRIDIPSRKLEVDLSPREIEERLQSAVKPRRSVK-GWLARYR 536
           SPEA E GP+A V +GD IR+DIP+RKLE+ +    + ER    V P   +K GWLARY 
Sbjct: 479 SPEAAEGGPIALVEEGDRIRLDIPNRKLELLVDESILAERRSRWVAPEPKIKTGWLARYA 538

Query: 537 KLAGSADTGAV 547
           K+  SA TGAV
Sbjct: 539 KVVTSAYTGAV 549


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: 981
Number of extensions: 46
Number of successful extensions: 7
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: 553
Length adjustment: 36
Effective length of query: 513
Effective length of database: 517
Effective search space:   265221
Effective search space used:   265221
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_004512108.1 GMET_RS06340 (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.8518.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.1e-234  763.5   1.8     7e-234  763.3   1.8    1.0  1  lcl|NCBI__GCF_000012925.1:WP_004512108.1  GMET_RS06340 dihydroxy-acid dehy


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000012925.1:WP_004512108.1  GMET_RS06340 dihydroxy-acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  763.3   1.8    7e-234    7e-234       1     542 [.      14     551 ..      14     552 .. 0.99

  Alignments for each domain:
  == domain 1  score: 763.3 bits;  conditional E-value: 7e-234
                                 TIGR00110   1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiam 69 
                                               ++ral+k tG+ + ++ kP+i+v+ s+t+++Pghv ++dl + ++++i++ Gg a+ f++ +v+DGiam
  lcl|NCBI__GCF_000012925.1:WP_004512108.1  14 PHRALIKGTGVPQSEMAKPFIGVATSFTDLIPGHVGMRDLERFIEKGIHSGGGYAFFFGIPGVCDGIAM 82 
                                               69******************************************************************* PP

                                 TIGR00110  70 gheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktk 138
                                               gh+Gm+ysLp+re+iaD ve+v++ah+lD+lv++++CDki+PGmlmaa+rl+iP+ivv+ Gpm+ag+  
  lcl|NCBI__GCF_000012925.1:WP_004512108.1  83 GHKGMHYSLPTRELIADMVESVAEAHRLDGLVLLTNCDKITPGMLMAAARLDIPTIVVTAGPMMAGRGV 151
                                               *******************************************************************99 PP

                                 TIGR00110 139 lsekid.lvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstll 206
                                                +++++ ++d fea+ +y+ag ++ +el+  e++acP+ gsC+Glftan+ma+lte+lG+slP ++t+l
  lcl|NCBI__GCF_000012925.1:WP_004512108.1 152 EGRRFSfVTDTFEAMARYKAGVIDAKELQVCEDNACPGMGSCQGLFTANTMAILTETLGMSLPRCGTAL 220
                                               9999983569*********************************************************** PP

                                 TIGR00110 207 atsaekkelakksgkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklsl 275
                                               a+sa k+++a  sg++iv+lv++ ++Pr+ilt++afenai +dlalGGs+ntvLhllaia+eagv+l l
  lcl|NCBI__GCF_000012925.1:WP_004512108.1 221 AVSALKRRIAFASGEKIVDLVRNGVTPRQILTRAAFENAIRVDLALGGSSNTVLHLLAIAREAGVDLPL 289
                                               ********************************************************************* PP

                                 TIGR00110 276 ddfdrlsrkvPllaklkPsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlr 344
                                               + fd ls+++P++a+++P+g++++edl++aGGv +vlk+l   g++ kd+ tv+G t  e +++v++  
  lcl|NCBI__GCF_000012925.1:WP_004512108.1 290 ETFDILSKETPQIASMNPAGEYFMEDLDAAGGVVGVLKQL--GGTI-KDSPTVLGLTTRELASTVESV- 354
                                               ****************************************..6666.5679************99999. PP

                                 TIGR00110 345 vdqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvke 413
                                                d+ vir++++pvkkegg+avL+Gnla++Gavvk++gv+  +++feG+a+ f+see a++a++ggk++ 
  lcl|NCBI__GCF_000012925.1:WP_004512108.1 355 -DERVIRPVSDPVKKEGGIAVLFGNLAPKGAVVKQSGVSAPMMQFEGTARCFDSEELAMAALMGGKITS 422
                                               .******************************************************************** PP

                                 TIGR00110 414 GdvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialv 482
                                               GdvvviryeGPkGgPGmremLaPt++l+glGLg++vaL+tDGrfsGgtrG++iGh+sPeaaegG+ialv
  lcl|NCBI__GCF_000012925.1:WP_004512108.1 423 GDVVVIRYEGPKGGPGMREMLAPTATLMGLGLGDSVALVTDGRFSGGTRGPCIGHISPEAAEGGPIALV 491
                                               ********************************************************************* PP

                                 TIGR00110 483 edGDkikiDienrkldlevseeelaerrakakkkearevkgaLakyaklvssadkGavld 542
                                               e+GD+i++Di+nrkl+l v+e  laerr +++++e++ + g+La+yak+v+sa +Gav++
  lcl|NCBI__GCF_000012925.1:WP_004512108.1 492 EEGDRIRLDIPNRKLELLVDESILAERRSRWVAPEPKIKTGWLARYAKVVTSAYTGAVTT 551
                                               *********************************************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (553 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: 00:00:00.04
# Mc/sec: 6.38
//
[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