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.1412249.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  NCBI__GCF_000012925.1:WP_004512108.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000012925.1:WP_004512108.1  
   #    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 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamgheG 73 
                                           ++ral+k tG+ + ++ kP+i+v+ s+t+++Pghv ++dl + ++++i++ Gg a+ f++ +v+DGiamgh+G
  NCBI__GCF_000012925.1:WP_004512108.1  14 PHRALIKGTGVPQSEMAKPFIGVATSFTDLIPGHVGMRDLERFIEKGIHSGGGYAFFFGIPGVCDGIAMGHKG 86 
                                           69*********************************************************************** PP

                             TIGR00110  74 mkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktklsekid.l 145
                                           m+ysLp+re+iaD ve+v++ah+lD+lv++++CDki+PGmlmaa+rl+iP+ivv+ Gpm+ag+   +++++ +
  NCBI__GCF_000012925.1:WP_004512108.1  87 MHYSLPTRELIADMVESVAEAHRLDGLVLLTNCDKITPGMLMAAARLDIPTIVVTAGPMMAGRGVEGRRFSfV 159
                                           ***************************************************************9999999835 PP

                             TIGR00110 146 vdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllatsaekkelakk 218
                                           +d fea+ +y+ag ++ +el+  e++acP+ gsC+Glftan+ma+lte+lG+slP ++t+la+sa k+++a  
  NCBI__GCF_000012925.1:WP_004512108.1 160 TDTFEAMARYKAGVIDAKELQVCEDNACPGMGSCQGLFTANTMAILTETLGMSLPRCGTALAVSALKRRIAFA 232
                                           69*********************************************************************** PP

                             TIGR00110 219 sgkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklslddfdrlsrkvPllakl 291
                                           sg++iv+lv++ ++Pr+ilt++afenai +dlalGGs+ntvLhllaia+eagv+l l+ fd ls+++P++a++
  NCBI__GCF_000012925.1:WP_004512108.1 233 SGEKIVDLVRNGVTPRQILTRAAFENAIRVDLALGGSSNTVLHLLAIAREAGVDLPLETFDILSKETPQIASM 305
                                           ************************************************************************* PP

                             TIGR00110 292 kPsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlrvdqdvirsldnpvkkeggla 364
                                           +P+g++++edl++aGGv +vlk+l   g++ kd+ tv+G t  e +++v++   d+ vir++++pvkkegg+a
  NCBI__GCF_000012925.1:WP_004512108.1 306 NPAGEYFMEDLDAAGGVVGVLKQL--GGTI-KDSPTVLGLTTRELASTVESV--DERVIRPVSDPVKKEGGIA 373
                                           ************************..6666.5679************99999..******************* PP

                             TIGR00110 365 vLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeGdvvviryeGPkGgPGmremLaPt 437
                                           vL+Gnla++Gavvk++gv+  +++feG+a+ f+see a++a++ggk++ GdvvviryeGPkGgPGmremLaPt
  NCBI__GCF_000012925.1:WP_004512108.1 374 VLFGNLAPKGAVVKQSGVSAPMMQFEGTARCFDSEELAMAALMGGKITSGDVVVIRYEGPKGGPGMREMLAPT 446
                                           ************************************************************************* PP

                             TIGR00110 438 salvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDienrkldlevseeelaerr 510
                                           ++l+glGLg++vaL+tDGrfsGgtrG++iGh+sPeaaegG+ialve+GD+i++Di+nrkl+l v+e  laerr
  NCBI__GCF_000012925.1:WP_004512108.1 447 ATLMGLGLGDSVALVTDGRFSGGTRGPCIGHISPEAAEGGPIALVEEGDRIRLDIPNRKLELLVDESILAERR 519
                                           ************************************************************************* PP

                             TIGR00110 511 akakkkearevkgaLakyaklvssadkGavld 542
                                            +++++e++ + g+La+yak+v+sa +Gav++
  NCBI__GCF_000012925.1:WP_004512108.1 520 SRWVAPEPKIKTGWLARYAKVVTSAYTGAVTT 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 29.25
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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