Alignments for a candidate for ilvD in Prosthecochloris aestuarii DSM 271

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Prosthecochloris aestuarii DSM 271

Align dihydroxy-acid dehydratase subunit (EC 4.2.1.9) (characterized)
to candidate WP_041702216.1 PAES_RS03730 dihydroxy-acid dehydratase

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



>NCBI__GCF_000020625.1:WP_041702216.1
          Length = 563

 Score =  569 bits (1467), Expect = e-167
 Identities = 295/558 (52%), Positives = 395/558 (70%), Gaps = 10/558 (1%)

Query: 1   MKSDTIKRGIQRAPHRSLLARCGL--TDDDFEKPFIGIANSYTDIVPGHIHLRELAEAVK 58
           M+SDTIK+G ++APHRSLL   G   +  DF+KPFIGI NSY +++PGH HL+EL    K
Sbjct: 1   MRSDTIKKGFEKAPHRSLLNATGAIRSQSDFKKPFIGICNSYNELIPGHTHLQELGRIAK 60

Query: 59  EGVNAAGGVAFEFNTMAICDGIAMNHDGMKYSLASREIVADTVESMAMAHALDGLVLLPT 118
           E +  AGGV FEFNT+ +CDGIAM H GM+YSLASRE++AD+VE++A AH LDGLV +P 
Sbjct: 61  EAIREAGGVPFEFNTIGVCDGIAMGHMGMRYSLASRELIADSVETVAQAHRLDGLVCIPN 120

Query: 119 CDKIVPGMLMAAARLDIPAIVVTGGPMLPGEF-KGRKVDLINVYEGVGTVSAGEMSEDEL 177
           CDKI PGM+M   R++IPA+ V+GGPM  G    G+ VDLI+V+E VG  S GE+S++EL
Sbjct: 121 CDKITPGMMMGVLRINIPAVFVSGGPMKAGHTPSGKTVDLISVFEAVGQCSTGEISDEEL 180

Query: 178 EELERCACPGPRSCAGLFTANTMACLTEALGMSLPGCATAHAVSSRKRQIARLSGKRIVE 237
             +E  ACP   SC+G+FTAN+M CL EALG +LPG  T  AV   ++++ + +   I++
Sbjct: 181 RSIESNACPTCGSCSGMFTANSMNCLAEALGFALPGNGTILAVDQGRKELVKQASAVILD 240

Query: 238 MVQENLKPTMIMSQEAFENAVMVDLALGGSTNTTLHIPAIAAEIDGLNINLDLFDELSRV 297
           +VQ ++KP  I+S+++  NA  +DLA+GGSTNT LH  AIA E + L  +    ++LS  
Sbjct: 241 LVQNDIKPRDILSRKSMLNAFALDLAMGGSTNTILHTLAIANEAE-LEFDFSELNDLSAR 299

Query: 298 IPHIASISPAGEHMML-DLDRAGGIPAVLKTL---EDHINRECVTCTGRTVQENIENVKV 353
            P+I  +SPA   + + D+DRAGGI A+L  L   +  ++    T TG+T+ ENI   +V
Sbjct: 300 TPYICKVSPATPDVHIEDVDRAGGISAILHELSKIDGLLDLSTPTVTGKTLGENISGAEV 359

Query: 354 GHRDVIRPLDSPVHSEGGLAILRGNLAPRGSVVKQGAVAEDMMVHEGPAKVFNSEDECME 413
             R VIR ++ P    GGLA+L GNLAP G+VVK GAV+  MM H GPA++F  +D+ ++
Sbjct: 360 RDRKVIRSVEEPYSPTGGLAVLYGNLAPDGAVVKTGAVSPSMMKHTGPARIFECQDDAIK 419

Query: 414 AIFGGRIDEGDVIVIRYEGPKGGPGMREMLNPTSAIAGMGL-ERVALITDGRFSGGTRGP 472
            I  G + +GDV++IRYEGPKGGPGM EML+PTSAI G GL + VALITDGRFSGG+RG 
Sbjct: 420 GIMDGDVVKGDVVIIRYEGPKGGPGMPEMLSPTSAIMGRGLGDSVALITDGRFSGGSRGA 479

Query: 473 CVGHVSPEAMEDGPLAAVNDGDIIRIDIPSRKLEVDLSPREIEERLQS-AVKPRRSVKGW 531
           CVGHVSPEA E GP+AAV +GD++ IDIP+R + VDLS   IE+R  S  V   +  KG+
Sbjct: 480 CVGHVSPEAAEKGPIAAVENGDLVTIDIPNRTISVDLSDEVIEQRQASLPVFEPKVKKGY 539

Query: 532 LARYRKLAGSADTGAVLR 549
           LARY  +  SA+TGA+L+
Sbjct: 540 LARYAHMVTSANTGAILK 557


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: 1011
Number of extensions: 55
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: 563
Length adjustment: 36
Effective length of query: 513
Effective length of database: 527
Effective search space:   270351
Effective search space used:   270351
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_041702216.1 PAES_RS03730 (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.20461.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.9e-248  811.3   4.2   2.2e-248  811.1   4.2    1.0  1  lcl|NCBI__GCF_000020625.1:WP_041702216.1  PAES_RS03730 dihydroxy-acid dehy


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000020625.1:WP_041702216.1  PAES_RS03730 dihydroxy-acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  811.1   4.2  2.2e-248  2.2e-248       1     542 [.      14     557 ..      14     558 .. 0.99

  Alignments for each domain:
  == domain 1  score: 811.1 bits;  conditional E-value: 2.2e-248
                                 TIGR00110   1 aarallkatGl..kdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGi 67 
                                               ++r+ll+atG   ++ d++kP+i+++nsy+e++Pgh hl++l++++ke+i++aGgv++efnti+v+DGi
  lcl|NCBI__GCF_000020625.1:WP_041702216.1  14 PHRSLLNATGAirSQSDFKKPFIGICNSYNELIPGHTHLQELGRIAKEAIREAGGVPFEFNTIGVCDGI 82 
                                               69********744679***************************************************** PP

                                 TIGR00110  68 amgheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagk 136
                                               amgh Gm+ysL+sre+iaDsvetv++ah+lD+lv+i++CDki+PGm+m++lr+niPa++vsGGpm+ag+
  lcl|NCBI__GCF_000020625.1:WP_041702216.1  83 AMGHMGMRYSLASRELIADSVETVAQAHRLDGLVCIPNCDKITPGMMMGVLRINIPAVFVSGGPMKAGH 151
                                               ********************************************************************* PP

                                 TIGR00110 137 tklsekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstl 205
                                               t  ++ +dl++vfeavg+++ g++s+eel++ie +acPt+gsCsG+ftansm+cl+ealG++lPg++t+
  lcl|NCBI__GCF_000020625.1:WP_041702216.1 152 TPSGKTVDLISVFEAVGQCSTGEISDEELRSIESNACPTCGSCSGMFTANSMNCLAEALGFALPGNGTI 220
                                               ********************************************************************* PP

                                 TIGR00110 206 latsaekkelakksgkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvkls 274
                                               la+++ +kel+k++++ i +lv+++ikPrdil+++++ na++ldla+GGstnt+Lh+laia+ea+++++
  lcl|NCBI__GCF_000020625.1:WP_041702216.1 221 LAVDQGRKELVKQASAVILDLVQNDIKPRDILSRKSMLNAFALDLAMGGSTNTILHTLAIANEAELEFD 289
                                               ********************************************************************* PP

                                 TIGR00110 275 lddfdrlsrkvPllaklkPsgkkv.iedlhraGGvsavlkeldk.egllhkdaltvtGktlaetlekvk 341
                                               +++++ ls ++P ++k++P++  v ied++raGG+sa+l+el+k +gll+  + tvtGktl+e+++ ++
  lcl|NCBI__GCF_000020625.1:WP_041702216.1 290 FSELNDLSARTPYICKVSPATPDVhIEDVDRAGGISAILHELSKiDGLLDLSTPTVTGKTLGENISGAE 358
                                               *********************9988*****************998999********************* PP

                                 TIGR00110 342 vlrvdqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggk 410
                                               v+  d++virs+++p++ +gglavL+Gnla++Gavvk+++v+ +++k++Gpa++fe +++a+++i++g+
  lcl|NCBI__GCF_000020625.1:WP_041702216.1 359 VR--DRKVIRSVEEPYSPTGGLAVLYGNLAPDGAVVKTGAVSPSMMKHTGPARIFECQDDAIKGIMDGD 425
                                               **..***************************************************************** PP

                                 TIGR00110 411 vkeGdvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGai 479
                                               v +Gdvv+iryeGPkGgPGm+emL Ptsa++g GLg++vaLitDGrfsGg+rG ++GhvsPeaae G+i
  lcl|NCBI__GCF_000020625.1:WP_041702216.1 426 VVKGDVVIIRYEGPKGGPGMPEMLSPTSAIMGRGLGDSVALITDGRFSGGSRGACVGHVSPEAAEKGPI 494
                                               ********************************************************************* PP

                                 TIGR00110 480 alvedGDkikiDienrkldlevseeelaerrakakkkearevkgaLakyaklvssadkGavld 542
                                               a ve+GD ++iDi+nr++ +++s+e +++r+a+    e++ +kg+La+ya++v+sa++Ga+l+
  lcl|NCBI__GCF_000020625.1:WP_041702216.1 495 AAVENGDLVTIDIPNRTISVDLSDEVIEQRQASLPVFEPKVKKGYLARYAHMVTSANTGAILK 557
                                               *************************************************************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (563 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: 00:00:00.02
# Mc/sec: 11.63
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 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 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