Alignments for a candidate for ilvD in Thermus aquaticus YT-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Thermus aquaticus YT-1

Align dihydroxyacid dehydratase (EC 4.2.1.9) (characterized)
to candidate WP_053767874.1 BVI061214_RS07550 dihydroxy-acid dehydratase

Query= metacyc::MONOMER-18815
         (557 letters)



>NCBI__GCF_001280255.1:WP_053767874.1
          Length = 567

 Score =  547 bits (1410), Expect = e-160
 Identities = 275/552 (49%), Positives = 377/552 (68%), Gaps = 1/552 (0%)

Query: 6   RSQNITQGVARSPNRSMYYALGYKKEDFDKPMVGIANGHSTITPCNAGLQRLADAAIDAI 65
           RS  I +G+ ++P RSM  A+G   EDF +P VG+ N  +   PCN  L+ LA      +
Sbjct: 2   RSDRIKKGLQQAPARSMLRAVGVGDEDFGRPFVGVVNTFTDGMPCNYHLRELALDLKAGL 61

Query: 66  KASDANPQVFGTPTISDGMSMGTEGMKYSLISREVIADCIETAAQGQWMDGVVVIGGCDK 125
           + +   P  FG P ISDG+SMGT GM+ SL+SREVIAD IE  AQG   DG+ V+  CDK
Sbjct: 62  REAGVFPFEFGAPAISDGISMGTPGMRASLVSREVIADSIELVAQGYLYDGMAVLSACDK 121

Query: 126 NMPGGMIALARTNVPGIYVYGGTIKPGNWKGKDLTIVSSFEAVGEFTAGRMSQEDFEGVE 185
            +PGG + + R+ VPG+ +YGGTI PG W+G+ LTIV  FEAVG+  AGR++ E+   +E
Sbjct: 122 TIPGGAMGVIRSGVPGMVLYGGTIAPGEWRGRKLTIVEVFEAVGQRAAGRITDEELLEIE 181

Query: 186 KNACPSTGSCGGMYTANTMSSSFEALGMSLLYSSTMANPDQEKVDSAAESARVLVEAIKQ 245
           + A P  G+CGG YTANTM+ + E LG+S +  + +     EK  +  E+ R+L  AI+ 
Sbjct: 182 RRAIPGPGACGGQYTANTMAMALEVLGLSPMGYNAIPAVHPEKPRTTKEAGRILAWAIEH 241

Query: 246 DIKPRDIITRKSIENAVALIMATGGSTNAVLHYLAIAHAAEVEWTIDDFERIRRKVPVIC 305
           D KP+D +TR+S  NA+A + ATGGSTNAVLH LA+A    VE ++DDF+R+ RK PVI 
Sbjct: 242 DWKPQDFLTRRSFLNAIAAVAATGGSTNAVLHLLAMAKEVGVELSLDDFDRVSRKTPVIA 301

Query: 306 NLKPSGQYVATDLHKAGGIPQVMKILLKAGMLHGDCLTITGRTLAEELENVPDTPRADQD 365
           +L+P G Y A +L++AGG P V K LL+AG+L G+  T+TGRTLAEE+E         Q 
Sbjct: 302 DLRPWGTYTAWELYEAGGTPLVFKRLLEAGLLFGEEKTLTGRTLAEEVEQA-FREAEGQK 360

Query: 366 VILPIEKALYAEGHLAILKGNLAEEGAVAKITGLKNPVITGPARVFEDEQSAMEAILADK 425
           V+ P+E+AL  +G L +L+GNLA  GAV K+ G +     GPARVF+ E+ AM  +LA +
Sbjct: 361 VVFPVERALKPQGGLVVLRGNLAPRGAVLKLAGTERTYFEGPARVFDSEEEAMAKVLAKE 420

Query: 426 INAGDILVLRYLGPKGGPGMPEMLAPTSAIIGKGLGESVGFITDGRFSGGTWGMVVGHVA 485
           I  GD++V+RY+GPKG PGMPEML+ TSAI+G+GLG  V  +TDGRFSGGT G++VGH+A
Sbjct: 421 IRPGDVVVIRYVGPKGAPGMPEMLSVTSAIVGEGLGPEVALLTDGRFSGGTRGLMVGHIA 480

Query: 486 PEAYVGGTIALVQEGDSITIDAHKLLLQLNVADEELARRRANWKQPAPRYTRGVLAKFSK 545
           PEA+VGG IAL++EGD + ID    LL++ + +EELARR+ +WK   P +  GV A+++ 
Sbjct: 481 PEAFVGGPIALLKEGDRVRIDVENRLLEVLLPEEELARRKESWKPRPPAFRHGVFARYAA 540

Query: 546 LASTASKGAVTD 557
           L + A +GAV +
Sbjct: 541 LVAQADEGAVLE 552


Lambda     K      H
   0.316    0.133    0.386 

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: 980
Number of extensions: 53
Number of successful extensions: 3
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: 557
Length of database: 567
Length adjustment: 36
Effective length of query: 521
Effective length of database: 531
Effective search space:   276651
Effective search space used:   276651
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 53 (25.0 bits)

Align candidate WP_053767874.1 BVI061214_RS07550 (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.1832732.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.9e-206  672.1   0.0   3.4e-206  671.9   0.0    1.0  1  NCBI__GCF_001280255.1:WP_053767874.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001280255.1:WP_053767874.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  671.9   0.0  3.4e-206  3.4e-206       1     542 [.      14     552 ..      14     553 .. 0.99

  Alignments for each domain:
  == domain 1  score: 671.9 bits;  conditional E-value: 3.4e-206
                             TIGR00110   1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamgheG 73 
                                           +ar++l+a+G+ ded+++P+++vvn++t+ +P++ hl++la   k+++++aG  ++ef+  a+sDGi+mg+ G
  NCBI__GCF_001280255.1:WP_053767874.1  14 PARSMLRAVGVGDEDFGRPFVGVVNTFTDGMPCNYHLRELALDLKAGLREAGVFPFEFGAPAISDGISMGTPG 86 
                                           579********************************************************************** PP

                             TIGR00110  74 mkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktklsekidlv 146
                                           m+ sL+sre+iaDs+e v+++  +D++ v+s+CDk +PG  m+++r  +P +v +GG++++g+ + ++k+++v
  NCBI__GCF_001280255.1:WP_053767874.1  87 MRASLVSREVIADSIELVAQGYLYDGMAVLSACDKTIPGGAMGVIRSGVPGMVLYGGTIAPGEWR-GRKLTIV 158
                                           *****************************************************************.9****** PP

                             TIGR00110 147 dvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllatsaekkelakks 219
                                           +vfeavg+ aag++++eel eier a P++g+C+G +tan+ma++ e+lGls  g  +++a++ ek +++k++
  NCBI__GCF_001280255.1:WP_053767874.1 159 EVFEAVGQRAAGRITDEELLEIERRAIPGPGACGGQYTANTMAMALEVLGLSPMGYNAIPAVHPEKPRTTKEA 231
                                           ************************************************************************* PP

                             TIGR00110 220 gkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklslddfdrlsrkvPllaklk 292
                                           g+ +  +++++ kP+d+lt+++f nai+ + a+GGstn+vLhlla+ake+gv+lslddfdr+srk+P++a+l+
  NCBI__GCF_001280255.1:WP_053767874.1 232 GRILAWAIEHDWKPQDFLTRRSFLNAIAAVAATGGSTNAVLHLLAMAKEVGVELSLDDFDRVSRKTPVIADLR 304
                                           ************************************************************************* PP

                             TIGR00110 293 PsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlrvdqdvirsldnpvkkegglav 365
                                           P g +   +l +aGG++ v+k l ++gll  + +t+tG+tlae++e++    ++q+v+ +++ ++k +ggl v
  NCBI__GCF_001280255.1:WP_053767874.1 305 PWGTYTAWELYEAGGTPLVFKRLLEAGLLFGEEKTLTGRTLAEEVEQAFREAEGQKVVFPVERALKPQGGLVV 377
                                           ************************************************************************* PP

                             TIGR00110 366 LkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeGdvvviryeGPkGgPGmremLaPts 438
                                           L+Gnla++Gav k ag e   ++feGpa+vf+seeea++ +l+++++ Gdvvviry GPkG+PGm+emL  ts
  NCBI__GCF_001280255.1:WP_053767874.1 378 LRGNLAPRGAVLKLAGTER--TYFEGPARVFDSEEEAMAKVLAKEIRPGDVVVIRYVGPKGAPGMPEMLSVTS 448
                                           ******************9..**************************************************** PP

                             TIGR00110 439 alvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDienrkldlevseeelaerra 511
                                           a+vg GLg +vaL+tDGrfsGgtrGl++Gh++Pea +gG+ial+++GD+++iD+enr l++ + eeela+r++
  NCBI__GCF_001280255.1:WP_053767874.1 449 AIVGEGLGPEVALLTDGRFSGGTRGLMVGHIAPEAFVGGPIALLKEGDRVRIDVENRLLEVLLPEEELARRKE 521
                                           ************************************************************************* PP

                             TIGR00110 512 kakkkearevkgaLakyaklvssadkGavld 542
                                           ++k++ +   +g++a+ya lv++ad+Gavl+
  NCBI__GCF_001280255.1:WP_053767874.1 522 SWKPRPPAFRHGVFARYAALVAQADEGAVLE 552
                                           *****************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (567 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 18.91
//
[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