Alignments for a candidate for ilvD in Haloechinothrix alba DSM 45207

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Haloechinothrix alba DSM 45207

Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate WP_089302216.1 CHB84_RS14910 dihydroxy-acid dehydratase

Query= SwissProt::P9WKJ5
         (575 letters)



>NCBI__GCF_900188115.1:WP_089302216.1
          Length = 566

 Score =  776 bits (2005), Expect = 0.0
 Identities = 393/558 (70%), Positives = 455/558 (81%), Gaps = 5/558 (0%)

Query: 18  KPRSRDVTDGLEKAAARGMLRAVGMDDEDFAKPQIGVASSWNEITPCNLSLDRLANAVKE 77
           KPRS +VT G E+  AR MLRAVGM D DF K QIG+ASSWN+ITPCNLSL RLA+  K 
Sbjct: 14  KPRSTEVTGGYERTPARAMLRAVGMTDSDFEKSQIGIASSWNQITPCNLSLARLADESKI 73

Query: 78  GVFSAGGYPLEFGTISVSDGISMGHEGMHFSLVSREVIADSVEVVMQAERLDGSVLLAGC 137
           GV  AGG+P+EFGTISVSDGISMGHEGM  SLVSREVIADSVE V+ AERLDG++LLAGC
Sbjct: 74  GVRDAGGFPMEFGTISVSDGISMGHEGMRASLVSREVIADSVECVVHAERLDGTILLAGC 133

Query: 138 DKSLPGMLMAAARLDLAAVFLYAGSILPGRAKLSDGSERDVTIIDAFEAVGACSRGLMSR 197
           DKSLPGMLMAAARLDLA+VFLYAGS LPG        + D+TI DAFE VGAC+ G +S 
Sbjct: 134 DKSLPGMLMAAARLDLASVFLYAGSTLPGHL-----GDNDITIQDAFEGVGACALGRIST 188

Query: 198 ADVDAIERAICPGEGACGGMYTANTMASAAEALGMSLPGSAAPPATDRRRDGFARRSGQA 257
            +++ IER  CPGEGACGGM+TANTMA+AAEALGMSLPGSA+PPA D+RRD +A++SG+A
Sbjct: 189 DELEEIERHACPGEGACGGMFTANTMAAAAEALGMSLPGSASPPAPDKRRDSYAQKSGEA 248

Query: 258 VVELLRRGITARDILTKEAFENAIAVVMAFGGSTNAVLHLLAIAHEANVALSLQDFSRIG 317
           V+EL+ +GITAR +LT+EAFENAI VV A GGSTNAVLHLLAIA EA V L + +F+RIG
Sbjct: 249 VIELINKGITARQVLTREAFENAITVVTALGGSTNAVLHLLAIAREARVDLDIDEFNRIG 308

Query: 318 SGVPHLADVKPFGRHVMSDVDHIGGVPVVMKALLDAGLLHGDCLTVTGHTMAENLAAITP 377
              P LADVKPFGR+VMSD+D IGGVPVVMKALLDAGLLHG+  TVTG TMAENLA I P
Sbjct: 309 ERTPLLADVKPFGRYVMSDIDSIGGVPVVMKALLDAGLLHGNVRTVTGRTMAENLAEIAP 368

Query: 378 PDPDGKVLRALANPIHPSGGITILHGSLAPEGAVVKTAGFDSDVFEGTARVFDGERAALD 437
           PDPDGK++ A ++P+  +GG+TIL GSLAPEGAVVK+A     V EGTARVFD E+ A+ 
Sbjct: 369 PDPDGKIIAAASSPLAETGGLTILRGSLAPEGAVVKSASLTQAVTEGTARVFDDEQDAMA 428

Query: 438 ALEDGTITVGDAVVIRYEGPKGGPGMREMLAITGAIKGAGLGKDVLLLTDGRFSGGTTGL 497
           A+  G I  GDAVVIRYEGP GGPGMREMLA+T AIKGAGLG DVLL+TDGRFSG T G 
Sbjct: 429 AVTSGRINPGDAVVIRYEGPAGGPGMREMLAVTAAIKGAGLGSDVLLMTDGRFSGATHGP 488

Query: 498 CVGHIAPEAVDGGPIALLRNGDRIRLDVAGRVLDVLADPAEFASRQQDFSPPPPRYTTGV 557
           C+GH+APEA  GGPIAL+ +GDR+RLD+  R LDVL DP E A R++++ P  PRYT+GV
Sbjct: 489 CIGHVAPEAAHGGPIALVEDGDRVRLDLNERTLDVLVDPDELARRKENWKPREPRYTSGV 548

Query: 558 LSKYVKLVSSAAVGAVCG 575
           L+KY KLV SA  GAVCG
Sbjct: 549 LAKYAKLVGSAEDGAVCG 566


Lambda     K      H
   0.318    0.136    0.393 

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: 1156
Number of extensions: 49
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: 575
Length of database: 566
Length adjustment: 36
Effective length of query: 539
Effective length of database: 530
Effective search space:   285670
Effective search space used:   285670
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 (21.7 bits)
S2: 53 (25.0 bits)

Align candidate WP_089302216.1 CHB84_RS14910 (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.23723.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     3e-220  718.3   3.5   3.4e-220  718.1   3.5    1.0  1  lcl|NCBI__GCF_900188115.1:WP_089302216.1  CHB84_RS14910 dihydroxy-acid deh


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900188115.1:WP_089302216.1  CHB84_RS14910 dihydroxy-acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  718.1   3.5  3.4e-220  3.4e-220       1     540 [.      28     564 ..      28     566 .] 0.99

  Alignments for each domain:
  == domain 1  score: 718.1 bits;  conditional E-value: 3.4e-220
                                 TIGR00110   1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiam 69 
                                               +ara+l+a+G++d d+ek +i++++s+++i+P++++l  la+  k ++++aGg ++ef+ti+vsDGi+m
  lcl|NCBI__GCF_900188115.1:WP_089302216.1  28 PARAMLRAVGMTDSDFEKSQIGIASSWNQITPCNLSLARLADESKIGVRDAGGFPMEFGTISVSDGISM 96 
                                               579****************************************************************** PP

                                 TIGR00110  70 gheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktk 138
                                               gheGm+ sL+sre+iaDsve vv+a++lD+ ++++ CDk +PGmlmaa+rl++ +++ + G+  +g++ 
  lcl|NCBI__GCF_900188115.1:WP_089302216.1  97 GHEGMRASLVSREVIADSVECVVHAERLDGTILLAGCDKSLPGMLMAAARLDLASVFLYAGSTLPGHLG 165
                                               ********************************************************************9 PP

                                 TIGR00110 139 lsekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstlla 207
                                                 ++i++ d+fe+vg++a g++s +eleeier+acP+ g+C+G+ftan+ma+++ealG+slPgs++ +a
  lcl|NCBI__GCF_900188115.1:WP_089302216.1 166 -DNDITIQDAFEGVGACALGRISTDELEEIERHACPGEGACGGMFTANTMAAAAEALGMSLPGSASPPA 233
                                               .8******************************************************************* PP

                                 TIGR00110 208 tsaekkelakksgkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklsld 276
                                                ++++ + a+ksg+ ++el++k i+ r++lt+eafenait++ alGGstn+vLhllaia+ea v+l++d
  lcl|NCBI__GCF_900188115.1:WP_089302216.1 234 PDKRRDSYAQKSGEAVIELINKGITARQVLTREAFENAITVVTALGGSTNAVLHLLAIAREARVDLDID 302
                                               ********************************************************************* PP

                                 TIGR00110 277 dfdrlsrkvPllaklkPsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlrv 345
                                               +f+r+ +++Plla++kP g++v+ d++  GGv+ v+k l  +gllh ++ tvtG+t+ae+l+++     
  lcl|NCBI__GCF_900188115.1:WP_089302216.1 303 EFNRIGERTPLLADVKPFGRYVMSDIDSIGGVPVVMKALLDAGLLHGNVRTVTGRTMAENLAEIAPPDP 371
                                               ****************************************************************99988 PP

                                 TIGR00110 346 dqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeG 414
                                               d ++i++ ++p+ ++ggl +L+G+la+eGavvk a+  +   + eG+a+vf++e++a++a+ +g+++ G
  lcl|NCBI__GCF_900188115.1:WP_089302216.1 372 DGKIIAAASSPLAETGGLTILRGSLAPEGAVVKSASLTQ--AVTEGTARVFDDEQDAMAAVTSGRINPG 438
                                               999************************************..7889************************ PP

                                 TIGR00110 415 dvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialve 483
                                               d vviryeGP GgPGmremLa t+a++g+GLg++v L+tDGrfsG+t+G++iGhv+Peaa+gG+ialve
  lcl|NCBI__GCF_900188115.1:WP_089302216.1 439 DAVVIRYEGPAGGPGMREMLAVTAAIKGAGLGSDVLLMTDGRFSGATHGPCIGHVAPEAAHGGPIALVE 507
                                               ********************************************************************* PP

                                 TIGR00110 484 dGDkikiDienrkldlevseeelaerrakakkkearevkgaLakyaklvssadkGav 540
                                               dGD++++D+++r+ld+ v+ +ela+r++++k++e+r+++g+Lakyaklv sa++Gav
  lcl|NCBI__GCF_900188115.1:WP_089302216.1 508 DGDRVRLDLNERTLDVLVDPDELARRKENWKPREPRYTSGVLAKYAKLVGSAEDGAV 564
                                               ********************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (566 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: 00:00:00.02
# Mc/sec: 11.84
//
[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