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_089301226.1 CHB84_RS09885 dihydroxy-acid dehydratase

Query= SwissProt::P9WKJ5
         (575 letters)



>NCBI__GCF_900188115.1:WP_089301226.1
          Length = 569

 Score =  829 bits (2141), Expect = 0.0
 Identities = 422/575 (73%), Positives = 475/575 (82%), Gaps = 6/575 (1%)

Query: 1   MPQTTDEAASVSTVADIKPRSRDVTDGLEKAAARGMLRAVGMDDEDFAKPQIGVASSWNE 60
           MP TT +  +V      +PRS +VT+GL+K AARG+LRA G+ D D AK Q+GVASSWNE
Sbjct: 1   MPPTTPDTPAV------RPRSGEVTEGLDKTAARGLLRAAGLGDADLAKFQVGVASSWNE 54

Query: 61  ITPCNLSLDRLANAVKEGVFSAGGYPLEFGTISVSDGISMGHEGMHFSLVSREVIADSVE 120
           ITPCNLSLDRLA AVK+GV +AG YPLEFGTISVSDGISMGH GMHFSLVSREVIADSVE
Sbjct: 55  ITPCNLSLDRLAGAVKDGVHAAGAYPLEFGTISVSDGISMGHRGMHFSLVSREVIADSVE 114

Query: 121 VVMQAERLDGSVLLAGCDKSLPGMLMAAARLDLAAVFLYAGSILPGRAKLSDGSERDVTI 180
            VM+AER+DGSVLLAGCDKSLPGMLMAAARLDLA+VF YAG+ LPG    SDG+ R VTI
Sbjct: 115 TVMEAERMDGSVLLAGCDKSLPGMLMAAARLDLASVFCYAGTALPGLVTTSDGTRRQVTI 174

Query: 181 IDAFEAVGACSRGLMSRADVDAIERAICPGEGACGGMYTANTMASAAEALGMSLPGSAAP 240
           +DAFEAVGACSRGLM R DV+ IER  CP EGAC GMY+ANTMA   EALGMSLPGSAAP
Sbjct: 175 VDAFEAVGACSRGLMPRDDVETIERGYCPSEGACAGMYSANTMAGVGEALGMSLPGSAAP 234

Query: 241 PATDRRRDGFARRSGQAVVELLRRGITARDILTKEAFENAIAVVMAFGGSTNAVLHLLAI 300
           PATDRRR   AR +G+AVVELL R ITARDILT+EAFENA+AVVMA GGSTNAVLHLLAI
Sbjct: 235 PATDRRRSVHAREAGRAVVELLARDITARDILTREAFENAVAVVMALGGSTNAVLHLLAI 294

Query: 301 AHEANVALSLQDFSRIGSGVPHLADVKPFGRHVMSDVDHIGGVPVVMKALLDAGLLHGDC 360
           A EA V LSL DF+RI + VPHLADV+PFGRHVM DVD +GG+PVVMKALLDAGL+HGD 
Sbjct: 295 AREAEVELSLDDFARINARVPHLADVRPFGRHVMVDVDRVGGIPVVMKALLDAGLVHGDA 354

Query: 361 LTVTGHTMAENLAAITPPDPDGKVLRALANPIHPSGGITILHGSLAPEGAVVKTAGFDSD 420
           LTVTG T+AENLA I PP PDG VLR   +PIHP+GGIT+L+GSLAP+GAVVK+AG++  
Sbjct: 355 LTVTGRTLAENLAEIDPPCPDGTVLRPPDDPIHPTGGITVLNGSLAPDGAVVKSAGYEGT 414

Query: 421 VFEGTARVFDGERAALDALEDGTITVGDAVVIRYEGPKGGPGMREMLAITGAIKGAGLGK 480
            F G ARVFDGE AA+DA   GTI+ GD VVIRYEGP+GGPGMREMLAITGAIKGAGLGK
Sbjct: 415 EFSGPARVFDGESAAMDAFAAGTISAGDVVVIRYEGPRGGPGMREMLAITGAIKGAGLGK 474

Query: 481 DVLLLTDGRFSGGTTGLCVGHIAPEAVDGGPIALLRNGDRIRLDVAGRVLDVLADPAEFA 540
           DVLLLTDGRFSGGTTGLCVGHIAPEA D GPIAL ++GDR+RLD+    LD+L D  E A
Sbjct: 475 DVLLLTDGRFSGGTTGLCVGHIAPEAADTGPIALAQDGDRVRLDLHSGSLDLLVDGEELA 534

Query: 541 SRQQDFSPPPPRYTTGVLSKYVKLVSSAAVGAVCG 575
            R++  +P       GVL +Y ++V+SAA GA CG
Sbjct: 535 RRKERHTPRGSGTARGVLGRYARMVTSAANGATCG 569


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: 1266
Number of extensions: 52
Number of successful extensions: 2
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: 569
Length adjustment: 36
Effective length of query: 539
Effective length of database: 533
Effective search space:   287287
Effective search space used:   287287
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_089301226.1 CHB84_RS09885 (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.14958.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.7e-211  688.3   2.7   4.2e-211  688.1   2.7    1.0  1  lcl|NCBI__GCF_900188115.1:WP_089301226.1  CHB84_RS09885 dihydroxy-acid deh


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900188115.1:WP_089301226.1  CHB84_RS09885 dihydroxy-acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  688.1   2.7  4.2e-211  4.2e-211       2     540 ..      27     567 ..      26     569 .] 0.99

  Alignments for each domain:
  == domain 1  score: 688.1 bits;  conditional E-value: 4.2e-211
                                 TIGR00110   2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamg 70 
                                               ar ll+a+Gl d+dl k +++v++s++ei+P++++l+ la +vk++++aaG+ + ef+ti+vsDGi+mg
  lcl|NCBI__GCF_900188115.1:WP_089301226.1  27 ARGLLRAAGLGDADLAKFQVGVASSWNEITPCNLSLDRLAGAVKDGVHAAGAYPLEFGTISVSDGISMG 95 
                                               799****************************************************************** PP

                                 TIGR00110  71 heGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktkl 139
                                               h+Gm++sL+sre+iaDsvetv++a+++D+ v+++ CDk +PGmlmaa+rl++ +++ + G+  +g +++
  lcl|NCBI__GCF_900188115.1:WP_089301226.1  96 HRGMHFSLVSREVIADSVETVMEAERMDGSVLLAGCDKSLPGMLMAAARLDLASVFCYAGTALPGLVTT 164
                                               *****************************************************************9998 PP

                                 TIGR00110 140 ....sekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsst 204
                                                    +++++vd+feavg+++ g +  +++e+ier  cP+ g+C+G++ an+ma + ealG+slPgs++
  lcl|NCBI__GCF_900188115.1:WP_089301226.1 165 sdgtRRQVTIVDAFEAVGACSRGLMPRDDVETIERGYCPSEGACAGMYSANTMAGVGEALGMSLPGSAA 233
                                               4544579************************************************************** PP

                                 TIGR00110 205 llatsaekkelakksgkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvkl 273
                                                +at+ ++   a+++g+ +vel+ ++i+ rdilt+eafena+++++alGGstn+vLhllaia+ea+v+l
  lcl|NCBI__GCF_900188115.1:WP_089301226.1 234 PPATDRRRSVHAREAGRAVVELLARDITARDILTREAFENAVAVVMALGGSTNAVLHLLAIAREAEVEL 302
                                               ********************************************************************* PP

                                 TIGR00110 274 slddfdrlsrkvPllaklkPsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkv 342
                                               slddf r++ +vP+la+++P g++v++d++r+GG++ v+k l  +gl+h daltvtG+tlae+l++++ 
  lcl|NCBI__GCF_900188115.1:WP_089301226.1 303 SLDDFARINARVPHLADVRPFGRHVMVDVDRVGGIPVVMKALLDAGLVHGDALTVTGRTLAENLAEIDP 371
                                               ********************************************************************* PP

                                 TIGR00110 343 lrvdqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkv 411
                                                  d  v+r+ d+p++ +gg+ vL G+la++Gavvk ag e   ++f Gpa+vf+ e +a++a  +g +
  lcl|NCBI__GCF_900188115.1:WP_089301226.1 372 PCPDGTVLRPPDDPIHPTGGITVLNGSLAPDGAVVKSAGYEG--TEFSGPARVFDGESAAMDAFAAGTI 438
                                               *99***************************************..************************* PP

                                 TIGR00110 412 keGdvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaia 480
                                               ++GdvvviryeGP+GgPGmremLa t a++g+GLgk+v L+tDGrfsGgt+Gl++Gh++Peaa  G+ia
  lcl|NCBI__GCF_900188115.1:WP_089301226.1 439 SAGDVVVIRYEGPRGGPGMREMLAITGAIKGAGLGKDVLLLTDGRFSGGTTGLCVGHIAPEAADTGPIA 507
                                               ********************************************************************* PP

                                 TIGR00110 481 lvedGDkikiDienrkldlevseeelaerrakakkkearevkgaLakyaklvssadkGav 540
                                               l +dGD++++D+++  ldl v+ eela+r++++++++  + +g+L +ya++v+sa +Ga 
  lcl|NCBI__GCF_900188115.1:WP_089301226.1 508 LAQDGDRVRLDLHSGSLDLLVDGEELARRKERHTPRGSGTARGVLGRYARMVTSAANGAT 567
                                               **********************************************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (569 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.04
# Mc/sec: 7.62
//
[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