Alignments for a candidate for ilvD in Thiohalomonas denitrificans HLD2

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Thiohalomonas denitrificans HLD2

Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate WP_092995422.1 BLP65_RS06935 dihydroxy-acid dehydratase

Query= SwissProt::P55186
         (617 letters)



>NCBI__GCF_900102855.1:WP_092995422.1
          Length = 617

 Score =  934 bits (2415), Expect = 0.0
 Identities = 465/617 (75%), Positives = 529/617 (85%), Gaps = 1/617 (0%)

Query: 1   MPPYRSRTTTHGRNMAGARGLWRATGMKDEDFG-KPIIAVANSFTQFVPGHVHLKDLGQL 59
           MP YRS T+THGRNMAGAR LWRATGMKD+DFG KPIIA+ANSFTQFVPGHVHLKD+GQL
Sbjct: 1   MPRYRSWTSTHGRNMAGARALWRATGMKDDDFGSKPIIAIANSFTQFVPGHVHLKDMGQL 60

Query: 60  VAREIEAAGGVAKEFNTIAVDDGIAMGHGGMLYSLPSRDLIADSVEYMVNAHCADAIVCI 119
           VAREIEAAGGVAKEFNTIAVDDGIAMGHGGMLYSLPSR++IADSVEYMVNAHCADA+VCI
Sbjct: 61  VAREIEAAGGVAKEFNTIAVDDGIAMGHGGMLYSLPSREIIADSVEYMVNAHCADALVCI 120

Query: 120 SNCDKITPGMLMAAMRLNIPVVFVSGGPMEAGKVTVKGKIRALDLVDAMVVAADDSYSDE 179
           SNCDKITPGML AAMRLNIP +FVSGGPMEAGK  VKG    LDLVDAMV AAD + +DE
Sbjct: 121 SNCDKITPGMLNAAMRLNIPTIFVSGGPMEAGKAVVKGGEVHLDLVDAMVAAADPNETDE 180

Query: 180 EVEAIEKAACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSVLATHADREALFKEAGRVV 239
           +VE +E++ACPTCGSCSGMFTANSMNCLTEALGLSLPGNG++LATHADRE LFKEAGR+V
Sbjct: 181 DVETLERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGTLLATHADRERLFKEAGRMV 240

Query: 240 VDLCQRWYEQEDATALPRGIATRAAFENAMSLDIAMGGSTNTVLHLLAAAHEGGIDFSMA 299
           V L +RWYE++DA+ LPR IAT  AFENAMSLDIAMGGSTNT+LHLLAAA EG ++F+MA
Sbjct: 241 VALAKRWYEEDDASVLPRSIATFEAFENAMSLDIAMGGSTNTILHLLAAAREGEVEFTMA 300

Query: 300 DIDRLSRHVPCLSKVAPAKSDVHMEDVHRAGGVMAILGELERGGLIDASQPTVHAPTMGE 359
           DIDRLSR VP L +VAPA    H+EDVHRAGG+MAILGE+ERGGL+    PTVHA ++GE
Sbjct: 301 DIDRLSRRVPHLCQVAPATPQYHIEDVHRAGGIMAILGEMERGGLLHRDVPTVHAGSIGE 360

Query: 360 ALARWDIGRTNSQIAHEFFKAAPGGKPTQVAFSQAARWEELDLDRENGVIRSVEHPFSKD 419
           A+  WD+ RT       F++AAPGG PTQ AFSQ  R+  LDLDRENG IR +EH FSK+
Sbjct: 361 AIDLWDVRRTRDAKRWTFYQAAPGGVPTQQAFSQDKRYASLDLDRENGCIRDMEHAFSKE 420

Query: 420 GGLAVLFGNLAPEGCIVKTAGVDESILTFRGTARVFESQDAAVSGILGGQVKAGEVVVIR 479
           GGLAVL+GN+A EGC+VKTAGVDESIL F G A + E+Q+ AV  IL G+VKAG+VV+IR
Sbjct: 421 GGLAVLYGNIAEEGCVVKTAGVDESILKFSGPAVICEAQEEAVEKILSGEVKAGDVVIIR 480

Query: 480 YEGPKGGPGMQEMLYPTTYLKSKGLGAACALVTDGRFSGGTSGLSIGHVSPEAGEGGLIA 539
           YEGP+GGPGMQEMLYPT+Y+KS GLG ACAL+TDGRFSGGTSGLSIGHVSPEA EGG I 
Sbjct: 481 YEGPRGGPGMQEMLYPTSYIKSMGLGKACALLTDGRFSGGTSGLSIGHVSPEAAEGGAIG 540

Query: 540 LVETGDPILIDIPTRGITLEVSDAVLAARREAQLARGKDAWTPLNRKRDLTPALRAYAAM 599
           LVE+GD I IDIP R I + +SD  L  RREA  ARG  AW P++R+R ++ AL+AYAAM
Sbjct: 541 LVESGDTIEIDIPNRSIRVALSDEELGQRREAMQARGPKAWKPVDRERQVSDALKAYAAM 600

Query: 600 TTNAARGAVRDVSQIER 616
           TT+AARGAVRDVSQ+E+
Sbjct: 601 TTSAARGAVRDVSQLEK 617


Lambda     K      H
   0.318    0.134    0.395 

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: 1371
Number of extensions: 54
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: 617
Length of database: 617
Length adjustment: 37
Effective length of query: 580
Effective length of database: 580
Effective search space:   336400
Effective search space used:   336400
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_092995422.1 BLP65_RS06935 (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.17437.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.6e-251  820.3   2.8   4.1e-251  820.1   2.8    1.0  1  lcl|NCBI__GCF_900102855.1:WP_092995422.1  BLP65_RS06935 dihydroxy-acid deh


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900102855.1:WP_092995422.1  BLP65_RS06935 dihydroxy-acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  820.1   2.8  4.1e-251  4.1e-251       2     542 ..      18     611 ..      17     612 .. 0.98

  Alignments for each domain:
  == domain 1  score: 820.1 bits;  conditional E-value: 4.1e-251
                                 TIGR00110   2 arallkatGlkdedle.kPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiam 69 
                                               aral++atG+kd+d++ kPiia++ns+t++vPghvhlkd+++lv++eieaaGgvakefntiav+DGiam
  lcl|NCBI__GCF_900102855.1:WP_092995422.1  18 ARALWRATGMKDDDFGsKPIIAIANSFTQFVPGHVHLKDMGQLVAREIEAAGGVAKEFNTIAVDDGIAM 86 
                                               79*************659*************************************************** PP

                                 TIGR00110  70 gheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktk 138
                                               gh+Gm+ysLpsreiiaDsve++v+ah++Dalv+is+CDki+PGml aa+rlniP+i+vsGGpmeagk  
  lcl|NCBI__GCF_900102855.1:WP_092995422.1  87 GHGGMLYSLPSREIIADSVEYMVNAHCADALVCISNCDKITPGMLNAAMRLNIPTIFVSGGPMEAGKAV 155
                                               *******************************************************************99 PP

                                 TIGR00110 139 lsekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstlla 207
                                               +      +d+++a++++a+++ ++e++e++ersacPt+gsCsG+ftansm+cltealGlslPg++tlla
  lcl|NCBI__GCF_900102855.1:WP_092995422.1 156 VKGGEVHLDLVDAMVAAADPNETDEDVETLERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGTLLA 224
                                               97777889************************************************************* PP

                                 TIGR00110 208 tsaekkelakksgkrivelvkknik.......PrdiltkeafenaitldlalGGstntvLhllaiakea 269
                                               t+a++++l+k++g+ +v l k+ ++       Pr+i+t eafena++ld+a+GGstnt+Lhlla+a+e 
  lcl|NCBI__GCF_900102855.1:WP_092995422.1 225 THADRERLFKEAGRMVVALAKRWYEeddasvlPRSIATFEAFENAMSLDIAMGGSTNTILHLLAAAREG 293
                                               ************************99******************************************* PP

                                 TIGR00110 270 gvklslddfdrlsrkvPllaklkPsgkkv.iedlhraGGvsavlkeldkegllhkdaltvtGktlaetl 337
                                               +v++++ d+drlsr+vP+l++++P++ ++ ied+hraGG++a+l+e+++ gllh+d+ tv   +++e +
  lcl|NCBI__GCF_900102855.1:WP_092995422.1 294 EVEFTMADIDRLSRRVPHLCQVAPATPQYhIEDVHRAGGIMAILGEMERGGLLHRDVPTVHAGSIGEAI 362
                                               **************************9988*************************************** PP

                                 TIGR00110 338 ekvkvlr...................................vdqdvirsldnpvkkegglavLkGnla 371
                                               +  +v+r                                    ++ +ir ++++++kegglavL+Gn+a
  lcl|NCBI__GCF_900102855.1:WP_092995422.1 363 DLWDVRRtrdakrwtfyqaapggvptqqafsqdkryasldldRENGCIRDMEHAFSKEGGLAVLYGNIA 431
                                               *****999******************************99665666*********************** PP

                                 TIGR00110 372 eeGavvkiagveedilkfeGpakvfeseeealeailggkvkeGdvvviryeGPkGgPGmremLaPtsal 440
                                               eeG+vvk+agv+e+ilkf Gpa + e +eea+e il+g+vk+Gdvv+iryeGP+GgPGm+emL+Pts++
  lcl|NCBI__GCF_900102855.1:WP_092995422.1 432 EEGCVVKTAGVDESILKFSGPAVICEAQEEAVEKILSGEVKAGDVVIIRYEGPRGGPGMQEMLYPTSYI 500
                                               ********************************************************************* PP

                                 TIGR00110 441 vglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDienrkldlevseeelaer 509
                                               +++GLgk++aL+tDGrfsGgt+GlsiGhvsPeaaegGai+lve GD+i+iDi+nr + +++s+eel +r
  lcl|NCBI__GCF_900102855.1:WP_092995422.1 501 KSMGLGKACALLTDGRFSGGTSGLSIGHVSPEAAEGGAIGLVESGDTIEIDIPNRSIRVALSDEELGQR 569
                                               ********************************************************************* PP

                                 TIGR00110 510 rakakkkea.........revkgaLakyaklvssadkGavld 542
                                               r++++++++         r+v+ aL++ya + +sa +Gav+d
  lcl|NCBI__GCF_900102855.1:WP_092995422.1 570 REAMQARGPkawkpvdreRQVSDALKAYAAMTTSAARGAVRD 611
                                               ******999999****************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (617 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: 13.20
//
[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