Alignments for a candidate for ilvD in Derxia gummosa DSM 723

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Derxia gummosa DSM 723

Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate WP_028312025.1 H566_RS0114690 dihydroxy-acid dehydratase

Query= SwissProt::P55186
         (617 letters)



>NCBI__GCF_000482785.1:WP_028312025.1
          Length = 617

 Score =  936 bits (2419), Expect = 0.0
 Identities = 467/617 (75%), Positives = 529/617 (85%)

Query: 1   MPPYRSRTTTHGRNMAGARGLWRATGMKDEDFGKPIIAVANSFTQFVPGHVHLKDLGQLV 60
           MP YRSRT+T GRNMAGAR LWRATGMKD+DF KPIIA+ANSFTQFVPGHVHLKDLGQLV
Sbjct: 1   MPQYRSRTSTAGRNMAGARALWRATGMKDDDFSKPIIAIANSFTQFVPGHVHLKDLGQLV 60

Query: 61  AREIEAAGGVAKEFNTIAVDDGIAMGHGGMLYSLPSRDLIADSVEYMVNAHCADAIVCIS 120
           AREIEAAGGVAKEFNTIAVDDGIAMGH GMLYSLPSRDLIADSVEYMVNAHCADA+VCIS
Sbjct: 61  AREIEAAGGVAKEFNTIAVDDGIAMGHSGMLYSLPSRDLIADSVEYMVNAHCADALVCIS 120

Query: 121 NCDKITPGMLMAAMRLNIPVVFVSGGPMEAGKVTVKGKIRALDLVDAMVVAADDSYSDEE 180
           NCDKITPGMLMAAMRLNIP VFVSGGPMEAGKV  + KI  +DL+DAM+ A DD  SD E
Sbjct: 121 NCDKITPGMLMAAMRLNIPAVFVSGGPMEAGKVKWEAKIIPVDLIDAMIKAGDDKVSDAE 180

Query: 181 VEAIEKAACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSVLATHADREALFKEAGRVVV 240
           V   E++ACPTCGSCSGMFTANSMNCLTEALGLSLPGNGS++ATHADR+ LF EAGR  V
Sbjct: 181 VAEYERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSIVATHADRKQLFLEAGRKAV 240

Query: 241 DLCQRWYEQEDATALPRGIATRAAFENAMSLDIAMGGSTNTVLHLLAAAHEGGIDFSMAD 300
           ++ +R+YEQ D + LPR IAT AAFENAMSLD+AMGGSTNTVLHLLAAA E G+DF+M D
Sbjct: 241 EIARRYYEQGDESVLPRSIATFAAFENAMSLDVAMGGSTNTVLHLLAAAREAGVDFTMKD 300

Query: 301 IDRLSRHVPCLSKVAPAKSDVHMEDVHRAGGVMAILGELERGGLIDASQPTVHAPTMGEA 360
           IDRLSR VPCLSKVAPAK+DVHMEDVHRAGG+MAILGEL+R GLI+   PT+H+PT+G A
Sbjct: 301 IDRLSRRVPCLSKVAPAKNDVHMEDVHRAGGIMAILGELDRAGLINRDVPTIHSPTLGAA 360

Query: 361 LARWDIGRTNSQIAHEFFKAAPGGKPTQVAFSQAARWEELDLDRENGVIRSVEHPFSKDG 420
           +A++D+  T  +   +FF+AAPGG PTQVAFSQ  R+  LD DR  GVIR+ E+ FS+DG
Sbjct: 361 IAKYDVTVTADEAVKDFFRAAPGGVPTQVAFSQDRRYPSLDTDRAKGVIRNKENAFSQDG 420

Query: 421 GLAVLFGNLAPEGCIVKTAGVDESILTFRGTARVFESQDAAVSGILGGQVKAGEVVVIRY 480
           GLAVL+GN+A  GCIVKTAGVDESIL F G ARVFESQD AV  ILG ++ AG++VVIRY
Sbjct: 421 GLAVLYGNIARNGCIVKTAGVDESILKFTGRARVFESQDDAVEAILGDKIVAGDIVVIRY 480

Query: 481 EGPKGGPGMQEMLYPTTYLKSKGLGAACALVTDGRFSGGTSGLSIGHVSPEAGEGGLIAL 540
           EGPKGGPGMQEMLYPT+YLKSKGLG ACAL+TDGRFSGGTSGLSIGH SPEA  GG IAL
Sbjct: 481 EGPKGGPGMQEMLYPTSYLKSKGLGKACALLTDGRFSGGTSGLSIGHASPEAAMGGDIAL 540

Query: 541 VETGDPILIDIPTRGITLEVSDAVLAARREAQLARGKDAWTPLNRKRDLTPALRAYAAMT 600
           VE GD I+IDIP R I L+V ++++A RR A+LARG  A+ P  R+R ++ AL+AYAA+T
Sbjct: 541 VENGDTIVIDIPNRTIHLDVGESLIAQRRSAELARGDRAFKPRTRERHVSAALQAYAALT 600

Query: 601 TNAARGAVRDVSQIERG 617
           T+A  GAVRDV+QI RG
Sbjct: 601 TSADTGAVRDVTQILRG 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: 1272
Number of extensions: 40
Number of successful extensions: 1
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_028312025.1 H566_RS0114690 (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.16071.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.2e-256  837.0   4.3   3.7e-256  836.8   4.3    1.0  1  lcl|NCBI__GCF_000482785.1:WP_028312025.1  H566_RS0114690 dihydroxy-acid de


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000482785.1:WP_028312025.1  H566_RS0114690 dihydroxy-acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  836.8   4.3  3.7e-256  3.7e-256       2     542 ..      18     610 ..      17     611 .. 0.99

  Alignments for each domain:
  == domain 1  score: 836.8 bits;  conditional E-value: 3.7e-256
                                 TIGR00110   2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamg 70 
                                               aral++atG+kd+d++kPiia++ns+t++vPghvhlkdl++lv++eieaaGgvakefntiav+DGiamg
  lcl|NCBI__GCF_000482785.1:WP_028312025.1  18 ARALWRATGMKDDDFSKPIIAIANSFTQFVPGHVHLKDLGQLVAREIEAAGGVAKEFNTIAVDDGIAMG 86 
                                               79******************************************************************* PP

                                 TIGR00110  71 heGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktkl 139
                                               h+Gm+ysLpsr++iaDsve++v+ah++Dalv+is+CDki+PGmlmaa+rlniPa++vsGGpmeagk+k 
  lcl|NCBI__GCF_000482785.1:WP_028312025.1  87 HSGMLYSLPSRDLIADSVEYMVNAHCADALVCISNCDKITPGMLMAAMRLNIPAVFVSGGPMEAGKVKW 155
                                               ********************************************************************* PP

                                 TIGR00110 140 sekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllat 208
                                                 ki+ vd+++a++++ ++k+s++e+ e+ersacPt+gsCsG+ftansm+cltealGlslPg++++ at
  lcl|NCBI__GCF_000482785.1:WP_028312025.1 156 EAKIIPVDLIDAMIKAGDDKVSDAEVAEYERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSIVAT 224
                                               ********************************************************************* PP

                                 TIGR00110 209 saekkelakksgkrivelvkknik.......PrdiltkeafenaitldlalGGstntvLhllaiakeag 270
                                               +a++k+l+ ++g++ ve+ +++++       Pr+i+t +afena++ld+a+GGstntvLhlla+a+eag
  lcl|NCBI__GCF_000482785.1:WP_028312025.1 225 HADRKQLFLEAGRKAVEIARRYYEqgdesvlPRSIATFAAFENAMSLDVAMGGSTNTVLHLLAAAREAG 293
                                               ********************************************************************* PP

                                 TIGR00110 271 vklslddfdrlsrkvPllaklkPsgkkv.iedlhraGGvsavlkeldkegllhkdaltvtGktlaetle 338
                                               v+++++d+drlsr+vP+l+k++P+ + v +ed+hraGG++a+l+eld++gl+++d+ t+   tl+  ++
  lcl|NCBI__GCF_000482785.1:WP_028312025.1 294 VDFTMKDIDRLSRRVPCLSKVAPAKNDVhMEDVHRAGGIMAILGELDRAGLINRDVPTIHSPTLGAAIA 362
                                               *************************9999**************************************** PP

                                 TIGR00110 339 kvkvlr...................................vdqdvirsldnpvkkegglavLkGnlae 372
                                               k++v+                                      + vir+++n+++++gglavL+Gn+a 
  lcl|NCBI__GCF_000482785.1:WP_028312025.1 363 KYDVTVtadeavkdffraapggvptqvafsqdrrypsldtdRAKGVIRNKENAFSQDGGLAVLYGNIAR 431
                                               ****999******************************66444444************************ PP

                                 TIGR00110 373 eGavvkiagveedilkfeGpakvfeseeealeailggkvkeGdvvviryeGPkGgPGmremLaPtsalv 441
                                               +G++vk+agv+e+ilkf+G+a+vfes+++a+eailg k+ +Gd+vviryeGPkGgPGm+emL+Pts+l+
  lcl|NCBI__GCF_000482785.1:WP_028312025.1 432 NGCIVKTAGVDESILKFTGRARVFESQDDAVEAILGDKIVAGDIVVIRYEGPKGGPGMQEMLYPTSYLK 500
                                               ********************************************************************* PP

                                 TIGR00110 442 glGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDienrkldlevseeelaerr 510
                                               + GLgk++aL+tDGrfsGgt+GlsiGh sPeaa gG ialve+GD+i iDi+nr+++l+v e  +a+rr
  lcl|NCBI__GCF_000482785.1:WP_028312025.1 501 SKGLGKACALLTDGRFSGGTSGLSIGHASPEAAMGGDIALVENGDTIVIDIPNRTIHLDVGESLIAQRR 569
                                               ********************************************************************* PP

                                 TIGR00110 511 akakkkea.........revkgaLakyaklvssadkGavld 542
                                                +  ++++         r+v+ aL++ya l +sad+Gav+d
  lcl|NCBI__GCF_000482785.1:WP_028312025.1 570 SAELARGDrafkprtreRHVSAALQAYAALTTSADTGAVRD 610
                                               *999999999999999999********************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 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 11.60
//
[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