Alignments for a candidate for ilvD in Desulfobulbus mediterraneus DSM 13871

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Desulfobulbus mediterraneus DSM 13871

Align dihydroxyacid dehydratase (characterized)
to candidate WP_028585696.1 G494_RS0118395 dihydroxy-acid dehydratase

Query= CharProtDB::CH_024768
         (616 letters)



>NCBI__GCF_000429965.1:WP_028585696.1
          Length = 609

 Score =  795 bits (2054), Expect = 0.0
 Identities = 412/606 (67%), Positives = 478/606 (78%), Gaps = 7/606 (1%)

Query: 5   RSATTTHGRNMAGARALWRATGMTDADFGKPIIAVVNSFTQFVPGHVHLRDLGKLVAEQI 64
           RSA TT GR MAGARALWRA GM +  FGKP+IAVVNSFTQFVPGHVHL  +G+ V + I
Sbjct: 6   RSAETTSGRKMAGARALWRANGMQEEQFGKPVIAVVNSFTQFVPGHVHLHAIGQQVKKII 65

Query: 65  EAAGGVAKEFNTIAVDDGIAMGHGGMLYSLPSRELIADSVEYMVNAHCADAMVCISNCDK 124
           EA G  A EFNTIA+DDGIAMGH GMLYSLPSRELIADSVEYM NAH  DAMVCISNCDK
Sbjct: 66  EAQGCFAAEFNTIAIDDGIAMGHDGMLYSLPSRELIADSVEYMCNAHKVDAMVCISNCDK 125

Query: 125 ITPGMLMASLRLNIPVIFVSGGPMEAGKTKLSDQIIKLDLVDAMIQGADPKVSDSQSDQV 184
           ITPGMLMA++RLNIP IFVSGGPMEAGK  + D+   LDLVDAM+  AD  VSD + ++V
Sbjct: 126 ITPGMLMAAMRLNIPAIFVSGGPMEAGK--VGDKA--LDLVDAMVMAADSTVSDEEVEEV 181

Query: 185 ERSACPTCGSCSGMFTANSMNCLTEALGLSQPGNGSLLATHADRKQLFLNAGKRIVELTK 244
           ERSACPTCGSCSGMFTANSMNCL EALGL+ PGNG+L+ATHA R  LF  AG++IVE+ +
Sbjct: 182 ERSACPTCGSCSGMFTANSMNCLNEALGLALPGNGTLVATHAARLDLFARAGEQIVEMCR 241

Query: 245 RYYEQNDESALPRNIASKAAFENAMTLDIAMGGSTNTVLHLLAAAQEAEIDFTMSDIDKL 304
            +YEQ DE  LPR+IAS+AAF NAM LDIAMGGSTNTVLHLLA A EA +++ M DID L
Sbjct: 242 LWYEQEDERVLPRSIASRAAFNNAMALDIAMGGSTNTVLHLLAIAHEAGVEYGMEDIDAL 301

Query: 305 SRKVPQLCKVAPSTQKYHMEDVHRAGGVIGILGELDRAGLLNRDVKNVLGLTLPQTLEQY 364
           S KVP L KVAP++  YH+EDV+RAGG++GILGELDR GL++  V    GL+L + L QY
Sbjct: 302 SGKVPNLSKVAPNSH-YHIEDVNRAGGIMGILGELDRGGLIDTTVSRADGLSLAEALAQY 360

Query: 365 DVML-TQDDAVKNMFRAGPAGIRTTQAFSQDCRWDTLDDDRANGCIRSLEHAYSKDGGLA 423
           D+M  T  +  ++++ + P G R     SQ+  +  LD DRA GCIR L HAYS+DGGLA
Sbjct: 361 DIMRPTVSEEARSLYLSAPGGGRNLVMGSQNEMYAELDTDRAGGCIRDLAHAYSQDGGLA 420

Query: 424 VLYGNFAENGCIVKTAGVDDSILKFTGPAKVYESQDDAVEAILGGKVVAGDVVVIRYEGP 483
           VLYGN A NG IVKTAGVD SIL F G A+V++SQD A E ILGG + AGDVV I YEGP
Sbjct: 421 VLYGNIALNGSIVKTAGVDPSILHFQGAARVFQSQDAACEGILGGSIKAGDVVFILYEGP 480

Query: 484 KGGPGMQEMLYPTSFLKSMGLGKACALITDGRFSGGTSGLSIGHVSPEAASGGSIGLIED 543
           +GGPGMQEMLYPTS+LKS  LG ACAL+TDGRFSGGTSGLSIGHVSPEAA GG+I L+ D
Sbjct: 481 RGGPGMQEMLYPTSYLKSQHLGAACALVTDGRFSGGTSGLSIGHVSPEAAGGGAIALVRD 540

Query: 544 GDLIAIDIPNRGIQLQVSDAELAARREAQDARGDKAWTPKNRERQVSFALRAYASLATSA 603
           GD + I+IP R + L V +AEL ARR  ++ARGDKA+TP+ RER VS AL+ YA  A SA
Sbjct: 541 GDGVDINIPKRSLNLLVDEAELEARRREEEARGDKAYTPE-RERTVSTALKVYARFAASA 599

Query: 604 DKGAVR 609
           D+GAVR
Sbjct: 600 DRGAVR 605


Lambda     K      H
   0.317    0.134    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: 1182
Number of extensions: 57
Number of successful extensions: 5
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: 616
Length of database: 609
Length adjustment: 37
Effective length of query: 579
Effective length of database: 572
Effective search space:   331188
Effective search space used:   331188
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_028585696.1 G494_RS0118395 (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.16518.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.4e-238  778.0   5.8   2.8e-238  777.8   5.8    1.0  1  lcl|NCBI__GCF_000429965.1:WP_028585696.1  G494_RS0118395 dihydroxy-acid de


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000429965.1:WP_028585696.1  G494_RS0118395 dihydroxy-acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  777.8   5.8  2.8e-238  2.8e-238       2     541 ..      19     605 ..      18     607 .. 0.98

  Alignments for each domain:
  == domain 1  score: 777.8 bits;  conditional E-value: 2.8e-238
                                 TIGR00110   2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamg 70 
                                               aral++a G+++e+++kP+iavvns+t++vPghvhl+ ++++vk+ iea G  a efntia++DGiamg
  lcl|NCBI__GCF_000429965.1:WP_028585696.1  19 ARALWRANGMQEEQFGKPVIAVVNSFTQFVPGHVHLHAIGQQVKKIIEAQGCFAAEFNTIAIDDGIAMG 87 
                                               79******************************************************************* PP

                                 TIGR00110  71 heGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktkl 139
                                               h+Gm+ysLpsre+iaDsve++++ah++Da+v+is+CDki+PGmlmaa+rlniPai+vsGGpmeagk+  
  lcl|NCBI__GCF_000429965.1:WP_028585696.1  88 HDGMLYSLPSRELIADSVEYMCNAHKVDAMVCISNCDKITPGMLMAAMRLNIPAIFVSGGPMEAGKVGD 156
                                               ******************************************************************993 PP

                                 TIGR00110 140 sekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllat 208
                                                   + +d+++a++++a++ +s+ee+ee+ersacPt+gsCsG+ftansm+cl ealGl+lPg++tl at
  lcl|NCBI__GCF_000429965.1:WP_028585696.1 157 ----KALDLVDAMVMAADSTVSDEEVEEVERSACPTCGSCSGMFTANSMNCLNEALGLALPGNGTLVAT 221
                                               ....568999*********************************************************** PP

                                 TIGR00110 209 saekkelakksgkrivelvkknik.......PrdiltkeafenaitldlalGGstntvLhllaiakeag 270
                                               +a +++l+ ++g++ive+++  ++       Pr+i++++af+na++ld+a+GGstntvLhllaia+eag
  lcl|NCBI__GCF_000429965.1:WP_028585696.1 222 HAARLDLFARAGEQIVEMCRLWYEqedervlPRSIASRAAFNNAMALDIAMGGSTNTVLHLLAIAHEAG 290
                                               ********************99999999999************************************** PP

                                 TIGR00110 271 vklslddfdrlsrkvPllaklkPsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlek 339
                                               v++ ++d+d ls kvP l+k++P++++ ied++raGG++++l+eld+ gl+++ +    G +lae l++
  lcl|NCBI__GCF_000429965.1:WP_028585696.1 291 VEYGMEDIDALSGKVPNLSKVAPNSHYHIEDVNRAGGIMGILGELDRGGLIDTTVSRADGLSLAEALAQ 359
                                               ********************************************************************* PP

                                 TIGR00110 340 vkvlr................................vdqd....virsldnpvkkegglavLkGnlae 372
                                               ++++r                                +d+d    +ir l ++++++gglavL+Gn+a 
  lcl|NCBI__GCF_000429965.1:WP_028585696.1 360 YDIMRptvseearslylsapgggrnlvmgsqnemyaeLDTDraggCIRDLAHAYSQDGGLAVLYGNIAL 428
                                               ***********************************9955556688************************ PP

                                 TIGR00110 373 eGavvkiagveedilkfeGpakvfeseeealeailggkvkeGdvvviryeGPkGgPGmremLaPtsalv 441
                                               +G++vk+agv+ +il+f+G a+vf+s+++a e+ilgg +k+Gdvv i yeGP+GgPGm+emL+Pts+l+
  lcl|NCBI__GCF_000429965.1:WP_028585696.1 429 NGSIVKTAGVDPSILHFQGAARVFQSQDAACEGILGGSIKAGDVVFILYEGPRGGPGMQEMLYPTSYLK 497
                                               ********************************************************************* PP

                                 TIGR00110 442 glGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDienrkldlevseeelaerr 510
                                               +  Lg ++aL+tDGrfsGgt+GlsiGhvsPeaa gGaialv+dGD + i+i++r l+l v+e+el++rr
  lcl|NCBI__GCF_000429965.1:WP_028585696.1 498 SQHLGAACALVTDGRFSGGTSGLSIGHVSPEAAGGGAIALVRDGDGVDINIPKRSLNLLVDEAELEARR 566
                                               ********************************************************************* PP

                                 TIGR00110 511 akakkkea........revkgaLakyaklvssadkGavl 541
                                               ++ +++++        r+v+ aL+ ya++++sad+Gav+
  lcl|NCBI__GCF_000429965.1:WP_028585696.1 567 REEEARGDkaytpereRTVSTALKVYARFAASADRGAVR 605
                                               ***99999999***999********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (609 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: 11.42
//
[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