Alignments for a candidate for ilvD in Desulfotomaculum ruminis DSM 2154

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Desulfotomaculum ruminis DSM 2154

Align dihydroxy-acid dehydratase subunit (EC 4.2.1.9) (characterized)
to candidate WP_013842744.1 DESRU_RS14010 dihydroxy-acid dehydratase

Query= metacyc::MONOMER-11919
         (549 letters)



>NCBI__GCF_000215085.1:WP_013842744.1
          Length = 553

 Score =  536 bits (1380), Expect = e-156
 Identities = 275/543 (50%), Positives = 386/543 (71%), Gaps = 7/543 (1%)

Query: 11  QRAPHRSLLARCGLTDDDFEKPFIGIANSYTDIVPGHIHLRELAEAVKEGVNAAGGVAFE 70
           Q AP R+L    GLT ++  +P +GI +S  D+VPGH++L ++ +AVK GV  AGG    
Sbjct: 8   QSAPKRALFHALGLTHEEMARPLVGIVSSQNDVVPGHMNLDKIVDAVKLGVAMAGGTPLV 67

Query: 71  FNTMAICDGIAMNHDGMKYSLASREIVADTVESMAMAHALDGLVLLPTCDKIVPGMLMAA 130
           F  +A+CDG+AM H GMKYSLA+RE++AD+ E+MA++HA D LV++P CDK VPG+LMAA
Sbjct: 68  FPAIAVCDGLAMGHQGMKYSLATRELIADSTEAMALSHAFDALVMVPNCDKNVPGLLMAA 127

Query: 131 ARLDIPAIVVTGGPMLPGEFKGRKVDLINVYEGVGTVSAGEMSEDELEELERCACPGPRS 190
           ARL+IP + V+GGPML G+  G+K+   +V E      AG++S ++L E E  ACP   S
Sbjct: 128 ARLNIPTLFVSGGPMLAGKVDGQKISFSSVSEADSAFQAGKISREKLLEFEHKACPTCGS 187

Query: 191 CAGLFTANTMACLTEALGMSLPGCATAHAVSSRKRQIARLSGKRIVEMVQENLKPTMIMS 250
           C+G++TAN+M CLTE LGM L G  T  AV S + Q+A+ +G +I+E+++ N++P  I++
Sbjct: 188 CSGMYTANSMNCLTEVLGMGLQGNGTIPAVYSERIQLAKHAGMQIMELLKRNIRPRDILT 247

Query: 251 QEAFENAVMVDLALGGSTNTTLHIPAIAAEIDGLNINLDLFDELSRVIPHIASISPAGEH 310
           ++AF+NA+ +D+ALG STN+ LH+PAIA E  G+ +NLDL +E+S   P++  ++PAG  
Sbjct: 248 EDAFKNALTLDMALGCSTNSLLHLPAIAHEC-GMELNLDLANEISDKTPNLCHLAPAGPT 306

Query: 311 MMLDLDRAGGIPAVLKTLE--DHINRECVTCTGRTVQENIENVKVGHRDVIRPLDSPVHS 368
            + DL  AGGI AV+  +     +N + +TCTG+TV ENI      ++ VIRP+++P   
Sbjct: 307 YIEDLHEAGGIYAVMNEVNKLGLLNTDLMTCTGKTVGENIAGCINKNKSVIRPVENPYSQ 366

Query: 369 EGGLAILRGNLAPRGSVVKQGAVAEDMMVHEGPAKVFNSEDECMEAIFGGRIDEGDVIVI 428
            GG+A+L+GNLAP   VVK+ AVA +M+ H+GPAKVF+ E++ M+AI  G+I  GDVIVI
Sbjct: 367 TGGIAVLKGNLAPDSCVVKRSAVAPEMLKHQGPAKVFDCEEDAMQAIHSGKITSGDVIVI 426

Query: 429 RYEGPKGGPGMREMLNPTSAIAGMGL-ERVALITDGRFSGGTRGPCVGHVSPEAMEDGPL 487
           RYEGPKGGPGMREMLNPTSAI G GL E VALITDGRFSG TRG  +GHVSPEA   G +
Sbjct: 427 RYEGPKGGPGMREMLNPTSAIMGCGLGESVALITDGRFSGATRGAAIGHVSPEAAVGGNI 486

Query: 488 AAVNDGDIIRIDIPSRKLEVDLSPREIEERLQSAVKPRRS--VKGWLARYRKLAGSADTG 545
           A + DGD+I+IDI + ++   +S  E+E+R ++  +PR+     G+L+RY  L  S + G
Sbjct: 487 ALIEDGDMIQIDIMANEINFIISDGELEKR-RANWQPRKPQITTGYLSRYAALVTSGNKG 545

Query: 546 AVL 548
           AVL
Sbjct: 546 AVL 548


Lambda     K      H
   0.319    0.136    0.397 

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: 933
Number of extensions: 50
Number of successful extensions: 7
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: 549
Length of database: 553
Length adjustment: 36
Effective length of query: 513
Effective length of database: 517
Effective search space:   265221
Effective search space used:   265221
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)

Align candidate WP_013842744.1 DESRU_RS14010 (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.20985.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   8.8e-236  769.5   7.2     1e-235  769.3   7.2    1.0  1  lcl|NCBI__GCF_000215085.1:WP_013842744.1  DESRU_RS14010 dihydroxy-acid deh


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000215085.1:WP_013842744.1  DESRU_RS14010 dihydroxy-acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  769.3   7.2    1e-235    1e-235       1     542 [.      11     549 ..      11     550 .. 0.99

  Alignments for each domain:
  == domain 1  score: 769.3 bits;  conditional E-value: 1e-235
                                 TIGR00110   1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiam 69 
                                               ++ral++a+Gl++e++ +P++++v+s +++vPgh++l+++ ++vk ++  aGg++  f  iav+DG+am
  lcl|NCBI__GCF_000215085.1:WP_013842744.1  11 PKRALFHALGLTHEEMARPLVGIVSSQNDVVPGHMNLDKIVDAVKLGVAMAGGTPLVFPAIAVCDGLAM 79 
                                               589****************************************************************** PP

                                 TIGR00110  70 gheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktk 138
                                               gh+GmkysL++re+iaDs e+++ +ha+Dalv++++CDk+vPG+lmaa+rlniP+++vsGGpm agk+ 
  lcl|NCBI__GCF_000215085.1:WP_013842744.1  80 GHQGMKYSLATRELIADSTEAMALSHAFDALVMVPNCDKNVPGLLMAAARLNIPTLFVSGGPMLAGKVD 148
                                               ********************************************************************* PP

                                 TIGR00110 139 lsekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstlla 207
                                                ++ki+ ++v ea  + +agk+s e+l e+e+ acPt+gsCsG++tansm+clte+lG+ l g++t++a
  lcl|NCBI__GCF_000215085.1:WP_013842744.1 149 -GQKISFSSVSEADSAFQAGKISREKLLEFEHKACPTCGSCSGMYTANSMNCLTEVLGMGLQGNGTIPA 216
                                               .9******************************************************************* PP

                                 TIGR00110 208 tsaekkelakksgkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklsld 276
                                               + +e+ +lak++g++i+el+k+ni+Prdilt++af+na+tld+alG stn+ Lhl+aia+e g++l+ld
  lcl|NCBI__GCF_000215085.1:WP_013842744.1 217 VYSERIQLAKHAGMQIMELLKRNIRPRDILTEDAFKNALTLDMALGCSTNSLLHLPAIAHECGMELNLD 285
                                               ********************************************************************* PP

                                 TIGR00110 277 dfdrlsrkvPllaklkPsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlrv 345
                                                 +++s+k+P l++l+P+g ++iedlh+aGG+ av++e++k gll++d +t+tGkt++e+++    +  
  lcl|NCBI__GCF_000215085.1:WP_013842744.1 286 LANEISDKTPNLCHLAPAGPTYIEDLHEAGGIYAVMNEVNKLGLLNTDLMTCTGKTVGENIAGCINK-- 352
                                               **************************************************************99888.. PP

                                 TIGR00110 346 dqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeG 414
                                               +++vir+++np++++gg+avLkGnla++ +vvk ++v+ ++lk++Gpakvf+ ee+a++ai +gk++ G
  lcl|NCBI__GCF_000215085.1:WP_013842744.1 353 NKSVIRPVENPYSQTGGIAVLKGNLAPDSCVVKRSAVAPEMLKHQGPAKVFDCEEDAMQAIHSGKITSG 421
                                               9******************************************************************** PP

                                 TIGR00110 415 dvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialve 483
                                               dv+viryeGPkGgPGmremL+Ptsa++g GLg++vaLitDGrfsG+trG +iGhvsPeaa+gG+ial+e
  lcl|NCBI__GCF_000215085.1:WP_013842744.1 422 DVIVIRYEGPKGGPGMREMLNPTSAIMGCGLGESVALITDGRFSGATRGAAIGHVSPEAAVGGNIALIE 490
                                               ********************************************************************* PP

                                 TIGR00110 484 dGDkikiDienrkldlevseeelaerrakakkkearevkgaLakyaklvssadkGavld 542
                                               dGD+i+iDi +++++  +s+ el++rra++++++++ + g+L++ya lv+s +kGavl+
  lcl|NCBI__GCF_000215085.1:WP_013842744.1 491 DGDMIQIDIMANEINFIISDGELEKRRANWQPRKPQITTGYLSRYAALVTSGNKGAVLE 549
                                               *********************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (553 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: 12.16
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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