Alignments for a candidate for ilvD in Desulfobacter vibrioformis DSM 8776

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Desulfobacter vibrioformis DSM 8776

Align dihydroxy-acid dehydratase subunit (EC 4.2.1.9) (characterized)
to candidate WP_035240749.1 Q366_RS15950 dihydroxy-acid dehydratase

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



>NCBI__GCF_000745975.1:WP_035240749.1
          Length = 556

 Score =  598 bits (1542), Expect = e-175
 Identities = 302/549 (55%), Positives = 406/549 (73%), Gaps = 8/549 (1%)

Query: 8   RGIQRAPHRSLLARCGLTDDDFEKPFIGIANSYTDIVPGHIHLRELAEAVKEGVNAAGGV 67
           +G+ RAPHR LL   G TD + ++P IGIANS  +++PGH+HL  + +AVK G++ AGG 
Sbjct: 9   QGVARAPHRGLLKALGYTDIELDRPLIGIANSANELIPGHMHLDSIVKAVKAGISMAGGT 68

Query: 68  AFEFNTMAICDGIAMNHDGMKYSLASREIVADTVESMAMAHALDGLVLLPTCDKIVPGML 127
             EF+T+ +CDGIAMNH GM YSLASRE++AD++E +A AH  DG+V++P CDKIVPGML
Sbjct: 69  PMEFSTIGVCDGIAMNHIGMHYSLASRELIADSIEVVATAHPFDGIVMVPNCDKIVPGML 128

Query: 128 MAAARLDIPAIVVTGGPMLPGEF---KGRKVDLINVYEGVGTVSAGEMSEDELEELERCA 184
           MAAARL+IPAI V+GGPML G     + +K+DLI ++E VG V +G+M+E+EL E+E   
Sbjct: 129 MAAARLNIPAIFVSGGPMLAGRHPHDRSKKIDLITIFEAVGAVQSGKMTEEELLEMENGG 188

Query: 185 CPGPRSCAGLFTANTMACLTEALGMSLPGCATAHAVSSRKRQIARLSGKRIVEMVQENLK 244
           CP   SC+G+FTAN+M CLTEA+GM LPG  T  A  S + ++A+ +G +I+ +V+ N+ 
Sbjct: 189 CPTCGSCSGMFTANSMNCLTEAIGMGLPGNGTIPAPMSSRLRLAKAAGMQILSLVENNIT 248

Query: 245 PTMIMSQEAFENAVMVDLALGGSTNTTLHIPAIAAEIDGLNINLDLFDELSRVIPHIASI 304
           P  IM+++AF NA+ VD+ALG STNT LH+ A+AAE  G++I LDL +E+S+  PH+ S+
Sbjct: 249 PDKIMTRQAFMNALAVDMALGCSTNTVLHLKAVAAEA-GVDIPLDLINEVSKKTPHLCSL 307

Query: 305 SPAGEHMMLDLDRAGGIPAVLKTLEDH--INRECVTCTGRTVQENIENVKVGHRDVIRPL 362
           SP G+  + DLD AGGI AV+K L D+  I+   VT TG+T++EN+ENV+V + DVIRP+
Sbjct: 308 SPGGKDHIEDLDAAGGIQAVMKELSDNNMIDTGLVTATGKTIKENLENVRVKYPDVIRPV 367

Query: 363 DSPVHSEGGLAILRGNLAPRGSVVKQGAVAEDMMVHEGPAKVFNSEDECMEAIFGGRIDE 422
           + P H EGGLA+L GN+AP G VVKQ AV  +MM H+GPA+VF+ E++   AI   +I+ 
Sbjct: 368 NDPYHKEGGLAVLFGNIAPEGCVVKQSAVLPEMMTHQGPARVFDCEEDATTAIMARQINP 427

Query: 423 GDVIVIRYEGPKGGPGMREMLNPTSAIAGMGL-ERVALITDGRFSGGTRGPCVGHVSPEA 481
           GDVIVIRYEGP GGPGMREML PTSAIAGMGL +R ALITDGRFSGGT+G  +GHVSPEA
Sbjct: 428 GDVIVIRYEGPAGGPGMREMLTPTSAIAGMGLDDRCALITDGRFSGGTKGASIGHVSPEA 487

Query: 482 MEDGPLAAVNDGDIIRIDIPSRKLEVDLSPREIEERLQSAVKPRRSV-KGWLARYRKLAG 540
            + G +A V +GD IRIDIP++ +E+ +S  E   R     KP   + KG++ARY ++  
Sbjct: 488 AQGGLIALVLEGDQIRIDIPNKAIELLVSEDEQALRKADWKKPEPKIKKGYMARYARMVT 547

Query: 541 SADTGAVLR 549
           SA  GAV +
Sbjct: 548 SAGNGAVFK 556


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: 1015
Number of extensions: 49
Number of successful extensions: 6
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: 556
Length adjustment: 36
Effective length of query: 513
Effective length of database: 520
Effective search space:   266760
Effective search space used:   266760
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_035240749.1 Q366_RS15950 (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.2503.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     8e-243  792.8  10.0   9.1e-243  792.6  10.0    1.0  1  lcl|NCBI__GCF_000745975.1:WP_035240749.1  Q366_RS15950 dihydroxy-acid dehy


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000745975.1:WP_035240749.1  Q366_RS15950 dihydroxy-acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  792.6  10.0  9.1e-243  9.1e-243       1     541 [.      15     555 ..      15     556 .] 0.99

  Alignments for each domain:
  == domain 1  score: 792.6 bits;  conditional E-value: 9.1e-243
                                 TIGR00110   1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiam 69 
                                               ++r llka+G++d +l++P+i+++ns +e++Pgh+hl+ + k+vk++i+ aGg+++ef ti+v+DGiam
  lcl|NCBI__GCF_000745975.1:WP_035240749.1  15 PHRGLLKALGYTDIELDRPLIGIANSANELIPGHMHLDSIVKAVKAGISMAGGTPMEFSTIGVCDGIAM 83 
                                               689****************************************************************** PP

                                 TIGR00110  70 gheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktk 138
                                               +h Gm+ysL+sre+iaDs+e v++ah +D++v++++CDkivPGmlmaa+rlniPai+vsGGpm ag+  
  lcl|NCBI__GCF_000745975.1:WP_035240749.1  84 NHIGMHYSLASRELIADSIEVVATAHPFDGIVMVPNCDKIVPGMLMAAARLNIPAIFVSGGPMLAGRHP 152
                                               ******************************************************************986 PP

                                 TIGR00110 139 l..sekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstl 205
                                                  s+kidl+ +feavg++++gk++eeel e+e+ +cPt+gsCsG+ftansm+cltea+G+ lPg++t+
  lcl|NCBI__GCF_000745975.1:WP_035240749.1 153 HdrSKKIDLITIFEAVGAVQSGKMTEEELLEMENGGCPTCGSCSGMFTANSMNCLTEAIGMGLPGNGTI 221
                                               5559***************************************************************** PP

                                 TIGR00110 206 latsaekkelakksgkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvkls 274
                                               +a  + +++lak +g++i  lv++ni+P++i+t++af na+++d+alG stntvLhl a+a+eagv++ 
  lcl|NCBI__GCF_000745975.1:WP_035240749.1 222 PAPMSSRLRLAKAAGMQILSLVENNITPDKIMTRQAFMNALAVDMALGCSTNTVLHLKAVAAEAGVDIP 290
                                               ********************************************************************* PP

                                 TIGR00110 275 lddfdrlsrkvPllaklkPsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvl 343
                                               ld ++++s+k+P+l++l+P+gk  iedl++aGG++av+kel+ ++++++  +t tGkt++e+le+v+v+
  lcl|NCBI__GCF_000745975.1:WP_035240749.1 291 LDLINEVSKKTPHLCSLSPGGKDHIEDLDAAGGIQAVMKELSDNNMIDTGLVTATGKTIKENLENVRVK 359
                                               ********************************************************************9 PP

                                 TIGR00110 344 rvdqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvk 412
                                                   dvir++++p++kegglavL+Gn+a+eG+vvk+++v  ++++++Gpa+vf+ ee+a  ai++++++
  lcl|NCBI__GCF_000745975.1:WP_035240749.1 360 --YPDVIRPVNDPYHKEGGLAVLFGNIAPEGCVVKQSAVLPEMMTHQGPARVFDCEEDATTAIMARQIN 426
                                               ..99***************************************************************** PP

                                 TIGR00110 413 eGdvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaial 481
                                                Gdv+viryeGP GgPGmremL+Ptsa++g+GL++++aLitDGrfsGgt+G siGhvsPeaa+gG ial
  lcl|NCBI__GCF_000745975.1:WP_035240749.1 427 PGDVIVIRYEGPAGGPGMREMLTPTSAIAGMGLDDRCALITDGRFSGGTKGASIGHVSPEAAQGGLIAL 495
                                               ********************************************************************* PP

                                 TIGR00110 482 vedGDkikiDienrkldlevseeelaerrakakkkearevkgaLakyaklvssadkGavl 541
                                               v +GD+i+iDi+n++++l vse+e a r+a++kk+e++ +kg++a+ya++v+sa +Gav 
  lcl|NCBI__GCF_000745975.1:WP_035240749.1 496 VLEGDQIRIDIPNKAIELLVSEDEQALRKADWKKPEPKIKKGYMARYARMVTSAGNGAVF 555
                                               **********************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (556 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: 10.21
//
[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