Alignments for a candidate for ilvD in Thermodesulforhabdus norvegica DSM 9990

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Thermodesulforhabdus norvegica DSM 9990

Align dihydroxy-acid dehydratase subunit (EC 4.2.1.9) (characterized)
to candidate WP_093393511.1 BM091_RS01820 dihydroxy-acid dehydratase

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



>NCBI__GCF_900114975.1:WP_093393511.1
          Length = 554

 Score =  556 bits (1432), Expect = e-162
 Identities = 293/549 (53%), Positives = 380/549 (69%), Gaps = 2/549 (0%)

Query: 2   KSDTIKRGIQRAPHRSLLARCGLTDDDFEKPFIGIANSYTDIVPGHIHLRELAEAVKEGV 61
           +S  I  G  RA  R+ L   GL D D +KPFIGI NS+ ++ PGH HLREL+E VK+GV
Sbjct: 6   RSRIIVDGPARAGQRAHLRSLGLLDRDLDKPFIGIVNSWNEMHPGHRHLRELSEEVKKGV 65

Query: 62  NAAGGVAFEFNTMAICDGIAMNHDGMKYSLASREIVADTVESMAMAHALDGLVLLPTCDK 121
             AGG+ FEFNT+AICDGI   H GM Y L SR+ +AD++E +  A  LDGLV +  CDK
Sbjct: 66  YEAGGIPFEFNTIAICDGITQGHRGMCYVLPSRDWIADSIELVVEAQQLDGLVFIGGCDK 125

Query: 122 IVPGMLMAAARLDIPAIVVTGGPMLPGEFKGRKVDLINVYEGVGTVSAGEMSEDELEELE 181
           I P MLMA ARL++P+I+VTGGPMLPG F+GRKV + ++ EGVG    GE++++E+ +LE
Sbjct: 126 IEPAMLMAMARLNLPSIMVTGGPMLPGYFQGRKVAIPDMREGVGRWRRGELTDEEVLKLE 185

Query: 182 RCACPGPRSCAGLFTANTMACLTEALGMSLPGCATAHAVSSRKRQIARLSGKRIVEMVQE 241
              CPGP SCA + TANTMAC  E LG++LPG +TAHAVSS K++IAR SG  ++ +V+E
Sbjct: 186 CSVCPGPGSCAMMGTANTMACFAEVLGVTLPGSSTAHAVSSEKKRIARQSGLEVLRLVRE 245

Query: 242 NLKPTMIMSQEAFENAVMVDLALGGSTNTTLHIPAIAAEIDGLNINLDLFDELSRVIPHI 301
           ++KP  IM++ AFENAV V  A+GGSTN  LH PAIAAE + ++I+L  FD LSR  P+I
Sbjct: 246 DIKPRDIMTRGAFENAVRVCAAVGGSTNLLLHAPAIAAEAE-IDISLKDFDTLSRTTPYI 304

Query: 302 ASISPAGEHMMLDLDRAGGIPAVLKTLEDHINRECVTCTGRTVQENIENVKVGHRDVIRP 361
             + PAG   +LDLD AGGIPAV K L   +N + V   G  +++      +   +VIRP
Sbjct: 305 CHLKPAGPFTLLDLDMAGGIPAVCKRLMPLLNPDEVNVLGMKIRDVAARAVINDDEVIRP 364

Query: 362 LDSPVHSEGGLAILRGNLAPRGSVVKQGAVAEDMMVHEGPAKVFNSEDECMEAIFGGRID 421
           LD+PV  EG  AIL G LAP G+ VKQ  V   +    G A+VF++E +   AI+ G+I 
Sbjct: 365 LDNPVKEEGSYAILFGTLAPDGACVKQTGVDLSVKYFRGRARVFDNEQDAEHAIYDGKIK 424

Query: 422 EGDVIVIRYEGPKGGPGMREMLNPTSAIAGMGL-ERVALITDGRFSGGTRGPCVGHVSPE 480
            GDV+VIRYEGPKGGPGMREML+ T+A+ GMGL +  AL+TDGRFSG TRG CVGHVSPE
Sbjct: 425 PGDVVVIRYEGPKGGPGMREMLSATAALVGMGLGKECALVTDGRFSGSTRGLCVGHVSPE 484

Query: 481 AMEDGPLAAVNDGDIIRIDIPSRKLEVDLSPREIEERLQSAVKPRRSVKGWLARYRKLAG 540
           A   GP+A V DGD+I ID+P R++++ +   E+E R ++     ++VKG LARY  L G
Sbjct: 485 AALGGPIAYVMDGDVIEIDLPGRRIDLKVDEAELERRRKTVKIREKAVKGVLARYSMLVG 544

Query: 541 SADTGAVLR 549
               GA LR
Sbjct: 545 KVSEGARLR 553


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: 1006
Number of extensions: 58
Number of successful extensions: 3
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: 554
Length adjustment: 36
Effective length of query: 513
Effective length of database: 518
Effective search space:   265734
Effective search space used:   265734
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_093393511.1 BM091_RS01820 (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.21021.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   7.7e-220  716.9   0.0   8.8e-220  716.7   0.0    1.0  1  lcl|NCBI__GCF_900114975.1:WP_093393511.1  BM091_RS01820 dihydroxy-acid deh


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900114975.1:WP_093393511.1  BM091_RS01820 dihydroxy-acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  716.7   0.0  8.8e-220  8.8e-220       2     541 ..      19     552 ..      18     554 .] 0.99

  Alignments for each domain:
  == domain 1  score: 716.7 bits;  conditional E-value: 8.8e-220
                                 TIGR00110   2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamg 70 
                                               +ra l+++Gl d dl+kP+i++vns++e+ Pgh hl++l++ vk+++++aGg+++efntia++DGi+ g
  lcl|NCBI__GCF_900114975.1:WP_093393511.1  19 QRAHLRSLGLLDRDLDKPFIGIVNSWNEMHPGHRHLRELSEEVKKGVYEAGGIPFEFNTIAICDGITQG 87 
                                               7999***************************************************************** PP

                                 TIGR00110  71 heGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktkl 139
                                               h+Gm+y Lpsr+ iaDs+e vv+a++lD+lv i+ CDki P mlma++rln+P+i+v+GGpm +g ++ 
  lcl|NCBI__GCF_900114975.1:WP_093393511.1  88 HRGMCYVLPSRDWIADSIELVVEAQQLDGLVFIGGCDKIEPAMLMAMARLNLPSIMVTGGPMLPGYFQ- 155
                                               ********************************************************************. PP

                                 TIGR00110 140 sekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllat 208
                                               ++k+ + d+ e+vg+   g+l++ee+ ++e s cP++gsC+ + tan+mac +e+lG++lPgsst++a+
  lcl|NCBI__GCF_900114975.1:WP_093393511.1 156 GRKVAIPDMREGVGRWRRGELTDEEVLKLECSVCPGPGSCAMMGTANTMACFAEVLGVTLPGSSTAHAV 224
                                               9******************************************************************** PP

                                 TIGR00110 209 saekkelakksgkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklsldd 277
                                               s+ekk++a++sg ++  lv+++ikPrdi+t+ afena+ +  a+GGstn  Lh +aia+ea++++sl+d
  lcl|NCBI__GCF_900114975.1:WP_093393511.1 225 SSEKKRIARQSGLEVLRLVREDIKPRDIMTRGAFENAVRVCAAVGGSTNLLLHAPAIAAEAEIDISLKD 293
                                               ********************************************************************* PP

                                 TIGR00110 278 fdrlsrkvPllaklkPsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlrvd 346
                                               fd+lsr++P +++lkP+g   + dl+ aGG++av k l    ll+ d ++v+G+ + ++++++ ++  d
  lcl|NCBI__GCF_900114975.1:WP_093393511.1 294 FDTLSRTTPYICHLKPAGPFTLLDLDMAGGIPAVCKRL--MPLLNPDEVNVLGMKIRDVAARAVIN--D 358
                                               **************************************..99*******************99999..* PP

                                 TIGR00110 347 qdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeGd 415
                                               ++vir+ldnpvk+eg  a+L+G la++Ga vk++gv+ ++ +f+G+a+vf++e++a +ai +gk+k Gd
  lcl|NCBI__GCF_900114975.1:WP_093393511.1 359 DEVIRPLDNPVKEEGSYAILFGTLAPDGACVKQTGVDLSVKYFRGRARVFDNEQDAEHAIYDGKIKPGD 427
                                               ********************************************************************* PP

                                 TIGR00110 416 vvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialved 484
                                               vvviryeGPkGgPGmremL  t+alvg+GLgk++aL+tDGrfsG+trGl++GhvsPeaa gG+ia v d
  lcl|NCBI__GCF_900114975.1:WP_093393511.1 428 VVVIRYEGPKGGPGMREMLSATAALVGMGLGKECALVTDGRFSGSTRGLCVGHVSPEAALGGPIAYVMD 496
                                               ********************************************************************* PP

                                 TIGR00110 485 GDkikiDienrkldlevseeelaerrakakkkearevkgaLakyaklvssadkGavl 541
                                               GD i+iD++ r++dl+v+e+el++rr++ k +e + vkg+La+y+ lv   ++Ga l
  lcl|NCBI__GCF_900114975.1:WP_093393511.1 497 GDVIEIDLPGRRIDLKVDEAELERRRKTVKIRE-KAVKGVLARYSMLVGKVSEGARL 552
                                               *************************99999998.99******************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (554 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: 11.93
//
[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