Align dihydroxyacid dehydratase (EC 4.2.1.9) (characterized)
to candidate WP_011316921.1 AVA_RS00115 dihydroxy-acid dehydratase
Query= metacyc::MONOMER-18815 (557 letters) >NCBI__GCF_000204075.1:WP_011316921.1 Length = 563 Score = 801 bits (2068), Expect = 0.0 Identities = 395/557 (70%), Positives = 468/557 (84%) Query: 1 MAFNKRSQNITQGVARSPNRSMYYALGYKKEDFDKPMVGIANGHSTITPCNAGLQRLADA 60 M+ N RS+ ITQGV RSPNR+M A+G++ DF K +VG+ANG+STITPCN G+ +LA Sbjct: 1 MSENLRSKAITQGVQRSPNRAMLRAVGFQDADFTKAIVGVANGYSTITPCNMGINQLAQR 60 Query: 61 AIDAIKASDANPQVFGTPTISDGMSMGTEGMKYSLISREVIADCIETAAQGQWMDGVVVI 120 A I + A PQ+FGT TISDG+SMGTEGMKYSL+SREVIAD IET GQ +DGV+ I Sbjct: 61 AEAGINRAGAKPQIFGTITISDGISMGTEGMKYSLVSREVIADSIETVCNGQSLDGVIAI 120 Query: 121 GGCDKNMPGGMIALARTNVPGIYVYGGTIKPGNWKGKDLTIVSSFEAVGEFTAGRMSQED 180 GGCDKNMPG MIA+AR N+P I+VYGGTIKPG++ GKDLT+VSSFEAVGE++AG++ + + Sbjct: 121 GGCDKNMPGAMIAIARMNIPAIFVYGGTIKPGHYNGKDLTVVSSFEAVGEYSAGKIDENE 180 Query: 181 FEGVEKNACPSTGSCGGMYTANTMSSSFEALGMSLLYSSTMANPDQEKVDSAAESARVLV 240 VE+NACP GSCGGMYTANTMSS+FEALGMSL YSSTMA D EK DS ESA+VLV Sbjct: 181 LLAVERNACPGAGSCGGMYTANTMSSAFEALGMSLPYSSTMAAEDDEKADSTEESAKVLV 240 Query: 241 EAIKQDIKPRDIITRKSIENAVALIMATGGSTNAVLHYLAIAHAAEVEWTIDDFERIRRK 300 EAI+ + PR IITRKSIENA+A+IMA GGSTNAVLH+LAIA AA VE +DDFE IR + Sbjct: 241 EAIRHQLLPRQIITRKSIENAIAVIMAVGGSTNAVLHFLAIARAAGVELNLDDFETIRGR 300 Query: 301 VPVICNLKPSGQYVATDLHKAGGIPQVMKILLKAGMLHGDCLTITGRTLAEELENVPDTP 360 VPV+C+LKPSG+YVATDLHKAGGIPQVMK+LL G+LHGDC+TITG+T+AE L ++P+ P Sbjct: 301 VPVLCDLKPSGRYVATDLHKAGGIPQVMKMLLVHGLLHGDCITITGKTIAEVLADIPEEP 360 Query: 361 RADQDVILPIEKALYAEGHLAILKGNLAEEGAVAKITGLKNPVITGPARVFEDEQSAMEA 420 +QDVI P K +YA+GHLAILKGNLA EGAVAKITG+KNPVITGPA+VFE E+ ++A Sbjct: 361 SPNQDVIRPWNKPMYAQGHLAILKGNLATEGAVAKITGVKNPVITGPAKVFESEEDCLDA 420 Query: 421 ILADKINAGDILVLRYLGPKGGPGMPEMLAPTSAIIGKGLGESVGFITDGRFSGGTWGMV 480 ILA KI AGD++V+RY GPKGGPGM EMLAPTSAIIG GLG+SVG ITDGRFSGGT+GMV Sbjct: 421 ILAGKIKAGDVIVVRYEGPKGGPGMREMLAPTSAIIGAGLGDSVGLITDGRFSGGTYGMV 480 Query: 481 VGHVAPEAYVGGTIALVQEGDSITIDAHKLLLQLNVADEELARRRANWKQPAPRYTRGVL 540 VGHVAPEA VGG IALVQEGDSITIDAH LQLN++DEELA RRANW+ PRYT+G+L Sbjct: 481 VGHVAPEAAVGGAIALVQEGDSITIDAHTRSLQLNISDEELAHRRANWQPRPPRYTKGIL 540 Query: 541 AKFSKLASTASKGAVTD 557 AK++KL +++S GAVTD Sbjct: 541 AKYAKLVASSSVGAVTD 557 Lambda K H 0.316 0.133 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: 1069 Number of extensions: 41 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: 557 Length of database: 563 Length adjustment: 36 Effective length of query: 521 Effective length of database: 527 Effective search space: 274567 Effective search space used: 274567 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 (21.6 bits) S2: 53 (25.0 bits)
Align candidate WP_011316921.1 AVA_RS00115 (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.23972.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-250 818.5 9.3 1.5e-250 818.3 9.3 1.0 1 lcl|NCBI__GCF_000204075.1:WP_011316921.1 AVA_RS00115 dihydroxy-acid dehyd Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000204075.1:WP_011316921.1 AVA_RS00115 dihydroxy-acid dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 818.3 9.3 1.5e-250 1.5e-250 1 542 [. 18 557 .. 18 558 .. 0.99 Alignments for each domain: == domain 1 score: 818.3 bits; conditional E-value: 1.5e-250 TIGR00110 1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiam 69 ++ra+l+a+G++d+d++k i++v+n+y++i+P+++ +++la++++++i++aG++++ f+ti++sDGi+m lcl|NCBI__GCF_000204075.1:WP_011316921.1 18 PNRAMLRAVGFQDADFTKAIVGVANGYSTITPCNMGINQLAQRAEAGINRAGAKPQIFGTITISDGISM 86 68******************************************************************* PP TIGR00110 70 gheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktk 138 g+eGmkysL+sre+iaDs+etv++++ lD++++i+ CDk++PG+++a +r+niPai+v+GG++++g+++ lcl|NCBI__GCF_000204075.1:WP_011316921.1 87 GTEGMKYSLVSREVIADSIETVCNGQSLDGVIAIGGCDKNMPGAMIAIARMNIPAIFVYGGTIKPGHYN 155 ********************************************************************* PP TIGR00110 139 lsekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstlla 207 ++++++v+ feavgey+agk++e+el ++er+acP+agsC+G++tan+m++++ealG+slP+sst++a lcl|NCBI__GCF_000204075.1:WP_011316921.1 156 -GKDLTVVSSFEAVGEYSAGKIDENELLAVERNACPGAGSCGGMYTANTMSSAFEALGMSLPYSSTMAA 223 .9******************************************************************* PP TIGR00110 208 tsaekkelakksgkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklsld 276 + ek++++++s+k +ve++++++ Pr+i+t++++enai++++a+GGstn+vLh laia+ agv+l+ld lcl|NCBI__GCF_000204075.1:WP_011316921.1 224 EDDEKADSTEESAKVLVEAIRHQLLPRQIITRKSIENAIAVIMAVGGSTNAVLHFLAIARAAGVELNLD 292 ********************************************************************* PP TIGR00110 277 dfdrlsrkvPllaklkPsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlrv 345 df++++ +vP+l++lkPsg++v +dlh+aGG+++v+k+l +gllh d++t+tGkt+ae+l++++ + lcl|NCBI__GCF_000204075.1:WP_011316921.1 293 DFETIRGRVPVLCDLKPSGRYVATDLHKAGGIPQVMKMLLVHGLLHGDCITITGKTIAEVLADIPEEPS 361 ****************************************************************99875 PP TIGR00110 346 .dqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvke 413 +qdvir++++p++++g+la+LkGnla+eGav+ki+gv++ +++Gpakvfesee++l+ail+gk+k+ lcl|NCBI__GCF_000204075.1:WP_011316921.1 362 pNQDVIRPWNKPMYAQGHLAILKGNLATEGAVAKITGVKN--PVITGPAKVFESEEDCLDAILAGKIKA 428 3899************************************..999************************ PP TIGR00110 414 GdvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialv 482 Gdv+v+ryeGPkGgPGmremLaPtsa++g+GLg++v+LitDGrfsGgt+G+++Ghv+Peaa+gGaialv lcl|NCBI__GCF_000204075.1:WP_011316921.1 429 GDVIVVRYEGPKGGPGMREMLAPTSAIIGAGLGDSVGLITDGRFSGGTYGMVVGHVAPEAAVGGAIALV 497 ********************************************************************* PP TIGR00110 483 edGDkikiDienrkldlevseeelaerrakakkkearevkgaLakyaklvssadkGavld 542 ++GD i+iD++ r l+l++s+eela+rra+++++ +r++kg+Lakyaklv+s++ Gav+d lcl|NCBI__GCF_000204075.1:WP_011316921.1 498 QEGDSITIDAHTRSLQLNISDEELAHRRANWQPRPPRYTKGILAKYAKLVASSSVGAVTD 557 **********************************************************87 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (543 nodes) Target sequences: 1 (563 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: 12.83 // [ok]
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
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:
Otherwise, a candidate is "medium confidence" if either:
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:
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:
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