Align dihydroxyacid dehydratase (EC 4.2.1.9) (characterized)
to candidate WP_026186347.1 THITHI_RS0113600 dihydroxy-acid dehydratase
Query= metacyc::MONOMER-18815 (557 letters) >NCBI__GCF_000378965.1:WP_026186347.1 Length = 560 Score = 766 bits (1978), Expect = 0.0 Identities = 378/557 (67%), Positives = 456/557 (81%) Query: 1 MAFNKRSQNITQGVARSPNRSMYYALGYKKEDFDKPMVGIANGHSTITPCNAGLQRLADA 60 M+ N+RS+ +T+GV RSPNR+M A+G+ DF KP+VG+A+ HSTITPCN G+ LA+ Sbjct: 1 MSDNRRSRIVTEGVQRSPNRAMLRAVGFDNGDFTKPIVGVASAHSTITPCNMGIGNLAER 60 Query: 61 AIDAIKASDANPQVFGTPTISDGMSMGTEGMKYSLISREVIADCIETAAQGQWMDGVVVI 120 A++A+ A PQ+FGT TISDG+SMGTEGMKYSL+SREVIAD IET GQ MDGV+ Sbjct: 61 GEAALRAAGAMPQLFGTITISDGISMGTEGMKYSLVSREVIADAIETVCMGQSMDGVIAF 120 Query: 121 GGCDKNMPGGMIALARTNVPGIYVYGGTIKPGNWKGKDLTIVSSFEAVGEFTAGRMSQED 180 GGCDKNMPG MIA+AR N+P I+VYGGTIKPG++KG+DLTIVS+FEAVG AGR+S ED Sbjct: 121 GGCDKNMPGAMIAIARMNIPAIFVYGGTIKPGHYKGRDLTIVSAFEAVGSHAAGRLSDED 180 Query: 181 FEGVEKNACPSTGSCGGMYTANTMSSSFEALGMSLLYSSTMANPDQEKVDSAAESARVLV 240 G+E+NACP GSCGGMYTANTMSS+FEA+GMSL YSSTMA D+EK DSAA SA VLV Sbjct: 181 LAGIERNACPGAGSCGGMYTANTMSSAFEAMGMSLPYSSTMAAEDEEKADSAARSAEVLV 240 Query: 241 EAIKQDIKPRDIITRKSIENAVALIMATGGSTNAVLHYLAIAHAAEVEWTIDDFERIRRK 300 +AI+ PR+I+TR++ ENA+A++MA GGSTNA LH LAIAHAA V ++DDFE IR + Sbjct: 241 DAIRHQRLPREILTRQAFENAIAVVMALGGSTNATLHLLAIAHAARVPLSLDDFEEIRGR 300 Query: 301 VPVICNLKPSGQYVATDLHKAGGIPQVMKILLKAGMLHGDCLTITGRTLAEELENVPDTP 360 VPV+C+LKPSG++V T H+AGGIPQVMK+LL+ G+LHG CLTITGRT+AE L +VP P Sbjct: 301 VPVLCDLKPSGRFVTTQFHRAGGIPQVMKMLLERGLLHGGCLTITGRTVAETLSDVPPDP 360 Query: 361 RADQDVILPIEKALYAEGHLAILKGNLAEEGAVAKITGLKNPVITGPARVFEDEQSAMEA 420 DQ VI P K +YA GHLA+LKGNLA EGAVAKI+G+K P ITGPARVF+ E++ MEA Sbjct: 361 PDDQMVIRPWNKPVYASGHLAVLKGNLAPEGAVAKISGIKKPEITGPARVFDAEEACMEA 420 Query: 421 ILADKINAGDILVLRYLGPKGGPGMPEMLAPTSAIIGKGLGESVGFITDGRFSGGTWGMV 480 ILA +I AGDILV+RY GP+GGPGM EML+PTSAIIG GLG+SVG ITDGRFSGGT+G+V Sbjct: 421 ILAGRIRAGDILVIRYEGPRGGPGMREMLSPTSAIIGAGLGDSVGLITDGRFSGGTYGLV 480 Query: 481 VGHVAPEAYVGGTIALVQEGDSITIDAHKLLLQLNVADEELARRRANWKQPAPRYTRGVL 540 VGHVAPEA GG IALV+EGDSITIDA LQLNV++ EL +RR W P+PR TRGVL Sbjct: 481 VGHVAPEAAAGGAIALVREGDSITIDAGARRLQLNVSEAELEQRRRQWTPPSPRDTRGVL 540 Query: 541 AKFSKLASTASKGAVTD 557 AK+++L +ASKGAVTD Sbjct: 541 AKYARLVGSASKGAVTD 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: 1019 Number of extensions: 37 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: 560 Length adjustment: 36 Effective length of query: 521 Effective length of database: 524 Effective search space: 273004 Effective search space used: 273004 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_026186347.1 THITHI_RS0113600 (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.25405.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.1e-242 789.5 3.7 9.3e-242 789.3 3.7 1.0 1 lcl|NCBI__GCF_000378965.1:WP_026186347.1 THITHI_RS0113600 dihydroxy-acid Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000378965.1:WP_026186347.1 THITHI_RS0113600 dihydroxy-acid dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 789.3 3.7 9.3e-242 9.3e-242 1 542 [. 18 557 .. 18 558 .. 0.99 Alignments for each domain: == domain 1 score: 789.3 bits; conditional E-value: 9.3e-242 TIGR00110 1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiam 69 ++ra+l+a+G+ + d++kPi++v++++++i+P+++ + +la++ +++++aaG++++ f+ti++sDGi+m lcl|NCBI__GCF_000378965.1:WP_026186347.1 18 PNRAMLRAVGFDNGDFTKPIVGVASAHSTITPCNMGIGNLAERGEAALRAAGAMPQLFGTITISDGISM 86 68******************************************************************* PP TIGR00110 70 gheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktk 138 g+eGmkysL+sre+iaD++etv++++ +D++++ + CDk++PG+++a +r+niPai+v+GG++++g++k lcl|NCBI__GCF_000378965.1:WP_026186347.1 87 GTEGMKYSLVSREVIADAIETVCMGQSMDGVIAFGGCDKNMPGAMIAIARMNIPAIFVYGGTIKPGHYK 155 ********************************************************************* PP TIGR00110 139 lsekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstlla 207 ++++++v++feavg+ aag+ls+e+l ier+acP+agsC+G++tan+m++++ea+G+slP+sst++a lcl|NCBI__GCF_000378965.1:WP_026186347.1 156 -GRDLTIVSAFEAVGSHAAGRLSDEDLAGIERNACPGAGSCGGMYTANTMSSAFEAMGMSLPYSSTMAA 223 .9******************************************************************* PP TIGR00110 208 tsaekkelakksgkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklsld 276 ++ek+++a +s++ +v++++++ Pr+ilt++afenai++++alGGstn++Lhllaia+ a v lsld lcl|NCBI__GCF_000378965.1:WP_026186347.1 224 EDEEKADSAARSAEVLVDAIRHQRLPREILTRQAFENAIAVVMALGGSTNATLHLLAIAHAARVPLSLD 292 ********************************************************************* PP TIGR00110 277 dfdrlsrkvPllaklkPsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlr. 344 df++++ +vP+l++lkPsg+ v+++ hraGG+++v+k+l ++gllh +lt+tG+t+aetl++v+ + lcl|NCBI__GCF_000378965.1:WP_026186347.1 293 DFEEIRGRVPVLCDLKPSGRFVTTQFHRAGGIPQVMKMLLERGLLHGGCLTITGRTVAETLSDVPPDPp 361 ****************************************************************98762 PP TIGR00110 345 vdqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvke 413 dq vir++++pv++ g+lavLkGnla+eGav+ki+g+++ +++Gpa+vf+ ee+++eail+g++++ lcl|NCBI__GCF_000378965.1:WP_026186347.1 362 DDQMVIRPWNKPVYASGHLAVLKGNLAPEGAVAKISGIKK--PEITGPARVFDAEEACMEAILAGRIRA 428 5566************************************..9************************** PP TIGR00110 414 GdvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialv 482 Gd++viryeGP+GgPGmremL Ptsa++g+GLg++v+LitDGrfsGgt+Gl++Ghv+Peaa+gGaialv lcl|NCBI__GCF_000378965.1:WP_026186347.1 429 GDILVIRYEGPRGGPGMREMLSPTSAIIGAGLGDSVGLITDGRFSGGTYGLVVGHVAPEAAAGGAIALV 497 ********************************************************************* PP TIGR00110 483 edGDkikiDienrkldlevseeelaerrakakkkearevkgaLakyaklvssadkGavld 542 ++GD i+iD+ +r+l+l+vse+el++rr++++++++r ++g+Lakya+lv sa+kGav+d lcl|NCBI__GCF_000378965.1:WP_026186347.1 498 REGDSITIDAGARRLQLNVSEAELEQRRRQWTPPSPRDTRGVLAKYARLVGSASKGAVTD 557 **********************************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (543 nodes) Target sequences: 1 (560 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: 12.56 // [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