Align dihydroxy-acid dehydratase subunit (EC 4.2.1.9) (characterized)
to candidate WP_012102089.1 CKL_RS08320 dihydroxy-acid dehydratase
Query= metacyc::MONOMER-11919 (549 letters) >NCBI__GCF_000016505.1:WP_012102089.1 Length = 556 Score = 555 bits (1431), Expect = e-162 Identities = 280/553 (50%), Positives = 401/553 (72%), Gaps = 7/553 (1%) Query: 1 MKSDTIKRGIQRAPHRSLLARCGLTDDDFEKPFIGIANSYTDIVPGHIHLRELAEAVKEG 60 M+SD I +G + AP R+LL GLT ++ E+P +GI +S DIVPGH++L ++ EAVK G Sbjct: 1 MRSDVITKGTKSAPQRALLNALGLTKEEIERPLVGIVSSKNDIVPGHMNLDKIVEAVKTG 60 Query: 61 VNAAGGVAFEFNTMAICDGIAMNHDGMKYSLASREIVADTVESMAMAHALDGLVLLPTCD 120 V+ AGG F +A+CDGIAM H GMKYSL +R+++AD+ E+MAMAHA D LV++P CD Sbjct: 61 VSMAGGTPIVFPAIAVCDGIAMGHQGMKYSLVTRDLIADSTEAMAMAHAFDALVMVPNCD 120 Query: 121 KIVPGMLMAAARLDIPAIVVTGGPMLPGEFKGRKVDLINVYEGVGTVSAGEMSEDELEEL 180 K VPG+LMAAARL+IP I V+GGPML G+ G KV ++ E VG + G+++E++LEE Sbjct: 121 KNVPGLLMAAARLNIPTIFVSGGPMLAGKVDGCKVSFSSISEAVGAFNGGKITEEKLEEF 180 Query: 181 ERCACPGPRSCAGLFTANTMACLTEALGMSLPGCATAHAVSSRKRQIARLSGKRIVEMVQ 240 E CP SC+G++TAN+M CLTE LGM+L G T AV S + ++A+ +G +I+E+++ Sbjct: 181 ESKVCPTCGSCSGMYTANSMNCLTEVLGMALGGNGTIPAVYSDRIKLAKHAGMKIMELLE 240 Query: 241 ENLKPTMIMSQEAFENAVMVDLALGGSTNTTLHIPAIAAEIDGLNINLDLFDELSRVIPH 300 N++P +M++ AF+NA+ +D+ALG STN+ LH+PAIA E G+ +N+D+ +E+S P+ Sbjct: 241 RNIRPRDVMTEAAFKNALTMDMALGCSTNSMLHLPAIAHEA-GIELNVDMANEISAKTPN 299 Query: 301 IASISPAGEHMMLDLDRAGGIPAVLKTLE--DHINRECVTCTGRTVQENIENVKVGHRDV 358 + ++PAG + + +L+ AGGI AV+ + + ++ + +TCTG+TV ENI+ +++V Sbjct: 300 LCHLAPAGHNYVEELNEAGGIYAVMNEINKLNLLSTDLITCTGKTVAENIKGCINKNKEV 359 Query: 359 IRPLDSPVHSEGGLAILRGNLAPRGSVVKQGAVAEDMMVHEGPAKVFNSEDECMEAIFGG 418 IRP+++P + GG+AIL+GNLAP VVK+ AVA +M+ HEGPA+VF+ E++ + AI G Sbjct: 360 IRPVENPYSTTGGIAILKGNLAPDSCVVKRSAVAPEMLKHEGPARVFDCEEDALNAINTG 419 Query: 419 RIDEGDVIVIRYEGPKGGPGMREMLNPTSAIAGMGL-ERVALITDGRFSGGTRGPCVGHV 477 +I GDV++IRYEGPKGGPGMREMLNPTSAI G GL VALITDGRFSG TRG +GHV Sbjct: 420 KIVAGDVVIIRYEGPKGGPGMREMLNPTSAIMGRGLGGSVALITDGRFSGATRGAAIGHV 479 Query: 478 SPEAMEDGPLAAVNDGDIIRIDIPSRKLEVDLSPREIEERLQSAVKPR--RSVKGWLARY 535 SPEA G +A V +GDII+IDI + ++ ++S E+E R +S KPR + G+LARY Sbjct: 480 SPEAAVGGNIALVEEGDIIKIDIEANSIDFEISEEELERR-RSNWKPRQPKITTGYLARY 538 Query: 536 RKLAGSADTGAVL 548 + S + GA+L Sbjct: 539 ASMVTSGNRGAIL 551 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: 954 Number of extensions: 50 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_012102089.1 CKL_RS08320 (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.12311.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.6e-237 774.6 12.1 3e-237 774.4 12.1 1.0 1 lcl|NCBI__GCF_000016505.1:WP_012102089.1 CKL_RS08320 dihydroxy-acid dehyd Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000016505.1:WP_012102089.1 CKL_RS08320 dihydroxy-acid dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 774.4 12.1 3e-237 3e-237 1 542 [. 14 552 .. 14 553 .. 0.99 Alignments for each domain: == domain 1 score: 774.4 bits; conditional E-value: 3e-237 TIGR00110 1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiam 69 ++rall+a+Gl++e++e+P++++v+s ++ivPgh++l+++ ++vk +++ aGg++ f iav+DGiam lcl|NCBI__GCF_000016505.1:WP_012102089.1 14 PQRALLNALGLTKEEIERPLVGIVSSKNDIVPGHMNLDKIVEAVKTGVSMAGGTPIVFPAIAVCDGIAM 82 589****************************************************************** PP TIGR00110 70 gheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktk 138 gh+GmkysL++r++iaDs e++++aha+Dalv++++CDk+vPG+lmaa+rlniP+i+vsGGpm agk+ lcl|NCBI__GCF_000016505.1:WP_012102089.1 83 GHQGMKYSLVTRDLIADSTEAMAMAHAFDALVMVPNCDKNVPGLLMAAARLNIPTIFVSGGPMLAGKVD 151 ********************************************************************* PP TIGR00110 139 lsekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstlla 207 + k++ +++ eavg+ + gk++ee+lee+e cPt+gsCsG++tansm+clte+lG++l g++t++a lcl|NCBI__GCF_000016505.1:WP_012102089.1 152 -GCKVSFSSISEAVGAFNGGKITEEKLEEFESKVCPTCGSCSGMYTANSMNCLTEVLGMALGGNGTIPA 219 .9******************************************************************* PP TIGR00110 208 tsaekkelakksgkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklsld 276 + +++ +lak++g++i+el+++ni+Prd++t++af+na+t+d+alG stn++Lhl+aia+eag++l++d lcl|NCBI__GCF_000016505.1:WP_012102089.1 220 VYSDRIKLAKHAGMKIMELLERNIRPRDVMTEAAFKNALTMDMALGCSTNSMLHLPAIAHEAGIELNVD 288 ********************************************************************* PP TIGR00110 277 dfdrlsrkvPllaklkPsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlrv 345 +++s k+P l++l+P+g++++e+l++aGG+ av++e++k +ll +d +t+tGkt+ae+++ + lcl|NCBI__GCF_000016505.1:WP_012102089.1 289 MANEISAKTPNLCHLAPAGHNYVEELNEAGGIYAVMNEINKLNLLSTDLITCTGKTVAENIKGCINK-- 355 **************************************************************99888.. PP TIGR00110 346 dqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeG 414 +++vir+++np++ +gg+a+LkGnla++ +vvk ++v+ ++lk+eGpa+vf+ ee+al+ai +gk+ +G lcl|NCBI__GCF_000016505.1:WP_012102089.1 356 NKEVIRPVENPYSTTGGIAILKGNLAPDSCVVKRSAVAPEMLKHEGPARVFDCEEDALNAINTGKIVAG 424 9******************************************************************** PP TIGR00110 415 dvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialve 483 dvv+iryeGPkGgPGmremL+Ptsa++g GLg +vaLitDGrfsG+trG +iGhvsPeaa+gG+ialve lcl|NCBI__GCF_000016505.1:WP_012102089.1 425 DVVIIRYEGPKGGPGMREMLNPTSAIMGRGLGGSVALITDGRFSGATRGAAIGHVSPEAAVGGNIALVE 493 ********************************************************************* PP TIGR00110 484 dGDkikiDienrkldlevseeelaerrakakkkearevkgaLakyaklvssadkGavld 542 +GD+ikiDie++ +d e+seeel++rr ++k+++++ + g+La+ya++v+s ++Ga+l+ lcl|NCBI__GCF_000016505.1:WP_012102089.1 494 EGDIIKIDIEANSIDFEISEEELERRRSNWKPRQPKITTGYLARYASMVTSGNRGAILE 552 ********************************************************986 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: 11.24 // [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