Align dihydroxy-acid dehydratase subunit (EC 4.2.1.9) (characterized)
to candidate WP_013840428.1 DESRU_RS01855 dihydroxy-acid dehydratase
Query= metacyc::MONOMER-11919 (549 letters) >NCBI__GCF_000215085.1:WP_013840428.1 Length = 552 Score = 623 bits (1607), Expect = 0.0 Identities = 316/552 (57%), Positives = 411/552 (74%), Gaps = 5/552 (0%) Query: 1 MKSDTIKRGIQRAPHRSLLARCGLTDDDFEKPFIGIANSYTDIVPGHIHLRELAEAVKEG 60 M+SD +K+G++RAPHRSL GL D++ KP IG+ NS+ +IVPGH+HL+++AEAVK G Sbjct: 1 MRSDAMKKGLERAPHRSLFRALGLVDEELSKPMIGVVNSFNEIVPGHMHLKDIAEAVKAG 60 Query: 61 VNAAGGVAFEFNTMAICDGIAMNHDGMKYSLASREIVADTVESMAMAHALDGLVLLPTCD 120 V AGG EF +A+CDGIAM H GM+YSLASREI+AD++E MA AH DGLVL+P CD Sbjct: 61 VRMAGGTPVEFPAIAVCDGIAMGHPGMRYSLASREIIADSIEVMAQAHPFDGLVLIPNCD 120 Query: 121 KIVPGMLMAAARLDIPAIVVTGGPMLPGEFKGRKVDLINVYEGVGTVSAGEMSEDELEEL 180 K+VPGMLMAAARL+IPAIVV+GGPM+ G F+ + V + N++E VG V AG M+ +EL +L Sbjct: 121 KVVPGMLMAAARLNIPAIVVSGGPMMAGRFQDKDVSVTNIFEAVGAVQAGRMTPEELAQL 180 Query: 181 ERCACPGPRSCAGLFTANTMACLTEALGMSLPGCATAHAVSSRKRQIARLSGKRIVEMVQ 240 E ACPG SC+G+FTAN+M CLTE LGM+LPG T AVS+ +R++A+++G R V +VQ Sbjct: 181 EDSACPGCGSCSGMFTANSMNCLTEVLGMALPGNGTIPAVSAARRRLAKMTGIRAVSLVQ 240 Query: 241 ENLKPTMIMSQEAFENAVMVDLALGGSTNTTLHIPAIAAEIDGLNINLDLFDELSRVIPH 300 ENL+P I++ +AF N + VDLALG STNT LH+PAIA E G+ ++L+L +++S PH Sbjct: 241 ENLRPCDILTAKAFANGLTVDLALGCSTNTVLHLPAIAHEA-GIELDLNLVNQMSEKTPH 299 Query: 301 IASISPAGEHMMLDLDRAGGIPAVLKTL--EDHINRECVTCTGRTVQENIENVKVGHRDV 358 + +SPAGEH + +L AGGI AV+K L +D IN +G TV E + V V Sbjct: 300 LCKLSPAGEHHIENLYAAGGIQAVMKELSRKDLINLNIKAVSGLTVGEQLAQAGVKDNGV 359 Query: 359 IRPLDSPVHSEGGLAILRGNLAPRGSVVKQGAVAEDMMVHEGPAKVFNSEDECMEAIFGG 418 IR + P + GGLAILRGNLAP G+VVK+ AVA +M+ H GPA+VF+ E+ ++AI GG Sbjct: 360 IRSVSEPYSATGGLAILRGNLAPDGAVVKRAAVAPEMLKHTGPARVFDGEEAAIQAIMGG 419 Query: 419 RIDEGDVIVIRYEGPKGGPGMREMLNPTSAIAGMGLER-VALITDGRFSGGTRGPCVGHV 477 RI GDV+VIRYEGPKGGPGMREML PTSA+AGMGL++ VAL+TDGRFSG +RG +GHV Sbjct: 420 RIKPGDVVVIRYEGPKGGPGMREMLMPTSALAGMGLDKEVALLTDGRFSGASRGASIGHV 479 Query: 478 SPEAMEDGPLAAVNDGDIIRIDIPSRKLEVDLSPREIEERLQSAVKPR-RSVKGWLARYR 536 SPEA E G ++ + DGDI+ IDIP+ +LEV LS EI+ER + P+ R KG+LARY Sbjct: 480 SPEAAEGGLISVLQDGDIVEIDIPNYRLEVQLSEAEIKERQANWQPPQPRVTKGYLARYA 539 Query: 537 KLAGSADTGAVL 548 +L SA GAVL Sbjct: 540 RLVTSAGKGAVL 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: 971 Number of extensions: 48 Number of successful extensions: 5 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: 552 Length adjustment: 36 Effective length of query: 513 Effective length of database: 516 Effective search space: 264708 Effective search space used: 264708 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_013840428.1 DESRU_RS01855 (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.22621.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.8e-250 816.6 6.5 5.5e-250 816.4 6.5 1.0 1 lcl|NCBI__GCF_000215085.1:WP_013840428.1 DESRU_RS01855 dihydroxy-acid deh Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000215085.1:WP_013840428.1 DESRU_RS01855 dihydroxy-acid dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 816.4 6.5 5.5e-250 5.5e-250 1 541 [. 14 551 .. 14 552 .] 1.00 Alignments for each domain: == domain 1 score: 816.4 bits; conditional E-value: 5.5e-250 TIGR00110 1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiam 69 ++r+l++a+Gl de+l+kP+i+vvns++eivPgh+hlkd+a++vk++++ aGg+++ef iav+DGiam lcl|NCBI__GCF_000215085.1:WP_013840428.1 14 PHRSLFRALGLVDEELSKPMIGVVNSFNEIVPGHMHLKDIAEAVKAGVRMAGGTPVEFPAIAVCDGIAM 82 69******************************************************************* PP TIGR00110 70 gheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktk 138 gh Gm+ysL+sreiiaDs+e +++ah +D+lv+i++CDk+vPGmlmaa+rlniPaivvsGGpm+ag+++ lcl|NCBI__GCF_000215085.1:WP_013840428.1 83 GHPGMRYSLASREIIADSIEVMAQAHPFDGLVLIPNCDKVVPGMLMAAARLNIPAIVVSGGPMMAGRFQ 151 ********************************************************************* PP TIGR00110 139 lsekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstlla 207 ++++++++feavg+++ag+++ eel ++e+sacP++gsCsG+ftansm+clte+lG++lPg++t++a lcl|NCBI__GCF_000215085.1:WP_013840428.1 152 -DKDVSVTNIFEAVGAVQAGRMTPEELAQLEDSACPGCGSCSGMFTANSMNCLTEVLGMALPGNGTIPA 219 .8******************************************************************* PP TIGR00110 208 tsaekkelakksgkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklsld 276 +sa +++lak +g r v lv++n++P dilt +af n +t+dlalG stntvLhl+aia+eag++l+l+ lcl|NCBI__GCF_000215085.1:WP_013840428.1 220 VSAARRRLAKMTGIRAVSLVQENLRPCDILTAKAFANGLTVDLALGCSTNTVLHLPAIAHEAGIELDLN 288 ********************************************************************* PP TIGR00110 277 dfdrlsrkvPllaklkPsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlrv 345 ++++s+k+P+l+kl+P+g++ ie+l +aGG++av+kel++++l++ ++++v+G t++e+l+++ v+ lcl|NCBI__GCF_000215085.1:WP_013840428.1 289 LVNQMSEKTPHLCKLSPAGEHHIENLYAAGGIQAVMKELSRKDLINLNIKAVSGLTVGEQLAQAGVK-- 355 *******************************************************************.. PP TIGR00110 346 dqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeG 414 d+ virs+++p++++ggla+L+Gnla++Gavvk a+v+ ++lk++Gpa+vf+ ee+a++ai+gg++k G lcl|NCBI__GCF_000215085.1:WP_013840428.1 356 DNGVIRSVSEPYSATGGLAILRGNLAPDGAVVKRAAVAPEMLKHTGPARVFDGEEAAIQAIMGGRIKPG 424 ********************************************************************* PP TIGR00110 415 dvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialve 483 dvvviryeGPkGgPGmremL+Ptsal+g+GL+k+vaL+tDGrfsG++rG siGhvsPeaaegG i++++ lcl|NCBI__GCF_000215085.1:WP_013840428.1 425 DVVVIRYEGPKGGPGMREMLMPTSALAGMGLDKEVALLTDGRFSGASRGASIGHVSPEAAEGGLISVLQ 493 ********************************************************************* PP TIGR00110 484 dGDkikiDienrkldlevseeelaerrakakkkearevkgaLakyaklvssadkGavl 541 dGD+++iDi+n +l++++se+e++er+a+++++++r +kg+La+ya+lv+sa kGavl lcl|NCBI__GCF_000215085.1:WP_013840428.1 494 DGDIVEIDIPNYRLEVQLSEAEIKERQANWQPPQPRVTKGYLARYARLVTSAGKGAVL 551 ********************************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (543 nodes) Target sequences: 1 (552 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 0.02s 00:00:00.04 Elapsed: 00:00:00.02 # Mc/sec: 10.83 // [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