Align dihydroxy-acid dehydratase subunit (EC 4.2.1.9) (characterized)
to candidate WP_084055683.1 B9A12_RS01020 dihydroxy-acid dehydratase
Query= metacyc::MONOMER-11919 (549 letters) >NCBI__GCF_900176285.1:WP_084055683.1 Length = 552 Score = 605 bits (1561), Expect = e-177 Identities = 308/552 (55%), Positives = 403/552 (73%), Gaps = 5/552 (0%) Query: 1 MKSDTIKRGIQRAPHRSLLARCGLTDDDFEKPFIGIANSYTDIVPGHIHLRELAEAVKEG 60 M+SD +K+G ++APHRSL G T ++ E+P +GI NS+ +I+PGHIHL ++A+AVK G Sbjct: 1 MRSDLMKKGPEKAPHRSLFKAMGYTREELERPIVGIVNSFNEIIPGHIHLDKIAQAVKAG 60 Query: 61 VNAAGGVAFEFNTMAICDGIAMNHDGMKYSLASREIVADTVESMAMAHALDGLVLLPTCD 120 V AGG EF+T+ +CDGIAMNH GM+YSLASRE++AD+VE MA AH D LVL+P CD Sbjct: 61 VRMAGGTPVEFSTIGVCDGIAMNHAGMRYSLASRELIADSVEVMATAHPFDALVLIPNCD 120 Query: 121 KIVPGMLMAAARLDIPAIVVTGGPMLPGEFKGRKVDLINVYEGVGTVSAGEMSEDELEEL 180 KI+PGMLMAA RL+IP ++V+GGPML G R VDLI+V+EGVG AG +S +ELEEL Sbjct: 121 KIIPGMLMAAFRLNIPTLLVSGGPMLAGRVGRRPVDLISVFEGVGAHKAGTLSTEELEEL 180 Query: 181 ERCACPGPRSCAGLFTANTMACLTEALGMSLPGCATAHAVSSRKRQIARLSGKRIVEMVQ 240 E CACPG SCAG+FTAN+M CL+EALG++LPG T AVS+ + ++A+ +G +I++++ Sbjct: 181 EDCACPGCGSCAGMFTANSMNCLSEALGLALPGNGTIPAVSAARFRLAKTAGMKIMDLIA 240 Query: 241 ENLKPTMIMSQEAFENAVMVDLALGGSTNTTLHIPAIAAEIDGLNINLDLFDELSRVIPH 300 N P +++Q +FENA+ VD+ALG STNT LH+PAIA E G+ ++LDLF+ +S PH Sbjct: 241 ANKLPKDLVTQASFENAIAVDMALGCSTNTVLHVPAIAHEA-GITLDLDLFNSMSAKTPH 299 Query: 301 IASISPAGEHMMLDLDRAGGIPAVLKTLEDH--INRECVTCTGRTVQENIENVKVGHRDV 358 + S+ P G H + DL+ AGGI AV++ L I+ + T TG+TV N+E VK DV Sbjct: 300 LCSLRPGGPHFLEDLNAAGGIQAVMRELAKGGLIHLDAQTVTGQTVGANLERVKAVDHDV 359 Query: 359 IRPLDSPVHSEGGLAILRGNLAPRGSVVKQGAVAEDMMVHEGPAKVFNSEDECMEAIFGG 418 IRPLD P H EGG+AIL GNLAP+G+VVKQ AVA +MM G A+VF SE+E AI G Sbjct: 360 IRPLDKPYHQEGGIAILYGNLAPQGAVVKQSAVAHEMMQRTGRARVFESENEAASAILIG 419 Query: 419 RIDEGDVIVIRYEGPKGGPGMREMLNPTSAIAGMGLER-VALITDGRFSGGTRGPCVGHV 477 +I GDV+VIRYEGPKGGPGM+EML PT+AI G GL++ VALITDGRFSGGT+G +GH+ Sbjct: 420 QIRPGDVVVIRYEGPKGGPGMQEMLTPTAAIVGRGLDKDVALITDGRFSGGTQGAAIGHI 479 Query: 478 SPEAMEDGPLAAVNDGDIIRIDIPSRKLEVDLSPREIE-ERLQSAVKPRRSVKGWLARYR 536 SPEA GP+A V +GD I IDIP +KLE+ + +E R + K R G+LARY Sbjct: 480 SPEAAAGGPIALVEEGDEIVIDIPGKKLELKVDEATLEARRARWQPKEPRIRHGYLARYA 539 Query: 537 KLAGSADTGAVL 548 ++ S GAVL Sbjct: 540 RMVTSGAQGAVL 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: 1025 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_084055683.1 B9A12_RS01020 (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.17804.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8e-250 815.9 4.5 9.1e-250 815.7 4.5 1.0 1 lcl|NCBI__GCF_900176285.1:WP_084055683.1 B9A12_RS01020 dihydroxy-acid deh Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900176285.1:WP_084055683.1 B9A12_RS01020 dihydroxy-acid dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 815.7 4.5 9.1e-250 9.1e-250 1 541 [. 14 551 .. 14 552 .] 1.00 Alignments for each domain: == domain 1 score: 815.7 bits; conditional E-value: 9.1e-250 TIGR00110 1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiam 69 ++r+l+ka+G++ e+le+Pi+++vns++ei+Pgh+hl+++a++vk++++ aGg+++ef ti+v+DGiam lcl|NCBI__GCF_900176285.1:WP_084055683.1 14 PHRSLFKAMGYTREELERPIVGIVNSFNEIIPGHIHLDKIAQAVKAGVRMAGGTPVEFSTIGVCDGIAM 82 69******************************************************************* PP TIGR00110 70 gheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktk 138 +h Gm+ysL+sre+iaDsve +++ah +Dalv+i++CDki+PGmlmaa rlniP+++vsGGpm ag++ lcl|NCBI__GCF_900176285.1:WP_084055683.1 83 NHAGMRYSLASRELIADSVEVMATAHPFDALVLIPNCDKIIPGMLMAAFRLNIPTLLVSGGPMLAGRVG 151 ********************************************************************9 PP TIGR00110 139 lsekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstlla 207 + +dl++vfe+vg+ +ag ls eelee+e++acP++gsC+G+ftansm+cl+ealGl+lPg++t++a lcl|NCBI__GCF_900176285.1:WP_084055683.1 152 -RRPVDLISVFEGVGAHKAGTLSTEELEELEDCACPGCGSCAGMFTANSMNCLSEALGLALPGNGTIPA 219 .7******************************************************************* PP TIGR00110 208 tsaekkelakksgkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklsld 276 +sa + +lak++g++i++l+ n P+d++t+++fenai++d+alG stntvLh++aia+eag++l+ld lcl|NCBI__GCF_900176285.1:WP_084055683.1 220 VSAARFRLAKTAGMKIMDLIAANKLPKDLVTQASFENAIAVDMALGCSTNTVLHVPAIAHEAGITLDLD 288 ********************************************************************* PP TIGR00110 277 dfdrlsrkvPllaklkPsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlrv 345 f+ +s k+P+l++l+P+g +++edl++aGG++av++el k gl+h da+tvtG+t++ +le+vk lcl|NCBI__GCF_900176285.1:WP_084055683.1 289 LFNSMSAKTPHLCSLRPGGPHFLEDLNAAGGIQAVMRELAKGGLIHLDAQTVTGQTVGANLERVKAV-- 355 ****************************************************************999.. PP TIGR00110 346 dqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeG 414 d+dvir+ld+p+++egg+a+L+Gnla++Gavvk+++v++++++ +G+a+vfese+ea ail g+++ G lcl|NCBI__GCF_900176285.1:WP_084055683.1 356 DHDVIRPLDKPYHQEGGIAILYGNLAPQGAVVKQSAVAHEMMQRTGRARVFESENEAASAILIGQIRPG 424 ********************************************************************* PP TIGR00110 415 dvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialve 483 dvvviryeGPkGgPGm+emL+Pt+a+vg GL+k+vaLitDGrfsGgt+G +iGh+sPeaa+gG+ialve lcl|NCBI__GCF_900176285.1:WP_084055683.1 425 DVVVIRYEGPKGGPGMQEMLTPTAAIVGRGLDKDVALITDGRFSGGTQGAAIGHISPEAAAGGPIALVE 493 ********************************************************************* PP TIGR00110 484 dGDkikiDienrkldlevseeelaerrakakkkearevkgaLakyaklvssadkGavl 541 +GD+i iDi+ +kl+l+v+e+ l++rra++++ke+r +g+La+ya++v+s +Gavl lcl|NCBI__GCF_900176285.1:WP_084055683.1 494 EGDEIVIDIPGKKLELKVDEATLEARRARWQPKEPRIRHGYLARYARMVTSGAQGAVL 551 ********************************************************98 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03 # Mc/sec: 8.11 // [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