Align dihydroxy-acid dehydratase subunit (EC 4.2.1.9) (characterized)
to candidate WP_041314961.1 HM1_RS06870 dihydroxy-acid dehydratase
Query= metacyc::MONOMER-11919 (549 letters) >NCBI__GCF_000019165.1:WP_041314961.1 Length = 552 Score = 624 bits (1608), Expect = 0.0 Identities = 315/553 (56%), Positives = 415/553 (75%), Gaps = 5/553 (0%) Query: 1 MKSDTIKRGIQRAPHRSLLARCGLTDDDFEKPFIGIANSYTDIVPGHIHLRELAEAVKEG 60 M+S T+K G+++APHRSLL GLT ++ +P IGI N+ D+VPGHIHL +A+AVK G Sbjct: 1 MRSQTVKCGVEKAPHRSLLRSIGLTAEEMNRPLIGIVNAKNDVVPGHIHLDTIADAVKAG 60 Query: 61 VNAAGGVAFEFNTMAICDGIAMNHDGMKYSLASREIVADTVESMAMAHALDGLVLLPTCD 120 V AGG F T+A+CDGIAMNH GMKYSLASRE++AD++E M MAH D LV +P CD Sbjct: 61 VRLAGGTPLAFPTIAVCDGIAMNHTGMKYSLASRELIADSIEVMTMAHGFDALVFIPNCD 120 Query: 121 KIVPGMLMAAARLDIPAIVVTGGPMLPGEFKGRKVDLINVYEGVGTVSAGEMSEDELEEL 180 K+VPGMLMAAARL+IP+I V+GGPML G F+G+KV+L V+EGVG + G+M+ +ELEEL Sbjct: 121 KVVPGMLMAAARLNIPSIFVSGGPMLAGRFQGKKVNLNTVFEGVGQYNTGKMTMEELEEL 180 Query: 181 ERCACPGPRSCAGLFTANTMACLTEALGMSLPGCATAHAVSSRKRQIARLSGKRIVEMVQ 240 E+ ACP SC+G+FTAN+M CLTE LGMSLPG T AV S + +A+ +G RI++++ Sbjct: 181 EKNACPTCGSCSGMFTANSMNCLTEVLGMSLPGNGTIPAVYSARILLAKQTGMRIMDLLA 240 Query: 241 ENLKPTMIMSQEAFENAVMVDLALGGSTNTTLHIPAIAAEIDGLNINLDLFDELSRVIPH 300 N++P +M++ F NAV VD+ALG STNT LH+PAIA E G+ +NLD+ +E+S PH Sbjct: 241 NNVRPLDMMTEGTFRNAVTVDMALGCSTNTLLHLPAIAHEA-GVELNLDMVNEISAKTPH 299 Query: 301 IASISPAGEHMMLDLDRAGGIPAVLKTLEDH--INRECVTCTGRTVQENIENVKVGHRDV 358 + ++PAGEH + DL AGGIPAV+K+L + I+ + T TG+TV EN+ +V DV Sbjct: 300 LCKLAPAGEHHIEDLYEAGGIPAVMKSLLEAGLIDGDLPTVTGKTVAENVASVVNLRPDV 359 Query: 359 IRPLDSPVHSEGGLAILRGNLAPRGSVVKQGAVAEDMMVHEGPAKVFNSEDECMEAIFGG 418 IRPLD+P GGLA+LRGNLAP G+VVK+GAVA +M+VH+GPA+VF+SE++ AI GG Sbjct: 360 IRPLDNPYSKTGGLAVLRGNLAPDGAVVKKGAVAPEMLVHKGPARVFDSEEQAYAAITGG 419 Query: 419 RIDEGDVIVIRYEGPKGGPGMREMLNPTSAIAGMGLER-VALITDGRFSGGTRGPCVGHV 477 RI +GDV+VIRYEGP+GGPGMREML+PTS I GMGL++ VALITDGRFSG TRG +GHV Sbjct: 420 RIQKGDVVVIRYEGPRGGPGMREMLSPTSTICGMGLDKDVALITDGRFSGATRGAAIGHV 479 Query: 478 SPEAMEDGPLAAVNDGDIIRIDIPSRKLEVDLSPREIEERLQSAVKPRRSV-KGWLARYR 536 SPEA + GP+A + +GDII IDIP+ +L+V++ E+ ER + P V G++ RY Sbjct: 480 SPEAADGGPIAFIREGDIIAIDIPAGRLDVEVDAAELAERRKEWQPPAPKVTSGYMKRYA 539 Query: 537 KLAGSADTGAVLR 549 + SA TGA +R Sbjct: 540 QNVLSASTGARMR 552 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: 977 Number of extensions: 50 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_041314961.1 HM1_RS06870 (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.11970.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-245 801.9 5.2 1.6e-245 801.7 5.2 1.0 1 lcl|NCBI__GCF_000019165.1:WP_041314961.1 HM1_RS06870 dihydroxy-acid dehyd Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000019165.1:WP_041314961.1 HM1_RS06870 dihydroxy-acid dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 801.7 5.2 1.6e-245 1.6e-245 1 541 [. 14 551 .. 14 552 .] 0.99 Alignments for each domain: == domain 1 score: 801.7 bits; conditional E-value: 1.6e-245 TIGR00110 1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiam 69 ++r+ll+++Gl+ e++++P+i++vn+ +++vPgh+hl+ +a++vk++++ aGg++ f tiav+DGiam lcl|NCBI__GCF_000019165.1:WP_041314961.1 14 PHRSLLRSIGLTAEEMNRPLIGIVNAKNDVVPGHIHLDTIADAVKAGVRLAGGTPLAFPTIAVCDGIAM 82 69******************************************************************* PP TIGR00110 70 gheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktk 138 +h+GmkysL+sre+iaDs+e + +ah +Dalv i++CDk+vPGmlmaa+rlniP+i+vsGGpm ag+++ lcl|NCBI__GCF_000019165.1:WP_041314961.1 83 NHTGMKYSLASRELIADSIEVMTMAHGFDALVFIPNCDKVVPGMLMAAARLNIPSIFVSGGPMLAGRFQ 151 ********************************************************************* PP TIGR00110 139 lsekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstlla 207 ++k++l vfe+vg+y+ gk++ eelee+e++acPt+gsCsG+ftansm+clte+lG+slPg++t++a lcl|NCBI__GCF_000019165.1:WP_041314961.1 152 -GKKVNLNTVFEGVGQYNTGKMTMEELEELEKNACPTCGSCSGMFTANSMNCLTEVLGMSLPGNGTIPA 219 .9******************************************************************* PP TIGR00110 208 tsaekkelakksgkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklsld 276 + + + lak++g+ri++l+ +n++P d++t+ +f na+t+d+alG stnt Lhl+aia+eagv+l+ld lcl|NCBI__GCF_000019165.1:WP_041314961.1 220 VYSARILLAKQTGMRIMDLLANNVRPLDMMTEGTFRNAVTVDMALGCSTNTLLHLPAIAHEAGVELNLD 288 ********************************************************************* PP TIGR00110 277 dfdrlsrkvPllaklkPsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlrv 345 ++++s k+P+l+kl+P+g++ iedl +aGG++av+k+l ++gl++ d tvtGkt+ae++++v l lcl|NCBI__GCF_000019165.1:WP_041314961.1 289 MVNEISAKTPHLCKLAPAGEHHIEDLYEAGGIPAVMKSLLEAGLIDGDLPTVTGKTVAENVASVVNL-- 355 *************************************************************999888.. PP TIGR00110 346 dqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeG 414 dvir+ldnp++k+gglavL+Gnla++Gavvk ++v+ ++l+++Gpa+vf+see+a +ai gg++++G lcl|NCBI__GCF_000019165.1:WP_041314961.1 356 RPDVIRPLDNPYSKTGGLAVLRGNLAPDGAVVKKGAVAPEMLVHKGPARVFDSEEQAYAAITGGRIQKG 424 99******************************************************************* PP TIGR00110 415 dvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialve 483 dvvviryeGP+GgPGmremL Pts+++g+GL+k+vaLitDGrfsG+trG +iGhvsPeaa gG+ia+++ lcl|NCBI__GCF_000019165.1:WP_041314961.1 425 DVVVIRYEGPRGGPGMREMLSPTSTICGMGLDKDVALITDGRFSGATRGAAIGHVSPEAADGGPIAFIR 493 ********************************************************************* PP TIGR00110 484 dGDkikiDienrkldlevseeelaerrakakkkearevkgaLakyaklvssadkGavl 541 +GD+i+iDi++ +ld+ev+ +elaerr++++++ ++ ++g++++ya+ v sa++Ga + lcl|NCBI__GCF_000019165.1:WP_041314961.1 494 EGDIIAIDIPAGRLDVEVDAAELAERRKEWQPPAPKVTSGYMKRYAQNVLSASTGARM 551 *******************************************************965 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 11.49 // [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