Align dihydroxy-acid dehydratase subunit (EC 4.2.1.9) (characterized)
to candidate WP_078430190.1 BK574_RS22725 dihydroxy-acid dehydratase
Query= metacyc::MONOMER-11919 (549 letters) >NCBI__GCF_002019605.1:WP_078430190.1 Length = 555 Score = 530 bits (1366), Expect = e-155 Identities = 265/555 (47%), Positives = 390/555 (70%), Gaps = 7/555 (1%) Query: 1 MKSDTIKRGIQRAPHRSLLARCGLTDDDFEKPFIGIANSYTDIVPGHIHLRELAEAVKEG 60 M+S+ IK+GI RAPHRSLL G+ ++D +KPFIG+ NSY DI+PGH+HL + AE KE Sbjct: 1 MRSNMIKKGIDRAPHRSLLRAAGVKEEDMDKPFIGVCNSYIDIIPGHMHLNKFAEVAKEA 60 Query: 61 VNAAGGVAFEFNTMAICDGIAMNHDGMKYSLASREIVADTVESMAMAHALDGLVLLPTCD 120 + AGG+ FEFNT+ + DGIAM H GM+YSL SREI+ D E++ AH DG+ +P CD Sbjct: 61 IREAGGIPFEFNTIGVDDGIAMGHIGMRYSLPSREIICDAAETVINAHWFDGVFYIPNCD 120 Query: 121 KIVPGMLMAAARLDIPAIVVTGGPMLPGEFK-GRKVDLINVYEGVGTVSAGEMSEDELEE 179 KI PGMLMA+ R ++P++ V+GGPM G K G+ + L +V+EGVG ++G MS +EL E Sbjct: 121 KITPGMLMASVRTNVPSVFVSGGPMEAGRTKDGKSLSLASVFEGVGAFASGSMSREELLE 180 Query: 180 LERCACPGPRSCAGLFTANTMACLTEALGMSLPGCATAHAVSSRKRQIARLSGKRIVEMV 239 +E+ ACP SC+G+FTAN+M L E LG++LPG T A S + Q+ + + K ++ ++ Sbjct: 181 IEQSACPTCGSCSGMFTANSMNTLMEMLGVALPGNGTLVATSEGRHQLIKDAAKHLMTLI 240 Query: 240 QENLKPTMIMSQEAFENAVMVDLALGGSTNTTLHIPAIAAEIDGLNINLDLFDELSRVIP 299 +++++P I+++EA ++A +D+A+GGSTNT LH AIA E + ++ N+ ++++ +P Sbjct: 241 EKDIRPRDIITKEAIDDAFALDMAMGGSTNTVLHTLAIANEAE-IDYNISDINKIAERVP 299 Query: 300 HIASISPAGEHMMLDLDRAGGIPAVLKTL---EDHINRECVTCTGRTVQENIENVKVGHR 356 +++ ISPA ++ M D+ +AGG+ A++K L E I+ E +T +G+T+ E +++ ++ + Sbjct: 300 YLSKISPASDYSMDDVHKAGGVSAIMKELCQIEGAIHPERITISGKTIWETVKDAEITND 359 Query: 357 DVIRPLDSPVHSEGGLAILRGNLAPRGSVVKQGAVAEDMMVHEGPAKVFNSEDECMEAIF 416 +VIR D+P S GGL++L GNLAP G V+K GAV + V EG A V+NS++E +E I Sbjct: 360 EVIRRKDNPYSSVGGLSVLFGNLAPDGGVIKVGAVDASIKVFEGDAIVYNSQEEALEGIN 419 Query: 417 GGRIDEGDVIVIRYEGPKGGPGMREMLNPTSAIAGMGL-ERVALITDGRFSGGTRGPCVG 475 G + EG V+VIRYEGPKGGPGM EML PTS+I G GL +VALITDGRFSG +RG +G Sbjct: 420 NGDVREGHVVVIRYEGPKGGPGMPEMLAPTSSIVGRGLGTKVALITDGRFSGASRGISIG 479 Query: 476 HVSPEAMEDGPLAAVNDGDIIRIDIPSRKLEVDLSPREIEERLQSAVKPRRSV-KGWLAR 534 H+SPEA E GP+A V +GD I +D+ +R + +++ E+ R + +P V KG+LAR Sbjct: 480 HISPEAAEGGPIAFVENGDKITLDLTNRTITLNVDDVELANRKEGWKEPEPKVKKGYLAR 539 Query: 535 YRKLAGSADTGAVLR 549 Y KL SA+TG V++ Sbjct: 540 YSKLVTSANTGGVMK 554 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: 893 Number of extensions: 43 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: 555 Length adjustment: 36 Effective length of query: 513 Effective length of database: 519 Effective search space: 266247 Effective search space used: 266247 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_078430190.1 BK574_RS22725 (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.26846.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-250 818.4 5.9 1.6e-250 818.2 5.9 1.0 1 lcl|NCBI__GCF_002019605.1:WP_078430190.1 BK574_RS22725 dihydroxy-acid deh Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002019605.1:WP_078430190.1 BK574_RS22725 dihydroxy-acid dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 818.2 5.9 1.6e-250 1.6e-250 1 542 [. 14 554 .. 14 555 .] 1.00 Alignments for each domain: == domain 1 score: 818.2 bits; conditional E-value: 1.6e-250 TIGR00110 1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiam 69 ++r+ll+a+G+k+ed++kP+i+v+nsy++i+Pgh+hl+++a+++ke+i++aGg+++efnti+v+DGiam lcl|NCBI__GCF_002019605.1:WP_078430190.1 14 PHRSLLRAAGVKEEDMDKPFIGVCNSYIDIIPGHMHLNKFAEVAKEAIREAGGIPFEFNTIGVDDGIAM 82 69******************************************************************* PP TIGR00110 70 gheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktk 138 gh Gm+ysLpsreii D+ etv++ah++D++ i++CDki+PGmlma++r+n+P+++vsGGpmeag+tk lcl|NCBI__GCF_002019605.1:WP_078430190.1 83 GHIGMRYSLPSREIICDAAETVINAHWFDGVFYIPNCDKITPGMLMASVRTNVPSVFVSGGPMEAGRTK 151 ********************************************************************* PP TIGR00110 139 lsekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstlla 207 ++ ++l +vfe+vg+ a+g +s eel eie+sacPt+gsCsG+ftansm++l+e lG++lPg++tl a lcl|NCBI__GCF_002019605.1:WP_078430190.1 152 DGKSLSLASVFEGVGAFASGSMSREELLEIEQSACPTCGSCSGMFTANSMNTLMEMLGVALPGNGTLVA 220 ********************************************************************* PP TIGR00110 208 tsaekkelakksgkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklsld 276 ts+ +++l+k ++k+++ l++k+i+Prdi+tkea+++a++ld+a+GGstntvLh+laia+ea+++++++ lcl|NCBI__GCF_002019605.1:WP_078430190.1 221 TSEGRHQLIKDAAKHLMTLIEKDIRPRDIITKEAIDDAFALDMAMGGSTNTVLHTLAIANEAEIDYNIS 289 ********************************************************************* PP TIGR00110 277 dfdrlsrkvPllaklkPsgkkviedlhraGGvsavlkeldk.egllhkdaltvtGktlaetlekvkvlr 344 d+++++++vP l+k++P++++ + d+h+aGGvsa++kel + eg++h + +t++Gkt+ et+++++++ lcl|NCBI__GCF_002019605.1:WP_078430190.1 290 DINKIAERVPYLSKISPASDYSMDDVHKAGGVSAIMKELCQiEGAIHPERITISGKTIWETVKDAEIT- 357 ***************************************9889************************9. PP TIGR00110 345 vdqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvke 413 +++vir +dnp+++ ggl vL+Gnla++G v+k+++v+ +i +feG a v++s+eeale+i +g+v+e lcl|NCBI__GCF_002019605.1:WP_078430190.1 358 -NDEVIRRKDNPYSSVGGLSVLFGNLAPDGGVIKVGAVDASIKVFEGDAIVYNSQEEALEGINNGDVRE 425 .99****************************************************************** PP TIGR00110 414 GdvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialv 482 G+vvviryeGPkGgPGm+emLaPts +vg GLg kvaLitDGrfsG++rG+siGh+sPeaaegG+ia+v lcl|NCBI__GCF_002019605.1:WP_078430190.1 426 GHVVVIRYEGPKGGPGMPEMLAPTSSIVGRGLGTKVALITDGRFSGASRGISIGHISPEAAEGGPIAFV 494 ********************************************************************* PP TIGR00110 483 edGDkikiDienrkldlevseeelaerrakakkkearevkgaLakyaklvssadkGavld 542 e+GDki++D++nr++ l+v++ ela+r++ +k++e++ +kg+La+y+klv+sa++G+v++ lcl|NCBI__GCF_002019605.1:WP_078430190.1 495 ENGDKITLDLTNRTITLNVDDVELANRKEGWKEPEPKVKKGYLARYSKLVTSANTGGVMK 554 **********************************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (543 nodes) Target sequences: 1 (555 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: 11.59 // [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