Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate WP_036259446.1 DL86_RS06455 dihydroxy-acid dehydratase
Query= SwissProt::Q1MIB2 (612 letters) >NCBI__GCF_000746085.1:WP_036259446.1 Length = 616 Score = 994 bits (2570), Expect = 0.0 Identities = 495/613 (80%), Positives = 545/613 (88%), Gaps = 4/613 (0%) Query: 1 MPVYRSRTTTHGRNMAGARGLWRATGMKDSDFGKPIIAVVNSFTQFVPGHVHLKDLGQLV 60 MP YRSRTTTHGRNMAGARGLWRATGM D+DFGKPIIAVVNSFTQFVPGHVHLKDLGQLV Sbjct: 1 MPQYRSRTTTHGRNMAGARGLWRATGMTDADFGKPIIAVVNSFTQFVPGHVHLKDLGQLV 60 Query: 61 AREIEAAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSRELIADSVEYMVNAHCADAMVCIS 120 AREIEAAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSRE+IADSVEYMVNAHCADAMVCIS Sbjct: 61 AREIEAAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSREIIADSVEYMVNAHCADAMVCIS 120 Query: 121 NCDKITPGMLMASLRLNIPTVFVSGGPMEAGKVVMHGKTHALDLVDAMVAAADDKISDED 180 NCDKITPGMLMA+LRLNIP VFVSGGPMEAGK ++ GK+ ALDLVDAMVAAADDKISD D Sbjct: 121 NCDKITPGMLMAALRLNIPAVFVSGGPMEAGKALLGGKSKALDLVDAMVAAADDKISDAD 180 Query: 181 VQTIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSTLATHLDRKRLFVEAGHLIV 240 + IERSACPTCGSCSGMFTANSMNCLTEALGL+LPGNGS LATH DRKRLFVEAGHLIV Sbjct: 181 IAVIERSACPTCGSCSGMFTANSMNCLTEALGLALPGNGSLLATHADRKRLFVEAGHLIV 240 Query: 241 DLARRYYEQDDVKALPRTIASKQAFENAMTLDIAMGGSTNTVLHILAAAHEGEIDFTMAD 300 DLARRYYEQ+D LPR++AS +AFENAMTLDI+MGGSTNTVLH+LAAA+E E+DFTMAD Sbjct: 241 DLARRYYEQNDASVLPRSVASFKAFENAMTLDISMGGSTNTVLHLLAAAYEAEVDFTMAD 300 Query: 301 IDALSRRVPCLSKVAPAKSDVHMEDVHRAGGIMSILGELDKGGLLNRDCPTVHAETLGDA 360 ID LSRRVP L KVAP+ +DVH+EDVHRAGG+M+ILGEL++ GL++ D PTVHA TL DA Sbjct: 301 IDRLSRRVPVLCKVAPSVADVHLEDVHRAGGVMAILGELERAGLIHADLPTVHAPTLADA 360 Query: 361 IDRWDITRTNSETVRKFYRAAPGGIPTQVAFSQEARWDELDTDRENGVIRSVEHPFSKDG 420 ++RWDI RT S +V +F+RAAPGG+PTQVAFSQ RWDE+D DRE+G IR H FSKDG Sbjct: 361 LERWDIRRTASASVTEFFRAAPGGVPTQVAFSQNRRWDEIDLDREHGAIRDAAHAFSKDG 420 Query: 421 GLAVLKGNLAIDGCIVKTAGVDESILKFSGPARVFESQDASVKAILANEVKAGDVVVIRY 480 GLAVL GNLA DG IVKTAGVD SIL FSGPAR+FESQDA+V AIL + +K GD++VIRY Sbjct: 421 GLAVLYGNLAEDGSIVKTAGVDASILTFSGPARIFESQDAAVDAILGDRIKPGDILVIRY 480 Query: 481 EGPKGGPGMQEMLYPTSYLKSKGLGKACALITDGRFSGGTSGLSIGHASPEAANGGTIGL 540 EGP+GGPGMQEMLYPTSYLKSKGLGKACALITDGRFSGGTSGLSIGH SPEAA GG IGL Sbjct: 481 EGPRGGPGMQEMLYPTSYLKSKGLGKACALITDGRFSGGTSGLSIGHVSPEAAEGGVIGL 540 Query: 541 VREGDMIDIDIPNRTISLRVSETELAARRAEQDAKG---WYPTEVRKRNVTTALKAYAAF 597 V EGD+I+IDIPNR I L V + ELA RRA+ +AKG W P E R R ++TAL+AYAA Sbjct: 541 VSEGDLIEIDIPNRGIHLAVPDGELARRRADMEAKGKEAWKPAE-RVRKISTALRAYAAM 599 Query: 598 ATSADRGAVRDLN 610 TSA RGAVRD++ Sbjct: 600 TTSAARGAVRDVD 612 Lambda K H 0.318 0.134 0.391 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: 1304 Number of extensions: 44 Number of successful extensions: 2 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: 612 Length of database: 616 Length adjustment: 37 Effective length of query: 575 Effective length of database: 579 Effective search space: 332925 Effective search space used: 332925 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 53 (25.0 bits)
Align candidate WP_036259446.1 DL86_RS06455 (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.5006.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.5e-250 817.6 2.0 2.9e-250 817.4 2.0 1.0 1 lcl|NCBI__GCF_000746085.1:WP_036259446.1 DL86_RS06455 dihydroxy-acid dehy Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000746085.1:WP_036259446.1 DL86_RS06455 dihydroxy-acid dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 817.4 2.0 2.9e-250 2.9e-250 2 542 .. 18 610 .. 17 611 .. 0.99 Alignments for each domain: == domain 1 score: 817.4 bits; conditional E-value: 2.9e-250 TIGR00110 2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamg 70 ar l++atG++d+d++kPiiavvns+t++vPghvhlkdl++lv++eieaaGgvakefntiav+DGiamg lcl|NCBI__GCF_000746085.1:WP_036259446.1 18 ARGLWRATGMTDADFGKPIIAVVNSFTQFVPGHVHLKDLGQLVAREIEAAGGVAKEFNTIAVDDGIAMG 86 689****************************************************************** PP TIGR00110 71 heGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktkl 139 h+Gm+ysLpsreiiaDsve++v+ah++Da+v+is+CDki+PGmlmaalrlniPa++vsGGpmeagk l lcl|NCBI__GCF_000746085.1:WP_036259446.1 87 HDGMLYSLPSREIIADSVEYMVNAHCADAMVCISNCDKITPGMLMAALRLNIPAVFVSGGPMEAGKALL 155 ********************************************************************* PP TIGR00110 140 sekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllat 208 + k + +d+++a++++a++k+s++++ iersacPt+gsCsG+ftansm+cltealGl+lPg+++llat lcl|NCBI__GCF_000746085.1:WP_036259446.1 156 GGKSKALDLVDAMVAAADDKISDADIAVIERSACPTCGSCSGMFTANSMNCLTEALGLALPGNGSLLAT 224 ********************************************************************* PP TIGR00110 209 saekkelakksgkrivelvkknik.......PrdiltkeafenaitldlalGGstntvLhllaiakeag 270 +a++k+l+ ++g+ iv+l +++++ Pr++++ +afena+tld+ +GGstntvLhlla+a ea+ lcl|NCBI__GCF_000746085.1:WP_036259446.1 225 HADRKRLFVEAGHLIVDLARRYYEqndasvlPRSVASFKAFENAMTLDISMGGSTNTVLHLLAAAYEAE 293 ********************************************************************* PP TIGR00110 271 vklslddfdrlsrkvPllaklkPsgkkv.iedlhraGGvsavlkeldkegllhkdaltvtGktlaetle 338 v++++ d+drlsr+vP+l+k++Ps v +ed+hraGGv+a+l+el+++gl+h d tv tla+ le lcl|NCBI__GCF_000746085.1:WP_036259446.1 294 VDFTMADIDRLSRRVPVLCKVAPSVADVhLEDVHRAGGVMAILGELERAGLIHADLPTVHAPTLADALE 362 ************************98888**************************************** PP TIGR00110 339 kvkvlr...................................vdqdvirsldnpvkkegglavLkGnlae 372 + +++r ++ ir ++++k+gglavL+Gnlae lcl|NCBI__GCF_000746085.1:WP_036259446.1 363 RWDIRRtasasvteffraapggvptqvafsqnrrwdeidldREHGAIRDAAHAFSKDGGLAVLYGNLAE 431 *****9*******************************88554455************************ PP TIGR00110 373 eGavvkiagveedilkfeGpakvfeseeealeailggkvkeGdvvviryeGPkGgPGmremLaPtsalv 441 +G++vk+agv+ +il+f Gpa++fes+++a++ailg ++k Gd++viryeGP+GgPGm+emL+Pts+l+ lcl|NCBI__GCF_000746085.1:WP_036259446.1 432 DGSIVKTAGVDASILTFSGPARIFESQDAAVDAILGDRIKPGDILVIRYEGPRGGPGMQEMLYPTSYLK 500 ********************************************************************* PP TIGR00110 442 glGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDienrkldlevseeelaerr 510 + GLgk++aLitDGrfsGgt+GlsiGhvsPeaaegG i+lv +GD i+iDi+nr ++l+v + ela+rr lcl|NCBI__GCF_000746085.1:WP_036259446.1 501 SKGLGKACALITDGRFSGGTSGLSIGHVSPEAAEGGVIGLVSEGDLIEIDIPNRGIHLAVPDGELARRR 569 ********************************************************************* PP TIGR00110 511 akakkkea.........revkgaLakyaklvssadkGavld 542 a++++k++ r+++ aL++ya + +sa +Gav+d lcl|NCBI__GCF_000746085.1:WP_036259446.1 570 ADMEAKGKeawkpaervRKISTALRAYAAMTTSAARGAVRD 610 ****9999999****9999********************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (543 nodes) Target sequences: 1 (616 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 0.02s 00:00:00.03 Elapsed: 00:00:00.03 # Mc/sec: 10.27 // [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