Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate WP_034997151.1 DL88_RS13730 dihydroxy-acid dehydratase
Query= SwissProt::Q1MIB2 (612 letters) >NCBI__GCF_000745425.1:WP_034997151.1 Length = 617 Score = 966 bits (2496), Expect = 0.0 Identities = 487/612 (79%), Positives = 534/612 (87%), Gaps = 2/612 (0%) Query: 1 MPVYRSRTTTHGRNMAGARGLWRATGMKDSDFGKPIIAVVNSFTQFVPGHVHLKDLGQLV 60 MP YRSRTTTHGRNMAGARGLWRATG+KD DFGKPIIA+ NSFTQFVPGHVHLKDLGQLV Sbjct: 1 MPAYRSRTTTHGRNMAGARGLWRATGVKDEDFGKPIIAIANSFTQFVPGHVHLKDLGQLV 60 Query: 61 AREIEAAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSRELIADSVEYMVNAHCADAMVCIS 120 A EIE AGG+AKEFNTIAVDDGIAMGHDGMLYSLPSRELIADSVEYMVNAHCADA+VCIS Sbjct: 61 AGEIEKAGGIAKEFNTIAVDDGIAMGHDGMLYSLPSRELIADSVEYMVNAHCADALVCIS 120 Query: 121 NCDKITPGMLMASLRLNIPTVFVSGGPMEAGKVVMHGKTHALDLVDAMVAAADDKISDED 180 NCDKITPGMLMA+LRLNIP +FVSGGPMEAGK + GK ALDLVDAMVAAADDK+S ED Sbjct: 121 NCDKITPGMLMAALRLNIPAIFVSGGPMEAGKAQVGGKQVALDLVDAMVAAADDKVSAED 180 Query: 181 VQTIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSTLATHLDRKRLFVEAGHLIV 240 V IERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGS LATH DRKRLFVEAGHLIV Sbjct: 181 VAVIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSLLATHGDRKRLFVEAGHLIV 240 Query: 241 DLARRYYEQDDVKALPRTIASKQAFENAMTLDIAMGGSTNTVLHILAAAHEGEIDFTMAD 300 DLARRYYEQ+DV LPR+IAS +AFENAMTLDIAMGGSTNTVLH+LAAA+E + FTMAD Sbjct: 241 DLARRYYEQNDVSVLPRSIASFKAFENAMTLDIAMGGSTNTVLHLLAAAYEAGVPFTMAD 300 Query: 301 IDALSRRVPCLSKVAPAKSDVHMEDVHRAGGIMSILGELDKGGLLNRDCPTVHAETLGDA 360 ID LSRRVPCL KVAPAK+DVHMEDVHRAGGIM ILGELD+ L++ D PTVHA LG+A Sbjct: 301 IDGLSRRVPCLCKVAPAKNDVHMEDVHRAGGIMGILGELDRARLIHADLPTVHAANLGEA 360 Query: 361 IDRWDITRTNSETVRKFYRAAPGGIPTQVAFSQEARWDELDTDRENGVIRSVEHPFSKDG 420 + RWD+ R+NSE V+ FY+AAPG +PT AFSQE R++ LD DRE GVIR H FS+DG Sbjct: 361 LMRWDVRRSNSEMVQTFYKAAPGNVPTTQAFSQEKRYEALDLDREAGVIRDSAHAFSQDG 420 Query: 421 GLAVLKGNLAIDGCIVKTAGVDESILKFSGPARVFESQDASVKAILANEVKAGDVVVIRY 480 GLAVL GNLA DG IVKTAGVDESIL F+GPARVFESQD++V+AIL+ + AGDVVVIRY Sbjct: 421 GLAVLYGNLAEDGSIVKTAGVDESILTFAGPARVFESQDSAVEAILSGRIVAGDVVVIRY 480 Query: 481 EGPKGGPGMQEMLYPTSYLKSKGLGKACALITDGRFSGGTSGLSIGHASPEAANGGTIGL 540 EGP+GGPGMQEMLYPTSYLKSKGLGKACALITDGRFSGGTSGLSIGH SPEAA GG I L Sbjct: 481 EGPRGGPGMQEMLYPTSYLKSKGLGKACALITDGRFSGGTSGLSIGHVSPEAAEGGMIAL 540 Query: 541 VREGDMIDIDIPNRTISLRVSETELAARRAEQDAKG--WYPTEVRKRNVTTALKAYAAFA 598 V +GD I+IDI R++ L V + ELA RRA +A G + R+R+V+TAL+AYAAF Sbjct: 541 VEDGDRIEIDIKARSLVLAVPDAELARRRAAMEALGAAGFKPRARERHVSTALRAYAAFT 600 Query: 599 TSADRGAVRDLN 610 TSA RGAVRDL+ Sbjct: 601 TSAARGAVRDLD 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: 1267 Number of extensions: 38 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: 617 Length adjustment: 37 Effective length of query: 575 Effective length of database: 580 Effective search space: 333500 Effective search space used: 333500 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_034997151.1 DL88_RS13730 (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.30836.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.9e-252 823.2 3.5 5.8e-252 822.9 3.5 1.0 1 lcl|NCBI__GCF_000745425.1:WP_034997151.1 DL88_RS13730 dihydroxy-acid dehy Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000745425.1:WP_034997151.1 DL88_RS13730 dihydroxy-acid dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 822.9 3.5 5.8e-252 5.8e-252 2 542 .. 18 610 .. 17 611 .. 0.99 Alignments for each domain: == domain 1 score: 822.9 bits; conditional E-value: 5.8e-252 TIGR00110 2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamg 70 ar l++atG+kded++kPiia++ns+t++vPghvhlkdl++lv+ eie+aGg+akefntiav+DGiamg lcl|NCBI__GCF_000745425.1:WP_034997151.1 18 ARGLWRATGVKDEDFGKPIIAIANSFTQFVPGHVHLKDLGQLVAGEIEKAGGIAKEFNTIAVDDGIAMG 86 689****************************************************************** PP TIGR00110 71 heGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktkl 139 h+Gm+ysLpsre+iaDsve++v+ah++Dalv+is+CDki+PGmlmaalrlniPai+vsGGpmeagk ++ lcl|NCBI__GCF_000745425.1:WP_034997151.1 87 HDGMLYSLPSRELIADSVEYMVNAHCADALVCISNCDKITPGMLMAALRLNIPAIFVSGGPMEAGKAQV 155 ********************************************************************* PP TIGR00110 140 sekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllat 208 + k +d+++a++++a++k+s e++ iersacPt+gsCsG+ftansm+cltealGlslPg+++llat lcl|NCBI__GCF_000745425.1:WP_034997151.1 156 GGKQVALDLVDAMVAAADDKVSAEDVAVIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSLLAT 224 ********************************************************************* PP TIGR00110 209 saekkelakksgkrivelvkknik.......PrdiltkeafenaitldlalGGstntvLhllaiakeag 270 + ++k+l+ ++g+ iv+l +++++ Pr+i++ +afena+tld+a+GGstntvLhlla+a eag lcl|NCBI__GCF_000745425.1:WP_034997151.1 225 HGDRKRLFVEAGHLIVDLARRYYEqndvsvlPRSIASFKAFENAMTLDIAMGGSTNTVLHLLAAAYEAG 293 ********************************************************************* PP TIGR00110 271 vklslddfdrlsrkvPllaklkPsgkkv.iedlhraGGvsavlkeldkegllhkdaltvtGktlaetle 338 v +++ d+d lsr+vP+l+k++P+ + v +ed+hraGG++++l+eld++ l+h d tv l+e l lcl|NCBI__GCF_000745425.1:WP_034997151.1 294 VPFTMADIDGLSRRVPCLCKVAPAKNDVhMEDVHRAGGIMGILGELDRARLIHADLPTVHAANLGEALM 362 *************************9999**************************************** PP TIGR00110 339 kvkvlr...................................vdqd..virsldnpvkkegglavLkGnl 370 + +v+r + vir ++++++gglavL+Gnl lcl|NCBI__GCF_000745425.1:WP_034997151.1 363 RWDVRRsnsemvqtfykaapgnvpttqafsqekryealdldR--EagVIRDSAHAFSQDGGLAVLYGNL 429 *****9*******************************88444..455********************** PP TIGR00110 371 aeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeGdvvviryeGPkGgPGmremLaPtsa 439 ae+G++vk+agv+e+il+f Gpa+vfes++ a+eail+g++ +GdvvviryeGP+GgPGm+emL+Pts+ lcl|NCBI__GCF_000745425.1:WP_034997151.1 430 AEDGSIVKTAGVDESILTFAGPARVFESQDSAVEAILSGRIVAGDVVVIRYEGPRGGPGMQEMLYPTSY 498 ********************************************************************* PP TIGR00110 440 lvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDienrkldlevseeelae 508 l++ GLgk++aLitDGrfsGgt+GlsiGhvsPeaaegG ialvedGD+i+iDi++r l l+v ++ela+ lcl|NCBI__GCF_000745425.1:WP_034997151.1 499 LKSKGLGKACALITDGRFSGGTSGLSIGHVSPEAAEGGMIALVEDGDRIEIDIKARSLVLAVPDAELAR 567 ********************************************************************* PP TIGR00110 509 rrakakkkea.........revkgaLakyaklvssadkGavld 542 rra++++ +a r+v+ aL++ya + +sa +Gav+d lcl|NCBI__GCF_000745425.1:WP_034997151.1 568 RRAAMEALGAagfkprareRHVSTALRAYAAFTTSAARGAVRD 610 *****9999889999999999********************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (543 nodes) Target sequences: 1 (617 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 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 12.88 // [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