Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate WP_027456693.1 K420_RS0102705 dihydroxy-acid dehydratase
Query= SwissProt::Q1MIB2 (612 letters) >NCBI__GCF_000519045.1:WP_027456693.1 Length = 618 Score = 935 bits (2416), Expect = 0.0 Identities = 462/612 (75%), Positives = 523/612 (85%), Gaps = 4/612 (0%) Query: 1 MPVYRSRTTTHGRNMAGARGLWRATGMKDSDFGKPIIAVVNSFTQFVPGHVHLKDLGQLV 60 MP YRSRT+THGRNMAGAR LWRATGMKD DFGKPIIAVVNSFTQFVPGHVHLKD+GQLV Sbjct: 1 MPQYRSRTSTHGRNMAGARALWRATGMKDGDFGKPIIAVVNSFTQFVPGHVHLKDMGQLV 60 Query: 61 AREIEAAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSRELIADSVEYMVNAHCADAMVCIS 120 AREIEAAGG+AKEFNTIA+DDGIAMGH GMLYSLPSR+LIADSVEYMVNAHCADAMVCIS Sbjct: 61 AREIEAAGGIAKEFNTIAIDDGIAMGHSGMLYSLPSRDLIADSVEYMVNAHCADAMVCIS 120 Query: 121 NCDKITPGMLMASLRLNIPTVFVSGGPMEAGKVVMHGKTHALDLVDAMVAAADDKISDED 180 NCDKITPGMLMA++RLNIP VFVSGGPMEAGKV +T +DL+DAM+ A D +SD + Sbjct: 121 NCDKITPGMLMAAMRLNIPVVFVSGGPMEAGKVKWQDQTIKVDLIDAMIKAGDKTVSDAE 180 Query: 181 VQTIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSTLATHLDRKRLFVEAGHLIV 240 V++ ERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNG+ +ATH RK LF+ A L V Sbjct: 181 VESFERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGTIVATHASRKELFLRAARLSV 240 Query: 241 DLARRYYEQDDVKALPRTIASKQAFENAMTLDIAMGGSTNTVLHILAAAHEGEIDFTMAD 300 +L RRYYEQDD LPRTIASK AFENAM LD++MGGSTNTVLH+LA A E +DFTMAD Sbjct: 241 ELCRRYYEQDDASVLPRTIASKAAFENAMALDVSMGGSTNTVLHLLATAQEAGVDFTMAD 300 Query: 301 IDALSRRVPCLSKVAPAKSDVHMEDVHRAGGIMSILGELDKGGLLNRDCPTVHAETLGDA 360 ID +SR+VPCL+KVAPA + H+EDVHRAGGIM+ILGELD+ GLL+RD PTVH +TLG+A Sbjct: 301 IDRISRKVPCLAKVAPATQEYHIEDVHRAGGIMAILGELDRAGLLDRDVPTVHTKTLGEA 360 Query: 361 IDRWDITRTNSETVRKFYRAAPGGIPTQVAFSQEARWDELDTDRENGVIRSVEHPFSKDG 420 IDRWD+ R + V FY+AAPGG+PTQ AFSQ ++ ELD DR +G IR+ + +S+DG Sbjct: 361 IDRWDVVREHDVKVHDFYKAAPGGVPTQTAFSQSRQYPELDLDRTHGCIRNKANAYSQDG 420 Query: 421 GLAVLKGNLAIDGCIVKTAGVDESILKFSGPARVFESQDASVKAILANEVKAGDVVVIRY 480 GLAVL GN+A+DGCIVKTAGVDESI KF+G ARVFESQD +V++IL +V AGDVVVIRY Sbjct: 421 GLAVLYGNIALDGCIVKTAGVDESIWKFTGRARVFESQDTAVESILGGQVVAGDVVVIRY 480 Query: 481 EGPKGGPGMQEMLYPTSYLKSKGLGKACALITDGRFSGGTSGLSIGHASPEAANGGTIGL 540 EGPKGGPGMQEMLYPTSYLKS GLGK CAL+TDGRFSGGTSGLSIGHASPEAA+GG IGL Sbjct: 481 EGPKGGPGMQEMLYPTSYLKSMGLGKECALLTDGRFSGGTSGLSIGHASPEAADGGAIGL 540 Query: 541 VREGDMIDIDIPNRTISLRVSETELAARRAEQDAKG---WYPTEVRKRNVTTALKAYAAF 597 V EGD I+IDIPNR I L VS+ ELA RRA +AKG W P R+R V+ AL+AYA Sbjct: 541 VEEGDRIEIDIPNRRIHLAVSDDELARRRAAMEAKGDAAWKPAS-RERVVSAALQAYALM 599 Query: 598 ATSADRGAVRDL 609 ATSAD+GAVRD+ Sbjct: 600 ATSADKGAVRDV 611 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: 1253 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: 618 Length adjustment: 37 Effective length of query: 575 Effective length of database: 581 Effective search space: 334075 Effective search space used: 334075 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_027456693.1 K420_RS0102705 (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.12178.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.7e-260 848.8 3.6 1e-259 848.5 3.6 1.0 1 lcl|NCBI__GCF_000519045.1:WP_027456693.1 K420_RS0102705 dihydroxy-acid de Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000519045.1:WP_027456693.1 K420_RS0102705 dihydroxy-acid dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 848.5 3.6 1e-259 1e-259 2 542 .. 18 610 .. 17 611 .. 0.99 Alignments for each domain: == domain 1 score: 848.5 bits; conditional E-value: 1e-259 TIGR00110 2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamg 70 aral++atG+kd d++kPiiavvns+t++vPghvhlkd+++lv++eieaaGg+akefntia++DGiamg lcl|NCBI__GCF_000519045.1:WP_027456693.1 18 ARALWRATGMKDGDFGKPIIAVVNSFTQFVPGHVHLKDMGQLVAREIEAAGGIAKEFNTIAIDDGIAMG 86 79******************************************************************* PP TIGR00110 71 heGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktkl 139 h+Gm+ysLpsr++iaDsve++v+ah++Da+v+is+CDki+PGmlmaa+rlniP+++vsGGpmeagk+k lcl|NCBI__GCF_000519045.1:WP_027456693.1 87 HSGMLYSLPSRDLIADSVEYMVNAHCADAMVCISNCDKITPGMLMAAMRLNIPVVFVSGGPMEAGKVKW 155 ********************************************************************* PP TIGR00110 140 sekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllat 208 ++ ++vd+++a++++ ++ +s++e+e++ersacPt+gsCsG+ftansm+cltealGlslPg++t+ at lcl|NCBI__GCF_000519045.1:WP_027456693.1 156 QDQTIKVDLIDAMIKAGDKTVSDAEVESFERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGTIVAT 224 ********************************************************************* PP TIGR00110 209 saekkelakksgkrivelvkknik.......PrdiltkeafenaitldlalGGstntvLhllaiakeag 270 +a +kel+ ++++ vel++++++ Pr+i++k+afena++ld+ +GGstntvLhlla a+eag lcl|NCBI__GCF_000519045.1:WP_027456693.1 225 HASRKELFLRAARLSVELCRRYYEqddasvlPRTIASKAAFENAMALDVSMGGSTNTVLHLLATAQEAG 293 ********************************************************************* PP TIGR00110 271 vklslddfdrlsrkvPllaklkPsgkkv.iedlhraGGvsavlkeldkegllhkdaltvtGktlaetle 338 v++++ d+dr+srkvP+lak++P+++++ ied+hraGG++a+l+eld++gll++d+ tv ktl+e ++ lcl|NCBI__GCF_000519045.1:WP_027456693.1 294 VDFTMADIDRISRKVPCLAKVAPATQEYhIEDVHRAGGIMAILGELDRAGLLDRDVPTVHTKTLGEAID 362 **************************999**************************************** PP TIGR00110 339 kvkvlr...................................vdqdvirsldnpvkkegglavLkGnlae 372 + +v r + +ir++ n+++++gglavL+Gn+a lcl|NCBI__GCF_000519045.1:WP_027456693.1 363 RWDVVRehdvkvhdfykaapggvptqtafsqsrqypeldldRTHGCIRNKANAYSQDGGLAVLYGNIAL 431 *****99*****************************987555555************************ PP TIGR00110 373 eGavvkiagveedilkfeGpakvfeseeealeailggkvkeGdvvviryeGPkGgPGmremLaPtsalv 441 +G++vk+agv+e+i+kf+G+a+vfes++ a+e+ilgg+v +GdvvviryeGPkGgPGm+emL+Pts+l+ lcl|NCBI__GCF_000519045.1:WP_027456693.1 432 DGCIVKTAGVDESIWKFTGRARVFESQDTAVESILGGQVVAGDVVVIRYEGPKGGPGMQEMLYPTSYLK 500 ********************************************************************* PP TIGR00110 442 glGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDienrkldlevseeelaerr 510 ++GLgk++aL+tDGrfsGgt+GlsiGh sPeaa gGai+lve+GD+i+iDi+nr+++l+vs++ela+rr lcl|NCBI__GCF_000519045.1:WP_027456693.1 501 SMGLGKECALLTDGRFSGGTSGLSIGHASPEAADGGAIGLVEEGDRIEIDIPNRRIHLAVSDDELARRR 569 ********************************************************************* PP TIGR00110 511 akakkkea.........revkgaLakyaklvssadkGavld 542 a++++k++ r v+ aL++ya +++sadkGav+d lcl|NCBI__GCF_000519045.1:WP_027456693.1 570 AAMEAKGDaawkpasreRVVSAALQAYALMATSADKGAVRD 610 ******9999******99*********************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (543 nodes) Target sequences: 1 (618 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: 9.22 // [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