Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate WP_012385640.1 BIND_RS13700 dihydroxy-acid dehydratase
Query= SwissProt::Q1MIB2 (612 letters) >NCBI__GCF_000019845.1:WP_012385640.1 Length = 617 Score = 969 bits (2504), Expect = 0.0 Identities = 491/613 (80%), Positives = 536/613 (87%), Gaps = 4/613 (0%) Query: 1 MPVYRSRTTTHGRNMAGARGLWRATGMKDSDFGKPIIAVVNSFTQFVPGHVHLKDLGQLV 60 MP YRSRTTTHGRNMAGARGLWRATG+KD DFGKPIIA+ NSFTQFVPGHVHLKDLGQLV Sbjct: 1 MPDYRSRTTTHGRNMAGARGLWRATGVKDEDFGKPIIAIANSFTQFVPGHVHLKDLGQLV 60 Query: 61 AREIEAAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSRELIADSVEYMVNAHCADAMVCIS 120 A EIE AGG+AKEFNTIAVDDGIAMGHDGMLYSLPSRELIADSVEYMVNAHCADA+VCIS Sbjct: 61 AGEIEKAGGIAKEFNTIAVDDGIAMGHDGMLYSLPSRELIADSVEYMVNAHCADALVCIS 120 Query: 121 NCDKITPGMLMASLRLNIPTVFVSGGPMEAGKVVMHGKTHALDLVDAMVAAADDKISDED 180 NCDKITPGMLMA+LRLNIPT+FVSGGPMEAGK + GKT ALDLVDAMVAAADD++S ED Sbjct: 121 NCDKITPGMLMAALRLNIPTIFVSGGPMEAGKAQVGGKTLALDLVDAMVAAADDRVSAED 180 Query: 181 VQTIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSTLATHLDRKRLFVEAGHLIV 240 V IERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGS LATH DR+RLFVEAGHLIV Sbjct: 181 VAVIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSVLATHADRRRLFVEAGHLIV 240 Query: 241 DLARRYYEQDDVKALPRTIASKQAFENAMTLDIAMGGSTNTVLHILAAAHEGEIDFTMAD 300 DLARRYYEQ+D LPR IAS +AFENAMTLDIAMGGSTNTVLH+LAAAHE + F MAD Sbjct: 241 DLARRYYEQNDGSVLPRAIASFKAFENAMTLDIAMGGSTNTVLHLLAAAHEAGVPFMMAD 300 Query: 301 IDALSRRVPCLSKVAPAKSDVHMEDVHRAGGIMSILGELDKGGLLNRDCPTVHAETLGDA 360 ID LSR VPCL KVAPAK+DVHMEDVHRAGGIM+ILGELD+ GLL+ D PTVH+ +LG+A Sbjct: 301 IDRLSRGVPCLCKVAPAKNDVHMEDVHRAGGIMAILGELDRAGLLHADLPTVHSSSLGEA 360 Query: 361 IDRWDITRTNSETVRKFYRAAPGGIPTQVAFSQEARWDELDTDRENGVIRSVEHPFSKDG 420 + RWDI R+NSE V+ FY+AAPG +PT AFSQE R++ LD DRE GVIR H FS+DG Sbjct: 361 LMRWDIRRSNSEMVQTFYKAAPGNVPTTQAFSQEKRYEALDLDRETGVIRDQAHAFSQDG 420 Query: 421 GLAVLKGNLAIDGCIVKTAGVDESILKFSGPARVFESQDASVKAILANEVKAGDVVVIRY 480 GLAVL GNLA +G IVKTAGVDESIL F+GPARVFESQD++V+AILA + AGDVVVIRY Sbjct: 421 GLAVLFGNLAEEGSIVKTAGVDESILTFAGPARVFESQDSAVEAILAGRIVAGDVVVIRY 480 Query: 481 EGPKGGPGMQEMLYPTSYLKSKGLGKACALITDGRFSGGTSGLSIGHASPEAANGGTIGL 540 EGP+GGPGMQEMLYPTSYLKSKGLGKACALITDGRFSGGTSGLSIGH SPEAA GG I L Sbjct: 481 EGPRGGPGMQEMLYPTSYLKSKGLGKACALITDGRFSGGTSGLSIGHVSPEAAEGGMIAL 540 Query: 541 VREGDMIDIDIPNRTISLRVSETELAARRAEQDAKG---WYPTEVRKRNVTTALKAYAAF 597 V EGD I+IDI R++ L V E ELA RR +AKG + P E R+R V+TAL+AYAAF Sbjct: 541 VEEGDRIEIDIKTRSLILAVPEAELARRRGVMEAKGANAFKPRE-RQRQVSTALRAYAAF 599 Query: 598 ATSADRGAVRDLN 610 TSA RGAVRDL+ Sbjct: 600 TTSAARGAVRDLD 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: 1280 Number of extensions: 39 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_012385640.1 BIND_RS13700 (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.6111.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.1e-252 824.4 3.5 2.5e-252 824.2 3.5 1.0 1 lcl|NCBI__GCF_000019845.1:WP_012385640.1 BIND_RS13700 dihydroxy-acid dehy Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000019845.1:WP_012385640.1 BIND_RS13700 dihydroxy-acid dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 824.2 3.5 2.5e-252 2.5e-252 2 542 .. 18 610 .. 17 611 .. 0.99 Alignments for each domain: == domain 1 score: 824.2 bits; conditional E-value: 2.5e-252 TIGR00110 2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamg 70 ar l++atG+kded++kPiia++ns+t++vPghvhlkdl++lv+ eie+aGg+akefntiav+DGiamg lcl|NCBI__GCF_000019845.1:WP_012385640.1 18 ARGLWRATGVKDEDFGKPIIAIANSFTQFVPGHVHLKDLGQLVAGEIEKAGGIAKEFNTIAVDDGIAMG 86 689****************************************************************** PP TIGR00110 71 heGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktkl 139 h+Gm+ysLpsre+iaDsve++v+ah++Dalv+is+CDki+PGmlmaalrlniP+i+vsGGpmeagk ++ lcl|NCBI__GCF_000019845.1:WP_012385640.1 87 HDGMLYSLPSRELIADSVEYMVNAHCADALVCISNCDKITPGMLMAALRLNIPTIFVSGGPMEAGKAQV 155 ********************************************************************* PP TIGR00110 140 sekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllat 208 + k +d+++a++++a++++s e++ iersacPt+gsCsG+ftansm+cltealGlslPg++++lat lcl|NCBI__GCF_000019845.1:WP_012385640.1 156 GGKTLALDLVDAMVAAADDRVSAEDVAVIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSVLAT 224 ********************************************************************* PP TIGR00110 209 saekkelakksgkrivelvkknik.......PrdiltkeafenaitldlalGGstntvLhllaiakeag 270 +a++++l+ ++g+ iv+l +++++ Pr i++ +afena+tld+a+GGstntvLhlla+a+eag lcl|NCBI__GCF_000019845.1:WP_012385640.1 225 HADRRRLFVEAGHLIVDLARRYYEqndgsvlPRAIASFKAFENAMTLDIAMGGSTNTVLHLLAAAHEAG 293 ********************************************************************* PP TIGR00110 271 vklslddfdrlsrkvPllaklkPsgkkv.iedlhraGGvsavlkeldkegllhkdaltvtGktlaetle 338 v + + d+drlsr vP+l+k++P+ + v +ed+hraGG++a+l+eld++gllh d tv ++l+e l lcl|NCBI__GCF_000019845.1:WP_012385640.1 294 VPFMMADIDRLSRGVPCLCKVAPAKNDVhMEDVHRAGGIMAILGELDRAGLLHADLPTVHSSSLGEALM 362 *************************9999**************************************** PP TIGR00110 339 kvkvlr...................................vdqdvirsldnpvkkegglavLkGnlae 372 + +++r ++ vir ++++++gglavL+Gnlae lcl|NCBI__GCF_000019845.1:WP_012385640.1 363 RWDIRRsnsemvqtfykaapgnvpttqafsqekryealdldRETGVIRDQAHAFSQDGGLAVLFGNLAE 431 *****9*******************************88544455************************ PP TIGR00110 373 eGavvkiagveedilkfeGpakvfeseeealeailggkvkeGdvvviryeGPkGgPGmremLaPtsalv 441 eG++vk+agv+e+il+f Gpa+vfes++ a+eail+g++ +GdvvviryeGP+GgPGm+emL+Pts+l+ lcl|NCBI__GCF_000019845.1:WP_012385640.1 432 EGSIVKTAGVDESILTFAGPARVFESQDSAVEAILAGRIVAGDVVVIRYEGPRGGPGMQEMLYPTSYLK 500 ********************************************************************* PP TIGR00110 442 glGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDienrkldlevseeelaerr 510 + GLgk++aLitDGrfsGgt+GlsiGhvsPeaaegG ialve+GD+i+iDi+ r l l+v e+ela+rr lcl|NCBI__GCF_000019845.1:WP_012385640.1 501 SKGLGKACALITDGRFSGGTSGLSIGHVSPEAAEGGMIALVEEGDRIEIDIKTRSLILAVPEAELARRR 569 ********************************************************************* PP TIGR00110 511 akakkkea.........revkgaLakyaklvssadkGavld 542 +++k+a r+v+ aL++ya + +sa +Gav+d lcl|NCBI__GCF_000019845.1:WP_012385640.1 570 GVMEAKGAnafkprerqRQVSTALRAYAAFTTSAARGAVRD 610 **999999999****999*********************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: 0.04u 0.02s 00:00:00.06 Elapsed: 00:00:00.04 # Mc/sec: 7.48 // [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