Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate SMc04045 SMc04045 dihydroxy-acid dehydratase
Query= SwissProt::Q1MIB2 (612 letters) >FitnessBrowser__Smeli:SMc04045 Length = 612 Score = 1153 bits (2982), Expect = 0.0 Identities = 573/612 (93%), Positives = 591/612 (96%) Query: 1 MPVYRSRTTTHGRNMAGARGLWRATGMKDSDFGKPIIAVVNSFTQFVPGHVHLKDLGQLV 60 MP YRSRTTTHGRNMAGARGLWRATGMKDSDFGKPIIAVVNSFTQFVPGHVHLKDLGQLV Sbjct: 1 MPAYRSRTTTHGRNMAGARGLWRATGMKDSDFGKPIIAVVNSFTQFVPGHVHLKDLGQLV 60 Query: 61 AREIEAAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSRELIADSVEYMVNAHCADAMVCIS 120 AREIEAAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSRE+IADSVEYMVNAHCADAMVCIS Sbjct: 61 AREIEAAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSREIIADSVEYMVNAHCADAMVCIS 120 Query: 121 NCDKITPGMLMASLRLNIPTVFVSGGPMEAGKVVMHGKTHALDLVDAMVAAADDKISDED 180 NCDKITPGMLMA+LRLNIP VFVSGGPMEAGKVV+HGKTHALDLVDAMVAAADDK+SDED Sbjct: 121 NCDKITPGMLMAALRLNIPAVFVSGGPMEAGKVVLHGKTHALDLVDAMVAAADDKVSDED 180 Query: 181 VQTIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSTLATHLDRKRLFVEAGHLIV 240 VQ IERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSTLATH DRKRLFVEAGHLIV Sbjct: 181 VQIIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSTLATHADRKRLFVEAGHLIV 240 Query: 241 DLARRYYEQDDVKALPRTIASKQAFENAMTLDIAMGGSTNTVLHILAAAHEGEIDFTMAD 300 DLARRYYEQ+D + LPR IA+KQAFENAM LDIAMGGSTNTVLHILAAA+EGEIDFTM D Sbjct: 241 DLARRYYEQEDERVLPRNIATKQAFENAMALDIAMGGSTNTVLHILAAAYEGEIDFTMDD 300 Query: 301 IDALSRRVPCLSKVAPAKSDVHMEDVHRAGGIMSILGELDKGGLLNRDCPTVHAETLGDA 360 ID LSR+VPCLSKVAPAK+DVHMEDVHRAGGIMSILGELDKGGL+NRDCPTVHAETLGDA Sbjct: 301 IDRLSRKVPCLSKVAPAKADVHMEDVHRAGGIMSILGELDKGGLINRDCPTVHAETLGDA 360 Query: 361 IDRWDITRTNSETVRKFYRAAPGGIPTQVAFSQEARWDELDTDRENGVIRSVEHPFSKDG 420 IDRWDITRT+S+TVRKF+RAAPGGIPTQVAFSQEARWDELDTDRENGVIRSVEHPFSKDG Sbjct: 361 IDRWDITRTSSDTVRKFFRAAPGGIPTQVAFSQEARWDELDTDRENGVIRSVEHPFSKDG 420 Query: 421 GLAVLKGNLAIDGCIVKTAGVDESILKFSGPARVFESQDASVKAILANEVKAGDVVVIRY 480 GLAVLKGN+A+DGCIVKTAGVDESILKFSGPARVFESQDA+VK ILANE+KAGDVVVIRY Sbjct: 421 GLAVLKGNIALDGCIVKTAGVDESILKFSGPARVFESQDAAVKGILANEIKAGDVVVIRY 480 Query: 481 EGPKGGPGMQEMLYPTSYLKSKGLGKACALITDGRFSGGTSGLSIGHASPEAANGGTIGL 540 EGPKGGPGMQEMLYPTSYLKSKGLGKACALITDGRFSGGTSGLSIGH SPEAANGGTIGL Sbjct: 481 EGPKGGPGMQEMLYPTSYLKSKGLGKACALITDGRFSGGTSGLSIGHVSPEAANGGTIGL 540 Query: 541 VREGDMIDIDIPNRTISLRVSETELAARRAEQDAKGWYPTEVRKRNVTTALKAYAAFATS 600 VREGDMIDIDIPNRTISLRV E ELAARR EQDAKGW P E RKR VTTALKAYAAFATS Sbjct: 541 VREGDMIDIDIPNRTISLRVDEAELAARRTEQDAKGWKPVEQRKRRVTTALKAYAAFATS 600 Query: 601 ADRGAVRDLNVR 612 ADRGAVRDL R Sbjct: 601 ADRGAVRDLGDR 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: 1364 Number of extensions: 26 Number of successful extensions: 1 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: 612 Length adjustment: 37 Effective length of query: 575 Effective length of database: 575 Effective search space: 330625 Effective search space used: 330625 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 SMc04045 SMc04045 (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.9434.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.7e-260 850.0 3.2 4.3e-260 849.8 3.2 1.0 1 lcl|FitnessBrowser__Smeli:SMc04045 SMc04045 dihydroxy-acid dehydrat Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Smeli:SMc04045 SMc04045 dihydroxy-acid dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 849.8 3.2 4.3e-260 4.3e-260 2 542 .. 18 608 .. 17 609 .. 0.99 Alignments for each domain: == domain 1 score: 849.8 bits; conditional E-value: 4.3e-260 TIGR00110 2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamgheGmky 76 ar l++atG+kd d++kPiiavvns+t++vPghvhlkdl++lv++eieaaGgvakefntiav+DGiamgh+Gm+y lcl|FitnessBrowser__Smeli:SMc04045 18 ARGLWRATGMKDSDFGKPIIAVVNSFTQFVPGHVHLKDLGQLVAREIEAAGGVAKEFNTIAVDDGIAMGHDGMLY 92 689************************************************************************ PP TIGR00110 77 sLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktklsekidlvdvfea 151 sLpsreiiaDsve++v+ah++Da+v+is+CDki+PGmlmaalrlniPa++vsGGpmeagk+ l k + +d+++a lcl|FitnessBrowser__Smeli:SMc04045 93 SLPSREIIADSVEYMVNAHCADAMVCISNCDKITPGMLMAALRLNIPAVFVSGGPMEAGKVVLHGKTHALDLVDA 167 *************************************************************************** PP TIGR00110 152 vgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllatsaekkelakksgkrivel 226 ++++a++k+s+e+++ iersacPt+gsCsG+ftansm+cltealGlslPg++++lat+a++k+l+ ++g+ iv+l lcl|FitnessBrowser__Smeli:SMc04045 168 MVAAADDKVSDEDVQIIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSTLATHADRKRLFVEAGHLIVDL 242 *************************************************************************** PP TIGR00110 227 vkknik.......PrdiltkeafenaitldlalGGstntvLhllaiakeagvklslddfdrlsrkvPllaklkPs 294 +++++ Pr+i+tk+afena++ld+a+GGstntvLh+la+a e ++++++dd+drlsrkvP+l+k++P+ lcl|FitnessBrowser__Smeli:SMc04045 243 ARRYYEqedervlPRNIATKQAFENAMALDIAMGGSTNTVLHILAAAYEGEIDFTMDDIDRLSRKVPCLSKVAPA 317 *************************************************************************** PP TIGR00110 295 gkkv.iedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlr........................ 344 v +ed+hraGG++++l+eldk gl+++d+ tv +tl++ +++ +++r lcl|FitnessBrowser__Smeli:SMc04045 318 KADVhMEDVHRAGGIMSILGELDKGGLINRDCPTVHAETLGDAIDRWDITRtssdtvrkffraapggiptqvafs 392 98888*********************************************9************************ PP TIGR00110 345 ...........vdqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailg 408 ++ virs+++p++k+gglavLkGn+a +G++vk+agv+e+ilkf Gpa+vfes+++a+++il+ lcl|FitnessBrowser__Smeli:SMc04045 393 qearwdeldtdRENGVIRSVEHPFSKDGGLAVLKGNIALDGCIVKTAGVDESILKFSGPARVFESQDAAVKGILA 467 *******88555555************************************************************ PP TIGR00110 409 gkvkeGdvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialve 483 ++k+GdvvviryeGPkGgPGm+emL+Pts+l++ GLgk++aLitDGrfsGgt+GlsiGhvsPeaa+gG+i+lv+ lcl|FitnessBrowser__Smeli:SMc04045 468 NEIKAGDVVVIRYEGPKGGPGMQEMLYPTSYLKSKGLGKACALITDGRFSGGTSGLSIGHVSPEAANGGTIGLVR 542 *************************************************************************** PP TIGR00110 484 dGDkikiDienrkldlevseeelaerrakakkkea.......revkgaLakyaklvssadkGavld 542 +GD+i iDi+nr++ l+v+e+ela+rr ++++k++ r+v aL++ya +++sad+Gav+d lcl|FitnessBrowser__Smeli:SMc04045 543 EGDMIDIDIPNRTISLRVDEAELAARRTEQDAKGWkpveqrkRRVTTALKAYAAFATSADRGAVRD 608 **********************************999**9998999******************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (543 nodes) Target sequences: 1 (612 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: 00:00:00.03 # Mc/sec: 10.13 // [ok]
This GapMind analysis is from Apr 09 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