Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate Ac3H11_955 Dihydroxy-acid dehydratase (EC 4.2.1.9)
Query= SwissProt::Q1MIB2 (612 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_955 Length = 619 Score = 918 bits (2373), Expect = 0.0 Identities = 463/619 (74%), Positives = 515/619 (83%), Gaps = 11/619 (1%) Query: 1 MPVYRSRTTTHGRNMAGARGLWRATGMKDSDFGKPIIAVVNSFTQFVPGHVHLKDLGQLV 60 MP+YRS+T+T GRNMAGAR LWRATGMKD DF KPIIAVVNSFTQFVPGHVHLKDLGQLV Sbjct: 1 MPIYRSKTSTAGRNMAGARSLWRATGMKDDDFSKPIIAVVNSFTQFVPGHVHLKDLGQLV 60 Query: 61 AREIEAAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSRELIADSVEYMVNAHCADAMVCIS 120 AREIEAAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSR++IADSVEYMVNAHCADAMVCIS Sbjct: 61 AREIEAAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSRDIIADSVEYMVNAHCADAMVCIS 120 Query: 121 NCDKITPGMLMASLRLNIPTVFVSGGPMEAGKV--------VMHGKTHALDLVDAMVAAA 172 NCDKITPGMLMA++RLNIP +FVSGGPMEAGK VM K LDLVDAMV AA Sbjct: 121 NCDKITPGMLMAAMRLNIPVIFVSGGPMEAGKTRLANPVTKVMEFKK--LDLVDAMVIAA 178 Query: 173 DDKISDEDVQTIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSTLATHLDRKRLF 232 D SD DV +ERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNG+ +ATH DR++LF Sbjct: 179 DSNYSDADVAEVERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGTVVATHADREQLF 238 Query: 233 VEAGHLIVDLARRYYEQDDVKALPRTIASKQAFENAMTLDIAMGGSTNTVLHILAAAHEG 292 AG IVDLA++YYEQDD + LPR++ K AFENAMTLDIAMGGSTNT+LH+LA A E Sbjct: 239 KRAGRRIVDLAKQYYEQDDERVLPRSVGFK-AFENAMTLDIAMGGSTNTILHLLAIASEA 297 Query: 293 EIDFTMADIDALSRRVPCLSKVAPAKSDVHMEDVHRAGGIMSILGELDKGGLLNRDCPTV 352 EI FTMADID LSR VP L KVAP + H+EDVHRAGGIM+ILGELD+ G L+ D PTV Sbjct: 298 EIPFTMADIDRLSRVVPQLCKVAPNTNKYHIEDVHRAGGIMAILGELDRAGKLHTDVPTV 357 Query: 353 HAETLGDAIDRWDITRTNSETVRKFYRAAPGGIPTQVAFSQEARWDELDTDRENGVIRSV 412 H TL DA+D+WDI RT E VR FY A P G+PTQVAFSQ RW LD DR G IRS Sbjct: 358 HTATLKDALDQWDIVRTQDEAVRTFYMAGPAGVPTQVAFSQATRWPSLDLDRAEGCIRSY 417 Query: 413 EHPFSKDGGLAVLKGNLAIDGCIVKTAGVDESILKFSGPARVFESQDASVKAILANEVKA 472 +H FSK+GGLAVL GN+A+DGC+VK+AGVDESIL F G A V ESQD +V ILA++V+A Sbjct: 418 DHAFSKEGGLAVLTGNIAVDGCVVKSAGVDESILVFEGTAHVTESQDEAVANILADKVQA 477 Query: 473 GDVVVIRYEGPKGGPGMQEMLYPTSYLKSKGLGKACALITDGRFSGGTSGLSIGHASPEA 532 GDVV++RYEGPKGGPGMQEMLYPTSY+KSKGLGKACAL+TDGRFSGGTSGLSIGH SPEA Sbjct: 478 GDVVIVRYEGPKGGPGMQEMLYPTSYIKSKGLGKACALLTDGRFSGGTSGLSIGHCSPEA 537 Query: 533 ANGGTIGLVREGDMIDIDIPNRTISLRVSETELAARRAEQDAKGWYPTEVRKRNVTTALK 592 A GG IGLV+ GD I IDIPNRTI++ VS+ ELA RR Q+AKGW P + R R V+ ALK Sbjct: 538 AAGGAIGLVQNGDRIRIDIPNRTINVLVSDEELAKRREAQNAKGWKPAQPRPRKVSAALK 597 Query: 593 AYAAFATSADRGAVRDLNV 611 AYA SAD+GAVRDL++ Sbjct: 598 AYAKLVMSADKGAVRDLSL 616 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: 1164 Number of extensions: 26 Number of successful extensions: 3 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: 619 Length adjustment: 37 Effective length of query: 575 Effective length of database: 582 Effective search space: 334650 Effective search space used: 334650 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 Ac3H11_955 (Dihydroxy-acid dehydratase (EC 4.2.1.9))
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.16099.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.4e-257 840.7 3.5 2.8e-257 840.5 3.5 1.0 1 lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_955 Dihydroxy-acid dehydratase (EC 4 Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_955 Dihydroxy-acid dehydratase (EC 4.2.1.9) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 840.5 3.5 2.8e-257 2.8e-257 2 542 .. 18 613 .. 17 614 .. 0.97 Alignments for each domain: == domain 1 score: 840.5 bits; conditional E-value: 2.8e-257 TIGR00110 2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavs 64 ar+l++atG+kd+d++kPiiavvns+t++vPghvhlkdl++lv++eieaaGgvakefntiav+ lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_955 18 ARSLWRATGMKDDDFSKPIIAVVNSFTQFVPGHVHLKDLGQLVAREIEAAGGVAKEFNTIAVD 80 69************************************************************* PP TIGR00110 65 DGiamgheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivv 127 DGiamgh+Gm+ysLpsr+iiaDsve++v+ah++Da+v+is+CDki+PGmlmaa+rlniP+i+v lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_955 81 DGIAMGHDGMLYSLPSRDIIADSVEYMVNAHCADAMVCISNCDKITPGMLMAAMRLNIPVIFV 143 *************************************************************** PP TIGR00110 128 sGGpmeagktkl......sekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlft 184 sGGpmeagkt+l +++++d+++a++ +a+++ s++++ e+ersacPt+gsCsG+ft lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_955 144 SGGPMEAGKTRLanpvtkVMEFKKLDLVDAMVIAADSNYSDADVAEVERSACPTCGSCSGMFT 206 ***********955554444567889************************************* PP TIGR00110 185 ansmacltealGlslPgsstllatsaekkelakksgkrivelvkknik.......Prdiltke 240 ansm+cltealGlslPg++t+ at+a++++l+k++g+riv+l k++++ Pr++ + lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_955 207 ANSMNCLTEALGLSLPGNGTVVATHADREQLFKRAGRRIVDLAKQYYEqddervlPRSV-GFK 268 ************************************************99999999986.589 PP TIGR00110 241 afenaitldlalGGstntvLhllaiakeagvklslddfdrlsrkvPllaklkPsgkkv.iedl 302 afena+tld+a+GGstnt+Lhllaia+ea++ +++ d+drlsr vP+l+k++P+++k+ ied+ lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_955 269 AFENAMTLDIAMGGSTNTILHLLAIASEAEIPFTMADIDRLSRVVPQLCKVAPNTNKYhIEDV 331 *********************************************************99**** PP TIGR00110 303 hraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlr..................... 344 hraGG++a+l+eld++g+lh+d+ tv tl++ l++ ++ r lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_955 332 HRAGGIMAILGELDRAGKLHTDVPTVHTATLKDALDQWDIVRtqdeavrtfymagpagvptqv 394 ****************************************999******************** PP TIGR00110 345 ..............vdqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpa 393 + +irs d++++kegglavL+Gn+a +G+vvk agv+e+il+feG+a lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_955 395 afsqatrwpsldldRAEGCIRSYDHAFSKEGGLAVLTGNIAVDGCVVKSAGVDESILVFEGTA 457 **********88655555********************************************* PP TIGR00110 394 kvfeseeealeailggkvkeGdvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGr 456 +v es++ea++ il+ kv++Gdvv++ryeGPkGgPGm+emL+Pts++++ GLgk++aL+tDGr lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_955 458 HVTESQDEAVANILADKVQAGDVVIVRYEGPKGGPGMQEMLYPTSYIKSKGLGKACALLTDGR 520 *************************************************************** PP TIGR00110 457 fsGgtrGlsiGhvsPeaaegGaialvedGDkikiDienrkldlevseeelaerrakakkkea. 518 fsGgt+GlsiGh sPeaa+gGai+lv++GD+i+iDi+nr++++ vs+eela+rr+++++k++ lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_955 521 FSGGTSGLSIGHCSPEAAAGGAIGLVQNGDRIRIDIPNRTINVLVSDEELAKRREAQNAKGWk 583 *************************************************************99 PP TIGR00110 519 ......revkgaLakyaklvssadkGavld 542 r+v+ aL++yaklv sadkGav+d lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_955 584 paqprpRKVSAALKAYAKLVMSADKGAVRD 613 99**99**********************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (543 nodes) Target sequences: 1 (619 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: 00:00:00.02 # Mc/sec: 12.70 // [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