Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate WP_007688035.1 V474_RS20600 dihydroxy-acid dehydratase
Query= SwissProt::P55186 (617 letters) >NCBI__GCF_001046635.1:WP_007688035.1 Length = 617 Score = 1056 bits (2731), Expect = 0.0 Identities = 522/616 (84%), Positives = 564/616 (91%) Query: 1 MPPYRSRTTTHGRNMAGARGLWRATGMKDEDFGKPIIAVANSFTQFVPGHVHLKDLGQLV 60 MP YRSRT+THGRNMAGARGLWRATGMKDEDFGKPIIA+ANSFTQFVPGHVHLKDLGQLV Sbjct: 1 MPHYRSRTSTHGRNMAGARGLWRATGMKDEDFGKPIIAIANSFTQFVPGHVHLKDLGQLV 60 Query: 61 AREIEAAGGVAKEFNTIAVDDGIAMGHGGMLYSLPSRDLIADSVEYMVNAHCADAIVCIS 120 AREIEAAGGVAKEFNTIAVDDGIAMGH GMLYSLPSRDLIADSVEYMVNAH ADA+VCIS Sbjct: 61 AREIEAAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSRDLIADSVEYMVNAHTADALVCIS 120 Query: 121 NCDKITPGMLMAAMRLNIPVVFVSGGPMEAGKVTVKGKIRALDLVDAMVVAADDSYSDEE 180 NCDKITPGMLMAAMRLNIP +FVSGGPMEAGK ++GK ALDLVDAMVVAADDSY+DEE Sbjct: 121 NCDKITPGMLMAAMRLNIPTIFVSGGPMEAGKTELRGKTVALDLVDAMVVAADDSYTDEE 180 Query: 181 VEAIEKAACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSVLATHADREALFKEAGRVVV 240 V+ IE++ACPTCGSCSGMFTANSMNCLTEALGLSLPGNGS LATHADRE LF EAGR +V Sbjct: 181 VKVIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSTLATHADREKLFLEAGRTIV 240 Query: 241 DLCQRWYEQEDATALPRGIATRAAFENAMSLDIAMGGSTNTVLHLLAAAHEGGIDFSMAD 300 DL +RWYEQ+DA+ALPR IAT AAFENAMSLDIAMGGSTNTVLHLLAAA+EGG+DF+MAD Sbjct: 241 DLAKRWYEQDDASALPRNIATFAAFENAMSLDIAMGGSTNTVLHLLAAAYEGGVDFTMAD 300 Query: 301 IDRLSRHVPCLSKVAPAKSDVHMEDVHRAGGVMAILGELERGGLIDASQPTVHAPTMGEA 360 IDRLSR VPCL KVAPAK+DVHMEDVHRAGG+MAILGELER GL+DA+ PTVHAPT+G+A Sbjct: 301 IDRLSRRVPCLCKVAPAKNDVHMEDVHRAGGIMAILGELERAGLVDATLPTVHAPTLGDA 360 Query: 361 LARWDIGRTNSQIAHEFFKAAPGGKPTQVAFSQAARWEELDLDRENGVIRSVEHPFSKDG 420 L RWDIGRTNS+ FF+AAPGG T AFSQ ARWEELD DRE GVIRS EHPFSKDG Sbjct: 361 LNRWDIGRTNSEEVRNFFRAAPGGVRTTQAFSQNARWEELDTDRETGVIRSAEHPFSKDG 420 Query: 421 GLAVLFGNLAPEGCIVKTAGVDESILTFRGTARVFESQDAAVSGILGGQVKAGEVVVIRY 480 GLAVLFGN+APEGCIVKTAGVDESILTF GTARV+ESQDAAV+GILG +VKAG+VVVIRY Sbjct: 421 GLAVLFGNIAPEGCIVKTAGVDESILTFHGTARVYESQDAAVAGILGNEVKAGDVVVIRY 480 Query: 481 EGPKGGPGMQEMLYPTTYLKSKGLGAACALVTDGRFSGGTSGLSIGHVSPEAGEGGLIAL 540 EGPKGGPGMQEMLYPT+YLKSKGLG ACAL+TDGRFSGGTSGLSIGHVSPEA EGGLIAL Sbjct: 481 EGPKGGPGMQEMLYPTSYLKSKGLGKACALITDGRFSGGTSGLSIGHVSPEAAEGGLIAL 540 Query: 541 VETGDPILIDIPTRGITLEVSDAVLAARREAQLARGKDAWTPLNRKRDLTPALRAYAAMT 600 V TGDPILIDIP R I L++ DAV+AAR+ RG AW PL RKR+++PALRAYAA+T Sbjct: 541 VATGDPILIDIPNRVIRLDLDDAVIAARKAEMEGRGAKAWKPLGRKRNVSPALRAYAALT 600 Query: 601 TNAARGAVRDVSQIER 616 TNAARGAVRDV Q+E+ Sbjct: 601 TNAARGAVRDVGQVEK 616 Lambda K H 0.318 0.134 0.395 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: 1394 Number of extensions: 40 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: 617 Length of database: 617 Length adjustment: 37 Effective length of query: 580 Effective length of database: 580 Effective search space: 336400 Effective search space used: 336400 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_007688035.1 V474_RS20600 (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.3301688.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-249 815.0 1.6 1.7e-249 814.8 1.6 1.0 1 NCBI__GCF_001046635.1:WP_007688035.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_001046635.1:WP_007688035.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 814.8 1.6 1.7e-249 1.7e-249 2 542 .. 18 610 .. 17 611 .. 0.98 Alignments for each domain: == domain 1 score: 814.8 bits; conditional E-value: 1.7e-249 TIGR00110 2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamgheGm 74 ar l++atG+kded++kPiia++ns+t++vPghvhlkdl++lv++eieaaGgvakefntiav+DGiamgh+Gm NCBI__GCF_001046635.1:WP_007688035.1 18 ARGLWRATGMKDEDFGKPIIAIANSFTQFVPGHVHLKDLGQLVAREIEAAGGVAKEFNTIAVDDGIAMGHDGM 90 689********************************************************************** PP TIGR00110 75 kysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktklsekidlvd 147 +ysLpsr++iaDsve++v+ah++Dalv+is+CDki+PGmlmaa+rlniP+i+vsGGpmeagkt+l k +d NCBI__GCF_001046635.1:WP_007688035.1 91 LYSLPSRDLIADSVEYMVNAHTADALVCISNCDKITPGMLMAAMRLNIPTIFVSGGPMEAGKTELRGKTVALD 163 *****************************************************************99****** PP TIGR00110 148 vfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllatsaekkelakksg 220 +++a++ +a++ ++ee++ iersacPt+gsCsG+ftansm+cltealGlslPg++++lat+a++++l+ ++g NCBI__GCF_001046635.1:WP_007688035.1 164 LVDAMVVAADDSYTDEEVKVIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSTLATHADREKLFLEAG 236 ************************************************************************* PP TIGR00110 221 krivelvkknik.......PrdiltkeafenaitldlalGGstntvLhllaiakeagvklslddfdrlsrkvP 286 ++iv+l k+ ++ Pr+i+t +afena++ld+a+GGstntvLhlla+a e gv++++ d+drlsr+vP NCBI__GCF_001046635.1:WP_007688035.1 237 RTIVDLAKRWYEqddasalPRNIATFAAFENAMSLDIAMGGSTNTVLHLLAAAYEGGVDFTMADIDRLSRRVP 309 ***********9************************************************************* PP TIGR00110 287 llaklkPsgkkv.iedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlr.............. 344 +l+k++P+ + v +ed+hraGG++a+l+el+++gl++ tv tl++ l++ ++ r NCBI__GCF_001046635.1:WP_007688035.1 310 CLCKVAPAKNDVhMEDVHRAGGIMAILGELERAGLVDATLPTVHAPTLGDALNRWDIGRtnseevrnffraap 382 *********9999********************************************999************* PP TIGR00110 345 .....................vdqd..virsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpak 394 + virs ++p++k+gglavL+Gn+a+eG++vk+agv+e+il+f+G+a+ NCBI__GCF_001046635.1:WP_007688035.1 383 ggvrttqafsqnarweeldtdR--EtgVIRSAEHPFSKDGGLAVLFGNIAPEGCIVKTAGVDESILTFHGTAR 453 ****************977444..366********************************************** PP TIGR00110 395 vfeseeealeailggkvkeGdvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiG 467 v+es+++a+++ilg +vk+GdvvviryeGPkGgPGm+emL+Pts+l++ GLgk++aLitDGrfsGgt+GlsiG NCBI__GCF_001046635.1:WP_007688035.1 454 VYESQDAAVAGILGNEVKAGDVVVIRYEGPKGGPGMQEMLYPTSYLKSKGLGKACALITDGRFSGGTSGLSIG 526 ************************************************************************* PP TIGR00110 468 hvsPeaaegGaialvedGDkikiDienrkldlevseeelaerrakakkkea.........revkgaLakyakl 531 hvsPeaaegG ialv GD i iDi+nr + l+++++ +a+r+a+++ ++a r+v+ aL++ya l NCBI__GCF_001046635.1:WP_007688035.1 527 HVSPEAAEGGLIALVATGDPILIDIPNRVIRLDLDDAVIAARKAEMEGRGAkawkplgrkRNVSPALRAYAAL 599 **********************************************999888999***9999*********** PP TIGR00110 532 vssadkGavld 542 ++a +Gav+d NCBI__GCF_001046635.1:WP_007688035.1 600 TTNAARGAVRD 610 *********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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 21.86 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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