Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate WP_004309872.1 C665_RS11310 dihydroxy-acid dehydratase
Query= SwissProt::P55186 (617 letters) >NCBI__GCF_000310185.1:WP_004309872.1 Length = 616 Score = 941 bits (2431), Expect = 0.0 Identities = 468/616 (75%), Positives = 532/616 (86%) Query: 1 MPPYRSRTTTHGRNMAGARGLWRATGMKDEDFGKPIIAVANSFTQFVPGHVHLKDLGQLV 60 MP YRSRT+T GRNMAGAR LWRATGMKD DF KPIIA+ANSFTQFVPGHVHLKDLGQLV Sbjct: 1 MPQYRSRTSTAGRNMAGARALWRATGMKDGDFEKPIIAIANSFTQFVPGHVHLKDLGQLV 60 Query: 61 AREIEAAGGVAKEFNTIAVDDGIAMGHGGMLYSLPSRDLIADSVEYMVNAHCADAIVCIS 120 AREIE+AGGVAKEFNTIAVDDGIAMGHGGMLYSLPSR+LIADSVEYM NAH ADA+VCIS Sbjct: 61 AREIESAGGVAKEFNTIAVDDGIAMGHGGMLYSLPSRELIADSVEYMCNAHTADALVCIS 120 Query: 121 NCDKITPGMLMAAMRLNIPVVFVSGGPMEAGKVTVKGKIRALDLVDAMVVAADDSYSDEE 180 NCDKITPGMLMAA+RLNIP +FVSGGPMEAGKV + K+ +LDLVDAMV AAD S SDEE Sbjct: 121 NCDKITPGMLMAALRLNIPAIFVSGGPMEAGKVKWEAKVISLDLVDAMVKAADKSCSDEE 180 Query: 181 VEAIEKAACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSVLATHADREALFKEAGRVVV 240 V+AIE++ACPTCGSCSGMFTANSMNCLTEALGLSLPGNG+ LATHADRE LFKEAGR +V Sbjct: 181 VDAIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGTTLATHADRERLFKEAGRRIV 240 Query: 241 DLCQRWYEQEDATALPRGIATRAAFENAMSLDIAMGGSTNTVLHLLAAAHEGGIDFSMAD 300 DL +R+YE++DA+ LPR IA+ AFENAMSLD+AMGGSTNTVLHLLAAA E G+DF+M D Sbjct: 241 DLARRYYEKDDASVLPRSIASFQAFENAMSLDVAMGGSTNTVLHLLAAAREAGVDFTMKD 300 Query: 301 IDRLSRHVPCLSKVAPAKSDVHMEDVHRAGGVMAILGELERGGLIDASQPTVHAPTMGEA 360 IDR+SR VPCL KVAPA +DVH+EDVHRAGG+M+ILGEL+R GL+ PTVH+ ++ EA Sbjct: 301 IDRVSRRVPCLCKVAPAIADVHIEDVHRAGGIMSILGELDRAGLLHTDVPTVHSASLAEA 360 Query: 361 LARWDIGRTNSQIAHEFFKAAPGGKPTQVAFSQAARWEELDLDRENGVIRSVEHPFSKDG 420 L +WDI RT + H FF+AAPGG PTQVAFSQ RW+ LD DRE+G+IR+ EH F+ DG Sbjct: 361 LDKWDIKRTEDEAVHTFFRAAPGGVPTQVAFSQDRRWKSLDADREHGIIRNKEHAFTADG 420 Query: 421 GLAVLFGNLAPEGCIVKTAGVDESILTFRGTARVFESQDAAVSGILGGQVKAGEVVVIRY 480 GLAVL+GN+A +GCIVKTAGVDESI F G ARV+ESQ+ AV GILG QV+AG+VVVIRY Sbjct: 421 GLAVLYGNIAEKGCIVKTAGVDESIWKFTGKARVYESQEDAVEGILGEQVQAGDVVVIRY 480 Query: 481 EGPKGGPGMQEMLYPTTYLKSKGLGAACALVTDGRFSGGTSGLSIGHVSPEAGEGGLIAL 540 EGPKGGPGMQEMLYPT+YLKS+GLGA CAL+TDGRFSGGTSGLSIGH SPEA GG IAL Sbjct: 481 EGPKGGPGMQEMLYPTSYLKSRGLGAQCALLTDGRFSGGTSGLSIGHASPEAACGGAIAL 540 Query: 541 VETGDPILIDIPTRGITLEVSDAVLAARREAQLARGKDAWTPLNRKRDLTPALRAYAAMT 600 VE GD I IDIP R I L V+DA LA RR A A+G AW P+ R+R ++ AL+AYAA+T Sbjct: 541 VEDGDTIEIDIPARRIHLAVADAELARRRAAMEAKGNAAWKPVKRERVVSAALQAYAALT 600 Query: 601 TNAARGAVRDVSQIER 616 T+A GAVRDV+Q++R Sbjct: 601 TSADTGAVRDVTQVQR 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: 1318 Number of extensions: 42 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: 616 Length adjustment: 37 Effective length of query: 580 Effective length of database: 579 Effective search space: 335820 Effective search space used: 335820 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_004309872.1 C665_RS11310 (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.24256.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.7e-260 849.4 2.2 6.6e-260 849.2 2.2 1.0 1 lcl|NCBI__GCF_000310185.1:WP_004309872.1 C665_RS11310 dihydroxy-acid dehy Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000310185.1:WP_004309872.1 C665_RS11310 dihydroxy-acid dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 849.2 2.2 6.6e-260 6.6e-260 2 542 .. 18 610 .. 17 611 .. 0.99 Alignments for each domain: == domain 1 score: 849.2 bits; conditional E-value: 6.6e-260 TIGR00110 2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamg 70 aral++atG+kd d+ekPiia++ns+t++vPghvhlkdl++lv++eie+aGgvakefntiav+DGiamg lcl|NCBI__GCF_000310185.1:WP_004309872.1 18 ARALWRATGMKDGDFEKPIIAIANSFTQFVPGHVHLKDLGQLVAREIESAGGVAKEFNTIAVDDGIAMG 86 79******************************************************************* PP TIGR00110 71 heGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktkl 139 h+Gm+ysLpsre+iaDsve++++ah++Dalv+is+CDki+PGmlmaalrlniPai+vsGGpmeagk+k lcl|NCBI__GCF_000310185.1:WP_004309872.1 87 HGGMLYSLPSRELIADSVEYMCNAHTADALVCISNCDKITPGMLMAALRLNIPAIFVSGGPMEAGKVKW 155 ********************************************************************* PP TIGR00110 140 sekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllat 208 k++ +d+++a++++a++ s+ee+++iersacPt+gsCsG+ftansm+cltealGlslPg++t+lat lcl|NCBI__GCF_000310185.1:WP_004309872.1 156 EAKVISLDLVDAMVKAADKSCSDEEVDAIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGTTLAT 224 ********************************************************************* PP TIGR00110 209 saekkelakksgkrivelvkknik.......PrdiltkeafenaitldlalGGstntvLhllaiakeag 270 +a++++l+k++g+riv+l +++++ Pr+i++ +afena++ld+a+GGstntvLhlla+a+eag lcl|NCBI__GCF_000310185.1:WP_004309872.1 225 HADRERLFKEAGRRIVDLARRYYEkddasvlPRSIASFQAFENAMSLDVAMGGSTNTVLHLLAAAREAG 293 ********************************************************************* PP TIGR00110 271 vklslddfdrlsrkvPllaklkPsgkkv.iedlhraGGvsavlkeldkegllhkdaltvtGktlaetle 338 v+++++d+dr+sr+vP+l+k++P+ v ied+hraGG++++l+eld++gllh+d+ tv +lae l+ lcl|NCBI__GCF_000310185.1:WP_004309872.1 294 VDFTMKDIDRVSRRVPCLCKVAPAIADVhIEDVHRAGGIMSILGELDRAGLLHTDVPTVHSASLAEALD 362 ************************88887**************************************** PP TIGR00110 339 kvkvlr...................................vdqd..virsldnpvkkegglavLkGnl 370 k +++r + +ir+++++++++gglavL+Gn+ lcl|NCBI__GCF_000310185.1:WP_004309872.1 363 KWDIKRtedeavhtffraapggvptqvafsqdrrwksldadR--EhgIIRNKEHAFTADGGLAVLYGNI 429 *****9*******************************88444..356********************** PP TIGR00110 371 aeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeGdvvviryeGPkGgPGmremLaPtsa 439 ae+G++vk+agv+e+i+kf+G+a+v+es+e+a+e+ilg +v++GdvvviryeGPkGgPGm+emL+Pts+ lcl|NCBI__GCF_000310185.1:WP_004309872.1 430 AEKGCIVKTAGVDESIWKFTGKARVYESQEDAVEGILGEQVQAGDVVVIRYEGPKGGPGMQEMLYPTSY 498 ********************************************************************* PP TIGR00110 440 lvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDienrkldlevseeelae 508 l++ GLg ++aL+tDGrfsGgt+GlsiGh sPeaa gGaialvedGD+i+iDi++r+++l+v ++ela+ lcl|NCBI__GCF_000310185.1:WP_004309872.1 499 LKSRGLGAQCALLTDGRFSGGTSGLSIGHASPEAACGGAIALVEDGDTIEIDIPARRIHLAVADAELAR 567 ********************************************************************* PP TIGR00110 509 rrakakkkea.........revkgaLakyaklvssadkGavld 542 rra++++k++ r v+ aL++ya l +sad+Gav+d lcl|NCBI__GCF_000310185.1:WP_004309872.1 568 RRAAMEAKGNaawkpvkreRVVSAALQAYAALTTSADTGAVRD 610 ********99999****9999********************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (543 nodes) Target sequences: 1 (616 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: 12.43 // [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