Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate WP_018232560.1 THITHI_RS0108000 dihydroxy-acid dehydratase
Query= SwissProt::Q1MIB2 (612 letters) >NCBI__GCF_000378965.1:WP_018232560.1 Length = 618 Score = 951 bits (2459), Expect = 0.0 Identities = 474/613 (77%), Positives = 525/613 (85%), Gaps = 4/613 (0%) Query: 1 MPVYRSRTTTHGRNMAGARGLWRATGMKDSDFGKPIIAVVNSFTQFVPGHVHLKDLGQLV 60 MP YRSRTTTHGRNMAGAR LWRATGMKD DF KPIIA+ NSFTQFVPGHVHLKDLGQ+V Sbjct: 1 MPQYRSRTTTHGRNMAGARALWRATGMKDGDFDKPIIAIANSFTQFVPGHVHLKDLGQMV 60 Query: 61 AREIEAAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSRELIADSVEYMVNAHCADAMVCIS 120 AREIE AGGVAKEFNTIAVDDGIAMGH GMLYSLPSR+LIADSVEYMVNAHCADA+VCIS Sbjct: 61 AREIERAGGVAKEFNTIAVDDGIAMGHGGMLYSLPSRDLIADSVEYMVNAHCADALVCIS 120 Query: 121 NCDKITPGMLMASLRLNIPTVFVSGGPMEAGKVVMHGKTHALDLVDAMVAAADDKISDED 180 NCDKITPGMLMA+LRLNIP VFVSGGPMEAGKVV+ K LDLVDAMV AAD SDED Sbjct: 121 NCDKITPGMLMAALRLNIPVVFVSGGPMEAGKVVIRDKVIHLDLVDAMVTAADPGASDED 180 Query: 181 VQTIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSTLATHLDRKRLFVEAGHLIV 240 V ERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGS LATH DRK LF+EAG L+V Sbjct: 181 VAEYERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSLLATHADRKELFLEAGRLVV 240 Query: 241 DLARRYYEQDDVKALPRTIASKQAFENAMTLDIAMGGSTNTVLHILAAAHEGEIDFTMAD 300 +LARRYYEQDD ALPR IA+ QAFENA+ LDIAMGGSTNTVLH+LAAAHE E+DFTMAD Sbjct: 241 ELARRYYEQDDASALPRNIATFQAFENAIALDIAMGGSTNTVLHLLAAAHEAEVDFTMAD 300 Query: 301 IDALSRRVPCLSKVAPAKSDVHMEDVHRAGGIMSILGELDKGGLLNRDCPTVHAETLGDA 360 ID +SRR+P L KVAPA HMEDVHRAGG++ ILGELD+GGL++R+ TVH+ TLG+A Sbjct: 301 IDRMSRRIPNLCKVAPATQLYHMEDVHRAGGVLGILGELDRGGLIHREAKTVHSATLGEA 360 Query: 361 IDRWDITRTNSETVRKFYRAAPGGIPTQVAFSQEARWDELDTDRENGVIRSVEHPFSKDG 420 +DRWD+ R+ +E R Y AAPGG+PTQ AFSQ+ RWD+LD DRE G IR + H +S+DG Sbjct: 361 LDRWDVMRSEAEGARMRYMAAPGGVPTQTAFSQDRRWDDLDLDRERGCIRDIAHAYSRDG 420 Query: 421 GLAVLKGNLAIDGCIVKTAGVDESILKFSGPARVFESQDASVKAILANEVKAGDVVVIRY 480 GLAVL GNLA+DGCIVKTAGVDES L FSGPARVFESQDA+V+AIL + ++ GDVVVIRY Sbjct: 421 GLAVLYGNLAVDGCIVKTAGVDESNLIFSGPARVFESQDAAVEAILGDRIREGDVVVIRY 480 Query: 481 EGPKGGPGMQEMLYPTSYLKSKGLGKACALITDGRFSGGTSGLSIGHASPEAANGGTIGL 540 EGPKGGPGMQEMLYPTSYLKSKGLGKACALITDGRFSGGTSGLSIGH SPEAA GG IGL Sbjct: 481 EGPKGGPGMQEMLYPTSYLKSKGLGKACALITDGRFSGGTSGLSIGHVSPEAAEGGEIGL 540 Query: 541 VREGDMIDIDIPNRTISLRVSETELAARRAEQDAKG---WYPTEVRKRNVTTALKAYAAF 597 V EGD+I+IDIP+R+I L V + E RR+ +A+G W P R R V+ AL+AYA Sbjct: 541 VEEGDIIEIDIPHRSIRLAVDDAERTRRRSAMEARGEAAWNPVN-RARAVSQALRAYALM 599 Query: 598 ATSADRGAVRDLN 610 ATSA RGAVRD++ Sbjct: 600 ATSAARGAVRDIS 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: 1285 Number of extensions: 45 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: 618 Length adjustment: 37 Effective length of query: 575 Effective length of database: 581 Effective search space: 334075 Effective search space used: 334075 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_018232560.1 THITHI_RS0108000 (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.20989.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-255 834.1 1.4 2.7e-255 833.9 1.4 1.0 1 lcl|NCBI__GCF_000378965.1:WP_018232560.1 THITHI_RS0108000 dihydroxy-acid Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000378965.1:WP_018232560.1 THITHI_RS0108000 dihydroxy-acid dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 833.9 1.4 2.7e-255 2.7e-255 2 542 .. 18 610 .. 17 611 .. 0.99 Alignments for each domain: == domain 1 score: 833.9 bits; conditional E-value: 2.7e-255 TIGR00110 2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamg 70 aral++atG+kd d++kPiia++ns+t++vPghvhlkdl+++v++eie+aGgvakefntiav+DGiamg lcl|NCBI__GCF_000378965.1:WP_018232560.1 18 ARALWRATGMKDGDFDKPIIAIANSFTQFVPGHVHLKDLGQMVAREIERAGGVAKEFNTIAVDDGIAMG 86 79******************************************************************* PP TIGR00110 71 heGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktkl 139 h+Gm+ysLpsr++iaDsve++v+ah++Dalv+is+CDki+PGmlmaalrlniP+++vsGGpmeagk+ + lcl|NCBI__GCF_000378965.1:WP_018232560.1 87 HGGMLYSLPSRDLIADSVEYMVNAHCADALVCISNCDKITPGMLMAALRLNIPVVFVSGGPMEAGKVVI 155 ********************************************************************* PP TIGR00110 140 sekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllat 208 +k++ +d+++a++++a++ s+e++ e+ersacPt+gsCsG+ftansm+cltealGlslPg+++llat lcl|NCBI__GCF_000378965.1:WP_018232560.1 156 RDKVIHLDLVDAMVTAADPGASDEDVAEYERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSLLAT 224 ********************************************************************* PP TIGR00110 209 saekkelakksgkrivelvkknik.......PrdiltkeafenaitldlalGGstntvLhllaiakeag 270 +a++kel+ ++g+ +vel +++++ Pr+i+t +afenai+ld+a+GGstntvLhlla+a+ea+ lcl|NCBI__GCF_000378965.1:WP_018232560.1 225 HADRKELFLEAGRLVVELARRYYEqddasalPRNIATFQAFENAIALDIAMGGSTNTVLHLLAAAHEAE 293 ********************************************************************* PP TIGR00110 271 vklslddfdrlsrkvPllaklkPsgkkv.iedlhraGGvsavlkeldkegllhkdaltvtGktlaetle 338 v++++ d+dr+sr++P l+k++P+++ + +ed+hraGGv ++l+eld+ gl+h++a+tv tl+e l+ lcl|NCBI__GCF_000378965.1:WP_018232560.1 294 VDFTMADIDRMSRRIPNLCKVAPATQLYhMEDVHRAGGVLGILGELDRGGLIHREAKTVHSATLGEALD 362 **************************999**************************************** PP TIGR00110 339 kvkvlr...................................vdqdvirsldnpvkkegglavLkGnlae 372 + +v+r ++ +ir + ++++++gglavL+Gnla lcl|NCBI__GCF_000378965.1:WP_018232560.1 363 RWDVMRseaegarmrymaapggvptqtafsqdrrwddldldRERGCIRDIAHAYSRDGGLAVLYGNLAV 431 ***********************************9998655566************************ PP TIGR00110 373 eGavvkiagveedilkfeGpakvfeseeealeailggkvkeGdvvviryeGPkGgPGmremLaPtsalv 441 +G++vk+agv+e+ l f Gpa+vfes+++a+eailg +++eGdvvviryeGPkGgPGm+emL+Pts+l+ lcl|NCBI__GCF_000378965.1:WP_018232560.1 432 DGCIVKTAGVDESNLIFSGPARVFESQDAAVEAILGDRIREGDVVVIRYEGPKGGPGMQEMLYPTSYLK 500 ********************************************************************* PP TIGR00110 442 glGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDienrkldlevseeelaerr 510 + GLgk++aLitDGrfsGgt+GlsiGhvsPeaaegG i+lve+GD+i+iDi++r + l+v+++e +rr lcl|NCBI__GCF_000378965.1:WP_018232560.1 501 SKGLGKACALITDGRFSGGTSGLSIGHVSPEAAEGGEIGLVEEGDIIEIDIPHRSIRLAVDDAERTRRR 569 ********************************************************************* PP TIGR00110 511 akakkkea.........revkgaLakyaklvssadkGavld 542 +++++++ r v+ aL++ya +++sa +Gav+d lcl|NCBI__GCF_000378965.1:WP_018232560.1 570 SAMEARGEaawnpvnraRAVSQALRAYALMATSAARGAVRD 610 *****999999****************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (543 nodes) Target sequences: 1 (618 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: 11.69 // [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