Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate WP_006747006.1 THITH_RS14925 dihydroxy-acid dehydratase
Query= SwissProt::Q1MIB2 (612 letters) >NCBI__GCF_000227685.2:WP_006747006.1 Length = 622 Score = 948 bits (2451), Expect = 0.0 Identities = 471/613 (76%), Positives = 523/613 (85%), Gaps = 4/613 (0%) Query: 1 MPVYRSRTTTHGRNMAGARGLWRATGMKDSDFGKPIIAVVNSFTQFVPGHVHLKDLGQLV 60 MP YRSRTTTHGRNMAGAR LWRATGM D DFGKPIIA+ NSFTQFVPGHVHLKDLGQLV Sbjct: 1 MPQYRSRTTTHGRNMAGARALWRATGMTDGDFGKPIIAIANSFTQFVPGHVHLKDLGQLV 60 Query: 61 AREIEAAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSRELIADSVEYMVNAHCADAMVCIS 120 ARE+E AGGVAKEFNTIAVDDGIAMGH GMLYSLPSRELI+D+VEYMVNAHCADA+VCIS Sbjct: 61 AREVEKAGGVAKEFNTIAVDDGIAMGHAGMLYSLPSRELISDAVEYMVNAHCADALVCIS 120 Query: 121 NCDKITPGMLMASLRLNIPTVFVSGGPMEAGKVVMHGKTHALDLVDAMVAAADDKISDED 180 NCDKITPGML A+LRLNIP VFVSGGPMEAGKVV G LDLVDAMV AAD SD D Sbjct: 121 NCDKITPGMLNAALRLNIPAVFVSGGPMEAGKVVRDGNVLHLDLVDAMVVAADPNQSDAD 180 Query: 181 VQTIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSTLATHLDRKRLFVEAGHLIV 240 V+ ERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGS LATH R+ LF+EAG L+V Sbjct: 181 VEAYERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSLLATHAGRRELFLEAGRLVV 240 Query: 241 DLARRYYEQDDVKALPRTIASKQAFENAMTLDIAMGGSTNTVLHILAAAHEGEIDFTMAD 300 DLARRYYEQDD LPR++AS AFENAM LDIAMGGSTNTVLH+LAAA E +DFTMAD Sbjct: 241 DLARRYYEQDDASVLPRSVASFAAFENAMALDIAMGGSTNTVLHLLAAAREAGVDFTMAD 300 Query: 301 IDALSRRVPCLSKVAPAKSDVHMEDVHRAGGIMSILGELDKGGLLNRDCPTVHAETLGDA 360 ID LSR+VP + KVAPA HMEDVHRAGG++ ILGELD+GGL++RD PTVH+ +LGDA Sbjct: 301 IDRLSRQVPNICKVAPATQKYHMEDVHRAGGVLGILGELDRGGLVHRDVPTVHSASLGDA 360 Query: 361 IDRWDITRTNSETVRKFYRAAPGGIPTQVAFSQEARWDELDTDRENGVIRSVEHPFSKDG 420 +DRWD+ R+++E R Y AAPGGIPTQVAFSQ+A WD+LD DR NG IR +EH +S+DG Sbjct: 361 LDRWDVIRSDAEPARTRYLAAPGGIPTQVAFSQDAVWDDLDLDRANGCIRDIEHAYSRDG 420 Query: 421 GLAVLKGNLAIDGCIVKTAGVDESILKFSGPARVFESQDASVKAILANEVKAGDVVVIRY 480 GLAVL GN+A++GCIVKTAGVDESIL FSGPAR+FESQDA+V AIL + + GDVV+IRY Sbjct: 421 GLAVLYGNIAVEGCIVKTAGVDESILTFSGPARIFESQDAAVDAILGDRIAKGDVVIIRY 480 Query: 481 EGPKGGPGMQEMLYPTSYLKSKGLGKACALITDGRFSGGTSGLSIGHASPEAANGGTIGL 540 EGPKGGPGMQEMLYPTSYLKSKGLGK CAL+TDGRFSGGTSGLSIGHASPEAA GG IGL Sbjct: 481 EGPKGGPGMQEMLYPTSYLKSKGLGKDCALVTDGRFSGGTSGLSIGHASPEAAQGGAIGL 540 Query: 541 VREGDMIDIDIPNRTISLRVSETELAARRAEQDAKG---WYPTEVRKRNVTTALKAYAAF 597 V +GD+IDIDIP R I +RVS+ ELA RRA +A+G W P R R V+ AL+AYA Sbjct: 541 VEDGDLIDIDIPQRRIDVRVSDDELAQRRARMEARGEQAWKPVN-RDRVVSQALQAYALM 599 Query: 598 ATSADRGAVRDLN 610 TSA RGAVRD++ Sbjct: 600 TTSASRGAVRDVS 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: 1298 Number of extensions: 50 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: 622 Length adjustment: 37 Effective length of query: 575 Effective length of database: 585 Effective search space: 336375 Effective search space used: 336375 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_006747006.1 THITH_RS14925 (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.7494.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.2e-250 817.2 0.7 3.7e-250 817.0 0.7 1.0 1 lcl|NCBI__GCF_000227685.2:WP_006747006.1 THITH_RS14925 dihydroxy-acid deh Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000227685.2:WP_006747006.1 THITH_RS14925 dihydroxy-acid dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 817.0 0.7 3.7e-250 3.7e-250 2 542 .. 18 610 .. 17 611 .. 0.99 Alignments for each domain: == domain 1 score: 817.0 bits; conditional E-value: 3.7e-250 TIGR00110 2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamg 70 aral++atG++d d++kPiia++ns+t++vPghvhlkdl++lv++e+e+aGgvakefntiav+DGiamg lcl|NCBI__GCF_000227685.2:WP_006747006.1 18 ARALWRATGMTDGDFGKPIIAIANSFTQFVPGHVHLKDLGQLVAREVEKAGGVAKEFNTIAVDDGIAMG 86 79******************************************************************* PP TIGR00110 71 heGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktkl 139 h Gm+ysLpsre+i+D+ve++v+ah++Dalv+is+CDki+PGml aalrlniPa++vsGGpmeagk+ lcl|NCBI__GCF_000227685.2:WP_006747006.1 87 HAGMLYSLPSRELISDAVEYMVNAHCADALVCISNCDKITPGMLNAALRLNIPAVFVSGGPMEAGKVVR 155 ********************************************************************* PP TIGR00110 140 sekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllat 208 ++ +d+++a++ +a+++ s++++e++ersacPt+gsCsG+ftansm+cltealGlslPg+++llat lcl|NCBI__GCF_000227685.2:WP_006747006.1 156 DGNVLHLDLVDAMVVAADPNQSDADVEAYERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSLLAT 224 ********************************************************************* PP TIGR00110 209 saekkelakksgkrivelvkknik.......PrdiltkeafenaitldlalGGstntvLhllaiakeag 270 +a ++el+ ++g+ +v+l +++++ Pr++++ +afena++ld+a+GGstntvLhlla+a+eag lcl|NCBI__GCF_000227685.2:WP_006747006.1 225 HAGRRELFLEAGRLVVDLARRYYEqddasvlPRSVASFAAFENAMALDIAMGGSTNTVLHLLAAAREAG 293 ********************************************************************* PP TIGR00110 271 vklslddfdrlsrkvPllaklkPsgkkv.iedlhraGGvsavlkeldkegllhkdaltvtGktlaetle 338 v++++ d+drlsr+vP ++k++P+++k+ +ed+hraGGv ++l+eld+ gl+h+d+ tv +l++ l+ lcl|NCBI__GCF_000227685.2:WP_006747006.1 294 VDFTMADIDRLSRQVPNICKVAPATQKYhMEDVHRAGGVLGILGELDRGGLVHRDVPTVHSASLGDALD 362 ***************************99**************************************** PP TIGR00110 339 kvkvlr...................................vdqdvirsldnpvkkegglavLkGnlae 372 + +v+r + +ir ++++++++gglavL+Gn+a lcl|NCBI__GCF_000227685.2:WP_006747006.1 363 RWDVIRsdaepartrylaapggiptqvafsqdavwddldldRANGCIRDIEHAYSRDGGLAVLYGNIAV 431 ***********************************9977555555************************ PP TIGR00110 373 eGavvkiagveedilkfeGpakvfeseeealeailggkvkeGdvvviryeGPkGgPGmremLaPtsalv 441 eG++vk+agv+e+il+f Gpa++fes+++a++ailg ++ +Gdvv+iryeGPkGgPGm+emL+Pts+l+ lcl|NCBI__GCF_000227685.2:WP_006747006.1 432 EGCIVKTAGVDESILTFSGPARIFESQDAAVDAILGDRIAKGDVVIIRYEGPKGGPGMQEMLYPTSYLK 500 ********************************************************************* PP TIGR00110 442 glGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDienrkldlevseeelaerr 510 + GLgk++aL+tDGrfsGgt+GlsiGh sPeaa+gGai+lvedGD i iDi++r++d++vs++ela+rr lcl|NCBI__GCF_000227685.2:WP_006747006.1 501 SKGLGKDCALVTDGRFSGGTSGLSIGHASPEAAQGGAIGLVEDGDLIDIDIPQRRIDVRVSDDELAQRR 569 ********************************************************************* PP TIGR00110 511 akakkkea.........revkgaLakyaklvssadkGavld 542 a+++++++ r v+ aL++ya + +sa++Gav+d lcl|NCBI__GCF_000227685.2:WP_006747006.1 570 ARMEARGEqawkpvnrdRVVSQALQAYALMTTSASRGAVRD 610 ****9999999*****9**********************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (543 nodes) Target sequences: 1 (622 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: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.04 # Mc/sec: 7.41 // [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