Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate WP_029935949.1 N746_RS0109090 dihydroxy-acid dehydratase
Query= SwissProt::Q1MIB2 (612 letters) >NCBI__GCF_000711195.1:WP_029935949.1 Length = 620 Score = 916 bits (2368), Expect = 0.0 Identities = 447/612 (73%), Positives = 518/612 (84%), Gaps = 3/612 (0%) Query: 1 MPVYRSRTTTHGRNMAGARGLWRATGMKDSDFGKPIIAVVNSFTQFVPGHVHLKDLGQLV 60 MP YRS+T+THGRNMAGAR LWRATGMK DFGKPIIA+ NSFTQFVPGHVHLKD+GQLV Sbjct: 1 MPAYRSKTSTHGRNMAGARALWRATGMKTEDFGKPIIAIANSFTQFVPGHVHLKDMGQLV 60 Query: 61 AREIEAAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSRELIADSVEYMVNAHCADAMVCIS 120 A IE +GGVAKEFNTIAVDDGIAMGHDGMLYSLPSR+LIADSVEYMVNAHCADA+VCIS Sbjct: 61 AGVIEKSGGVAKEFNTIAVDDGIAMGHDGMLYSLPSRDLIADSVEYMVNAHCADALVCIS 120 Query: 121 NCDKITPGMLMASLRLNIPTVFVSGGPMEAGKVVMHGKTHALDLVDAMVAAADDKISDED 180 NCDKITPGMLMA++RLNIPT+FVSGGPME+GK V+ G+ LDLVDAMV AADD SD+D Sbjct: 121 NCDKITPGMLMAAMRLNIPTIFVSGGPMESGKTVLGGQEIKLDLVDAMVMAADDSCSDQD 180 Query: 181 VQTIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSTLATHLDRKRLFVEAGHLIV 240 + +E SACPTCGSCSGMFTANSMNCL EALG++LPGNGS LATH DRK LF EAG IV Sbjct: 181 IHDVEISACPTCGSCSGMFTANSMNCLAEALGVALPGNGSMLATHADRKHLFEEAGRRIV 240 Query: 241 DLARRYYEQDDVKALPRTIASKQAFENAMTLDIAMGGSTNTVLHILAAAHEGEIDFTMAD 300 ++A+ YYEQD+ + LPR+IA+ AF+N M LD+AMGGSTNTVLH+LA AHE ++ FTM+D Sbjct: 241 EIAKEYYEQDNDRVLPRSIATFSAFQNVMALDVAMGGSTNTVLHLLAIAHEADVKFTMSD 300 Query: 301 IDALSRRVPCLSKVAPAKSDVHMEDVHRAGGIMSILGELDKGGLLNRDCPTVHAETLGDA 360 +D +SR+VPCL+KVAP + HMEDVHRAGGIM +LGELD+GGL++ TVHA TLG A Sbjct: 301 MDEVSRKVPCLAKVAPNSKNYHMEDVHRAGGIMRLLGELDRGGLIDTSTYTVHASTLGAA 360 Query: 361 IDRWDITRTNSETVRKFYRAAPGGIPTQVAFSQEARWDELDTDRENGVIRSVEHPFSKDG 420 I+ WDI+R SE+V+ FY+AAPG + T AFSQ RW LDTD ENG IRSVEH ++KDG Sbjct: 361 IELWDISRNPSESVQTFYKAAPGNVRTTQAFSQSKRWKTLDTDDENGCIRSVEHAYTKDG 420 Query: 421 GLAVLKGNLAIDGCIVKTAGVDESILKFSGPARVFESQDASVKAILANEVKAGDVVVIRY 480 GLAVL GN+A GC+VKTAGVDE I KFSGPAR+FESQD +V IL NEV+AG+VV+IRY Sbjct: 421 GLAVLFGNIAQHGCVVKTAGVDEEIFKFSGPARIFESQDTAVAGILGNEVQAGEVVIIRY 480 Query: 481 EGPKGGPGMQEMLYPTSYLKSKGLGKACALITDGRFSGGTSGLSIGHASPEAANGGTIGL 540 EGPKGGPGMQEMLYPTSYLKSKGLGK CAL+TDGRFSGGTSGLSIGHASPEAA GG IGL Sbjct: 481 EGPKGGPGMQEMLYPTSYLKSKGLGKQCALLTDGRFSGGTSGLSIGHASPEAAEGGNIGL 540 Query: 541 VREGDMIDIDIPNRTISLRVSETELAARRAEQDAKG---WYPTEVRKRNVTTALKAYAAF 597 V GD+I+IDIPNR+I++++S+ EL+ RR ++KG W P E R R+V+ AL+AYAA Sbjct: 541 VESGDIIEIDIPNRSINVKLSDYELSQRRQAMESKGDQAWKPQETRPRHVSPALRAYAAM 600 Query: 598 ATSADRGAVRDL 609 TSA GAVRD+ Sbjct: 601 TTSAAFGAVRDV 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: 1176 Number of extensions: 33 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: 620 Length adjustment: 37 Effective length of query: 575 Effective length of database: 583 Effective search space: 335225 Effective search space used: 335225 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_029935949.1 N746_RS0109090 (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.18720.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-250 818.5 4.0 1.5e-250 818.3 4.0 1.0 1 lcl|NCBI__GCF_000711195.1:WP_029935949.1 N746_RS0109090 dihydroxy-acid de Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000711195.1:WP_029935949.1 N746_RS0109090 dihydroxy-acid dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 818.3 4.0 1.5e-250 1.5e-250 2 542 .. 18 611 .. 17 612 .. 0.99 Alignments for each domain: == domain 1 score: 818.3 bits; conditional E-value: 1.5e-250 TIGR00110 2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamg 70 aral++atG+k ed++kPiia++ns+t++vPghvhlkd+++lv+ ie++Ggvakefntiav+DGiamg lcl|NCBI__GCF_000711195.1:WP_029935949.1 18 ARALWRATGMKTEDFGKPIIAIANSFTQFVPGHVHLKDMGQLVAGVIEKSGGVAKEFNTIAVDDGIAMG 86 79******************************************************************* PP TIGR00110 71 heGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktkl 139 h+Gm+ysLpsr++iaDsve++v+ah++Dalv+is+CDki+PGmlmaa+rlniP+i+vsGGpme+gkt l lcl|NCBI__GCF_000711195.1:WP_029935949.1 87 HDGMLYSLPSRDLIADSVEYMVNAHCADALVCISNCDKITPGMLMAAMRLNIPTIFVSGGPMESGKTVL 155 ********************************************************************* PP TIGR00110 140 sekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllat 208 + + +++d+++a++++a++ s+++++++e sacPt+gsCsG+ftansm+cl+ealG++lPg++++lat lcl|NCBI__GCF_000711195.1:WP_029935949.1 156 GGQEIKLDLVDAMVMAADDSCSDQDIHDVEISACPTCGSCSGMFTANSMNCLAEALGVALPGNGSMLAT 224 ********************************************************************* PP TIGR00110 209 saekkelakksgkrivelvkknik.......PrdiltkeafenaitldlalGGstntvLhllaiakeag 270 +a++k+l++++g+rive+ k++++ Pr+i+t +af+n ++ld+a+GGstntvLhllaia+ea+ lcl|NCBI__GCF_000711195.1:WP_029935949.1 225 HADRKHLFEEAGRRIVEIAKEYYEqdndrvlPRSIATFSAFQNVMALDVAMGGSTNTVLHLLAIAHEAD 293 ********************************************************************* PP TIGR00110 271 vklslddfdrlsrkvPllaklkPsgkkv.iedlhraGGvsavlkeldkegllhkdaltvtGktlaetle 338 vk++++d+d++srkvP+lak++P++k++ +ed+hraGG++ +l+eld+ gl+++ + tv +tl+ +e lcl|NCBI__GCF_000711195.1:WP_029935949.1 294 VKFTMSDMDEVSRKVPCLAKVAPNSKNYhMEDVHRAGGIMRLLGELDRGGLIDTSTYTVHASTLGAAIE 362 **************************999**************************************** PP TIGR00110 339 kvkvlr...................................vdqdvirsldnpvkkegglavLkGnlae 372 ++ r ++ +irs++++++k+gglavL+Gn+a+ lcl|NCBI__GCF_000711195.1:WP_029935949.1 363 LWDISRnpsesvqtfykaapgnvrttqafsqskrwktldtdDENGCIRSVEHAYTKDGGLAVLFGNIAQ 431 ***9999******************************87544444************************ PP TIGR00110 373 eGavvkiagveedilkfeGpakvfeseeealeailggkvkeGdvvviryeGPkGgPGmremLaPtsalv 441 +G+vvk+agv+e+i kf Gpa++fes++ a+++ilg +v++G+vv+iryeGPkGgPGm+emL+Pts+l+ lcl|NCBI__GCF_000711195.1:WP_029935949.1 432 HGCVVKTAGVDEEIFKFSGPARIFESQDTAVAGILGNEVQAGEVVIIRYEGPKGGPGMQEMLYPTSYLK 500 ********************************************************************* PP TIGR00110 442 glGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDienrkldlevseeelaerr 510 + GLgk++aL+tDGrfsGgt+GlsiGh sPeaaegG+i+lve GD+i+iDi+nr +++++s+ el +rr lcl|NCBI__GCF_000711195.1:WP_029935949.1 501 SKGLGKQCALLTDGRFSGGTSGLSIGHASPEAAEGGNIGLVESGDIIEIDIPNRSINVKLSDYELSQRR 569 ********************************************************************* PP TIGR00110 511 akakkkea..........revkgaLakyaklvssadkGavld 542 +++++k++ r+v+ aL++ya + +sa Gav+d lcl|NCBI__GCF_000711195.1:WP_029935949.1 570 QAMESKGDqawkpqetrpRHVSPALRAYAAMTTSAAFGAVRD 611 ****9999999*****************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (543 nodes) Target sequences: 1 (620 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: 12.47 // [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