Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate WP_012172053.1 AZC_RS18155 dihydroxy-acid dehydratase
Query= SwissProt::Q1MIB2 (612 letters) >NCBI__GCF_000010525.1:WP_012172053.1 Length = 617 Score = 989 bits (2556), Expect = 0.0 Identities = 488/613 (79%), Positives = 549/613 (89%), Gaps = 5/613 (0%) Query: 1 MPVYRSRTTTHGRNMAGARGLWRATGMKDSDFGKPIIAVVNSFTQFVPGHVHLKDLGQLV 60 MP YRSRT+THGRNMAGARGLWRATGMKD DFGKPIIAVVNSFTQFVPGHVHLKDLGQLV Sbjct: 1 MPAYRSRTSTHGRNMAGARGLWRATGMKDGDFGKPIIAVVNSFTQFVPGHVHLKDLGQLV 60 Query: 61 AREIEAAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSRELIADSVEYMVNAHCADAMVCIS 120 AREIE AGGVAKEFNTIAVDDGIAMGHDGMLYSLPSRE+IADSVEYMVNAHCADAMVCIS Sbjct: 61 AREIEKAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSREIIADSVEYMVNAHCADAMVCIS 120 Query: 121 NCDKITPGMLMASLRLNIPTVFVSGGPMEAGKVVMHGKTHALDLVDAMVAAADDKISDED 180 NCDKITPGMLMA++RLNIP VFVSGGPMEAGKV++ +DL+DAM+AAADD++SDED Sbjct: 121 NCDKITPGMLMAAMRLNIPAVFVSGGPMEAGKVLLSTGEKKVDLIDAMIAAADDRVSDED 180 Query: 181 VQTIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSTLATHLDRKRLFVEAGHLIV 240 V+ +ERSACPTCGSCSGMFTANSMNCLTEALGL+LPGNGS LATH DR+RLFVEAGHL+V Sbjct: 181 VKVMERSACPTCGSCSGMFTANSMNCLTEALGLALPGNGSVLATHADRERLFVEAGHLVV 240 Query: 241 DLARRYYEQDDVKALPRTIASKQAFENAMTLDIAMGGSTNTVLHILAAAHEGEIDFTMAD 300 DLARRYYEQDD LPRTIAS +AFENAMTLDI+MGGSTNTVLH+LAAA+EGE+ FTMAD Sbjct: 241 DLARRYYEQDDAGVLPRTIASFKAFENAMTLDISMGGSTNTVLHLLAAANEGEVPFTMAD 300 Query: 301 IDALSRRVPCLSKVAPAKSDVHMEDVHRAGGIMSILGELDKGGLLNRDCPTVHAETLGDA 360 ID LSR+VP L KVAPA +++HMEDVHRAGGIM ILGELD+ GL++ D PTVHA ++ DA Sbjct: 301 IDRLSRKVPVLCKVAPAVANIHMEDVHRAGGIMGILGELDRAGLIHTDLPTVHAPSMKDA 360 Query: 361 IDRWDITRTNSETVRKFYRAAPGGIPTQVAFSQEARWDELDTDRENGVIRSVEHPFSKDG 420 ++RWD+TRT +E+V FYRAAPGG+PTQVAFSQ RWD+LDTDR +GVIR EH +SKDG Sbjct: 361 LERWDVTRTKAESVTTFYRAAPGGVPTQVAFSQSRRWDDLDTDRASGVIRDFEHAYSKDG 420 Query: 421 GLAVLKGNLAIDGCIVKTAGVDESILKFSGPARVFESQDASVKAILAN-EVKAGDVVVIR 479 GLAVL GN+A DGCIVKTAGVD SILKF+GPAR+FESQDA+V+AILAN ++KAGD+V+IR Sbjct: 421 GLAVLFGNIAEDGCIVKTAGVDASILKFTGPARIFESQDAAVEAILANGKIKAGDIVLIR 480 Query: 480 YEGPKGGPGMQEMLYPTSYLKSKGLGKACALITDGRFSGGTSGLSIGHASPEAANGGTIG 539 YEGP+GGPGMQEMLYPTSYLKSKGLGKACAL+TDGRFSGG+SGLSIGH SPEAA GG IG Sbjct: 481 YEGPRGGPGMQEMLYPTSYLKSKGLGKACALVTDGRFSGGSSGLSIGHVSPEAAEGGAIG 540 Query: 540 LVREGDMIDIDIPNRTISLRVSETELAARRAEQDAKG---WYPTEVRKRNVTTALKAYAA 596 LV EGD I+IDIPNR I L +S+ E+A RRA +AKG W P + R+R V+ AL+AYAA Sbjct: 541 LVEEGDTIEIDIPNRRIHLAISDEEMARRRAAMEAKGDAAWKPKD-RQRVVSQALQAYAA 599 Query: 597 FATSADRGAVRDL 609 TSA RGAVRD+ Sbjct: 600 LTTSAARGAVRDV 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: 1294 Number of extensions: 34 Number of successful extensions: 3 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: 617 Length adjustment: 37 Effective length of query: 575 Effective length of database: 580 Effective search space: 333500 Effective search space used: 333500 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_012172053.1 AZC_RS18155 (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.307.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.1e-253 827.7 4.7 2.4e-253 827.5 4.7 1.0 1 lcl|NCBI__GCF_000010525.1:WP_012172053.1 AZC_RS18155 dihydroxy-acid dehyd Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000010525.1:WP_012172053.1 AZC_RS18155 dihydroxy-acid dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 827.5 4.7 2.4e-253 2.4e-253 2 542 .. 18 611 .. 17 612 .. 0.98 Alignments for each domain: == domain 1 score: 827.5 bits; conditional E-value: 2.4e-253 TIGR00110 2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamg 70 ar l++atG+kd d++kPiiavvns+t++vPghvhlkdl++lv++eie+aGgvakefntiav+DGiamg lcl|NCBI__GCF_000010525.1:WP_012172053.1 18 ARGLWRATGMKDGDFGKPIIAVVNSFTQFVPGHVHLKDLGQLVAREIEKAGGVAKEFNTIAVDDGIAMG 86 689****************************************************************** PP TIGR00110 71 heGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktkl 139 h+Gm+ysLpsreiiaDsve++v+ah++Da+v+is+CDki+PGmlmaa+rlniPa++vsGGpmeagk+ l lcl|NCBI__GCF_000010525.1:WP_012172053.1 87 HDGMLYSLPSREIIADSVEYMVNAHCADAMVCISNCDKITPGMLMAAMRLNIPAVFVSGGPMEAGKVLL 155 ********************************************************************* PP TIGR00110 140 sekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllat 208 s ++vd+++a++++a++++s+e+++ +ersacPt+gsCsG+ftansm+cltealGl+lPg++++lat lcl|NCBI__GCF_000010525.1:WP_012172053.1 156 STGEKKVDLIDAMIAAADDRVSDEDVKVMERSACPTCGSCSGMFTANSMNCLTEALGLALPGNGSVLAT 224 ********************************************************************* PP TIGR00110 209 saekkelakksgkrivelvkknik.......PrdiltkeafenaitldlalGGstntvLhllaiakeag 270 +a++++l+ ++g+ +v+l +++++ Pr+i++ +afena+tld+ +GGstntvLhlla+a+e + lcl|NCBI__GCF_000010525.1:WP_012172053.1 225 HADRERLFVEAGHLVVDLARRYYEqddagvlPRTIASFKAFENAMTLDISMGGSTNTVLHLLAAANEGE 293 ********************************************************************* PP TIGR00110 271 vklslddfdrlsrkvPllaklkPsgkkv.iedlhraGGvsavlkeldkegllhkdaltvtGktlaetle 338 v +++ d+drlsrkvP+l+k++P+ ++ +ed+hraGG++++l+eld++gl+h+d tv ++++ le lcl|NCBI__GCF_000010525.1:WP_012172053.1 294 VPFTMADIDRLSRKVPVLCKVAPAVANIhMEDVHRAGGIMGILGELDRAGLIHTDLPTVHAPSMKDALE 362 ************************99888**************************************** PP TIGR00110 339 kvkvlr.................................vdqd....virsldnpvkkegglavLkGnl 370 + +v+r + d vir +++++k+gglavL+Gn+ lcl|NCBI__GCF_000010525.1:WP_012172053.1 363 RWDVTRtkaesvttfyraapggvptqvafsqsrrwddldT--DrasgVIRDFEHAYSKDGGLAVLFGNI 429 *****99****************************99552..45567********************** PP TIGR00110 371 aeeGavvkiagveedilkfeGpakvfeseeealeail.ggkvkeGdvvviryeGPkGgPGmremLaPts 438 ae+G++vk+agv+ +ilkf+Gpa++fes+++a+eail +gk+k+Gd+v+iryeGP+GgPGm+emL+Pts lcl|NCBI__GCF_000010525.1:WP_012172053.1 430 AEDGCIVKTAGVDASILKFTGPARIFESQDAAVEAILaNGKIKAGDIVLIRYEGPRGGPGMQEMLYPTS 498 ***********************************98569***************************** PP TIGR00110 439 alvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDienrkldlevseeela 507 +l++ GLgk++aL+tDGrfsGg++GlsiGhvsPeaaegGai+lve+GD+i+iDi+nr+++l++s+ee+a lcl|NCBI__GCF_000010525.1:WP_012172053.1 499 YLKSKGLGKACALVTDGRFSGGSSGLSIGHVSPEAAEGGAIGLVEEGDTIEIDIPNRRIHLAISDEEMA 567 ********************************************************************* PP TIGR00110 508 errakakkkea.........revkgaLakyaklvssadkGavld 542 +rra++++k++ r v+ aL++ya l +sa +Gav+d lcl|NCBI__GCF_000010525.1:WP_012172053.1 568 RRRAAMEAKGDaawkpkdrqRVVSQALQAYAALTTSAARGAVRD 611 *********99999****9999********************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: 0.02u 0.02s 00:00:00.04 Elapsed: 00:00:00.03 # Mc/sec: 8.42 // [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