Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate YP_004139388.1 Mesci_0165 dihydroxy-acid dehydratase
Query= SwissProt::Q1MIB2 (612 letters) >NCBI__GCF_000185905.1:YP_004139388.1 Length = 614 Score = 1070 bits (2766), Expect = 0.0 Identities = 537/610 (88%), Positives = 564/610 (92%), Gaps = 3/610 (0%) Query: 1 MPVYRSRTTTHGRNMAGARGLWRATGMKDSDFGKPIIAVVNSFTQFVPGHVHLKDLGQLV 60 MP YRSRTTTHGRNMAGARGLWRATGMKDSDFGKPIIAVVNSFTQFVPGHVHLKDLGQLV Sbjct: 1 MPAYRSRTTTHGRNMAGARGLWRATGMKDSDFGKPIIAVVNSFTQFVPGHVHLKDLGQLV 60 Query: 61 AREIEAAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSRELIADSVEYMVNAHCADAMVCIS 120 AREIE AGGVAKEFNTIAVDDGIAMGHDGMLYSLPSRELIADSVEYMVNAHCADAMVCIS Sbjct: 61 AREIEKAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSRELIADSVEYMVNAHCADAMVCIS 120 Query: 121 NCDKITPGMLMASLRLNIPTVFVSGGPMEAGKVVMHGKTHALDLVDAMVAAADDKISDED 180 NCDKITPGMLMASLRLNIPTVFVSGGPMEAGKVV+ GKT ALDLVDAMVAAADDKISDED Sbjct: 121 NCDKITPGMLMASLRLNIPTVFVSGGPMEAGKVVLAGKTQALDLVDAMVAAADDKISDED 180 Query: 181 VQTIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSTLATHLDRKRLFVEAGHLIV 240 V+ IERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSTLATH DRKRLFVEAGHLIV Sbjct: 181 VKVIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSTLATHADRKRLFVEAGHLIV 240 Query: 241 DLARRYYEQDDVKALPRTIASKQAFENAMTLDIAMGGSTNTVLHILAAAHEGEIDFTMAD 300 DLA+RYYEQDD ALPR IASK AFENAMTLDIAMGGSTNTVLHILAAAHEGEIDF D Sbjct: 241 DLAQRYYEQDDETALPRNIASKGAFENAMTLDIAMGGSTNTVLHILAAAHEGEIDFDQDD 300 Query: 301 IDALSRRVPCLSKVAPAKSDVHMEDVHRAGGIMSILGELDKGGLLNRDCPTVHAETLGDA 360 IDALSR+VP L KVAPAKSDVHMEDVHRAGGIM+ILG+LD GLLNRD PTVH TLG+A Sbjct: 301 IDALSRKVPVLCKVAPAKSDVHMEDVHRAGGIMAILGQLDNAGLLNRDLPTVHTSTLGEA 360 Query: 361 IDRWDITRTNSETVRKFYRAAPGGIPTQVAFSQEARWDELDTDRENGVIRSVEHPFSKDG 420 +D WDI+RT S++VR F+ AAPGG+PTQVAFSQE RWDELD DRE GVIRS EHPFSKDG Sbjct: 361 LDHWDISRTTSQSVRDFFLAAPGGVPTQVAFSQERRWDELDLDREKGVIRSTEHPFSKDG 420 Query: 421 GLAVLKGNLAIDGCIVKTAGVDESILKFSGPARVFESQDASVKAILANEVKAGDVVVIRY 480 GLAVLKGNLA+DGCIVKTAGVDESILKF+GPARVFESQD+SVKAIL+NE+KAGDVVVIRY Sbjct: 421 GLAVLKGNLALDGCIVKTAGVDESILKFTGPARVFESQDSSVKAILSNEIKAGDVVVIRY 480 Query: 481 EGPKGGPGMQEMLYPTSYLKSKGLGKACALITDGRFSGGTSGLSIGHASPEAANGGTIGL 540 EGP+GGPGMQEMLYPTSYLKSKGLGKACAL+TDGRFSGGTSGLSIGHASPEAA GG IGL Sbjct: 481 EGPRGGPGMQEMLYPTSYLKSKGLGKACALVTDGRFSGGTSGLSIGHASPEAAEGGLIGL 540 Query: 541 VREGDMIDIDIPNRTISLRVSETELAARRAEQDAKG---WYPTEVRKRNVTTALKAYAAF 597 V+EGD I+IDIPNR+I L V E ELAARRA +A+G W P E RKR VTTAL+AYAA Sbjct: 541 VQEGDTIEIDIPNRSIRLAVDEAELAARRAAMEARGALAWKPEEKRKRKVTTALRAYAAM 600 Query: 598 ATSADRGAVR 607 ATSA +GAVR Sbjct: 601 ATSAAKGAVR 610 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: 1324 Number of extensions: 39 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: 614 Length adjustment: 37 Effective length of query: 575 Effective length of database: 577 Effective search space: 331775 Effective search space used: 331775 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 YP_004139388.1 Mesci_0165 (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.28496.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-255 834.9 2.8 1.6e-255 834.7 2.8 1.0 1 lcl|NCBI__GCF_000185905.1:YP_004139388.1 Mesci_0165 dihydroxy-acid dehydr Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000185905.1:YP_004139388.1 Mesci_0165 dihydroxy-acid dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 834.7 2.8 1.6e-255 1.6e-255 2 541 .. 18 610 .. 17 612 .. 0.99 Alignments for each domain: == domain 1 score: 834.7 bits; conditional E-value: 1.6e-255 TIGR00110 2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamg 70 ar l++atG+kd d++kPiiavvns+t++vPghvhlkdl++lv++eie+aGgvakefntiav+DGiamg lcl|NCBI__GCF_000185905.1:YP_004139388.1 18 ARGLWRATGMKDSDFGKPIIAVVNSFTQFVPGHVHLKDLGQLVAREIEKAGGVAKEFNTIAVDDGIAMG 86 689****************************************************************** PP TIGR00110 71 heGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktkl 139 h+Gm+ysLpsre+iaDsve++v+ah++Da+v+is+CDki+PGmlma+lrlniP+++vsGGpmeagk+ l lcl|NCBI__GCF_000185905.1:YP_004139388.1 87 HDGMLYSLPSRELIADSVEYMVNAHCADAMVCISNCDKITPGMLMASLRLNIPTVFVSGGPMEAGKVVL 155 ********************************************************************* PP TIGR00110 140 sekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllat 208 + k + +d+++a++++a++k+s+e+++ iersacPt+gsCsG+ftansm+cltealGlslPg++++lat lcl|NCBI__GCF_000185905.1:YP_004139388.1 156 AGKTQALDLVDAMVAAADDKISDEDVKVIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSTLAT 224 ********************************************************************* PP TIGR00110 209 saekkelakksgkrivelvkknik.......PrdiltkeafenaitldlalGGstntvLhllaiakeag 270 +a++k+l+ ++g+ iv+l +++++ Pr+i++k afena+tld+a+GGstntvLh+la+a+e + lcl|NCBI__GCF_000185905.1:YP_004139388.1 225 HADRKRLFVEAGHLIVDLAQRYYEqddetalPRNIASKGAFENAMTLDIAMGGSTNTVLHILAAAHEGE 293 ********************************************************************* PP TIGR00110 271 vklslddfdrlsrkvPllaklkPsgkkv.iedlhraGGvsavlkeldkegllhkdaltvtGktlaetle 338 ++++ dd+d lsrkvP+l+k++P+ + v +ed+hraGG++a+l++ld++gll++d tv +tl+e l+ lcl|NCBI__GCF_000185905.1:YP_004139388.1 294 IDFDQDDIDALSRKVPVLCKVAPAKSDVhMEDVHRAGGIMAILGQLDNAGLLNRDLPTVHTSTLGEALD 362 ************************88888**************************************** PP TIGR00110 339 kvkvlr...................................vdqdvirsldnpvkkegglavLkGnlae 372 + ++ r ++ virs+++p++k+gglavLkGnla lcl|NCBI__GCF_000185905.1:YP_004139388.1 363 HWDISRttsqsvrdfflaapggvptqvafsqerrwdeldldREKGVIRSTEHPFSKDGGLAVLKGNLAL 431 ****999******************************99655566************************ PP TIGR00110 373 eGavvkiagveedilkfeGpakvfeseeealeailggkvkeGdvvviryeGPkGgPGmremLaPtsalv 441 +G++vk+agv+e+ilkf+Gpa+vfes++ ++ail+ ++k+GdvvviryeGP+GgPGm+emL+Pts+l+ lcl|NCBI__GCF_000185905.1:YP_004139388.1 432 DGCIVKTAGVDESILKFTGPARVFESQDSSVKAILSNEIKAGDVVVIRYEGPRGGPGMQEMLYPTSYLK 500 ********************************************************************* PP TIGR00110 442 glGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDienrkldlevseeelaerr 510 + GLgk++aL+tDGrfsGgt+GlsiGh sPeaaegG i+lv++GD+i+iDi+nr + l+v+e+ela+rr lcl|NCBI__GCF_000185905.1:YP_004139388.1 501 SKGLGKACALVTDGRFSGGTSGLSIGHASPEAAEGGLIGLVQEGDTIEIDIPNRSIRLAVDEAELAARR 569 ********************************************************************* PP TIGR00110 511 akakkkea..........revkgaLakyaklvssadkGavl 541 a++++++a r+v aL++ya +++sa kGav+ lcl|NCBI__GCF_000185905.1:YP_004139388.1 570 AAMEARGAlawkpeekrkRKVTTALRAYAAMATSAAKGAVR 610 *****9999999***9999999*****************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (543 nodes) Target sequences: 1 (614 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: 11.49 // [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