Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate WP_012592210.1 MSIL_RS16465 dihydroxy-acid dehydratase
Query= SwissProt::Q1MIB2 (612 letters) >NCBI__GCF_000021745.1:WP_012592210.1 Length = 616 Score = 995 bits (2573), Expect = 0.0 Identities = 502/613 (81%), Positives = 543/613 (88%), Gaps = 4/613 (0%) Query: 1 MPVYRSRTTTHGRNMAGARGLWRATGMKDSDFGKPIIAVVNSFTQFVPGHVHLKDLGQLV 60 MP YRSRTTTHGRNMAGARGLWRATGMKD DFGKPIIAV NSFTQFVPGHVHLKDLGQLV Sbjct: 1 MPPYRSRTTTHGRNMAGARGLWRATGMKDGDFGKPIIAVANSFTQFVPGHVHLKDLGQLV 60 Query: 61 AREIEAAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSRELIADSVEYMVNAHCADAMVCIS 120 AREIEAAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSRE+IADSVEYMVNAHCADA+VCIS Sbjct: 61 AREIEAAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSREIIADSVEYMVNAHCADAIVCIS 120 Query: 121 NCDKITPGMLMASLRLNIPTVFVSGGPMEAGKVVMHGKTHALDLVDAMVAAADDKISDED 180 NCDKITPGMLMASLRLNIP VFVSGGPMEAGKV++ GKT ALDLVDAMVAAADDK+S+ D Sbjct: 121 NCDKITPGMLMASLRLNIPVVFVSGGPMEAGKVLLGGKTKALDLVDAMVAAADDKVSEAD 180 Query: 181 VQTIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSTLATHLDRKRLFVEAGHLIV 240 V IERSACPTCGSCSGMFTANSMNCLTEALGL+LPGNGS LATH DRKRLFVEAGHLIV Sbjct: 181 VAAIERSACPTCGSCSGMFTANSMNCLTEALGLALPGNGSMLATHGDRKRLFVEAGHLIV 240 Query: 241 DLARRYYEQDDVKALPRTIASKQAFENAMTLDIAMGGSTNTVLHILAAAHEGEIDFTMAD 300 DLARRYYEQDD LPR+IAS AFENAMTLDI+MGGSTNTVLH+LAAAHEGEIDFTMAD Sbjct: 241 DLARRYYEQDDSSVLPRSIASFAAFENAMTLDISMGGSTNTVLHLLAAAHEGEIDFTMAD 300 Query: 301 IDALSRRVPCLSKVAPAKSDVHMEDVHRAGGIMSILGELDKGGLLNRDCPTVHAETLGDA 360 ID LSRRVP L KVAPA +DVH+EDVHRAGG+M+ILGEL++ GL++ D P VHA +L +A Sbjct: 301 IDRLSRRVPVLCKVAPAVADVHVEDVHRAGGVMAILGELERAGLIHGDLPVVHAPSLKEA 360 Query: 361 IDRWDITRTNSETVRKFYRAAPGGIPTQVAFSQEARWDELDTDRENGVIRSVEHPFSKDG 420 ++RWD+ RT+SE+V +F+RAAPGG+PTQVAFSQ ARW E D DR GVIR VEH FSKDG Sbjct: 361 LERWDLRRTSSESVTEFFRAAPGGVPTQVAFSQNARWKETDVDRAGGVIRDVEHAFSKDG 420 Query: 421 GLAVLKGNLAIDGCIVKTAGVDESILKFSGPARVFESQDASVKAILANEVKAGDVVVIRY 480 GLAVL GNLA DG IVKTAGVD SIL FSGPARVFESQDA+V+AILAN++K GDV+VIRY Sbjct: 421 GLAVLYGNLAEDGAIVKTAGVDASILVFSGPARVFESQDAAVEAILANQIKPGDVLVIRY 480 Query: 481 EGPKGGPGMQEMLYPTSYLKSKGLGKACALITDGRFSGGTSGLSIGHASPEAANGGTIGL 540 EGP+GGPGMQEMLYPTSYLKSKGLGKACALITDGRFSGGTSGLSIGH SPEAA GG IGL Sbjct: 481 EGPRGGPGMQEMLYPTSYLKSKGLGKACALITDGRFSGGTSGLSIGHVSPEAAEGGLIGL 540 Query: 541 VREGDMIDIDIPNRTISLRVSETELAARRAEQDAKG---WYPTEVRKRNVTTALKAYAAF 597 V EGD I IDIPNR + L +S+ LA RR KG W P R R V+TAL+AYAA Sbjct: 541 VEEGDSIQIDIPNRRLHLDISDEALAHRRTAMAEKGKGAWKPAH-RTRKVSTALRAYAAM 599 Query: 598 ATSADRGAVRDLN 610 ATSA RGAVRD++ Sbjct: 600 ATSAARGAVRDVD 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: 1283 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: 616 Length adjustment: 37 Effective length of query: 575 Effective length of database: 579 Effective search space: 332925 Effective search space used: 332925 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_012592210.1 MSIL_RS16465 (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.25446.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.9e-252 822.5 3.2 9.2e-252 822.3 3.2 1.0 1 lcl|NCBI__GCF_000021745.1:WP_012592210.1 MSIL_RS16465 dihydroxy-acid dehy Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000021745.1:WP_012592210.1 MSIL_RS16465 dihydroxy-acid dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 822.3 3.2 9.2e-252 9.2e-252 2 542 .. 18 610 .. 17 611 .. 0.98 Alignments for each domain: == domain 1 score: 822.3 bits; conditional E-value: 9.2e-252 TIGR00110 2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamg 70 ar l++atG+kd d++kPiiav+ns+t++vPghvhlkdl++lv++eieaaGgvakefntiav+DGiamg lcl|NCBI__GCF_000021745.1:WP_012592210.1 18 ARGLWRATGMKDGDFGKPIIAVANSFTQFVPGHVHLKDLGQLVAREIEAAGGVAKEFNTIAVDDGIAMG 86 689****************************************************************** PP TIGR00110 71 heGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktkl 139 h+Gm+ysLpsreiiaDsve++v+ah++Da+v+is+CDki+PGmlma+lrlniP+++vsGGpmeagk+ l lcl|NCBI__GCF_000021745.1:WP_012592210.1 87 HDGMLYSLPSREIIADSVEYMVNAHCADAIVCISNCDKITPGMLMASLRLNIPVVFVSGGPMEAGKVLL 155 ********************************************************************* PP TIGR00110 140 sekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllat 208 + k + +d+++a++++a++k+se+++ +iersacPt+gsCsG+ftansm+cltealGl+lPg++++lat lcl|NCBI__GCF_000021745.1:WP_012592210.1 156 GGKTKALDLVDAMVAAADDKVSEADVAAIERSACPTCGSCSGMFTANSMNCLTEALGLALPGNGSMLAT 224 ********************************************************************* PP TIGR00110 209 saekkelakksgkrivelvkknik.......PrdiltkeafenaitldlalGGstntvLhllaiakeag 270 + ++k+l+ ++g+ iv+l +++++ Pr+i++ +afena+tld+ +GGstntvLhlla+a+e + lcl|NCBI__GCF_000021745.1:WP_012592210.1 225 HGDRKRLFVEAGHLIVDLARRYYEqddssvlPRSIASFAAFENAMTLDISMGGSTNTVLHLLAAAHEGE 293 ********************************************************************* PP TIGR00110 271 vklslddfdrlsrkvPllaklkPsgkkv.iedlhraGGvsavlkeldkegllhkdaltvtGktlaetle 338 +++++ d+drlsr+vP+l+k++P+ v +ed+hraGGv+a+l+el+++gl+h d v +l+e le lcl|NCBI__GCF_000021745.1:WP_012592210.1 294 IDFTMADIDRLSRRVPVLCKVAPAVADVhVEDVHRAGGVMAILGELERAGLIHGDLPVVHAPSLKEALE 362 ************************98888**************************************** PP TIGR00110 339 kvkvlr.................................vdqd....virsldnpvkkegglavLkGnl 370 + +++r v d vir ++++++k+gglavL+Gnl lcl|NCBI__GCF_000021745.1:WP_012592210.1 363 RWDLRRtssesvteffraapggvptqvafsqnarwketdV--DraggVIRDVEHAFSKDGGLAVLYGNL 429 *****9*****************************88653..34477********************** PP TIGR00110 371 aeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeGdvvviryeGPkGgPGmremLaPtsa 439 ae+Ga+vk+agv+ +il+f Gpa+vfes+++a+eail+ ++k Gdv+viryeGP+GgPGm+emL+Pts+ lcl|NCBI__GCF_000021745.1:WP_012592210.1 430 AEDGAIVKTAGVDASILVFSGPARVFESQDAAVEAILANQIKPGDVLVIRYEGPRGGPGMQEMLYPTSY 498 ********************************************************************* PP TIGR00110 440 lvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDienrkldlevseeelae 508 l++ GLgk++aLitDGrfsGgt+GlsiGhvsPeaaegG i+lve+GD i+iDi+nr+l+l++s+e la+ lcl|NCBI__GCF_000021745.1:WP_012592210.1 499 LKSKGLGKACALITDGRFSGGTSGLSIGHVSPEAAEGGLIGLVEEGDSIQIDIPNRRLHLDISDEALAH 567 ********************************************************************* PP TIGR00110 509 rrakakkkea.........revkgaLakyaklvssadkGavld 542 rr ++ +k++ r+v+ aL++ya +++sa +Gav+d lcl|NCBI__GCF_000021745.1:WP_012592210.1 568 RRTAMAEKGKgawkpahrtRKVSTALRAYAAMATSAARGAVRD 610 *****99999999****999*********************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (543 nodes) Target sequences: 1 (616 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.04 # Mc/sec: 7.92 // [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