Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate WP_085772653.1 B1812_RS17045 dihydroxy-acid dehydratase
Query= SwissProt::Q1MIB2 (612 letters) >NCBI__GCF_002117405.1:WP_085772653.1 Length = 610 Score = 952 bits (2460), Expect = 0.0 Identities = 469/609 (77%), Positives = 528/609 (86%) Query: 1 MPVYRSRTTTHGRNMAGARGLWRATGMKDSDFGKPIIAVVNSFTQFVPGHVHLKDLGQLV 60 MP YRSRT+THGRNMAGARGLWRATGM++ DFGKPIIA+ NSFTQFVPGHVHL+DLGQLV Sbjct: 1 MPPYRSRTSTHGRNMAGARGLWRATGMREEDFGKPIIAIANSFTQFVPGHVHLQDLGQLV 60 Query: 61 AREIEAAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSRELIADSVEYMVNAHCADAMVCIS 120 ARE+E AGGVAKEFNTIA+DDGIAMGHDGMLYSLPSRE+IADSVEYM NAHCADA+VCIS Sbjct: 61 AREVENAGGVAKEFNTIAIDDGIAMGHDGMLYSLPSREIIADSVEYMANAHCADALVCIS 120 Query: 121 NCDKITPGMLMASLRLNIPTVFVSGGPMEAGKVVMHGKTHALDLVDAMVAAADDKISDED 180 NCDKITPGMLMA+LRLNIPT+FVSGGPMEAGK +HGK ALDL+DAMVAAAD+ SD + Sbjct: 121 NCDKITPGMLMAALRLNIPTIFVSGGPMEAGKADVHGKAVALDLIDAMVAAADEHYSDAE 180 Query: 181 VQTIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSTLATHLDRKRLFVEAGHLIV 240 V+TIERSACPTCGSCSGMFTANSMNCL EALGL+LPGNG+ LATH DRK LF+EAG IV Sbjct: 181 VKTIERSACPTCGSCSGMFTANSMNCLVEALGLALPGNGTALATHADRKELFLEAGRRIV 240 Query: 241 DLARRYYEQDDVKALPRTIASKQAFENAMTLDIAMGGSTNTVLHILAAAHEGEIDFTMAD 300 +LARR+YE+DD ALPR+IAS +AFENAMTLDIAMGGSTNTVLH+LAAAHE E+ FTMAD Sbjct: 241 ELARRWYEEDDASALPRSIASFKAFENAMTLDIAMGGSTNTVLHLLAAAHEAEVGFTMAD 300 Query: 301 IDALSRRVPCLSKVAPAKSDVHMEDVHRAGGIMSILGELDKGGLLNRDCPTVHAETLGDA 360 ID LSRRVP L KVAPAK+DVH+EDVHRAGG+M+ILGEL + GL++ PTVH++TL DA Sbjct: 301 IDRLSRRVPVLCKVAPAKADVHLEDVHRAGGVMAILGELLRAGLIHDGLPTVHSKTLRDA 360 Query: 361 IDRWDITRTNSETVRKFYRAAPGGIPTQVAFSQEARWDELDTDRENGVIRSVEHPFSKDG 420 I WDI R F++AAPGG+PTQ AFSQ R++ LD DR +GVIR H FSKDG Sbjct: 361 ISAWDICGGAGVAARNFFQAAPGGVPTQTAFSQSRRYEALDMDRAHGVIRDAAHAFSKDG 420 Query: 421 GLAVLKGNLAIDGCIVKTAGVDESILKFSGPARVFESQDASVKAILANEVKAGDVVVIRY 480 GLAVL GNLA DGCIVKTAGVD+S+LKF+GPARV+ESQDA+V IL +VK GDVVVIRY Sbjct: 421 GLAVLSGNLAEDGCIVKTAGVDDSVLKFTGPARVYESQDAAVSGILTGDVKEGDVVVIRY 480 Query: 481 EGPKGGPGMQEMLYPTSYLKSKGLGKACALITDGRFSGGTSGLSIGHASPEAANGGTIGL 540 EGP+GGPGMQEMLYPTSYLKSKGLGKACALITDGRFSGGTSGLSIGH SPEAA GG I L Sbjct: 481 EGPRGGPGMQEMLYPTSYLKSKGLGKACALITDGRFSGGTSGLSIGHVSPEAAEGGLIAL 540 Query: 541 VREGDMIDIDIPNRTISLRVSETELAARRAEQDAKGWYPTEVRKRNVTTALKAYAAFATS 600 V +GD I+IDIP R++ L VSE ELAARR Q AKG+ P + R R V+ AL+AYAA ATS Sbjct: 541 VEDGDRIEIDIPGRSLKLAVSEAELAARRKAQQAKGFAPAQARHRVVSKALRAYAAMATS 600 Query: 601 ADRGAVRDL 609 A +GAVR++ Sbjct: 601 AAKGAVREV 609 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: 1272 Number of extensions: 38 Number of successful extensions: 1 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: 610 Length adjustment: 37 Effective length of query: 575 Effective length of database: 573 Effective search space: 329475 Effective search space used: 329475 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_085772653.1 B1812_RS17045 (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.18836.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.4e-253 826.3 4.7 6.2e-253 826.1 4.7 1.0 1 lcl|NCBI__GCF_002117405.1:WP_085772653.1 B1812_RS17045 dihydroxy-acid deh Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002117405.1:WP_085772653.1 B1812_RS17045 dihydroxy-acid dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 826.1 4.7 6.2e-253 6.2e-253 2 542 .. 18 608 .. 17 609 .. 0.98 Alignments for each domain: == domain 1 score: 826.1 bits; conditional E-value: 6.2e-253 TIGR00110 2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamg 70 ar l++atG+++ed++kPiia++ns+t++vPghvhl+dl++lv++e+e+aGgvakefntia++DGiamg lcl|NCBI__GCF_002117405.1:WP_085772653.1 18 ARGLWRATGMREEDFGKPIIAIANSFTQFVPGHVHLQDLGQLVAREVENAGGVAKEFNTIAIDDGIAMG 86 689****************************************************************** PP TIGR00110 71 heGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktkl 139 h+Gm+ysLpsreiiaDsve++++ah++Dalv+is+CDki+PGmlmaalrlniP+i+vsGGpmeagk + lcl|NCBI__GCF_002117405.1:WP_085772653.1 87 HDGMLYSLPSREIIADSVEYMANAHCADALVCISNCDKITPGMLMAALRLNIPTIFVSGGPMEAGKADV 155 ********************************************************************* PP TIGR00110 140 sekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllat 208 k +d+++a++++a+++ s++e+++iersacPt+gsCsG+ftansm+cl ealGl+lPg++t+lat lcl|NCBI__GCF_002117405.1:WP_085772653.1 156 HGKAVALDLIDAMVAAADEHYSDAEVKTIERSACPTCGSCSGMFTANSMNCLVEALGLALPGNGTALAT 224 9******************************************************************** PP TIGR00110 209 saekkelakksgkrivelvkknik.......PrdiltkeafenaitldlalGGstntvLhllaiakeag 270 +a++kel+ ++g+rivel ++ ++ Pr+i++ +afena+tld+a+GGstntvLhlla+a+ea+ lcl|NCBI__GCF_002117405.1:WP_085772653.1 225 HADRKELFLEAGRRIVELARRWYEeddasalPRSIASFKAFENAMTLDIAMGGSTNTVLHLLAAAHEAE 293 ***********************99******************************************** PP TIGR00110 271 vklslddfdrlsrkvPllaklkPsgkkv.iedlhraGGvsavlkeldkegllhkdaltvtGktlaetle 338 v +++ d+drlsr+vP+l+k++P+ v +ed+hraGGv+a+l+el ++gl+h+ tv ktl + ++ lcl|NCBI__GCF_002117405.1:WP_085772653.1 294 VGFTMADIDRLSRRVPVLCKVAPAKADVhLEDVHRAGGVMAILGELLRAGLIHDGLPTVHSKTLRDAIS 362 ************************98888**************************************** PP TIGR00110 339 kvkvlr...................................vdqd..virsldnpvkkegglavLkGnl 370 ++ vir ++++k+gglavL Gnl lcl|NCBI__GCF_002117405.1:WP_085772653.1 363 AWDICGgagvaarnffqaapggvptqtafsqsrryealdmdR--AhgVIRDAAHAFSKDGGLAVLSGNL 429 ***99999***************************9966444..256********************** PP TIGR00110 371 aeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeGdvvviryeGPkGgPGmremLaPtsa 439 ae+G++vk+agv++++lkf+Gpa+v+es+++a+ +il+g+vkeGdvvviryeGP+GgPGm+emL+Pts+ lcl|NCBI__GCF_002117405.1:WP_085772653.1 430 AEDGCIVKTAGVDDSVLKFTGPARVYESQDAAVSGILTGDVKEGDVVVIRYEGPRGGPGMQEMLYPTSY 498 ********************************************************************* PP TIGR00110 440 lvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDienrkldlevseeelae 508 l++ GLgk++aLitDGrfsGgt+GlsiGhvsPeaaegG ialvedGD+i+iDi+ r l+l+vse+ela+ lcl|NCBI__GCF_002117405.1:WP_085772653.1 499 LKSKGLGKACALITDGRFSGGTSGLSIGHVSPEAAEGGLIALVEDGDRIEIDIPGRSLKLAVSEAELAA 567 ********************************************************************* PP TIGR00110 509 rrakakkkea.......revkgaLakyaklvssadkGavld 542 rr+++++k++ r v+ aL++ya +++sa kGav++ lcl|NCBI__GCF_002117405.1:WP_085772653.1 568 RRKAQQAKGFapaqarhRVVSKALRAYAAMATSAAKGAVRE 608 ********9999***999*********************86 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (543 nodes) Target sequences: 1 (610 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: 00:00:00.03 # Mc/sec: 8.96 // [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