Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate WP_013834773.1 THICY_RS01100 dihydroxy-acid dehydratase
Query= SwissProt::Q1MIB2 (612 letters) >NCBI__GCF_000214825.1:WP_013834773.1 Length = 634 Score = 912 bits (2356), Expect = 0.0 Identities = 453/627 (72%), Positives = 524/627 (83%), Gaps = 20/627 (3%) Query: 1 MPVYRSRTTTHGRNMAGARGLWRATGMKDSDFGKPIIAVVNSFTQFVPGHVHLKDLGQLV 60 MP YRSRT+THGRNMAGAR LWRATGM DFGKPIIA+ NSFTQFVPGHVHLKDLGQLV Sbjct: 1 MPAYRSRTSTHGRNMAGARALWRATGMNSEDFGKPIIAIANSFTQFVPGHVHLKDLGQLV 60 Query: 61 AREIEAAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSRELIADSVEYMVNAHCADAMVCIS 120 A IE +GGVAKEFNTIAVDDGIAMGHDGMLYSLPSRE+IADSVEYMVNAHCADA+VCIS Sbjct: 61 AGVIEQSGGVAKEFNTIAVDDGIAMGHDGMLYSLPSREVIADSVEYMVNAHCADALVCIS 120 Query: 121 NCDKITPGMLMASLRLNIPTVFVSGGPMEAGKVVMHGKTHALDLVDAMVAAADDKISDED 180 NCDKITPGMLMA++RLNIPT+FVSGGPME+GK V+ G+T LDLVDAMV AADDK++DE+ Sbjct: 121 NCDKITPGMLMAAMRLNIPTIFVSGGPMESGKTVIGGQTIKLDLVDAMVMAADDKVTDEE 180 Query: 181 VQTIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSTLATHLDRKRLFVEAGHLIV 240 V+++E SACPTCGSCSGMFTANSMNCL EALG++LPGNGS LATH DRK LF EAG IV Sbjct: 181 VESVEVSACPTCGSCSGMFTANSMNCLAEALGMALPGNGSALATHADRKHLFEEAGRRIV 240 Query: 241 DLARRYYEQDDVKALPRTIASKQAFENAMTLDIAMGGSTNTVLHILAAAHEGEIDFTMAD 300 ++A+ YYE+D+ K LPR+IA+ AF+NA+ LD+AMGGSTNTVLH+LA AHE ++FTM+D Sbjct: 241 EIAKEYYEKDNDKVLPRSIATFSAFQNAVALDVAMGGSTNTVLHLLAVAHEAGVEFTMSD 300 Query: 301 IDALSRRVPCLSKVAPAKSDVHMEDVHRAGGIMSILGELDKGGLLNRDCPTVHAETLGDA 360 IDA+SRRVPCLSKVAP HMEDVHRAGGIM +LGELD+GGLL+ D TVH+ TLG A Sbjct: 301 IDAMSRRVPCLSKVAPNSKIYHMEDVHRAGGIMRLLGELDRGGLLDPDTYTVHSSTLGAA 360 Query: 361 IDRWDITRTNSETVRKFYRAAPGGIPTQVAFSQEARWDELDTDRENGVIRSVEHPFSKDG 420 ++ WDI R SE V+KFY AAPG + T AFSQ+ RW LD+D ENG IRSVEH +++DG Sbjct: 361 LELWDIRRNPSEAVKKFYLAAPGNVRTTQAFSQDKRWKTLDSDYENGCIRSVEHAYTQDG 420 Query: 421 GLAVLKGNLAIDGCIVKTAGVDESILK-----------------FSGPARVFESQDASVK 463 GLAVL GN+A DGCIVKTAG+DES+L+ FSGP R++ESQDA+V Sbjct: 421 GLAVLFGNIAQDGCIVKTAGIDESMLEVEQLQYTTSVPTSTIRVFSGPTRIYESQDAAVA 480 Query: 464 AILANEVKAGDVVVIRYEGPKGGPGMQEMLYPTSYLKSKGLGKACALITDGRFSGGTSGL 523 AIL +EV+ GDVV+IRYEGPKGGPGMQEMLYPTSYLKSKGLGK CAL+TDGRFSGGTSGL Sbjct: 481 AILGDEVQKGDVVLIRYEGPKGGPGMQEMLYPTSYLKSKGLGKYCALLTDGRFSGGTSGL 540 Query: 524 SIGHASPEAANGGTIGLVREGDMIDIDIPNRTISLRVSETELAARRAEQDAKG---WYPT 580 SIGHASPEAA GG IGLV EGD+I+IDIPNR+I++++S+ EL+ RR + AKG W P Sbjct: 541 SIGHASPEAAEGGNIGLVEEGDIIEIDIPNRSINVKLSDYELSQRRQKMLAKGDKAWKPE 600 Query: 581 EVRKRNVTTALKAYAAFATSADRGAVR 607 R+R V+ AL+AYAA TSA GAVR Sbjct: 601 HPRERRVSAALRAYAAMTTSAAFGAVR 627 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: 1201 Number of extensions: 31 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: 634 Length adjustment: 37 Effective length of query: 575 Effective length of database: 597 Effective search space: 343275 Effective search space used: 343275 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: 54 (25.4 bits)
Align candidate WP_013834773.1 THICY_RS01100 (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.7279.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1e-246 805.6 3.4 1.7e-245 801.6 3.4 1.9 1 lcl|NCBI__GCF_000214825.1:WP_013834773.1 THICY_RS01100 dihydroxy-acid deh Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000214825.1:WP_013834773.1 THICY_RS01100 dihydroxy-acid dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 801.6 3.4 1.7e-245 1.7e-245 2 542 .. 18 628 .. 17 629 .. 0.96 Alignments for each domain: == domain 1 score: 801.6 bits; conditional E-value: 1.7e-245 TIGR00110 2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamg 70 aral++atG++ ed++kPiia++ns+t++vPghvhlkdl++lv+ ie++Ggvakefntiav+DGiamg lcl|NCBI__GCF_000214825.1:WP_013834773.1 18 ARALWRATGMNSEDFGKPIIAIANSFTQFVPGHVHLKDLGQLVAGVIEQSGGVAKEFNTIAVDDGIAMG 86 79******************************************************************* PP TIGR00110 71 heGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktkl 139 h+Gm+ysLpsre+iaDsve++v+ah++Dalv+is+CDki+PGmlmaa+rlniP+i+vsGGpme+gkt + lcl|NCBI__GCF_000214825.1:WP_013834773.1 87 HDGMLYSLPSREVIADSVEYMVNAHCADALVCISNCDKITPGMLMAAMRLNIPTIFVSGGPMESGKTVI 155 ********************************************************************* PP TIGR00110 140 sekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllat 208 + + +++d+++a++++a++k+++ee+e++e sacPt+gsCsG+ftansm+cl+ealG++lPg++++lat lcl|NCBI__GCF_000214825.1:WP_013834773.1 156 GGQTIKLDLVDAMVMAADDKVTDEEVESVEVSACPTCGSCSGMFTANSMNCLAEALGMALPGNGSALAT 224 ********************************************************************* PP TIGR00110 209 saekkelakksgkrivelvkknik.......PrdiltkeafenaitldlalGGstntvLhllaiakeag 270 +a++k+l++++g+rive+ k++++ Pr+i+t +af+na++ld+a+GGstntvLhlla+a+eag lcl|NCBI__GCF_000214825.1:WP_013834773.1 225 HADRKHLFEEAGRRIVEIAKEYYEkdndkvlPRSIATFSAFQNAVALDVAMGGSTNTVLHLLAVAHEAG 293 ***********************9********************************************* PP TIGR00110 271 vklslddfdrlsrkvPllaklkPsgkkv.iedlhraGGvsavlkeldkegllhkdaltvtGktlaetle 338 v+++++d+d +sr+vP+l+k++P++k + +ed+hraGG++ +l+eld+ gll+ d+ tv +tl+ le lcl|NCBI__GCF_000214825.1:WP_013834773.1 294 VEFTMSDIDAMSRRVPCLSKVAPNSKIYhMEDVHRAGGIMRLLGELDRGGLLDPDTYTVHSSTLGAALE 362 **************************999**************************************** PP TIGR00110 339 kvkvlr...................................vdqdvirsldnpvkkegglavLkGnlae 372 +++r ++ +irs++++++++gglavL+Gn+a+ lcl|NCBI__GCF_000214825.1:WP_013834773.1 363 LWDIRRnpseavkkfylaapgnvrttqafsqdkrwktldsdYENGCIRSVEHAYTQDGGLAVLFGNIAQ 431 ****999******************************77555555************************ PP TIGR00110 373 eGavvkiagveedil.................kfeGpakvfeseeealeailggkvkeGdvvviryeGP 424 +G++vk+ag++e++l +f Gp +++es+++a++ailg +v++Gdvv+iryeGP lcl|NCBI__GCF_000214825.1:WP_013834773.1 432 DGCIVKTAGIDESMLeveqlqyttsvptstirVFSGPTRIYESQDAAVAAILGDEVQKGDVVLIRYEGP 500 ***********988522222222222222222588********************************** PP TIGR00110 425 kGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDie 493 kGgPGm+emL+Pts+l++ GLgk +aL+tDGrfsGgt+GlsiGh sPeaaegG+i+lve+GD+i+iDi+ lcl|NCBI__GCF_000214825.1:WP_013834773.1 501 KGGPGMQEMLYPTSYLKSKGLGKYCALLTDGRFSGGTSGLSIGHASPEAAEGGNIGLVEEGDIIEIDIP 569 ********************************************************************* PP TIGR00110 494 nrkldlevseeelaerrakakkkea..........revkgaLakyaklvssadkGavld 542 nr +++++s+ el +rr+k+ +k++ r+v+ aL++ya + +sa Gav++ lcl|NCBI__GCF_000214825.1:WP_013834773.1 570 NRSINVKLSDYELSQRRQKMLAKGDkawkpehpreRRVSAALRAYAAMTTSAAFGAVRR 628 ********************999999999****9999********************86 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (543 nodes) Target sequences: 1 (634 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: 0.06u 0.01s 00:00:00.06 Elapsed: 00:00:00.06 # Mc/sec: 5.16 // [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