Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate WP_019555805.1 F612_RS0100635 dihydroxy-acid dehydratase
Query= SwissProt::Q1MIB2 (612 letters) >NCBI__GCF_000381085.1:WP_019555805.1 Length = 618 Score = 919 bits (2374), Expect = 0.0 Identities = 445/612 (72%), Positives = 518/612 (84%), Gaps = 3/612 (0%) Query: 1 MPVYRSRTTTHGRNMAGARGLWRATGMKDSDFGKPIIAVVNSFTQFVPGHVHLKDLGQLV 60 MPVYRS+T+THGRNMAGAR LWRATGM+ DFGKPIIA+ NSFTQFVPGHVHLKD+GQLV Sbjct: 1 MPVYRSKTSTHGRNMAGARALWRATGMETGDFGKPIIAIANSFTQFVPGHVHLKDMGQLV 60 Query: 61 AREIEAAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSRELIADSVEYMVNAHCADAMVCIS 120 AR IE AGGVAKEFNTIAVDDGIAMGHDGMLYSLPSR+LIADSVEYMVNAHCADA+VCIS Sbjct: 61 ARVIEQAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSRDLIADSVEYMVNAHCADALVCIS 120 Query: 121 NCDKITPGMLMASLRLNIPTVFVSGGPMEAGKVVMHGKTHALDLVDAMVAAADDKISDED 180 NCDKITPGM+MA++RLNIPT+FV+GGPME+GK V+ G LDLVDAMV AADD +SD D Sbjct: 121 NCDKITPGMMMAAMRLNIPTIFVTGGPMESGKTVLGGIGIKLDLVDAMVMAADDSVSDSD 180 Query: 181 VQTIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSTLATHLDRKRLFVEAGHLIV 240 V+ +E SACPTCGSCSGMFTANSMNCL EALG++LPGNG+TLATH DR+ LF EAG IV Sbjct: 181 VEDVEVSACPTCGSCSGMFTANSMNCLAEALGIALPGNGTTLATHSDRRHLFEEAGRRIV 240 Query: 241 DLARRYYEQDDVKALPRTIASKQAFENAMTLDIAMGGSTNTVLHILAAAHEGEIDFTMAD 300 ++A+++Y++DD LPR+IA+ +AFENAMTLD+AMGGSTNTVLH+LA A E E++FTMAD Sbjct: 241 EIAKKHYDEDDYSVLPRSIATFEAFENAMTLDVAMGGSTNTVLHLLAIAKEAEVNFTMAD 300 Query: 301 IDALSRRVPCLSKVAPAKSDVHMEDVHRAGGIMSILGELDKGGLLNRDCPTVHAETLGDA 360 +D +SRRVPCL KVAP HMEDVHRAGGIM ILGELD+GGL+ RD PTVHA ++G A Sbjct: 301 MDHISRRVPCLVKVAPNSKQFHMEDVHRAGGIMRILGELDRGGLIKRDVPTVHASSMGAA 360 Query: 361 IDRWDITRTNSETVRKFYRAAPGGIPTQVAFSQEARWDELDTDRENGVIRSVEHPFSKDG 420 +D WDI RT+ + + F+RAAPG + T AFSQ RW +D D NG +R +EH ++K+G Sbjct: 361 LDLWDIRRTDDDAIDTFFRAAPGNVRTTEAFSQSKRWKTVDDDPINGCVRDMEHAYTKEG 420 Query: 421 GLAVLKGNLAIDGCIVKTAGVDESILKFSGPARVFESQDASVKAILANEVKAGDVVVIRY 480 GLAVL GN+A+DGCIVKTAGVDESI KF+GPAR+FESQD++V AILANE+ GDV++IRY Sbjct: 421 GLAVLYGNIALDGCIVKTAGVDESIFKFTGPARIFESQDSAVAAILANEISEGDVLIIRY 480 Query: 481 EGPKGGPGMQEMLYPTSYLKSKGLGKACALITDGRFSGGTSGLSIGHASPEAANGGTIGL 540 EGPKGGPGMQEMLYPTSYLKSKGLGKACAL+TDGRFSGGTSGLSIGHASPEAA GG IGL Sbjct: 481 EGPKGGPGMQEMLYPTSYLKSKGLGKACALLTDGRFSGGTSGLSIGHASPEAAEGGNIGL 540 Query: 541 VREGDMIDIDIPNRTISLRVSETELAARRAEQDAKG---WYPTEVRKRNVTTALKAYAAF 597 + EGD I+IDIPNRTI +++ A RR +KG W P EVR R ++ AL+AYAA Sbjct: 541 INEGDAIEIDIPNRTIKALLTDEVFAERRQAMVSKGRNAWKPLEVRPRKISAALRAYAAM 600 Query: 598 ATSADRGAVRDL 609 TSA GAVRD+ Sbjct: 601 TTSAAFGAVRDV 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: 1217 Number of extensions: 37 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: 618 Length adjustment: 37 Effective length of query: 575 Effective length of database: 581 Effective search space: 334075 Effective search space used: 334075 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_019555805.1 F612_RS0100635 (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.14996.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-246 805.3 5.0 1.5e-246 805.0 5.0 1.1 1 lcl|NCBI__GCF_000381085.1:WP_019555805.1 F612_RS0100635 dihydroxy-acid de Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000381085.1:WP_019555805.1 F612_RS0100635 dihydroxy-acid dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 805.0 5.0 1.5e-246 1.5e-246 2 542 .. 18 611 .. 17 612 .. 0.99 Alignments for each domain: == domain 1 score: 805.0 bits; conditional E-value: 1.5e-246 TIGR00110 2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamg 70 aral++atG++ d++kPiia++ns+t++vPghvhlkd+++lv++ ie+aGgvakefntiav+DGiamg lcl|NCBI__GCF_000381085.1:WP_019555805.1 18 ARALWRATGMETGDFGKPIIAIANSFTQFVPGHVHLKDMGQLVARVIEQAGGVAKEFNTIAVDDGIAMG 86 79******************************************************************* PP TIGR00110 71 heGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktkl 139 h+Gm+ysLpsr++iaDsve++v+ah++Dalv+is+CDki+PGm+maa+rlniP+i+v+GGpme+gkt l lcl|NCBI__GCF_000381085.1:WP_019555805.1 87 HDGMLYSLPSRDLIADSVEYMVNAHCADALVCISNCDKITPGMMMAAMRLNIPTIFVTGGPMESGKTVL 155 ********************************************************************* PP TIGR00110 140 sekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllat 208 + +++d+++a++++a++ +s++++e++e sacPt+gsCsG+ftansm+cl+ealG++lPg++t+lat lcl|NCBI__GCF_000381085.1:WP_019555805.1 156 GGIGIKLDLVDAMVMAADDSVSDSDVEDVEVSACPTCGSCSGMFTANSMNCLAEALGIALPGNGTTLAT 224 **99***************************************************************** PP TIGR00110 209 saekkelakksgkrivelvkknik.......PrdiltkeafenaitldlalGGstntvLhllaiakeag 270 ++++++l++++g+rive+ kk++ Pr+i+t eafena+tld+a+GGstntvLhllaiakea+ lcl|NCBI__GCF_000381085.1:WP_019555805.1 225 HSDRRHLFEEAGRRIVEIAKKHYDeddysvlPRSIATFEAFENAMTLDVAMGGSTNTVLHLLAIAKEAE 293 ***********************99******************************************** PP TIGR00110 271 vklslddfdrlsrkvPllaklkPsgkkv.iedlhraGGvsavlkeldkegllhkdaltvtGktlaetle 338 v++++ d+d++sr+vP+l+k++P++k++ +ed+hraGG++ +l+eld+ gl+++d+ tv ++++ l+ lcl|NCBI__GCF_000381085.1:WP_019555805.1 294 VNFTMADMDHISRRVPCLVKVAPNSKQFhMEDVHRAGGIMRILGELDRGGLIKRDVPTVHASSMGAALD 362 ****************************9**************************************** PP TIGR00110 339 kvkvlr...............................vdqd....virsldnpvkkegglavLkGnlae 372 +++r vd+d ++r ++++++kegglavL+Gn+a lcl|NCBI__GCF_000381085.1:WP_019555805.1 363 LWDIRRtdddaidtffraapgnvrtteafsqskrwktVDDDpingCVRDMEHAYTKEGGLAVLYGNIAL 431 ****99******************************977778888************************ PP TIGR00110 373 eGavvkiagveedilkfeGpakvfeseeealeailggkvkeGdvvviryeGPkGgPGmremLaPtsalv 441 +G++vk+agv+e+i kf+Gpa++fes++ a++ail+ +++eGdv++iryeGPkGgPGm+emL+Pts+l+ lcl|NCBI__GCF_000381085.1:WP_019555805.1 432 DGCIVKTAGVDESIFKFTGPARIFESQDSAVAAILANEISEGDVLIIRYEGPKGGPGMQEMLYPTSYLK 500 ********************************************************************* PP TIGR00110 442 glGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDienrkldlevseeelaerr 510 + GLgk++aL+tDGrfsGgt+GlsiGh sPeaaegG+i+l+++GD i+iDi+nr+++ + +e +aerr lcl|NCBI__GCF_000381085.1:WP_019555805.1 501 SKGLGKACALLTDGRFSGGTSGLSIGHASPEAAEGGNIGLINEGDAIEIDIPNRTIKALLTDEVFAERR 569 ********************************************************************* PP TIGR00110 511 akakkkea..........revkgaLakyaklvssadkGavld 542 +++++k+ r+++ aL++ya + +sa Gav+d lcl|NCBI__GCF_000381085.1:WP_019555805.1 570 QAMVSKGRnawkplevrpRKISAALRAYAAMTTSAAFGAVRD 611 ****9999999*******9*********************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (543 nodes) Target sequences: 1 (618 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: 7.60 // [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