Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate WP_011384917.1 AMB_RS12770 dihydroxy-acid dehydratase
Query= SwissProt::Q1MIB2 (612 letters) >NCBI__GCF_000009985.1:WP_011384917.1 Length = 616 Score = 924 bits (2387), Expect = 0.0 Identities = 454/613 (74%), Positives = 516/613 (84%), Gaps = 4/613 (0%) Query: 1 MPVYRSRTTTHGRNMAGARGLWRATGMKDSDFGKPIIAVVNSFTQFVPGHVHLKDLGQLV 60 MP YRSRT+THGRNM+GARGLWRATGM D+DFGKPIIA+ NSFTQFVPGHVHLKDLGQ+V Sbjct: 1 MPAYRSRTSTHGRNMSGARGLWRATGMTDADFGKPIIAIANSFTQFVPGHVHLKDLGQMV 60 Query: 61 AREIEAAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSRELIADSVEYMVNAHCADAMVCIS 120 AREIE AGGVAKEF+TIA+DDGIAMGH GMLYSLPSRELIADSVEYMVNAHCADAMVCIS Sbjct: 61 AREIEKAGGVAKEFDTIAIDDGIAMGHAGMLYSLPSRELIADSVEYMVNAHCADAMVCIS 120 Query: 121 NCDKITPGMLMASLRLNIPTVFVSGGPMEAGKVVMHGKTHALDLVDAMVAAADDKISDED 180 NCDKITPGMLMASLRLNIPT+F+SGGPMEAGKV G+THA+DL+DAM+ AD +SDE+ Sbjct: 121 NCDKITPGMLMASLRLNIPTIFISGGPMEAGKVTYQGETHAVDLIDAMIKGADQNVSDEE 180 Query: 181 VQTIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSTLATHLDRKRLFVEAGHLIV 240 E+ +CPTCGSCSGMFTANSMNCL EALGL LPGNG+ +ATH DRK LF+EAG IV Sbjct: 181 ALAFEKESCPTCGSCSGMFTANSMNCLIEALGLGLPGNGTVVATHADRKELFLEAGRRIV 240 Query: 241 DLARRYYEQDDVKALPRTIASKQAFENAMTLDIAMGGSTNTVLHILAAAHEGEIDFTMAD 300 DLARR YE DD LPR+IA+ QAFENAMTLDIAMGGSTNTVLH+LAAA E + F M+D Sbjct: 241 DLARRAYEGDDASVLPRSIATFQAFENAMTLDIAMGGSTNTVLHLLAAAQEAGVAFGMSD 300 Query: 301 IDALSRRVPCLSKVAPAKSDVHMEDVHRAGGIMSILGELDKGGLLNRDCPTVHAETLGDA 360 ID LSRRVPCL KVAP DVH+EDVHRAGGIM ILG+LD+GGL+NR+C T+HA TL + Sbjct: 301 IDRLSRRVPCLCKVAPNVPDVHIEDVHRAGGIMGILGQLDRGGLINRECGTIHARTLAEG 360 Query: 361 IDRWDITRTNSETVRKFYRAAPGGIPTQVAFSQEARWDELDTDRENGVIRSVEHPFSKDG 420 +DRWDI+R+N V +FY+AAPGG+ T AFSQ RW E+D DR GVIRSV++ FSKDG Sbjct: 361 LDRWDISRSNDPKVVEFYKAAPGGVRTTEAFSQSKRWAEVDKDRTAGVIRSVDNAFSKDG 420 Query: 421 GLAVLKGNLAIDGCIVKTAGVDESILKFSGPARVFESQDASVKAILANEVKAGDVVVIRY 480 GLAVL GNLA+DGCIVKTAGVD+ L FSGPA + ESQD +V IL +VK+GDVV++RY Sbjct: 421 GLAVLFGNLALDGCIVKTAGVDDKNLTFSGPAVICESQDEAVAKILGGQVKSGDVVIVRY 480 Query: 481 EGPKGGPGMQEMLYPTSYLKSKGLGKACALITDGRFSGGTSGLSIGHASPEAANGGTIGL 540 EGP+GGPGMQEMLYPTSYLKS GLGK CALITDGRFSGGTSGLSIGH SPEAA GG IGL Sbjct: 481 EGPRGGPGMQEMLYPTSYLKSMGLGKECALITDGRFSGGTSGLSIGHVSPEAAEGGAIGL 540 Query: 541 VREGDMIDIDIPNRTISLRVSETELAARRAEQDA---KGWYPTEVRKRNVTTALKAYAAF 597 ++ GD+IDI IPNR+I++RVS+ EL RR A K W P + R R V+ AL+AYAA Sbjct: 541 IQAGDIIDIHIPNRSIAIRVSDAELEKRRQAMQALGPKAWKPVD-RDRQVSAALRAYAAM 599 Query: 598 ATSADRGAVRDLN 610 TSA RGAVRD++ Sbjct: 600 TTSAARGAVRDVS 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: 1250 Number of extensions: 40 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_011384917.1 AMB_RS12770 (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.15900.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.1e-249 814.5 4.9 2.5e-249 814.3 4.9 1.0 1 lcl|NCBI__GCF_000009985.1:WP_011384917.1 AMB_RS12770 dihydroxy-acid dehyd Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000009985.1:WP_011384917.1 AMB_RS12770 dihydroxy-acid dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 814.3 4.9 2.5e-249 2.5e-249 2 542 .. 18 610 .. 17 611 .. 0.99 Alignments for each domain: == domain 1 score: 814.3 bits; conditional E-value: 2.5e-249 TIGR00110 2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamg 70 ar l++atG++d+d++kPiia++ns+t++vPghvhlkdl+++v++eie+aGgvakef+tia++DGiamg lcl|NCBI__GCF_000009985.1:WP_011384917.1 18 ARGLWRATGMTDADFGKPIIAIANSFTQFVPGHVHLKDLGQMVAREIEKAGGVAKEFDTIAIDDGIAMG 86 689****************************************************************** PP TIGR00110 71 heGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktkl 139 h Gm+ysLpsre+iaDsve++v+ah++Da+v+is+CDki+PGmlma+lrlniP+i++sGGpmeagk+++ lcl|NCBI__GCF_000009985.1:WP_011384917.1 87 HAGMLYSLPSRELIADSVEYMVNAHCADAMVCISNCDKITPGMLMASLRLNIPTIFISGGPMEAGKVTY 155 ********************************************************************* PP TIGR00110 140 sekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllat 208 + + vd+++a+++ a++++s+ee ++e+ +cPt+gsCsG+ftansm+cl ealGl lPg++t+ at lcl|NCBI__GCF_000009985.1:WP_011384917.1 156 QGETHAVDLIDAMIKGADQNVSDEEALAFEKESCPTCGSCSGMFTANSMNCLIEALGLGLPGNGTVVAT 224 ********************************************************************* PP TIGR00110 209 saekkelakksgkrivelvkknik.......PrdiltkeafenaitldlalGGstntvLhllaiakeag 270 +a++kel+ ++g+riv+l ++ ++ Pr+i+t +afena+tld+a+GGstntvLhlla+a+eag lcl|NCBI__GCF_000009985.1:WP_011384917.1 225 HADRKELFLEAGRRIVDLARRAYEgddasvlPRSIATFQAFENAMTLDIAMGGSTNTVLHLLAAAQEAG 293 ********************************************************************* PP TIGR00110 271 vklslddfdrlsrkvPllaklkPsgkkv.iedlhraGGvsavlkeldkegllhkdaltvtGktlaetle 338 v + ++d+drlsr+vP+l+k++P+ v ied+hraGG++++l++ld+ gl+++++ t+ +tlae l+ lcl|NCBI__GCF_000009985.1:WP_011384917.1 294 VAFGMSDIDRLSRRVPCLCKVAPNVPDVhIEDVHRAGGIMGILGQLDRGGLINRECGTIHARTLAEGLD 362 ************************98888**************************************** PP TIGR00110 339 kvkvlr...............................vdqd....virsldnpvkkegglavLkGnlae 372 + ++ r vd+d virs+dn+++k+gglavL+Gnla lcl|NCBI__GCF_000009985.1:WP_011384917.1 363 RWDISRsndpkvvefykaapggvrtteafsqskrwaeVDKDrtagVIRSVDNAFSKDGGLAVLFGNLAL 431 *****99****************************9966666688************************ PP TIGR00110 373 eGavvkiagveedilkfeGpakvfeseeealeailggkvkeGdvvviryeGPkGgPGmremLaPtsalv 441 +G++vk+agv+++ l+f Gpa + es++ea++ ilgg+vk Gdvv++ryeGP+GgPGm+emL+Pts+l+ lcl|NCBI__GCF_000009985.1:WP_011384917.1 432 DGCIVKTAGVDDKNLTFSGPAVICESQDEAVAKILGGQVKSGDVVIVRYEGPRGGPGMQEMLYPTSYLK 500 ********************************************************************* PP TIGR00110 442 glGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDienrkldlevseeelaerr 510 ++GLgk++aLitDGrfsGgt+GlsiGhvsPeaaegGai+l++ GD+i i i+nr + ++vs++el++rr lcl|NCBI__GCF_000009985.1:WP_011384917.1 501 SMGLGKECALITDGRFSGGTSGLSIGHVSPEAAEGGAIGLIQAGDIIDIHIPNRSIAIRVSDAELEKRR 569 ********************************************************************* PP TIGR00110 511 akakkkea.........revkgaLakyaklvssadkGavld 542 +++++ ++ r+v+ aL++ya + +sa +Gav+d lcl|NCBI__GCF_000009985.1:WP_011384917.1 570 QAMQALGPkawkpvdrdRQVSAALRAYAAMTTSAARGAVRD 610 **99988888999**************************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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.04 # Mc/sec: 7.87 // [ok]
This GapMind analysis is from Apr 09 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