Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate WP_092345630.1 BLU87_RS05690 dihydroxy-acid dehydratase
Query= SwissProt::Q1MIB2 (612 letters) >NCBI__GCF_900107645.1:WP_092345630.1 Length = 618 Score = 875 bits (2262), Expect = 0.0 Identities = 436/612 (71%), Positives = 507/612 (82%), Gaps = 4/612 (0%) Query: 1 MPVYRSRTTTHGRNMAGARGLWRATGMKDSDFGKPIIAVVNSFTQFVPGHVHLKDLGQLV 60 MP+YRS + G+NMAGAR LW ATG+K DFGKPIIAVVNSFTQFVPGHVHLKDLGQLV Sbjct: 1 MPIYRSAQSVQGKNMAGARALWLATGVKPKDFGKPIIAVVNSFTQFVPGHVHLKDLGQLV 60 Query: 61 AREIEAAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSRELIADSVEYMVNAHCADAMVCIS 120 +IEA GG+AKEFNT+A+ DGIAMGH GMLYSLPSRELIAD+VEYM NAHC DA+VCIS Sbjct: 61 VSQIEAHGGIAKEFNTMAICDGIAMGHQGMLYSLPSRELIADTVEYMANAHCVDALVCIS 120 Query: 121 NCDKITPGMLMASLRLNIPTVFVSGGPMEAGKVVMHGKTHALDLVDAMVAAADDKISDED 180 NCDKITPGMLMAS+RLNIPT+FVSGGPMEAG+ + GK ALDLVDAMVAAA+ ++SDED Sbjct: 121 NCDKITPGMLMASMRLNIPTIFVSGGPMEAGRATLQGKKLALDLVDAMVAAANPEVSDED 180 Query: 181 VQTIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSTLATHLDRKRLFVEAGHLIV 240 V ERS+CPTCGSCSGMFTANSMNCLTEALG+ LPGNGS +ATH DRK LF+EA I+ Sbjct: 181 VAVYERSSCPTCGSCSGMFTANSMNCLTEALGMGLPGNGSLVATHADRKGLFLEAAKRIM 240 Query: 241 DLARRYYEQDDVKALPRTIASKQAFENAMTLDIAMGGSTNTVLHILAAAHEGEIDFTMAD 300 DL +R+YE DD + LPR+IA + A+ENAM LDIAMGGSTNT+LH+LA A EGE+DFTMAD Sbjct: 241 DLTKRWYEDDDQRVLPRSIACRGAYENAMRLDIAMGGSTNTILHLLAIAREGEVDFTMAD 300 Query: 301 IDALSRRVPCLSKVAPAKSDVHMEDVHRAGGIMSILGELDKGGLLNRDCPTVHAETLGDA 360 I+ LS + P L KVAPA HMEDVHRAGGI +ILGELD+ GL+ R+ PTVH+ TLG+A Sbjct: 301 INRLSLQTPNLCKVAPAVQHYHMEDVHRAGGIFAILGELDRAGLIQRNVPTVHSPTLGEA 360 Query: 361 IDRWDITRTNSETVRKFYRAAPGGIPTQVAFSQEARWDELDTDRENGVIRSVEHPFSKDG 420 +D WD+ RT++ V +FYRAAPGG+ AF+Q R LD DRE G IR +H +S+DG Sbjct: 361 LDCWDVLRTDAPDVHEFYRAAPGGVRCVEAFAQNNRSTSLDLDREKGCIRDQKHAYSQDG 420 Query: 421 GLAVLKGNLAIDGCIVKTAGVDESILKFSGPARVFESQDASVKAILANEVKAGDVVVIRY 480 GLAVL GNLA+DGCIVKTAGVDES L FSGPAR+FESQ+ +++ IL + V+ GDVVVIRY Sbjct: 421 GLAVLYGNLALDGCIVKTAGVDESNLTFSGPARIFESQEDAIEGILGDVVQPGDVVVIRY 480 Query: 481 EGPKGGPGMQEMLYPTSYLKSKGLGKACALITDGRFSGGTSGLSIGHASPEAANGGTIGL 540 EGPKGGPGMQEMLYPTSYLKSKGLGKACALITDGRFSGGTSGLSIGH SPEAA GG+I L Sbjct: 481 EGPKGGPGMQEMLYPTSYLKSKGLGKACALITDGRFSGGTSGLSIGHISPEAAEGGSIAL 540 Query: 541 VREGDMIDIDIPNRTISLRVSETELAARRAEQDAKG---WYPTEVRKRNVTTALKAYAAF 597 +++GD +DIDIP R IS++VSE L R+ E ++G W PT +R+R V+ AL+AYAA Sbjct: 541 LQDGDRVDIDIPARKISMQVSEEVLQQRQTEMLSRGDQAWQPT-LRQRVVSRALQAYAAT 599 Query: 598 ATSADRGAVRDL 609 TSA RGAVRDL Sbjct: 600 TTSAARGAVRDL 611 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: 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_092345630.1 BLU87_RS05690 (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.16750.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-242 792.1 0.5 1.5e-242 791.9 0.5 1.0 1 lcl|NCBI__GCF_900107645.1:WP_092345630.1 BLU87_RS05690 dihydroxy-acid deh Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900107645.1:WP_092345630.1 BLU87_RS05690 dihydroxy-acid dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 791.9 0.5 1.5e-242 1.5e-242 2 542 .. 18 610 .. 17 611 .. 0.99 Alignments for each domain: == domain 1 score: 791.9 bits; conditional E-value: 1.5e-242 TIGR00110 2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamg 70 aral+ atG+k +d++kPiiavvns+t++vPghvhlkdl++lv +iea Gg+akefnt+a++DGiamg lcl|NCBI__GCF_900107645.1:WP_092345630.1 18 ARALWLATGVKPKDFGKPIIAVVNSFTQFVPGHVHLKDLGQLVVSQIEAHGGIAKEFNTMAICDGIAMG 86 79******************************************************************* PP TIGR00110 71 heGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktkl 139 h+Gm+ysLpsre+iaD+ve++++ah++Dalv+is+CDki+PGmlma++rlniP+i+vsGGpmeag+ +l lcl|NCBI__GCF_900107645.1:WP_092345630.1 87 HQGMLYSLPSRELIADTVEYMANAHCVDALVCISNCDKITPGMLMASMRLNIPTIFVSGGPMEAGRATL 155 ********************************************************************9 PP TIGR00110 140 sekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllat 208 k +d+++a++++a++++s+e++ +ers+cPt+gsCsG+ftansm+cltealG+ lPg+++l at lcl|NCBI__GCF_900107645.1:WP_092345630.1 156 QGKKLALDLVDAMVAAANPEVSDEDVAVYERSSCPTCGSCSGMFTANSMNCLTEALGMGLPGNGSLVAT 224 8888899************************************************************** PP TIGR00110 209 saekkelakksgkrivelvkknik.......PrdiltkeafenaitldlalGGstntvLhllaiakeag 270 +a++k l+ +++kri++l+k+ ++ Pr+i+ + a+ena+ ld+a+GGstnt+Lhllaia+e + lcl|NCBI__GCF_900107645.1:WP_092345630.1 225 HADRKGLFLEAAKRIMDLTKRWYEdddqrvlPRSIACRGAYENAMRLDIAMGGSTNTILHLLAIAREGE 293 ***********************99******************************************** PP TIGR00110 271 vklslddfdrlsrkvPllaklkPsgkkv.iedlhraGGvsavlkeldkegllhkdaltvtGktlaetle 338 v++++ d++rls ++P l+k++P+ +++ +ed+hraGG+ a+l+eld++gl+++++ tv tl+e l+ lcl|NCBI__GCF_900107645.1:WP_092345630.1 294 VDFTMADINRLSLQTPNLCKVAPAVQHYhMEDVHRAGGIFAILGELDRAGLIQRNVPTVHSPTLGEALD 362 ***************************99**************************************** PP TIGR00110 339 kvkvlr...................................vdqdvirsldnpvkkegglavLkGnlae 372 +vlr ++ +ir +++++++gglavL+Gnla lcl|NCBI__GCF_900107645.1:WP_092345630.1 363 CWDVLRtdapdvhefyraapggvrcveafaqnnrstsldldREKGCIRDQKHAYSQDGGLAVLYGNLAL 431 *****9*******************************99655566************************ PP TIGR00110 373 eGavvkiagveedilkfeGpakvfeseeealeailggkvkeGdvvviryeGPkGgPGmremLaPtsalv 441 +G++vk+agv+e+ l+f Gpa++fes+e+a+e+ilg v+ GdvvviryeGPkGgPGm+emL+Pts+l+ lcl|NCBI__GCF_900107645.1:WP_092345630.1 432 DGCIVKTAGVDESNLTFSGPARIFESQEDAIEGILGDVVQPGDVVVIRYEGPKGGPGMQEMLYPTSYLK 500 ********************************************************************* PP TIGR00110 442 glGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDienrkldlevseeelaerr 510 + GLgk++aLitDGrfsGgt+GlsiGh+sPeaaegG+ial++dGD++ iDi++rk+ ++vsee l++r+ lcl|NCBI__GCF_900107645.1:WP_092345630.1 501 SKGLGKACALITDGRFSGGTSGLSIGHISPEAAEGGSIALLQDGDRVDIDIPARKISMQVSEEVLQQRQ 569 ********************************************************************* PP TIGR00110 511 akakkkea.........revkgaLakyaklvssadkGavld 542 ++ ++++ r v+ aL++ya +sa +Gav+d lcl|NCBI__GCF_900107645.1:WP_092345630.1 570 TEMLSRGDqawqptlrqRVVSRALQAYAATTTSAARGAVRD 610 *9999988899999*9999********************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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 11.68 // [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