Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate WP_028488534.1 Q394_RS0106325 dihydroxy-acid dehydratase
Query= SwissProt::Q1MIB2 (612 letters) >NCBI__GCF_000621325.1:WP_028488534.1 Length = 616 Score = 935 bits (2416), Expect = 0.0 Identities = 462/612 (75%), Positives = 529/612 (86%), Gaps = 4/612 (0%) Query: 1 MPVYRSRTTTHGRNMAGARGLWRATGMKDSDFGKPIIAVVNSFTQFVPGHVHLKDLGQLV 60 MPVYRSRT+T GRNMAGAR LWRATGM D+DF KPIIA+ NSFTQFVPGHVHLKD+GQLV Sbjct: 1 MPVYRSRTSTGGRNMAGARALWRATGMTDADFQKPIIAIANSFTQFVPGHVHLKDMGQLV 60 Query: 61 AREIEAAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSRELIADSVEYMVNAHCADAMVCIS 120 AREIEAAGGVAKEFNTIAVDDGIAMGH GMLYSLPSRELIAD+VEYMVNAHCADA+VCIS Sbjct: 61 AREIEAAGGVAKEFNTIAVDDGIAMGHGGMLYSLPSRELIADAVEYMVNAHCADALVCIS 120 Query: 121 NCDKITPGMLMASLRLNIPTVFVSGGPMEAGKVVMHGKTHALDLVDAMVAAADDKISDED 180 NCDKITPGML A++RLNIPT+FVSGGPME+GK V+ GK LDLVDAMV+AA+ SDE+ Sbjct: 121 NCDKITPGMLNAAMRLNIPTIFVSGGPMESGKAVIGGKLVKLDLVDAMVSAANSAESDEN 180 Query: 181 VQTIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSTLATHLDRKRLFVEAGHLIV 240 V+T+ERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSTLATH DRKRLF+EAG +IV Sbjct: 181 VETMERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSTLATHSDRKRLFLEAGRIIV 240 Query: 241 DLARRYYEQDDVKALPRTIASKQAFENAMTLDIAMGGSTNTVLHILAAAHEGEIDFTMAD 300 LA+RYYEQDD LPR+IA+ +AFENAM LDIAMGGSTNT+LH+LAAA EGE++FT+ D Sbjct: 241 GLAKRYYEQDDETVLPRSIATFEAFENAMCLDIAMGGSTNTILHLLAAAEEGEVNFTLND 300 Query: 301 IDALSRRVPCLSKVAPAKSDVHMEDVHRAGGIMSILGELDKGGLLNRDCPTVHAETLGDA 360 ID LSR+VP L KVAP+ HMEDVHRAGG+ +ILGELD+ GLL+R+ TVHA + +A Sbjct: 301 IDRLSRKVPQLCKVAPSTPLYHMEDVHRAGGVFAILGELDRAGLLHREAGTVHATNMAEA 360 Query: 361 IDRWDITRTNSETVRKFYRAAPGGIPTQVAFSQEARWDELDTDRENGVIRSVEHPFSKDG 420 + WD+ T+ +F+RA PGG+PTQVAFSQ RWD LDTDR NG IR H +S +G Sbjct: 361 LSLWDVRLTDDAKRHEFFRAGPGGVPTQVAFSQSKRWDTLDTDRANGCIRDKAHAYSTEG 420 Query: 421 GLAVLKGNLAIDGCIVKTAGVDESILKFSGPARVFESQDASVKAILANEVKAGDVVVIRY 480 GLAVL GN+A++GC+VKTAGVD+SILKFSGPAR+FESQDA+V ILA+ + AGD+V+IRY Sbjct: 421 GLAVLFGNIALEGCVVKTAGVDDSILKFSGPARIFESQDAAVAGILADNIVAGDIVLIRY 480 Query: 481 EGPKGGPGMQEMLYPTSYLKSKGLGKACALITDGRFSGGTSGLSIGHASPEAANGGTIGL 540 EGP+GGPGMQEMLYPTSY+KSKGLGKACALITDGRFSGGTSGLSIGH SPEAA GG IGL Sbjct: 481 EGPRGGPGMQEMLYPTSYIKSKGLGKACALITDGRFSGGTSGLSIGHVSPEAAEGGAIGL 540 Query: 541 VREGDMIDIDIPNRTISLRVSETELAARRAEQDAK---GWYPTEVRKRNVTTALKAYAAF 597 V+EGDMIDIDIPNRTI++R+S+ ELA+RR+ DA+ GW P R R V+ ALKAYAA Sbjct: 541 VQEGDMIDIDIPNRTINVRISDAELASRRSAMDAQGKAGWKPVN-RDRVVSAALKAYAAM 599 Query: 598 ATSADRGAVRDL 609 TSA RGAVRD+ Sbjct: 600 TTSASRGAVRDV 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: 1262 Number of extensions: 36 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: 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_028488534.1 Q394_RS0106325 (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.20009.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.1e-250 816.1 3.7 8.2e-250 815.8 3.7 1.0 1 lcl|NCBI__GCF_000621325.1:WP_028488534.1 Q394_RS0106325 dihydroxy-acid de Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000621325.1:WP_028488534.1 Q394_RS0106325 dihydroxy-acid dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 815.8 3.7 8.2e-250 8.2e-250 2 542 .. 18 610 .. 17 611 .. 0.99 Alignments for each domain: == domain 1 score: 815.8 bits; conditional E-value: 8.2e-250 TIGR00110 2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamg 70 aral++atG++d+d++kPiia++ns+t++vPghvhlkd+++lv++eieaaGgvakefntiav+DGiamg lcl|NCBI__GCF_000621325.1:WP_028488534.1 18 ARALWRATGMTDADFQKPIIAIANSFTQFVPGHVHLKDMGQLVAREIEAAGGVAKEFNTIAVDDGIAMG 86 79******************************************************************* PP TIGR00110 71 heGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktkl 139 h+Gm+ysLpsre+iaD+ve++v+ah++Dalv+is+CDki+PGml aa+rlniP+i+vsGGpme+gk + lcl|NCBI__GCF_000621325.1:WP_028488534.1 87 HGGMLYSLPSRELIADAVEYMVNAHCADALVCISNCDKITPGMLNAAMRLNIPTIFVSGGPMESGKAVI 155 ********************************************************************* PP TIGR00110 140 sekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllat 208 + k+ ++d+++a++++a++ s+e++e++ersacPt+gsCsG+ftansm+cltealGlslPg++++lat lcl|NCBI__GCF_000621325.1:WP_028488534.1 156 GGKLVKLDLVDAMVSAANSAESDENVETMERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSTLAT 224 ********************************************************************* PP TIGR00110 209 saekkelakksgkrivelvkknik.......PrdiltkeafenaitldlalGGstntvLhllaiakeag 270 ++++k+l+ ++g+ iv l k++++ Pr+i+t eafena+ ld+a+GGstnt+Lhlla+a+e + lcl|NCBI__GCF_000621325.1:WP_028488534.1 225 HSDRKRLFLEAGRIIVGLAKRYYEqddetvlPRSIATFEAFENAMCLDIAMGGSTNTILHLLAAAEEGE 293 ********************************************************************* PP TIGR00110 271 vklslddfdrlsrkvPllaklkPsgkkv.iedlhraGGvsavlkeldkegllhkdaltvtGktlaetle 338 v+++l+d+drlsrkvP+l+k++Ps+ + +ed+hraGGv a+l+eld++gllh++a tv + +ae l+ lcl|NCBI__GCF_000621325.1:WP_028488534.1 294 VNFTLNDIDRLSRKVPQLCKVAPSTPLYhMEDVHRAGGVFAILGELDRAGLLHREAGTVHATNMAEALS 362 *************************9999**************************************** PP TIGR00110 339 kvkvlr...................................vdqdvirsldnpvkkegglavLkGnlae 372 +v+ + +ir + ++++ egglavL+Gn+a lcl|NCBI__GCF_000621325.1:WP_028488534.1 363 LWDVRLtddakrheffragpggvptqvafsqskrwdtldtdRANGCIRDKAHAYSTEGGLAVLFGNIAL 431 **999999*****************************66544445************************ PP TIGR00110 373 eGavvkiagveedilkfeGpakvfeseeealeailggkvkeGdvvviryeGPkGgPGmremLaPtsalv 441 eG+vvk+agv+++ilkf Gpa++fes+++a+++il+ ++ +Gd+v+iryeGP+GgPGm+emL+Pts+++ lcl|NCBI__GCF_000621325.1:WP_028488534.1 432 EGCVVKTAGVDDSILKFSGPARIFESQDAAVAGILADNIVAGDIVLIRYEGPRGGPGMQEMLYPTSYIK 500 ********************************************************************* PP TIGR00110 442 glGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDienrkldlevseeelaerr 510 + GLgk++aLitDGrfsGgt+GlsiGhvsPeaaegGai+lv++GD+i iDi+nr++++++s++ela+rr lcl|NCBI__GCF_000621325.1:WP_028488534.1 501 SKGLGKACALITDGRFSGGTSGLSIGHVSPEAAEGGAIGLVQEGDMIDIDIPNRTINVRISDAELASRR 569 ********************************************************************* PP TIGR00110 511 akakkkea.........revkgaLakyaklvssadkGavld 542 +++++++ r v+ aL++ya + +sa++Gav+d lcl|NCBI__GCF_000621325.1:WP_028488534.1 570 SAMDAQGKagwkpvnrdRVVSAALKAYAAMTTSASRGAVRD 610 ****9999999****************************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: 0.02u 0.02s 00:00:00.04 Elapsed: 00:00:00.04 # Mc/sec: 8.29 // [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