Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate WP_011445434.1 SARO_RS08930 dihydroxy-acid dehydratase
Query= SwissProt::Q1MIB2 (612 letters) >NCBI__GCF_000013325.1:WP_011445434.1 Length = 615 Score = 1016 bits (2627), Expect = 0.0 Identities = 498/610 (81%), Positives = 553/610 (90%) Query: 1 MPVYRSRTTTHGRNMAGARGLWRATGMKDSDFGKPIIAVVNSFTQFVPGHVHLKDLGQLV 60 MP YRSRTTTHGRNMAGARGLWRATGMKDSDFGKPIIAVVNSFTQFVPGHVHLKDLGQ+V Sbjct: 1 MPAYRSRTTTHGRNMAGARGLWRATGMKDSDFGKPIIAVVNSFTQFVPGHVHLKDLGQMV 60 Query: 61 AREIEAAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSRELIADSVEYMVNAHCADAMVCIS 120 AREIEAAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSR+LIADSVEYMVNAHCADAMVCIS Sbjct: 61 AREIEAAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSRDLIADSVEYMVNAHCADAMVCIS 120 Query: 121 NCDKITPGMLMASLRLNIPTVFVSGGPMEAGKVVMHGKTHALDLVDAMVAAADDKISDED 180 NCDKITPGMLMA++R+NIP VFVSGGPMEAGKV++ GK HALDLVDAMVAAAD+ +DE+ Sbjct: 121 NCDKITPGMLMAAMRINIPVVFVSGGPMEAGKVILKGKEHALDLVDAMVAAADESFTDEE 180 Query: 181 VQTIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSTLATHLDRKRLFVEAGHLIV 240 V IERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSTLATH DR+RLF+EAG L+V Sbjct: 181 VTAIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSTLATHADRQRLFLEAGRLVV 240 Query: 241 DLARRYYEQDDVKALPRTIASKQAFENAMTLDIAMGGSTNTVLHILAAAHEGEIDFTMAD 300 DL +RYYEQDD LPR+IA+ +AFENAM+LDIAMGGSTNTVLH+LAAAHE ++FTM+D Sbjct: 241 DLCKRYYEQDDESVLPRSIATFEAFENAMSLDIAMGGSTNTVLHLLAAAHEAGVNFTMSD 300 Query: 301 IDALSRRVPCLSKVAPAKSDVHMEDVHRAGGIMSILGELDKGGLLNRDCPTVHAETLGDA 360 ID LSR+VPCLSKVAPAKSDVHMEDVHRAGGI +ILGELD+ GLL+ PTVH+ TLGDA Sbjct: 301 IDHLSRKVPCLSKVAPAKSDVHMEDVHRAGGIYAILGELDRAGLLHTHLPTVHSRTLGDA 360 Query: 361 IDRWDITRTNSETVRKFYRAAPGGIPTQVAFSQEARWDELDTDRENGVIRSVEHPFSKDG 420 +++WD+ RTNS TV++F+RAAPGG+PTQVAFSQ+ RW ELD DRE GVIRS EH FSKDG Sbjct: 361 LNQWDVKRTNSPTVQEFFRAAPGGVPTQVAFSQDRRWKELDLDRETGVIRSAEHAFSKDG 420 Query: 421 GLAVLKGNLAIDGCIVKTAGVDESILKFSGPARVFESQDASVKAILANEVKAGDVVVIRY 480 GLAVL GN+A +GCIVKTAGVD+SILKF+GPA+V+ESQDA+V AIL +V +GDVVVIRY Sbjct: 421 GLAVLFGNIAREGCIVKTAGVDDSILKFTGPAKVYESQDAAVTAILTGQVTSGDVVVIRY 480 Query: 481 EGPKGGPGMQEMLYPTSYLKSKGLGKACALITDGRFSGGTSGLSIGHASPEAANGGTIGL 540 EGPKGGPGMQEMLYPTSYLKSKGLG ACAL+TDGRFSGGTSGLSIGH SPEAA GG IGL Sbjct: 481 EGPKGGPGMQEMLYPTSYLKSKGLGAACALLTDGRFSGGTSGLSIGHVSPEAAEGGEIGL 540 Query: 541 VREGDMIDIDIPNRTISLRVSETELAARRAEQDAKGWYPTEVRKRNVTTALKAYAAFATS 600 V GD+I+IDIPNRTI L V++ LA RRAEQ+AKGW P + R R V+TAL+AYAA TS Sbjct: 541 VENGDVIEIDIPNRTIHLAVADDVLAQRRAEQEAKGWKPVKERPRKVSTALRAYAAMTTS 600 Query: 601 ADRGAVRDLN 610 A RGAVRDL+ Sbjct: 601 AARGAVRDLS 610 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: 1286 Number of extensions: 29 Number of successful extensions: 1 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: 615 Length adjustment: 37 Effective length of query: 575 Effective length of database: 578 Effective search space: 332350 Effective search space used: 332350 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_011445434.1 SARO_RS08930 (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.3509001.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-257 841.5 2.2 1.6e-257 841.3 2.2 1.0 1 NCBI__GCF_000013325.1:WP_011445434.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000013325.1:WP_011445434.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 841.3 2.2 1.6e-257 1.6e-257 2 542 .. 18 608 .. 17 609 .. 0.99 Alignments for each domain: == domain 1 score: 841.3 bits; conditional E-value: 1.6e-257 TIGR00110 2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamgheGm 74 ar l++atG+kd d++kPiiavvns+t++vPghvhlkdl+++v++eieaaGgvakefntiav+DGiamgh+Gm NCBI__GCF_000013325.1:WP_011445434.1 18 ARGLWRATGMKDSDFGKPIIAVVNSFTQFVPGHVHLKDLGQMVAREIEAAGGVAKEFNTIAVDDGIAMGHDGM 90 689********************************************************************** PP TIGR00110 75 kysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktklsekidlvd 147 +ysLpsr++iaDsve++v+ah++Da+v+is+CDki+PGmlmaa+r+niP+++vsGGpmeagk+ l k + +d NCBI__GCF_000013325.1:WP_011445434.1 91 LYSLPSRDLIADSVEYMVNAHCADAMVCISNCDKITPGMLMAAMRINIPVVFVSGGPMEAGKVILKGKEHALD 163 *****************************************************************99****** PP TIGR00110 148 vfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllatsaekkelakksg 220 +++a++++a++ +++ee+++iersacPt+gsCsG+ftansm+cltealGlslPg++++lat+a++++l+ ++g NCBI__GCF_000013325.1:WP_011445434.1 164 LVDAMVAAADESFTDEEVTAIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSTLATHADRQRLFLEAG 236 ************************************************************************* PP TIGR00110 221 krivelvkknik.......PrdiltkeafenaitldlalGGstntvLhllaiakeagvklslddfdrlsrkvP 286 + +v+l+k++++ Pr+i+t eafena++ld+a+GGstntvLhlla+a+eagv+++++d+d+lsrkvP NCBI__GCF_000013325.1:WP_011445434.1 237 RLVVDLCKRYYEqddesvlPRSIATFEAFENAMSLDIAMGGSTNTVLHLLAAAHEAGVNFTMSDIDHLSRKVP 309 ************************************************************************* PP TIGR00110 287 llaklkPsgkkv.iedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlr.............. 344 +l+k++P+ + v +ed+hraGG+ a+l+eld++gllh++ tv +tl++ l++ +v+r NCBI__GCF_000013325.1:WP_011445434.1 310 CLSKVAPAKSDVhMEDVHRAGGIYAILGELDRAGLLHTHLPTVHSRTLGDALNQWDVKRtnsptvqeffraap 382 ********88888************************************************************ PP TIGR00110 345 .....................vdqd..virsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpak 394 + virs +++++k+gglavL+Gn+a eG++vk+agv+++ilkf+Gpak NCBI__GCF_000013325.1:WP_011445434.1 383 ggvptqvafsqdrrwkeldldR--EtgVIRSAEHAFSKDGGLAVLFGNIAREGCIVKTAGVDDSILKFTGPAK 453 ***************9988544..355********************************************** PP TIGR00110 395 vfeseeealeailggkvkeGdvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiG 467 v+es+++a+ ail+g+v+ GdvvviryeGPkGgPGm+emL+Pts+l++ GLg ++aL+tDGrfsGgt+GlsiG NCBI__GCF_000013325.1:WP_011445434.1 454 VYESQDAAVTAILTGQVTSGDVVVIRYEGPKGGPGMQEMLYPTSYLKSKGLGAACALLTDGRFSGGTSGLSIG 526 ************************************************************************* PP TIGR00110 468 hvsPeaaegGaialvedGDkikiDienrkldlevseeelaerrakakkkea.......revkgaLakyaklvs 533 hvsPeaaegG i+lve+GD i+iDi+nr+++l+v ++ la+rra++++k++ r+v+ aL++ya + + NCBI__GCF_000013325.1:WP_011445434.1 527 HVSPEAAEGGEIGLVENGDVIEIDIPNRTIHLAVADDVLAQRRAEQEAKGWkpvkerpRKVSTALRAYAAMTT 599 **************************************************999***999************** PP TIGR00110 534 sadkGavld 542 sa +Gav+d NCBI__GCF_000013325.1:WP_011445434.1 600 SAARGAVRD 608 *******97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (543 nodes) Target sequences: 1 (615 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: 00:00:00.01 # Mc/sec: 29.51 // [ok]
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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