Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate GFF2902 PGA1_c29490 dihydroxy-acid dehydratase LivD
Query= SwissProt::Q1MIB2 (612 letters) >FitnessBrowser__Phaeo:GFF2902 Length = 614 Score = 926 bits (2394), Expect = 0.0 Identities = 461/610 (75%), Positives = 522/610 (85%), Gaps = 1/610 (0%) Query: 1 MPVYRSRTTTHGRNMAGARGLWRATGMKDSDFGKPIIAVVNSFTQFVPGHVHLKDLGQLV 60 MP+YRSRT+THGRNMAGARGLWRATGM D DFGKPIIA+VNSFTQFVPGHVHLKDLGQ+V Sbjct: 1 MPMYRSRTSTHGRNMAGARGLWRATGMTDDDFGKPIIAIVNSFTQFVPGHVHLKDLGQMV 60 Query: 61 AREIEAAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSRELIADSVEYMVNAHCADAMVCIS 120 ARE+EAAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSRE+IADSVEYMVNAHCADAMVCIS Sbjct: 61 AREVEAAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSREVIADSVEYMVNAHCADAMVCIS 120 Query: 121 NCDKITPGMLMASLRLNIPTVFVSGGPMEAGKV-VMHGKTHALDLVDAMVAAADDKISDE 179 NCDKITPGMLMA++RLNIP +FVSGGPMEAGK+ + +DLVDAMVAAA D ++DE Sbjct: 121 NCDKITPGMLMAAMRLNIPAIFVSGGPMEAGKIDIADLDMKKIDLVDAMVAAASDTMTDE 180 Query: 180 DVQTIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSTLATHLDRKRLFVEAGHLI 239 VQ IE +ACPTCGSCSGMFTANSMNCL EALGL+LPGNGSTLATH DRK LF+EAG I Sbjct: 181 QVQHIEENACPTCGSCSGMFTANSMNCLAEALGLALPGNGSTLATHADRKHLFLEAGRKI 240 Query: 240 VDLARRYYEQDDVKALPRTIASKQAFENAMTLDIAMGGSTNTVLHILAAAHEGEIDFTMA 299 VD+ +R+Y ++ LPR IA+ AFENAM+LDIAMGGSTNTVLH+LA A+EG++DFTM Sbjct: 241 VDITKRHYVGEEKGLLPREIATFDAFENAMSLDIAMGGSTNTVLHLLAIANEGKVDFTMT 300 Query: 300 DIDALSRRVPCLSKVAPAKSDVHMEDVHRAGGIMSILGELDKGGLLNRDCPTVHAETLGD 359 D+D LSR+VPCL KVAP +VHMEDVHRAGGI SILGEL + GLL+ +C TVH+ T+G+ Sbjct: 301 DMDRLSRKVPCLCKVAPNIENVHMEDVHRAGGIFSILGELSRAGLLHNECSTVHSSTMGE 360 Query: 360 AIDRWDITRTNSETVRKFYRAAPGGIPTQVAFSQEARWDELDTDRENGVIRSVEHPFSKD 419 AI +WDI N+ ++AAPGG+ T AFSQ R+ ELDTDRE GVIRS +H FS+D Sbjct: 361 AIAKWDIKVANNPDAEALFKAAPGGVRTTEAFSQSNRYKELDTDREGGVIRSKDHAFSQD 420 Query: 420 GGLAVLKGNLAIDGCIVKTAGVDESILKFSGPARVFESQDASVKAILANEVKAGDVVVIR 479 GGLAVL GN+A DGCIVKTAGVD++ILKF+G A V ESQD +V IL ++VK GDVVVIR Sbjct: 421 GGLAVLFGNIARDGCIVKTAGVDDNILKFTGSAYVCESQDQAVNDILTSKVKEGDVVVIR 480 Query: 480 YEGPKGGPGMQEMLYPTSYLKSKGLGKACALITDGRFSGGTSGLSIGHASPEAANGGTIG 539 YEGP+GGPGMQEMLYPTSYLKSKGLGKACAL+TDGRFSGGTSGLSIGH SPEAA GGTIG Sbjct: 481 YEGPRGGPGMQEMLYPTSYLKSKGLGKACALLTDGRFSGGTSGLSIGHVSPEAAEGGTIG 540 Query: 540 LVREGDMIDIDIPNRTISLRVSETELAARRAEQDAKGWYPTEVRKRNVTTALKAYAAFAT 599 LV++GD I+IDIPNRTI L VS+ ELAARRA QDA GW P + RKR V+TALKAYA AT Sbjct: 541 LVQQGDTIEIDIPNRTIHLAVSDEELAARRAAQDAAGWKPVKPRKRKVSTALKAYALLAT 600 Query: 600 SADRGAVRDL 609 SA +GAVR L Sbjct: 601 SAAKGAVRAL 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: 1211 Number of extensions: 29 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: 614 Length adjustment: 37 Effective length of query: 575 Effective length of database: 577 Effective search space: 331775 Effective search space used: 331775 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 GFF2902 PGA1_c29490 (dihydroxy-acid dehydratase LivD)
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.24834.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.2e-257 839.6 7.8 6e-257 839.4 7.8 1.0 1 lcl|FitnessBrowser__Phaeo:GFF2902 PGA1_c29490 dihydroxy-acid dehyd Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Phaeo:GFF2902 PGA1_c29490 dihydroxy-acid dehydratase LivD # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 839.4 7.8 6e-257 6e-257 2 541 .. 18 608 .. 17 610 .. 0.98 Alignments for each domain: == domain 1 score: 839.4 bits; conditional E-value: 6e-257 TIGR00110 2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamgheGmkys 77 ar l++atG++d+d++kPiia+vns+t++vPghvhlkdl+++v++e+eaaGgvakefntiav+DGiamgh+Gm+ys lcl|FitnessBrowser__Phaeo:GFF2902 18 ARGLWRATGMTDDDFGKPIIAIVNSFTQFVPGHVHLKDLGQMVAREVEAAGGVAKEFNTIAVDDGIAMGHDGMLYS 93 689************************************************************************* PP TIGR00110 78 LpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktklse.kidlvdvfeav 152 Lpsre+iaDsve++v+ah++Da+v+is+CDki+PGmlmaa+rlniPai+vsGGpmeagk+ +++ +++++d+++a+ lcl|FitnessBrowser__Phaeo:GFF2902 94 LPSREVIADSVEYMVNAHCADAMVCISNCDKITPGMLMAAMRLNIPAIFVSGGPMEAGKIDIADlDMKKIDLVDAM 169 *************************************************************97658999******* PP TIGR00110 153 geyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllatsaekkelakksgkrivelvk 228 +++a++ +++e++++ie++acPt+gsCsG+ftansm+cl+ealGl+lPg++++lat+a++k+l+ ++g++iv+++k lcl|FitnessBrowser__Phaeo:GFF2902 170 VAAASDTMTDEQVQHIEENACPTCGSCSGMFTANSMNCLAEALGLALPGNGSTLATHADRKHLFLEAGRKIVDITK 245 **************************************************************************** PP TIGR00110 229 knik.......PrdiltkeafenaitldlalGGstntvLhllaiakeagvklslddfdrlsrkvPllaklkPsgkk 297 +++ Pr+i+t +afena++ld+a+GGstntvLhllaia+e +v++++ d+drlsrkvP+l+k++P+ ++ lcl|FitnessBrowser__Phaeo:GFF2902 246 RHYVgeekgllPREIATFDAFENAMSLDIAMGGSTNTVLHLLAIANEGKVDFTMTDMDRLSRKVPCLCKVAPNIEN 321 **999999******************************************************************99 PP TIGR00110 298 v.iedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlr............................ 344 v +ed+hraGG+ ++l+el+++gllh+++ tv +t++e ++k +++ lcl|FitnessBrowser__Phaeo:GFF2902 322 VhMEDVHRAGGIFSILGELSRAGLLHNECSTVHSSTMGEAIAKWDIKVannpdaealfkaapggvrtteafsqsnr 397 99*******************************************99999************************** PP TIGR00110 345 .....vdqd..virsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvke 413 +d++ virs+d++++++gglavL+Gn+a +G++vk+agv+++ilkf+G+a v es+++a++ il+ kvke lcl|FitnessBrowser__Phaeo:GFF2902 398 ykeldTDREggVIRSKDHAFSQDGGLAVLFGNIARDGCIVKTAGVDDNILKFTGSAYVCESQDQAVNDILTSKVKE 473 *9966444477***************************************************************** PP TIGR00110 414 GdvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkik 489 GdvvviryeGP+GgPGm+emL+Pts+l++ GLgk++aL+tDGrfsGgt+GlsiGhvsPeaaegG+i+lv++GD+i+ lcl|FitnessBrowser__Phaeo:GFF2902 474 GDVVVIRYEGPRGGPGMQEMLYPTSYLKSKGLGKACALLTDGRFSGGTSGLSIGHVSPEAAEGGTIGLVQQGDTIE 549 **************************************************************************** PP TIGR00110 490 iDienrkldlevseeelaerrakakkkea.......revkgaLakyaklvssadkGavl 541 iDi+nr+++l+vs+eela+rra++++ ++ r+v+ aL++ya l++sa kGav+ lcl|FitnessBrowser__Phaeo:GFF2902 550 IDIPNRTIHLAVSDEELAARRAAQDAAGWkpvkprkRKVSTALKAYALLATSAAKGAVR 608 *************************9999999999999*******************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (543 nodes) Target sequences: 1 (614 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: 00:00:00.03 # Mc/sec: 10.38 // [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