Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate Dsui_1122 Dsui_1122 dihydroxy-acid dehydratase
Query= SwissProt::Q1MIB2 (612 letters) >FitnessBrowser__PS:Dsui_1122 Length = 619 Score = 949 bits (2454), Expect = 0.0 Identities = 468/612 (76%), Positives = 529/612 (86%), Gaps = 3/612 (0%) Query: 1 MPVYRSRTTTHGRNMAGARGLWRATGMKDSDFGKPIIAVVNSFTQFVPGHVHLKDLGQLV 60 MP YRSRT+THGRNMAGAR LWRATGMKD DFGKPIIAVVNSFTQFVPGHVHLKDLGQLV Sbjct: 1 MPAYRSRTSTHGRNMAGARALWRATGMKDGDFGKPIIAVVNSFTQFVPGHVHLKDLGQLV 60 Query: 61 AREIEAAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSRELIADSVEYMVNAHCADAMVCIS 120 AREIEAAGG+AKEFNTIA+DDGIAMGHDGMLYSLPSR+LIADSVEYMVNAHCADAMVCIS Sbjct: 61 AREIEAAGGIAKEFNTIAIDDGIAMGHDGMLYSLPSRDLIADSVEYMVNAHCADAMVCIS 120 Query: 121 NCDKITPGMLMASLRLNIPTVFVSGGPMEAGKVVMHGKTHALDLVDAMVAAADDKISDED 180 NCDKITPGMLMA++R+NIPT+FVSGGPMEAGKV GKT A+DL+DAM+ A D SD + Sbjct: 121 NCDKITPGMLMAAMRVNIPTIFVSGGPMEAGKVKWEGKTIAVDLIDAMIKAGDSNCSDAE 180 Query: 181 VQTIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSTLATHLDRKRLFVEAGHLIV 240 V+ ERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNG+ +ATH DRK LF+EAG IV Sbjct: 181 VEEFERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGTLVATHADRKGLFLEAGRRIV 240 Query: 241 DLARRYYEQDDVKALPRTIASKQAFENAMTLDIAMGGSTNTVLHILAAAHEGEIDFTMAD 300 LA+R+YE++D LPR+IA+++AFENA LD+AMGGSTNTVLH+LA A E + FTMAD Sbjct: 241 RLAQRWYEENDASVLPRSIANQKAFENAFALDVAMGGSTNTVLHLLATAQEAGVTFTMAD 300 Query: 301 IDALSRRVPCLSKVAPAKSDVHMEDVHRAGGIMSILGELDKGGLLNRDCPTVHAETLGDA 360 IDA+SR+VPCL KVAPA D H+EDVHRAGGIM+ILGEL +GGL++RD PTVH TLG+A Sbjct: 301 IDAISRKVPCLCKVAPATQDYHIEDVHRAGGIMAILGELSRGGLIHRDTPTVHCHTLGEA 360 Query: 361 IDRWDITRTNSETVRKFYRAAPGGIPTQVAFSQEARWDELDTDRENGVIRSVEHPFSKDG 420 ID +D+ R S+ +F+RAAPGGIPTQ AFSQ+ R+ ELD DR NG IR+V H +SK+G Sbjct: 361 IDTYDVQRAGSQRTLEFFRAAPGGIPTQTAFSQDRRYTELDQDRSNGCIRNVAHAYSKEG 420 Query: 421 GLAVLKGNLAIDGCIVKTAGVDESILKFSGPARVFESQDASVKAILANEVKAGDVVVIRY 480 GLAVL GN+A+DGCIVKTAGVDESI KF+G A+V+ESQD++V AIL EV AGDVVVIRY Sbjct: 421 GLAVLHGNIALDGCIVKTAGVDESIWKFTGKAKVYESQDSAVTAILGGEVVAGDVVVIRY 480 Query: 481 EGPKGGPGMQEMLYPTSYLKSKGLGKACALITDGRFSGGTSGLSIGHASPEAANGGTIGL 540 EGPKGGPGMQEMLYPTSYLKS+GLGK CAL+TDGRFSGGTSGLSIGHASPEAA GG IGL Sbjct: 481 EGPKGGPGMQEMLYPTSYLKSRGLGKECALLTDGRFSGGTSGLSIGHASPEAAEGGAIGL 540 Query: 541 VREGDMIDIDIPNRTISLRVSETELAARRAEQDAKG---WYPTEVRKRNVTTALKAYAAF 597 VR GD I+IDIP R I L VS+ EL RRAE++AKG W PTE R R V+ AL+AYA Sbjct: 541 VRTGDTIEIDIPGRRIHLAVSDAELEKRRAEENAKGDKAWKPTEERGRVVSKALQAYALM 600 Query: 598 ATSADRGAVRDL 609 ATSAD+GAVRDL Sbjct: 601 ATSADKGAVRDL 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: 1329 Number of extensions: 38 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: 619 Length adjustment: 37 Effective length of query: 575 Effective length of database: 582 Effective search space: 334650 Effective search space used: 334650 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 Dsui_1122 Dsui_1122 (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.3228.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-258 844.2 3.2 2.5e-258 844.0 3.2 1.0 1 lcl|FitnessBrowser__PS:Dsui_1122 Dsui_1122 dihydroxy-acid dehydra Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__PS:Dsui_1122 Dsui_1122 dihydroxy-acid dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 844.0 3.2 2.5e-258 2.5e-258 2 542 .. 18 611 .. 17 612 .. 0.99 Alignments for each domain: == domain 1 score: 844.0 bits; conditional E-value: 2.5e-258 TIGR00110 2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamgheGmkysL 78 aral++atG+kd d++kPiiavvns+t++vPghvhlkdl++lv++eieaaGg+akefntia++DGiamgh+Gm+ysL lcl|FitnessBrowser__PS:Dsui_1122 18 ARALWRATGMKDGDFGKPIIAVVNSFTQFVPGHVHLKDLGQLVAREIEAAGGIAKEFNTIAIDDGIAMGHDGMLYSL 94 79*************************************************************************** PP TIGR00110 79 psreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktklsekidlvdvfeavgey 155 psr++iaDsve++v+ah++Da+v+is+CDki+PGmlmaa+r+niP+i+vsGGpmeagk+k k + vd+++a++++ lcl|FitnessBrowser__PS:Dsui_1122 95 PSRDLIADSVEYMVNAHCADAMVCISNCDKITPGMLMAAMRVNIPTIFVSGGPMEAGKVKWEGKTIAVDLIDAMIKA 171 ***************************************************************************** PP TIGR00110 156 aagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllatsaekkelakksgkrivelvkknik 232 +++ s++e+ee+ersacPt+gsCsG+ftansm+cltealGlslPg++tl at+a++k l+ ++g+riv l ++ ++ lcl|FitnessBrowser__PS:Dsui_1122 172 GDSNCSDAEVEEFERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGTLVATHADRKGLFLEAGRRIVRLAQRWYE 248 ****************************************************************************9 PP TIGR00110 233 .......PrdiltkeafenaitldlalGGstntvLhllaiakeagvklslddfdrlsrkvPllaklkPsgkkv.ied 301 Pr+i++++afena++ld+a+GGstntvLhlla a+eagv++++ d+d +srkvP+l+k++P+++ + ied lcl|FitnessBrowser__PS:Dsui_1122 249 endasvlPRSIANQKAFENAFALDVAMGGSTNTVLHLLATAQEAGVTFTMADIDAISRKVPCLCKVAPATQDYhIED 325 9**********************************************************************999*** PP TIGR00110 302 lhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlr...............................vdq 347 +hraGG++a+l+el++ gl+h+d+ tv +tl+e +++++v+r +dq lcl|FitnessBrowser__PS:Dsui_1122 326 VHRAGGIMAILGELSRGGLIHRDTPTVHCHTLGEAIDTYDVQRagsqrtleffraapggiptqtafsqdrryteLDQ 402 *************************************************************************9455 PP TIGR00110 348 d....virsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeGdvvvir 420 d +ir++ ++++kegglavL+Gn+a +G++vk+agv+e+i+kf+G+akv+es++ a+ ailgg+v +Gdvvvir lcl|FitnessBrowser__PS:Dsui_1122 403 DrsngCIRNVAHAYSKEGGLAVLHGNIALDGCIVKTAGVDESIWKFTGKAKVYESQDSAVTAILGGEVVAGDVVVIR 479 45567************************************************************************ PP TIGR00110 421 yeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDienrkl 497 yeGPkGgPGm+emL+Pts+l++ GLgk++aL+tDGrfsGgt+GlsiGh sPeaaegGai+lv+ GD+i+iDi+ r++ lcl|FitnessBrowser__PS:Dsui_1122 480 YEGPKGGPGMQEMLYPTSYLKSRGLGKECALLTDGRFSGGTSGLSIGHASPEAAEGGAIGLVRTGDTIEIDIPGRRI 556 ***************************************************************************** PP TIGR00110 498 dlevseeelaerrakakkkea..........revkgaLakyaklvssadkGavld 542 +l+vs++el++rra+ ++k++ r v+ aL++ya +++sadkGav+d lcl|FitnessBrowser__PS:Dsui_1122 557 HLAVSDAELEKRRAEENAKGDkawkpteergRVVSKALQAYALMATSADKGAVRD 611 *******************99999*****************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (543 nodes) Target sequences: 1 (619 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03 # Mc/sec: 8.90 // [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