Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate Synpcc7942_0626 Synpcc7942_0626 dihydroxy-acid dehydratase
Query= SwissProt::P55186 (617 letters) >FitnessBrowser__SynE:Synpcc7942_0626 Length = 619 Score = 934 bits (2415), Expect = 0.0 Identities = 473/615 (76%), Positives = 526/615 (85%), Gaps = 1/615 (0%) Query: 1 MPPYRSRTTTHGRNMAGARGLWRATGMKDEDFGKPIIAVANSFTQFVPGHVHLKDLGQLV 60 MP YRSRTTT+GRNMAGAR LWRATGMKDEDF KPIIAVANSFTQFVPGHVHLKDLGQLV Sbjct: 1 MPQYRSRTTTYGRNMAGARALWRATGMKDEDFEKPIIAVANSFTQFVPGHVHLKDLGQLV 60 Query: 61 AREIEAAGGVAKEFNTIAVDDGIAMGHGGMLYSLPSRDLIADSVEYMVNAHCADAIVCIS 120 AREIE AGGVAKEFNTIAVDDGIAMGHGGMLYSLPSRDLIADSVEYMVNAHCADA+VCIS Sbjct: 61 AREIERAGGVAKEFNTIAVDDGIAMGHGGMLYSLPSRDLIADSVEYMVNAHCADALVCIS 120 Query: 121 NCDKITPGMLMAAMRLNIPVVFVSGGPMEAGKVTVKGKIRALDLVDAMVVAADDSYSDEE 180 NCDKITPGMLMAA+RLNIP VFVSGGPMEAGKV + G+ R LDLVDAMVVAADD SDE+ Sbjct: 121 NCDKITPGMLMAALRLNIPAVFVSGGPMEAGKVILNGEERHLDLVDAMVVAADDRESDED 180 Query: 181 VEAIEKAACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSVLATHADREALFKEAGRVVV 240 V IE++ACPTCGSCSGMFTANSMNCLTEALGLSLPGNGS+LATH DR+ LF EAGR+ V Sbjct: 181 VATIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSLLATHGDRKELFLEAGRLAV 240 Query: 241 DLCQRWYEQEDATALPRGIATRAAFENAMSLDIAMGGSTNTVLHLLAAAHEGGIDFSMAD 300 L +++YEQ+D + LPR IA+ AFENA+ LDIAMGGSTNTVLHLLAAAHE G+DF+M D Sbjct: 241 KLAKQYYEQDDESVLPRSIASFKAFENAICLDIAMGGSTNTVLHLLAAAHEAGVDFTMKD 300 Query: 301 IDRLSRHVPCLSKVAPAKSDVHMEDVHRAGGVMAILGELERGGLIDASQPTVHAPTMGEA 360 IDRLSR +P L KVAP+ HMEDVHRAGGV+AILGEL+R GL+ PTVH+P++G A Sbjct: 301 IDRLSRKIPNLCKVAPSTQKYHMEDVHRAGGVIAILGELDRAGLLHREVPTVHSPSLGAA 360 Query: 361 LARWDIGR-TNSQIAHEFFKAAPGGKPTQVAFSQAARWEELDLDRENGVIRSVEHPFSKD 419 L +WDI R T ++ A + AAPGG PTQ AFSQ+ RW LDLDRENG IR +EH +S+D Sbjct: 361 LDQWDINRETATEEAKSRYLAAPGGVPTQEAFSQSKRWTALDLDRENGCIRDIEHAYSQD 420 Query: 420 GGLAVLFGNLAPEGCIVKTAGVDESILTFRGTARVFESQDAAVSGILGGQVKAGEVVVIR 479 GGLAVL+GNLA +GCIVKTAGVDE+IL F G A V ESQD AV+ IL G+VK G+VV+IR Sbjct: 421 GGLAVLYGNLAEQGCIVKTAGVDENILVFSGPAVVCESQDEAVNWILNGRVKEGDVVLIR 480 Query: 480 YEGPKGGPGMQEMLYPTTYLKSKGLGAACALVTDGRFSGGTSGLSIGHVSPEAGEGGLIA 539 YEGP+GGPGMQEMLYPT+YLKSKGLG ACAL+TDGRFSGGTSGLSIGHVSPEA EGGLIA Sbjct: 481 YEGPRGGPGMQEMLYPTSYLKSKGLGKACALITDGRFSGGTSGLSIGHVSPEAAEGGLIA 540 Query: 540 LVETGDPILIDIPTRGITLEVSDAVLAARREAQLARGKDAWTPLNRKRDLTPALRAYAAM 599 LVE GD I IDIP R I L VS+ LA RR A ARG AWTP +R R ++ AL+AYAAM Sbjct: 541 LVEQGDRIEIDIPNRRIHLAVSEEELAHRRAAMEARGDQAWTPKDRDRPISQALQAYAAM 600 Query: 600 TTNAARGAVRDVSQI 614 TT+AARG VRD+SQI Sbjct: 601 TTSAARGGVRDLSQI 615 Lambda K H 0.318 0.134 0.395 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: 1297 Number of extensions: 42 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: 617 Length of database: 619 Length adjustment: 37 Effective length of query: 580 Effective length of database: 582 Effective search space: 337560 Effective search space used: 337560 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 Synpcc7942_0626 Synpcc7942_0626 (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.16864.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.5e-254 829.4 0.3 7.6e-254 829.2 0.3 1.0 1 lcl|FitnessBrowser__SynE:Synpcc7942_0626 Synpcc7942_0626 dihydroxy-acid d Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SynE:Synpcc7942_0626 Synpcc7942_0626 dihydroxy-acid dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 829.2 0.3 7.6e-254 7.6e-254 2 542 .. 18 611 .. 17 612 .. 0.99 Alignments for each domain: == domain 1 score: 829.2 bits; conditional E-value: 7.6e-254 TIGR00110 2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamg 70 aral++atG+kded+ekPiiav+ns+t++vPghvhlkdl++lv++eie+aGgvakefntiav+DGiamg lcl|FitnessBrowser__SynE:Synpcc7942_0626 18 ARALWRATGMKDEDFEKPIIAVANSFTQFVPGHVHLKDLGQLVAREIERAGGVAKEFNTIAVDDGIAMG 86 79******************************************************************* PP TIGR00110 71 heGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktkl 139 h+Gm+ysLpsr++iaDsve++v+ah++Dalv+is+CDki+PGmlmaalrlniPa++vsGGpmeagk+ l lcl|FitnessBrowser__SynE:Synpcc7942_0626 87 HGGMLYSLPSRDLIADSVEYMVNAHCADALVCISNCDKITPGMLMAALRLNIPAVFVSGGPMEAGKVIL 155 ********************************************************************* PP TIGR00110 140 sekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllat 208 + +d+++a++ +a+++ s+e++ +iersacPt+gsCsG+ftansm+cltealGlslPg+++llat lcl|FitnessBrowser__SynE:Synpcc7942_0626 156 NGEERHLDLVDAMVVAADDRESDEDVATIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSLLAT 224 99******************************************************************* PP TIGR00110 209 saekkelakksgkrivelvkknik.......PrdiltkeafenaitldlalGGstntvLhllaiakeag 270 + ++kel+ ++g+ v+l k++++ Pr+i++ +afenai ld+a+GGstntvLhlla+a+eag lcl|FitnessBrowser__SynE:Synpcc7942_0626 225 HGDRKELFLEAGRLAVKLAKQYYEqddesvlPRSIASFKAFENAICLDIAMGGSTNTVLHLLAAAHEAG 293 ********************************************************************* PP TIGR00110 271 vklslddfdrlsrkvPllaklkPsgkkv.iedlhraGGvsavlkeldkegllhkdaltvtGktlaetle 338 v+++++d+drlsrk+P l+k++Ps++k+ +ed+hraGGv+a+l+eld++gllh+++ tv +l+ l+ lcl|FitnessBrowser__SynE:Synpcc7942_0626 294 VDFTMKDIDRLSRKIPNLCKVAPSTQKYhMEDVHRAGGVIAILGELDRAGLLHREVPTVHSPSLGAALD 362 ***************************99**************************************** PP TIGR00110 339 kvkvlr....................................vdqdvirsldnpvkkegglavLkGnla 371 + +++r ++ +ir ++++++++gglavL+Gnla lcl|FitnessBrowser__SynE:Synpcc7942_0626 363 QWDINRetateeaksrylaapggvptqeafsqskrwtaldldRENGCIRDIEHAYSQDGGLAVLYGNLA 431 *****9********************************99666666*********************** PP TIGR00110 372 eeGavvkiagveedilkfeGpakvfeseeealeailggkvkeGdvvviryeGPkGgPGmremLaPtsal 440 e+G++vk+agv+e+il+f Gpa v es++ea++ il+g+vkeGdvv+iryeGP+GgPGm+emL+Pts+l lcl|FitnessBrowser__SynE:Synpcc7942_0626 432 EQGCIVKTAGVDENILVFSGPAVVCESQDEAVNWILNGRVKEGDVVLIRYEGPRGGPGMQEMLYPTSYL 500 ********************************************************************* PP TIGR00110 441 vglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDienrkldlevseeelaer 509 ++ GLgk++aLitDGrfsGgt+GlsiGhvsPeaaegG ialve+GD+i+iDi+nr+++l+vseeela+r lcl|FitnessBrowser__SynE:Synpcc7942_0626 501 KSKGLGKACALITDGRFSGGTSGLSIGHVSPEAAEGGLIALVEQGDRIEIDIPNRRIHLAVSEEELAHR 569 ********************************************************************* PP TIGR00110 510 rakakkkea.........revkgaLakyaklvssadkGavld 542 ra+++++++ r ++ aL++ya + +sa +G+v+d lcl|FitnessBrowser__SynE:Synpcc7942_0626 570 RAAMEARGDqawtpkdrdRPISQALQAYAAMTTSAARGGVRD 611 ******999999***999999*******************87 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03 # Mc/sec: 10.03 // [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