Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate N515DRAFT_0569 N515DRAFT_0569 dihydroxy-acid dehydratase
Query= SwissProt::P9WKJ5 (575 letters) >FitnessBrowser__Dyella79:N515DRAFT_0569 Length = 568 Score = 493 bits (1268), Expect = e-143 Identities = 270/553 (48%), Positives = 351/553 (63%), Gaps = 10/553 (1%) Query: 20 RSRDVTDGLEKAAARGMLRAVGMDDEDFAKPQIGVASSWNEITPCNLSLDRLANAVKEGV 79 RS + G ++A AR MLRA G+DD AKP + V +W+ ++PCNL+L LA V EG+ Sbjct: 2 RSDLIKTGADRAPARAMLRATGLDDGAIAKPLVAVVHTWSNVSPCNLNLRELAEQVAEGI 61 Query: 80 FSAGGYPLEFGTISVSDGISMGHEGMHFSLVSREVIADSVEVVMQAERLDGSVLLAGCDK 139 +AGG P+EF TI+V+DGI+MG GM SL+SREVI DS+E+ + LD V+L GCDK Sbjct: 62 RAAGGTPIEFNTIAVTDGIAMGTPGMRASLISREVITDSIELAVDGHCLDAMVVLCGCDK 121 Query: 140 SLPGMLMAAARLDLAAVFLYAGSILPGRAKLSDGSERDVTIIDAFEAVGACSRGLMSRAD 199 ++P MA ARLD+ AV LY G+I G +TI FEAVGA G + A+ Sbjct: 122 TIPAAAMAMARLDIPAVALYGGTIAHGTH-----DAHPITIQQVFEAVGAHGAGKIDDAE 176 Query: 200 VDAIERAICPGEGACGGMYTANTMASAAEALGMSLPGSAAPPATDRRRDGFARRSGQAVV 259 + A+ER CPG GACGG +TANTMA LG+S G PAT + ARR G+ V+ Sbjct: 177 LAAVERDACPGAGACGGQFTANTMAMVLTTLGLSPMGFNDIPATHPAKAAAARRCGELVM 236 Query: 260 ELLRRGITARDILTKEAFENAIAVVMAFGGSTNAVLHLLAIAHEANVALSLQDFSRIGSG 319 + LR T R ++ + + NA +V A GSTNAVLHLLAIA EA +L+DF Sbjct: 237 DCLREQRTPRALINRTSLRNAARMVAATAGSTNAVLHLLAIAREAGAPWTLEDFEPASKH 296 Query: 320 VPHLADVKPFGRHVMSDVDHIGGVPVVMKALLDAGLLHGDCLTVTGHTMAENLAAITPPD 379 P +AD+ P GR+ ++ GG V + L+ AG+L D TVTG ++ E AA P Sbjct: 297 TPVIADLLPGGRYTAVEMFGAGGAARVAQELIAAGMLD-DVPTVTGRSLFEEAAA-APRA 354 Query: 380 PDGKVLRALANPIHPSGGITILHGSLAPEGAVVKTAGFDSDVFEGTARVFDGERAALDAL 439 V+ + P+ P GG +IL+G+LAPEG ++K AG + FEGTARVF+ E A A+ Sbjct: 355 EQQDVILPVGQPLKPRGGYSILYGNLAPEGCILKLAGKGATHFEGTARVFESEEQAFAAV 414 Query: 440 EDGTITVGDAVVIRYEGPKGGPGMREMLAITGAIKGAGLGKDVLLLTDGRFSGGTTGLCV 499 + G I GD +VIR EGP GGPGMREML +T A+ G GLG DV L+TDGRFSG T G V Sbjct: 415 QQGRIAKGDVIVIRNEGPAGGPGMREMLGVTAALIGRGLGDDVALITDGRFSGATHGFMV 474 Query: 500 GHIAPEAVDGGPIALLRNGDRIRLDVAGRVLDVLADPAEFASRQQDFSPPPPRYTTGVLS 559 GH+APEAV GGPIALLR+GDRIR+D L +A A+ A R+Q ++PP P+ TTG L+ Sbjct: 475 GHMAPEAVRGGPIALLRDGDRIRIDAG---LREIATDADLAERRQHWTPPAPKVTTGALA 531 Query: 560 KYVKLVSSAAVGA 572 KY +LV SA+ GA Sbjct: 532 KYARLVGSASDGA 544 Lambda K H 0.318 0.136 0.393 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: 1019 Number of extensions: 39 Number of successful extensions: 4 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: 575 Length of database: 568 Length adjustment: 36 Effective length of query: 539 Effective length of database: 532 Effective search space: 286748 Effective search space used: 286748 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 N515DRAFT_0569 N515DRAFT_0569 (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.3098.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.8e-191 621.9 4.5 6e-191 621.6 4.5 1.0 1 lcl|FitnessBrowser__Dyella79:N515DRAFT_0569 N515DRAFT_0569 dihydroxy-acid de Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Dyella79:N515DRAFT_0569 N515DRAFT_0569 dihydroxy-acid dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 621.6 4.5 6e-191 6e-191 1 540 [. 14 545 .. 14 547 .. 0.99 Alignments for each domain: == domain 1 score: 621.6 bits; conditional E-value: 6e-191 TIGR00110 1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDG 66 +ara+l+atGl d + kP++avv +++++ P++++l++la++v+e+i+aaGg++ efntiav+DG lcl|FitnessBrowser__Dyella79:N515DRAFT_0569 14 PARAMLRATGLDDGAIAKPLVAVVHTWSNVSPCNLNLRELAEQVAEGIRAAGGTPIEFNTIAVTDG 79 579*************************************************************** PP TIGR00110 67 iamgheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpm 132 iamg+ Gm+ sL sre+i Ds+e v++h+lDa+vv+ CDk +P + ma++rl+iPa++ +GG++ lcl|FitnessBrowser__Dyella79:N515DRAFT_0569 80 IAMGTPGMRASLISREVITDSIELAVDGHCLDAMVVLCGCDKTIPAAAMAMARLDIPAVALYGGTI 145 ****************************************************************** PP TIGR00110 133 eagktklsekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGls 198 + g ++ i++ +vfeavg+ agk++++el ++er acP+ag+C+G ftan+ma++ +lGls lcl|FitnessBrowser__Dyella79:N515DRAFT_0569 146 AHGTHD-AHPITIQQVFEAVGAHGAGKIDDAELAAVERDACPGAGACGGQFTANTMAMVLTTLGLS 210 ***999.8********************************************************** PP TIGR00110 199 lPgsstllatsaekkelakksgkrivelvkknikPrdiltkeafenaitldlalGGstntvLhlla 264 g ++at+ k++ a++ g+ +++ ++++ +Pr +++++++ na ++ a+ Gstn+vLhlla lcl|FitnessBrowser__Dyella79:N515DRAFT_0569 211 PMGFNDIPATHPAKAAAARRCGELVMDCLREQRTPRALINRTSLRNAARMVAATAGSTNAVLHLLA 276 ****************************************************************** PP TIGR00110 265 iakeagvklslddfdrlsrkvPllaklkPsgkkviedlhraGGvsavlkeldkegllhkdaltvtG 330 ia+eag +l+df+ s+++P++a+l P+g++ +++ aGG v +el +g+l +d+ tvtG lcl|FitnessBrowser__Dyella79:N515DRAFT_0569 277 IAREAGAPWTLEDFEPASKHTPVIADLLPGGRYTAVEMFGAGGAARVAQELIAAGML-DDVPTVTG 341 ***************************************************999988.588***** PP TIGR00110 331 ktlaetlekvkvlrvdqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvf 396 ++l e+++ ++ ++qdvi ++ +p+k gg +L+Gnla+eG++ k ag+ ++feG+a+vf lcl|FitnessBrowser__Dyella79:N515DRAFT_0569 342 RSLFEEAAAAPRA-EQQDVILPVGQPLKPRGGYSILYGNLAPEGCILKLAGKGA--THFEGTARVF 404 *********9999.99***********************************998..********** PP TIGR00110 397 eseeealeailggkvkeGdvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtr 462 esee+a +a+ +g++ +Gdv+vir eGP GgPGmremL t+al+g GLg++vaLitDGrfsG+t+ lcl|FitnessBrowser__Dyella79:N515DRAFT_0569 405 ESEEQAFAAVQQGRIAKGDVIVIRNEGPAGGPGMREMLGVTAALIGRGLGDDVALITDGRFSGATH 470 ****************************************************************** PP TIGR00110 463 GlsiGhvsPeaaegGaialvedGDkikiDienrkldlevseeelaerrakakkkearevkgaLaky 528 G+++Gh++Pea+ gG+ial++dGD+i+iD+ r++ +++laerr++++++ ++ + gaLaky lcl|FitnessBrowser__Dyella79:N515DRAFT_0569 471 GFMVGHMAPEAVRGGPIALLRDGDRIRIDAGLREIA---TDADLAERRQHWTPPAPKVTTGALAKY 533 *********************************997...6899*********************** PP TIGR00110 529 aklvssadkGav 540 a+lv sa++Ga lcl|FitnessBrowser__Dyella79:N515DRAFT_0569 534 ARLVGSASDGAN 545 **********95 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (543 nodes) Target sequences: 1 (568 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: 8.64 // [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