Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate WP_020175679.1 A3OQ_RS0112230 dihydroxy-acid dehydratase
Query= SwissProt::P9WKJ5 (575 letters) >NCBI__GCF_000385335.1:WP_020175679.1 Length = 576 Score = 536 bits (1380), Expect = e-156 Identities = 285/555 (51%), Positives = 368/555 (66%), Gaps = 8/555 (1%) Query: 21 SRDVTDGLEKAAARGMLRAVGMDDEDFAKPQIGVASSWNEITPCNLSLDRLANAVKEGVF 80 SR VT+G E+A R L A+G+ E +P +GVAS WNE PCN+SL R A AVK+GV Sbjct: 13 SRHVTEGPERAPHRSYLYAMGLTREQIHQPFVGVASCWNEAAPCNISLMRQAQAVKQGVA 72 Query: 81 SAGGYPLEFGTISVSDGISMGHEGMHFSLVSREVIADSVEVVMQAERLDGSVLLAGCDKS 140 SAGG P EF TI+V+DGI+MGH+GM SLVSR+VIADSVE+ M+ D V LAGCDKS Sbjct: 73 SAGGTPREFCTITVTDGIAMGHQGMKSSLVSRDVIADSVELTMRGHCYDALVGLAGCDKS 132 Query: 141 LPGMLMAAARLDLAAVFLYAGSILPGRAKLSDGSERDVTIIDAFEAVGACSRGLMSRADV 200 LPGM+MA RL++ +VF+Y GSILPG K + VT+ D FEAVG S G M+ D+ Sbjct: 133 LPGMMMAMVRLNVPSVFIYGGSILPGTFK-----GKPVTVQDLFEAVGKYSVGDMTPEDL 187 Query: 201 DAIERAICPGEGACGGMYTANTMASAAEALGMSLPGSAAPPATDRRRDGFARRSGQAVVE 260 D +E CP GACG +TANTMA+ +EA+G++LP SA PA RD F +G+ V+E Sbjct: 188 DELETVACPSAGACGAQFTANTMATVSEAIGLALPYSAGAPAPYEIRDRFCLTAGEMVME 247 Query: 261 LLRRGITARDILTKEAFENAIAVVMAFGGSTNAVLHLLAIAHEANVALSLQDFSRIGSGV 320 L+ R I RDI+T+ A ENA VV A GGSTNA LHL AIAHEA + L D + I Sbjct: 248 LIARNIRPRDIVTRRALENAATVVAASGGSTNAALHLPAIAHEAGIKFDLFDVAEIFKKT 307 Query: 321 PHLADVKPFGRHVMSDVDHIGGVPVVMKALLDAGLLHGDCLTVTGHTMAENLAAITPPDP 380 P++AD+KP G++V D+ GG+P++MK LLD G LHGDCLTVTG T+AEN+A + +P Sbjct: 308 PYIADLKPGGKYVAKDMFEAGGIPLLMKTLLDHGFLHGDCLTVTGRTIAENMAKV-KWNP 366 Query: 381 DGKVLRALANPIHPSGGITILHGSLAPEGAVVKTAGFDSD--VFEGTARVFDGERAALDA 438 D V+ PI +GG+ L G+LAPEGA+VK AG D VF+G A FD E + +A Sbjct: 367 DQDVVYPADKPITVTGGVVGLKGNLAPEGAIVKVAGMKQDHLVFKGPALCFDTEESCFEA 426 Query: 439 LEDGTITVGDAVVIRYEGPKGGPGMREMLAITGAIKGAGLGKDVLLLTDGRFSGGTTGLC 498 + G VIRYEGP+GGPGMREML+ T A+ G G+G+ V L+TDGRFSG T G C Sbjct: 427 VSQRKYQEGCVFVIRYEGPRGGPGMREMLSTTAALYGQGMGEKVALITDGRFSGATRGFC 486 Query: 499 VGHIAPEAVDGGPIALLRNGDRIRLDVAGRVLDVLADPAEFASRQQDFSPPPPRYTTGVL 558 +GH+ PEA GGPIAL+++GD I +D +++ E A R++ + P + +G L Sbjct: 487 IGHVGPEAAVGGPIALVKDGDIIEIDAVKGTIELHVSDEELAERRKAWQPRKTDFGSGAL 546 Query: 559 SKYVKLVSSAAVGAV 573 KY ++V A GAV Sbjct: 547 WKYAQIVGPAVNGAV 561 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: 971 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: 576 Length adjustment: 36 Effective length of query: 539 Effective length of database: 540 Effective search space: 291060 Effective search space used: 291060 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_020175679.1 A3OQ_RS0112230 (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.19278.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2e-213 695.8 0.5 2.2e-213 695.6 0.5 1.0 1 lcl|NCBI__GCF_000385335.1:WP_020175679.1 A3OQ_RS0112230 dihydroxy-acid de Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000385335.1:WP_020175679.1 A3OQ_RS0112230 dihydroxy-acid dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 695.6 0.5 2.2e-213 2.2e-213 1 541 [. 24 562 .. 24 564 .. 1.00 Alignments for each domain: == domain 1 score: 695.6 bits; conditional E-value: 2.2e-213 TIGR00110 1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiam 69 ++r+ l+a+Gl+ e++++P+++v+++++e +P++++l a++vk+++ +aGg++ ef ti+v+DGiam lcl|NCBI__GCF_000385335.1:WP_020175679.1 24 PHRSYLYAMGLTREQIHQPFVGVASCWNEAAPCNISLMRQAQAVKQGVASAGGTPREFCTITVTDGIAM 92 699****************************************************************** PP TIGR00110 70 gheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktk 138 gh+Gmk sL+sr++iaDsve +++h++Dalv ++ CDk +PGm+ma++rln+P+++++GG++ +g +k lcl|NCBI__GCF_000385335.1:WP_020175679.1 93 GHQGMKSSLVSRDVIADSVELTMRGHCYDALVGLAGCDKSLPGMMMAMVRLNVPSVFIYGGSILPGTFK 161 ********************************************************************* PP TIGR00110 139 lsekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstlla 207 ++ +++ d+feavg+y+ g+++ e+l+e+e +acP+ag+C+ ftan+ma+++ea+Gl+lP+s+ ++a lcl|NCBI__GCF_000385335.1:WP_020175679.1 162 -GKPVTVQDLFEAVGKYSVGDMTPEDLDELETVACPSAGACGAQFTANTMATVSEAIGLALPYSAGAPA 229 .9******************************************************************* PP TIGR00110 208 tsaekkelakksgkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklsld 276 + + +++ ++g+ ++el+ +ni+Prdi+t++a+ena t++ a GGstn+ Lhl+aia+eag+k++l lcl|NCBI__GCF_000385335.1:WP_020175679.1 230 PYEIRDRFCLTAGEMVMELIARNIRPRDIVTRRALENAATVVAASGGSTNAALHLPAIAHEAGIKFDLF 298 ********************************************************************* PP TIGR00110 277 dfdrlsrkvPllaklkPsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlrv 345 d+ ++ +k+P +a+lkP+gk+v +d+ +aGG++ ++k+l +g lh d+ltvtG+t+ae+++kvk + lcl|NCBI__GCF_000385335.1:WP_020175679.1 299 DVAEIFKKTPYIADLKPGGKYVAKDMFEAGGIPLLMKTLLDHGFLHGDCLTVTGRTIAENMAKVKWN-P 366 ******************************************************************9.8 PP TIGR00110 346 dqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeG 414 dqdv+ + d+p++ +gg+ LkGnla+eGa+vk+ag+++d l+f+Gpa f+ ee + ea+ ++k +eG lcl|NCBI__GCF_000385335.1:WP_020175679.1 367 DQDVVYPADKPITVTGGVVGLKGNLAPEGAIVKVAGMKQDHLVFKGPALCFDTEESCFEAVSQRKYQEG 435 ********************************************************************* PP TIGR00110 415 dvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialve 483 v viryeGP+GgPGmremL t+al g G+g+kvaLitDGrfsG+trG++iGhv Peaa+gG+ialv+ lcl|NCBI__GCF_000385335.1:WP_020175679.1 436 CVFVIRYEGPRGGPGMREMLSTTAALYGQGMGEKVALITDGRFSGATRGFCIGHVGPEAAVGGPIALVK 504 ********************************************************************* PP TIGR00110 484 dGDkikiDienrkldlevseeelaerrakakkkearevkgaLakyaklvssadkGavl 541 dGD+i+iD+ + +++l+vs+eelaerr++++++++ +gaL kya++v a +Gav+ lcl|NCBI__GCF_000385335.1:WP_020175679.1 505 DGDIIEIDAVKGTIELHVSDEELAERRKAWQPRKTDFGSGALWKYAQIVGPAVNGAVT 562 ********************************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (543 nodes) Target sequences: 1 (576 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: 8.19 // [ok]
This GapMind analysis is from Apr 10 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