Align dihydroxy-acid dehydratase subunit (EC 4.2.1.9) (characterized)
to candidate WP_012966058.1 FERP_RS07825 dihydroxy-acid dehydratase
Query= metacyc::MONOMER-11919 (549 letters) >NCBI__GCF_000025505.1:WP_012966058.1 Length = 546 Score = 576 bits (1484), Expect = e-169 Identities = 293/546 (53%), Positives = 391/546 (71%), Gaps = 5/546 (0%) Query: 1 MKSDTIKRGIQRAPHRSLLARCGLTDDDFEKPFIGIANSYTDIVPGHIHLRELAEAVKEG 60 M+SD +K+GI R HR+LL GLTDDDFEKPFIGIAN+Y IVPGH+ L + + VK G Sbjct: 1 MRSDIVKKGIDRVAHRALLRALGLTDDDFEKPFIGIANAYNTIVPGHMSLDRITQFVKLG 60 Query: 61 VNAAGGVAFEFNTMAICDGIAMNHDGMKYSLASREIVADTVESMAMAHALDGLVLLPTCD 120 + +AGGV FEF + ICDGIAM H GM YSL SREI+AD++E+M AH DGLV++ +CD Sbjct: 61 IASAGGVPFEFGVIGICDGIAMGHKGMSYSLPSREIIADSIEAMVEAHQFDGLVVVGSCD 120 Query: 121 KIVPGMLMAAARLDIPAIVVTGGPMLPGEFKGRKVDLINVYEGVGTVSAGEMSEDELEEL 180 KIVPGMLMA RL+IP+IVVT GPM+P + G+K+ + + +E G AGE+SE+EL+ Sbjct: 121 KIVPGMLMAVMRLNIPSIVVTSGPMIPEKLNGKKLSIKHAFEAAGMYKAGELSEEELKLY 180 Query: 181 ERCACPGPRSCAGLFTANTMACLTEALGMSLPGCATAHAVSSRKRQIARLSGKRIVEMVQ 240 E SC GL+TANTM LTE LG+SLP +T+ SSRK +IA+ +GKR+VE+V+ Sbjct: 181 ENYCAAYCGSCQGLYTANTMQILTETLGLSLPYTSTSPCSSSRKLRIAKEAGKRVVELVK 240 Query: 241 ENLKPTMIMSQEAFENAVMVDLALGGSTNTTLHIPAIAAEIDGLNINLDLFDELSRVIPH 300 ++LKP I+++ +FENA+ +D+ +GGSTNT LH+PAIA E G+ I LD FDE+SR PH Sbjct: 241 QDLKPLDIVNENSFENAITMDMMIGGSTNTVLHLPAIAREA-GIKIELDKFDEISRKTPH 299 Query: 301 IASISPAGEHMMLDLDRAGGIPAVLKTLEDHINRECVTCTGRTVQENIENVKVGHRDVIR 360 + ++ PA + M++DLD +GG+P ++K +++ + E +T +G+ + E E RD+I Sbjct: 300 LVALDPASDEMVVDLDESGGVPMIIKKAKEYFHNE-MTVSGKRLYEIAEEAFARGRDIIA 358 Query: 361 PLDSPVHSEGGLAILRGNLAPRGSVVKQGAVAEDMMVHEGPAKVFNSEDECMEAIFGGRI 420 + P+ EGG+AIL+GNL +V+K AV E+M EG AKVF+SE + ++AI GG+I Sbjct: 359 SPEKPLSKEGGIAILKGNLGK--AVIKAAAVDEEMRKFEGEAKVFDSEKDALDAILGGKI 416 Query: 421 DEGDVIVIRYEGPKGGPGMREMLNPTSAIAGMGLERVALITDGRFSGGTRGPCVGHVSPE 480 +EGDV+VIRY GPK GM EML PT+AI+GMGLERVALITDGRFSG TRGP VGHV+PE Sbjct: 417 EEGDVVVIRYMGPKAA-GMPEMLLPTAAISGMGLERVALITDGRFSGATRGPAVGHVTPE 475 Query: 481 AMEDGPLAAVNDGDIIRIDIPSRKLEVDLSPREIEERLQSAVKPRRSVKGWLARYRKLAG 540 A+ G +A V DGD I IDIP+RKL V +S E+ ER + +G LA+Y KL Sbjct: 476 ALAGGTIALVEDGDAIEIDIPNRKLNVKISEEELRERREKWKPKEIRHRGLLAKYSKLVT 535 Query: 541 SADTGA 546 SA+ GA Sbjct: 536 SAEEGA 541 Lambda K H 0.319 0.136 0.397 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: 874 Number of extensions: 27 Number of successful extensions: 5 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: 549 Length of database: 546 Length adjustment: 36 Effective length of query: 513 Effective length of database: 510 Effective search space: 261630 Effective search space used: 261630 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 53 (25.0 bits)
Align candidate WP_012966058.1 FERP_RS07825 (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.6378.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.8e-245 801.5 4.2 2e-245 801.4 4.2 1.0 1 lcl|NCBI__GCF_000025505.1:WP_012966058.1 FERP_RS07825 dihydroxy-acid dehy Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000025505.1:WP_012966058.1 FERP_RS07825 dihydroxy-acid dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 801.4 4.2 2e-245 2e-245 1 541 [. 14 543 .. 14 545 .. 0.99 Alignments for each domain: == domain 1 score: 801.4 bits; conditional E-value: 2e-245 TIGR00110 1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiam 69 a+rall+a+Gl+d+d+ekP+i+++n+y++ivPgh++l+ +++ vk +i +aGgv++ef++i+++DGiam lcl|NCBI__GCF_000025505.1:WP_012966058.1 14 AHRALLRALGLTDDDFEKPFIGIANAYNTIVPGHMSLDRITQFVKLGIASAGGVPFEFGVIGICDGIAM 82 69******************************************************************* PP TIGR00110 70 gheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktk 138 gh+Gm ysLpsreiiaDs+e++v+ah++D+lvv++sCDkivPGmlma++rlniP+ivv+ Gpm ++k++ lcl|NCBI__GCF_000025505.1:WP_012966058.1 83 GHKGMSYSLPSREIIADSIEAMVEAHQFDGLVVVGSCDKIVPGMLMAVMRLNIPSIVVTSGPMIPEKLN 151 ********************************************************************* PP TIGR00110 139 lsekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstlla 207 ++k++++++fea+g+y+ag+lseeel+ +e++++ ++gsC+Gl+tan+m++lte+lGlslP++st+++ lcl|NCBI__GCF_000025505.1:WP_012966058.1 152 -GKKLSIKHAFEAAGMYKAGELSEEELKLYENYCAAYCGSCQGLYTANTMQILTETLGLSLPYTSTSPC 219 .9******************************************************************* PP TIGR00110 208 tsaekkelakksgkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklsld 276 s++k+++ak++gkr+velvk+++kP di+++++fenait+d+ +GGstntvLhl+aia+eag+k++ld lcl|NCBI__GCF_000025505.1:WP_012966058.1 220 SSSRKLRIAKEAGKRVVELVKQDLKPLDIVNENSFENAITMDMMIGGSTNTVLHLPAIAREAGIKIELD 288 ********************************************************************* PP TIGR00110 277 dfdrlsrkvPllaklkPsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlrv 345 +fd++srk+P+l+ l+P+++++++dl+++GGv++++k++ ++++h++ +tv+Gk l+e++e++ + lcl|NCBI__GCF_000025505.1:WP_012966058.1 289 KFDEISRKTPHLVALDPASDEMVVDLDESGGVPMIIKKA--KEYFHNE-MTVSGKRLYEIAEEAFAR-- 352 **************************************9..99***99.9*************9999.. PP TIGR00110 346 dqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeG 414 ++d+i+s ++p++kegg+a+LkGnl + av+k+a+v+e++ kfeG+akvf+se++al+ailggk++eG lcl|NCBI__GCF_000025505.1:WP_012966058.1 353 GRDIIASPEKPLSKEGGIAILKGNLGK--AVIKAAAVDEEMRKFEGEAKVFDSEKDALDAILGGKIEEG 419 *************************86..9*************************************** PP TIGR00110 415 dvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialve 483 dvvviry+GPk Gm+emL Pt+a++g+GL++ vaLitDGrfsG+trG+++Ghv+Pea +gG+ialve lcl|NCBI__GCF_000025505.1:WP_012966058.1 420 DVVVIRYMGPKA-AGMPEMLLPTAAISGMGLER-VALITDGRFSGATRGPAVGHVTPEALAGGTIALVE 486 ***********6.5******************9.*********************************** PP TIGR00110 484 dGDkikiDienrkldlevseeelaerrakakkkearevkgaLakyaklvssadkGavl 541 dGD i+iDi+nrkl++++seeel+err+k+k+ke r +g+Laky+klv+sa++Ga + lcl|NCBI__GCF_000025505.1:WP_012966058.1 487 DGDAIEIDIPNRKLNVKISEEELRERREKWKPKEIR-HRGLLAKYSKLVTSAEEGATT 543 **********************************88.9*****************976 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (543 nodes) Target sequences: 1 (546 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: 00:00:00.02 # Mc/sec: 12.11 // [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