Align dihydroxy-acid dehydratase subunit (EC 4.2.1.9) (characterized)
to candidate WP_013705483.1 DESAC_RS02410 dihydroxy-acid dehydratase
Query= metacyc::MONOMER-11919 (549 letters) >NCBI__GCF_000195295.1:WP_013705483.1 Length = 553 Score = 604 bits (1557), Expect = e-177 Identities = 297/553 (53%), Positives = 404/553 (73%), Gaps = 5/553 (0%) Query: 1 MKSDTIKRGIQRAPHRSLLARCGLTDDDFEKPFIGIANSYTDIVPGHIHLRELAEAVKEG 60 M+SD +K G++++PHRSL+ G T+++ ++P IG+AN+ +I+PGHIHL +++EAVK G Sbjct: 1 MRSDLMKTGVEKSPHRSLMKAMGYTEEELQRPLIGVANAKNEIIPGHIHLDKISEAVKAG 60 Query: 61 VNAAGGVAFEFNTMAICDGIAMNHDGMKYSLASREIVADTVESMAMAHALDGLVLLPTCD 120 + AGG EF + +CDGIAM+H GMKYSLASRE++AD++E MAMAH DGL L+P CD Sbjct: 61 IRMAGGTPIEFGVIGVCDGIAMHHVGMKYSLASRELIADSIEVMAMAHPFDGLALIPNCD 120 Query: 121 KIVPGMLMAAARLDIPAIVVTGGPMLPGEFKGRKVDLINVYEGVGTVSAGEMSEDELEEL 180 KI+PGM+MAA RL+IPA+V++GGPML G + R +DLI V+EGVG V AG+M+E EL+E+ Sbjct: 121 KIIPGMIMAALRLNIPALVISGGPMLAGRLQNRAIDLITVFEGVGAVKAGKMTEAELKEI 180 Query: 181 ERCACPGPRSCAGLFTANTMACLTEALGMSLPGCATAHAVSSRKRQIARLSGKRIVEMVQ 240 E ACPG SCAG+FTAN+M CL+EALG++LPG A+S+ + ++A+ G++I+E+V+ Sbjct: 181 EDAACPGCGSCAGMFTANSMNCLSEALGLALPGNGAIPAISAARYRLAKQGGRQIMELVR 240 Query: 241 ENLKPTMIMSQEAFENAVMVDLALGGSTNTTLHIPAIAAEIDGLNINLDLFDELSRVIPH 300 + P I + AF+NA+ VD+ALG STNT LHIPA+A E G+++ LDLF+ +S PH Sbjct: 241 RQILPRQIATLTAFQNAMTVDMALGCSTNTVLHIPAMAHEA-GIDLPLDLFNTISEKTPH 299 Query: 301 IASISPAGEHMMLDLDRAGGIPAVLKTL--EDHINRECVTCTGRTVQENIENVKVGHRDV 358 I S+SP G + + DL RAGG+PAV+ L IN E +T TG+T+ EN+ V+V ++ Sbjct: 300 ICSLSPGGMYHLEDLHRAGGVPAVMARLWQAGLINGEPLTATGKTMAENLAGVRVLDDEI 359 Query: 359 IRPLDSPVHSEGGLAILRGNLAPRGSVVKQGAVAEDMMVHEGPAKVFNSEDECMEAIFGG 418 IR LD P H++GG+AIL+GNLAP G VVKQ AV M+V EG A+VF+SE+E AI GG Sbjct: 360 IRSLDHPYHTQGGIAILKGNLAPEGGVVKQSAVDPQMLVREGRARVFDSEEEAANAILGG 419 Query: 419 RIDEGDVIVIRYEGPKGGPGMREMLNPTSAIAGMGLER-VALITDGRFSGGTRGPCVGHV 477 I GDV++IRYEGPKGGPGMREML PT+AIAGMGL++ VAL+TDGRFSGGTRG +GH+ Sbjct: 420 AIHPGDVVIIRYEGPKGGPGMREMLTPTAAIAGMGLDKEVALLTDGRFSGGTRGAAIGHI 479 Query: 478 SPEAMEDGPLAAVNDGDIIRIDIPSRKLEVDLSPREIEERLQSAVKPRRSVK-GWLARYR 536 SPEA GP+ + +GD I IDIP + L + + E+ R P +K G+ RY Sbjct: 480 SPEAAAGGPIGLIQEGDAILIDIPGKTLTLKVDETELVRRRAQWKLPEPKIKHGYAYRYS 539 Query: 537 KLAGSADTGAVLR 549 + S GAVL+ Sbjct: 540 RQVTSGSQGAVLQ 552 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: 1053 Number of extensions: 48 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: 549 Length of database: 553 Length adjustment: 36 Effective length of query: 513 Effective length of database: 517 Effective search space: 265221 Effective search space used: 265221 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_013705483.1 DESAC_RS02410 (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.8585.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3e-244 797.5 5.4 3.4e-244 797.3 5.4 1.0 1 lcl|NCBI__GCF_000195295.1:WP_013705483.1 DESAC_RS02410 dihydroxy-acid deh Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000195295.1:WP_013705483.1 DESAC_RS02410 dihydroxy-acid dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 797.3 5.4 3.4e-244 3.4e-244 1 542 [. 14 552 .. 14 553 .] 1.00 Alignments for each domain: == domain 1 score: 797.3 bits; conditional E-value: 3.4e-244 TIGR00110 1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiam 69 ++r+l+ka+G+++e+l++P+i+v+n+ +ei+Pgh+hl++++++vk++i+ aGg++ ef++i+v+DGiam lcl|NCBI__GCF_000195295.1:WP_013705483.1 14 PHRSLMKAMGYTEEELQRPLIGVANAKNEIIPGHIHLDKISEAVKAGIRMAGGTPIEFGVIGVCDGIAM 82 69******************************************************************* PP TIGR00110 70 gheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktk 138 h GmkysL+sre+iaDs+e +++ah +D+l +i++CDki+PGm+maalrlniPa+v+sGGpm ag+++ lcl|NCBI__GCF_000195295.1:WP_013705483.1 83 HHVGMKYSLASRELIADSIEVMAMAHPFDGLALIPNCDKIIPGMIMAALRLNIPALVISGGPMLAGRLQ 151 ********************************************************************* PP TIGR00110 139 lsekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstlla 207 + idl+ vfe+vg+++agk++e+el+eie+ acP++gsC+G+ftansm+cl+ealGl+lPg+++++a lcl|NCBI__GCF_000195295.1:WP_013705483.1 152 -NRAIDLITVFEGVGAVKAGKMTEAELKEIEDAACPGCGSCAGMFTANSMNCLSEALGLALPGNGAIPA 219 .7******************************************************************* PP TIGR00110 208 tsaekkelakksgkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklsld 276 +sa + +lak+ g++i+elv+++i Pr+i+t +af+na+t+d+alG stntvLh++a+a+eag++l ld lcl|NCBI__GCF_000195295.1:WP_013705483.1 220 ISAARYRLAKQGGRQIMELVRRQILPRQIATLTAFQNAMTVDMALGCSTNTVLHIPAMAHEAGIDLPLD 288 ********************************************************************* PP TIGR00110 277 dfdrlsrkvPllaklkPsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlrv 345 f+++s+k+P++++l+P+g + +edlhraGGv+av+ l ++gl++ + lt tGkt+ae+l+ v+vl lcl|NCBI__GCF_000195295.1:WP_013705483.1 289 LFNTISEKTPHICSLSPGGMYHLEDLHRAGGVPAVMARLWQAGLINGEPLTATGKTMAENLAGVRVL-- 355 *****************************************************************99.. PP TIGR00110 346 dqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeG 414 d+++irsld+p++ +gg+a+LkGnla+eG vvk+++v+ ++l+ eG+a+vf+seeea +ailgg ++ G lcl|NCBI__GCF_000195295.1:WP_013705483.1 356 DDEIIRSLDHPYHTQGGIAILKGNLAPEGGVVKQSAVDPQMLVREGRARVFDSEEEAANAILGGAIHPG 424 ********************************************************************* PP TIGR00110 415 dvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialve 483 dvv+iryeGPkGgPGmremL+Pt+a++g+GL+k+vaL+tDGrfsGgtrG +iGh+sPeaa+gG+i+l++ lcl|NCBI__GCF_000195295.1:WP_013705483.1 425 DVVIIRYEGPKGGPGMREMLTPTAAIAGMGLDKEVALLTDGRFSGGTRGAAIGHISPEAAAGGPIGLIQ 493 ********************************************************************* PP TIGR00110 484 dGDkikiDienrkldlevseeelaerrakakkkearevkgaLakyaklvssadkGavld 542 +GD i iDi+ ++l l+v+e el +rra++k +e++ ++g+ +y++ v+s ++Gavl+ lcl|NCBI__GCF_000195295.1:WP_013705483.1 494 EGDAILIDIPGKTLTLKVDETELVRRRAQWKLPEPKIKHGYAYRYSRQVTSGSQGAVLQ 552 *********************************************************86 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (543 nodes) Target sequences: 1 (553 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: 8.15 // [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