Align dihydroxy-acid dehydratase subunit (EC 4.2.1.9) (characterized)
to candidate WP_093395105.1 BM091_RS08860 dihydroxy-acid dehydratase
Query= metacyc::MONOMER-11919 (549 letters) >NCBI__GCF_900114975.1:WP_093395105.1 Length = 557 Score = 608 bits (1569), Expect = e-178 Identities = 310/552 (56%), Positives = 407/552 (73%), Gaps = 5/552 (0%) Query: 1 MKSDTIKRGIQRAPHRSLLARCGLTDDDFEKPFIGIANSYTDIVPGHIHLRELAEAVKEG 60 M+SD +K G+++APHRSL G TD++ ++P IGI NS +I+PGHIHL +AEAVK G Sbjct: 1 MRSDLMKSGLEKAPHRSLFKAMGYTDEELQRPLIGIVNSANEIIPGHIHLDRIAEAVKAG 60 Query: 61 VNAAGGVAFEFNTMAICDGIAMNHDGMKYSLASREIVADTVESMAMAHALDGLVLLPTCD 120 V AGG EF + +CDGIAMNH+GMKYSLASRE++AD+VE MA AH DGLVL+P CD Sbjct: 61 VRMAGGTPVEFPVIGVCDGIAMNHEGMKYSLASRELIADSVELMAKAHPFDGLVLIPNCD 120 Query: 121 KIVPGMLMAAARLDIPAIVVTGGPMLPGEFKGRKVDLINVYEGVGTVSAGEMSEDELEEL 180 KI+PGMLMAA RL+IP+IVV+GGPML G + VDLI+V+E VG+V AG+M + L+EL Sbjct: 121 KIIPGMLMAALRLNIPSIVVSGGPMLAGRLGSQPVDLISVFEAVGSVRAGKMDRETLKEL 180 Query: 181 ERCACPGPRSCAGLFTANTMACLTEALGMSLPGCATAHAVSSRKRQIARLSGKRIVEMVQ 240 E ACPG SCAG+FTAN+M CL EALG++LPG T AV + + ++A+ +G RIVE+V+ Sbjct: 181 EDEACPGCGSCAGMFTANSMNCLAEALGLALPGNGTIPAVHAARIRLAKYAGMRIVELVR 240 Query: 241 ENLKPTMIMSQEAFENAVMVDLALGGSTNTTLHIPAIAAEIDGLNINLDLFDELSRVIPH 300 + + P I+ +EAFENA+ VD+ALG STNT LH+PAIA E G++I+L++F+++SR PH Sbjct: 241 KGIYPRDIVVKEAFENAIAVDMALGCSTNTVLHVPAIAHEA-GISIDLNIFNDISRKTPH 299 Query: 301 IASISPAGEHMMLDLDRAGGIPAVLKTLEDH--INRECVTCTGRTVQENIENVKVGHRDV 358 + S+ P G H + DL RAGGIPAV+K L D +NR+ T +G+TV E ++ V +V Sbjct: 300 LCSLRPGGPHFLEDLHRAGGIPAVMKVLADAGLVNRDLPTVSGKTVGEIVDAAAVRDSEV 359 Query: 359 IRPLDSPVHSEGGLAILRGNLAPRGSVVKQGAVAEDMMVHEGPAKVFNSEDECMEAIFGG 418 IRP++ H+EGG+A+L GNLAP G+VVKQ AVA +MM G A+VF+SE E +AI G Sbjct: 360 IRPVERAYHAEGGIAVLYGNLAPEGAVVKQSAVAPEMMKRTGRARVFDSEQEAAKAILDG 419 Query: 419 RIDEGDVIVIRYEGPKGGPGMREMLNPTSAIAGMGLER-VALITDGRFSGGTRGPCVGHV 477 I G+V+VIRYEGPKGGPGM+EML+PT+AI G GL++ VALITDGRFSGGTRG +GHV Sbjct: 420 VIQPGEVVVIRYEGPKGGPGMQEMLSPTAAIVGRGLDKDVALITDGRFSGGTRGAAIGHV 479 Query: 478 SPEAMEDGPLAAVNDGDIIRIDIPSRKLEVDLSPREIEE-RLQSAVKPRRSVKGWLARYR 536 SPEA G +A V DGD I IDIP ++LE+ + +E+ R++ P R G+LARY Sbjct: 480 SPEAAAGGTIALVKDGDEILIDIPGKRLELLVDEGTLEKRRMEWTPPPPRITSGYLARYA 539 Query: 537 KLAGSADTGAVL 548 + S GAVL Sbjct: 540 AMVTSGARGAVL 551 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: 1027 Number of extensions: 45 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: 557 Length adjustment: 36 Effective length of query: 513 Effective length of database: 521 Effective search space: 267273 Effective search space used: 267273 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_093395105.1 BM091_RS08860 (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.19838.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.7e-250 816.6 3.9 5.4e-250 816.4 3.9 1.0 1 lcl|NCBI__GCF_900114975.1:WP_093395105.1 BM091_RS08860 dihydroxy-acid deh Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900114975.1:WP_093395105.1 BM091_RS08860 dihydroxy-acid dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 816.4 3.9 5.4e-250 5.4e-250 1 542 [. 14 552 .. 14 553 .. 1.00 Alignments for each domain: == domain 1 score: 816.4 bits; conditional E-value: 5.4e-250 TIGR00110 1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiam 69 ++r+l+ka+G++de+l++P+i++vns +ei+Pgh+hl+ +a++vk++++ aGg+++ef +i+v+DGiam lcl|NCBI__GCF_900114975.1:WP_093395105.1 14 PHRSLFKAMGYTDEELQRPLIGIVNSANEIIPGHIHLDRIAEAVKAGVRMAGGTPVEFPVIGVCDGIAM 82 69******************************************************************* PP TIGR00110 70 gheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktk 138 +heGmkysL+sre+iaDsve ++kah +D+lv+i++CDki+PGmlmaalrlniP+ivvsGGpm ag++ lcl|NCBI__GCF_900114975.1:WP_093395105.1 83 NHEGMKYSLASRELIADSVELMAKAHPFDGLVLIPNCDKIIPGMLMAALRLNIPSIVVSGGPMLAGRLG 151 ********************************************************************9 PP TIGR00110 139 lsekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstlla 207 s+ +dl++vfeavg++ agk++ e+l+e+e+ acP++gsC+G+ftansm+cl+ealGl+lPg++t++a lcl|NCBI__GCF_900114975.1:WP_093395105.1 152 -SQPVDLISVFEAVGSVRAGKMDRETLKELEDEACPGCGSCAGMFTANSMNCLAEALGLALPGNGTIPA 219 .9******************************************************************* PP TIGR00110 208 tsaekkelakksgkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklsld 276 ++a + +lak +g+rivelv+k i Prdi+ keafenai++d+alG stntvLh++aia+eag++++l+ lcl|NCBI__GCF_900114975.1:WP_093395105.1 220 VHAARIRLAKYAGMRIVELVRKGIYPRDIVVKEAFENAIAVDMALGCSTNTVLHVPAIAHEAGISIDLN 288 ********************************************************************* PP TIGR00110 277 dfdrlsrkvPllaklkPsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlrv 345 f+ +srk+P+l++l+P+g +++edlhraGG++av+k+l +gl+++d tv+Gkt++e+++ + v+ lcl|NCBI__GCF_900114975.1:WP_093395105.1 289 IFNDISRKTPHLCSLRPGGPHFLEDLHRAGGIPAVMKVLADAGLVNRDLPTVSGKTVGEIVDAAAVR-- 355 ******************************************************************9.. PP TIGR00110 346 dqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeG 414 d++vir+++ ++++egg+avL+Gnla+eGavvk+++v+ +++k +G+a+vf+se+ea +ail+g ++ G lcl|NCBI__GCF_900114975.1:WP_093395105.1 356 DSEVIRPVERAYHAEGGIAVLYGNLAPEGAVVKQSAVAPEMMKRTGRARVFDSEQEAAKAILDGVIQPG 424 ********************************************************************* PP TIGR00110 415 dvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialve 483 +vvviryeGPkGgPGm+emL Pt+a+vg GL+k+vaLitDGrfsGgtrG +iGhvsPeaa+gG+ialv+ lcl|NCBI__GCF_900114975.1:WP_093395105.1 425 EVVVIRYEGPKGGPGMQEMLSPTAAIVGRGLDKDVALITDGRFSGGTRGAAIGHVSPEAAAGGTIALVK 493 ********************************************************************* PP TIGR00110 484 dGDkikiDienrkldlevseeelaerrakakkkearevkgaLakyaklvssadkGavld 542 dGD+i iDi+ ++l+l v+e l++rr +++++ +r ++g+La+ya +v+s +Gavl+ lcl|NCBI__GCF_900114975.1:WP_093395105.1 494 DGDEILIDIPGKRLELLVDEGTLEKRRMEWTPPPPRITSGYLARYAAMVTSGARGAVLE 552 *********************************************************86 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (543 nodes) Target sequences: 1 (557 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 0.02s 00:00:00.04 Elapsed: 00:00:00.03 # Mc/sec: 8.14 // [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