Align dihydroxy-acid dehydratase subunit (EC 4.2.1.9) (characterized)
to candidate WP_039651789.1 PN53_RS01900 dihydroxy-acid dehydratase
Query= metacyc::MONOMER-11919 (549 letters) >NCBI__GCF_000816635.1:WP_039651789.1 Length = 552 Score = 613 bits (1582), Expect = e-180 Identities = 313/553 (56%), Positives = 417/553 (75%), Gaps = 5/553 (0%) Query: 1 MKSDTIKRGIQRAPHRSLLARCGLTDDDFEKPFIGIANSYTDIVPGHIHLRELAEAVKEG 60 MKSD+IK+GI+ AP R+L+ G T ++ E+P IGI NS ++V GH+HL E+A+A K G Sbjct: 1 MKSDSIKKGIKGAPARALMYGMGYTKEEIERPLIGIVNSQNEVVAGHMHLDEIAKAAKLG 60 Query: 61 VNAAGGVAFEFNTMAICDGIAMNHDGMKYSLASREIVADTVESMAMAHALDGLVLLPTCD 120 V AGG EF +A+CDGIAM H GMK+SLASRE++AD++E+MA AH DGLVL+P CD Sbjct: 61 VAMAGGTPMEFPAIAVCDGIAMGHVGMKFSLASRELIADSIEAMATAHGFDGLVLIPNCD 120 Query: 121 KIVPGMLMAAARLDIPAIVVTGGPMLPGEFKGRKVDLINVYEGVGTVSAGEMSEDELEEL 180 K+VPGMLMAAARLDIP++VV+GGPM G+ G+ +D E VG S G+++ED+LEE Sbjct: 121 KVVPGMLMAAARLDIPSVVVSGGPMRAGKSNGKVLDFSTCIEQVGACSDGKITEDQLEEE 180 Query: 181 ERCACPGPRSCAGLFTANTMACLTEALGMSLPGCATAHAVSSRKRQIARLSGKRIVEMVQ 240 + +CPG SC+GLFTAN+M CLTE LGM LP TA A + +RQ+A+ +G +++ V+ Sbjct: 181 AKKSCPGCGSCSGLFTANSMNCLTEVLGMGLPLNGTALAQTGERRQLAKYAGMYVMDCVK 240 Query: 241 ENLKPTMIMSQEAFENAVMVDLALGGSTNTTLHIPAIAAEIDGLNINLDLFDELSRVIPH 300 N +P+ I+ +AF+NA+ +D+A+ GSTNT LH+PAIA E G+ ++LDLFDE+S+ P Sbjct: 241 NNRRPSDILKLDAFKNAITMDMAMAGSTNTVLHLPAIAHEA-GIKLDLDLFDEISQKTPC 299 Query: 301 IASISPAGEHMMLDLDRAGGIPAVLKTLEDH--INRECVTCTGRTVQENIENVKVGHRDV 358 + +SP+G+H M DL AGGIPA++ L I + +T TG+T+ E I+ V +RDV Sbjct: 300 LIKLSPSGKHHMEDLHMAGGIPALMHELSSKGLIAEDSMTVTGKTIGETIKEYNVLNRDV 359 Query: 359 IRPLDSPVHSEGGLAILRGNLAPRGSVVKQGAVAEDMMVHEGPAKVFNSEDECMEAIFGG 418 IR +D+ +GGLAILRGNLA G+VVK+ AVA++MMVHEGPA+V+NSE+E ++AIFG Sbjct: 360 IRSVDNAYSPKGGLAILRGNLAVDGAVVKESAVAKEMMVHEGPARVYNSEEEAVKAIFGD 419 Query: 419 RIDEGDVIVIRYEGPKGGPGMREMLNPTSAIAGMGLER-VALITDGRFSGGTRGPCVGHV 477 I++GDVIVIRYEGPKGGPGMREML+PTSAIAGMGL++ VAL+TDGRFSG TRG +GHV Sbjct: 420 EINKGDVIVIRYEGPKGGPGMREMLSPTSAIAGMGLDKDVALLTDGRFSGATRGASIGHV 479 Query: 478 SPEAMEDGPLAAVNDGDIIRIDIPSRKLEVDLSPREIEERLQSAVKPRRSV-KGWLARYR 536 SPEAME G + V +GD I IDI ++KLE+ + +E+EER + VKP V KG+LARY Sbjct: 480 SPEAMEGGLIGLVEEGDTIFIDIKNKKLELKVDAKELEERKKRYVKPEPKVKKGYLARYG 539 Query: 537 KLAGSADTGAVLR 549 KL SA+TGAVL+ Sbjct: 540 KLVTSANTGAVLK 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: 956 Number of extensions: 43 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: 552 Length adjustment: 36 Effective length of query: 513 Effective length of database: 516 Effective search space: 264708 Effective search space used: 264708 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_039651789.1 PN53_RS01900 (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.17088.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-244 798.7 12.0 1.4e-244 798.5 12.0 1.0 1 NCBI__GCF_000816635.1:WP_039651789.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000816635.1:WP_039651789.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 798.5 12.0 1.4e-244 1.4e-244 1 542 [. 14 552 .] 14 552 .] 1.00 Alignments for each domain: == domain 1 score: 798.5 bits; conditional E-value: 1.4e-244 TIGR00110 1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamgheG 73 +aral++ +G+++e++e+P+i++vns +e+v gh+hl+++ak++k ++ aGg+++ef iav+DGiamgh G NCBI__GCF_000816635.1:WP_039651789.1 14 PARALMYGMGYTKEEIERPLIGIVNSQNEVVAGHMHLDEIAKAAKLGVAMAGGTPMEFPAIAVCDGIAMGHVG 86 579********************************************************************** PP TIGR00110 74 mkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktklsekidlv 146 mk+sL+sre+iaDs+e++++ah +D+lv+i++CDk+vPGmlmaa+rl+iP++vvsGGpm agk + ++ +d + NCBI__GCF_000816635.1:WP_039651789.1 87 MKFSLASRELIADSIEAMATAHGFDGLVLIPNCDKVVPGMLMAAARLDIPSVVVSGGPMRAGKSN-GKVLDFS 158 ****************************************************************9.9****** PP TIGR00110 147 dvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllatsaekkelakks 219 +e vg++++gk++e++lee + +cP++gsCsGlftansm+clte+lG+ lP ++t+la + e+++lak + NCBI__GCF_000816635.1:WP_039651789.1 159 TCIEQVGACSDGKITEDQLEEEAKKSCPGCGSCSGLFTANSMNCLTEVLGMGLPLNGTALAQTGERRQLAKYA 231 ************************************************************************* PP TIGR00110 220 gkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklslddfdrlsrkvPllaklk 292 g+++++ vk+n +P+dil +af+nait+d+a+ GstntvLhl+aia+eag+kl+ld fd++s+k+P+l kl+ NCBI__GCF_000816635.1:WP_039651789.1 232 GMYVMDCVKNNRRPSDILKLDAFKNAITMDMAMAGSTNTVLHLPAIAHEAGIKLDLDLFDEISQKTPCLIKLS 304 ************************************************************************* PP TIGR00110 293 PsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlrvdqdvirsldnpvkkegglav 365 Psgk+ +edlh aGG++a+++el+ +gl+ +d++tvtGkt++et+++++vl ++dvirs+dn+++ +ggla+ NCBI__GCF_000816635.1:WP_039651789.1 305 PSGKHHMEDLHMAGGIPALMHELSSKGLIAEDSMTVTGKTIGETIKEYNVL--NRDVIRSVDNAYSPKGGLAI 375 **************************************************9..******************** PP TIGR00110 366 LkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeGdvvviryeGPkGgPGmremLaPts 438 L+Gnla +Gavvk ++v+++++++eGpa+v++seeea++ai+g ++++Gdv+viryeGPkGgPGmremL Pts NCBI__GCF_000816635.1:WP_039651789.1 376 LRGNLAVDGAVVKESAVAKEMMVHEGPARVYNSEEEAVKAIFGDEINKGDVIVIRYEGPKGGPGMREMLSPTS 448 ************************************************************************* PP TIGR00110 439 alvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDienrkldlevseeelaerra 511 a++g+GL+k+vaL+tDGrfsG+trG siGhvsPea+egG i+lve+GD+i iDi+n+kl+l+v+ +el+er++ NCBI__GCF_000816635.1:WP_039651789.1 449 AIAGMGLDKDVALLTDGRFSGATRGASIGHVSPEAMEGGLIGLVEEGDTIFIDIKNKKLELKVDAKELEERKK 521 ************************************************************************* PP TIGR00110 512 kakkkearevkgaLakyaklvssadkGavld 542 + +k+e++ +kg+La+y+klv+sa++Gavl+ NCBI__GCF_000816635.1:WP_039651789.1 522 RYVKPEPKVKKGYLARYGKLVTSANTGAVLK 552 *****************************85 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (543 nodes) Target sequences: 1 (552 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: 00:00:00.01 # Mc/sec: 15.42 // [ok]
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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