Align dihydroxy-acid dehydratase subunit (EC 4.2.1.9) (characterized)
to candidate WP_015738270.1 ADEG_RS01125 dihydroxy-acid dehydratase
Query= metacyc::MONOMER-11919 (549 letters) >NCBI__GCF_000024605.1:WP_015738270.1 Length = 553 Score = 619 bits (1597), Expect = 0.0 Identities = 313/551 (56%), Positives = 412/551 (74%), Gaps = 5/551 (0%) Query: 1 MKSDTIKRGIQRAPHRSLLARCGLTDDDFEKPFIGIANSYTDIVPGHIHLRELAEAVKEG 60 M+S K G+++APHRSL GLT ++ ++PFIG+ N+++++VPGH+HLR++AEAVK G Sbjct: 1 MRSGRAKEGLEKAPHRSLWKALGLTTEELKRPFIGVVNAFSELVPGHVHLRDIAEAVKAG 60 Query: 61 VNAAGGVAFEFNTMAICDGIAMNHDGMKYSLASREIVADTVESMAMAHALDGLVLLPTCD 120 V AGGV EF + +CDGIAMNH+GMKYSLASRE++AD+VE MA AHALDGLV + CD Sbjct: 61 VRLAGGVPLEFPVIGVCDGIAMNHEGMKYSLASRELIADSVEVMAEAHALDGLVFVAACD 120 Query: 121 KIVPGMLMAAARLDIPAIVVTGGPMLPGEFKGRKVDLINVYEGVGTVSAGEMSEDELEEL 180 KIVPG+LMAAARLD+PAI+V+GGPML G F+G V L V+E VG V AG+M+E+EL EL Sbjct: 121 KIVPGLLMAAARLDLPAILVSGGPMLAGRFRGENVSLSTVFEAVGRVKAGKMAEEELAEL 180 Query: 181 ERCACPGPRSCAGLFTANTMACLTEALGMSLPGCATAHAVSSRKRQIARLSGKRIVEMVQ 240 E ACPG SCAG+FTAN+M CL E LG++LPG +T AVS+ +R++A+L+G R VE+V+ Sbjct: 181 EEVACPGCGSCAGMFTANSMNCLAEVLGLALPGNSTIPAVSAARRRLAKLAGMRAVELVK 240 Query: 241 ENLKPTMIMSQEAFENAVMVDLALGGSTNTTLHIPAIAAEIDGLNINLDLFDELSRVIPH 300 E L P+ I+S +F NA+ VD+ALG STNT LH+ AIA E G+ +L + +S +P+ Sbjct: 241 EGLTPSRILSPASFHNALAVDMALGCSTNTVLHLAAIAHEA-GIPFSLAEVNRISERVPN 299 Query: 301 IASISPAGEHMMLDLDRAGGIPAVLKTLEDH--INRECVTCTGRTVQENIENVKVGHRDV 358 + + PAG H + DLD AGGIPAV+ L + I E +T TGRT++EN+++ +V +V Sbjct: 300 LCRLDPAGVHRLQDLDEAGGIPAVVNLLLEAGLIEGEVLTVTGRTLRENVKDARVRRPEV 359 Query: 359 IRPLDSPVHSEGGLAILRGNLAPRGSVVKQGAVAEDMMVHEGPAKVFNSEDECMEAIFGG 418 IRP++ P GGLA+L GNLAP G+VVKQ AVA +M+ H GPA+VF+SE+E +EAI G Sbjct: 360 IRPVEDPYSPTGGLAVLFGNLAPEGAVVKQAAVAPEMLRHTGPARVFDSEEEAVEAILAG 419 Query: 419 RIDEGDVIVIRYEGPKGGPGMREMLNPTSAIAGMGLER-VALITDGRFSGGTRGPCVGHV 477 G+VIVIRYEGP+GGPGMREML T+A+AGMG ++ VALITDGRFSG TRG +GHV Sbjct: 420 NFRAGEVIVIRYEGPRGGPGMREMLTATAALAGMGRDKEVALITDGRFSGATRGASIGHV 479 Query: 478 SPEAMEDGPLAAVNDGDIIRIDIPSRKLEVDLSPREIEERLQSAVKPR-RSVKGWLARYR 536 SPEA GP+AA+ DGD+I IDIP+R+LEV L E+ RL++ R R +G+L+RY Sbjct: 480 SPEAAARGPIAALKDGDLITIDIPARRLEVHLDEGELARRLEALPPFRPRVTRGYLSRYA 539 Query: 537 KLAGSADTGAV 547 L SA GAV Sbjct: 540 SLVSSAAQGAV 550 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: 943 Number of extensions: 38 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: 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_015738270.1 ADEG_RS01125 (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.10217.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.8e-243 793.8 0.1 4.3e-243 793.7 0.1 1.0 1 lcl|NCBI__GCF_000024605.1:WP_015738270.1 ADEG_RS01125 dihydroxy-acid dehy Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000024605.1:WP_015738270.1 ADEG_RS01125 dihydroxy-acid dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 793.7 0.1 4.3e-243 4.3e-243 1 541 [. 14 551 .. 14 553 .] 1.00 Alignments for each domain: == domain 1 score: 793.7 bits; conditional E-value: 4.3e-243 TIGR00110 1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiam 69 ++r+l+ka+Gl+ e+l++P+i+vvn+++e+vPghvhl+d+a++vk++++ aGgv+ ef +i+v+DGiam lcl|NCBI__GCF_000024605.1:WP_015738270.1 14 PHRSLWKALGLTTEELKRPFIGVVNAFSELVPGHVHLRDIAEAVKAGVRLAGGVPLEFPVIGVCDGIAM 82 69******************************************************************* PP TIGR00110 70 gheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktk 138 +heGmkysL+sre+iaDsve +++ahalD+lv +++CDkivPG+lmaa+rl++Pai+vsGGpm ag+++ lcl|NCBI__GCF_000024605.1:WP_015738270.1 83 NHEGMKYSLASRELIADSVEVMAEAHALDGLVFVAACDKIVPGLLMAAARLDLPAILVSGGPMLAGRFR 151 ********************************************************************* PP TIGR00110 139 lsekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstlla 207 +e+++l+ vfeavg+++agk+ eeel e+e++acP++gsC+G+ftansm+cl+e+lGl+lPg+st++a lcl|NCBI__GCF_000024605.1:WP_015738270.1 152 -GENVSLSTVFEAVGRVKAGKMAEEELAELEEVACPGCGSCAGMFTANSMNCLAEVLGLALPGNSTIPA 219 .9******************************************************************* PP TIGR00110 208 tsaekkelakksgkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklsld 276 +sa +++lak +g+r velvk+ ++P++il+ ++f na+++d+alG stntvLhl aia+eag+ +sl lcl|NCBI__GCF_000024605.1:WP_015738270.1 220 VSAARRRLAKLAGMRAVELVKEGLTPSRILSPASFHNALAVDMALGCSTNTVLHLAAIAHEAGIPFSLA 288 ********************************************************************* PP TIGR00110 277 dfdrlsrkvPllaklkPsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlrv 345 +++r+s++vP l+ l+P+g + ++dl++aGG++av++ l ++gl++ ++ltvtG+tl e++++++v+ lcl|NCBI__GCF_000024605.1:WP_015738270.1 289 EVNRISERVPNLCRLDPAGVHRLQDLDEAGGIPAVVNLLLEAGLIEGEVLTVTGRTLRENVKDARVR-- 355 ******************************************************************9.. PP TIGR00110 346 dqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeG 414 +vir++++p++ +gglavL+Gnla+eGavvk+a+v+ ++l+++Gpa+vf+seeea+eail+g+ ++G lcl|NCBI__GCF_000024605.1:WP_015738270.1 356 RPEVIRPVEDPYSPTGGLAVLFGNLAPEGAVVKQAAVAPEMLRHTGPARVFDSEEEAVEAILAGNFRAG 424 89******************************************************************* PP TIGR00110 415 dvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialve 483 +v+viryeGP+GgPGmremL+ t+al+g+G +k+vaLitDGrfsG+trG siGhvsPeaa+ G+ia ++ lcl|NCBI__GCF_000024605.1:WP_015738270.1 425 EVIVIRYEGPRGGPGMREMLTATAALAGMGRDKEVALITDGRFSGATRGASIGHVSPEAAARGPIAALK 493 ********************************************************************* PP TIGR00110 484 dGDkikiDienrkldlevseeelaerrakakkkearevkgaLakyaklvssadkGavl 541 dGD i+iDi++r+l+++++e ela+r ++ + ++r ++g+L++ya+lvssa +Gav lcl|NCBI__GCF_000024605.1:WP_015738270.1 494 DGDLITIDIPARRLEVHLDEGELARRLEALPPFRPRVTRGYLSRYASLVSSAAQGAVF 551 ********************************************************95 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 12.57 // [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