Align dihydroxy-acid dehydratase subunit (EC 4.2.1.9) (characterized)
to candidate WP_092483005.1 BM299_RS08280 dihydroxy-acid dehydratase
Query= metacyc::MONOMER-11919 (549 letters) >NCBI__GCF_900115975.1:WP_092483005.1 Length = 562 Score = 637 bits (1644), Expect = 0.0 Identities = 316/553 (57%), Positives = 415/553 (75%), Gaps = 5/553 (0%) Query: 1 MKSDTIKRGIQRAPHRSLLARCGLTDDDFEKPFIGIANSYTDIVPGHIHLRELAEAVKEG 60 M+SD +K+G+++APHRSL G+TD + E+P IG+ NS+ +IVPGH+HLREL EAVK G Sbjct: 1 MRSDAMKKGLEKAPHRSLFKALGMTDQELERPMIGVVNSFNEIVPGHMHLRELTEAVKAG 60 Query: 61 VNAAGGVAFEFNTMAICDGIAMNHDGMKYSLASREIVADTVESMAMAHALDGLVLLPTCD 120 V GG EF +A+CDGIAMNH GMKYSLASREI+AD+VE M+MAH DGLVL+ CD Sbjct: 61 VRMNGGTPVEFPAIAVCDGIAMNHAGMKYSLASREIIADSVEVMSMAHPFDGLVLVTACD 120 Query: 121 KIVPGMLMAAARLDIPAIVVTGGPMLPGEFKGRKVDLINVYEGVGTVSAGEMSEDELEEL 180 K+VPGMLMAAARLDIPAIVV+GGPML G GR + L N++E VG V AG+++E EL E+ Sbjct: 121 KVVPGMLMAAARLDIPAIVVSGGPMLAGRHGGRDLALTNIFEAVGAVRAGKITETELAEI 180 Query: 181 ERCACPGPRSCAGLFTANTMACLTEALGMSLPGCATAHAVSSRKRQIARLSGKRIVEMVQ 240 E CPG SCAG+FTAN+M CLTEALGM+LPG T AVS+ +R++A+L+G R+V++V+ Sbjct: 181 EESVCPGCGSCAGMFTANSMNCLTEALGMALPGNGTLPAVSAARRRLAKLTGMRVVDLVR 240 Query: 241 ENLKPTMIMSQEAFENAVMVDLALGGSTNTTLHIPAIAAEIDGLNINLDLFDELSRVIPH 300 EN++P+ IM+++AF N + +D+ALG STNT LH+PAIA E G+ INLD + +S P+ Sbjct: 241 ENVRPSDIMTEKAFTNGLALDMALGCSTNTVLHLPAIAHEA-GVAINLDQINRISEKTPN 299 Query: 301 IASISPAGEHMMLDLDRAGGIPAVLKTLEDH--INRECVTCTGRTVQENIENVKVGHRDV 358 + +SP G H M DL+ AGG+ AVL+ L DH ++ +T TG++++ENI + DV Sbjct: 300 LCKLSPIGPHFMQDLNEAGGVSAVLRELADHGLVDGSALTVTGKSLRENIAGAVIHRGDV 359 Query: 359 IRPLDSPVHSEGGLAILRGNLAPRGSVVKQGAVAEDMMVHEGPAKVFNSEDECMEAIFGG 418 IR + P S GG+A+L GNLAP G+VVK+ VA +M+ H GPA+V+NSE+E ++A+ Sbjct: 360 IRSVKEPYSSSGGIAVLYGNLAPGGAVVKKAGVAPEMLKHRGPARVYNSEEEAVQALMNQ 419 Query: 419 RIDEGDVIVIRYEGPKGGPGMREMLNPTSAIAGMGLER-VALITDGRFSGGTRGPCVGHV 477 I +GDVIVIRYEGPKGGPGMREML PT+ +AG+GL++ VALITDGRFSG TRG +GHV Sbjct: 420 EIQKGDVIVIRYEGPKGGPGMREMLTPTATVAGLGLDKDVALITDGRFSGATRGASIGHV 479 Query: 478 SPEAMEDGPLAAVNDGDIIRIDIPSRKLEVDLSPREIEERLQSAVKPR-RSVKGWLARYR 536 +PEA E GP+A + DGD++ I+IP +L V+LS E+ RL VKP R KG+LARY Sbjct: 480 TPEAAEGGPIAVLQDGDVVEINIPECRLNVELSDEELSARLGKWVKPEPRVQKGYLARYA 539 Query: 537 KLAGSADTGAVLR 549 + SA TGAVLR Sbjct: 540 QAVTSAGTGAVLR 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: 1037 Number of extensions: 42 Number of successful extensions: 6 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: 562 Length adjustment: 36 Effective length of query: 513 Effective length of database: 526 Effective search space: 269838 Effective search space used: 269838 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_092483005.1 BM299_RS08280 (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.8838.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.9e-246 802.9 7.7 7.9e-246 802.7 7.7 1.0 1 lcl|NCBI__GCF_900115975.1:WP_092483005.1 BM299_RS08280 dihydroxy-acid deh Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900115975.1:WP_092483005.1 BM299_RS08280 dihydroxy-acid dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 802.7 7.7 7.9e-246 7.9e-246 1 542 [. 14 552 .. 14 553 .. 1.00 Alignments for each domain: == domain 1 score: 802.7 bits; conditional E-value: 7.9e-246 TIGR00110 1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiam 69 ++r+l+ka+G++d++le+P+i+vvns++eivPgh+hl++l+++vk++++ +Gg+++ef iav+DGiam lcl|NCBI__GCF_900115975.1:WP_092483005.1 14 PHRSLFKALGMTDQELERPMIGVVNSFNEIVPGHMHLRELTEAVKAGVRMNGGTPVEFPAIAVCDGIAM 82 69******************************************************************* PP TIGR00110 70 gheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktk 138 +h GmkysL+sreiiaDsve + +ah +D+lv++++CDk+vPGmlmaa+rl+iPaivvsGGpm ag+ lcl|NCBI__GCF_900115975.1:WP_092483005.1 83 NHAGMKYSLASREIIADSVEVMSMAHPFDGLVLVTACDKVVPGMLMAAARLDIPAIVVSGGPMLAGRHG 151 ********************************************************************9 PP TIGR00110 139 lsekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstlla 207 ++++ l+++feavg++ agk++e el eie+s cP++gsC+G+ftansm+cltealG++lPg++tl+a lcl|NCBI__GCF_900115975.1:WP_092483005.1 152 -GRDLALTNIFEAVGAVRAGKITETELAEIEESVCPGCGSCAGMFTANSMNCLTEALGMALPGNGTLPA 219 .9******************************************************************* PP TIGR00110 208 tsaekkelakksgkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklsld 276 +sa +++lak +g+r+v+lv++n++P+di+t++af n ++ld+alG stntvLhl+aia+eagv ++ld lcl|NCBI__GCF_900115975.1:WP_092483005.1 220 VSAARRRLAKLTGMRVVDLVRENVRPSDIMTEKAFTNGLALDMALGCSTNTVLHLPAIAHEAGVAINLD 288 ********************************************************************* PP TIGR00110 277 dfdrlsrkvPllaklkPsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlrv 345 +++r+s+k+P l+kl+P g ++++dl++aGGvsavl+el +gl++ altvtGk+l e+++ + ++ lcl|NCBI__GCF_900115975.1:WP_092483005.1 289 QINRISEKTPNLCKLSPIGPHFMQDLNEAGGVSAVLRELADHGLVDGSALTVTGKSLRENIAGAVIH-- 355 ****************************************************************999.. PP TIGR00110 346 dqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeG 414 dvirs+++p+++ gg+avL+Gnla+ Gavvk agv+ ++lk++Gpa+v++seeea++a+++ ++++G lcl|NCBI__GCF_900115975.1:WP_092483005.1 356 RGDVIRSVKEPYSSSGGIAVLYGNLAPGGAVVKKAGVAPEMLKHRGPARVYNSEEEAVQALMNQEIQKG 424 89******************************************************************* PP TIGR00110 415 dvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialve 483 dv+viryeGPkGgPGmremL+Pt++++glGL+k+vaLitDGrfsG+trG siGhv+PeaaegG+ia+++ lcl|NCBI__GCF_900115975.1:WP_092483005.1 425 DVIVIRYEGPKGGPGMREMLTPTATVAGLGLDKDVALITDGRFSGATRGASIGHVTPEAAEGGPIAVLQ 493 ********************************************************************* PP TIGR00110 484 dGDkikiDienrkldlevseeelaerrakakkkearevkgaLakyaklvssadkGavld 542 dGD ++i+i++ +l++e+s+eel +r k++k+e+r +kg+La+ya+ v+sa +Gavl+ lcl|NCBI__GCF_900115975.1:WP_092483005.1 494 DGDVVEINIPECRLNVELSDEELSARLGKWVKPEPRVQKGYLARYAQAVTSAGTGAVLR 552 *********************************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (543 nodes) Target sequences: 1 (562 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: 12.07 // [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