Align dihydroxy-acid dehydratase subunit (EC 4.2.1.9) (characterized)
to candidate WP_011736418.1 PPRO_RS12640 dihydroxy-acid dehydratase
Query= metacyc::MONOMER-11919 (549 letters) >NCBI__GCF_000015045.1:WP_011736418.1 Length = 553 Score = 583 bits (1503), Expect = e-171 Identities = 304/551 (55%), Positives = 395/551 (71%), Gaps = 6/551 (1%) Query: 1 MKSDTIKRGIQRAPHRSLLARCGLTDDDFEKPFIGIANSYTDIVPGHIHLRELAEAVKEG 60 M+SDTI +G +R PHR+LL G+ +KPFIG+A S+TD++PGH+ +R+L +++G Sbjct: 1 MRSDTITQGFERTPHRALLKGSGVPQSQMDKPFIGVATSFTDLIPGHVGMRDLERFIEKG 60 Query: 61 VNAAGGVAFEFNTMAICDGIAMNHDGMKYSLASREIVADTVESMAMAHALDGLVLLPTCD 120 V+ GG AF F +CDGIAM H GM YSL +RE++AD VES+A AH LDGLVLL CD Sbjct: 61 VHTGGGHAFFFGLPGVCDGIAMGHKGMHYSLPTRELIADMVESVAEAHRLDGLVLLTNCD 120 Query: 121 KIVPGMLMAAARLDIPAIVVTGGPMLPGE-FKGRKVDLI-NVYEGVGTVSAGEMSEDELE 178 KI PGMLMAAARLDIP IVVT GPM+ G +GRK + + +E + AG +SE EL Sbjct: 121 KITPGMLMAAARLDIPCIVVTAGPMMSGRGQEGRKFSFVTDTFEAMARYKAGVISERELM 180 Query: 179 ELERCACPGPRSCAGLFTANTMACLTEALGMSLPGCATAHAVSSRKRQIARLSGKRIVEM 238 E ACPG SC GLFTANTMA LTE +GMSLP C TA AVS+ KR+IA SG++IVE+ Sbjct: 181 VCEENACPGIGSCQGLFTANTMAILTETMGMSLPRCGTALAVSALKRRIAFASGEKIVEL 240 Query: 239 VQENLKPTMIMSQEAFENAVMVDLALGGSTNTTLHIPAIAAEIDGLNINLDLFDELSRVI 298 VQ N+ P I+++EAFENA+ VDLALGGS+NT LH+ AIA E G+ + L+ FD L++ Sbjct: 241 VQNNITPRSILTREAFENAIRVDLALGGSSNTVLHLLAIANEA-GVELPLETFDILAKET 299 Query: 299 PHIASISPAGEHMMLDLDRAGGIPAVLKTLEDHINRECVTCTGRTVQENIENVKVGHRDV 358 P +AS++PAGEH M DLD AGG+ V+K L D I ++ T G T ++ +V+ V Sbjct: 300 PQLASMNPAGEHFMEDLDVAGGVSGVMKQLGDKI-KDTQTLFGLTTRQLAASVENVDETV 358 Query: 359 IRPLDSPVHSEGGLAILRGNLAPRGSVVKQGAVAEDMMVHEGPAKVFNSEDECMEAIFGG 418 IRPL +PV EGG+A+L GN+AP+G+VVKQ V++ MM EG A+ F+SE+ M A+ G Sbjct: 359 IRPLTNPVKKEGGIAVLFGNIAPKGAVVKQSGVSDKMMKFEGTARCFDSEELAMAALMEG 418 Query: 419 RIDEGDVIVIRYEGPKGGPGMREMLNPTSAIAGMGL-ERVALITDGRFSGGTRGPCVGHV 477 I G+V+VIRYEGPKGGPGMREML PT+A+ G+GL + VALITDGRFSGGTRGPC+GH+ Sbjct: 419 EIVAGNVVVIRYEGPKGGPGMREMLAPTAALMGLGLGDSVALITDGRFSGGTRGPCIGHI 478 Query: 478 SPEAMEDGPLAAVNDGDIIRIDIPSRKLEVDLSPREIEERLQSAVKPRRSV-KGWLARYR 536 SPEA + GP+ + DGD I +DIP+R+LE+ + ++ R + V P + KGWLARY Sbjct: 479 SPEAAQGGPIGLIQDGDRISLDIPARRLELLVDEAVLQARAATWVAPPPKIAKGWLARYA 538 Query: 537 KLAGSADTGAV 547 K+ SA TGAV Sbjct: 539 KVVTSAHTGAV 549 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: 958 Number of extensions: 51 Number of successful extensions: 7 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_011736418.1 PPRO_RS12640 (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.27479.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-232 758.6 3.8 2.1e-232 758.4 3.8 1.0 1 lcl|NCBI__GCF_000015045.1:WP_011736418.1 PPRO_RS12640 dihydroxy-acid dehy Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000015045.1:WP_011736418.1 PPRO_RS12640 dihydroxy-acid dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 758.4 3.8 2.1e-232 2.1e-232 1 542 [. 14 551 .. 14 552 .. 0.99 Alignments for each domain: == domain 1 score: 758.4 bits; conditional E-value: 2.1e-232 TIGR00110 1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiam 69 ++rallk G+ + +++kP+i+v+ s+t+++Pghv ++dl + +++++++ Gg a+ f+ +v+DGiam lcl|NCBI__GCF_000015045.1:WP_011736418.1 14 PHRALLKGSGVPQSQMDKPFIGVATSFTDLIPGHVGMRDLERFIEKGVHTGGGHAFFFGLPGVCDGIAM 82 69******************************************************************* PP TIGR00110 70 gheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktk 138 gh+Gm+ysLp+re+iaD ve+v++ah+lD+lv++++CDki+PGmlmaa+rl+iP ivv+ Gpm++g+ + lcl|NCBI__GCF_000015045.1:WP_011736418.1 83 GHKGMHYSLPTRELIADMVESVAEAHRLDGLVLLTNCDKITPGMLMAAARLDIPCIVVTAGPMMSGRGQ 151 ********************************************************************* PP TIGR00110 139 lsekidl.vdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstll 206 ++k++ +d fea+ +y+ag +se el e++acP+ gsC+Glftan+ma+lte++G+slP ++t+l lcl|NCBI__GCF_000015045.1:WP_011736418.1 152 EGRKFSFvTDTFEAMARYKAGVISERELMVCEENACPGIGSCQGLFTANTMAILTETMGMSLPRCGTAL 220 ****986269*********************************************************** PP TIGR00110 207 atsaekkelakksgkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklsl 275 a+sa k+++a sg++ivelv++ni+Pr+ilt+eafenai +dlalGGs+ntvLhllaia+eagv+l l lcl|NCBI__GCF_000015045.1:WP_011736418.1 221 AVSALKRRIAFASGEKIVELVQNNITPRSILTREAFENAIRVDLALGGSSNTVLHLLAIANEAGVELPL 289 ********************************************************************* PP TIGR00110 276 ddfdrlsrkvPllaklkPsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlr 344 + fd l++++P+la+++P+g++++edl+ aGGvs+v+k+l +++ kd++t+ G t + +++v+ lcl|NCBI__GCF_000015045.1:WP_011736418.1 290 ETFDILAKETPQLASMNPAGEHFMEDLDVAGGVSGVMKQL--GDKI-KDTQTLFGLTTRQLAASVENV- 354 ****************************************..6666.688**********99999988. PP TIGR00110 345 vdqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvke 413 d+ vir+l npvkkegg+avL+Gn+a++Gavvk++gv+++++kfeG+a+ f+see a++a+++g++ + lcl|NCBI__GCF_000015045.1:WP_011736418.1 355 -DETVIRPLTNPVKKEGGIAVLFGNIAPKGAVVKQSGVSDKMMKFEGTARCFDSEELAMAALMEGEIVA 422 .******************************************************************** PP TIGR00110 414 GdvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialv 482 G+vvviryeGPkGgPGmremLaPt+al+glGLg++vaLitDGrfsGgtrG++iGh+sPeaa+gG+i+l+ lcl|NCBI__GCF_000015045.1:WP_011736418.1 423 GNVVVIRYEGPKGGPGMREMLAPTAALMGLGLGDSVALITDGRFSGGTRGPCIGHISPEAAQGGPIGLI 491 ********************************************************************* PP TIGR00110 483 edGDkikiDienrkldlevseeelaerrakakkkearevkgaLakyaklvssadkGavld 542 +dGD+i++Di++r+l+l v+e+ l++r a+++++ ++ kg+La+yak+v+sa++Gav++ lcl|NCBI__GCF_000015045.1:WP_011736418.1 492 QDGDRISLDIPARRLELLVDEAVLQARAATWVAPPPKIAKGWLARYAKVVTSAHTGAVTT 551 *********************************************************985 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: 11.58 // [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