Align dihydroxy-acid dehydratase subunit (EC 4.2.1.9) (characterized)
to candidate WP_013430882.1 CALKRO_RS09920 dihydroxy-acid dehydratase
Query= metacyc::MONOMER-11919 (549 letters) >NCBI__GCF_000166775.1:WP_013430882.1 Length = 552 Score = 612 bits (1577), Expect = e-179 Identities = 308/554 (55%), Positives = 413/554 (74%), Gaps = 9/554 (1%) Query: 1 MKSDTIKRGIQRAPHRSLLARCGLTDDDFEKPFIGIANSYTDIVPGHIHLRELAEAVKEG 60 M+SDT+K+G ++AP RSL G TD++ +P I + NS+ ++VPGHIHL +AEAVK G Sbjct: 1 MRSDTVKKGFEKAPQRSLFKAMGYTDEEIRRPLIAVVNSWNEVVPGHIHLDRIAEAVKAG 60 Query: 61 VNAAGGVAFEFNTMAICDGIAMNHDGMKYSLASREIVADTVESMAMAHALDGLVLLPTCD 120 + AG EFN + +CDGIAM H GMKYSL +RE++AD++E+M MAH DG+VL+P CD Sbjct: 61 IRLAGATPMEFNVIGVCDGIAMGHIGMKYSLITRELIADSIEAMVMAHQFDGMVLIPNCD 120 Query: 121 KIVPGMLMAAARLDIPAIVVTGGPMLPGEFKGRKVDLINVYEGVGTVSAGEMSEDELEEL 180 KIVPGMLMAAAR++IPAI+++GGPML G+ + DL +V+EGVG SAG++SE++L L Sbjct: 121 KIVPGMLMAAARVNIPAILISGGPMLAGKVGDKVCDLNSVFEGVGAYSAGKISEEDLYAL 180 Query: 181 ERCACPGPRSCAGLFTANTMACLTEALGMSLPGCATAHAVSSRKRQIARLSGKRIVEMVQ 240 E ACPG SC+G+FTANTM CL+E LG++LPG T AV + + ++A+++G +IVE+V+ Sbjct: 181 EENACPGCGSCSGMFTANTMNCLSEVLGLALPGNGTIPAVMAARIRLAKMAGMKIVELVE 240 Query: 241 ENLKPTMIMSQEAFENAVMVDLALGGSTNTTLHIPAIAAEIDGLNINLDLFDELSRVIPH 300 +++KP+ I++ EAFENA+ VD+ALGGSTNT LH+PAIA E+ G+ +NLD+ + +S P+ Sbjct: 241 KDIKPSDILTVEAFENALAVDMALGGSTNTILHLPAIANEV-GIKLNLDIINAISDRTPN 299 Query: 301 IASISPAGEHMMLDLDRAGGIPAVLKTLED----HINRECVTCTGRTVQENIENVKVGHR 356 + +SPAG+H + DL AGG+ AV+ L H+N +T TG+TV ENI++ V + Sbjct: 300 LCKLSPAGQHHIEDLYFAGGVQAVMNELSKKGLLHLN--LMTVTGKTVGENIKDANVKNY 357 Query: 357 DVIRPLDSPVHSEGGLAILRGNLAPRGSVVKQGAVAEDMMVHEGPAKVFNSEDECMEAIF 416 +VIRP+D+P GGL I+RGNLAP G+VVK+ AV +M H GPA+VF S +E EAI Sbjct: 358 NVIRPIDNPYSETGGLVIVRGNLAPDGAVVKKSAVPPKLMKHRGPARVFESGEEVFEAIL 417 Query: 417 GGRIDEGDVIVIRYEGPKGGPGMREMLNPTSAIAGMGL-ERVALITDGRFSGGTRGPCVG 475 G+I +GDVIVIRYEGPKGGPGMREML+PTSA+AG+GL E VALITDGRFSG TRG C G Sbjct: 418 KGKIQKGDVIVIRYEGPKGGPGMREMLSPTSALAGVGLIEDVALITDGRFSGATRGACFG 477 Query: 476 HVSPEAMEDGPLAAVNDGDIIRIDIPSRKLEVDLSPREIEERLQSAVKPRRSV-KGWLAR 534 HVSPEA E GP+AAV DGD+I IDI ++ L +++ EI+ RL+ V KG+L R Sbjct: 478 HVSPEAAERGPIAAVQDGDMISIDIENKTLTLEVPEEEIKRRLEILPPFEPKVKKGYLYR 537 Query: 535 YRKLAGSADTGAVL 548 Y KL SA TGA+L Sbjct: 538 YSKLVRSASTGAIL 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: 946 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_013430882.1 CALKRO_RS09920 (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.677240.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.9e-252 822.3 6.2 1e-251 822.2 6.2 1.0 1 NCBI__GCF_000166775.1:WP_013430882.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000166775.1:WP_013430882.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 822.2 6.2 1e-251 1e-251 1 541 [. 14 551 .. 14 552 .] 0.99 Alignments for each domain: == domain 1 score: 822.2 bits; conditional E-value: 1e-251 TIGR00110 1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamgheG 73 ++r+l+ka+G++de++ +P+iavvns++e+vPgh+hl+ +a++vk++i+ aG++++efn+i+v+DGiamgh G NCBI__GCF_000166775.1:WP_013430882.1 14 PQRSLFKAMGYTDEEIRRPLIAVVNSWNEVVPGHIHLDRIAEAVKAGIRLAGATPMEFNVIGVCDGIAMGHIG 86 589********************************************************************** PP TIGR00110 74 mkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktklsekidlv 146 mkysL +re+iaDs+e++v+ah++D++v+i++CDkivPGmlmaa+r+niPai++sGGpm agk+ + dl NCBI__GCF_000166775.1:WP_013430882.1 87 MKYSLITRELIADSIEAMVMAHQFDGMVLIPNCDKIVPGMLMAAARVNIPAILISGGPMLAGKVG-DKVCDLN 158 ****************************************************************9.78899** PP TIGR00110 147 dvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllatsaekkelakks 219 +vfe+vg+y+agk+see+l+++e++acP++gsCsG+ftan+m+cl+e+lGl+lPg++t++a+ a + +lak + NCBI__GCF_000166775.1:WP_013430882.1 159 SVFEGVGAYSAGKISEEDLYALEENACPGCGSCSGMFTANTMNCLSEVLGLALPGNGTIPAVMAARIRLAKMA 231 ************************************************************************* PP TIGR00110 220 gkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklslddfdrlsrkvPllaklk 292 g++ivelv+k+ikP+dilt eafena+++d+alGGstnt+Lhl+aia+e+g+kl+ld ++ +s+++P l+kl+ NCBI__GCF_000166775.1:WP_013430882.1 232 GMKIVELVEKDIKPSDILTVEAFENALAVDMALGGSTNTILHLPAIANEVGIKLNLDIINAISDRTPNLCKLS 304 ************************************************************************* PP TIGR00110 293 PsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlrvdqdvirsldnpvkkegglav 365 P+g++ iedl aGGv+av++el+k+gllh + +tvtGkt++e++++++v+ +++vir++dnp++++ggl + NCBI__GCF_000166775.1:WP_013430882.1 305 PAGQHHIEDLYFAGGVQAVMNELSKKGLLHLNLMTVTGKTVGENIKDANVK--NYNVIRPIDNPYSETGGLVI 375 ***************************************************..******************** PP TIGR00110 366 LkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeGdvvviryeGPkGgPGmremLaPts 438 ++Gnla++Gavvk ++v +++k++Gpa+vfes ee+ eail+gk+++Gdv+viryeGPkGgPGmremL Pts NCBI__GCF_000166775.1:WP_013430882.1 376 VRGNLAPDGAVVKKSAVPPKLMKHRGPARVFESGEEVFEAILKGKIQKGDVIVIRYEGPKGGPGMREMLSPTS 448 ************************************************************************* PP TIGR00110 439 alvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDienrkldlevseeelaerra 511 al+g+GL ++vaLitDGrfsG+trG + GhvsPeaae G+ia v+dGD+i+iDien++l lev eee+++r + NCBI__GCF_000166775.1:WP_013430882.1 449 ALAGVGLIEDVALITDGRFSGATRGACFGHVSPEAAERGPIAAVQDGDMISIDIENKTLTLEVPEEEIKRRLE 521 ************************************************************************* PP TIGR00110 512 kakkkearevkgaLakyaklvssadkGavl 541 + e++ +kg+L +y+klv+sa++Ga+l NCBI__GCF_000166775.1:WP_013430882.1 522 ILPPFEPKVKKGYLYRYSKLVRSASTGAIL 551 ****************************97 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: 18.95 // [ok]
This GapMind analysis is from Jul 26 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