Align dihydroxy-acid dehydratase subunit (EC 4.2.1.9) (characterized)
to candidate WP_011021805.1 MA_RS09370 dihydroxy-acid dehydratase
Query= metacyc::MONOMER-11919 (549 letters) >NCBI__GCF_000007345.1:WP_011021805.1 Length = 553 Score = 660 bits (1704), Expect = 0.0 Identities = 322/553 (58%), Positives = 426/553 (77%), Gaps = 6/553 (1%) Query: 1 MKSDTIKRGIQRAPHRSLLARCGLTDDDFEKPFIGIANSYTDIVPGHIHLRELAEAVKEG 60 M+S IK G +RA +RSLL G+TD + +KPFI + NS+ +IVPGHIHL +LAEAVK G Sbjct: 1 MRSAIIKEGPERAANRSLLKATGVTDSEMKKPFIAVVNSWNEIVPGHIHLDKLAEAVKAG 60 Query: 61 VNAAGGVAFEFNTMAICDGIAMNHDGMKYSLASREIVADTVESMAMAHALDGLVLLPTCD 120 + AGGV FEF+T+ +CDG+AM H+GMKYSL SRE++ DT+E M AH DG+VL+PTCD Sbjct: 61 IRNAGGVPFEFHTIGVCDGLAMGHEGMKYSLPSREVIEDTIELMVRAHQFDGMVLIPTCD 120 Query: 121 KIVPGMLMAAARLDIPAIVVTGGPMLPGEFKGRKVDLINVYEGVGTVSAGEMSEDELEEL 180 KIVPG LMAA RLDIPAIVVTGGPMLPG + DLI+V+EGVG SAG++SE EL+ L Sbjct: 121 KIVPGHLMAAGRLDIPAIVVTGGPMLPGYVDDKYTDLISVFEGVGAYSAGKLSEAELKRL 180 Query: 181 ERCACPGPRSCAGLFTANTMACLTEALGMSLPGCATAHAVSSRKRQIARLSGKRIVEMVQ 240 E +C G SCAG+FTANTMAC+TEALG+SLPGCATAHAV ++K +IA+ SG+RIV +V+ Sbjct: 181 ENLSCAGAGSCAGMFTANTMACMTEALGLSLPGCATAHAVDAKKVRIAKESGERIVALVK 240 Query: 241 ENLKPTMIMSQEAFENAVMVDLALGGSTNTTLHIPAIAAEIDGLNINLDLFDELSRVIPH 300 ENL P I++Q++FENA+MVD+A+GGSTNTTLH+PA+A E GL + L FDELSR PH Sbjct: 241 ENLTPRKIVTQKSFENAIMVDMAVGGSTNTTLHLPALAHEF-GLELPLKTFDELSRTTPH 299 Query: 301 IASISPAGEHMMLDLDRAGGIPAVLKTLEDHINRECVTCTGRTVQENIENVKVG----HR 356 + S+ P G + ML DRAGG+ AV++ L ++ + +T G+T+ EN++ +++ + Sbjct: 300 LISLRPGGPNFMLHFDRAGGVEAVVQRLASKLHLDQLTVNGKTIGENLDELEIVNPKLNA 359 Query: 357 DVIRPLDSPVHSEGGLAILRGNLAPRGSVVKQGAVAEDMMVHEGPAKVFNSEDECMEAIF 416 ++I L++P+H+EGG+A+L+G+LAP GSVVKQ AV M VH GPAKV++ E++ M++I Sbjct: 360 EIITTLENPIHAEGGIAVLKGSLAPDGSVVKQAAVDPKMRVHTGPAKVYDCEEDAMKSIL 419 Query: 417 GGRIDEGDVIVIRYEGPKGGPGMREMLNPTSAIAGMG-LERVALITDGRFSGGTRGPCVG 475 G + GD++VIRYEGPKGGPGMREML T+AI GMG LE VALITDGRFSGGTRGPC+G Sbjct: 420 AGDVKPGDIVVIRYEGPKGGPGMREMLAATAAIGGMGLLESVALITDGRFSGGTRGPCIG 479 Query: 476 HVSPEAMEDGPLAAVNDGDIIRIDIPSRKLEVDLSPREIEERLQSAVKPRRSVKGWLARY 535 HVSPEA E GP+ V DGD+I I+IP R L + ++ E+E+R + V P++ V G+LARY Sbjct: 480 HVSPEASEGGPIGLVKDGDLIEINIPERILNLKVTEEELEKRKAAFVPPKKEVTGYLARY 539 Query: 536 RKLAGSADTGAVL 548 ++ SA+TG ++ Sbjct: 540 QRSVHSANTGGIV 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: 1070 Number of extensions: 57 Number of successful extensions: 4 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_011021805.1 MA_RS09370 (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.1323.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.6e-245 799.1 3.9 1.1e-244 798.9 3.9 1.0 1 lcl|NCBI__GCF_000007345.1:WP_011021805.1 MA_RS09370 dihydroxy-acid dehydr Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000007345.1:WP_011021805.1 MA_RS09370 dihydroxy-acid dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 798.9 3.9 1.1e-244 1.1e-244 1 542 [. 14 553 .] 14 553 .] 0.99 Alignments for each domain: == domain 1 score: 798.9 bits; conditional E-value: 1.1e-244 TIGR00110 1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiam 69 a+r+llkatG++d +++kP+iavvns++eivPgh+hl++la++vk++i++aGgv++ef ti+v+DG+am lcl|NCBI__GCF_000007345.1:WP_011021805.1 14 ANRSLLKATGVTDSEMKKPFIAVVNSWNEIVPGHIHLDKLAEAVKAGIRNAGGVPFEFHTIGVCDGLAM 82 68******************************************************************* PP TIGR00110 70 gheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktk 138 gheGmkysLpsre+i D++e +v+ah++D++v+i++CDkivPG lmaa rl+iPaivv+GGpm +g + lcl|NCBI__GCF_000007345.1:WP_011021805.1 83 GHEGMKYSLPSREVIEDTIELMVRAHQFDGMVLIPTCDKIVPGHLMAAGRLDIPAIVVTGGPMLPGYVD 151 ********************************************************************9 PP TIGR00110 139 lsekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstlla 207 + dl++vfe+vg+y+agklse+el+++e+ +c +agsC+G+ftan+mac+tealGlslPg++t++a lcl|NCBI__GCF_000007345.1:WP_011021805.1 152 -DKYTDLISVFEGVGAYSAGKLSEAELKRLENLSCAGAGSCAGMFTANTMACMTEALGLSLPGCATAHA 219 .7999**************************************************************** PP TIGR00110 208 tsaekkelakksgkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklsld 276 ++a+k ++ak+sg+riv lvk+n++Pr+i+t+++fenai++d+a+GGstnt+Lhl+a+a+e g++l l+ lcl|NCBI__GCF_000007345.1:WP_011021805.1 220 VDAKKVRIAKESGERIVALVKENLTPRKIVTQKSFENAIMVDMAVGGSTNTTLHLPALAHEFGLELPLK 288 ********************************************************************* PP TIGR00110 277 dfdrlsrkvPllaklkPsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlr. 344 fd+lsr++P+l +l+P+g +++ +raGGv+av++ l + +lh d ltv Gkt++e+l++ ++ + lcl|NCBI__GCF_000007345.1:WP_011021805.1 289 TFDELSRTTPHLISLRPGGPNFMLHFDRAGGVEAVVQRL--ASKLHLDQLTVNGKTIGENLDELEIVNp 355 ***************************************..99********************998864 PP TIGR00110 345 .vdqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvk 412 ++ ++i +l+np+++egg+avLkG+la++G+vvk+a+v+ ++ +++Gpakv++ ee+a+++il+g+vk lcl|NCBI__GCF_000007345.1:WP_011021805.1 356 kLNAEIITTLENPIHAEGGIAVLKGSLAPDGSVVKQAAVDPKMRVHTGPAKVYDCEEDAMKSILAGDVK 424 48899**************************************************************** PP TIGR00110 413 eGdvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaial 481 Gd+vviryeGPkGgPGmremLa t+a+ g+GL ++vaLitDGrfsGgtrG++iGhvsPea egG+i+l lcl|NCBI__GCF_000007345.1:WP_011021805.1 425 PGDIVVIRYEGPKGGPGMREMLAATAAIGGMGLLESVALITDGRFSGGTRGPCIGHVSPEASEGGPIGL 493 ********************************************************************* PP TIGR00110 482 vedGDkikiDienrkldlevseeelaerrakakkkearevkgaLakyaklvssadkGavld 542 v+dGD i+i+i++r l+l+v eeel++r+a+ ++++ +ev g+La+y++ v sa++G+++d lcl|NCBI__GCF_000007345.1:WP_011021805.1 494 VKDGDLIEINIPERILNLKVTEEELEKRKAAFVPPK-KEVTGYLARYQRSVHSANTGGIVD 553 *******************************99999.99******************9975 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: 10.19 // [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