Align dihydroxy-acid dehydratase subunit (EC 4.2.1.9) (characterized)
to candidate WP_011023301.1 MA_RS17605 dihydroxy-acid dehydratase
Query= metacyc::MONOMER-11919 (549 letters) >NCBI__GCF_000007345.1:WP_011023301.1 Length = 553 Score = 657 bits (1696), Expect = 0.0 Identities = 319/553 (57%), Positives = 425/553 (76%), Gaps = 6/553 (1%) Query: 1 MKSDTIKRGIQRAPHRSLLARCGLTDDDFEKPFIGIANSYTDIVPGHIHLRELAEAVKEG 60 M+SD IK G +RAP+RSLL G+TD + +KPFI + NS+ DI+PGH+HL +LAEAVK G Sbjct: 1 MRSDIIKEGPERAPNRSLLKATGVTDSEMKKPFIAVVNSWNDIIPGHMHLNKLAEAVKAG 60 Query: 61 VNAAGGVAFEFNTMAICDGIAMNHDGMKYSLASREIVADTVESMAMAHALDGLVLLPTCD 120 + AGGV FEF+T+ +CDGIAM H+GMKYSL SREI+ DT+E M AH DG+VL+P+CD Sbjct: 61 IRNAGGVPFEFHTVGVCDGIAMGHEGMKYSLPSREIIEDTIELMVKAHQFDGMVLIPSCD 120 Query: 121 KIVPGMLMAAARLDIPAIVVTGGPMLPGEFKGRKVDLINVYEGVGTVSAGEMSEDELEEL 180 KIVPG LMAA RLDIPAIVVTGGPMLPG DLI+V EGVG SAG++SE E + L Sbjct: 121 KIVPGHLMAAGRLDIPAIVVTGGPMLPGYVDDNYRDLISVSEGVGAYSAGKISETEFKRL 180 Query: 181 ERCACPGPRSCAGLFTANTMACLTEALGMSLPGCATAHAVSSRKRQIARLSGKRIVEMVQ 240 E +C G SCAG+FTANTMAC+TEALG+SLPGCATAHAV ++K IA+ SG+RIVE+V+ Sbjct: 181 ENLSCAGAGSCAGMFTANTMACMTEALGLSLPGCATAHAVDAKKILIAKESGERIVELVK 240 Query: 241 ENLKPTMIMSQEAFENAVMVDLALGGSTNTTLHIPAIAAEIDGLNINLDLFDELSRVIPH 300 ENL P I++Q++FENA+MVD+A+GGSTNTTLH+PA+A E GL + L+ FDELSR PH Sbjct: 241 ENLTPRKIVTQKSFENAIMVDMAVGGSTNTTLHLPALAHEF-GLGLPLEAFDELSRKTPH 299 Query: 301 IASISPAGEHMMLDLDRAGGIPAVLKTLEDHINRECVTCTGRTVQENIENVKVG----HR 356 + S+ P G + +L DRAGG+ AV++ L ++ + +T G+T+ EN++ +++ + Sbjct: 300 LISLRPGGPNFILHFDRAGGVEAVMQRLASKLHLDQLTVNGKTIGENLDELEIVNPKLNA 359 Query: 357 DVIRPLDSPVHSEGGLAILRGNLAPRGSVVKQGAVAEDMMVHEGPAKVFNSEDECMEAIF 416 ++I L++P+H+EGG+A+L+G+LAP GSVVKQ AV M V+ GPAKV++ E++ M++I Sbjct: 360 EIITTLENPIHAEGGIAVLKGSLAPDGSVVKQAAVDPKMHVYTGPAKVYDCEEDAMKSIL 419 Query: 417 GGRIDEGDVIVIRYEGPKGGPGMREMLNPTSAIAGMG-LERVALITDGRFSGGTRGPCVG 475 G + GD++VIRYEGPKGGPGMREML T+A+ G G LE VAL+TDGRFSGGTRGPC+G Sbjct: 420 AGDVKPGDIVVIRYEGPKGGPGMREMLAATAALGGRGLLESVALVTDGRFSGGTRGPCIG 479 Query: 476 HVSPEAMEDGPLAAVNDGDIIRIDIPSRKLEVDLSPREIEERLQSAVKPRRSVKGWLARY 535 HVSPEA + GP+A V DGD+I I+IP R L + +S E+++R S V P+ + G+LARY Sbjct: 480 HVSPEASDGGPIALVKDGDLIEINIPERALNLKISEEELKQRKASFVPPKTEITGYLARY 539 Query: 536 RKLAGSADTGAVL 548 ++ SA+TG ++ Sbjct: 540 QRAVHSANTGGIV 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: 1079 Number of extensions: 55 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_011023301.1 MA_RS17605 (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.3374.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.8e-243 792.5 3.2 1.1e-242 792.3 3.2 1.0 1 lcl|NCBI__GCF_000007345.1:WP_011023301.1 MA_RS17605 dihydroxy-acid dehydr Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000007345.1:WP_011023301.1 MA_RS17605 dihydroxy-acid dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 792.3 3.2 1.1e-242 1.1e-242 1 542 [. 14 553 .] 14 553 .] 0.99 Alignments for each domain: == domain 1 score: 792.3 bits; conditional E-value: 1.1e-242 TIGR00110 1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiam 69 ++r+llkatG++d +++kP+iavvns+++i+Pgh+hl++la++vk++i++aGgv++ef t++v+DGiam lcl|NCBI__GCF_000007345.1:WP_011023301.1 14 PNRSLLKATGVTDSEMKKPFIAVVNSWNDIIPGHMHLNKLAEAVKAGIRNAGGVPFEFHTVGVCDGIAM 82 68******************************************************************* PP TIGR00110 70 gheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktk 138 gheGmkysLpsreii D++e +vkah++D++v+i+sCDkivPG lmaa rl+iPaivv+GGpm +g + lcl|NCBI__GCF_000007345.1:WP_011023301.1 83 GHEGMKYSLPSREIIEDTIELMVKAHQFDGMVLIPSCDKIVPGHLMAAGRLDIPAIVVTGGPMLPGYVD 151 ********************************************************************9 PP TIGR00110 139 lsekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstlla 207 + dl++v e+vg+y+agk+se e +++e+ +c +agsC+G+ftan+mac+tealGlslPg++t++a lcl|NCBI__GCF_000007345.1:WP_011023301.1 152 -DNYRDLISVSEGVGAYSAGKISETEFKRLENLSCAGAGSCAGMFTANTMACMTEALGLSLPGCATAHA 219 .68889*************************************************************** PP TIGR00110 208 tsaekkelakksgkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklsld 276 ++a+k +ak+sg+rivelvk+n++Pr+i+t+++fenai++d+a+GGstnt+Lhl+a+a+e g+ l l+ lcl|NCBI__GCF_000007345.1:WP_011023301.1 220 VDAKKILIAKESGERIVELVKENLTPRKIVTQKSFENAIMVDMAVGGSTNTTLHLPALAHEFGLGLPLE 288 ********************************************************************* PP TIGR00110 277 dfdrlsrkvPllaklkPsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlr. 344 fd+lsrk+P+l +l+P+g ++i +raGGv+av++ l + +lh d ltv Gkt++e+l++ ++ + lcl|NCBI__GCF_000007345.1:WP_011023301.1 289 AFDELSRKTPHLISLRPGGPNFILHFDRAGGVEAVMQRL--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_011023301.1 356 kLNAEIITTLENPIHAEGGIAVLKGSLAPDGSVVKQAAVDPKMHVYTGPAKVYDCEEDAMKSILAGDVK 424 48899**************************************************************** PP TIGR00110 413 eGdvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaial 481 Gd+vviryeGPkGgPGmremLa t+al g GL ++vaL+tDGrfsGgtrG++iGhvsPea gG+ial lcl|NCBI__GCF_000007345.1:WP_011023301.1 425 PGDIVVIRYEGPKGGPGMREMLAATAALGGRGLLESVALVTDGRFSGGTRGPCIGHVSPEASDGGPIAL 493 ********************************************************************* PP TIGR00110 482 vedGDkikiDienrkldlevseeelaerrakakkkearevkgaLakyaklvssadkGavld 542 v+dGD i+i+i++r+l+l++seeel++r+a+ ++++ e+ g+La+y++ v sa++G+++d lcl|NCBI__GCF_000007345.1:WP_011023301.1 494 VKDGDLIEINIPERALNLKISEEELKQRKASFVPPK-TEITGYLARYQRAVHSANTGGIVD 553 *********************************999.789*****************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: 0.03u 0.02s 00:00:00.05 Elapsed: 00:00:00.04 # Mc/sec: 7.08 // [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