Align dihydroxyacid dehydratase (EC 4.2.1.9) (characterized)
to candidate RR42_RS16210 RR42_RS16210 dihydroxy-acid dehydratase
Query= metacyc::MONOMER-18815 (557 letters) >FitnessBrowser__Cup4G11:RR42_RS16210 Length = 557 Score = 1065 bits (2754), Expect = 0.0 Identities = 529/557 (94%), Positives = 552/557 (99%) Query: 1 MAFNKRSQNITQGVARSPNRSMYYALGYKKEDFDKPMVGIANGHSTITPCNAGLQRLADA 60 MA+NKRSQ+ITQGVARSPNRSMYYALGYKKEDFDKPMVGIANGHSTITPCN+GLQRLADA Sbjct: 1 MAYNKRSQHITQGVARSPNRSMYYALGYKKEDFDKPMVGIANGHSTITPCNSGLQRLADA 60 Query: 61 AIDAIKASDANPQVFGTPTISDGMSMGTEGMKYSLISREVIADCIETAAQGQWMDGVVVI 120 A+ AIKASDANPQ+FGTPTISDGMSMGTEGMKYSLISREVIADCIETA QGQWMDGVVVI Sbjct: 61 AVAAIKASDANPQIFGTPTISDGMSMGTEGMKYSLISREVIADCIETATQGQWMDGVVVI 120 Query: 121 GGCDKNMPGGMIALARTNVPGIYVYGGTIKPGNWKGKDLTIVSSFEAVGEFTAGRMSQED 180 GGCDKNMPGGMIALARTNVPGIYVYGGTIKPGNWKGKDLTIVSSFEAVGEFTAGR+SQED Sbjct: 121 GGCDKNMPGGMIALARTNVPGIYVYGGTIKPGNWKGKDLTIVSSFEAVGEFTAGRLSQED 180 Query: 181 FEGVEKNACPSTGSCGGMYTANTMSSSFEALGMSLLYSSTMANPDQEKVDSAAESARVLV 240 FEGVEKNACPS+GSCGGMYTANTMSSSFEALGMSLLYSSTMANPDQEKVDSAAESARVLV Sbjct: 181 FEGVEKNACPSSGSCGGMYTANTMSSSFEALGMSLLYSSTMANPDQEKVDSAAESARVLV 240 Query: 241 EAIKQDIKPRDIITRKSIENAVALIMATGGSTNAVLHYLAIAHAAEVEWTIDDFERIRRK 300 EAIK+DIKPRDIITRKSIENAVALIMATGGSTNAVLHYLAIAH+AEVEW+IDDFERIRRK Sbjct: 241 EAIKKDIKPRDIITRKSIENAVALIMATGGSTNAVLHYLAIAHSAEVEWSIDDFERIRRK 300 Query: 301 VPVICNLKPSGQYVATDLHKAGGIPQVMKILLKAGMLHGDCLTITGRTLAEELENVPDTP 360 VPVICNLKPSGQYVATDLH+AGGIPQVMKILLKAG++HGDCLTITGRTLAEELENVPDTP Sbjct: 301 VPVICNLKPSGQYVATDLHRAGGIPQVMKILLKAGLMHGDCLTITGRTLAEELENVPDTP 360 Query: 361 RADQDVILPIEKALYAEGHLAILKGNLAEEGAVAKITGLKNPVITGPARVFEDEQSAMEA 420 RADQDVI+PIEKALY EGHLAILKGNLA+EGAVAKITGLKNPVITGPARVFEDEQSAM+A Sbjct: 361 RADQDVIMPIEKALYKEGHLAILKGNLAQEGAVAKITGLKNPVITGPARVFEDEQSAMDA 420 Query: 421 ILADKINAGDILVLRYLGPKGGPGMPEMLAPTSAIIGKGLGESVGFITDGRFSGGTWGMV 480 ILADKINAGDILVLRYLGPKGGPGMPEMLAPTSAIIGKGLGESVGFITDGRFSGGTWGMV Sbjct: 421 ILADKINAGDILVLRYLGPKGGPGMPEMLAPTSAIIGKGLGESVGFITDGRFSGGTWGMV 480 Query: 481 VGHVAPEAYVGGTIALVQEGDSITIDAHKLLLQLNVADEELARRRANWKQPAPRYTRGVL 540 VGHVAPEA+VGG IALVQEGDS+TIDAHKLLL+LNV++EELA+RRA WKQPAPRYTRGVL Sbjct: 481 VGHVAPEAHVGGNIALVQEGDSVTIDAHKLLLELNVSEEELAKRRAAWKQPAPRYTRGVL 540 Query: 541 AKFSKLASTASKGAVTD 557 AKF+KLASTASKGAVTD Sbjct: 541 AKFAKLASTASKGAVTD 557 Lambda K H 0.316 0.133 0.386 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: 1203 Number of extensions: 34 Number of successful extensions: 1 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: 557 Length of database: 557 Length adjustment: 36 Effective length of query: 521 Effective length of database: 521 Effective search space: 271441 Effective search space used: 271441 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 53 (25.0 bits)
Align candidate RR42_RS16210 RR42_RS16210 (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.11881.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-229 748.8 3.9 2e-229 748.6 3.9 1.0 1 lcl|FitnessBrowser__Cup4G11:RR42_RS16210 RR42_RS16210 dihydroxy-acid dehy Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cup4G11:RR42_RS16210 RR42_RS16210 dihydroxy-acid dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 748.6 3.9 2e-229 2e-229 1 542 [. 18 557 .] 18 557 .] 0.99 Alignments for each domain: == domain 1 score: 748.6 bits; conditional E-value: 2e-229 TIGR00110 1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiam 69 ++r++++a+G+k+ed++kP+++++n++++i+P++ l+ la+++ ++i+a+ + ++ f+t ++sDG++m lcl|FitnessBrowser__Cup4G11:RR42_RS16210 18 PNRSMYYALGYKKEDFDKPMVGIANGHSTITPCNSGLQRLADAAVAAIKASDANPQIFGTPTISDGMSM 86 68******************************************************************* PP TIGR00110 70 gheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktk 138 g+eGmkysL sre+iaD +et +++++D++vvi+ CDk++PG ++a +r+n+P i v+GG++++g+ k lcl|FitnessBrowser__Cup4G11:RR42_RS16210 87 GTEGMKYSLISREVIADCIETATQGQWMDGVVVIGGCDKNMPGGMIALARTNVPGIYVYGGTIKPGNWK 155 ********************************************************************* PP TIGR00110 139 lsekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstlla 207 ++++++v+ feavge +ag+ls+e+ e +e++acP++gsC+G++tan+m++ +ealG+sl +sst++ lcl|FitnessBrowser__Cup4G11:RR42_RS16210 156 -GKDLTIVSSFEAVGEFTAGRLSQEDFEGVEKNACPSSGSCGGMYTANTMSSSFEALGMSLLYSSTMAN 223 .9******************************************************************* PP TIGR00110 208 tsaekkelakksgkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklsld 276 ++ek ++a +s++ +ve++kk+ikPrdi+t++++ena++l++a+GGstn+vLh laia++a+v+ s+d lcl|FitnessBrowser__Cup4G11:RR42_RS16210 224 PDQEKVDSAAESARVLVEAIKKDIKPRDIITRKSIENAVALIMATGGSTNAVLHYLAIAHSAEVEWSID 292 ********************************************************************* PP TIGR00110 277 dfdrlsrkvPllaklkPsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlr. 344 df+r++rkvP++++lkPsg++v +dlhraGG+++v+k l k+gl+h d+lt+tG+tlae+le+v+ ++ lcl|FitnessBrowser__Cup4G11:RR42_RS16210 293 DFERIRRKVPVICNLKPSGQYVATDLHRAGGIPQVMKILLKAGLMHGDCLTITGRTLAEELENVPDTPr 361 ****************************************************************88753 PP TIGR00110 345 vdqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvke 413 +dqdvi +++++++keg+la+LkGnla+eGav+ki+g ++ +++Gpa+vfe+e+ a++ail+ k+++ lcl|FitnessBrowser__Cup4G11:RR42_RS16210 362 ADQDVIMPIEKALYKEGHLAILKGNLAQEGAVAKITGLKN--PVITGPARVFEDEQSAMDAILADKINA 428 89**************************************..999************************ PP TIGR00110 414 GdvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialv 482 Gd++v+ry GPkGgPGm+emLaPtsa++g GLg++v++itDGrfsGgt G+++Ghv+Pea +gG+ialv lcl|FitnessBrowser__Cup4G11:RR42_RS16210 429 GDILVLRYLGPKGGPGMPEMLAPTSAIIGKGLGESVGFITDGRFSGGTWGMVVGHVAPEAHVGGNIALV 497 ********************************************************************* PP TIGR00110 483 edGDkikiDienrkldlevseeelaerrakakkkearevkgaLakyaklvssadkGavld 542 ++GD ++iD+++ l+l+vseeela+rra++k++ +r+++g+Lak+akl+s+a+kGav+d lcl|FitnessBrowser__Cup4G11:RR42_RS16210 498 QEGDSVTIDAHKLLLELNVSEEELAKRRAAWKQPAPRYTRGVLAKFAKLASTASKGAVTD 557 **********************************************************86 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (543 nodes) Target sequences: 1 (557 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: 11.45 // [ok]
This GapMind analysis is from Apr 09 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