Align dihydroxyacid dehydratase (EC 4.2.1.9) (characterized)
to candidate WP_011812996.1 HHAL_RS00935 dihydroxy-acid dehydratase
Query= metacyc::MONOMER-18815 (557 letters) >NCBI__GCF_000015585.1:WP_011812996.1 Length = 565 Score = 741 bits (1913), Expect = 0.0 Identities = 353/557 (63%), Positives = 460/557 (82%) Query: 1 MAFNKRSQNITQGVARSPNRSMYYALGYKKEDFDKPMVGIANGHSTITPCNAGLQRLADA 60 MA N+RS+ ITQGVAR+PNR+M A+G++ EDF+KP++G+ N HSTITPCN G+ +A Sbjct: 1 MADNRRSRVITQGVARTPNRAMLRAVGFRDEDFEKPIIGVGNAHSTITPCNVGIGAMARR 60 Query: 61 AIDAIKASDANPQVFGTPTISDGMSMGTEGMKYSLISREVIADCIETAAQGQWMDGVVVI 120 A +A++ A P FGT T+SDG++MGTEGMKYSL+SREVIAD IET GQ MDG++ Sbjct: 61 AEEALREVGAMPMKFGTITVSDGITMGTEGMKYSLVSREVIADSIETVGGGQRMDGMLAT 120 Query: 121 GGCDKNMPGGMIALARTNVPGIYVYGGTIKPGNWKGKDLTIVSSFEAVGEFTAGRMSQED 180 GGCDKNMPG M+ALAR ++PGI+VYGGTIKPG++KG+DLT+VS+FEAVG++ AG +S+ D Sbjct: 121 GGCDKNMPGAMMALARLDIPGIFVYGGTIKPGHYKGEDLTVVSAFEAVGQYNAGNLSEAD 180 Query: 181 FEGVEKNACPSTGSCGGMYTANTMSSSFEALGMSLLYSSTMANPDQEKVDSAAESARVLV 240 +GVE+NACP G+CGGM+TANTMSS+FEA+GMSL+ SST++ D E D AAE++RVL+ Sbjct: 181 LKGVEENACPGAGACGGMFTANTMSSAFEAMGMSLMGSSTVSAEDDEARDVAAEASRVLM 240 Query: 241 EAIKQDIKPRDIITRKSIENAVALIMATGGSTNAVLHYLAIAHAAEVEWTIDDFERIRRK 300 +A+ D +P I+TR++ ENA A++MA GGSTNAVLH LAIA+ AEV + +DD ERIRRK Sbjct: 241 DAVHHDRRPSSILTREAFENAFAVVMALGGSTNAVLHLLAIANTAEVPFDLDDVERIRRK 300 Query: 301 VPVICNLKPSGQYVATDLHKAGGIPQVMKILLKAGMLHGDCLTITGRTLAEELENVPDTP 360 VPV+C+LKPSG++V + H+ GG PQVM+ILL+ G+LHG C TITG+T+ + ++P P Sbjct: 301 VPVLCDLKPSGRFVTSQFHEVGGTPQVMRILLEQGLLHGHCQTITGQTIEALIGHLPPEP 360 Query: 361 RADQDVILPIEKALYAEGHLAILKGNLAEEGAVAKITGLKNPVITGPARVFEDEQSAMEA 420 ADQ++I+P ++ LY EGHLAIL+GNLAEEGAVAK++G++ I+GPARVF+ E+ +EA Sbjct: 361 PADQEIIMPFDRPLYPEGHLAILRGNLAEEGAVAKVSGIQQRRISGPARVFDSEEECLEA 420 Query: 421 ILADKINAGDILVLRYLGPKGGPGMPEMLAPTSAIIGKGLGESVGFITDGRFSGGTWGMV 480 ILAD + AGD++++RY GPKGGPGM EMLAPTSAIIGKGLG++VG ITDGRFSGGT+GMV Sbjct: 421 ILADGVQAGDVVIVRYEGPKGGPGMREMLAPTSAIIGKGLGDAVGLITDGRFSGGTYGMV 480 Query: 481 VGHVAPEAYVGGTIALVQEGDSITIDAHKLLLQLNVADEELARRRANWKQPAPRYTRGVL 540 VGHVAPEAY GGTIAL+ EGD++TIDA + LLQ+ V D EL RRR+ W+ P PRY RGVL Sbjct: 481 VGHVAPEAYDGGTIALIAEGDTVTIDADQNLLQVEVDDAELERRRSQWQVPRPRYRRGVL 540 Query: 541 AKFSKLASTASKGAVTD 557 K+++LA++AS+GAVTD Sbjct: 541 GKYARLAASASRGAVTD 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: 1039 Number of extensions: 40 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: 565 Length adjustment: 36 Effective length of query: 521 Effective length of database: 529 Effective search space: 275609 Effective search space used: 275609 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 WP_011812996.1 HHAL_RS00935 (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.9934.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.7e-232 756.2 4.1 1.1e-231 756.0 4.1 1.0 1 lcl|NCBI__GCF_000015585.1:WP_011812996.1 HHAL_RS00935 dihydroxy-acid dehy Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000015585.1:WP_011812996.1 HHAL_RS00935 dihydroxy-acid dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 756.0 4.1 1.1e-231 1.1e-231 1 542 [. 18 557 .. 18 558 .. 0.99 Alignments for each domain: == domain 1 score: 756.0 bits; conditional E-value: 1.1e-231 TIGR00110 1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiam 69 ++ra+l+a+G++ded+ekPii+v+n++++i+P++v + +a++++e++++ G+++++f+ti+vsDGi+m lcl|NCBI__GCF_000015585.1:WP_011812996.1 18 PNRAMLRAVGFRDEDFEKPIIGVGNAHSTITPCNVGIGAMARRAEEALREVGAMPMKFGTITVSDGITM 86 68******************************************************************* PP TIGR00110 70 gheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktk 138 g+eGmkysL+sre+iaDs+etv ++++D++++ + CDk++PG++ma +rl+iP i+v+GG++++g++k lcl|NCBI__GCF_000015585.1:WP_011812996.1 87 GTEGMKYSLVSREVIADSIETVGGGQRMDGMLATGGCDKNMPGAMMALARLDIPGIFVYGGTIKPGHYK 155 ********************************************************************* PP TIGR00110 139 lsekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstlla 207 +e++++v++feavg+y+ag+lse++l+ +e++acP+ag+C+G+ftan+m++++ea+G+sl gsst+ a lcl|NCBI__GCF_000015585.1:WP_011812996.1 156 -GEDLTVVSAFEAVGQYNAGNLSEADLKGVEENACPGAGACGGMFTANTMSSAFEAMGMSLMGSSTVSA 223 .9******************************************************************* PP TIGR00110 208 tsaekkelakksgkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklsld 276 + e +++a ++++ ++++v+++ +P++ilt+eafena+++++alGGstn+vLhllaia++a+v ++ld lcl|NCBI__GCF_000015585.1:WP_011812996.1 224 EDDEARDVAAEASRVLMDAVHHDRRPSSILTREAFENAFAVVMALGGSTNAVLHLLAIANTAEVPFDLD 292 ********************************************************************* PP TIGR00110 277 dfdrlsrkvPllaklkPsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlr. 344 d++r++rkvP+l++lkPsg+ v+ + h++GG+++v++ l ++gllh +++t+tG+t++ + + + + lcl|NCBI__GCF_000015585.1:WP_011812996.1 293 DVERIRRKVPVLCDLKPSGRFVTSQFHEVGGTPQVMRILLEQGLLHGHCQTITGQTIEALIGHLPPEPp 361 *************************************************************99986643 PP TIGR00110 345 vdqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvke 413 +dq++i + d p++ eg+la+L+GnlaeeGav+k++g+++ ++ Gpa+vf+seee+leail+ v++ lcl|NCBI__GCF_000015585.1:WP_011812996.1 362 ADQEIIMPFDRPLYPEGHLAILRGNLAEEGAVAKVSGIQQ--RRISGPARVFDSEEECLEAILADGVQA 428 9***************************************..9************************** PP TIGR00110 414 GdvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialv 482 Gdvv++ryeGPkGgPGmremLaPtsa++g GLg++v+LitDGrfsGgt+G+++Ghv+Pea+ gG+ial+ lcl|NCBI__GCF_000015585.1:WP_011812996.1 429 GDVVIVRYEGPKGGPGMREMLAPTSAIIGKGLGDAVGLITDGRFSGGTYGMVVGHVAPEAYDGGTIALI 497 ********************************************************************* PP TIGR00110 483 edGDkikiDienrkldlevseeelaerrakakkkearevkgaLakyaklvssadkGavld 542 +GD+++iD++++ l++ev+++el++rr +++ +++r+ +g+L kya+l++sa++Gav+d lcl|NCBI__GCF_000015585.1:WP_011812996.1 498 AEGDTVTIDADQNLLQVEVDDAELERRRSQWQVPRPRYRRGVLGKYARLAASASRGAVTD 557 **********************************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (543 nodes) Target sequences: 1 (565 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: 00:00:00.03 # Mc/sec: 10.14 // [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