Align dihydroxyacid dehydratase (EC 4.2.1.9) (characterized)
to candidate H281DRAFT_00127 H281DRAFT_00127 dihydroxyacid dehydratase
Query= metacyc::MONOMER-18815 (557 letters) >FitnessBrowser__Burk376:H281DRAFT_00127 Length = 557 Score = 1005 bits (2598), Expect = 0.0 Identities = 493/556 (88%), Positives = 531/556 (95%) Query: 1 MAFNKRSQNITQGVARSPNRSMYYALGYKKEDFDKPMVGIANGHSTITPCNAGLQRLADA 60 M +N+RS+NITQGVARSPNRSMYYALGY+KEDFDKPM+GIANGHSTITPCNAGLQRLADA Sbjct: 1 MPYNRRSKNITQGVARSPNRSMYYALGYQKEDFDKPMIGIANGHSTITPCNAGLQRLADA 60 Query: 61 AIDAIKASDANPQVFGTPTISDGMSMGTEGMKYSLISREVIADCIETAAQGQWMDGVVVI 120 A+ A+K +DANPQ+FGTPTISDGMSMGTEGMKYSL+SREVIADCIET QGQWMDGVVVI Sbjct: 61 AVAAVKGADANPQIFGTPTISDGMSMGTEGMKYSLVSREVIADCIETCVQGQWMDGVVVI 120 Query: 121 GGCDKNMPGGMIALARTNVPGIYVYGGTIKPGNWKGKDLTIVSSFEAVGEFTAGRMSQED 180 GGCDKNMPGGMI LAR NVPGIYVYGGTI+PGNWKG DLTIVSSFEAVGEFTAGRMSQED Sbjct: 121 GGCDKNMPGGMIGLARMNVPGIYVYGGTIRPGNWKGTDLTIVSSFEAVGEFTAGRMSQED 180 Query: 181 FEGVEKNACPSTGSCGGMYTANTMSSSFEALGMSLLYSSTMANPDQEKVDSAAESARVLV 240 FEGVE+NACPSTGSCGGMYTANTMSSSFEALGMSLLYSSTMANPDQEKVDSAAESARVLV Sbjct: 181 FEGVERNACPSTGSCGGMYTANTMSSSFEALGMSLLYSSTMANPDQEKVDSAAESARVLV 240 Query: 241 EAIKQDIKPRDIITRKSIENAVALIMATGGSTNAVLHYLAIAHAAEVEWTIDDFERIRRK 300 EA+K+D+KPRDIIT+KSIENAVA+IMATGGSTNAVLH+LAIAHAAEVEWTI+DFER+R+K Sbjct: 241 EAVKKDLKPRDIITKKSIENAVAVIMATGGSTNAVLHFLAIAHAAEVEWTIEDFERMRKK 300 Query: 301 VPVICNLKPSGQYVATDLHKAGGIPQVMKILLKAGMLHGDCLTITGRTLAEELENVPDTP 360 VPVICNLKPSGQYVATDLHKAGGIPQVMKILL AG+LHGDC+TITG+TLAEEL++VP P Sbjct: 301 VPVICNLKPSGQYVATDLHKAGGIPQVMKILLDAGLLHGDCITITGKTLAEELKDVPSRP 360 Query: 361 RADQDVILPIEKALYAEGHLAILKGNLAEEGAVAKITGLKNPVITGPARVFEDEQSAMEA 420 RADQ VI PI++ALY EGHLAILKGNLAE+GAVAKITGLKNPVITGPARVF+DEQSA+EA Sbjct: 361 RADQKVIFPIDQALYKEGHLAILKGNLAEDGAVAKITGLKNPVITGPARVFDDEQSALEA 420 Query: 421 ILADKINAGDILVLRYLGPKGGPGMPEMLAPTSAIIGKGLGESVGFITDGRFSGGTWGMV 480 ILADKI AGD++VLRYLGPKGGPGMPEMLAPTSAIIGKGLGESVG ITDGRFSGGTWGMV Sbjct: 421 ILADKIVAGDVVVLRYLGPKGGPGMPEMLAPTSAIIGKGLGESVGLITDGRFSGGTWGMV 480 Query: 481 VGHVAPEAYVGGTIALVQEGDSITIDAHKLLLQLNVADEELARRRANWKQPAPRYTRGVL 540 VGHVAPEA+VGGTI LVQEGDSITIDAHKLLLQLNV D EL RRRA W+QP PRYTRGVL Sbjct: 481 VGHVAPEAFVGGTIGLVQEGDSITIDAHKLLLQLNVDDAELQRRRAAWQQPQPRYTRGVL 540 Query: 541 AKFSKLASTASKGAVT 556 AK+S LA A+KGA+T Sbjct: 541 AKYSALALPANKGAIT 556 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: 1176 Number of extensions: 39 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 H281DRAFT_00127 H281DRAFT_00127 (dihydroxyacid 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.16959.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.7e-227 741.1 3.3 4.2e-227 740.9 3.3 1.0 1 lcl|FitnessBrowser__Burk376:H281DRAFT_00127 H281DRAFT_00127 dihydroxyacid de Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Burk376:H281DRAFT_00127 H281DRAFT_00127 dihydroxyacid dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 740.9 3.3 4.2e-227 4.2e-227 1 541 [. 18 556 .. 18 557 .] 0.99 Alignments for each domain: == domain 1 score: 740.9 bits; conditional E-value: 4.2e-227 TIGR00110 1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDG 66 ++r++++a+G+++ed++kP+i+++n++++i+P++ l+ la+++ ++++ a + ++ f+t ++sDG lcl|FitnessBrowser__Burk376:H281DRAFT_00127 18 PNRSMYYALGYQKEDFDKPMIGIANGHSTITPCNAGLQRLADAAVAAVKGADANPQIFGTPTISDG 83 68**************************************************************** PP TIGR00110 67 iamgheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpm 132 ++mg+eGmkysL+sre+iaD +et v+++++D++vvi+ CDk++PG +++ +r+n+P i v+GG++ lcl|FitnessBrowser__Burk376:H281DRAFT_00127 84 MSMGTEGMKYSLVSREVIADCIETCVQGQWMDGVVVIGGCDKNMPGGMIGLARMNVPGIYVYGGTI 149 ****************************************************************** PP TIGR00110 133 eagktklsekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGls 198 +g+ k + ++++v+ feavge +ag++s+e+ e +er+acP++gsC+G++tan+m++ +ealG+s lcl|FitnessBrowser__Burk376:H281DRAFT_00127 150 RPGNWK-GTDLTIVSSFEAVGEFTAGRMSQEDFEGVERNACPSTGSCGGMYTANTMSSSFEALGMS 214 ******.9********************************************************** PP TIGR00110 199 lPgsstllatsaekkelakksgkrivelvkknikPrdiltkeafenaitldlalGGstntvLhlla 264 l +sst++ ++ek ++a +s++ +ve+vkk++kPrdi+tk+++ena+++++a+GGstn+vLh la lcl|FitnessBrowser__Burk376:H281DRAFT_00127 215 LLYSSTMANPDQEKVDSAAESARVLVEAVKKDLKPRDIITKKSIENAVAVIMATGGSTNAVLHFLA 280 ****************************************************************** PP TIGR00110 265 iakeagvklslddfdrlsrkvPllaklkPsgkkviedlhraGGvsavlkeldkegllhkdaltvtG 330 ia+ a+v+ +++df+r+++kvP++++lkPsg++v +dlh+aGG+++v+k l +gllh d++t+tG lcl|FitnessBrowser__Burk376:H281DRAFT_00127 281 IAHAAEVEWTIEDFERMRKKVPVICNLKPSGQYVATDLHKAGGIPQVMKILLDAGLLHGDCITITG 346 ****************************************************************** PP TIGR00110 331 ktlaetlekvkvlr.vdqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakv 395 ktlae+l++v++++ +dq+vi ++d++++keg+la+LkGnlae+Gav+ki+g ++ +++Gpa+v lcl|FitnessBrowser__Burk376:H281DRAFT_00127 347 KTLAEELKDVPSRPrADQKVIFPIDQALYKEGHLAILKGNLAEDGAVAKITGLKN--PVITGPARV 410 **********998647999************************************..999****** PP TIGR00110 396 feseeealeailggkvkeGdvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgt 461 f++e+ aleail+ k+ +Gdvvv+ry GPkGgPGm+emLaPtsa++g GLg++v+LitDGrfsGgt lcl|FitnessBrowser__Burk376:H281DRAFT_00127 411 FDDEQSALEAILADKIVAGDVVVLRYLGPKGGPGMPEMLAPTSAIIGKGLGESVGLITDGRFSGGT 476 ****************************************************************** PP TIGR00110 462 rGlsiGhvsPeaaegGaialvedGDkikiDienrkldlevseeelaerrakakkkearevkgaLak 527 G+++Ghv+Pea +gG+i+lv++GD i+iD+++ l+l+v+++el++rra+++++++r+++g+Lak lcl|FitnessBrowser__Burk376:H281DRAFT_00127 477 WGMVVGHVAPEAFVGGTIGLVQEGDSITIDAHKLLLQLNVDDAELQRRRAAWQQPQPRYTRGVLAK 542 ****************************************************************** PP TIGR00110 528 yaklvssadkGavl 541 y+ l+ a+kGa++ lcl|FitnessBrowser__Burk376:H281DRAFT_00127 543 YSALALPANKGAIT 556 ************96 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: 11.39 // [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