Align dihydroxyacid dehydratase (EC 4.2.1.9) (characterized)
to candidate WP_053767874.1 BVI061214_RS07550 dihydroxy-acid dehydratase
Query= metacyc::MONOMER-18815 (557 letters) >NCBI__GCF_001280255.1:WP_053767874.1 Length = 567 Score = 547 bits (1410), Expect = e-160 Identities = 275/552 (49%), Positives = 377/552 (68%), Gaps = 1/552 (0%) Query: 6 RSQNITQGVARSPNRSMYYALGYKKEDFDKPMVGIANGHSTITPCNAGLQRLADAAIDAI 65 RS I +G+ ++P RSM A+G EDF +P VG+ N + PCN L+ LA + Sbjct: 2 RSDRIKKGLQQAPARSMLRAVGVGDEDFGRPFVGVVNTFTDGMPCNYHLRELALDLKAGL 61 Query: 66 KASDANPQVFGTPTISDGMSMGTEGMKYSLISREVIADCIETAAQGQWMDGVVVIGGCDK 125 + + P FG P ISDG+SMGT GM+ SL+SREVIAD IE AQG DG+ V+ CDK Sbjct: 62 REAGVFPFEFGAPAISDGISMGTPGMRASLVSREVIADSIELVAQGYLYDGMAVLSACDK 121 Query: 126 NMPGGMIALARTNVPGIYVYGGTIKPGNWKGKDLTIVSSFEAVGEFTAGRMSQEDFEGVE 185 +PGG + + R+ VPG+ +YGGTI PG W+G+ LTIV FEAVG+ AGR++ E+ +E Sbjct: 122 TIPGGAMGVIRSGVPGMVLYGGTIAPGEWRGRKLTIVEVFEAVGQRAAGRITDEELLEIE 181 Query: 186 KNACPSTGSCGGMYTANTMSSSFEALGMSLLYSSTMANPDQEKVDSAAESARVLVEAIKQ 245 + A P G+CGG YTANTM+ + E LG+S + + + EK + E+ R+L AI+ Sbjct: 182 RRAIPGPGACGGQYTANTMAMALEVLGLSPMGYNAIPAVHPEKPRTTKEAGRILAWAIEH 241 Query: 246 DIKPRDIITRKSIENAVALIMATGGSTNAVLHYLAIAHAAEVEWTIDDFERIRRKVPVIC 305 D KP+D +TR+S NA+A + ATGGSTNAVLH LA+A VE ++DDF+R+ RK PVI Sbjct: 242 DWKPQDFLTRRSFLNAIAAVAATGGSTNAVLHLLAMAKEVGVELSLDDFDRVSRKTPVIA 301 Query: 306 NLKPSGQYVATDLHKAGGIPQVMKILLKAGMLHGDCLTITGRTLAEELENVPDTPRADQD 365 +L+P G Y A +L++AGG P V K LL+AG+L G+ T+TGRTLAEE+E Q Sbjct: 302 DLRPWGTYTAWELYEAGGTPLVFKRLLEAGLLFGEEKTLTGRTLAEEVEQA-FREAEGQK 360 Query: 366 VILPIEKALYAEGHLAILKGNLAEEGAVAKITGLKNPVITGPARVFEDEQSAMEAILADK 425 V+ P+E+AL +G L +L+GNLA GAV K+ G + GPARVF+ E+ AM +LA + Sbjct: 361 VVFPVERALKPQGGLVVLRGNLAPRGAVLKLAGTERTYFEGPARVFDSEEEAMAKVLAKE 420 Query: 426 INAGDILVLRYLGPKGGPGMPEMLAPTSAIIGKGLGESVGFITDGRFSGGTWGMVVGHVA 485 I GD++V+RY+GPKG PGMPEML+ TSAI+G+GLG V +TDGRFSGGT G++VGH+A Sbjct: 421 IRPGDVVVIRYVGPKGAPGMPEMLSVTSAIVGEGLGPEVALLTDGRFSGGTRGLMVGHIA 480 Query: 486 PEAYVGGTIALVQEGDSITIDAHKLLLQLNVADEELARRRANWKQPAPRYTRGVLAKFSK 545 PEA+VGG IAL++EGD + ID LL++ + +EELARR+ +WK P + GV A+++ Sbjct: 481 PEAFVGGPIALLKEGDRVRIDVENRLLEVLLPEEELARRKESWKPRPPAFRHGVFARYAA 540 Query: 546 LASTASKGAVTD 557 L + A +GAV + Sbjct: 541 LVAQADEGAVLE 552 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: 980 Number of extensions: 53 Number of successful extensions: 3 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: 567 Length adjustment: 36 Effective length of query: 521 Effective length of database: 531 Effective search space: 276651 Effective search space used: 276651 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_053767874.1 BVI061214_RS07550 (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.173476.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.9e-206 672.1 0.0 3.4e-206 671.9 0.0 1.0 1 NCBI__GCF_001280255.1:WP_053767874.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_001280255.1:WP_053767874.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 671.9 0.0 3.4e-206 3.4e-206 1 542 [. 14 552 .. 14 553 .. 0.99 Alignments for each domain: == domain 1 score: 671.9 bits; conditional E-value: 3.4e-206 TIGR00110 1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamgheG 73 +ar++l+a+G+ ded+++P+++vvn++t+ +P++ hl++la k+++++aG ++ef+ a+sDGi+mg+ G NCBI__GCF_001280255.1:WP_053767874.1 14 PARSMLRAVGVGDEDFGRPFVGVVNTFTDGMPCNYHLRELALDLKAGLREAGVFPFEFGAPAISDGISMGTPG 86 579********************************************************************** PP TIGR00110 74 mkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktklsekidlv 146 m+ sL+sre+iaDs+e v+++ +D++ v+s+CDk +PG m+++r +P +v +GG++++g+ + ++k+++v NCBI__GCF_001280255.1:WP_053767874.1 87 MRASLVSREVIADSIELVAQGYLYDGMAVLSACDKTIPGGAMGVIRSGVPGMVLYGGTIAPGEWR-GRKLTIV 158 *****************************************************************.9****** PP TIGR00110 147 dvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllatsaekkelakks 219 +vfeavg+ aag++++eel eier a P++g+C+G +tan+ma++ e+lGls g +++a++ ek +++k++ NCBI__GCF_001280255.1:WP_053767874.1 159 EVFEAVGQRAAGRITDEELLEIERRAIPGPGACGGQYTANTMAMALEVLGLSPMGYNAIPAVHPEKPRTTKEA 231 ************************************************************************* PP TIGR00110 220 gkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklslddfdrlsrkvPllaklk 292 g+ + +++++ kP+d+lt+++f nai+ + a+GGstn+vLhlla+ake+gv+lslddfdr+srk+P++a+l+ NCBI__GCF_001280255.1:WP_053767874.1 232 GRILAWAIEHDWKPQDFLTRRSFLNAIAAVAATGGSTNAVLHLLAMAKEVGVELSLDDFDRVSRKTPVIADLR 304 ************************************************************************* PP TIGR00110 293 PsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlrvdqdvirsldnpvkkegglav 365 P g + +l +aGG++ v+k l ++gll + +t+tG+tlae++e++ ++q+v+ +++ ++k +ggl v NCBI__GCF_001280255.1:WP_053767874.1 305 PWGTYTAWELYEAGGTPLVFKRLLEAGLLFGEEKTLTGRTLAEEVEQAFREAEGQKVVFPVERALKPQGGLVV 377 ************************************************************************* PP TIGR00110 366 LkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeGdvvviryeGPkGgPGmremLaPts 438 L+Gnla++Gav k ag e ++feGpa+vf+seeea++ +l+++++ Gdvvviry GPkG+PGm+emL ts NCBI__GCF_001280255.1:WP_053767874.1 378 LRGNLAPRGAVLKLAGTER--TYFEGPARVFDSEEEAMAKVLAKEIRPGDVVVIRYVGPKGAPGMPEMLSVTS 448 ******************9..**************************************************** PP TIGR00110 439 alvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDienrkldlevseeelaerra 511 a+vg GLg +vaL+tDGrfsGgtrGl++Gh++Pea +gG+ial+++GD+++iD+enr l++ + eeela+r++ NCBI__GCF_001280255.1:WP_053767874.1 449 AIVGEGLGPEVALLTDGRFSGGTRGLMVGHIAPEAFVGGPIALLKEGDRVRIDVENRLLEVLLPEEELARRKE 521 ************************************************************************* PP TIGR00110 512 kakkkearevkgaLakyaklvssadkGavld 542 ++k++ + +g++a+ya lv++ad+Gavl+ NCBI__GCF_001280255.1:WP_053767874.1 522 SWKPRPPAFRHGVFARYAALVAQADEGAVLE 552 *****************************86 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (543 nodes) Target sequences: 1 (567 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 17.13 // [ok]
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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