Align dihydroxyacid dehydratase (EC 4.2.1.9) (characterized)
to candidate WP_010532005.1 ON01_RS15945 dihydroxy-acid dehydratase
Query= metacyc::MONOMER-18815 (557 letters) >NCBI__GCF_000224785.1:WP_010532005.1 Length = 563 Score = 588 bits (1515), Expect = e-172 Identities = 290/552 (52%), Positives = 394/552 (71%), Gaps = 2/552 (0%) Query: 6 RSQNITQGVARSPNRSMYYALGYKKEDFDKPMVGIANGHSTITPCNAGLQRLADAAIDAI 65 +SQ + R+PNR+M A+G E F+KPMVGIA+ S +TPCN + LA +A Sbjct: 8 KSQVFSDDTMRAPNRAMLRAVGLTDEHFEKPMVGIASTWSEVTPCNIHIDDLAVSAKKGA 67 Query: 66 KASDANPQVFGTPTISDGMSMGTEGMKYSLISREVIADCIETAAQGQWMDGVVVIGGCDK 125 + + A P +F T T+SDG+SMGT+GM+YSL SR++IAD IET + +D V IG CDK Sbjct: 68 REAGATPLIFNTITVSDGISMGTQGMRYSLPSRDLIADSIETVVGAENLDAFVAIGACDK 127 Query: 126 NMPGGMIALARTNVPGIYVYGGTIKPGNWKGKDLTIVSSFEAVGEFTAGRMSQEDFEGVE 185 N+PG MIA+A ++VP ++VYGGTI PG+ GKD+ +VS FE VG+ G + ++ + +E Sbjct: 128 NIPGCMIAIANSDVPAVFVYGGTIAPGSHNGKDIDLVSVFEGVGKHNNGDIDDQELKNIE 187 Query: 186 KNACPSTGSCGGMYTANTMSSSFEALGMSLLYSSTMANPDQEKVDSAAESARVLVEAIKQ 245 ACP G+CGGMYTANTM+S+ EA+GMSL S++ +EK AE+ + + ++Q Sbjct: 188 CKACPGAGACGGMYTANTMASAVEAMGMSLPGSASNPAESEEKAADCAEAGEAVYKLLEQ 247 Query: 246 DIKPRDIITRKSIENAVALIMATGGSTNAVLHYLAIAHAAEVEWTIDDFERIRRKVPVIC 305 I P+DI+T+K+ ENA+ ++MA GGSTNA+LH L +AHA V+ TIDDF RI+ KVP + Sbjct: 248 GIYPKDIMTKKAFENAMTVVMALGGSTNAILHLLGMAHAVGVDITIDDFNRIQEKVPHLA 307 Query: 306 NLKPSGQYVATDLHKAGGIPQVMKILLKAGMLHGDCLTITGRTLAEELENVPDTPRADQD 365 +LKPSGQYV DLH++GG+ VMK+L +AG LHGDCLT+TG+T+AE L P DQ Sbjct: 308 DLKPSGQYVMQDLHRSGGVQAVMKLLYEAGYLHGDCLTVTGKTVAENLAEAPSLAE-DQK 366 Query: 366 VILPIEKALYAEGHLAILKGNLAEEGAVAKITGLKNPVITGPARVFEDEQSAMEAILADK 425 VI P++ +G L +LKGNLA GAVAK++G+K TGPARVF EQ A +A+ +K Sbjct: 367 VIAPLDNPKRTDGPLIVLKGNLAPRGAVAKVSGVKVSRHTGPARVFNTEQEATDAVRQNK 426 Query: 426 INAGDILVLRYLGPKGGPGMPEMLAPTSAIIGKGLGESVGFITDGRFSGGTWGMVVGHVA 485 I GD+LV+RY+GPKGGPGMPEML+ +S ++GKGLGE V +TDGRFSGGT G+VVGH+A Sbjct: 427 IQEGDVLVIRYVGPKGGPGMPEMLSVSSLLVGKGLGEKVALLTDGRFSGGTHGLVVGHIA 486 Query: 486 PEAYVGGTIALVQEGDSITIDAHKLLLQLNVADEELARRRANWKQPAPRYTRGVLAKFSK 545 PEA GG IA ++EGD++TID+ + + +V++EEL RR+ NW P P Y +GVL K++ Sbjct: 487 PEAQDGGPIAFLKEGDNVTIDSDEKEITADVSEEELERRKQNWSAP-PLYKKGVLGKYAH 545 Query: 546 LASTASKGAVTD 557 S +SKGAVTD Sbjct: 546 NVSCSSKGAVTD 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: 918 Number of extensions: 42 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: 563 Length adjustment: 36 Effective length of query: 521 Effective length of database: 527 Effective search space: 274567 Effective search space used: 274567 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_010532005.1 ON01_RS15945 (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.670102.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.5e-228 744.9 7.1 2.9e-228 744.7 7.1 1.0 1 NCBI__GCF_000224785.1:WP_010532005.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000224785.1:WP_010532005.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 744.7 7.1 2.9e-228 2.9e-228 1 542 [. 20 557 .. 20 558 .. 0.99 Alignments for each domain: == domain 1 score: 744.7 bits; conditional E-value: 2.9e-228 TIGR00110 1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamgheG 73 ++ra+l+a+Gl+de +ekP+++++++++e++P+++h++dla +k++ ++aG+++ fnti+vsDGi+mg++G NCBI__GCF_000224785.1:WP_010532005.1 20 PNRAMLRAVGLTDEHFEKPMVGIASTWSEVTPCNIHIDDLAVSAKKGAREAGATPLIFNTITVSDGISMGTQG 92 68*********************************************************************** PP TIGR00110 74 mkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktklsekidlv 146 m+ysLpsr++iaDs+etvv a+ lDa v+i++CDk++PG ++a + ++Pa++v+GG++++g + +++idlv NCBI__GCF_000224785.1:WP_010532005.1 93 MRYSLPSRDLIADSIETVVGAENLDAFVAIGACDKNIPGCMIAIANSDVPAVFVYGGTIAPGSHN-GKDIDLV 164 ****************************************************************9.9****** PP TIGR00110 147 dvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllatsaekkelakks 219 +vfe+vg+ ++g+++++el++ie acP+ag+C+G++tan+ma++ ea+G+slPgs++ +a s+ek++ + ++ NCBI__GCF_000224785.1:WP_010532005.1 165 SVFEGVGKHNNGDIDDQELKNIECKACPGAGACGGMYTANTMASAVEAMGMSLPGSASNPAESEEKAADCAEA 237 ************************************************************************* PP TIGR00110 220 gkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklslddfdrlsrkvPllaklk 292 g+ + +l+++ i P+di+tk+afena+t+++alGGstn++Lhll +a+ +gv++++ddf+r+++kvP+la+lk NCBI__GCF_000224785.1:WP_010532005.1 238 GEAVYKLLEQGIYPKDIMTKKAFENAMTVVMALGGSTNAILHLLGMAHAVGVDITIDDFNRIQEKVPHLADLK 310 ************************************************************************* PP TIGR00110 293 PsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlrvdqdvirsldnpvkkegglav 365 Psg++v++dlhr+GGv+av+k l+++g+lh d+ltvtGkt+ae+l+++++l +dq+vi++ldnp + +g l v NCBI__GCF_000224785.1:WP_010532005.1 311 PSGQYVMQDLHRSGGVQAVMKLLYEAGYLHGDCLTVTGKTVAENLAEAPSLAEDQKVIAPLDNPKRTDGPLIV 383 ************************************************************************* PP TIGR00110 366 LkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeGdvvviryeGPkGgPGmremLaPts 438 LkGnla++Gav+k++gv+ +++Gpa+vf+ e+ea +a+ + k++eGdv+viry GPkGgPGm+emL +s NCBI__GCF_000224785.1:WP_010532005.1 384 LKGNLAPRGAVAKVSGVKV--SRHTGPARVFNTEQEATDAVRQNKIQEGDVLVIRYVGPKGGPGMPEMLSVSS 454 *****************87..9*************************************************** PP TIGR00110 439 alvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDienrkldlevseeelaerra 511 lvg GLg+kvaL+tDGrfsGgt+Gl++Gh++Pea gG+ia++++GD+++iD +++++ +vseeel++r++ NCBI__GCF_000224785.1:WP_010532005.1 455 LLVGKGLGEKVALLTDGRFSGGTHGLVVGHIAPEAQDGGPIAFLKEGDNVTIDSDEKEITADVSEEELERRKQ 527 ************************************************************************* PP TIGR00110 512 kakkkearevkgaLakyaklvssadkGavld 542 +++++ ++kg+L kya+ vs ++kGav+d NCBI__GCF_000224785.1:WP_010532005.1 528 NWSAPP-LYKKGVLGKYAHNVSCSSKGAVTD 557 ****99.789*******************87 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (543 nodes) Target sequences: 1 (563 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 33.14 // [ok]
This GapMind analysis is from Jul 26 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