Align dihydroxyacid dehydratase (EC 4.2.1.9) (characterized)
to candidate WP_011609947.1 TERY_RS00080 dihydroxy-acid dehydratase
Query= metacyc::MONOMER-18815 (557 letters) >NCBI__GCF_000014265.1:WP_011609947.1 Length = 561 Score = 767 bits (1980), Expect = 0.0 Identities = 377/557 (67%), Positives = 460/557 (82%) Query: 1 MAFNKRSQNITQGVARSPNRSMYYALGYKKEDFDKPMVGIANGHSTITPCNAGLQRLADA 60 M N RSQ +T+GV R+PNR+M A+G++ DF KP++G+AN HSTITPCN G+ LA Sbjct: 1 MPENLRSQLVTKGVQRAPNRAMLRAVGFEDSDFTKPIIGVANAHSTITPCNMGINDLAMR 60 Query: 61 AIDAIKASDANPQVFGTPTISDGMSMGTEGMKYSLISREVIADCIETAAQGQWMDGVVVI 120 A+ +K + PQ+FGT TISDG+SMGTEGMKYSL+SR+VIAD IET GQ MDGV+ I Sbjct: 61 AVSGVKEAGGMPQIFGTITISDGISMGTEGMKYSLVSRDVIADSIETVCNGQTMDGVLAI 120 Query: 121 GGCDKNMPGGMIALARTNVPGIYVYGGTIKPGNWKGKDLTIVSSFEAVGEFTAGRMSQED 180 GGCDKNMPG MIA+AR N+P I+VYGGTIKPGN+ GKDLT+VS+FEAVGE++AG++ + + Sbjct: 121 GGCDKNMPGAMIAIARMNIPAIFVYGGTIKPGNYNGKDLTVVSAFEAVGEYSAGKIDETE 180 Query: 181 FEGVEKNACPSTGSCGGMYTANTMSSSFEALGMSLLYSSTMANPDQEKVDSAAESARVLV 240 VE+ ACP GSCGGM+TANTMSS+FEA+GMSL+YSSTMA D EK DS +SA VLV Sbjct: 181 LTEVERRACPGAGSCGGMFTANTMSSAFEAMGMSLMYSSTMAAEDAEKADSTEKSAHVLV 240 Query: 241 EAIKQDIKPRDIITRKSIENAVALIMATGGSTNAVLHYLAIAHAAEVEWTIDDFERIRRK 300 EAI++ I P IITRK+IENA+++IMA GGSTNAVLH LAIA+AA V+ ++DDFE IR + Sbjct: 241 EAIRKQILPSQIITRKAIENAISVIMAVGGSTNAVLHLLAIAYAANVKLSLDDFEIIRAR 300 Query: 301 VPVICNLKPSGQYVATDLHKAGGIPQVMKILLKAGMLHGDCLTITGRTLAEELENVPDTP 360 VPV+C+LKPSG+YV T+LH+AGGIP VMK+LL+ +LH D LTITG+T+ E+L N+P P Sbjct: 301 VPVLCDLKPSGKYVTTNLHQAGGIPLVMKMLLEHDLLHPDALTITGKTIGEQLTNIPSEP 360 Query: 361 RADQDVILPIEKALYAEGHLAILKGNLAEEGAVAKITGLKNPVITGPARVFEDEQSAMEA 420 ++QDVI P +YA+GHLAILKGNLA EGAVAKITG+KNP ITG ARVF+ E++ +EA Sbjct: 361 PSNQDVIRPWNNPMYAQGHLAILKGNLATEGAVAKITGVKNPEITGLARVFDSEEACLEA 420 Query: 421 ILADKINAGDILVLRYLGPKGGPGMPEMLAPTSAIIGKGLGESVGFITDGRFSGGTWGMV 480 ILA KI AG+I+V+RY GPKGGPGM EMLAPTSAIIG GLG+ VG ITDGRFSGGT+GMV Sbjct: 421 ILAGKIQAGNIIVVRYEGPKGGPGMREMLAPTSAIIGAGLGDKVGLITDGRFSGGTYGMV 480 Query: 481 VGHVAPEAYVGGTIALVQEGDSITIDAHKLLLQLNVADEELARRRANWKQPAPRYTRGVL 540 VGHVAPEA VGGTIALV+EGD ITIDAHK LLQLN++DEEL +RR WK P+YTRGVL Sbjct: 481 VGHVAPEAAVGGTIALVKEGDMITIDAHKRLLQLNISDEELEKRRQVWKPRKPQYTRGVL 540 Query: 541 AKFSKLASTASKGAVTD 557 AK++KL S++S GAVTD Sbjct: 541 AKYAKLVSSSSVGAVTD 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: 1037 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: 561 Length adjustment: 36 Effective length of query: 521 Effective length of database: 525 Effective search space: 273525 Effective search space used: 273525 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_011609947.1 TERY_RS00080 (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.27581.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.8e-247 806.4 11.8 6.6e-247 806.3 11.8 1.0 1 lcl|NCBI__GCF_000014265.1:WP_011609947.1 TERY_RS00080 dihydroxy-acid dehy Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000014265.1:WP_011609947.1 TERY_RS00080 dihydroxy-acid dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 806.3 11.8 6.6e-247 6.6e-247 1 542 [. 18 557 .. 18 558 .. 0.99 Alignments for each domain: == domain 1 score: 806.3 bits; conditional E-value: 6.6e-247 TIGR00110 1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiam 69 ++ra+l+a+G++d d++kPii+v+n++++i+P+++ ++dla ++ ++++aGg+++ f+ti++sDGi+m lcl|NCBI__GCF_000014265.1:WP_011609947.1 18 PNRAMLRAVGFEDSDFTKPIIGVANAHSTITPCNMGINDLAMRAVSGVKEAGGMPQIFGTITISDGISM 86 68******************************************************************* PP TIGR00110 70 gheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktk 138 g+eGmkysL+sr++iaDs+etv++++++D++++i+ CDk++PG+++a +r+niPai+v+GG++++g+++ lcl|NCBI__GCF_000014265.1:WP_011609947.1 87 GTEGMKYSLVSRDVIADSIETVCNGQTMDGVLAIGGCDKNMPGAMIAIARMNIPAIFVYGGTIKPGNYN 155 ********************************************************************* PP TIGR00110 139 lsekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstlla 207 ++++++v++feavgey+agk++e el+e+er acP+agsC+G+ftan+m++++ea+G+sl +sst++a lcl|NCBI__GCF_000014265.1:WP_011609947.1 156 -GKDLTVVSAFEAVGEYSAGKIDETELTEVERRACPGAGSCGGMFTANTMSSAFEAMGMSLMYSSTMAA 223 .9******************************************************************* PP TIGR00110 208 tsaekkelakksgkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklsld 276 +aek+++++ks++ +ve+++k+i P++i+t++a+enai++++a+GGstn+vLhllaia a+vklsld lcl|NCBI__GCF_000014265.1:WP_011609947.1 224 EDAEKADSTEKSAHVLVEAIRKQILPSQIITRKAIENAISVIMAVGGSTNAVLHLLAIAYAANVKLSLD 292 ********************************************************************* PP TIGR00110 277 dfdrlsrkvPllaklkPsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlr. 344 df+ ++ +vP+l++lkPsgk+v+++lh+aGG++ v+k+l +++llh dalt+tGkt++e+l ++++ + lcl|NCBI__GCF_000014265.1:WP_011609947.1 293 DFEIIRARVPVLCDLKPSGKYVTTNLHQAGGIPLVMKMLLEHDLLHPDALTITGKTIGEQLTNIPSEPp 361 ****************************************************************99864 PP TIGR00110 345 vdqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvke 413 +qdvir+++np++++g+la+LkGnla+eGav+ki+gv++ +++G a+vf+see++leail+gk+++ lcl|NCBI__GCF_000014265.1:WP_011609947.1 362 SNQDVIRPWNNPMYAQGHLAILKGNLATEGAVAKITGVKN--PEITGLARVFDSEEACLEAILAGKIQA 428 899*************************************..9************************** PP TIGR00110 414 GdvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialv 482 G+++v+ryeGPkGgPGmremLaPtsa++g+GLg+kv+LitDGrfsGgt+G+++Ghv+Peaa+gG+ialv lcl|NCBI__GCF_000014265.1:WP_011609947.1 429 GNIIVVRYEGPKGGPGMREMLAPTSAIIGAGLGDKVGLITDGRFSGGTYGMVVGHVAPEAAVGGTIALV 497 ********************************************************************* PP TIGR00110 483 edGDkikiDienrkldlevseeelaerrakakkkearevkgaLakyaklvssadkGavld 542 ++GD+i+iD+++r l+l++s+eel++rr+ +k++++++++g+Lakyaklvss++ Gav+d lcl|NCBI__GCF_000014265.1:WP_011609947.1 498 KEGDMITIDAHKRLLQLNISDEELEKRRQVWKPRKPQYTRGVLAKYAKLVSSSSVGAVTD 557 **********************************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (543 nodes) Target sequences: 1 (561 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03 # Mc/sec: 7.65 // [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