Align dihydroxyacid dehydratase (EC 4.2.1.9) (characterized)
to candidate WP_013520142.1 ALIDE2_RS05525 dihydroxy-acid dehydratase
Query= metacyc::MONOMER-18815 (557 letters) >NCBI__GCF_000204645.1:WP_013520142.1 Length = 563 Score = 888 bits (2295), Expect = 0.0 Identities = 432/557 (77%), Positives = 493/557 (88%) Query: 1 MAFNKRSQNITQGVARSPNRSMYYALGYKKEDFDKPMVGIANGHSTITPCNAGLQRLADA 60 M N+RS +ITQG AR+PNRSMYY +GY + DFDKPMVG+ANGHSTITPCN+GLQRLADA Sbjct: 5 MPLNRRSAHITQGKARAPNRSMYYGMGYAEADFDKPMVGVANGHSTITPCNSGLQRLADA 64 Query: 61 AIDAIKASDANPQVFGTPTISDGMSMGTEGMKYSLISREVIADCIETAAQGQWMDGVVVI 120 AI+ I+ + NPQVFGTPTISDGM+MGTEGMKYSL+SREVIADC+ET QGQWMDG VVI Sbjct: 65 AIEGIREAGGNPQVFGTPTISDGMAMGTEGMKYSLVSREVIADCVETCVQGQWMDGCVVI 124 Query: 121 GGCDKNMPGGMIALARTNVPGIYVYGGTIKPGNWKGKDLTIVSSFEAVGEFTAGRMSQED 180 GGCDKNMPGGM+ + R NVP IYVYGGTI PG+ G DL IVS FEAVGE AG++S + Sbjct: 125 GGCDKNMPGGMMGMLRANVPSIYVYGGTILPGSLHGCDLNIVSVFEAVGENAAGKISDRE 184 Query: 181 FEGVEKNACPSTGSCGGMYTANTMSSSFEALGMSLLYSSTMANPDQEKVDSAAESARVLV 240 + +E++A P TGSCGGMYTANTMSS+FEALGMSL YSSTMANP QEK DSA ESA+VL+ Sbjct: 185 LKDIEQHAIPGTGSCGGMYTANTMSSAFEALGMSLPYSSTMANPHQEKADSAKESAKVLI 244 Query: 241 EAIKQDIKPRDIITRKSIENAVALIMATGGSTNAVLHYLAIAHAAEVEWTIDDFERIRRK 300 EAI++D+KPRDI+TRK+IENAVA+IMA GGSTNAVLH+LAIAHAA V+W+IDDFER+R+K Sbjct: 245 EAIRRDLKPRDIVTRKAIENAVAVIMAVGGSTNAVLHFLAIAHAAGVDWSIDDFERMRQK 304 Query: 301 VPVICNLKPSGQYVATDLHKAGGIPQVMKILLKAGMLHGDCLTITGRTLAEELENVPDTP 360 VPV C+LKPSG+Y+A DLH+AGGIPQVMK+LL AG+LHGDC+TITGRT+AE L++VP P Sbjct: 305 VPVFCDLKPSGRYLAVDLHRAGGIPQVMKMLLNAGLLHGDCMTITGRTIAETLKDVPGQP 364 Query: 361 RADQDVILPIEKALYAEGHLAILKGNLAEEGAVAKITGLKNPVITGPARVFEDEQSAMEA 420 RADQDVI PI+K LY GHLAILKGNL+ EGAVAKITGLKNPVITGPARVF+DEQSA+ A Sbjct: 365 RADQDVIRPIDKPLYGHGHLAILKGNLSPEGAVAKITGLKNPVITGPARVFDDEQSALAA 424 Query: 421 ILADKINAGDILVLRYLGPKGGPGMPEMLAPTSAIIGKGLGESVGFITDGRFSGGTWGMV 480 IL KI AGD++VLRYLGPKGGPGMPEMLAPT A+IG+GLGESVG ITDGRFSGGTWGMV Sbjct: 425 ILDGKIKAGDVMVLRYLGPKGGPGMPEMLAPTGALIGQGLGESVGLITDGRFSGGTWGMV 484 Query: 481 VGHVAPEAYVGGTIALVQEGDSITIDAHKLLLQLNVADEELARRRANWKQPAPRYTRGVL 540 VGHVAPEA+VGGTIALV EGDSITIDAH+LLLQLNV D+ELARRRA W PAPRYTRGV Sbjct: 485 VGHVAPEAFVGGTIALVHEGDSITIDAHRLLLQLNVGDDELARRRAGWTPPAPRYTRGVQ 544 Query: 541 AKFSKLASTASKGAVTD 557 AKF+ A++ASKGAV D Sbjct: 545 AKFAFNAASASKGAVLD 561 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: 1140 Number of extensions: 44 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: 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_013520142.1 ALIDE2_RS05525 (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.30749.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-230 752.1 2.6 1.9e-230 751.9 2.6 1.0 1 lcl|NCBI__GCF_000204645.1:WP_013520142.1 ALIDE2_RS05525 dihydroxy-acid de Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000204645.1:WP_013520142.1 ALIDE2_RS05525 dihydroxy-acid dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 751.9 2.6 1.9e-230 1.9e-230 1 542 [. 22 561 .. 22 562 .. 0.99 Alignments for each domain: == domain 1 score: 751.9 bits; conditional E-value: 1.9e-230 TIGR00110 1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiam 69 ++r++++ +G+ ++d++kP+++v+n++++i+P++ l+ la+++ e+i++aGg ++ f+t ++sDG+am lcl|NCBI__GCF_000204645.1:WP_013520142.1 22 PNRSMYYGMGYAEADFDKPMVGVANGHSTITPCNSGLQRLADAAIEGIREAGGNPQVFGTPTISDGMAM 90 68******************************************************************* PP TIGR00110 70 gheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktk 138 g+eGmkysL+sre+iaD vet v+++++D+ vvi+ CDk++PG +m++lr n+P+i v+GG++ +g ++ lcl|NCBI__GCF_000204645.1:WP_013520142.1 91 GTEGMKYSLVSREVIADCVETCVQGQWMDGCVVIGGCDKNMPGGMMGMLRANVPSIYVYGGTILPGSLH 159 ********************************************************************* PP TIGR00110 139 lsekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstlla 207 + ++++v+vfeavge aagk+s+ el++ie++a P++gsC+G++tan+m++++ealG+slP+sst++ lcl|NCBI__GCF_000204645.1:WP_013520142.1 160 -GCDLNIVSVFEAVGENAAGKISDRELKDIEQHAIPGTGSCGGMYTANTMSSAFEALGMSLPYSSTMAN 227 .99****************************************************************** PP TIGR00110 208 tsaekkelakksgkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklsld 276 ++ek+++ak+s+k ++e++++++kPrdi+t++a+ena+++++a+GGstn+vLh laia+ agv+ s+d lcl|NCBI__GCF_000204645.1:WP_013520142.1 228 PHQEKADSAKESAKVLIEAIRRDLKPRDIVTRKAIENAVAVIMAVGGSTNAVLHFLAIAHAAGVDWSID 296 ********************************************************************* PP TIGR00110 277 dfdrlsrkvPllaklkPsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlr. 344 df+r+++kvP+ ++lkPsg+++ +dlhraGG+++v+k+l ++gllh d++t+tG+t+aetl++v+ ++ lcl|NCBI__GCF_000204645.1:WP_013520142.1 297 DFERMRQKVPVFCDLKPSGRYLAVDLHRAGGIPQVMKMLLNAGLLHGDCMTITGRTIAETLKDVPGQPr 365 ****************************************************************98854 PP TIGR00110 345 vdqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvke 413 +dqdvir++d+p++ +g+la+LkGnl++eGav+ki+g ++ +++Gpa+vf++e+ al+ail+gk+k+ lcl|NCBI__GCF_000204645.1:WP_013520142.1 366 ADQDVIRPIDKPLYGHGHLAILKGNLSPEGAVAKITGLKN--PVITGPARVFDDEQSALAAILDGKIKA 432 89**************************************..999************************ PP TIGR00110 414 GdvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialv 482 Gdv+v+ry GPkGgPGm+emLaPt al+g GLg++v+LitDGrfsGgt G+++Ghv+Pea +gG+ialv lcl|NCBI__GCF_000204645.1:WP_013520142.1 433 GDVMVLRYLGPKGGPGMPEMLAPTGALIGQGLGESVGLITDGRFSGGTWGMVVGHVAPEAFVGGTIALV 501 ********************************************************************* PP TIGR00110 483 edGDkikiDienrkldlevseeelaerrakakkkearevkgaLakyaklvssadkGavld 542 ++GD i+iD+++ l+l+v ++ela+rra ++++ +r+++g+ ak+a ++sa+kGavld lcl|NCBI__GCF_000204645.1:WP_013520142.1 502 HEGDSITIDAHRLLLQLNVGDDELARRRAGWTPPAPRYTRGVQAKFAFNAASASKGAVLD 561 **********************************************************97 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 0.01s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 12.01 // [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