Align dihydroxyacid dehydratase (EC 4.2.1.9) (characterized)
to candidate WP_028999050.1 H537_RS0118680 dihydroxy-acid dehydratase
Query= metacyc::MONOMER-18815 (557 letters) >NCBI__GCF_000430725.1:WP_028999050.1 Length = 559 Score = 877 bits (2267), Expect = 0.0 Identities = 425/557 (76%), Positives = 497/557 (89%), Gaps = 1/557 (0%) Query: 1 MAFNKRSQNITQGVARSPNRSMYYALGYKKEDFDKPMVGIANGHSTITPCNAGLQRLADA 60 M+ N+RS+NIT+GVAR+PNRSMYYA+GY + DF KPM+G+ANGHSTITPCN+GLQRLADA Sbjct: 1 MSDNRRSRNITEGVARAPNRSMYYAMGYTEGDFGKPMIGVANGHSTITPCNSGLQRLADA 60 Query: 61 AIDAIKASDANPQVFGTPTISDGMSMGTEGMKYSLISREVIADCIETAAQGQWMDGVVVI 120 A++ ++A+ ANPQ+FGTPTISDGM+MGTEGMKYSL+SREVI+DC+ET GQWMDGV+VI Sbjct: 61 AVEGLQAAGANPQIFGTPTISDGMAMGTEGMKYSLVSREVISDCVETCVGGQWMDGVLVI 120 Query: 121 GGCDKNMPGGMIALARTNVPGIYVYGGTIKPGNWKGKDLTIVSSFEAVGEFTAGRMSQED 180 GGCDKNMPGGM+ + R NVP IYVYGGTI PG +KG+DL IVS FEAVG+F+AG+MS+ED Sbjct: 121 GGCDKNMPGGMMGMLRANVPAIYVYGGTILPGRYKGQDLNIVSVFEAVGQFSAGKMSEED 180 Query: 181 FEGVEKNACPSTGSCGGMYTANTMSSSFEALGMSLLYSSTMANPDQEKVDSAAESARVLV 240 F +EK A P +GSCGGMYTANTMSS+FEALGMSL YSST AN EKV+S +A VLV Sbjct: 181 FCEIEKRAIPGSGSCGGMYTANTMSSAFEALGMSLPYSSTEANVHDEKVESTRRAAAVLV 240 Query: 241 EAIKQDIKPRDIITRKSIENAVALIMATGGSTNAVLHYLAIAHAAEVEWTIDDFERIRRK 300 EA+K+D+KPRDI+T++SIENAVA+IMATGGSTNAVLH+LAIAHAAEVEWTIDDFER+R+K Sbjct: 241 EAVKKDLKPRDIVTKQSIENAVAVIMATGGSTNAVLHFLAIAHAAEVEWTIDDFERMRKK 300 Query: 301 VPVICNLKPSGQYVATDLHKAGGIPQVMKILLKAGMLHGDCLTITGRTLAEELENVPDTP 360 V V+CNLKPSGQY+A DLH+AGGIP VMK LLKAG+L+GDC+TITG+T+AE L +VPD Sbjct: 301 VAVLCNLKPSGQYLAVDLHRAGGIPAVMKELLKAGLLNGDCMTITGKTVAENLADVPDL- 359 Query: 361 RADQDVILPIEKALYAEGHLAILKGNLAEEGAVAKITGLKNPVITGPARVFEDEQSAMEA 420 A+QDVI P+ LYA+GHLAILKGNL+ EG VAKITGLKNPVITGPARVF+DEQSA+ A Sbjct: 360 TAEQDVIRPVSDPLYAQGHLAILKGNLSPEGCVAKITGLKNPVITGPARVFDDEQSALAA 419 Query: 421 ILADKINAGDILVLRYLGPKGGPGMPEMLAPTSAIIGKGLGESVGFITDGRFSGGTWGMV 480 I+A +I AGD++VLRYLGPKGGPGMPEMLAPT A+IG+GLGESVG ITDGRFSGGTWGMV Sbjct: 420 IMAGQIKAGDVMVLRYLGPKGGPGMPEMLAPTGALIGQGLGESVGLITDGRFSGGTWGMV 479 Query: 481 VGHVAPEAYVGGTIALVQEGDSITIDAHKLLLQLNVADEELARRRANWKQPAPRYTRGVL 540 VGHVAPEAY GG IALVQEGD+ITIDAH+LLLQLNV + E+ARRRA WKQPAPRYTRGVL Sbjct: 480 VGHVAPEAYDGGNIALVQEGDAITIDAHQLLLQLNVDEAEIARRRAQWKQPAPRYTRGVL 539 Query: 541 AKFSKLASTASKGAVTD 557 AKF++ A +AS GAV D Sbjct: 540 AKFARNACSASSGAVLD 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: 1109 Number of extensions: 43 Number of successful extensions: 2 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: 559 Length adjustment: 36 Effective length of query: 521 Effective length of database: 523 Effective search space: 272483 Effective search space used: 272483 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_028999050.1 H537_RS0118680 (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.31974.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-230 751.5 5.7 2.9e-230 751.3 5.7 1.0 1 lcl|NCBI__GCF_000430725.1:WP_028999050.1 H537_RS0118680 dihydroxy-acid de Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000430725.1:WP_028999050.1 H537_RS0118680 dihydroxy-acid dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 751.3 5.7 2.9e-230 2.9e-230 1 542 [. 18 556 .. 18 557 .. 1.00 Alignments for each domain: == domain 1 score: 751.3 bits; conditional E-value: 2.9e-230 TIGR00110 1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiam 69 ++r++++a+G+++ d++kP+i+v+n++++i+P++ l+ la+++ e+++aaG+ ++ f+t ++sDG+am lcl|NCBI__GCF_000430725.1:WP_028999050.1 18 PNRSMYYAMGYTEGDFGKPMIGVANGHSTITPCNSGLQRLADAAVEGLQAAGANPQIFGTPTISDGMAM 86 68******************************************************************* PP TIGR00110 70 gheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktk 138 g+eGmkysL+sre+i+D vet v ++++D+++vi+ CDk++PG +m++lr n+Pai v+GG++ +g++k lcl|NCBI__GCF_000430725.1:WP_028999050.1 87 GTEGMKYSLVSREVISDCVETCVGGQWMDGVLVIGGCDKNMPGGMMGMLRANVPAIYVYGGTILPGRYK 155 ********************************************************************* PP TIGR00110 139 lsekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstlla 207 ++++++v+vfeavg+ +agk+see+ eie+ a P++gsC+G++tan+m++++ealG+slP+sst + lcl|NCBI__GCF_000430725.1:WP_028999050.1 156 -GQDLNIVSVFEAVGQFSAGKMSEEDFCEIEKRAIPGSGSCGGMYTANTMSSAFEALGMSLPYSSTEAN 223 .9******************************************************************* PP TIGR00110 208 tsaekkelakksgkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklsld 276 ++ ek e+++++++ +ve+vkk++kPrdi+tk+++ena+++++a+GGstn+vLh laia+ a+v+ ++d lcl|NCBI__GCF_000430725.1:WP_028999050.1 224 VHDEKVESTRRAAAVLVEAVKKDLKPRDIVTKQSIENAVAVIMATGGSTNAVLHFLAIAHAAEVEWTID 292 ********************************************************************* PP TIGR00110 277 dfdrlsrkvPllaklkPsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlrv 345 df+r+++kv +l++lkPsg+++ +dlhraGG++av+kel k+gll+ d++t+tGkt+ae+l++v+ l++ lcl|NCBI__GCF_000430725.1:WP_028999050.1 293 DFERMRKKVAVLCNLKPSGQYLAVDLHRAGGIPAVMKELLKAGLLNGDCMTITGKTVAENLADVPDLTA 361 ********************************************************************* PP TIGR00110 346 dqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeG 414 +qdvir++++p++++g+la+LkGnl++eG+v+ki+g ++ +++Gpa+vf++e+ al+ai++g++k+G lcl|NCBI__GCF_000430725.1:WP_028999050.1 362 EQDVIRPVSDPLYAQGHLAILKGNLSPEGCVAKITGLKN--PVITGPARVFDDEQSALAAIMAGQIKAG 428 ***************************************..999************************* PP TIGR00110 415 dvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialve 483 dv+v+ry GPkGgPGm+emLaPt al+g GLg++v+LitDGrfsGgt G+++Ghv+Pea+ gG+ialv+ lcl|NCBI__GCF_000430725.1:WP_028999050.1 429 DVMVLRYLGPKGGPGMPEMLAPTGALIGQGLGESVGLITDGRFSGGTWGMVVGHVAPEAYDGGNIALVQ 497 ********************************************************************* PP TIGR00110 484 dGDkikiDienrkldlevseeelaerrakakkkearevkgaLakyaklvssadkGavld 542 +GD i+iD+++ l+l+v+e+e+a+rra++k++ +r+++g+Lak+a+ + sa++Gavld lcl|NCBI__GCF_000430725.1:WP_028999050.1 498 EGDAITIDAHQLLLQLNVDEAEIARRRAQWKQPAPRYTRGVLAKFARNACSASSGAVLD 556 *********************************************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (543 nodes) Target sequences: 1 (559 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: 7.69 // [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