Align dihydroxyacid dehydratase (EC 4.2.1.9) (characterized)
to candidate Ac3H11_954 Dihydroxy-acid dehydratase (EC 4.2.1.9)
Query= metacyc::MONOMER-18815 (557 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_954 Length = 567 Score = 875 bits (2260), Expect = 0.0 Identities = 427/554 (77%), Positives = 491/554 (88%) Query: 4 NKRSQNITQGVARSPNRSMYYALGYKKEDFDKPMVGIANGHSTITPCNAGLQRLADAAID 63 N+RS NITQG +R+PNRSMYYA+GY++ DF KPMVG+ANGHSTITPCN+GLQ+LADAAI Sbjct: 12 NRRSANITQGKSRAPNRSMYYAMGYEEGDFVKPMVGVANGHSTITPCNSGLQKLADAAIA 71 Query: 64 AIKASDANPQVFGTPTISDGMSMGTEGMKYSLISREVIADCIETAAQGQWMDGVVVIGGC 123 I+ + N QVFGTPTISDGM+MGTEGMKYSL+SREVI+DCIET GQWMDGV+V+GGC Sbjct: 72 GIEEAGGNAQVFGTPTISDGMAMGTEGMKYSLVSREVISDCIETCVGGQWMDGVLVVGGC 131 Query: 124 DKNMPGGMIALARTNVPGIYVYGGTIKPGNWKGKDLTIVSSFEAVGEFTAGRMSQEDFEG 183 DKNMPGG++ + R NVP IYVYGGTI PG+++GKDL IVS FEAVGE AG++S D + Sbjct: 132 DKNMPGGLMGMLRANVPAIYVYGGTILPGHYQGKDLNIVSVFEAVGENAAGKLSDFDLKE 191 Query: 184 VEKNACPSTGSCGGMYTANTMSSSFEALGMSLLYSSTMANPDQEKVDSAAESARVLVEAI 243 +EK A P TGSCGGMYTANTMSS+FEALG+SL YSSTMANP EK++SA ESA+VL+EAI Sbjct: 192 IEKRAIPGTGSCGGMYTANTMSSAFEALGISLPYSSTMANPHDEKMNSAKESAKVLIEAI 251 Query: 244 KQDIKPRDIITRKSIENAVALIMATGGSTNAVLHYLAIAHAAEVEWTIDDFERIRRKVPV 303 K+DIKPRDI+T+KSIENAVA+IMATGGSTNAVLH+LAIAHAA VEW+IDDFER+R K PV Sbjct: 252 KKDIKPRDIVTKKSIENAVAVIMATGGSTNAVLHFLAIAHAAGVEWSIDDFERVRVKTPV 311 Query: 304 ICNLKPSGQYVATDLHKAGGIPQVMKILLKAGMLHGDCLTITGRTLAEELENVPDTPRAD 363 +C+LKPSG+Y+A DLH+AGGIPQVMK+LL AG+LHGDCLTI G+T+AE L++VPD PRAD Sbjct: 312 LCDLKPSGKYLAVDLHRAGGIPQVMKVLLNAGLLHGDCLTIEGKTVAEVLKDVPDQPRAD 371 Query: 364 QDVILPIEKALYAEGHLAILKGNLAEEGAVAKITGLKNPVITGPARVFEDEQSAMEAILA 423 QDVI PI +YA+GHLAILKGNL+ EGAVAKITGLKNPVITGPARVFEDEQSA+EAILA Sbjct: 372 QDVIRPINNPMYAQGHLAILKGNLSPEGAVAKITGLKNPVITGPARVFEDEQSALEAILA 431 Query: 424 DKINAGDILVLRYLGPKGGPGMPEMLAPTSAIIGKGLGESVGFITDGRFSGGTWGMVVGH 483 KI AGD++VLRYLGPKGGPGMPEMLAPT A+IG GLGESVG ITDGRFSGGTWGMVVGH Sbjct: 432 GKIKAGDVMVLRYLGPKGGPGMPEMLAPTGALIGAGLGESVGLITDGRFSGGTWGMVVGH 491 Query: 484 VAPEAYVGGTIALVQEGDSITIDAHKLLLQLNVADEELARRRANWKQPAPRYTRGVLAKF 543 VAPEA GGTIA V EGDSITIDA +LLL+LNV++EE+ARRRA W PAPRYTRGV AKF Sbjct: 492 VAPEAAAGGTIAFVHEGDSITIDARQLLLELNVSEEEIARRRAAWTAPAPRYTRGVQAKF 551 Query: 544 SKLASTASKGAVTD 557 + AS+ASKGAV D Sbjct: 552 AFNASSASKGAVLD 565 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: 1137 Number of extensions: 42 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: 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 Ac3H11_954 (Dihydroxy-acid dehydratase (EC 4.2.1.9))
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.21961.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-229 749.4 5.9 1.3e-229 749.2 6.0 1.0 1 lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_954 Dihydroxy-acid dehydratase (EC 4 Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_954 Dihydroxy-acid dehydratase (EC 4.2.1.9) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 749.2 6.0 1.3e-229 1.3e-229 1 542 [. 26 565 .. 26 566 .. 0.99 Alignments for each domain: == domain 1 score: 749.2 bits; conditional E-value: 1.3e-229 TIGR00110 1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiav 63 ++r++++a+G+++ d+ kP+++v+n++++i+P++ l++la+++ ++ie+aGg a+ f+t ++ lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_954 26 PNRSMYYAMGYEEGDFVKPMVGVANGHSTITPCNSGLQKLADAAIAGIEEAGGNAQVFGTPTI 88 68************************************************************* PP TIGR00110 64 sDGiamgheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaiv 126 sDG+amg+eGmkysL+sre+i+D +et v ++++D+++v++ CDk++PG lm++lr n+Pai lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_954 89 SDGMAMGTEGMKYSLVSREVISDCIETCVGGQWMDGVLVVGGCDKNMPGGLMGMLRANVPAIY 151 *************************************************************** PP TIGR00110 127 vsGGpmeagktklsekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansma 189 v+GG++ +g+++ ++++++v+vfeavge aagkls+ +l+eie+ a P++gsC+G++tan+m+ lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_954 152 VYGGTILPGHYQ-GKDLNIVSVFEAVGENAAGKLSDFDLKEIEKRAIPGTGSCGGMYTANTMS 213 ************.9************************************************* PP TIGR00110 190 cltealGlslPgsstllatsaekkelakksgkrivelvkknikPrdiltkeafenaitldlal 252 +++ealG+slP+sst++ + ek+++ak+s+k ++e++kk+ikPrdi+tk+++ena+++++a+ lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_954 214 SAFEALGISLPYSSTMANPHDEKMNSAKESAKVLIEAIKKDIKPRDIVTKKSIENAVAVIMAT 276 *************************************************************** PP TIGR00110 253 GGstntvLhllaiakeagvklslddfdrlsrkvPllaklkPsgkkviedlhraGGvsavlkel 315 GGstn+vLh laia+ agv+ s+ddf+r++ k+P+l++lkPsgk++ +dlhraGG+++v+k+l lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_954 277 GGSTNAVLHFLAIAHAAGVEWSIDDFERVRVKTPVLCDLKPSGKYLAVDLHRAGGIPQVMKVL 339 *************************************************************** PP TIGR00110 316 dkegllhkdaltvtGktlaetlekvkvlr.vdqdvirsldnpvkkegglavLkGnlaeeGavv 377 ++gllh d+lt+ Gkt+ae+l++v+ ++ +dqdvir+++np++++g+la+LkGnl++eGav+ lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_954 340 LNAGLLHGDCLTIEGKTVAEVLKDVPDQPrADQDVIRPINNPMYAQGHLAILKGNLSPEGAVA 402 *************************9886489******************************* PP TIGR00110 378 kiagveedilkfeGpakvfeseeealeailggkvkeGdvvviryeGPkGgPGmremLaPtsal 440 ki+g ++ +++Gpa+vfe+e+ aleail+gk+k+Gdv+v+ry GPkGgPGm+emLaPt al lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_954 403 KITGLKN--PVITGPARVFEDEQSALEAILAGKIKAGDVMVLRYLGPKGGPGMPEMLAPTGAL 463 *******..999*************************************************** PP TIGR00110 441 vglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDienrkldlevse 503 +g+GLg++v+LitDGrfsGgt G+++Ghv+Peaa+gG+ia+v++GD i+iD+ + l+l+vse lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_954 464 IGAGLGESVGLITDGRFSGGTWGMVVGHVAPEAAAGGTIAFVHEGDSITIDARQLLLELNVSE 526 *************************************************************** PP TIGR00110 504 eelaerrakakkkearevkgaLakyaklvssadkGavld 542 ee+a+rra+++++ +r+++g+ ak+a +ssa+kGavld lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_954 527 EEIARRRAAWTAPAPRYTRGVQAKFAFNASSASKGAVLD 565 *************************************98 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03 # Mc/sec: 7.75 // [ok]
This GapMind analysis is from Apr 09 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