Align dihydroxy-acid dehydratase (EC 4.2.1.9) (characterized)
to candidate CA265_RS15795 CA265_RS15795 dihydroxy-acid dehydratase
Query= BRENDA::Q9LIR4 (608 letters) >FitnessBrowser__Pedo557:CA265_RS15795 Length = 560 Score = 672 bits (1734), Expect = 0.0 Identities = 335/559 (59%), Positives = 430/559 (76%), Gaps = 2/559 (0%) Query: 51 NKLNKYSSRITEPKSQGGSQAILHGVGLSDDDLLKPQIGISSVWYEGNTCNMHLLKLSEA 110 ++LNKYS T+ +Q +QA+L+G+GL+D D+ K Q+GI+S+ Y+GNTCNMHL L++ Sbjct: 2 SELNKYSKTFTQDPTQPAAQAMLYGIGLTDADMAKAQVGIASMGYDGNTCNMHLNDLAKD 61 Query: 111 VKEGVENAGMVGFRFNTIGVSDAISMGTRGMCFSLQSRDLIADSIETVMSAQWYDGNISI 170 VK+GV +VG FNTIGVSD +S GT GM +SL SRD+IADSIET+ Q+YDG ISI Sbjct: 62 VKKGVWKNDLVGLVFNTIGVSDGMSNGTDGMRYSLVSRDVIADSIETICGGQYYDGIISI 121 Query: 171 PGCDKNMPGTIMAMGRLNRPGIMVYGGTIKPGHFQDKTYDIVSAFQSYGEFVSGSISDEQ 230 PGCDKNMPG IMAM RL+RP IMVYGGTI PGH++ + +IVSAF++ G+ + G++S+E Sbjct: 122 PGCDKNMPGAIMAMARLDRPSIMVYGGTIAPGHYKGEELNIVSAFEALGQKICGNLSEED 181 Query: 231 RKTVLHHSCPGAGACGGMYTANTMASAIEAMGMSLPYSSSIPAEDPLKLDECRLAGKYLL 290 + ++ H+CPGAGACGGMYTANTMASAIEA+GMSLPYSSS PA K EC AGKY+ Sbjct: 182 YQGIIKHTCPGAGACGGMYTANTMASAIEALGMSLPYSSSNPAISEEKKQECLDAGKYIK 241 Query: 291 ELLKMDLKPRDIITPKSLRNAMVSVMALGGSTNAVLHLIAIARSVGLELTLDDFQKVSDA 350 LL+ D+KP DI+T K+ NA+ S++ LGGSTNAVLH IA+ +++G+E+T DDFQ++SD Sbjct: 242 ILLEKDIKPSDIMTRKAFENAIRSIIILGGSTNAVLHFIAMGKAIGIEITQDDFQRMSDV 301 Query: 351 VPFLADLKPSGKYVMEDIHKIGGTPAVLRYLLELGLMDGDCMTVTGQTLAQNLENVPSLT 410 P LAD KPSGKY+M+D+H+ GG PAVL+YLL GL+ GDC+TVTG+T+A+NL +V S+ Sbjct: 302 TPVLADFKPSGKYLMQDLHQYGGIPAVLKYLLNEGLLHGDCLTVTGKTVAENLADVKSIM 361 Query: 411 E-GQEIIRPLSNPIKETGHIQILRGDLAPDGSVAKITGKEGLYFSGPALVFEGEESMLAA 469 + Q+II+ LS PIK TGH+QIL G+LA GSVAKI+GKEG F GPA VF+GE ++A Sbjct: 362 DYDQKIIQKLSEPIKATGHLQILYGNLAEKGSVAKISGKEGEKFEGPARVFDGEHDLIAG 421 Query: 470 ISADPMSFKGTVVVIRGEGPKGGPGMPEMLTPTSAIMGAGLGKECALLTDGRFSGGSHGF 529 IS+ + G V+VI+ GP G PGMPEML PTSAI+GAGLGK AL+TDGRFSGG+HGF Sbjct: 422 ISSGRVQ-PGDVIVIKNSGPVGAPGMPEMLKPTSAIIGAGLGKSVALITDGRFSGGTHGF 480 Query: 530 VVGHICPEAQEGGPIGLIKNGDIITIDIGKKRIDTQVSPEEMNDRRKKWTAPAYKVNRGV 589 VVGHI PE+ +GG IGL+++ D I ID I+ QVS E + +RRK + PA KV +GV Sbjct: 481 VVGHITPESYKGGLIGLVEDEDRILIDAVNNIINLQVSDEVIAERRKNYVQPALKVTKGV 540 Query: 590 LYKYIKNVQSASDGCVTDE 608 LYKY K V A+ GCVTDE Sbjct: 541 LYKYAKTVSDAASGCVTDE 559 Lambda K H 0.316 0.135 0.397 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: 1113 Number of extensions: 48 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: 608 Length of database: 560 Length adjustment: 36 Effective length of query: 572 Effective length of database: 524 Effective search space: 299728 Effective search space used: 299728 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 CA265_RS15795 CA265_RS15795 (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.9851.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-217 709.8 9.5 1.3e-217 709.6 9.5 1.0 1 lcl|FitnessBrowser__Pedo557:CA265_RS15795 CA265_RS15795 dihydroxy-acid deh Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Pedo557:CA265_RS15795 CA265_RS15795 dihydroxy-acid dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 709.6 9.5 1.3e-217 1.3e-217 2 542 .. 20 558 .. 19 559 .. 0.99 Alignments for each domain: == domain 1 score: 709.6 bits; conditional E-value: 1.3e-217 TIGR00110 2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiam 69 a+a+l+ +Gl+d+d+ k ++++++ + + +++hl+dlak vk+++ ++ v fnti+vsDG++ lcl|FitnessBrowser__Pedo557:CA265_RS15795 20 AQAMLYGIGLTDADMAKAQVGIASMGYDGNTCNMHLNDLAKDVKKGVWKNDLVGLVFNTIGVSDGMSN 87 79****************************************************************** PP TIGR00110 70 gheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagkt 137 g++Gm+ysL+sr++iaDs+et++ ++ +D+++ i+ CDk++PG++ma++rl++P+i+v+GG++++g++ lcl|FitnessBrowser__Pedo557:CA265_RS15795 88 GTDGMRYSLVSRDVIADSIETICGGQYYDGIISIPGCDKNMPGAIMAMARLDRPSIMVYGGTIAPGHY 155 ******************************************************************** PP TIGR00110 138 klsekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstl 205 k +e++++v++fea+g+ g+lsee+ + i +++cP+ag+C+G++tan+ma++ ealG+slP+ss+ lcl|FitnessBrowser__Pedo557:CA265_RS15795 156 K-GEELNIVSAFEALGQKICGNLSEEDYQGIIKHTCPGAGACGGMYTANTMASAIEALGMSLPYSSSN 222 *.9***************************************************************** PP TIGR00110 206 latsaekkelakksgkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvkl 273 +a+s+ekk+ + +gk+i+ l++k+ikP+di+t++afenai +++lGGstn+vLh +a+ k +g+++ lcl|FitnessBrowser__Pedo557:CA265_RS15795 223 PAISEEKKQECLDAGKYIKILLEKDIKPSDIMTRKAFENAIRSIIILGGSTNAVLHFIAMGKAIGIEI 290 ******************************************************************** PP TIGR00110 274 slddfdrlsrkvPllaklkPsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvk 341 + ddf+r+s+ +P+la++kPsgk++++dlh+ GG++avlk+l +egllh d+ltvtGkt+ae+l++vk lcl|FitnessBrowser__Pedo557:CA265_RS15795 291 TQDDFQRMSDVTPVLADFKPSGKYLMQDLHQYGGIPAVLKYLLNEGLLHGDCLTVTGKTVAENLADVK 358 ******************************************************************99 PP TIGR00110 342 vlr.vdqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailg 408 +++ dq++i++l++p+k++g+l++L+Gnlae+G+v+ki+g+e kfeGpa+vf+ e++ +++i + lcl|FitnessBrowser__Pedo557:CA265_RS15795 359 SIMdYDQKIIQKLSEPIKATGHLQILYGNLAEKGSVAKISGKEG--EKFEGPARVFDGEHDLIAGISS 424 87325666***********************************9..9********************* PP TIGR00110 409 gkvkeGdvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaeg 476 g+v+ Gdv+vi+ GP G+PGm+emL+Ptsa++g+GLgk+vaLitDGrfsGgt+G+++Gh++Pe+++g lcl|FitnessBrowser__Pedo557:CA265_RS15795 425 GRVQPGDVIVIKNSGPVGAPGMPEMLKPTSAIIGAGLGKSVALITDGRFSGGTHGFVVGHITPESYKG 492 ******************************************************************** PP TIGR00110 477 GaialvedGDkikiDienrkldlevseeelaerrakakkkearevkgaLakyaklvssadkGavld 542 G i+lved D+i iD+ n+ ++l+vs+e +aerr++ +++ + +kg+L kyak vs a +G+v+d lcl|FitnessBrowser__Pedo557:CA265_RS15795 493 GLIGLVEDEDRILIDAVNNIINLQVSDEVIAERRKNYVQPALKVTKGVLYKYAKTVSDAASGCVTD 558 ****************************************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (543 nodes) Target sequences: 1 (560 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 11.34 // [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