Align Dihydroxy-acid dehydratase, mitochondrial; DAD; EC 4.2.1.9 (characterized)
to candidate WP_014148274.1 MEALZ_RS08790 dihydroxy-acid dehydratase
Query= SwissProt::P39522 (585 letters) >NCBI__GCF_000968535.2:WP_014148274.1 Length = 565 Score = 616 bits (1589), Expect = 0.0 Identities = 303/564 (53%), Positives = 406/564 (71%), Gaps = 8/564 (1%) Query: 21 KKLNKYSYIITEPKGQGASQAMLYATGFKKEDFKKPQVGVGSCWWSGNPCNMHLLDLNNR 80 K ++S + + + S+AML+A GFK EDFKKPQ+GV S W PCNMH+ L + Sbjct: 7 KSARRFSSQVVDGMERAPSRAMLHAVGFKNEDFKKPQIGVASTWSMVTPCNMHINRLADD 66 Query: 81 CSQSIEKAGLKAMQFNTIGVSDGISMGTKGMRYSLQSREIIADSFETIMMAQHYDANIAI 140 ++ ++K+G KA+ FNTI +SDGISMGT+GM+YSL SRE+IADS ET++ Q +D +AI Sbjct: 67 AARGVDKSGGKAVIFNTITISDGISMGTEGMKYSLVSREVIADSIETVVGCQGFDGVVAI 126 Query: 141 PSCDKNMPGVMMAMGRHNRPSIMVYGGTILPGHPTCGSSKISKNIDIVSAFQSYGEYISK 200 CDKNMPG M+A+ R NRP+I VYGGTILPG C K +D+VS F++ G + Sbjct: 127 GGCDKNMPGCMIALSRLNRPAIFVYGGTILPG---CHKDK---KLDVVSVFEAVGARANN 180 Query: 201 QFTEEEREDVVEHACPGPGSCGGMYTANTMASAAEVLGLTIPNSSSFPAVSKEKLAECDN 260 + +EE + A PG GSCGGMYTANTMASA E LG+++PNSS+ AVS++K +C+ Sbjct: 181 KIDDEELAQIEAKAIPGAGSCGGMYTANTMASAIEALGMSLPNSSAQAAVSEDKRLDCER 240 Query: 261 IGEYIKKTMELGILPRDILTKEAFENAITYVVATGGSTNAVLHLVAVAHSAGVKLSPDDF 320 G + + + I PRDI+TKEAFENAIT V+A GGSTN+VLHL+A+A++ GV ++ DDF Sbjct: 241 AGAAVLELLAKDIKPRDIMTKEAFENAITIVIALGGSTNSVLHLIAMANATGVDVTLDDF 300 Query: 321 QRISDTTPLIGDFKPSGKYVMADLINVGGTQSVIKYLYENNMLHGNTMTVTGDTLAERAK 380 RI P++ D KPSGKY MA+LI +GG Q ++K L + +LHG+ +TVTG TLAE Sbjct: 301 TRIGKNVPMLADLKPSGKYQMAELIEIGGIQPLMKALLDRGLLHGDCLTVTGKTLAENLA 360 Query: 381 KAPSLPEGQEIIKPLSHPIKANGHLQILYGSLAPGGAVGKITGKEGTYFKGRARVFEEEG 440 PEGQ++I +PIK + HL +LYG+LAP GAV KITGKEG F G+A+VF+ E Sbjct: 361 DVQPYPEGQDMIHSFDNPIKKDSHLVVLYGNLAPEGAVAKITGKEGLLFTGKAKVFDAEE 420 Query: 441 AFIEALERGEIKKGEKTVVVIRYEGPRGAPGMPEMLKPSSALMGYGLGKDVALLTDGRFS 500 ++++ G+I KG+ V+VIRYEGP+G PGM EML P+SA+MG GLGKDVAL+TDGRFS Sbjct: 421 QALQSILNGDIVKGD--VIVIRYEGPKGGPGMREMLSPTSAVMGKGLGKDVALITDGRFS 478 Query: 501 GGSHGFLIGHIVPEAAEGGPIGLVRDGDEIIIDADNNKIDLLVSDKEMAQRKQSWVAPPP 560 GG+HGF++GHI PEA GGP+ +V+DGD I IDA+NN++ L +++ EM +R + W P P Sbjct: 479 GGTHGFVVGHITPEAFTGGPLAIVQDGDSITIDAENNELTLHINEHEMNRRMEKWQQPAP 538 Query: 561 RYTRGTLSKYAKLVSNASNGCVLD 584 +YTRG L+K+AKL S+AS G V D Sbjct: 539 KYTRGVLAKFAKLTSSASKGAVTD 562 Lambda K H 0.315 0.134 0.390 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: 982 Number of extensions: 44 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: 585 Length of database: 565 Length adjustment: 36 Effective length of query: 549 Effective length of database: 529 Effective search space: 290421 Effective search space used: 290421 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_014148274.1 MEALZ_RS08790 (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.2471.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.8e-238 777.8 8.5 3.2e-238 777.6 8.5 1.0 1 lcl|NCBI__GCF_000968535.2:WP_014148274.1 MEALZ_RS08790 dihydroxy-acid deh Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000968535.2:WP_014148274.1 MEALZ_RS08790 dihydroxy-acid dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 777.6 8.5 3.2e-238 3.2e-238 1 542 [. 24 562 .. 24 563 .. 1.00 Alignments for each domain: == domain 1 score: 777.6 bits; conditional E-value: 3.2e-238 TIGR00110 1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiam 69 ++ra+l+a+G+k+ed++kP+i+v+++++ ++P+++h++ la+ ++++++++Gg+a+ fnti++sDGi+m lcl|NCBI__GCF_000968535.2:WP_014148274.1 24 PSRAMLHAVGFKNEDFKKPQIGVASTWSMVTPCNMHINRLADDAARGVDKSGGKAVIFNTITISDGISM 92 589****************************************************************** PP TIGR00110 70 gheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktk 138 g+eGmkysL+sre+iaDs+etvv + +D++v+i+ CDk++PG ++a rln+Pai+v+GG++ +g k lcl|NCBI__GCF_000968535.2:WP_014148274.1 93 GTEGMKYSLVSREVIADSIETVVGCQGFDGVVAIGGCDKNMPGCMIALSRLNRPAIFVYGGTILPGCHK 161 *******************************************************************99 PP TIGR00110 139 lsekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstlla 207 +k+d+v+vfeavg+ a++k+++eel +ie a P+agsC+G++tan+ma++ ealG+slP+ss+ +a lcl|NCBI__GCF_000968535.2:WP_014148274.1 162 -DKKLDVVSVFEAVGARANNKIDDEELAQIEAKAIPGAGSCGGMYTANTMASAIEALGMSLPNSSAQAA 229 .8******************************************************************* PP TIGR00110 208 tsaekkelakksgkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklsld 276 +s++k+ ++++g+ + el+ k+ikPrdi+tkeafenait+++alGGstn+vLhl+a+a+ gv+++ld lcl|NCBI__GCF_000968535.2:WP_014148274.1 230 VSEDKRLDCERAGAAVLELLAKDIKPRDIMTKEAFENAITIVIALGGSTNSVLHLIAMANATGVDVTLD 298 ********************************************************************* PP TIGR00110 277 dfdrlsrkvPllaklkPsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlrv 345 df r+ ++vP+la+lkPsgk+ +++l + GG++ ++k l +gllh d+ltvtGktlae+l++v+ ++ lcl|NCBI__GCF_000968535.2:WP_014148274.1 299 DFTRIGKNVPMLADLKPSGKYQMAELIEIGGIQPLMKALLDRGLLHGDCLTVTGKTLAENLADVQPYPE 367 ********************************************************************* PP TIGR00110 346 dqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeG 414 +qd+i+s dnp+kk+++l vL+Gnla+eGav+ki+g+e l f+G+akvf+ ee+al++il+g++ +G lcl|NCBI__GCF_000968535.2:WP_014148274.1 368 GQDMIHSFDNPIKKDSHLVVLYGNLAPEGAVAKITGKEG--LLFTGKAKVFDAEEQALQSILNGDIVKG 434 ***************************************..99************************** PP TIGR00110 415 dvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialve 483 dv+viryeGPkGgPGmremL Ptsa++g GLgk+vaLitDGrfsGgt+G+++Gh++Pea +gG++a+v+ lcl|NCBI__GCF_000968535.2:WP_014148274.1 435 DVIVIRYEGPKGGPGMREMLSPTSAVMGKGLGKDVALITDGRFSGGTHGFVVGHITPEAFTGGPLAIVQ 503 ********************************************************************* PP TIGR00110 484 dGDkikiDienrkldlevseeelaerrakakkkearevkgaLakyaklvssadkGavld 542 dGD i+iD+en++l l+++e+e+++r +k++++ +++++g+Lak+akl ssa+kGav+d lcl|NCBI__GCF_000968535.2:WP_014148274.1 504 DGDSITIDAENNELTLHINEHEMNRRMEKWQQPAPKYTRGVLAKFAKLTSSASKGAVTD 562 *********************************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (543 nodes) Target sequences: 1 (565 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: 13.23 // [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