Align Dihydroxy-acid dehydratase, mitochondrial; DAD; EC 4.2.1.9 (characterized)
to candidate WP_019865909.1 METMI_RS0108790 dihydroxy-acid dehydratase
Query= SwissProt::P39522 (585 letters) >NCBI__GCF_000384075.1:WP_019865909.1 Length = 563 Score = 594 bits (1532), Expect = e-174 Identities = 296/564 (52%), Positives = 397/564 (70%), Gaps = 8/564 (1%) Query: 21 KKLNKYSYIITEPKGQGASQAMLYATGFKKEDFKKPQVGVGSCWWSGNPCNMHLLDLNNR 80 K +S + + + S+AML+A GF EDF KPQ+G+ S W PCNMH+ L + Sbjct: 7 KTTRTFSSQVVDGMERAPSRAMLHAVGFSNEDFLKPQIGIASTWSMVTPCNMHINKLADD 66 Query: 81 CSQSIEKAGLKAMQFNTIGVSDGISMGTKGMRYSLQSREIIADSFETIMMAQHYDANIAI 140 + + +A KA+ FNTI +SDGISMGT+GM+YSL SRE+IADS ET++ Q +D +AI Sbjct: 67 AANGVNQANGKAVIFNTITISDGISMGTEGMKYSLVSREVIADSIETVVGCQGFDGVVAI 126 Query: 141 PSCDKNMPGVMMAMGRHNRPSIMVYGGTILPGHPTCGSSKISKNIDIVSAFQSYGEYISK 200 CDKNMPG M+A+ R +RP+I VYGGTILPG C K +D+VS F++ G + Sbjct: 127 GGCDKNMPGCMIAISRLDRPAIFVYGGTILPG---CHKDK---KLDVVSVFEAVGARANN 180 Query: 201 QFTEEEREDVVEHACPGPGSCGGMYTANTMASAAEVLGLTIPNSSSFPAVSKEKLAECDN 260 + + E ++ A PG GSCGGMYTANTMASA E LG+++PNSS+ AVS +K +C+ Sbjct: 181 KIDDAELAEIEAKAIPGAGSCGGMYTANTMASAIEALGMSLPNSSAQAAVSNDKRLDCER 240 Query: 261 IGEYIKKTMELGILPRDILTKEAFENAITYVVATGGSTNAVLHLVAVAHSAGVKLSPDDF 320 G + +E I P DI+TKEAFENAIT +A GGSTNAVLH++A+A++A V +S DDF Sbjct: 241 AGAAVMNLIEKNIKPSDIMTKEAFENAITVAIALGGSTNAVLHILAMANAAKVDISLDDF 300 Query: 321 QRISDTTPLIGDFKPSGKYVMADLINVGGTQSVIKYLYENNMLHGNTMTVTGDTLAERAK 380 RI P++ D KPSG+Y MA+L+ +GG Q ++K L + +LHG+ +TVTG TLAE Sbjct: 301 TRIGKRVPMLADLKPSGRYSMAELVEIGGIQPLMKVLLDAGLLHGDCLTVTGLTLAENLA 360 Query: 381 KAPSLPEGQEIIKPLSHPIKANGHLQILYGSLAPGGAVGKITGKEGTYFKGRARVFEEEG 440 + P+GQ++I L+HPIK + HL +LYG+LAP GAV KITGKEG F G A+VF+ E Sbjct: 361 EVAPYPDGQDMIHDLAHPIKKDSHLVVLYGNLAPEGAVAKITGKEGLRFIGTAKVFDAEE 420 Query: 441 AFIEALERGEIKKGEKTVVVIRYEGPRGAPGMPEMLKPSSALMGYGLGKDVALLTDGRFS 500 + ++ G+I KG+ V+VIRYEGP+G PGM EML P+SA+MG GLGK+VAL+TDGRFS Sbjct: 421 QALHSILHGDIVKGD--VIVIRYEGPKGGPGMREMLSPTSAIMGKGLGKEVALITDGRFS 478 Query: 501 GGSHGFLIGHIVPEAAEGGPIGLVRDGDEIIIDADNNKIDLLVSDKEMAQRKQSWVAPPP 560 GG+HGF++GHI PEA GGP+ LV +GD I IDA+NN + L +++ EMA+R + W P P Sbjct: 479 GGTHGFVVGHITPEAYVGGPLALVENGDTIAIDAENNALTLHINEHEMARRMEKWQQPAP 538 Query: 561 RYTRGTLSKYAKLVSNASNGCVLD 584 +Y RG L+KYAKLV++AS G V D Sbjct: 539 KYIRGVLAKYAKLVNSASLGAVTD 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: 951 Number of extensions: 43 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: 563 Length adjustment: 36 Effective length of query: 549 Effective length of database: 527 Effective search space: 289323 Effective search space used: 289323 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_019865909.1 METMI_RS0108790 (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.19843.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.9e-235 767.1 11.1 5.5e-235 766.9 11.1 1.0 1 lcl|NCBI__GCF_000384075.1:WP_019865909.1 METMI_RS0108790 dihydroxy-acid d Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000384075.1:WP_019865909.1 METMI_RS0108790 dihydroxy-acid dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 766.9 11.1 5.5e-235 5.5e-235 1 542 [. 24 562 .. 24 563 .] 1.00 Alignments for each domain: == domain 1 score: 766.9 bits; conditional E-value: 5.5e-235 TIGR00110 1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiam 69 ++ra+l+a+G+++ed+ kP+i+++++++ ++P+++h+++la+ +++++++a g+a+ fnti++sDGi+m lcl|NCBI__GCF_000384075.1:WP_019865909.1 24 PSRAMLHAVGFSNEDFLKPQIGIASTWSMVTPCNMHINKLADDAANGVNQANGKAVIFNTITISDGISM 92 589****************************************************************** PP TIGR00110 70 gheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktk 138 g+eGmkysL+sre+iaDs+etvv + +D++v+i+ CDk++PG ++a rl++Pai+v+GG++ +g k lcl|NCBI__GCF_000384075.1:WP_019865909.1 93 GTEGMKYSLVSREVIADSIETVVGCQGFDGVVAIGGCDKNMPGCMIAISRLDRPAIFVYGGTILPGCHK 161 *******************************************************************99 PP TIGR00110 139 lsekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstlla 207 +k+d+v+vfeavg+ a++k++++el eie a P+agsC+G++tan+ma++ ealG+slP+ss+ +a lcl|NCBI__GCF_000384075.1:WP_019865909.1 162 -DKKLDVVSVFEAVGARANNKIDDAELAEIEAKAIPGAGSCGGMYTANTMASAIEALGMSLPNSSAQAA 229 .8******************************************************************* PP TIGR00110 208 tsaekkelakksgkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklsld 276 +s++k+ ++++g+ +++l++knikP+di+tkeafenait+ +alGGstn+vLh+la+a+ a+v++sld lcl|NCBI__GCF_000384075.1:WP_019865909.1 230 VSNDKRLDCERAGAAVMNLIEKNIKPSDIMTKEAFENAITVAIALGGSTNAVLHILAMANAAKVDISLD 298 ********************************************************************* PP TIGR00110 277 dfdrlsrkvPllaklkPsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlrv 345 df r+ ++vP+la+lkPsg++ +++l + GG++ ++k+l +gllh d+ltvtG tlae+l++v + lcl|NCBI__GCF_000384075.1:WP_019865909.1 299 DFTRIGKRVPMLADLKPSGRYSMAELVEIGGIQPLMKVLLDAGLLHGDCLTVTGLTLAENLAEVAPYPD 367 ********************************************************************* PP TIGR00110 346 dqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeG 414 +qd+i+ l +p+kk+++l vL+Gnla+eGav+ki+g+e l+f G+akvf+ ee+al++il+g++ +G lcl|NCBI__GCF_000384075.1:WP_019865909.1 368 GQDMIHDLAHPIKKDSHLVVLYGNLAPEGAVAKITGKEG--LRFIGTAKVFDAEEQALHSILHGDIVKG 434 ***************************************..**************************** PP TIGR00110 415 dvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialve 483 dv+viryeGPkGgPGmremL Ptsa++g GLgk+vaLitDGrfsGgt+G+++Gh++Pea++gG++alve lcl|NCBI__GCF_000384075.1:WP_019865909.1 435 DVIVIRYEGPKGGPGMREMLSPTSAIMGKGLGKEVALITDGRFSGGTHGFVVGHITPEAYVGGPLALVE 503 ********************************************************************* PP TIGR00110 484 dGDkikiDienrkldlevseeelaerrakakkkearevkgaLakyaklvssadkGavld 542 +GD+i+iD+en++l l+++e+e+a+r +k++++ +++++g+Lakyaklv+sa+ Gav+d lcl|NCBI__GCF_000384075.1:WP_019865909.1 504 NGDTIAIDAENNALTLHINEHEMARRMEKWQQPAPKYIRGVLAKYAKLVNSASLGAVTD 562 *********************************************************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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03 # Mc/sec: 7.94 // [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