Align acetohydroxyacid isomeroreductase (EC 1.1.1.86) (characterized)
to candidate Dsui_3527 Dsui_3527 ketol-acid reductoisomerase
Query= metacyc::MONOMER-18814 (338 letters) >FitnessBrowser__PS:Dsui_3527 Length = 338 Score = 536 bits (1381), Expect = e-157 Identities = 261/338 (77%), Positives = 295/338 (87%) Query: 1 MKVFYDKDADLSLIKGKNVTIIGYGSQGHAHALNLKDSGVNVTVGLRKSGASWNKAANAG 60 MKV+YDKDADLSLIKGK VTI+GYGSQGHAHA NLKDSG VTVGLRK GASW KA AG Sbjct: 1 MKVYYDKDADLSLIKGKKVTIVGYGSQGHAHAQNLKDSGCKVTVGLRKGGASWAKAEKAG 60 Query: 61 LQVKEVAEAVKGADVVMILLPDEQIADVYKNEVHDNIKEGAALAFAHGFNVHYGAVIPRA 120 L+V+E+A+AVKGADVVMILLPDE I VY +V N+K+GAALAFAHGFNVHY V+PR Sbjct: 61 LKVEEIAKAVKGADVVMILLPDENIPAVYYADVEPNLKKGAALAFAHGFNVHYNQVVPRE 120 Query: 121 DLDVIMIAPKAPGHTVRATYTQGGGVPHLIAVHQNKSGAARDIALSYATANGGGRAGIIE 180 D+DVIM+APK PGHTVR+ Y +GGGVP LIAV+Q+K+G A+DIALSYA ANGG + G+IE Sbjct: 121 DVDVIMVAPKGPGHTVRSEYLKGGGVPSLIAVYQDKTGKAKDIALSYAAANGGTKGGVIE 180 Query: 181 TNFREETETDLFGEQAVLCGGTVELIKAGFETLVEAGYAPEMAYFECLHELKLIVDLIYE 240 TNFREETETDLFGEQAVLCGG VEL+K GFETLVEAGYAPEMAYFECLHELKLIVDL+YE Sbjct: 181 TNFREETETDLFGEQAVLCGGAVELVKMGFETLVEAGYAPEMAYFECLHELKLIVDLMYE 240 Query: 241 GGIANMNYSISNNAEYGEYVTGPRVVTEETKKAMKQCLTDIQTGEYAKSFLLENKAGAPT 300 GGIANMNYSISNNAEYGEYVTGP V+ EE++ AM+ L IQTGEYAK F+LE K G P+ Sbjct: 241 GGIANMNYSISNNAEYGEYVTGPEVINEESRYAMRNALKRIQTGEYAKMFILEGKTGYPS 300 Query: 301 LISRRRLTAEHQIEEVGAKLRAMMPWIAKNKMVDQSKN 338 + +RRRLTA+H IE+VG+KLR MMPWI KNK+VDQSKN Sbjct: 301 MTARRRLTADHPIEQVGSKLRDMMPWIKKNKLVDQSKN 338 Lambda K H 0.316 0.133 0.379 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: 508 Number of extensions: 17 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: 338 Length of database: 338 Length adjustment: 28 Effective length of query: 310 Effective length of database: 310 Effective search space: 96100 Effective search space used: 96100 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: 49 (23.5 bits)
Align candidate Dsui_3527 Dsui_3527 (ketol-acid reductoisomerase)
to HMM TIGR00465 (ilvC: ketol-acid reductoisomerase (EC 1.1.1.86))
# 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/TIGR00465.hmm # target sequence database: /tmp/gapView.562.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00465 [M=314] Accession: TIGR00465 Description: ilvC: ketol-acid reductoisomerase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-137 443.6 1.5 1.9e-137 443.4 1.5 1.0 1 lcl|FitnessBrowser__PS:Dsui_3527 Dsui_3527 ketol-acid reductoisom Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__PS:Dsui_3527 Dsui_3527 ketol-acid reductoisomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 443.4 1.5 1.9e-137 1.9e-137 1 313 [. 14 327 .. 14 328 .. 0.99 Alignments for each domain: == domain 1 score: 443.4 bits; conditional E-value: 1.9e-137 TIGR00465 1 lkgkkvaiiGyGsqGeaqalnlrdsglnvivglrkeaaswkkAeedGfkvltveeaikkadlimiLlpDevqkevye 77 +kgkkv+i+GyGsqG+a+a nl+dsg +v+vglrk++asw+kAe+ G+kv +++ a+k ad++miLlpDe ++vy lcl|FitnessBrowser__PS:Dsui_3527 14 IKGKKVTIVGYGSQGHAHAQNLKDSGCKVTVGLRKGGASWAKAEKAGLKVEEIAKAVKGADVVMILLPDENIPAVYY 90 689************************************************************************** PP TIGR00465 78 aeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliAveqdvtgeakeiAlay 154 a+++p+lk+g+al f+HGfn++++q+v+++dvdv++vAPKgpG++vR+ey +g GvpsliAv+qd tg+ak+iAl+y lcl|FitnessBrowser__PS:Dsui_3527 91 ADVEPNLKKGAALAFAHGFNVHYNQVVPREDVDVIMVAPKGPGHTVRSEYLKGGGVPSLIAVYQDKTGKAKDIALSY 167 ***************************************************************************** PP TIGR00465 155 AkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqpelAyfeivhelklivdllkekGle 231 A+a Gg++ gv+et F+eE+e+DLfGEqavLcGg +l+k++f+tLveaGy+pe+Ayfe++helklivdl++e+G++ lcl|FitnessBrowser__PS:Dsui_3527 168 AAANGGTKGGVIETNFREETETDLFGEQAVLCGGAVELVKMGFETLVEAGYAPEMAYFECLHELKLIVDLMYEGGIA 244 ***************************************************************************** PP TIGR00465 232 lmrdavsntAklgalelr.eilkeelkkemqkilkeiqnGefakewalekeagkpafeearkkekeqeiekvGkelr 307 +m ++sn A++g++ ++ e+++ee + +m++ lk iq+Ge+ak ++le ++g+p++++ r+ ++ ie+vG++lr lcl|FitnessBrowser__PS:Dsui_3527 245 NMNYSISNNAEYGEYVTGpEVINEESRYAMRNALKRIQTGEYAKMFILEGKTGYPSMTARRRLTADHPIEQVGSKLR 321 ******************9********************************************************** PP TIGR00465 308 alvkae 313 +++++ lcl|FitnessBrowser__PS:Dsui_3527 322 DMMPWI 327 ***986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (314 nodes) Target sequences: 1 (338 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: 00:00:00.01 # Mc/sec: 8.29 // [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