Align Ketol-acid reductoisomerase (NADP(+)); KARI; Acetohydroxy-acid isomeroreductase; AHIR; Alpha-keto-beta-hydroxylacyl reductoisomerase; Ketol-acid reductoisomerase type 1; Ketol-acid reductoisomerase type I; EC 1.1.1.86 (characterized)
to candidate WP_027459067.1 K420_RS0116795 ketol-acid reductoisomerase
Query= SwissProt::Q9HVA2 (338 letters) >NCBI__GCF_000519045.1:WP_027459067.1 Length = 338 Score = 541 bits (1394), Expect = e-159 Identities = 265/338 (78%), Positives = 295/338 (87%) Query: 1 MRVFYDKDCDLSIIQGKKVAIIGYGSQGHAHACNLKDSGVDVTVGLRSGSATVAKAEAHG 60 M+V+YDKD DLS+I+GKKV I+GYGSQGHAHA NLKDSGV VTVGLR G A+ AKAEA G Sbjct: 1 MKVYYDKDADLSLIKGKKVTIVGYGSQGHAHAQNLKDSGVKVTVGLRKGGASWAKAEAAG 60 Query: 61 LKVADVKTAVAAADVVMILTPDEFQGRLYKEEIEPNLKKGATLAFAHGFSIHYNQVVPRA 120 LKV ++ AV ADVVMIL PDE ++Y EE+ PNLKKGA LAFAHGF++HYNQVVPRA Sbjct: 61 LKVEEIAKAVKGADVVMILLPDENIPQVYNEEVAPNLKKGAALAFAHGFNVHYNQVVPRA 120 Query: 121 DLDVIMIAPKAPGHTVRSEFVKGGGIPDLIAIYQDASGNAKNVALSYACGVGGGRTGIIE 180 D+DVIM+APK PGHTVRSE++KGGG+P LIA+YQD SG AK++ALSYA GG + G+IE Sbjct: 121 DVDVIMVAPKGPGHTVRSEYLKGGGVPSLIAVYQDKSGKAKDIALSYAAANGGTKGGVIE 180 Query: 181 TTFKDETETDLFGEQAVLCGGCVELVKAGFETLVEAGYAPEMAYFECLHELKLIVDLMYE 240 T F++ETETDLFGEQAVLCGG VELVK GFETLVEAGYAPEMAYFECLHELKLIVDLMYE Sbjct: 181 TNFREETETDLFGEQAVLCGGAVELVKMGFETLVEAGYAPEMAYFECLHELKLIVDLMYE 240 Query: 241 GGIANMNYSISNNAEYGEYVTGPEVINAESRAAMRNALKRIQDGEYAKMFITEGAANYPS 300 GGIANMNYSISNNAEYGEYVTGPEVINA+SR AMRNALKRIQ GEYAKMFI EG NYPS Sbjct: 241 GGIANMNYSISNNAEYGEYVTGPEVINAQSREAMRNALKRIQTGEYAKMFILEGRTNYPS 300 Query: 301 MTAYRRNNAAHPIEQIGEKLRAMMPWIAANKIVDKSKN 338 MTA RR AAHPIEQ+GEKLR MMPWI NK+VD++KN Sbjct: 301 MTARRRLTAAHPIEQVGEKLRDMMPWIKKNKLVDQTKN 338 Lambda K H 0.317 0.134 0.389 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: 469 Number of extensions: 11 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 (21.7 bits) S2: 49 (23.5 bits)
Align candidate WP_027459067.1 K420_RS0116795 (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.837.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-136 440.7 2.4 1.4e-136 440.5 2.4 1.0 1 lcl|NCBI__GCF_000519045.1:WP_027459067.1 K420_RS0116795 ketol-acid reduct Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000519045.1:WP_027459067.1 K420_RS0116795 ketol-acid reductoisomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 440.5 2.4 1.4e-136 1.4e-136 1 313 [. 14 327 .. 14 328 .. 0.99 Alignments for each domain: == domain 1 score: 440.5 bits; conditional E-value: 1.4e-136 TIGR00465 1 lkgkkvaiiGyGsqGeaqalnlrdsglnvivglrkeaaswkkAeedGfkvltveeaikkadlimiLlpD 69 +kgkkv+i+GyGsqG+a+a nl+dsg++v+vglrk++asw+kAe G+kv +++ a+k ad++miLlpD lcl|NCBI__GCF_000519045.1:WP_027459067.1 14 IKGKKVTIVGYGSQGHAHAQNLKDSGVKVTVGLRKGGASWAKAEAAGLKVEEIAKAVKGADVVMILLPD 82 689****************************************************************** PP TIGR00465 70 evqkevyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliA 138 e ++vy++e++p+lk+g+al f+HGfn++++q+v+++dvdv++vAPKgpG++vR+ey +g GvpsliA lcl|NCBI__GCF_000519045.1:WP_027459067.1 83 ENIPQVYNEEVAPNLKKGAALAFAHGFNVHYNQVVPRADVDVIMVAPKGPGHTVRSEYLKGGGVPSLIA 151 ********************************************************************* PP TIGR00465 139 veqdvtgeakeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqp 207 v+qd +g+ak+iAl+yA+a Gg++ gv+et F+eE+e+DLfGEqavLcGg +l+k++f+tLveaGy+p lcl|NCBI__GCF_000519045.1:WP_027459067.1 152 VYQDKSGKAKDIALSYAAANGGTKGGVIETNFREETETDLFGEQAVLCGGAVELVKMGFETLVEAGYAP 220 ********************************************************************* PP TIGR00465 208 elAyfeivhelklivdllkekGlelmrdavsntAklgalelr.eilkeelkkemqkilkeiqnGefake 275 e+Ayfe++helklivdl++e+G+++m ++sn A++g++ ++ e+++++ +++m++ lk iq+Ge+ak lcl|NCBI__GCF_000519045.1:WP_027459067.1 221 EMAYFECLHELKLIVDLMYEGGIANMNYSISNNAEYGEYVTGpEVINAQSREAMRNALKRIQTGEYAKM 289 ******************************************9************************** PP TIGR00465 276 walekeagkpafeearkkekeqeiekvGkelralvkae 313 ++le ++++p++++ r+ + ie+vG++lr+++++ lcl|NCBI__GCF_000519045.1:WP_027459067.1 290 FILEGRTNYPSMTARRRLTAAHPIEQVGEKLRDMMPWI 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: 9.07 // [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