Align Ketol-acid reductoisomerase (NAD(+)); KARI; Acetohydroxy-acid isomeroreductase; AHIR; Alpha-keto-beta-hydroxylacyl reductoisomerase; Ketol-acid reductoisomerase type 1; Ketol-acid reductoisomerase type I; EC 1.1.1.382 (characterized)
to candidate WP_027178077.1 G496_RS0103610 ketol-acid reductoisomerase
Query= SwissProt::K4LVZ1 (332 letters) >NCBI__GCF_000429985.1:WP_027178077.1 Length = 329 Score = 468 bits (1205), Expect = e-137 Identities = 229/329 (69%), Positives = 274/329 (83%) Query: 1 MKIYYDQDADLQYLDGKTVAVIGYGSQGHAQSQNLRDSGVKVVVADIPSSENWKKAEEAQ 60 MK+YY+QDADL L KTVA+IGYGSQGHA +QNLRDSGVKV+V P N+ A+E Sbjct: 1 MKVYYEQDADLGLLKDKTVAIIGYGSQGHAHAQNLRDSGVKVIVGQRPGGPNYDLAKEHG 60 Query: 61 FQPLTADEAAREADIIQILVPDEKQAALYRESIAPNLRPGKALVFSHGFNIHFKQIVPPP 120 F+P++A EAA ADII IL+PD+ QAA+Y+ I PNL+PG L F+HGF IHF+QI+P Sbjct: 61 FEPVSAAEAAAAADIIMILLPDQVQAAVYKNDILPNLKPGNVLAFAHGFCIHFEQIIPKE 120 Query: 121 DVDVFMVAPKGPGHLVRRMYEEGAGVPSLVAVEQDYSGQALNLALAYAKGIGATRAGVIQ 180 DVDV M+APKGPGHLVRR Y EG VPSLVAV Q+ SG+A +LA+AYAKGIGATR+GVI+ Sbjct: 121 DVDVIMIAPKGPGHLVRRTYTEGGAVPSLVAVYQNASGKAFDLAMAYAKGIGATRSGVIE 180 Query: 181 TTFKEETETDLFGEQAVLCGGITELIRAGFDTLVDAGYQPEIAYFECLHEMKLIVDLIYE 240 T+F+EETETDLFGEQAVLCGG++ELI+AGF+TLV+AGYQPE+AYFECLHEMKLIVDLIYE Sbjct: 181 TSFREETETDLFGEQAVLCGGLSELIKAGFETLVEAGYQPEMAYFECLHEMKLIVDLIYE 240 Query: 241 GGISTMRYSISDTAEYGDLTRGKRIITEATREEMKKILKEIQDGVFAREWLLENQVGRPV 300 GGIS MRYSISDTAEYGDLTRG R+I E +R+EMK+ILKEIQ G FA+E+++EN G+ Sbjct: 241 GGISNMRYSISDTAEYGDLTRGPRVINEESRKEMKEILKEIQQGDFAKEFIVENMSGKAH 300 Query: 301 YNALRRKEQNHLIETVGARLRGMMPWLKK 329 ++ALRR + H IE VGA LR MM WLKK Sbjct: 301 FSALRRINREHKIEEVGANLRNMMSWLKK 329 Lambda K H 0.318 0.136 0.393 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: 377 Number of extensions: 8 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: 332 Length of database: 329 Length adjustment: 28 Effective length of query: 304 Effective length of database: 301 Effective search space: 91504 Effective search space used: 91504 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_027178077.1 G496_RS0103610 (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.10495.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-141 457.4 0.2 1.2e-141 457.2 0.2 1.0 1 lcl|NCBI__GCF_000429985.1:WP_027178077.1 G496_RS0103610 ketol-acid reduct Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000429985.1:WP_027178077.1 G496_RS0103610 ketol-acid reductoisomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 457.2 0.2 1.2e-141 1.2e-141 1 314 [] 14 328 .. 14 328 .. 0.99 Alignments for each domain: == domain 1 score: 457.2 bits; conditional E-value: 1.2e-141 TIGR00465 1 lkgkkvaiiGyGsqGeaqalnlrdsglnvivglrkeaaswkkAeedGfkvltveeaikkadlimiLlpD 69 lk+k+vaiiGyGsqG+a+a nlrdsg++vivg r+++ ++ A+e Gf+ ++ +ea+++ad+imiLlpD lcl|NCBI__GCF_000429985.1:WP_027178077.1 14 LKDKTVAIIGYGSQGHAHAQNLRDSGVKVIVGQRPGGPNYDLAKEHGFEPVSAAEAAAAADIIMILLPD 82 79******************************************************************* PP TIGR00465 70 evqkevyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliA 138 +vq +vy+++i p+lk g++l f+HGf i+f+qi +++dvdv+++APKgpG+lvR++y eg vpsl+A lcl|NCBI__GCF_000429985.1:WP_027178077.1 83 QVQAAVYKNDILPNLKPGNVLAFAHGFCIHFEQIIPKEDVDVIMIAPKGPGHLVRRTYTEGGAVPSLVA 151 ********************************************************************* PP TIGR00465 139 veqdvtgeakeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqp 207 v+q+++g+a + A+ayAk+iG++r gv+et+F+eE+e+DLfGEqavLcGgl++lika+f+tLveaGyqp lcl|NCBI__GCF_000429985.1:WP_027178077.1 152 VYQNASGKAFDLAMAYAKGIGATRSGVIETSFREETETDLFGEQAVLCGGLSELIKAGFETLVEAGYQP 220 ********************************************************************* PP TIGR00465 208 elAyfeivhelklivdllkekGlelmrdavsntAklgalelr.eilkeelkkemqkilkeiqnGefake 275 e+Ayfe++he+klivdl++e+G+++mr ++s+tA++g+l+++ ++++ee +kem++ilkeiq+G+fake lcl|NCBI__GCF_000429985.1:WP_027178077.1 221 EMAYFECLHEMKLIVDLIYEGGISNMRYSISDTAEYGDLTRGpRVINEESRKEMKEILKEIQQGDFAKE 289 ********************************************************************* PP TIGR00465 276 walekeagkpafeearkkekeqeiekvGkelralvkaek 314 +++e++ gk++f + r+ ++e++ie+vG +lr+++++ k lcl|NCBI__GCF_000429985.1:WP_027178077.1 290 FIVENMSGKAHFSALRRINREHKIEEVGANLRNMMSWLK 328 ***********************************9865 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (314 nodes) Target sequences: 1 (329 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 9.64 // [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