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_027722535.1 H589_RS0113600 ketol-acid reductoisomerase
Query= SwissProt::K4LVZ1 (332 letters) >NCBI__GCF_000425265.1:WP_027722535.1 Length = 329 Score = 464 bits (1193), Expect = e-135 Identities = 223/329 (67%), Positives = 271/329 (82%) Query: 1 MKIYYDQDADLQYLDGKTVAVIGYGSQGHAQSQNLRDSGVKVVVADIPSSENWKKAEEAQ 60 MK+YY++DADL L KTVA+IGYGSQGHA +QNLRDSG+KVVV P N+ A+E Sbjct: 1 MKVYYEKDADLNLLKDKTVAIIGYGSQGHAHAQNLRDSGIKVVVGQRPGGANYDLAKEHG 60 Query: 61 FQPLTADEAAREADIIQILVPDEKQAALYRESIAPNLRPGKALVFSHGFNIHFKQIVPPP 120 F+P++A EAA +AD+I IL+PD+ QA +Y+ IAPNL+PG L F HGFNIHF+QIVP P Sbjct: 61 FEPVSAAEAAAQADLIMILLPDQVQAEVYKNDIAPNLKPGNILAFGHGFNIHFEQIVPTP 120 Query: 121 DVDVFMVAPKGPGHLVRRMYEEGAGVPSLVAVEQDYSGQALNLALAYAKGIGATRAGVIQ 180 DVDV M APKGPGHLVRR Y EG VP+++AV QD SG+A +LALAYAKGIGATR+GV++ Sbjct: 121 DVDVIMAAPKGPGHLVRRTYTEGGAVPAIIAVHQDASGKAFDLALAYAKGIGATRSGVLE 180 Query: 181 TTFKEETETDLFGEQAVLCGGITELIRAGFDTLVDAGYQPEIAYFECLHEMKLIVDLIYE 240 TTF+EETETDLFGEQAVLCGG++ELI+AGF+TLV+AGY+PEIAYFECLHE KLI+DLIYE Sbjct: 181 TTFREETETDLFGEQAVLCGGLSELIKAGFETLVEAGYKPEIAYFECLHECKLIIDLIYE 240 Query: 241 GGISTMRYSISDTAEYGDLTRGKRIITEATREEMKKILKEIQDGVFAREWLLENQVGRPV 300 GG++ MR SISDTAEYGDLTRG R+I E +R+EMKKILKEIQ G FA+E+++EN G+ Sbjct: 241 GGLAKMRDSISDTAEYGDLTRGPRVINEESRKEMKKILKEIQQGEFAKEFIVENMSGKAH 300 Query: 301 YNALRRKEQNHLIETVGARLRGMMPWLKK 329 ++A+RR H IE VG LR MM WLKK Sbjct: 301 FSAMRRINAEHQIEQVGGELRKMMSWLKK 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: 379 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_027722535.1 H589_RS0113600 (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.29810.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.1e-143 461.7 0.3 5.9e-143 461.5 0.3 1.0 1 lcl|NCBI__GCF_000425265.1:WP_027722535.1 H589_RS0113600 ketol-acid reduct Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000425265.1:WP_027722535.1 H589_RS0113600 ketol-acid reductoisomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 461.5 0.3 5.9e-143 5.9e-143 1 314 [] 14 328 .. 14 328 .. 0.99 Alignments for each domain: == domain 1 score: 461.5 bits; conditional E-value: 5.9e-143 TIGR00465 1 lkgkkvaiiGyGsqGeaqalnlrdsglnvivglrkeaaswkkAeedGfkvltveeaikkadlimiLlpD 69 lk+k+vaiiGyGsqG+a+a nlrdsg++v+vg r+++a ++ A+e Gf+ ++ +ea+++adlimiLlpD lcl|NCBI__GCF_000425265.1:WP_027722535.1 14 LKDKTVAIIGYGSQGHAHAQNLRDSGIKVVVGQRPGGANYDLAKEHGFEPVSAAEAAAQADLIMILLPD 82 79******************************************************************* PP TIGR00465 70 evqkevyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliA 138 +vq evy+++i+p+lk g++l f HGfni+f+qiv+ dvdv+++APKgpG+lvR++y eg vp++iA lcl|NCBI__GCF_000425265.1:WP_027722535.1 83 QVQAEVYKNDIAPNLKPGNILAFGHGFNIHFEQIVPTPDVDVIMAAPKGPGHLVRRTYTEGGAVPAIIA 151 ********************************************************************* PP TIGR00465 139 veqdvtgeakeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqp 207 v+qd++g+a + AlayAk+iG++r gvlettF+eE+e+DLfGEqavLcGgl++lika+f+tLveaGy+p lcl|NCBI__GCF_000425265.1:WP_027722535.1 152 VHQDASGKAFDLALAYAKGIGATRSGVLETTFREETETDLFGEQAVLCGGLSELIKAGFETLVEAGYKP 220 ********************************************************************* PP TIGR00465 208 elAyfeivhelklivdllkekGlelmrdavsntAklgalelr.eilkeelkkemqkilkeiqnGefake 275 e+Ayfe++he+kli+dl++e+Gl++mrd++s+tA++g+l+++ ++++ee +kem+kilkeiq+Gefake lcl|NCBI__GCF_000425265.1:WP_027722535.1 221 EIAYFECLHECKLIIDLIYEGGLAKMRDSISDTAEYGDLTRGpRVINEESRKEMKKILKEIQQGEFAKE 289 ********************************************************************* PP TIGR00465 276 walekeagkpafeearkkekeqeiekvGkelralvkaek 314 +++e++ gk++f ++r+ + e++ie+vG elr+++++ k lcl|NCBI__GCF_000425265.1:WP_027722535.1 290 FIVENMSGKAHFSAMRRINAEHQIEQVGGELRKMMSWLK 328 ***********************************9965 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 8.98 // [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