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_093393433.1 BM091_RS03285 ketol-acid reductoisomerase
Query= SwissProt::K4LVZ1 (332 letters) >NCBI__GCF_900114975.1:WP_093393433.1 Length = 335 Score = 493 bits (1270), Expect = e-144 Identities = 236/330 (71%), Positives = 285/330 (86%) Query: 1 MKIYYDQDADLQYLDGKTVAVIGYGSQGHAQSQNLRDSGVKVVVADIPSSENWKKAEEAQ 60 M+I+Y+ DAD +L GK VA++GYGSQGHAQ+QNLRDSG+ V+VA P S N++ A E Sbjct: 1 MRIFYEADADFSFLQGKKVAIVGYGSQGHAQAQNLRDSGIDVIVAQRPGSRNYELALEDG 60 Query: 61 FQPLTADEAAREADIIQILVPDEKQAALYRESIAPNLRPGKALVFSHGFNIHFKQIVPPP 120 F+PL+ +EAA+EAD+IQ+L+PD QA +YR S+AP+L+PGK L+FSHGFNIH+ QIVPP Sbjct: 61 FKPLSVEEAAKEADVIQMLIPDHVQADVYRTSVAPHLKPGKMLMFSHGFNIHYGQIVPPR 120 Query: 121 DVDVFMVAPKGPGHLVRRMYEEGAGVPSLVAVEQDYSGQALNLALAYAKGIGATRAGVIQ 180 DVDV MVAPKGPGHLVR Y GAGVP+LVAV QD +G ALN+ALAYAKGIGATRAGVI+ Sbjct: 121 DVDVTMVAPKGPGHLVRSEYVRGAGVPALVAVHQDATGNALNVALAYAKGIGATRAGVIE 180 Query: 181 TTFKEETETDLFGEQAVLCGGITELIRAGFDTLVDAGYQPEIAYFECLHEMKLIVDLIYE 240 TTFKEETETDLFGEQ VLCGG++ELI+AGF+TLV+AGYQPEIAYFECLHE+KLIVDLIY+ Sbjct: 181 TTFKEETETDLFGEQCVLCGGVSELIKAGFETLVEAGYQPEIAYFECLHELKLIVDLIYQ 240 Query: 241 GGISTMRYSISDTAEYGDLTRGKRIITEATREEMKKILKEIQDGVFAREWLLENQVGRPV 300 GG+S MRYSISDTAEYGDLTRG RI++E TR+ M+ ILKEIQ G FAREW+LEN+ GRPV Sbjct: 241 GGLSYMRYSISDTAEYGDLTRGPRIVSEQTRQTMRDILKEIQTGAFAREWILENRAGRPV 300 Query: 301 YNALRRKEQNHLIETVGARLRGMMPWLKKK 330 + ALRR+ ++HL+E VG RLR MMP+L+ K Sbjct: 301 FQALRRQARSHLVEEVGKRLRSMMPFLEAK 330 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: 391 Number of extensions: 7 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: 335 Length adjustment: 28 Effective length of query: 304 Effective length of database: 307 Effective search space: 93328 Effective search space used: 93328 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_093393433.1 BM091_RS03285 (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.11643.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.6e-147 475.8 0.0 3e-147 475.6 0.0 1.0 1 lcl|NCBI__GCF_900114975.1:WP_093393433.1 BM091_RS03285 ketol-acid reducto Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900114975.1:WP_093393433.1 BM091_RS03285 ketol-acid reductoisomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 475.6 0.0 3e-147 3e-147 1 312 [. 14 326 .. 14 328 .. 0.99 Alignments for each domain: == domain 1 score: 475.6 bits; conditional E-value: 3e-147 TIGR00465 1 lkgkkvaiiGyGsqGeaqalnlrdsglnvivglrkeaaswkkAeedGfkvltveeaikkadlimiLlpD 69 l+gkkvai+GyGsqG+aqa nlrdsg++viv+ r+++ ++ A edGfk l+veea+k+ad+i +L+pD lcl|NCBI__GCF_900114975.1:WP_093393433.1 14 LQGKKVAIVGYGSQGHAQAQNLRDSGIDVIVAQRPGSRNYELALEDGFKPLSVEEAAKEADVIQMLIPD 82 79******************************************************************* PP TIGR00465 70 evqkevyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliA 138 +vq +vy+ +++p lk gk+l+fsHGfni++ qiv+p+dvdv++vAPKgpG+lvR+ey +g+Gvp+l+A lcl|NCBI__GCF_900114975.1:WP_093393433.1 83 HVQADVYRTSVAPHLKPGKMLMFSHGFNIHYGQIVPPRDVDVTMVAPKGPGHLVRSEYVRGAGVPALVA 151 ********************************************************************* PP TIGR00465 139 veqdvtgeakeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqp 207 v+qd+tg+a ++AlayAk+iG++ragv+ettFkeE+e+DLfGEq vLcGg+++lika+f+tLveaGyqp lcl|NCBI__GCF_900114975.1:WP_093393433.1 152 VHQDATGNALNVALAYAKGIGATRAGVIETTFKEETETDLFGEQCVLCGGVSELIKAGFETLVEAGYQP 220 ********************************************************************* PP TIGR00465 208 elAyfeivhelklivdllkekGlelmrdavsntAklgalelr.eilkeelkkemqkilkeiqnGefake 275 e+Ayfe++helklivdl++++Gl++mr ++s+tA++g+l+++ +i++e+++++m++ilkeiq+G fa+e lcl|NCBI__GCF_900114975.1:WP_093393433.1 221 EIAYFECLHELKLIVDLIYQGGLSYMRYSISDTAEYGDLTRGpRIVSEQTRQTMRDILKEIQTGAFARE 289 ********************************************************************* PP TIGR00465 276 walekeagkpafeearkkekeqeiekvGkelralvka 312 w+le++ag+p f++ r++ + + +e+vGk+lr ++++ lcl|NCBI__GCF_900114975.1:WP_093393433.1 290 WILENRAGRPVFQALRRQARSHLVEEVGKRLRSMMPF 326 **********************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (314 nodes) Target sequences: 1 (335 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 7.66 // [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