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_084057656.1 B9A12_RS09545 ketol-acid reductoisomerase
Query= SwissProt::K4LVZ1 (332 letters) >NCBI__GCF_900176285.1:WP_084057656.1 Length = 333 Score = 483 bits (1242), Expect = e-141 Identities = 235/330 (71%), Positives = 281/330 (85%) Query: 1 MKIYYDQDADLQYLDGKTVAVIGYGSQGHAQSQNLRDSGVKVVVADIPSSENWKKAEEAQ 60 M+I+YD DAD + L GK VAVIGYGSQGHAQ+QNLRDSG+ V+V P S N++KA E Sbjct: 1 MRIFYDADADAKVLQGKKVAVIGYGSQGHAQAQNLRDSGMDVIVGQRPGSANYQKAVEDG 60 Query: 61 FQPLTADEAAREADIIQILVPDEKQAALYRESIAPNLRPGKALVFSHGFNIHFKQIVPPP 120 F+P++A EAA AD+IQ+LVPD QA LYR+ +AP + GK L+FSHGFNIHF QIVPP Sbjct: 61 FEPVSAREAAEAADVIQMLVPDHIQAQLYRDDVAPFMSAGKTLLFSHGFNIHFGQIVPPA 120 Query: 121 DVDVFMVAPKGPGHLVRRMYEEGAGVPSLVAVEQDYSGQALNLALAYAKGIGATRAGVIQ 180 DVDV MVAPKGPGHLVR Y GAGVP+LVAVEQD +GQAL ALAYAKGIGATRAGV++ Sbjct: 121 DVDVVMVAPKGPGHLVRSEYVRGAGVPALVAVEQDATGQALQTALAYAKGIGATRAGVME 180 Query: 181 TTFKEETETDLFGEQAVLCGGITELIRAGFDTLVDAGYQPEIAYFECLHEMKLIVDLIYE 240 TTF+EETETDLFGEQAVLCGG++ELI+AGF+TLV+AGYQPEIA+FEC+HE+KLIVDLIY+ Sbjct: 181 TTFQEETETDLFGEQAVLCGGVSELIKAGFETLVEAGYQPEIAFFECMHELKLIVDLIYQ 240 Query: 241 GGISTMRYSISDTAEYGDLTRGKRIITEATREEMKKILKEIQDGVFAREWLLENQVGRPV 300 GG+S MRYSISDTAEYGD TRG+RIIT+ TR+EMKKIL+EIQ G FAREW+LENQ G + Sbjct: 241 GGLSYMRYSISDTAEYGDYTRGRRIITDETRKEMKKILREIQTGQFAREWILENQAGTAM 300 Query: 301 YNALRRKEQNHLIETVGARLRGMMPWLKKK 330 + ++RR+E+ H +E VGARLR MMP+L+ K Sbjct: 301 FRSMRRRERAHQVEEVGARLRAMMPFLEPK 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: 386 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: 332 Length of database: 333 Length adjustment: 28 Effective length of query: 304 Effective length of database: 305 Effective search space: 92720 Effective search space used: 92720 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_084057656.1 B9A12_RS09545 (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.22945.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.3e-147 475.4 0.5 3.8e-147 475.2 0.5 1.0 1 lcl|NCBI__GCF_900176285.1:WP_084057656.1 B9A12_RS09545 ketol-acid reducto Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900176285.1:WP_084057656.1 B9A12_RS09545 ketol-acid reductoisomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 475.2 0.5 3.8e-147 3.8e-147 1 312 [. 14 326 .. 14 328 .. 0.99 Alignments for each domain: == domain 1 score: 475.2 bits; conditional E-value: 3.8e-147 TIGR00465 1 lkgkkvaiiGyGsqGeaqalnlrdsglnvivglrkeaaswkkAeedGfkvltveeaikkadlimiLlpD 69 l+gkkva+iGyGsqG+aqa nlrdsg++vivg r+++a ++kA edGf+ ++ +ea+++ad+i +L+pD lcl|NCBI__GCF_900176285.1:WP_084057656.1 14 LQGKKVAVIGYGSQGHAQAQNLRDSGMDVIVGQRPGSANYQKAVEDGFEPVSAREAAEAADVIQMLVPD 82 79******************************************************************* PP TIGR00465 70 evqkevyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliA 138 ++q + y+ +++p++ +gk+llfsHGfni+f qiv+p+dvdvv+vAPKgpG+lvR+ey +g+Gvp+l+A lcl|NCBI__GCF_900176285.1:WP_084057656.1 83 HIQAQLYRDDVAPFMSAGKTLLFSHGFNIHFGQIVPPADVDVVMVAPKGPGHLVRSEYVRGAGVPALVA 151 ********************************************************************* PP TIGR00465 139 veqdvtgeakeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqp 207 veqd+tg+a ++AlayAk+iG++ragv+ettF+eE+e+DLfGEqavLcGg+++lika+f+tLveaGyqp lcl|NCBI__GCF_900176285.1:WP_084057656.1 152 VEQDATGQALQTALAYAKGIGATRAGVMETTFQEETETDLFGEQAVLCGGVSELIKAGFETLVEAGYQP 220 ********************************************************************* PP TIGR00465 208 elAyfeivhelklivdllkekGlelmrdavsntAklgalelr.eilkeelkkemqkilkeiqnGefake 275 e+A+fe++helklivdl++++Gl++mr ++s+tA++g+++++ +i+++e++kem+kil eiq+G+fa+e lcl|NCBI__GCF_900176285.1:WP_084057656.1 221 EIAFFECMHELKLIVDLIYQGGLSYMRYSISDTAEYGDYTRGrRIITDETRKEMKKILREIQTGQFARE 289 *****************************************99************************** PP TIGR00465 276 walekeagkpafeearkkekeqeiekvGkelralvka 312 w+le++ag+++f+++r++e+ +++e+vG +lra++++ lcl|NCBI__GCF_900176285.1:WP_084057656.1 290 WILENQAGTAMFRSMRRRERAHQVEEVGARLRAMMPF 326 **********************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (314 nodes) Target sequences: 1 (333 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: 8.44 // [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