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 PP_4678 PP_4678 Ketol-acid reductoisomerase
Query= SwissProt::Q9HVA2 (338 letters) >FitnessBrowser__Putida:PP_4678 Length = 338 Score = 631 bits (1627), Expect = 0.0 Identities = 316/338 (93%), Positives = 325/338 (96%) Query: 1 MRVFYDKDCDLSIIQGKKVAIIGYGSQGHAHACNLKDSGVDVTVGLRSGSATVAKAEAHG 60 M+VFYDKDCDLSIIQGKKVAIIGYGSQGHA ACNLKDSGVDVTVGLR GSATVAKAEAHG Sbjct: 1 MKVFYDKDCDLSIIQGKKVAIIGYGSQGHAQACNLKDSGVDVTVGLRKGSATVAKAEAHG 60 Query: 61 LKVADVKTAVAAADVVMILTPDEFQGRLYKEEIEPNLKKGATLAFAHGFSIHYNQVVPRA 120 LKVADV TAVAAAD+VMILTPDEFQG LYK EIEPN+KKGATLAF+HGFSIHYNQVVPRA Sbjct: 61 LKVADVATAVAAADLVMILTPDEFQGALYKNEIEPNIKKGATLAFSHGFSIHYNQVVPRA 120 Query: 121 DLDVIMIAPKAPGHTVRSEFVKGGGIPDLIAIYQDASGNAKNVALSYACGVGGGRTGIIE 180 DLDVIMIAPKAPGHTVRSEFVKGGGIPDLIAIYQDASGNAKNVALSYA GVGGGRTGIIE Sbjct: 121 DLDVIMIAPKAPGHTVRSEFVKGGGIPDLIAIYQDASGNAKNVALSYASGVGGGRTGIIE 180 Query: 181 TTFKDETETDLFGEQAVLCGGCVELVKAGFETLVEAGYAPEMAYFECLHELKLIVDLMYE 240 TTFKDETETDLFGEQAVLCGG VELVKAGFETLVEAGYAPEMAYFECLHELKLIVDLMYE Sbjct: 181 TTFKDETETDLFGEQAVLCGGTVELVKAGFETLVEAGYAPEMAYFECLHELKLIVDLMYE 240 Query: 241 GGIANMNYSISNNAEYGEYVTGPEVINAESRAAMRNALKRIQDGEYAKMFITEGAANYPS 300 GGIANMNYSISNNAEYGEYVTGPEVIN ESR AMRNALKRIQDGEYAKMFI+EGA NYPS Sbjct: 241 GGIANMNYSISNNAEYGEYVTGPEVINEESRKAMRNALKRIQDGEYAKMFISEGATNYPS 300 Query: 301 MTAYRRNNAAHPIEQIGEKLRAMMPWIAANKIVDKSKN 338 MTA RRNNAAH IE IGE+LR+MMPWI+ANKIVDK+KN Sbjct: 301 MTAKRRNNAAHGIEIIGEQLRSMMPWISANKIVDKTKN 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: 493 Number of extensions: 6 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 PP_4678 PP_4678 (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.26771.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.3e-133 429.9 1.9 2.7e-133 429.7 1.9 1.0 1 lcl|FitnessBrowser__Putida:PP_4678 PP_4678 Ketol-acid reductoisomer Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Putida:PP_4678 PP_4678 Ketol-acid reductoisomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 429.7 1.9 2.7e-133 2.7e-133 1 312 [. 14 326 .. 14 328 .. 0.99 Alignments for each domain: == domain 1 score: 429.7 bits; conditional E-value: 2.7e-133 TIGR00465 1 lkgkkvaiiGyGsqGeaqalnlrdsglnvivglrkeaaswkkAeedGfkvltveeaikkadlimiLlpDevqkev 75 ++gkkvaiiGyGsqG+aqa nl+dsg++v+vglrk++a+++kAe G+kv +v+ a+++adl+miL+pDe q + lcl|FitnessBrowser__Putida:PP_4678 14 IQGKKVAIIGYGSQGHAQACNLKDSGVDVTVGLRKGSATVAKAEAHGLKVADVATAVAAADLVMILTPDEFQGAL 88 689************************************************************************ PP TIGR00465 76 yeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliAveqdvtgeakei 150 y++ei+p++k+g++l fsHGf+i+++q+v+++d+dv+++APK+pG++vR+e+ +g G+p liA++qd++g+ak++ lcl|FitnessBrowser__Putida:PP_4678 89 YKNEIEPNIKKGATLAFSHGFSIHYNQVVPRADLDVIMIAPKAPGHTVRSEFVKGGGIPDLIAIYQDASGNAKNV 163 *************************************************************************** PP TIGR00465 151 AlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqpelAyfeivhelklivdll 225 Al+yA ++Gg+r g++ettFk+E+e+DLfGEqavLcGg +l+ka+f+tLveaGy+pe+Ayfe++helklivdl+ lcl|FitnessBrowser__Putida:PP_4678 164 ALSYASGVGGGRTGIIETTFKDETETDLFGEQAVLCGGTVELVKAGFETLVEAGYAPEMAYFECLHELKLIVDLM 238 *************************************************************************** PP TIGR00465 226 kekGlelmrdavsntAklgalelr.eilkeelkkemqkilkeiqnGefakewalekeagkpafeearkkekeqei 299 +e+G+++m ++sn A++g++ ++ e+++ee +k+m++ lk iq+Ge+ak ++ e ++++p+++++r+ + + i lcl|FitnessBrowser__Putida:PP_4678 239 YEGGIANMNYSISNNAEYGEYVTGpEVINEESRKAMRNALKRIQDGEYAKMFISEGATNYPSMTAKRRNNAAHGI 313 ************************9************************************************** PP TIGR00465 300 ekvGkelralvka 312 e +G++lr ++++ lcl|FitnessBrowser__Putida:PP_4678 314 EIIGEQLRSMMPW 326 ***********98 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 10.46 // [ok]
This GapMind analysis is from Apr 09 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