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 WP_013834810.1 THICY_RS01280 ketol-acid reductoisomerase
Query= SwissProt::Q9HVA2 (338 letters) >NCBI__GCF_000214825.1:WP_013834810.1 Length = 338 Score = 563 bits (1452), Expect = e-165 Identities = 279/338 (82%), Positives = 302/338 (89%) Query: 1 MRVFYDKDCDLSIIQGKKVAIIGYGSQGHAHACNLKDSGVDVTVGLRSGSATVAKAEAHG 60 M+V+YDKDCDLSII+G +VAIIG+GSQGHAHA NL+DSGVDVTVGLR GS+++ KAE +G Sbjct: 1 MQVYYDKDCDLSIIRGMRVAIIGFGSQGHAHAANLQDSGVDVTVGLRPGSSSIKKAEGYG 60 Query: 61 LKVADVKTAVAAADVVMILTPDEFQGRLYKEEIEPNLKKGATLAFAHGFSIHYNQVVPRA 120 LK ADV +AVA AD+VMILTPDEFQ LYK EIEPNLKKGA LAFAHGF+I YNQVVPRA Sbjct: 61 LKTADVPSAVANADLVMILTPDEFQSVLYKNEIEPNLKKGAVLAFAHGFAILYNQVVPRA 120 Query: 121 DLDVIMIAPKAPGHTVRSEFVKGGGIPDLIAIYQDASGNAKNVALSYACGVGGGRTGIIE 180 DLDVIMIAPKAPGHTVRSEFVKGGGIPDLIA++QD SG AK++ALSYA GVGGGRTGIIE Sbjct: 121 DLDVIMIAPKAPGHTVRSEFVKGGGIPDLIAVHQDVSGKAKSIALSYASGVGGGRTGIIE 180 Query: 181 TTFKDETETDLFGEQAVLCGGCVELVKAGFETLVEAGYAPEMAYFECLHELKLIVDLMYE 240 TTF++E ETDLFGEQAVLCGG VELVK GFETLVEAGYAPEMAYFECLHELKLIVDLMYE Sbjct: 181 TTFREECETDLFGEQAVLCGGAVELVKMGFETLVEAGYAPEMAYFECLHELKLIVDLMYE 240 Query: 241 GGIANMNYSISNNAEYGEYVTGPEVINAESRAAMRNALKRIQDGEYAKMFITEGAANYPS 300 GGIANMNYSISNNAEYGEYVTGP+VIN ESR AMR AL IQ GEYAK FI EG NYP Sbjct: 241 GGIANMNYSISNNAEYGEYVTGPQVINEESRMAMREALYNIQSGEYAKRFILEGMTNYPE 300 Query: 301 MTAYRRNNAAHPIEQIGEKLRAMMPWIAANKIVDKSKN 338 MTA RR NA HPIE +GE+LR+MMPWI ANKIVDK KN Sbjct: 301 MTAMRRMNAEHPIEVVGEQLRSMMPWIQANKIVDKDKN 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: 442 Number of extensions: 10 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 WP_013834810.1 THICY_RS01280 (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.11624.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-131 424.1 0.3 1.6e-131 423.9 0.3 1.0 1 lcl|NCBI__GCF_000214825.1:WP_013834810.1 THICY_RS01280 ketol-acid reducto Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000214825.1:WP_013834810.1 THICY_RS01280 ketol-acid reductoisomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 423.9 0.3 1.6e-131 1.6e-131 2 312 .. 15 326 .. 14 328 .. 0.99 Alignments for each domain: == domain 1 score: 423.9 bits; conditional E-value: 1.6e-131 TIGR00465 2 kgkkvaiiGyGsqGeaqalnlrdsglnvivglrkeaaswkkAeedGfkvltveeaikkadlimiLlpDe 70 +g +vaiiG+GsqG+a+a nl+dsg++v+vglr++++s+kkAe G+k +v a+++adl+miL+pDe lcl|NCBI__GCF_000214825.1:WP_013834810.1 15 RGMRVAIIGFGSQGHAHAANLQDSGVDVTVGLRPGSSSIKKAEGYGLKTADVPSAVANADLVMILTPDE 83 6789***************************************************************** PP TIGR00465 71 vqkevyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliAv 139 q+ y++ei+p+lk+g++l f+HGf i ++q+v+++d+dv+++APK+pG++vR+e+ +g G+p liAv lcl|NCBI__GCF_000214825.1:WP_013834810.1 84 FQSVLYKNEIEPNLKKGAVLAFAHGFAILYNQVVPRADLDVIMIAPKAPGHTVRSEFVKGGGIPDLIAV 152 ********************************************************************* PP TIGR00465 140 eqdvtgeakeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqpe 208 +qdv+g+ak iAl+yA ++Gg+r g++ettF+eE+e+DLfGEqavLcGg +l+k++f+tLveaGy+pe lcl|NCBI__GCF_000214825.1:WP_013834810.1 153 HQDVSGKAKSIALSYASGVGGGRTGIIETTFREECETDLFGEQAVLCGGAVELVKMGFETLVEAGYAPE 221 ********************************************************************* PP TIGR00465 209 lAyfeivhelklivdllkekGlelmrdavsntAklgalelr.eilkeelkkemqkilkeiqnGefakew 276 +Ayfe++helklivdl++e+G+++m ++sn A++g++ ++ ++++ee + +m++ l +iq+Ge+ak + lcl|NCBI__GCF_000214825.1:WP_013834810.1 222 MAYFECLHELKLIVDLMYEGGIANMNYSISNNAEYGEYVTGpQVINEESRMAMREALYNIQSGEYAKRF 290 *****************************************999************************* PP TIGR00465 277 alekeagkpafeearkkekeqeiekvGkelralvka 312 +le ++++p+++++r+++ e+ ie vG++lr ++++ lcl|NCBI__GCF_000214825.1:WP_013834810.1 291 ILEGMTNYPEMTAMRRMNAEHPIEVVGEQLRSMMPW 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 9.00 // [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