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_013459446.1 SULKU_RS02945 ketol-acid reductoisomerase
Query= SwissProt::C1DFH7 (338 letters) >NCBI__GCF_000183725.1:WP_013459446.1 Length = 340 Score = 477 bits (1227), Expect = e-139 Identities = 237/338 (70%), Positives = 273/338 (80%) Query: 1 MKVYYDKDCDLSIIQSKKVAIIGYGSQGHAHACNLKDSGVDVYVGLRAGSASVAKAEAHG 60 + VYYDKDC++ +I+SKKVA+IG+GSQGHAHA NL+DSGV+V +GLR +S KAEA G Sbjct: 3 LSVYYDKDCNIELIKSKKVAMIGFGSQGHAHAENLRDSGVEVVIGLRKEGSSWGKAEAKG 62 Query: 61 LTVKSVKDAVAAADVVMILTPDEFQGRLYKDEIEPNLKKGATLAFAHGFSIHYNQVVPRA 120 V +V +A A ADVVMIL PDE Q +YK+EIEPNLK GAT+AF HGF+IHY ++ PRA Sbjct: 63 FKVMTVAEASAYADVVMILLPDENQAEIYKNEIEPNLKNGATIAFGHGFNIHYGRIHPRA 122 Query: 121 DLDVIMIAPKAPGHTVRSEFVRGGGIPDLIAVYQDASGNAKNLALSYACGVGGGRTGIIE 180 D++V MIAPKAPGHTVRSEFVRGGGIPDLIAV Q+ SG K LALSYA +GGGRT IIE Sbjct: 123 DINVTMIAPKAPGHTVRSEFVRGGGIPDLIAVGQNPSGTTKELALSYASAIGGGRTAIIE 182 Query: 181 TTFKDETETDLFGEQAVLCGGCVELVKAGFETLVEAGYAPEMAYFECLHELKLIVDLMFE 240 TTFKDETETDLFGEQAVLCGG LV+AGFETL EAGYAPE+AYFECLHELKLIVDLMFE Sbjct: 183 TTFKDETETDLFGEQAVLCGGAASLVQAGFETLTEAGYAPELAYFECLHELKLIVDLMFE 242 Query: 241 GGIANMNYSISNNAEYGEYVTGPEVINEQSRQAMRNALKRIQDGEYAKMFITEGAANYPS 300 GGIA+M YSISN AEYG+YV+G VIN +S+ AM+ LK IQDG +AK FI EG A YP Sbjct: 243 GGIADMRYSISNTAEYGDYVSGKRVINAESKAAMKEILKEIQDGRFAKDFILEGQAGYPR 302 Query: 301 MTAYRRNNAAHQIEVVGEKLRTMMPWIAANKIVDKTKN 338 M A R N A IE G KLR+MMPWI+ NKIV++ N Sbjct: 303 MNAERANARASLIEQTGVKLRSMMPWISKNKIVNQATN 340 Lambda K H 0.317 0.134 0.388 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: 409 Number of extensions: 5 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: 340 Length adjustment: 28 Effective length of query: 310 Effective length of database: 312 Effective search space: 96720 Effective search space used: 96720 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_013459446.1 SULKU_RS02945 (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.25044.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.8e-135 435.8 0.7 4.5e-135 435.6 0.7 1.0 1 lcl|NCBI__GCF_000183725.1:WP_013459446.1 SULKU_RS02945 ketol-acid reducto Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000183725.1:WP_013459446.1 SULKU_RS02945 ketol-acid reductoisomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 435.6 0.7 4.5e-135 4.5e-135 1 312 [. 16 328 .. 16 330 .. 0.99 Alignments for each domain: == domain 1 score: 435.6 bits; conditional E-value: 4.5e-135 TIGR00465 1 lkgkkvaiiGyGsqGeaqalnlrdsglnvivglrkeaaswkkAeedGfkvltveeaikkadlimiLlpD 69 +k+kkva+iG+GsqG+a+a nlrdsg++v++glrke++sw kAe +Gfkv+tv+ea + ad++miLlpD lcl|NCBI__GCF_000183725.1:WP_013459446.1 16 IKSKKVAMIGFGSQGHAHAENLRDSGVEVVIGLRKEGSSWGKAEAKGFKVMTVAEASAYADVVMILLPD 84 689****************************************************************** PP TIGR00465 70 evqkevyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliA 138 e q e y++ei+p+lk+g+++ f HGfni++ +i++++d++v+++APK+pG++vR+e+ +g G+p liA lcl|NCBI__GCF_000183725.1:WP_013459446.1 85 ENQAEIYKNEIEPNLKNGATIAFGHGFNIHYGRIHPRADINVTMIAPKAPGHTVRSEFVRGGGIPDLIA 153 ********************************************************************* PP TIGR00465 139 veqdvtgeakeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqp 207 v q+++g +ke Al+yA aiGg+r ++ettFk+E+e+DLfGEqavLcGg + l++a+f+tL+eaGy+p lcl|NCBI__GCF_000183725.1:WP_013459446.1 154 VGQNPSGTTKELALSYASAIGGGRTAIIETTFKDETETDLFGEQAVLCGGAASLVQAGFETLTEAGYAP 222 ********************************************************************* PP TIGR00465 208 elAyfeivhelklivdllkekGlelmrdavsntAklgalelr.eilkeelkkemqkilkeiqnGefake 275 elAyfe++helklivdl+ e+G++ mr ++sntA++g++ ++ +++++e k++m++ilkeiq+G+fak+ lcl|NCBI__GCF_000183725.1:WP_013459446.1 223 ELAYFECLHELKLIVDLMFEGGIADMRYSISNTAEYGDYVSGkRVINAESKAAMKEILKEIQDGRFAKD 291 *****************************************99************************** PP TIGR00465 276 walekeagkpafeearkkekeqeiekvGkelralvka 312 ++le +ag+p+++++r + ie++G++lr ++++ lcl|NCBI__GCF_000183725.1:WP_013459446.1 292 FILEGQAGYPRMNAERANARASLIEQTGVKLRSMMPW 328 ***********************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (314 nodes) Target sequences: 1 (340 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: 00:00:00.00 # Mc/sec: 12.39 // [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