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_013553345.1 NITSA_RS01940 ketol-acid reductoisomerase
Query= SwissProt::C1DFH7 (338 letters) >NCBI__GCF_000186245.1:WP_013553345.1 Length = 340 Score = 491 bits (1264), Expect = e-143 Identities = 242/338 (71%), Positives = 276/338 (81%) Query: 1 MKVYYDKDCDLSIIQSKKVAIIGYGSQGHAHACNLKDSGVDVYVGLRAGSASVAKAEAHG 60 + VYYDKDCD+++I+SK VA+IG+GSQGHAHA NL+DSGV+V VGL+ G S KAEA G Sbjct: 3 LNVYYDKDCDINLIKSKTVAMIGFGSQGHAHAENLRDSGVNVVVGLKPGGNSWKKAEAKG 62 Query: 61 LTVKSVKDAVAAADVVMILTPDEFQGRLYKDEIEPNLKKGATLAFAHGFSIHYNQVVPRA 120 V V +A A ADV+MIL PDE Q +YK+EIEPNLK G T+AF HGF+IHY ++ P A Sbjct: 63 FEVLPVAEATAKADVIMILLPDETQAEVYKNEIEPNLKSGDTIAFGHGFNIHYGRIKPAA 122 Query: 121 DLDVIMIAPKAPGHTVRSEFVRGGGIPDLIAVYQDASGNAKNLALSYACGVGGGRTGIIE 180 D++V+M+APKAPGHTVRSEFV+GGGIPDLIAVYQD SGN K LALSYA +GGGRT IIE Sbjct: 123 DINVMMVAPKAPGHTVRSEFVKGGGIPDLIAVYQDPSGNTKELALSYASAIGGGRTAIIE 182 Query: 181 TTFKDETETDLFGEQAVLCGGCVELVKAGFETLVEAGYAPEMAYFECLHELKLIVDLMFE 240 TTFKDETETDLFGEQAVLCGG LV+AGFETL EAGYAPEMAYFECLHELKLIVDLMFE Sbjct: 183 TTFKDETETDLFGEQAVLCGGVTSLVQAGFETLTEAGYAPEMAYFECLHELKLIVDLMFE 242 Query: 241 GGIANMNYSISNNAEYGEYVTGPEVINEQSRQAMRNALKRIQDGEYAKMFITEGAANYPS 300 GGIA M YSISN AEYG+YV+GP VINE+SR+AM+ LK IQ+G++AK FI EG A YP Sbjct: 243 GGIAEMRYSISNTAEYGDYVSGPRVINEESRKAMKEILKEIQNGKFAKDFILEGMAGYPR 302 Query: 301 MTAYRRNNAAHQIEVVGEKLRTMMPWIAANKIVDKTKN 338 MTA R N IE GEKLR MMPWI ANKIVD+ N Sbjct: 303 MTAERNNMKDSLIEKTGEKLRAMMPWIQANKIVDQETN 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: 412 Number of extensions: 8 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_013553345.1 NITSA_RS01940 (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.8824.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.8e-139 450.0 0.5 2.1e-139 449.8 0.5 1.0 1 lcl|NCBI__GCF_000186245.1:WP_013553345.1 NITSA_RS01940 ketol-acid reducto Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000186245.1:WP_013553345.1 NITSA_RS01940 ketol-acid reductoisomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 449.8 0.5 2.1e-139 2.1e-139 1 312 [. 16 328 .. 16 330 .. 0.99 Alignments for each domain: == domain 1 score: 449.8 bits; conditional E-value: 2.1e-139 TIGR00465 1 lkgkkvaiiGyGsqGeaqalnlrdsglnvivglrkeaaswkkAeedGfkvltveeaikkadlimiLlpD 69 +k+k+va+iG+GsqG+a+a nlrdsg+nv+vgl+++++swkkAe +Gf+vl v+ea +kad+imiLlpD lcl|NCBI__GCF_000186245.1:WP_013553345.1 16 IKSKTVAMIGFGSQGHAHAENLRDSGVNVVVGLKPGGNSWKKAEAKGFEVLPVAEATAKADVIMILLPD 84 689****************************************************************** PP TIGR00465 70 evqkevyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliA 138 e+q evy++ei+p+lk g+++ f HGfni++ +i++ +d++v++vAPK+pG++vR+e+ +g G+p liA lcl|NCBI__GCF_000186245.1:WP_013553345.1 85 ETQAEVYKNEIEPNLKSGDTIAFGHGFNIHYGRIKPAADINVMMVAPKAPGHTVRSEFVKGGGIPDLIA 153 ********************************************************************* PP TIGR00465 139 veqdvtgeakeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqp 207 v+qd++g++ke Al+yA aiGg+r ++ettFk+E+e+DLfGEqavLcGg++ l++a+f+tL+eaGy+p lcl|NCBI__GCF_000186245.1:WP_013553345.1 154 VYQDPSGNTKELALSYASAIGGGRTAIIETTFKDETETDLFGEQAVLCGGVTSLVQAGFETLTEAGYAP 222 ********************************************************************* PP TIGR00465 208 elAyfeivhelklivdllkekGlelmrdavsntAklgalelr.eilkeelkkemqkilkeiqnGefake 275 e+Ayfe++helklivdl+ e+G+++mr ++sntA++g++ ++ ++++ee +k+m++ilkeiqnG+fak+ lcl|NCBI__GCF_000186245.1:WP_013553345.1 223 EMAYFECLHELKLIVDLMFEGGIAEMRYSISNTAEYGDYVSGpRVINEESRKAMKEILKEIQNGKFAKD 291 ********************************************************************* PP TIGR00465 276 walekeagkpafeearkkekeqeiekvGkelralvka 312 ++le +ag+p+++++r+ k+ iek+G++lra++++ lcl|NCBI__GCF_000186245.1:WP_013553345.1 292 FILEGMAGYPRMTAERNNMKDSLIEKTGEKLRAMMPW 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 9.13 // [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