Align ketol-acid reductoisomerase (NAD+) (EC 1.1.1.382); ketol-acid reductoisomerase (NADP+) (EC 1.1.1.86) (characterized)
to candidate WP_075385748.1 BK574_RS22740 ketol-acid reductoisomerase
Query= BRENDA::C8WR67 (344 letters) >NCBI__GCF_002019605.1:WP_075385748.1 Length = 340 Score = 500 bits (1288), Expect = e-146 Identities = 240/333 (72%), Positives = 280/333 (84%) Query: 1 MEKIYYDADISIQPLADKRIAVIGYGSQGHAHAQNLRDSGFDVVIGLRPGSSWAKAEADG 60 M IYY+ DI+ L K +A+IGYGSQGHAHAQNLR+SG VV+GLRPG S+ +A DG Sbjct: 1 MANIYYNGDINEGVLQGKTVAIIGYGSQGHAHAQNLRESGTSVVVGLRPGKSFDQAVNDG 60 Query: 61 FRVMAVGEAVEESDVIMILLPDERQPAVYEREIRPYLTAGKALAFAHGFNIHFSQIQPPK 120 F V+ V EA +++VIM+LLPDE QP VY+ I P LTAGKAL FAHGFNIHF+QIQPP Sbjct: 61 FEVLPVREAAAKAEVIMVLLPDENQPKVYKESIEPELTAGKALVFAHGFNIHFNQIQPPA 120 Query: 121 DVDVFMVAPKGPGHLVRRVYEAGGGVPALIAVHQDASGQAKDLALAYARGIGAGRAGILT 180 DVDVF+ APKGPGHLVRR Y G GVP LIAV+QDA+GQAK+LALAYA+ IG+ R G++ Sbjct: 121 DVDVFLAAPKGPGHLVRRTYTEGAGVPGLIAVYQDATGQAKELALAYAKQIGSARGGVIE 180 Query: 181 TTFREETETDLFGEQAVLCGGLSALIKAGFETLVEAGYQPEIAYFECLHEMKLIVDLIYE 240 TTF+EETETDLFGEQAVLCGG +AL+KAGFETLVEAGYQPE+AYFECLHE+KLIVDL+YE Sbjct: 181 TTFQEETETDLFGEQAVLCGGTTALVKAGFETLVEAGYQPEVAYFECLHELKLIVDLMYE 240 Query: 241 GGLEYMRYSISDTAQWGDFTSGPRIINEETKKEMRRILADIQSGAFAKSWILENQANRPM 300 GGLE MRYSISDTAQWGDF +GP+++ E+TKK M+ IL+DIQ+G FAK WILENQANRP Sbjct: 241 GGLEGMRYSISDTAQWGDFVAGPQVVTEDTKKAMKSILSDIQTGKFAKGWILENQANRPE 300 Query: 301 FNAINRRELEHPIEVVGRKLRSMMPFIKAKRPG 333 FNAIN E +HPIEVVGR+LR MMPF+KAK G Sbjct: 301 FNAINESEKKHPIEVVGRELREMMPFVKAKSKG 333 Lambda K H 0.320 0.138 0.404 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: 434 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: 344 Length of database: 340 Length adjustment: 29 Effective length of query: 315 Effective length of database: 311 Effective search space: 97965 Effective search space used: 97965 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 49 (23.5 bits)
Align candidate WP_075385748.1 BK574_RS22740 (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.22185.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-144 466.9 0.2 1.6e-144 466.7 0.2 1.0 1 lcl|NCBI__GCF_002019605.1:WP_075385748.1 BK574_RS22740 ketol-acid reducto Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002019605.1:WP_075385748.1 BK574_RS22740 ketol-acid reductoisomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 466.7 0.2 1.6e-144 1.6e-144 1 313 [. 15 327 .. 15 328 .. 0.99 Alignments for each domain: == domain 1 score: 466.7 bits; conditional E-value: 1.6e-144 TIGR00465 1 lkgkkvaiiGyGsqGeaqalnlrdsglnvivglrkeaaswkkAeedGfkvltveeaikkadlimiLlpD 69 l+gk+vaiiGyGsqG+a+a nlr+sg v+vglr++ +s+++A +dGf+vl v+ea++ka++im+LlpD lcl|NCBI__GCF_002019605.1:WP_075385748.1 15 LQGKTVAIIGYGSQGHAHAQNLRESGTSVVVGLRPG-KSFDQAVNDGFEVLPVREAAAKAEVIMVLLPD 82 79********************************98.9******************************* PP TIGR00465 70 evqkevyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliA 138 e q++vy+++i+p+l++gkal+f+HGfni+f+qi++p+dvdv+l+APKgpG+lvR++y eg+Gvp+liA lcl|NCBI__GCF_002019605.1:WP_075385748.1 83 ENQPKVYKESIEPELTAGKALVFAHGFNIHFNQIQPPADVDVFLAAPKGPGHLVRRTYTEGAGVPGLIA 151 ********************************************************************* PP TIGR00465 139 veqdvtgeakeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqp 207 v+qd+tg+ake AlayAk iG+ar gv+ettF+eE+e+DLfGEqavLcGg +al+ka+f+tLveaGyqp lcl|NCBI__GCF_002019605.1:WP_075385748.1 152 VYQDATGQAKELALAYAKQIGSARGGVIETTFQEETETDLFGEQAVLCGGTTALVKAGFETLVEAGYQP 220 ********************************************************************* PP TIGR00465 208 elAyfeivhelklivdllkekGlelmrdavsntAklgalelr.eilkeelkkemqkilkeiqnGefake 275 e+Ayfe++helklivdl++e+Gle+mr ++s+tA++g++ ++ ++++e +kk+m+ il +iq+G+fak lcl|NCBI__GCF_002019605.1:WP_075385748.1 221 EVAYFECLHELKLIVDLMYEGGLEGMRYSISDTAQWGDFVAGpQVVTEDTKKAMKSILSDIQTGKFAKG 289 ******************************************999************************ PP TIGR00465 276 walekeagkpafeearkkekeqeiekvGkelralvkae 313 w+le++a++p+f++++++ek++ ie vG+elr+++++ lcl|NCBI__GCF_002019605.1:WP_075385748.1 290 WILENQANRPEFNAINESEKKHPIEVVGRELREMMPFV 327 ***********************************976 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: 00:00:00.01 # Mc/sec: 10.37 // [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