Align ketol-acid reductoisomerase (NAD+) (EC 1.1.1.382); ketol-acid reductoisomerase (NADP+) (EC 1.1.1.86) (characterized)
to candidate WP_011023690.1 MA_RS19745 ketol-acid reductoisomerase
Query= BRENDA::C8WR67 (344 letters) >NCBI__GCF_000007345.1:WP_011023690.1 Length = 335 Score = 440 bits (1132), Expect = e-128 Identities = 218/335 (65%), Positives = 266/335 (79%), Gaps = 1/335 (0%) Query: 1 MEKIYYDADISIQPLADKRIAVIGYGSQGHAHAQNLRDSGFDVVIGLRPGSS-WAKAEAD 59 M I YD + + L DK IA++GYGSQGHAHA+NL +SG +VV+GLR GSS WAKAE+D Sbjct: 1 MATIIYDNETTFDALKDKTIAIMGYGSQGHAHARNLHESGLNVVVGLRKGSSSWAKAESD 60 Query: 60 GFRVMAVGEAVEESDVIMILLPDERQPAVYEREIRPYLTAGKALAFAHGFNIHFSQIQPP 119 G +VM V EA + +DVIMILLPDE+Q +VY +I P L AG AL FAHGFNIH++QI PP Sbjct: 61 GLKVMTVEEAAKAADVIMILLPDEKQASVYYSQIEPSLEAGNALVFAHGFNIHYNQIVPP 120 Query: 120 KDVDVFMVAPKGPGHLVRRVYEAGGGVPALIAVHQDASGQAKDLALAYARGIGAGRAGIL 179 KDVDVFMVAPKGPGH+VRR Y G GVP LIAV+QDA+G+A+DLALAYA+GIGA RAG+ Sbjct: 121 KDVDVFMVAPKGPGHIVRRTYTEGIGVPGLIAVYQDATGKARDLALAYAKGIGATRAGVY 180 Query: 180 TTTFREETETDLFGEQAVLCGGLSALIKAGFETLVEAGYQPEIAYFECLHEMKLIVDLIY 239 TTFREETETDLFGEQ LCGGLSALIK FE LVEAGYQPE+AYFE HE+KLIVDLIY Sbjct: 181 ETTFREETETDLFGEQVDLCGGLSALIKTAFEVLVEAGYQPEMAYFETCHEVKLIVDLIY 240 Query: 240 EGGLEYMRYSISDTAQWGDFTSGPRIINEETKKEMRRILADIQSGAFAKSWILENQANRP 299 EGGLE M +S+S+TA++G T GPRIINEE+++ M LA IQ+G FAK ++LE N P Sbjct: 241 EGGLERMWHSVSNTAEYGGMTVGPRIINEESREAMYEALARIQNGEFAKEFVLEGMVNHP 300 Query: 300 MFNAINRRELEHPIEVVGRKLRSMMPFIKAKRPGD 334 + A+ R+E EHP+EVVG+++R+ +P++ K D Sbjct: 301 VLKAMERQEKEHPLEVVGKEIRANIPWLNKKIDDD 335 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: 375 Number of extensions: 14 Number of successful extensions: 2 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: 335 Length adjustment: 28 Effective length of query: 316 Effective length of database: 307 Effective search space: 97012 Effective search space used: 97012 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_011023690.1 MA_RS19745 (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.5789.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-149 483.5 0.4 1.4e-149 483.3 0.4 1.0 1 lcl|NCBI__GCF_000007345.1:WP_011023690.1 MA_RS19745 ketol-acid reductoiso Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000007345.1:WP_011023690.1 MA_RS19745 ketol-acid reductoisomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 483.3 0.4 1.4e-149 1.4e-149 1 312 [. 15 327 .. 15 329 .. 0.99 Alignments for each domain: == domain 1 score: 483.3 bits; conditional E-value: 1.4e-149 TIGR00465 1 lkgkkvaiiGyGsqGeaqalnlrdsglnvivglrkeaaswkkAeedGfkvltveeaikkadlimiLlpD 69 lk+k++ai+GyGsqG+a+a+nl++sglnv+vglrk+++sw+kAe dG+kv+tveea+k+ad+imiLlpD lcl|NCBI__GCF_000007345.1:WP_011023690.1 15 LKDKTIAIMGYGSQGHAHARNLHESGLNVVVGLRKGSSSWAKAESDGLKVMTVEEAAKAADVIMILLPD 83 79******************************************************************* PP TIGR00465 70 evqkevyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliA 138 e q +vy +i+p l++g+al+f+HGfni+++qiv+pkdvdv++vAPKgpG+ vR++y eg Gvp+liA lcl|NCBI__GCF_000007345.1:WP_011023690.1 84 EKQASVYYSQIEPSLEAGNALVFAHGFNIHYNQIVPPKDVDVFMVAPKGPGHIVRRTYTEGIGVPGLIA 152 ********************************************************************* PP TIGR00465 139 veqdvtgeakeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqp 207 v+qd+tg+a++ AlayAk+iG++ragv+ettF+eE+e+DLfGEq+ LcGgl+alik+af++LveaGyqp lcl|NCBI__GCF_000007345.1:WP_011023690.1 153 VYQDATGKARDLALAYAKGIGATRAGVYETTFREETETDLFGEQVDLCGGLSALIKTAFEVLVEAGYQP 221 ********************************************************************* PP TIGR00465 208 elAyfeivhelklivdllkekGlelmrdavsntAklgalelr.eilkeelkkemqkilkeiqnGefake 275 e+Ayfe++he+klivdl++e+Gle m+++vsntA++g+++++ +i++ee +++m++ l iqnGefake lcl|NCBI__GCF_000007345.1:WP_011023690.1 222 EMAYFETCHEVKLIVDLIYEGGLERMWHSVSNTAEYGGMTVGpRIINEESREAMYEALARIQNGEFAKE 290 ********************************************************************* PP TIGR00465 276 walekeagkpafeearkkekeqeiekvGkelralvka 312 ++le ++++p +++++++eke+ +e vGke+ra +++ lcl|NCBI__GCF_000007345.1:WP_011023690.1 291 FVLEGMVNHPVLKAMERQEKEHPLEVVGKEIRANIPW 327 *********************************9887 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (314 nodes) Target sequences: 1 (335 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: 8.75 // [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