Align ketol-acid reductoisomerase (NAD+) (EC 1.1.1.382); ketol-acid reductoisomerase (NADP+) (EC 1.1.1.86) (characterized)
to candidate WP_041304997.1 BTUS_RS04775 ketol-acid reductoisomerase
Query= BRENDA::C8WR67 (344 letters) >NCBI__GCF_000092905.1:WP_041304997.1 Length = 328 Score = 479 bits (1234), Expect = e-140 Identities = 232/325 (71%), Positives = 272/325 (83%) Query: 3 KIYYDADISIQPLADKRIAVIGYGSQGHAHAQNLRDSGFDVVIGLRPGSSWAKAEADGFR 62 KIYY+ D ++ L K +AV+GYGSQGHA AQNLRDSG VV+GLRPG SW +AEADGF Sbjct: 2 KIYYEQDADLKLLDGKTVAVLGYGSQGHAQAQNLRDSGVSVVVGLRPGRSWKQAEADGFE 61 Query: 63 VMAVGEAVEESDVIMILLPDERQPAVYEREIRPYLTAGKALAFAHGFNIHFSQIQPPKDV 122 V++V EA E +D+I IL+PDERQ Y E+ P L +G+ L FAHGFNIHF QI PP DV Sbjct: 62 VLSVAEATERADLIQILIPDERQAQTYREEMLPNLRSGQMLMFAHGFNIHFGQIDPPADV 121 Query: 123 DVFMVAPKGPGHLVRRVYEAGGGVPALIAVHQDASGQAKDLALAYARGIGAGRAGILTTT 182 DV M+APKGPGHLVRR ++ G GVPAL+AVHQDASG+AK++ALA+A+GIGA RAG++ TT Sbjct: 122 DVTMIAPKGPGHLVRRTFQEGTGVPALLAVHQDASGKAKEVALAFAKGIGATRAGVIETT 181 Query: 183 FREETETDLFGEQAVLCGGLSALIKAGFETLVEAGYQPEIAYFECLHEMKLIVDLIYEGG 242 F+EETETDLFGEQAVLCGG+S LIKAGFETLVEAGY+PEIA+FECLHEMKLIVDL+YEGG Sbjct: 182 FKEETETDLFGEQAVLCGGVSNLIKAGFETLVEAGYKPEIAFFECLHEMKLIVDLMYEGG 241 Query: 243 LEYMRYSISDTAQWGDFTSGPRIINEETKKEMRRILADIQSGAFAKSWILENQANRPMFN 302 L MRYSISDTA++GD+ SGPRII EET+ EMR+ILA+IQSG FA+ WILENQANRP FN Sbjct: 242 LSRMRYSISDTAEFGDYRSGPRIITEETRAEMRKILAEIQSGQFAREWILENQANRPFFN 301 Query: 303 AINRRELEHPIEVVGRKLRSMMPFI 327 A + E HPIEVVG KLR MM +I Sbjct: 302 ARRKAEQNHPIEVVGGKLREMMTWI 326 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: 387 Number of extensions: 9 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: 328 Length adjustment: 28 Effective length of query: 316 Effective length of database: 300 Effective search space: 94800 Effective search space used: 94800 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_041304997.1 BTUS_RS04775 (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.24289.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.1e-146 471.5 0.0 6e-146 471.3 0.0 1.0 1 lcl|NCBI__GCF_000092905.1:WP_041304997.1 BTUS_RS04775 ketol-acid reductoi Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000092905.1:WP_041304997.1 BTUS_RS04775 ketol-acid reductoisomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 471.3 0.0 6e-146 6e-146 1 312 [. 14 325 .. 14 327 .. 0.99 Alignments for each domain: == domain 1 score: 471.3 bits; conditional E-value: 6e-146 TIGR00465 1 lkgkkvaiiGyGsqGeaqalnlrdsglnvivglrkeaaswkkAeedGfkvltveeaikkadlimiLlpD 69 l+gk+va++GyGsqG+aqa nlrdsg+ v+vglr++ swk+Ae dGf+vl+v+ea ++adli iL+pD lcl|NCBI__GCF_000092905.1:WP_041304997.1 14 LDGKTVAVLGYGSQGHAQAQNLRDSGVSVVVGLRPG-RSWKQAEADGFEVLSVAEATERADLIQILIPD 81 689*******************************98.9******************************* PP TIGR00465 70 evqkevyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliA 138 e q ++y++e+ p+l+ g++l+f+HGfni+f qi +p+dvdv+++APKgpG+lvR++++eg+Gvp+l+A lcl|NCBI__GCF_000092905.1:WP_041304997.1 82 ERQAQTYREEMLPNLRSGQMLMFAHGFNIHFGQIDPPADVDVTMIAPKGPGHLVRRTFQEGTGVPALLA 150 ********************************************************************* PP TIGR00465 139 veqdvtgeakeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqp 207 v+qd++g+ake+Ala+Ak+iG++ragv+ettFkeE+e+DLfGEqavLcGg+++lika+f+tLveaGy+p lcl|NCBI__GCF_000092905.1:WP_041304997.1 151 VHQDASGKAKEVALAFAKGIGATRAGVIETTFKEETETDLFGEQAVLCGGVSNLIKAGFETLVEAGYKP 219 ********************************************************************* PP TIGR00465 208 elAyfeivhelklivdllkekGlelmrdavsntAklgalelr.eilkeelkkemqkilkeiqnGefake 275 e+A+fe++he+klivdl++e+Gl+ mr ++s+tA++g+++++ +i++ee+++em+kil eiq+G+fa+e lcl|NCBI__GCF_000092905.1:WP_041304997.1 220 EIAFFECLHEMKLIVDLMYEGGLSRMRYSISDTAEFGDYRSGpRIITEETRAEMRKILAEIQSGQFARE 288 ********************************************************************* PP TIGR00465 276 walekeagkpafeearkkekeqeiekvGkelralvka 312 w+le++a++p f++ rk+e+++ ie vG +lr+++ + lcl|NCBI__GCF_000092905.1:WP_041304997.1 289 WILENQANRPFFNARRKAEQNHPIEVVGGKLREMMTW 325 **********************************987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (314 nodes) Target sequences: 1 (328 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: 10.03 // [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