Align Ketol-acid reductoisomerase (NAD(P)(+)); KARI; Acetohydroxy-acid isomeroreductase; AHIR; Alpha-keto-beta-hydroxylacyl reductoisomerase; Ketol-acid reductoisomerase type 1; Ketol-acid reductoisomerase type I; EC 1.1.1.383 (characterized)
to candidate WP_013537217.1 THEAM_RS02365 ketol-acid reductoisomerase
Query= SwissProt::B4U6I9 (333 letters) >NCBI__GCF_000185805.1:WP_013537217.1 Length = 335 Score = 487 bits (1253), Expect = e-142 Identities = 247/336 (73%), Positives = 280/336 (83%), Gaps = 4/336 (1%) Query: 1 MAKIYYDEDASLGILAMKTVAIVGYGSQGHAHALNLRDSGIRVIVALDDKSPHRKTAMED 60 MAKIYYDEDASL L KTVAI+GYGSQGHAHALNLRDSG+ V++ L K A +D Sbjct: 1 MAKIYYDEDASLEYLNGKTVAILGYGSQGHAHALNLRDSGVNVVIGLRPGKSAEK-AKKD 59 Query: 61 GFSVYTTSRATQEADVIMILTPDTVQPAVYKECIEPNLTPGKAIAFAHGFNIHFGQIVPP 120 GF V T A + ADVIM L PD VQ VY+E ++PNL PGKA+AFAHGFNIHF QIVPP Sbjct: 60 GFEVLTPEEAAKRADVIMFLLPDPVQKKVYEEAVKPNLEPGKALAFAHGFNIHFNQIVPP 119 Query: 121 KDIDVFMVAPKGPGHLVRWMYEEGKGVPALISIHQDATGSCRDIALAYAKGIGATRAGVI 180 +D+DVFMVAPKGPGHLVRW Y EG GVPAL+++HQDATG ++IALAYAKGIGATRAGVI Sbjct: 120 EDVDVFMVAPKGPGHLVRWTYLEGAGVPALVAVHQDATGKAKEIALAYAKGIGATRAGVI 179 Query: 181 ETTFREETETDLFGEQAVLCGGATALIKAGFETLVEAGYQPEMAYFECLHELKLIVDLIY 240 ETTF+EETETDLFGEQAVLCGGA+AL+KAGFETLVEAGYQPE+AYFECLHELKLIVDL+Y Sbjct: 180 ETTFKEETETDLFGEQAVLCGGASALVKAGFETLVEAGYQPEVAYFECLHELKLIVDLMY 239 Query: 241 QHGIAGMRYSISDTAKYGDVTRGDRVY-EAVKPLMKQMLKEIQDGEFAREWILENQANRP 299 QHG+AGMRYSISDTA+YGD TRG RV E VK MK++LKEIQ GEFARE++LE QAN P Sbjct: 240 QHGLAGMRYSISDTAEYGDYTRGPRVIDEHVKENMKKILKEIQTGEFAREFVLEAQANYP 299 Query: 300 VYNALLNKDKEHLVEKVGKELRQMMPWL--SGKELK 333 V NA + EH +EKVGK+LR+MMP+L KELK Sbjct: 300 VLNAYRKIEAEHPIEKVGKKLREMMPFLKQQKKELK 335 Lambda K H 0.319 0.136 0.402 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: 12 Number of successful extensions: 3 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: 333 Length of database: 335 Length adjustment: 28 Effective length of query: 305 Effective length of database: 307 Effective search space: 93635 Effective search space used: 93635 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_013537217.1 THEAM_RS02365 (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.24858.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.4e-151 487.9 0.1 6.3e-151 487.7 0.1 1.0 1 lcl|NCBI__GCF_000185805.1:WP_013537217.1 THEAM_RS02365 ketol-acid reducto Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000185805.1:WP_013537217.1 THEAM_RS02365 ketol-acid reductoisomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 487.7 0.1 6.3e-151 6.3e-151 1 313 [. 15 327 .. 15 328 .. 0.99 Alignments for each domain: == domain 1 score: 487.7 bits; conditional E-value: 6.3e-151 TIGR00465 1 lkgkkvaiiGyGsqGeaqalnlrdsglnvivglrkeaaswkkAeedGfkvltveeaikkadlimiLlpD 69 l+gk+vai+GyGsqG+a+alnlrdsg+nv++glr++ +s +kA++dGf+vlt eea+k+ad+im LlpD lcl|NCBI__GCF_000185805.1:WP_013537217.1 15 LNGKTVAILGYGSQGHAHALNLRDSGVNVVIGLRPG-KSAEKAKKDGFEVLTPEEAAKRADVIMFLLPD 82 689*******************************98.9******************************* PP TIGR00465 70 evqkevyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliA 138 vqk+vye+ +kp+l+ gkal f+HGfni+f+qiv+p+dvdv++vAPKgpG+lvR +y eg+Gvp+l+A lcl|NCBI__GCF_000185805.1:WP_013537217.1 83 PVQKKVYEEAVKPNLEPGKALAFAHGFNIHFNQIVPPEDVDVFMVAPKGPGHLVRWTYLEGAGVPALVA 151 ********************************************************************* PP TIGR00465 139 veqdvtgeakeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqp 207 v+qd+tg+akeiAlayAk+iG++ragv+ettFkeE+e+DLfGEqavLcGg +al+ka+f+tLveaGyqp lcl|NCBI__GCF_000185805.1:WP_013537217.1 152 VHQDATGKAKEIALAYAKGIGATRAGVIETTFKEETETDLFGEQAVLCGGASALVKAGFETLVEAGYQP 220 ********************************************************************* PP TIGR00465 208 elAyfeivhelklivdllkekGlelmrdavsntAklgalelr.eilkeelkkemqkilkeiqnGefake 275 e+Ayfe++helklivdl++++Gl++mr ++s+tA++g+++++ ++++e++k++m+kilkeiq+Gefa+e lcl|NCBI__GCF_000185805.1:WP_013537217.1 221 EVAYFECLHELKLIVDLMYQHGLAGMRYSISDTAEYGDYTRGpRVIDEHVKENMKKILKEIQTGEFARE 289 ********************************************************************* PP TIGR00465 276 walekeagkpafeearkkekeqeiekvGkelralvkae 313 ++le +a++p +++ rk e e+ iekvGk+lr+++++ lcl|NCBI__GCF_000185805.1:WP_013537217.1 290 FVLEAQANYPVLNAYRKIEAEHPIEKVGKKLREMMPFL 327 ***********************************975 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 7.38 // [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