Align ketol-acid reductoisomerase (NADP+) (EC 1.1.1.86) (characterized)
to candidate WP_011779353.1 MVAN_RS10650 ketol-acid reductoisomerase
Query= BRENDA::A5U713 (337 letters) >NCBI__GCF_000015305.1:WP_011779353.1 Length = 337 Score = 587 bits (1512), Expect = e-172 Identities = 286/337 (84%), Positives = 316/337 (93%) Query: 1 MALEMFYDDDADLSIIQGRKVGVIGYGSQGHAHSLSLRDSGVQVRVGLKQGSRSRPKVEE 60 MA+EMFYD DADLSIIQGRKV VIGYGSQGHAHSLSLRDSGVQV+VGLK+GS+SR KV E Sbjct: 1 MAVEMFYDADADLSIIQGRKVAVIGYGSQGHAHSLSLRDSGVQVKVGLKEGSKSREKVTE 60 Query: 61 QGLDVDTPAEVAKWADVVMVLAPDTAQAEIFAGDIEPNLKPGDALFFGHGLNVHFGLIKP 120 QGL+VDTPAEVAKWADV+M+LAPDTAQAEIF DIEPNL+ G+ALFFGHGLN+HFGLIKP Sbjct: 61 QGLEVDTPAEVAKWADVIMLLAPDTAQAEIFTNDIEPNLEDGNALFFGHGLNIHFGLIKP 120 Query: 121 PADVAVAMVAPKGPGHLVRRQFVDGKGVPCLVAVEQDPRGDGLALALSYAKAIGGTRAGV 180 PA+V + MVAPKGPGHLVRRQFVDGKGVPCL+A++QDP+G+G ALALSYA AIGG RAGV Sbjct: 121 PANVTIGMVAPKGPGHLVRRQFVDGKGVPCLIAIDQDPKGEGQALALSYAAAIGGARAGV 180 Query: 181 IKTTFKDETETDLFGEQTVLCGGTEELVKAGFEVMVEAGYPAELAYFEVLHELKLIVDLM 240 IKTTFK+ETETDLFGEQ VLCGGTEELVK GFEVMVEAGY E+AYFEVLHELKLIVDLM Sbjct: 181 IKTTFKEETETDLFGEQAVLCGGTEELVKTGFEVMVEAGYAPEMAYFEVLHELKLIVDLM 240 Query: 241 YEGGLARMYYSVSDTAEFGGYLSGPRVIDAGTKERMRDILREIQDGSFVHKLVADVEGGN 300 YEGG+ARM YSVSDTAEFGGYLSGPRVIDA TK+RM+DIL++IQDG+FV +LVA+VEGGN Sbjct: 241 YEGGIARMNYSVSDTAEFGGYLSGPRVIDADTKKRMQDILKDIQDGTFVKRLVANVEGGN 300 Query: 301 KQLEELRRQNAEHPIEVVGKKLRDLMSWVDRPITETA 337 K+LE LR++NAEHPIEV GKKLRDLMSWVDRPITETA Sbjct: 301 KELEALRKKNAEHPIEVTGKKLRDLMSWVDRPITETA 337 Lambda K H 0.318 0.138 0.401 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: 505 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: 337 Length of database: 337 Length adjustment: 28 Effective length of query: 309 Effective length of database: 309 Effective search space: 95481 Effective search space used: 95481 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_011779353.1 MVAN_RS10650 (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.31958.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.2e-126 406.5 0.3 3.6e-126 406.3 0.3 1.0 1 lcl|NCBI__GCF_000015305.1:WP_011779353.1 MVAN_RS10650 ketol-acid reductoi Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000015305.1:WP_011779353.1 MVAN_RS10650 ketol-acid reductoisomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 406.3 0.3 3.6e-126 3.6e-126 1 312 [. 16 328 .. 16 330 .. 0.99 Alignments for each domain: == domain 1 score: 406.3 bits; conditional E-value: 3.6e-126 TIGR00465 1 lkgkkvaiiGyGsqGeaqalnlrdsglnvivglrkeaaswkkAeedGfkvltveeaikkadlimiLlpD 69 ++g+kva+iGyGsqG+a++l lrdsg++v vgl+++++s +k +e+G++v t +e++k ad+im L pD lcl|NCBI__GCF_000015305.1:WP_011779353.1 16 IQGRKVAVIGYGSQGHAHSLSLRDSGVQVKVGLKEGSKSREKVTEQGLEVDTPAEVAKWADVIMLLAPD 84 6899***************************************************************** PP TIGR00465 70 evqkevyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliA 138 ++q e ++++i+p+l++g+al f HG ni+f i++p++v++ +vAPKgpG+lvR+++ g+Gvp liA lcl|NCBI__GCF_000015305.1:WP_011779353.1 85 TAQAEIFTNDIEPNLEDGNALFFGHGLNIHFGLIKPPANVTIGMVAPKGPGHLVRRQFVDGKGVPCLIA 153 ********************************************************************* PP TIGR00465 139 veqdvtgeakeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqp 207 + qd++ge+++ Al+yA+aiGgaragv++ttFkeE+e+DLfGEqavLcGg e+l+k++f+++veaGy+p lcl|NCBI__GCF_000015305.1:WP_011779353.1 154 IDQDPKGEGQALALSYAAAIGGARAGVIKTTFKEETETDLFGEQAVLCGGTEELVKTGFEVMVEAGYAP 222 ********************************************************************* PP TIGR00465 208 elAyfeivhelklivdllkekGlelmrdavsntAklgalelr.eilkeelkkemqkilkeiqnGefake 275 e+Ayfe++helklivdl++e+G++ m +vs+tA++g++ ++ +++++ +kk+mq+ilk+iq+G+f k lcl|NCBI__GCF_000015305.1:WP_011779353.1 223 EMAYFEVLHELKLIVDLMYEGGIARMNYSVSDTAEFGGYLSGpRVIDADTKKRMQDILKDIQDGTFVKR 291 *****************************************99*************************9 PP TIGR00465 276 walekeagkpafeearkkekeqeiekvGkelralvka 312 + + e g+ ++e+ rkk+ e+ ie +Gk+lr+l+++ lcl|NCBI__GCF_000015305.1:WP_011779353.1 292 LVANVEGGNKELEALRKKNAEHPIEVTGKKLRDLMSW 328 99999*****************************987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (314 nodes) Target sequences: 1 (337 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: 8.85 // [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