Align ketol-acid reductoisomerase (NADP+) (EC 1.1.1.86) (characterized)
to candidate WP_025274011.1 HALAL_RS0110745 ketol-acid reductoisomerase
Query= BRENDA::A5U713 (337 letters) >NCBI__GCF_000527155.1:WP_025274011.1 Length = 333 Score = 434 bits (1117), Expect = e-126 Identities = 209/333 (62%), Positives = 260/333 (78%), Gaps = 1/333 (0%) Query: 1 MALEMFYDDDADLSIIQGRKVGVIGYGSQGHAHSLSLRDSGVQVRVGLKQGSRSRPKVEE 60 MA +++YD D+DLS+IQG+KV V+GYGSQGHAHSLSLRDSGV+V +GL+ GS+SR K EE Sbjct: 1 MAADVYYDHDSDLSLIQGKKVAVLGYGSQGHAHSLSLRDSGVEVAIGLQDGSKSRAKAEE 60 Query: 61 QGLDVDTPAEVAKWADVVMVLAPDTAQAEIFAGDIEPNLKPGDALFFGHGLNVHFGLIKP 120 GLDV TP E WADV+M+L PDT QA+++ +I PNL+ G L FGHG N+ + LI+ Sbjct: 61 AGLDVKTPGEATAWADVIMILVPDTVQADLYRDEIAPNLRSGQTLMFGHGFNIRYNLIQA 120 Query: 121 PADVAVAMVAPKGPGHLVRRQFVDGKGVPCLVAVEQDPRGDGLALALSYAKAIGGTRAGV 180 P DV VAMVAPKGPGHLVRRQ+VDGKGVP L+AVEQDP G+ LALSYA+ IG TRAGV Sbjct: 121 PGDVNVAMVAPKGPGHLVRRQYVDGKGVPSLIAVEQDPSGNTQELALSYAQGIGATRAGV 180 Query: 181 IKTTFKDETETDLFGEQTVLCGGTEELVKAGFEVMVEAGYPAELAYFEVLHELKLIVDLM 240 +KTTFK+ETETDLFGEQ VLCGG EL++AGFE +VEAGY E AYFE LHE KLIVDL+ Sbjct: 181 LKTTFKEETETDLFGEQVVLCGGISELIRAGFETLVEAGYAPEAAYFECLHETKLIVDLI 240 Query: 241 YEGGLARMYYSVSDTAEFGGYLSGPRVIDAGTKERMRDILREIQDGSFVHKLVADVEGGN 300 YEGGL+ M+YSVSDTAE+GG G RVI++ TK+ M+ IL E+QDG+F + V + + Sbjct: 241 YEGGLSNMWYSVSDTAEYGGLTRGSRVINSETKKEMKRILTEVQDGTFAKEWVQESK-ER 299 Query: 301 KQLEELRRQNAEHPIEVVGKKLRDLMSWVDRPI 333 L+ L+ + EH IE +G ++RDLM WV + + Sbjct: 300 SNLKRLQDKQEEHQIEKIGSEIRDLMPWVKKKL 332 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: 424 Number of extensions: 16 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: 337 Length of database: 333 Length adjustment: 28 Effective length of query: 309 Effective length of database: 305 Effective search space: 94245 Effective search space used: 94245 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_025274011.1 HALAL_RS0110745 (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.17816.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.1e-135 436.1 0.1 3.7e-135 435.9 0.1 1.0 1 lcl|NCBI__GCF_000527155.1:WP_025274011.1 HALAL_RS0110745 ketol-acid reduc Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000527155.1:WP_025274011.1 HALAL_RS0110745 ketol-acid reductoisomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 435.9 0.1 3.7e-135 3.7e-135 1 314 [] 16 329 .. 16 329 .. 0.99 Alignments for each domain: == domain 1 score: 435.9 bits; conditional E-value: 3.7e-135 TIGR00465 1 lkgkkvaiiGyGsqGeaqalnlrdsglnvivglrkeaaswkkAeedGfkvltveeaikkadlimiLlpD 69 ++gkkva++GyGsqG+a++l lrdsg++v +gl+ +++s +kAee G++v+t ea + ad+imiL+pD lcl|NCBI__GCF_000527155.1:WP_025274011.1 16 IQGKKVAVLGYGSQGHAHSLSLRDSGVEVAIGLQDGSKSRAKAEEAGLDVKTPGEATAWADVIMILVPD 84 689****************************************************************** PP TIGR00465 70 evqkevyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliA 138 +vq + y+ ei+p+l+ g++l+f HGfni ++ i++p dv+v++vAPKgpG+lvR++y g+GvpsliA lcl|NCBI__GCF_000527155.1:WP_025274011.1 85 TVQADLYRDEIAPNLRSGQTLMFGHGFNIRYNLIQAPGDVNVAMVAPKGPGHLVRRQYVDGKGVPSLIA 153 ********************************************************************* PP TIGR00465 139 veqdvtgeakeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqp 207 veqd++g+++e Al+yA++iG++ragvl+ttFkeE+e+DLfGEq+vLcGg+++li+a+f+tLveaGy+p lcl|NCBI__GCF_000527155.1:WP_025274011.1 154 VEQDPSGNTQELALSYAQGIGATRAGVLKTTFKEETETDLFGEQVVLCGGISELIRAGFETLVEAGYAP 222 ********************************************************************* PP TIGR00465 208 elAyfeivhelklivdllkekGlelmrdavsntAklgalelr.eilkeelkkemqkilkeiqnGefake 275 e Ayfe++he klivdl++e+Gl++m+ +vs+tA++g+l+++ ++++ e+kkem+ il e+q+G+fake lcl|NCBI__GCF_000527155.1:WP_025274011.1 223 EAAYFECLHETKLIVDLIYEGGLSNMWYSVSDTAEYGGLTRGsRVINSETKKEMKRILTEVQDGTFAKE 291 ******************************************9************************** PP TIGR00465 276 walekeagkpafeearkkekeqeiekvGkelralvkaek 314 w+ e+ + ++++++ + k++e++iek+G+e+r+l+++ k lcl|NCBI__GCF_000527155.1:WP_025274011.1 292 WVQES-KERSNLKRLQDKQEEHQIEKIGSEIRDLMPWVK 329 ***99.899**************************9975 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (314 nodes) Target sequences: 1 (333 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: 7.12 // [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