Align acetohydroxyacid isomeroreductase (EC 1.1.1.86) (characterized)
to candidate WP_013518620.1 ALIDE2_RS15520 ketol-acid reductoisomerase
Query= metacyc::MONOMER-18814 (338 letters) >NCBI__GCF_000204645.1:WP_013518620.1 Length = 338 Score = 544 bits (1401), Expect = e-159 Identities = 267/338 (78%), Positives = 294/338 (86%) Query: 1 MKVFYDKDADLSLIKGKNVTIIGYGSQGHAHALNLKDSGVNVTVGLRKSGASWNKAANAG 60 MKVFYDKD DLSLIKGK V IIGYGSQGHAHA NL DSGV V VGLRK GASW+K AG Sbjct: 1 MKVFYDKDCDLSLIKGKTVAIIGYGSQGHAHAQNLNDSGVKVVVGLRKGGASWDKVGKAG 60 Query: 61 LQVKEVAEAVKGADVVMILLPDEQIADVYKNEVHDNIKEGAALAFAHGFNVHYGAVIPRA 120 L VKEV +AVK ADVVMILLPDEQIA+VYKN V NIK+GA+LAFAHGFNVHY V+PRA Sbjct: 61 LTVKEVNDAVKEADVVMILLPDEQIAEVYKNNVEPNIKQGASLAFAHGFNVHYNQVVPRA 120 Query: 121 DLDVIMIAPKAPGHTVRATYTQGGGVPHLIAVHQNKSGAARDIALSYATANGGGRAGIIE 180 DLDV M+APKAPGHTVR TYTQGGGVPHL+AVHQ+KSG AR++ALSYA ANGGG+AGIIE Sbjct: 121 DLDVWMVAPKAPGHTVRNTYTQGGGVPHLVAVHQDKSGRARELALSYAMANGGGKAGIIE 180 Query: 181 TNFREETETDLFGEQAVLCGGTVELIKAGFETLVEAGYAPEMAYFECLHELKLIVDLIYE 240 TNFREETETDLFGEQAVLCGG VELIK G+ETLVEAGYAPEMAYFECLHELKLIVDLIYE Sbjct: 181 TNFREETETDLFGEQAVLCGGAVELIKMGYETLVEAGYAPEMAYFECLHELKLIVDLIYE 240 Query: 241 GGIANMNYSISNNAEYGEYVTGPRVVTEETKKAMKQCLTDIQTGEYAKSFLLENKAGAPT 300 GGIANMNYSISNNAEYGEYVTGP V+ E+++ AM+ L IQ GEYAK F+ E + P+ Sbjct: 241 GGIANMNYSISNNAEYGEYVTGPEVINEQSRAAMRNALKRIQDGEYAKMFIQEGRLNYPS 300 Query: 301 LISRRRLTAEHQIEEVGAKLRAMMPWIAKNKMVDQSKN 338 + +RRR A H IE+VGA+LRAMMPWIAKNK+VDQS+N Sbjct: 301 MTARRRNLAAHSIEQVGAQLRAMMPWIAKNKLVDQSRN 338 Lambda K H 0.316 0.133 0.379 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: 483 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: 338 Length of database: 338 Length adjustment: 28 Effective length of query: 310 Effective length of database: 310 Effective search space: 96100 Effective search space used: 96100 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 (21.6 bits) S2: 49 (23.5 bits)
Align candidate WP_013518620.1 ALIDE2_RS15520 (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.12636.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.6e-134 431.2 2.3 1.1e-133 431.0 2.3 1.0 1 lcl|NCBI__GCF_000204645.1:WP_013518620.1 ALIDE2_RS15520 ketol-acid reduct Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000204645.1:WP_013518620.1 ALIDE2_RS15520 ketol-acid reductoisomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 431.0 2.3 1.1e-133 1.1e-133 1 312 [. 14 326 .. 14 328 .. 0.99 Alignments for each domain: == domain 1 score: 431.0 bits; conditional E-value: 1.1e-133 TIGR00465 1 lkgkkvaiiGyGsqGeaqalnlrdsglnvivglrkeaaswkkAeedGfkvltveeaikkadlimiLlpD 69 +kgk+vaiiGyGsqG+a+a nl dsg++v+vglrk++asw+k + G+ v++v++a+k+ad++miLlpD lcl|NCBI__GCF_000204645.1:WP_013518620.1 14 IKGKTVAIIGYGSQGHAHAQNLNDSGVKVVVGLRKGGASWDKVGKAGLTVKEVNDAVKEADVVMILLPD 82 689****************************************************************** PP TIGR00465 70 evqkevyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliA 138 e+ evy+++++p++k+g++l f+HGfn++++q+v+++d+dv +vAPK+pG++vR++y +g Gvp+l+A lcl|NCBI__GCF_000204645.1:WP_013518620.1 83 EQIAEVYKNNVEPNIKQGASLAFAHGFNVHYNQVVPRADLDVWMVAPKAPGHTVRNTYTQGGGVPHLVA 151 ********************************************************************* PP TIGR00465 139 veqdvtgeakeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqp 207 v+qd +g a+e Al+yA a Gg++ag++et F+eE+e+DLfGEqavLcGg +lik++++tLveaGy+p lcl|NCBI__GCF_000204645.1:WP_013518620.1 152 VHQDKSGRARELALSYAMANGGGKAGIIETNFREETETDLFGEQAVLCGGAVELIKMGYETLVEAGYAP 220 ********************************************************************* PP TIGR00465 208 elAyfeivhelklivdllkekGlelmrdavsntAklgalelr.eilkeelkkemqkilkeiqnGefake 275 e+Ayfe++helklivdl++e+G+++m ++sn A++g++ ++ e+++e+ +++m++ lk iq+Ge+ak lcl|NCBI__GCF_000204645.1:WP_013518620.1 221 EMAYFECLHELKLIVDLIYEGGIANMNYSISNNAEYGEYVTGpEVINEQSRAAMRNALKRIQDGEYAKM 289 ******************************************9************************** PP TIGR00465 276 walekeagkpafeearkkekeqeiekvGkelralvka 312 ++ e + ++p++++ r+ ++ie+vG +lra++++ lcl|NCBI__GCF_000204645.1:WP_013518620.1 290 FIQEGRLNYPSMTARRRNLAAHSIEQVGAQLRAMMPW 326 ***********************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (314 nodes) Target sequences: 1 (338 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: 7.57 // [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