Align acetohydroxyacid isomeroreductase (EC 1.1.1.86) (characterized)
to candidate WP_011801118.1 PNAP_RS08590 ketol-acid reductoisomerase
Query= metacyc::MONOMER-18814 (338 letters) >NCBI__GCF_000015505.1:WP_011801118.1 Length = 338 Score = 583 bits (1502), Expect = e-171 Identities = 290/338 (85%), Positives = 306/338 (90%) Query: 1 MKVFYDKDADLSLIKGKNVTIIGYGSQGHAHALNLKDSGVNVTVGLRKSGASWNKAANAG 60 MKVFYDKD DLSLIKGK V IIGYGSQGHAHA NL DSGV V VGLRK GASW K AG Sbjct: 1 MKVFYDKDCDLSLIKGKTVAIIGYGSQGHAHAQNLNDSGVKVVVGLRKGGASWPKVEKAG 60 Query: 61 LQVKEVAEAVKGADVVMILLPDEQIADVYKNEVHDNIKEGAALAFAHGFNVHYGAVIPRA 120 LQV EVA+AVK ADVVMILLPDEQI VYKN+V NIK+GA+L FAHGFNVHYGAVIPR Sbjct: 61 LQVAEVADAVKAADVVMILLPDEQIGAVYKNDVAPNIKQGASLVFAHGFNVHYGAVIPRD 120 Query: 121 DLDVIMIAPKAPGHTVRATYTQGGGVPHLIAVHQNKSGAARDIALSYATANGGGRAGIIE 180 DLDV M+APKAPGHTVR TYTQGGGVPHL+AVHQ+KSG ARD+ALSYA ANGGG+AGIIE Sbjct: 121 DLDVWMVAPKAPGHTVRNTYTQGGGVPHLVAVHQDKSGKARDLALSYAMANGGGKAGIIE 180 Query: 181 TNFREETETDLFGEQAVLCGGTVELIKAGFETLVEAGYAPEMAYFECLHELKLIVDLIYE 240 TNFREETETDLFGEQAVLCGG VELIKAGFETLVEAGYAPEMAYFECLHELKLIVDLIYE Sbjct: 181 TNFREETETDLFGEQAVLCGGAVELIKAGFETLVEAGYAPEMAYFECLHELKLIVDLIYE 240 Query: 241 GGIANMNYSISNNAEYGEYVTGPRVVTEETKKAMKQCLTDIQTGEYAKSFLLENKAGAPT 300 GGIANMNYSISNNAEYGEYVTGPR+VTE+TK AM+ L DIQTGEYAKSFLLEN AGAPT Sbjct: 241 GGIANMNYSISNNAEYGEYVTGPRIVTEDTKNAMRAVLKDIQTGEYAKSFLLENIAGAPT 300 Query: 301 LISRRRLTAEHQIEEVGAKLRAMMPWIAKNKMVDQSKN 338 LISRRRL AEHQIE+VG KLRAMMPWIAKNK+VDQ++N Sbjct: 301 LISRRRLNAEHQIEQVGGKLRAMMPWIAKNKLVDQTRN 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: 503 Number of extensions: 10 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_011801118.1 PNAP_RS08590 (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.12653.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-135 437.4 1.2 1.5e-135 437.2 1.2 1.0 1 lcl|NCBI__GCF_000015505.1:WP_011801118.1 PNAP_RS08590 ketol-acid reductoi Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000015505.1:WP_011801118.1 PNAP_RS08590 ketol-acid reductoisomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 437.2 1.2 1.5e-135 1.5e-135 1 312 [. 14 326 .. 14 328 .. 0.99 Alignments for each domain: == domain 1 score: 437.2 bits; conditional E-value: 1.5e-135 TIGR00465 1 lkgkkvaiiGyGsqGeaqalnlrdsglnvivglrkeaaswkkAeedGfkvltveeaikkadlimiLlpD 69 +kgk+vaiiGyGsqG+a+a nl dsg++v+vglrk++asw k e+ G++v +v++a+k+ad++miLlpD lcl|NCBI__GCF_000015505.1:WP_011801118.1 14 IKGKTVAIIGYGSQGHAHAQNLNDSGVKVVVGLRKGGASWPKVEKAGLQVAEVADAVKAADVVMILLPD 82 689****************************************************************** PP TIGR00465 70 evqkevyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliA 138 e+ +vy+++++p++k+g++l+f+HGfn+++ + +++d+dv +vAPK+pG++vR++y +g Gvp+l+A lcl|NCBI__GCF_000015505.1:WP_011801118.1 83 EQIGAVYKNDVAPNIKQGASLVFAHGFNVHYGAVIPRDDLDVWMVAPKAPGHTVRNTYTQGGGVPHLVA 151 ********************************************************************* PP TIGR00465 139 veqdvtgeakeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqp 207 v+qd +g+a++ Al+yA a Gg++ag++et F+eE+e+DLfGEqavLcGg +lika+f+tLveaGy+p lcl|NCBI__GCF_000015505.1:WP_011801118.1 152 VHQDKSGKARDLALSYAMANGGGKAGIIETNFREETETDLFGEQAVLCGGAVELIKAGFETLVEAGYAP 220 ********************************************************************* PP TIGR00465 208 elAyfeivhelklivdllkekGlelmrdavsntAklgalelr.eilkeelkkemqkilkeiqnGefake 275 e+Ayfe++helklivdl++e+G+++m ++sn A++g++ ++ +i++e +k++m+ +lk+iq+Ge+ak lcl|NCBI__GCF_000015505.1:WP_011801118.1 221 EMAYFECLHELKLIVDLIYEGGIANMNYSISNNAEYGEYVTGpRIVTEDTKNAMRAVLKDIQTGEYAKS 289 ******************************************9************************** PP TIGR00465 276 walekeagkpafeearkkekeqeiekvGkelralvka 312 ++le+ ag+p++ + r+ + e++ie+vG +lra++++ lcl|NCBI__GCF_000015505.1:WP_011801118.1 290 FLLENIAGAPTLISRRRLNAEHQIEQVGGKLRAMMPW 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 12.19 // [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