Align acetohydroxy-acid isomeroreductase subunit (EC 1.1.1.383) (characterized)
to candidate WP_048061053.1 MTH_RS06895 ketol-acid reductoisomerase
Query= metacyc::MONOMER-11920 (328 letters) >NCBI__GCF_000008645.1:WP_048061053.1 Length = 328 Score = 654 bits (1688), Expect = 0.0 Identities = 328/328 (100%), Positives = 328/328 (100%) Query: 1 MKIYYENDIDMEILADKKIAVIGYGSQGEAQARNMADSGLNVIVGLRRGGSSWKKAHDDG 60 MKIYYENDIDMEILADKKIAVIGYGSQGEAQARNMADSGLNVIVGLRRGGSSWKKAHDDG Sbjct: 1 MKIYYENDIDMEILADKKIAVIGYGSQGEAQARNMADSGLNVIVGLRRGGSSWKKAHDDG 60 Query: 61 MNVMTIEDASREADIIHILIPDEIQETVFEQSIRPYLKEGNTISFSHGYNIHYGYIKAPE 120 MNVMTIEDASREADIIHILIPDEIQETVFEQSIRPYLKEGNTISFSHGYNIHYGYIKAPE Sbjct: 61 MNVMTIEDASREADIIHILIPDEIQETVFEQSIRPYLKEGNTISFSHGYNIHYGYIKAPE 120 Query: 121 GVNVTMVAPKGPGAMVRRTYLEGFGIPGLVAVEVDATGDAMEQALAMAKACGLARAGVLE 180 GVNVTMVAPKGPGAMVRRTYLEGFGIPGLVAVEVDATGDAMEQALAMAKACGLARAGVLE Sbjct: 121 GVNVTMVAPKGPGAMVRRTYLEGFGIPGLVAVEVDATGDAMEQALAMAKACGLARAGVLE 180 Query: 181 TTFREETETDLFGEQAVLCGGVTELINTAFKTLVRAGYQPEIAYFETCHELKLIVDLIYE 240 TTFREETETDLFGEQAVLCGGVTELINTAFKTLVRAGYQPEIAYFETCHELKLIVDLIYE Sbjct: 181 TTFREETETDLFGEQAVLCGGVTELINTAFKTLVRAGYQPEIAYFETCHELKLIVDLIYE 240 Query: 241 RGFRGMWHNVSNTAEFGGLTRRGRIITEETEKEMDEILKEIQNGKFAKEWALENRAGAPM 300 RGFRGMWHNVSNTAEFGGLTRRGRIITEETEKEMDEILKEIQNGKFAKEWALENRAGAPM Sbjct: 241 RGFRGMWHNVSNTAEFGGLTRRGRIITEETEKEMDEILKEIQNGKFAKEWALENRAGAPM 300 Query: 301 LKRMRKLESELEIEEVGSKLRKLCGLEK 328 LKRMRKLESELEIEEVGSKLRKLCGLEK Sbjct: 301 LKRMRKLESELEIEEVGSKLRKLCGLEK 328 Lambda K H 0.317 0.136 0.390 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: 566 Number of extensions: 17 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: 328 Length of database: 328 Length adjustment: 28 Effective length of query: 300 Effective length of database: 300 Effective search space: 90000 Effective search space used: 90000 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_048061053.1 MTH_RS06895 (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.13483.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3e-157 508.4 0.6 3.3e-157 508.3 0.6 1.0 1 lcl|NCBI__GCF_000008645.1:WP_048061053.1 MTH_RS06895 ketol-acid reductois Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000008645.1:WP_048061053.1 MTH_RS06895 ketol-acid reductoisomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 508.3 0.6 3.3e-157 3.3e-157 1 314 [] 14 328 .] 14 328 .] 0.99 Alignments for each domain: == domain 1 score: 508.3 bits; conditional E-value: 3.3e-157 TIGR00465 1 lkgkkvaiiGyGsqGeaqalnlrdsglnvivglrkeaaswkkAeedGfkvltveeaikkadlimiLlpD 69 l++kk+a+iGyGsqGeaqa+n+ dsglnvivglr++++swkkA++dG++v+t+e+a ++ad+i+iL+pD lcl|NCBI__GCF_000008645.1:WP_048061053.1 14 LADKKIAVIGYGSQGEAQARNMADSGLNVIVGLRRGGSSWKKAHDDGMNVMTIEDASREADIIHILIPD 82 689****************************************************************** PP TIGR00465 70 evqkevyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliA 138 e+q++v+e++i+p+lkeg++++fsHG+ni++ +i++p++v+v++vAPKgpGa+vR++y eg+G+p+l+A lcl|NCBI__GCF_000008645.1:WP_048061053.1 83 EIQETVFEQSIRPYLKEGNTISFSHGYNIHYGYIKAPEGVNVTMVAPKGPGAMVRRTYLEGFGIPGLVA 151 ********************************************************************* PP TIGR00465 139 veqdvtgeakeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqp 207 ve d+tg+a+e+Ala+Aka+G aragvlettF+eE+e+DLfGEqavLcGg+++li++af+tLv+aGyqp lcl|NCBI__GCF_000008645.1:WP_048061053.1 152 VEVDATGDAMEQALAMAKACGLARAGVLETTFREETETDLFGEQAVLCGGVTELINTAFKTLVRAGYQP 220 ********************************************************************* PP TIGR00465 208 elAyfeivhelklivdllkekGlelmrdavsntAklgalelr.eilkeelkkemqkilkeiqnGefake 275 e+Ayfe++helklivdl++e+G+++m+++vsntA++g+l++r +i++ee++kem++ilkeiqnG+fake lcl|NCBI__GCF_000008645.1:WP_048061053.1 221 EIAYFETCHELKLIVDLIYERGFRGMWHNVSNTAEFGGLTRRgRIITEETEKEMDEILKEIQNGKFAKE 289 ******************************************9************************** PP TIGR00465 276 walekeagkpafeearkkekeqeiekvGkelralvkaek 314 wale++ag+p+++++rk e+e eie+vG++lr+l+ +ek lcl|NCBI__GCF_000008645.1:WP_048061053.1 290 WALENRAGAPMLKRMRKLESELEIEEVGSKLRKLCGLEK 328 **********************************99875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (314 nodes) Target sequences: 1 (328 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: 8.99 // [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