Align acetohydroxy-acid synthase large subunit (EC 2.2.1.6) (characterized)
to candidate WP_011973398.1 MAEO_RS03395 acetolactate synthase, large subunit, biosynthetic type
Query= metacyc::MONOMER-11900 (599 letters) >NCBI__GCF_000017185.1:WP_011973398.1 Length = 599 Score = 1199 bits (3102), Expect = 0.0 Identities = 597/599 (99%), Positives = 598/599 (99%) Query: 1 MNGAEAMIKALEAEKVEILFGYPGGALLPFYDALHHSDLIHLLTRHEQAAAHAADGYARA 60 MNGAEAMIKALEAEKVEILFGYPGGALLPFYDALHHSDLIHLLTRHEQAAAHAADGYARA Sbjct: 1 MNGAEAMIKALEAEKVEILFGYPGGALLPFYDALHHSDLIHLLTRHEQAAAHAADGYARA 60 Query: 61 SGKVGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALGLFMP 120 SGKVGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALGLFMP Sbjct: 61 SGKVGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALGLFMP 120 Query: 121 IVKHNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQELELDIDKHPIPSKVKLI 180 IVKHNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQELELDIDKHPIPSKVKLI Sbjct: 121 IVKHNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQELELDIDKHPIPSKVKLI 180 Query: 181 GYNPTTIGHPRQIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNIPVCTTLMG 240 GYNPTTIGHPRQIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNIPVCTTLMG Sbjct: 181 GYNPTTIGHPRQIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNIPVCTTLMG 240 Query: 241 KGCISENHPLALGMVGMHGTKPANYCLSESDVLISIGCRFSDRITGDIKSFATNAKIIHI 300 KGCISENHPLALGMVGMHGTKPANYCLSESDVLISIGCRFSDRITGDIKSFATNAKIIHI Sbjct: 241 KGCISENHPLALGMVGMHGTKPANYCLSESDVLISIGCRFSDRITGDIKSFATNAKIIHI 300 Query: 301 DIDPAEIGKNVNVDVPIVGDAKLILKEVIKQLDYIINKDSKENNDKENISQWIENVNSLK 360 DIDPAEIGKNV VDVPIVGDAKLILKE+IKQLDYIINKDSKENNDKENISQWIENVNSLK Sbjct: 301 DIDPAEIGKNVAVDVPIVGDAKLILKELIKQLDYIINKDSKENNDKENISQWIENVNSLK 360 Query: 361 KSSIPVMDYDDIPIKPQKIVKELMAVIDDLNINKNTIITTDVGQNQMWMAHYFKTQTPRS 420 KSSIPVMDYDDIPIKPQKIVKELMAVIDDLNINKNTIITTDVGQNQMWMAHYFKTQTPRS Sbjct: 361 KSSIPVMDYDDIPIKPQKIVKELMAVIDDLNINKNTIITTDVGQNQMWMAHYFKTQTPRS 420 Query: 421 FLSSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQELGTIAEYNIPVVICIF 480 FLSSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQELGTIAEYNIPVVICIF Sbjct: 421 FLSSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQELGTIAEYNIPVVICIF 480 Query: 481 DNRTLGMVYQWQNLFYGKRQCSVNFGGAPDFIKLAESYGIKARRIESPNEINEALKEAIN 540 DNRTLGMVYQWQNLFYGKRQCSVNFGGAPDFIKLAESYGIKARRIESPNEINEALKEAIN Sbjct: 481 DNRTLGMVYQWQNLFYGKRQCSVNFGGAPDFIKLAESYGIKARRIESPNEINEALKEAIN 540 Query: 541 CDEPYLLDFAIDPSSALSMVPPGAKLTNIIDAVQEHPNEKIVCFDEIKRRYMENKRNRK 599 CDEPYLLDFAIDPSSALSMVPPGAKLTNIIDAVQEHPNEKIVCFDEIKRRYMENKRNRK Sbjct: 541 CDEPYLLDFAIDPSSALSMVPPGAKLTNIIDAVQEHPNEKIVCFDEIKRRYMENKRNRK 599 Lambda K H 0.319 0.137 0.405 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: 1315 Number of extensions: 34 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: 599 Length of database: 599 Length adjustment: 37 Effective length of query: 562 Effective length of database: 562 Effective search space: 315844 Effective search space used: 315844 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 53 (25.0 bits)
Align candidate WP_011973398.1 MAEO_RS03395 (acetolactate synthase, large subunit, biosynthetic type)
to HMM TIGR00118 (ilvB: acetolactate synthase, large subunit, biosynthetic type (EC 2.2.1.6))
# 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/TIGR00118.hmm # target sequence database: /tmp/gapView.24374.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00118 [M=557] Accession: TIGR00118 Description: acolac_lg: acetolactate synthase, large subunit, biosynthetic type 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-264 865.0 0.1 1.3e-264 864.8 0.1 1.0 1 lcl|NCBI__GCF_000017185.1:WP_011973398.1 MAEO_RS03395 acetolactate syntha Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000017185.1:WP_011973398.1 MAEO_RS03395 acetolactate synthase, large subunit, biosynthetic type # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 864.8 0.1 1.3e-264 1.3e-264 1 555 [. 1 571 [. 1 573 [. 0.97 Alignments for each domain: == domain 1 score: 864.8 bits; conditional E-value: 1.3e-264 TIGR00118 1 lkgaeilveslkkegvetvfGyPGGavlpiydalydselehilvrheqaaahaadGyarasGkvGvvla 69 ++gae+++++l++e+ve++fGyPGGa+lp+ydal++s+l h+l+rheqaaahaadGyarasGkvGv+++ lcl|NCBI__GCF_000017185.1:WP_011973398.1 1 MNGAEAMIKALEAEKVEILFGYPGGALLPFYDALHHSDLIHLLTRHEQAAAHAADGYARASGKVGVCIG 69 78******************************************************************* PP TIGR00118 70 tsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeil 138 tsGPGatnlvtg+ata+ ds+P+v+ltGqv+t+liG+dafqeid lG+++p++kh+f+++k+ ++pei+ lcl|NCBI__GCF_000017185.1:WP_011973398.1 70 TSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALGLFMPIVKHNFQIQKTCQIPEIF 138 ********************************************************************* PP TIGR00118 139 keafeiastGrPGPvlvdlPkdvteaeieleve...ekvelpgykptvkghklqikkaleliekakkPv 204 + afeia+tGrPGPv++dlPkdv+e e++++++ +kv+l gy+pt+ gh++qikka++li++ak+P+ lcl|NCBI__GCF_000017185.1:WP_011973398.1 139 RSAFEIAQTGRPGPVHIDLPKDVQELELDIDKHpipSKVKLIGYNPTTIGHPRQIKKAIKLIASAKRPI 207 ***************************998877777********************************* PP TIGR00118 205 llvGgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliav 273 +l+GgGv+ ++a+eel +l+e l+ipv+ttl+G+G++ e+hplalgm+GmhGtk an+++se+d+li++ lcl|NCBI__GCF_000017185.1:WP_011973398.1 208 ILAGGGVLLSGANEELLKLVELLNIPVCTTLMGKGCISENHPLALGMVGMHGTKPANYCLSESDVLISI 276 ********************************************************************* PP TIGR00118 274 GarfddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkee.........e 333 G+rf+dr+tg++++fa++akiihididPaeigknv+vd+pivGdak +l+el+k+l + + lcl|NCBI__GCF_000017185.1:WP_011973398.1 277 GCRFSDRITGDIKSFATNAKIIHIDIDPAEIGKNVAVDVPIVGDAKLILKELIKQLDYIinkdskennD 345 ******************************************************987766667776642 PP TIGR00118 334 kkeke.WlekieewkkeyilkldeeeesikPqkvikelskllkd.....eaivttdvGqhqmwaaqfyk 396 k+++ W+e+++++kk++i+ +d+++ +ikPqk++kel+ +++d ++i+ttdvGq+qmw+a+++k lcl|NCBI__GCF_000017185.1:WP_011973398.1 346 KENISqWIENVNSLKKSSIPVMDYDDIPIKPQKIVKELMAVIDDlninkNTIITTDVGQNQMWMAHYFK 414 233335*************************************999999******************** PP TIGR00118 397 tkkprkfitsgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnne 465 t++pr+f++sgGlGtmGfG+P+a+Gakvakp+++v+++tGdg+f+mn+qel ti+ey+ipv+i+i++n+ lcl|NCBI__GCF_000017185.1:WP_011973398.1 415 TQTPRSFLSSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQELGTIAEYNIPVVICIFDNR 483 ********************************************************************* PP TIGR00118 466 llGmvkqWqelfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvev 534 +lGmv+qWq+lfy +r+ +++++ + pdf+klae+yG+k+ rie+p+e++e+lkea++ +ep+lld+ + lcl|NCBI__GCF_000017185.1:WP_011973398.1 484 TLGMVYQWQNLFYGKRQCSVNFG-GAPDFIKLAESYGIKARRIESPNEINEALKEAINCDEPYLLDFAI 551 ***********************.6******************************************** PP TIGR00118 535 dkeeevlPmvapGagldelve 555 d ++++l mv+pGa+l+++++ lcl|NCBI__GCF_000017185.1:WP_011973398.1 552 D-PSSALSMVPPGAKLTNIID 571 *.9999************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (557 nodes) Target sequences: 1 (599 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.04 # Mc/sec: 7.72 // [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