Align acetohydroxy-acid synthase large subunit (EC 2.2.1.6) (characterized)
to candidate WP_013684084.1 ARCVE_RS07075 acetolactate synthase, large subunit, biosynthetic type
Query= metacyc::MONOMER-11900 (599 letters) >NCBI__GCF_000194625.1:WP_013684084.1 Length = 555 Score = 588 bits (1516), Expect = e-172 Identities = 303/574 (52%), Positives = 391/574 (68%), Gaps = 25/574 (4%) Query: 1 MNGAEAMIKALEAEKVEILFGYPGGALLPFYDALHHSDLIHLLTRHEQAAAHAADGYARA 60 M A+A++KALEAE VE +FG PGGA++ YDAL+ S++ H+LTRHEQAA HAADGYARA Sbjct: 1 MRAADALVKALEAEGVEHIFGIPGGAIIEVYDALYDSNIEHILTRHEQAAVHAADGYARA 60 Query: 61 SGKVGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALGLFMP 120 +GK GV TSGPGATN VTG+ATA+ DSSP+V +TGQVP LIGNDAFQE D G+ MP Sbjct: 61 TGKTGVAFATSGPGATNTVTGIATAYMDSSPLVVMTGQVPRALIGNDAFQEADITGITMP 120 Query: 121 IVKHNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQELELDIDKHPIPSKVKLI 180 + KHN+ + + R AF IA TGRPGPV IDLPKDV +++ D P K+ L+ Sbjct: 121 VTKHNYLVTDPNSLLTTVREAFHIASTGRPGPVLIDLPKDVTMADIEFD---YPPKIDLV 177 Query: 181 GYNPTTIGHPRQIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNIPVCTTLMG 240 GY P GHP+QIK+A +LI ++RP+ILAGGGV+LS A+EEL+KL E + V TTLMG Sbjct: 178 GYKPKMKGHPKQIKRAAELIMKSERPVILAGGGVILSNASEELVKLAETIPAFVVTTLMG 237 Query: 241 KGCISENHPLALGMVGMHGTKPANYCLSESDVLISIGCRFSDRITGDIKSFATNAKIIHI 300 KG + E HPL LG +GMHG+K ANY + E+D++I++GCRFSDR TG + FA AK++HI Sbjct: 238 KGAMPETHPLCLGFIGMHGSKYANYTIMEADLVIAVGCRFSDRTTGRVSGFAPYAKVVHI 297 Query: 301 DIDPAEIGKNVNVDVPIVGDAKLILKEVIKQLDYIINKDSKENNDKENISQWIENVNSLK 360 D+DPAEIGKNV VDVPIVGDAK +L E++K + Y K KE W VN + Sbjct: 298 DVDPAEIGKNVRVDVPIVGDAKQVLAELVKYIKY---KQRKE---------WENKVNEWR 345 Query: 361 KSSIPVMDYDDIPIKPQKIVKELMAVIDDLNINKNTIITTDVGQNQMWMAHYFKTQTPRS 420 K + P+ D ++PQ +++++ + + I+TT+VGQNQMW A YFK PR Sbjct: 346 K-TYPLRYKKDGKLRPQYVIEKV------YELKPDAIVTTEVGQNQMWAAQYFKVSRPRQ 398 Query: 421 FLSSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQELGTIAEYNIPVVICIF 480 F+SSGGLGTMGFGFP+A+GA+VA PD V+ I GDG F+MN QEL T +Y IPV +CI Sbjct: 399 FISSGGLGTMGFGFPAAMGAQVAFPDKTVVDIAGDGSFLMNIQELATCVDYRIPVKVCIL 458 Query: 481 DNRTLGMVYQWQNLFYGKRQCSVNFG-GAPDFIKLAESYGIKARRIESPNEINEALKEAI 539 +N LGMV QWQ LFY +R + F K+AE +G +E E+ +ALKEA Sbjct: 459 NNMFLGMVRQWQQLFYDERYSATCLRCKEMSFEKIAEGFGAVGITVEKETEVEDALKEAF 518 Query: 540 NC-DEPYLLDFAIDP-SSALSMVPPGAKLTNIID 571 D P ++DF ++ + MVP GA L I+D Sbjct: 519 EINDLPVVIDFRVERLENVYPMVPAGAALNEILD 552 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: 890 Number of extensions: 43 Number of successful extensions: 4 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: 555 Length adjustment: 36 Effective length of query: 563 Effective length of database: 519 Effective search space: 292197 Effective search space used: 292197 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_013684084.1 ARCVE_RS07075 (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.5591.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.4e-274 895.7 0.6 6.1e-274 895.5 0.6 1.0 1 lcl|NCBI__GCF_000194625.1:WP_013684084.1 ARCVE_RS07075 acetolactate synth Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000194625.1:WP_013684084.1 ARCVE_RS07075 acetolactate synthase, large subunit, biosynthetic type # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 895.5 0.6 6.1e-274 6.1e-274 1 556 [. 1 553 [. 1 554 [. 0.99 Alignments for each domain: == domain 1 score: 895.5 bits; conditional E-value: 6.1e-274 TIGR00118 1 lkgaeilveslkkegvetvfGyPGGavlpiydalydselehilvrheqaaahaadGyarasGkvGvvla 69 +++a++lv++l++egve++fG+PGGa++++ydalyds++ehil+rheqaa+haadGyara+Gk+Gv++a lcl|NCBI__GCF_000194625.1:WP_013684084.1 1 MRAADALVKALEAEGVEHIFGIPGGAIIEVYDALYDSNIEHILTRHEQAAVHAADGYARATGKTGVAFA 69 789****************************************************************** PP TIGR00118 70 tsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeil 138 tsGPGatn+vtgiatay+ds+Plvv+tGqv+++liG+dafqe+di+Git+pvtkh++lv++++ l +++ lcl|NCBI__GCF_000194625.1:WP_013684084.1 70 TSGPGATNTVTGIATAYMDSSPLVVMTGQVPRALIGNDAFQEADITGITMPVTKHNYLVTDPNSLLTTV 138 ********************************************************************* PP TIGR00118 139 keafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllv 207 +eaf+iastGrPGPvl+dlPkdvt a+ie++++ k++l gykp++kgh++qik+a+eli+k+++Pv+l+ lcl|NCBI__GCF_000194625.1:WP_013684084.1 139 REAFHIASTGRPGPVLIDLPKDVTMADIEFDYPPKIDLVGYKPKMKGHPKQIKRAAELIMKSERPVILA 207 ********************************************************************* PP TIGR00118 208 GgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGar 276 GgGvi ++aseel++lae++ ++v+ttl+G+Ga+pe+hpl lg++GmhG+k+an+++ eadl+iavG+r lcl|NCBI__GCF_000194625.1:WP_013684084.1 208 GGGVILSNASEELVKLAETIPAFVVTTLMGKGAMPETHPLCLGFIGMHGSKYANYTIMEADLVIAVGCR 276 ********************************************************************* PP TIGR00118 277 fddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkeeekkekeWlekiee 345 f+dr+tg ++ fap ak++hid+dPaeigknv+vd+pivGdak+vl+el+k +k++++ke W +k++e lcl|NCBI__GCF_000194625.1:WP_013684084.1 277 FSDRTTGRVSGFAPYAKVVHIDVDPAEIGKNVRVDVPIVGDAKQVLAELVKYIKYKQRKE--WENKVNE 343 *******************************************************99999..******* PP TIGR00118 346 wkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGf 414 w+k+y+l+++ ++++++Pq+vi+++++l +d aivtt+vGq+qmwaaq++k+++pr+fi+sgGlGtmGf lcl|NCBI__GCF_000194625.1:WP_013684084.1 344 WRKTYPLRYK-KDGKLRPQYVIEKVYELKPD-AIVTTEVGQNQMWAAQYFKVSRPRQFISSGGLGTMGF 410 ******9987.5689*************995.************************************* PP TIGR00118 415 GlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeerys 483 G+Paa+Ga+va p++tvv+++Gdgsf mn+qel+t+v+y ipvk++ilnn +lGmv+qWq+lfy+erys lcl|NCBI__GCF_000194625.1:WP_013684084.1 411 GFPAAMGAQVAFPDKTVVDIAGDGSFLMNIQELATCVDYRIPVKVCILNNMFLGMVRQWQQLFYDERYS 479 ********************************************************************* PP TIGR00118 484 etklaselpdfvklaeayGvkgiriekpeeleeklkealesk.epvlldvevdkeeevlPmvapGagld 551 +t+l ++ f+k+ae++G++gi++ek+ e+e++lkea+e + pv++d++v++ e+v+Pmv+ Ga+l+ lcl|NCBI__GCF_000194625.1:WP_013684084.1 480 ATCLRCKEMSFEKIAEGFGAVGITVEKETEVEDALKEAFEINdLPVVIDFRVERLENVYPMVPAGAALN 548 ****************************************99679************************ PP TIGR00118 552 elvee 556 e+++e lcl|NCBI__GCF_000194625.1:WP_013684084.1 549 EILDE 553 **986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (557 nodes) Target sequences: 1 (555 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: 7.17 // [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