Align Acetolactate synthase isozyme 2 large subunit; AHAS-II; ALS-II; Acetohydroxy-acid synthase II large subunit; EC 2.2.1.6 (characterized)
to candidate WP_101445091.1 BD749_RS13350 biosynthetic-type acetolactate synthase large subunit
Query= SwissProt::P0DP90 (548 letters) >NCBI__GCF_002846395.1:WP_101445091.1 Length = 564 Score = 462 bits (1189), Expect = e-134 Identities = 254/561 (45%), Positives = 359/561 (63%), Gaps = 22/561 (3%) Query: 1 MNGAQWVVHALRAQGVNTVFGYPGGAIMPVYDALYDGG--VEHLLCRHEQGAAMAAIGYA 58 + GA+ V+ +L A+ V T+FGYPGGAIMPVYDALYD + H+L RHEQGA AA GYA Sbjct: 5 VTGAEAVILSLLAENVETIFGYPGGAIMPVYDALYDYADQLNHILVRHEQGAIHAAQGYA 64 Query: 59 RATGKTGVCIATSGPGATNLITGLADALLDSIPVVAITGQVSAPFIGTDAFQEVDVLGLS 118 R +GK GVC+ATSGPGATNLITGLADA DS PVV ITGQV++ +GTDAFQE DV+ ++ Sbjct: 65 RVSGKVGVCLATSGPGATNLITGLADAKADSTPVVCITGQVASSLLGTDAFQEADVISIT 124 Query: 119 LACTKHSFLVQSLEELPRIMAEAFDVACSGRPGPVLVDIPKDIQLASGDLEPWFTTVENE 178 A TK + V ++P +++AF +A SGRPGPVL+DI KD Q A P+ + Sbjct: 125 SAVTKWNLQVTQASDIPAAISKAFYLAQSGRPGPVLIDITKDAQFAK---TPFRYAPCKQ 181 Query: 179 VTF--PHAEVEQ-----ARQMLAKAQKPMLYVGGGVGMAQAVPALREFLAATKMPATCTL 231 V + P ++Q A ++ ++KP++ G G+ +A A L + +P TL Sbjct: 182 VAYYAPKPPLDQQAVACAAALINSSRKPLILAGQGIHLAGAHQELLDLATKADIPVATTL 241 Query: 232 KGLGAVEADYPYYLGMLGMHGTKAANFAVQECDLLIAVGARFDDRVTGKLNTFAPHASVI 291 GL A+ ++P +G+LGMHG A N E DL+IAVG RFDDRVTG+++T+A AS+I Sbjct: 242 LGLSAIPTEHPLNVGLLGMHGNYAPNLKTNEADLIIAVGMRFDDRVTGRVDTYARQASII 301 Query: 292 HMDIDPAEMNKLRQAHVALQGDLNALLPALQQPL--NQY-DWQQH---CAQLRDEHSWRY 345 H+D+DPAE+NK+ +A VAL D L AL + + N++ +W Q C E R+ Sbjct: 302 HIDLDPAEINKIIKADVALVADAREALAALTRLVFKNEHPEWLQEFRDCMDQEFEKVVRH 361 Query: 346 D-HPGD--AIYAPLLLKQLSDRKPADCVVTTDVGQHQMWAAQHIAHTRPENFITSSGLGT 402 D P D I +L+ +++ D V+ TDVGQHQM A+++ + ITS GLGT Sbjct: 362 DLFPADDREITMGEVLRLVNELAEEDSVLVTDVGQHQMVASRYFNFRSLNSNITSGGLGT 421 Query: 403 MGFGLPAAVGAQVARPNDTVVCISGDGSFMMNVQELGTVKRKQLPLKIVLLDNQRLGMVR 462 MGF LPAA+GA+ RP VV + GDG F MN+QELGT+ + + +K+++L+N LGMVR Sbjct: 422 MGFALPAAIGAKAGRPLAQVVAVIGDGGFQMNIQELGTIMQTGIAVKVIILNNNFLGMVR 481 Query: 463 QWQQLFFQERYSETTLTDNPDFLMLASAFGIHGQHITRKDQVEAALDTMLNSDGPYLLHV 522 QWQQLFF++RYS + +NPDF+ + +GI + + ++ + + +L+S P +L V Sbjct: 482 QWQQLFFEKRYSSVEM-ENPDFVKITQGYGISARKVVQRSALAETMRAVLSSQQPEVLEV 540 Query: 523 SIDELENVWPLVPPGASNSEM 543 + +NV+P++P GA SE+ Sbjct: 541 VVGREDNVFPMIPTGACVSEV 561 Lambda K H 0.320 0.135 0.410 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: 748 Number of extensions: 36 Number of successful extensions: 5 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: 548 Length of database: 564 Length adjustment: 36 Effective length of query: 512 Effective length of database: 528 Effective search space: 270336 Effective search space used: 270336 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 (21.8 bits) S2: 53 (25.0 bits)
Align candidate WP_101445091.1 BD749_RS13350 (biosynthetic-type acetolactate synthase large subunit)
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.3425488.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-214 699.3 1.3 2e-214 699.1 1.3 1.0 1 NCBI__GCF_002846395.1:WP_101445091.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_002846395.1:WP_101445091.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 699.1 1.3 2e-214 2e-214 2 553 .. 6 561 .. 5 564 .] 0.97 Alignments for each domain: == domain 1 score: 699.1 bits; conditional E-value: 2e-214 TIGR00118 2 kgaeilveslkkegvetvfGyPGGavlpiydaly..dselehilvrheqaaahaadGyarasGkvGvvlatsG 72 +gae+++ sl +e+vet+fGyPGGa++p+ydaly +++l+hilvrheq+a+haa+Gyar+sGkvGv+latsG NCBI__GCF_002846395.1:WP_101445091.1 6 TGAEAVILSLLAENVETIFGYPGGAIMPVYDALYdyADQLNHILVRHEQGAIHAAQGYARVSGKVGVCLATSG 78 79********************************989************************************ PP TIGR00118 73 PGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafeia 145 PGatnl+tg+a+a +ds+P+v +tGqva+sl+G+dafqe+d++ it +vtk++++v++a+d+p+ + +af++a NCBI__GCF_002846395.1:WP_101445091.1 79 PGATNLITGLADAKADSTPVVCITGQVASSLLGTDAFQEADVISITSAVTKWNLQVTQASDIPAAISKAFYLA 151 ************************************************************************* PP TIGR00118 146 stGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllvGgGviiaease 218 ++GrPGPvl+d+ kd + a++ +++ ++ y+p+ +++ ++ a+ li++++kP++l+G G+ a+a++ NCBI__GCF_002846395.1:WP_101445091.1 152 QSGRPGPVLIDITKDAQFAKTPFRYAPCKQVAYYAPKPPLDQQAVACAAALINSSRKPLILAGQGIHLAGAHQ 224 **************************9999999**************************************** PP TIGR00118 219 elkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfape 291 el +la +++ipv+ttllGl a+p +hpl +g+lGmhG ++ nl +eadl+iavG+rfddrvtg ++++a++ NCBI__GCF_002846395.1:WP_101445091.1 225 ELLDLATKADIPVATTLLGLSAIPTEHPLNVGLLGMHGNYAPNLKTNEADLIIAVGMRFDDRVTGRVDTYARQ 297 ************************************************************************* PP TIGR00118 292 akiihididPaeigknvkvdipivGdakkvleellkklkeeekkekeWlekieewkkeyilk......ldeee 358 a iihid+dPaei+k++k+d+++v da++ l+ l + + ++e+ e Wl++ ++ ++ k + ++ NCBI__GCF_002846395.1:WP_101445091.1 298 ASIIHIDLDPAEINKIIKADVALVADAREALAALTRLVFKNEHPE--WLQEFRDCMDQEFEKvvrhdlFPADD 368 ***************************************999888..99988766554443311112466788 PP TIGR00118 359 esikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpeetv 431 +i +v++ + +l+++++++ tdvGqhqm a++++++++ ++ itsgGlGtmGf lPaa+Gak + p ++v NCBI__GCF_002846395.1:WP_101445091.1 369 REITMGEVLRLVNELAEEDSVLVTDVGQHQMVASRYFNFRSLNSNITSGGLGTMGFALPAAIGAKAGRPLAQV 441 99*********************************************************************** PP TIGR00118 432 vavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeerysetklaselpdfvklaeayGvk 504 vav Gdg+fqmn+qel ti++ +i vk++ilnn++lGmv+qWq+lf+e+rys++++++ pdfvk++++yG+ NCBI__GCF_002846395.1:WP_101445091.1 442 VAVIGDGGFQMNIQELGTIMQTGIAVKVIILNNNFLGMVRQWQQLFFEKRYSSVEMEN--PDFVKITQGYGIS 512 ********************************************************97..************* PP TIGR00118 505 giriekpeeleeklkealeskepvlldvevdkeeevlPmvapGagldel 553 + ++ +++ l+e ++ +l+s++p +l+v+v +e++v+Pm+++Ga ++e+ NCBI__GCF_002846395.1:WP_101445091.1 513 ARKVVQRSALAETMRAVLSSQQPEVLEVVVGREDNVFPMIPTGACVSEV 561 *******************************************999886 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (557 nodes) Target sequences: 1 (564 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: 16.98 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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