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_027722598.1 H589_RS0113925 acetolactate synthase, large subunit, biosynthetic type
Query= SwissProt::P0DP90 (548 letters) >NCBI__GCF_000425265.1:WP_027722598.1 Length = 553 Score = 486 bits (1250), Expect = e-141 Identities = 244/549 (44%), Positives = 350/549 (63%), Gaps = 5/549 (0%) Query: 1 MNGAQWVVHALRAQGVNTVFGYPGGAIMPVYDALYDGGVEHLLCRHEQGAAMAAIGYARA 60 ++GA+ +++ L QG+ + G PGG+ + +YDAL D ++H+L RHEQGA A G AR Sbjct: 3 LSGAKLLINLLERQGIEIICGIPGGSNLIIYDALRDSSIKHILARHEQGAGFMAQGMART 62 Query: 61 TGKTGVCIATSGPGATNLITGLADALLDSIPVVAITGQVSAPFIGTDAFQEVDVLGLSLA 120 TGK VC+ TSGPG TNL+T +ADA LDSIPVVAITGQVS+ IGTDAFQEVD GL++ Sbjct: 63 TGKAAVCMGTSGPGVTNLLTAIADARLDSIPVVAITGQVSSSLIGTDAFQEVDTYGLTIP 122 Query: 121 CTKHSFLVQSLEELPRIMAEAFDVACSGRPGPVLVDIPKDIQLASGDLEPW--FTTVENE 178 TKH+FLVQS +L I+ EAF +A SGRPGPV+VDIPKD+Q ++ W + Sbjct: 123 ITKHNFLVQSAADLLEIIPEAFRLAESGRPGPVVVDIPKDVQKEIVEITSWPEHGLKDAV 182 Query: 179 VTFPHAEVEQARQMLAKAQKPMLYVGGGVGMAQAVPALREFLAATKMPATCTLKGLGAVE 238 T +++QA +M+ +++P++Y GGGV A L + +P TL GLGA Sbjct: 183 HTCDDNDLKQALEMINSSRRPIIYAGGGVVAADCSDDLLKLAHKNSIPVVSTLMGLGAYP 242 Query: 239 ADYPYYLGMLGMHGTKAANFAVQECDLLIAVGARFDDRVTGKLNTFAPHASVIHMDIDPA 298 YLGMLGMHG ++ N ++E DL+IA+G RFDDR GK F HA ++H+DID + Sbjct: 243 DGDSNYLGMLGMHGARSTNMIMEEADLIIALGVRFDDRAVGKACEFCKHADILHIDIDRS 302 Query: 299 EMNKLRQAHVALQGDLNALLPALQQPLN---QYDWQQHCAQLRDEHSWRYDHPGDAIYAP 355 E+ K++ +++++ GD+ L L + + W A LR ++ + + Sbjct: 303 EIGKIKSSNLSVVGDVGHALSELAANVESSIRISWSARIASLRMKYPEIIPDSNETFHPA 362 Query: 356 LLLKQLSDRKPADCVVTTDVGQHQMWAAQHIAHTRPENFITSSGLGTMGFGLPAAVGAQV 415 L++ + + P D ++TTDVGQHQMW AQ +P +TS GLGTMGFGLP A+GA Sbjct: 363 NLIRIMGESLPDDAIITTDVGQHQMWVAQKYPFRKPRTLLTSGGLGTMGFGLPNAIGAAF 422 Query: 416 ARPNDTVVCISGDGSFMMNVQELGTVKRKQLPLKIVLLDNQRLGMVRQWQQLFFQERYSE 475 A+P+ VVC+SGDGSF+MN+QEL T+ + L +K+++++N RLG+VRQ Q+LFF+ER+ Sbjct: 423 AKPDKKVVCVSGDGSFLMNIQELATLAEQHLNVKVLIMNNHRLGLVRQQQELFFEERFFA 482 Query: 476 TTLTDNPDFLMLASAFGIHGQHITRKDQVEAALDTMLNSDGPYLLHVSIDELENVWPLVP 535 ++ NPDF +A FGI + +D E L +L DGP ++++ I V+P+VP Sbjct: 483 SSFESNPDFASIAKGFGIPAFDLDDQDNPELFLRKILGQDGPCVINIPIGLENKVFPMVP 542 Query: 536 PGASNSEML 544 P +N EM+ Sbjct: 543 PECANREMI 551 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: 782 Number of extensions: 29 Number of successful extensions: 3 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: 553 Length adjustment: 36 Effective length of query: 512 Effective length of database: 517 Effective search space: 264704 Effective search space used: 264704 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_027722598.1 H589_RS0113925 (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.11291.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.6e-209 680.5 0.0 9.8e-209 680.3 0.0 1.0 1 lcl|NCBI__GCF_000425265.1:WP_027722598.1 H589_RS0113925 acetolactate synt Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000425265.1:WP_027722598.1 H589_RS0113925 acetolactate synthase, large subunit, biosynthetic type # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 680.3 0.0 9.8e-209 9.8e-209 1 555 [. 3 552 .. 3 553 .] 0.98 Alignments for each domain: == domain 1 score: 680.3 bits; conditional E-value: 9.8e-209 TIGR00118 1 lkgaeilveslkkegvetvfGyPGGavlpiydalydselehilvrheqaaahaadGyarasGkvGvvla 69 l+ga++l++ l+++g+e++ G+PGG+ l iydal ds ++hil+rheq+a +a+G+ar++Gk+ v+++ lcl|NCBI__GCF_000425265.1:WP_027722598.1 3 LSGAKLLINLLERQGIEIICGIPGGSNLIIYDALRDSSIKHILARHEQGAGFMAQGMARTTGKAAVCMG 71 689****************************************************************** PP TIGR00118 70 tsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeil 138 tsGPG tnl+t+ia+a lds+P+v++tGqv++sliG+dafqe+d G+t+p+tkh+flv++a+dl ei+ lcl|NCBI__GCF_000425265.1:WP_027722598.1 72 TSGPGVTNLLTAIADARLDSIPVVAITGQVSSSLIGTDAFQEVDTYGLTIPITKHNFLVQSAADLLEII 140 ********************************************************************* PP TIGR00118 139 keafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllv 207 eaf +a++GrPGPv+vd+Pkdv+++ +e++ + l+ t + + +k+ale+i+++++P++++ lcl|NCBI__GCF_000425265.1:WP_027722598.1 141 PEAFRLAESGRPGPVVVDIPKDVQKEIVEITSWPEHGLKDAVHT--CDDNDLKQALEMINSSRRPIIYA 207 *****************************999988888876554..566789***************** PP TIGR00118 208 GgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGar 276 GgGv++a++s++l +la++ ipv++tl+GlGa+p+ + + lgmlGmhG++ +n+ ++eadl+ia+G+r lcl|NCBI__GCF_000425265.1:WP_027722598.1 208 GGGVVAADCSDDLLKLAHKNSIPVVSTLMGLGAYPDGDSNYLGMLGMHGARSTNMIMEEADLIIALGVR 276 ********************************************************************* PP TIGR00118 277 fddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkeeekkekeWlekiee 345 fddr g+ +f+++a i+hidid +eigk+ ++++++vGd+ + l+el +++++ + + W ++i++ lcl|NCBI__GCF_000425265.1:WP_027722598.1 277 FDDRAVGKACEFCKHADILHIDIDRSEIGKIKSSNLSVVGDVGHALSELAANVESSIRIS--WSARIAS 343 **************************************************9998877766..******* PP TIGR00118 346 wkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGf 414 ++ +y+ + ++e+++P ++i+ + + l+d+ai+ttdvGqhqmw+aq y+++kpr+ +tsgGlGtmGf lcl|NCBI__GCF_000425265.1:WP_027722598.1 344 LRMKYPEIIPDSNETFHPANLIRIMGESLPDDAIITTDVGQHQMWVAQKYPFRKPRTLLTSGGLGTMGF 412 ********************************************************************* PP TIGR00118 415 GlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeerys 483 GlP a+Ga akp+++vv+v+Gdgsf mn+qel+t++e +++vk++i+nn+ lG+v+q qelf+eer+ lcl|NCBI__GCF_000425265.1:WP_027722598.1 413 GLPNAIGAAFAKPDKKVVCVSGDGSFLMNIQELATLAEQHLNVKVLIMNNHRLGLVRQQQELFFEERFF 481 ********************************************************************* PP TIGR00118 484 etklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlPmvapGaglde 552 ++ ++s +pdf+ +a+++G+ + + ++++ e l+++l +++p ++++ + e++v+Pmv+p +++ e lcl|NCBI__GCF_000425265.1:WP_027722598.1 482 ASSFES-NPDFASIAKGFGIPAFDLDDQDNPELFLRKILGQDGPCVINIPIGLENKVFPMVPPECANRE 549 *****5.************************************************************** PP TIGR00118 553 lve 555 +++ lcl|NCBI__GCF_000425265.1:WP_027722598.1 550 MIG 552 *96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (557 nodes) Target sequences: 1 (553 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: 7.21 // [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