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_027179478.1 G496_RS0111895 acetolactate synthase, large subunit, biosynthetic type
Query= SwissProt::P0DP90 (548 letters) >NCBI__GCF_000429985.1:WP_027179478.1 Length = 553 Score = 518 bits (1334), Expect = e-151 Identities = 257/549 (46%), Positives = 368/549 (67%), Gaps = 5/549 (0%) Query: 1 MNGAQWVVHALRAQGVNTVFGYPGGAIMPVYDALYDGGVEHLLCRHEQGAAMAAIGYARA 60 ++GA+ +++ L QG+ TV G PGG+ +P+YDAL ++H+L RHEQGA A G AR Sbjct: 3 LSGAEIIINMLERQGITTVAGIPGGSTLPIYDALGKSSIKHILSRHEQGAGFIAQGMART 62 Query: 61 TGKTGVCIATSGPGATNLITGLADALLDSIPVVAITGQVSAPFIGTDAFQEVDVLGLSLA 120 TGK VC+ATSGPG TNL+T +ADA LDSIP++AITGQV+ IGTDAFQEVD GL++ Sbjct: 63 TGKAAVCLATSGPGVTNLLTAIADACLDSIPIIAITGQVTNSLIGTDAFQEVDTYGLTIP 122 Query: 121 CTKHSFLVQSLEELPRIMAEAFDVACSGRPGPVLVDIPKDIQLASGDLEPWFTTV--ENE 178 TKH+FLVQS E+L ++ EAF +A SGRPGPV++D+PK+IQ +++ W + Sbjct: 123 ITKHNFLVQSCEDLLEVIPEAFRIAESGRPGPVVIDVPKNIQNEVIEIKSWPEPYIKDEP 182 Query: 179 VTFPHAEVEQARQMLAKAQKPMLYVGGGVGMAQAVPALREFLAATKMPATCTLKGLGAVE 238 V F +E+A +M+ KA++P+LYVGGGV AV ++EF +PA TL GLG + Sbjct: 183 VMFNEDNMERALEMINKAERPVLYVGGGVIAGDAVKEVQEFSKRNSIPAVSTLMGLGVFK 242 Query: 239 ADYPYYLGMLGMHGTKAANFAVQECDLLIAVGARFDDRVTGKLNTFAPHASVIHMDIDPA 298 P +LGMLGMHG + N ++E DLLIA+G RFDDR GK N F HA +IH+DID + Sbjct: 243 DSDPGFLGMLGMHGARYTNMVMEEADLLIALGVRFDDRAVGKSNEFCCHADIIHVDIDRS 302 Query: 299 EMNKLRQAHVALQGDLNALLPALQQPL---NQYDWQQHCAQLRDEHSWRYDHPGDAIYAP 355 E+ K++ +++++ GD+ +L L + + ++ +W A++R + + D + Sbjct: 303 EIGKIKSSNLSVVGDVKLVLQDLCKSVPESSRLEWNNRVAEIRSSNPRQLPDSEDFFHPI 362 Query: 356 LLLKQLSDRKPADCVVTTDVGQHQMWAAQHIAHTRPENFITSSGLGTMGFGLPAAVGAQV 415 ++ ++S+ P + V+ TDVGQHQMW AQH P +TS GLGTMGFGLP+A+GA + Sbjct: 363 NVIHKISEFVPDNTVICTDVGQHQMWVAQHYPFCGPRTLLTSGGLGTMGFGLPSAIGAAL 422 Query: 416 ARPNDTVVCISGDGSFMMNVQELGTVKRKQLPLKIVLLDNQRLGMVRQWQQLFFQERYSE 475 A VVC+SGDGS +MN+QEL T+ +QL +KI++++N RLG+VRQ Q+LFF+ RY Sbjct: 423 ADKERKVVCVSGDGSILMNIQELATLAEQQLNIKILIMNNNRLGLVRQQQELFFEGRYVA 482 Query: 476 TTLTDNPDFLMLASAFGIHGQHITRKDQVEAALDTMLNSDGPYLLHVSIDELENVWPLVP 535 +T NPDF +A+ FGI + +D EAAL +L+ DGP L+++ I NV+P+VP Sbjct: 483 STFKSNPDFASVAAGFGIVSADLGSEDDPEAALGRLLSFDGPCLINIPIGFENNVFPMVP 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: 741 Number of extensions: 18 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_027179478.1 G496_RS0111895 (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.8184.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.5e-211 687.5 0.0 7.4e-211 687.3 0.0 1.0 1 lcl|NCBI__GCF_000429985.1:WP_027179478.1 G496_RS0111895 acetolactate synt Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000429985.1:WP_027179478.1 G496_RS0111895 acetolactate synthase, large subunit, biosynthetic type # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 687.3 0.0 7.4e-211 7.4e-211 1 555 [. 3 552 .. 3 553 .] 0.98 Alignments for each domain: == domain 1 score: 687.3 bits; conditional E-value: 7.4e-211 TIGR00118 1 lkgaeilveslkkegvetvfGyPGGavlpiydalydselehilvrheqaaahaadGyarasGkvGvvla 69 l+gaei++++l+++g+ tv G+PGG+ lpiydal +s ++hil rheq+a +a+G+ar++Gk+ v+la lcl|NCBI__GCF_000429985.1:WP_027179478.1 3 LSGAEIIINMLERQGITTVAGIPGGSTLPIYDALGKSSIKHILSRHEQGAGFIAQGMARTTGKAAVCLA 71 68******************************************************************* PP TIGR00118 70 tsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeil 138 tsGPG tnl+t+ia+a lds+P++++tGqv++sliG+dafqe+d G+t+p+tkh+flv++ edl e++ lcl|NCBI__GCF_000429985.1:WP_027179478.1 72 TSGPGVTNLLTAIADACLDSIPIIAITGQVTNSLIGTDAFQEVDTYGLTIPITKHNFLVQSCEDLLEVI 140 ********************************************************************* PP TIGR00118 139 keafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllv 207 eaf ia++GrPGPv++d+Pk+++++ ie++ + ++ v ++ +++ale+i+ka++Pvl+v lcl|NCBI__GCF_000429985.1:WP_027179478.1 141 PEAFRIAESGRPGPVVIDVPKNIQNEVIEIKSWPEPYIKDE--PVMFNEDNMERALEMINKAERPVLYV 207 *****************************999877666654..456677889***************** PP TIGR00118 208 GgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGar 276 GgGvi+++a +e++e+++r ip ++tl+GlG f++ +p +lgmlGmhG++++n+ ++eadllia+G+r lcl|NCBI__GCF_000429985.1:WP_027179478.1 208 GGGVIAGDAVKEVQEFSKRNSIPAVSTLMGLGVFKDSDPGFLGMLGMHGARYTNMVMEEADLLIALGVR 276 ********************************************************************* PP TIGR00118 277 fddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkeeekkekeWlekiee 345 fddr g+ ++f+ +a iih+did +eigk+ ++++++vGd+k vl++l k + e ++ e W ++++e lcl|NCBI__GCF_000429985.1:WP_027179478.1 277 FDDRAVGKSNEFCCHADIIHVDIDRSEIGKIKSSNLSVVGDVKLVLQDLCKSVPESSRLE--WNNRVAE 343 ****************************************************99988887..******* PP TIGR00118 346 wkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGf 414 +++++ +l +e+ ++P +vi+++s++++d++++ tdvGqhqmw+aq+y++ pr+ +tsgGlGtmGf lcl|NCBI__GCF_000429985.1:WP_027179478.1 344 IRSSNPRQLPDSEDFFHPINVIHKISEFVPDNTVICTDVGQHQMWVAQHYPFCGPRTLLTSGGLGTMGF 412 ********************************************************************* PP TIGR00118 415 GlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeerys 483 GlP+a+Ga +a +e +vv+v+Gdgs+ mn+qel+t++e ++++ki+i+nn+ lG+v+q qelf+e+ry lcl|NCBI__GCF_000429985.1:WP_027179478.1 413 GLPSAIGAALADKERKVVCVSGDGSILMNIQELATLAEQQLNIKILIMNNNRLGLVRQQQELFFEGRYV 481 ********************************************************************* PP TIGR00118 484 etklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlPmvapGaglde 552 +++++s +pdf+ +a ++G+++ + ++++ e++l ++l+ ++p l+++ + e++v+Pmv+p +++ e lcl|NCBI__GCF_000429985.1:WP_027179478.1 482 ASTFKS-NPDFASVAAGFGIVSADLGSEDDPEAALGRLLSFDGPCLINIPIGFENNVFPMVPPECANRE 549 *****5.************************************************************** PP TIGR00118 553 lve 555 +++ lcl|NCBI__GCF_000429985.1:WP_027179478.1 550 MIG 552 *85 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: 00:00:00.03 # Mc/sec: 9.07 // [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