Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate WP_010532006.1 ON01_RS15950 biosynthetic-type acetolactate synthase large subunit
Query= BRENDA::P9WG41 (618 letters) >NCBI__GCF_000224785.1:WP_010532006.1 Length = 575 Score = 521 bits (1341), Expect = e-152 Identities = 273/570 (47%), Positives = 371/570 (65%), Gaps = 18/570 (3%) Query: 36 QQLTGAQAVIRSLEELGVDVIFGIPGGAVLPVYDPLFDSKK-LRHVLVRHEQGAGHAASG 94 +++TGA +I++L + VD +FG PGGAVLP+YD L+ S +HVL RHEQGA HAA G Sbjct: 14 KKVTGADLLIQTLTAVNVDTVFGYPGGAVLPIYDALYRSDAPFKHVLTRHEQGAAHAAEG 73 Query: 95 YAHVTGRVGVCMATSGPGATNLVTPLADAQMDSIPVVAITGQVGRGLIGTDAFQEADISG 154 YA VTG+ GV +ATSGPGATNL+T + DA MDS+P+V TGQV +IGTDAFQE+D+ G Sbjct: 74 YARVTGKPGVVLATSGPGATNLITGITDAMMDSLPMVVFTGQVASNVIGTDAFQESDVMG 133 Query: 155 ITMPITKHNFLVRSGDDIPRVLAEAFHIAASGRPGAVLVDIPKDVLQGQCTFSWPPRME- 213 IT P+TK+N+ VR ++PR++ EAFHIA++GRPG V+VDIPKD+ S + Sbjct: 134 ITTPVTKYNYQVRDLKELPRIVKEAFHIASTGRPGPVVVDIPKDISSTVSGISVELNDDC 193 Query: 214 -LPGYKPNTKPHSRQVREAAKLIAAARKPVLYVGGGVIRGEATEQLRELAELTGIPVVTT 272 LPGY+PN KP+ Q+ + A+ I+ A+KP++ G GV+ EA+++L AE +PVV T Sbjct: 194 YLPGYQPNKKPNPLQIVKLAEAISRAKKPLILAGAGVVSAEASKELTAFAEKHKLPVVNT 253 Query: 273 LMARGAFPDSHRQNLGMPGMHGTVAAVAALQRSDLLIALGTRFDDRVTGKLDSFAPEAKV 332 L+ G F +H +LGM GMHG AA + DLLI +G RFDDR+TG L FAP AKV Sbjct: 254 LLGLGGFSGTHELSLGMGGMHGCYAANQGVYECDLLINIGARFDDRLTGNLKHFAPNAKV 313 Query: 333 IHADIDPAEIGKNRHADVPIVGDVKAVITELI--AMLRHHHIPGTIEMADWWAYLNGVRK 390 H DIDPAEIGKN ++P+V D K + L+ + + H DW L + Sbjct: 314 AHVDIDPAEIGKNVETEIPVVADAKEALEALVKTEITANDH-------GDWLDTLRQNQM 366 Query: 391 TYPLSYGPQSDGSLSPEYVIEKLGEIAGPDAVFVAGVGQHQMWAAQFIRYEKPRSWLNSG 450 YP Y +S+ +SP+++ E++ +++ +A+ VGQHQMWAAQ+ + P W+ SG Sbjct: 367 DYPYWY-DRSETYISPQWLTEQIYKVSDGEAIVTTDVGQHQMWAAQYYPFANPNKWVTSG 425 Query: 451 GLGTMGFAIPAAMGAKIALPGTEVWAIDGDGCFQMTNQELATCAVEGIPVKVALINNGNL 510 GLGTMGF PAA+GA++ P V A+ GDG FQMT QEL+ +PVKV ++NN +L Sbjct: 426 GLGTMGFGFPAAVGAQLGAPDELVVAVVGDGGFQMTAQELSVIKERQLPVKVVIVNNQSL 485 Query: 511 GMVRQWQSLFYAERYSQTDLATHSHRIPDFVKLAEALGCVGLRCEREEDVVDVINQARAI 570 GMVRQWQ FY +RYS++ + PDFVKLAE G +G+R E E ++ DV+ A Sbjct: 486 GMVRQWQEKFYDKRYSESIFPEN----PDFVKLAECYGILGMRAENESELPDVLTDAFNY 541 Query: 571 NDCPVVIDFIVGADAQVWPMVAAGTSNDEI 600 D PVVID V + V+PM+A G E+ Sbjct: 542 -DGPVVIDCHVVQEECVYPMIAPGKGMHEM 570 Lambda K H 0.319 0.136 0.414 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: 1059 Number of extensions: 43 Number of successful extensions: 6 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: 618 Length of database: 575 Length adjustment: 37 Effective length of query: 581 Effective length of database: 538 Effective search space: 312578 Effective search space used: 312578 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_010532006.1 ON01_RS15950 (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.3245558.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.9e-254 830.6 0.3 3.3e-254 830.4 0.3 1.0 1 NCBI__GCF_000224785.1:WP_010532006.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000224785.1:WP_010532006.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 830.4 0.3 3.3e-254 3.3e-254 2 556 .. 17 573 .. 16 574 .. 0.98 Alignments for each domain: == domain 1 score: 830.4 bits; conditional E-value: 3.3e-254 TIGR00118 2 kgaeilveslkkegvetvfGyPGGavlpiydaly..dselehilvrheqaaahaadGyarasGkvGvvlatsG 72 +ga++l+++l++ +v+tvfGyPGGavlpiydaly d ++h+l+rheq+aahaa+Gyar++Gk+GvvlatsG NCBI__GCF_000224785.1:WP_010532006.1 17 TGADLLIQTLTAVNVDTVFGYPGGAVLPIYDALYrsDAPFKHVLTRHEQGAAHAAEGYARVTGKPGVVLATSG 89 79********************************766679********************************* PP TIGR00118 73 PGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafeia 145 PGatnl+tgi++a++ds+P+vv+tGqva+++iG+dafqe d++Git pvtk++++v++ ++lp+i+keaf+ia NCBI__GCF_000224785.1:WP_010532006.1 90 PGATNLITGITDAMMDSLPMVVFTGQVASNVIGTDAFQESDVMGITTPVTKYNYQVRDLKELPRIVKEAFHIA 162 ************************************************************************* PP TIGR00118 146 stGrPGPvlvdlPkdvteaeieleve..ekvelpgykptvkghklqikkaleliekakkPvllvGgGviiaea 216 stGrPGPv+vd+Pkd++++ ++ve ++ lpgy+p++k+++lqi k++e+i++akkP++l+G+Gv+ aea NCBI__GCF_000224785.1:WP_010532006.1 163 STGRPGPVVVDIPKDISSTVSGISVElnDDCYLPGYQPNKKPNPLQIVKLAEAISRAKKPLILAGAGVVSAEA 235 ****************9887655555549******************************************** PP TIGR00118 217 seelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfa 289 s+el+ +ae+ k+pv+ tllGlG+f +h+l+lgm GmhG+++an v e+dlli +Garfddr tgnl++fa NCBI__GCF_000224785.1:WP_010532006.1 236 SKELTAFAEKHKLPVVNTLLGLGGFSGTHELSLGMGGMHGCYAANQGVYECDLLINIGARFDDRLTGNLKHFA 308 ************************************************************************* PP TIGR00118 290 peakiihididPaeigknvkvdipivGdakkvleellkklkeeekkekeWlekieewkkeyilkldeeeesik 362 p+ak+ h+didPaeigknv+++ip+v dak+ le l+k+ + +++ +Wl+ +++ + +y++++d++e+ i NCBI__GCF_000224785.1:WP_010532006.1 309 PNAKVAHVDIDPAEIGKNVETEIPVVADAKEALEALVKTEITANDHG-DWLDTLRQNQMDYPYWYDRSETYIS 380 *************************************9988887776.6************************ PP TIGR00118 363 PqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpeetvvavt 435 Pq + ++++k+ ++eaivttdvGqhqmwaaq+y++ +p+k++tsgGlGtmGfG+Paa+Ga+++ p+e vvav+ NCBI__GCF_000224785.1:WP_010532006.1 381 PQWLTEQIYKVSDGEAIVTTDVGQHQMWAAQYYPFANPNKWVTSGGLGTMGFGFPAAVGAQLGAPDELVVAVV 453 ************************************************************************* PP TIGR00118 436 GdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeerysetklaselpdfvklaeayGvkgiri 508 Gdg+fqm+ qels+i+e ++pvk+vi+nn+ lGmv+qWqe fy++ryse+ + e+pdfvklae+yG+ g+r NCBI__GCF_000224785.1:WP_010532006.1 454 GDGGFQMTAQELSVIKERQLPVKVVIVNNQSLGMVRQWQEKFYDKRYSESIFP-ENPDFVKLAECYGILGMRA 525 ****************************************************9.7****************** PP TIGR00118 509 ekpeeleeklkealeskepvlldvevdkeeevlPmvapGagldelvee 556 e+++el + l++a++ ++pv++d +v +ee v+Pm+apG+g++e++++ NCBI__GCF_000224785.1:WP_010532006.1 526 ENESELPDVLTDAFNYDGPVVIDCHVVQEECVYPMIAPGKGMHEMIGV 573 *********************************************975 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (557 nodes) Target sequences: 1 (575 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 35.63 // [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