Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate WP_053767937.1 BVI061214_RS07970 biosynthetic-type acetolactate synthase large subunit
Query= BRENDA::P9WG41 (618 letters) >NCBI__GCF_001280255.1:WP_053767937.1 Length = 561 Score = 563 bits (1451), Expect = e-165 Identities = 301/564 (53%), Positives = 387/564 (68%), Gaps = 16/564 (2%) Query: 38 LTGAQAVIRSLEELGVDVIFGIPGGAVLPVYDPLFDSKKLRHVLVRHEQGAGHAASGYAH 97 + GA+A++++LE GV+VIFG PGGA++P YD L+DS +RH+LVRHEQG HAA+ YA Sbjct: 1 MKGAEALLKALEREGVEVIFGHPGGAIMPTYDALYDSP-IRHILVRHEQGGIHAATAYAR 59 Query: 98 VTGRVGVCMATSGPGATNLVTPLADAQMDSIPVVAITGQVGRGLIGTDAFQEADISGITM 157 +GRVGV MATSGPGA NLVT LADA MDS PVVAITG V R LIGTDAFQEAD++G+TM Sbjct: 60 ASGRVGVVMATSGPGALNLVTGLADALMDSTPVVAITGNVPRALIGTDAFQEADVTGVTM 119 Query: 158 PITKHNFLVRSGDDIPRVLAEAFHIAASGRPGAVLVDIPKDVLQGQCTFSWPPRMELPGY 217 PITKHN+LV+ ++IPRV+ EAFHIA++GRPG VL+D+PKDV + T + ++LPGY Sbjct: 120 PITKHNYLVQDVNEIPRVVKEAFHIASTGRPGPVLIDLPKDVQLAEFTGEFDVELDLPGY 179 Query: 218 KPNTKPHSRQVREAAKLIAAARKPVLYVGGGVIRGEATEQLRELAELTGIPVVTTLMARG 277 KP + H +Q+ A + A +P+L VGGG A +L AE TG+PV+TTLM G Sbjct: 180 KPTLRGHPKQIERALDALEKAERPILMVGGGAQHAHA--ELLAFAEKTGLPVITTLMGLG 237 Query: 278 AFPDSHRQNLGMPGMHGTVAAVAALQRSDLLIALGTRFDDRVTGKLDSFAPEA-KVIHAD 336 AFP +H LGMPGMHGTVAA A+ +D+++A+G RFDDRVTGK+ FAP A +IH D Sbjct: 238 AFPGNHPLWLGMPGMHGTVAANRAIHHADVILAIGLRFDDRVTGKVSRFAPHAHTIIHVD 297 Query: 337 IDPAEIGKNRHADVPIVGDVKAVITELIAMLRHHHIPGTIEMADWWAYLNGVRKTYPLSY 396 IDPAEIGK +PIVGD + V+ E++ + + +A WW L R YPL Y Sbjct: 298 IDPAEIGKVVRTHIPIVGDSRLVLKEMLKGAK------PLRLAAWWRELEEWRTRYPLRY 351 Query: 397 GPQSDGSLSPEYVIEKLGEIAGPDAVFVAGVGQHQMWAAQFIRYEKPRSWLNSGGLGTMG 456 P+ L VI E G +A+ GVGQHQM+AAQ+ +PRS+L SGGLGTMG Sbjct: 352 RPRP--HLQAPEVIRAFHEATGGNAIVTTGVGQHQMFAAQYFTVTRPRSFLTSGGLGTMG 409 Query: 457 FAIPAAMGAKIALPGTEVWAIDGDGCFQMTNQELATCAVEGIPVKVALINNGNLGMVRQW 516 +P A+GA+IA P V DGDG FQMT QELAT +PVKV ++NNG LGMVRQW Sbjct: 410 VGLPFAIGAQIARPEELVIDFDGDGSFQMTLQELATVVKYRLPVKVVILNNGYLGMVRQW 469 Query: 517 QSLFYAERYSQTDLATHSHRIPDFVKLAEALGCVGLRCEREEDVVDVINQARAINDCPVV 576 Q LF+A+RYS+ LA + PDF KLAEA G G+R ER+ED+ + +A D PVV Sbjct: 470 QDLFHAKRYSEVYLADSN---PDFAKLAEAYGIKGVRVERKEDLKKGV-EAVLNADGPVV 525 Query: 577 IDFIVGADAQVWPMVAAGTSNDEI 600 +F V + V+PM+ AG + +++ Sbjct: 526 AEFKVYHEEGVFPMIPAGGAAEDM 549 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: 1107 Number of extensions: 60 Number of successful extensions: 8 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: 561 Length adjustment: 37 Effective length of query: 581 Effective length of database: 524 Effective search space: 304444 Effective search space used: 304444 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_053767937.1 BVI061214_RS07970 (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.910858.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.2e-244 797.9 0.0 2.6e-244 797.8 0.0 1.0 1 NCBI__GCF_001280255.1:WP_053767937.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_001280255.1:WP_053767937.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 797.8 0.0 2.6e-244 2.6e-244 1 555 [. 1 551 [. 1 553 [. 0.98 Alignments for each domain: == domain 1 score: 797.8 bits; conditional E-value: 2.6e-244 TIGR00118 1 lkgaeilveslkkegvetvfGyPGGavlpiydalydselehilvrheqaaahaadGyarasGkvGvvlatsGP 73 +kgae+l+++l++egve++fG+PGGa++p ydalyds ++hilvrheq+ +haa yarasG+vGvv+atsGP NCBI__GCF_001280255.1:WP_053767937.1 1 MKGAEALLKALEREGVEVIFGHPGGAIMPTYDALYDSPIRHILVRHEQGGIHAATAYARASGRVGVVMATSGP 73 89*********************************************************************** PP TIGR00118 74 GatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafeias 146 Ga nlvtg+a+a +ds+P+v++tG v+++liG+dafqe+d++G+t+p+tkh++lv++++++p+++keaf+ias NCBI__GCF_001280255.1:WP_053767937.1 74 GALNLVTGLADALMDSTPVVAITGNVPRALIGTDAFQEADVTGVTMPITKHNYLVQDVNEIPRVVKEAFHIAS 146 ************************************************************************* PP TIGR00118 147 tGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllvGgGviiaeasee 219 tGrPGPvl+dlPkdv+ ae++ e + +++lpgykpt++gh++qi++al+++eka++P+l+vGgG+ + a++e NCBI__GCF_001280255.1:WP_053767937.1 147 TGRPGPVLIDLPKDVQLAEFTGEFDVELDLPGYKPTLRGHPKQIERALDALEKAERPILMVGGGAQH--AHAE 217 ****************************************************************976..5679 PP TIGR00118 220 lkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfapea 292 l +ae++ +pv+ttl+GlGafp +hpl lgm GmhGt +an a+++ad+++a+G rfddrvtg++++fap+a NCBI__GCF_001280255.1:WP_053767937.1 218 LLAFAEKTGLPVITTLMGLGAFPGNHPLWLGMPGMHGTVAANRAIHHADVILAIGLRFDDRVTGKVSRFAPHA 290 ************************************************************************9 PP TIGR00118 293 k.iihididPaeigknvkvdipivGdakkvleellkklkeeekkekeWlekieewkkeyilkldeeeesikPq 364 + iih+didPaeigk+v+++ipivGd++ vl+e+lk +k + W++++eew+++y+l++ + + + NCBI__GCF_001280255.1:WP_053767937.1 291 HtIIHVDIDPAEIGKVVRTHIPIVGDSRLVLKEMLKGAKPLRLAA--WWRELEEWRTRYPLRYRPRPHLQA-P 360 769**********************************99999888..*************99988776555.5 PP TIGR00118 365 kvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpeetvvavtGd 437 +vi++ ++ + ++aivtt+vGqhqm+aaq++++++pr+f+tsgGlGtmG GlP a+Ga++a pee v++ +Gd NCBI__GCF_001280255.1:WP_053767937.1 361 EVIRAFHEATGGNAIVTTGVGQHQMFAAQYFTVTRPRSFLTSGGLGTMGVGLPFAIGAQIARPEELVIDFDGD 433 8************************************************************************ PP TIGR00118 438 gsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeerysetklaselpdfvklaeayGvkgiriek 510 gsfqm+lqel+t+v+y +pvk+vilnn +lGmv+qWq+lf+ +ryse++la ++pdf+klaeayG+kg+r+e+ NCBI__GCF_001280255.1:WP_053767937.1 434 GSFQMTLQELATVVKYRLPVKVVILNNGYLGMVRQWQDLFHAKRYSEVYLADSNPDFAKLAEAYGIKGVRVER 506 ************************************************************************* PP TIGR00118 511 peeleeklkealeskepvlldvevdkeeevlPmvapGagldelve 555 +e+l++ ++ +l+ ++pv+ +++v +ee v+Pm++ G++ ++++ NCBI__GCF_001280255.1:WP_053767937.1 507 KEDLKKGVEAVLNADGPVVAEFKVYHEEGVFPMIPAGGAAEDMIL 551 ******************************************996 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (557 nodes) Target sequences: 1 (561 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: 34.62 // [ok]
This GapMind analysis is from Jul 25 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