Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate WP_037572586.1 BS73_RS14735 acetolactate synthase large subunit
Query= BRENDA::P9WG41 (618 letters) >NCBI__GCF_000744815.1:WP_037572586.1 Length = 618 Score = 835 bits (2156), Expect = 0.0 Identities = 406/602 (67%), Positives = 480/602 (79%), Gaps = 15/602 (2%) Query: 27 AARPKHVALQQLTGAQAVIRSLEELGVDVIFGIPGGAVLPVYDPLFDSKKLRHVLVRHEQ 86 AA+P + ++GAQ++IRSLE +GVD +FG+PGGA+LP YDPL DS+KLRHVLVRHEQ Sbjct: 19 AAQP--TVAETMSGAQSLIRSLEAVGVDTVFGLPGGAILPAYDPLMDSEKLRHVLVRHEQ 76 Query: 87 GAGHAASGYAHVTGRVGVCMATSGPGATNLVTPLADAQMDSIPVVAITGQVGRGLIGTDA 146 GAGHAA+GYA TG+VGVCMATSGPGATNLVTP+ADA MDS+P+VAITGQV IGTDA Sbjct: 77 GAGHAATGYAQATGKVGVCMATSGPGATNLVTPIADAYMDSVPMVAITGQVASTSIGTDA 136 Query: 147 FQEADISGITMPITKHNFLVRSGDDIPRVLAEAFHIAASGRPGAVLVDIPKDVLQGQCTF 206 FQEADI GITMPITKHNFLV DIPRV++EAFHIAA+GRPG VLVD+ KD +Q Q F Sbjct: 137 FQEADICGITMPITKHNFLVTDAADIPRVISEAFHIAATGRPGPVLVDVAKDAMQKQTVF 196 Query: 207 SWPPRMELPGYKPNTKPHSRQVREAAKLIAAARKPVLYVGGGVIRGEATEQLRELAELTG 266 WP +LPGY+P T+PH +Q+REAA+L+A AR+PVLYVGGGV++ AT +L+ LAELT Sbjct: 197 RWPVEHQLPGYRPVTRPHGKQIREAARLLAQARRPVLYVGGGVLKARATAELKILAELTK 256 Query: 267 IPVVTTLMARGAFPDSHRQNLGMPGMHGTVAAVAALQRSDLLIALGTRFDDRVTGKLDSF 326 PV TTLM GAFPDSH Q+LGMPGMHGTVAAV +LQ++DL+IALG RFDDRVTGKLD F Sbjct: 257 APVTTTLMGIGAFPDSHPQHLGMPGMHGTVAAVTSLQKADLIIALGARFDDRVTGKLDGF 316 Query: 327 APEAKVIHADIDPAEIGKNRHADVPIVGDVKAVITELIAMLRHH--HIPGTIEMADWWAY 384 AP A ++HADIDPAEIGKNR ADVPIVGD + V+ +LI +++ H PG + WW Sbjct: 317 APYATIVHADIDPAEIGKNRAADVPIVGDAREVLADLIVAVQNELDHTPGACDYTAWWEQ 376 Query: 385 LNGVRKTYPLSYGPQSDGSLSPEYVIEKLGEIAGPDAVFVAGVGQHQMWAAQFIRYEKPR 444 L G RKTYPL + P DG L+P+ VIE++G++ GPDA++ AGVGQHQMWA+QFI++E P Sbjct: 377 LGGWRKTYPLGWDPAPDGLLTPQQVIERIGQLVGPDAIYAAGVGQHQMWASQFIQFEHPA 436 Query: 445 SWLNSGGLGTMGFAIPAAMGAKIALPGTEVWAIDGDGCFQMTNQELATCAVEGIPVKVAL 504 +WLNSGG GTMG+A+PAAMGAK PGTEVWAIDGDGCFQMTNQEL TCA+ IP+KVA+ Sbjct: 437 TWLNSGGAGTMGYAVPAAMGAKAGQPGTEVWAIDGDGCFQMTNQELVTCALNNIPIKVAV 496 Query: 505 INNGNLGMVRQWQSLFYAERYSQTDL-----------ATHSHRIPDFVKLAEALGCVGLR 553 INNG+LGMVRQWQ+LFY ERYS T L RIPDFVKLAEA+GC GLR Sbjct: 497 INNGSLGMVRQWQTLFYNERYSNTVLHSGPGHDGKEQPAQGTRIPDFVKLAEAMGCHGLR 556 Query: 554 CEREEDVVDVINQARAINDCPVVIDFIVGADAQVWPMVAAGTSNDEIQAARGIRPLFDDI 613 CE + + VI QAR++ND PVVIDFIV DA VWPMVAAGT+NDEI AAR +RP F D Sbjct: 557 CESPDQLDAVIEQARSLNDAPVVIDFIVHQDAMVWPMVAAGTNNDEIMAARDVRPDFGDN 616 Query: 614 TE 615 E Sbjct: 617 EE 618 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: 1203 Number of extensions: 45 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: 618 Length of database: 618 Length adjustment: 37 Effective length of query: 581 Effective length of database: 581 Effective search space: 337561 Effective search space used: 337561 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_037572586.1 BS73_RS14735 (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.380344.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2e-232 758.5 0.5 3.2e-232 757.8 0.5 1.3 1 NCBI__GCF_000744815.1:WP_037572586.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000744815.1:WP_037572586.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 757.8 0.5 3.2e-232 3.2e-232 1 555 [. 28 605 .. 28 607 .. 0.95 Alignments for each domain: == domain 1 score: 757.8 bits; conditional E-value: 3.2e-232 TIGR00118 1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvlatsG 72 ++ga+ l++sl++ gv+tvfG PGGa+lp yd l +++l+h+lvrheq+a haa Gya+a+GkvGv++atsG NCBI__GCF_000744815.1:WP_037572586.1 28 MSGAQSLIRSLEAVGVDTVFGLPGGAILPAYDPLMdSEKLRHVLVRHEQGAGHAATGYAQATGKVGVCMATSG 100 79*********************************7789********************************** PP TIGR00118 73 PGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafeia 145 PGatnlvt+ia+ay+dsvP+v++tGqva++ iG+dafqe+di Git+p+tkh+flv++a+d+p+++ eaf+ia NCBI__GCF_000744815.1:WP_037572586.1 101 PGATNLVTPIADAYMDSVPMVAITGQVASTSIGTDAFQEADICGITMPITKHNFLVTDAADIPRVISEAFHIA 173 ************************************************************************* PP TIGR00118 146 stGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllvGgGviiaease 218 +tGrPGPvlvd+ kd +++++ ++ + + +lpgy+p +++h +qi++a+ l+++a++Pvl+vGgGv++a a++ NCBI__GCF_000744815.1:WP_037572586.1 174 ATGRPGPVLVDVAKDAMQKQTVFRWPVEHQLPGYRPVTRPHGKQIREAARLLAQARRPVLYVGGGVLKARATA 246 ************************************************************************* PP TIGR00118 219 elkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfape 291 elk lae +k+pvtttl+G+Gafp+ hp+ lgm GmhGt +a +++++adl+ia+Garfddrvtg+l+ fap NCBI__GCF_000744815.1:WP_037572586.1 247 ELKILAELTKAPVTTTLMGIGAFPDSHPQHLGMPGMHGTVAAVTSLQKADLIIALGARFDDRVTGKLDGFAPY 319 ************************************************************************* PP TIGR00118 292 akiihididPaeigknvkvdipivGdakkvleellkklkee......ekkekeWlekieewkkeyilkldeee 358 a+i+h didPaeigkn+++d+pivGda++vl++l+ ++++e + + W+e++ w+k+y+l d NCBI__GCF_000744815.1:WP_037572586.1 320 ATIVHADIDPAEIGKNRAADVPIVGDAREVLADLIVAVQNEldhtpgACDYTAWWEQLGGWRKTYPLGWDPAP 392 *************************************9999877664334445***************99888 PP TIGR00118 359 es.ikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpeet 430 + + Pq+vi+++ +l+ +ai++++vGqhqmwa+qf ++++p ++++sgG+GtmG+ +Paa+Gak ++p ++ NCBI__GCF_000744815.1:WP_037572586.1 393 DGlLTPQQVIERIGQLVGPDAIYAAGVGQHQMWASQFIQFEHPATWLNSGGAGTMGYAVPAAMGAKAGQPGTE 465 7769********************************************************************* PP TIGR00118 431 vvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeerysetklas.............. 489 v a++Gdg fqm+ qel t++ +ip+k+ ++nn lGmv+qWq lfy+erys+t l+s NCBI__GCF_000744815.1:WP_037572586.1 466 VWAIDGDGCFQMTNQELVTCALNNIPIKVAVINNGSLGMVRQWQTLFYNERYSNTVLHSgpghdgkeqpaqgt 538 ******************************************************9886422222222222222 PP TIGR00118 490 elpdfvklaeayGvkgiriekpeeleeklkealesk.epvlldvevdkeeevlPmvapGagldelve 555 pdfvklaea+G +g+r e+p++l++ +++a + + +pv++d+ v++++ v+Pmva G+++de++ NCBI__GCF_000744815.1:WP_037572586.1 539 RIPDFVKLAEAMGCHGLRCESPDQLDAVIEQARSLNdAPVVIDFIVHQDAMVWPMVAAGTNNDEIMA 605 479*****************************998769**************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (557 nodes) Target sequences: 1 (618 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03 # Mc/sec: 9.08 // [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