Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate YP_002826533.1 NGR_c20170 acetolactate synthase 3 catalytic subunit
Query= metacyc::MONOMER-18810 (585 letters) >NCBI__GCF_000018545.1:YP_002826533.1 Length = 592 Score = 622 bits (1605), Expect = 0.0 Identities = 312/575 (54%), Positives = 416/575 (72%), Gaps = 6/575 (1%) Query: 13 SSAAPEMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHA 72 S +M GAEI++ AL + GVE+++GYPGGAVL IYDE+ +Q + +HILVRHEQ A H Sbjct: 2 SGTENQMTGAEIVLQALKDNGVEHIFGYPGGAVLPIYDEIFQQEEIQHILVRHEQGAGHM 61 Query: 73 ADGYARATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECD 132 A+GYAR+TGKVGV LVTSGPG TNAVT + A +DSIP+V I+G VPT IG DAFQECD Sbjct: 62 AEGYARSTGKVGVMLVTSGPGATNAVTPLQDALMDSIPLVCISGQVPTPLIGSDAFQECD 121 Query: 133 TVGITRPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKS 192 TVGITRP KHN+LVK+V DLA I +AF +A +GRPGPVVVDIPKD+ Y P + Sbjct: 122 TVGITRPCTKHNWLVKNVNDLARIIHEAFRVAQSGRPGPVVVDIPKDIQFATGTYTPPSA 181 Query: 193 I-DMRSYNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLA--NASDELRQLAALTGHP 249 + +SY P +G +I +A+AL++ A +P IY+GGGV+ + A+ LR+L LTG P Sbjct: 182 VPTQKSYQPKTQGDLKKIEEAIALMKTARQPIIYSGGGVINSGPQAAHFLRELVDLTGFP 241 Query: 250 VTNTLMGLGAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTS 309 +T+TLMGLGA+P + K ++GMLGMHGTYEANMAM +CDV+I IGARFDDR+ G F+ Sbjct: 242 ITSTLMGLGAYPASGKNWLGMLGMHGTYEANMAMHDCDVMICIGARFDDRITGRLNAFSP 301 Query: 310 QARKIIHIDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIE 369 ++K IHIDIDPSSI+K V+VD+PIVG+V VL+++I +A+ + L WW + Sbjct: 302 NSKK-IHIDIDPSSINKNVRVDVPIVGDVGTVLEDMIRLWRAAAKTLDKARLDGWWGAVA 360 Query: 370 QWRSVDCLKYDRSSEIIKPQYVVEKIWELTKG-DAFICSDVGQHQMWAAQFYKFDEPRRW 428 +WR+ + L Y + ++I PQY +++++EL+K D +I ++VGQHQMWAAQF+ F++P RW Sbjct: 361 KWRARNSLAYTPNDDVIMPQYAIQRLYELSKDRDTYITTEVGQHQMWAAQFFGFEQPNRW 420 Query: 429 INSGGLGTMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLN 488 + SGGLGTMG G P A+G++ A PE V+ I G+ SIQMCIQE+S +QY PVKI LN Sbjct: 421 MTSGGLGTMGYGFPAAIGVQVAHPESLVIDIAGDASIQMCIQEMSCAVQYGLPVKIFILN 480 Query: 489 NGYLGMVRQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRL 548 N Y+GMVRQWQ++ + NR SHSY +A+PDFVKLAEAYG VG+R EK +++ A+R Sbjct: 481 NQYMGMVRQWQQLLHGNRLSHSYTEAMPDFVKLAEAYGGVGIRCEKPGELDDAIRRMIDT 540 Query: 549 KDRTVFLDFQTDPTENVWPMVQAGKGISEMLLGAE 583 +F D + N +PM+ +GK +EMLL E Sbjct: 541 PAPVIF-DCRVANLANCFPMIPSGKAHNEMLLPDE 574 Lambda K H 0.319 0.135 0.407 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: 944 Number of extensions: 39 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: 585 Length of database: 592 Length adjustment: 37 Effective length of query: 548 Effective length of database: 555 Effective search space: 304140 Effective search space used: 304140 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 YP_002826533.1 NGR_c20170 (acetolactate synthase 3 catalytic 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.26449.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.4e-244 796.7 0.0 6.3e-244 796.5 0.0 1.0 1 lcl|NCBI__GCF_000018545.1:YP_002826533.1 NGR_c20170 acetolactate synthase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000018545.1:YP_002826533.1 NGR_c20170 acetolactate synthase 3 catalytic subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 796.5 0.0 6.3e-244 6.3e-244 1 555 [. 8 571 .. 8 573 .. 0.97 Alignments for each domain: == domain 1 score: 796.5 bits; conditional E-value: 6.3e-244 TIGR00118 1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvl 68 ++gaei++++lk++gve++fGyPGGavlpiyd+++ ++e++hilvrheq+a h+a+Gyar++GkvGv+l lcl|NCBI__GCF_000018545.1:YP_002826533.1 8 MTGAEIVLQALKDNGVEHIFGYPGGAVLPIYDEIFqQEEIQHILVRHEQGAGHMAEGYARSTGKVGVML 76 79*********************************999******************************* PP TIGR00118 69 atsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpei 137 +tsGPGatn+vt++ +a +ds+Plv ++Gqv+t liGsdafqe+d +Git+p+tkh++lvk+++dl++i lcl|NCBI__GCF_000018545.1:YP_002826533.1 77 VTSGPGATNAVTPLQDALMDSIPLVCISGQVPTPLIGSDAFQECDTVGITRPCTKHNWLVKNVNDLARI 145 ********************************************************************* PP TIGR00118 138 lkeafeiastGrPGPvlvdlPkdvteaeieleveekv.elpgykptvkghklqikkaleliekakkPvl 205 ++eaf +a++GrPGPv+vd+Pkd++ a+ +++ ++ v + ++y+p+++g+ ++i++a+ l+++a++P++ lcl|NCBI__GCF_000018545.1:YP_002826533.1 146 IHEAFRVAQSGRPGPVVVDIPKDIQFATGTYTPPSAVpTQKSYQPKTQGDLKKIEEAIALMKTARQPII 214 ******************************99997763679**************************** PP TIGR00118 206 lvGgGviia..easeelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadllia 272 + GgGvi + +a + l+el++ + p+t+tl+GlGa+p+ ++ lgmlGmhGt+ean+a++++d++i+ lcl|NCBI__GCF_000018545.1:YP_002826533.1 215 YSGGGVINSgpQAAHFLRELVDLTGFPITSTLMGLGAYPASGKNWLGMLGMHGTYEANMAMHDCDVMIC 283 *******883357789***************************************************** PP TIGR00118 273 vGarfddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkee....ekkek 337 +Garfddr+tg l+ f+p++k ihididP++i+knv+vd+pivGd+ +vle++++ ++ +k lcl|NCBI__GCF_000018545.1:YP_002826533.1 284 IGARFDDRITGRLNAFSPNSKKIHIDIDPSSINKNVRVDVPIVGDVGTVLEDMIRLWRAAaktlDKARL 352 ******************************************************987766555555556 PP TIGR00118 338 e.WlekieewkkeyilkldeeeesikPqkvikelskllkd.eaivttdvGqhqmwaaqfyktkkprkfi 404 + W+ +++w++++ l++ +++ i Pq+ i++l++l kd ++++tt+vGqhqmwaaqf+ +++p++++ lcl|NCBI__GCF_000018545.1:YP_002826533.1 353 DgWWGAVAKWRARNSLAYTPNDDVIMPQYAIQRLYELSKDrDTYITTEVGQHQMWAAQFFGFEQPNRWM 421 68*************************************999*************************** PP TIGR00118 405 tsgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqW 473 tsgGlGtmG+G+Paa+G++va+pe+ v++++Gd+s+qm +qe+s +v+y++pvki ilnn+++Gmv+qW lcl|NCBI__GCF_000018545.1:YP_002826533.1 422 TSGGLGTMGYGFPAAIGVQVAHPESLVIDIAGDASIQMCIQEMSCAVQYGLPVKIFILNNQYMGMVRQW 490 ********************************************************************* PP TIGR00118 474 qelfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlP 542 q+l++ +r s+++ ++ +pdfvklaeayG +gir ekp el++++++++ + +pv++d +v++ ++++P lcl|NCBI__GCF_000018545.1:YP_002826533.1 491 QQLLHGNRLSHSYTEA-MPDFVKLAEAYGGVGIRCEKPGELDDAIRRMIDTPAPVIFDCRVANLANCFP 558 ***************5.**************************************************** PP TIGR00118 543 mvapGagldelve 555 m+++G++ +e++ lcl|NCBI__GCF_000018545.1:YP_002826533.1 559 MIPSGKAHNEMLL 571 **********985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (557 nodes) Target sequences: 1 (592 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: 8.84 // [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