Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_029151720.1 METMI_RS0114455 acetolactate synthase 3 large subunit
Query= metacyc::MONOMER-18810 (585 letters) >NCBI__GCF_000384075.1:WP_029151720.1 Length = 578 Score = 791 bits (2043), Expect = 0.0 Identities = 381/565 (67%), Positives = 459/565 (81%), Gaps = 3/565 (0%) Query: 18 EMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYA 77 E+ GA+ILV +L +EGVEY++GYPGGAVL++YD + +Q +HILVRHEQ A HAADGYA Sbjct: 2 ELSGAQILVQSLKDEGVEYIFGYPGGAVLHLYDAIFQQDAVKHILVRHEQGATHAADGYA 61 Query: 78 RATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGIT 137 RATGK GV LVTSGPG TNAVTGIATAY+DSIPMV+I+G VP+ IG DAFQE D VGIT Sbjct: 62 RATGKPGVVLVTSGPGATNAVTGIATAYMDSIPMVIISGQVPSPVIGSDAFQEVDMVGIT 121 Query: 138 RPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACK--YEYPKSIDM 195 RP VKHNFLVKDV LA T+KKAF++A TGRPGPVVVDIPKD++ K Y+YPK + + Sbjct: 122 RPCVKHNFLVKDVTKLAETVKKAFYVATTGRPGPVVVDIPKDITDPNIKVPYKYPKKVTI 181 Query: 196 RSYNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTNTLM 255 RSYNP G Q++KAV LL A +P IY+GGGVVL AS EL + + L G+P+TNTLM Sbjct: 182 RSYNPAVNGDKEQVKKAVDLLMAAHKPVIYSGGGVVLGEASKELTEFSQLLGYPITNTLM 241 Query: 256 GLGAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKII 315 GLGA+P T KQF+GMLGMHGTYEANMAM D++IA+GARFDDRV G F A KII Sbjct: 242 GLGAYPATDKQFIGMLGMHGTYEANMAMHESDLIIAVGARFDDRVTGKLDMFCPYA-KII 300 Query: 316 HIDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIEQWRSVD 375 HIDIDP+SISK VKVD+ IVG VK+VL+++I IK KP+++AL WW+QI QWR+V+ Sbjct: 301 HIDIDPASISKTVKVDVAIVGEVKNVLEQMITLIKDHKAKPQKKALEAWWQQIGQWRAVE 360 Query: 376 CLKYDRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPRRWINSGGLG 435 CL++DR S +IKPQ+V+E+++ +TKGDA++ SDVGQHQMWAAQ+YKFD+PRRWINSGGLG Sbjct: 361 CLEFDRESPLIKPQFVIEQLYAVTKGDAYVTSDVGQHQMWAAQYYKFDKPRRWINSGGLG 420 Query: 436 TMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGMV 495 TMG GLP A+G+K AFP+ +V +TGE SIQMCIQELST LQY TP+KI +LNN Y+GMV Sbjct: 421 TMGFGLPAAIGVKLAFPDADVACVTGEASIQMCIQELSTALQYKTPIKIINLNNRYMGMV 480 Query: 496 RQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTVFL 555 RQWQE Y++RYSHSYMD +P+FVKLAEAYGHVGMRVE+ DV AL EAF LKDRTVFL Sbjct: 481 RQWQEFSYESRYSHSYMDTIPEFVKLAEAYGHVGMRVERPEDVRAALEEAFALKDRTVFL 540 Query: 556 DFQTDPTENVWPMVQAGKGISEMLL 580 D TD TENV+PM++AGKG +M L Sbjct: 541 DIITDRTENVYPMIEAGKGHHDMKL 565 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: 1040 Number of extensions: 33 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: 585 Length of database: 578 Length adjustment: 36 Effective length of query: 549 Effective length of database: 542 Effective search space: 297558 Effective search space used: 297558 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_029151720.1 METMI_RS0114455 (acetolactate synthase 3 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.11284.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-269 880.7 3.5 2.4e-269 880.4 3.5 1.0 1 lcl|NCBI__GCF_000384075.1:WP_029151720.1 METMI_RS0114455 acetolactate syn Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000384075.1:WP_029151720.1 METMI_RS0114455 acetolactate synthase 3 large subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 880.4 3.5 2.4e-269 2.4e-269 1 553 [. 3 563 .. 3 566 .. 0.98 Alignments for each domain: == domain 1 score: 880.4 bits; conditional E-value: 2.4e-269 TIGR00118 1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvl 68 l+ga+ilv+slk+egve++fGyPGGavl++yda++ ++ ++hilvrheq+a+haadGyara+Gk+Gvvl lcl|NCBI__GCF_000384075.1:WP_029151720.1 3 LSGAQILVQSLKDEGVEYIFGYPGGAVLHLYDAIFqQDAVKHILVRHEQGATHAADGYARATGKPGVVL 71 68*********************************8899****************************** PP TIGR00118 69 atsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpei 137 +tsGPGatn+vtgiatay+ds+P+v+++Gqv++ +iGsdafqe+d++Git+p++kh+flvk++ l+e+ lcl|NCBI__GCF_000384075.1:WP_029151720.1 72 VTSGPGATNAVTGIATAYMDSIPMVIISGQVPSPVIGSDAFQEVDMVGITRPCVKHNFLVKDVTKLAET 140 ********************************************************************* PP TIGR00118 138 lkeafeiastGrPGPvlvdlPkdvteaeieleve..ekvelpgykptvkghklqikkaleliekakkPv 204 +k+af++a+tGrPGPv+vd+Pkd+t+++i+++++ +kv++++y+p v+g+k q+kka++l+++a+kPv lcl|NCBI__GCF_000384075.1:WP_029151720.1 141 VKKAFYVATTGRPGPVVVDIPKDITDPNIKVPYKypKKVTIRSYNPAVNGDKEQVKKAVDLLMAAHKPV 209 ******************************998888********************************* PP TIGR00118 205 llvGgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliav 273 ++ GgGv+ +eas+el+e+++ l p+t tl+GlGa+p+++++++gmlGmhGt+ean+a++e+dl+iav lcl|NCBI__GCF_000384075.1:WP_029151720.1 210 IYSGGGVVLGEASKELTEFSQLLGYPITNTLMGLGAYPATDKQFIGMLGMHGTYEANMAMHESDLIIAV 278 ********************************************************************* PP TIGR00118 274 GarfddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkee....ekkeke 338 Garfddrvtg+l++f+p akiihididPa+i+k+vkvd++ivG++k+vle++++ +k++ +kk e lcl|NCBI__GCF_000384075.1:WP_029151720.1 279 GARFDDRVTGKLDMFCPYAKIIHIDIDPASISKTVKVDVAIVGEVKNVLEQMITLIKDHkakpQKKALE 347 *****************************************************9998877777666777 PP TIGR00118 339 .WlekieewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfits 406 W+++i +w++ +l++d+e+ ikPq vi++l+ ++k++a+vt+dvGqhqmwaaq+yk++kpr++i+s lcl|NCBI__GCF_000384075.1:WP_029151720.1 348 aWWQQIGQWRAVECLEFDRESPLIKPQFVIEQLYAVTKGDAYVTSDVGQHQMWAAQYYKFDKPRRWINS 416 8******************************************************************** PP TIGR00118 407 gGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqe 475 gGlGtmGfGlPaa+G+k+a p+++v +vtG++s+qm +qelst+ +y++p+ki++lnn+++Gmv+qWqe lcl|NCBI__GCF_000384075.1:WP_029151720.1 417 GGLGTMGFGLPAAIGVKLAFPDADVACVTGEASIQMCIQELSTALQYKTPIKIINLNNRYMGMVRQWQE 485 ********************************************************************* PP TIGR00118 476 lfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealesk.epvlldvevdkeeevlPm 543 + ye rys++++ + p+fvklaeayG++g+r+e+pe++ ++l+ea++ k + v+ld+ d++e+v+Pm lcl|NCBI__GCF_000384075.1:WP_029151720.1 486 FSYESRYSHSYMDT-IPEFVKLAEAYGHVGMRVERPEDVRAALEEAFALKdRTVFLDIITDRTENVYPM 553 *************5.*******************************9987699**************** PP TIGR00118 544 vapGagldel 553 + G+g +++ lcl|NCBI__GCF_000384075.1:WP_029151720.1 554 IEAGKGHHDM 563 ******9998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (557 nodes) Target sequences: 1 (578 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: 00:00:00.02 # Mc/sec: 11.22 // [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