Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_012470550.1 GLOV_RS12400 acetolactate synthase, large subunit, biosynthetic type
Query= metacyc::MONOMER-18810 (585 letters) >NCBI__GCF_000020385.1:WP_012470550.1 Length = 566 Score = 622 bits (1603), Expect = 0.0 Identities = 302/567 (53%), Positives = 409/567 (72%), Gaps = 4/567 (0%) Query: 18 EMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYA 77 +M GA IL+ +L EGV+ V+GYPGG V+ +YDEL + HIL RHEQ HAADGYA Sbjct: 2 KMNGARILLESLKREGVDLVFGYPGGTVINLYDELMNVREIRHILPRHEQGGTHAADGYA 61 Query: 78 RATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGIT 137 RATGKVGVA+ TSGPG TN +TGIATAY+DSIPMV+ITG VPT IG DAFQE D +GIT Sbjct: 62 RATGKVGVAIATSGPGATNTITGIATAYMDSIPMVIITGQVPTPLIGNDAFQEVDIIGIT 121 Query: 138 RPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRS 197 RPI KH+FL++ +D+ ++KAF+IA +GRPGPV++D PKDV + ++++P+SI++R Sbjct: 122 RPITKHSFLIRHAKDIPTIVRKAFYIARSGRPGPVLIDFPKDVQISQAEFKWPESIEIRG 181 Query: 198 YNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTNTLMGL 257 Y P +GH Q+ KAV +L A RP +Y GGGV+LANA++EL +LA PVT TLMGL Sbjct: 182 YKPNLEGHQKQVEKAVDMLLVARRPVMYVGGGVILANAAEELTELARTLQFPVTTTLMGL 241 Query: 258 GAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKIIHI 317 GAFP + MLGMHG Y ANMAM + D+++A+GARFDDRV G A F A KIIHI Sbjct: 242 GAFPENDPLSLKMLGMHGAYAANMAMTHSDLILAVGARFDDRVTGKIATFAPHA-KIIHI 300 Query: 318 DIDPSSISKRVKVDIPIVGNVKDVLQELIAQIK--ASDIKPKREALAKWWEQIEQWRSVD 375 D+DP+SI K V+VD+PIVG+ KDVL ++I +K + + A+ W E I W++ Sbjct: 301 DVDPTSIRKNVRVDLPIVGDTKDVLVKMIECLKGQTEKVSAQHSAMEAWHEDISGWKAKH 360 Query: 376 CLKYDRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPRRWINSGGLG 435 + Y +SS +IKPQYV++K+ EL++ DA + +DVGQHQMW AQF++F++PR + SGGLG Sbjct: 361 PIAYKQSSSVIKPQYVIQKLRELSEDDAIMATDVGQHQMWTAQFFEFNQPRTLLTSGGLG 420 Query: 436 TMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGMV 495 TMG GLP AMG + A+P+++V+ + G+G +QM +QEL+T +Q+ PVKI LNN +LGMV Sbjct: 421 TMGFGLPAAMGAQAAYPKRQVICVCGDGGVQMNMQELATLVQHRLPVKIVVLNNNFLGMV 480 Query: 496 RQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTVFL 555 RQWQE+ +D RYS + ++ DF ++AEAYG G++ +K S+VE ++E F D V + Sbjct: 481 RQWQELFFDKRYSQTCLELPMDFARIAEAYGAKGLKADKPSEVEQVIKEGF-AHDGPVIM 539 Query: 556 DFQTDPTENVWPMVQAGKGISEMLLGA 582 +F+ E V PMV AG ++EM+L A Sbjct: 540 EFKIAREEKVLPMVPAGASLNEMVLNA 566 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: 902 Number of extensions: 30 Number of successful extensions: 4 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: 566 Length adjustment: 36 Effective length of query: 549 Effective length of database: 530 Effective search space: 290970 Effective search space used: 290970 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_012470550.1 GLOV_RS12400 (acetolactate synthase, large subunit, biosynthetic type)
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.20674.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-262 857.0 1.7 3.3e-262 856.8 1.7 1.0 1 lcl|NCBI__GCF_000020385.1:WP_012470550.1 GLOV_RS12400 acetolactate syntha Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000020385.1:WP_012470550.1 GLOV_RS12400 acetolactate synthase, large subunit, biosynthetic type # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 856.8 1.7 3.3e-262 3.3e-262 1 555 [. 3 564 .. 3 566 .] 0.98 Alignments for each domain: == domain 1 score: 856.8 bits; conditional E-value: 3.3e-262 TIGR00118 1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvl 68 ++ga+il+eslk+egv+ vfGyPGG+v+++yd+l e++hil+rheq+ +haadGyara+GkvGv++ lcl|NCBI__GCF_000020385.1:WP_012470550.1 3 MNGARILLESLKREGVDLVFGYPGGTVINLYDELMnVREIRHILPRHEQGGTHAADGYARATGKVGVAI 71 78********************************9899******************************* PP TIGR00118 69 atsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpei 137 atsGPGatn++tgiatay+ds+P+v++tGqv+t liG+dafqe+di+Git+p+tkhsfl+++a+d+p+i lcl|NCBI__GCF_000020385.1:WP_012470550.1 72 ATSGPGATNTITGIATAYMDSIPMVIITGQVPTPLIGNDAFQEVDIIGITRPITKHSFLIRHAKDIPTI 140 ********************************************************************* PP TIGR00118 138 lkeafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvll 206 +++af+ia +GrPGPvl+d+Pkdv+ ++ e++ +e++e++gykp+++gh++q++ka++++ a++Pv++ lcl|NCBI__GCF_000020385.1:WP_012470550.1 141 VRKAFYIARSGRPGPVLIDFPKDVQISQAEFKWPESIEIRGYKPNLEGHQKQVEKAVDMLLVARRPVMY 209 ********************************************************************* PP TIGR00118 207 vGgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGa 275 vGgGvi a+a eel+ela +l+ pvtttl+GlGafpe++pl+l mlGmhG+++an+a++++dl++avGa lcl|NCBI__GCF_000020385.1:WP_012470550.1 210 VGGGVILANAAEELTELARTLQFPVTTTLMGLGAFPENDPLSLKMLGMHGAYAANMAMTHSDLILAVGA 278 ********************************************************************* PP TIGR00118 276 rfddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkee......ekkeke 338 rfddrvtg++a+fap+akiihid+dP++i knv+vd+pivGd+k vl ++++ lk + +++ +e lcl|NCBI__GCF_000020385.1:WP_012470550.1 279 RFDDRVTGKIATFAPHAKIIHIDVDPTSIRKNVRVDLPIVGDTKDVLVKMIECLKGQtekvsaQHSAME 347 ***************************************************988776667776555556 PP TIGR00118 339 .WlekieewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfits 406 W e i+ wk++++++++++++ ikPq+vi++l +l +d+ai++tdvGqhqmw+aqf+++++pr+ +ts lcl|NCBI__GCF_000020385.1:WP_012470550.1 348 aWHEDISGWKAKHPIAYKQSSSVIKPQYVIQKLRELSEDDAIMATDVGQHQMWTAQFFEFNQPRTLLTS 416 7******************************************************************** PP TIGR00118 407 gGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqe 475 gGlGtmGfGlPaa+Ga+ a p+ +v++v+Gdg++qmn+qel+t+v+ +pvkiv+lnn++lGmv+qWqe lcl|NCBI__GCF_000020385.1:WP_012470550.1 417 GGLGTMGFGLPAAMGAQAAYPKRQVICVCGDGGVQMNMQELATLVQHRLPVKIVVLNNNFLGMVRQWQE 485 ********************************************************************* PP TIGR00118 476 lfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlPmv 544 lf+++rys+t+l+ df+++aeayG+kg++ kp+e+e+ +ke +++++pv++++++++ee+vlPmv lcl|NCBI__GCF_000020385.1:WP_012470550.1 486 LFFDKRYSQTCLEL-PMDFARIAEAYGAKGLKADKPSEVEQVIKEGFAHDGPVIMEFKIAREEKVLPMV 553 *************6.88**************************************************** PP TIGR00118 545 apGagldelve 555 + Ga+l+e+v lcl|NCBI__GCF_000020385.1:WP_012470550.1 554 PAGASLNEMVL 564 *********96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (557 nodes) Target sequences: 1 (566 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 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 10.81 // [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