Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_011736417.1 PPRO_RS12635 acetolactate synthase, large subunit, biosynthetic type
Query= metacyc::MONOMER-18810 (585 letters) >NCBI__GCF_000015045.1:WP_011736417.1 Length = 566 Score = 631 bits (1627), Expect = 0.0 Identities = 319/567 (56%), Positives = 407/567 (71%), Gaps = 4/567 (0%) Query: 18 EMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYA 77 +M GA IL+ L +EGV+ V+GYPGG VL +YDEL + HI+ RHEQA HAADGYA Sbjct: 2 KMNGARILLECLMKEGVDTVFGYPGGTVLNVYDELFGCKEIRHIMPRHEQAGTHAADGYA 61 Query: 78 RATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGIT 137 RATGKVGVA+ TSGPG TN VTGIATAY+DSIPMV+ITG VPT IG DAFQE D VGIT Sbjct: 62 RATGKVGVAIATSGPGATNTVTGIATAYMDSIPMVIITGQVPTALIGNDAFQEVDIVGIT 121 Query: 138 RPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRS 197 R KHNFLVKDV D+A IKKAF+IA TGRPGPV+VD+PKDV ++ YP+S+++RS Sbjct: 122 RSCTKHNFLVKDVNDIAPIIKKAFYIARTGRPGPVLVDLPKDVQIAKTEFCYPESVELRS 181 Query: 198 YNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTNTLMGL 257 Y P GH Q+ KAV++L + RP +Y GGGV+L+NA+ EL L+ L PVT TLMGL Sbjct: 182 YKPTTGGHPRQVSKAVSMLLASHRPVMYVGGGVILSNAAPELTALSRLLSIPVTTTLMGL 241 Query: 258 GAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKIIHI 317 GAFPG +GMLGMHG Y ANMAM + D+++A+GARFDDRV G F A KIIHI Sbjct: 242 GAFPGDDVNSLGMLGMHGAYCANMAMTHSDLIVAVGARFDDRVTGKVDTFAPHA-KIIHI 300 Query: 318 DIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKAS--DIKPKREALAKWWEQIEQWRSVD 375 D+DP+SI K V+VD+PIVG+V+DVL ++I +++ S D RE+LA W EQI W+ Sbjct: 301 DVDPTSIRKNVRVDLPIVGDVRDVLTKMIKKVEKSEGDQAAYRESLAPWHEQIAGWKEKH 360 Query: 376 CLKYDRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPRRWINSGGLG 435 + + RSS +IKPQ+V++K+ EL+ DA + +DVGQHQMW AQF+ F PR + SGGLG Sbjct: 361 PVSFTRSSAVIKPQFVIQKLRELSDRDAIVSTDVGQHQMWTAQFFSFTGPRTLLTSGGLG 420 Query: 436 TMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGMV 495 TMG GLP AMG + AFP ++V+ I G+G IQM IQE++T +Q PVKI +NN +LGMV Sbjct: 421 TMGFGLPAAMGAQAAFPGRQVIAICGDGGIQMNIQEMATLVQNRLPVKIVIINNNFLGMV 480 Query: 496 RQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTVFL 555 RQWQE+ +D RYS S ++ D++KLA+AYG G K S+VE +R+ F + V + Sbjct: 481 RQWQEMFFDKRYSQSCLELPIDYIKLADAYGAKGFVASKPSEVETVIRQGF-AEPGPVIM 539 Query: 556 DFQTDPTENVWPMVQAGKGISEMLLGA 582 +F+ E V PMV +G ++EMLL A Sbjct: 540 EFRVAREEKVLPMVPSGASLNEMLLNA 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: 884 Number of extensions: 32 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_011736417.1 PPRO_RS12635 (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.8347.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.7e-256 835.5 0.6 1.1e-255 835.3 0.6 1.0 1 lcl|NCBI__GCF_000015045.1:WP_011736417.1 PPRO_RS12635 acetolactate syntha Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000015045.1:WP_011736417.1 PPRO_RS12635 acetolactate synthase, large subunit, biosynthetic type # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 835.3 0.6 1.1e-255 1.1e-255 1 555 [. 3 564 .. 3 566 .] 0.98 Alignments for each domain: == domain 1 score: 835.3 bits; conditional E-value: 1.1e-255 TIGR00118 1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvl 68 ++ga+il+e l kegv+tvfGyPGG+vl++yd+l+ +e++hi++rheqa +haadGyara+GkvGv++ lcl|NCBI__GCF_000015045.1:WP_011736417.1 3 MNGARILLECLMKEGVDTVFGYPGGTVLNVYDELFgCKEIRHIMPRHEQAGTHAADGYARATGKVGVAI 71 78*********************************99******************************** PP TIGR00118 69 atsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpei 137 atsGPGatn+vtgiatay+ds+P+v++tGqv+t+liG+dafqe+di+Git+++tkh+flvk+++d++ i lcl|NCBI__GCF_000015045.1:WP_011736417.1 72 ATSGPGATNTVTGIATAYMDSIPMVIITGQVPTALIGNDAFQEVDIVGITRSCTKHNFLVKDVNDIAPI 140 ********************************************************************* PP TIGR00118 138 lkeafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvll 206 +k+af+ia tGrPGPvlvdlPkdv+ a++e+ ++e+vel++ykpt+ gh++q+ ka+ ++ ++++Pv++ lcl|NCBI__GCF_000015045.1:WP_011736417.1 141 IKKAFYIARTGRPGPVLVDLPKDVQIAKTEFCYPESVELRSYKPTTGGHPRQVSKAVSMLLASHRPVMY 209 ********************************************************************* PP TIGR00118 207 vGgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGa 275 vGgGvi ++a el+ l+ l ipvtttl+GlGafp d+ ++lgmlGmhG++ an+a++++dl++avGa lcl|NCBI__GCF_000015045.1:WP_011736417.1 210 VGGGVILSNAAPELTALSRLLSIPVTTTLMGLGAFPGDDVNSLGMLGMHGAYCANMAMTHSDLIVAVGA 278 ********************************************************************* PP TIGR00118 276 rfddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkee......ekkeke 338 rfddrvtg++++fap+akiihid+dP++i knv+vd+pivGd++ vl++++kk+++ +++ lcl|NCBI__GCF_000015045.1:WP_011736417.1 279 RFDDRVTGKVDTFAPHAKIIHIDVDPTSIRKNVRVDLPIVGDVRDVLTKMIKKVEKSegdqaaYRESLA 347 ******************************************************999787765344445 PP TIGR00118 339 .WlekieewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfits 406 W e+i+ wk+++++++ +++ ikPq vi++l +l + +aiv+tdvGqhqmw+aqf++++ pr+ +ts lcl|NCBI__GCF_000015045.1:WP_011736417.1 348 pWHEQIAGWKEKHPVSFTRSSAVIKPQFVIQKLRELSDRDAIVSTDVGQHQMWTAQFFSFTGPRTLLTS 416 7******************************************************************** PP TIGR00118 407 gGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqe 475 gGlGtmGfGlPaa+Ga+ a p +v+a++Gdg++qmn+qe++t+v+ +pvkivi+nn++lGmv+qWqe lcl|NCBI__GCF_000015045.1:WP_011736417.1 417 GGLGTMGFGLPAAMGAQAAFPGRQVIAICGDGGIQMNIQEMATLVQNRLPVKIVIINNNFLGMVRQWQE 485 ********************************************************************* PP TIGR00118 476 lfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlPmv 544 +f+++rys+++l+ d++kla+ayG+kg +kp+e+e +++ +++ +pv+++++v++ee+vlPmv lcl|NCBI__GCF_000015045.1:WP_011736417.1 486 MFFDKRYSQSCLEL-PIDYIKLADAYGAKGFVASKPSEVETVIRQGFAEPGPVIMEFRVAREEKVLPMV 553 *************6.88**************************************************** PP TIGR00118 545 apGagldelve 555 ++Ga+l+e++ lcl|NCBI__GCF_000015045.1:WP_011736417.1 554 PSGASLNEMLL 564 *********85 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.04 # Mc/sec: 7.37 // [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