Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_013135583.1 ARNIT_RS08885 acetolactate synthase, large subunit, biosynthetic type
Query= metacyc::MONOMER-18810 (585 letters) >NCBI__GCF_000092245.1:WP_013135583.1 Length = 564 Score = 558 bits (1438), Expect = e-163 Identities = 284/563 (50%), Positives = 377/563 (66%), Gaps = 6/563 (1%) Query: 18 EMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYA 77 +M GA+++ +L EGVE V+GYPGGA++ +YDE++KQT FEHIL RHEQAA+HAA+GYA Sbjct: 2 KMTGAKMVTESLKNEGVEVVFGYPGGAIMNVYDEIYKQTHFEHILTRHEQAAIHAAEGYA 61 Query: 78 RATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGIT 137 +ATGKVGV++VTSGPG TNAVTG+A AY+DSIP+VVITG VPT IG D FQE D VGI+ Sbjct: 62 KATGKVGVSIVTSGPGFTNAVTGLADAYMDSIPLVVITGQVPTTIIGTDGFQEIDAVGIS 121 Query: 138 RPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRS 197 RP KHN+LV + DL IK+AF IA+TGRPGPV VDIPKD++ Y YPK +++ + Sbjct: 122 RPCTKHNYLVNKLEDLPRIIKEAFHIASTGRPGPVHVDIPKDITAEVGDYIYPKEVNLPT 181 Query: 198 YNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTNTLMGL 257 Y P + Q+++A+ + A++P +Y GGG +L+N + E+R+LA P TLM Sbjct: 182 YKPTVNYNKKQLKRAMQAISKAKKPLLYIGGGAILSNCAYEIRELAEKLNIPAVETLMAR 241 Query: 258 GAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKIIHI 317 G T+ +GMLGMHG Y ANMA D+LI++GARFDDRV G F +A K+IH+ Sbjct: 242 GVMGHTNPLLLGMLGMHGEYAANMAAHETDLLISLGARFDDRVTGRLDEFAKKA-KVIHV 300 Query: 318 DIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIEQWRSVDCL 377 DIDP+SI+K V + PIVG++K +Q +I I + W ++ +R L Sbjct: 301 DIDPASIAKLVHTNFPIVGDLKVTVQGMIDSIGEFEFND----YTNWVALLQDYRVQHPL 356 Query: 378 KYDRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPRRWINSGGLGTM 437 + S IKPQ+ + ++ EL +A I +DVGQHQMW+AQFY F PR+W SGGLGTM Sbjct: 357 AFKDSDVKIKPQWPIVRVGELVGDNAIISTDVGQHQMWSAQFYPFSYPRQWNTSGGLGTM 416 Query: 438 GVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGMVRQ 497 G GLP AMG+ KA P+K + TG+GSI M IQEL TC++ PV LNN YLGMVRQ Sbjct: 417 GFGLPGAMGVAKARPDKVSINFTGDGSILMNIQELMTCVEQKLPVINIILNNNYLGMVRQ 476 Query: 498 WQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTVFLDF 557 WQ + Y+NR S + + A PDFVKL EA+G +G RV + + AL++A K ++ Sbjct: 477 WQTMFYENRLSETDLSAQPDFVKLVEAFGGIGYRVTTKKEFDEALKDAME-KKVVAMIEV 535 Query: 558 QTDPTENVWPMVQAGKGISEMLL 580 D E V PMV G ++EM+L Sbjct: 536 IVDRNEEVLPMVPNGHALNEMML 558 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: 893 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: 564 Length adjustment: 36 Effective length of query: 549 Effective length of database: 528 Effective search space: 289872 Effective search space used: 289872 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_013135583.1 ARNIT_RS08885 (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.11833.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.9e-246 802.6 2.6 1e-245 802.4 2.6 1.0 1 lcl|NCBI__GCF_000092245.1:WP_013135583.1 ARNIT_RS08885 acetolactate synth Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000092245.1:WP_013135583.1 ARNIT_RS08885 acetolactate synthase, large subunit, biosynthetic type # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 802.4 2.6 1e-245 1e-245 1 554 [. 3 557 .. 3 560 .. 0.99 Alignments for each domain: == domain 1 score: 802.4 bits; conditional E-value: 1e-245 TIGR00118 1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvl 68 ++ga+++ eslk+egve+vfGyPGGa++++yd++y + ++ehil+rheqaa+haa+Gya+a+GkvGv + lcl|NCBI__GCF_000092245.1:WP_013135583.1 3 MTGAKMVTESLKNEGVEVVFGYPGGAIMNVYDEIYkQTHFEHILTRHEQAAIHAAEGYAKATGKVGVSI 71 79*********************************9999****************************** PP TIGR00118 69 atsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpei 137 +tsGPG tn+vtg+a+ay+ds+Plvv+tGqv+t++iG+d fqeid +Gi++p+tkh++lv+k edlp+i lcl|NCBI__GCF_000092245.1:WP_013135583.1 72 VTSGPGFTNAVTGLADAYMDSIPLVVITGQVPTTIIGTDGFQEIDAVGISRPCTKHNYLVNKLEDLPRI 140 ********************************************************************* PP TIGR00118 138 lkeafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvll 206 +keaf+iastGrPGPv+vd+Pkd+t++ ++ ++++v+lp+ykptv+ +k+q+k+a+++i+kakkP+l+ lcl|NCBI__GCF_000092245.1:WP_013135583.1 141 IKEAFHIASTGRPGPVHVDIPKDITAEVGDYIYPKEVNLPTYKPTVNYNKKQLKRAMQAISKAKKPLLY 209 ********************************************************************* PP TIGR00118 207 vGgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGa 275 +GgG+i +++ e++elae+l+ip + tl+ G + +++pl lgmlGmhG ++an+a +e+dlli++Ga lcl|NCBI__GCF_000092245.1:WP_013135583.1 210 IGGGAILSNCAYEIRELAEKLNIPAVETLMARGVMGHTNPLLLGMLGMHGEYAANMAAHETDLLISLGA 278 ********************************************************************* PP TIGR00118 276 rfddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkeeekkeke.Wleki 343 rfddrvtg l++fa++ak+ih+didPa+i+k v+++ pivGd k ++ +++ + e e ++ W++ + lcl|NCBI__GCF_000092245.1:WP_013135583.1 279 RFDDRVTGRLDEFAKKAKVIHVDIDPASIAKLVHTNFPIVGDLKVTVQGMIDSIGEFEFNDYTnWVALL 347 *********************************************************9888777***** PP TIGR00118 344 eewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtm 412 ++++ +++l+++ ++ +ikPq i ++ +l+ d+ai++tdvGqhqmw+aqfy++++pr++ tsgGlGtm lcl|NCBI__GCF_000092245.1:WP_013135583.1 348 QDYRVQHPLAFKDSDVKIKPQWPIVRVGELVGDNAIISTDVGQHQMWSAQFYPFSYPRQWNTSGGLGTM 416 ********************************************************************* PP TIGR00118 413 GfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeer 481 GfGlP a+G+ a p++ ++ tGdgs+ mn+qel t+ve ++pv+ +ilnn++lGmv+qWq +fye+r lcl|NCBI__GCF_000092245.1:WP_013135583.1 417 GFGLPGAMGVAKARPDKVSINFTGDGSILMNIQELMTCVEQKLPVINIILNNNYLGMVRQWQTMFYENR 485 ********************************************************************* PP TIGR00118 482 ysetklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlPmvapGagl 550 set l++ +pdfvkl ea+G g r+++++e +e+lk+a+e+k ++++v vd++eevlPmv++G++l lcl|NCBI__GCF_000092245.1:WP_013135583.1 486 LSETDLSA-QPDFVKLVEAFGGIGYRVTTKKEFDEALKDAMEKKVVAMIEVIVDRNEEVLPMVPNGHAL 553 *******5.************************************************************ PP TIGR00118 551 delv 554 +e++ lcl|NCBI__GCF_000092245.1:WP_013135583.1 554 NEMM 557 **98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (557 nodes) Target sequences: 1 (564 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: 8.89 // [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