Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_013840432.1 DESRU_RS01875 biosynthetic-type acetolactate synthase large subunit
Query= metacyc::MONOMER-18810 (585 letters) >NCBI__GCF_000215085.1:WP_013840432.1 Length = 553 Score = 562 bits (1449), Expect = e-164 Identities = 289/560 (51%), Positives = 368/560 (65%), Gaps = 10/560 (1%) Query: 18 EMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYA 77 E+ AE LV L EGVE V+GYPGGA+L +YD L+ +K +HIL RHEQ A HAA GYA Sbjct: 2 EITCAEALVRCLELEGVELVFGYPGGAILPVYDALN-DSKIKHILTRHEQGAAHAASGYA 60 Query: 78 RATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGIT 137 R TGKVGV + TSGPG TN VTG+A AY+DSIP+V ITG VPT +G DAFQE D GIT Sbjct: 61 RTTGKVGVCMATSGPGATNLVTGLANAYMDSIPLVAITGQVPTSQVGTDAFQEVDITGIT 120 Query: 138 RPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRS 197 PI KHN+LVKD + L +++AF IA TGRPGPV++D+PKDV+ K+ YP+ + ++ Sbjct: 121 IPITKHNYLVKDAKTLPLIVRRAFHIARTGRPGPVLIDLPKDVANTRIKFNYPEEVHLKG 180 Query: 198 YNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTNTLMGL 257 Y P KGH QI +A L+ AERP IY GGGVV A AS+EL LA PV TLMGL Sbjct: 181 YKPTVKGHIAQINQAAKLMMQAERPVIYAGGGVVNAEASEELVWLAETLDAPVVTTLMGL 240 Query: 258 GAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKIIHI 317 GAFPG + F+GM G+HG AN+A+ + D+LI +GARFDDRV G A F AR +IH+ Sbjct: 241 GAFPGDHRLFLGMPGLHGNLAANLAVTHSDLLITLGARFDDRVTGRIAGFAPGAR-VIHV 299 Query: 318 DIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIEQWRSVDCL 377 DIDP+ ISK V +PIVG+ K VL +L+ ++ ++ W EQ+ W+ Sbjct: 300 DIDPAEISKNVISHLPIVGDTKKVLTDLLVRL-------DKKQNPGWIEQVSSWKEEHAH 352 Query: 378 KYDRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPRRWINSGGLGTM 437 +Y + E++KPQYV+E+I+ +KGD + +DVGQHQMW AQ + F EPR + SGGLG M Sbjct: 353 RYQQEGELLKPQYVIEEIYRHSKGDVIVSTDVGQHQMWVAQHFPFKEPRALVTSGGLGVM 412 Query: 438 GVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGMVRQ 497 G GLP A+G + PEK VV +TG+GS QM + ELST + + P+KI LNN LGMVRQ Sbjct: 413 GFGLPGAIGAQIGRPEKTVVLVTGDGSFQMSLNELSTAAEQELPLKIVVLNNRCLGMVRQ 472 Query: 498 WQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTVFLDF 557 QE + RY+ +PDF LA YG G V +++ AL EAF+ V +D Sbjct: 473 LQEFYCEKRYTAVDFGFVPDFAALARVYGFKGYTVNTAEELQSALTEAFQ-DPGPVLIDC 531 Query: 558 QTDPTENVWPMVQAGKGISE 577 DP ENV PMV AGK I + Sbjct: 532 SVDPNENVLPMVLAGKDICD 551 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: 909 Number of extensions: 35 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: 553 Length adjustment: 36 Effective length of query: 549 Effective length of database: 517 Effective search space: 283833 Effective search space used: 283833 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_013840432.1 DESRU_RS01875 (biosynthetic-type acetolactate synthase 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.3173901.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.2e-251 820.1 0.0 5.2e-251 819.8 0.0 1.0 1 NCBI__GCF_000215085.1:WP_013840432.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000215085.1:WP_013840432.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 819.8 0.0 5.2e-251 5.2e-251 2 549 .. 4 548 .. 3 552 .. 0.99 Alignments for each domain: == domain 1 score: 819.8 bits; conditional E-value: 5.2e-251 TIGR00118 2 kgaeilveslkkegvetvfGyPGGavlpiydalydselehilvrheqaaahaadGyarasGkvGvvlatsGPG 74 + ae+lv+ l+ egve vfGyPGGa+lp+ydal ds+++hil+rheq+aahaa Gyar++GkvGv++atsGPG NCBI__GCF_000215085.1:WP_013840432.1 4 TCAEALVRCLELEGVELVFGYPGGAILPVYDALNDSKIKHILTRHEQGAAHAASGYARTTGKVGVCMATSGPG 76 679********************************************************************** PP TIGR00118 75 atnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafeiast 147 atnlvtg+a+ay+ds+Plv++tGqv+ts +G+dafqe+di+Git+p+tkh++lvk+a+ lp i+++af+ia t NCBI__GCF_000215085.1:WP_013840432.1 77 ATNLVTGLANAYMDSIPLVAITGQVPTSQVGTDAFQEVDITGITIPITKHNYLVKDAKTLPLIVRRAFHIART 149 ************************************************************************* PP TIGR00118 148 GrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllvGgGviiaeaseel 220 GrPGPvl+dlPkdv+++ i+++++e+v+l+gykptvkgh +qi++a++l+++a++Pv+++GgGv+ aeaseel NCBI__GCF_000215085.1:WP_013840432.1 150 GRPGPVLIDLPKDVANTRIKFNYPEEVHLKGYKPTVKGHIAQINQAAKLMMQAERPVIYAGGGVVNAEASEEL 222 ************************************************************************* PP TIGR00118 221 kelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfapeak 293 + lae+l++pv+ttl+GlGafp dh+l+lgm G+hG +anlav+++dlli++Garfddrvtg +a fap a+ NCBI__GCF_000215085.1:WP_013840432.1 223 VWLAETLDAPVVTTLMGLGAFPGDHRLFLGMPGLHGNLAANLAVTHSDLLITLGARFDDRVTGRIAGFAPGAR 295 ************************************************************************* PP TIGR00118 294 iihididPaeigknvkvdipivGdakkvleellkklkeeekkekeWlekieewkkeyilkldeeeesikPqkv 366 +ih+didPaei+knv +++pivGd+kkvl++ll +l ++++ W+e++++wk+e+ ++++e e +kPq+v NCBI__GCF_000215085.1:WP_013840432.1 296 VIHVDIDPAEISKNVISHLPIVGDTKKVLTDLLVRLDKKQNPG--WIEQVSSWKEEHAHRYQQEGELLKPQYV 366 ************************************9988877..**************************** PP TIGR00118 367 ikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpeetvvavtGdgs 439 i+e+++ k+++iv+tdvGqhqmw+aq++++k+pr +tsgGlG mGfGlP a+Ga+++ pe+tvv vtGdgs NCBI__GCF_000215085.1:WP_013840432.1 367 IEEIYRHSKGDVIVSTDVGQHQMWVAQHFPFKEPRALVTSGGLGVMGFGLPGAIGAQIGRPEKTVVLVTGDGS 439 ************************************************************************* PP TIGR00118 440 fqmnlqelstiveydipvkivilnnellGmvkqWqelfyeerysetklaselpdfvklaeayGvkgiriekpe 512 fqm+l+elst++e ++p+kiv+lnn++lGmv+q qe++ e+ry+++ ++ +pdf++la+ yG kg ++++ e NCBI__GCF_000215085.1:WP_013840432.1 440 FQMSLNELSTAAEQELPLKIVVLNNRCLGMVRQLQEFYCEKRYTAVDFGF-VPDFAALARVYGFKGYTVNTAE 511 *************************************************6.********************** PP TIGR00118 513 eleeklkealeskepvlldvevdkeeevlPmvapGag 549 el+++l+ea++ +pvl+d +vd +e+vlPmv G+ NCBI__GCF_000215085.1:WP_013840432.1 512 ELQSALTEAFQDPGPVLIDCSVDPNENVLPMVLAGKD 548 *********************************9986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (557 nodes) Target sequences: 1 (553 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 21.81 // [ok]
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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