Align acetolactate synthase isozyme 2 large subunit; EC 2.2.1.6 (characterized)
to candidate Ac3H11_1601 Acetolactate synthase large subunit (EC 2.2.1.6)
Query= CharProtDB::CH_003896 (548 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1601 Length = 561 Score = 242 bits (618), Expect = 2e-68 Identities = 165/532 (31%), Positives = 246/532 (46%), Gaps = 11/532 (2%) Query: 3 GAQWVVHALRAQGVNTVFGYPGGAIMPVYDALYDGGVEHLLCRHEQGAAMAAIGYARATG 62 G Q +V L GV +F PG + + V DAL+D + +CR E GAAM A + TG Sbjct: 11 GGQILVQQLITHGVKQLFCVPGESYLAVLDALHDADIGVTVCRQEGGAAMMAEAQGKLTG 70 Query: 63 KTGVCIATSGPGATNLITGLADALLDSIPVVAITGQVSAPFIGTDAFQEVDVLGLSLACT 122 + G+C T GPGATN G+ A DS P++ GQV+ +G +AFQE+D + Sbjct: 71 QPGICFVTRGPGATNASAGVHIAHQDSTPMILFVGQVARGAMGREAFQELDYSAVFGTMA 130 Query: 123 KHSFLVQSLEELPRIMAEAFDVACSGRPGPVLVDIPKDIQLASGDLEPWFTTVENEVTFP 182 K + +P +++ AF VA SGRPGPV+V +P+D+ + + E Sbjct: 131 KWVVQIDDPARVPELISRAFHVATSGRPGPVVVALPEDMLTEAATVADALPYQVTETHPG 190 Query: 183 HAEVEQARQMLAKAQKPMLYVGGGVGMAQAVPALREFLAATKMPATCTLKGLGAVEADYP 242 A++ + Q L A+ P+ +GG +AV F A +P C+ + A + Sbjct: 191 AAQLAELAQRLQAAKNPVAILGGSRWSEEAVREFTAFAEAWSIPVYCSFRRQMLFPATHA 250 Query: 243 YYLGMLGMHGTKAANFAVQECDLLIAVGARFDDRVTGKLNTF---APHASVIHMDIDPAE 299 Y G LG+ ++ DL++ VG R + + F P S +H+ D E Sbjct: 251 CYGGDLGLGVNPKLLARIKASDLVLVVGGRLSEVPSQGYELFDIPTPAQSFVHVHADADE 310 Query: 300 MNKLRQAHVALQGDLNALLPALQ--QPLNQYDWQQHCAQLRDEH-SWRYDHP---GDAIY 353 + KL + A+ A AL +P W+ H E+ +W P + Sbjct: 311 LGKLYRPTQAIHATPQAFTAALNAVRPTASVAWKAHTEAAHAEYLAWSDPAPIRIPGNLQ 370 Query: 354 APLLLKQLSDRKPADCVVTTDVGQHQMWAAQHIAHTRPENFITSSGLGTMGFGLPAAVGA 413 +++ L PAD + G W + T + + + G+MG+GLPA VG Sbjct: 371 MGEVMQHLKSVLPADTIFCNGAGNFATWVHRFWPFTTYASQLAPTS-GSMGYGLPAGVGG 429 Query: 414 QVARPNDTVVCISGDGSFMMNVQELGTVKRKQLPLKIVLLDNQRLGMVRQWQQLFFQERY 473 + P VV +GDG F+M+ QE T + LP+ +VLLDN G +R Q+ + R Sbjct: 430 KRLWPQREVVVFAGDGDFLMHGQEFATAVQYGLPILVVLLDNAMYGTIRMHQEREYPGRI 489 Query: 474 SETTLTDNPDFLMLASAFGIHGQHITRKDQVEAALDTMLNSDGPYLLHVSID 525 S T L NPDF A AFG HG+ + R + AL S P +LH ID Sbjct: 490 SATQL-KNPDFKAYAQAFGGHGERVERTEDFAPALARARASGLPSVLHCLID 540 Lambda K H 0.320 0.135 0.410 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: 767 Number of extensions: 51 Number of successful extensions: 5 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: 548 Length of database: 561 Length adjustment: 36 Effective length of query: 512 Effective length of database: 525 Effective search space: 268800 Effective search space used: 268800 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)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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