Align Acetolactate synthase isozyme 2 large subunit; AHAS-II; ALS-II; Acetohydroxy-acid synthase II large subunit; EC 2.2.1.6 (characterized)
to candidate WP_058930994.1 AU252_RS12450 acetolactate synthase
Query= SwissProt::P0DP90 (548 letters) >NCBI__GCF_001484605.1:WP_058930994.1 Length = 584 Score = 223 bits (567), Expect = 2e-62 Identities = 165/540 (30%), Positives = 249/540 (46%), Gaps = 30/540 (5%) Query: 7 VVHALRAQGVNTVFGYPGGAIMPVYDALYDGGVEHLLCRHEQGAAMAAIGYARATGKTGV 66 +V +L A GV + PG + + V D L++ +E ++CRHE GAA A + + G+ Sbjct: 50 IVDSLVAHGVERTYVVPGESFLDVLDGLHNSDIETIVCRHEGGAAYMAEADGKMHQRPGI 109 Query: 67 CIATSGPGATNLITGLADALLDSIPVVAITGQVSAPFIGTDAFQEVDVLGLSLACTKHSF 126 + T GPGA N GL A DS P++ G + +AFQE D+ K Sbjct: 110 AMVTRGPGAANAHVGLHTAWQDSTPMLLFVGLIPFAHRDREAFQEFDIKAWFDTGAKRVM 169 Query: 127 LVQSLEELPRIMAEAFDVACSGRPGPVLVDIPKDI--QLASGDLEPWFTTVENEVTFPHA 184 ++ E I+AEA A SGRPGPV+V +P+DI Q L P ++ A Sbjct: 170 VLDHAERASEIVAEAMFAAMSGRPGPVVVGLPEDIIRQQIDPALHPAIPVAAGGMSTSDA 229 Query: 185 EVEQARQMLAKAQKPMLYVGGGVGMAQAVPALREFLAATKMPATCTLKGLGAVEADYPYY 244 +A LA++ KP+ GG A L E+L +PA + G V D P Y Sbjct: 230 AALEA--ALAESSKPLFVTGGNDWTQGAADQLTEWLERHHIPAAAEWRTQGTVSFDSPSY 287 Query: 245 LGMLGMHGTKAANFAVQECDLLIAVGARFDDRVT---------GKLNTFAPHASVIHMDI 295 +G +G + +E DLL+ VG D +T K N + Sbjct: 288 VGPIGYGRPRPTYDLFEETDLLVFVGTVPGDVITDGFVCRQDWNKKNFLVTADPSLRGRS 347 Query: 296 DPAEMNKLRQAHVALQGDLNALLPALQQPLNQYDWQQHCAQLRDEHSWRYDHPGDAIYA- 354 P L + ++ + LPA + +W+ ++R E P A A Sbjct: 348 GPVSRQILAKPEAFVRDLVGIDLPAKE------EWKAWTDRMRGEQERFAALPPAAPAAG 401 Query: 355 ----PLLLKQLSDRKPADCVVTTDVGQHQMWAAQHIAHTRPENFITSSGLGTMGFGLPAA 410 L+ L R P D +VT G+H WA ++ R + I++ G+MG+ +P+A Sbjct: 402 QARMDTLMANLVPRLPEDSLVTFGAGEHTNWAHRYFPTRRYASMISARN-GSMGYSVPSA 460 Query: 411 VGAQVARPNDTVVCISGDGSFMMNVQELGTVKRKQLPLKIVLLDNQRLGMVRQWQQLFFQ 470 + A +A P VV I+GDG F+MN QEL T + ++++DNQ G +R Q+ + Sbjct: 461 IAASLAEPRRRVVTIAGDGEFLMNGQELATAAQYGATPLVIVMDNQEYGTIRTHQERHYP 520 Query: 471 ERYSETTLTDNPDFLMLASAFGIHGQHITRKDQVEAALDTML---NSDGPY-LLHVSIDE 526 R S T L NPDF ++A AFG G +T V AALD L + DG + L+H+ +++ Sbjct: 521 SRVSGTQL-KNPDFGLMARAFGGFGITVTEDCDVPAALDAALAAIDEDGVFALIHLIVEQ 579 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: 819 Number of extensions: 36 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: 584 Length adjustment: 36 Effective length of query: 512 Effective length of database: 548 Effective search space: 280576 Effective search space used: 280576 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 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