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_085641493.1 MGEO_RS19930 5-guanidino-2-oxopentanoate decarboxylase
Query= SwissProt::P0DP90 (548 letters) >NCBI__GCF_002115805.1:WP_085641493.1 Length = 531 Score = 194 bits (492), Expect = 9e-54 Identities = 156/530 (29%), Positives = 235/530 (44%), Gaps = 19/530 (3%) Query: 3 GAQWVVHALRAQGVNTVFGYPGGAIMPVYDALYDGGVEHLLCRHEQGAAMAAIGYARATG 62 GAQ + L+ +GV+T+FG PG + +Y + G+ H+L RHEQGA A GYARATG Sbjct: 7 GAQ-ISQMLKERGVDTIFGIPGVHNVELYRGIEQAGITHVLARHEQGAGFMADGYARATG 65 Query: 63 KTGVCIATSGPGATNLITGLADALLDSIPVVAITGQVSAPFIGTDAFQEV-DVLGLSLAC 121 K GV +GPG TN++T L A DS+PV+AI+ + ++ D + Sbjct: 66 KPGVAYVITGPGLTNILTPLGQAYSDSVPVLAISSCLDEVAARRGQLHQMRDQRMAAETV 125 Query: 122 TKHSFLVQSLEELPRIMAEAFDVACSGRPGPVLVDIPKDIQLASGDLEPWFTTVENEV-T 180 S +S ++ AFD S R P + + + A D P + + Sbjct: 126 CAWSEEARSASAAYALIDRAFDQFASARARPCHMQVSIETLGALADPAPQPPAARPGLPS 185 Query: 181 FPHAEVEQARQMLAKAQKPMLYVGGG-VGMAQAVPALREFLAATKMPATCTLKGLGAVEA 239 H++V + A+KP+ GGG V A A+P + L T + T G V A Sbjct: 186 ASHSDVYDVVAAVLAAKKPLFVFGGGSVAAADAIP---DLLRQTGAASIVTYAARGVVPA 242 Query: 240 DYPYYLGMLGMHGTKAANFAVQECDLLIAVGARFDDRVTGKLNTFAPHASVIHMDIDPAE 299 D P Y G A A + DL+IAVG + V T A +I +DIDP Sbjct: 243 DEPLYFGSYLARPDSAEITA--QADLVIAVGTTLSE-VDLWRPTLGHTAPMIRVDIDPEV 299 Query: 300 MNKLRQAHVALQGDLNALLPAL------QQPLNQYDWQQHCAQLRDEHSWRYDHPGDAIY 353 + A+ D A L A+ + W + R +WR + + Sbjct: 300 FTGMGPEDRAILADAGAFLKAMTIAIPARTDTKPPKWDA-ASVARKRAAWRAEVDAERPG 358 Query: 354 APLLLKQLSDRKPADCVVTTDVGQHQMWAAQHIAHTRPENFITSSGLGTMGFGLPAAVGA 413 + L P D ++ +D+ Q A + RP ++ G GT+G+ LPAA+G Sbjct: 359 IVPVCDALRAVLPDDTMIYSDMTQFAYAAKEIWDMPRPGHWHHPYGFGTLGYALPAAIGG 418 Query: 414 QVARPNDTVVCISGDGSFMMNVQELGTVKRKQLPLKIVLLDNQRLGMVRQWQQLFFQERY 473 VARP + I+GD +QELGT LPL I++ DN +LG + + + Sbjct: 419 AVARPGLPTLAIAGDYGLQYTIQELGTAVELGLPLPILVWDNGKLGEIE--DSMVRSQIA 476 Query: 474 SETTLTDNPDFLMLASAFGIHGQHITRKDQVEAALDTMLNSDGPYLLHVS 523 + NPDFL LA A+G + ++ A+ +DGP ++ V+ Sbjct: 477 PNAVVARNPDFLALAKAYGAEAVQPDSLEALQQAMLAAFKADGPTVIRVT 526 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: 713 Number of extensions: 38 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: 548 Length of database: 531 Length adjustment: 35 Effective length of query: 513 Effective length of database: 496 Effective search space: 254448 Effective search space used: 254448 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: 52 (24.6 bits)
This GapMind analysis is from Jul 26 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