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 PfGW456L13_1794 Acetolactate synthase, large subunit (EC 2.2.1.6)
Query= SwissProt::P0DP90 (548 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1794 Length = 545 Score = 197 bits (501), Expect = 9e-55 Identities = 164/544 (30%), Positives = 248/544 (45%), Gaps = 45/544 (8%) Query: 7 VVHALRAQGVNTVFGYPGGAIMPVYDALYDGGVEHLLCRHEQGAAMAAIGYARATGKTGV 66 +V L GV VFG PG + +Y L + H+ RHEQGA A GYAR +GK GV Sbjct: 8 LVKLLENYGVEQVFGIPGVHTVELYRGLARSSINHVTPRHEQGAGFMADGYARTSGKPGV 67 Query: 67 CIATSGPGATNLITGLADALLDSIPVVAITGQVSAPFI--GTDAFQEVDVLG-LSLACTK 123 C +GPG TN+ T + A DSIP++ I+ S + G E+ G L Sbjct: 68 CFIITGPGMTNITTAMGQAYADSIPMLVISSVQSRSQLGGGRGKLHELPNQGALCAGVAA 127 Query: 124 HSFLVQSLEELPRIMAEAFDVACSGRPGPVLVDIPKDIQLASGD--LEPWFTTVENEVTF 181 S + S ELP ++A AF + +GRP PV ++IP D+ + D L ++ Sbjct: 128 FSHTLMSASELPGVLARAFALFQAGRPRPVHIEIPLDVLVEEADDLLASLPVNIDRAGAS 187 Query: 182 PHAEVEQARQMLAKAQKPMLYVGGGVGMAQAVPALREFLAATKMPATCTLKGLGAVEADY 241 P A V + ++LA A++P++ GGG A L E P T+ G + + + Sbjct: 188 PSA-VSRMAELLAGAKRPLILAGGGA--IDAAVELTELAELLDAPVALTINAKGMLASGH 244 Query: 242 PYYLGMLGMHGTKAANFAVQECDLLIAVG---ARFDDRVTGKLNTFAPHASVIHMDIDPA 298 P +G A V E D+++A+G A D VT F ++ +DIDP Sbjct: 245 PLLIG--STQSLVATRALVAEADVVLAIGTELAETDYDVT-FAGGFEIPGKLLRVDIDPD 301 Query: 299 EMNKLRQAHVALQGD----LNALLPALQQPL---NQYDW-QQHCAQLRDEHSWRYDHP-- 348 + + HVAL D ALL AL + DW Q A+LR++ + +D P Sbjct: 302 QTVRNYPPHVALVADSRNAAQALLSALSHKSLAERRNDWGQVRAARLREDLAATWDAPTL 361 Query: 349 GDAIYAPLLLKQLSDRKPADCVVTTDVGQHQMWAAQHIAHTRPEN-FITSSGLGTMGFGL 407 + +L++L D V D Q RP F +S+G GT+G+ L Sbjct: 362 AQTRFLETVLQEL-----PDAVFVGDSTQPVYTGNLTFNPERPRRWFNSSTGYGTLGYAL 416 Query: 408 PAAVGAQV-------ARPNDTVVCISGDGSFMMNVQELGTVKRKQLPLKIVLLDNQRLGM 460 PAA+GA + ARP VVC+ GDG + EL + + P+ ++L +NQ Sbjct: 417 PAAIGAWLGGRIEGGARP--PVVCLIGDGGLQFTLPELASAVEARTPVIVLLWNNQGYEE 474 Query: 461 VRQWQQLFFQERYSETTLTD--NPDFLMLASAFGIHGQHITRKDQVEAALDTMLNSDGPY 518 +++ + R E D PDF+ +A A G + ++ +Q+ AL + GP Sbjct: 475 IKK----YMVNRAIEPVGVDIYTPDFIGVAKALGCAAEAVSSVEQLRGALRVATDRQGPT 530 Query: 519 LLHV 522 L+ + Sbjct: 531 LIEI 534 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: 662 Number of extensions: 38 Number of successful extensions: 7 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: 545 Length adjustment: 36 Effective length of query: 512 Effective length of database: 509 Effective search space: 260608 Effective search space used: 260608 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 Apr 09 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