Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate Pf6N2E2_5475 Acetolactate synthase, large subunit (EC 2.2.1.6)
Query= BRENDA::P00893 (574 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5475 Length = 545 Score = 210 bits (534), Expect = 1e-58 Identities = 164/551 (29%), Positives = 259/551 (47%), Gaps = 44/551 (7%) Query: 3 MLSGAEMVVRSLIDQGVKQVFGYPGGAVLDIYDALHTVGGIDHVLVRHEQAAVHMADGLA 62 M + E++V+ L GV+QVFG PG +++Y L I HV RHEQ A MADG A Sbjct: 1 MATCGEVLVKLLHAYGVEQVFGIPGVHTVELYRGLAR-SNIRHVTPRHEQGAGFMADGYA 59 Query: 63 RATGEVGVVLVTSGPGATNAITGIATAYMDSIPLVVLSGQVATSLIG------YDAFQEC 116 R +G+ GV + +GPG TN T + AY DSIP++V+S + + +G ++ + Sbjct: 60 RVSGKPGVCFIITGPGMTNITTAMGQAYADSIPMLVISSVQSRNQLGGGRGKLHELPNQA 119 Query: 117 DMVGISRPVVKHSFLVKQTEDIPQVLKKAFWLAASGRPGPVVVDLPKDIL-NPANKLPYV 175 +VG V S + ++P VL +AF + +GRP PV +++P D+L A+ L Sbjct: 120 ALVG---GVAAFSHTLMSAAELPGVLARAFAVFQAGRPRPVHIEIPLDVLVEDADALLAS 176 Query: 176 WPESVSMRSYNPTTTGHKGQIKRALQTLVAAKKPVVYVGGGAITAGCHQQLKETVEALNL 235 P +++ P+ + + L +A++P++ GGGAI A +L E E L Sbjct: 177 VPVNINRAGAAPSA------VAQMAAKLASAQRPLILAGGGAIDAAA--ELTELAERLGA 228 Query: 236 PVVCSLMGLGAFPATHRQALGMLGMHGTYEANMTMHNADVIFAVGVRF--DDRTTNNLAK 293 PV ++ G P+ H +G + ADV+ A+G D Sbjct: 229 PVALTINAKGLLPSRHPLLIG--STQSLVATRALVAEADVVLAIGTELAETDYDITFAGG 286 Query: 294 YCPNATVLHIDIDPTSISKTVTADIPIVGDARQVLEQMLELLSQESAHQPLDEIRDWWQQ 353 + +L IDIDP + + +V DAR +L+ LSQ PL E RD W Sbjct: 287 FEIPGALLRIDIDPDQTVRNYPPYLALVADARVATRAVLDALSQ----HPLAERRDDWGT 342 Query: 354 IEQWRARQCLKYD----THSEKIKPQAVIETLWRLTKGDAYVTSDVGQHQMFAALYYPFD 409 R R L+ T ++ + V++ L +A D Q L + + Sbjct: 343 TRAARLRAELQGSWDAATRAQTLFLDTVLQAL-----PEAVFVGDSTQPVYTGNLTFNPE 397 Query: 410 KPRRWINSG-GLGTMGFGLPAALGVKMALPEE-----TVVCVTGDGSIQMNIQELSTALQ 463 +PRRW NS G GT+G+ LPAA+G + + VVC+ GDG +Q + EL++A++ Sbjct: 398 QPRRWFNSSTGYGTLGYALPAAIGAWLGGKDRGHGRPAVVCLIGDGGLQFTLPELASAVE 457 Query: 464 YELPVLVVNLNNRYLGMVKQWQDMIYSGRHSQSYMQSLPDFVRLAEAYGHVGIQISHPHE 523 PV+V+ NN+ +K++ M+ PDF+ +A A G I + Sbjct: 458 ARTPVIVLLWNNQGYEEIKKY--MVNRAIEPVGVDIYTPDFIGVARALGCAAQAIDGVAQ 515 Query: 524 LESKLSEALEQ 534 L + L A ++ Sbjct: 516 LHAALLAACDR 526 Lambda K H 0.319 0.135 0.403 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: 745 Number of extensions: 47 Number of successful extensions: 8 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: 574 Length of database: 545 Length adjustment: 36 Effective length of query: 538 Effective length of database: 509 Effective search space: 273842 Effective search space used: 273842 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 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