Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate 8501200 DvMF_1934 sulfoacetaldehyde acetyltransferase (RefSeq)
Query= BRENDA::P00893 (574 letters) >FitnessBrowser__Miya:8501200 Length = 580 Score = 268 bits (684), Expect = 6e-76 Identities = 178/571 (31%), Positives = 285/571 (49%), Gaps = 29/571 (5%) Query: 1 MEMLSGAEMVVRSLIDQGVKQVFGYPGGAVLDIYDALHTVGGIDHVLVRHEQAAVHMADG 60 M ++ +E + L+ +GV V G G A +D+ D L GID + VRHEQ A HM D Sbjct: 1 MPKMTPSEAMAEVLVQEGVTHVSGILGSAFMDLLD-LFPAAGIDFISVRHEQTAGHMEDA 59 Query: 61 LARATGEVGVVLVTSGPGATNAITGIATAYMDSIPLVVLSGQVATSLIGYDAFQECDMVG 120 R TG GV + +GPG TN +T +ATA M P+VVLS + +G+D FQECD Sbjct: 60 FTRMTGRAGVCIGQNGPGITNYVTAVATANMAHTPMVVLSPSAGSISVGWDGFQECDTWN 119 Query: 121 ISRPVVKHSFLVKQTEDIPQVLKKAFWLAASGRPGPVVVDLPKDILNPANKLPYVWPESV 180 + +P+ K S V + +L+ AF +A + R GPV+VD+P+D + P Sbjct: 120 LFKPITKASLRVPHPKRAADILRTAFRIAYAER-GPVLVDIPRDYFYGELDEDILAP--- 175 Query: 181 SMRSYNPTTTGHKGQIKRALQTLVAAKKPVVYVGGGAITAGCHQQLKETVEALNLPVVCS 240 S P G+ Q + A++ L AAK+PV+ G G + +G + +K E LN PV C+ Sbjct: 176 SQYRVAPGGIGNPEQFREAVEVLKAAKRPVIVSGRGVVDSGALETVKALAEHLNAPVACT 235 Query: 241 LMGLGAFPATHRQALGMLGMHGTYEANMTMHNADVIFAVGVR---FDDRTTNNLAKYCPN 297 + AFP H G +G G+ A + ADVI AVG R F ++ + Sbjct: 236 YLHNDAFPCDHPLWTGPIGYMGSKAAMRILQQADVILAVGTRLSYFGTLPQYDINYFPKT 295 Query: 298 ATVLHIDIDPTSISKTVTADIPIVGDARQVLEQMLELLSQESAHQPLD---------EIR 348 A ++ IDI+P I+KT + + DA+ ++L + + + D E+ Sbjct: 296 AKIVQIDINPRHIAKTHPVAVGLCADAKDAAVELLARVREAMPNPRRDDAVYAMVKAELE 355 Query: 349 DWWQQIEQWRARQCLKYDTHSEKIKPQAVIETLWR-LTKGDAYVTSDVGQHQMFAALYYP 407 DW+++I ++ H P+ ++ + R +T+ +A T+D+G A Y Sbjct: 356 DWYKEIAAIADEPVMEGRMH-----PRKALDVVGRFVTEHNAIATTDIGNTSSTANSYLR 410 Query: 408 FDKPRRWINSGGLGTMGFGLPAALGVKMALPEETVVCVTGDGSIQMNIQELSTALQYELP 467 F +R + + G GF A LG ++A PE+TVV + GDG+ M++ E+ TA+QY LP Sbjct: 411 FRNAKRSVATLTFGNTGFAYQAGLGAQLACPEDTVVAIVGDGAWGMSLFEVPTAVQYNLP 470 Query: 468 VLVVNLNNRYLGMVKQWQDMIYSGRHSQSYMQSLPDFVRLAEAYGHVGIQISHPHELESK 527 V+ NN K+ Q Y+ R + + S + +AEA G G +++ ++ Sbjct: 471 VIATVYNNGAWCAEKKNQVDFYNNRFVGADIWS-NSYAAIAEAMGATGYKVN----TQAD 525 Query: 528 LSEALEQVRNNRL-VFVDVTVDGSEHVYPMQ 557 L++AL+ R +R +++ DG+ P + Sbjct: 526 LADALDAARKSRKPSVIEIMTDGTRLAPPFR 556 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: 729 Number of extensions: 33 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: 574 Length of database: 580 Length adjustment: 36 Effective length of query: 538 Effective length of database: 544 Effective search space: 292672 Effective search space used: 292672 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