Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate WP_018231967.1 THITHI_RS0104940 sulfoacetaldehyde acetyltransferase
Query= BRENDA::P9WG41 (618 letters) >NCBI__GCF_000378965.1:WP_018231967.1 Length = 581 Score = 254 bits (650), Expect = 6e-72 Identities = 169/545 (31%), Positives = 277/545 (50%), Gaps = 33/545 (6%) Query: 35 LQQLTGAQAVIRSLEELGVDVIFGIPGGAVLPVYDPLFDSKKLRHVLVRHEQGAGHAASG 94 ++++T ++A++ ++ GV +FGI G A + D +F+ +R + HEQG+ H A G Sbjct: 1 MKRMTPSEALVETMAAHGVTNVFGIVGSAFMDALD-IFEPAGIRFIPTVHEQGSAHMADG 59 Query: 95 YAHVTGRVGVCMATSGPGATNLVTPLADAQMDSIPVVAITGQVGRGLIGTDAFQEADISG 154 Y+ VTGR GVC+A +GPG TN VT +A A PVVAIT + G G FQE + Sbjct: 60 YSRVTGRHGVCVAQNGPGITNFVTGIAAAYWAHSPVVAITPETGTNSQGLGGFQETEQLP 119 Query: 155 ITMPITKHNFLVRSGDDIPRVLAEAFHIAASGRPGAVLVDIPKDVLQGQCTFSWPPRMEL 214 ITK+ + D + + A F+ A + L +IP+D+ G+ E+ Sbjct: 120 YFEKITKYQGHLSRSDRMAEIAARCFNRAINENAPTQL-NIPRDLFYGEI------ECEI 172 Query: 215 PGYK--PNTKPHSRQVREAAKLIAAARKPVLYVGGGVIRGEATEQLRELAELTGIPVVTT 272 PG K R++ AA L+A AR PV+ GGGV+ + + LAE PVV + Sbjct: 173 PGPKVIERGAGGERELDRAADLLAEARFPVIISGGGVVMSDGVAECIALAERLSAPVVNS 232 Query: 273 LMARGAFPDSHRQNLGMPGMHGTVAAVAALQRSDLLIALGTR---FDDRVTGKLDSFAPE 329 + +FP SH+ G G G+ A + ++++D+++ALG+R F LD + + Sbjct: 233 YLHNDSFPASHKLWAGPLGYQGSKAGMQLMEKADVVLALGSRLGPFGTLPQHGLDYWPKD 292 Query: 330 AKVIHADIDPAEIGKNRHADVPIVGDVKAVITELIAMLRHHHIP---------GTIE--M 378 A++I D++P +G ++ DV ++GD +V L+A L+ + GTIE Sbjct: 293 ARIIQVDVNPDMLGLVKNTDVDLLGDAASVARALLARLKDRKLACDASRDERLGTIETTK 352 Query: 379 ADWWAYLNG---VRKTYPLSYGPQSDGSLSPEYVIEKLGEIAGPDAVFVAGVGQHQMWAA 435 A W L+ R + L SDG L P V+ +L + +A+ +G + Sbjct: 353 AQWEKELDSWSHERDDWSLKVA-DSDGGLHPRQVLRELEKAMPGNAMVSTDIGNICSVSN 411 Query: 436 QFIRYEKPRSWLNSGGLGTMGFAIPAAMGAKIALPGTEVWAIDGDGCFQMTNQELATCAV 495 ++R+E+PRS+ + G G+A+PA +G K+ P A GDG + M+ E+ TC Sbjct: 412 SYLRFEQPRSFFAAMSFGNCGYALPAIIGCKVGAPDRPAVAYVGDGAWAMSMVEILTCVR 471 Query: 496 EGIPVKVALINNGNLGMVRQWQSLFYAERYSQTDLATHSHRIPDFVKLAEALGCVGLRCE 555 E IPV + NN G ++ Q +Y ER+ ++L + P + +A ++G G+ + Sbjct: 472 ENIPVTAVVFNNRQWGAEKKNQVDYYGERFVGSNLNS-----PSWAGIARSMGAEGVTVD 526 Query: 556 REEDV 560 + +DV Sbjct: 527 KLDDV 531 Lambda K H 0.319 0.136 0.414 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: 941 Number of extensions: 46 Number of successful extensions: 4 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: 618 Length of database: 581 Length adjustment: 37 Effective length of query: 581 Effective length of database: 544 Effective search space: 316064 Effective search space used: 316064 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