Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate WP_041099065.1 SUTH_RS10350 sulfoacetaldehyde acetyltransferase
Query= BRENDA::P9WG41 (618 letters) >NCBI__GCF_000828635.1:WP_041099065.1 Length = 588 Score = 246 bits (627), Expect = 3e-69 Identities = 174/541 (32%), Positives = 261/541 (48%), Gaps = 27/541 (4%) Query: 36 QQLTGAQAVIRSLEELGVDVIFGIPGGAVLPVYDPLFDSKKLRHVLVRHEQGAGHAASGY 95 Q++T ++A++ +L GV +FGI G A + D +F + +R + HEQGA H A GY Sbjct: 9 QRMTPSEALVETLAANGVTDVFGIVGSAYMDALD-IFPAAGIRFIPTVHEQGAAHMADGY 67 Query: 96 AHVTGRVGVCMATSGPGATNLVTPLADAQMDSIPVVAITGQVGRGLIGTDAFQEADISGI 155 A V+GR GVC+A +GPG TN VT +A A PVVAIT + G +G FQE I Sbjct: 68 ARVSGRHGVCIAQNGPGVTNFVTAVAAAYWAHSPVVAITPETGSMGMGLGGFQETSQLPI 127 Query: 156 TMPITKHNFLVRSGDDIPRVLAEAFHIAASGRPGAVLVDIPKDVLQGQCTFSWPPRMELP 215 ITK+ V + + + A F A G ++IP+D G F P + + Sbjct: 128 FSGITKYQGHVNNPKRMAEIAARCFD-RAMLEMGPTQLNIPRDYFYGDAEFEITPPIRI- 185 Query: 216 GYKPNTKPHSRQVREAAKLIAAARKPVLYVGGGVIRGEATEQLRELAELTGIPVVTTLMA 275 R + AA+L+AAAR PV+ GGGV+ + E LAEL G PVV++ + Sbjct: 186 ---ERGAGGERSLDAAAELLAAARFPVIVSGGGVVLADGVESCIALAELLGAPVVSSYLH 242 Query: 276 RGAFPDSHRQNLGMPGMHGTVAAVAALQRSDLLIALGTR---FDDRVTGKLDSFAPEAKV 332 +FP H G G G+ AA+ + ++D+++ALGTR F LD + AK+ Sbjct: 243 NDSFPADHSLWCGPLGYQGSKAAMKLIAKADVVLALGTRLGPFGTLPQHGLDYWPKNAKI 302 Query: 333 IHADIDPAEIGKNRHADVPIVGDVKAVITELIAMLRHHHIPGTIEM-----------ADW 381 I D D +G + V I GD +A L+ L + + + A+W Sbjct: 303 IQVDADAKMLGLVKQISVGICGDARAAADALVHRLASQVLACQLSIENRAGEIAQAKAEW 362 Query: 382 WAYLNG-VRKTYPLSYGPQSDG-SLSPEYVIEKLGEIAGPDAVFVAGVGQHQMWAAQFIR 439 A L+ + P S D ++ P ++ +L DA+ +G A ++R Sbjct: 363 EAELDAWPHERDPWSIEVAKDSPAIHPRQMLRELERALPDDAMVSTDIGNICSVANSYLR 422 Query: 440 YEKPRSWLNSGGLGTMGFAIPAAMGAKIALPGTEVWAIDGDGCFQMTNQELATCAVEGIP 499 + +PRS+ + G G+A PA +GAK A P A GDG + M+ E+ TC E IP Sbjct: 423 FRRPRSFFAAMSFGNCGYAFPAIIGAKHAAPERPAVAYVGDGAWGMSFGEILTCVRERIP 482 Query: 500 VKVALINNGNLGMVRQWQSLFYAERYSQTDLATHSHRIPDFVKLAEALGCVGLRCEREED 559 V + +N G ++ Q FY R+ ++L P F +A A+G G+ +R D Sbjct: 483 VTAVVFHNKQWGAEKKNQVDFYGNRFVGSNLDN-----PGFAAIARAMGAEGVVVDRLAD 537 Query: 560 V 560 V Sbjct: 538 V 538 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: 937 Number of extensions: 48 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: 618 Length of database: 588 Length adjustment: 37 Effective length of query: 581 Effective length of database: 551 Effective search space: 320131 Effective search space used: 320131 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