Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate WP_043461338.1 H537_RS0133840 sulfoacetaldehyde acetyltransferase
Query= BRENDA::P9WG41 (618 letters) >NCBI__GCF_000430725.1:WP_043461338.1 Length = 588 Score = 236 bits (603), Expect = 2e-66 Identities = 174/556 (31%), Positives = 259/556 (46%), Gaps = 38/556 (6%) Query: 38 LTGAQAVIRSLEELGVDVIFGIPGGAVLPVYDPLFDSKKLRHVLVRHEQGAGHAASGYAH 97 +T ++A + ++ GV +FGI G A + D +F +R + V HEQGAGH A GYA Sbjct: 1 MTPSEAFVETMVANGVTDMFGIMGSAFMDAMD-IFAPAGIRLIPVVHEQGAGHMADGYAR 59 Query: 98 VTGRVGVCMATSGPGATNLVTPLADAQMDSIPVVAITGQVGRGLIGTDAFQEADISGITM 157 V+GR GV + +GPG +N VT +A A PVV +T + G G FQEA + Sbjct: 60 VSGRHGVVIGQNGPGISNCVTAIAAAYWAHTPVVIVTPEAGTMGQGLGGFQEAKQLPMFQ 119 Query: 158 PITKHNFLVRSGDDIPRVLAEAFHIAASGRPGAVLVDIPKDVLQGQCTFSWPPRMELPGY 217 TK+ V + F A S G ++IP+D GQ T P L Sbjct: 120 EFTKYQGHVTHPARMAEFTGRCFDRAMS-EMGPTQLNIPRDYFYGQITAEIPQPQRL--- 175 Query: 218 KPNTKPHSRQ-VREAAKLIAAARKPVLYVGGGVIRGEATEQLRELAELTGIPVVTTLMAR 276 + P Q + EAA+L+A A+ PV+ GGGV+ + E + LAE G PVV + + Sbjct: 176 --DRGPGGEQSLNEAAELLATAKFPVIIAGGGVVMADGVEACQALAERLGAPVVNSYLHN 233 Query: 277 GAFPDSHRQNLGMPGMHGTVAAVAALQRSDLLIALGTR---FDDRVTGKLDSFAPEAKVI 333 +FP SH G G G+ AA+ + R+D+++ALG+R F +D + EAK+I Sbjct: 234 DSFPASHPLWCGPLGYQGSKAAMKLISRADVVVALGSRLGPFGTLPQHGMDYWPKEAKII 293 Query: 334 HADIDPAEIGKNRHADVPIVGDVKAVITELIAMLRHHHIPG-----------TIEMADWW 382 D D +G + V I GD KA L+ L + E A W Sbjct: 294 QIDADHKMLGLVKKISVGICGDAKAAAQALVQRLGERTLACDATRAQRGDDIATEKAAWE 353 Query: 383 AYLNG---VRKTYPLSYGPQSDGS--------LSPEYVIEKLGEIAGPDAVFVAGVGQHQ 431 L+ R + L ++ G L P V+ +L + PD + +G Sbjct: 354 RELDAWTHERDPFSLDMIEEAKGERTPFGGHYLHPRQVLRELEKAMPPDVMVSTDIGNIN 413 Query: 432 MWAAQFIRYEKPRSWLNSGGLGTMGFAIPAAMGAKIALPGTEVWAIDGDGCFQMTNQELA 491 A ++R+EKPRS+ + G G+A P +GAK+A P + GDG + M+ E Sbjct: 414 SVANSYLRFEKPRSFFAAMSWGNCGYAFPTIIGAKVAAPHRPAISYAGDGAWGMSLMETL 473 Query: 492 TCAVEGIPVKVALINNGNLGMVRQWQSLFYAERYSQTDLATHSHRIPDFVKLAEALGCVG 551 TC IPV + +N G ++ Q FY R+ +L + P F +A+A+G G Sbjct: 474 TCVRHDIPVTAVVFHNRQWGAEKKNQVDFYNRRFVAGELDS-----PSFAGIAKAMGAEG 528 Query: 552 LRCEREEDVVDVINQA 567 + +R EDV + +A Sbjct: 529 IVVDRLEDVGPALQRA 544 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: 939 Number of extensions: 56 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 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