Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate WP_029001425.1 H537_RS0133840 sulfoacetaldehyde acetyltransferase
Query= BRENDA::P9WG41 (618 letters) >NCBI__GCF_000430725.1:WP_029001425.1 Length = 601 Score = 239 bits (610), Expect = 2e-67 Identities = 176/561 (31%), Positives = 262/561 (46%), Gaps = 38/561 (6%) Query: 33 VALQQLTGAQAVIRSLEELGVDVIFGIPGGAVLPVYDPLFDSKKLRHVLVRHEQGAGHAA 92 V Q++T ++A + ++ GV +FGI G A + D +F +R + V HEQGAGH A Sbjct: 9 VGPQKMTPSEAFVETMVANGVTDMFGIMGSAFMDAMD-IFAPAGIRLIPVVHEQGAGHMA 67 Query: 93 SGYAHVTGRVGVCMATSGPGATNLVTPLADAQMDSIPVVAITGQVGRGLIGTDAFQEADI 152 GYA V+GR GV + +GPG +N VT +A A PVV +T + G G FQEA Sbjct: 68 DGYARVSGRHGVVIGQNGPGISNCVTAIAAAYWAHTPVVIVTPEAGTMGQGLGGFQEAKQ 127 Query: 153 SGITMPITKHNFLVRSGDDIPRVLAEAFHIAASGRPGAVLVDIPKDVLQGQCTFSWPPRM 212 + TK+ V + F A S G ++IP+D GQ T P Sbjct: 128 LPMFQEFTKYQGHVTHPARMAEFTGRCFDRAMS-EMGPTQLNIPRDYFYGQITAEIPQPQ 186 Query: 213 ELPGYKPNTKPHSRQ-VREAAKLIAAARKPVLYVGGGVIRGEATEQLRELAELTGIPVVT 271 L + P Q + EAA+L+A A+ PV+ GGGV+ + E + LAE G PVV Sbjct: 187 RL-----DRGPGGEQSLNEAAELLATAKFPVIIAGGGVVMADGVEACQALAERLGAPVVN 241 Query: 272 TLMARGAFPDSHRQNLGMPGMHGTVAAVAALQRSDLLIALGTR---FDDRVTGKLDSFAP 328 + + +FP SH G G G+ AA+ + R+D+++ALG+R F +D + Sbjct: 242 SYLHNDSFPASHPLWCGPLGYQGSKAAMKLISRADVVVALGSRLGPFGTLPQHGMDYWPK 301 Query: 329 EAKVIHADIDPAEIGKNRHADVPIVGDVKAVITELIAMLRHHHIPG-----------TIE 377 EAK+I D D +G + V I GD KA L+ L + E Sbjct: 302 EAKIIQIDADHKMLGLVKKISVGICGDAKAAAQALVQRLGERTLACDATRAQRGDDIATE 361 Query: 378 MADWWAYLNG---VRKTYPLSYGPQSDGS--------LSPEYVIEKLGEIAGPDAVFVAG 426 A W L+ R + L ++ G L P V+ +L + PD + Sbjct: 362 KAAWERELDAWTHERDPFSLDMIEEAKGERTPFGGHYLHPRQVLRELEKAMPPDVMVSTD 421 Query: 427 VGQHQMWAAQFIRYEKPRSWLNSGGLGTMGFAIPAAMGAKIALPGTEVWAIDGDGCFQMT 486 +G A ++R+EKPRS+ + G G+A P +GAK+A P + GDG + M+ Sbjct: 422 IGNINSVANSYLRFEKPRSFFAAMSWGNCGYAFPTIIGAKVAAPHRPAISYAGDGAWGMS 481 Query: 487 NQELATCAVEGIPVKVALINNGNLGMVRQWQSLFYAERYSQTDLATHSHRIPDFVKLAEA 546 E TC IPV + +N G ++ Q FY R+ +L + P F +A+A Sbjct: 482 LMETLTCVRHDIPVTAVVFHNRQWGAEKKNQVDFYNRRFVAGELDS-----PSFAGIAKA 536 Query: 547 LGCVGLRCEREEDVVDVINQA 567 +G G+ +R EDV + +A Sbjct: 537 MGAEGIVVDRLEDVGPALQRA 557 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: 954 Number of extensions: 57 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: 601 Length adjustment: 37 Effective length of query: 581 Effective length of database: 564 Effective search space: 327684 Effective search space used: 327684 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 Jul 25 2024. The underlying query database was built on Jul 25 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