Align acetolactate synthase (EC 2.2.1.6) (characterized)
to candidate WP_037576212.1 BS73_RS25220 thiamine pyrophosphate-binding protein
Query= BRENDA::O06335 (552 letters) >NCBI__GCF_000744815.1:WP_037576212.1 Length = 554 Score = 144 bits (364), Expect = 7e-39 Identities = 167/564 (29%), Positives = 241/564 (42%), Gaps = 54/564 (9%) Query: 4 GDHLVARMRAAGISVVCGLPTSRLDSLLVRLSRDAGFQIVLARHEGGAGYLADGFARASG 63 GD LV +RA G V G+ + L+ + R A + V RHE A ADG+ARA+G Sbjct: 11 GDLLVEVLRAHGCDTVFGIVSVHNLPLVEAVDRSADVRFVPVRHEAAAVNAADGYARATG 70 Query: 64 K-SAAVFVAGPGATNVISAVANASVNQVPMLILTGEVAVGEFGL-HSQQDTSDDGLGLGA 121 + A+ G GA N ++ + +L +TG++ GL + D LG+ Sbjct: 71 RLGCALTSTGTGAGNAAGSLIESLSAGTSVLHVTGQIDSPYLGLGRGFIHETKDQLGMLT 130 Query: 122 TFRRFCRCSVSIESIANARSKIDSAFRALASIPRGPVHIALPRDL---VDERLPAHQLGT 178 + +V I S A A + +A +A + P GP + P DL P L T Sbjct: 131 AVSKH---AVRIGSAAEAEGVLLAAAQAALTAPGGPASVEWPIDLQYAAQRPRPLTALDT 187 Query: 179 AAAGLGGLRTLAPCGPDVADEVIGRLDRSRAPMLVLGNGCRLDGIGEQIVAFCEKAGLPF 238 A T P G D A E++ +R P++ G G GE + A E G Sbjct: 188 APV------TALPDGLDAAAELLAA---ARRPVIWAGGGAAR--AGEPLRALAELLGAGL 236 Query: 239 ATTPNGRGIVAETHPLSLGVLGIFGDGRADEYLFDTPCDLLIAVGVSFGGLVTRSFSPRW 298 T+ +GRG V E HPL +G G+A D +++VG F T + + Sbjct: 237 FTSNSGRGAVGEDHPLVIGNYATSPGGKA----LLAEADAILSVGTHFRSNETGDYRLQ- 291 Query: 299 RGLKADVVHVDPDPSAVGRFVATSLGITTSGRAFVNALNCGRPPRFCRRVGVRPPAPAAL 358 L A V VD DP+A+GR ++G+ A + AL R++ V A Sbjct: 292 --LPAAHVQVDLDPAALGRVYPATVGLAGESGAVLAAL---LQKLSGRQLSVEEGWSARA 346 Query: 359 PGTPQARGE----SIHPLELMHELDRELAPNATICADVGTCIS--WTFRGIPVRRPGRFF 412 T + E +I P + E R P A++ A T S W R +P+ P Sbjct: 347 TETREEVRERQRWAIGPQAAVCEAIRAHYPAASVIARDVTIPSSTWGNRLLPLTDP---- 402 Query: 413 ATVDF---SPMGCGIAGAIGVALARPEEHVICIAGDGAFLMHGTEISTAVAHGIRVTWAV 469 AT F +G G+A AIG A RPE + IAGDG F +H E+ T R+T AV Sbjct: 403 ATNVFPRGGGIGQGLAMAIGAACGRPEVPTVLIAGDGGFAVHLGELLTVAQERPRLTLAV 462 Query: 470 LNDGQMSASAGPVSGRMDPSPVARIGANDLAA-----MARALGAEGIRVDTRCELRAGVQ 524 NDG G + + R G DL A +A A+G + R+ E + Sbjct: 463 FNDG----GYGVLRNMQEAGGGDRHGV-DLTAPAFDRLAAAVGIDYARIGAEAEADPVFK 517 Query: 525 KALAATGPCV--LDIAIDPEINKP 546 A AA GP + +D+A +N+P Sbjct: 518 AAAAAEGPVLVEIDLAALGPMNQP 541 Lambda K H 0.322 0.139 0.425 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: 849 Number of extensions: 44 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: 552 Length of database: 554 Length adjustment: 36 Effective length of query: 516 Effective length of database: 518 Effective search space: 267288 Effective search space used: 267288 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 (21.9 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Jul 26 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