Align acetolactate synthase (EC 2.2.1.6) (characterized)
to candidate WP_011842727.1 RSPH17029_RS19665 thiamine pyrophosphate-binding protein
Query= BRENDA::P9WG39 (547 letters) >NCBI__GCF_000015985.1:WP_011842727.1 Length = 550 Score = 195 bits (496), Expect = 3e-54 Identities = 165/540 (30%), Positives = 247/540 (45%), Gaps = 49/540 (9%) Query: 16 LIARRLKASGIDTVFTLSGGHLFSIYDGCREEGIRLIDTRHEQTAAFAAEGWSKVTRVPG 75 L+ L G+ +F+LSG + +YD C GI ++ RHE A F AEGW+++T G Sbjct: 14 LLVSTLVDCGVTRIFSLSGNQIMPLYDACLGSGIEIVHVRHEAAAVFMAEGWAQLTGEVG 73 Query: 76 VAALTAGPGITNGMSAMAAAQQNQSPLVVLGGRAPALRWGMGSLQEIDHVPFVAPVARFA 135 VA +TAGPG N + + +A+Q+++PL++L G +P + GMG+ Q +D V AP + + Sbjct: 74 VALVTAGPGAANAVGPLMSARQSETPLLLLSGDSPRAQDGMGAFQTLDQVAATAPFTKHS 133 Query: 136 ATAQSAENAGLLVDQALQAAVSAPSGVAFVDFPMDHAFSMSSDNGRPGALTELPAGPTPA 195 A S + AL A + G + P D G P + + A PA Sbjct: 134 ARVGSVPTLAHELRAALTLARAGRPGPVHLALPQD--LLTQRAEGVPSS-SRTAAATVPA 190 Query: 196 GD-ALDRAAGLLSTAQRPVIMAGTNVWWGHAEAALLRLVEERHIPVLMNGMARGV-VPAD 253 + R A ++ A+RP+I+ RL + +PV+ RG+ PA Sbjct: 191 SERETARLAAEIAEARRPLIVTSGLFSPTRGGDLARRLGQRLAVPVVALESPRGLRDPAQ 250 Query: 254 HRLAFSRARSKALGEADVALIVGVPMDFRLGFGGVFGSTTQLIVADRVEPAREH------ 307 L + + +AD+ + +G +D+ L FG + IV + + A E Sbjct: 251 PGL------RQRMADADLVISLGKSVDYMLDFGRATSADCGWIVVEPEDGAGEEAVRNLG 304 Query: 308 ----------PRPVAAGLYGDLTATLSALAGSGGTDHQGWIEELATAETMARDLEKAELV 357 PR +A GL A L G + W R L Sbjct: 305 PKLRRLIAADPRALAQGL-----AELPEAGCDAG--RRDW------CARFGRRPAPPVLD 351 Query: 358 DDRIPLHPMRVYAELAALLERD---ALVVIDAGDFGSYAGRMIDSYLPGCWLDSGPFGCL 414 + P+ + A L+ +L D ++V D G+FG +A ++ + L +GP G + Sbjct: 352 ETPGPIDSGLLCATLSDVLGADGGETILVSDGGEFGQWAQALVQA---DRRLINGPAGGI 408 Query: 415 GSGPGYALAAKLARPQRQVVLLQGDGAFGFSGMEWDTLVRHNVAVVSVIGNNGIWGLEKH 474 G G+A+AA LA P+ +V + GDG+ GF E +T VR A V VIGN+ W E Sbjct: 409 GGALGHAVAASLACPEARVAVASGDGSIGFHLAELETAVRAGAAFVVVIGNDRRWNAEHL 468 Query: 475 PMEALYGYSVV--AELRPGTRYDEVVRALGGHGELVSVPAELRPALERAFASGLPAVVNV 532 +G V EL G RYD V ALGG G V+ +ELR AL RAFA+G +VNV Sbjct: 469 LQIREFGPDRVHGCEL-SGARYDLVAAALGGTGAHVTCRSELRGALRRAFAAGGVVLVNV 527 Lambda K H 0.319 0.135 0.405 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: 787 Number of extensions: 52 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 547 Length of database: 550 Length adjustment: 36 Effective length of query: 511 Effective length of database: 514 Effective search space: 262654 Effective search space used: 262654 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