Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Beta-ketothiolase; EC 2.3.1.9 (characterized)
to candidate WP_015446959.1 R2APBS1_RS03900 3-oxoadipyl-CoA thiolase
Query= SwissProt::P45369 (394 letters) >NCBI__GCF_000230695.2:WP_015446959.1 Length = 400 Score = 309 bits (791), Expect = 1e-88 Identities = 172/395 (43%), Positives = 248/395 (62%), Gaps = 9/395 (2%) Query: 7 IVDAGRSAIGTFSGSLSSLSATEIGTAVLKGLLAR-TGLAPEQIDEVILGQVLTAGV-GQ 64 +VDA R+ G G+L+ + A ++ + L+AR L +DEVILG AG + Sbjct: 6 LVDATRTPFGRLGGALAGVRADDLAALPIAALMARHPTLDWAALDEVILGCANQAGEDNR 65 Query: 65 NPARQTTLKAGLPHSVPAMTINKVCGSGLKAVHLAMQAIACGDADIVIAGGQESMSQSSH 124 N AR TL AGLP SVPA+T+N++C SGL+A+ A +AIACG+A++V+AGG ESMS++ + Sbjct: 66 NVARMATLLAGLPQSVPAVTVNRLCASGLEAIGQAARAIACGEAELVVAGGVESMSRAPY 125 Query: 125 VLPRS----RDGQRMGDWSMKDTMIVDGLWDAFNNYHMGTTAENIAQKYGFTREQQDAFA 180 VL ++ GQ++ D ++ ++ + + M TAEN+A+++G R+ QDA+A Sbjct: 126 VLAKADVAYARGQQLEDTTLGWRLVNPRMQAGYGIDSMTQTAENLAREHGIDRDSQDAYA 185 Query: 181 AASQQKTEAAQKAGRFQDEIIPIEIPQRKGDPKVFDADEFPRHGTTAESLGKLRPAFSRD 240 SQQ+T AQ G +EI + P K + V DE PR TTA L L+P Sbjct: 186 LRSQQRTAHAQAQGWLAEEITAVHAPHGK-ESLVVQVDEHPRADTTAAKLAALKPLLGAG 244 Query: 241 GSVTAGNASGINDGAAMVVVMKESKAKELGLKPMARLVAFASAGVDPAIMGTGPIPASTK 300 S+TAGNASG+NDGAA V++ E+ GL+P+AR+V A+AGV P +MG GP+PA K Sbjct: 245 SSITAGNASGLNDGAAAVLLASEAALARYGLQPLARIVGMAAAGVAPRVMGIGPVPAIHK 304 Query: 301 CLEKAGWTPADLDLIEANEAFAAQAMSVNQDMGW--DLSKVNVNGGAIAIGHPIGASGAR 358 L + G +D D IE NEAFAAQ ++ + +G D VN NGGAIA+GHP+GASGAR Sbjct: 305 LLARTGLGASDFDRIEINEAFAAQVLACTRSLGLPDDAEHVNANGGAIALGHPLGASGAR 364 Query: 359 VLVTLLYEMQKRDAKKGLATLCIGGGQGVALAVER 393 + +T + +++ + L +LC+G GQG+ALA+ER Sbjct: 365 LALTAAFALRRHRQHRALVSLCVGVGQGLALALER 399 Lambda K H 0.315 0.131 0.375 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: 401 Number of extensions: 22 Number of successful extensions: 6 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: 394 Length of database: 400 Length adjustment: 31 Effective length of query: 363 Effective length of database: 369 Effective search space: 133947 Effective search space used: 133947 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
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