Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Beta-ketothiolase; EC 2.3.1.9 (characterized)
to candidate WP_065401082.1 BBI00_RS22490 3-oxoadipyl-CoA thiolase
Query= SwissProt::P45363 (394 letters) >NCBI__GCF_001684965.1:WP_065401082.1 Length = 401 Score = 335 bits (858), Expect = 2e-96 Identities = 185/402 (46%), Positives = 264/402 (65%), Gaps = 12/402 (2%) Query: 3 DTIVIVDAGRTAIGTFGGALSALQATDIGTTVLKALIERTGIAP-EQVSEVILGQVLTAG 61 + + I+D RT I G LS ++A D+ V+K ++ R P E++ +VI G AG Sbjct: 2 NNVYIIDYVRTPISKLQGGLSEVRADDLAAIVIKEVVARNPEVPVEEIEDVIFGCANQAG 61 Query: 62 -CGQNPARQTTLMAGLPHTVPAMTINKVCGSGLKAVHLAMQAVACGDAEIVIAGGQESMS 120 +N AR L+AGLP+ + T+N++C SG+ AV A +++A G+ EI IAGG E M+ Sbjct: 62 EDNRNVARMGLLLAGLPYKIGGETVNRLCASGMSAVANAFRSIASGEGEIYIAGGVEHMT 121 Query: 121 QSSHVLPRSREGQRMG-DWPMKDT-----MIVDGLWDAFNQCHMGVTAENIAKKYAFTRE 174 +S +V+ S+ G G D M DT I + + + MG TAEN+A + +RE Sbjct: 122 RSPYVM--SKPGAAFGRDSQMFDTTFGWRFINPKMKEMYGVDGMGETAENLADMHHISRE 179 Query: 175 AQDAFAAASQQKAEAAIQSGRFADEIIPVSIPQRKGDPLVFDTDEFPRPGTTAETLGRLR 234 QD FA SQQKA A +SGR A+EI+ V IPQRKG+P++F+ DEF +PG++ E LG+LR Sbjct: 180 DQDKFALWSQQKATKAQESGRLAEEIVKVEIPQRKGEPVIFEKDEFIKPGSSMEGLGKLR 239 Query: 235 PAFDKQGTVTAGNASGINDGAAMVVVMKESKAKELGLTPMARLVAFSSAGVDPAIMGTGP 294 PAF K+GTVTAGNASG+NDGAA +++ E K+ GL P AR++ S AGV+P IMG GP Sbjct: 240 PAFRKEGTVTAGNASGMNDGAAALILASEEAVKKYGLKPKARILGSSVAGVEPRIMGIGP 299 Query: 295 IPASTDCLKKAGWAPADLDLVEANEAFAAQAMSVNQEMGW--DLSKVNVNGGAIAIGHPI 352 + A+ LK+ + D+D++E NEAFAAQA++V + +G D S++N NGGAIAIGHP+ Sbjct: 300 VEATQKLLKRLDLSLEDMDIIELNEAFAAQALAVTRTLGLKDDDSRINPNGGAIAIGHPL 359 Query: 353 GASGARVLVTLLYEMQKRDAKKGLATLCIGGGQGVALAVERL 394 G SGAR++ + E+QK++ K L TLCIG GQG A+ +E++ Sbjct: 360 GVSGARIIGSAAMELQKQNKKYALCTLCIGVGQGYAMVIEKV 401 Lambda K H 0.317 0.131 0.380 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: 321 Number of extensions: 6 Number of successful extensions: 4 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: 401 Length adjustment: 31 Effective length of query: 363 Effective length of database: 370 Effective search space: 134310 Effective search space used: 134310 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 (21.7 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