Align Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized)
to candidate YP_004140539.1 Mesci_1329 acetyl-CoA acetyltransferase
Query= SwissProt::Q8VPF1 (401 letters) >NCBI__GCF_000185905.1:YP_004140539.1 Length = 392 Score = 316 bits (810), Expect = 7e-91 Identities = 183/400 (45%), Positives = 254/400 (63%), Gaps = 11/400 (2%) Query: 1 MSREVYICDAVRTPIGRFGGSLAAVRADDLAAVPVKALVERNPQVDWSQLDEVYLGCANQ 60 MS + I A RTP+G F G+ AA A +L AV ++ L+ R V+ ++DEV LG Sbjct: 1 MSASIVIASAARTPVGSFNGAFAATPAHELGAVVIRELLSR-AGVEPGEVDEVILGQVLT 59 Query: 61 AGEDNRNVARMALLLAGLPDSVPGVTLNRLCASGMDAVGTAFRAIASGEAELVIAGGVES 120 A + +N AR A + AGLP LN++C SG+ A+ + IA G+A ++IAGG ES Sbjct: 60 AAQ-GQNPARQASINAGLPKETTAWGLNQVCGSGLRAIALGMQQIAIGDARVIIAGGQES 118 Query: 121 MSRAPYVMGKADSAFGRGQKIEDTTIGWRFINPLMKAQYGVDAMPETADNVADDYKVSRA 180 MS + + K+ DT I + L A G M TA+NVA ++++R Sbjct: 119 MSLSTHAQHLRAGVKMGDFKLIDTMIK----DGLWDAFNGYH-MGNTAENVARQFQITRE 173 Query: 181 DQDAFALRSQQLAGRAQAAGYFAEEIVPVVIKGKKGETVVDADEHLRPDTTLEALAKLKP 240 DQD FAL SQ A AQ AG F +EIV V IKGKKG+T+VD DE++R T++A+ KLKP Sbjct: 174 DQDQFALASQNKAEAAQKAGKFKDEIVAVTIKGKKGDTIVDQDEYIRHGATIDAMTKLKP 233 Query: 241 VNGPDKTVTAGNASGVNDGSV-ALILASAEAVKKHGLKARAKVLGMASAGVAPRVMGIGP 299 D TVTA NASG+NDG+ AL+++ AEAV++ G+ A+++ A+AGV P++MG GP Sbjct: 234 AFDKDGTVTAANASGINDGAAGALLMSEAEAVRR-GITPLARIVSWATAGVDPQIMGTGP 292 Query: 300 VPAVRKLLERLNLSVADFDVIELNEAFAAQGLAVTRELGIADDDARVNPNGGAIALGHPL 359 +PA RK LE+ SV D D++E NEAFAAQ AV +++G D + VN NGGAIA+GHP+ Sbjct: 293 IPASRKALEKAGWSVGDLDLVEANEAFAAQACAVNKDMGW--DPSIVNVNGGAIAIGHPI 350 Query: 360 GASGARLVLTAVHQLEKSGGQRGLCTMCVGVGQGVALAVE 399 GASGAR+ T V ++ + G ++GL T+C+G G GVA+ VE Sbjct: 351 GASGARVFNTLVFEMRRRGAKKGLATLCIGGGMGVAMCVE 390 Lambda K H 0.317 0.134 0.379 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: 416 Number of extensions: 19 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: 401 Length of database: 392 Length adjustment: 31 Effective length of query: 370 Effective length of database: 361 Effective search space: 133570 Effective search space used: 133570 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