Align Beta-ketothiolase BktB; Acetyl-CoA acetyltransferase; Acetyl-CoA acyltransferase; EC 2.3.1.16; EC 2.3.1.9 (characterized)
to candidate PfGW456L13_2411 3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltransferase (EC 2.3.1.9)
Query= SwissProt::Q0KBP1 (394 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2411 Length = 393 Score = 494 bits (1272), Expect = e-144 Identities = 251/393 (63%), Positives = 301/393 (76%), Gaps = 2/393 (0%) Query: 2 TREVVVVSGVRTAIGTFGGSLKDVAPAELGALVVREALARAQVSGDDVGHVVFGNVIQTE 61 T E+ VVS RTAIGTFGGSLKDV A+L V+ AL RA V VGH+V GNVI TE Sbjct: 3 TPEIYVVSAARTAIGTFGGSLKDVPLADLATTAVKAALERAAVDPALVGHLVMGNVIPTE 62 Query: 62 PRDMYLGRVAAVNGGVTINAPALTVNRLCGSGLQAIVSAAQTILLGDTDVAIGGGAESMS 121 RD Y+ RVAA+N G+ PA VNRLCGSGLQAI++AAQT++LGD D+ +G GAESMS Sbjct: 63 TRDAYISRVAAMNAGIPKETPAYNVNRLCGSGLQAIINAAQTLMLGDADIVVGAGAESMS 122 Query: 122 RAPYLAPAARWGARMGDAGLVDMMLGALHDPFHRIHMGVTAENVAKEYDISRAQQDEAAL 181 R PYL PAARWG+RMG+A ++D MLG LHDPFH IHMG+TAENVA I+R QD A Sbjct: 123 RGPYLMPAARWGSRMGNAQVIDYMLGILHDPFHGIHMGITAENVAARNGITREMQDALAF 182 Query: 182 ESHRRASAAIKAGYFKDQIVPVVSKGRKGDVTFDTDEHVRHDATIDDMTKLRPVFVKENG 241 E +RA+ AI GYF +QI V + RKG F DEH R +++ + ++P F K++G Sbjct: 183 EDQQRAAHAIANGYFSEQIATVEIQDRKGVKLFSVDEHPR-ATSLEQLAAMKPAF-KKDG 240 Query: 242 TVTAGNASGLNDAAAAVVMMERAEAERRGLKPLARLVSYGHAGVDPKAMGIGPVPATKIA 301 +VTAGNASGLND AAA+VM + LKPLARLVSY HAGV+P+ MG+GP+PAT++A Sbjct: 241 SVTAGNASGLNDGAAALVMASGNAVQANNLKPLARLVSYAHAGVEPEFMGLGPIPATRLA 300 Query: 302 LERAGLQVSDLDVIEANEAFAAQACAVTKALGLDPAKVNPNGSGISLGHPIGATGALITV 361 L+RAGL V+DLDVIEAN AFAAQACAV++ L LDPAKVNPNGSGI+LGHP+GATGA+I Sbjct: 301 LKRAGLTVADLDVIEANIAFAAQACAVSQELDLDPAKVNPNGSGIALGHPVGATGAIIAT 360 Query: 362 KALHELNRVQGRYALVTMCIGGGQGIAAIFERI 394 KA+HEL+R GRYALVTMCIGGGQGIAAIFER+ Sbjct: 361 KAIHELHRTGGRYALVTMCIGGGQGIAAIFERV 393 Lambda K H 0.318 0.134 0.381 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: 507 Number of extensions: 18 Number of successful extensions: 2 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: 393 Length adjustment: 31 Effective length of query: 363 Effective length of database: 362 Effective search space: 131406 Effective search space used: 131406 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 17 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