Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate PfGW456L13_2411 3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltransferase (EC 2.3.1.9)
Query= metacyc::MONOMER-15952 (401 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2411 Length = 393 Score = 324 bits (831), Expect = 2e-93 Identities = 189/400 (47%), Positives = 250/400 (62%), Gaps = 12/400 (3%) Query: 3 EALIIDAVRTPIGRYAGALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCANQAGE 62 E ++ A RT IG + G+L V DL +KA + R +D + V ++ G Sbjct: 5 EIYVVSAARTAIGTFGGSLKDVPLADLATTAVKAALER-AAVDPALVGHLVMGNVIPTET 63 Query: 63 DNRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVESMSR 122 + ++R+AA+ AG+P P +NRLCGSGL A+ +AA+ L G+A +++ G ESMSR Sbjct: 64 RDAYISRVAAMNAGIPKETPAYNVNRLCGSGLQAIINAAQTLMLGDADIVVGAGAESMSR 123 Query: 123 APFVMGKSEQAFGR-SAEIFDTTIGWRFVNKLMQQGFGIDSMPETAENVAAQFNISRADQ 181 P++M + +A++ D +G ++ F M TAENVAA+ I+R Q Sbjct: 124 GPYLMPAARWGSRMGNAQVIDYMLG------ILHDPFHGIHMGITAENVAARNGITREMQ 177 Query: 182 DAFALRSQHKAAAAIANGRLAKEIVAVEIAQRKGPAKIVEHDEHPRGDTTLEQLAKLGTP 241 DA A Q +AA AIANG +++I VEI RKG K+ DEHPR T+LEQLA + Sbjct: 178 DALAFEDQQRAAHAIANGYFSEQIATVEIQDRKG-VKLFSVDEHPRA-TSLEQLAAMKPA 235 Query: 242 FRQGGSVTAGNASGVNDGACALLLASSEAAQRHGLKARARVVGMATAGVEPRIMGIGPVP 301 F++ GSVTAGNASG+NDGA AL++AS A Q + LK AR+V A AGVEP MG+GP+P Sbjct: 236 FKKDGSVTAGNASGLNDGAAALVMASGNAVQANNLKPLARLVSYAHAGVEPEFMGLGPIP 295 Query: 302 ATRKVLELTGLALADMDVIELNEAFAAQGLAVLRELGLADDDERVNPNGGAIALGHPLGM 361 ATR L+ GL +AD+DVIE N AFAAQ AV +EL L D +VNPNG IALGHP+G Sbjct: 296 ATRLALKRAGLTVADLDVIEANIAFAAQACAVSQELDL--DPAKVNPNGSGIALGHPVGA 353 Query: 362 SGARLVTTALHELEERQGRYALCTMCIGVGQGIALIIERI 401 +GA + T A+HEL GRYAL TMCIG GQGIA I ER+ Sbjct: 354 TGAIIATKAIHELHRTGGRYALVTMCIGGGQGIAAIFERV 393 Lambda K H 0.319 0.134 0.384 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: 404 Number of extensions: 23 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: 393 Length adjustment: 31 Effective length of query: 370 Effective length of database: 362 Effective search space: 133940 Effective search space used: 133940 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: 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