Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate PfGW456L13_2430 Acetyl-CoA acetyltransferase (EC 2.3.1.9) @ Beta-ketoadipyl CoA thiolase (EC 2.3.1.-)
Query= metacyc::MONOMER-15952 (401 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2430 Length = 403 Score = 694 bits (1790), Expect = 0.0 Identities = 348/401 (86%), Positives = 375/401 (93%) Query: 1 MNEALIIDAVRTPIGRYAGALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCANQA 60 MN+ALIIDAVRTPIGRYAG L+SVRADDLGA+PL+ L+ RHPQ+DW+ VDDVIYGCANQA Sbjct: 1 MNDALIIDAVRTPIGRYAGVLSSVRADDLGAVPLRELLRRHPQVDWNTVDDVIYGCANQA 60 Query: 61 GEDNRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVESM 120 GEDNRNVARM+ALLAGLPVSVPGTTLNRLCGSGLDA+G+AARA+R GE GLML GGVESM Sbjct: 61 GEDNRNVARMSALLAGLPVSVPGTTLNRLCGSGLDAIGTAARAIRSGETGLMLVGGVESM 120 Query: 121 SRAPFVMGKSEQAFGRSAEIFDTTIGWRFVNKLMQQGFGIDSMPETAENVAAQFNISRAD 180 SRAP VMGK+EQAF R+AE+FDTTIGWRFVN LM++ +GIDSMPETAENVA QFNISRAD Sbjct: 121 SRAPLVMGKAEQAFSRTAEVFDTTIGWRFVNPLMKKTYGIDSMPETAENVAEQFNISRAD 180 Query: 181 QDAFALRSQHKAAAAIANGRLAKEIVAVEIAQRKGPAKIVEHDEHPRGDTTLEQLAKLGT 240 QDAFALRSQ +AAAA A+GRLAKEIVAVEI QRKGPAK+VEHDEHPRGDTTLEQLAKLGT Sbjct: 181 QDAFALRSQQRAAAAQASGRLAKEIVAVEIPQRKGPAKVVEHDEHPRGDTTLEQLAKLGT 240 Query: 241 PFRQGGSVTAGNASGVNDGACALLLASSEAAQRHGLKARARVVGMATAGVEPRIMGIGPV 300 PFR+GGS+TAGNASGVNDGACALLLAS E A+R GL AR RVV MATAGVEPRIMGIGPV Sbjct: 241 PFREGGSITAGNASGVNDGACALLLASPEVAKRQGLTARGRVVAMATAGVEPRIMGIGPV 300 Query: 301 PATRKVLELTGLALADMDVIELNEAFAAQGLAVLRELGLADDDERVNPNGGAIALGHPLG 360 PATRKVLE+ L+LADMDVIELNEAFAAQGLAVLRELGL+D D RVNPNGGAIALGHPLG Sbjct: 301 PATRKVLEVANLSLADMDVIELNEAFAAQGLAVLRELGLSDTDPRVNPNGGAIALGHPLG 360 Query: 361 MSGARLVTTALHELEERQGRYALCTMCIGVGQGIALIIERI 401 MSGARLVTTALHELEER GRYALCTMCIGVGQGIALIIER+ Sbjct: 361 MSGARLVTTALHELEERNGRYALCTMCIGVGQGIALIIERL 401 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: 639 Number of extensions: 16 Number of successful extensions: 1 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: 403 Length adjustment: 31 Effective length of query: 370 Effective length of database: 372 Effective search space: 137640 Effective search space used: 137640 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