Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate WP_007508344.1 R2APBS1_RS08710 acetyl-CoA C-acyltransferase
Query= metacyc::MONOMER-15952 (401 letters) >NCBI__GCF_000230695.2:WP_007508344.1 Length = 401 Score = 301 bits (771), Expect = 2e-86 Identities = 189/415 (45%), Positives = 245/415 (59%), Gaps = 32/415 (7%) Query: 1 MNEALIIDAVRTPIGRYA-GALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCANQ 59 + EA I+ A RTP+G+ G + R DD+ A ++A++A+ P +D + DVI GCA Sbjct: 5 VQEAYIVAATRTPVGKAPRGVFRNTRPDDMLAHVIRAVMAQAPGIDPHQIGDVIIGCAMP 64 Query: 60 AGEDNRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVES 119 E NVAR+ LLAGLP +VPG T+NR C SGL +V AA +R G LMLAGG ES Sbjct: 65 EAEQGMNVARIGLLLAGLPDTVPGVTVNRFCSSGLQSVAMAADRIRLGLDDLMLAGGTES 124 Query: 120 MSRAPFVMGKSEQAFGRSAEIF-DTTIGWRFVNKLMQQGFGIDSMPETAENVAAQFNISR 178 MS P + K + IF D IG + G GI TAENVA Q+ +SR Sbjct: 125 MSMVPMMGHK----IAMNPAIFNDENIGIAY-------GMGI-----TAENVAKQWKVSR 168 Query: 179 ADQDAFALRSQHKAAAAIANGRLAKEIVAVEIAQR------KG---PAKIVEHDEHPRGD 229 QDAF++ S +A AA A G EI + +G ++ ++ DE PR Sbjct: 169 EQQDAFSVESHRRALAAQAAGEFNDEISPFALDDHYPNLATRGIVTDSRRIDSDEGPRAG 228 Query: 230 TTLEQLAKLGTPFRQG---GSVTAGNASGVNDGACALLLASSEAAQRHGLKARARVVGMA 286 TT+E LAKL T FR G G+VTAGN+S ++DGA A+LLAS A + + L+ AR VG + Sbjct: 229 TTMEVLAKLKTVFRNGQFGGTVTAGNSSQMSDGAGAVLLASERAVKEYNLQPLARFVGFS 288 Query: 287 TAGVEPRIMGIGPVPATRKVLELTGLALADMDVIELNEAFAAQGLAVLRELGLADDDERV 346 AGV P +MGIGP A K L+ GL +D IELNEAFAAQ LAV+ +LGL D +V Sbjct: 289 VAGVPPEVMGIGPKEAIPKALKQAGLNRDQLDWIELNEAFAAQALAVMGDLGL--DPNKV 346 Query: 347 NPNGGAIALGHPLGMSGARLVTTALHELEERQGRYALCTMCIGVGQGIALIIERI 401 NP GGAIALGHPLG +GA + T +H + R+ +Y + TMCIG G G A I E + Sbjct: 347 NPLGGAIALGHPLGATGAVRIATLVHGMRRRKQKYGMVTMCIGTGMGAAGIFEAL 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: 448 Number of extensions: 23 Number of successful extensions: 6 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: 401 Length adjustment: 31 Effective length of query: 370 Effective length of database: 370 Effective search space: 136900 Effective search space used: 136900 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 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