Align 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 (characterized)
to candidate WP_099618908.1 CLH62_RS14435 acetyl-CoA C-acetyltransferase
Query= SwissProt::P0C7L2 (401 letters) >NCBI__GCF_002744735.1:WP_099618908.1 Length = 402 Score = 279 bits (713), Expect = 1e-79 Identities = 173/421 (41%), Positives = 238/421 (56%), Gaps = 44/421 (10%) Query: 3 EAFICDGIRTPIGR--YGGALSSVRADDLAAIPLRELLVRNPRLDAECIDDVILGCANQA 60 EA+I D +RTP GR G+L SV+ L L L RN LD +DD+++GC Sbjct: 4 EAYIFDAVRTPRGRGKKDGSLHSVKPITLLTTVLHALQERNS-LDTAQVDDIVMGCVTAV 62 Query: 61 GEDNRNVARMATLLAGLPQSVSGTTINRLCGSGLDALGFAARAIKAGDGDLLIAGGVESM 120 G+ ++A+ A L A + V+G T+NR C SGL+A+ AA +++G D+++AGGVE+M Sbjct: 63 GDQGADIAKTAALAADWDEKVAGVTLNRFCASGLEAVNLAAMKVRSGWEDMVVAGGVEAM 122 Query: 121 SRAPFVMGKAASAFSRQAEMFDTTIGWRFVNPLMAQQFGTDSMPETAENVAELLKISRED 180 SR P MG A++ E T + F M Q G D +A L SR D Sbjct: 123 SRVP--MGSDGGAWATDPE---TNLHTGF----MPQGIGADL-------IATLEGFSRMD 166 Query: 181 QDSFALRSQQRTAKAQSSGILAEEIVPVVLKNKKGVVTEIQHDEHLRPETTLEQLRGLKA 240 D+FA++SQQ+ A A +G + I+PV +N GVV + DEH+R TT+E L GL+ Sbjct: 167 VDAFAVKSQQKAANAWQNGYFGKSIIPVTDQN--GVVI-LDRDEHVRGNTTVESLSGLRP 223 Query: 241 PF--------------------RANGVITAGNASGVNDGAAALIIASEQMAAAQGLTPRA 280 F + N V AGN+SG+ DGA A++I SE A GL PRA Sbjct: 224 SFQMMGEMGFDGVAREKYHYVEKINHVHHAGNSSGIVDGATAMLIGSEAKGKAMGLKPRA 283 Query: 281 RIVAMATAGVEPRLMGLGPVPATRRVLERAGLSIHDMDVIELNEAFAAQALGVLRELGLP 340 RIVA A +P +M GP PA R+ L +AG++ +D+ E+NEAFA+ + REL +P Sbjct: 284 RIVATAVTSTDPTIMLTGPAPAARKALGKAGMTADQIDLFEVNEAFASVVMRFQRELSVP 343 Query: 341 DDAPHVNPNGGAIALGHPLGMSGARLALAASHELHRRNGRYALCTMCIGVGQGIAMILER 400 D+ VN NGGAIA+GHPLG +GA + EL RR R+ L T+C+G G GIA I+ER Sbjct: 344 DE--KVNVNGGAIAMGHPLGATGAMILGTLLDELERRELRFGLATLCVGGGMGIATIIER 401 Query: 401 V 401 V Sbjct: 402 V 402 Lambda K H 0.319 0.135 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: 439 Number of extensions: 20 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: 402 Length adjustment: 31 Effective length of query: 370 Effective length of database: 371 Effective search space: 137270 Effective search space used: 137270 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