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_059153516.1 V474_RS22770 thiolase family protein
Query= SwissProt::P0C7L2 (401 letters) >NCBI__GCF_001046635.1:WP_059153516.1 Length = 378 Score = 299 bits (766), Expect = 8e-86 Identities = 184/403 (45%), Positives = 250/403 (62%), Gaps = 28/403 (6%) Query: 1 MREAFICDGIRTPIGRYG-GALSSVRADDLAAIPLRELLVRNPRLDAECIDDVILGCANQ 59 M+ I R+P G GAL+ VR DDLAA +R L+ + A+ I+D+I+GCA Sbjct: 1 MQSVVIAGYARSPFHLAGKGALARVRPDDLAAQVIRGLIGKTGVEPAD-IEDIIVGCAFP 59 Query: 60 AGEDNRNVARMATLLAGLPQSVSGTTINRLCGSGLDALGFAARAIKAGDGDLLIAGGVES 119 GE NVAR+ LLA LP SV G T+NR CGS + A+ A I G G++ + GVES Sbjct: 60 EGEQGLNVARLIGLLADLPISVGGMTVNRFCGSSMSAIHIAMGQIAIGAGEVFVCAGVES 119 Query: 120 MSRAPFVMGKAASAFSRQAEMFDTTIGWRFVNPLMAQQFGTD-SMPETAENVAELLKISR 178 MSR P +MG F+ NP +A++ M ETAENVA +ISR Sbjct: 120 MSRVP-MMG------------FNP-----LPNPALAKKSAAYMGMGETAENVAAKYQISR 161 Query: 179 EDQDSFALRSQQRTAKAQSSGILAEEIVPVVLKNKKGVVTEIQHDEHLRPETTLEQLRGL 238 DQ++ A+ SQ + A++ G L++EIVP+ + K G V+E D +RPETT E L GL Sbjct: 162 GDQEALAVESQNKATAARTEGRLSDEIVPI--ETKAGTVSE---DGTIRPETTAEGLAGL 216 Query: 239 KAPFRANGVITAGNASGVNDGAAALIIASEQMAAAQGLTPRARIVAMATAGVEPRLMGLG 298 K F A G +TAG +S + DGA+A+++ +E A A GL ARI ++A +G P MGLG Sbjct: 217 KPAFDAQGSVTAGTSSPLTDGASAVLVTTEDYARAHGLPILARIKSVAISGCAPETMGLG 276 Query: 299 PVPATRRVLERAGLSIHDMDVIELNEAFAAQALGVLRELGLPDDAPHVNPNGGAIALGHP 358 P+ ++++ LERAG+S D+DV+ELNEAFA+QAL +++LGL D VN +GGAIA+GHP Sbjct: 277 PILSSQKALERAGISAADLDVVELNEAFASQALACIKDLGL--DRAKVNIDGGAIAIGHP 334 Query: 359 LGMSGARLALAASHELHRRNGRYALCTMCIGVGQGIAMILERV 401 LG +GAR+ A+ L R G+YAL + CIG GQGIA +LE V Sbjct: 335 LGATGARIVGKAASLLKREGGKYALASQCIGGGQGIATVLEAV 377 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: 412 Number of extensions: 16 Number of successful extensions: 5 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: 378 Length adjustment: 30 Effective length of query: 371 Effective length of database: 348 Effective search space: 129108 Effective search space used: 129108 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