Align 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 (characterized)
to candidate 5210417 Shew_2858 acetyl-CoA acetyltransferase (RefSeq)
Query= SwissProt::P0C7L2 (401 letters) >FitnessBrowser__PV4:5210417 Length = 394 Score = 231 bits (588), Expect = 4e-65 Identities = 155/409 (37%), Positives = 226/409 (55%), Gaps = 27/409 (6%) Query: 1 MREAFICDGIRTPIGR-YGGALSSVRADDLAAIPLRELLVRNPRLDAECIDDVILGCANQ 59 MREA I RT + + + G+L++ ++ + +++ V+ ++ IDD I+G Sbjct: 1 MREAVIVSTARTGMAKSFRGSLNNTKSPTMLGHCIKQA-VQRAGVEGGEIDDAIMGTVLT 59 Query: 60 AGEDNRNVARMATLLAGLPQSVSGTTINRLCGSGLDALGFAARAIKAGDGDLLIAGGVES 119 AG N+AR A L AGLP +VS TI+R C SGL A+G AA+ I +++AGG E+ Sbjct: 60 AGTAGMNIARNAVLAAGLPNTVSAQTIDRQCSSGLMAIGMAAKQIIVDQQQIVVAGGQEN 119 Query: 120 MSRAPFVMGKAASAFSRQAEMFDTTIGWRFVNPLMAQQFGTDSMPETAENVAELLKISRE 179 ++ K A A+ D N + + M +TAE+VA++ +SRE Sbjct: 120 ITAVQNEYMKWA------ADNADP-------NVMQFEPHAYMPMLKTAEHVAKVYGVSRE 166 Query: 180 DQDSFALRSQQRTAKAQSSGILAEEIVPVVL------KNKKGVVTE---IQHDEHLRPET 230 QD +AL SQQRTA AQ +G +EIVP + K + + + DE RP T Sbjct: 167 AQDIYALMSQQRTAAAQEAGYFDDEIVPFTTTMAIQDRETKAISYQQVTLDRDECNRPST 226 Query: 231 TLEQLRGLKAPFRANGVITAGNASGVNDGAAALIIASEQMAAAQGLTPRARIVAMATAGV 290 T+E L+ L AP G ITAGNAS ++DGA+A ++ ++A +GL P +A AG Sbjct: 227 TMESLQNL-APVIEGGFITAGNASQLSDGASACVVMERKLAEQRGLAPLGIYRGIAVAGC 285 Query: 291 EPRLMGLGPVPATRRVLERAGLSIHDMDVIELNEAFAAQALGVLRELGLPDDAPHVNPNG 350 P MG+GP+ A ++L++ GL+I D+ + E+NEAFA QAL LG+ D N NG Sbjct: 286 APEEMGIGPIYAIPKLLKQHGLTIDDIGLWEINEAFAVQALYCRDHLGI--DPARYNVNG 343 Query: 351 GAIALGHPLGMSGARLALAASHELHRRNGRYALCTMCIGVGQGIAMILE 399 G I++GHP GM+G+RL A E RR +Y + MCIG G G A + E Sbjct: 344 GGISIGHPYGMTGSRLVGHALIEGKRRGVKYVVVGMCIGGGMGAAGLFE 392 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: 395 Number of extensions: 21 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: 394 Length adjustment: 31 Effective length of query: 370 Effective length of database: 363 Effective search space: 134310 Effective search space used: 134310 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