Align 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 (characterized)
to candidate RR42_RS07645 RR42_RS07645 acetyl-CoA acetyltransferase
Query= SwissProt::P0C7L2 (401 letters) >FitnessBrowser__Cup4G11:RR42_RS07645 Length = 394 Score = 315 bits (807), Expect = 1e-90 Identities = 182/402 (45%), Positives = 246/402 (61%), Gaps = 12/402 (2%) Query: 2 REAFICDGIRTPIGRYGGALSSVRADDLAAIPLRELLVRNPRLDAECIDDVILGCANQAG 61 RE + G+RT IG +GG+L + + A+ +RE L R ++ + + V+ G Q Sbjct: 3 REVVVVSGVRTAIGTFGGSLKDLSPTQMGAMVVREALAR-AQVSGDDVGHVVFGNVIQTE 61 Query: 62 EDNRNVARMATLLAGLPQSVSGTTINRLCGSGLDALGFAARAIKAGDGDLLIAGGVESMS 121 + + R+A + G+ T+NRLCGSGL A+ AA+ I GD D+ I GG ESMS Sbjct: 62 PRDMYLGRVAAVEGGVTIDAPALTVNRLCGSGLQAIVSAAQTILLGDADVAIGGGAESMS 121 Query: 122 RAPFVMGKAA-SAFSRQAEMFDTTIGWRFVNPLMAQQFGTDSMPETAENVAELLKISRED 180 RAP++ A A A+M D +G + F M TAENVA+ ISR Sbjct: 122 RAPYLAQSARWGARMGDAKMLDMMLG------ALHDPFHGIHMGVTAENVAKEYDISRVQ 175 Query: 181 QDSFALRSQQRTAKAQSSGILAEEIVPVVLKNKKGVVTEIQHDEHLRPETTLEQLRGLKA 240 QD AL S +R + A +G ++I+PV LK +KG VT DEH+R + +E + LK Sbjct: 176 QDEAALESHRRASAAIRAGHFKDQILPVTLKGRKGDVT-FDTDEHVRHDAVMEDMTKLKP 234 Query: 241 PF-RANGVITAGNASGVNDGAAALIIASEQMAAAQGLTPRARIVAMATAGVEPRLMGLGP 299 F + NG +TAGNASG+ND AAA+++ A +GL P AR+V+ A AGV+P+ MG+GP Sbjct: 235 VFVKENGTVTAGNASGLNDAAAAVVLMERAEAEKRGLKPMARLVSYAHAGVDPKTMGIGP 294 Query: 300 VPATRRVLERAGLSIHDMDVIELNEAFAAQALGVLRELGLPDDAPHVNPNGGAIALGHPL 359 VPAT++ LERAGL++ D+DVIE NEAFAAQA V + LGL D VNPNG I+LGHP+ Sbjct: 295 VPATKKALERAGLTVADLDVIEANEAFAAQACAVTKALGL--DPAKVNPNGSGISLGHPI 352 Query: 360 GMSGARLALAASHELHRRNGRYALCTMCIGVGQGIAMILERV 401 G +GA + + A +EL R GRYAL TMCIG GQGIA I ER+ Sbjct: 353 GATGALITVKALYELQRVQGRYALVTMCIGGGQGIAAIFERL 394 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: 431 Number of extensions: 19 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: 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