Align 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 (characterized)
to candidate H281DRAFT_00852 H281DRAFT_00852 acetyl-CoA acetyltransferase
Query= SwissProt::P0C7L2 (401 letters) >FitnessBrowser__Burk376:H281DRAFT_00852 Length = 393 Score = 327 bits (839), Expect = 3e-94 Identities = 186/402 (46%), Positives = 258/402 (64%), Gaps = 10/402 (2%) Query: 1 MREAFICDGIRTPIGRYGGALSSVRADDLAAIPLRELLVRNPRLDAECIDDVILGCANQA 60 M + I RT +G++GG+L+ + A +L A +R +L R + E + +VILG A Sbjct: 1 MTDVVIVSAARTAVGKFGGSLAKIAAPELGATVIRAVLER-AGMKPEQVSEVILGQVLTA 59 Query: 61 GEDNRNVARMATLLAGLPQSVSGTTINRLCGSGLDALGFAARAIKAGDGDLLIAGGVESM 120 G +N AR + + AGLP +V G TIN++CGSGL A+ AA AI AGD D++IAGG E+M Sbjct: 60 GS-GQNPARQSLIKAGLPAAVPGMTINKVCGSGLKAVMLAANAIIAGDADIVIAGGQENM 118 Query: 121 SRAPFVMGKAASAFSR-QAEMFDTTIGWRFVNPLMAQQFGTDSMPETAENVAELLKISRE 179 S AP V+ + F A++ D+ I V+ L + M TAENVA+ I+RE Sbjct: 119 SAAPHVLPGSRDGFRMGDAKLIDSMI----VDGLW-DVYNQYHMGVTAENVAKEFDITRE 173 Query: 180 DQDSFALRSQQRTAKAQSSGILAEEIVPVVLKNKKGVVTEIQHDEHLRPETTLEQLRGLK 239 QD+FA SQ + AQ SG +EIVPV + +KG DE +R T E L GLK Sbjct: 174 QQDAFAALSQNKAEAAQKSGRFDDEIVPVEIPQRKGDPVRFATDEFVRHGVTAESLAGLK 233 Query: 240 APFRANGVITAGNASGVNDGAAALIIASEQMAAAQGLTPRARIVAMATAGVEPRLMGLGP 299 F G +TA NASG+NDGAAA+++ S + A A GLTP ARI A A AGV+P++MG+GP Sbjct: 234 PAFSKEGTVTAANASGLNDGAAAVLVMSAKKAEALGLTPLARIKAYANAGVDPKVMGMGP 293 Query: 300 VPATRRVLERAGLSIHDMDVIELNEAFAAQALGVLRELGLPDDAPHVNPNGGAIALGHPL 359 VPA+RR LERAG S++D+D++E+NEAFAAQAL V +++G D +N NGGAIA+GHP+ Sbjct: 294 VPASRRCLERAGWSVNDLDLMEINEAFAAQALAVHKQMGW--DTSKINVNGGAIAIGHPI 351 Query: 360 GMSGARLALAASHELHRRNGRYALCTMCIGVGQGIAMILERV 401 G SG R+ + +E+ +R+ + L ++CIG G G+A+ LERV Sbjct: 352 GASGCRILVTLLYEMQKRDAKKGLASLCIGGGMGVALALERV 393 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: 436 Number of extensions: 18 Number of successful extensions: 4 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: 393 Length adjustment: 31 Effective length of query: 370 Effective length of database: 362 Effective search space: 133940 Effective search space used: 133940 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