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_RS26090 RR42_RS26090 acetyl-CoA acetyltransferase
Query= SwissProt::P0C7L2 (401 letters) >FitnessBrowser__Cup4G11:RR42_RS26090 Length = 391 Score = 321 bits (822), Expect = 3e-92 Identities = 183/404 (45%), Positives = 257/404 (63%), Gaps = 17/404 (4%) Query: 1 MREAFICDGIRTPIGRYGGALSSVRADDLAAIPLRELLVRNPRLDAECIDDVILGCANQA 60 M + I RT +G++GG+L+ V A +L A ++ LL R+ L E +D+V+LG A Sbjct: 1 MEDVVIVAAARTAVGKFGGSLAKVPAPELGATVIKALLERSG-LKPEMVDEVLLGQVLTA 59 Query: 61 GEDNRNVARMATLLAGLPQSVSGTTINRLCGSGLDALGFAARAIKAGDGDLLIAGGVESM 120 G +N AR A + AGLP +V TI ++CGSGL A+ AA+AIK GD D++IAGG E+M Sbjct: 60 G-GGQNPARQAAIKAGLPNTVPAMTIGKVCGSGLKAVHLAAQAIKCGDADIVIAGGQENM 118 Query: 121 SRAPFVMGKAASAFSRQAEMFDTTIGWRFVNPLMAQ----QFGTDSMPETAENVAELLKI 176 S +P V+ A SR + W+ + ++ F M TAENVA+ I Sbjct: 119 SASPHVL-----AGSRDGQRMGD---WKLTDTMIVDGLWDAFNQYHMGTTAENVAKAYHI 170 Query: 177 SREDQDSFALRSQQRTAKAQSSGILAEEIVPVVLKNKKGVVTEIQHDEHLRPETTLEQLR 236 SRE QD+FA SQQ+ AQ +G +EIVPV + +KKG V DE ++ TT + L Sbjct: 171 SREQQDAFAAASQQKAELAQKTGRFKDEIVPVSIVSKKGTVV-FDTDEFIKHGTTADALA 229 Query: 237 GLKAPFRANGVITAGNASGVNDGAAALIIASEQMAAAQGLTPRARIVAMATAGVEPRLMG 296 GL+ F G +TAGNASG+NDGAAA+++ S A GLTP ARI + A+AG++P +MG Sbjct: 230 GLRPAFDKAGSVTAGNASGLNDGAAAVLMMSASKARELGLTPLARIASYASAGLDPAIMG 289 Query: 297 LGPVPATRRVLERAGLSIHDMDVIELNEAFAAQALGVLRELGLPDDAPHVNPNGGAIALG 356 +GPVPA++R L +AG SI+D+D++E+NEAFAAQA V +E+ DA +N NGGAIA+G Sbjct: 290 MGPVPASQRCLHKAGWSINDLDLMEINEAFAAQACAVNQEMDW--DASKINVNGGAIAIG 347 Query: 357 HPLGMSGARLALAASHELHRRNGRYALCTMCIGVGQGIAMILER 400 HP+G SG R+ + HE+ RR+ R L ++CIG G G+A+ +ER Sbjct: 348 HPIGASGCRILVTLLHEMARRDARRGLASLCIGGGMGVALAVER 391 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: 443 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: 391 Length adjustment: 31 Effective length of query: 370 Effective length of database: 360 Effective search space: 133200 Effective search space used: 133200 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