Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate RR42_RS26090 RR42_RS26090 acetyl-CoA acetyltransferase
Query= metacyc::MONOMER-3207 (400 letters) >FitnessBrowser__Cup4G11:RR42_RS26090 Length = 391 Score = 327 bits (838), Expect = 4e-94 Identities = 183/403 (45%), Positives = 260/403 (64%), Gaps = 16/403 (3%) Query: 1 MRDVFICDAIRTPIGRFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQA 60 M DV I A RT +G+FGG+LA V A +L A +KAL+E + ++ + VDEV G A Sbjct: 1 MEDVVIVAAARTAVGKFGGSLAKVPAPELGATVIKALLERS-GLKPEMVDEVLLGQVLTA 59 Query: 61 GEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESM 120 G +N AR A + AGLP ++P +T+ ++C SG+ A+ A +AI G+ ++ IAGG E+M Sbjct: 60 G-GGQNPARQAAIKAGLPNTVPAMTIGKVCGSGLKAVHLAAQAIKCGDADIVIAGGQENM 118 Query: 121 SRAPFVMGKAESGYSR-NMKLEDTTIG---WRFINPLMKSQYGVDSMPETADNVADDYQV 176 S +P V+ + G + KL DT I W N QY M TA+NVA Y + Sbjct: 119 SASPHVLAGSRDGQRMGDWKLTDTMIVDGLWDAFN-----QY---HMGTTAENVAKAYHI 170 Query: 177 SRADQDAFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGETIVERDEHLRPETTLEALTK 236 SR QDAFA SQQKA AQ G F +EIVPV I KKG + + DE ++ TT +AL Sbjct: 171 SREQQDAFAAASQQKAELAQKTGRFKDEIVPVSIVSKKGTVVFDTDEFIKHGTTADALAG 230 Query: 237 LKPVNGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGMASGGVAPRVMGI 296 L+P +VTAGNASG+NDGAAA+++ SA ++ GLTP AR+ AS G+ P +MG+ Sbjct: 231 LRPAFDKAGSVTAGNASGLNDGAAAVLMMSASKARELGLTPLARIASYASAGLDPAIMGM 290 Query: 297 GPVPAVRKLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALGH 356 GPVPA ++ + G +++D D++E+NEAFA+Q AV +E+ DA ++N NGGAIA+GH Sbjct: 291 GPVPASQRCLHKAGWSINDLDLMEINEAFAAQACAVNQEMDW--DASKINVNGGAIAIGH 348 Query: 357 PLGMSGARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIER 399 P+G SG R+++T LH++ + R+GLA++C+G G G+ALA+ER Sbjct: 349 PIGASGCRILVTLLHEMARRDARRGLASLCIGGGMGVALAVER 391 Lambda K H 0.318 0.134 0.383 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: 406 Number of extensions: 15 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: 400 Length of database: 391 Length adjustment: 31 Effective length of query: 369 Effective length of database: 360 Effective search space: 132840 Effective search space used: 132840 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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