Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate WP_110804969.1 C8J30_RS06880 acetyl-CoA C-acetyltransferase
Query= metacyc::MONOMER-3207 (400 letters) >NCBI__GCF_003217355.1:WP_110804969.1 Length = 403 Score = 258 bits (659), Expect = 2e-73 Identities = 173/424 (40%), Positives = 238/424 (56%), Gaps = 45/424 (10%) Query: 1 MRDVFICDAIRTPIG--RFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCAN 58 M + +I DA RTP G R G+L V + L+A L A+ E N + V++V +G Sbjct: 1 MTEAYIYDACRTPRGKGRADGSLHEVTSVALSARLLDAVAERN-GLTGHAVEDVIWGNVT 59 Query: 59 QAGEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVE 118 Q GE +AR A+LL+GL ESIPG+++NR CASGM+A+ A + +G IAGGVE Sbjct: 60 QVGEQGGCLARSAVLLSGLDESIPGLSINRFCASGMEAVNLAANQVKAGAGAAYIAGGVE 119 Query: 119 SMSRAPFVMGKAESGYSRNMKLEDTTIGWRFINPLMKSQYGVDSMPETADNVADDYQVSR 178 MSR MG + + + L MK+ + + +AD +A +Y +R Sbjct: 120 MMSRV--AMGSDGAAIAVDPSLA------------MKTYFVPQGI--SADVIATEYGFTR 163 Query: 179 ADQDAFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGETIVERDEHLRPETTLEALTKLK 238 DA A+ SQ++AA A A FA+ IVPVR + G I+ERDE+LRP TT+E L KLK Sbjct: 164 EMADALAVESQRRAAEAWAENRFAKSIVPVR--DQNGLIILERDEYLRPGTTMEDLAKLK 221 Query: 239 P--------VNGPDKTVT--------------AGNASGVNDGAAALILASAEAVKKHGLT 276 P + G DK AGN+SG+ DGAAA+++ S E + HGL Sbjct: 222 PAFKDMGEVMPGFDKVAMLKYPHLERIEHIHHAGNSSGIVDGAAAVLIGSKEFGEAHGLK 281 Query: 277 PRARVLGMASGGVAPRVMGIGPVPAVRKLTERLGVAVSDFDVIELNEAFASQGLAVLREL 336 PRAR+ A G P +M GPVP K+ G+++SD D+ E+NEAFA+ L ++ Sbjct: 282 PRARIRATAKIGTDPTIMLTGPVPVTEKILRDSGMSISDIDLFEVNEAFAAVVLRFMQAF 341 Query: 337 GVADDAPQVNPNGGAIALGHPLGMSGARLVLTALHQLEKSGGRKGLATMCVGVGQGLALA 396 V D +VN NGGA+ALGHPLG +GA ++ T L +LE+ GLAT+C+ G G A Sbjct: 342 DVGQD--KVNVNGGAMALGHPLGATGAIIIGTLLDELERRDLSTGLATLCIASGMGAATI 399 Query: 397 IERV 400 IERV Sbjct: 400 IERV 403 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: 397 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: 400 Length of database: 403 Length adjustment: 31 Effective length of query: 369 Effective length of database: 372 Effective search space: 137268 Effective search space used: 137268 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 24 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