Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate WP_110804969.1 C8J30_RS06880 acetyl-CoA C-acetyltransferase
Query= metacyc::MONOMER-15952 (401 letters) >NCBI__GCF_003217355.1:WP_110804969.1 Length = 403 Score = 256 bits (654), Expect = 8e-73 Identities = 171/425 (40%), Positives = 229/425 (53%), Gaps = 46/425 (10%) Query: 1 MNEALIIDAVRTPIG--RYAGALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCAN 58 M EA I DA RTP G R G+L V + L A L A+ R+ L AV+DVI+G Sbjct: 1 MTEAYIYDACRTPRGKGRADGSLHEVTSVALSARLLDAVAERNG-LTGHAVEDVIWGNVT 59 Query: 59 QAGEDNRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVE 118 Q GE +AR A LL+GL S+PG ++NR C SG++AV AA ++ G +AGGVE Sbjct: 60 QVGEQGGCLARSAVLLSGLDESIPGLSINRFCASGMEAVNLAANQVKAGAGAAYIAGGVE 119 Query: 119 SMSRAPFVMGKSEQAFGRSAEIFDTTIGWRFVNKLMQQGFGIDSMPETAENVAAQFNISR 178 MSR MG A + T + QG +A+ +A ++ +R Sbjct: 120 MMSRV--AMGSDGAAIAVDPSLAMKTY-------FVPQGI-------SADVIATEYGFTR 163 Query: 179 ADQDAFALRSQHKAAAAIANGRLAKEIVAVEIAQRKGPAKIVEHDEHPRGDTTLEQLAKL 238 DA A+ SQ +AA A A R AK IV V + + I+E DE+ R TT+E LAKL Sbjct: 164 EMADALAVESQRRAAEAWAENRFAKSIVPV---RDQNGLIILERDEYLRPGTTMEDLAKL 220 Query: 239 GTPFRQGGSVT----------------------AGNASGVNDGACALLLASSEAAQRHGL 276 F+ G V AGN+SG+ DGA A+L+ S E + HGL Sbjct: 221 KPAFKDMGEVMPGFDKVAMLKYPHLERIEHIHHAGNSSGIVDGAAAVLIGSKEFGEAHGL 280 Query: 277 KARARVVGMATAGVEPRIMGIGPVPATRKVLELTGLALADMDVIELNEAFAAQGLAVLRE 336 K RAR+ A G +P IM GPVP T K+L +G++++D+D+ E+NEAFAA L ++ Sbjct: 281 KPRARIRATAKIGTDPTIMLTGPVPVTEKILRDSGMSISDIDLFEVNEAFAAVVLRFMQA 340 Query: 337 LGLADDDERVNPNGGAIALGHPLGMSGARLVTTALHELEERQGRYALCTMCIGVGQGIAL 396 + D +VN NGGA+ALGHPLG +GA ++ T L ELE R L T+CI G G A Sbjct: 341 FDVGQD--KVNVNGGAMALGHPLGATGAIIIGTLLDELERRDLSTGLATLCIASGMGAAT 398 Query: 397 IIERI 401 IIER+ Sbjct: 399 IIERV 403 Lambda K H 0.319 0.134 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: 395 Number of extensions: 13 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: 403 Length adjustment: 31 Effective length of query: 370 Effective length of database: 372 Effective search space: 137640 Effective search space used: 137640 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 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