Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate WP_057509233.1 ABB28_RS14140 acetyl-CoA C-acyltransferase
Query= metacyc::MONOMER-3207 (400 letters) >NCBI__GCF_001431535.1:WP_057509233.1 Length = 426 Score = 189 bits (479), Expect = 2e-52 Identities = 146/434 (33%), Positives = 213/434 (49%), Gaps = 48/434 (11%) Query: 2 RDVFICDAIRTPIGRFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQAG 61 R V I +R P R A + V ++ L AL+E + Q+ EV G + Sbjct: 5 RPVAILGGVRIPFCRQNTAYSDVGNLGMSVRTLGALVE-RFGLHGQQLGEVAMGAVIKHS 63 Query: 62 EDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESMS 121 D N+ R A L +GL PG+T+ R C + +D I IA G++E I GG ++ S Sbjct: 64 SD-WNLGREAALSSGLSPLTPGITMQRACGTSLDTIIAVANKIALGQIESGIGGGSDTTS 122 Query: 122 RAPFVMGK--------AESGYSRNMKLEDTTIGWRFIN-----PLMKSQYGVDSMPETAD 168 P V GK A S K+ T G++F P + SM + + Sbjct: 123 DVPIVYGKKLRARLLAANRAKSTGDKIRALTRGFKFSEFKPEFPGVAEPRTGKSMGDHCE 182 Query: 169 NVADDYQVSRADQDAFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGETIVERDEHLRPE 228 ++A ++ +SR QD +A+ S +K AAA GFF + I P R VERD LR + Sbjct: 183 DMAKEWNISRDSQDEWAVSSHRKLAAAYERGFFNDLIAPFRG--------VERDNILRAD 234 Query: 229 TTLEALTKLKP----VNGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGM 284 T+LE L LKP V+G T+TA N++ + DGA+A++LAS E + HG P A + Sbjct: 235 TSLEKLATLKPAFDKVSGRG-TLTAANSTPLTDGASAVLLASEEWARAHGHAPLAYLRDS 293 Query: 285 ASGGVAPRVMGIG----PVPAVRKLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVAD 340 V V G G P AV ++ +R G+ + DFD+ E++EAFA+Q L LR D Sbjct: 294 QVAAV-DFVHGEGLLMAPTVAVPEMLKRNGLTLQDFDIYEIHEAFAAQVLCTLRAWESED 352 Query: 341 --------DAP-------QVNPNGGAIALGHPLGMSGARLVLTALHQLEKSGGRKGLATM 385 DAP ++NP G ++A GHP +GAR++ TA QL + GG + L ++ Sbjct: 353 YCRNRLGLDAPLGRIDPEKINPLGSSLATGHPFAATGARVIATAAKQLAERGGGRALVSI 412 Query: 386 CVGVGQGLALAIER 399 C G G+ +ER Sbjct: 413 CTAGGMGVVAIVER 426 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: 403 Number of extensions: 15 Number of successful extensions: 6 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: 426 Length adjustment: 31 Effective length of query: 369 Effective length of database: 395 Effective search space: 145755 Effective search space used: 145755 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