Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate GFF3052 HP15_2996 acetyl-CoA acetyltransferase
Query= metacyc::MONOMER-3207 (400 letters) >FitnessBrowser__Marino:GFF3052 Length = 398 Score = 321 bits (823), Expect = 2e-92 Identities = 182/401 (45%), Positives = 256/401 (63%), Gaps = 11/401 (2%) Query: 1 MRDVFICDAIRTPIGRFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQA 60 MRDV I A RT IG FGG L+ + AD L +KA++E V DQ++EV G A Sbjct: 7 MRDVVIVAARRTAIGTFGGGLSSLSADQLGTAVIKAILEET-GVAGDQINEVVLGQVLTA 65 Query: 61 GEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESM 120 G +N AR + + AG+P S+P +T+N++C SG+ A+ A +AI G+ E+ IAGG ESM Sbjct: 66 G-CGQNPARQSAINAGIPASVPAMTINKVCGSGLKAVHMAVQAIRCGDAEMMIAGGQESM 124 Query: 121 SRAPFVMGKAESGYSR-NMKLEDTTIGWRFINPLMKSQYGVDSMPETADNVADDYQVSRA 179 S+AP V+ + +G N + DT I + G+ TA+N+ + Y +SR Sbjct: 125 SQAPHVLPNSRNGQRMGNWSMVDTMIKDGLWDAFNDYHMGI-----TAENIVEKYGISRD 179 Query: 180 DQDAFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGETIV-ERDEHLRPETTLEALTKLK 238 +QD FA SQQKAAAA+ AG+F +IVPV I +KG+ IV +RDE R T E L KL+ Sbjct: 180 EQDEFAAASQQKAAAAREAGYFDGQIVPVSIPQRKGDPIVVDRDEGPRDGVTAEGLGKLR 239 Query: 239 PVNGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGMASGGVAPRVMGIGP 298 D TVTAGNAS +NDGAAA+++ SAE ++ GLTP A + A+ GV P +MG GP Sbjct: 240 AAFKKDGTVTAGNASSLNDGAAAVMVCSAEKAEELGLTPIATIKAYANAGVDPTIMGTGP 299 Query: 299 VPAVRKLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALGHPL 358 +PA ++ + G + D D++E NEAFA+Q ++V R++G D +VN NGGAIALGHP+ Sbjct: 300 IPASQRCLKLAGWSTEDLDLVEANEAFAAQAISVNRDMGW--DTGKVNVNGGAIALGHPI 357 Query: 359 GMSGARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIER 399 G SG R++++ LH++ + KGLAT+C+G G G+ALA+ER Sbjct: 358 GASGCRILVSLLHEMVRRDVHKGLATLCIGGGMGVALAVER 398 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: 419 Number of extensions: 20 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: 398 Length adjustment: 31 Effective length of query: 369 Effective length of database: 367 Effective search space: 135423 Effective search space used: 135423 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