Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate GFF3267 PGA1_c33180 acetyl-CoA acetyltransferase
Query= uniprot:D8ITH5 (401 letters) >FitnessBrowser__Phaeo:GFF3267 Length = 390 Score = 267 bits (683), Expect = 3e-76 Identities = 166/400 (41%), Positives = 232/400 (58%), Gaps = 17/400 (4%) Query: 4 LICDAIRTPFGRYGGALGAVRADDLAAAPIRSLMERNPGVDWSRVEDILYGCANQAGEDN 63 +I A RTP G + G V A +L + IR+ + G + V++IL GC AG+ Sbjct: 5 VIAGAARTPMGGFQGMYDGVAAAELGGSAIRAALA---GAGATTVDEILMGCVLPAGQ-G 60 Query: 64 RNVARMAGLLAGLPIAVPGSTVNRLCGSSLDAVGMAARAIKSGEVQLMIAGGVESMTRAP 123 + AR AG AGL VP +T+N++CGS + A MA I G+ MIAGG+ESMT AP Sbjct: 61 QAPARQAGFAAGLGEEVPATTLNKMCGSGMKAAMMAYDQIALGQADTMIAGGMESMTNAP 120 Query: 124 FVMGKAESAFARSAAIFDTTIGWRFVNPLMKAQYGIDSMPETAENVATDFQINRADQDAF 183 +++ K + AR + F++ L A M AE+ A +Q R QD + Sbjct: 121 YLLPKMRNG-ARLG--HGQVVDHMFLDGLEDAYDKGRLMGTFAEDCAETYQFTREAQDEY 177 Query: 184 ALRSQQRWAAAQAAGFFAGEIAPLTIPQKKGDPLVVTTDEHP---RPDTTLATLAKLKGV 240 AL S AAQ +G F EIAP+T+ +KG+ V DE P RPD + LK Sbjct: 178 ALTSLSNALAAQESGAFDAEIAPVTVKTRKGET-VTNADEQPKSARPDK----IPTLKPA 232 Query: 241 VRPDGTVTAGNASGVNDGACALLLASPKAADLYRLKPRARVLGMATAGVAPRIMGFGPAP 300 R DGTVTA NAS ++DGA AL+LAS AA+ L RAR++G A+ AP + P P Sbjct: 233 FRKDGTVTAANASSISDGAAALVLASEDAAEAQGLTVRARIMGHASHAQAPGLFTTAPVP 292 Query: 301 AVRKVLAQVGLTLAQMDVIELNEAFAAQGLAVMRDLGLPDDAAHVNPNGGAIAIGHPLGA 360 A +K++AQ+G T++ +D+ E+NEAFA +A M ++GLP D VN NGGA A+GHP+GA Sbjct: 293 AAKKLMAQLGWTVSDVDLWEVNEAFAVVPMAFMHEMGLPRD--KVNVNGGACALGHPIGA 350 Query: 361 SGARLVTTAINQLERSGGRYALCTMCIGVGQGIALVIERV 400 SGAR++ T +N LE+ + + +CIG G+G A+ IER+ Sbjct: 351 SGARIMVTLLNALEKRNLKRGIAAICIGGGEGTAIAIERM 390 Lambda K H 0.320 0.135 0.394 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: 383 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: 390 Length adjustment: 31 Effective length of query: 370 Effective length of database: 359 Effective search space: 132830 Effective search space used: 132830 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 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