Align Beta-ketoadipyl CoA thiolase (EC 2.3.1.-) (characterized)
to candidate WP_068004809.1 PsAD2_RS08250 thiolase family protein
Query= reanno::Marino:GFF2751 (415 letters) >NCBI__GCF_001623255.1:WP_068004809.1 Length = 383 Score = 157 bits (397), Expect = 5e-43 Identities = 134/418 (32%), Positives = 199/418 (47%), Gaps = 56/418 (13%) Query: 11 YIVDAIRTPIGRYG--GALSAVRADDLGAIPIKALAERYPDLDWSKIDDVLYGCANQAGE 68 YI DA+RT G+ G L+AV+ D+L A A+ +R K + +L G Q G Sbjct: 4 YIYDAVRTARGKAKPEGGLAAVKPDELVAALSDAITDRVGQF---KPEALLLGSVGQVGA 60 Query: 69 DNRDVARMSLLLAGLPVDVPGSTINRLCGSGMDAVGSAARAIRTGETQLMIAGGVESMSR 128 ++A +S A LP + TIN C SG+ A+G A+ + TG+ ++AGGVE MS Sbjct: 61 QGGNIALVSKFRAKLPDETVAWTINNFCASGLTAIGQASSMVATGQANRVLAGGVEMMSC 120 Query: 129 APFVMGKADSAFSRKAEIFDTTIGWRFVNPVLKKQYGIDSMPETAENVAADFGISREDQD 188 PF+ AD A +V+ L +++ + A+ +A D ISR + D Sbjct: 121 VPFM---ADDAH-------------YYVDTTLPERHRYLLVALAADKLAEDLDISRAEMD 164 Query: 189 AFALRSQQRTAAAQKEGRLAAEITPVTIPRRKQDPLVVDTDEHPRETSLEKLASLPTPF- 247 ALRS + G+ A+ I + R +E ++ E +A+L F Sbjct: 165 TAALRSHAQALLGDDNGKNASRIIVNGLNR----------EECAKKMDHESIAALQPAFA 214 Query: 248 ------------RENGTVTAGNASGVNDGACALLLAGADALKQYNLKPRARVVAMATAGV 295 + + T +A + DGA ++ A+ + PRA++VA A G Sbjct: 215 ALAPQYAQVLGRKVDHRHTIAHAPPMTDGAGLAMVGTYGAI---DAPPRAQIVAFAEVGG 271 Query: 296 EPRI-MGFGPAPATRKVLATAGLELADMDVIELNEAFAAQALAVTRDLGLPDDAEHVNPN 354 +P + +G G A A +VLA + L L DMD IE EAFA + RD P + VN + Sbjct: 272 DPAVSLGAGFA-AMDQVLAKSELSLEDMDRIEFMEAFAVTIVKFLRD--HPHLEDRVNTS 328 Query: 355 GGAIALGHPLGMSGARLVTTALNELERRHAAGQKARYALCTMCIGVGQGIALIIERMD 412 GG +A GHPLG SGA LV+T L+ L+ + RY L G G A+I++RMD Sbjct: 329 GGHLAKGHPLGASGAILVSTLLDTLDM-----VQGRYGLVVASGAEGIGSAMIVKRMD 381 Lambda K H 0.318 0.133 0.382 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: 364 Number of extensions: 19 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: 415 Length of database: 383 Length adjustment: 31 Effective length of query: 384 Effective length of database: 352 Effective search space: 135168 Effective search space used: 135168 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