Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate WP_011461057.1 DHAF_RS22625 acetyl-CoA C-acyltransferase
Query= uniprot:B2SYZ2 (400 letters) >NCBI__GCF_000021925.1:WP_011461057.1 Length = 384 Score = 309 bits (791), Expect = 1e-88 Identities = 184/404 (45%), Positives = 244/404 (60%), Gaps = 24/404 (5%) Query: 1 MNDAFICDAIRTPIGRYG-GALKDVRADDLGAVPIKALIERNPGVDWRTVDDVIYGCANQ 59 M +AFI +A RT IG+ G G+L +R DDL A I+ +++ P ++ +DD + GC+ Sbjct: 1 MKEAFIIEAKRTAIGKAGRGSLAHMRPDDLAAFVIQDVLKSAPNLNSADIDDCVIGCSFP 60 Query: 60 AGEDNRNVARMSALLAGLPVEAPGSTINRLCGSGMDAVGTAARAIKAGEARLMIAGGVES 119 GE N+AR+ AL AGLP++ G TINR C SG+ A+ AA I+ GEA M+AGG ES Sbjct: 61 EGEQGMNMARVIALRAGLPIDVSGLTINRFCSSGLQAISLAADRIRLGEAHAMLAGGAES 120 Query: 120 MTRAPFVMGKATSAFARQADIYDTTIGWRFINPLMKRQYGVD--SMPETAENVAAEFSVS 177 M+ P GK NP M SM TAENVA ++ ++ Sbjct: 121 MSAVPMGGGKPAP------------------NPYMMEHCPEVYLSMGLTAENVAKKYEIT 162 Query: 178 RADQDAFALASQQKAARAQQDGTLAQEIVGVEIAQKKGDPVRALLDEHPR-ETSLESLGK 236 R QD FA AS QKA AQ G +EIV V IA K V DE R ++++ESLGK Sbjct: 163 REQQDEFAAASHQKAHAAQVGGRFEEEIVPVLIASGKKGEVWFSKDEGIRADSTVESLGK 222 Query: 237 LKGVVRPDGSVTAGNASGVNDGACALLLANQQAADQYGLRRRARVVGMATAGVEPRIMGI 296 LK + G VTAGN+S +DGA A LL +++ + L+ A G A AGVE +MGI Sbjct: 223 LKPAFKNGGCVTAGNSSQTSDGAAATLLMSEEKVKELDLKPLALWRGFAVAGVEAELMGI 282 Query: 297 GPAPATQKLLKQLGMTLEQLDVIELNEAFASQGLAVLRTLGLRDDDPRVNPNGGAIALGH 356 GP A K+LKQ+G+TLEQ+D+ ELNEAFASQ LA+++TLG+ D +VNPNGGAIA GH Sbjct: 283 GPIKAIPKVLKQVGLTLEQIDLFELNEAFASQSLAIIKTLGI--DPAKVNPNGGAIAFGH 340 Query: 357 PLGASGARLITTALYQLERTNGRFALCTMCIGVGQGIALVIERL 400 PLG +GA+L T L++++R ++ + TMCIG G G A V E L Sbjct: 341 PLGCTGAKLTATLLHEMKRRGLKYGMVTMCIGGGMGAAGVYELL 384 Lambda K H 0.318 0.135 0.386 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: 407 Number of extensions: 21 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: 384 Length adjustment: 31 Effective length of query: 369 Effective length of database: 353 Effective search space: 130257 Effective search space used: 130257 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