Align acetyl-CoA C-acetyltransferase [EC: 2.3.1.9] (characterized)
to candidate WP_033100856.1 JG50_RS0109300 thiolase family protein
Query= reanno::pseudo5_N2C3_1:AO356_21640 (393 letters) >NCBI__GCF_000763315.1:WP_033100856.1 Length = 402 Score = 377 bits (968), Expect = e-109 Identities = 209/399 (52%), Positives = 274/399 (68%), Gaps = 7/399 (1%) Query: 1 MQEVVIVAATRTAIGSFQGSLAAIPAPELGAAVIRRLLEQT-GLSGEQVDEVILGQVLTA 59 M+EVVIV A RT IG + GSL+ A +L A VI+ LL++ GL V++V+LG A Sbjct: 1 MREVVIVDAVRTPIGRYLGSLSRTRADDLAAHVIKALLDRNPGLPPSLVEDVLLGCANQA 60 Query: 60 GS-GQNPARQASILAGLPHAVPALTLNKVCGSGLKALHLGAQAIRCGDAEVIIAGGMENM 118 G +N AR A++LAGLP +T+N++CGSGL+A++ AI G + +IAGG+ENM Sbjct: 61 GEDNRNVARMAALLAGLPLEAGGVTVNRLCGSGLEAVNQAVAAIAFGAGDAMIAGGVENM 120 Query: 119 SLAPYVLPAARTGLRMGHAKMIDS-----MITDGLWDAFNDYHMGITAENLVDKYGISRE 173 S AP V+ TGL G+ + D+ + L ++ MG TAEN+ +KYGISRE Sbjct: 121 SRAPLVMLKPETGLARGNQTLFDTTLGWRFVNPKLAAMYDPVSMGETAENVAEKYGISRE 180 Query: 174 EQDAFAAASQQKAVAAIEGGRFADEITPILIPQRKGDPVAFATDEQPRAGTTAESLGKLK 233 EQD FA SQQKA AA E G+FADEI I + + G VAFA DE PR TT E L +L+ Sbjct: 181 EQDRFALVSQQKARAAWEEGKFADEIVAIEVTEPGGATVAFARDEHPRPQTTLEKLSQLR 240 Query: 234 PAFKKDGSVTAGNASSLNDGAAAVILMSAEKAKALGLPVLAKISAYANAGVDPAIMGIGP 293 PAF++ G+VTAGNAS +NDGA+A++LM+ + A+ LGL +AK+ A+A G +P MGIGP Sbjct: 241 PAFRQGGTVTAGNASGINDGASALLLMARDVAERLGLKPMAKVVAFAVEGTNPLYMGIGP 300 Query: 294 VSATRRCLDKAGWSLEQLDLIEANEAFAAQSLAVARELKWDMDKVNVNGGAIALGHPIGA 353 V ATR+ L +AG S+ LDL+E NEAFAAQSLA EL D D+VNVNGGAIALGHP+GA Sbjct: 301 VGATRKVLKRAGISVSDLDLVELNEAFAAQSLACISELGLDPDRVNVNGGAIALGHPLGA 360 Query: 354 SGCRVLVSLLHEMIKRDAKKGLATLCIGGGQGVALALER 392 SG R+L +L+HE+ KR + GLAT+CIG GQG+A +ER Sbjct: 361 SGARILTTLVHELEKRQGRFGLATMCIGVGQGIATLIER 399 Lambda K H 0.317 0.133 0.376 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: 445 Number of extensions: 20 Number of successful extensions: 3 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: 393 Length of database: 402 Length adjustment: 31 Effective length of query: 362 Effective length of database: 371 Effective search space: 134302 Effective search space used: 134302 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 (21.6 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