Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate AO356_21640 AO356_21640 acetyl-CoA acetyltransferase
Query= metacyc::MONOMER-20679 (395 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_21640 Length = 393 Score = 239 bits (610), Expect = 1e-67 Identities = 152/401 (37%), Positives = 224/401 (55%), Gaps = 27/401 (6%) Query: 1 MTEAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAGIDPKEVEDVVMGAAMQQ 60 M E VIV+ RT IG +++G+L A L I +++ G+ ++V++V++G + Sbjct: 1 MQEVVIVAATRTAIG-SFQGSLAAIPAPELGAAVIRRLLEQTGLSGEQVDEVILGQVLTA 59 Query: 61 GATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESI 120 G+ G N AR+A + AGLP T+++ C SGL+A+ L A+++ E+ + GG E++ Sbjct: 60 GS-GQNPARQASILAGLPHAVPALTLNKVCGSGLKALHLGAQAIRCGDAEVIIAGGMENM 118 Query: 121 SLVQ-------------NDKMNTFHAVDPALEAIKGDVYMAMLDTAETVAKRYGISRERQ 167 SL + KM D +A D +M + TAE + +YGISRE Q Sbjct: 119 SLAPYVLPAARTGLRMGHAKMIDSMITDGLWDAFN-DYHMGI--TAENLVDKYGISREEQ 175 Query: 168 DEYSLESQRRTAAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTA 227 D ++ SQ++ AA +GG+F DEI PI ++ + G + + DE PR TTA Sbjct: 176 DAFAAASQQKAVAAIEGGRFADEITPI-----LIPQRKG----DPVAFATDEQPRAGTTA 226 Query: 228 EGLAGLKAVRGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEP 287 E L LK + ++TAGNAS L+DGA+A ++MS + A A GL L + G +P Sbjct: 227 ESLGKLKPAFKKDGSVTAGNASSLNDGAAAVILMSAEKAKALGLPVLAKISAYANAGVDP 286 Query: 288 DEMGIGPVFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAIS 347 MGIGPV A R L + G S++ + L E NEAFA Q L +L D +K+NVNGGAI+ Sbjct: 287 AIMGIGPVSATRRCLDKAGWSLEQLDLIEANEAFAAQSLAVARELKWDMDKVNVNGGAIA 346 Query: 348 VGHPYGMSGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSA 388 +GHP G SG R+ L E +R AK + T+C+GGG G A Sbjct: 347 LGHPIGASGCRVLVSLLHEMIKRDAKKGLATLCIGGGQGVA 387 Lambda K H 0.316 0.134 0.378 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: 17 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: 395 Length of database: 393 Length adjustment: 31 Effective length of query: 364 Effective length of database: 362 Effective search space: 131768 Effective search space used: 131768 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 Apr 09 2024. 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