Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate 6937205 Sama_1375 Acetyl-CoA C-acetyltransferase (RefSeq)
Query= metacyc::MONOMER-20679 (395 letters) >FitnessBrowser__SB2B:6937205 Length = 392 Score = 192 bits (487), Expect = 2e-53 Identities = 129/406 (31%), Positives = 208/406 (51%), Gaps = 29/406 (7%) Query: 1 MTEAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAGIDPKEVEDVVMGAAMQQ 60 +++ VIV+ RT +G ++G+L+ L A++ + G+D V++++MG + Sbjct: 3 VSDIVIVAAKRTAMG-GFQGSLSEVPSPKLAATAVKALLDDTGLDGARVDELLMGCVLPA 61 Query: 61 GATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESI 120 G G AR+A L AGLP++ TT+++ C SG++ + LA + ++ + GG ES+ Sbjct: 62 GL-GQAPARQAALGAGLPLSVGATTVNKVCGSGMKTVMLAHDLIKAGSAKVVIAGGMESM 120 Query: 121 SLVQ-------------NDKMNTFHAVDPALEAIKGDVYMAMLDTAETVAKRYGISRERQ 167 S + K+ +D +A G AM A+ A YG++RE Sbjct: 121 SQAPYLLDKARGGMRMGHGKVLDHMFLDGLEDAYTGG---AMGTFAQKTADDYGLTRESM 177 Query: 168 DEYSLESQRRTAAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTA 227 D ++L S + AA G F EI P++ V G D+ + DE P Sbjct: 178 DAFALSSLEKANAAINSGAFEAEIVPVT-----VSSRKG-----DVEVKVDEQPG-NARP 226 Query: 228 EGLAGLKAVRGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEP 287 E + L+ + TITA N+S +SDGA+A ++MS A A GLK L +G ++ EP Sbjct: 227 EKIPTLRPAFAKDGTITAANSSSISDGAAALMLMSRDQADALGLKVLATIKGHTTHAQEP 286 Query: 288 DEMGIGPVFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAIS 347 PV A+ +LL G S D++ L+E+NEAFA+ + +L +D ++NVNGGA + Sbjct: 287 AMFTTAPVGAMTKLLSNVGWSKDEVDLFEINEAFAMVTMLAISELKLDAARVNVNGGACA 346 Query: 348 VGHPYGMSGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFEI 393 +GHP G SGAR+ + + R K V ++C+GGG +A E+ Sbjct: 347 LGHPIGCSGARVLVTLIHALKARGLKRGVASLCIGGGEATAMAIEV 392 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: 427 Number of extensions: 25 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: 395 Length of database: 392 Length adjustment: 31 Effective length of query: 364 Effective length of database: 361 Effective search space: 131404 Effective search space used: 131404 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 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