Align acetyl-CoA C-acetyltransferase [EC: 2.3.1.9] (characterized)
to candidate PP_4636 PP_4636 acetyl-CoA acetyltransferase
Query= reanno::pseudo5_N2C3_1:AO356_21640 (393 letters) >FitnessBrowser__Putida:PP_4636 Length = 392 Score = 648 bits (1672), Expect = 0.0 Identities = 327/392 (83%), Positives = 360/392 (91%) Query: 1 MQEVVIVAATRTAIGSFQGSLAAIPAPELGAAVIRRLLEQTGLSGEQVDEVILGQVLTAG 60 M +VVIVAATRTAIGSFQG+LA +PA +LGAAVI++LL+QTGL QVDEVILGQVLTAG Sbjct: 1 MNDVVIVAATRTAIGSFQGALATVPAVDLGAAVIKQLLKQTGLDPAQVDEVILGQVLTAG 60 Query: 61 SGQNPARQASILAGLPHAVPALTLNKVCGSGLKALHLGAQAIRCGDAEVIIAGGMENMSL 120 +GQNPARQA+I AGLP +VPALTLNKVCGSGLKALHL AQAIRCGDAEV+IAGG ENMSL Sbjct: 61 AGQNPARQAAIKAGLPFSVPALTLNKVCGSGLKALHLAAQAIRCGDAEVVIAGGQENMSL 120 Query: 121 APYVLPAARTGLRMGHAKMIDSMITDGLWDAFNDYHMGITAENLVDKYGISREEQDAFAA 180 APYV+P+ARTG RMGH ++IDSMITDGLWDAFNDYHMGITAENLVDKYG+SRE+QDAFAA Sbjct: 121 APYVMPSARTGQRMGHGQLIDSMITDGLWDAFNDYHMGITAENLVDKYGLSREQQDAFAA 180 Query: 181 ASQQKAVAAIEGGRFADEITPILIPQRKGDPVAFATDEQPRAGTTAESLGKLKPAFKKDG 240 SQ+KAVAAIE GRF EITPI++PQ+KG+P FA DEQPR TTAESL KL+PAFKKDG Sbjct: 181 ESQRKAVAAIEAGRFDAEITPIVLPQKKGEPKVFARDEQPRPDTTAESLAKLRPAFKKDG 240 Query: 241 SVTAGNASSLNDGAAAVILMSAEKAKALGLPVLAKISAYANAGVDPAIMGIGPVSATRRC 300 SVTAGNASSLNDGAAAV+LMSA KA+ALGLPVLAKI+AYA+AGVDPAIMGIGPVSAT+RC Sbjct: 241 SVTAGNASSLNDGAAAVLLMSAAKAEALGLPVLAKIAAYASAGVDPAIMGIGPVSATQRC 300 Query: 301 LDKAGWSLEQLDLIEANEAFAAQSLAVARELKWDMDKVNVNGGAIALGHPIGASGCRVLV 360 LDKAGW L +LDLIEANEAFAAQ+LAV L WD +VNVNGGAIALGHPIGASGCRVLV Sbjct: 301 LDKAGWQLAELDLIEANEAFAAQALAVGNALAWDAARVNVNGGAIALGHPIGASGCRVLV 360 Query: 361 SLLHEMIKRDAKKGLATLCIGGGQGVALALER 392 +LLHEMIKRD KKGLATLCIGGGQGVALA+ER Sbjct: 361 TLLHEMIKRDVKKGLATLCIGGGQGVALAIER 392 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: 590 Number of extensions: 16 Number of successful extensions: 1 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: 392 Length adjustment: 31 Effective length of query: 362 Effective length of database: 361 Effective search space: 130682 Effective search space used: 130682 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