Align acetyl-CoA C-acetyltransferase [EC: 2.3.1.9] (characterized)
to candidate WP_011385133.1 AMB_RS13850 3-oxoadipyl-CoA thiolase
Query= reanno::pseudo5_N2C3_1:AO356_21640 (393 letters) >NCBI__GCF_000009985.1:WP_011385133.1 Length = 400 Score = 338 bits (866), Expect = 2e-97 Identities = 192/401 (47%), Positives = 268/401 (66%), Gaps = 11/401 (2%) Query: 1 MQEVVIVAATRTAIGSFQGSLAAIPAPELGAAVIRRLLEQ-TGLSGEQVDEVILGQVLTA 59 M E +I TRT IG + GSLA + +L A I+ L+ + GL +VDEV G A Sbjct: 1 MTEALICDYTRTPIGRYAGSLAGVRTDDLAAHPIKALMARHAGLDWSRVDEVAYGCANQA 60 Query: 60 GS-GQNPARQASILAGLPHAVPALTLNKVCGSGLKALHLGAQAIRCGDAEVIIAGGMENM 118 G +N AR A +LAGLPH++ TLN++CGSG+ A+ A+A+ G+AE++IAGG+E+M Sbjct: 61 GEDNRNVARMALLLAGLPHSIGGTTLNRLCGSGMDAVGYAARAVMTGEAELMIAGGVESM 120 Query: 119 SLAPYVLPAARTGLRMGHAKMIDSMI----TDGLWD-AFNDYHMGITAENLVDKYGISRE 173 S AP+V+ A + A++ D+ I + L + A+ M TAEN+ +++ ISRE Sbjct: 121 SRAPFVMNKADSAFSRD-ARLYDTTIGWRFVNALMEKAYGTDSMPETAENVAEQFNISRE 179 Query: 174 EQDAFAAASQQKAVAAIEGGRFADEITPILIPQRKGDPVAFATDEQPRAGTTAESLGKLK 233 +QDAFAA SQ KA AA + GRFA EI+P+ +P RKGDPV + DE PR TT E+L KLK Sbjct: 180 DQDAFAARSQAKASAAQKNGRFAQEISPVTLPARKGDPVVVSHDEHPRE-TTVEALAKLK 238 Query: 234 PAFKKDGSVTAGNASSLNDGAAAVILMSAEKAKALGLPVLAKISAYANAGVDPAIMGIGP 293 F+ GS+TAGNAS +NDGAAA+++ S AKA GL +A+I A AGV+P IMGIGP Sbjct: 239 APFRAGGSITAGNASGVNDGAAALLIASPAAAKAHGLTPIARILGMATAGVEPRIMGIGP 298 Query: 294 VSATRRCLDKAGWSLEQLDLIEANEAFAAQSLAVARELKW--DMDKVNVNGGAIALGHPI 351 V AT++ L + G ++ LD++E NEAFAAQ+LA R+L D +VN NGGAIALGHP+ Sbjct: 299 VPATQKLLARLGLTMADLDVMEFNEAFAAQALACTRQLGLADDDQRVNPNGGAIALGHPL 358 Query: 352 GASGCRVLVSLLHEMIKRDAKKGLATLCIGGGQGVALALER 392 G SG R++ + ++ + ++ L+T+CIG GQG+A+A+ER Sbjct: 359 GMSGARIVGTAALQLAQTGGRRALSTMCIGVGQGIAMAIER 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: 428 Number of extensions: 20 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: 393 Length of database: 400 Length adjustment: 31 Effective length of query: 362 Effective length of database: 369 Effective search space: 133578 Effective search space used: 133578 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