Align 3-ketoacyl-CoA thiolase, peroxisomal; Acetyl-CoA acyltransferase; Beta-ketothiolase; Peroxisomal 3-oxoacyl-CoA thiolase; EC 2.3.1.16 (characterized)
to candidate WP_012281246.1 HM1_RS00320 acetyl-CoA C-acyltransferase
Query= SwissProt::P09110 (424 letters) >NCBI__GCF_000019165.1:WP_012281246.1 Length = 392 Score = 352 bits (902), Expect = e-101 Identities = 198/390 (50%), Positives = 262/390 (67%), Gaps = 8/390 (2%) Query: 37 DVVVVHGRRTAICRAGRGGFKDTTPDELLS-AVMTAVLKDVNLRPEQLGDICVGNVL-QP 94 + V+V RT + +A +G KD P++L + AV A+ + + PE++ D+ +G + Sbjct: 3 EAVIVSAVRTPVGKAPKGVLKDVRPEDLAAIAVRGALARVPAIAPEEVEDVILGCAFPEA 62 Query: 95 GAGAIMARIAQFLSDIPETVPLSTVNRQCSSGLQAVASIAGGIRNGSYDIGMACGVESMS 154 G + RI + +P +V TVNR CSSGLQA+A A + G ++ +A GVESMS Sbjct: 63 EQGMNLGRIVAQRAGLPYSVCGMTVNRFCSSGLQAIAIAAERVMAGFAEVMLAGGVESMS 122 Query: 155 LADRGNPGNITSRLMEKEKARDCLIPMGITSENVAERFGISREKQDTFALASQQKAARAQ 214 G I E + + MGIT+ENVA RFG+SRE QD FALASQQKAARAQ Sbjct: 123 TIPMGGT-KIAPNPYLMEHMPEAYMTMGITAENVAARFGVSREAQDRFALASQQKAARAQ 181 Query: 215 SKGCFQAEIVPVTTTVH----DDKGTKRSITVTQDEGIRPSTTMEGLAKLKPAFKKDGST 270 ++G F E++PVT + D K ++ + +DEGIRP T+++ LAKL+P F+++G+ Sbjct: 182 AEGRFNEELIPVTVSKRWVDADGKLQEQEVLFDKDEGIRPDTSLDALAKLRPVFRENGTV 241 Query: 271 TAGNSSQVSDGAAAILLARRSKAEELGLPILGVLRSYAVVGVPPDIMGIGPAYAIPVALQ 330 TAGN+SQ SDGAAA+L+ R KAE+LGLP+LG RS+AV GVP +IMGIGP AIP AL+ Sbjct: 242 TAGNASQTSDGAAALLVTSREKAEQLGLPVLGAFRSFAVGGVPAEIMGIGPVVAIPKALK 301 Query: 331 KAGLTVSDVDIFEINEAFASQAAYCVEKLRLPPEKVNPLGGAVALGHPLGCTGARQVITL 390 AG+ DVD+FE+NEAFA+QA Y + L L PE+VN GGA+ALGHPLGCTG++ TL Sbjct: 302 LAGIDQDDVDLFELNEAFAAQALYVMNHLGLDPERVNVNGGAIALGHPLGCTGSKLTTTL 361 Query: 391 LNELKRRGKRAYGVVSMCIGTGMGAAAVFE 420 L E+KRR R YGVVSMCIG GMGAAAVFE Sbjct: 362 LYEMKRRQAR-YGVVSMCIGGGMGAAAVFE 390 Lambda K H 0.317 0.134 0.385 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: 485 Number of extensions: 16 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: 424 Length of database: 392 Length adjustment: 31 Effective length of query: 393 Effective length of database: 361 Effective search space: 141873 Effective search space used: 141873 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 (21.7 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