Align acetyl-CoA:acetyl-CoA C-acetyltransferase / acetyl-CoA:propanoyl-CoA 2-C-acetyltransferase (EC 2.3.1.9; EC 2.3.1.16) (characterized)
to candidate SMa1450 SMa1450 thiolase
Query= reanno::pseudo3_N2E3:AO353_25685 (397 letters) >FitnessBrowser__Smeli:SMa1450 Length = 396 Score = 555 bits (1431), Expect = e-163 Identities = 276/389 (70%), Positives = 327/389 (84%) Query: 6 DPIVIVSAVRTPMGGFQGELKSLSAPQLGAAAIRAAVERAGVAADAVEEVLFGCVLSAGL 65 DP+VIV RTP+G FQGELK LSA LGAAAI A++RAG+A DAV+EV+FGCVL+AG Sbjct: 5 DPVVIVGQARTPLGSFQGELKDLSAADLGAAAIVDALKRAGLAPDAVDEVMFGCVLTAGQ 64 Query: 66 GQAPARQAALGAGLDKSTRCTTLNKMCGSGMEAAILAHDMLLAGSADVVVAGGMESMSNA 125 GQAPARQAALGAGL TT+NKMCGSGM+AA+LAHD++ A SA +VVAGGMESM+NA Sbjct: 65 GQAPARQAALGAGLPPGVGATTVNKMCGSGMKAAMLAHDLIKAESASIVVAGGMESMTNA 124 Query: 126 PYLLDRARSGYRMGHGKVLDHMFLDGLEDAYDKGRLMGTFAEDCAEANGFTREAQDEFAI 185 PYLLDRAR GYR+GH KVLDHMFLDGLEDAYDKGRLMG+FAEDCAEA FTR AQDE+AI Sbjct: 125 PYLLDRARQGYRIGHQKVLDHMFLDGLEDAYDKGRLMGSFAEDCAEAYQFTRSAQDEYAI 184 Query: 186 ASTTRAQQAIKDGSFNAEIVPLQVIVGKEQKLITDDEQPPKAKLDKIASLKPAFRDGGTV 245 AS +AQ+A DGSF EIVPL + GK ++ + DEQP KA+LDKI LKPAFRDGGT+ Sbjct: 185 ASLEKAQKASADGSFAEEIVPLSIASGKGERTVNLDEQPQKARLDKIPLLKPAFRDGGTI 244 Query: 246 TAANSSSISDGAAALLLMRRSEAEKRGLKPLAVIHGHAAFADTPGLFPVAPVGAIKKLLK 305 TAAN+SSISDGAAAL+LMRRS A+K+G+ PLAVI GHA AD P LFP AP+GAIK L + Sbjct: 245 TAANASSISDGAAALVLMRRSAADKQGIGPLAVICGHATHADAPSLFPTAPIGAIKALCR 304 Query: 306 KTGWSLDEVELFEVNEAFAVVSLVTMTKLEIPHSKVNVHGGACALGHPIGASGARILVTL 365 + GW + EV+LFE+NEAFAVV + M +L + KVNVHGGACALGHPIGASGAR++VTL Sbjct: 305 RIGWDIGEVDLFEINEAFAVVPMAAMRELGLDAEKVNVHGGACALGHPIGASGARVIVTL 364 Query: 366 LSALRQKGLKRGVAAICIGGGEATAMAVE 394 ++ALR++GL+RG+A++CIGGGEATA+AVE Sbjct: 365 VNALRRRGLRRGIASVCIGGGEATAVAVE 393 Lambda K H 0.318 0.133 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: 546 Number of extensions: 17 Number of successful extensions: 2 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: 397 Length of database: 396 Length adjustment: 31 Effective length of query: 366 Effective length of database: 365 Effective search space: 133590 Effective search space used: 133590 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 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