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 GFF1030 HP15_1009 acyl-CoA thiolase
Query= reanno::pseudo3_N2E3:AO353_25685 (397 letters) >FitnessBrowser__Marino:GFF1030 Length = 397 Score = 461 bits (1185), Expect = e-134 Identities = 230/395 (58%), Positives = 303/395 (76%), Gaps = 1/395 (0%) Query: 2 TMSHDPIVIVSAVRTPMGGFQGELKSLSAPQLGAAAIRAAVERAGVAADAVEEVLFGCVL 61 TMS++ +VI + RTPMGG G L S+ +P LGA +I+AA+ER+G+ V+EV+ GCVL Sbjct: 4 TMSNNDVVIAGSARTPMGGMMGSLSSVRSPDLGAISIKAAIERSGLQPADVQEVIMGCVL 63 Query: 62 SAGLGQAPARQAALGAGLDKSTRCTTLNKMCGSGMEAAILAHDMLLAGSADVVVAGGMES 121 AGLGQAPARQA+ +G+ S+ CTT+NKMCGSGM+A I+AHD + AG+ ++++AGGME+ Sbjct: 64 PAGLGQAPARQASRASGIPDSSGCTTINKMCGSGMQAVIMAHDQIKAGTNNIMIAGGMEN 123 Query: 122 MSNAPYLLDRARSGYRMGHGKVLDHMFLDGLEDAYDKGRLMGTFAEDCAEANGFTREAQD 181 MS APYLL +AR G RMGHG+V+D MFLDGLEDAY+ G LMG FA+ A+ +R+A D Sbjct: 124 MSQAPYLLPKARGGMRMGHGQVMDSMFLDGLEDAYEGG-LMGVFAQRTADKYDISRQAMD 182 Query: 182 EFAIASTTRAQQAIKDGSFNAEIVPLQVIVGKEQKLITDDEQPPKAKLDKIASLKPAFRD 241 EFAI S ++ AI++G F EIVP+ V + DEQP AK +KI LKPAF Sbjct: 183 EFAIGSLQKSLAAIENGWFRDEIVPVTVSGRGGDTEVDTDEQPGNAKPEKIPHLKPAFAK 242 Query: 242 GGTVTAANSSSISDGAAALLLMRRSEAEKRGLKPLAVIHGHAAFADTPGLFPVAPVGAIK 301 G+VTAANSSSISDGA+AL+L +EA+ RGL P A I HA A P F +AP+G+I+ Sbjct: 243 DGSVTAANSSSISDGASALVLASAAEADARGLTPQARIVAHATHARLPAEFTLAPIGSIE 302 Query: 302 KLLKKTGWSLDEVELFEVNEAFAVVSLVTMTKLEIPHSKVNVHGGACALGHPIGASGARI 361 K+LKK GWS+D+V+LFE+NEAFAVV+L + +L++P KVNVHGGACALGHPIG+SG+RI Sbjct: 303 KVLKKAGWSVDDVDLFEINEAFAVVTLAAINELKLPADKVNVHGGACALGHPIGSSGSRI 362 Query: 362 LVTLLSALRQKGLKRGVAAICIGGGEATAMAVECL 396 +VTL++AL+Q+GLKRGVA++CIGGGE TA+A+E + Sbjct: 363 IVTLINALKQRGLKRGVASLCIGGGEGTAVAIELI 397 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: 479 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: 397 Length adjustment: 31 Effective length of query: 366 Effective length of database: 366 Effective search space: 133956 Effective search space used: 133956 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