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 HSERO_RS04635 HSERO_RS04635 acetyl-CoA acetyltransferase
Query= reanno::pseudo3_N2E3:AO353_25685 (397 letters) >FitnessBrowser__HerbieS:HSERO_RS04635 Length = 400 Score = 484 bits (1247), Expect = e-141 Identities = 251/398 (63%), Positives = 302/398 (75%), Gaps = 6/398 (1%) Query: 3 MSHDPIVIVSAVRTPMGGFQGELKSLSAPQLGAAAIRAAVERAGVAADAV---EEVLFGC 59 MS DP+VIVSA RT MG FQG L L AP LGA AI AA++RA ++A + E+V GC Sbjct: 1 MSEDPVVIVSAARTAMGSFQGALADLPAPHLGAVAISAALQRAQLSAAQIAQIEQVWMGC 60 Query: 60 VLSAGLGQAPARQAALGAGLDKSTRCTTLNKMCGSGMEAAILAHDMLLAGSADVVVAGGM 119 VL AGLGQAPARQAAL AGL ++ C TLNK+CGS M+A +L HD +LAGSA +VVAGGM Sbjct: 61 VLQAGLGQAPARQAALRAGLPQTVACATLNKVCGSAMQAVMLGHDSILAGSASMVVAGGM 120 Query: 120 ESMSNAPYLLDRARSGYRMGHGKVLDHMFLDGLEDAYD---KGRLMGTFAEDCAEANGFT 176 ESMSNAPYLL +AR GYR+GH ++LDHMFLDGLEDAY +GRLMGTFAEDCA GFT Sbjct: 121 ESMSNAPYLLPKARRGYRLGHDRLLDHMFLDGLEDAYSDQYRGRLMGTFAEDCASEFGFT 180 Query: 177 REAQDEFAIASTTRAQQAIKDGSFNAEIVPLQVIVGKEQKLITDDEQPPKAKLDKIASLK 236 R QD FA+ ST RA+QAI G F+ E+VP+ V K +I+ DE P L++IA+LK Sbjct: 181 RAQQDAFAVQSTLRARQAISGGGFDWEVVPVDVAGKKGSVVISQDEGPMAVNLERIATLK 240 Query: 237 PAFRDGGTVTAANSSSISDGAAALLLMRRSEAEKRGLKPLAVIHGHAAFADTPGLFPVAP 296 PAF GTVTAANSSSISDGAAALLLMR S A K+GL PLA I GHA++A P FP AP Sbjct: 241 PAFSVDGTVTAANSSSISDGAAALLLMRESAALKQGLTPLARILGHASYAGAPEKFPTAP 300 Query: 297 VGAIKKLLKKTGWSLDEVELFEVNEAFAVVSLVTMTKLEIPHSKVNVHGGACALGHPIGA 356 +G ++K+ KTG +LFE+NEAFAVV + +L+I K+NVHGGACALGHPIGA Sbjct: 301 IGVLRKIFAKTGLDAASTDLFEINEAFAVVPMAASRELDIDMEKINVHGGACALGHPIGA 360 Query: 357 SGARILVTLLSALRQKGLKRGVAAICIGGGEATAMAVE 394 SGARI+V+LL AL+ +GLK G+A++CIGGGEATA+A+E Sbjct: 361 SGARIIVSLLGALKARGLKTGIASLCIGGGEATAIALE 398 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: 482 Number of extensions: 15 Number of successful extensions: 3 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: 400 Length adjustment: 31 Effective length of query: 366 Effective length of database: 369 Effective search space: 135054 Effective search space used: 135054 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