Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Ergosterol biosynthesis protein 10; EC 2.3.1.9 (characterized)
to candidate Echvi_3705 Echvi_3705 acetyl-CoA acetyltransferases
Query= SwissProt::Q9UQW6 (395 letters) >FitnessBrowser__Cola:Echvi_3705 Length = 393 Score = 461 bits (1186), Expect = e-134 Identities = 233/391 (59%), Positives = 298/391 (76%), Gaps = 1/391 (0%) Query: 5 EVYIVSAVRTPMGSFGGSFASLPATKLGSIAIKGALERVNIKPSDVDEVFMGNVVSANLG 64 EVYI+SAVRTP+GSFGG + L A +LG+ AIKGAL R + P VDEV MGNV+SANLG Sbjct: 3 EVYIISAVRTPLGSFGGKLSGLTAVELGAQAIKGALGRAQVTPEQVDEVIMGNVLSANLG 62 Query: 65 QNPARQCALGAGLPRSIVCTTVNKVCASGMKATILGAQTIMTGNAEIVVAGGTESMSNAP 124 Q PARQ A+GAG+ + CTTVNKVCASGMK+ + AQ+IMTG ++I+VAGG ESMSN P Sbjct: 63 QAPARQAAIGAGIGYHVPCTTVNKVCASGMKSVMFAAQSIMTGQSDIIVAGGMESMSNVP 122 Query: 125 YYAPKNRFGAKYGNVELVDGLLRDGLSDAYDGLPMGNAAELCAEEHSIDRASQDAFAISS 184 YY PK RFG K+GN E VDGL +DGL + Y PMGN A+ A+E +I R +QD +AI S Sbjct: 123 YYIPKARFGYKFGNGEFVDGLAKDGLHEVYYNFPMGNCADNTAKEKNISREAQDEYAIQS 182 Query: 185 YKRAQNAQATKAFEQEIVPVEVPVGRGKPNKLVTEDEEPKNLNEDKLKSVRAVFKSNGTV 244 Y+RA A +AF+ E++PV +G+ + V EDEE +N+ +K+ S+R VF GTV Sbjct: 183 YRRAAEAWKAQAFQDEVIPVTFKSRKGE-SITVDEDEEYQNVLFEKIPSLRPVFDKEGTV 241 Query: 245 TAANASTLNDGASALVLMSAAKVKELGLKPLAKIIGWGEAAQDPERFTTSPSLAIPKALK 304 TAANAST+NDGA+ALVLMS K + LGL+P+AKI+G+ +AA DP FTT+P+LAIPKALK Sbjct: 242 TAANASTMNDGAAALVLMSKEKAEALGLQPVAKILGFADAATDPIWFTTAPALAIPKALK 301 Query: 305 HAGIEASQVDYYEINEAFSVVAVANTKILGLDPERVNINGGGVAMGHPLGSSGSRIICTL 364 +AGI+A VDYYEINEAFS VA+AN + L + +R+N+ GG V++GHPLG+SG+RI+ TL Sbjct: 302 NAGIQAEAVDYYEINEAFSAVALANQQELNIPNDRLNVFGGAVSLGHPLGASGARIMATL 361 Query: 365 AYILAQKDAKIGVAAVCNGGGGASSIVIERV 395 +L QK KIGVA +CNGGGGAS++VIE + Sbjct: 362 HSVLRQKGGKIGVAGICNGGGGASAMVIENL 392 Lambda K H 0.313 0.130 0.365 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: 459 Number of extensions: 12 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: 395 Length of database: 393 Length adjustment: 31 Effective length of query: 364 Effective length of database: 362 Effective search space: 131768 Effective search space used: 131768 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. 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