Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Ergosterol biosynthesis protein 10; EC 2.3.1.9 (characterized)
to candidate CA265_RS06590 CA265_RS06590 acetyl-CoA acetyltransferase
Query= SwissProt::Q9UQW6 (395 letters) >FitnessBrowser__Pedo557:CA265_RS06590 Length = 391 Score = 446 bits (1147), Expect = e-130 Identities = 232/391 (59%), Positives = 294/391 (75%), Gaps = 2/391 (0%) Query: 5 EVYIVSAVRTPMGSFGGSFASLPATKLGSIAIKGALERVNIKPSDVDEVFMGNVVSANLG 64 EV IVSAVRTP+GSFGGS A AT+LG AIK A+E+ +KP + EV+MGNV+SANLG Sbjct: 3 EVVIVSAVRTPIGSFGGSLAQFSATQLGGFAIKAAIEKAGLKPEQIQEVYMGNVLSANLG 62 Query: 65 QNPARQCALGAGLPRSIVCTTVNKVCASGMKATILGAQTIMTGNAEIVVAGGTESMSNAP 124 Q PA Q A AGLP + TT+NKVCASG KA +L AQ+I G+ EI+VAGG ESMSN P Sbjct: 63 QAPATQAAKFAGLP-DLPATTINKVCASGTKAIMLAAQSIANGDNEIIVAGGMESMSNVP 121 Query: 125 YYAPKNRFGAKYGNVELVDGLLRDGLSDAYDGLPMGNAAELCAEEHSIDRASQDAFAISS 184 YY K R G + G+ ++ DGL++DGL D Y+ MG+AAELCA E +I+R +QD FAISS Sbjct: 122 YYLDKARNGYRLGHGQITDGLVKDGLWDVYNDYHMGSAAELCATECNINREAQDNFAISS 181 Query: 185 YKRAQNAQATKAFEQEIVPVEVPVGRGKPNKLVTEDEEPKNLNEDKLKSVRAVFKSNGTV 244 YKRAQ AQ + F EIV +EV +G LV D+EP + DK+ S++ VFK +GTV Sbjct: 182 YKRAQAAQTSGKFANEIVAIEVKDRKGDIT-LVDTDDEPTAVKFDKIPSLKPVFKKDGTV 240 Query: 245 TAANASTLNDGASALVLMSAAKVKELGLKPLAKIIGWGEAAQDPERFTTSPSLAIPKALK 304 TAANASTLNDGA+ALVLMSA K KELGL PLAKI+G+ +A Q PE FTT+PS AIP AL Sbjct: 241 TAANASTLNDGAAALVLMSADKAKELGLTPLAKILGYADAQQAPEWFTTAPSKAIPLALH 300 Query: 305 HAGIEASQVDYYEINEAFSVVAVANTKILGLDPERVNINGGGVAMGHPLGSSGSRIICTL 364 A + + VD++EINEAF+VV++AN ++L L+ +VN+NGG V++GHPLG+SG+RI+ TL Sbjct: 301 KANVNINDVDFFEINEAFAVVSIANNQLLALNDNQVNVNGGAVSLGHPLGASGARIVVTL 360 Query: 365 AYILAQKDAKIGVAAVCNGGGGASSIVIERV 395 +LAQ D KIGVA +CNGGGGAS++VI ++ Sbjct: 361 LSVLAQNDGKIGVAGICNGGGGASALVIGKL 391 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: 469 Number of extensions: 14 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: 395 Length of database: 391 Length adjustment: 31 Effective length of query: 364 Effective length of database: 360 Effective search space: 131040 Effective search space used: 131040 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 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