Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate 208482 DVU2969 acetoacetyl-CoA synthase
Query= SwissProt::P27550 (652 letters) >MicrobesOnline__882:208482 Length = 661 Score = 746 bits (1927), Expect = 0.0 Identities = 367/623 (58%), Positives = 462/623 (74%), Gaps = 8/623 (1%) Query: 25 EAMYQQSINVPDTFWGEQG-KILDWIKPYQKVKNTSFAPGNVSIKWYEDGTLNLAANCLD 83 EA+ +++ P+ FWGE+ +++DW KP+ V + I+W++ G LN+A NCLD Sbjct: 35 EALVRRAAEDPEGFWGERAAQLIDWFKPWDTVLDADM--NEPRIEWFKGGRLNVAHNCLD 92 Query: 84 RHLQENG-DRTAIIWEGDDASQSKHISYKELHRDVCRFANTLLELGIKKGDVVAIYMPMV 142 RH+ N ++ AIIW+G+ + ++Y+ L+ +V RFA L ++G+ KGD V++YMPM+ Sbjct: 93 RHVAGNRRNKAAIIWQGEPEEDVRVLTYQMLYDEVRRFAAVLRKMGVHKGDRVSLYMPMI 152 Query: 143 PEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNSRLVITSDEGVRAGRSIPLKKNV 202 PE AVAMLACARIGAVHS++F GFS ++ RI D +++V+T+D +RAGR IPLK NV Sbjct: 153 PELAVAMLACARIGAVHSIVFAGFSAVSLQNRIHDCEAKVVVTADAVLRAGRRIPLKVNV 212 Query: 203 DDALKNPNVTSVEHVVVLKRTGGKIDWQEGRDLWWHDLVEQAS--DQHQAEEMNAEDPLF 260 D+A++ SVE VVV+ R ++ +EGRDLWWH+++ + EEM+AED LF Sbjct: 213 DEAVRQ--CPSVEKVVVVNRGSLEVTMEEGRDLWWHEVMADRTLDVDRPCEEMDAEDMLF 270 Query: 261 ILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDIYWCTADVGWVTGHSYLLYGP 320 ILYTSGSTGKPKGV+HTTGGYL YAA T ++VFD D+YWCTAD+GW+TGHSY++YGP Sbjct: 271 ILYTSGSTGKPKGVVHTTGGYLTYAAHTTQWVFDVQDDDVYWCTADIGWITGHSYIVYGP 330 Query: 321 LACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTAIRALMAEGDKAIEGTDRSSL 380 LA GAT+LMFEGVP+WP+P R ++V+K +VNI YTAPT +RALM EG E D SSL Sbjct: 331 LALGATSLMFEGVPSWPSPDRFWRIVEKFRVNIFYTAPTVVRALMREGTDWTERHDLSSL 390 Query: 381 RILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGGFMITPLPGATELKAGSATRP 440 R+LGSVGEPINPEAW WY IG + P+VDTWWQTETGG MI+ LP AT LK GSAT+P Sbjct: 391 RVLGSVGEPINPEAWMWYHTHIGKGRLPIVDTWWQTETGGIMISGLPYATTLKPGSATQP 450 Query: 441 FFGVQPALVDNEGNPLEGATEGSLVITDSWPGQARTLFGDHERFEQTYFSTFKNMYFSGD 500 GV A+V +G+P G LVI WPG R +FG ER+ TYF F MY SGD Sbjct: 451 LPGVDAAIVRPDGSPAGPNEGGHLVIRKPWPGMLRGIFGSPERYRSTYFERFPGMYESGD 510 Query: 501 GARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHPKIAEAAVVGIPHNIKGQAIY 560 GAR D DGY+WI GR+DDV+NVSGHR+GTAE+ESALVAHP +AEAAVVG+PH +KG+AIY Sbjct: 511 GARTDTDGYFWIMGRLDDVINVSGHRMGTAEVESALVAHPSVAEAAVVGMPHAVKGEAIY 570 Query: 561 AYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTDSLPKTRSGKIMRRILRKIAA 620 AYVTL E + EL AE+R WVRKEIGP+ATPDVL + + LPKTRSGKIMRRILRKIAA Sbjct: 571 AYVTLGADAEETEELRAELRAWVRKEIGPIATPDVLQFAEGLPKTRSGKIMRRILRKIAA 630 Query: 621 GDTSNLGDTSTLADPGVVEKLLE 643 G TS GDTSTLADPGVV L+E Sbjct: 631 GATSEFGDTSTLADPGVVSDLIE 653 Lambda K H 0.317 0.135 0.421 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: 1389 Number of extensions: 64 Number of successful extensions: 5 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: 652 Length of database: 661 Length adjustment: 38 Effective length of query: 614 Effective length of database: 623 Effective search space: 382522 Effective search space used: 382522 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: 54 (25.4 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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