Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate 6937938 Sama_2079 acetyl-CoA synthetase (RefSeq)
Query= SwissProt::P27550 (652 letters) >FitnessBrowser__SB2B:6937938 Length = 650 Score = 964 bits (2493), Expect = 0.0 Identities = 444/645 (68%), Positives = 535/645 (82%) Query: 1 MSQIHKHTIPANIADRCLINPQQYEAMYQQSINVPDTFWGEQGKILDWIKPYQKVKNTSF 60 MS +++PA+IA L+N +QY+ MYQ+S+ P+ FWGE K +DWIKP+ +VK+TS+ Sbjct: 1 MSTQSLYSVPADIAANALVNNEQYQKMYQESVANPEGFWGEHAKRIDWIKPFTQVKDTSY 60 Query: 61 APGNVSIKWYEDGTLNLAANCLDRHLQENGDRTAIIWEGDDASQSKHISYKELHRDVCRF 120 N+ IKW+ DGTLN +ANCLDRHL GD AIIWEGDDAS+ + ++Y+ELH +VC+F Sbjct: 61 DDQNLYIKWFHDGTLNASANCLDRHLASKGDDVAIIWEGDDASEQRKVTYRELHAEVCQF 120 Query: 121 ANTLLELGIKKGDVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNS 180 AN L G+K+GDVV IYMPMV EA VAMLACARIGAVHSV+FGGFSP+++A R+ID S Sbjct: 121 ANALKAEGVKRGDVVTIYMPMVVEATVAMLACARIGAVHSVVFGGFSPDSIASRVIDGKS 180 Query: 181 RLVITSDEGVRAGRSIPLKKNVDDALKNPNVTSVEHVVVLKRTGGKIDWQEGRDLWWHDL 240 +L+IT+DEGVR GR IPLK N+D+AL P+VT+VE V+VLKRTGG ++W EGRD WWH + Sbjct: 181 KLLITADEGVRGGRKIPLKGNIDEALNRPDVTTVETVIVLKRTGGAVNWVEGRDKWWHQV 240 Query: 241 VEQASDQHQAEEMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDI 300 + A+ + EEM AEDPLF+LYTSGSTG PKGVLHTTGGYLVYA++T +YVFDY PG++ Sbjct: 241 TDGAATECAVEEMGAEDPLFLLYTSGSTGNPKGVLHTTGGYLVYASMTHEYVFDYKPGEV 300 Query: 301 YWCTADVGWVTGHSYLLYGPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTA 360 YWCTADVGW+TGHSY++YGPLA GAT L+ EG+PN+P+PAR+ ++VD+HQVNILYTAPT Sbjct: 301 YWCTADVGWITGHSYMVYGPLANGATILIHEGIPNFPSPARLGEIVDRHQVNILYTAPTL 360 Query: 361 IRALMAEGDKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGG 420 IRALMAEG + + D SLRI+GSVGEPINPEAW WY + IG+E CP+VDTWWQTETGG Sbjct: 361 IRALMAEGKQHFDNFDGKSLRIMGSVGEPINPEAWRWYHEVIGHEHCPIVDTWWQTETGG 420 Query: 421 FMITPLPGATELKAGSATRPFFGVQPALVDNEGNPLEGATEGSLVITDSWPGQARTLFGD 480 +ITPLPGAT+ K GSATRPFFGVQPALVDNEGN LEGATEG+LV+ DSWPGQ RT++GD Sbjct: 421 ILITPLPGATDTKPGSATRPFFGVQPALVDNEGNILEGATEGNLVLLDSWPGQMRTVYGD 480 Query: 481 HERFEQTYFSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHP 540 HERF TYF TF+ MYF+GDGARRDEDGYYWITGRVDDV+NVSGHRLGTAE+ESALVAH Sbjct: 481 HERFVLTYFKTFRGMYFTGDGARRDEDGYYWITGRVDDVINVSGHRLGTAEVESALVAHD 540 Query: 541 KIAEAAVVGIPHNIKGQAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTD 600 +AEAAVVG PH+IKGQ IYAYVTL G E + EL E+R WVRKEIG LATPD++ W Sbjct: 541 LVAEAAVVGYPHDIKGQGIYAYVTLTKGTEATEELRQELRQWVRKEIGALATPDLIQWAS 600 Query: 601 SLPKTRSGKIMRRILRKIAAGDTSNLGDTSTLADPGVVEKLLEEK 645 LPKTRSGKIMRR LRKIAA + +NLGD STLADP V++ L+E + Sbjct: 601 GLPKTRSGKIMRRFLRKIAANEITNLGDASTLADPSVIDTLIESR 645 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: 1459 Number of extensions: 55 Number of successful extensions: 1 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: 650 Length adjustment: 38 Effective length of query: 614 Effective length of database: 612 Effective search space: 375768 Effective search space used: 375768 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 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