Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate 201881 SO2743 acetyl-coenzyme A synthetase (NCBI ptt file)
Query= SwissProt::P27550 (652 letters) >FitnessBrowser__MR1:201881 Length = 650 Score = 975 bits (2520), Expect = 0.0 Identities = 453/645 (70%), Positives = 537/645 (83%) Query: 1 MSQIHKHTIPANIADRCLINPQQYEAMYQQSINVPDTFWGEQGKILDWIKPYQKVKNTSF 60 MS + + NIA L+N QY+ MYQ+SI P+ FW E GK +DWIKPY K+K T+F Sbjct: 1 MSSQSLYKVSGNIAANALVNNDQYKTMYQESIVNPEGFWREHGKRIDWIKPYTKIKKTTF 60 Query: 61 APGNVSIKWYEDGTLNLAANCLDRHLQENGDRTAIIWEGDDASQSKHISYKELHRDVCRF 120 N+SI W+ DGTLN +ANCLDRHL + DR AIIWEGD+A++ + I+Y ELH VC+F Sbjct: 61 DDHNLSINWFYDGTLNASANCLDRHLAAHSDRVAIIWEGDNANEQRKITYGELHTQVCKF 120 Query: 121 ANTLLELGIKKGDVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNS 180 AN L G+++GD+V IYMPMVPEAAVAMLACARIGAVHSV+FGGFSP+++A R+ID S Sbjct: 121 ANALRSQGVRRGDIVTIYMPMVPEAAVAMLACARIGAVHSVVFGGFSPDSIASRVIDGKS 180 Query: 181 RLVITSDEGVRAGRSIPLKKNVDDALKNPNVTSVEHVVVLKRTGGKIDWQEGRDLWWHDL 240 ++VITSDEG+R GR+IPLK+N+DDALK+P+VTSVE V+VLKRTGGKIDW EGRD+WWH L Sbjct: 181 KIVITSDEGMRGGRAIPLKRNIDDALKHPDVTSVEKVIVLKRTGGKIDWVEGRDVWWHSL 240 Query: 241 VEQASDQHQAEEMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDI 300 VE AS+ EEM AEDPLF+LYTSGSTG PKGVLHTTGGY+VYA++T +YVFDY PG+I Sbjct: 241 VETASEHCAVEEMGAEDPLFLLYTSGSTGNPKGVLHTTGGYMVYASMTHEYVFDYKPGEI 300 Query: 301 YWCTADVGWVTGHSYLLYGPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTA 360 YWCTADVGW+TGHSY++YGPLA GAT L+ EGVPN P+PAR+ +++D+H+VNILYTAPT Sbjct: 301 YWCTADVGWITGHSYMVYGPLANGATVLIHEGVPNHPSPARLGEMIDRHKVNILYTAPTL 360 Query: 361 IRALMAEGDKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGG 420 IRALMAEG + + + SSLRI+GSVGEPINPEAW WY + IG+E CP+VDTWWQTETGG Sbjct: 361 IRALMAEGKQHFDKYNGSSLRIMGSVGEPINPEAWRWYHEVIGHEHCPIVDTWWQTETGG 420 Query: 421 FMITPLPGATELKAGSATRPFFGVQPALVDNEGNPLEGATEGSLVITDSWPGQARTLFGD 480 +ITPLPGAT+ K GSATRPFFGVQPALVDN GN LEGATEG+LV+ DSWPGQ RT++GD Sbjct: 421 ILITPLPGATDTKPGSATRPFFGVQPALVDNMGNILEGATEGNLVLLDSWPGQMRTVYGD 480 Query: 481 HERFEQTYFSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHP 540 HERF TYF TF+ MYF+GDGARRDEDGYYWITGRVDDV+NVSGHRLGTAE+ESALV+H Sbjct: 481 HERFVLTYFKTFRGMYFTGDGARRDEDGYYWITGRVDDVINVSGHRLGTAEVESALVSHE 540 Query: 541 KIAEAAVVGIPHNIKGQAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTD 600 +AEAAVVG PH+IKGQ IYAYVTL G E S EL E+R WVRKEIG LATPD++ W Sbjct: 541 LVAEAAVVGYPHDIKGQGIYAYVTLTRGTEESEELRQELRQWVRKEIGALATPDLIQWAT 600 Query: 601 SLPKTRSGKIMRRILRKIAAGDTSNLGDTSTLADPGVVEKLLEEK 645 LPKTRSGKIMRR LRKIAA + +NLGD STLADP V+E L+E + Sbjct: 601 GLPKTRSGKIMRRFLRKIAANEVTNLGDASTLADPAVIETLIETR 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: 1460 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 Apr 09 2024.
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