Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate GFF4246 PS417_21750 acetyl-CoA synthetase
Query= SwissProt::P27550 (652 letters) >FitnessBrowser__WCS417:GFF4246 Length = 651 Score = 948 bits (2450), Expect = 0.0 Identities = 445/643 (69%), Positives = 525/643 (81%) Query: 1 MSQIHKHTIPANIADRCLINPQQYEAMYQQSINVPDTFWGEQGKILDWIKPYQKVKNTSF 60 MS + + +A L + Y+AMYQQS+ PD FW EQ K LDWIKP+ VK TSF Sbjct: 1 MSAASLYPVRPEVAANTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSF 60 Query: 61 APGNVSIKWYEDGTLNLAANCLDRHLQENGDRTAIIWEGDDASQSKHISYKELHRDVCRF 120 +V IKW+ DGTLN++ NCLDRHL E GD+ AIIWEGDD S+S+ I+Y+ELH +VC+F Sbjct: 61 DDHHVDIKWFADGTLNVSYNCLDRHLAERGDQAAIIWEGDDPSESRTITYRELHEEVCKF 120 Query: 121 ANTLLELGIKKGDVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNS 180 AN L + +GDVV IYMPM+PEA VAMLAC RIGA+HSV+FGGFSPEA+AGRIID S Sbjct: 121 ANALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKS 180 Query: 181 RLVITSDEGVRAGRSIPLKKNVDDALKNPNVTSVEHVVVLKRTGGKIDWQEGRDLWWHDL 240 ++VIT+DEG+RAG+ IPLK NVDDAL NP +S++ V+V KRT G I W + RD+W+ DL Sbjct: 181 KVVITADEGIRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTNGNIKWNQHRDIWYEDL 240 Query: 241 VEQASDQHQAEEMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDI 300 ++ A +EM AE+ LFILYTSGSTGKPKGV HTTGGYL+YAALT + VFDY PG+I Sbjct: 241 MKVAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTGGYLLYAALTHERVFDYRPGEI 300 Query: 301 YWCTADVGWVTGHSYLLYGPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTA 360 YWCTADVGWVTGH+Y++YGPLA GATTL+FEGVPN+P R+A++VDKH+VNILYTAPTA Sbjct: 301 YWCTADVGWVTGHTYIVYGPLANGATTLLFEGVPNYPDITRVAKIVDKHKVNILYTAPTA 360 Query: 361 IRALMAEGDKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGG 420 IRA+MA G A EG D SSLR+LGSVGEPINPEAW+WY+K +G +CP+VDTWWQTETGG Sbjct: 361 IRAMMASGTAACEGADGSSLRLLGSVGEPINPEAWDWYYKNVGQSRCPIVDTWWQTETGG 420 Query: 421 FMITPLPGATELKAGSATRPFFGVQPALVDNEGNPLEGATEGSLVITDSWPGQARTLFGD 480 M++PLPGA LK GSA RPFFGV PALVDN GN +EGA EG+LVI DSWPGQARTLFGD Sbjct: 421 NMMSPLPGAHALKPGSAARPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLFGD 480 Query: 481 HERFEQTYFSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHP 540 H+RF TYF TF+ MYF+GDGARRDEDGYYWITGRVDDVLNVSGHR+GTAEIESA+VAHP Sbjct: 481 HDRFVDTYFKTFRGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHP 540 Query: 541 KIAEAAVVGIPHNIKGQAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTD 600 K+AEAAVVG+PH+IKGQ IY YVTL +GEEP+ L E++NWVRKEIGP+A+PDV+ W Sbjct: 541 KVAEAAVVGVPHDIKGQGIYVYVTLKNGEEPNEALRLELKNWVRKEIGPIASPDVIQWAP 600 Query: 601 SLPKTRSGKIMRRILRKIAAGDTSNLGDTSTLADPGVVEKLLE 643 LPKTRSGKIMRRILRKIA G+ LGD STLADPGVV L+E Sbjct: 601 GLPKTRSGKIMRRILRKIATGEYDGLGDISTLADPGVVAHLIE 643 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: 1511 Number of extensions: 50 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: 651 Length adjustment: 38 Effective length of query: 614 Effective length of database: 613 Effective search space: 376382 Effective search space used: 376382 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 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