Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate GFF832 HP15_811 acetyl-CoA synthetase
Query= SwissProt::P27550 (652 letters) >FitnessBrowser__Marino:GFF832 Length = 649 Score = 965 bits (2494), Expect = 0.0 Identities = 452/637 (70%), Positives = 534/637 (83%), Gaps = 1/637 (0%) Query: 7 HTIPANIADRCLINPQQYEAMYQQSINVPDTFWGEQGKILDWIKPYQKVKNTSFAPGNVS 66 + + +A + L+N +QYE MY+QS+ PDTFWGE GK L+WIKPY KVKNT++ N+S Sbjct: 7 YPVSPEVAKQALLNREQYEEMYRQSVEDPDTFWGEHGKRLEWIKPYTKVKNTTYDYNNLS 66 Query: 67 IKWYEDGTLNLAANCLDRHLQENGDRTAIIWEGDDASQSKHISYKELHRDVCRFANTLLE 126 IKW+EDG LN +ANCLDRHL++ GD+TAII+EGDD + S++++Y+ELH + +FAN L Sbjct: 67 IKWFEDGQLNASANCLDRHLEKRGDQTAIIFEGDDPADSRNVTYRELHEETSKFANVLKG 126 Query: 127 LGIKKGDVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNSRLVITS 186 LG+KKGDVV IYMPM+ E AVAMLACARIGA+HSV+FGGFSPEA+ RI++ SR V+T+ Sbjct: 127 LGVKKGDVVTIYMPMIVETAVAMLACARIGAIHSVVFGGFSPEALGARIVNGKSRFVVTA 186 Query: 187 DEGVRAGRSIPLKKNVDDALKNPNVTSVEHVVVLKRTGG-KIDWQEGRDLWWHDLVEQAS 245 DEGVR GR IPLKKNVD ALKN + +VE VVV+ RTG ++ W E RD + DL++ AS Sbjct: 187 DEGVRGGRKIPLKKNVDAALKNEDAANVEKVVVVTRTGNSEVPWNEARDERYEDLMKSAS 246 Query: 246 DQHQAEEMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDIYWCTA 305 Q E MNAEDPLF+LYTSGSTG PKGVLHTTGGY+VYA++T +YVFDYH GD+YWCTA Sbjct: 247 ADCQPEPMNAEDPLFMLYTSGSTGAPKGVLHTTGGYMVYASMTHEYVFDYHEGDVYWCTA 306 Query: 306 DVGWVTGHSYLLYGPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTAIRALM 365 D GWVTGHSY+LYGPLA GA T++FEGVPN+P +RM QVVDKH+VNILYTAPTAIRALM Sbjct: 307 DFGWVTGHSYILYGPLANGAITVLFEGVPNYPDSSRMGQVVDKHKVNILYTAPTAIRALM 366 Query: 366 AEGDKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGGFMITP 425 AEG+ + GT R SL++LGSVGEPINPEAWEWY + IGN KCP+VDTWWQTETGG +I+P Sbjct: 367 AEGESCMNGTTRESLKLLGSVGEPINPEAWEWYHRVIGNSKCPIVDTWWQTETGGILISP 426 Query: 426 LPGATELKAGSATRPFFGVQPALVDNEGNPLEGATEGSLVITDSWPGQARTLFGDHERFE 485 LPGA +LK GSAT PFFGVQPALVDN+GN LEG TEG+LVI DSWPGQ RT++GDHERF Sbjct: 427 LPGAIDLKPGSATVPFFGVQPALVDNDGNILEGKTEGNLVILDSWPGQMRTIYGDHERFA 486 Query: 486 QTYFSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHPKIAEA 545 QTYFST+K MYF+GDGARRDEDGYYWITGRVDDVLNVSGHRLGTAE+ESALV+H K+AEA Sbjct: 487 QTYFSTYKGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEVESALVSHEKVAEA 546 Query: 546 AVVGIPHNIKGQAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTDSLPKT 605 AVVG PH+IKGQ IY YVTL HG+EPS EL E+ WVRKEIGP+A+PDV+ W LPKT Sbjct: 547 AVVGYPHDIKGQGIYVYVTLVHGQEPSDELKKELVQWVRKEIGPIASPDVIQWAPGLPKT 606 Query: 606 RSGKIMRRILRKIAAGDTSNLGDTSTLADPGVVEKLL 642 RSGKIMRRILRKIAA + LGDTSTLADPGVV+ L+ Sbjct: 607 RSGKIMRRILRKIAANEHDQLGDTSTLADPGVVDDLI 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: 1476 Number of extensions: 60 Number of successful extensions: 2 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: 649 Length adjustment: 38 Effective length of query: 614 Effective length of database: 611 Effective search space: 375154 Effective search space used: 375154 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