Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate GFF2607 Psest_2657 acetate--CoA ligase
Query= SwissProt::P27550 (652 letters) >FitnessBrowser__psRCH2:GFF2607 Length = 651 Score = 912 bits (2357), Expect = 0.0 Identities = 424/642 (66%), Positives = 517/642 (80%) Query: 7 HTIPANIADRCLINPQQYEAMYQQSINVPDTFWGEQGKILDWIKPYQKVKNTSFAPGNVS 66 + + A L + Y AMYQQS+ P+ FW EQ L+WI+P+ +VK TSF +V Sbjct: 7 YPVSPEAAKHSLTDEAAYRAMYQQSVINPEGFWREQAARLNWIRPFTEVKRTSFDDHHVD 66 Query: 67 IKWYEDGTLNLAANCLDRHLQENGDRTAIIWEGDDASQSKHISYKELHRDVCRFANTLLE 126 IKW+ DGTLN++ANCLDRHL E GD+ AIIWEGD+ S+ + I+Y+EL+++VC+FAN L Sbjct: 67 IKWFADGTLNVSANCLDRHLAERGDQVAIIWEGDEPSEHREITYRELYQEVCKFANALRG 126 Query: 127 LGIKKGDVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNSRLVITS 186 + +GDVV IYMPM+PEAAVAMLACARIGA+HSV+FGGFSPEA+AGRIID S++VIT+ Sbjct: 127 QDVHRGDVVTIYMPMIPEAAVAMLACARIGAIHSVVFGGFSPEALAGRIIDGQSKVVITA 186 Query: 187 DEGVRAGRSIPLKKNVDDALKNPNVTSVEHVVVLKRTGGKIDWQEGRDLWWHDLVEQASD 246 DEG+R G+ IPLK+NVD+AL +P V+ ++V++RTG I W RD+ + DL+ A + Sbjct: 187 DEGIRGGKPIPLKENVDEALTHPQTRCVQKIIVVRRTGADIRWHPHRDVCYDDLMRVAGE 246 Query: 247 QHQAEEMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDIYWCTAD 306 +EM AE+PLFILYTSGSTGKPKGVLHT GGYL+YAALT + VFDY PGD+YWCTAD Sbjct: 247 VCAPKEMGAEEPLFILYTSGSTGKPKGVLHTCGGYLLYAALTHERVFDYRPGDVYWCTAD 306 Query: 307 VGWVTGHSYLLYGPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTAIRALMA 366 +GW+TGHSYL+YGPLA GATTLM+EGVPN+P R+A+++DKH+VNILYTAPTAIRA+MA Sbjct: 307 IGWITGHSYLIYGPLANGATTLMYEGVPNYPDVTRIARIIDKHRVNILYTAPTAIRAMMA 366 Query: 367 EGDKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGGFMITPL 426 EG A+EG D SSLR+LG+VGEPINPEAW WY++ +G +CP+VDTWWQTETGG +I+PL Sbjct: 367 EGAAAMEGADGSSLRLLGTVGEPINPEAWHWYYETVGRSRCPIVDTWWQTETGGILISPL 426 Query: 427 PGATELKAGSATRPFFGVQPALVDNEGNPLEGATEGSLVITDSWPGQARTLFGDHERFEQ 486 PGAT LK GSATRP FGV P LVDN GN LEG EG+LVI DSWPGQ RT++ DH+RF Sbjct: 427 PGATALKPGSATRPLFGVVPGLVDNLGNLLEGPAEGNLVILDSWPGQMRTIYRDHDRFVD 486 Query: 487 TYFSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHPKIAEAA 546 TYF TF+ MYF+GDGARRDEDGYYWITGRVDDVLNVSGHR+GTAEIESA+VAH K+AEAA Sbjct: 487 TYFKTFRGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHAKVAEAA 546 Query: 547 VVGIPHNIKGQAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTDSLPKTR 606 VG+PH +KGQAIY YVTL G EPS L E++ WVR EIGP+A PD + W LPKTR Sbjct: 547 AVGVPHALKGQAIYVYVTLVAGVEPSDTLRQELQQWVRHEIGPIAVPDTIQWAPGLPKTR 606 Query: 607 SGKIMRRILRKIAAGDTSNLGDTSTLADPGVVEKLLEEKQAI 648 SGKIMRR+LRKIA D LGDTSTLADPGVV++L+E +A+ Sbjct: 607 SGKIMRRLLRKIATDDYDALGDTSTLADPGVVDQLIEAHEAV 648 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: 1529 Number of extensions: 65 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 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