Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_029133502.1 A3GO_RS0111360 acetate--CoA ligase
Query= SwissProt::P27550 (652 letters) >NCBI__GCF_000428045.1:WP_029133502.1 Length = 646 Score = 839 bits (2168), Expect = 0.0 Identities = 400/648 (61%), Positives = 504/648 (77%), Gaps = 8/648 (1%) Query: 1 MSQIHKHTIPANIADRCLINPQQYEAMYQQSINVPDTFWGEQGK-ILDWIKPYQKVKNTS 59 MS+ + + A A IN +Y+ MYQ+S+ PD FWG+ + L W K + KV + Sbjct: 1 MSEEKVYPVSAETAAHAHINAAKYQEMYQRSVKDPDGFWGDAAEEFLTWSKKWDKVSDWD 60 Query: 60 FAPGNVSIKWYEDGTLNLAANCLDRHLQENGDRTAIIWEGDDASQSKHISYKELHRDVCR 119 F N IKW++ G LN++ NCLDRHL+ GD+TA+IWE D+ ++ K ISY+ELH +VC+ Sbjct: 61 FNEAN--IKWFQGGKLNVSYNCLDRHLETRGDQTALIWESDNPNEDKKISYRELHTEVCK 118 Query: 120 FANTLLELGIKKGDVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSN 179 FAN L + G+KKGD V IYMPM+ EAAVAMLAC RIGAVHS++FGGFSP+A++ RI+DS+ Sbjct: 119 FANVLKDRGVKKGDRVCIYMPMILEAAVAMLACTRIGAVHSIVFGGFSPDALSSRILDSD 178 Query: 180 SRLVITSDEGVRAGRSIPLKKNVDDALKN-PNVTSVEHVVVLKRTGGKIDWQEGRDLWWH 238 + +ITSDE VR G+++PLK N D AL++ PNV + VV+KRTGGK+ W+EGRD+++H Sbjct: 179 CQTLITSDESVRGGKNVPLKANADIALEDCPNVRTC---VVVKRTGGKVAWKEGRDIYYH 235 Query: 239 DLVEQASDQHQAEEMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPG 298 D + AS + EEM+AEDPLFILYTSGSTG+PKGVLHTTGGYL++AA+T KY FDY G Sbjct: 236 DAMANASATCEPEEMDAEDPLFILYTSGSTGQPKGVLHTTGGYLLFAAMTHKYTFDYKEG 295 Query: 299 DIYWCTADVGWVTGHSYLLYGPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAP 358 ++YWCTADVGWVTGH+Y++YGPLA GA +LMFEG+P +P R V +KH+VN YTAP Sbjct: 296 EVYWCTADVGWVTGHTYIVYGPLANGAISLMFEGIPTYPDAGRFWAVCEKHKVNTFYTAP 355 Query: 359 TAIRALMAEGDKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTET 418 TAIRALM G++ ++ D SSLR+LGSVGEPINPEAWEWY++ +G E+CP+VDTWWQTET Sbjct: 356 TAIRALMRVGEEPVKKHDLSSLRLLGSVGEPINPEAWEWYYRVVGGERCPIVDTWWQTET 415 Query: 419 GGFMITPLPGATELKAGSATRPFFGVQPALVD-NEGNPLEGATEGSLVITDSWPGQARTL 477 GG +ITPLPGAT+LK GSA+ PFFGV PA+VD G LEG EG+L++T WPG R++ Sbjct: 416 GGHLITPLPGATDLKPGSASMPFFGVVPAIVDATTGEVLEGECEGALIMTRPWPGMMRSV 475 Query: 478 FGDHERFEQTYFSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALV 537 +GDH+RF+ TYFS + YF+GDGARRD+DGYYWITGR+DDVLNVSGHRLGTAEIESALV Sbjct: 476 YGDHQRFKDTYFSQYPGNYFTGDGARRDKDGYYWITGRIDDVLNVSGHRLGTAEIESALV 535 Query: 538 AHPKIAEAAVVGIPHNIKGQAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLH 597 H K+AEAAVVG PH+I GQ IYAYVT G EP+ EL AE+ VR EIGP+A +++ Sbjct: 536 LHEKVAEAAVVGYPHDITGQGIYAYVTPMAGVEPTDELKAELVKLVRDEIGPIAKINLIQ 595 Query: 598 WTDSLPKTRSGKIMRRILRKIAAGDTSNLGDTSTLADPGVVEKLLEEK 645 W LPKTRSGKIMRRILRK+A + LGDTSTLADPGVV+ L+E + Sbjct: 596 WAPGLPKTRSGKIMRRILRKVACNEIDTLGDTSTLADPGVVDDLIENR 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: 1399 Number of extensions: 63 Number of successful extensions: 4 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: 646 Length adjustment: 38 Effective length of query: 614 Effective length of database: 608 Effective search space: 373312 Effective search space used: 373312 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 10 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