Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_084200888.1 C0029_RS18225 acetate--CoA ligase
Query= SwissProt::P27550 (652 letters) >NCBI__GCF_002869505.1:WP_084200888.1 Length = 643 Score = 819 bits (2115), Expect = 0.0 Identities = 398/647 (61%), Positives = 484/647 (74%), Gaps = 8/647 (1%) Query: 1 MSQIHKHTIPANIADRCLINPQQYEAMYQQSINVPDTFWGEQGK-ILDWIKPYQKVKNTS 59 MS+ H +PAN D I+ Y+AMYQ+SI+ PD F+ + L W +P+ KV Sbjct: 1 MSEFPTHPVPANFKD-AHIDADTYKAMYQRSIDDPDGFFSQMANDFLSWDQPWDKVMEYD 59 Query: 60 FAPGNVSIKWYEDGTLNLAANCLDRHLQENGDRTAIIWEGDDASQSKHISYKELHRDVCR 119 F G + W+ G LN++ NC+DRHL E D+TA+IWEGDD + SKHI+Y EL VC+ Sbjct: 60 FIKGEAA--WFAGGKLNVSYNCVDRHLPERADQTALIWEGDDPADSKHITYAELKDHVCK 117 Query: 120 FANTLLELGIKKGDVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSN 179 AN L G+KKGD V IYMPM+PEAA AMLAC RIGAVHS++FGGFSPEA+ RI+DS+ Sbjct: 118 LANALKARGVKKGDRVCIYMPMIPEAAYAMLACTRIGAVHSIVFGGFSPEALKDRILDSD 177 Query: 180 SRLVITSDEGVRAGRSIPLKKNVDDALKN-PNVTSVEHVVVLKRTGGKIDWQEGRDLWWH 238 + VIT+DEGVR GR +PLK N D AL+ PNV + +V++RT G + W RD+W+H Sbjct: 178 CQTVITADEGVRGGRKVPLKVNADKALEACPNVHTC---LVVERTSGDVAWNADRDVWYH 234 Query: 239 DLVEQASDQHQAEEMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPG 298 +LV+ S + E M+AEDPLFILYTSGSTGKPKGVLHTTGGYL+ AA+TFKYVFDY G Sbjct: 235 ELVDGQSTDCEPESMDAEDPLFILYTSGSTGKPKGVLHTTGGYLLQAAMTFKYVFDYRDG 294 Query: 299 DIYWCTADVGWVTGHSYLLYGPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAP 358 +IYWCTADVGWVTGH+Y++YGPLA GA +LMFEGVP +P R +VVDKHQVN YTAP Sbjct: 295 EIYWCTADVGWVTGHTYIVYGPLANGAISLMFEGVPTYPDAGRCWEVVDKHQVNTFYTAP 354 Query: 359 TAIRALMAEGDKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTET 418 TAIRAL A GD+ + R SLR+LG+VGEPINPEAWEWY + +G+ +CP++DTWWQTET Sbjct: 355 TAIRALQAVGDEPVTRASRVSLRLLGTVGEPINPEAWEWYHRVVGDGRCPIIDTWWQTET 414 Query: 419 GGFMITPLPGATELKAGSATRPFFGVQPALVDNEGNPLEGATEGSLVITDSWPGQARTLF 478 G MITPLPGA LK GSAT PFFGV+ AL++ +G+ +EG G LV+ SWP Q RT+F Sbjct: 415 GAHMITPLPGAVPLKPGSATFPFFGVELALLNEDGSEIEGPGAGYLVVKRSWPSQIRTVF 474 Query: 479 GDHERFEQTYFSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVA 538 GDH+R TYF + YF+GDGA RDEDGYYWITGRVDDVLNVSGHR+GTAE+ESALV Sbjct: 475 GDHKRLIDTYFRNYPGYYFTGDGATRDEDGYYWITGRVDDVLNVSGHRMGTAEVESALVL 534 Query: 539 HPKIAEAAVVGIPHNIKGQAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHW 598 H +IAEAAVVG PH+IKGQ IYAYVT G EP+ EL E+ KEIGP+A PD++ W Sbjct: 535 HEEIAEAAVVGFPHDIKGQGIYAYVTPMQGVEPNEELRQELIALCVKEIGPIAKPDIIQW 594 Query: 599 TDSLPKTRSGKIMRRILRKIAAGDTSNLGDTSTLADPGVVEKLLEEK 645 LPKTRSGKIMRRILRKIA + +LGDTSTLADP VV+ L+ + Sbjct: 595 APGLPKTRSGKIMRRILRKIAENELDSLGDTSTLADPSVVDNLVANR 641 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: 1416 Number of extensions: 60 Number of successful extensions: 3 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: 643 Length adjustment: 38 Effective length of query: 614 Effective length of database: 605 Effective search space: 371470 Effective search space used: 371470 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 24 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