Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_011386526.1 AMB_RS21140 acetate--CoA ligase
Query= SwissProt::P27550 (652 letters) >NCBI__GCF_000009985.1:WP_011386526.1 Length = 645 Score = 937 bits (2422), Expect = 0.0 Identities = 439/646 (67%), Positives = 538/646 (83%), Gaps = 6/646 (0%) Query: 1 MSQIHKHTIPANIADRCLINPQQYEAMYQQSINVPDTFWGEQGKILDWIKPYQKVKNTSF 60 MS+++ +PA A LI+ +Y Y++S+ PD FWGE GK +DWIKP+ KVKN S+ Sbjct: 1 MSEVYP--VPAETAKNALIDNDKYNEWYERSVKDPDGFWGEHGKRIDWIKPFTKVKNVSY 58 Query: 61 APGNVSIKWYEDGTLNLAANCLDRHLQENGDRTAIIWEGDDASQSKHISYKELHRDVCRF 120 + G+VSIKW+EDGTLN++ANCLDRHL + D+TAIIWEGDD ++S HI+Y +LH VCR Sbjct: 59 S-GDVSIKWFEDGTLNVSANCLDRHLAKRRDQTAIIWEGDDPNESAHITYGDLHERVCRL 117 Query: 121 ANTLLELGIKKGDVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNS 180 AN + +LG+KKGD V IY+PM+PEAAVAMLACAR+GAVHS++FGGFSP+A+AGRI D +S Sbjct: 118 ANAMTDLGVKKGDRVTIYLPMIPEAAVAMLACARVGAVHSIVFGGFSPDALAGRIQDCDS 177 Query: 181 RLVITSDEGVRAGRSIPLKKNVDDALKNPNVTSVEHVVVLKRTGGKIDWQEGRDLWWHDL 240 L+IT+DEG+R GR +PLK NVD AL+ S + V+V+KRTGG I GRD W+HDL Sbjct: 178 SLLITADEGLRGGRKVPLKANVDKALET--CWSCKSVIVVKRTGGDIHMVTGRDHWYHDL 235 Query: 241 VEQASDQHQAEEMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDI 300 V +A+ H EM+AEDPLF+LYTSGSTGKPKGV+HTTGGYLVYA++T +YVFDYH GDI Sbjct: 236 VAKAAPTHTPVEMSAEDPLFLLYTSGSTGKPKGVVHTTGGYLVYASMTHQYVFDYHEGDI 295 Query: 301 YWCTADVGWVTGHSYLLYGPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTA 360 YWCTADVGWVTGHSY++YGPLA GA TLMFEG+PN+PT +R VVDKH+VNI YTAPTA Sbjct: 296 YWCTADVGWVTGHSYIVYGPLANGAITLMFEGIPNYPTVSRFWDVVDKHKVNIFYTAPTA 355 Query: 361 IRALMAEGDKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGG 420 IR+LM EG++ ++ T R+SLR+LGSVGEPINPEAW WY + +G+ +CP+VDTWWQTETGG Sbjct: 356 IRSLMREGEEPVKKTSRASLRLLGSVGEPINPEAWTWYHRVVGDGRCPIVDTWWQTETGG 415 Query: 421 FMITPLPGATELKAGSATRPFFGVQPALVDNEGNPLEGATEGSLVITD-SWPGQARTLFG 479 +ITPLPGAT LK GSATRPFFGV+P +VD EG LEGA EG+L + + WPGQ RTL+G Sbjct: 416 ILITPLPGATALKPGSATRPFFGVKPVMVDAEGKTLEGAVEGNLCLAEPGWPGQMRTLWG 475 Query: 480 DHERFEQTYFSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAH 539 DHERF+Q+YF+T++ MYF+GDGARRDEDGYYWITGRVDDV+NVSGHR+GTAE+ESALVAH Sbjct: 476 DHERFKQSYFATYQGMYFTGDGARRDEDGYYWITGRVDDVINVSGHRMGTAEVESALVAH 535 Query: 540 PKIAEAAVVGIPHNIKGQAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWT 599 PK+AEAAVVG PH+IKGQ IYAYVTL GEEPS +L E+ NWVRKEIGP+A+PD++ W+ Sbjct: 536 PKVAEAAVVGYPHDIKGQGIYAYVTLVAGEEPSEDLRKELVNWVRKEIGPIASPDLIQWS 595 Query: 600 DSLPKTRSGKIMRRILRKIAAGDTSNLGDTSTLADPGVVEKLLEEK 645 LPKTRSGKIMRRILRKIA D +LGDTSTLADPGVV+ L++ + Sbjct: 596 PGLPKTRSGKIMRRILRKIAENDFGSLGDTSTLADPGVVDDLIDSR 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: 1505 Number of extensions: 59 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: 645 Length adjustment: 38 Effective length of query: 614 Effective length of database: 607 Effective search space: 372698 Effective search space used: 372698 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