Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_046009377.1 OLEAN_RS11725 acetate--CoA ligase
Query= SwissProt::P27550 (652 letters) >NCBI__GCF_000967895.1:WP_046009377.1 Length = 653 Score = 957 bits (2474), Expect = 0.0 Identities = 449/650 (69%), Positives = 540/650 (83%), Gaps = 5/650 (0%) Query: 1 MSQIHKHTIPANIADRCLINPQQYEAMYQQSINVPDTFWGEQGKILDWIKPYQKVKNTSF 60 MS I ++ + NI L+N QYEAMY++SI+ + FW EQGK +DWI+P+ +V++ SF Sbjct: 1 MSDIKRYPVKENIGLTTLVNNDQYEAMYKRSIDDSEGFWAEQGKRIDWIEPFTQVRDISF 60 Query: 61 APGNVSIKWYEDGTLNLAANCLDRHLQENGDRTAIIWEGDDASQSKHISYKELHRDVCRF 120 V+I WY+DGTLN +ANCLDRHL GD+TAIIWEGD+ + +HISYKELH +VC+F Sbjct: 61 DEHKVNINWYKDGTLNASANCLDRHLATRGDQTAIIWEGDEPTDDRHISYKELHGEVCQF 120 Query: 121 ANTLLELGIKKGDVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNS 180 AN L G++KGDVV IYMPMVP+A VAMLACARIGA+HSV+FGGFSP+A+AGRI DS Sbjct: 121 ANALKTQGVRKGDVVCIYMPMVPQAVVAMLACARIGAIHSVVFGGFSPDALAGRIDDSQV 180 Query: 181 RLVITSDEGVRAGRSIPLKKNVDDALKNPNVTSVEHVVVLKRTGGKIDWQEGRDLWWHDL 240 ++VIT+DEGVR G+++PLK+NVD+AL +P+V +VE V+V+KRTG IDW RD+W+HD Sbjct: 181 KVVITADEGVRGGKTVPLKENVDEALTHPSVNTVEKVIVVKRTGANIDWHRSRDIWYHDA 240 Query: 241 VEQASDQHQAEEMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDI 300 + + S Q EM AEDPLFILYTSGSTGKPKGV+HTTGGY+VYA+LT +YVFDY G++ Sbjct: 241 IAKESKHCQPAEMRAEDPLFILYTSGSTGKPKGVVHTTGGYMVYASLTHEYVFDYQEGEV 300 Query: 301 YWCTADVGWVTGHSYLLYGPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTA 360 YWCTADVGW+TGH+YL+YGPLA GAT+LM EG+PN+P R++QVVDKH VNILYTAPTA Sbjct: 301 YWCTADVGWITGHTYLVYGPLANGATSLMCEGLPNYPNINRVSQVVDKHGVNILYTAPTA 360 Query: 361 IRALMAEGDKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGG 420 IRALMAEGD A+ T R SLR+LG+VGEPINPEAWEWY++ IG E+CP+VDTWWQTETGG Sbjct: 361 IRALMAEGDAAVTETKRHSLRVLGTVGEPINPEAWEWYYRTIGEERCPIVDTWWQTETGG 420 Query: 421 FMITPLPGATELKAGSATRPFFGVQPALVDNEGNPLEGATEGSLVITDSWPGQARTLFGD 480 MITPLPGAT LK GSATRPFFGVQPALVD EGN +EG EG+LVI DSWPGQ+RTL+GD Sbjct: 421 IMITPLPGATTLKPGSATRPFFGVQPALVDAEGNIVEGVGEGNLVILDSWPGQSRTLYGD 480 Query: 481 HERFEQTYFSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHP 540 HERF QTYFST+ MYF+GDGARRDEDGYYWITGRVDDVLNVSGHR+GTAEIESALVAHP Sbjct: 481 HERFMQTYFSTYAGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESALVAHP 540 Query: 541 KIAEAAVVGIPHNIKGQAIYAYVTLNHGE-----EPSPELYAEVRNWVRKEIGPLATPDV 595 K+AEAAVVG PH+IKGQ IY YVTLN GE E + L E++ WVR++IGP+ATPD+ Sbjct: 541 KVAEAAVVGYPHDIKGQGIYVYVTLNKGELSADKEVNDALVLELKKWVRQDIGPIATPDL 600 Query: 596 LHWTDSLPKTRSGKIMRRILRKIAAGDTSNLGDTSTLADPGVVEKLLEEK 645 + T LPKTRSGKIMRRILRKIA + LGDTSTLADP VV++L+E++ Sbjct: 601 IQLTSGLPKTRSGKIMRRILRKIAENECGALGDTSTLADPAVVDELIEQR 650 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: 1459 Number of extensions: 55 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: 653 Length adjustment: 38 Effective length of query: 614 Effective length of database: 615 Effective search space: 377610 Effective search space used: 377610 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