Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate PP_4487 PP_4487 acetyl-CoA synthetase
Query= SwissProt::P27550 (652 letters) >FitnessBrowser__Putida:PP_4487 Length = 696 Score = 951 bits (2459), Expect = 0.0 Identities = 446/652 (68%), Positives = 536/652 (82%) Query: 1 MSQIHKHTIPANIADRCLINPQQYEAMYQQSINVPDTFWGEQGKILDWIKPYQKVKNTSF 60 MS + + +A L + Y+AMYQQS+ PD FW EQ + +DWIKP+ KVK TSF Sbjct: 44 MSAAPLYPVRPEVAATTLTDEATYKAMYQQSVINPDGFWREQAQRIDWIKPFTKVKQTSF 103 Query: 61 APGNVSIKWYEDGTLNLAANCLDRHLQENGDRTAIIWEGDDASQSKHISYKELHRDVCRF 120 +V IKW+ DGTLN+++NCLDRHL+E GD+ AIIWEGDD S+ ++I+Y+ELH VC+F Sbjct: 104 DDHHVDIKWFADGTLNVSSNCLDRHLEERGDQLAIIWEGDDPSEHRNITYRELHEQVCKF 163 Query: 121 ANTLLELGIKKGDVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNS 180 AN L + +GDVV IYMPM+PEA VAMLACARIGA+HSV+FGGFSPEA+AGRIID S Sbjct: 164 ANALRGQDVHRGDVVTIYMPMIPEAVVAMLACARIGAIHSVVFGGFSPEALAGRIIDCKS 223 Query: 181 RLVITSDEGVRAGRSIPLKKNVDDALKNPNVTSVEHVVVLKRTGGKIDWQEGRDLWWHDL 240 ++VIT+DEGVR GR PLK NVD AL NP +SV+ ++V KRTGG I W + RD+W+ DL Sbjct: 224 KVVITADEGVRGGRRTPLKANVDLALTNPETSSVQKIIVCKRTGGDIAWHQHRDIWYEDL 283 Query: 241 VEQASDQHQAEEMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDI 300 ++ AS +EM AE+ LFILYTSGSTGKPKGVLHTTGGYLVYAALT + VFDY PG++ Sbjct: 284 MKVASSHCAPKEMGAEEALFILYTSGSTGKPKGVLHTTGGYLVYAALTHERVFDYRPGEV 343 Query: 301 YWCTADVGWVTGHSYLLYGPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTA 360 YWCTADVGWVTGHSY++YGPLA GATTL+FEGVPN+P R++++VDKH+VNILYTAPTA Sbjct: 344 YWCTADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVSKIVDKHKVNILYTAPTA 403 Query: 361 IRALMAEGDKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGG 420 IRA+MAEG A+EG D SSLR+LGSVGEPINPEAW WY+K +G E+CP+VDTWWQTETGG Sbjct: 404 IRAMMAEGQAAVEGADGSSLRLLGSVGEPINPEAWNWYYKTVGKERCPIVDTWWQTETGG 463 Query: 421 FMITPLPGATELKAGSATRPFFGVQPALVDNEGNPLEGATEGSLVITDSWPGQARTLFGD 480 +I+PLPGAT LK GSATRPFFGV PALVDN GN ++GA EG+LVI DSWPGQ+R+L+GD Sbjct: 464 ILISPLPGATGLKPGSATRPFFGVVPALVDNLGNLIDGAAEGNLVILDSWPGQSRSLYGD 523 Query: 481 HERFEQTYFSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHP 540 H+RF TYF TF+ MYF+GDGARRDEDGYYWITGRVDDVLNVSGHR+GTAEIESA+VAH Sbjct: 524 HDRFVDTYFKTFRGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHS 583 Query: 541 KIAEAAVVGIPHNIKGQAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTD 600 K+AEAAVVG+PH+IKGQ IY YVTLN G E S +L E++NWVRKEIGP+A+PDV+ W Sbjct: 584 KVAEAAVVGVPHDIKGQGIYVYVTLNAGIEASEQLRLELKNWVRKEIGPIASPDVIQWAP 643 Query: 601 SLPKTRSGKIMRRILRKIAAGDTSNLGDTSTLADPGVVEKLLEEKQAIAMPS 652 LPKTRSGKIMRRILRKIA G+ LGD STLADPGVV+ L++ +A+ + S Sbjct: 644 GLPKTRSGKIMRRILRKIATGEYDALGDISTLADPGVVQHLIDTHKAMNLAS 695 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: 1570 Number of extensions: 66 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: 696 Length adjustment: 39 Effective length of query: 613 Effective length of database: 657 Effective search space: 402741 Effective search space used: 402741 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