Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate PP_4702 PP_4702 acetyl-CoA synthetase
Query= SwissProt::P27550 (652 letters) >FitnessBrowser__Putida:PP_4702 Length = 644 Score = 839 bits (2167), Expect = 0.0 Identities = 389/645 (60%), Positives = 487/645 (75%), Gaps = 4/645 (0%) Query: 1 MSQIHKHTIPANIADRCLINPQQYEAMYQQSINVPDTFWGEQGKILDWIKPYQKVKNTSF 60 M I K+ ++ + P+ Y +Y+QS+ PDTFW EQ K LDWIKP+ V+ Sbjct: 1 MFDIRKYPQALAVSQSAALTPEDYRRLYRQSVEDPDTFWAEQAKRLDWIKPWSSVQQCDL 60 Query: 61 APGNVSIKWYEDGTLNLAANCLDRHLQENGDRTAIIWEGDDASQSKHISYKELHRDVCRF 120 G +W++ LN++ NC+DRHL + G++TA++WEGDD SK I+Y+ELHR VCR Sbjct: 61 HTGKA--RWFDGAQLNVSYNCIDRHLAQRGEQTALLWEGDDPKDSKAITYRELHRQVCRL 118 Query: 121 ANTLLELGIKKGDVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNS 180 AN + G+KKGD V+IYMPM+PEAA AMLAC RIGA+HSV+FGGFSP+A+ RI+D++ Sbjct: 119 ANAMKARGVKKGDRVSIYMPMIPEAAFAMLACTRIGAIHSVVFGGFSPDALRDRILDADC 178 Query: 181 RLVITSDEGVRAGRSIPLKKNVDDALKNPNVTSVEHVVVLKRTGGKIDWQEGRDLWWHDL 240 R VIT+DEGVR G+ IPLK+NVD AL + +V V+V++RTGG + W EGRDLW+H+ Sbjct: 179 RTVITADEGVRGGKRIPLKQNVDKALAS--CPAVSSVLVVRRTGGDVAWTEGRDLWYHEA 236 Query: 241 VEQASDQHQAEEMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDI 300 + A D E M AEDPLFILYTSGSTGKPKGVLHTTGGYL+ A +TFK VFDY G++ Sbjct: 237 TKDAGDDCPPEPMEAEDPLFILYTSGSTGKPKGVLHTTGGYLLQATMTFKVVFDYRDGEV 296 Query: 301 YWCTADVGWVTGHSYLLYGPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTA 360 +WCTADVGWVTGHSY++YGPLA GA +LMFEGVPN+P +R QVVDKHQVNI YTAPTA Sbjct: 297 FWCTADVGWVTGHSYIVYGPLANGAISLMFEGVPNYPDTSRFWQVVDKHQVNIFYTAPTA 356 Query: 361 IRALMAEGDKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGG 420 +RALM EG ++ T R SLR+LGSVGEPINPEAWEWY++++G ++CP+VDTWWQTETGG Sbjct: 357 LRALMREGSAPLQSTSRKSLRLLGSVGEPINPEAWEWYFEEVGQKRCPIVDTWWQTETGG 416 Query: 421 FMITPLPGATELKAGSATRPFFGVQPALVDNEGNPLEGATEGSLVITDSWPGQARTLFGD 480 M+TPLPG LK G AT+P FGVQP L+D +G +EG G L I SWPGQ R+++GD Sbjct: 417 IMLTPLPGTQSLKPGCATQPMFGVQPVLLDEKGKLIEGPGAGVLAIKASWPGQIRSVYGD 476 Query: 481 HERFEQTYFSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHP 540 H+R TYF YF+GDGARRD DG YWITGR+DDV+NVSGHR+GTAE+ESALV H Sbjct: 477 HQRMVDTYFKPLPGYYFTGDGARRDADGDYWITGRIDDVINVSGHRIGTAEVESALVLHD 536 Query: 541 KIAEAAVVGIPHNIKGQAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTD 600 +AEAAVVG PH++KGQ +YA+VT +G P L AE+ V KEIG A P+++ W Sbjct: 537 SVAEAAVVGYPHDLKGQGVYAFVTTMNGVTPDDTLKAELLALVSKEIGSFAKPELIQWAP 596 Query: 601 SLPKTRSGKIMRRILRKIAAGDTSNLGDTSTLADPGVVEKLLEEK 645 +LPKTRSGKIMRRILRKIA + NLGDTSTLADP VV+ L++++ Sbjct: 597 ALPKTRSGKIMRRILRKIACNELENLGDTSTLADPSVVQGLIDKR 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: 1413 Number of extensions: 59 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: 644 Length adjustment: 38 Effective length of query: 614 Effective length of database: 606 Effective search space: 372084 Effective search space used: 372084 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