Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate AO353_14365 AO353_14365 acetyl-CoA synthetase
Query= SwissProt::P27550 (652 letters) >FitnessBrowser__pseudo3_N2E3:AO353_14365 Length = 645 Score = 814 bits (2103), Expect = 0.0 Identities = 383/628 (60%), Positives = 484/628 (77%), Gaps = 5/628 (0%) Query: 19 INPQQYEAMYQQSINVPDTFWGEQGK-ILDWIKPYQKVKNTSFAPGNVSIKWYEDGTLNL 77 ++ Y+ +Y+QSI PD FW EQ K LDW P+Q V++T+ G + +W+ LN+ Sbjct: 19 LSQDDYQRLYRQSIEQPDVFWAEQAKRFLDWSTPWQSVQHTNIKTG--AAQWFAGAQLNV 76 Query: 78 AANCLDRHLQENGDRTAIIWEGDDASQSKHISYKELHRDVCRFANTLLELGIKKGDVVAI 137 + NC+DRHL + G++TAIIWEGDD ++S HI+Y++LH VCR AN L G+KKGD V I Sbjct: 77 SYNCIDRHLAQRGEQTAIIWEGDDPAESLHITYQKLHHCVCRLANVLKSRGVKKGDRVCI 136 Query: 138 YMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNSRLVITSDEGVRAGRSIP 197 YMPM+PEAA AMLACARIGAVHSV+FGGFSP+++ RI+D++ R VIT+DEGVR G+ +P Sbjct: 137 YMPMIPEAAYAMLACARIGAVHSVVFGGFSPDSLRDRILDADCRTVITADEGVRGGKYVP 196 Query: 198 LKKNVDDALKNPNVTSVEHVVVLKRTGGKIDWQEGRDLWWHDLVEQASDQHQAEEMNAED 257 LK+NVD AL + +V VVV++ T +++W EGRDLW+H + SD E M+AED Sbjct: 197 LKQNVDKALLS--CPAVSTVVVVEHTQIEVNWVEGRDLWYHQALRDVSDDCPPEPMDAED 254 Query: 258 PLFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDIYWCTADVGWVTGHSYLL 317 PLFILYTSGSTGKPKGVLHTTGGYL+ AA+TFKYVFDY G+++WCTADVGWVTGHSY++ Sbjct: 255 PLFILYTSGSTGKPKGVLHTTGGYLLQAAMTFKYVFDYRDGEVFWCTADVGWVTGHSYIV 314 Query: 318 YGPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTAIRALMAEGDKAIEGTDR 377 YGPLA GATTL+FEGVP++P +R QV+DKHQVNI YTAPTA+RALM EG + ++ + R Sbjct: 315 YGPLANGATTLIFEGVPSYPNSSRFWQVIDKHQVNIFYTAPTALRALMREGLEPLKDSSR 374 Query: 378 SSLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGGFMITPLPGATELKAGSA 437 +SLR+LGSVGEPINPEAW+WY+ +G ++CP+VDTWWQTETGG M++PL A +K G A Sbjct: 375 ASLRLLGSVGEPINPEAWDWYFNAVGEQRCPIVDTWWQTETGGIMLSPLVSAQRIKPGCA 434 Query: 438 TRPFFGVQPALVDNEGNPLEGATEGSLVITDSWPGQARTLFGDHERFEQTYFSTFKNMYF 497 TRP FGVQP L+D G + GA G L I SWPGQ R+++GD +R TYF + YF Sbjct: 435 TRPMFGVQPVLLDEHGKEISGAGSGVLAIKSSWPGQIRSVYGDPQRMIDTYFKPYPGYYF 494 Query: 498 SGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHPKIAEAAVVGIPHNIKGQ 557 +GDGARRDEDG YWITGR+DDV+NVSGHR+GTAE+ESALV H IAEAAVVG PH++KGQ Sbjct: 495 TGDGARRDEDGDYWITGRIDDVINVSGHRIGTAEVESALVLHDSIAEAAVVGYPHDLKGQ 554 Query: 558 AIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTDSLPKTRSGKIMRRILRK 617 IYA+VT +G EPS L E+ V +EIG A PD++ W +LPKTRSGKIMRRILRK Sbjct: 555 GIYAFVTPMNGIEPSDALKKELLAHVSQEIGSFAKPDLIQWAPALPKTRSGKIMRRILRK 614 Query: 618 IAAGDTSNLGDTSTLADPGVVEKLLEEK 645 IA + +LGDTSTLADP VV L++++ Sbjct: 615 IACNELDSLGDTSTLADPSVVAGLIDKR 642 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: 1373 Number of extensions: 54 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 Apr 09 2024. The underlying query database was built on Apr 09 2024.
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