Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate GFF1279 PGA1_c12950 acetyl-coenzyme A synthetase Acs
Query= SwissProt::P27550 (652 letters) >FitnessBrowser__Phaeo:GFF1279 Length = 695 Score = 830 bits (2145), Expect = 0.0 Identities = 396/633 (62%), Positives = 483/633 (76%), Gaps = 5/633 (0%) Query: 16 RCLINPQQYEAMYQQSINVPDTFWGEQGKILDWIKPYQKVKNTSFAPGNVSIKWYEDGTL 75 R +N QY+ MY S+ P+ FW +Q + +DWIKP+ +VK+ F GNVSI WY DGTL Sbjct: 61 RAHVNAAQYDEMYAASMQDPEGFWRQQAERIDWIKPFTQVKDVDFTLGNVSINWYADGTL 120 Query: 76 NLAANCLDRHLQENGDRTAIIWEGDDASQS-KHISYKELHRDVCRFANTLLELGIKKGDV 134 N+AANC+DRHL GD+TAIIWE D ++ +HISYK+LH VCR AN L +G++KGD Sbjct: 121 NVAANCIDRHLDTRGDQTAIIWEPDSPDEAAQHISYKQLHTRVCRMANVLETMGVRKGDR 180 Query: 135 VAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNSRLVITSDEGVRAGR 194 V IY+PM+PEAA AMLACARIGA+HS++F GFSP+A+A R+ +++++IT+DE R GR Sbjct: 181 VVIYLPMIPEAAYAMLACARIGAIHSIVFAGFSPDALAARVNGCDAKVLITADEAPRGGR 240 Query: 195 SIPLKKNVDDALKNPNVTSVEHVVVLKRTGGKIDWQEGRDLWWHDLVEQASDQHQAEEMN 254 PLK N D AL + T +V+KRTGG+ W +GRD ++++ +A D + EMN Sbjct: 241 KTPLKSNADAALLHTKDTV--KCLVVKRTGGQTTWIDGRDYDYNEMALEADDYSKPAEMN 298 Query: 255 AEDPLFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDIYWCTADVGWVTGHS 314 AEDPLFILYTSGSTG+PKGV+HTTGGYL YAA+T + FDYH GDIYWCTADVGWVTGHS Sbjct: 299 AEDPLFILYTSGSTGQPKGVVHTTGGYLTYAAMTHEITFDYHDGDIYWCTADVGWVTGHS 358 Query: 315 YLLYGPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTAIRALMAEGDKAIEG 374 Y++YGPLA GATTLMFEGVP +P +R QV DKH+V YTAPTA+RALM +G++ +E Sbjct: 359 YIVYGPLANGATTLMFEGVPTYPDASRFWQVCDKHKVTQFYTAPTALRALMGQGNEWVEK 418 Query: 375 TDRSSLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGGFMITPLPGATELKA 434 D SSLR LG+VGEPINPEAW WY +G KCP+VDTWWQTETGG ++TPLPGA K Sbjct: 419 CDLSSLRTLGTVGEPINPEAWNWYNDIVGKGKCPIVDTWWQTETGGHLMTPLPGAHATKP 478 Query: 435 GSATRPFFGVQPALVD-NEGNPLEG-ATEGSLVITDSWPGQARTLFGDHERFEQTYFSTF 492 G+A +PFFGV P ++D G + G EG L I DSWPGQ RT++GDHERFE+TYFS + Sbjct: 479 GAAMKPFFGVAPVVLDPQSGEEITGNGVEGVLCIKDSWPGQMRTVWGDHERFEKTYFSDY 538 Query: 493 KNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHPKIAEAAVVGIPH 552 K YF+GDG RRDEDG YWITGRVDDV+NVSGHR+GTAE+ESALVAH +AEAAVVG PH Sbjct: 539 KGYYFTGDGCRRDEDGDYWITGRVDDVINVSGHRMGTAEVESALVAHAAVAEAAVVGYPH 598 Query: 553 NIKGQAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTDSLPKTRSGKIMR 612 IKGQ IY YVTL + EPS EL E+R WVR EIGP+A+PDV+ W LPKTRSGKIMR Sbjct: 599 EIKGQGIYCYVTLMNDREPSDELVKELRTWVRTEIGPIASPDVIQWAPGLPKTRSGKIMR 658 Query: 613 RILRKIAAGDTSNLGDTSTLADPGVVEKLLEEK 645 RILRKIA D +LGDTSTLADP VV+ L+ + Sbjct: 659 RILRKIAENDFGSLGDTSTLADPSVVDDLIANR 691 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: 1525 Number of extensions: 64 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: 695 Length adjustment: 39 Effective length of query: 613 Effective length of database: 656 Effective search space: 402128 Effective search space used: 402128 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