Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate N515DRAFT_3075 N515DRAFT_3075 acetyl-coenzyme A synthetase (EC 6.2.1.1)
Query= SwissProt::P27550 (652 letters) >FitnessBrowser__Dyella79:N515DRAFT_3075 Length = 646 Score = 883 bits (2281), Expect = 0.0 Identities = 411/639 (64%), Positives = 508/639 (79%) Query: 7 HTIPANIADRCLINPQQYEAMYQQSINVPDTFWGEQGKILDWIKPYQKVKNTSFAPGNVS 66 + + A + I+ + YE +Y++S+ P+ FWG G+ L+W + K+KN S+ P N+ Sbjct: 5 YPVKPEFAAKARISKEDYERLYEESVRDPEGFWGRIGERLEWHRKPSKIKNVSYDPKNLH 64 Query: 67 IKWYEDGTLNLAANCLDRHLQENGDRTAIIWEGDDASQSKHISYKELHRDVCRFANTLLE 126 I+WYEDG LN++ANCLDRHL GD+TAII+EGDD ++S+H++Y+ELH +VC+FANTL Sbjct: 65 IRWYEDGELNVSANCLDRHLASRGDKTAIIFEGDDPNESRHLTYRELHAEVCKFANTLKN 124 Query: 127 LGIKKGDVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNSRLVITS 186 LG+ KGD VAIYMPM+PEAAVAMLACARIGAVHSV+FGGFSP+++AGRI DS +++V+T+ Sbjct: 125 LGVAKGDRVAIYMPMIPEAAVAMLACARIGAVHSVVFGGFSPDSLAGRIADSTAKVVVTA 184 Query: 187 DEGVRAGRSIPLKKNVDDALKNPNVTSVEHVVVLKRTGGKIDWQEGRDLWWHDLVEQASD 246 DEGVR G+ IPLK NVD AL+ P SVE V+V++RTG + Q RD ++H L+E S Sbjct: 185 DEGVRGGKKIPLKANVDAALERPGTNSVETVIVVRRTGSAVPMQSPRDRYYHVLMEGQSA 244 Query: 247 QHQAEEMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDIYWCTAD 306 + AE PLFILYTSGSTGKPKGVLHT+GGYLV+A T + VFD D+YWCTAD Sbjct: 245 DCPPTPVEAEHPLFILYTSGSTGKPKGVLHTSGGYLVFAGFTHEMVFDLREDDVYWCTAD 304 Query: 307 VGWVTGHSYLLYGPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTAIRALMA 366 VGWVTGHSY++YGPLA GATT+MF+GVPN+P +R VVDKH+V + YTAPTAIRALM Sbjct: 305 VGWVTGHSYVVYGPLANGATTVMFDGVPNYPDTSRFWNVVDKHKVTLFYTAPTAIRALMR 364 Query: 367 EGDKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGGFMITPL 426 EG+ ++ R+SLR+LGSVGEPINPEAWEWY++ +G+E+CP+VDTWWQTETGG MITPL Sbjct: 365 EGEAPVKKASRASLRLLGSVGEPINPEAWEWYYRVVGDERCPIVDTWWQTETGGIMITPL 424 Query: 427 PGATELKAGSATRPFFGVQPALVDNEGNPLEGATEGSLVITDSWPGQARTLFGDHERFEQ 486 GA + K GSAT+PFFG++PA+VD G LEGATEG+LVI DSWPGQ RT++GDH+RF + Sbjct: 425 AGAIDAKPGSATKPFFGIRPAVVDAGGAVLEGATEGNLVIADSWPGQMRTVYGDHQRFVE 484 Query: 487 TYFSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHPKIAEAA 546 TYF+ + YF+GDG RRDEDGYYWITGRVDDV+NVSGHR+GTAE+ESALV+HPK+AEAA Sbjct: 485 TYFTAYPGNYFTGDGVRRDEDGYYWITGRVDDVINVSGHRIGTAEVESALVSHPKVAEAA 544 Query: 547 VVGIPHNIKGQAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTDSLPKTR 606 VVG PH IKGQ IYAYVTL GE+ S EL E+ WVRKEIGP+ATPD L W LPKTR Sbjct: 545 VVGCPHEIKGQGIYAYVTLIAGEQGSDELRKELVAWVRKEIGPIATPDYLQWAPGLPKTR 604 Query: 607 SGKIMRRILRKIAAGDTSNLGDTSTLADPGVVEKLLEEK 645 SGKIMRRILRKI LGD STLADP VV+ L+EE+ Sbjct: 605 SGKIMRRILRKIGENQPDQLGDISTLADPSVVKNLVEER 643 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: 1438 Number of extensions: 60 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: 646 Length adjustment: 38 Effective length of query: 614 Effective length of database: 608 Effective search space: 373312 Effective search space used: 373312 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