Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_057507083.1 ABB28_RS02385 acetate--CoA ligase
Query= SwissProt::P27550 (652 letters) >NCBI__GCF_001431535.1:WP_057507083.1 Length = 647 Score = 852 bits (2201), Expect = 0.0 Identities = 397/641 (61%), Positives = 497/641 (77%), Gaps = 1/641 (0%) Query: 7 HTIPANIADRCLINPQQYEAMYQQSINVPDTFWGEQGKILDWIKPYQKVKNTSFAPGNVS 66 + + A I+ Y+ YQ SI+ PD FWGE + L W K +KN S+ + Sbjct: 5 YPVDPQFAKNARIDKTTYQQQYQASIDAPDAFWGEAAQRLQWFKQPSIIKNVSYDLADFR 64 Query: 67 IKWYEDGTLNLAANCLDRHLQENGDRTAIIWEGDDA-SQSKHISYKELHRDVCRFANTLL 125 IKW+EDG LN + NCLDR L++ G++TA+++E D + ++H++Y+EL+ CR N L Sbjct: 65 IKWFEDGELNASVNCLDRQLEKRGEKTALLFEPDSPDAPAQHVTYRELYERTCRLGNALR 124 Query: 126 ELGIKKGDVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNSRLVIT 185 LG+KKGD V IY+PM+ +AAVAMLACARIGA+HSV+FGGF+P ++A R+ D S+L+IT Sbjct: 125 NLGVKKGDRVTIYLPMIVDAAVAMLACARIGAIHSVVFGGFAPNSIADRVSDCASKLIIT 184 Query: 186 SDEGVRAGRSIPLKKNVDDALKNPNVTSVEHVVVLKRTGGKIDWQEGRDLWWHDLVEQAS 245 +DEG+R G+ IPLK NVD ALK P +VE V+V++ TGG +D Q RD W+HD+V+ Sbjct: 185 ADEGLRGGKKIPLKANVDAALKLPGTNTVETVLVVRHTGGAVDMQAPRDRWFHDVVDSQP 244 Query: 246 DQHQAEEMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDIYWCTA 305 + + E MNAEDPLFILYTSGSTGKPKGVLHTTGGYL+YAA T + VFD DIYWCTA Sbjct: 245 AECEPERMNAEDPLFILYTSGSTGKPKGVLHTTGGYLLYAAYTHEAVFDLREDDIYWCTA 304 Query: 306 DVGWVTGHSYLLYGPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTAIRALM 365 DVGWVTGHSY++YGPLA GAT+LMFEGVPN+P +R V+DKH+V++ YTAPTAIRALM Sbjct: 305 DVGWVTGHSYIVYGPLANGATSLMFEGVPNYPDTSRFWNVIDKHKVSLFYTAPTAIRALM 364 Query: 366 AEGDKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGGFMITP 425 EG++ ++ T R+SLR+LGSVGEPINPEAW WY++ +G+ +CP+VDTWWQTETGG +I+P Sbjct: 365 REGEEPVKRTSRASLRLLGSVGEPINPEAWRWYYEVVGDSRCPIVDTWWQTETGGILISP 424 Query: 426 LPGATELKAGSATRPFFGVQPALVDNEGNPLEGATEGSLVITDSWPGQARTLFGDHERFE 485 LPGA +LK GSA+ PFFGVQPALV+ +G +GATEG+L+I DSWPGQ RT++GD +RF Sbjct: 425 LPGAVDLKPGSASLPFFGVQPALVNADGEIKDGATEGNLIIRDSWPGQMRTVYGDDQRFI 484 Query: 486 QTYFSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHPKIAEA 545 TYF T+ YF+GDG RRDEDGYYWITGRVDDV+NVSGHR+GTAE+ESALV+HPK+AEA Sbjct: 485 DTYFRTYPGAYFTGDGCRRDEDGYYWITGRVDDVINVSGHRIGTAEVESALVSHPKVAEA 544 Query: 546 AVVGIPHNIKGQAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTDSLPKT 605 AVVG PH +KGQ IYAYVTL E PS EL+ E+ WVRKEIGP+ATPD L W LPKT Sbjct: 545 AVVGFPHEVKGQGIYAYVTLIADEAPSEELHKELVAWVRKEIGPIATPDHLQWAPGLPKT 604 Query: 606 RSGKIMRRILRKIAAGDTSNLGDTSTLADPGVVEKLLEEKQ 646 RSGKIMRRILRKIA LGDTSTLADP VV L++E++ Sbjct: 605 RSGKIMRRILRKIAENAPDQLGDTSTLADPSVVASLVDERK 645 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: 1387 Number of extensions: 63 Number of successful extensions: 2 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: 647 Length adjustment: 38 Effective length of query: 614 Effective length of database: 609 Effective search space: 373926 Effective search space used: 373926 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 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