Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate 2629598430 Ga0074568_11495 acetyl-coenzyme A synthetase
Query= SwissProt::P31638 (660 letters) >IMG__TrieryIMS101_FD:2629598430 Length = 655 Score = 730 bits (1884), Expect = 0.0 Identities = 361/657 (54%), Positives = 472/657 (71%), Gaps = 13/657 (1%) Query: 4 IESVMQEHRVFNPPEGFASQAAIPSMEAYQALCDEAERDYEGFWARHARELLHWTKPFTK 63 IES++QE R+F PPE F A I +E Y+ L ++A+ + E FWA A L W + + K Sbjct: 6 IESILQEKRLFQPPEKFVQTAQIKGIEQYKELYEKAKSNPEEFWAELAETELDWFQKWDK 65 Query: 64 VLDQSNAPFYKWFEDGELNASYNCLDRNLQNGNADKVAIVFEADDGSVTRVTYRELHGKV 123 VL+ PF KWF +G++N SYNCLDR+L +K A+++E + G +TY +LH +V Sbjct: 66 VLEWQ-PPFAKWFINGKINISYNCLDRHLTTWRRNKAALIWEGEPGDSRTITYAQLHREV 124 Query: 124 CRFANGLKALGIRKGDRVVIYMPMSVEGVVAMQACARLGATHSVVFGGFSAKSLQERLVD 183 C+ AN K LG++KGDRV IYMPM E +AM ACAR+GA H+VVFGGFSA +L+ RLVD Sbjct: 125 CQMANVFKQLGVKKGDRVGIYMPMIPEAAIAMLACARIGAPHTVVFGGFSADALKNRLVD 184 Query: 184 VGAVALITADEQMRGGKALPLKAIADDALALGGCEAVRNVIVYRRTGGKVAWTEGRDRWM 243 A ++TAD R +PLK D AL + G +V NV+V +RT K+ GRD W Sbjct: 185 AEAKLVVTADGGWRKDAIVPLKEQVDKAL-MAGAPSVENVLVVKRTAQKIQMEPGRDHWW 243 Query: 244 EDVSAGQPDTCEAEPVSAEHPLFVLYTSGSTGKPKGVQHSTGGYLLWALMTMKWTFDIKP 303 D+ C AEP+ +E LF+LYTSG+TG PKGV H+TGGY L+ +T KW FD++ Sbjct: 244 HDLQKSASGECPAEPMDSEDMLFILYTSGTTGTPKGVVHTTGGYNLYTHVTNKWAFDLQD 303 Query: 304 DDLFWCTADIGWVTGHTYIAYGPLAAGATQVVFEGVPTYPNAGRFWDMIARHKVSIFYTA 363 D++WCTAD+GW+TGH+YI YGPL+ GAT +++EG P N G WD++ ++ V+IFYTA Sbjct: 304 TDVYWCTADVGWITGHSYIVYGPLSNGATTLMYEGAPRASNPGCLWDVVEKYGVTIFYTA 363 Query: 364 PTAIRSLIKAAEADEKIHPKQYDLSSLRLLGTVGEPINPEAWMWYYKNIGNERCPIVDTF 423 PTAIR+L+K E HP +L+SLRLLGTVGEPINPEAW+WY++ IG+ +CPIVDT+ Sbjct: 364 PTAIRALMKMGEQ----HPNSRNLTSLRLLGTVGEPINPEAWIWYHRVIGDSKCPIVDTW 419 Query: 424 WQTETGGHMITPLPGATPLVPGSCTLPLPGIMAAIVDETGHDVPNGNGGILVVKRPWPAM 483 WQTETGG MITPLPGATP PGS T P PGI+A IV+E G V NGG LVVK PWP M Sbjct: 420 WQTETGGFMITPLPGATPTKPGSATFPFPGIIADIVNEEGESVDGNNGGYLVVKHPWPGM 479 Query: 484 IRTIWGDPERFRKSYFP---EELGGKLYLAGDGSIRDKDTGYFTIMGRIDDVLNVSGHRM 540 +RT++GDP+RFR++Y+ + G +Y AGDG+ +D+D GYF +MGR+DDV+NV+GHR+ Sbjct: 480 MRTVYGDPDRFRRTYWEYLRPKNGEYIYFAGDGAHKDED-GYFWVMGRVDDVINVAGHRL 538 Query: 541 GTMEIESALVSNPLVAEAAVVGRPDDMTGEAICAFVVLKRSRPTGEEAVKIATELRNWVG 600 GTME+ESALVS+P VAEAAVVG+PD++ GE I AFV L+ R E K EL+ V Sbjct: 539 GTMEVESALVSHPAVAEAAVVGKPDEVKGEDIVAFVSLEGGREPDENLEK---ELKQHVV 595 Query: 601 KEIGPIAKPKDIRFGDNLPKTRSGKIMRRLLRSLAKGEEITQDTSTLENPAILEQLK 657 KEIG IA+P +IRF D+LPKTRSGKIMRRLLRSLA G+EIT DTSTL++ ++L++L+ Sbjct: 596 KEIGAIARPGEIRFTDDLPKTRSGKIMRRLLRSLAAGQEITGDTSTLQDRSVLDKLR 652 Lambda K H 0.319 0.136 0.422 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: 1419 Number of extensions: 73 Number of successful extensions: 7 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: 660 Length of database: 655 Length adjustment: 38 Effective length of query: 622 Effective length of database: 617 Effective search space: 383774 Effective search space used: 383774 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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