Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate Synpcc7942_1352 Synpcc7942_1352 acetyl-CoA synthetase
Query= SwissProt::P31638 (660 letters) >FitnessBrowser__SynE:Synpcc7942_1352 Length = 656 Score = 758 bits (1956), Expect = 0.0 Identities = 376/658 (57%), Positives = 480/658 (72%), Gaps = 12/658 (1%) Query: 4 IESVMQEHRVFNPPEGFASQAAIPSMEAYQALCDEAERDYEGFWARHARELLHWTKPFTK 63 IES++QE RVF P FAS A I + EAY+ALC +A D FW A + L W +P+ + Sbjct: 6 IESILQEKRVFPPSAEFASAARI-NPEAYEALCQKAAADPVAFWGELAAQELDWFEPWQQ 64 Query: 64 VLDQSNAPFYKWFEDGELNASYNCLDRNLQNGNADKVAIVFEADDGSVTRVTYRELHGKV 123 LD SN PF KWF G+LN S+NCLDR+L +K AI++E + G +TY +LH +V Sbjct: 65 TLDWSNPPFAKWFVGGKLNISHNCLDRHLTTWRKNKAAIIWEGEPGDSRTLTYAQLHREV 124 Query: 124 CRFANGLKALGIRKGDRVVIYMPMSVEGVVAMQACARLGATHSVVFGGFSAKSLQERLVD 183 C+FAN LK+LGI+KGD V +YMPM E +AM ACAR+GA HSVVFGGFSA++L++RLVD Sbjct: 125 CQFANVLKSLGIQKGDVVGVYMPMIPEAAIAMLACARIGAVHSVVFGGFSAEALRDRLVD 184 Query: 184 VGAVALITADEQMRGGKALPLKAIADDALALGGCEAVRNVIVYRRTGGKVAWTEGRDRWM 243 A ++TAD R +PLK D AL C +V++V+V RT + GRD W Sbjct: 185 GQAKLVVTADGGWRKDAIVPLKDSVDQALEGNACPSVQHVLVVERTKQDIHMEPGRDHWW 244 Query: 244 EDVSAGQPDTCEAEPVSAEHPLFVLYTSGSTGKPKGVQHSTGGYLLWALMTMKWTFDIKP 303 ++ TC AEP+ +E LFVLYTSGSTGKPKGV H+TGGY L+A +T +WTFD++ Sbjct: 245 HELQQTVSATCPAEPMDSEDLLFVLYTSGSTGKPKGVVHTTGGYNLYAHITTQWTFDLQD 304 Query: 304 DDLFWCTADIGWVTGHTYIAYGPLAAGATQVVFEGVPTYPNAGRFWDMIARHKVSIFYTA 363 D++WCTAD+GW+TGH+YI YGPL+ GAT +++EG P N G FWD+I ++ V+ FYTA Sbjct: 305 TDVYWCTADVGWITGHSYIVYGPLSNGATTLMYEGAPRASNPGCFWDVIEKYGVTTFYTA 364 Query: 364 PTAIRSLIKAAEADEKIHPKQYDLSSLRLLGTVGEPINPEAWMWYYKNIGNERCPIVDTF 423 PTAIR+ IK E HP DLSSLRLLGTVGEPINPEAW+WY++ IG +RCPIVDT+ Sbjct: 365 PTAIRAFIKMGEQ----HPAARDLSSLRLLGTVGEPINPEAWIWYHRVIGGDRCPIVDTW 420 Query: 424 WQTETGGHMITPLPGATPLVPGSCTLPLPGIMAAIVDETGHDVPNGNGGILVVKRPWPAM 483 WQTETGGHMIT LPGA P PGS T P PGI+A +VD G VP+ GG LV++ PWP M Sbjct: 421 WQTETGGHMITSLPGAVPTKPGSATKPFPGILADVVDLDGRSVPDNEGGYLVIRHPWPGM 480 Query: 484 IRTIWGDPERFRKSYF---PEELGGKLYLAGDGSIRDKDTGYFTIMGRIDDVLNVSGHRM 540 +RT++GDP+RFR++Y+ P + G LY AGDG+ RD D GYF +MGR+DDV+NVSGHR+ Sbjct: 481 MRTVYGDPDRFRRTYWEHIPPQNGQYLYFAGDGARRDAD-GYFWVMGRVDDVINVSGHRL 539 Query: 541 GTMEIESALVSNPLVAEAAVVGRPDDMTGEAICAFVVLKRSRPTGEEAVKIATELRNWVG 600 GTMEIESALVS+P VAEAAVVGRPDD+ GE I AF+ L+ TG+E VK +L+ V Sbjct: 540 GTMEIESALVSHPAVAEAAVVGRPDDLKGEGIVAFITLESGIETGDELVK---DLKKHVA 596 Query: 601 KEIGPIAKPKDIRFGDNLPKTRSGKIMRRLLRSLAKGEEITQDTSTLENPAILEQLKQ 658 +EIG IA+P +IRF + LPKTRSGKIMRRLLRSLA G+E++ DTSTLE+ ++L++L+Q Sbjct: 597 QEIGAIARPDEIRFSEALPKTRSGKIMRRLLRSLAAGQEVSGDTSTLEDRSVLDKLRQ 654 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: 1408 Number of extensions: 67 Number of successful extensions: 6 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: 656 Length adjustment: 38 Effective length of query: 622 Effective length of database: 618 Effective search space: 384396 Effective search space used: 384396 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 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