Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate 8499484 DvMF_0256 AMP-dependent synthetase and ligase (RefSeq)
Query= SwissProt::P31638 (660 letters) >FitnessBrowser__Miya:8499484 Length = 583 Score = 124 bits (310), Expect = 2e-32 Identities = 154/538 (28%), Positives = 233/538 (43%), Gaps = 51/538 (9%) Query: 113 RVTYRELHGKVCRFANGLKALGIRKGDRVVIYMPMSVEGVVAMQACARLGATHSVVFGGF 172 R++Y +L A L+A G+R+GD+V I +P + V+A A + G + + Sbjct: 54 RISYAKLRQLAEVMAANLRAQGVRRGDKVSIMLPNLPQTVIAFWAVLKAGGVVVMTNPLY 113 Query: 173 SAKSLQERLVDVGAVALITADEQMRGGKALPLKA-IADDALAL----GGCEAVRNVIVYR 227 K L ++ D GA +I D + K PL+ + D L G N + Sbjct: 114 MEKELVHQIHDSGARFMIALD--LVWPKIEPLREKLGIDKYFLTRIGDGLAFPLNFLYAF 171 Query: 228 RTGGKVAWTE----GRD--RWMEDVSAG-QPDTCEAEPVSAEHPLFVLYTSGSTGKPKGV 280 + + W E GR W + + T P E + YT G+TG KGV Sbjct: 172 KAKREGTWRELPFDGRHVLPWKTLLKGKVRHSTTTCNPT--EDLAVLQYTGGTTGISKGV 229 Query: 281 QHSTGGYLLWALMTMKWTFDIKP-DDLFWCTADIGWVTGHTYIAYGPLAAGATQVVFEG- 338 + + D + D F V G T P A AT V F Sbjct: 230 MLTHHNMSVNVQQITTILGDARDMDHCFLGLMPYFHVYGLTTCLTLPTALAATIVPFPRY 289 Query: 339 VPTYPNAGRFWDMIARHKVSIFYTAPTAIRSLIKAAEADEKIHPKQYDLSSLRLLGTVGE 398 VP G I +HK +IF AP+ SL++ E + YDL+S+R + Sbjct: 290 VPRDVLVG-----IQKHKPTIFPGAPSIYISLMQQKEVGD------YDLTSIRYCISGSA 338 Query: 399 PINPEAWMWYYKNIGNERCPIVDTFWQTETGGHM-ITPLPGATPLVPGSCTLPLPGIMAA 457 P+ E + + G + +++ F TE + P+ G + GS +P P A Sbjct: 339 PMPVEHIKRFRELTGAQ---VIEGFGLTEASPVTHLNPIHGVSKT--GSIGIPFPDTEAR 393 Query: 458 IVD-ETGH-DVPNGNGGILVVKRPWPAMIRTIWGDPERFRKSYFPEELGGKLYLAGDGSI 515 IVD E G +P G G L+++ P +++ W P+ + G LY GD +I Sbjct: 394 IVDMEVGQVPLPAGKVGELIIRGP--QVMKGYWNRPDETANTL----RNGWLY-TGDIAI 446 Query: 516 RDKDTGYFTIMGRIDDVLNVSGHRMGTMEIESALVSNPLVAEAAVVGRPDDMTGEAICAF 575 D+D GYFTI+ R D+ V G+ + EI+ L +P + EA VG P GE I AF Sbjct: 447 MDED-GYFTIVDRKKDMFLVGGYNVYPREIDEVLHEHPKIKEAVTVGVPHPTRGEMIKAF 505 Query: 576 VVLKRSRPTGEEAVKIATELRNWVGKEIGPIAKPKDIRFGDNLPKTRSGKIMRRLLRS 633 VV+K GE+ K E+ +++ PK + F D+LPKT GK++RR+LR+ Sbjct: 506 VVVK----PGEKLTK--AEVVAHCREKLASYKVPKQVEFRDDLPKTVVGKVLRRILRT 557 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: 955 Number of extensions: 46 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 660 Length of database: 583 Length adjustment: 37 Effective length of query: 623 Effective length of database: 546 Effective search space: 340158 Effective search space used: 340158 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: 53 (25.0 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