Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_052473675.1 SUTH_RS14585 AMP-binding protein
Query= SwissProt::P39062 (572 letters) >NCBI__GCF_000828635.1:WP_052473675.1 Length = 559 Score = 306 bits (785), Expect = 1e-87 Identities = 187/548 (34%), Positives = 289/548 (52%), Gaps = 24/548 (4%) Query: 26 DWAEAEKHFSWHETGKLNAAYEAIDRHAESFRKNKVALYYKDAK-RDEKYTFKEMKEESN 84 DW F W + N A R A+ +++ ALYY+D E +TF ++++ +N Sbjct: 12 DWQALRASFRWQVPARYNIAQACCGRWADD--RSRFALYYEDESGHTEAWTFWDVQQAAN 69 Query: 85 RAGNVLRRYGNVEKGDRVFIFMPRSPELYFIMLGAIKIGAIAGPLFEAFMEGAVKDRLEN 144 R NVL G V GDRV I +P+ PE + ++GAIA P+ F A++ RL N Sbjct: 70 RLSNVLGAMG-VMAGDRVAIMLPQRPETGIAHMACYQMGAIAVPISHLFGADALEYRLSN 128 Query: 145 SEAKVVVTTPELLERIPV--DKLPHLQHVFVVGGEAESGTNIINYDEAAKQESTRLDIEW 202 + A+V + LE++ DKLP L+HV VGG E+ + ++R Sbjct: 129 AGARVAIIDDGGLEKLAAVRDKLPQLKHVIGVGGAREAWVR--EWATLLPLAASRYTPRD 186 Query: 203 MDKKDGFLLHYTSGSTGTPKGVLHVHEAMIQQYQTGKWVLDL--KEEDIYWCTADPGWVT 260 D ++ YTSG+TG PKG L +++ D + D++W AD W Sbjct: 187 TAADDPAMIIYTSGTTGNPKGALIAQRSLLGNLPGFVCSHDFYPRRGDMFWSPADWAWTG 246 Query: 261 GTVYGIFAPWLNGATNVIVGGRFSPESWYGTIEQLGVNVWYSAPTAFRMLMGAGDEMAAK 320 G + W G + GRF PE + +E+ G+ + PTA +M+M A + K Sbjct: 247 GLFDALLPTWNFGQPLLGYRGRFDPEKAFWLLEKYGIRNAFLFPTALKMMMKAVPQPKEK 306 Query: 321 YDLTSLRHVLSVGEPLNPEVIRWGHKVFNKRIHDTWWMTETGSQLICNYPCMDI-KPGSM 379 Y+L LR ++S GE + V W + +++ + TE + ++ N + KPG+M Sbjct: 307 YNLV-LRSIMSAGETVGEAVCHWAQEALGVTVNEMYGQTEI-NYIVGNCAAVTSPKPGAM 364 Query: 380 GKPIPGVEAAIVDNQGNELPPYRMGNLAIKKGW-----PSMMHTIWNNPEKYESYFMPGG 434 G+ PG + A++D+ GN + P +G + +++ P M W NPE F+ GG Sbjct: 365 GRGYPGHQLAVLDDAGNPVAPGELGEVCVQRSCNGEMDPVFMLGYWKNPEATAEKFIGGG 424 Query: 435 ------WYVSGDSAYMDEEGYFWFQGRVDDVIMTSGERVGPFEVESKLVEHPAIAEAGVI 488 W +GD A MDE+G W+QGR DD+ ++G R+GP E+E+ LV+HPA+A A VI Sbjct: 425 VDDPQAWGRTGDLAKMDEDGVLWYQGRSDDMFKSAGYRIGPGEIENCLVKHPAVANAAVI 484 Query: 489 GKPDPVRGEIIKAFIALREGFEPSDKLKEEIRLFVKQGLAAHAAPREIEFKDKLPKTRSG 548 G+PDPVRG ++KAFI L+ G +PS +L+ ++ V+Q LA + P+ IEF D LP T +G Sbjct: 485 GEPDPVRGTVVKAFIVLQAGEKPSAELEASLQQHVRQFLAPYEYPKIIEFIDALPMTTTG 544 Query: 549 KIMRRVLK 556 K+ RR+L+ Sbjct: 545 KVQRRLLR 552 Lambda K H 0.318 0.136 0.425 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: 919 Number of extensions: 63 Number of successful extensions: 9 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: 572 Length of database: 559 Length adjustment: 36 Effective length of query: 536 Effective length of database: 523 Effective search space: 280328 Effective search space used: 280328 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: 53 (25.0 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