Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate GFF2177 Psest_2220 Acyl-coenzyme A synthetases/AMP-(fatty) acid ligases
Query= SwissProt::P39062 (572 letters) >FitnessBrowser__psRCH2:GFF2177 Length = 585 Score = 493 bits (1269), Expect = e-144 Identities = 267/561 (47%), Positives = 353/561 (62%), Gaps = 18/561 (3%) Query: 25 FDWAEAEKHFSWHETGKLNAAYEAIDRHAESFRKNKVALYYKDAKRDEK-YTFKEMKEES 83 F W A + G LN A+EA+DRHA R AL + + + ++ ++K ++ Sbjct: 29 FSWPMAADALNGLPGGGLNLAHEAVDRHAAGPRAGYCALRFLERNGSRRELSYLQLKRQT 88 Query: 84 NRAGNVLRRYGNVEKGDRVFIFMPRSPELYFIMLGAIKIGAIAGPLFEAFMEGAVKDRLE 143 NR NVL + G V +G+R+F+ R ELY +LG +K G + PLF AF ++ RL Sbjct: 89 NRFANVLAQLG-VARGERLFVLCNRGVELYLGVLGGLKNGCVVSPLFAAFGPEPLETRLR 147 Query: 144 NSEAKVVVTTPELLERIPV----DKLPHLQHVFVV----GGEAESGTNIINYDEAAKQES 195 + V++T+ E+L R V D+LP L+HV + G + GT ++ AA E Sbjct: 148 LGDCSVLLTS-EMLYRKKVARLRDRLPLLKHVLLYDESGGHTSIDGTLDLHDLLAAAGEE 206 Query: 196 TRLDIEWMDKKDGFLLHYTSGSTGTPKGVLHVHEAMIQQYQTGKWVLDLKEEDIYWCTAD 255 ++ D LLH+TSG+TGTPKG LHVH A + Y TG++ LDL +DIYWC+AD Sbjct: 207 FKIAPTTADSPS--LLHFTSGTTGTPKGALHVHGAALTHYVTGRYALDLHPDDIYWCSAD 264 Query: 256 PGWVTGTVYGIFAPWLNGATNVIVGGRFSPESWYGTIEQLGVNVWYSAPTAFRMLMGAGD 315 PGWVTGT YGI AP L G T+V+ G F E WYG +E+ ++VWY+APTA RMLM AG Sbjct: 265 PGWVTGTSYGILAPLLLGVTSVVDCGEFDAERWYGILEKERISVWYTAPTAIRMLMKAGP 324 Query: 316 EMAAKYDLTSLRHVLSVGEPLNPEVIRWGHKVFNKRIHDTWWMTETGSQLICNYPCMDIK 375 E+A ++ LR V SVGEPLNPE + WG +V IHD WW TETG +I N P M IK Sbjct: 325 ELARRHFHPQLRFVASVGEPLNPEAVWWGKEVLGLPIHDNWWQTETGGIMIANIPAMPIK 384 Query: 376 PGSMGKPIPGVEAAIV----DNQGNELPPYRMGNLAIKKGWPSMMHTIWNNPEKYESYFM 431 PGSMGKP+PGVEAAIV D L +G LA+K+ WP M T E+Y F Sbjct: 385 PGSMGKPLPGVEAAIVRHGEDGNLTFLGDDEIGELALKQPWPGMFRTYLGQEERYRRCF- 443 Query: 432 PGGWYVSGDSAYMDEEGYFWFQGRVDDVIMTSGERVGPFEVESKLVEHPAIAEAGVIGKP 491 G WY+SGD A D +GY+WF GR DDVI ++G +GPFEVES L+EH A+AEA VIGKP Sbjct: 444 AGDWYLSGDLARRDADGYYWFIGRSDDVIKSAGHLIGPFEVESALMEHSAVAEAAVIGKP 503 Query: 492 DPVRGEIIKAFIALREGFEPSDKLKEEIRLFVKQGLAAHAAPREIEFKDKLPKTRSGKIM 551 DP+ GE +KAF++L+ G E S+ L +E+ ++ L A AP+E+EF LP+TRSGK+M Sbjct: 504 DPLLGETVKAFVSLKRGREASEALHDELIGHARKRLGAAVAPKELEFLASLPRTRSGKLM 563 Query: 552 RRVLKAWELNLPAGDLSTMED 572 RR+LKA EL LP GD+ST+E+ Sbjct: 564 RRLLKARELGLPEGDISTLEN 584 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: 1015 Number of extensions: 52 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: 572 Length of database: 585 Length adjustment: 36 Effective length of query: 536 Effective length of database: 549 Effective search space: 294264 Effective search space used: 294264 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 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