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::P27550 (652 letters) >FitnessBrowser__psRCH2:GFF2177 Length = 585 Score = 344 bits (883), Expect = 6e-99 Identities = 216/580 (37%), Positives = 309/580 (53%), Gaps = 55/580 (9%) Query: 73 GTLNLAANCLDRH-------------LQENGDRTAIIWEGDDASQSKHISYKELHRDVCR 119 G LNLA +DRH L+ NG R + +SY +L R R Sbjct: 44 GGLNLAHEAVDRHAAGPRAGYCALRFLERNGSR-------------RELSYLQLKRQTNR 90 Query: 120 FANTLLELGIKKGDVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSN 179 FAN L +LG+ +G+ + + E + +L + G V S +F F PE + R+ + Sbjct: 91 FANVLAQLGVARGERLFVLCNRGVELYLGVLGGLKNGCVVSPLFAAFGPEPLETRLRLGD 150 Query: 180 SRLVITSDEGVRAGRSIPLKKNVDDALKNPNVTSVEHVVVLKRTGGKIDWQEGRDLWWHD 239 +++TS+ + +K V A + ++HV++ +GG DL HD Sbjct: 151 CSVLLTSE--------MLYRKKV--ARLRDRLPLLKHVLLYDESGGHTSIDGTLDL--HD 198 Query: 240 LVEQASDQHQAEEMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGD 299 L+ A ++ + A+ P + +TSG+TG PKG LH G L + +T +Y D HP D Sbjct: 199 LLAAAGEEFKIAPTTADSPSLLHFTSGTTGTPKGALHVHGAALTHY-VTGRYALDLHPDD 257 Query: 300 IYWCTADVGWVTGHSYLLYGPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPT 359 IYWC+AD GWVTG SY + PL G T+++ G + R +++K ++++ YTAPT Sbjct: 258 IYWCSADPGWVTGTSYGILAPLLLGVTSVVDCGEFD---AERWYGILEKERISVWYTAPT 314 Query: 360 AIRALMAEGDKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETG 419 AIR LM G + LR + SVGEP+NPEA W + +G P+ D WWQTETG Sbjct: 315 AIRMLMKAGPELARRHFHPQLRFVASVGEPLNPEAVWWGKEVLG---LPIHDNWWQTETG 371 Query: 420 GFMITPLPGATELKAGSATRPFFGVQPALVDN--EGN-PLEGATE-GSLVITDSWPGQAR 475 G MI +P A +K GS +P GV+ A+V + +GN G E G L + WPG R Sbjct: 372 GIMIANIP-AMPIKPGSMGKPLPGVEAAIVRHGEDGNLTFLGDDEIGELALKQPWPGMFR 430 Query: 476 TLFGDHERFEQTYFSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESA 535 T G ER+ + + + Y SGD ARRD DGYYW GR DDV+ +GH +G E+ESA Sbjct: 431 TYLGQEERYRRCFAGDW---YLSGDLARRDADGYYWFIGRSDDVIKSAGHLIGPFEVESA 487 Query: 536 LVAHPKIAEAAVVGIPHNIKGQAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDV 595 L+ H +AEAAV+G P + G+ + A+V+L G E S L+ E+ RK +G P Sbjct: 488 LMEHSAVAEAAVIGKPDPLLGETVKAFVSLKRGREASEALHDELIGHARKRLGAAVAPKE 547 Query: 596 LHWTDSLPKTRSGKIMRRILRKIAAGDTSNLGDTSTLADP 635 L + SLP+TRSGK+MRR+L+ G GD STL +P Sbjct: 548 LEFLASLPRTRSGKLMRRLLKARELGLPE--GDISTLENP 585 Lambda K H 0.317 0.135 0.421 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: 1085 Number of extensions: 60 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: 652 Length of database: 585 Length adjustment: 37 Effective length of query: 615 Effective length of database: 548 Effective search space: 337020 Effective search space used: 337020 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 Apr 09 2024.
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