Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate RR42_RS10650 RR42_RS10650 acetyl-CoA synthetase
Query= SwissProt::P27550 (652 letters) >FitnessBrowser__Cup4G11:RR42_RS10650 Length = 588 Score = 326 bits (835), Expect = 2e-93 Identities = 206/565 (36%), Positives = 294/565 (52%), Gaps = 30/565 (5%) Query: 73 GTLNLAANCLDRHLQENGDRTAIIWEGDDASQSKHISYKELHRDVCRFANTLLELGIKKG 132 G LN+A +DRH + A + + ++Y +L RF N L +LG+ KG Sbjct: 45 GALNIAWQAVDRHAASSLRGKAAFRILARGTPTHFVTYGQLSALTNRFCNVLRDLGVGKG 104 Query: 133 DVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNSRLVITSDEGVRA 192 + + I +PE +A+L + G S +F F P+ +A R+ +++T+D Sbjct: 105 ERLFILAGRIPELYIAILGSLKNGTAVSPLFSAFGPDPIATRVNLGEGAVLVTTD----- 159 Query: 193 GRSIPLKKNVDDALKNPNVTSVEHVVVLKRTGGKIDWQEGRDLWWHDLVEQASDQHQAEE 252 + ++ + A + S++HV+++ GG DL L+ ASD + Sbjct: 160 ---MLFERKI--AKWRDRMPSLKHVLLVAEDGGTTAVPGTLDL--SSLMASASDACEITP 212 Query: 253 MNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDIYWCTADVGWVTG 312 AED + +TSG+TG PKG +H G L + + T +Y D H DIYWCTAD GWVTG Sbjct: 213 TTAEDMALLHFTSGTTGTPKGAVHVHGAVLTHWS-TGRYALDLHVDDIYWCTADPGWVTG 271 Query: 313 HSYLLYGPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTAIRALMAEGDKAI 372 SY + PL G T+++ + R ++ V+I YTAPTAIR LM G Sbjct: 272 TSYGVIAPLLHGVTSIVDREEFD---AERWYAILQDEGVSIWYTAPTAIRMLMKAGADIA 328 Query: 373 EGTDRSSLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGGFMITPLPGATEL 432 + LR SVGEP+NPEA W + +G P D WWQTETGG MI P A ++ Sbjct: 329 KKYAFPRLRFAASVGEPLNPEAVWWGKQVLG---LPFHDNWWQTETGGIMIANTP-AFDI 384 Query: 433 KAGSATRPFFGVQPALVDNEGNP----LEGAT-EGSLVITDSWPGQARTLFGDHERFEQT 487 K GS RP GV+ A+V + + +E EG L + WP R ER+ ++ Sbjct: 385 KPGSMGRPLPGVEAAIVSRQADGSVQVIEAPNKEGELALKRGWPSMFRGYLNSEERYRKS 444 Query: 488 YFSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHPKIAEAAV 547 + + Y +GD ARRD DGYYW GR DDV+ +GH +G E+ESAL+ HP +AEAAV Sbjct: 445 FSGEW---YLTGDLARRDADGYYWFVGRADDVIKSAGHLIGPFEVESALMEHPAVAEAAV 501 Query: 548 VGIPHNIKGQAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTDSLPKTRS 607 +G P I G+ + A+V+LN+G E S L + R +G P + + LP+TRS Sbjct: 502 IGKPDPIAGEVVKAFVSLNNGFEQSEALRMALLGHARTRLGAAVAPKEIAFLTQLPRTRS 561 Query: 608 GKIMRRILRKIAAGDTSNLGDTSTL 632 GKIMRR+L+ G GDTSTL Sbjct: 562 GKIMRRLLKARELGLPE--GDTSTL 584 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: 1094 Number of extensions: 73 Number of successful extensions: 8 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: 588 Length adjustment: 37 Effective length of query: 615 Effective length of database: 551 Effective search space: 338865 Effective search space used: 338865 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