Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; EC 6.2.1.1; Acetate--CoA ligase; Acyl-activating enzyme (uncharacterized)
to candidate HSERO_RS15645 HSERO_RS15645 acetyl-CoA synthetase
Query= curated2:Q9RRL7 (649 letters) >FitnessBrowser__HerbieS:HSERO_RS15645 Length = 628 Score = 505 bits (1301), Expect = e-147 Identities = 276/628 (43%), Positives = 392/628 (62%), Gaps = 21/628 (3%) Query: 34 EYERRYRQSLDQPDDFWSEVAHDLHWMKDWDRVLDWQEP-HAQWFVGGQTNIAYNALDRN 92 +YE+ YRQS++QP+ FW++ A +HW + + R LD+ P A+WF+ GQTN+ +NA+DR+ Sbjct: 2 QYEQFYRQSVEQPEAFWAQEAQRIHWQQPFSRTLDYSRPPFARWFIDGQTNLCHNAVDRH 61 Query: 93 VQRGLGDKRAIIWEGEDGEVRTYTYAELLREVCKAANALEELGVVAGDRVTLYMPLIPEA 152 + I E R YTYAEL +EV A +++ LGV GDRV +YMP+I EA Sbjct: 62 LPERAQQAALIAISTETNSERVYTYAELQQEVMAMAASMQALGVQRGDRVLIYMPMIAEA 121 Query: 153 AIAMLACARIGAVHSIVFGGFSVSALADRINNAQSKLLITADAGYRRGKPVTLKINADEA 212 AMLACARIGAVHS+VFGGF+ ++LA RI++AQ +L+++ADAG R GK + K DEA Sbjct: 122 VFAMLACARIGAVHSVVFGGFASNSLASRIDDAQPRLIVSADAGSRGGKVIPYKGLLDEA 181 Query: 213 AKLAPCL-EHVLVVKRAGIPLEWWTEGRDLWWHDV-VDRQSDQHEATALDSEHPLFILYT 270 +A +HVL+V R P+ T RD+ + + Q T L+S +ILYT Sbjct: 182 IAMAQHRPQHVLLVDRGLAPMAR-TAQRDVDYAPLRTQHLGQQVPVTWLESNASSYILYT 240 Query: 271 SGSTGAPKGVQHTTGGYMVGTYLTTQTVFDLRDDDIYWCTADIGWITGHSYSVYGPLLNG 330 SG+TG PKGVQ GGY V + Q +F + + Y+CT+DIGW+ GHSY VYGPL+ G Sbjct: 241 SGTTGKPKGVQRDVGGYAVALASSMQHIFCGQPGETYFCTSDIGWVVGHSYIVYGPLIAG 300 Query: 331 ATVVMYEGAPNQPDWGRFWDIVQKHRVTILYTAPTAIRSFMQHGDEIPGRYDLASLRLLG 390 V+YEG P +PD G +W IV+K++VT +++APTAIR + E RYD +SL+ L Sbjct: 301 MATVLYEGLPIRPDAGIWWSIVEKYKVTRMFSAPTAIRVLKKQPPECMERYDTSSLKALY 360 Query: 391 SVGEPINPEAWMWYYRVIGGERCPVVDTWWQTETGSIMLTTLPGA--FPSKPGSAGLPMF 448 GEP++ W + G + PV+D +WQTE+G +++ G P++ GS G+PM Sbjct: 361 LAGEPLDETTSSW---ISGALKVPVIDNYWQTESGWPIISIAKGIDDKPTRLGSPGVPMP 417 Query: 449 GVEPALMTR-DGEEIGDDDGGLLVIKRPW-PSMLRTVYGDDERYRKSYWGEIP-HVYFAG 505 G A++ GE G D G++ I+ P P ++TVYGDDER+ +YW +P VY Sbjct: 418 GYRLAILDEATGEPCGPDQKGVVAIEGPLPPGCMQTVYGDDERFVNTYWRSLPREVYSTF 477 Query: 506 DGARRDHDGYYTIVGRVDDVLNVSGHRLGTMEIESALVAHPDVSEAAVVGRPDPVKGESV 565 D RD DGYY I+GR DDV+NV+GHRLGT EIE ++ +HP+VSE AVVG D +KG+ Sbjct: 478 DWGIRDKDGYYFILGRTDDVINVAGHRLGTREIEESISSHPNVSEVAVVGVEDKLKGQVA 537 Query: 566 VAYVLLQDGHT--------ADPAALRAHVSSEIGALARPDAIYIADALPKTRSGKIMRRF 617 A+ + + +T A A + A V +IGA+ RP ++ LPKTRSGK++RR Sbjct: 538 FAFAIPKQAYTIATPEQRKALEAEIMAVVDKQIGAVGRPARVFFVSGLPKTRSGKLLRRA 597 Query: 618 LRQLAAGQPVQGDTSTLEDPTVLERLQA 645 ++ + G+ GD T+EDP LE+++A Sbjct: 598 IQSICEGRD-PGDLPTIEDPAALEQVRA 624 Lambda K H 0.319 0.137 0.432 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: 1182 Number of extensions: 71 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: 649 Length of database: 628 Length adjustment: 38 Effective length of query: 611 Effective length of database: 590 Effective search space: 360490 Effective search space used: 360490 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 (21.8 bits) S2: 54 (25.4 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