Align Acetate/butyrate--CoA ligase AAE7, peroxisomal; AMP-binding protein 7; AtAMPBP7; Acetyl-CoA synthetase; Acyl-activating enzyme 7; Butyryl-CoA synthetase; Protein ACETATE NON-UTILIZING 1; EC 6.2.1.1; EC 6.2.1.2 (characterized)
to candidate GFF1060 HP15_1039 acyl-CoA synthetase
Query= SwissProt::Q8VZF1 (569 letters) >FitnessBrowser__Marino:GFF1060 Length = 542 Score = 621 bits (1601), Expect = 0.0 Identities = 300/550 (54%), Positives = 389/550 (70%), Gaps = 17/550 (3%) Query: 12 LPKIPANYTALTPLWFLDRAAVVHPTRKSVIHGSREYTWRQTYDRCRRLASALADRSIGP 71 L + ANY +P+ F++R A V+P +VIHG+ Y W QTY+RCRRLASAL R IG Sbjct: 9 LAPVDANYAVQSPVDFIERTATVYPEYPAVIHGAIRYNWAQTYERCRRLASALKGRGIGR 68 Query: 72 GSTVAIIAPNIPAMYEAHFGVPMCGAVLNCVNIRLNAPTVAFLLSHSQSSVIMVDQEFFT 131 G TVA++ PNIPAM EAHFGVPM GAVLN +N+RL+A +AF+L H ++ V++ D+EF Sbjct: 69 GDTVAVMLPNIPAMVEAHFGVPMIGAVLNTLNVRLDAEAIAFMLDHGEAKVVIADREFGE 128 Query: 132 LAEDSLRLMEEKAGSSFKRPLLIVIGDHTCAPESLNRALSKGAIEYEDFLATGDPNYPWQ 191 + D++ ++ K PL+I + D PE + ++YE FL GDP + W Sbjct: 129 VIRDAVSRLDTK-------PLVIDVDD----PE-YGEGVQVSDLDYEAFLQEGDPTFQWS 176 Query: 192 PPADEWQSIALGYTSGTTASPKGVVLHHRGAYIMALSNPLIWGMQDGAVYLWTLPMFHCN 251 P +EW +I+L YTSGTT +PKGVV HHRGAYI A+ N +W M VYLWTLPMFHCN Sbjct: 177 FPENEWDAISLNYTSGTTGNPKGVVYHHRGAYINAIGNQTVWSMDMHPVYLWTLPMFHCN 236 Query: 252 GWCFPWSLAVLSGTSICLRQVTAKEVYSMIAKYKVTHFCAAPVVLNAIVNAPKEDTILPL 311 GWCFPW++ ++GT +CLR+V +++ +I ++VTH C AP+VLNA++N P E + Sbjct: 237 GWCFPWTITAMAGTHVCLRRVDPEKILQLIRDHQVTHMCGAPIVLNALLNVP-ESAKAGI 295 Query: 312 PHTVHVMTAGAAPPPSVLFSMNQKGFRVAHTYGLSETYGPSTVCAWKPEWDSLPPETQAK 371 H V MTAGAAPP V+ ++ + G +V H YGL+E YGP TVCAWK EWD+LP +A+ Sbjct: 296 DHDVKSMTAGAAPPAQVIGAIEEMGIQVTHVYGLTEVYGPVTVCAWKSEWDALPLHDRAR 355 Query: 372 LNARQGVRYTGMEQLDVIDTQTGKPVPADGKTAGEIVFRGNMVMKGYLKNPEANKETFAG 431 ARQGVRY + V D T +PVP DGKT GEI RGN VMKGYLKNP+A +E F G Sbjct: 356 KKARQGVRYHTLAGTMVGDPNTMEPVPKDGKTIGEIFLRGNTVMKGYLKNPKATEEAFRG 415 Query: 432 GWFHSGDIAVKHPDNYIEIKDRSKDVIISGGENISSVEVENVVYHHPAVLEASVVARPDE 491 GWFH+GD+AV H D Y+EIKDR KD+IISGGENIS++EVE+ +Y HPAVLEA+VVARPDE Sbjct: 416 GWFHTGDLAVWHEDGYMEIKDRLKDIIISGGENISTIEVEDTLYRHPAVLEAAVVARPDE 475 Query: 492 RWQESPCAFVTLKSDYEKHDQNKLAQDIMKFCREKLPAYWVPKSVVFGPLPKTATGKIQK 551 +W E+PCAFVTLK E D ++ +DI+ FCRE L + VPK++VF LPKT+TGKIQK Sbjct: 476 KWGETPCAFVTLKP--EAGDVSE--EDIINFCREHLARFKVPKTIVFSELPKTSTGKIQK 531 Query: 552 HILRTKAKEM 561 +LR +AKE+ Sbjct: 532 FVLRDQAKEL 541 Lambda K H 0.319 0.134 0.422 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: 938 Number of extensions: 29 Number of successful extensions: 4 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: 569 Length of database: 542 Length adjustment: 36 Effective length of query: 533 Effective length of database: 506 Effective search space: 269698 Effective search space used: 269698 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: 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