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 BPHYT_RS33490 BPHYT_RS33490 acyl-CoA synthetase
Query= SwissProt::Q8VZF1 (569 letters) >FitnessBrowser__BFirm:BPHYT_RS33490 Length = 543 Score = 556 bits (1434), Expect = e-163 Identities = 282/549 (51%), Positives = 363/549 (66%), Gaps = 20/549 (3%) Query: 12 LPKIPANYTALTPLWFLDRAAVVHPTRKSVIHGSREYTWRQTYDRCRRLASALADRSIGP 71 L + ANY LTP+ F+ RAA V+ R +V+HG WR+TY+R RRLASAL I Sbjct: 9 LERREANYVPLTPIDFIVRAAEVYGERPAVVHGEIRRNWRETYERARRLASALQQAGIQR 68 Query: 72 GSTVAIIAPNIPAMYEAHFGVPMCGAVLNCVNIRLNAPTVAFLLSHSQSSVIMVDQEFFT 131 G TVA + PNIP M EAHFGVPM GAVLN +N RL+ ++ F+L H ++ ++VD E+ Sbjct: 69 GDTVAALLPNIPPMIEAHFGVPMAGAVLNTLNTRLDVSSLLFMLRHGEAKALIVDTEYGE 128 Query: 132 LAEDSLRLMEEKAGSSFKRPLLIVIGDHTCA-PESLNRALSKGAIEYEDFLATGDPNYPW 190 A +A F +I + D A P RA +YE FL +GDP + W Sbjct: 129 FAH--------RAALEFPDLRVISVADAMPADPSQFIRAT-----DYEAFLQSGDPEFAW 175 Query: 191 QPPADEWQSIALGYTSGTTASPKGVVLHHRGAYIMALSNPLIWGMQDGAVYLWTLPMFHC 250 PADEW +IAL YTSGTT PKGVV HHRGAY+ ALSN L W M A+YLWTLP+FHC Sbjct: 176 AMPADEWDAIALNYTSGTTGDPKGVVYHHRGAYLNALSNILEWDMPKHAIYLWTLPLFHC 235 Query: 251 NGWCFPWSLAVLSGTSICLRQVTAKEVYSMIAKYKVTHFCAAPVVLNAIVNAPKEDTILP 310 NGWCFPW++A +G ++CLR+ AK V+ +I + +TH+C AP+V +A+ NAP + Sbjct: 236 NGWCFPWTVAARAGVNVCLRKFDAKTVFDLIRREGITHYCGAPIVQSALANAPAQWRE-G 294 Query: 311 LPHTVHVMTAGAAPPPSVLFSMNQKGFRVAHTYGLSETYGPSTVCAWKPEWDSLPPETQA 370 + H V M AGAAP P+V+ M + GF + H YGL+ETYGP+ VCA + EW++L +A Sbjct: 295 IEHRVSTMVAGAAPAPAVIAKMKEIGFDLTHVYGLTETYGPAAVCAKQEEWEALDDGARA 354 Query: 371 KLNARQGVRYTGMEQLDVIDTQTGKPVPADGKTAGEIVFRGNMVMKGYLKNPEANKETFA 430 ++NARQGVRY + V+D T PVP DG+T GEI+FRGN+ MKGYLKN A + TF Sbjct: 355 EMNARQGVRYHLQAAVTVLDPDTLTPVPDDGETIGEIMFRGNICMKGYLKNERATEATFQ 414 Query: 431 GGWFHSGDIAVKHPDNYIEIKDRSKDVIISGGENISSVEVENVVYHHPAVLEASVVARPD 490 GGWFH+GD+ V+ PD YI I+DRSKD+IISGGENISS+EVE+ +Y HPAV A+VVA D Sbjct: 415 GGWFHTGDLGVRMPDGYIRIRDRSKDIIISGGENISSIEVEDTLYRHPAVSVAAVVAMAD 474 Query: 491 ERWQESPCAFVTLKSDYEKHDQNKLAQDIMKFCREKLPAYWVPKSVVFGPLPKTATGKIQ 550 +W E PCAFV LK + A++I+ CR L Y +PK+V FG LPKT+TGKIQ Sbjct: 475 PKWGEVPCAFVELKEGAQVS-----AEEIIAHCRLFLAGYKLPKAVRFGELPKTSTGKIQ 529 Query: 551 KHILRTKAK 559 K LR + K Sbjct: 530 KFELRARIK 538 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: 875 Number of extensions: 41 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: 543 Length adjustment: 36 Effective length of query: 533 Effective length of database: 507 Effective search space: 270231 Effective search space used: 270231 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