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 WP_011765428.1 AZO_RS08590 acyl-CoA synthetase
Query= SwissProt::Q8VZF1 (569 letters) >NCBI__GCF_000061505.1:WP_011765428.1 Length = 550 Score = 573 bits (1478), Expect = e-168 Identities = 280/553 (50%), Positives = 372/553 (67%), Gaps = 16/553 (2%) Query: 12 LPKIPANYTALTPLWFLDRAAVVHPTRKSVIHGSREYTWRQTYDRCRRLASALADRSIGP 71 L K ANY LTPL F++R+A ++P R +VIHG R YTW ++Y R RRLASAL +G Sbjct: 13 LEKNAANYVPLTPLTFIERSAYIYPDRVAVIHGKRRYTWLESYTRSRRLASALKQLGVGK 72 Query: 72 GSTVAIIAPNIPAMYEAHFGVPMCGAVLNCVNIRLNAPTVAFLLSHSQSSVIMVDQEFFT 131 TVA+I N P M+E HFGVP CGAVLN VN RL+A VAF+L+H ++ V++ D+E+ Sbjct: 73 NDTVAVILNNTPEMFECHFGVPACGAVLNTVNTRLDAEGVAFILNHGEAKVLITDREYSR 132 Query: 132 LAEDSLRLMEEKAGSSFKRPLLIVIGDHTCAPESLNRALSKGAIEYEDFLATGDPNYPWQ 191 + ++ L RP +IVI PE G ++YE L TG+P + ++ Sbjct: 133 MVGKAIELAN--------RPDMIVIDVDD--PEYTGPGERVGKLDYEALLETGNPEFEYE 182 Query: 192 PPADEWQSIALGYTSGTTASPKGVVLHHRGAYIMALSNPLIWGMQDGAVYLWTLPMFHCN 251 P DEW +I+L YTSGTT +PKGVV HHRGAY+ A+SN + WGM +VYLWTLPMFHCN Sbjct: 183 QPGDEWDAISLNYTSGTTGNPKGVVYHHRGAYLNAMSNIVSWGMPPHSVYLWTLPMFHCN 242 Query: 252 GWCFPWSLAVLSGTSICLRQVTAKEVYSMIAKYKVTHFCAAPVVLNAIVNAPKEDTILPL 311 GWCF W++A +G ++CLR+V + ++ + ++ VTH+C AP+V + + NAP E+ + Sbjct: 243 GWCFAWTMAANAGVNVCLRRVDPRLIFDAMREHGVTHYCGAPIVHSMLANAP-EEWRKGI 301 Query: 312 PHTVHVMTAGAAPPPSVLFSMNQKGFRVAHTYGLSETYGPSTVCAWKPEWDSLPPETQAK 371 H V + A A PP +V+ M + G + H YGL+ETYGP++VCA EW LP Q Sbjct: 302 NHKVSGLVAAAPPPAAVIEGMAKIGIDITHVYGLTETYGPASVCAKHDEWRDLPLAEQVA 361 Query: 372 LNARQGVRYTGMEQLDVIDTQTGKPVPADGKTAGEIVFRGNMVMKGYLKNPEANKETFAG 431 N RQGVRY E + V+D T +PVP D +T GEI+FRGN+VMKGYLKN +A +E+F G Sbjct: 362 KNGRQGVRYHAQEGITVLDPTTMEPVPWDNETMGEIMFRGNLVMKGYLKNEKATEESFRG 421 Query: 432 GWFHSGDIAVKHPDNYIEIKDRSKDVIISGGENISSVEVENVVYHHPAVLEASVVARPDE 491 GW+H+GD+AV PD Y++IKDRSKDVIISGGENISS+EVE+ +Y HPAV+ A+VVA PDE Sbjct: 422 GWYHTGDLAVMQPDGYVKIKDRSKDVIISGGENISSIEVEDALYKHPAVMAAAVVAAPDE 481 Query: 492 RWQESPCAFVTLKSDYEKHDQNKLAQDIMKFCREKLPAYWVPKSVVFGPLPKTATGKIQK 551 +W E PCAFV LK A++I+ CRE L + PK V+FG LPKT+TGKIQK Sbjct: 482 KWGEVPCAFVELKD-----GATVTAEEIIAHCREHLAGFKTPKKVIFGALPKTSTGKIQK 536 Query: 552 HILRTKAKEMGPV 564 +LR +AK + Sbjct: 537 FVLREQAKSSSAI 549 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: 931 Number of extensions: 45 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: 550 Length adjustment: 36 Effective length of query: 533 Effective length of database: 514 Effective search space: 273962 Effective search space used: 273962 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 24 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