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 3607419 Dshi_0833 AMP-dependent synthetase and ligase (RefSeq)
Query= SwissProt::Q8VZF1 (569 letters) >FitnessBrowser__Dino:3607419 Length = 541 Score = 561 bits (1447), Expect = e-164 Identities = 284/550 (51%), Positives = 364/550 (66%), Gaps = 18/550 (3%) Query: 12 LPKIPANYTALTPLWFLDRAAVVHPTRKSVIHGSREYTWRQTYDRCRRLASALADRSIGP 71 L K ANY LTPL L RAA+V+P R++V++G+R +T+ + + R RLASALA I P Sbjct: 10 LDKCAANYVPLTPLSHLARAALVYPDREAVVYGARRFTYAEYHARVSRLASALAGAGIAP 69 Query: 72 GSTVAIIAPNIPAMYEAHFGVPMCGAVLNCVNIRLNAPTVAFLLSHSQSSVIMVDQEFFT 131 G VA + PNIPAM EAHFGVP CGAVLN +NIRL+ TVA++LSH + ++VD +F Sbjct: 70 GDVVATLLPNIPAMVEAHFGVPACGAVLNTINIRLDVDTVAYILSHGGAKAVLVDSQFLP 129 Query: 132 LAEDSLRLMEEKAGSSFKRPLLIVIGDHTCAPESLNRALSKGAIEYEDFLATGDPNYPWQ 191 LA ++ ++ A PLLI + D +L G EYEDFLA GDP++PW Sbjct: 130 LAAEACERLDGPA------PLLIEVADDAAGVHALG-----GYTEYEDFLAGGDPDFPWI 178 Query: 192 PPADEWQSIALGYTSGTTASPKGVVLHHRGAYIMALSNPLIWGMQDGAVYLWTLPMFHCN 251 P DEW+S+AL YTSGTT PKGVV HHRGAY+M + + W M +L +P+FHCN Sbjct: 179 MPRDEWESLALNYTSGTTGRPKGVVYHHRGAYLMTMGTVISWRMVLYPRWLAIVPLFHCN 238 Query: 252 GWCFPWSLAVLSGTSICLRQVTAKEVYSMIAKYKVTHFCAAPVVLNAIVNAPKEDTILPL 311 GW W + +L GT +C R V+A+ +Y+ IA+ VTHF AP+VLN IVNAP + P Sbjct: 239 GWNHSWMMPMLGGTVVCCRDVSAQAIYTAIAENGVTHFGGAPIVLNMIVNAP-DAARRPF 297 Query: 312 PHTVHVMTAGAAPPPSVLFSMNQKGFRVAHTYGLSETYGPSTVCAWKPEWDSLPPETQAK 371 HTV V TAGA P + L ++ + GF V YGL+ETYG T C W P+WD+LP +A Sbjct: 298 SHTVEVFTAGAPPAAATLAAIEELGFNVTQVYGLTETYGHVTECVWNPDWDTLPQAERAA 357 Query: 372 LNARQGVRYTGMEQLDVIDTQTGKPVPADGKTAGEIVFRGNMVMKGYLKNPEANKETFAG 431 + ARQGV ME + V+D + + VP DG T GE++ RGN VMKGY +NP+A E FAG Sbjct: 358 IKARQGVALPQMEHITVMDPEM-RQVPMDGATTGEVMMRGNSVMKGYYRNPDATAEAFAG 416 Query: 432 GWFHSGDIAVKHPDNYIEIKDRSKDVIISGGENISSVEVENVVYHHPAVLEASVVARPDE 491 G+FHSGDIA++HPD YI+I DR+KD+IISGGENISSVEVE + HHPAVL +VVA+PD Sbjct: 417 GYFHSGDIALQHPDGYIQIADRAKDIIISGGENISSVEVEGALMHHPAVLLCAVVAKPDP 476 Query: 492 RWQESPCAFVTLKSDYEKHDQNKLAQDIMKFCREKLPAYWVPKSVVFGPLPKTATGKIQK 551 W E PCAFV LK + +I+ F RE+L + PK VVF LPKT+TGKIQK Sbjct: 477 TWGEVPCAFVELKDGKTAEE-----AEIIAFARERLAGFKTPKKVVFTELPKTSTGKIQK 531 Query: 552 HILRTKAKEM 561 LR +AK + Sbjct: 532 FELRNRAKAL 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: 919 Number of extensions: 36 Number of successful extensions: 5 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: 541 Length adjustment: 36 Effective length of query: 533 Effective length of database: 505 Effective search space: 269165 Effective search space used: 269165 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