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 PP_3553 PP_3553 AMP-binding domain protein
Query= SwissProt::Q8VZF1 (569 letters) >FitnessBrowser__Putida:PP_3553 Length = 540 Score = 614 bits (1584), Expect = e-180 Identities = 301/545 (55%), Positives = 387/545 (71%), Gaps = 19/545 (3%) Query: 18 NYTALTPLWFLDRAAVVHPTRKSVIHGSREYTWRQTYDRCRRLASALADRSIGPGSTVAI 77 N+ ALTPL F++R A V+ +VIHG+ W++TY RCRRLASALA R IG G TVA+ Sbjct: 14 NHVALTPLSFIERTAAVYGNYPAVIHGAIRRNWQETYQRCRRLASALAGRGIGRGDTVAV 73 Query: 78 IAPNIPAMYEAHFGVPMCGAVLNCVNIRLNAPTVAFLLSHSQSSVIMVDQEFFTLAEDSL 137 + PN P M EAHFGVPM GAVLN +N+RL+A +AF+L H ++ V++ D+EF + E +L Sbjct: 74 MLPNTPTMLEAHFGVPMTGAVLNTLNVRLDAEAIAFMLQHGEAKVLITDREFHAVIEGAL 133 Query: 138 RLMEEKAGSSFKRPLLIVIGDHTCAPE-SLNRALSKGAIEYEDFLATGDPNYPWQPPADE 196 L+E PL++ + D PE RA+S+ ++YE L GDP + W+ P DE Sbjct: 134 ALLEHP-------PLVVDVDD----PEYGEGRAVSQ--LDYEALLNEGDPEFAWEWPDDE 180 Query: 197 WQSIALGYTSGTTASPKGVVLHHRGAYIMALSNPLIWGMQDGAVYLWTLPMFHCNGWCFP 256 WQ+I+L YTSGTT +PKGVV HHRGAY+ AL N + W M VYLWTLPMFHCNGWC+P Sbjct: 181 WQAISLNYTSGTTGNPKGVVYHHRGAYLNALGNQMTWAMGHRPVYLWTLPMFHCNGWCYP 240 Query: 257 WSLAVLSGTSICLRQVTAKEVYSMIAKYKVTHFCAAPVVLNAIVNAPKEDTILPLPHTVH 316 W++ L+GT + LR+V +++ ++I ++KV+H C AP+VLNA+VN P E + H V Sbjct: 241 WTITALAGTHVFLRRVDPQKILTLIREHKVSHLCGAPIVLNALVNMP-EAAKAAIEHPVQ 299 Query: 317 VMTAGAAPPPSVLFSMNQKGFRVAHTYGLSETYGPSTVCAWKPEWDSLPPETQAKLNARQ 376 M AGAAPP V+ ++ Q G +V HTYGL+E YGP TVCAW EWD+L E +A++ +RQ Sbjct: 300 AMVAGAAPPAKVIGAVEQMGIKVTHTYGLTEVYGPVTVCAWHDEWDALSLEERARIKSRQ 359 Query: 377 GVRYTGMEQLDVIDTQTGKPVPADGKTAGEIVFRGNMVMKGYLKNPEANKETFAGGWFHS 436 GVRY ++ L V D QT +PVP DG T GEI RGN VMKGYLKNPEA E F GGWFH+ Sbjct: 360 GVRYPTLDGLMVADPQTLQPVPRDGDTLGEIFMRGNTVMKGYLKNPEATAEAFRGGWFHT 419 Query: 437 GDIAVKHPDNYIEIKDRSKDVIISGGENISSVEVENVVYHHPAVLEASVVARPDERWQES 496 GD+AV H D YIEIKDR KD+IISGGENIS++EVE+ +Y H AVLEA+VVARPDE+W E+ Sbjct: 420 GDLAVWHADGYIEIKDRLKDIIISGGENISTIEVEDALYKHSAVLEAAVVARPDEKWGET 479 Query: 497 PCAFVTLKSDYEKHDQNKLAQDIMKFCREKLPAYWVPKSVVFGPLPKTATGKIQKHILRT 556 PCAFV LK E + DI +CRE L + VPK+VVFG LPKT+TGKIQK++LR Sbjct: 480 PCAFVALKPGRE----DTREADITSWCREHLAGFKVPKTVVFGELPKTSTGKIQKYVLRD 535 Query: 557 KAKEM 561 +AK + Sbjct: 536 RAKAL 540 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: 913 Number of extensions: 37 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: 540 Length adjustment: 36 Effective length of query: 533 Effective length of database: 504 Effective search space: 268632 Effective search space used: 268632 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