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 Pf6N2E2_1726 3-methylmercaptopropionyl-CoA ligase (DmdB)
Query= SwissProt::Q8VZF1 (569 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1726 Length = 540 Score = 614 bits (1583), Expect = e-180 Identities = 293/544 (53%), Positives = 388/544 (71%), Gaps = 17/544 (3%) Query: 18 NYTALTPLWFLDRAAVVHPTRKSVIHGSREYTWRQTYDRCRRLASALADRSIGPGSTVAI 77 N+TALTPL F++R A V+P +VIHGS TW TY RCRRLASALA R IG TVA+ Sbjct: 14 NHTALTPLSFIERTASVYPDYPAVIHGSIRRTWADTYRRCRRLASALAGRGIGKNDTVAV 73 Query: 78 IAPNIPAMYEAHFGVPMCGAVLNCVNIRLNAPTVAFLLSHSQSSVIMVDQEFFTLAEDSL 137 + PNIPAM EAHFGVPM GAVLN +N+RL+A +AF+L+H ++ V++ D+EF + + ++ Sbjct: 74 MLPNIPAMLEAHFGVPMIGAVLNALNVRLDAEAIAFMLAHGEAKVLIADREFHDVVQAAI 133 Query: 138 RLMEEKAGSSFKRPLLIVIGDHTCAPESLNRALSKGAIEYEDFLATGDPNYPWQPPADEW 197 +++ PL+I + D PE + ++YE FLA GDP++ WQ P DEW Sbjct: 134 GMLDHP-------PLVIDLDD----PE-YGEGQAVSELDYEAFLAEGDPDFAWQWPDDEW 181 Query: 198 QSIALGYTSGTTASPKGVVLHHRGAYIMALSNPLIWGMQDGAVYLWTLPMFHCNGWCFPW 257 Q+I+L YTSGTT +PKGVV HHRGAY+ +L N + W M + VYLWTLPMFHCNGWC+PW Sbjct: 182 QAISLNYTSGTTGNPKGVVYHHRGAYLNSLGNQMTWAMGNHPVYLWTLPMFHCNGWCYPW 241 Query: 258 SLAVLSGTSICLRQVTAKEVYSMIAKYKVTHFCAAPVVLNAIVNAPKEDTILPLPHTVHV 317 ++ L+G + LR+V +++ ++I ++++TH C AP+VLNA+VN P + + H V Sbjct: 242 TVTALAGVHVFLRRVDPQKILNLIREHQITHLCGAPIVLNALVNMP-DSAKAAIDHPVSA 300 Query: 318 MTAGAAPPPSVLFSMNQKGFRVAHTYGLSETYGPSTVCAWKPEWDSLPPETQAKLNARQG 377 M AGAAPP V+ ++ + G +V H YGL+E YGP T+CAW WD LP E +A++ ARQG Sbjct: 301 MVAGAAPPAKVIGAVEEMGIKVTHVYGLTEVYGPVTLCAWHAAWDELPLEQRAQIKARQG 360 Query: 378 VRYTGMEQLDVIDTQTGKPVPADGKTAGEIVFRGNMVMKGYLKNPEANKETFAGGWFHSG 437 VRY +E L V D +T +P P DG+T GEI RGN VMKGYLKNP A E F GGWFH+G Sbjct: 361 VRYPTLEGLMVADPRTLEPTPHDGQTIGEIFMRGNTVMKGYLKNPSATAEAFEGGWFHTG 420 Query: 438 DIAVKHPDNYIEIKDRSKDVIISGGENISSVEVENVVYHHPAVLEASVVARPDERWQESP 497 D+AV H D Y+EI+DR KD+IISGGENIS++E+E V+Y HPAVLEA+VVARPDE+W E+P Sbjct: 421 DLAVTHADGYVEIRDRLKDIIISGGENISTIELEGVLYRHPAVLEAAVVARPDEKWGETP 480 Query: 498 CAFVTLKSDYEKHDQNKLAQDIMKFCREKLPAYWVPKSVVFGPLPKTATGKIQKHILRTK 557 CAF+TLKSD+ + +I+ FCRE L + VP++VVF LPKT+TGKIQK +LR Sbjct: 481 CAFITLKSDH----TDVREAEIISFCREHLAGFKVPRTVVFTQLPKTSTGKIQKFVLRDM 536 Query: 558 AKEM 561 AK + Sbjct: 537 AKNL 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: 890 Number of extensions: 39 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