Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate AO356_29235 AO356_29235 acyl-CoA synthetase
Query= BRENDA::A4YDR9 (549 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_29235 Length = 550 Score = 382 bits (982), Expect = e-110 Identities = 212/536 (39%), Positives = 314/536 (58%), Gaps = 7/536 (1%) Query: 11 GVDPTGSWYSVLTPLLFLERAGKYFKDKTAVVYRDSRYTYSTFYDNVMVQASALMRRGFS 70 G++ + + Y LTPL FL+RA D+ AVV+ D R T+ + ASAL G Sbjct: 9 GLEQSKANYLPLTPLGFLDRAALVHPDRVAVVHGDLRRTWRQTRERCYRLASALSNEGMG 68 Query: 71 REDKLSFISRNRPEFLESFFGVPYAGGVLVPINFRLSPKEMAYIINHSDSKFVVVDEPYL 130 D +S +S N P LE+ FGVP G VL +N+RL + +A+I+ H + K ++VD + Sbjct: 69 AGDTVSILSPNTPAMLEAHFGVPLCGAVLNTVNYRLDAEGVAFILRHGECKLLLVDREFA 128 Query: 131 NSLLEVKDQIKAEIILLEDPDNPSASETARKEVRMTYRELVKGGSRDPLPIPAKEEYSMI 190 + ++++ ++++ D+ + ++ +V Y + GS D + +E+ I Sbjct: 129 ALAVAALERLEHPPVVIDINDHLAPLGSSIGDV--DYETFIGRGSPDFQGVWPSDEWQPI 186 Query: 191 TLYYTSGTTGLPKGVMHHHRGAFLNAMAEVLEHQMDLNSVYLWTLPMFHAASWGFSWATV 250 L YTSGTTG PKGV+ HRG +L +M ++ + YLWTLPMFHA W F+WA Sbjct: 187 ALNYTSGTTGDPKGVVASHRGTYLMSMLQMTNWPLSRAPRYLWTLPMFHANGWCFTWAIT 246 Query: 251 AVGATNVCLDKVDYPLIYRLVEKERVTHMCAAPTVYVNLADYMKRNNLKFSNRVHMLVAG 310 A T+VCL KV ++ ++ + V H CAAP V +A+ R L+ RV L AG Sbjct: 247 AAAGTHVCLRKVSAEAVFDAIDTQGVDHFCAAPIVMAMIANSADRPPLETPVRV--LTAG 304 Query: 311 AAPAPATLKAMQEIGGYMCHVYGLTETYGPHSICEWRREWDSLPLEEQAKLKARQGIPYV 370 + P L A+ +G + HVYG+TE G C W+ W++L +Q L+ RQG Sbjct: 305 SPPPATVLDAVVSLGFDVDHVYGITEVSGTPISCVWQDGWNALAQSDQGALRVRQGARAA 364 Query: 371 SFE-MDVFDANG-KPVPWDGKTIGEVVMRGHNVALGYYKNPEKTAESFRDGWFHSGDAAV 428 FE + V DA+ +PVP DG T GE++++G+ V +GY KN T ++F GWFH+GD AV Sbjct: 365 GFEGLMVADADTLQPVPKDGHTTGELLLKGNTVMMGYLKNENATRKAFEGGWFHTGDVAV 424 Query: 429 VHPDGYIEIVDRFKDLINTGGEKVSSILVEKTLMEIPGVKAVAVYGTPDEKWGEVVTARI 488 VHP+GYI+I DR KD+I +GGE +SS+ +E+ + P V AV PD+ WGEV A I Sbjct: 425 VHPNGYIQITDRCKDVIISGGENISSVEIEEAIHCHPAVLHAAVVAQPDDIWGEVPCAFI 484 Query: 489 ELQEGV-KLTEEEVIKFCKERLAHFECPKIVEFGPIPMTATGKMQKYVLRNEAKAK 543 EL+ G + TE ++I FC+ RLA F+CP+ V F +P TATGK+QK++LR +A ++ Sbjct: 485 ELKGGAERPTEADMIAFCQARLARFKCPRRVIFMELPKTATGKIQKFLLREQAGSR 540 Lambda K H 0.319 0.136 0.411 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: 677 Number of extensions: 30 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: 549 Length of database: 550 Length adjustment: 36 Effective length of query: 513 Effective length of database: 514 Effective search space: 263682 Effective search space used: 263682 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 (21.7 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