Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate WP_079648207.1 B5X82_RS11035 AMP-binding protein
Query= BRENDA::A4YDT1 (564 letters) >NCBI__GCF_900167915.1:WP_079648207.1 Length = 528 Score = 372 bits (954), Expect = e-107 Identities = 211/520 (40%), Positives = 303/520 (58%), Gaps = 11/520 (2%) Query: 38 FNWVRDVFEDIHVKERGSKTALIWRDINTGEEAKLSYHELSLMSNRVLSTLRKHGLKKGD 97 FN+ RDV + R A++W + +G + S+ E+++ ++R + L + G+ +GD Sbjct: 11 FNFTRDVMGR-WAELRPDDPAMVWTE-PSGTVIERSFAEMAIAASRAAAVLAEAGVGRGD 68 Query: 98 VVYLMTKVHPMHWAVFLAVIKGGFVMVPSATNLTVAEMKYRFSDLKPSAIISDSLRASVM 157 V ++ W + L I G + P T L ++ YR +++ A + Sbjct: 69 TVLILLNREIEWWELMLGCIAIGAIASPGTTQLMAKDIAYRHRAAAARCVVASGEMAERV 128 Query: 158 EEALGSLKVEKFLIDGKRETWNSLEDESSNAEP----EDTRGEDVIINYFTSGTTGMPKR 213 + AL + + + G R W + + A P DT ++ + YFTSGTTG PK Sbjct: 129 DTALAGEDIARLHVGGPRSGWIDYGERRAAATPIATAADTGFDEDALCYFTSGTTGQPKM 188 Query: 214 VIHTAVSYPVGSITTASIVGVRESDLHLNLSATGWAKFAWSSFFSPLLVGATVVGINYEG 273 IHT IT + + ++ DLH NLS TGWAK AWSS F+P L+GAT+ +++ Sbjct: 189 TIHTHGYMLAHRITGSYWLDLKPGDLHWNLSDTGWAKAAWSSLFAPWLMGATIF-VHHSP 247 Query: 274 KLDTRRYLGEVENLGVTSFCAPPTAWRQFITLDLDQFRFERLRSVVSAGEPLNPEVIKIW 333 D L +E + VT+ CAPPTA+R F+ DL RF+ LR VSAGEPLNPEVI +W Sbjct: 248 GFDPVATLDLLERMPVTTLCAPPTAYRMFVRSDLTGRRFDTLRHCVSAGEPLNPEVIDLW 307 Query: 334 KDKFNLTIRDFYGQTETTAMVGNFPFLKVKPGSMGKPHPLYDIRLLDDEGKEITKPYEVG 393 K I D YGQTET + N + GSMG+P P +D+ ++D EG + E G Sbjct: 308 KAATGRDIHDGYGQTETVLLCAN-RVGAARQGSMGRPAPDFDLAVIDGEGNRLPADVE-G 365 Query: 394 HITVKL-NPRPIGLFLGYSDE-KKNMESFREGYYYTGDKAYFDEEGYFYFVGRGDDVIKT 451 + +++ P GLF Y D+ ++ ++ R+G+Y TGD+A D +GYF+FVGR DDVI + Sbjct: 366 DVALRIAEGHPPGLFARYRDDPQRTADTKRDGWYLTGDRAIVDADGYFWFVGRSDDVILS 425 Query: 452 SDYRVGPFEVESALLEHPAVAEAAVVGVPDTVRWQLVKAYIVLKKGYMPSKELAEEIREK 511 S YR+GPFEVESAL EHPAVAE+AVV PD R ++VKA++VL G+ PS+ L +++ Sbjct: 426 SGYRIGPFEVESALFEHPAVAESAVVSSPDPTRGEVVKAFVVLAAGFEPSEALVGMLQDH 485 Query: 512 MKTLLSPYKVPRIIEFVDELPKTISGKIRRVELRKREEEK 551 +K+ +PYK PR IEFV LPKT+SGKIRR ELR RE E+ Sbjct: 486 VKSTTAPYKYPRKIEFVTSLPKTVSGKIRRKELRDREWER 525 Lambda K H 0.318 0.137 0.402 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: 714 Number of extensions: 37 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: 564 Length of database: 528 Length adjustment: 35 Effective length of query: 529 Effective length of database: 493 Effective search space: 260797 Effective search space used: 260797 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: 52 (24.6 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