Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate WP_109940443.1 DLD82_RS07265 AMP-binding protein
Query= BRENDA::A4YDT1 (564 letters) >NCBI__GCF_003173335.1:WP_109940443.1 Length = 555 Score = 441 bits (1134), Expect = e-128 Identities = 244/533 (45%), Positives = 331/533 (62%), Gaps = 21/533 (3%) Query: 38 FNWVRDVFEDIHVKERGSKTALIWRDINTGEEAKLSYHELSLMSNRVLSTLRKHGLKKGD 97 FN+ DV + +R +K A+IW TGEE K ++ +L +S + L K+G+KKGD Sbjct: 27 FNFGFDVIDKWSETDR-NKLAMIWVS-QTGEEKKYTFRDLRNLSVEAANILLKYGVKKGD 84 Query: 98 VVYLMTKVHPMHWAVFLAVIKGGFVMVPSATNLTVAEMKYRFSDLKPSAIISDSLRASVM 157 V LM P W +A+IK G + P+ T LT +++YR + K S II+D+ A + Sbjct: 85 RVMLMLHRIPEWWIFVIALIKLGAIFCPAPTMLTPKDLQYRVNAGKFSFIITDTENAEKV 144 Query: 158 EEALG---SLKVEKFLIDGKRETWNSLEDESSNAEPED-----------TRGEDVIINYF 203 E+ S+K + L+DG+ W S + E P T D ++ YF Sbjct: 145 EKICRFCPSIK-HRMLVDGQLPNWISFQYELFYPAPVSRSAISMPVSMKTHATDPMLIYF 203 Query: 204 TSGTTGMPKRVIHTAVSYPVGSITTASI-VGVRESDLHLNLSATGWAKFAWSSFFSPLLV 262 TSGTTG PK V+H +P+G I TA + + +DLH S TGWAK W F +V Sbjct: 204 TSGTTGEPKMVLHDH-GHPLGHIVTARLWQDLNSNDLHFTSSDTGWAKCGWGKIFGQWIV 262 Query: 263 GATVVGINYEGKLDTRRYLGEVENLGVTSFCAPPTAWRQFITLDLDQFRFERLRSVVSAG 322 GA + + GK L +E + +FC PPT +R I DL ++ LR +SAG Sbjct: 263 GACIFIYDARGKFKATELLPLIEKYEINTFCCPPTVYRMLIIADLAKYDLRSLRHCISAG 322 Query: 323 EPLNPEVIKIWKDKFNLTIRDFYGQTETTAMVGNFPFLKVKPGSMGKPHPLYDIRLLDDE 382 EPLNPEVI+IWK++ L I + YGQ+ET + FP +K KPGSMGKP P + I L D+E Sbjct: 323 EPLNPEVIRIWKEETGLPIYEGYGQSETCCCIATFPCMKHKPGSMGKPSPGWKIELHDEE 382 Query: 383 GKEITKPYEVGHITVKLNPRPIGLFLGYSDEKK-NMESFREGYYYTGDKAYFDEEGYFYF 441 GK + + E G I + LNPRP+GL + Y D + N E F++G+YYTGDKAY DEEGYF+F Sbjct: 383 GKPVPQGTE-GRIAISLNPRPVGLVVEYLDNPEANAEVFKDGFYYTGDKAYMDEEGYFWF 441 Query: 442 VGRGDDVIKTSDYRVGPFEVESALLEHPAVAEAAVVGVPDTVRWQLVKAYIVLKKGYMPS 501 VGR DDVIK+S YR+GPFEVESAL EHPAV E+AVVG PD +R ++KA+++LK GY PS Sbjct: 442 VGRDDDVIKSSGYRIGPFEVESALQEHPAVQESAVVGSPDPIRGLIIKAFVILKSGYEPS 501 Query: 502 KELAEEIREKMKTLLSPYKVPRIIEFVDELPKTISGKIRRVELRKREEEKRKK 554 ++L +I++ +K + +PYK PRIIEFVDELPKT+SGKI+R ELR+RE K K+ Sbjct: 502 EQLIRDIQKHVKKVTAPYKYPRIIEFVDELPKTLSGKIKRAELRERELRKYKE 554 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: 821 Number of extensions: 38 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: 555 Length adjustment: 36 Effective length of query: 528 Effective length of database: 519 Effective search space: 274032 Effective search space used: 274032 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 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