Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate WP_034211018.1 N787_RS04435 long-chain fatty acid--CoA ligase
Query= BRENDA::A4YDT1 (564 letters) >NCBI__GCF_000747155.1:WP_034211018.1 Length = 560 Score = 145 bits (365), Expect = 5e-39 Identities = 137/511 (26%), Positives = 221/511 (43%), Gaps = 45/511 (8%) Query: 72 LSYHELSLMSNRVLS-TLRKHGLKKGDVVYLMTKVHPMHWAVFLAVIKGGFVMVPSATNL 130 ++Y E+ +S + + L + LKKGD V LM + V++ G +V + Sbjct: 51 ITYAEVDRLSTQFANYLLHELKLKKGDRVALMMPNVLQYPIAIFGVLRAGLTVVNTNPMY 110 Query: 131 TVAEMKYRFSDLKPSAIISDSLRASVMEEALGSLKVEKFLIDG--------KRETWNSLE 182 T E+K++ D SAI+ A V+ + + +V++ L+ G K N + Sbjct: 111 TARELKHQLVDSGASAIVVLENFAHVVADVVAETQVKQVLVTGVGDMLGFPKGALVNFVL 170 Query: 183 DESSNAEPE------------------------DTRGEDVIINYFTSGTTGMPKRVIHTA 218 PE D RG D+ +T GTTG+ K + T Sbjct: 171 RHVKKQVPEYDLPGAIRFGDAVAMGAKHQLPDIDIRGHDIAFLQYTGGTTGVAKGAMLTH 230 Query: 219 VSYPVGSITTASIVGVRESDLHLNLSATGWAKFAWSSFFSPLLVGATVVGINY--EGKLD 276 + ++ +G H + T + + + LV G+N+ D Sbjct: 231 RNLVANMQQSSVWLGSNAKPGH-EVIITALPLYHIFALTANCLVFMKFGGLNHLITNPRD 289 Query: 277 TRRYLGEVENLGVTSFCAPPTAWRQFI-TLDLDQFRFERLRSVVSAGEPLNPEVIKIWKD 335 + ++ E+ + T+ T + + T D+ F + + G + V + WK Sbjct: 290 MKGFVAELSKIPFTAITGVNTLFNGLLNTPGFDKIDFSNMHLSLGGGMAVQRAVAERWKK 349 Query: 336 KFNLTIRDFYGQTETTAMVGNFPF-LKVKPGSMGKPHPLYDIRLLDDEGKEITKPYEVGH 394 +T+ + YG TET+ P L+ G++G P P D + DD GK++ EVG Sbjct: 350 VTGITLVEAYGLTETSPAACMNPMDLEDFNGAIGLPIPSTDACVKDDAGKQLPVG-EVGE 408 Query: 395 ITVKLNPRPIGLFLGYSDEKKNMESFREGYYYTGDKAYFDEEGYFYFVGRGDDVIKTSDY 454 + ++ G + + K +++ EG+ +TGD A D G+FY V R D+I S + Sbjct: 409 LCIRGPQVMAGYWQRPEETAKVIDA--EGWLHTGDMAKMDAGGFFYIVDRKKDMILVSGF 466 Query: 455 RVGPFEVESALLEHPAVAEAAVVGVPDTVRWQLVKAYIVLKKGYMPSKELAEEIREKMKT 514 V P EVE + P V E A VGVPD + VK IV K + A+++R K Sbjct: 467 NVYPNEVEDVIALMPGVLEVAAVGVPDDKSGEAVKVVIVRKDPAL----TADQVRAFCKE 522 Query: 515 LLSPYKVPRIIEFVDELPKTISGKIRRVELR 545 L+ YK PR++EF ELPK+ GKI R ELR Sbjct: 523 NLTGYKQPRLVEFRTELPKSNVGKILRRELR 553 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: 628 Number of extensions: 25 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 564 Length of database: 560 Length adjustment: 36 Effective length of query: 528 Effective length of database: 524 Effective search space: 276672 Effective search space used: 276672 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