Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate WP_110207305.1 DNK54_RS12540 AMP-binding protein
Query= BRENDA::A4YDT1 (564 letters) >NCBI__GCF_003194585.1:WP_110207305.1 Length = 577 Score = 355 bits (911), Expect = e-102 Identities = 225/538 (41%), Positives = 303/538 (56%), Gaps = 19/538 (3%) Query: 38 FNWVRDVFEDIHVKERGSKTALIWRDINTGEEAKLSYHELSLMSNRVLSTLRKHGLKKGD 97 FN+V D F+ RG+ + G A S+ EL S +V L G++ GD Sbjct: 41 FNFVHDWFD---AYARGNDRPGLVIVEEDGRRASYSFGELVTRSEQVAQHLSALGVRAGD 97 Query: 98 VVYLMTKVHPMHWAVFLAVIKGGFVMVPSATNLTVAEMKYRFSDLKPSAIISDSLRASVM 157 V +M W LA+I+ G V++P+ T + AE+ R A++ ++ A+ Sbjct: 98 SVVVMLGNQVELWESMLALIRLGAVIMPTTTAVGPAELVDRLDRGAARAVVCNAADAAKF 157 Query: 158 EEALGS-LKVEKFLIDGKRETWNSLEDESSNA----EPEDTRGEDVIINYFTSGTTGMPK 212 +E G+ L+V ++ + D + A E +D ++ YFTSGTT PK Sbjct: 158 DEVPGAYLRVAVGEAPTGWASYAAAYDRDAGAVATLEHPGNGSDDRLLLYFTSGTTSRPK 217 Query: 213 RVIHTAVSYPVGSITTASIVGVRESDLHLNLSATGWAKFAWSSFFSPLLVGATVVGINYE 272 V HT SYP+G ++T +G++ D+HLN+S+ GWAK AWS+FF+P L ATV NY Sbjct: 218 LVEHTHTSYPIGHLSTMYWLGLQPGDVHLNISSPGWAKHAWSNFFAPWLAEATVFVYNY- 276 Query: 273 GKLDTRRYLGEVENLGVTSFCAPPTAWRQFITLDLDQFRFERLRSVVSAGEPLNPEVIKI 332 + D LG++ GVT+FCAPPT WR I DL LR ++AGEPLNPEVI Sbjct: 277 ARFDAMALLGQIRTEGVTTFCAPPTVWRMLINADLSGGPGV-LREAIAAGEPLNPEVISQ 335 Query: 333 WKDKFNLTIRDFYGQTETTAMVGNFPFLKVKPGSMGKPHPLYDIRLLDDEGKEITKPYEV 392 + + LTIRD +GQTE TA + N P VK GSMG+P P I L+D + + Sbjct: 336 VERHWGLTIRDGFGQTEMTAAIANAPGQPVKAGSMGRPLPGVPIVLVDPVEGSVVEGVGE 395 Query: 393 GHITVKLNPR----PIGLFLGYS-DEKKNMESFREGYYYTGDKAYFDEEGYFYFVGRGDD 447 G I + L+ R P+ L GY DE+KN E+ G+++TGD A DEEG +VGR DD Sbjct: 396 GEICLDLSVRDGAGPLTLMTGYQGDEEKNAEAMAGGFFHTGDVASRDEEGQITYVGRTDD 455 Query: 448 VIKTSDYRVGPFEVESALLEHPAVAEAAVVGVPDTVRWQLVKAYIVLKKGYMPSKELAEE 507 V K SDY+V PFE+ES LLEHPAVAEAAVV PD VR + KAY+ L G+ P+ E A+ Sbjct: 456 VFKASDYKVSPFELESVLLEHPAVAEAAVVPAPDPVRLAVPKAYVALVPGHEPTAETAKS 515 Query: 508 IREKMKTLLSPYKVPRIIEFVDELPKTISGKIRRVELRKREEE---KRKKGEVGQNEY 562 I + L+PY R +EF ELPKTISGKIRRVELR+RE E R GE ++ Sbjct: 516 ILHYAREHLAPYLRVRRLEFY-ELPKTISGKIRRVELRQRENEVEGSRLDGEYRDEDF 572 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: 748 Number of extensions: 30 Number of successful extensions: 6 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: 577 Length adjustment: 36 Effective length of query: 528 Effective length of database: 541 Effective search space: 285648 Effective search space used: 285648 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