Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate WP_011778819.1 MVAN_RS07875 AMP-dependent synthetase
Query= BRENDA::A4YDT1 (564 letters) >NCBI__GCF_000015305.1:WP_011778819.1 Length = 566 Score = 377 bits (968), Expect = e-109 Identities = 224/529 (42%), Positives = 307/529 (58%), Gaps = 15/529 (2%) Query: 38 FNWVRDVFEDIHVKERGSKTALIWRDINTGEEAKLSYHELSLMSNRVLSTLRKHGLKKGD 97 FNW D F+ + R + +W G E K+++ +++ S++V S LR G+ KGD Sbjct: 41 FNWATDWFDAV---ARDNDGVALWIVEQDGTELKVTFDQMARRSDQVASWLRGLGVGKGD 97 Query: 98 VVYLMTKVHPMHWAVFLAVIKGGFVMVPSATNLTVAEMKYRFSDLKPSAIISDSLRASVM 157 V LM W LAV K G V++P+ L ++ R + +I+++ A+ Sbjct: 98 RVILMLGNQVELWESMLAVAKLGAVIMPTTGALGSEDLADRIGRGRAGFVIANAADAAKF 157 Query: 158 EEALGSLKVEKFLIDGKRETWNSLEDESSNA-EPED--TRGEDVIINYFTSGTTGMPKRV 214 + G + + W+ D ++ A EP D T +D ++ YFTSGTT PK V Sbjct: 158 ADVPGDYV--RIAVGDPVPGWHPYSDTAAAAAEPHDPQTSADDPLLVYFTSGTTSKPKLV 215 Query: 215 IHTAVSYPVGSITTASIVGVRESDLHLNLSATGWAKFAWSSFFSPLLVGATVVGINYEGK 274 H+ +SYPVG +TT + +GVR D+HL +S+ GWAK AWS FF+P L AT+ NY G+ Sbjct: 216 EHSQISYPVGHLTTMAWIGVRPGDIHLAISSPGWAKHAWSCFFAPWLAEATIFVYNY-GR 274 Query: 275 LDTRRYLGEVENLGVTSFCAPPTAWRQFITLDLDQFRFERLRSVVSAGEPLNPEVIKIWK 334 D L ++ GV++FCAPPT WR I DL + R LR V+ AGEPLNPEVI + Sbjct: 275 FDAAALLQQMRRAGVSTFCAPPTVWRMLIQSDLGE-RPPGLREVLGAGEPLNPEVIGAVE 333 Query: 335 DKFNLTIRDFYGQTETTAMVGNFPFLKVKPGSMGKPHPLYDIRLLDDEGKEITKPYEVGH 394 + LTIRD +GQTETT VGN P VK GSMG+P P + L++ E+ + G Sbjct: 334 RAWGLTIRDGFGQTETTLQVGNTPGQPVKAGSMGRPMPGVPVVLVNPLTGELA---DEGE 390 Query: 395 ITVKLNPRPIGLFLGY-SDEKKNMESFREGYYYTGDKAYFDEEGYFYFVGRGDDVIKTSD 453 I + L+ P+ L GY D+ +N R+GYY+TGD A D +GY ++GR DDV K+SD Sbjct: 391 ICLDLSRTPLNLMTGYLGDDARNALVMRDGYYHTGDVASRDADGYITYIGRTDDVFKSSD 450 Query: 454 YRVGPFEVESALLEHPAVAEAAVVGVPDTVRWQLVKAYIVLKKGYMPSKELAEEIREKMK 513 Y+V PFE+ES L+EHPAV EAAVV PD R + KAYI L +G+ + A I E + Sbjct: 451 YKVSPFELESVLIEHPAVVEAAVVPQPDDTRLAVPKAYISLAEGWAADADTARSILEHSR 510 Query: 514 TLLSPYKVPRIIEFVDELPKTISGKIRRVELRKREEEKRKKGEVGQNEY 562 L+PY R +EF ELPKTISGKIRRVELR+REE+ G+ EY Sbjct: 511 DHLAPYLKVRRLEFY-ELPKTISGKIRRVELRRREEDAHTAGQPIDTEY 558 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: 775 Number of extensions: 43 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: 566 Length adjustment: 36 Effective length of query: 528 Effective length of database: 530 Effective search space: 279840 Effective search space used: 279840 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