Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate WP_028489631.1 Q394_RS0112845 AMP-binding protein
Query= BRENDA::A4YDT1 (564 letters) >NCBI__GCF_000621325.1:WP_028489631.1 Length = 555 Score = 124 bits (311), Expect = 1e-32 Identities = 145/561 (25%), Positives = 240/561 (42%), Gaps = 70/561 (12%) Query: 32 QLDLRRFNWVRDVFEDIHVKERGSKTALIWRDINTGEEAKLSYHELSLMSNRVLSTL-RK 90 ++D +++ + D+F+ VK+ GS A N G+ L+Y+++ ++ + + L Sbjct: 16 EIDTHQYHSLVDLFQR-SVKQYGSLPAFS----NMGKV--LTYNDVDELTRQFAAYLIHG 68 Query: 91 HGLKKGDVVYLMTKVHPMHWAVFLAVIKGGFVMVPSATNLTVAEMKYRFSDLKPSAIISD 150 GLK G+ + LM + ++ G V+V + T E++++ D +AI+ Sbjct: 69 AGLKPGERIALMMPNLLQYPIALFGALRAGLVVVNTNPLYTDRELEHQLKDSGATAIVIT 128 Query: 151 SLRASVMEEALGSLK---------------------------VEKFLIDGKRETWNSLED 183 + A +++ L + V+K + K T Sbjct: 129 ANFAHTLQDVLDKVPIKTIITTEIGDLFGFPKSLLVNLVVKYVKKMVPAFKLPTAIKFNQ 188 Query: 184 ESSNAEPEDTR-------GEDVIINYFTSGTTGMPKRVIHT-----AVSYPVGSITTASI 231 + + TR ED+ +T GTTG+ K T A + TTA + Sbjct: 189 ALTLGKQYATRFQDAEPGHEDIAFLQYTGGTTGIAKGAALTHRNIIANMLQAEAWTTADL 248 Query: 232 VGVRES-----DLHLNLSATGWAKFAWSSFFSPLLVGATVVGINYEGKLDTRRYLGEVEN 286 V +E L+ + T A FA L +GA V I D ++ ++ + Sbjct: 249 VAGKEIVITALPLYHVFALTANAMFA-------LKMGAKNVLIT--NPRDLPAFIKDLAH 299 Query: 287 LGVTSFCAPPTAWRQFITL-DLDQFRFERLRSVVSAGEPLNPEVIKIWKDKFNLTIRDFY 345 T T + + D+ + F RL+ + G + V + WK +T+ + Y Sbjct: 300 EPFTFITGVNTLYNALLNHPDIGKVDFSRLKISLGGGMAVQKSVAERWKALTGVTLLEAY 359 Query: 346 GQTETTAMVGNFPF-LKVKPGSMGKPHPLYDIRLLDDEGKEITKPYEVGHITVKLNPRPI 404 G TET+ V P L G +G P P ++ + D +G E+ G + V+ P+ + Sbjct: 360 GLTETSPAVAINPVDLHDYNGMIGLPVPSTEVSIRDVDGNELDIG-AAGELWVR-GPQVM 417 Query: 405 GLFLGYSDEKKNMESFREGYYYTGDKAYFDEEGYFYFVGRGDDVIKTSDYRVGPFEVESA 464 + DE N+ +G+ TGD A +E G+ V R D++ S + V P EVE Sbjct: 418 QGYWQRPDETANV-MVEDGWLRTGDVAVINELGFIKLVDRLKDMVLVSGFNVYPNEVEDV 476 Query: 465 LLEHPAVAEAAVVGVPDTVRWQLVKAYIVLKKGYMPSKELAEEIREKMKTLLSPYKVPRI 524 L HP V EA V+G PD ++VKA++V K + EE+R + LS YK P+ Sbjct: 477 LASHPKVLEAGVIGAPDEHSGEIVKAFVVKKDESL----TLEELRAYCRYELSAYKCPKQ 532 Query: 525 IEFVDELPKTISGKIRRVELR 545 I FV LPK+ GKI R ELR Sbjct: 533 IVFVTSLPKSNVGKILRKELR 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: 666 Number of extensions: 34 Number of successful extensions: 4 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 Apr 09 2024. 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