Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate WP_035703058.1 BA79_RS12435 AMP-binding protein
Query= BRENDA::A4YDR9 (549 letters) >NCBI__GCF_000691145.1:WP_035703058.1 Length = 502 Score = 209 bits (533), Expect = 2e-58 Identities = 152/492 (30%), Positives = 229/492 (46%), Gaps = 25/492 (5%) Query: 48 YTYSTFYDNVMVQASALMRRGFSREDKLSFISRNRPEFLESFFGVPYAGGVLVPINFRLS 107 YT+ + + A L R+G + D++ FI +N F AG V VP++++L+ Sbjct: 28 YTFEEYAKRIDQLAHYLHRKGIRKGDRVCFICQNHHHFSTIMLAAIKAGAVAVPLSWQLT 87 Query: 108 PKEMAYIINHSDSKFVVVDEPYLNSLLEVKDQIKAEIILLEDPDNPSASETARKEVRMTY 167 E+ I+ ++ K + D E +D I A + LED + A+ + Sbjct: 88 SFELEGILKKAEPKALFFDR-------EFRDIIAAVNVSLEDCLMVESGVNAK--TTQLF 138 Query: 168 RELVKGGSRDPLPIPAKEEYSMITLYYTSGTTGLPKGVMHHHRGAFLNAMAEVLEHQMDL 227 +++ L EE + + +TSGTTG PKG M H G + DL Sbjct: 139 EDILASNDGSDLAEQVSEE-DLAMILFTSGTTGNPKGCMVGH-GRIYQFLTRRGNRGFDL 196 Query: 228 NSV-YLWTLPMFHAASWGFSWATVAVGATNVCLDKVDYPLIYRLVEKERVTHMCAAPTVY 286 YL + P++H +S A G T V L I +EKER+T M A P+ Y Sbjct: 197 KGKRYLASHPLYHMSSINHLIAAAIEGYTLVFLHDATPKRILETIEKERITFMMAFPSAY 256 Query: 287 VNLADYMKRNNLKFSNRVHMLVAGAAPAPATL-KAMQEIGGYMCHVYGLTETYGPHSICE 345 + + MKR++ S+ + ++G P L + +E+G M H YG TE + + Sbjct: 257 TYMLEEMKRSSYDLSS-FEIAISGGTKVPVRLIRDYKEVGIQMMHGYGSTEAW---VVSA 312 Query: 346 WRREWDSLPLEEQAKLKARQGIPYVSFEMDVFDANGKPVPWDGKTIGEVVMRGHNVALGY 405 W + K+ + V E + G+ IGEVVMR LGY Sbjct: 313 WHPAMGEDKMGSAGKVDPDVEVKIVHPETEEALPAGE--------IGEVVMRSPFYFLGY 364 Query: 406 YKNPEKTAESFRDGWFHSGDAAVVHPDGYIEIVDRFKDLINTGGEKVSSILVEKTLMEIP 465 Y PE T + +DGWFH GDA + DG++ I R+KD+I GG+ + VE+ + +IP Sbjct: 365 YHQPEATEKVLKDGWFHMGDAGYLDEDGFLYITGRYKDVILYGGDNIYPDQVEEVIDQIP 424 Query: 466 GVKAVAVYGTPDEKWGEVVTARIELQEGVKLTEEEVIKFCKERLAHFECPKIVEFGPIPM 525 GV AV G PD+ +GEV +A I E V EE+V+ +CKERLA ++ P I +P Sbjct: 425 GVIESAVIGVPDDLYGEVPSAYIVKDESVDFCEEDVLNYCKERLADYKVPSIHFTHDLPK 484 Query: 526 TATGKMQKYVLR 537 GK+ K LR Sbjct: 485 NKLGKIMKKDLR 496 Lambda K H 0.319 0.136 0.411 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: 659 Number of extensions: 43 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: 549 Length of database: 502 Length adjustment: 35 Effective length of query: 514 Effective length of database: 467 Effective search space: 240038 Effective search space used: 240038 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: 52 (24.6 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