Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate WP_012469455.1 GLOV_RS06850 AMP-binding protein
Query= BRENDA::A4YDR9 (549 letters) >NCBI__GCF_000020385.1:WP_012469455.1 Length = 549 Score = 199 bits (506), Expect = 2e-55 Identities = 165/552 (29%), Positives = 263/552 (47%), Gaps = 46/552 (8%) Query: 28 LERAGKYFKDKTAVVY--RDSRYTYSTFYDNVMVQASALMRRGFSREDKLSFISRNRPEF 85 L+ F D A+VY R RY+Y F + A L++ G + D +S + N PE+ Sbjct: 13 LDEIAARFPDNDALVYPERGLRYSYKQFNEICRQVAKGLLKLGIKKGDHVSIWAYNVPEW 72 Query: 86 LESFFGVPYAGGVLVPINFRLSPKEMAYIINHSDSKFVVV-----DEPYLNSLLEVKDQI 140 + F P G VLV +N E+ Y++N SDS + + D Y+ +L EV I Sbjct: 73 VILQFATPKIGAVLVTVNTAYKSSELEYVLNQSDSTTLFMVKSFKDTDYVKTLAEVVPSI 132 Query: 141 K--------------AEIILLEDPDNPSASETARKEVRMTYRELVKGGSRDPLPI--PAK 184 + ++ + P+ + EL K S + L Sbjct: 133 HDSEPGKLNHAKLPFLKTVVFIGDETPAGMLNFNSII-----ELGKAVSDEELAAVEATL 187 Query: 185 EEYSMITLYYTSGTTGLPKGVMHHHRGAFLNAMAEVLEHQMDLNSVYLWT-LPMFHAASW 243 + + I + YTSGTTG PKGVM H N ++ E N L +P FH Sbjct: 188 DCHDTINMQYTSGTTGFPKGVMLTHYNLANNGF-QIGECMKFTNQDRLCIPVPFFHCFGC 246 Query: 244 GF-SWATVAVGATNVCLDKVDYPLIYRLVEKERVTHMCAAPTVYVNLADY--MKRNNLKF 300 + V G+ V ++ D + + +E E+ T + PT+++ ++ K+ NL Sbjct: 247 VLGTMVCVTHGSAMVPVELFDPLKVLQTIEAEKCTAVHGVPTMFIAELEHPEFKKFNLS- 305 Query: 301 SNRVHMLVAGAAPAPATLKAMQEIG-GYMCHVYGLTETYGPHSICEWRREWDSLPLEEQA 359 S R ++ P KA++++ + VYG TE I + R E P+E + Sbjct: 306 SLRTGIMAGSVCPIEVMKKAVRDMNLTEITSVYGQTEA--SPGITQTRTED---PVELRV 360 Query: 360 KLKARQGIPYVSFEMDVFDANGKPVPWDGKTIGEVVMRGHNVALGYYKNPEKTAESF-RD 418 R +P E+ + D GK GE+ RG+ V GYYK PE+TA+ D Sbjct: 361 STVGR-ALPEA--EVKIIDIETGATLPPGKQ-GELCARGYMVMKGYYKMPEETAKVIDAD 416 Query: 419 GWFHSGDAAVVHPDGYIEIVDRFKDLINTGGEKVSSILVEKTLMEIPGVKAVAVYGTPDE 478 W H+GD A++ +GY +I R K +I GGE + +E+ L P + V +YG PD+ Sbjct: 417 NWLHTGDLAIMDENGYCKITGRIKQMIIRGGENIYPKEIEEFLYTHPKISDVQIYGVPDK 476 Query: 479 KWGEVVTARIELQEGVKLTEEEVIKFCKERLAHFECPKIVEF-GPIPMTATGKMQKYVLR 537 K+GE V A + L++G+++TEEEV +FC+ ++A+++ PK V+F PMTA+GK+QK+ LR Sbjct: 477 KYGEQVMAAVILKKGMEMTEEEVKEFCRGKIANYKVPKYVKFVEGYPMTASGKIQKFKLR 536 Query: 538 NEAKAKANKEKS 549 A + + E++ Sbjct: 537 EMAIKELHLEEA 548 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: 671 Number of extensions: 30 Number of successful extensions: 5 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: 549 Length of database: 549 Length adjustment: 36 Effective length of query: 513 Effective length of database: 513 Effective search space: 263169 Effective search space used: 263169 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