Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate WP_073038813.1 BUB04_RS09750 hypothetical protein
Query= BRENDA::A4YDR9 (549 letters) >NCBI__GCF_900129305.1:WP_073038813.1 Length = 507 Score = 253 bits (646), Expect = 1e-71 Identities = 175/515 (33%), Positives = 273/515 (53%), Gaps = 33/515 (6%) Query: 31 AGKYFKDKTAVV-YRDSRYTYSTFYDNVMVQASALMRRGFSREDKLSFISRNRPEFLESF 89 AGK F KTAV+ Y T+S + A+AL R G + D+++++ N FLE Sbjct: 13 AGK-FPHKTAVINYGGPSLTFSQLNERANRLANALSRLGVRKGDRVAYLFPNTSTFLEIH 71 Query: 90 FGVPYAGGVLVPINFRLSPKEMAYIINHSDSKFVVVDEPYLNSLLEVKDQI-KAEIILLE 148 F V G V VP+N RL +E+ Y I+H+D+ V+ + + +++ +K + K L Sbjct: 72 FAVAKMGAVGVPLNVRLVGRELHYQIDHADAVCVIFHQAFHDTVASIKGDLPKVRAFLCH 131 Query: 149 DPDNPSASETARKEVRMTYRELVKGGSRDPL-PIPAKEEYSMITLYYTSGTTGLPKGVMH 207 + ++Y +++GG DP P Y + YT+GTTG+PKG + Sbjct: 132 GREGDGV---------LSYESVLQGG--DPREPDETVLLYDQNVVLYTAGTTGVPKGAVL 180 Query: 208 HHRGAFLNAMAEVLEHQMDLNSVYLWTLPMFHAASW-GFSWATVAVGATNVCLDKVDYPL 266 H+ + NAMA ++++ M + V P++H+AS GF+ V +GAT V VD Sbjct: 181 SHKNSLFNAMAMIMDYGMRHDDVLQVVPPLYHSASLNGFAVTGVLLGATQVLHAAVDLGE 240 Query: 267 IYRLVEKERVTHMCAAPTVYVNLADYMKRNNLKFSNRVHMLVAGAAPAPATLK-AMQEI- 324 I++ ++ +VT T++ L Y R S RV M++ GA PA ++ A+ E+ Sbjct: 241 IFQSIQDHQVTFTWGPATLWRMLLAYPDRGRYDTS-RVRMVINGAMYMPADMRRAVLEMF 299 Query: 325 -GGYMCHVYGLTETYGPHSICEWRREWDSLPLEEQAKLKARQGIPYVSFEMDVFDANGKP 383 M YG+TE +I L E+ + A G+P ++ +FD +G+ Sbjct: 300 PNARMGDTYGMTEASPCTTI---------LRPEDVLRKPASVGVPLTICDVKIFDESGRE 350 Query: 384 VPWDGKTIGEVVMRGHNVALGYYKNPEKTAESFRDGWFHSGDAAVVHPDGYIEIVDRFKD 443 P +GE+V RG N +GY KNP+ TAE+ R+GW+H+GD +G+I +VDR KD Sbjct: 351 RP--PGQVGEIVNRG-NFMMGYDKNPQATAEAVRNGWYHTGDLGKKDEEGFIYLVDRKKD 407 Query: 444 LINTGGEKVSSILVEKTLMEIPGVKAVAVYGTPDEKWGEVVTARIELQEGVKLTEEEVIK 503 +I TGGE V S VE+ + P V AV G PDE+WGE VTA + + G ++EEE++ Sbjct: 408 MIVTGGENVYSREVEEVIASHPAVFETAVIGLPDERWGERVTAVVVPRPGAAVSEEEILA 467 Query: 504 FCKERLAHFECPKIVEF-GPIPMTATGKMQKYVLR 537 C++ LA ++CPK V F +P +A GK+ K +R Sbjct: 468 HCRKNLAGYKCPKAVVFREELPKSAAGKILKKDIR 502 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: 646 Number of extensions: 34 Number of successful extensions: 5 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: 507 Length adjustment: 35 Effective length of query: 514 Effective length of database: 472 Effective search space: 242608 Effective search space used: 242608 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