Align 4-hydroxybutyrate-CoA ligase (AMP-forming) (EC 6.2.1.40) (characterized)
to candidate WP_011320678.1 AVA_RS20210 long-chain-fatty-acid--CoA ligase
Query= BRENDA::A4YDR9 (549 letters) >NCBI__GCF_000204075.1:WP_011320678.1 Length = 662 Score = 213 bits (543), Expect = 1e-59 Identities = 162/522 (31%), Positives = 236/522 (45%), Gaps = 36/522 (6%) Query: 28 LERAGKYFKDKTAVVYRDSRYTYSTFYDNVMVQASALMRRGFSREDKLSFISRNRPEFLE 87 +ER F +K A+++ +TY + A+AL+ G R D+++ + N PEF+ Sbjct: 7 VERGCCLFPNKPALIFEGLYFTYKQLNEMANRVANALLGLGIERGDRIALLLPNIPEFVI 66 Query: 88 SFFGVPYAGGVLVPINFRLSPKEMAYIINHSDSKFVVVDEPYLNSLLEVKDQIKAEIILL 147 S+ G+ G + V IN L E+ +I+N + +V E L +V II+ Sbjct: 67 SYLGILKIGAIAVSINPNLQSDELKFILNDCGAAVLVTTETLREKLPKVDLPHLKHIIIA 126 Query: 148 EDPDNPSASETARKEVRMTYRELVKGGSRDPLPIPAKEEYSMITLYYTSGTTGLPKGVMH 207 E A E + E + S + + + + LY TSGTTG PKG Sbjct: 127 EG----QAGEA------IALSEFMANASPNARAVEIERDEPAAILY-TSGTTGFPKGATL 175 Query: 208 HHRGAFLNAMAEVLEHQMDLNSVYLWTLPMFHAASWGFSWATVAVGATNVCLDKV----- 262 H N + +M N L LPMFH F V N C + Sbjct: 176 SHGNVISNMHSMKHCCEMRPNDQILLFLPMFHC----FGQNAVLNSGLNTCATIILQRSF 231 Query: 263 DYPLIYRLVEKERVTHMCAAPTVYVNLADYMKRNNLKFSNRVHMLVAGAAPAPATLKAMQ 322 D + + + +T PT ++ L D +L S R + A P + Sbjct: 232 DPETVLTTISEYNITIFFGVPTTFILLCDKASIRDLD-SVRYYFSAAAGLPVEIAKRWQD 290 Query: 323 EIGGYMCHVYGLTETYGPHSIC-EWRREWDSLPLEEQAKLKARQGIPYVSFEMDVFDANG 381 + G + YGLTET S E R + S+ G P + EM + + Sbjct: 291 KFGKVINQGYGLTETSPLASYNHELRYKLGSI------------GSPIENVEMKIVSLDD 338 Query: 382 KPVPWDGKTIGEVVMRGHNVALGYYKNPEKTAESFRDGWFHSGDAAVVHPDGYIEIVDRF 441 G+ +GE+V+RG NV LGY+ P +TA++ ++GWFH+GD + GY IVDR Sbjct: 339 GCEVAPGE-LGEIVIRGVNVMLGYWNRPAETAKAMKNGWFHTGDIGQIDELGYFYIVDRL 397 Query: 442 KDLINTGGEKVSSILVEKTLMEIPGVKAVAVYGTPDEKWGEVVTARIELQEGVKLTEEEV 501 KD+IN GG KV VE + + PG+ VAVYG PD GE V A I L+ +TE E+ Sbjct: 398 KDMINNGGLKVYPAEVENVIYQHPGIAEVAVYGVPDSVLGEQVKASIVLKPDQAVTEAEI 457 Query: 502 IKFCKERLAHFECPKIVEF-GPIPMTATGKMQKYVLRNEAKA 542 I FC ++LA ++ P VEF IP TGK+ K +LR E A Sbjct: 458 IAFCYQKLAQYKVPSAVEFVSSIPKNPTGKILKRLLRQENSA 499 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: 726 Number of extensions: 31 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: 662 Length adjustment: 37 Effective length of query: 512 Effective length of database: 625 Effective search space: 320000 Effective search space used: 320000 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 Apr 09 2024.
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