Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate WP_009564552.1 RSPH17029_RS01295 acyl--CoA ligase family protein
Query= BRENDA::A4YDR9 (549 letters) >NCBI__GCF_000015985.1:WP_009564552.1 Length = 549 Score = 399 bits (1025), Expect = e-115 Identities = 219/532 (41%), Positives = 306/532 (57%), Gaps = 2/532 (0%) Query: 11 GVDPTGSWYSVLTPLLFLERAGKYFKDKTAVVYRDSRYTYSTFYDNVMVQASALMRRGFS 70 G++ + Y+ LTPL L+RA + D+TA+V R TY ++ V ASAL G Sbjct: 9 GLEKCAANYAALTPLSHLKRAAEVHTDRTALVNGSIRLTYGEYHARVSRLASALAGMGIQ 68 Query: 71 REDKLSFISRNRPEFLESFFGVPYAGGVLVPINFRLSPKEMAYIINHSDSKFVVVDEPYL 130 D ++ + N E+ FGVP G +L IN RL ++YI+ H +K ++ D +L Sbjct: 69 PGDVVATLLPNIAAHAEAHFGVPACGAILNAINTRLDLDTVSYILEHGGAKLLLCDTAFL 128 Query: 131 NSLLEVKDQIKAEIILLEDPDNPSASETARKEVRMTYRELVKGGSRDPLPIPAKEEYSMI 190 + +++ + +L + + A + EV + Y +L+ G+ + ++E+ I Sbjct: 129 KLAKDACARLEGKAPILVEVCDREAGFSPSGEV-LEYEDLMDRGNPWAPWVMPEDEWESI 187 Query: 191 TLYYTSGTTGLPKGVMHHHRGAFLNAMAEVLEHQMDLNSVYLWTLPMFHAASWGFSWATV 250 L YTSGTTG PKGV++HHRGA+L+ + +M L VYL +P+FH W +W Sbjct: 188 ALNYTSGTTGRPKGVVYHHRGAYLSTYGNAIAWRMQLYPVYLTIVPLFHCNGWCHTWMVP 247 Query: 251 AVGATNVCLDKVDYPLIYRLVEKERVTHMCAAPTVYVNLADYMKRNNLKFSNRVHMLVAG 310 +G T VC + IY + E VTH AP V L + + F V + AG Sbjct: 248 MLGGTVVCCRDITAKAIYAAIADEGVTHFGGAPIVLNTLINAAPEDRRSFDQVVEVFTAG 307 Query: 311 AAPAPATLKAMQEIGGYMCHVYGLTETYGPHSICEWRREWDSLPLEEQAKLKARQGIPYV 370 A P ATL A++ +G + VYGLTE YGP + C W+ EWD EE+A LKAR G+ Sbjct: 308 APPPAATLAAIEPLGFNVTQVYGLTEVYGPATECIWKPEWDETAGEERAALKARTGVAMA 367 Query: 371 SFE-MDVFDANGKPVPWDGKTIGEVVMRGHNVALGYYKNPEKTAESFRDGWFHSGDAAVV 429 + E +V D +G+P+P D +GE+ MRG+ V GYYKNPE TAE+FRDGWF SGD A Sbjct: 368 TLEGAEVHDTHGQPIPRDTVHLGEIAMRGNMVMKGYYKNPEATAEAFRDGWFRSGDIAFQ 427 Query: 430 HPDGYIEIVDRFKDLINTGGEKVSSILVEKTLMEIPGVKAVAVYGTPDEKWGEVVTARIE 489 HPDGYI+I DR KD+I +GGE VSS+ VE + P V AV PDE+WGEV A +E Sbjct: 428 HPDGYIKITDRAKDIIISGGENVSSVEVEGVIAHHPAVSLCAVVAKPDERWGEVPCAFVE 487 Query: 490 LQEGVKLTEEEVIKFCKERLAHFECPKIVEFGPIPMTATGKMQKYVLRNEAK 541 L+ G + TEEE+I F +ERLA F+ PK V F +P T+TGK+QK+ LR AK Sbjct: 488 LKRGRQATEEEIIAFARERLAGFKTPKQVIFCELPKTSTGKIQKFELRAVAK 539 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: 772 Number of extensions: 37 Number of successful extensions: 3 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: 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 Apr 10 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