Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate WP_068172570.1 HTA01S_RS13910 long-chain fatty acid--CoA ligase
Query= BRENDA::A4YDR9 (549 letters) >NCBI__GCF_001592305.1:WP_068172570.1 Length = 545 Score = 247 bits (631), Expect = 7e-70 Identities = 159/492 (32%), Positives = 252/492 (51%), Gaps = 15/492 (3%) Query: 61 ASALMRRGFSREDKLSFISRNRPEFLESFFGVPYAGGVLVPINFRLSPKEMAYIINHSDS 120 A+AL + D+++ ++ N LE +FGV G VL +N RL P+++A+I+NH+D Sbjct: 53 ANALDGLHLAAGDRVATLAWNGYRHLELYFGVSGTGRVLHTLNPRLHPEQLAWIVNHADD 112 Query: 121 KFVVVDEPYLNSLLEVKDQ---IKAEIILLEDPDNPSASETARKEVRMTYRELVKGGSRD 177 + V D +L + V + +K + L + P+ S ++Y + G D Sbjct: 113 RAVCFDMTFLPLVQAVAGKCPGVKHWVALCDADKLPADSGLPGL---VSYEAWI-GAQPD 168 Query: 178 PLPIPAKEEYSMITLYYTSGTTGLPKGVMHHHRGAFLNAMAEVLEHQMDLNS--VYLWTL 235 P +E S ++ YTSGTTG PK ++ HR L+A L + ++ L + Sbjct: 169 TYLWPDLDENSASSMCYTSGTTGNPKAALYSHRSTLLHAYGAALPDALGCSARDAILPVV 228 Query: 236 PMFHAASWGFSWATVAVGATNVCLDK-VDYPLIYRLVEKERVTHMCAAPTVYVNLADYMK 294 PMFH +WG ++ AVG V +D +Y L+E E+V+ PTV+ L +M+ Sbjct: 229 PMFHVNAWGLPYSAAAVGCKLVFPGPAMDGKSVYELIEAEKVSMAAGVPTVWQMLLGHMQ 288 Query: 295 RNNLKFSNRVHMLVAGAAPAPATLKAMQEIGGY-MCHVYGLTETYGPHSICEWRREWDSL 353 LKFS ++ G+A PA + A + G + H +G+TE ++C + +L Sbjct: 289 AGGLKFSTLKRTVIGGSACPPAMINAFHDTYGVEVLHAWGMTEMSPLGTVCTLKNAQLAL 348 Query: 354 PLEEQAKLKARQGIPYVSFEMDVFDANGKPVPWDGKTIGEVVMRGHNVALGYYKNPEKTA 413 EEQ K++ +QG +M + D +G +PWDGK G++++RG + Y+K Sbjct: 349 SPEEQTKVRLKQGRAVYGVDMKIVDESGNELPWDGKAFGDLLVRGPWIIASYFKGEGGDP 408 Query: 414 ---ESFRDGWFHSGDAAVVHPDGYIEIVDRFKDLINTGGEKVSSILVEKTLMEIPGVKAV 470 ++ GWF +GD A + DG+++I DR KD+I +GGE +SSI VE M P V Sbjct: 409 LRYDAAGKGWFPTGDVATIDADGFMQITDRSKDVIKSGGEWISSIDVENIAMAHPAVAMA 468 Query: 471 AVYGTPDEKWGEVVTARIELQEGVKLTEEEVIKFCKERLAHFECPKIVEF-GPIPMTATG 529 A G KW E + + G +LT EE++ F + + A ++ P V F IP+ ATG Sbjct: 469 ACIGMKHPKWDERPIVVVVKKPGAELTREELLAFYEGKTAKWQIPDDVVFVDAIPLGATG 528 Query: 530 KMQKYVLRNEAK 541 KMQK LR + K Sbjct: 529 KMQKMTLRQQLK 540 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: 720 Number of extensions: 41 Number of successful extensions: 7 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: 545 Length adjustment: 36 Effective length of query: 513 Effective length of database: 509 Effective search space: 261117 Effective search space used: 261117 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