Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate GFF3161 Psest_3221 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II
Query= BRENDA::A4YDR9 (549 letters) >FitnessBrowser__psRCH2:GFF3161 Length = 561 Score = 229 bits (585), Expect = 2e-64 Identities = 160/537 (29%), Positives = 251/537 (46%), Gaps = 23/537 (4%) Query: 19 YSVLTPLLFLERAGKYFKDKTAVVYRDS-RYTYSTFYDNVMVQASALMRRGFSREDKLSF 77 Y +L L L +G ++ +VYRD RY Y T V A+ L G D ++ Sbjct: 16 YPLLIKRLLL--SGVRYERTREIVYRDQLRYDYRTLNQRVARLANVLTAAGVKAGDTVAV 73 Query: 78 ISRNRPEFLESFFGVPYAGGVLVPINFRLSPKEMAYIINHSDSKFVVVDEPYLNSLLEVK 137 + + +LE F +P G V+ IN RLSP ++ Y +NH+D +FV+V+ ++ + Sbjct: 74 MDWDSHRYLECMFAIPMIGAVVHTINVRLSPDQILYTMNHADDRFVLVNSEFVPLYQAIA 133 Query: 138 DQIKA--EIILLEDPDNPSASETARKEVRMTYRELVKGGSRDPLPIPAKEEYSMITLYYT 195 Q+ + +LL D D + + Y L+ + P +E S+ T +YT Sbjct: 134 GQLTTVQKTLLLTDGD---VHDAGLPDCVGEYESLLAAAAPS-YDFPDFDEDSVATTFYT 189 Query: 196 SGTTGLPKGVMHHHRGAFLNAMAEVLE-------HQMDLNSVYLWTLPMFHAASWGFSWA 248 +GTTG PKGV HR L+ +A + M + VY+ PMFH +WG + Sbjct: 190 TGTTGNPKGVYFTHRQLVLHTLAAAVTVGCRENPRLMGSDDVYMPITPMFHVHAWGLPYV 249 Query: 249 TVAVGATNVCLDKVDYPLIYRLVEKERVTHMCAAPTVYVNLADYMKRNNLKFSNRVHMLV 308 +G V + D + L +E+VT PT+ L + F + + Sbjct: 250 ATMLGLKQVYPGRYDPEYLIDLWRREQVTFSHCVPTIVQMLLNAKAAQGTDFKGW-KITI 308 Query: 309 AGAAPAPATLKAMQEIGGYMCHVYGLTETYGPHSICEWRREWDSLPLEEQAKLKARQGIP 368 G+A + G + YG++ET S E + ++ + G+P Sbjct: 309 GGSALTRGLYDQAKARGMNLIAAYGMSETCPLISGAHINDELLEADEDTRSTFHLKAGVP 368 Query: 369 YVSFEMDVFDANGKPVPWDGKTIGEVVMRGHNVALGYYKNPEKTAESFRDGWFHSGDAAV 428 V + + A+G +P DG + GE+V+R + GYY PEK+ E + DGW H+GD AV Sbjct: 369 VVLVDAAIQAADGSFLPADGTSQGELVLRAPWLTQGYYNEPEKSEELWADGWLHTGDVAV 428 Query: 429 VHPDGYIEIVDRFKDLINTGGEKVSSILVEKTLMEIPGVKAVAVYGTPDEKWGEVVTARI 488 + IEI DR KD+I TGGE +SS+ +E + V+ VAV G PDE+WGE A + Sbjct: 429 IDEMANIEIRDRIKDVIKTGGEWLSSLTLEGLISRHEAVRDVAVVGVPDERWGERPFALV 488 Query: 489 ELQEGVKLTEEEVIKFCKERLAHFECPK------IVEFGPIPMTATGKMQKYVLRNE 539 L EG +L +++ F + +A K + IP T+ GK+ K +R+E Sbjct: 489 VLAEGRELNADQLQTFLEPAVAEGHINKWAIPQQVAVVSEIPKTSVGKLDKKRIRSE 545 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: 697 Number of extensions: 33 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: 561 Length adjustment: 36 Effective length of query: 513 Effective length of database: 525 Effective search space: 269325 Effective search space used: 269325 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 17 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