Align 3-hydroxybutyryl-CoA dehydrogenase; EC 1.1.1.157 (characterized)
to candidate WP_029133989.1 A3GO_RS0114400 3-hydroxybutyryl-CoA dehydrogenase
Query= CharProtDB::CH_091789 (282 letters) >NCBI__GCF_000428045.1:WP_029133989.1 Length = 282 Score = 338 bits (867), Expect = 8e-98 Identities = 169/280 (60%), Positives = 210/280 (75%) Query: 1 MKKVCVIGAGTMGSGIAQAFAAKGFEVVLRDIKDEFVDRGLDFINKNLSKLVKKGKIEEA 60 + V VIGAGTMG+GIAQ FAA GF+V+L DI D + RGLD I KNL ++++K KI A Sbjct: 3 VNSVGVIGAGTMGNGIAQVFAAAGFKVILHDIADAPLQRGLDTIEKNLDRMLQKEKISAA 62 Query: 61 TKVEILTRISGTVDLNMAADCDLVIEAAVERMDIKKQIFADLDNICKPETILASNTSSLS 120 K L ISG L+ A DL++EAA E ++IK +IF +LD ICKPE +LA+NTSS+S Sbjct: 63 DKSATLANISGVTSLDELAGADLIVEAASENLEIKSKIFQELDRICKPEAVLATNTSSIS 122 Query: 121 ITEVASATKRPDKVIGMHFFNPAPVMKLVEVIRGIATSQETFDAVKETSIAIGKDPVEVA 180 +T +A T+RP+KVIGMHF NP PVMKLVEVIR + TS E + + + S IGK PVEV Sbjct: 123 LTRIARETQRPEKVIGMHFMNPVPVMKLVEVIRALQTSDEVYQLIDDLSKKIGKVPVEVN 182 Query: 181 EAPGFVVNRILIPMINEAVGILAEGIASVEDIDKAMKLGANHPMGPLELGDFIGLDICLA 240 ++PGFV NRIL+PMINEA+ L EG+A+VE ID+ MKLG NHPMGPL L D IGLD CL+ Sbjct: 183 DSPGFVSNRILLPMINEAIYTLYEGVATVEAIDEVMKLGMNHPMGPLALADLIGLDTCLS 242 Query: 241 IMDVLYSETGDSKYRPHTLLKKYVRAGWLGRKSGKGFYDY 280 IM+VL+ GD+KYRP LL++ V AG+LGRKSGKGFYDY Sbjct: 243 IMEVLHEGMGDTKYRPCPLLRRMVDAGYLGRKSGKGFYDY 282 Lambda K H 0.319 0.137 0.386 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: 261 Number of extensions: 4 Number of successful extensions: 1 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: 282 Length of database: 282 Length adjustment: 26 Effective length of query: 256 Effective length of database: 256 Effective search space: 65536 Effective search space used: 65536 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: 47 (22.7 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