Align 3-hydroxybutyryl-CoA dehydrogenase subunit (EC 1.1.1.35) (characterized)
to candidate WP_086511959.1 BZY95_RS21610 3-hydroxyacyl-CoA dehydrogenase
Query= metacyc::MONOMER-11936 (282 letters) >NCBI__GCF_002151265.1:WP_086511959.1 Length = 488 Score = 207 bits (527), Expect = 4e-58 Identities = 113/272 (41%), Positives = 169/272 (62%), Gaps = 1/272 (0%) Query: 12 MGAGIVQAFAQKGCEVIVRDIKEEFVDRGIAGITKGLEKQVAKGKMSEEDKEAILSRISG 71 MG GIVQ FA G +V + D +E ++ + I + LE+ VAKG++S E++EA L+RI Sbjct: 1 MGRGIVQLFAVAGHQVWLHDSREGAIEEALRFIGELLERSVAKGRLSAEEREATLARIRP 60 Query: 72 TTDMKLAADCDLVVEAAIENMKIKKEIFAELDGICKPEAILASNTSSLSITEVASATKRP 131 + + A+CDLV+EA +EN++ K+ + +L+ + EAILASNTSSLS+T +ASA + P Sbjct: 61 SDGLAGLAECDLVIEAIVENLEAKQALLRQLEEVVSHEAILASNTSSLSVTRLASACRHP 120 Query: 132 DKVIGMHFFNPAPVMKLVEIIKGIATSQETFDAVKELSVAIGKEPVEVAEAPGFVVNGIL 191 ++V G HFFNP P+MK+VE+++G T E ++ L+ G P + PGF+VN Sbjct: 121 ERVAGYHFFNPVPLMKIVEVVRGELTRPEVIARLERLAREAGHFPALTPDTPGFLVNHAG 180 Query: 192 IPMINEASFILQEGIASVEDIDTAMKYGANHPMGPLALGDLIGLDVCLAIMDVLFTETGD 251 + EA +L EGIA+ ID + MGP L DLIGLDV A+M+ ++ + D Sbjct: 181 RAYVPEALRLLDEGIATPAQIDRILCLSLGFRMGPFELLDLIGLDVSHAVMESIYRQFYD 240 Query: 252 NKYRASS-ILRKYVRAGWLGRKSGKGFYDYSK 282 + Y S + + + AG LGRK+G+GFY Y + Sbjct: 241 DPYYTPSWQVPRRIAAGLLGRKAGQGFYRYEE 272 Score = 63.5 bits (153), Expect = 9e-15 Identities = 36/108 (33%), Positives = 58/108 (53%), Gaps = 3/108 (2%) Query: 163 DAVKELSVAIGKE--PVEVA-EAPGFVVNGILIPMINEASFILQEGIASVEDIDTAMKYG 219 + + + S A+G + PVEV ++PGFV IL M+N S I++ G+A +D A+K Sbjct: 375 EVLAQASAALGADGVPVEVIHDSPGFVAQRILAFMVNIGSEIVRRGVAEPATLDRAVKLA 434 Query: 220 ANHPMGPLALGDLIGLDVCLAIMDVLFTETGDNKYRASSILRKYVRAG 267 +P GPLA G+ G ++ L G+ +YR S L++ + G Sbjct: 435 LGYPQGPLAFGERFGPQTFARVLGCLHDHYGEPRYRVSPWLKQRIALG 482 Lambda K H 0.318 0.136 0.378 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: 332 Number of extensions: 16 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 282 Length of database: 488 Length adjustment: 30 Effective length of query: 252 Effective length of database: 458 Effective search space: 115416 Effective search space used: 115416 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 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