Align 3-hydroxybutyryl-CoA dehydrogenase subunit (EC 1.1.1.35) (characterized)
to candidate WP_029134161.1 A3GO_RS0115390 3-hydroxyacyl-CoA dehydrogenase PaaC
Query= metacyc::MONOMER-11936 (282 letters) >NCBI__GCF_000428045.1:WP_029134161.1 Length = 505 Score = 231 bits (590), Expect = 2e-65 Identities = 121/278 (43%), Positives = 174/278 (62%), Gaps = 1/278 (0%) Query: 4 IFVLGAGTMGAGIVQAFAQKGCEVIVRDIKEEFVDRGIAGITKGLEKQVAKGKMSEEDKE 63 I V+GAGTMGAGI Q A G ++ D E ++RGI I GL+KQVA+GKMSE + Sbjct: 10 IAVIGAGTMGAGIAQIAAAAGHPTLLFDANPEAIERGIGQIDAGLKKQVARGKMSEAQRT 69 Query: 64 AILSRISGTTDMKLAADCDLVVEAAIENMKIKKEIFAELDGICKPEAILASNTSSLSITE 123 A+L+ I+ ++ A+ LV+EA +E++K+K+++FA+L+ +C + ILA+NTSSLS+T Sbjct: 70 ALLANITPAHKLEELAEAALVIEAILEDLKVKQDLFAQLESLCGDKTILATNTSSLSVTA 129 Query: 124 VASATKRPDKVIGMHFFNPAPVMKLVEIIKGIATSQETFDAVKELSVAIGKEPVEVAEAP 183 +A+ RPD ++GMHFFNPAPVMKLVE++ G+ TS + + + GK PV P Sbjct: 130 IAADLARPDNLVGMHFFNPAPVMKLVEVVSGVTTSPAAAQTLFDTAANWGKHPVFAKSTP 189 Query: 184 GFVVNGILIPMINEASFILQEGIASVEDIDTAMKYGANHPMGPLALGDLIGLDVCLAIMD 243 GF+VN + P E +L+EG A V +D ++ MGP L DLIG DV A+ Sbjct: 190 GFIVNRVARPFYAEGLRLLEEGAADVATLDGIIREAGGFRMGPFELMDLIGHDVNYAVTS 249 Query: 244 VLFTE-TGDNKYRASSILRKYVRAGWLGRKSGKGFYDY 280 ++ D ++ S I ++ V G GRKSG+GFYDY Sbjct: 250 TVYAGFYYDQRFLPSLIQKELVDGGLYGRKSGRGFYDY 287 Score = 71.2 bits (173), Expect = 4e-17 Identities = 65/239 (27%), Positives = 109/239 (45%), Gaps = 13/239 (5%) Query: 32 IKEEFVDRGIAGITKG-----LEKQVAKGKMSEEDKEAILSRISGTTDMKLAADC-DLVV 85 I++E VD G+ G G + K ++ A I T ++ +A DL Sbjct: 266 IQKELVDGGLYGRKSGRGFYDYREGAVKASATDASAAAAPDSIEITGELGIAEPLVDLWK 325 Query: 86 EAAIENMKIKKEIFAELDGICKPEAILASNTSSLSITEVASATKRPDKVIGMHFFNPAPV 145 +A I +IK+ E +G + + T S T A+A D ++ + + Sbjct: 326 QAGI---RIKR---TEGNGWIRIGHTRIALTDGRSATRRAAADHLSDTILFDLALDYSKA 379 Query: 146 MKLVEIIKGIATSQETFDAVKELSVAIGKEPVEVAEAPGFVVNGILIPMINEASFILQEG 205 ++ + G S E L A+GK+ +A+ PG VV + + NEA+ + + Sbjct: 380 TRIA-LAAGDNASPEALRQATGLFQALGKQVSVIADIPGMVVMRTVCTLANEAADAVFQQ 438 Query: 206 IASVEDIDTAMKYGANHPMGPLALGDLIGLDVCLAIMDVLFTETGDNKYRASSILRKYV 264 + V DTAM+ G N+P+GPLA + IGL A+++ L G ++YR S +LR+ V Sbjct: 439 VCDVAGADTAMQSGVNYPLGPLAWAERIGLPRVQAVLENLLQAYGLDRYRVSQLLRRKV 497 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: 343 Number of extensions: 13 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: 505 Length adjustment: 30 Effective length of query: 252 Effective length of database: 475 Effective search space: 119700 Effective search space used: 119700 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: 50 (23.9 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