Align Peroxisomal bifunctional enzyme; PBE; PBFE; EC 4.2.1.17; EC 5.3.3.8; EC 1.1.1.35 (characterized)
to candidate PP_2047 PP_2047 3-hydroxyacyl-CoA dehydrogenase family protein
Query= SwissProt::Q08426 (723 letters) >FitnessBrowser__Putida:PP_2047 Length = 412 Score = 303 bits (775), Expect = 1e-86 Identities = 170/414 (41%), Positives = 243/414 (58%), Gaps = 22/414 (5%) Query: 296 PVSSVGVVGLGTMGRGIVISFARARIPVIAVDSDKNQLATANKMITSVLEKEASKMQ--Q 353 P++ V V+G GTMGRGIVIS A A + V+ +D + L M++ ++ K + Q Sbjct: 6 PINQVAVIGAGTMGRGIVISLANAGLSVLWLDCNAAALEAGLGMVSQAWAQQVDKQRITQ 65 Query: 354 SGHPWSGPKPRLTSSVKELGGVDLVIEAVFEEMSLKKQVFAELSAVCKPEAFLCTNTSAL 413 + + + L DLVIEAV+E ++LK+++F L A KP A L +NTSAL Sbjct: 66 AQADACLARVQAVDGYPALAEADLVIEAVYENLALKQEIFCALDAHLKPRAILASNTSAL 125 Query: 414 DVDEIASSTDRPHLVIGTHFFSPAHVMKLLEVIPSQYSSPTTIATVMNLSKKIKKIGVVV 473 D+D IA+ T RP V+G HFFSPAHVMKLLE++ ++ + L +++ K+ +V Sbjct: 126 DIDAIAAVTQRPSQVLGLHFFSPAHVMKLLEIVRGTHTDQKVLDAAKALGERMGKVAIVA 185 Query: 474 GNCFGFVGNRMLNPYYNQAYFLLEEGSKPEEVDQVLEEFGFKMGPFRVSDLAGLDVGWKS 533 GNC GF+GNRML Y +A LL EG+ P +VD VL++FGF MGPFR+ D+ G+D+ W++ Sbjct: 186 GNCPGFIGNRMLRSYVGEARKLLLEGALPHQVDAVLQQFGFAMGPFRMYDVVGIDLEWRA 245 Query: 534 RK--GQGLTGPTLLPGTPARKRGNRRYCPIPDVLCELGRFGQKTGKGWYQYDKPLGRIHK 591 R+ GQG+ P + + + LCELGR GQKTG+G+Y+Y P R + Sbjct: 246 RQLAGQGMHDPLV---------------QVDNALCELGRLGQKTGQGYYRY-APGSRQAE 289 Query: 592 PDPWLSKFLSRYRKTHHIEPRTISQDEILERCLYSLINEAFRILGEGIAASPEHIDVVYL 651 DP + + + + R IS +EILERCL +L+NE ++L EGIAAS ID V+L Sbjct: 290 HDPQVDALVLQVSQNLGYRRRGISAEEILERCLLALVNEGAKVLQEGIAASSGDIDQVWL 349 Query: 652 HGYGWPRHKGGPMFYASTVGLPTVLEKLQKYYRQNPDIPQLEPSDYLKKLASQG 705 HGYG+P GGPM +A G P +L +L+ Y Q P+ L L + G Sbjct: 350 HGYGFPAATGGPMRWADEQGAPFILARLE--YLQGVLGEHWRPAGLLYSLVAGG 401 Lambda K H 0.319 0.136 0.405 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: 663 Number of extensions: 27 Number of successful extensions: 4 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: 723 Length of database: 412 Length adjustment: 35 Effective length of query: 688 Effective length of database: 377 Effective search space: 259376 Effective search space used: 259376 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 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