Align Peroxisomal bifunctional enzyme; PBE; PBFE; EC 4.2.1.17; EC 5.3.3.8; EC 1.1.1.35 (characterized)
to candidate Ac3H11_2523 Enoyl-CoA hydratase (EC 4.2.1.17) / Delta(3)-cis-delta(2)-trans-enoyl-CoA isomerase (EC 5.3.3.8) / 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) / 3-hydroxybutyryl-CoA epimerase (EC 5.1.2.3)
Query= SwissProt::Q08426 (723 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2523 Length = 699 Score = 507 bits (1306), Expect = e-148 Identities = 313/717 (43%), Positives = 432/717 (60%), Gaps = 37/717 (5%) Query: 2 AEYTRLHNALALIRLRNPPVNAISTTLLRDIKEGLQKAVIDHTIKAIVICGAEGKFSAGA 61 AEY ++H ++A+I + NPPVN + + I +GL +A D +K+IVI GA G FS GA Sbjct: 3 AEY-KVHGSVAVITMANPPVNGLGLATRQGIVDGLGRANADAAVKSIVITGAGGAFSGGA 61 Query: 62 DIRGFSAPRTFGL-TLGHVVDEIQRNEKPVVAAIQGMAFGGGLELALGCHYRIAHAEAQV 120 DI+ F ++ L V+ I+ + KPVVAA+ +A GGGLELALGCHYRIA + Sbjct: 62 DIKEFGTDKSLQEPNLLSVIAAIENSAKPVVAAMHSVAMGGGLELALGCHYRIAAPGCSI 121 Query: 121 GLPEVTLGLLPGARGTQLLPRLTGVPAALDLITSGRRILADEALKLG---ILDKVVNSDP 177 LPEV LGL+PGA GTQ LPR+ GV AAL+LI SG + ++ + + DK+ S Sbjct: 122 ALPEVKLGLIPGAGGTQRLPRVIGVEAALNLIVSGEPVKSEMIGAVPGQKLFDKMAASAE 181 Query: 178 --VEEAIRFAQRVSD-QPLESRRLCNKPIQSLPNMDSIFSEALLKMRRQHPGCLAQEACV 234 EA+ FAQ V+D +PL R N P + D+ F A ++ A CV Sbjct: 182 SLAAEALAFAQSVADARPLPLVR--NFPCKHSEG-DAYFQFARNMVKGMAKNFPAPAKCV 238 Query: 235 RAVQAAVQYPYEVGIKKEEELFLYLLQSGQARALQYAFFAERKANKWSTPSGASWKTASA 294 AV+AA + + G+ E E+F+ L+ + ++RAL++ F AER A+K P AS Sbjct: 239 DAVEAATKKKFAEGMLVEREIFINLMWTPESRALRHLFMAERAASK--IPDVAS--DTPK 294 Query: 295 RPVSSVGVVGLGTMGRGIVISFARARIPVIAVDSDKNQL----ATANKMITSVLEKEASK 350 R + VGV+G GTMG GI ++F A IPV ++ + L AT K + ++K K Sbjct: 295 RDIKLVGVIGAGTMGGGISMNFLNAGIPVKILEMKQEALDRGVATIKKNYEAQVKK--GK 352 Query: 351 MQQSGHPWSGPKPRLTSSVKELGGVDLVIEAVFEEMSLKKQVFAELSAVCKPEAFLCTNT 410 ++Q + T S + DL+IEAVFEEM +K+ VF +L AV KP A L +NT Sbjct: 353 LKQDKYDQRMALLSTTLSYDDFKDCDLIIEAVFEEMGVKEAVFKQLDAVAKPGAILASNT 412 Query: 411 SALDVDEIASSTDRPHLVIGTHFFSPAHVMKLLEVIPSQYSSPTTIATVMNLSKKIKKIG 470 S LDVD+IA+ T RP V+G HFFSPA+VMKLLEV+ + ++ +ATVM + KKIKK Sbjct: 413 STLDVDKIAAFTKRPQDVVGMHFFSPANVMKLLEVVRGKETAKDVLATVMAIGKKIKKTS 472 Query: 471 VVVGNCFGFVGNRMLNPYYNQAYFLLEEGSKPEEVDQVLEEFGFKMGPFRVSDLAGLDVG 530 VV G C GF+GNRM+ Y QA FLL+EG P++VD+ +E+FGF MGPFR+ DLAG D+G Sbjct: 473 VVSGVCDGFIGNRMIEQYSRQAGFLLDEGCTPQQVDKAVEKFGFAMGPFRMGDLAGNDIG 532 Query: 531 WKSRKGQGLTGPTLLPGTPARKRGNRRYCPIPDVLCELGRFGQKTGKGWYQYDKPLGRIH 590 W RK + + +R + +Y D LCELGRFGQKTG GWY Y R Sbjct: 533 WAIRKRRSV------------ERADMKYSRTADKLCELGRFGQKTGAGWYDYQAG-KRDA 579 Query: 591 KPDPWLSKFLSRYRKTHHIEPRTISQDEILERCLYSLINEAFRILGEGIAASPEHIDVVY 650 P ++K + +RK I PR IS +EI++R +++L+NE IL +GIA+ ID+VY Sbjct: 580 IPSDLVNKMIEDHRKELGITPRKISDEEIVQRLVFALVNEGAHILEDGIASKSGDIDMVY 639 Query: 651 LHGYGWPRHKGGPMFYASTVGLPTVLEKLQKYYRQNP--DIPQLEPSDYLKKLASQG 705 L GYG+P H+GGPM YAS VGL V++ + ++ R NP D +P+ L KLA++G Sbjct: 640 LTGYGFPIHRGGPMHYASEVGLFNVVQAMDRFAR-NPLDDAAFWKPAPLLAKLAAEG 695 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: 1060 Number of extensions: 52 Number of successful extensions: 7 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: 699 Length adjustment: 39 Effective length of query: 684 Effective length of database: 660 Effective search space: 451440 Effective search space used: 451440 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: 55 (25.8 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