Align Peroxisomal bifunctional enzyme; PBE; PBFE; EC 4.2.1.17; EC 5.3.3.8; EC 1.1.1.35 (characterized)
to candidate BPHYT_RS13545 BPHYT_RS13545 3-hydroxyacyl-CoA dehydrogenase
Query= SwissProt::Q08426 (723 letters) >FitnessBrowser__BFirm:BPHYT_RS13545 Length = 706 Score = 476 bits (1224), Expect = e-138 Identities = 288/712 (40%), Positives = 409/712 (57%), Gaps = 42/712 (5%) Query: 7 LHNALALIRLRNPPVNAISTTLLRDIKEGLQKAVIDHTIKAIVICGAEGKFSAGADIRGF 66 L + L+ + + PVNA+S + R + ++ A D ++A++I GA F AGADIR F Sbjct: 14 LRGKVLLVTIDHAPVNALSADVRRGLLAAIEAADADKAVEAVLIVGAGRNFIAGADIREF 73 Query: 67 SAPRTFGLTLGHVVDEIQRNEKPVVAAIQGMAFGGGLELALGCHYRIAHAEAQVGLPEVT 126 P +L V + I+ KPVVAAI G A GGGLE+AL HYRIA A++GLPEV Sbjct: 74 GKPPV-PPSLPDVCNRIEACTKPVVAAIHGAALGGGLEVALAAHYRIAVDGAKLGLPEVQ 132 Query: 127 LGLLPGARGTQLLPRLTGVPAALDLITSGRRILADEALKLGILDKVVNSDPV-EEAIRFA 185 LGLLPGA GTQ PRL G AALDLI SGR A EAL G++D++ +SD + E + + Sbjct: 133 LGLLPGAGGTQRTPRLIGAQAALDLILSGRHASAKEALAFGLIDRLGSSDDILAEGLAYV 192 Query: 186 QRVSDQPLESRRL-----CNKPIQSLPNMDSIFSEALLKMRRQHPGCLAQEACVRAVQAA 240 + RR + SL + + +E K R G + V AV+AA Sbjct: 193 HELLAAHAPVRRTRDAAALSDRAASLAAVATARAETAKKSR----GLFSPLKIVDAVEAA 248 Query: 241 VQYPYEVGIKKEEELFLYLLQSGQARALQYAFFAERKANKWSTPSGASWKTASARPVSSV 300 ++ P++ G++ E +LFL + S Q L +AFFAER+ K + A R ++++ Sbjct: 249 IEQPFDEGLRVERKLFLECIDSPQRAGLIHAFFAEREVLK-----APETRAAKPRTLNTI 303 Query: 301 GVVGLGTMGRGIVISFARARIPVIAVDSDKNQLATANKMITSVLEKEASKMQQSGHP--- 357 GVVG GTMG GI ++ A +PV ++ D LA I V + +K + S Sbjct: 304 GVVGGGTMGAGIAVAVLDAGLPVTMIERDDASLARGRAHIEKVYDGLIAKGRLSAEKKAA 363 Query: 358 ----WSGPKPRLTSSVKELGGVDLVIEAVFEEMSLKKQVFAELSAVCKPEAFLCTNTSAL 413 WSG ++S L G DLVIEAVFE++++K+ VFAEL VCK A L TNTS L Sbjct: 364 LMSRWSG-----STSYDALAGADLVIEAVFEDLAVKQAVFAELDRVCKAGAVLATNTSYL 418 Query: 414 DVDEIASSTDRPHLVIGTHFFSPAHVMKLLEVIPSQYSSPTTIATVMNLSKKIKKIGVVV 473 D+D +ASS RP VIG HFFSPA++MKLLEV+ + S +AT L+KK++K V Sbjct: 419 DIDALASSVSRPADVIGLHFFSPANIMKLLEVVVPKQVSADVVATAFELAKKLRKTPVRA 478 Query: 474 GNCFGFVGNRMLNPYYNQAYFLLEEGSKPEEVDQVLEEFGFKMGPFRVSDLAGLDVGWKS 533 G C GF+GNR+L Y + A ++E+G+ P ++D + FGF MGPF+V DLAG D+GW + Sbjct: 479 GVCDGFIGNRVLAVYRSAADAMMEDGASPYQIDAAVRAFGFPMGPFQVVDLAGGDIGWAA 538 Query: 534 RKGQGLTGPTLLPGTPARKRGNRRYCPIPDVLCELGRFGQKTGKGWYQYDKPLGRIHKPD 593 RK + T + RY I D LCE G FGQK+G+G+Y Y + R PD Sbjct: 539 RKRRAAT-----------RNPAARYVQIADRLCERGWFGQKSGRGFYLYPEG-SRSGTPD 586 Query: 594 PWLSKFLSRYRKTHHIEPRTISQDEILERCLYSLINEAFRILGEGIAASPEHIDVVYLHG 653 P + + R I PR+ + +EI+ R + ++INE ++ E IA P +DV +L+G Sbjct: 587 PEVEAIIDAERARAGITPRSFTDEEIIRRYMAAMINEGANVVHERIALRPLDVDVTFLYG 646 Query: 654 YGWPRHKGGPMFYASTVGLPTVLEKLQKYYRQNPDIPQLEPSDYLKKLASQG 705 YG+PR++GGPM YA VGLP +L ++++ +++P +PS L +L +G Sbjct: 647 YGFPRYRGGPMKYADMVGLPKILADIREFAKEDPLF--WKPSPLLIELVERG 696 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: 1141 Number of extensions: 65 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: 706 Length adjustment: 39 Effective length of query: 684 Effective length of database: 667 Effective search space: 456228 Effective search space used: 456228 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