Align Peroxisomal bifunctional enzyme; PBE; PBFE; EC 4.2.1.17; EC 5.3.3.8; EC 1.1.1.35 (characterized)
to candidate WP_011886130.1 3-hydroxyacyl-CoA dehydrogenase
Query= SwissProt::Q08426 (723 letters) >NCBI__GCF_000016205.1:WP_011886130.1 Length = 711 Score = 500 bits (1288), Expect = e-146 Identities = 295/703 (41%), Positives = 412/703 (58%), Gaps = 28/703 (3%) Query: 9 NALALIRLRNPPVNAISTTLLRDIKEGLQKAVIDHTIKAIVICGAEGKFSAGADIRGFSA 68 +AL ++ + +PPVNA+S + R + + L A DH ++A++I GA F AGADIR F Sbjct: 21 DALLVVTIDHPPVNALSADVRRGLADALDAAQADHAVRAVLIVGAGRNFIAGADIREFGK 80 Query: 69 PRTFGLTLGHVVDEIQRNEKPVVAAIQGMAFGGGLELALGCHYRIAHAEAQVGLPEVTLG 128 P +L V + I+ + KPVV A+ G GGGLE+AL HYR+A A++GLPEVTLG Sbjct: 81 PPV-PPSLPDVCERIESSAKPVVVALHGATLGGGLEVALAAHYRLALPGAKLGLPEVTLG 139 Query: 129 LLPGARGTQLLPRLTGVPAALDLITSGRRILADEALKLGILDKVVNSDP-VEEAIRFAQR 187 LLPGA GTQ PRL G AALDL+ +GR A+EA LG++D+V SD + E + +AQ Sbjct: 140 LLPGAGGTQRTPRLIGAKAALDLMLTGRHASAEEARALGLVDRVARSDDTLAEGLAYAQE 199 Query: 188 VSDQPLESRRLCNKPIQSLPNM---DSIFSEALLKMRRQHPGCLAQEACVRAVQAAVQYP 244 + RR + Q L + + A ++ ++ G + V AV+AA+ Sbjct: 200 LVSLGAPVRR--TRDAQGLAERTAAQAALAAARAELPKKSRGLFSPAKIVDAVEAALTLS 257 Query: 245 YEVGIKKEEELFLYLLQSGQARALQYAFFAERKANKWSTPSGASWKTASARPVSSVGVVG 304 ++ G+K E LFL L S Q L +AFFAER+A K + ASAR V VGVVG Sbjct: 258 FDAGMKLERSLFLQCLDSPQRAGLVHAFFAEREAAK-----APEARRASARAVERVGVVG 312 Query: 305 LGTMGRGIVISFARARIPVIAVDSDKNQLATANKMITSVLEKEASKMQQSGHPWSGPKPR 364 GTMG GI ++ A +PV ++ D LA + V + +K + + + R Sbjct: 313 GGTMGAGIAVAALDAGLPVTMIERDDASLARGRAHVEKVYDALVAKGRMTPDARAARVAR 372 Query: 365 LTSSVK--ELGGVDLVIEAVFEEMSLKKQVFAELSAVCKPEAFLCTNTSALDVDEIASST 422 L S + L D+VIEAVFE+M++K+ VFAEL+ VCKP A L TNTS LD+D +A+ Sbjct: 373 LDGSTRYDALAQADVVIEAVFEDMAVKQAVFAELARVCKPGAVLATNTSYLDIDALAAGI 432 Query: 423 DRPHLVIGTHFFSPAHVMKLLEVIPSQYSSPTTIATVMNLSKKIKKIGVVVGNCFGFVGN 482 DRP VIG HFFSPA+VMKLLE++ + S +AT L++++KK V G C GF+GN Sbjct: 433 DRPTDVIGLHFFSPANVMKLLEIVVPKRVSAEVVATAFALARQLKKTPVRAGVCDGFIGN 492 Query: 483 RMLNPYYNQAYFLLEEGSKPEEVDQVLEEFGFKMGPFRVSDLAGLDVGWKSRKGQGLTGP 542 R+L Y A +L+E+G+ P ++D+ + FGF MGPF+V DLAG D+GW +RK + T Sbjct: 493 RILAVYRTAADYLMEDGASPYQIDRAVRGFGFPMGPFQVVDLAGGDIGWATRKRRAAT-- 550 Query: 543 TLLPGTPARKRGNRRYCPIPDVLCELGRFGQKTGKGWYQYDKPLGRIHKPDPWLSKFLSR 602 + RY I D LCE G FGQK+G+G+Y Y R+ PDP + ++ Sbjct: 551 ---------RDPRARYVEISDRLCERGWFGQKSGRGYYLYPDG-ARVGTPDPEVDAIVAA 600 Query: 603 YRKTHHIEPRTISQDEILERCLYSLINEAFRILGEGIAASPEHIDVVYLHGYGWPRHKGG 662 R I PR+ S DEIL R L ++INE ++ E IA P +D V+L+GYG+PRH+GG Sbjct: 601 ERAKKGIVPRSFSDDEILRRYLAAMINEGANVVHERIALRPLDVDAVFLYGYGFPRHRGG 660 Query: 663 PMFYASTVGLPTVLEKLQKYYRQNPDIPQLEPSDYLKKLASQG 705 PM YA TVGL VL ++ + ++P PS L +L +G Sbjct: 661 PMHYADTVGLANVLADIRAFANEDPLF--WRPSPLLVELVERG 701 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: 1115 Number of extensions: 53 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: 711 Length adjustment: 40 Effective length of query: 683 Effective length of database: 671 Effective search space: 458293 Effective search space used: 458293 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 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