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_085640004.1 MGEO_RS15835 FAD-dependent oxidoreductase
Query= SwissProt::Q08426 (723 letters) >NCBI__GCF_002115805.1:WP_085640004.1 Length = 695 Score = 493 bits (1268), Expect = e-143 Identities = 291/699 (41%), Positives = 417/699 (59%), Gaps = 32/699 (4%) Query: 11 LALIRLRNPPVNAISTTLLRDIKEGLQKAVIDHTIKAIVICGAEGKFSAGADIRGFSAPR 70 +A+I + NPPVNA+ + + + E ++KA D +A +I G F AGADIR F P Sbjct: 13 IAMIAIDNPPVNALGQAVRQGLVEAVEKAEADGA-RAALIYGEGRSFPAGADIREFGKP- 70 Query: 71 TFGLTLGHVVDEIQRNEKPVVAAIQGMAFGGGLELALGCHYRIAHAEAQVGLPEVTLGLL 130 L V + ++ + VV+A+ G A GGGLE+AL YRIA A+VGLPEV +G++ Sbjct: 71 PLEPWLPDVCNRLETSPVLVVSALHGTALGGGLEIALASDYRIATPAAKVGLPEVLIGVM 130 Query: 131 PGARGTQLLPRLTGVPAALDLITSGRRILADEALKLGILDKVVNSDPVEEAIRFAQRVSD 190 PGA GTQ LPRL GV ++D+ITSGR+I A EA LGI+D+V + P + + + + + Sbjct: 131 PGAGGTQRLPRLVGVETSIDVITSGRQISAGEAFDLGIIDRVEDGAPRDIGLSYTRALLA 190 Query: 191 QPLESRRLCNKPIQSLPNMDSIFSEALLKMRRQHPGCLAQEACVRAVQAAVQYPYEVGIK 250 + R + P + D+ + AL K R Q ++ VR +QAA + P+E G+ Sbjct: 191 ENAPRRPIREMPAPQPIDFDAAYDSALRKARGQ----ISPAYAVRGIQAACELPFEEGLT 246 Query: 251 KEEELFLYLLQSGQARALQYAFFAERKANKWSTPSGASWKTASARPVSSVGVVGLGTMGR 310 +E ELF LL++ Q + L +AFFAER A K +AR V+SV V+G GTMG Sbjct: 247 RERELFRALLETDQRQGLIHAFFAERAVGVL-----AELKDTNARDVNSVAVIGGGTMGA 301 Query: 311 GIVISFARARIPVIAVDSDKNQLATANKMITSVLE---KEASKMQQSGHPWSGPKPRLTS 367 GI SF A PV ++ ++ A IT L K Q++ +GP LT+ Sbjct: 302 GIATSFLLAGFPVTLLEMSEDAAHAARGRITGNLSGALKRGKIDQKTYDRLTGPALALTT 361 Query: 368 SVKELGGVDLVIEAVFEEMSLKKQVFAELSAVCKPEAFLCTNTSALDVDEIASSTDRPHL 427 S +L DLVIEAVFE+M++K+ VF+ L A+CKP A L TNTS LD+++IA +T RP Sbjct: 362 SYDDLREADLVIEAVFEDMNVKRDVFSRLDAICKPGAVLATNTSYLDINKIADATQRPED 421 Query: 428 VIGTHFFSPAHVMKLLEVIPSQYSSPTTIATVMNLSKKIKKIGVVVGNCFGFVGNRMLNP 487 VIG HFFSPAHVMKLLEV+ + ++P T+AT L+K++KK V G C GF+GNR+L Sbjct: 422 VIGLHFFSPAHVMKLLEVVVADRTAPDTVATGFALAKRLKKTAVRAGVCDGFIGNRILAA 481 Query: 488 YYNQAYFLLEEGSKPEEVDQVLEEFGFKMGPFRVSDLAGLDVGWKSRKGQGLTGPTLLPG 547 Y A ++ +G+ P ++D + EFGF MGPF+VSDLAGLD+ W +RK + T Sbjct: 482 YRAAADHMVLDGATPYDIDAAIREFGFAMGPFQVSDLAGLDIAWAARKRRAAT------- 534 Query: 548 TPARKRGNRRYCP-IPDVLCELGRFGQKTGKGWYQYDKPLGRIHKPDPWLSKFLSRYRKT 606 R R P + D LCE G FGQKTG+G+Y Y++ KP+P ++ + R+T Sbjct: 535 -----RDPRERVPLVADRLCEAGLFGQKTGQGYYLYNE---TPPKPNPEVAGIIESARET 586 Query: 607 HHIEPRTISQDEILERCLYSLINEAFRILGEGIAASPEHIDVVYLHGYGWPRHKGGPMFY 666 I+PR S+ EI R L +++NEA +++G+GIA P +DVV L GYG+PR++GGP+ + Sbjct: 587 LGIKPRAFSRPEIQRRYLCAMVNEAAKVVGDGIARRPLDVDVVLLMGYGFPRYRGGPLKW 646 Query: 667 ASTVGLPTVLEKLQKYYRQNPDIPQLEPSDYLKKLASQG 705 A GLP +L + Y + D P+ L++L ++G Sbjct: 647 ADMDGLPKILSDITAYAQD--DRYFWSPAPLLEQLVAEG 683 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: 1152 Number of extensions: 52 Number of successful extensions: 8 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: 695 Length adjustment: 39 Effective length of query: 684 Effective length of database: 656 Effective search space: 448704 Effective search space used: 448704 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