Align Peroxisomal bifunctional enzyme; PBE; PBFE; EC 4.2.1.17; EC 5.3.3.8; EC 1.1.1.35 (characterized)
to candidate GFF4162 Psest_4235 3-hydroxyacyl-CoA dehydrogenase
Query= SwissProt::Q08426 (723 letters) >FitnessBrowser__psRCH2:GFF4162 Length = 701 Score = 499 bits (1286), Expect = e-145 Identities = 298/727 (40%), Positives = 430/727 (59%), Gaps = 41/727 (5%) Query: 1 MAEYTRLH--NALALIRLRNPPVNAISTTLLRDIKEGLQKAVIDHTIKAIVICGAEGKFS 58 M + RL +ALI + NPPVNA+ + +++ Q A D ++A+ + F Sbjct: 1 MTDVVRLEVQGEIALITVNNPPVNALGQAVREGLQKAFQSAEADPQVRAVALVCEGNTFI 60 Query: 59 AGADIRGFSAPRTFGLTLGHVVDEIQRNEKPVVAAIQGMAFGGGLELALGCHYRIAHAEA 118 AGADI+ F P +L V++ I+ K VA I G A GGGLE+ALGCHYRIA +A Sbjct: 61 AGADIKEFGKPPQ-APSLPEVIEIIEACNKSSVAVIHGTALGGGLEVALGCHYRIARKDA 119 Query: 119 QVGLPEVTLGLLPGARGTQLLPRLTGVPAALDLITSGRRILADEALKLGILDKVVNSDPV 178 +VGLPEV LGLLPGA GTQ LPRL GV AL++I SG+ I A EA++ I+D++ D V Sbjct: 120 KVGLPEVKLGLLPGAGGTQRLPRLAGVEKALEMIVSGQPISAAEAVEHNIVDELFEGDLV 179 Query: 179 EEAIRFAQRVSDQPLESRRLCNKPIQSLPNMDSIFSEALLKMR-----RQHPGCLAQEAC 233 E + + +R+ ++ RR + Q L D+ EAL++ + ++ PG + C Sbjct: 180 EAGLAYVRRMVEEGRTPRRT-GEQTQGLEGADN---EALIRAKHAEVAKRMPGLFSPLRC 235 Query: 234 VRAVQAAVQYPYEVGIKKEEELFLYLLQSGQARALQYAFFAERKANKWST-PSGASWKTA 292 + AV+AA + P G+K+E ELF L S Q AL ++FFAER+A K + PS Sbjct: 236 IAAVEAATKLPLAEGLKRERELFAECLNSPQRGALVHSFFAERQAGKINDLPSDTK---- 291 Query: 293 SARPVSSVGVVGLGTMGRGIVISFARARIPVIAVDSDKNQLATANKMITSVLEKEASKMQ 352 R ++S V+G GTMG GI +SFA A +PV ++ ++ L + + + A+ ++ Sbjct: 292 -PRSINSAAVIGGGTMGVGIALSFANAGVPVKLLEINEEAL---QRGLQRARDTYAASVK 347 Query: 353 QSGHPWSGPKPRLT-----SSVKELGGVDLVIEAVFEEMSLKKQVFAELSAVCKPEAFLC 407 + + RL + L D+V+EAVFEEM +K+QVF +L A+CKP A L Sbjct: 348 RGSLTEDAMEQRLALIEGVTEYAALADADVVVEAVFEEMGVKQQVFEQLDAICKPGAILA 407 Query: 408 TNTSALDVDEIASSTDRPHLVIGTHFFSPAHVMKLLEVIPSQYSSPTTIATVMNLSKKIK 467 +NTS+LD+D IA+ T RP V+G HFFSPA+VM+LLEV+ +S +AT M + K++K Sbjct: 408 SNTSSLDLDAIAAFTKRPEDVVGLHFFSPANVMRLLEVVRGAKTSDEVLATAMAIGKQLK 467 Query: 468 KIGVVVGNCFGFVGNRMLNPYYNQAYFLLEEGSKPEEVDQVLEEFGFKMGPFRVSDLAGL 527 K+ VVVG C GFVGNRM+ Y +A FLLEEG+ P++VD L FG MGPF + DL+GL Sbjct: 468 KVSVVVGVCDGFVGNRMVFQYGREAEFLLEEGATPQQVDAALRNFGMAMGPFAMRDLSGL 527 Query: 528 DVGWKSRKGQGLTGPTLLPGTPARKRGNRRYCPIPDVLCELGRFGQKTGKGWYQYDKPLG 587 D+G RK Q T P L + + D LC G GQKTG G+Y+Y+ P Sbjct: 528 DIGQAIRKRQRATLPAHLD-----------FPTVSDKLCAAGMLGQKTGAGYYRYE-PGN 575 Query: 588 RIHKPDPWLSKFLSRYRKTHHIEPRTISQDEILERCLYSLINEAFRILGEGIAASPEHID 647 R + +P L+ L IE + + + I+ERC+++L+NE +IL EGIA ID Sbjct: 576 RTPQENPDLAPMLEAASLEKGIERKALDEQYIVERCIFALVNEGAKILEEGIAQRSSDID 635 Query: 648 VVYLHGYGWPRHKGGPMFYASTVGLPTVLEKLQKYYRQNPDIPQLEPSDYLKKLASQGNP 707 V+YL+GYG+P +GGPMFYA +VGL VL ++++ + + D +P+ L+KLA++G Sbjct: 636 VIYLNGYGFPAFRGGPMFYADSVGLDRVLARVKELHARCGD--WWKPAPLLEKLAAEGR- 692 Query: 708 PLKEWQS 714 +WQ+ Sbjct: 693 TFTDWQA 699 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: 56 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: 701 Length adjustment: 39 Effective length of query: 684 Effective length of database: 662 Effective search space: 452808 Effective search space used: 452808 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