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_011911348.1 PST_RS00510 3-hydroxyacyl-CoA dehydrogenase NAD-binding domain-containing protein
Query= SwissProt::Q08426 (723 letters) >NCBI__GCF_000013785.1:WP_011911348.1 Length = 701 Score = 497 bits (1279), Expect = e-145 Identities = 294/715 (41%), Positives = 431/715 (60%), Gaps = 39/715 (5%) Query: 11 LALIRLRNPPVNAISTTLLRDIKEGLQKAVIDHTIKAIVICGAEGKFSAGADIRGFSAPR 70 +ALI + NPPVNA+ + + + + ++A + A+V+ F AGADI+ F P Sbjct: 13 IALILVNNPPVNALGHAVRKGLLDAFRQADEAPEVTAVVLVCEGPTFMAGADIKEFGKPP 72 Query: 71 TFGLTLGHVVDEIQRNEKPVVAAIQGMAFGGGLELALGCHYRIAHAEAQVGLPEVTLGLL 130 +L V++ I+ KP VA I G A GGGLE+ALGCHYRIA ++A+VGLPEV LGLL Sbjct: 73 Q-APSLPEVIEVIEGCRKPSVAVIHGSALGGGLEVALGCHYRIARSDAKVGLPEVKLGLL 131 Query: 131 PGARGTQLLPRLTGVPAALDLITSGRRILADEALKLGILDKVVNSDPVEEAIRFAQRVSD 190 PGA GTQ LPRL GV AL++I SG+ I A EAL+ I+D++ D +E + +A+R+ + Sbjct: 132 PGAGGTQRLPRLAGVEKALEMIVSGQPIGAAEALEHHIVDELFEGDLIEAGLTYARRLVE 191 Query: 191 QPLESRRLCNKPIQSLPNMDSIFSEALLKMR-----RQHPGCLAQEACVRAVQAAVQYPY 245 + RR + ++ + +EAL++ + ++ PG + C+ AV+AA + P Sbjct: 192 EGRGPRRSG----EQTRGLEGVDNEALIRAKHAEVAKRMPGLFSPLRCIAAVEAATRLPL 247 Query: 246 EVGIKKEEELFLYLLQSGQARALQYAFFAERKANKWST-PSGASWKTASARPVSSVGVVG 304 G+K+E ELF L S Q AL ++FFAER+A K PS RP+ + V+G Sbjct: 248 AEGLKRERELFTECLNSPQRGALIHSFFAERQAGKIDDLPSDVK-----LRPIRTAAVIG 302 Query: 305 LGTMGRGIVISFARARIPVIAVDSDKNQLATANKMITSVLEKEASKMQQSGHPWSGPKPR 364 GTMG GI +SFA +PV ++ + L + + E A+ +++ + R Sbjct: 303 GGTMGVGIALSFANTGVPVKLLEINDEAL---QRGLQRARETYAASVKRGSLTEDAMEQR 359 Query: 365 LT--SSVKELGGV---DLVIEAVFEEMSLKKQVFAELSAVCKPEAFLCTNTSALDVDEIA 419 L + V + G + D+V+EAVFEEM +K+QVF +L AVCKP A L +NTS+LD++ IA Sbjct: 360 LALIAGVTDYGALADADVVVEAVFEEMGVKQQVFEQLDAVCKPGAILASNTSSLDLNAIA 419 Query: 420 SSTDRPHLVIGTHFFSPAHVMKLLEVIPSQYSSPTTIATVMNLSKKIKKIGVVVGNCFGF 479 + T RP V+G HFFSPA+VM+LLEV+ + +S +AT M + K++KK+ VVVG C GF Sbjct: 420 AFTKRPEDVVGLHFFSPANVMRLLEVVRGERTSDEVLATAMAIGKQLKKVSVVVGVCDGF 479 Query: 480 VGNRMLNPYYNQAYFLLEEGSKPEEVDQVLEEFGFKMGPFRVSDLAGLDVGWKSRKGQGL 539 VGNRM+ Y +A FLLEEG+ P++VD L FG MGPF + DL+GLD+G RK Q Sbjct: 480 VGNRMVFQYGREAEFLLEEGATPQQVDAALRNFGMAMGPFAMRDLSGLDIGQAIRKRQRA 539 Query: 540 TGPTLLPGTPARKRGNRRYCPIPDVLCELGRFGQKTGKGWYQYDKPLGRIHKPDPWLSKF 599 T P L + + D LC G GQKTG G+Y+Y+ P R + +P L+ Sbjct: 540 TLPAHLD-----------FPTVSDKLCAAGMLGQKTGAGYYRYE-PGNRTPQENPDLAPM 587 Query: 600 LSRYRKTHHIEPRTISQDEILERCLYSLINEAFRILGEGIAASPEHIDVVYLHGYGWPRH 659 L + IE + + + I+ERC+++L+NE +IL EGIA IDV+YL+GYG+P Sbjct: 588 LEAASREKGIERKALDEQYIVERCIFALVNEGAKILEEGIAQRSSDIDVIYLNGYGFPAF 647 Query: 660 KGGPMFYASTVGLPTVLEKLQKYYRQNPDIPQLEPSDYLKKLASQGNPPLKEWQS 714 +GGPM+YA +VGL VL ++++ + + D +P+ L+KLA++G EWQ+ Sbjct: 648 RGGPMYYADSVGLDKVLARVKELHARCGD--WWKPAPLLEKLAAEGR-TFTEWQA 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: 1171 Number of extensions: 54 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 Apr 09 2024. 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