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_041097743.1 SUTH_RS05635 3-hydroxyacyl-CoA dehydrogenase
Query= SwissProt::Q08426 (723 letters) >NCBI__GCF_000828635.1:WP_041097743.1 Length = 697 Score = 509 bits (1312), Expect = e-148 Identities = 301/711 (42%), Positives = 425/711 (59%), Gaps = 35/711 (4%) Query: 6 RLHNALALIRLRNPPVNAISTTLLRDIKEGLQKAVIDHTIKAIVICGAEGKFSAGADIRG 65 +LH + A+I L NPPVN + L I G+ +A D +KA+V+ G++ FS GADIR Sbjct: 7 QLHGSTAVITLDNPPVNGLGYDLRCGIVAGIDQATADPAVKAVVLIGSDRAFSGGADIRE 66 Query: 66 FSAPRTFGL-TLGHVVDEIQRNEKPVVAAIQGMAFGGGLELALGCHYRIAHAEAQVGLPE 124 F +P+++ L V+ ++ KPVVAAI G+ GGGLEL LGCH+R+A A A + LPE Sbjct: 67 FGSPKSYAEPNLLTVIRIVEACPKPVVAAIGGVCMGGGLELTLGCHFRVAIAGASIALPE 126 Query: 125 VTLGLLPGARGTQLLPRLTGVPAALDLITSGRRILADEALKLGILDKVVNS---DPVEEA 181 + LGLLPGA GTQ +PR+ GV AAL+LI SG + +++ + D+ + D ++ A Sbjct: 127 IKLGLLPGAGGTQRMPRIVGVEAALNLILSGNPVPSEKFKGTPLFDEFIEGNGGDLLKGA 186 Query: 182 IRFAQRVSDQPLESRRLCNKPIQSLPNMDSIFSEALLKMRRQHPGCLAQEACVRAVQAAV 241 + FA +V + +R+ + I P ++ F + ++ A C+ AVQAA+ Sbjct: 187 LAFADKVVAEKRPLKRIRDIRID-YPGQEAFFQFSRNMVKGVAGPFPAPFKCIDAVQAAL 245 Query: 242 QYPYEVGIKKEEELFLYLLQSGQARALQYAFFAERKANKWSTPSGASWKTASARPVSSVG 301 P++ G+K E F+ L+ + ++RAL++AF ER A+K + AR ++ VG Sbjct: 246 TKPFDEGMKFERACFIELMGTPESRALRHAFTGERAASKIPDVPDDT----PARKIARVG 301 Query: 302 VVGLGTMGRGIVISFARARIPVIAVDSDKNQL----ATANKMITSVLEK---EASKMQQS 354 V+G GTMG GI ++F A IPV ++ + L AT K + ++K K+ Q Sbjct: 302 VIGAGTMGGGITMNFLNAGIPVTMLEMKQEALDKGIATIRKNYENSMKKGKLTQEKLDQR 361 Query: 355 GHPWSGPKPRLTSSVKELGGVDLVIEAVFEEMSLKKQVFAELSAVCKPEAFLCTNTSALD 414 SG T S + DL+IEAVFEE+S+K+ VF +L A+ KP A L +NTS LD Sbjct: 362 MGMLSG-----TLSYDDFKDADLIIEAVFEEISVKEAVFKQLDAIAKPGAILASNTSTLD 416 Query: 415 VDEIASSTDRPHLVIGTHFFSPAHVMKLLEVIPSQYSSPTTIATVMNLSKKIKKIGVVVG 474 V++IA+ T RP V+G HFFSPA+VMKLLEV+ ++ +ATVM ++KKIKK VV G Sbjct: 417 VNKIANFTKRPQDVVGMHFFSPANVMKLLEVVRGAATAKDVMATVMQVAKKIKKTAVVSG 476 Query: 475 NCFGFVGNRMLNPYYNQAYFLLEEGSKPEEVDQVLEEFGFKMGPFRVSDLAGLDVGWKSR 534 C GF+GNRM+ Y A FLLEEG+ P +VD+ LE++G MGPFR+ DLAG D+GW R Sbjct: 477 VCDGFIGNRMIEHYGRVAGFLLEEGATPAQVDKALEKWGMAMGPFRMGDLAGNDIGWAIR 536 Query: 535 KGQGLTGPTLLPGTPARKRGNRRYCPIPDVLCELGRFGQKTGKGWYQYDKPLGRIHKPDP 594 K + + P++ RY D LCE GR+GQKTGKGWY Y +P R PDP Sbjct: 537 KRRYVEKPSI------------RYAKFADKLCEQGRYGQKTGKGWYLY-QPGNRKAIPDP 583 Query: 595 WLSKFLSRYRKTHHIEPRTISQDEILERCLYSLINEAFRILGEGIAASPEHIDVVYLHGY 654 + L YRK I PR IS EI++RC+Y+L+NE RIL EGIAA ID++YL GY Sbjct: 584 EVDTMLEAYRKELGITPRKISDAEIVQRCIYALVNEGARILEEGIAARASDIDMIYLTGY 643 Query: 655 GWPRHKGGPMFYASTVGLPTVLEKLQKYYRQNPDIPQLEPSDYLKKLASQG 705 G+P H+GGPM YA VGL V ++++ + D EP+ + K + G Sbjct: 644 GFPLHRGGPMLYADEVGLYNVARSMKEFAATSGD-AFWEPAPLIAKRVADG 693 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: 1170 Number of extensions: 58 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: 697 Length adjustment: 39 Effective length of query: 684 Effective length of database: 658 Effective search space: 450072 Effective search space used: 450072 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