Align Peroxisomal bifunctional enzyme; PBE; PBFE; EC 4.2.1.17; EC 5.3.3.8; EC 1.1.1.35 (characterized)
to candidate AO356_30295 AO356_30295 fatty-acid oxidation protein subunit alpha
Query= SwissProt::Q08426 (723 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_30295 Length = 703 Score = 448 bits (1153), Expect = e-130 Identities = 274/709 (38%), Positives = 403/709 (56%), Gaps = 36/709 (5%) Query: 7 LHNALALIRLRNPPVNAISTTLLRDIKEGLQKAVIDHTIKAIVICGAEGKFSAGADIRGF 66 + +A+I + NPPVNA++ + I + + A D + AIV+ G F AGADIR F Sbjct: 11 VEGVVAVITVNNPPVNALTPEMRGSIIDAVTHANADPAVAAIVLMGGGQNFIAGADIRQF 70 Query: 67 SAPRTFGLTLGHVVDEIQRNEKPVVAAIQGMAFGGGLELALGCHYRIAHAEAQVGLPEVT 126 RT +T + + KP VAAI G A GGGLE AL CHYRIA A++GLPEV Sbjct: 71 GKART--ITTSMSAAALDASAKPTVAAIHGYALGGGLEHALACHYRIALPTAKLGLPEVA 128 Query: 127 LGLLPGARGTQLLPRLTGVPAALDLITSGRRILADEALKLGILDKVV----NSDPVEEAI 182 LGL+PG GTQ LPRL G A DL+ S R I A EAL++G++ ++V N + + A+ Sbjct: 129 LGLIPGGGGTQRLPRLVGAAVATDLLVSSRHIHAPEALQIGLISQIVPGTQNQELRDAAV 188 Query: 183 RFAQRVSD-QPLESRRLCNKPIQSLPNMDSIFSEALLKMRRQHPGCLAQEACVRAVQAAV 241 R+A+ V+ QP R L +P+ + MD + A + ++ P A + + ++AA Sbjct: 189 RYAKAVAHAQPQRVRDLALEPMDAT-TMD-LLQAARREAAKKSPHNKAPQYAIDCIEAAF 246 Query: 242 QYPYEVGIKKEEELFLYLLQSGQARALQYAFFAERKANKW-STPSGASWKTASARPVSSV 300 P++ ++ E LF L S A+AL+YAFFAER+A K P G +K A V+S Sbjct: 247 NLPFDEALEVESRLFSELEGSDVAKALRYAFFAEREAAKVPDAPPG--FKPAG---VTSA 301 Query: 301 GVVGLGTMGRGIVISFARARIPVIAVDSDKNQLATANKMITSVLEKEASK----MQQSGH 356 V+G GTMG GI I FA A I V +++ L + I + + + +Q+ Sbjct: 302 AVIGAGTMGAGIAICFADAGIVVKLLEASAEALDRGLQRIRDIYAVKVKRGRMTVQEMDA 361 Query: 357 PWSGPKPRLTSSVKELGGVDLVIEAVFEEMSLKKQVFAELSAVCKPEAFLCTNTSALDVD 416 +P S +E+G D+V+EAVFE + LKK VF +L AV KP A L TN+SA+D++ Sbjct: 362 CLQFVQP--VSHYEEIGDCDVVVEAVFERIDLKKDVFTKLDAVMKPGALLLTNSSAIDIN 419 Query: 417 EIASSTDRPHLVIGTHFFSPAHVMKLLEVIPSQYSSPTTIATVMNLSKKIKKIGVVVGNC 476 +A+ T RP V G HFF+PA+ MKL E++ +S T+ M + + +KK+ V G C Sbjct: 420 VMANMTGRPQSVAGAHFFAPANAMKLCEIVKGDQTSIETVVRAMKMGRDLKKVCAVSGTC 479 Query: 477 FGFVGNRMLNPYYNQAYFLLEEGSKPEEVDQVLEEFGFKMGPFRVSDLAGLDVGWKSRKG 536 GF NR P + LLEEG++PE++D+V+ EFG+ MGPF VSDL+GLDV + +RK Sbjct: 480 DGFAANRSRAPLVTEMMLLLEEGARPEQIDRVMVEFGYPMGPFAVSDLSGLDVSYDTRKR 539 Query: 537 QGLTGPTLLPGTPARKRGNRRYCPIPDVLCELGRFGQKTGKGWYQYDKPLGRIHKPDPWL 596 + P R +PD + ELGR GQK G GWY+Y++ R + D + Sbjct: 540 RAAADP------------QYRKLHVPDRMVELGRKGQKNGAGWYRYEEG-DRTPRHDEEV 586 Query: 597 SKFLSRYRKTHHIEPRTISQDEILERCLYSLINEAFRILGEGIAASPEHIDVVYLHGYGW 656 + ++ RT + EIL+R L++ INEA +IL EG A IDV++L+G+G+ Sbjct: 587 MRIIATVAHELGTPQRTFTDSEILKRLLFASINEACKILDEGKAYRASDIDVMWLYGFGF 646 Query: 657 PRHKGGPMFYASTVGLPTVLEKLQKYYRQNPDIPQLEPSDYLKKLASQG 705 PRH+GG +++A T+G + ++Q+++ Q + PS L K A++G Sbjct: 647 PRHRGGLLYWADTIGATEIHLQVQQWHEQYG--RRWAPSPLLSKAANEG 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: 1056 Number of extensions: 57 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: 703 Length adjustment: 39 Effective length of query: 684 Effective length of database: 664 Effective search space: 454176 Effective search space used: 454176 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