analysis of sequence from AAM43641.1.fa ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ >AAM43641.1 ACYLOXYACYL HYDROLASE [Dictyostelium discoideum]. MKSVFVLLFI VLSVLINFTT AVNIPVNGKS LEIKNKFEEF ISNDVKSANG GTHCAACTIV LSLVNQYSGI HNKSIEDSLD ELCSFFPDEA GSLCTWLVNT YGEQIISYFD QYQNADDVCH AMNVCTSPTC RLFTSAPSKF YNPDHVHQEY NKEDPKVGGS PWAWIQELIK VFSSEHLPIQ DFDGDHHSLE ATFRGYNWRG KDCNDFDKSS YPGTIEGTGD ASVDKNCNGI FGVNNQSQSY EELFCSNSGA MGVIVSGDSA GAHFSIPPQW MTARDINSTT YKGMIDILET EVDWPMRSCY TGWDTSAPNV DSMYLRMRER NLCNHRDYQN LGVNGASSSS TRTIIQTINR NQNTDKPVLL FLELIGNDVC SGHHDYDSMT TVEEFGENIL TILNYLETTL PKGSHVVFVG LADGRVLWDS LWNRTHPLGC TYEEVYDFLN CIQVSPCWGW MNPNETVRDY TSNRAAQLSL VYNQLIKNYT FNNFDMIYYD FPFATINEMW VAQGGQTYDL IEPIDGFHPN QIANYLMAGV FYNQIAQDKP EWLGEINQYN TQIQSIFGNQ GGYV ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ sec.str. with predator > AAM43641.1 . . . . . 1 MKSVFVLLFIVLSVLINFTTAVNIPVNGKSLEIKNKFEEFISNDVKSANG 50 ___HHHHHHHHHHHHHHHHEEEE______EEEEHHHHHHHH_________ . . . . . 51 GTHCAACTIVLSLVNQYSGIHNKSIEDSLDELCSFFPDEAGSLCTWLVNT 100 __EEEEEEEEEEE____________HHHHHHHH_______EEEEEEEE__ . . . . . 101 YGEQIISYFDQYQNADDVCHAMNVCTSPTCRLFTSAPSKFYNPDHVHQEY 150 ____EEEE_____________EEE__________________________ . . . . . 151 NKEDPKVGGSPWAWIQELIKVFSSEHLPIQDFDGDHHSLEATFRGYNWRG 200 _____________HHHHHHHHH______________HHHHHHH_______ . . . . . 201 KDCNDFDKSSYPGTIEGTGDASVDKNCNGIFGVNNQSQSYEELFCSNSGA 250 __________________________________________________ . . . . . 251 MGVIVSGDSAGAHFSIPPQWMTARDINSTTYKGMIDILETEVDWPMRSCY 300 EEEEE__________________________HHHHHHHHHHH________ . . . . . 301 TGWDTSAPNVDSMYLRMRERNLCNHRDYQNLGVNGASSSSTRTIIQTINR 350 ___________HHHHHHHHHH______EEE____________________ . . . . . 351 NQNTDKPVLLFLELIGNDVCSGHHDYDSMTTVEEFGENILTILNYLETTL 400 ________EEEE______________________HHHHHHHEEEEE____ . . . . . 401 PKGSHVVFVGLADGRVLWDSLWNRTHPLGCTYEEVYDFLNCIQVSPCWGW 450 ____EEEEEE_________________________EEEEEEE________ . . . . . 451 MNPNETVRDYTSNRAAQLSLVYNQLIKNYTFNNFDMIYYDFPFATINEMW 500 _____EEEEEHHHHHHHHHHHHHHHHHHH____EEEEEE___________ . . . . . 501 VAQGGQTYDLIEPIDGFHPNQIANYLMAGVFYNQIAQDKPEWLGEINQYN 550 ____________________HHHHHHHHHH__________________HH . 551 TQIQSIFGNQGGYV 564 HHHHHH________ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ method : 1 alpha-contents : 0.0 % beta-contents : 38.6 % coil-contents : 61.4 % class : beta method : 2 alpha-contents : 13.6 % beta-contents : 24.2 % coil-contents : 62.2 % class : beta ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ GPI: learning from metazoa -19.52 -2.91 -1.08 -0.16 -4.00 0.00 -24.00 0.00 0.00 -5.40 -1.44 -12.00 -12.00 0.00 0.00 0.00 -82.51 -26.96 -2.98 -2.79 -0.77 -4.00 0.00 0.00 -0.03 -0.93 -6.60 -1.44 -12.00 -12.00 0.00 -12.00 0.00 -82.50 ID: AAM43641.1 AC: xxx Len: 564 1:I 538 Sc: -82.50 Pv: 8.259450e-01 NO_GPI_SITE GPI: learning from protozoa -19.87 -3.38 -4.37 -2.00 -4.00 0.00 -24.00 0.00 0.00 -4.73 -5.97 -12.00 -12.00 0.00 0.00 0.00 -92.32 -37.84 -1.08 -0.55 -0.07 -4.00 0.00 0.00 0.00 -0.29 -3.78 -5.97 -12.00 -12.00 0.00 -12.00 0.00 -89.58 ID: AAM43641.1 AC: xxx Len: 564 1:I 545 Sc: -89.58 Pv: 6.880795e-01 NO_GPI_SITE ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ # SignalP euk predictions # name Cmax pos ? Ymax pos ? Smax pos ? Smean ? AAM43641.1 1.000 22 Y 0.922 22 Y 0.985 11 Y 0.949 Y # SignalP gram- predictions # name Cmax pos ? Ymax pos ? Smax pos ? Smean ? AAM43641.1 0.384 116 N 0.329 22 N 0.986 9 Y 0.893 Y # SignalP gram+ predictions # name Cmax pos ? Ymax pos ? Smax pos ? Smean ? AAM43641.1 0.712 116 Y 0.501 24 Y 0.993 9 Y 0.917 Y ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ low complexity regions: SEG 12 2.2 2.5 >AAM43641.1 ACYLOXYACYL HYDROLASE [Dictyostelium discoideum]. 1-2 MK svfvllfivlsvli 3-16 17-336 NFTTAVNIPVNGKSLEIKNKFEEFISNDVK SANGGTHCAACTIVLSLVNQYSGIHNKSIE DSLDELCSFFPDEAGSLCTWLVNTYGEQII SYFDQYQNADDVCHAMNVCTSPTCRLFTSA PSKFYNPDHVHQEYNKEDPKVGGSPWAWIQ ELIKVFSSEHLPIQDFDGDHHSLEATFRGY NWRGKDCNDFDKSSYPGTIEGTGDASVDKN CNGIFGVNNQSQSYEELFCSNSGAMGVIVS GDSAGAHFSIPPQWMTARDINSTTYKGMID ILETEVDWPMRSCYTGWDTSAPNVDSMYLR MRERNLCNHRDYQNLGVNGA sssstrtiiqtinrnqnt 337-354 355-564 DKPVLLFLELIGNDVCSGHHDYDSMTTVEE FGENILTILNYLETTLPKGSHVVFVGLADG RVLWDSLWNRTHPLGCTYEEVYDFLNCIQV SPCWGWMNPNETVRDYTSNRAAQLSLVYNQ LIKNYTFNNFDMIYYDFPFATINEMWVAQG GQTYDLIEPIDGFHPNQIANYLMAGVFYNQ IAQDKPEWLGEINQYNTQIQSIFGNQGGYV low complexity regions: SEG 25 3.0 3.3 >AAM43641.1 ACYLOXYACYL HYDROLASE [Dictyostelium discoideum]. 1-2 MK svfvllfivlsvli 3-16 17-564 NFTTAVNIPVNGKSLEIKNKFEEFISNDVK SANGGTHCAACTIVLSLVNQYSGIHNKSIE DSLDELCSFFPDEAGSLCTWLVNTYGEQII SYFDQYQNADDVCHAMNVCTSPTCRLFTSA PSKFYNPDHVHQEYNKEDPKVGGSPWAWIQ ELIKVFSSEHLPIQDFDGDHHSLEATFRGY NWRGKDCNDFDKSSYPGTIEGTGDASVDKN CNGIFGVNNQSQSYEELFCSNSGAMGVIVS GDSAGAHFSIPPQWMTARDINSTTYKGMID ILETEVDWPMRSCYTGWDTSAPNVDSMYLR MRERNLCNHRDYQNLGVNGASSSSTRTIIQ TINRNQNTDKPVLLFLELIGNDVCSGHHDY DSMTTVEEFGENILTILNYLETTLPKGSHV VFVGLADGRVLWDSLWNRTHPLGCTYEEVY DFLNCIQVSPCWGWMNPNETVRDYTSNRAA QLSLVYNQLIKNYTFNNFDMIYYDFPFATI NEMWVAQGGQTYDLIEPIDGFHPNQIANYL MAGVFYNQIAQDKPEWLGEINQYNTQIQSI FGNQGGYV low complexity regions: SEG 45 3.4 3.75 >AAM43641.1 ACYLOXYACYL HYDROLASE [Dictyostelium discoideum]. 1-564 MKSVFVLLFIVLSVLINFTTAVNIPVNGKS LEIKNKFEEFISNDVKSANGGTHCAACTIV LSLVNQYSGIHNKSIEDSLDELCSFFPDEA GSLCTWLVNTYGEQIISYFDQYQNADDVCH AMNVCTSPTCRLFTSAPSKFYNPDHVHQEY NKEDPKVGGSPWAWIQELIKVFSSEHLPIQ DFDGDHHSLEATFRGYNWRGKDCNDFDKSS YPGTIEGTGDASVDKNCNGIFGVNNQSQSY EELFCSNSGAMGVIVSGDSAGAHFSIPPQW MTARDINSTTYKGMIDILETEVDWPMRSCY TGWDTSAPNVDSMYLRMRERNLCNHRDYQN LGVNGASSSSTRTIIQTINRNQNTDKPVLL FLELIGNDVCSGHHDYDSMTTVEEFGENIL TILNYLETTLPKGSHVVFVGLADGRVLWDS LWNRTHPLGCTYEEVYDFLNCIQVSPCWGW MNPNETVRDYTSNRAAQLSLVYNQLIKNYT FNNFDMIYYDFPFATINEMWVAQGGQTYDL IEPIDGFHPNQIANYLMAGVFYNQIAQDKP EWLGEINQYNTQIQSIFGNQGGYV low complexity regions: XNU # Score cutoff = 21, Search from offsets 1 to 4 # both members of each repeat flagged # lambda = 0.347, K = 0.200, H = 0.664 >AAM43641.1 ACYLOXYACYL HYDROLASE [Dictyostelium discoideum]. MKSvfvllfivlsvlinFTTAVNIPVNGKSLEIKNKFEEFISNDVKSANGGTHCAACTIV LSLVNQYSGIHNKSIEDSLDELCSFFPDEAGSLCTWLVNTYGEQIISYFDQYQNADDVCH AMNVCTSPTCRLFTSAPSKFYNPDHVHQEYNKEDPKVGGSPWAWIQELIKVFSSEHLPIQ DFDGDHHSLEATFRGYNWRGKDCNDFDKSSYPGTIEGTGDASVDKNCNGIFGVNNQSQSY EELFCSNSGAMGVIVSGDSAGAHFSIPPQWMTARDINSTTYKGMIDILETEVDWPMRSCY TGWDTSAPNVDSMYLRMRERNLCNHRDYQNLGVNGASSSSTRTIIQTINRNQNTDKPVLL FLELIGNDVCSGHHDYDSMTTVEEFGENILTILNYLETTLPKGSHVVFVGLADGRVLWDS LWNRTHPLGCTYEEVYDFLNCIQVSPCWGWMNPNETVRDYTSNRAAQLSLVYNQLIKNYT FNNFDMIYYDFPFATINEMWVAQGGQTYDLIEPIDGFHPNQIANYLMAGVFYNQIAQDKP EWLGEINQYNTQIQSIFGNQGGYV 1 - 3 MKS 4 - 17 vfvllfi vlsvlin 18 - 564 FTT AVNIPVNGKS LEIKNKFEEF ISNDVKSANG GTHCAACTIV LSLVNQYSGI HNKSIED SLD ELCSFFPDEA GSLCTWLVNT YGEQIISYFD QYQNADDVCH AMNVCTSPTC RLFTSAP SKF YNPDHVHQEY NKEDPKVGGS PWAWIQELIK VFSSEHLPIQ DFDGDHHSLE ATFRGYN WRG KDCNDFDKSS YPGTIEGTGD ASVDKNCNGI FGVNNQSQSY EELFCSNSGA MGVIVSG DSA GAHFSIPPQW MTARDINSTT YKGMIDILET EVDWPMRSCY TGWDTSAPNV DSMYLRM RER NLCNHRDYQN LGVNGASSSS TRTIIQTINR NQNTDKPVLL FLELIGNDVC SGHHDYD SMT TVEEFGENIL TILNYLETTL PKGSHVVFVG LADGRVLWDS LWNRTHPLGC TYEEVYD FLN CIQVSPCWGW MNPNETVRDY TSNRAAQLSL VYNQLIKNYT FNNFDMIYYD FPFATIN EMW VAQGGQTYDL IEPIDGFHPN QIANYLMAGV FYNQIAQDKP EWLGEINQYN TQIQSIF GNQ GGYV low complexity regions: DUST >AAM43641.1 ACYLOXYACYL HYDROLASE [Dictyostelium discoideum]. MKSVFVLLFIVLSVLINFTTAVNIPVNGKSLEIKNKFEEFISNDVKSANGGTHCAACTIV LSLVNQYSGIHNKSIEDSLDELCSFFPDEAGSLCTWLVNTYGEQIISYFDQYQNADDVCH AMNVCTSPTCRLFTSAPSKFYNPDHVHQEYNKEDPKVGGSPWAWIQELIKVFSSEHLPIQ DFDGDHHSLEATFRGYNWRGKDCNDFDKSSYPGTIEGTGDASVDKNCNGIFGVNNQSQSY EELFCSNSGAMGVIVSGDSAGAHFSIPPQWMTARDINSTTYKGMIDILETEVDWPMRSCY TGWDTSAPNVDSMYLRMRERNLCNHRDYQNLGVNGASSSSTRTIIQTINRNQNTDKPVLL FLELIGNDVCSGHHDYDSMTTVEEFGENILTILNYLETTLPKGSHVVFVGLADGRVLWDS LWNRTHPLGCTYEEVYDFLNCIQVSPCWGWMNPNETVRDYTSNRAAQLSLVYNQLIKNYT FNNFDMIYYDFPFATINEMWVAQGGQTYDLIEPIDGFHPNQIANYLMAGVFYNQIAQDKP EWLGEINQYNTQIQSIFGNQGGYV ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ coiled coil prediction for AAM43641.1 sequence: 564 amino acids, 0 residue(s) in coiled coil state . | . | . | . | . | . 60 MKSVFVLLFI VLSVLINFTT AVNIPVNGKS LEIKNKFEEF ISNDVKSANG GTHCAACTIV ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border ---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif. ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local . | . | . | . | . | . 120 LSLVNQYSGI HNKSIEDSLD ELCSFFPDEA GSLCTWLVNT YGEQIISYFD QYQNADDVCH ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border ---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif. ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local . | . | . | . | . | . 180 AMNVCTSPTC RLFTSAPSKF YNPDHVHQEY NKEDPKVGGS PWAWIQELIK VFSSEHLPIQ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border ---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif. ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local . | . | . | . | . | . 240 DFDGDHHSLE ATFRGYNWRG KDCNDFDKSS YPGTIEGTGD ASVDKNCNGI FGVNNQSQSY ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border ---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif. ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local . | . | . | . | . | . 300 EELFCSNSGA MGVIVSGDSA GAHFSIPPQW MTARDINSTT YKGMIDILET EVDWPMRSCY ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border ---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif. ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local . | . | . | . | . | . 360 TGWDTSAPNV DSMYLRMRER NLCNHRDYQN LGVNGASSSS TRTIIQTINR NQNTDKPVLL ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border ---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif. ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local . | . | . | . | . | . 420 FLELIGNDVC SGHHDYDSMT TVEEFGENIL TILNYLETTL PKGSHVVFVG LADGRVLWDS ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border ---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif. ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local . | . | . | . | . | . 480 LWNRTHPLGC TYEEVYDFLN CIQVSPCWGW MNPNETVRDY TSNRAAQLSL VYNQLIKNYT ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border ---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif. ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local . | . | . | . | . | . 540 FNNFDMIYYD FPFATINEMW VAQGGQTYDL IEPIDGFHPN QIANYLMAGV FYNQIAQDKP ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border ---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif. ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local . | . | EWLGEINQYN TQIQSIFGNQ GGYV ~~~~~~~~~~ ~~~~~~~~~~ ~~~~ ---------- ---------- ---- ~~~~~~~~~~ ~~~~~~~~~~ ~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~ 2222222222 2222~~~~~~ ~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ prediction of transmembrane regions with toppred2 *********************************** *TOPPREDM with eukaryotic function* *********************************** AAM43641.1.fa.___inter___ is a single sequence Using hydrophobicity file: /bio_software/2D/toppredm/lib/Engelman-Steitz.scale Using cyt/ext file: /bio_software/2D/toppredm/lib/Cyt-Ext.prok Using sequence file: AAM43641.1.fa.___inter___ (1 sequences) MKSVFVLLFIVLSVLINFTTAVNIPVNGKSLEIKNKFEEFISNDVKSANG GTHCAACTIVLSLVNQYSGIHNKSIEDSLDELCSFFPDEAGSLCTWLVNT YGEQIISYFDQYQNADDVCHAMNVCTSPTCRLFTSAPSKFYNPDHVHQEY NKEDPKVGGSPWAWIQELIKVFSSEHLPIQDFDGDHHSLEATFRGYNWRG KDCNDFDKSSYPGTIEGTGDASVDKNCNGIFGVNNQSQSYEELFCSNSGA MGVIVSGDSAGAHFSIPPQWMTARDINSTTYKGMIDILETEVDWPMRSCY TGWDTSAPNVDSMYLRMRERNLCNHRDYQNLGVNGASSSSTRTIIQTINR NQNTDKPVLLFLELIGNDVCSGHHDYDSMTTVEEFGENILTILNYLETTL PKGSHVVFVGLADGRVLWDSLWNRTHPLGCTYEEVYDFLNCIQVSPCWGW MNPNETVRDYTSNRAAQLSLVYNQLIKNYTFNNFDMIYYDFPFATINEMW VAQGGQTYDLIEPIDGFHPNQIANYLMAGVFYNQIAQDKPEWLGEINQYN TQIQSIFGNQGGYV (p)rokaryotic or (e)ukaryotic: e Charge-pair energy: 0 Length of full window (odd number!): 21 Length of core window (odd number!): 11 Number of residues to add to each end of helix: 1 Critical length: 60 Upper cutoff for candidates: 1 Lower cutoff for candidates: 0.6 Total of 4 structures are to be tested Candidate membrane-spanning segments: Helix Begin End Score Certainity 1 3 23 2.034 Certain 2 47 67 0.983 Putative 3 248 268 0.735 Putative ---------------------------------------------------------------------- Structure 1 Transmembrane segments included in this structure: Segment 1 2 3 Loop length 2 23 180 296 K+R profile 2.00 + 4.00 + CYT-EXT prof - 0.47 - 0.63 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: -2.00 Tm probability: 0.32 -> Orientation: N-out Charge-difference over N-terminal Tm (+-15 residues): -1.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: N-out CYT-EXT difference: -0.16 -> Orientation: N-in ---------------------------------------------------------------------- Structure 2 Transmembrane segments included in this structure: Segment 1 3 Loop length 2 224 296 K+R profile 2.00 + + CYT-EXT prof - 0.63 0.59 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 2.00 Tm probability: 0.34 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): -1.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: N-out CYT-EXT difference: 0.04 -> Orientation: N-out ---------------------------------------------------------------------- Structure 3 Transmembrane segments included in this structure: Segment 1 2 Loop length 2 23 497 K+R profile 2.00 + 4.00 CYT-EXT prof - 0.78 - For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: -2.00 Tm probability: 0.96 -> Orientation: N-out Charge-difference over N-terminal Tm (+-15 residues): -1.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: N-out CYT-EXT difference: 0.78 -> Orientation: N-out ---------------------------------------------------------------------- Structure 4 Transmembrane segments included in this structure: Segment 1 Loop length 2 541 K+R profile 2.00 + CYT-EXT prof - 0.82 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 2.00 Tm probability: 1.00 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): -1.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: N-out CYT-EXT difference: -0.82 -> Orientation: N-in ---------------------------------------------------------------------- "AAM43641" 564 3 23 #t 2.03438 47 67 #f 0.983333 248 268 #f 0.735417 ************************************ *TOPPREDM with prokaryotic function* ************************************ AAM43641.1.fa.___inter___ is a single sequence Using hydrophobicity file: /bio_software/2D/toppredm/lib/Engelman-Steitz.scale Using cyt/ext file: /bio_software/2D/toppredm/lib/Cyt-Ext.prok Using sequence file: AAM43641.1.fa.___inter___ (1 sequences) MKSVFVLLFIVLSVLINFTTAVNIPVNGKSLEIKNKFEEFISNDVKSANG GTHCAACTIVLSLVNQYSGIHNKSIEDSLDELCSFFPDEAGSLCTWLVNT YGEQIISYFDQYQNADDVCHAMNVCTSPTCRLFTSAPSKFYNPDHVHQEY NKEDPKVGGSPWAWIQELIKVFSSEHLPIQDFDGDHHSLEATFRGYNWRG KDCNDFDKSSYPGTIEGTGDASVDKNCNGIFGVNNQSQSYEELFCSNSGA MGVIVSGDSAGAHFSIPPQWMTARDINSTTYKGMIDILETEVDWPMRSCY TGWDTSAPNVDSMYLRMRERNLCNHRDYQNLGVNGASSSSTRTIIQTINR NQNTDKPVLLFLELIGNDVCSGHHDYDSMTTVEEFGENILTILNYLETTL PKGSHVVFVGLADGRVLWDSLWNRTHPLGCTYEEVYDFLNCIQVSPCWGW MNPNETVRDYTSNRAAQLSLVYNQLIKNYTFNNFDMIYYDFPFATINEMW VAQGGQTYDLIEPIDGFHPNQIANYLMAGVFYNQIAQDKPEWLGEINQYN TQIQSIFGNQGGYV (p)rokaryotic or (e)ukaryotic: p Charge-pair energy: 0 Length of full window (odd number!): 21 Length of core window (odd number!): 11 Number of residues to add to each end of helix: 1 Critical length: 60 Upper cutoff for candidates: 1 Lower cutoff for candidates: 0.6 Total of 4 structures are to be tested Candidate membrane-spanning segments: Helix Begin End Score Certainity 1 3 23 2.034 Certain 2 47 67 0.983 Putative 3 248 268 0.735 Putative ---------------------------------------------------------------------- Structure 1 Transmembrane segments included in this structure: Segment 1 2 3 Loop length 2 23 180 296 K+R profile 1.00 + 4.00 + CYT-EXT prof - 0.47 - 0.63 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: -3.00 Tm probability: 0.32 -> Orientation: N-out Charge-difference over N-terminal Tm (+-15 residues): -1.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: N-out CYT-EXT difference: -0.16 -> Orientation: N-in ---------------------------------------------------------------------- Structure 2 Transmembrane segments included in this structure: Segment 1 2 Loop length 2 23 497 K+R profile 1.00 + 4.00 CYT-EXT prof - 0.78 - For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: -3.00 Tm probability: 0.96 -> Orientation: N-out Charge-difference over N-terminal Tm (+-15 residues): -1.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: N-out CYT-EXT difference: 0.78 -> Orientation: N-out ---------------------------------------------------------------------- Structure 3 Transmembrane segments included in this structure: Segment 1 3 Loop length 2 224 296 K+R profile 1.00 + + CYT-EXT prof - 0.63 0.59 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 1.00 Tm probability: 0.34 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): -1.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: N-out CYT-EXT difference: 0.04 -> Orientation: N-out ---------------------------------------------------------------------- Structure 4 Transmembrane segments included in this structure: Segment 1 Loop length 2 541 K+R profile 1.00 + CYT-EXT prof - 0.82 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 1.00 Tm probability: 1.00 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): -1.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: N-out CYT-EXT difference: -0.82 -> Orientation: N-in ---------------------------------------------------------------------- "AAM43641" 564 3 23 #t 2.03438 47 67 #f 0.983333 248 268 #f 0.735417 ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ SAPS. Version of April 11, 1996. Date run: Mon Oct 14 16:07:17 2002 File: /people/b_eisen/AAM43641.1.fa.___saps___ ID AAM43641.1 DE ACYLOXYACYL HYDROLASE [Dictyostelium discoideum]. number of residues: 564; molecular weight: 63.7 kdal 1 MKSVFVLLFI VLSVLINFTT AVNIPVNGKS LEIKNKFEEF ISNDVKSANG GTHCAACTIV 61 LSLVNQYSGI HNKSIEDSLD ELCSFFPDEA GSLCTWLVNT YGEQIISYFD QYQNADDVCH 121 AMNVCTSPTC RLFTSAPSKF YNPDHVHQEY NKEDPKVGGS PWAWIQELIK VFSSEHLPIQ 181 DFDGDHHSLE ATFRGYNWRG KDCNDFDKSS YPGTIEGTGD ASVDKNCNGI FGVNNQSQSY 241 EELFCSNSGA MGVIVSGDSA GAHFSIPPQW MTARDINSTT YKGMIDILET EVDWPMRSCY 301 TGWDTSAPNV DSMYLRMRER NLCNHRDYQN LGVNGASSSS TRTIIQTINR NQNTDKPVLL 361 FLELIGNDVC SGHHDYDSMT TVEEFGENIL TILNYLETTL PKGSHVVFVG LADGRVLWDS 421 LWNRTHPLGC TYEEVYDFLN CIQVSPCWGW MNPNETVRDY TSNRAAQLSL VYNQLIKNYT 481 FNNFDMIYYD FPFATINEMW VAQGGQTYDL IEPIDGFHPN QIANYLMAGV FYNQIAQDKP 541 EWLGEINQYN TQIQSIFGNQ GGYV -------------------------------------------------------------------------------- COMPOSITIONAL ANALYSIS (extremes relative to: swp23s) A : 25( 4.4%); C : 16( 2.8%); D : 37( 6.6%); E : 30( 5.3%); F : 28( 5.0%) G : 40( 7.1%); H : 15( 2.7%); I : 37( 6.6%); K : 18( 3.2%); L : 39( 6.9%) M : 13( 2.3%); N+ : 48( 8.5%); P : 22( 3.9%); Q : 25( 4.4%); R : 15( 2.7%) S : 45( 8.0%); T : 35( 6.2%); V : 36( 6.4%); W : 13( 2.3%); Y : 27( 4.8%) KR : 33 ( 5.9%); ED : 67 ( 11.9%); AGP : 87 ( 15.4%); KRED : 100 ( 17.7%); KR-ED - : -34 ( -6.0%); FIKMNY : 171 ( 30.3%); LVIFM : 153 ( 27.1%); ST : 80 ( 14.2%). -------------------------------------------------------------------------------- CHARGE DISTRIBUTIONAL ANALYSIS 1 0+00000000 0000000000 00000000+0 0-0+0+0--0 000-0+0000 0000000000 61 0000000000 00+00--00- -000000--0 0000000000 00-000000- 00000--000 121 0000000000 +0000000+0 000-0000-0 0+--0+0000 000000-00+ 0000-00000 181 -0-0-0000- 000+0000+0 +-00-0-+00 00000-000- 000-+00000 0000000000 241 --00000000 0000000-00 0000000000 000+-00000 0+000-00-0 -0-000+000 301 000-000000 -0000+0+-+ 00000+-000 0000000000 0+0000000+ 0000-+0000 361 00-0000-00 0000-0-000 00--00-000 000000-000 0+00000000 00-0+000-0 421 000+000000 00--00-000 0000000000 0000-00+-0 000+000000 000000+000 481 0000-0000- 0000000-00 00000000-0 0-00-00000 0000000000 0000000-+0 541 -000-00000 0000000000 0000 A. CHARGE CLUSTERS. Positive charge clusters (cmin = 6/30 or 8/45 or 10/60): none Negative charge clusters (cmin = 10/30 or 14/45 or 17/60): none Mixed charge clusters (cmin = 13/30 or 18/45 or 22/60): none B. HIGH SCORING (UN)CHARGED SEGMENTS. There are no high scoring positive charge segments. There are no high scoring negative charge segments. There are no high scoring mixed charge segments. There are no high scoring uncharged segments. C. CHARGE RUNS AND PATTERNS. pattern (+)| (-)| (*)| (0)| (+0)| (-0)| (*0)|(+00)|(-00)|(*00)| (H.)|(H..)| lmin0 4 | 5 | 6 | 47 | 8 | 10 | 12 | 10 | 12 | 15 | 7 | 9 | lmin1 5 | 7 | 8 | 57 | 10 | 12 | 14 | 12 | 15 | 18 | 9 | 11 | lmin2 6 | 8 | 9 | 64 | 11 | 14 | 16 | 14 | 17 | 20 | 10 | 12 | (Significance level: 0.010000; Minimal displayed length: 6) There are no charge runs or patterns exceeding the given minimal lengths. Run count statistics: + runs >= 3: 0 - runs >= 3: 0 * runs >= 4: 0 0 runs >= 31: 0 -------------------------------------------------------------------------------- DISTRIBUTION OF OTHER AMINO ACID TYPES 1. HIGH SCORING SEGMENTS. There are no high scoring hydrophobic segments. ____________________________________ High scoring transmembrane segments: 5.00 (LVIF) 2.00 (AGM) 0.00 (BZX) -1.00 (YCW) -2.00 (ST) -6.00 (P) -8.00 (H) -10.00 (NQ) -16.00 (KR) -17.00 (ED) Expected score/letter: -3.562 M_0.01= 57.24; M_0.05= 47.29; M_0.30= 35.45 1) From 4 to 18: length= 15, score=53.00 * 4 VFVLLFIVLS VLINF L: 4(26.7%); V: 4(26.7%); I: 2(13.3%); F: 3(20.0%); 2. SPACINGS OF C. H2N-53-C-2-C-25-C-10-C-24-C-5-C-4-C-72-C-23-C-17-C-53-C-23-C-46-C-59-C-10-C-5-C-117-COOH 2*. SPACINGS OF C and H. (additional deluxe function for ALEX) H2N-52-H-C-2-C-13-H-11-C-10-C-24-C-H-4-C-4-C-14-H-1-H-28-H-9-H-H-15-C-23-C-17-C-17-H-35-C-23-C-1-H-44-C-2-H-H-30-H-20-H-3-C-10-C-5-C-70-H-46-COOH -------------------------------------------------------------------------------- REPETITIVE STRUCTURES. A. SEPARATED, TANDEM, AND PERIODIC REPEATS: amino acid alphabet. Repeat core block length: 5 B. SEPARATED AND TANDEM REPEATS: 11-letter reduced alphabet. (i= LVIF; += KR; -= ED; s= AG; o= ST; n= NQ; a= YW; p= P; h= H; m= M; c= C) Repeat core block length: 9 -------------------------------------------------------------------------------- MULTIPLETS. A. AMINO ACID ALPHABET. 1. Total number of amino acid multiplets: 30 (Expected range: 14-- 47) 2. Histogram of spacings between consecutive amino acid multiplets: (1-5) 5 (6-10) 5 (11-20) 12 (>=21) 9 3. Clusters of amino acid multiplets (cmin = 10/30 or 13/45 or 15/60): none B. CHARGE ALPHABET. 1. Total number of charge multiplets: 9 (Expected range: 0-- 18) 0 +plets (f+: 5.9%), 9 -plets (f-: 11.9%) Total number of charge altplets: 10 (Critical number: 18) 2. Histogram of spacings between consecutive charge multiplets: (1-5) 1 (6-10) 1 (11-20) 0 (>=21) 8 -------------------------------------------------------------------------------- PERIODICITY ANALYSIS. A. AMINO ACID ALPHABET (core: 4; !-core: 5) Location Period Element Copies Core Errors 337- 340 1 S 4 4 0 B. CHARGE ALPHABET ({+= KR; -= ED; 0}; core: 5; !-core: 6) and HYDROPHOBICITY ALPHABET ({*= KRED; i= LVIF; 0}; core: 6; !-core: 9) Location Period Element Copies Core Errors 4- 18 1 i 13 9 ! 2 4- 27 2 i. 11 8 1 471- 505 5 i000. 7 7 /0/2/2/2/./ -------------------------------------------------------------------------------- SPACING ANALYSIS. There are no unusual spacings. ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ Start with Pfam_ls (from /local/index/hmmer) hmmpfam - search a single seq against HMM database HMMER 2.1.1 (Dec 1998) Copyright (C) 1992-1998 Washington University School of Medicine HMMER is freely distributed under the GNU General Public License (GPL). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - HMM file: /local/index/hmmer/Pfam_ls Sequence file: AAM43641.1.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: AAM43641.1 ACYLOXYACYL HYDROLASE [Dictyostelium discoideum]. Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- Lipase_GDSL Lipase/Acylhydrolase with GDSL-like m 50.7 3.3e-11 1 PsbN Photosystem II reaction centre N prot -6.1 9.9 1 Avian_gp85 Avian retrovirus envelope protein, gp -116.2 58 1 Arena_glycoprot Arenavirus glycoprotein -421.8 79 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- PsbN 1/1 1 42 [. 1 44 [] -6.1 9.9 Avian_gp85 1/1 106 321 .. 1 261 [] -116.2 58 Arena_glycoprot 1/1 5 333 .. 1 525 [] -421.8 79 Lipase_GDSL 1/1 252 375 .. 1 137 [] 50.7 3.3e-11 Alignments of top-scoring domains: PsbN: domain 1 of 1, from 1 to 42: score -6.1, E = 9.9 *->MEtiAtvltIFlasLLlsiTgYSiYtsFGPpSkeLrDPFEEHEd<-* M++ +vl + + s L+ +T ++ + S e + FEE AAM43641.1 1 MKS-VFVLLFIVLSVLINFTT-AVNIPVNGKSLEIKNKFEEFIS 42 Avian_gp85: domain 1 of 1, from 106 to 321: score -116.2, E = 58 *->LNvslPwDEPqELqlLGSQslpNiTnitqvsgvaggCvkfnprsrvc +s +D q + + N+ + +++ kf + + v AAM43641.1 106 --ISY-FDQYQNADDVCHAM--NVCTSPTCRLFTSAPSKFYNPDHVH 147 glflGnwsrqggaralLrdPgnnpfFiekskStepftvvtadrhnlfmgs + + + gg+ i+ S+ + + h + AAM43641.1 148 QEYNKEDPKVGGSPWAWIQE-----LIKVFSSEHLPIQDFDGDHHSLEAT 192 eycgaygysRfwemyncsqtrqntyrcgdvssgrGlP..EnwCtskgGkW gy w + c++ + ++ g + g+G + + C + G AAM43641.1 193 FR----GY--NWRGKDCNDFD-KSSYPGTIE-GTGDAsvDKNCNGIFGV- 233 vNQskeiNetepfSfTvnCtGsnlgnvsgyccGetitilPegaWvdsTqG NQs+ e ++ G vsg G + i P W+ AAM43641.1 234 NNQSQSYEELFCSN-----SGAMGVIVSGDSAGAHFSIPP--QWMTARDI 276 SFTKPKALPPaIFLICGDRAWQGIPsrpvGGPCYLGkLTMLaPnhTdilk T K + I W P r CY G T aPn + AAM43641.1 277 NSTTYKGM---IDILETEVDW---PMRS----CYTGWDTS-APNVDSM-- 313 ilaNSSrTGiRRskRS<-* +l R R AAM43641.1 314 YLRM-------R-ERN 321 Arena_glycoprot: domain 1 of 1, from 5 to 333: score -421.8, E = 79 *->MGQiisFfQeiPhilqEalNIALIaVSlIAIlKGlvNlwkCGLFQLv ++ +f I++S++ vN+ G AAM43641.1 5 ---FVLLF---------------IVLSVLINFTTAVNIPVNG----- 28 tFLiLAGRSCDSmYGLsetFiIgrnyefqsveldmsqLfenmsHeLPlSC S+ I+ e + +n AAM43641.1 29 ----------KSL-------EIKNKFE---------EFISND------VK 46 skNnSHHYikggnnstwGlELTlTnt.SilnhssgnfsldvfvnifcNLS s+N +H + L+l n S + +s sld f AAM43641.1 47 SANGGTHCAACT------IVLSLVNQySGIHNKSIEDSLDELCSFF---- 86 nCvksdeeddhtLmwlletlhlaIghdfnqdpam..lCd.kntgteielq +de++ ++ wl++t ++I f+q+ +++ C n t + + AAM43641.1 87 ----PDEAG-SLCTWLVNTYGEQIISYFDQYQNAddVCHaMNVCTSPTCR 131 yqlniSradgagnycrtllngllqlfrsmkwgWvdkCqRakcmrlesgsg + ++ + + + + n + +++ w+W+ + + s+ + AAM43641.1 132 LFTSAPSKFYNPDHVHQEYNKEDPKVGGSPWAWIQEL-----IKVFSSEH 176 gtcayseccgqTkykyLiI..QNtTWe.nhCe.fnrPhpntfhlLlsqrt + ++++ L ++ + W + +C +f+ ++ + + t AAM43641.1 177 LPI----QDFDGDHHSLEAtfRGYNWRgKDCNdFD---KSSYPGTIEG-T 218 gisfisRrLlGfFTWtLSDSsGndmPGGYCLErWMLVaAeLKCFGNTAvA g++++ AAM43641.1 219 GDASV--------------------------------------------- 223 KCNqnHDsEFCDMLRLFDyNKnAIktLndevksslNLlkkTINALISDnL D N n I n +++s L+ A AAM43641.1 224 -----------------DKNCNGIFGVNNQSQSYEELFCSNSGA------ 250 LMKNkLreLMgiPYCNYTKFWYvNHTlTGrH.SLPrCWLvsNGSYLNETe Mg+ v + G H S P W+ + N+T AAM43641.1 251 ---------MGV---------IVSGDSAGAHfSIPPQWMTARD--INSTT 280 FrndWiqESDnLitEMLrKEYidRQGkTPLtLVDlcfWSTvF.YtitlFL + + D L tE + R T W T+++ + + L AAM43641.1 281 YKGMI----DILETEV---DWPMRSCYTG--------WDTSApNVDSMYL 315 HLVGiPTHRHIrGepCPKPHRLnskGiCSCGkYkiPkk<-* R + +C Y ++++ AAM43641.1 316 --------------------RMRERNLCNHRDYQNLGV 333 Lipase_GDSL: domain 1 of 1, from 252 to 375: score 50.7, E = 3.3e-11 *->kvvalGDSLtdgggngsestklkdnyrqyrglspssvgdgnfsngtv v++ GDS ++++ +++++ +++ d+n ++++ AAM43641.1 252 GVIVSGDSAGAHFSIPPQW---------------MTARDINSTTYKG 283 lpdilakalgiklg.................frvgklqendsltglNfAv dil+++ ++++ + ++ +++ ++ ++ +r +++ +++++++N +v AAM43641.1 284 MIDILETEVDWPMRscytgwdtsapnvdsmyLRMRERNLCNHRDYQNLGV 333 gGataedllkrlpnlldqvikksqykmygksrkksqkdpdlvtielGgND +Ga++ ++ +++++ r+ ++p l ++el+gND AAM43641.1 334 NGASSSSTRTIIQTI---------------NRNQNTDKPVLLFLELIGND 368 lcdyfrd<-* +c++ d AAM43641.1 369 VCSGHHD 375 // Start with Pfam_fs (from /local/index/hmmer) hmmpfam - search a single seq against HMM database HMMER 2.1.1 (Dec 1998) Copyright (C) 1992-1998 Washington University School of Medicine HMMER is freely distributed under the GNU General Public License (GPL). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - HMM file: /local/index/hmmer/Pfam_fs Sequence file: AAM43641.1.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: AAM43641.1 ACYLOXYACYL HYDROLASE [Dictyostelium discoideum]. Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- Lipase_GDSL Lipase/Acylhydrolase with GDSL-like mot 48.9 4.7e-13 1 Vps52 Vps52 / Sac2 family 2.5 6.2 1 Vsr DNA mismatch endonuclease Vsr 2.1 23 1 PX PX domain 1.5 69 1 Antifreeze Antifreeze-like domain 1.5 74 1 DUF19 Domain of unknown function DUF19 0.6 15 1 DSL Delta serrate ligand 0.5 86 1 arginase Arginase family 0.4 35 1 MotA_ExbB MotA/TolQ/ExbB proton channel family 0.3 95 1 bac_dnaA Bacterial dnaA protein 0.2 23 1 Uteroglobin Uteroglobin family 0.0 99 1 Exo_endo_phos Endonuclease/Exonuclease/phosphatase fa -0.4 91 1 NlpE Uncharacterized lipoprotein NlpE involv -0.5 83 1 Glyco_hydro_7 Glycosyl hydrolase family 7 -1.3 62 1 DUF107 Protein of unknown function DUF107 -1.6 90 1 Peptidase_S15 X-Pro dipeptidyl-peptidase (S15 family) -2.8 65 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- DUF107 1/1 1 13 [. 1 13 [. -1.6 90 Uteroglobin 1/1 1 15 [. 1 15 [. 0.0 99 MotA_ExbB 1/1 27 42 .. 126 141 .] 0.3 95 arginase 1/1 55 68 .. 319 332 .] 0.4 35 Vps52 1/1 70 83 .. 1 14 [. 2.5 6.2 NlpE 1/1 136 146 .. 211 221 .] -0.5 83 Exo_endo_phos 1/1 185 193 .. 181 189 .] -0.4 91 DSL 1/1 198 203 .. 62 67 .] 0.5 86 Vsr 1/1 198 206 .. 75 83 .] 2.1 23 Glyco_hydro_7 1/1 275 283 .. 434 442 .] -1.3 62 Peptidase_S15 1/1 269 300 .. 767 796 .] -2.8 65 Lipase_GDSL 1/1 252 375 .. 1 137 [] 48.9 4.7e-13 PX 1/1 426 442 .. 115 134 .] 1.5 69 DUF19 1/1 430 442 .. 1 13 [. 0.6 15 Antifreeze 1/1 469 477 .. 1 9 [. 1.5 74 bac_dnaA 1/1 475 484 .. 1 10 [. 0.2 23 Alignments of top-scoring domains: DUF107: domain 1 of 1, from 1 to 13: score -1.6, E = 90 *->mrpiLlsLflLlf<-* m+ ++++Lf +l+ AAM43641.1 1 MKSVFVLLFIVLS 13 Uteroglobin: domain 1 of 1, from 1 to 15: score 0.0, E = 99 *->MKLaivLtLvtlalc<-* MK ++vL+ + l+ + AAM43641.1 1 MKSVFVLLFIVLSVL 15 MotA_ExbB: domain 1 of 1, from 27 to 42: score 0.3, E = 95 *->krkveelslkleafae<-* ++k+ e+++k+e+f++ AAM43641.1 27 NGKSLEIKNKFEEFIS 42 arginase: domain 1 of 1, from 55 to 68: score 0.4, E = 35 *->aAaslvrelLgktl<-* aA+++v++l +++ AAM43641.1 55 AACTIVLSLVNQYS 68 Vps52: domain 1 of 1, from 70 to 83: score 2.5, E = 6.2 *->verkSiqdvidYLC<-* +++kSi+d +d LC AAM43641.1 70 IHNKSIEDSLDELC 83 NlpE: domain 1 of 1, from 136 to 146: score -0.5, E = 83 *->kpakvlapdka<-* +p+k++ pd + AAM43641.1 136 APSKFYNPDHV 146 Exo_endo_phos: domain 1 of 1, from 185 to 193: score -0.4, E = 91 *->DHrPvlatl<-* DH+ ++at+ AAM43641.1 185 DHHSLEATF 193 DSL: domain 1 of 1, from 198 to 203: score 0.5, E = 86 *->WkGeyC<-* W+G++C AAM43641.1 198 WRGKDC 203 Vsr: domain 1 of 1, from 198 to 206: score 2.1, E = 23 *->WHGHdCnig<-* W G+dCn++ AAM43641.1 198 WRGKDCNDF 206 Glyco_hydro_7: domain 1 of 1, from 275 to 283: score -1.3, E = 62 *->pIGssTfsg<-* +I+s+T++g AAM43641.1 275 DINSTTYKG 283 Peptidase_S15: domain 1 of 1, from 269 to 300: score -2.8, E = 65 *->qgmTkRpleketYt..iDLaqtklilPyesvK<-* q mT R+ tY + iD +t++ P +s AAM43641.1 269 QWMTARDINSTTYKgmIDILETEVDWPMRSCY 300 Lipase_GDSL: domain 1 of 1, from 252 to 375: score 48.9, E = 4.7e-13 *->kvvalGDSLtdgggngsestklkdnyrqyrglspssvgdgnfsngtv v++ GDS ++++ +++++ +++ d+n ++++ AAM43641.1 252 GVIVSGDSAGAHFSIPPQW---------------MTARDINSTTYKG 283 lpdilakalgiklg.................frvgklqendsltglNfAv dil+++ ++++ + ++ +++ ++ ++ +r +++ +++++++N +v AAM43641.1 284 MIDILETEVDWPMRscytgwdtsapnvdsmyLRMRERNLCNHRDYQNLGV 333 gGataedllkrlpnlldqvikksqykmygksrkksqkdpdlvtielGgND +Ga++ ++ +++++ r+ ++p l ++el+gND AAM43641.1 334 NGASSSSTRTIIQTI---------------NRNQNTDKPVLLFLELIGND 368 lcdyfrd<-* +c++ d AAM43641.1 369 VCSGHHD 375 PX: domain 1 of 1, from 426 to 442: score 1.5, E = 69 *->hPelsnhrlsevvleFLess<-* hP+ + +e+v++FL++ AAM43641.1 426 HPLGCT---YEEVYDFLNCI 442 DUF19: domain 1 of 1, from 430 to 442: score 0.6, E = 15 *->CTevtslkatkCl<-* CT +++++++ C+ AAM43641.1 430 CTYEEVYDFLNCI 442 Antifreeze: domain 1 of 1, from 469 to 477: score 1.5, E = 74 *->SlVakkdIk<-* SlV++++Ik AAM43641.1 469 SLVYNQLIK 477 bac_dnaA: domain 1 of 1, from 475 to 484: score 0.2, E = 23 *->LnkrYtFenF<-* L k+YtF nF AAM43641.1 475 LIKNYTFNNF 484 // Start with Repeat Library (from /local/index/hmmer) hmmpfam - search a single seq against HMM database HMMER 2.1.1 (Dec 1998) Copyright (C) 1992-1998 Washington University School of Medicine HMMER is freely distributed under the GNU General Public License (GPL). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - HMM file: /local/index/hmmer/adrade-repeats.hmm Sequence file: AAM43641.1.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: AAM43641.1 ACYLOXYACYL HYDROLASE [Dictyostelium discoideum]. Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- [no hits above thresholds] Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- [no hits above thresholds] Alignments of top-scoring domains: [no hits above thresholds] // ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ Start with Prosite --------------------------------------------------------- | ppsearch (c) 1994 EMBL Data Library | | based on MacPattern (c) 1990-1994 R. Fuchs | --------------------------------------------------------- PROSITE pattern search started: Mon Oct 14 16:10:24 2002 Sequence file: AAM43641.1.fa ---------------------------------------- Sequence AAM43641.1 (564 residues): Matching pattern PS00001 ASN_GLYCOSYLATION: 17: NFTT 72: NKSI 235: NQSQ 277: NSTT 423: NRTH 454: NETV 478: NYTF Total matches: 7 Matching pattern PS00005 PKC_PHOSPHO_SITE: 129: TCR 192: TFR 272: TAR 280: TYK 340: STR 354: TDK 456: TVR 462: SNR Total matches: 8 Matching pattern PS00006 CK2_PHOSPHO_SITE: 74: SIED 78: SLDE 100: TYGE 107: SYFD 239: SYEE 272: TARD 290: TEVD 301: TGWD 380: TTVE 381: TVEE 431: TYEE 456: TVRD 495: TINE Total matches: 13 Matching pattern PS00008 MYRISTYL: 50: GGTHCA 51: GTHCAA 91: GSLCTW 159: GSPWAW 213: GTIEGT 217: GTGDAS 252: GVIVSG 261: GAHFSI 332: GVNGAS 335: GASSSS 366: GNDVCS 410: GLADGR 529: GVFYNQ 558: GNQGGY Total matches: 14 Total no of hits in this sequence: 42 ======================================== 1329 pattern(s) searched in 1 sequence(s), 564 residues. Total no of hits in all sequences: 42. Search time: 00:00 min ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ Start with Profile Search ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ Start with motif search against own library ***** bioMotif : Version V41a DB, 1999 Nov 11 ***** SeqTyp=2 : PROTEIN search; >APC D-Box is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >ER-GOLGI-traffic signal is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >INTRA-SIGNAL-M minimal SH3 binding is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >INTRA-SIGNAL-M deubiquitinating enzyme SH3 domain binding motif (Kato, 2000) is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >INTRA-SIGNAL-M minimal class I consensus-SH3 binding motif is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >INTRA-SIGNAL-M minimal class II consensus-SH3 binding motif is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >INTRA-SIGNAL-M exact 14-3-3 binding consensus (Muslin 1996 Cell 84 889) is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >INTRA-SIGNAL-M 14-3-3 binding motif in RAF and others (Muslin 1996 Cell 84 889) is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >INTRA-SIGNAL-M WW domain binding motif in formins (Bedford 1997) is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >INTRA-SIGNAL-M PY motif for WW domain is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >TM-CYTOPLASMIC-M di-hydrophobic endocytosis motifs for internalized transmembrane proteins is the MOTIF name >AAM43641.1 ACYLOXYACYL HYDROLASE [Dictyostelium discoideum]. ;LENGTH=564; DIRECT_SEQUENCE n 1 solutions m %_D 355-355 %_XXXL 356-359 %_L 360-360 f >STATISTICS Total : 1 solutions in 1 sequences, 564 units; out of 1 sequences, 564 units >TM-CYTOPLASMIC-M tyrosine-based endocytosis motif for internalized transmembrane proteins is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >TM-EXTRACELL-M Endocytosis signal for internalized transmembrane proteins is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >EXTRACELL-M minimal furin protease cleavage site motif is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >EXTRACELL-M extended furin protease cleavage site motif is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >EXTRACELL-M zinc binding motif in MMPs is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >EXTRACELL-M g alpha binding go loco is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS PDX-1 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS QKI-5 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS HCDA experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS SV40 LrgT experimentally determined is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS H2B experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS v-Rel experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS Amida experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS Amida experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS RanBP3 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS Pho4p experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS DNAhelicaseQ1 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS LEF-1 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS TCF-1 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR p53-NLS1 NLS experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS hum-Ku70 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS GAL4 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS act/inh betaA experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS BDV-P experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS BDV-P experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS BDV-P experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS TR2 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS THOV NP experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS polyomaVP1 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS HIV-1 Tat experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS HIV-1 Rev experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS Rex experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS SRY experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS SRY experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS SOX9 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS SOX9 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS NS5A experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS DNAse EBV experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS DNAse EBV experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS adenovE1a experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS ystDNApolalpha experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS hVDR experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS CPV capsid experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS hGlu.cort.experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS cFOS experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS cJUN experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS hDNApolalpha experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS hDNAtopoII experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS hDNAtopoII experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS hBLM experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS hARNT experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS influenzaNP experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS influenzaNP experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS p54 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS hProTalpha experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS Tst1/Oct6 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS protHsc9 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS protHsci experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS protHsc3 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS Ta alpha experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS Pax-QNR experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS Hunt.Dis.pro experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS MyoD experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS MyoD experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS opaque2 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS CTP experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS HCV experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS HCV experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS p110RB1 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS VirD2-Nterm experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS VirD2-Cterm experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS Nucloplasmin experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS Nucleolin experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS ICP-8 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS Nab2 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS M9 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS lscMyc experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS humKprotein experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS FluA experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS Mat-alpha experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS polyoma Lrg-T experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS polyoma Lrg-T experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS SV40 VP1 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS SV40 VP2 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS polyoma VP2 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS c-myb experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS N-myc experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS p53 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS c-erb-A experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS yeast SKI3 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS L29 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS L29 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS Max experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS L3 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >NUCLEAR NLS dyskerin experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >PDZ domain binding motif science 278_2075_pawson is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units >WW domain binding motif science 278_2075_pawson is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 564 units ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~ ~~~ Start with HMM-search search against own library hmmpfam - search a single seq against HMM database HMMER 2.1.1 (Dec 1998) Copyright (C) 1992-1998 Washington University School of Medicine HMMER is freely distributed under the GNU General Public License (GPL). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - HMM file: /local/index/hmmer/own-hmm.lib Sequence file: AAM43641.1.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: AAM43641.1 ACYLOXYACYL HYDROLASE [Dictyostelium discoideum]. Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- [no hits above thresholds] Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- [no hits above thresholds] Alignments of top-scoring domains: [no hits above thresholds] // hmmpfam - search a single seq against HMM database HMMER 2.1.1 (Dec 1998) Copyright (C) 1992-1998 Washington University School of Medicine HMMER is freely distributed under the GNU General Public License (GPL). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - HMM file: /local/index/hmmer/own-hmm-f.lib Sequence file: AAM43641.1.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: AAM43641.1 ACYLOXYACYL HYDROLASE [Dictyostelium discoideum]. Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- [no hits above thresholds] Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- [no hits above thresholds] Alignments of top-scoring domains: [no hits above thresholds] // ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ L. Aravind's signalling DB+ PSSM from other authors IMPALA version 1.1 [20-December-1999] Reference: Alejandro A. Schaffer, Yuri I. Wolf, Chris P. Ponting, Eugene V. Koonin, L. Aravind, Stephen F. Altschul (1999), "IMPALA: Matching a Protein Sequence Against a Collection of "PSI-BLAST-Constructed Position-Specific Score Matrices", Bioinformatics 15:1000-1011. Query= AAM43641.1 ACYLOXYACYL HYDROLASE [Dictyostelium discoideum]. (564 letters) Searching..................................done Results from profile search Score E Sequences producing significant alignments: (bits) Value DSP Dual specificity protein phosphatase 24 0.48 CATH Cathepsin like protease domain 22 2.8 SNARE Alpha helical domains which are involved in vesicle fu... 22 2.8 CHLMY Adenovirus like protease domain 21 4.0 ARR Arrestin domain 21 4.4 HMG High Mobility Group 1 Domain (An Alpha helical DNA bindi... 20 6.8 PUM Pumilio repeat RNA binding domain 20 7.9 SEC7 Sec7 like GDP exchange factor for ARF like GTPases 20 9.8 >DSP Dual specificity protein phosphatase Length = 185 Score = 24.2 bits (52), Expect = 0.48 Identities = 13/70 (18%), Positives = 13/70 (18%), Gaps = 14/70 (20%) Query: 22 VNIPVN-GKSLEIKNKFEE---FISNDVKSANGGT--HCAA-----CTIVLSLVNQYSGI 70 Sbjct: 86 LGIKANDTQEFNLSAYFERAADFIDQALAQKNGRVLVHCREGYSRSPTLVIAYLMMR--- 142 Query: 71 HNKSIEDSLD 80 Sbjct: 143 QKMDVKSALS 152 >CATH Cathepsin like protease domain Length = 371 Score = 21.8 bits (46), Expect = 2.8 Identities = 10/57 (17%), Positives = 10/57 (17%), Gaps = 1/57 (1%) Query: 213 GTIEGTGDASVDKNCNGIFGVNNQSQSYEELFCSNSGAMGVIVSGDSAGAHFSIPPQ 269 Sbjct: 255 GTSLITGPTDEIKQLQKAIGAKPIIKGQYMLPCDKLSSLPNVNL-VLGGKSYALTPN 310 >SNARE Alpha helical domains which are involved in vesicle fusion Length = 254 Score = 21.8 bits (46), Expect = 2.8 Identities = 2/23 (8%), Positives = 2/23 (8%), Gaps = 3/23 (13%) Query: 144 DHVHQEYNKEDPKVGGSPWAWIQ 166 Sbjct: 88 DELQKEFIT---TYNMMKTNTAV 107 >CHLMY Adenovirus like protease domain Length = 157 Score = 21.0 bits (44), Expect = 4.0 Identities = 13/110 (11%), Positives = 13/110 (11%), Gaps = 18/110 (16%) Query: 472 YNQLIKNYTF-----NNFDMIYYDFPFATINE---MWVA----QGGQTYDLIEPIDGFHP 519 Sbjct: 11 VPSLLKGYKNVSRWTRHVDIFKEDMILVPVHVDNVHWCMAIIDMSKNMISYYDSFNVPNP 70 Query: 520 ---NQIANYLMAGVFYNQIAQ--DKPEWLGEINQYNTQIQSIFGNQGGYV 564 Sbjct: 71 TVLNALRNFLIKESHARKLETPLTLKDFQVQHAT-NVPRQTNTSDCGVFS 119 >ARR Arrestin domain Length = 454 Score = 21.0 bits (44), Expect = 4.4 Identities = 9/52 (17%), Positives = 9/52 (17%), Gaps = 4/52 (7%) Query: 396 LETTLPKGSHVVFVGLADGRVLWDSLWNRTHPLGCTYEEVYDFLNCIQVSPC 447 Sbjct: 66 IDEEYIKDNRKVTAHLL-AAFRY--GREDLDVLGLTFRKDL-ISETFQVYPQ 113 >HMG High Mobility Group 1 Domain (An Alpha helical DNA binding domain) Length = 83 Score = 20.2 bits (42), Expect = 6.8 Identities = 6/30 (20%), Positives = 6/30 (20%) Query: 450 WMNPNETVRDYTSNRAAQLSLVYNQLIKNY 479 Sbjct: 48 WKMLTEAEKWPFFQEAQKLQAMHREKYPNY 77 >PUM Pumilio repeat RNA binding domain Length = 337 Score = 20.2 bits (42), Expect = 7.9 Identities = 12/52 (23%), Positives = 12/52 (23%), Gaps = 5/52 (9%) Query: 60 VLSLVNQYSGIH--NKSIEDSLDELCSFFPD---EAGSLCTWLVNTYGEQII 106 Sbjct: 131 VVTLINDLNGNHVIQKCIFKFSPSKFGFIIDAIVEQNNIITISTHKHGCCVL 182 >SEC7 Sec7 like GDP exchange factor for ARF like GTPases Length = 192 Score = 19.8 bits (41), Expect = 9.8 Identities = 14/50 (28%), Positives = 14/50 (28%), Gaps = 7/50 (14%) Query: 2 KSVFVLLFIVLSVLINFTTAVNIPVNGKSLEIKNKFEEFISNDVKSANGG 51 Sbjct: 130 DTIFILAFAI--ILLN--TDMYSPNVKPER--KMKLEDFIKN-LRGVDDG 172 Underlying Matrix: BLOSUM62 Number of sequences tested against query: 105 Number of sequences better than 10.0: 8 Number of calls to ALIGN: 8 Length of query: 564 Total length of test sequences: 20182 Effective length of test sequences: 16637.0 Effective search space size: 8829102.9 Initial X dropoff for ALIGN: 25.0 bits Y. Wolf's SCOP PSSM IMPALA version 1.1 [20-December-1999] Reference: Alejandro A. Schaffer, Yuri I. Wolf, Chris P. Ponting, Eugene V. Koonin, L. Aravind, Stephen F. Altschul (1999), "IMPALA: Matching a Protein Sequence Against a Collection of "PSI-BLAST-Constructed Position-Specific Score Matrices", Bioinformatics 15:1000-1011. Query= AAM43641.1 ACYLOXYACYL HYDROLASE [Dictyostelium discoideum]. (564 letters) Searching.................................................done Results from profile search Score E Sequences producing significant alignments: (bits) Value gi|1772352 [27..300] alpha/beta-Hydrolases 28 0.59 gi|1103829 [26..270] Trypsin-like serine proteases 25 3.7 gi|1145791 [40..633] alpha/beta-Hydrolases 24 5.2 gi|1001371 [11..156] Ribonuclease H-like motif 24 5.8 gi|2688349 [40..475] Class II aaRS and biotin synthetases 24 6.1 gi|1787711 [41..320] Periplasmic binding protein-like II 24 7.5 gi|1086887 [26..189] P-loop containing nucleotide triphospha... 23 9.6 gi|2104446 [1048..1249] 7-bladed beta-propeller 24 9.7 gi|462661 [1..391] IF3-like 23 9.9 >gi|1772352 [27..300] alpha/beta-Hydrolases Length = 274 Score = 27.6 bits (61), Expect = 0.59 Identities = 14/83 (16%), Positives = 14/83 (16%), Gaps = 14/83 (16%) Query: 155 PKVGGSPWA-WIQELIKVFSSEH-------LPIQDFDGDHHSLEATFRGYNWRGKDCNDF 206 Sbjct: 175 PRVANKPLAEFITNQGNNYRFTHNDDPVPKLPLLTMGYVHISPEYYITAPD------NTT 228 Query: 207 DKSSYPGTIEGTGDASVDKNCNG 229 Sbjct: 229 VTDNQVTVLDGYVNFKGNTGTSG 251 >gi|1103829 [26..270] Trypsin-like serine proteases Length = 245 Score = 24.7 bits (53), Expect = 3.7 Identities = 8/79 (10%), Positives = 8/79 (10%), Gaps = 13/79 (16%) Query: 373 HHDYDSMTTVEEFGENILTILNYLETTLPKGSHVVFVGL-------ADGRVLWDSLWNRT 425 Sbjct: 95 GRPIAQTL----SGFDIAIV--MLAQMVNLQSGITVISLPQASDIPTPGTGVFIVGYGRD 148 Query: 426 HPLGCTYEEVYDFLNCIQV 444 Sbjct: 149 DNDRDPSRKNGGILKKGEL 167 >gi|1145791 [40..633] alpha/beta-Hydrolases Length = 594 Score = 24.3 bits (52), Expect = 5.2 Identities = 18/121 (14%), Positives = 18/121 (14%), Gaps = 19/121 (15%) Query: 211 YPGTIEGTGDASVDKNCNGIFGVNNQSQSYEEL--FCSNSGAMG--VIVSGDSAGAHFSI 266 Sbjct: 198 YRVGVLGFL-STGDQAAKGNYGLLDQIQALRWVSENIAFFGGDPRRITVFGSGIGASCVS 256 Query: 267 PPQWMTARDINSTTYKGMI----------DILETEVDWPMRSC-YTGWDTSAPNVDSMYL 315 Sbjct: 257 ---LLTLSHHSEGLFQRAIIQSGSALSSWAVNYQPVKYTSLLADKVGCNVLDTVDMVDCL 313 Query: 316 R 316 Sbjct: 314 R 314 >gi|1001371 [11..156] Ribonuclease H-like motif Length = 146 Score = 24.2 bits (52), Expect = 5.8 Identities = 11/54 (20%), Positives = 11/54 (20%) Query: 29 KSLEIKNKFEEFISNDVKSANGGTHCAACTIVLSLVNQYSGIHNKSIEDSLDEL 82 Sbjct: 89 VIYREKSIQPVFLHQSSWKCHLGNGKANKAEVAAMVQNFFGLEDLPIDDSVDAI 142 >gi|2688349 [40..475] Class II aaRS and biotin synthetases Length = 436 Score = 24.2 bits (52), Expect = 6.1 Identities = 7/52 (13%), Positives = 7/52 (13%), Gaps = 3/52 (5%) Query: 125 CTSPTCRLFTSAPSKFYNPDHVHQEYNKEDPKVGGSPWAWIQELIKVFSSEH 176 Sbjct: 76 PQLYKQLIMIAGFDKYFQIARC---YRDEDSRGDRQPEFTQLDLEMSFVKKE 124 >gi|1787711 [41..320] Periplasmic binding protein-like II Length = 280 Score = 23.8 bits (51), Expect = 7.5 Identities = 13/97 (13%), Positives = 13/97 (13%), Gaps = 10/97 (10%) Query: 351 NQNTDKPVLLFLELIGNDVCSGHHDYDSMTTVEEFGENILTILNY-LETTLPKGSHVVFV 409 Sbjct: 175 EEQYQAVLKVLRAQHSLIHRYWHDTTVQMSDFKNEGVVASSAWPYQANALKAEGQPVATV 234 Query: 410 GLADGRVLWDSLWNRT----HPLGCTYEEVYDFLNCI 442 Sbjct: 235 FPKEGVTGWADTTMLHSEAKHP-----VCAYKWMNWS 266 >gi|1086887 [26..189] P-loop containing nucleotide triphosphate hydrolases Length = 164 Score = 23.3 bits (49), Expect = 9.6 Identities = 11/87 (12%), Positives = 11/87 (12%), Gaps = 5/87 (5%) Query: 475 LIKNYTFNNFDMIYYDFPFATINEMWVAQGGQTY-----DLIEPIDGFHPNQIANYLMAG 529 Sbjct: 15 FIERVEFGKFHEEKQTEKLYRVIAKKVFEQTLTVELIEKDLGGLTNEDNGFKKTEMRDVD 74 Query: 530 VFYNQIAQDKPEWLGEINQYNTQIQSI 556 Sbjct: 75 AVLLFYAADDLESFKQLKENLVHVQRK 101 >gi|2104446 [1048..1249] 7-bladed beta-propeller Length = 202 Score = 23.5 bits (50), Expect = 9.7 Identities = 7/49 (14%), Positives = 7/49 (14%), Gaps = 1/49 (2%) Query: 400 LPKGSHVVFVGLADGRV-LWDSLWNRTHPLGCTYEEVYDFLNCIQVSPC 447 Sbjct: 94 DLVGCNIIVAGFSDGVLRVYDKRLPARDSLTDVWKEHSSEIVNVEMQSS 142 >gi|462661 [1..391] IF3-like Length = 391 Score = 23.3 bits (50), Expect = 9.9 Identities = 8/46 (17%), Positives = 8/46 (17%), Gaps = 12/46 (26%) Query: 175 EHLPIQDFDGDH----HSLEATFRG--------YNWRGKDCNDFDK 208 Sbjct: 296 RTLPHPEFPTDMQAQIMAVNAIGRGFATISETIFENRFMHVPELAR 341 Underlying Matrix: BLOSUM62 Number of sequences tested against query: 1187 Number of sequences better than 10.0: 9 Number of calls to ALIGN: 9 Length of query: 564 Total length of test sequences: 256703 Effective length of test sequences: 209547.0 Effective search space size: 109959128.2 Initial X dropoff for ALIGN: 25.0 bits ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ calculation of internal repeats with prospero ***** PROSPERO v1.3 Mon Oct 14 16:11:03 2002 ***** Copyright 2000, Richard Mott, Wellcome Trust Centre for Human Genetics, University of Oxford For help see http://www.well.ox.ac.uk/ariadne For usage use -help using gap penalty 11+1k using matrix BLOSUM62 printing all alignments with eval < 0.100000 using sequence1 AAM43641.1 using self-comparison ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ TIGRFAM WARNING: tigrfam is not part of the automated update hmmpfam - search a single seq against HMM database HMMER 2.1.1 (Dec 1998) Copyright (C) 1992-1998 Washington University School of Medicine HMMER is freely distributed under the GNU General Public License (GPL). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - HMM file: /data/patterns/tigrfam/tigrfam.hmm Sequence file: AAM43641.1.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: AAM43641.1 ACYLOXYACYL HYDROLASE [Dictyostelium discoideum]. Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- [no hits above thresholds] Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- [no hits above thresholds] Alignments of top-scoring domains: [no hits above thresholds] // hmmpfam - search a single seq against HMM database HMMER 2.1.1 (Dec 1998) Copyright (C) 1992-1998 Washington University School of Medicine HMMER is freely distributed under the GNU General Public License (GPL). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - HMM file: /data/patterns/tigrfam/tigrfam.hmm-f Sequence file: AAM43641.1.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: AAM43641.1 ACYLOXYACYL HYDROLASE [Dictyostelium discoideum]. Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- TIGR00637 ModE_repress: ModE molybdate transport repr 2.3 24 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- TIGR00637 1/1 380 417 .. 62 101 .] 2.3 24 Alignments of top-scoring domains: TIGR00637: domain 1 of 1, from 380 to 417: score 2.3, E = 24 *->avlteaGerlialyglleralekalsvledegvvkplkal<-* + + e Ge ++ le +l k +v + + ++++ +l AAM43641.1 380 TTVEEFGENILTILNYLETTLPKGSHVVFVG--LADGRVL 417 // SMART WARNING: smart is not part of the automated update hmmpfam - search a single seq against HMM database HMMER 2.1.1 (Dec 1998) Copyright (C) 1992-1998 Washington University School of Medicine HMMER is freely distributed under the GNU General Public License (GPL). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - HMM file: /data/patterns/iprscan/data/smart.HMMs Sequence file: AAM43641.1.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: AAM43641.1 ACYLOXYACYL HYDROLASE [Dictyostelium discoideum]. Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- SAPB Saposins-like type B 46.0 8.5e-10 1 ZnF_U1 U1-like zinc finger -6.6 38 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- ZnF_U1 1/1 49 78 .. 1 37 [] -6.6 38 SAPB 1/1 52 125 .. 1 77 [] 46.0 8.5e-10 Alignments of top-scoring domains: ZnF_U1: domain 1 of 1, from 49 to 78: score -6.6, E = 38 *->tggfyCklCnvtfkddeisvreaHlkGkkHkknvkky<-* gg +C C ++++ +++ + H+k +++ AAM43641.1 49 NGGTHCAACTIVLS--LVNQ-----YSGIHNKSIEDS 78 SAPB: domain 1 of 1, from 52 to 125: score 46.0, E = 8.5e-10 *->ivCeiCeflVkklekllkdnktfeeeikdaldklCkklp..lsdeCk C C+ + ++++ + + + i+d ld lC+++p++++ +C AAM43641.1 52 THCAACTIVLSLVNQYSGIHNK---SIEDSLDELCSFFPdeAGSLCT 95 kfvdqyldtiiklleggtdnsPeevCsklglC<-* +v++y+ +ii ++++ + +++vC++++ C AAM43641.1 96 WLVNTYGEQIISYFDQYQN--ADDVCHAMNVC 125 // COG WARNING: cogs is not part of the automated update hmmpfam - search a single seq against HMM database HMMER 2.1.1 (Dec 1998) Copyright (C) 1992-1998 Washington University School of Medicine HMMER is freely distributed under the GNU General Public License (GPL). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - HMM file: /data/patterns/cogs/cogs.hmm Sequence file: AAM43641.1.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: AAM43641.1 ACYLOXYACYL HYDROLASE [Dictyostelium discoideum]. Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- [no hits above thresholds] Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- [no hits above thresholds] Alignments of top-scoring domains: [no hits above thresholds] // hmmpfam - search a single seq against HMM database HMMER 2.1.1 (Dec 1998) Copyright (C) 1992-1998 Washington University School of Medicine HMMER is freely distributed under the GNU General Public License (GPL). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - HMM file: /data/patterns/cogs/cogs.hmm-f Sequence file: AAM43641.1.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: AAM43641.1 ACYLOXYACYL HYDROLASE [Dictyostelium discoideum]. Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- COG1131 2.1 9.7 1 COG3015 1.2 23 1 COG0521 0.9 41 1 COG2127 0.7 81 1 COG1958 0.3 91 1 COG0323 -1.2 50 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- COG0323 1/1 75 89 .. 710 724 .] -1.2 50 COG3015 1/1 136 152 .. 212 228 .] 1.2 23 COG0521 1/1 144 157 .. 176 189 .] 0.9 41 COG1131 1/1 165 190 .. 303 325 .] 2.1 9.7 COG1958 1/1 402 416 .. 81 95 .] 0.3 91 COG2127 1/1 424 435 .. 99 110 .] 0.7 81 Alignments of top-scoring domains: COG0323: domain 1 of 1, from 75 to 89: score -1.2, E = 50 *->ikidldelekfFkrg<-* i+ +ldel+ fF+++ AAM43641.1 75 IEDSLDELCSFFPDE 89 COG3015: domain 1 of 1, from 136 to 152: score 1.2, E = 23 *->kpakvlapdkalKkykk<-* +p+k++ pd + y k AAM43641.1 136 APSKFYNPDHVHQEYNK 152 COG0521: domain 1 of 1, from 144 to 157: score 0.9, E = 41 *->dhilgelretphlk<-* dh++ e++++++++ AAM43641.1 144 DHVHQEYNKEDPKV 157 COG1131: domain 1 of 1, from 165 to 190: score 2.1, E = 9.7 *->v.ellalli.eginvlsi.veepsLE<-* ++el + +++e++ + +++ ++sLE AAM43641.1 165 IqELIKVFSsEHLPIQDFdGDHHSLE 190 COG1958: domain 1 of 1, from 402 to 416: score 0.3, E = 91 *->RGdnVvfIspadnek<-* +G+ Vvf+ +ad+ + AAM43641.1 402 KGSHVVFVGLADGRV 416 COG2127: domain 1 of 1, from 424 to 435: score 0.7, E = 81 *->aehPLlctvEea<-* ++hPL ct Ee+ AAM43641.1 424 RTHPLGCTYEEV 435 //