analysis of sequence from AAF45703.1.fa ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ >AAF45703.1 EG:133E12.3 gene product [Drosophila melanogaster]. MLVKFVVIFA LILASCRVEA DNTSVLPEGF VDAAQRSTHT NNWAVLVDAS RFWFNYRHVA NVLSIYRSVK RLGIPDSQII LMIADDMACN ARNPRPGQVY NNANQHINVY GDDVEVDYRG YEVTVENFVR LLTGRTQNGT ARSKKLLSDA GSNVLIYLTG HGGDGFLKFQ DSEEITSQEL ADGIQQMWEK KRYNELFFMV DTCQAASLYE KFTSPNVLAV ASSLVGEDSL SHHVDPSIGV YMIDRYTYYA LEFLEKVQPF SKRTIGEFLQ VCPKRVCIST VGVRKDLYPR DPHKVPITDF FGAIRPTRVS TDRINVTLAN EE ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ sec.str. with predator > AAF45703.1 . . . . . 1 MLVKFVVIFALILASCRVEADNTSVLPEGFVDAAQRSTHTNNWAVLVDAS 50 ___HHHHHHHHHHHHHEEE___________HHHHHHH______EEEEEE_ . . . . . 51 RFWFNYRHVANVLSIYRSVKRLGIPDSQIILMIADDMACNARNPRPGQVY 100 _HHHHHHHHHHHHHHHHHHH_________HHHHHHHHHHHH_________ . . . . . 101 NNANQHINVYGDDVEVDYRGYEVTVENFVRLLTGRTQNGTARSKKLLSDA 150 _____EEEE_____________EEEHHHHHHH________HHHHHHHHH_ . . . . . 151 GSNVLIYLTGHGGDGFLKFQDSEEITSQELADGIQQMWEKKRYNELFFMV 200 __EEEEEEE______EEEE___HHHHHHHHHHHHHHHHHHHHHHEEEE__ . . . . . 201 DTCQAASLYEKFTSPNVLAVASSLVGEDSLSHHVDPSIGVYMIDRYTYYA 250 HHHHHHHHHHH_____HHHHHH________________EEEEE___HHHH . . . . . 251 LEFLEKVQPFSKRTIGEFLQVCPKRVCISTVGVRKDLYPRDPHKVPITDF 300 HHHHHHH______HHHHHEEE___EEEEE_____________________ . . 301 FGAIRPTRVSTDRINVTLANEE 322 _____________EEEEE____ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ method : 1 alpha-contents : 15.3 % beta-contents : 49.9 % coil-contents : 34.8 % class : mixed method : 2 alpha-contents : 18.2 % beta-contents : 37.5 % coil-contents : 44.3 % class : mixed ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ GPI: learning from metazoa -26.98 -3.45 -1.45 0.00 -4.00 -4.00 0.00 0.00 0.00 -3.37 -1.26 -12.00 -12.00 -12.00 0.00 0.00 -80.52 -25.56 -1.37 -1.97 -0.38 -4.00 0.00 0.00 0.00 -0.01 -4.52 -1.26 -12.00 -12.00 -12.00 0.00 0.00 -75.07 ID: AAF45703.1 AC: xxx Len: 322 1:I 303 Sc: -75.07 Pv: 6.757603e-01 NO_GPI_SITE GPI: learning from protozoa -27.42 -1.54 -0.18 -1.36 -4.00 0.00 0.00 0.00 -0.05 -4.84 -5.44 -12.00 -12.00 -12.00 -12.00 0.00 -92.83 -24.14 -1.51 0.00 -0.07 -4.00 0.00 0.00 0.00 0.00 -4.00 -5.44 -12.00 -12.00 -12.00 0.00 0.00 -75.17 ID: AAF45703.1 AC: xxx Len: 322 1:I 303 Sc: -75.17 Pv: 4.256628e-01 NO_GPI_SITE ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ # SignalP euk predictions # name Cmax pos ? Ymax pos ? Smax pos ? Smean ? AAF45703.1 1.000 21 Y 0.893 21 Y 0.977 7 Y 0.889 Y # SignalP gram- predictions # name Cmax pos ? Ymax pos ? Smax pos ? Smean ? AAF45703.1 0.656 21 Y 0.685 21 Y 0.991 9 Y 0.809 Y # SignalP gram+ predictions # name Cmax pos ? Ymax pos ? Smax pos ? Smean ? AAF45703.1 0.561 34 Y 0.474 21 Y 0.998 9 Y 0.928 Y ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ low complexity regions: SEG 12 2.2 2.5 >AAF45703.1 EG:133E12.3 gene product [Drosophila melanogaster]. 1-322 MLVKFVVIFALILASCRVEADNTSVLPEGF VDAAQRSTHTNNWAVLVDASRFWFNYRHVA NVLSIYRSVKRLGIPDSQIILMIADDMACN ARNPRPGQVYNNANQHINVYGDDVEVDYRG YEVTVENFVRLLTGRTQNGTARSKKLLSDA GSNVLIYLTGHGGDGFLKFQDSEEITSQEL ADGIQQMWEKKRYNELFFMVDTCQAASLYE KFTSPNVLAVASSLVGEDSLSHHVDPSIGV YMIDRYTYYALEFLEKVQPFSKRTIGEFLQ VCPKRVCISTVGVRKDLYPRDPHKVPITDF FGAIRPTRVSTDRINVTLANEE low complexity regions: SEG 25 3.0 3.3 >AAF45703.1 EG:133E12.3 gene product [Drosophila melanogaster]. 1-322 MLVKFVVIFALILASCRVEADNTSVLPEGF VDAAQRSTHTNNWAVLVDASRFWFNYRHVA NVLSIYRSVKRLGIPDSQIILMIADDMACN ARNPRPGQVYNNANQHINVYGDDVEVDYRG YEVTVENFVRLLTGRTQNGTARSKKLLSDA GSNVLIYLTGHGGDGFLKFQDSEEITSQEL ADGIQQMWEKKRYNELFFMVDTCQAASLYE KFTSPNVLAVASSLVGEDSLSHHVDPSIGV YMIDRYTYYALEFLEKVQPFSKRTIGEFLQ VCPKRVCISTVGVRKDLYPRDPHKVPITDF FGAIRPTRVSTDRINVTLANEE low complexity regions: SEG 45 3.4 3.75 >AAF45703.1 EG:133E12.3 gene product [Drosophila melanogaster]. 1-322 MLVKFVVIFALILASCRVEADNTSVLPEGF VDAAQRSTHTNNWAVLVDASRFWFNYRHVA NVLSIYRSVKRLGIPDSQIILMIADDMACN ARNPRPGQVYNNANQHINVYGDDVEVDYRG YEVTVENFVRLLTGRTQNGTARSKKLLSDA GSNVLIYLTGHGGDGFLKFQDSEEITSQEL ADGIQQMWEKKRYNELFFMVDTCQAASLYE KFTSPNVLAVASSLVGEDSLSHHVDPSIGV YMIDRYTYYALEFLEKVQPFSKRTIGEFLQ VCPKRVCISTVGVRKDLYPRDPHKVPITDF FGAIRPTRVSTDRINVTLANEE 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 >AAF45703.1 EG:133E12.3 gene product [Drosophila melanogaster]. MlvkfvvifalilaSCRVEADNTSVLPEGFVDAAQRSTHTNNWAVLVDASRFWFNYRHVA NVLSIYRSVKRLGIPDSQIILMIADDMACNARNPRPGQVYNNANQHINVYGDDVEVDYRG YEVTVENFVRLLTGRTQNGTARSKKLLSDAGSNVLIYLTGHGGDGFLKFQDSEEITSQEL ADGIQQMWEKKRYNELFFMVDTCQAASLYEKFTSPNVLAVASSLVGEDSLSHHVDPSIGV YMIDRYTYYALEFLEKVQPFSKRTIGEFLQVCPKRVCISTVGVRKDLYPRDPHKVPITDF FGAIRPTRVSTDRINVTLANEE 1 - 1 M 2 - 14 lvkfvvifa lila 15 - 322 SCRVEA DNTSVLPEGF VDAAQRSTHT NNWAVLVDAS RFWFNYRHVA NVLSIYRSVK RLGI PDSQII LMIADDMACN ARNPRPGQVY NNANQHINVY GDDVEVDYRG YEVTVENFVR LLTG RTQNGT ARSKKLLSDA GSNVLIYLTG HGGDGFLKFQ DSEEITSQEL ADGIQQMWEK KRYN ELFFMV DTCQAASLYE KFTSPNVLAV ASSLVGEDSL SHHVDPSIGV YMIDRYTYYA LEFL EKVQPF SKRTIGEFLQ VCPKRVCIST VGVRKDLYPR DPHKVPITDF FGAIRPTRVS TDRI NVTLAN EE low complexity regions: DUST >AAF45703.1 EG:133E12.3 gene product [Drosophila melanogaster]. MLVKFVVIFALILASCRVEADNTSVLPEGFVDAAQRSTHTNNWAVLVDASRFWFNYRHVA NVLSIYRSVKRLGIPDSQIILMIADDMACNARNPRPGQVYNNANQHINVYGDDVEVDYRG YEVTVENFVRLLTGRTQNGTARSKKLLSDAGSNVLIYLTGHGGDGFLKFQDSEEITSQEL ADGIQQMWEKKRYNELFFMVDTCQAASLYEKFTSPNVLAVASSLVGEDSLSHHVDPSIGV YMIDRYTYYALEFLEKVQPFSKRTIGEFLQVCPKRVCISTVGVRKDLYPRDPHKVPITDF FGAIRPTRVSTDRINVTLANEE ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ coiled coil prediction for AAF45703.1 sequence: 322 amino acids, 0 residue(s) in coiled coil state . | . | . | . | . | . 60 MLVKFVVIFA LILASCRVEA DNTSVLPEGF VDAAQRSTHT NNWAVLVDAS RFWFNYRHVA ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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 NVLSIYRSVK RLGIPDSQII LMIADDMACN ARNPRPGQVY NNANQHINVY GDDVEVDYRG ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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 YEVTVENFVR LLTGRTQNGT ARSKKLLSDA GSNVLIYLTG HGGDGFLKFQ DSEEITSQEL ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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 ADGIQQMWEK KRYNELFFMV DTCQAASLYE KFTSPNVLAV ASSLVGEDSL SHHVDPSIGV ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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 YMIDRYTYYA LEFLEKVQPF SKRTIGEFLQ VCPKRVCIST VGVRKDLYPR DPHKVPITDF ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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 . | . | FGAIRPTRVS TDRINVTLAN EE ~~~~~~~~~~ ~~~~~~~~~~ ~~ ---------- ---------- -- ~~~~~~~~~~ ~~~~~~~~~~ ~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ prediction of transmembrane regions with toppred2 *********************************** *TOPPREDM with eukaryotic function* *********************************** AAF45703.1.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: AAF45703.1.fa.___inter___ (1 sequences) MLVKFVVIFALILASCRVEADNTSVLPEGFVDAAQRSTHTNNWAVLVDAS RFWFNYRHVANVLSIYRSVKRLGIPDSQIILMIADDMACNARNPRPGQVY NNANQHINVYGDDVEVDYRGYEVTVENFVRLLTGRTQNGTARSKKLLSDA GSNVLIYLTGHGGDGFLKFQDSEEITSQELADGIQQMWEKKRYNELFFMV DTCQAASLYEKFTSPNVLAVASSLVGEDSLSHHVDPSIGVYMIDRYTYYA LEFLEKVQPFSKRTIGEFLQVCPKRVCISTVGVRKDLYPRDPHKVPITDF FGAIRPTRVSTDRINVTLANEE (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 2 structures are to be tested Candidate membrane-spanning segments: Helix Begin End Score Certainity 1 1 21 0.806 Putative ---------------------------------------------------------------------- Structure 1 Transmembrane segments included in this structure: Segment 1 Loop length 0 301 K+R profile 2.00 + CYT-EXT prof - 1.33 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 2.00 Tm probability: 0.52 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 3.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: N-in CYT-EXT difference: -1.33 -> Orientation: N-in ---------------------------------------------------------------------- Structure 2 Transmembrane segments included in this structure: Segment Loop length 322 K+R profile + CYT-EXT prof 1.29 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 0.00 Tm probability: 1.00 -> Orientation: undecided Charge-difference over N-terminal Tm (+-15 residues): 2.00 (NEG-POS)/(NEG+POS): 0.0423 NEG: 37.0000 POS: 34.0000 -> Orientation: N-in CYT-EXT difference: 1.29 -> Orientation: N-out ---------------------------------------------------------------------- "AAF45703" 322 1 21 #f 0.80625 ************************************ *TOPPREDM with prokaryotic function* ************************************ AAF45703.1.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: AAF45703.1.fa.___inter___ (1 sequences) MLVKFVVIFALILASCRVEADNTSVLPEGFVDAAQRSTHTNNWAVLVDAS RFWFNYRHVANVLSIYRSVKRLGIPDSQIILMIADDMACNARNPRPGQVY NNANQHINVYGDDVEVDYRGYEVTVENFVRLLTGRTQNGTARSKKLLSDA GSNVLIYLTGHGGDGFLKFQDSEEITSQELADGIQQMWEKKRYNELFFMV DTCQAASLYEKFTSPNVLAVASSLVGEDSLSHHVDPSIGVYMIDRYTYYA LEFLEKVQPFSKRTIGEFLQVCPKRVCISTVGVRKDLYPRDPHKVPITDF FGAIRPTRVSTDRINVTLANEE (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 2 structures are to be tested Candidate membrane-spanning segments: Helix Begin End Score Certainity 1 1 21 0.806 Putative ---------------------------------------------------------------------- Structure 1 Transmembrane segments included in this structure: Segment 1 Loop length 0 301 K+R profile 1.00 + CYT-EXT prof - 1.33 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 1.00 Tm probability: 0.52 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 3.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: N-in CYT-EXT difference: -1.33 -> Orientation: N-in ---------------------------------------------------------------------- Structure 2 Transmembrane segments included in this structure: Segment Loop length 322 K+R profile + CYT-EXT prof 1.29 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 0.00 Tm probability: 1.00 -> Orientation: undecided Charge-difference over N-terminal Tm (+-15 residues): 2.00 (NEG-POS)/(NEG+POS): 0.0423 NEG: 37.0000 POS: 34.0000 -> Orientation: N-in CYT-EXT difference: 1.29 -> Orientation: N-out ---------------------------------------------------------------------- "AAF45703" 322 1 21 #f 0.80625 ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ SAPS. Version of April 11, 1996. Date run: Thu Feb 21 11:59:39 2002 File: /people/b_eisen/AAF45703.1.fa.___saps___ ID AAF45703.1 DE EG:133E12.3 gene product [Drosophila melanogaster]. number of residues: 322; molecular weight: 36.4 kdal 1 MLVKFVVIFA LILASCRVEA DNTSVLPEGF VDAAQRSTHT NNWAVLVDAS RFWFNYRHVA 61 NVLSIYRSVK RLGIPDSQII LMIADDMACN ARNPRPGQVY NNANQHINVY GDDVEVDYRG 121 YEVTVENFVR LLTGRTQNGT ARSKKLLSDA GSNVLIYLTG HGGDGFLKFQ DSEEITSQEL 181 ADGIQQMWEK KRYNELFFMV DTCQAASLYE KFTSPNVLAV ASSLVGEDSL SHHVDPSIGV 241 YMIDRYTYYA LEFLEKVQPF SKRTIGEFLQ VCPKRVCIST VGVRKDLYPR DPHKVPITDF 301 FGAIRPTRVS TDRINVTLAN EE -------------------------------------------------------------------------------- COMPOSITIONAL ANALYSIS (extremes relative to: swp23s) A : 22( 6.8%); C : 5( 1.6%); D : 21( 6.5%); E : 17( 5.3%); F : 16( 5.0%) G : 18( 5.6%); H : 7( 2.2%); I : 18( 5.6%); K : 13( 4.0%); L : 26( 8.1%) M : 6( 1.9%); N : 18( 5.6%); P : 12( 3.7%); Q : 12( 3.7%); R : 21( 6.5%) S : 22( 6.8%); T : 18( 5.6%); V+ : 33(10.2%); W : 3( 0.9%); Y : 14( 4.3%) KR : 34 ( 10.6%); ED : 38 ( 11.8%); AGP : 52 ( 16.1%); KRED : 72 ( 22.4%); KR-ED : -4 ( -1.2%); FIKMNY : 85 ( 26.4%); LVIFM : 99 ( 30.7%); ST : 40 ( 12.4%). -------------------------------------------------------------------------------- CHARGE DISTRIBUTIONAL ANALYSIS 1 000+000000 000000+0-0 -000000-00 0-000+0000 0000000-00 +00000+000 61 000000+00+ +0000-0000 0000--0000 0+00+00000 0000000000 0--0-0-0+0 121 0-000-000+ 0000+00000 0+0++000-0 0000000000 000-000+00 -0--0000-0 181 0-000000-+ ++00-00000 -00000000- +000000000 000000--00 0000-00000 241 000-+00000 0-00-+0000 0++000-000 000++00000 000++-000+ -00+0000-0 301 0000+00+00 0-+0000000 -- A. CHARGE CLUSTERS. Positive charge clusters (cmin = 9/30 or 12/45 or 15/60): none Negative charge clusters (cmin = 10/30 or 13/45 or 17/60): none Mixed charge clusters (cmin = 15/30 or 21/45 or 26/60): 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 5 | 5 | 7 | 35 | 9 | 9 | 12 | 11 | 11 | 14 | 6 | 8 | lmin1 6 | 6 | 8 | 43 | 11 | 11 | 15 | 13 | 14 | 18 | 8 | 10 | lmin2 7 | 7 | 10 | 47 | 12 | 13 | 17 | 15 | 15 | 20 | 9 | 11 | (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: 1, at 190; - runs >= 3: 0 * runs >= 5: 0 0 runs >= 23: 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: -3.612 M_0.01= 61.17; M_0.05= 49.80; M_0.30= 36.27 1) From 1 to 15: length= 15, score=38.00 1 MLVKFVVIFA LILAS L: 3(20.0%); A: 2(13.3%); V: 3(20.0%); I: 2(13.3%); F: 2(13.3%); 2. SPACINGS OF C. H2N-15-C-72-C-113-C-68-C-4-C-45-COOH 2*. SPACINGS OF C and H. (additional deluxe function for ALEX) H2N-15-C-22-H-18-H-30-C-16-H-54-H-41-C-28-H-H-38-C-4-C-15-H-29-COOH -------------------------------------------------------------------------------- REPETITIVE STRUCTURES. A. SEPARATED, TANDEM, AND PERIODIC REPEATS: amino acid alphabet. Repeat core block length: 4 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: 8 -------------------------------------------------------------------------------- MULTIPLETS. A. AMINO ACID ALPHABET. 1. Total number of amino acid multiplets: 21 (Expected range: 5-- 31) 2. Histogram of spacings between consecutive amino acid multiplets: (1-5) 4 (6-10) 7 (11-20) 8 (>=21) 3 3. Clusters of amino acid multiplets (cmin = 11/30 or 15/45 or 17/60): none B. CHARGE ALPHABET. 1. Total number of charge multiplets: 11 (Expected range: 0-- 16) 6 +plets (f+: 10.6%), 5 -plets (f-: 11.8%) Total number of charge altplets: 7 (Critical number: 18) 2. Histogram of spacings between consecutive charge multiplets: (1-5) 1 (6-10) 1 (11-20) 3 (>=21) 7 -------------------------------------------------------------------------------- PERIODICITY ANALYSIS. A. AMINO ACID ALPHABET (core: 4; !-core: 5) Location Period Element Copies Core Errors There are no periodicities of the prescribed length. 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 1- 14 2 i. 7 7 0 242- 295 9 i0..0.... 6 6 /0/2/././2/././././ -------------------------------------------------------------------------------- SPACING ANALYSIS. Location (Quartile) Spacing Rank P-value Interpretation 92- 95 (2.) R( 3)R 22 of 22 0.0081 large minimal spacing 305- 308 (4.) R( 3)R 21 of 22 0.0081 matching minimum ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ Start with Pfam (from /data/patterns/pfam) 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/pfam/Pfam Sequence file: AAF45703.1.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: AAF45703.1 EG:133E12.3 gene product [Drosophila melanogaster]. Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- Peptidase_C13 Peptidase C13 family 676.8 1.1e-199 1 ALAD Delta-aminolevulinic acid dehydratase 1.2 15 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- ALAD 1/1 247 258 .. 323 334 .] 1.2 15 Peptidase_C13 1/1 5 322 .] 1 364 [] 676.8 1.1e-199 Alignments of top-scoring domains: ALAD: domain 1 of 1, from 247 to 258: score 1.2, E = 15 *->TYfApdaAewLa<-* TY+A++++e+ AAF45703.1 247 TYYALEFLEKVQ 258 Peptidase_C13: domain 1 of 1, from 5 to 322: score 676.8, E = 1.1e-199 *->avfllvvLlilavvaaRdnfgdnislpsEevkffrDddghTnnWAVL +v++++++l+ ++v+a dn+s+++E++ +++++++hTnnWAVL AAF45703.1 5 FVVIFALILASCRVEA-----DNTSVLPEGFVDAAQRSTHTNNWAVL 46 VAGSnGwfNYRHqAfifDVChaYqllkrlGipDEnIIvmmyDDIAcNerN V++S++wfNYRH+A +V+++Y+++krlGipD++II+m++DD+AcN+rN AAF45703.1 47 VDASRFWFNYRHVA---NVLSIYRSVKRLGIPDSQIILMIADDMACNARN 93 PrPGvviNhpnngtDvYggdVpvDYrGeeVTveNFlrVLtGdksavtggS PrPG+v+N++n++++vYg+dV+vDYrG+eVTveNF+r+LtG++++ t++ AAF45703.1 94 PRPGQVYNNANQHINVYGDDVEVDYRGYEVTVENFVRLLTGRTQNGTAR- 142 GKvLlSdpnDhIFIYyTDHGGpGvLkFPdseeLyakDLadalkkmhekkr +K+LlSd++++++IY+T+HGG+G+LkF+dsee+++++Lad++++m+ekkr AAF45703.1 143 SKKLLSDAGSNVLIYLTGHGGDGFLKFQDSEEITSQELADGIQQMWEKKR 192 YkeLvfyiEACeSGSmFegllspdLNIyAtTASnagEsSYstycDgdips Y+eL+f++++C+++S++e+++sp N++A+++S++gE+S+s+++D++i+ AAF45703.1 193 YNELFFMVDTCQAASLYEKFTSP--NVLAVASSLVGEDSLSHHVDPSIG- 239 PPpvyvtcLgDlYSvaWlEdsekHnlskeTLqqqYksvkkrtclynysyG vy+++++++Y++++lE++++ +sk+T+ ++ ++++kr+c+ AAF45703.1 240 ---VYMIDRYTYYALEFLEKVQP--FSKRTIGEFLQVCPKRVCI------ 278 SHVmqygDlyisklklvlftgffpavsNftivdepplrkplevvnqrDad S+V++++Dly++++++v++t+ff+a++ p++v+ AAF45703.1 279 STVGVRKDLYPRDPHKVPITDFFGAIR------------PTRVS------ 310 Lhtlwrkyqlanngsek<-* t++++++lan e+ AAF45703.1 311 --TDRINVTLAN---EE 322 // Start with PfamFrag (from /data/patterns/pfam) 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/pfam/PfamFrag Sequence file: AAF45703.1.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: AAF45703.1 EG:133E12.3 gene product [Drosophila melanogaster]. Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- Peptidase_C13 Peptidase C13 family 675.0 3.7e-199 1 ALAD Delta-aminolevulinic acid dehydratase 1.2 15 1 Antistasin Antistasin family 0.4 84 1 CMAS Cyclopropane-fatty-acyl-phospholipid sy -0.3 80 1 GASA Gibberellin regulated protein -1.1 40 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- GASA 1/1 3 16 .. 1 14 [. -1.1 40 CMAS 1/1 114 122 .. 1 9 [. -0.3 80 ALAD 1/1 247 258 .. 323 334 .] 1.2 15 Antistasin 1/1 272 278 .. 1 7 [. 0.4 84 Peptidase_C13 1/1 5 322 .] 1 364 [] 675.0 3.7e-199 Alignments of top-scoring domains: GASA: domain 1 of 1, from 3 to 16: score -1.1, E = 40 *->vkrsvlillLLivL<-* vk++v+++l+L ++ AAF45703.1 3 VKFVVIFALILASC 16 CMAS: domain 1 of 1, from 114 to 122: score -0.3, E = 80 *->kevlLqDwe<-* +ev+++++e AAF45703.1 114 VEVDYRGYE 122 ALAD: domain 1 of 1, from 247 to 258: score 1.2, E = 15 *->TYfApdaAewLa<-* TY+A++++e+ AAF45703.1 247 TYYALEFLEKVQ 258 Antistasin: domain 1 of 1, from 272 to 278: score 0.4, E = 84 *->CeklqCs<-* C+k++C+ AAF45703.1 272 CPKRVCI 278 Peptidase_C13: domain 1 of 1, from 5 to 322: score 675.0, E = 3.7e-199 *->avfllvvLlilavvaaRdnfgdnislpsEevkffrDddghTnnWAVL +v++++++l+ ++v+a dn+s+++E++ +++++++hTnnWAVL AAF45703.1 5 FVVIFALILASCRVEA-----DNTSVLPEGFVDAAQRSTHTNNWAVL 46 VAGSnGwfNYRHqAfifDVChaYqllkrlGipDEnIIvmmyDDIAcNerN V++S++wfNYRH+A +V+++Y+++krlGipD++II+m++DD+AcN+rN AAF45703.1 47 VDASRFWFNYRHVA---NVLSIYRSVKRLGIPDSQIILMIADDMACNARN 93 PrPGvviNhpnngtDvYggdVpvDYrGeeVTveNFlrVLtGdksavtggS PrPG+v+N++n++++vYg+dV+vDYrG+eVTveNF+r+LtG++++ t++ AAF45703.1 94 PRPGQVYNNANQHINVYGDDVEVDYRGYEVTVENFVRLLTGRTQNGTAR- 142 GKvLlSdpnDhIFIYyTDHGGpGvLkFPdseeLyakDLadalkkmhekkr +K+LlSd++++++IY+T+HGG+G+LkF+dsee+++++Lad++++m+ekkr AAF45703.1 143 SKKLLSDAGSNVLIYLTGHGGDGFLKFQDSEEITSQELADGIQQMWEKKR 192 YkeLvfyiEACeSGSmFegllspdLNIyAtTASnagEsSYstycDgdips Y+eL+f++++C+++S++e+++sp N++A+++S++gE+S+s+++D++i+ AAF45703.1 193 YNELFFMVDTCQAASLYEKFTSP--NVLAVASSLVGEDSLSHHVDPSIG- 239 PPpvyvtcLgDlYSvaWlEdsekHnlskeTLqqqYksvkkrtclynysyG vy+++++++Y++++lE++++ +sk+T+ ++ ++++kr+c+ AAF45703.1 240 ---VYMIDRYTYYALEFLEKVQP--FSKRTIGEFLQVCPKRVCI------ 278 SHVmqygDlyisklklvlftgffpavsNftivdepplrkplevvnqrDad S+V++++Dly++++++v++t+ff+a++ p++v+ AAF45703.1 279 STVGVRKDLYPRDPHKVPITDFFGAIR------------PTRVS------ 310 Lhtlwrkyqlanngsek<-* t++++++lan e+ AAF45703.1 311 --TDRINVTLAN---EE 322 // Start with Repeat Library (from /data/patterns/repeats-Miguel-Andrade/hmm) 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/repeats-Miguel-Andrade/hmm/repeats.hmm-lib Sequence file: AAF45703.1.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: AAF45703.1 EG:133E12.3 gene product [Drosophila melanogaster]. 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: Thu Feb 21 12:01:35 2002 Sequence file: AAF45703.1.fa ---------------------------------------- Sequence AAF45703.1 (322 residues): Matching pattern PS00001 ASN_GLYCOSYLATION: 22: NTSV 138: NGTA 315: NVTL Total matches: 3 Matching pattern PS00005 PKC_PHOSPHO_SITE: 15: SCR 68: SVK 133: TGR 140: TAR 143: SKK 261: SKR 311: TDR Total matches: 7 Matching pattern PS00006 CK2_PHOSPHO_SITE: 176: TSQE 207: SLYE 264: TIGE Total matches: 3 Matching pattern PS00008 MYRISTYL: 73: GIPDSQ 97: GQVYNN 139: GTARSK Total matches: 3 Total no of hits in this sequence: 16 ======================================== 1314 pattern(s) searched in 1 sequence(s), 322 residues. Total no of hits in all sequences: 16. 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, 322 units >ER-GOLGI-traffic signal is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 322 units >INTRA-SIGNAL-M minimal SH3 binding is the MOTIF name >AAF45703.1 EG:133E12.3 gene product [Drosophila melanogaster]. ;LENGTH=322; DIRECT_SEQUENCE n 1 solutions m %_PXXP 289-292 f >STATISTICS Total : 1 solutions in 1 sequences, 322 units; out of 1 sequences, 322 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, 322 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, 322 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, 322 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, 322 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, 322 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, 322 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, 322 units >TM-CYTOPLASMIC-M di-hydrophobic endocytosis motifs for internalized transmembrane proteins is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 322 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, 322 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, 322 units >EXTRACELL-M minimal furin protease cleavage site motif is the MOTIF name >AAF45703.1 EG:133E12.3 gene product [Drosophila melanogaster]. ;LENGTH=322; DIRECT_SEQUENCE n 2 solutions m %_RXXR 92-95 f m %_RXXR 305-308 f >STATISTICS Total : 2 solutions in 1 sequences, 322 units; out of 1 sequences, 322 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, 322 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, 322 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, 322 units >NUCLEAR NLS experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 322 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, 322 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, 322 units >NUCLEAR NLS HCDA experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 322 units >NUCLEAR NLS SV40 LrgT experimentally determined is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 322 units >NUCLEAR NLS H2B experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 322 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, 322 units >NUCLEAR NLS Amida experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 322 units >NUCLEAR NLS Amida experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 322 units >NUCLEAR NLS RanBP3 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 322 units >NUCLEAR NLS Pho4p experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 322 units >NUCLEAR NLS DNAhelicaseQ1 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 322 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, 322 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, 322 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, 322 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, 322 units >NUCLEAR NLS GAL4 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 322 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, 322 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, 322 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, 322 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, 322 units >NUCLEAR NLS TR2 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 322 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, 322 units >NUCLEAR NLS polyomaVP1 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 322 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, 322 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, 322 units >NUCLEAR NLS Rex experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 322 units >NUCLEAR NLS SRY experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 322 units >NUCLEAR NLS SRY experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 322 units >NUCLEAR NLS SOX9 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 322 units >NUCLEAR NLS SOX9 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 322 units >NUCLEAR NLS NS5A experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 322 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, 322 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, 322 units >NUCLEAR NLS adenovE1a experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 322 units >NUCLEAR NLS ystDNApolalpha experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 322 units >NUCLEAR NLS hVDR experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 322 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, 322 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, 322 units >NUCLEAR NLS cFOS experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 322 units >NUCLEAR NLS cJUN experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 322 units >NUCLEAR NLS hDNApolalpha experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 322 units >NUCLEAR NLS hDNAtopoII experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 322 units >NUCLEAR NLS hDNAtopoII experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 322 units >NUCLEAR NLS hBLM experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 322 units >NUCLEAR NLS hARNT experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 322 units >NUCLEAR NLS influenzaNP experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 322 units >NUCLEAR NLS influenzaNP experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 322 units >NUCLEAR NLS p54 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 322 units >NUCLEAR NLS hProTalpha experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 322 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, 322 units >NUCLEAR NLS protHsc9 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 322 units >NUCLEAR NLS protHsci experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 322 units >NUCLEAR NLS protHsc3 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 322 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, 322 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, 322 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, 322 units >NUCLEAR NLS MyoD experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 322 units >NUCLEAR NLS MyoD experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 322 units >NUCLEAR NLS opaque2 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 322 units >NUCLEAR NLS CTP experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 322 units >NUCLEAR NLS HCV experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 322 units >NUCLEAR NLS HCV experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 322 units >NUCLEAR NLS p110RB1 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 322 units >NUCLEAR NLS experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 322 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, 322 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, 322 units >NUCLEAR NLS Nucloplasmin experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 322 units >NUCLEAR NLS Nucleolin experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 322 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, 322 units >NUCLEAR NLS Nab2 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 322 units >NUCLEAR NLS M9 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 322 units >NUCLEAR NLS lscMyc experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 322 units >NUCLEAR NLS humKprotein experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 322 units >NUCLEAR NLS FluA experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 322 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, 322 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, 322 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, 322 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, 322 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, 322 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, 322 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, 322 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, 322 units >NUCLEAR NLS p53 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 322 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, 322 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, 322 units >NUCLEAR NLS L29 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 322 units >NUCLEAR NLS L29 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 322 units >NUCLEAR NLS Max experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 322 units >NUCLEAR NLS L3 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 322 units >NUCLEAR NLS dyskerin experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 322 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, 322 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, 322 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: /data/patterns/own/own-hmm.lib Sequence file: AAF45703.1.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: AAF45703.1 EG:133E12.3 gene product [Drosophila melanogaster]. 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/own/own-hmm-f.lib Sequence file: AAF45703.1.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: AAF45703.1 EG:133E12.3 gene product [Drosophila melanogaster]. 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= AAF45703.1 EG:133E12.3 gene product [Drosophila melanogaster]. (322 letters) Searching..................................done Results from profile search Score E Sequences producing significant alignments: (bits) Value KIN Protein kinase domain 21 2.4 CYCL cyclophilin like peptidyl prolyl isomerases 21 2.4 SEC7 Sec7 like GDP exchange factor for ARF like GTPases 21 3.2 ACTIN Actin ATPase/ Cytoskeletal ATPase domain 19 7.3 ARR Arrestin domain 19 7.3 FKBP FK506 binding protein (Peptidyl prolyl isomerase) 19 8.6 RGS Regulator of heterotrimeric G protein signalling (G-prot... 19 9.9 ACYC Adenylyl/Guanylyl cyclase domain 19 9.9 >KIN Protein kinase domain Length = 313 Score = 20.8 bits (43), Expect = 2.4 Identities = 20/119 (16%), Positives = 20/119 (16%), Gaps = 13/119 (10%) Query: 190 KKRYNELFFMVDTCQAASLYEKFTSPNVLAVASSLVGEDSLSHHVDPSIGVYMIDRYTYY 249 Sbjct: 63 SKAFDNLKDTKRTLREIHLLRHFKHENLISIKDILKPNSKEQFE-----DVYIVSELMDT 117 Query: 250 AL-EFLEKVQPFSKRTIGEFLQ--VCPKRVCISTVGVRKDLYPR-----DPHKVPITDF 300 Sbjct: 118 DLHQIITSPQPLSDDHCQYFVYQMLRGLKHIHSANVLHRDLKPSNLLINEDCLLKICDL 176 >CYCL cyclophilin like peptidyl prolyl isomerases Length = 165 Score = 20.9 bits (44), Expect = 2.4 Identities = 9/24 (37%), Positives = 9/24 (37%), Gaps = 2/24 (8%) Query: 113 DVEVDYRGYEV--TVENFVRLLTG 134 Sbjct: 19 RVSFELFADKVPKTAENFRALSTG 42 >SEC7 Sec7 like GDP exchange factor for ARF like GTPases Length = 192 Score = 20.6 bits (43), Expect = 3.2 Identities = 8/18 (44%), Positives = 8/18 (44%) Query: 252 EFLEKVQPFSKRTIGEFL 269 Sbjct: 41 HFLLQRKGLSRQMIGEFL 58 >ACTIN Actin ATPase/ Cytoskeletal ATPase domain Length = 376 Score = 19.4 bits (40), Expect = 7.3 Identities = 6/15 (40%), Positives = 6/15 (40%) Query: 182 DGIQQMWEKKRYNEL 196 Sbjct: 82 DDMEKIWHHTFYNEL 96 >ARR Arrestin domain Length = 454 Score = 19.4 bits (40), Expect = 7.3 Identities = 6/51 (11%), Positives = 6/51 (11%) Query: 79 IILMIADDMACNARNPRPGQVYNNANQHINVYGDDVEVDYRGYEVTVENFV 129 Sbjct: 375 FTLTHSKPPESPERTDRGLPSIEATNGSEPVDIDLIQLHEELEPRYDDDLI 425 >FKBP FK506 binding protein (Peptidyl prolyl isomerase) Length = 149 Score = 19.0 bits (39), Expect = 8.6 Identities = 2/11 (18%), Positives = 2/11 (18%) Query: 111 GDDVEVDYRGY 121 Sbjct: 8 NSAVLVHFTLK 18 >RGS Regulator of heterotrimeric G protein signalling (G-protein GTP hydrolysis activating protein) Length = 117 Score = 19.0 bits (39), Expect = 9.9 Identities = 9/61 (14%), Positives = 9/61 (14%), Gaps = 7/61 (11%) Query: 205 AASLYEKF---TSPNVLAVASSLVGEDSLSHHVDPSIGVYMIDRYTYYALEFLEKVQPFS 261 Sbjct: 50 AKKIYNEFISVQATKEVNLDSCTR-EETSRNMLEP--TITCFDEAQKKIFNLMEK-DSYR 105 Query: 262 K 262 Sbjct: 106 R 106 >ACYC Adenylyl/Guanylyl cyclase domain Length = 244 Score = 19.0 bits (39), Expect = 9.9 Identities = 4/44 (9%), Positives = 4/44 (9%), Gaps = 11/44 (25%) Query: 250 ALEFLEKVQPFSKRT-IGEFLQVCPKRVCIST-------VGVRK 285 Sbjct: 113 VNRLQAMTAKLNQKYELPFPLRI---GTGINTGYAMVGNTGSGD 153 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: 322 Total length of test sequences: 20182 Effective length of test sequences: 16637.0 Effective search space size: 4792211.0 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= AAF45703.1 EG:133E12.3 gene product [Drosophila melanogaster]. (322 letters) Searching.................................................done Results from profile search Score E Sequences producing significant alignments: (bits) Value gi|322088 [20..469] Periplasmic binding protein-like II 27 0.44 gi|1256709 [134..309] Bleomycin resistance protein/Dihydroxy... 26 0.66 gi|1515350 [4..198] Cyclophilin 26 0.86 gi|2146731 [265..383] FKBP-like 26 0.90 gi|1215731 [52..500] Periplasmic binding protein-like II 25 1.6 gi|1723074 [152..573] Periplasmic binding protein-like II 25 1.6 gi|1652862 [45..566] Periplasmic binding protein-like II 25 1.8 gi|494812 [1..373] 7-bladed beta-propeller 25 2.0 gi|1361319 [558..735] Aldehyde oxidoreductase, molybdemum co... 25 2.4 gi|1351438 [967..1131] Aldehyde oxidoreductase, molybdemum c... 24 2.4 gi|1175188 [41..508] Periplasmic binding protein-like II 25 2.5 gi|1703166 [11..338] beta/alpha (TIM)-barrel 25 2.8 gi|1787052 [35..512] Periplasmic binding protein-like II 24 2.8 gi|585620 [104..580] Periplasmic binding protein-like II 24 4.4 gi|462710 [40..510] Periplasmic binding protein-like II 24 4.4 gi|1334744 [1415..1521] Spectrin repeat unit 24 4.5 gi|2500693 [47..427] Periplasmic binding protein-like II 24 4.6 gi|116871 [267..480] 4-bladed beta-propeller 24 4.6 gi|2665705 [26..489] Periplasmic binding protein-like II 24 4.8 gi|1130652 [108..360] (Phosphotyrosine) protein phosphatases... 23 5.3 gi|2088814 [406..557] Cyclophilin 23 5.3 gi|2665716 [42..473] Periplasmic binding protein-like II 23 5.4 gi|1168472 [55..543] Periplasmic binding protein-like II 23 5.8 gi|1361422 [77..475] Periplasmic binding protein-like II 23 5.9 gi|119334 [61..336] Periplasmic binding protein-like I 23 6.2 gi|2811252 [82..382] Periplasmic binding protein-like II 23 6.7 gi|1405512 [67..192] Transducin (alpha subunit), insertion d... 23 7.1 gi|462411 [169..318] Pyruvate oxidase and decarboxylase, mid... 23 7.2 gi|148721 [41..180] Glycosyl-asparaginase 23 7.3 gi|2493523 [117..286] Interleukin-1beta converting enzyme (a... 23 8.1 gi|2146709 [57..529] Periplasmic binding protein-like II 23 8.8 gi|1708629 [67..339] Periplasmic binding protein-like I 23 9.2 gi|2500694 [73..586] Periplasmic binding protein-like II 23 9.5 >gi|322088 [20..469] Periplasmic binding protein-like II Length = 450 Score = 26.9 bits (59), Expect = 0.44 Identities = 8/50 (16%), Positives = 8/50 (16%), Gaps = 5/50 (10%) Query: 141 ARSKKLLSDAGSNVLIYLTGHGGDGFLKFQDSEEITSQELADGIQQMWEK 190 Sbjct: 355 KEAAKLFKEGL-----AELGKDALTITITADADAACAKSAVDYIKETWET 399 Score = 23.0 bits (49), Expect = 6.9 Identities = 7/25 (28%), Positives = 7/25 (28%) Query: 167 LKFQDSEEITSQELADGIQQMWEKK 191 Sbjct: 89 LKWSDGSDLTAEDFEYSWQRMVDPK 113 >gi|1256709 [134..309] Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase Length = 176 Score = 26.4 bits (58), Expect = 0.66 Identities = 17/176 (9%), Positives = 17/176 (9%), Gaps = 19/176 (10%) Query: 29 GFVDAAQRSTHTNNWAVLVDASRFWFNYRHVANVLSIYRSVKRLGIPDSQIILMIADDMA 88 Sbjct: 4 GFLTGDRGAGHYFYTVPNIEEGLAF--YTGMLG----FQMSDVIDIAMGPDITVRGYFLH 57 Query: 89 CNARNPRPGQVYN---NANQHINVYGDDVEVDYRGYEVTVENFVRLLTGRTQNGTARSKK 145 Sbjct: 58 CNGRHHTMAIAEAPLPNRVHHFLQSPLTLDDVGHAYDRIDGLGDKSTDSNLRVPANSDIR 117 Query: 146 LLSDAGSNVLIYLTGHGGDG--FLKFQDSEEITSQELADGI---QQMWEKKRYNEL 196 Sbjct: 118 -----SSRITATIGRHVNDHMISFYAETPSGFELEFGWGARDVDDRSWVMTRHKRT 168 >gi|1515350 [4..198] Cyclophilin Length = 195 Score = 26.0 bits (57), Expect = 0.86 Identities = 21/107 (19%), Positives = 21/107 (19%), Gaps = 14/107 (13%) Query: 124 TVENFVRLLTGRTQNGTARSKKLLSDAGSNVLIYLTG---HGGDGFLKFQDSEEITSQEL 180 Sbjct: 30 TTENFYKLCAG-DVKSPLKDQQYLSYKGNGFHRVVKNFMIQAGD--IVFGTQKDSSSSSV 86 Query: 181 ADGIQQMWEKKRYNELFFMVDTCQAASLYE-----KFTSPNVLAVAS 222 Sbjct: 87 GKGGCSIYADKEEVKTD---DESFCYGNFEDENLGEFVEPFTLGMAN 130 >gi|2146731 [265..383] FKBP-like Length = 119 Score = 26.0 bits (57), Expect = 0.90 Identities = 13/59 (22%), Positives = 13/59 (22%), Gaps = 5/59 (8%) Query: 122 EVTVENFVRLLTGRTQNGTARSKKLLSDAGSNVLIYLTGHGGDGFLKFQDSEEITSQEL 180 Sbjct: 2 EVTDDNKVVKKVLKEGDGYERPNE-----GAVVKVKLIGKLQDGTVFLKKGHGENEEPF 55 >gi|1215731 [52..500] Periplasmic binding protein-like II Length = 449 Score = 25.3 bits (55), Expect = 1.6 Identities = 5/28 (17%), Positives = 5/28 (17%) Query: 167 LKFQDSEEITSQELADGIQQMWEKKRYN 194 Sbjct: 64 VQFHNGKELTPEDVIYSINHHRGDKSES 91 >gi|1723074 [152..573] Periplasmic binding protein-like II Length = 422 Score = 25.3 bits (55), Expect = 1.6 Identities = 8/45 (17%), Positives = 8/45 (17%) Query: 167 LKFQDSEEITSQELADGIQQMWEKKRYNELFFMVDTCQAASLYEK 211 Sbjct: 11 AVWSDGTPITWRDIASQIHAISGADKAFEIASSSGAERVASVTRG 55 >gi|1652862 [45..566] Periplasmic binding protein-like II Length = 522 Score = 24.9 bits (54), Expect = 1.8 Identities = 3/25 (12%), Positives = 3/25 (12%) Query: 167 LKFQDSEEITSQELADGIQQMWEKK 191 Sbjct: 75 VLWSDGQPFSAEDVAFTYKFLSDPK 99 >gi|494812 [1..373] 7-bladed beta-propeller Length = 373 Score = 24.8 bits (53), Expect = 2.0 Identities = 23/88 (26%), Positives = 23/88 (26%), Gaps = 13/88 (14%) Query: 173 EEITSQELAD-----GIQQMWEKKRYNELFFMVDTCQAASLYEKFTSPNVLAVASSLVGE 227 Sbjct: 253 EALTEAERADGWRPGGWQQVAYHRALDRIYLLVDQRDEWRHK---TASRFLVVLDAKTGE 309 Query: 228 D----SLSHHVDPSIGVYMIDRYTYYAL 251 Sbjct: 310 RLAKFEMGHEID-SINVSQDEKPLLYAL 336 >gi|1361319 [558..735] Aldehyde oxidoreductase, molybdemum cofactor-binding domain Length = 178 Score = 24.5 bits (53), Expect = 2.4 Identities = 6/36 (16%), Positives = 6/36 (16%) Query: 17 RVEADNTSVLPEGFVDAAQRSTHTNNWAVLVDASRF 52 Sbjct: 123 KFTWPNTATTPNSGPSGGSRQQVMTGNAIRVACENL 158 >gi|1351438 [967..1131] Aldehyde oxidoreductase, molybdemum cofactor-binding domain Length = 165 Score = 24.5 bits (53), Expect = 2.4 Identities = 8/36 (22%), Positives = 8/36 (22%) Query: 17 RVEADNTSVLPEGFVDAAQRSTHTNNWAVLVDASRF 52 Sbjct: 125 YISETSTNTVPNTSPTAASVSADINGMAVHNACQTI 160 >gi|1175188 [41..508] Periplasmic binding protein-like II Length = 468 Score = 24.5 bits (53), Expect = 2.5 Identities = 5/25 (20%), Positives = 5/25 (20%) Query: 167 LKFQDSEEITSQELADGIQQMWEKK 191 Sbjct: 76 AKWSNGEPITASDFVQSWQTLSQSE 100 Score = 24.1 bits (52), Expect = 3.0 Identities = 5/51 (9%), Positives = 5/51 (9%), Gaps = 7/51 (13%) Query: 141 ARSKKLLSDAGSNVLIYLTGHGGDGFLKFQDSEEITSQELADGIQQMWEKK 191 Sbjct: 298 VVAEQLFSQNQ-----ISETRPLK--LRIRYDDLSLNQTIAMRLNHQLSQS 341 >gi|1703166 [11..338] beta/alpha (TIM)-barrel Length = 328 Score = 24.5 bits (53), Expect = 2.8 Identities = 13/51 (25%), Positives = 13/51 (25%), Gaps = 2/51 (3%) Query: 22 NTSVLPEGFVDAAQRSTHTNNWAVLVDASRFWFNYRHVANVLSIYRSVKRL 72 Sbjct: 25 NDIILPEGFPKSVE--ELNEKYKKFRDLQDFLDYYYIGTNVLISEQDFFDL 73 >gi|1787052 [35..512] Periplasmic binding protein-like II Length = 478 Score = 24.5 bits (53), Expect = 2.8 Identities = 4/27 (14%), Positives = 4/27 (14%) Query: 167 LKFQDSEEITSQELADGIQQMWEKKRY 193 Sbjct: 62 IKFQDGTDFNAAAVKANLDRASDPANH 88 >gi|585620 [104..580] Periplasmic binding protein-like II Length = 477 Score = 23.8 bits (51), Expect = 4.4 Identities = 5/25 (20%), Positives = 5/25 (20%) Query: 167 LKFQDSEEITSQELADGIQQMWEKK 191 Sbjct: 25 LKWSDGSEVTAKDYEFTYETIANPA 49 >gi|462710 [40..510] Periplasmic binding protein-like II Length = 471 Score = 23.7 bits (51), Expect = 4.4 Identities = 7/42 (16%), Positives = 7/42 (16%), Gaps = 3/42 (7%) Query: 167 LKFQDSEEITSQELADGIQQMWEKK---RYNELFFMVDTCQA 205 Sbjct: 54 VKFSNGEPFDAEAAAENFRAVLDNRQRHAWLELANQIVDVKA 95 >gi|1334744 [1415..1521] Spectrin repeat unit Length = 107 Score = 23.7 bits (51), Expect = 4.5 Identities = 10/70 (14%), Positives = 10/70 (14%), Gaps = 9/70 (12%) Query: 173 EEITSQELADGIQQMWEKKRYNELFFMVDTCQAASLYEKFTSPNVLAVASSLVGEDSLSH 232 Sbjct: 24 AFLNTEDKGDSLDSVEALIKKHEDFDK----AINVQEEKIAV--LQSFADQLIAAD---H 74 Query: 233 HVDPSIGVYM 242 Sbjct: 75 YAKGVIANRR 84 >gi|2500693 [47..427] Periplasmic binding protein-like II Length = 381 Score = 23.7 bits (51), Expect = 4.6 Identities = 4/25 (16%), Positives = 4/25 (16%) Query: 167 LKFQDSEEITSQELADGIQQMWEKK 191 Sbjct: 56 LGWHDGTPVTAADCVASIRRWAQVG 80 >gi|116871 [267..480] 4-bladed beta-propeller Length = 214 Score = 23.7 bits (51), Expect = 4.6 Identities = 10/54 (18%), Positives = 10/54 (18%), Gaps = 5/54 (9%) Query: 26 LPEGFVDAAQRSTHTNNWAVLVDASRFWFNYRHVANVLSIYRSVKRLGIPDSQI 79 Sbjct: 73 LPSP-VDAAFE--DAQGHIWFFQGAQYW-VYDG-EKPVLGPAPLTELGLVRFPV 121 >gi|2665705 [26..489] Periplasmic binding protein-like II Length = 464 Score = 23.7 bits (51), Expect = 4.8 Identities = 6/24 (25%), Positives = 6/24 (25%) Query: 168 KFQDSEEITSQELADGIQQMWEKK 191 Sbjct: 68 KFHDGTTVTSADVKASLERILDPK 91 >gi|1130652 [108..360] (Phosphotyrosine) protein phosphatases II Length = 253 Score = 23.4 bits (50), Expect = 5.3 Identities = 8/56 (14%), Positives = 8/56 (14%), Gaps = 5/56 (8%) Query: 77 SQIILMIADDM-----ACNARNPRPGQVYNNANQHINVYGDDVEVDYRGYEVTVEN 127 Sbjct: 74 IVSIVIAVMPLECSVTLQQLFPLLSGTFSNHGKMFLNNKKVDSAVAMTAYTLEVLP 129 >gi|2088814 [406..557] Cyclophilin Length = 152 Score = 23.2 bits (50), Expect = 5.3 Identities = 4/17 (23%), Positives = 4/17 (23%) Query: 124 TVENFVRLLTGRTQNGT 140 Sbjct: 7 LTELFVKTARGEFVHPS 23 >gi|2665716 [42..473] Periplasmic binding protein-like II Length = 432 Score = 23.3 bits (50), Expect = 5.4 Identities = 14/51 (27%), Positives = 14/51 (27%), Gaps = 11/51 (21%) Query: 141 ARSKKLLSDAGSNVLIYLTGHGGDGF-LKFQDSEEITSQELADGIQQMWEK 190 Sbjct: 302 AQSKKLLAEAGFP----------NGVTVTMVASQLPGLESLAQLIQAQVAE 342 >gi|1168472 [55..543] Periplasmic binding protein-like II Length = 489 Score = 23.4 bits (50), Expect = 5.8 Identities = 6/25 (24%), Positives = 6/25 (24%) Query: 167 LKFQDSEEITSQELADGIQQMWEKK 191 Sbjct: 59 VKFHDGKELTADDVVFTYSVPLSKD 83 >gi|1361422 [77..475] Periplasmic binding protein-like II Length = 399 Score = 23.4 bits (50), Expect = 5.9 Identities = 5/36 (13%), Positives = 5/36 (13%), Gaps = 3/36 (8%) Query: 167 LKFQDSEEITSQELADGIQQMWEKK---RYNELFFM 199 Sbjct: 27 LRYEDGTPVVSADIKHAIARSNYGTDVLGAGPTYFR 62 >gi|119334 [61..336] Periplasmic binding protein-like I Length = 276 Score = 23.0 bits (49), Expect = 6.2 Identities = 8/72 (11%), Positives = 8/72 (11%), Gaps = 4/72 (5%) Query: 179 ELADGIQQMWEKKRYNELFFMVDTCQA--ASLYEKFTSPNV--LAVASSLVGEDSLSHHV 234 Sbjct: 18 EVVRAIEDECQLENVQVIVCNTDDDSLKEKKYVQSMIARQVDGLIIFPTEENKKLYVSLV 77 Query: 235 DPSIGVYMIDRY 246 Sbjct: 78 KNGYPFVFVDRK 89 >gi|2811252 [82..382] Periplasmic binding protein-like II Length = 301 Score = 23.0 bits (49), Expect = 6.7 Identities = 5/25 (20%), Positives = 5/25 (20%) Query: 167 LKFQDSEEITSQELADGIQQMWEKK 191 Sbjct: 21 AKFHNGEALTAKDVKFTYDFYMDTK 45 >gi|1405512 [67..192] Transducin (alpha subunit), insertion domain Length = 126 Score = 22.9 bits (49), Expect = 7.1 Identities = 8/34 (23%), Positives = 8/34 (23%) Query: 164 DGFLKFQDSEEITSQELADGIQQMWEKKRYNELF 197 Sbjct: 52 ENFKKADDSEKLLGPEVINAIQKYIKDETIAMML 85 >gi|462411 [169..318] Pyruvate oxidase and decarboxylase, middle domain Length = 150 Score = 22.9 bits (49), Expect = 7.2 Identities = 2/24 (8%), Positives = 2/24 (8%) Query: 93 NPRPGQVYNNANQHINVYGDDVEV 116 Sbjct: 110 DEIIADIDHAYQPDLELIGDIPST 133 >gi|148721 [41..180] Glycosyl-asparaginase Length = 140 Score = 22.8 bits (48), Expect = 7.3 Identities = 15/46 (32%), Positives = 15/46 (32%), Gaps = 1/46 (2%) Query: 92 RNPRPGQVYNNANQHINVYGDDVEVDYRGYEVTVENFVRLLTGRTQ 137 Sbjct: 68 KNKTTGEWY-EIGRFITPYWVGTEKLPRGLEIDVTDFKSLLSGNTE 112 >gi|2493523 [117..286] Interleukin-1beta converting enzyme (a cysteine protease) Length = 170 Score = 22.9 bits (49), Expect = 8.1 Identities = 15/92 (16%), Positives = 15/92 (16%), Gaps = 4/92 (4%) Query: 120 GYEVTVENFVRLLTGRTQNGTARSKKLLSDAGSNVLIYLTGHGGDGFLKFQDSEEITSQE 179 Sbjct: 62 GYQVHPHTNLTKTEMVKVMKEFAAQEEHADSDSTFIVLMS-HGDRQGVCGTDSKKT---E 117 Query: 180 LADGIQQMWEKKRYNELFFMVDTCQAASLYEK 211 Sbjct: 118 KEKGQYEVTNLLEIDEIFSTFNNVNCSKLRNK 149 >gi|2146709 [57..529] Periplasmic binding protein-like II Length = 473 Score = 22.6 bits (48), Expect = 8.8 Identities = 4/35 (11%), Positives = 4/35 (11%) Query: 167 LKFQDSEEITSQELADGIQQMWEKKRYNELFFMVD 201 Sbjct: 70 VTFHDGSKMTAEDVNFTLEKVISENAKVASMLKID 104 >gi|1708629 [67..339] Periplasmic binding protein-like I Length = 273 Score = 22.6 bits (48), Expect = 9.2 Identities = 8/42 (19%), Positives = 8/42 (19%) Query: 160 GHGGDGFLKFQDSEEITSQELADGIQQMWEKKRYNELFFMVD 201 Sbjct: 117 GYTDVALFTEPISSISPRAERAAVYQEMASVQNVNGLVRLHE 158 >gi|2500694 [73..586] Periplasmic binding protein-like II Length = 514 Score = 22.6 bits (48), Expect = 9.5 Identities = 4/25 (16%), Positives = 4/25 (16%) Query: 167 LKFQDSEEITSQELADGIQQMWEKK 191 Sbjct: 62 AKWADGKPVTPEDVVFSFDKAKELN 86 Underlying Matrix: BLOSUM62 Number of sequences tested against query: 1187 Number of sequences better than 10.0: 33 Number of calls to ALIGN: 35 Length of query: 322 Total length of test sequences: 256703 Effective length of test sequences: 208388.0 Effective search space size: 58711630.9 Initial X dropoff for ALIGN: 25.0 bits ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ calculation of internal repeats with prospero ***** PROSPERO v1.3 Thu Feb 21 12:02:14 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 AAF45703.1 using self-comparison ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ TIGRFAM 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: AAF45703.1.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: AAF45703.1 EG:133E12.3 gene product [Drosophila melanogaster]. 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: AAF45703.1.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: AAF45703.1 EG:133E12.3 gene product [Drosophila melanogaster]. 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] // SMART 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: AAF45703.1.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: AAF45703.1 EG:133E12.3 gene product [Drosophila melanogaster]. 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] // COG 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: AAF45703.1.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: AAF45703.1 EG:133E12.3 gene product [Drosophila melanogaster]. 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: AAF45703.1.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: AAF45703.1 EG:133E12.3 gene product [Drosophila melanogaster]. Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- COG1235 1.1 25 1 COG2503 -1.0 47 1 COG1520 -1.1 68 1 COG1689 -1.6 79 1 COG1293 -1.6 72 1 COG0554 -1.9 91 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- COG0554 1/1 31 57 .. 496 522 .] -1.9 91 COG1235 1/1 108 126 .. 297 315 .] 1.1 25 COG1293 1/1 125 153 .. 644 675 .] -1.6 72 COG1520 1/1 146 181 .. 536 573 .] -1.1 68 COG2503 1/1 180 192 .. 337 350 .] -1.0 47 COG1689 1/1 246 261 .. 272 287 .] -1.6 79 Alignments of top-scoring domains: COG0554: domain 1 of 1, from 31 to 57: score -1.9, E = 91 *->mdeeeReklykgWkkAVkRalgWakld<-* +d ++R+ + + W V ++++W AAF45703.1 31 VDAAQRSTHTNNWAVLVDASRFWFNYR 57 COG1235: domain 1 of 1, from 108 to 126: score 1.1, E = 25 *->kalaeevevaydgmeiyli<-* +++++ vev+y+g+e+ + AAF45703.1 108 NVYGDDVEVDYRGYEVTVE 126 COG1293: domain 1 of 1, from 125 to 153: score -1.6, E = 72 *->sekyveiePGdkkkgelavkeaKeiaekaGee<-* +e +v+++ G++ g + ++K++ ++aG+ AAF45703.1 125 VENFVRLLTGRTQNGTA---RSKKLLSDAGSN 153 COG1520: domain 1 of 1, from 146 to 181: score -1.1, E = 68 *->lllfgsvrkpvpadglkgnglllvatsaglvsaiqpra<-* ll++++ + ++++ g++g+g+l ++ + ++ +q++a AAF45703.1 146 LLSDAGSNVLIYLTGHGGDGFLKFQ--DSEEITSQELA 181 COG2503: domain 1 of 1, from 180 to 192: score -1.0, E = 47 *->lkDyvKqlyWenKk<-* l D + q+ We K+ AAF45703.1 180 LADGI-QQMWEKKR 192 COG1689: domain 1 of 1, from 246 to 261: score -1.6, E = 79 *->ntYrAlavLasLerWV<-* +tY+Al+ L+ + AAF45703.1 246 YTYYALEFLEKVQPFS 261 //