analysis of sequence from T38153.fa ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ >T38153 hypothetical protein SPAC22A12.13 - fission yeast MLVPPSPSLT TMFRTRSTTP DEEGTAIAEI DQQDWDIMVK VPTYEYYGFV MYLVSMLGFG VYIVWALTPA PVLKFFEIHY YLSRWWALAI PTWLFVLVIY IHVVLNAYNT EVLTKPFSSL ECIVDQYALV GEEDGAAHGR VVDLRLCDVN KQQLEET ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ sec.str. with predator > T38153 . . . . . 1 MLVPPSPSLTTMFRTRSTTPDEEGTAIAEIDQQDWDIMVKVPTYEYYGFV 50 ________________________HHHHHHHHH___EEEE______HHHH . . . . . 51 MYLVSMLGFGVYIVWALTPAPVLKFFEIHYYLSRWWALAIPTWLFVLVIY 100 HHHHHH____EEEEEE____EEEEEEEHHHHHHHHHHH_HHHHH______ . . . . . 101 IHVVLNAYNTEVLTKPFSSLECIVDQYALVGEEDGAAHGRVVDLRLCDVN 150 EEEEEEE___EEEE______EEEE___EEEE_______HHHHHH______ 151 KQQLEET 157 _______ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ method : 1 alpha-contents : 13.1 % beta-contents : 72.5 % coil-contents : 14.3 % class : beta method : 2 alpha-contents : 1.0 % beta-contents : 70.8 % coil-contents : 28.1 % class : beta ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ GPI: learning from metazoa -29.36 -0.30 0.00 0.00 -4.00 0.00 0.00 0.00 0.00 -4.59 -3.37 -12.00 -12.00 -12.00 0.00 0.00 -77.62 -12.54 0.00 0.00 -0.04 0.00 0.00 0.00 -0.01 0.00 -5.00 -3.37 -12.00 -12.00 -12.00 -12.00 0.00 -68.96 ID: T38153 AC: xxx Len: 157 1:I 134 Sc: -68.96 Pv: 5.437387e-01 NO_GPI_SITE GPI: learning from protozoa -25.74 0.00 0.00 0.00 0.00 0.00 0.00 -0.06 0.00 -4.40 -11.57 -12.00 -12.00 -12.00 -12.00 0.00 -89.78 -19.20 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 -6.30 -11.57 -12.00 -12.00 -12.00 -12.00 0.00 -85.07 ID: T38153 AC: xxx Len: 157 1:I 135 Sc: -85.07 Pv: 6.027372e-01 NO_GPI_SITE ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ # SignalP euk predictions # name Cmax pos ? Ymax pos ? Smax pos ? Smean ? T38153 0.835 107 Y 0.819 107 Y 0.990 94 Y 0.436 N # SignalP gram- predictions # name Cmax pos ? Ymax pos ? Smax pos ? Smean ? T38153 0.410 108 N 0.422 108 Y 0.886 9 Y 0.281 N # SignalP gram+ predictions # name Cmax pos ? Ymax pos ? Smax pos ? Smean ? T38153 0.525 137 Y 0.451 67 Y 0.963 101 Y 0.319 N ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ low complexity regions: SEG 12 2.2 2.5 >T38153 hypothetical protein SPAC22A12.13 - fission yeast 1-157 MLVPPSPSLTTMFRTRSTTPDEEGTAIAEI DQQDWDIMVKVPTYEYYGFVMYLVSMLGFG VYIVWALTPAPVLKFFEIHYYLSRWWALAI PTWLFVLVIYIHVVLNAYNTEVLTKPFSSL ECIVDQYALVGEEDGAAHGRVVDLRLCDVN KQQLEET low complexity regions: SEG 25 3.0 3.3 >T38153 hypothetical protein SPAC22A12.13 - fission yeast 1-157 MLVPPSPSLTTMFRTRSTTPDEEGTAIAEI DQQDWDIMVKVPTYEYYGFVMYLVSMLGFG VYIVWALTPAPVLKFFEIHYYLSRWWALAI PTWLFVLVIYIHVVLNAYNTEVLTKPFSSL ECIVDQYALVGEEDGAAHGRVVDLRLCDVN KQQLEET low complexity regions: SEG 45 3.4 3.75 >T38153 hypothetical protein SPAC22A12.13 - fission yeast 1-157 MLVPPSPSLTTMFRTRSTTPDEEGTAIAEI DQQDWDIMVKVPTYEYYGFVMYLVSMLGFG VYIVWALTPAPVLKFFEIHYYLSRWWALAI PTWLFVLVIYIHVVLNAYNTEVLTKPFSSL ECIVDQYALVGEEDGAAHGRVVDLRLCDVN KQQLEET 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 >T38153 hypothetical protein SPAC22A12.13 - fission yeast MLVPPSPSLTTMFRTRSTTPDEEGTAIAEIDQQDWDIMVKVPTYEYYGFVMYLVSMLGFG VYIVWALTPAPVLKFFEIHYYLSRWWALAIPTWLFVLVIYIHVVLNAYNTEVLTKPFSSL ECIVDQYALVGEEDGAAHGRVVDLRLCDVNKQQLEET 1 - 157 MLVPPSPSLT TMFRTRSTTP DEEGTAIAEI DQQDWDIMVK VPTYEYYGFV MYLVSMLGFG VYIVWALTPA PVLKFFEIHY YLSRWWALAI PTWLFVLVIY IHVVLNAYNT EVLTKPFSSL ECIVDQYALV GEEDGAAHGR VVDLRLCDVN KQQLEET low complexity regions: DUST >T38153 hypothetical protein SPAC22A12.13 - fission yeast MLVPPSPSLTTMFRTRSTTPDEEGTAIAEIDQQDWDIMVKVPTYEYYGFVMYLVSMLGFG VYIVWALTPAPVLKFFEIHYYLSRWWALAIPTWLFVLVIYIHVVLNAYNTEVLTKPFSSL ECIVDQYALVGEEDGAAHGRVVDLRLCDVNKQQLEET ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ coiled coil prediction for T38153 sequence: 157 amino acids, 0 residue(s) in coiled coil state . | . | . | . | . | . 60 MLVPPSPSLT TMFRTRSTTP DEEGTAIAEI DQQDWDIMVK VPTYEYYGFV MYLVSMLGFG ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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 VYIVWALTPA PVLKFFEIHY YLSRWWALAI PTWLFVLVIY IHVVLNAYNT EVLTKPFSSL ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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 . | . | . | . ECIVDQYALV GEEDGAAHGR VVDLRLCDVN KQQLEET ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~ ---------- ---------- ---------- ------- ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ prediction of transmembrane regions with toppred2 *********************************** *TOPPREDM with eukaryotic function* *********************************** T38153.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: T38153.fa.___inter___ (1 sequences) MLVPPSPSLTTMFRTRSTTPDEEGTAIAEIDQQDWDIMVKVPTYEYYGFV MYLVSMLGFGVYIVWALTPAPVLKFFEIHYYLSRWWALAIPTWLFVLVIY IHVVLNAYNTEVLTKPFSSLECIVDQYALVGEEDGAAHGRVVDLRLCDVN KQQLEET (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 1 structures are to be tested Candidate membrane-spanning segments: Helix Begin End Score Certainity 1 48 68 2.121 Certain 2 85 105 1.985 Certain ---------------------------------------------------------------------- Structure 1 Transmembrane segments included in this structure: Segment 1 2 Loop length 47 16 52 K+R profile 4.00 4.00 2.00 CYT-EXT prof - - - For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 6.00 Tm probability: 1.00 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): -3.00 (NEG-POS)/(NEG+POS): 0.4545 NEG: 8.0000 POS: 3.0000 -> Orientation: N-out CYT-EXT difference: 0.00 -> Orientation: undecided ---------------------------------------------------------------------- "T38153" 157 48 68 #t 2.12083 85 105 #t 1.98542 ************************************ *TOPPREDM with prokaryotic function* ************************************ T38153.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: T38153.fa.___inter___ (1 sequences) MLVPPSPSLTTMFRTRSTTPDEEGTAIAEIDQQDWDIMVKVPTYEYYGFV MYLVSMLGFGVYIVWALTPAPVLKFFEIHYYLSRWWALAIPTWLFVLVIY IHVVLNAYNTEVLTKPFSSLECIVDQYALVGEEDGAAHGRVVDLRLCDVN KQQLEET (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 1 structures are to be tested Candidate membrane-spanning segments: Helix Begin End Score Certainity 1 48 68 2.121 Certain 2 85 105 1.985 Certain ---------------------------------------------------------------------- Structure 1 Transmembrane segments included in this structure: Segment 1 2 Loop length 47 16 52 K+R profile 3.00 4.00 2.00 CYT-EXT prof - - - For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 5.00 Tm probability: 1.00 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): -3.00 (NEG-POS)/(NEG+POS): 0.4545 NEG: 8.0000 POS: 3.0000 -> Orientation: N-out CYT-EXT difference: 0.00 -> Orientation: undecided ---------------------------------------------------------------------- "T38153" 157 48 68 #t 2.12083 85 105 #t 1.98542 ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ SAPS. Version of April 11, 1996. Date run: Tue Mar 5 16:41:09 2002 File: /people/b_eisen/T38153.fa.___saps___ ID T38153 DE hypothetical protein SPAC22A12.13 - fission yeast number of residues: 157; molecular weight: 18.0 kdal 1 MLVPPSPSLT TMFRTRSTTP DEEGTAIAEI DQQDWDIMVK VPTYEYYGFV MYLVSMLGFG 61 VYIVWALTPA PVLKFFEIHY YLSRWWALAI PTWLFVLVIY IHVVLNAYNT EVLTKPFSSL 121 ECIVDQYALV GEEDGAAHGR VVDLRLCDVN KQQLEET -------------------------------------------------------------------------------- COMPOSITIONAL ANALYSIS (extremes relative to: swp23s) A : 10( 6.4%); C : 2( 1.3%); D : 8( 5.1%); E : 11( 7.0%); F : 7( 4.5%) G : 7( 4.5%); H : 3( 1.9%); I : 9( 5.7%); K : 4( 2.5%); L : 17(10.8%) M : 5( 3.2%); N : 3( 1.9%); P : 9( 5.7%); Q : 5( 3.2%); R : 5( 3.2%) S : 7( 4.5%); T : 12( 7.6%); V : 18(11.5%); W : 5( 3.2%); Y : 10( 6.4%) KR : 9 ( 5.7%); ED : 19 ( 12.1%); AGP : 26 ( 16.6%); KRED : 28 ( 17.8%); KR-ED : -10 ( -6.4%); FIKMNY : 38 ( 24.2%); LVIFM : 56 ( 35.7%); ST : 19 ( 12.1%). -------------------------------------------------------------------------------- CHARGE DISTRIBUTIONAL ANALYSIS 1 0000000000 000+0+0000 ---00000-0 -00-0-000+ 0000-00000 0000000000 61 0000000000 000+00-000 000+000000 0000000000 0000000000 -000+00000 121 -000-00000 0---00000+ 00-0+00-00 +000--0 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 3 | 5 | 5 | 40 | 7 | 9 | 11 | 9 | 11 | 13 | 6 | 7 | lmin1 5 | 6 | 7 | 49 | 9 | 11 | 13 | 11 | 13 | 16 | 7 | 9 | lmin2 5 | 7 | 8 | 54 | 10 | 12 | 14 | 12 | 15 | 18 | 8 | 10 | (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: 2, at 21; 132; * runs >= 4: 0 0 runs >= 27: 1, at 46; -------------------------------------------------------------------------------- DISTRIBUTION OF OTHER AMINO ACID TYPES 1. HIGH SCORING SEGMENTS. __________________________________ High scoring hydrophobic segments: 2.00 (LVIFM) 1.00 (AGYCW) 0.00 (BZX) -2.00 (PH) -4.00 (STNQ) -8.00 (KEDR) Expected score/letter: -1.338 M_0.01= 31.50; M_0.05= 24.98 1) From 46 to 67: length= 22, score=29.00 * 46 YYGFVMYLVS MLGFGVYIVW AL L: 3(13.6%); G: 3(13.6%); V: 4(18.2%); Y: 4(18.2%); ____________________________________ 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: -2.427 M_0.01= 74.13; M_0.05= 58.17; M_0.30= 39.19 1) From 48 to 105: length= 58, score=58.00 (pocket at 68 to 86: length= 19, score=-45.00) 48 GFVMYLVSML GFGVYIVWAL |TPAPVLKFFE IHYYLSRWW| A LAIPTWLFVL 98 VIYIHVVL L: 9(15.5%); V: 9(15.5%); 2. SPACINGS OF C. H2N-121-C-24-C-10-COOH 2*. SPACINGS OF C and H. (additional deluxe function for ALEX) H2N-78-H-22-H-19-C-15-H-8-C-10-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: 16 (Expected range: 0-- 19) 2. Histogram of spacings between consecutive amino acid multiplets: (1-5) 9 (6-10) 3 (11-20) 4 (>=21) 1 3. Clusters of amino acid multiplets (cmin = 15/30 or 19/45 or 24/60): none B. CHARGE ALPHABET. 1. Total number of charge multiplets: 3 (Expected range: 0-- 8) 0 +plets (f+: 5.7%), 3 -plets (f-: 12.1%) Total number of charge altplets: 0 (Critical number: 8) 2. Histogram of spacings between consecutive charge multiplets: (1-5) 1 (6-10) 0 (11-20) 0 (>=21) 3 -------------------------------------------------------------------------------- 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: 5) and HYDROPHOBICITY ALPHABET ({*= KRED; i= LVIF; 0}; core: 6; !-core: 9) Location Period Element Copies Core Errors 94- 105 1 i 10 6 2 -------------------------------------------------------------------------------- SPACING ANALYSIS. Location (Quartile) Spacing Rank P-value Interpretation 0- 21 (1.) D( 21)D 2 of 9 0.9555 small 2. maximal spacing 36- 125 (3.) D( 89)D 1 of 9 0.0087 large 1. maximal spacing ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ 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: T38153.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: T38153 hypothetical protein SPAC22A12.13 - fission yeast Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- OPR Octicosapeptide repeat -2.8 55 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- OPR 1/1 14 43 .. 1 30 [] -2.8 55 Alignments of top-scoring domains: OPR: domain 1 of 1, from 14 to 43: score -2.8, E = 55 *->dvtikYiDEDGDlvtisSdeeleeAlrlar<-* +++ + DE+G ++ ++ +++++++ + T38153 14 RTRSTTPDEEGTAIAEIDQQDWDIMVKVPT 43 // 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: T38153.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: T38153 hypothetical protein SPAC22A12.13 - fission yeast Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- lig_chan Ligand-gated ion channel 1.9 20 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- lig_chan 1/1 89 105 .. 1 17 [. 1.9 20 Alignments of top-scoring domains: lig_chan: domain 1 of 1, from 89 to 105: score 1.9, E = 20 *->slevWlcilaayllvsv<-* +Wl++l++y++v++ T38153 89 AIPTWLFVLVIYIHVVL 105 // 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: T38153.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: T38153 hypothetical protein SPAC22A12.13 - fission yeast 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: Tue Mar 5 16:43:00 2002 Sequence file: T38153.fa ---------------------------------------- Sequence T38153 (157 residues): Matching pattern PS00006 CK2_PHOSPHO_SITE: 18: TTPD 19: TPDE 118: SSLE Total matches: 3 Matching pattern PS00008 MYRISTYL: 24: GTAIAE 135: GAAHGR Total matches: 2 Total no of hits in this sequence: 5 ======================================== 1314 pattern(s) searched in 1 sequence(s), 157 residues. Total no of hits in all sequences: 5. 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, 157 units >ER-GOLGI-traffic signal is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 157 units >INTRA-SIGNAL-M minimal SH3 binding is the MOTIF name >T38153 hypothetical protein SPAC22A12.13 - fission yeast ;LENGTH=157; DIRECT_SEQUENCE n 1 solutions m %_PXXP 4-7 f >STATISTICS Total : 1 solutions in 1 sequences, 157 units; out of 1 sequences, 157 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, 157 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, 157 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, 157 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, 157 units >INTRA-SIGNAL-M 14-3-3 binding motif in RAF and others (Muslin 1996 Cell 84 889) is the MOTIF name >T38153 hypothetical protein SPAC22A12.13 - fission yeast ;LENGTH=157; DIRECT_SEQUENCE n 1 solutions m %_RSXXP 16-20 f >STATISTICS Total : 1 solutions in 1 sequences, 157 units; out of 1 sequences, 157 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, 157 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, 157 units >TM-CYTOPLASMIC-M di-hydrophobic endocytosis motifs for internalized transmembrane proteins is the MOTIF name >T38153 hypothetical protein SPAC22A12.13 - fission yeast ;LENGTH=157; DIRECT_SEQUENCE n 1 solutions m %_D 125-125 %_XXXL 126-129 %_V 130-130 f >STATISTICS Total : 1 solutions in 1 sequences, 157 units; out of 1 sequences, 157 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, 157 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, 157 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, 157 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, 157 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, 157 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, 157 units >NUCLEAR NLS experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 157 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, 157 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, 157 units >NUCLEAR NLS HCDA experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 157 units >NUCLEAR NLS SV40 LrgT experimentally determined is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 157 units >NUCLEAR NLS H2B experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 157 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, 157 units >NUCLEAR NLS Amida experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 157 units >NUCLEAR NLS Amida experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 157 units >NUCLEAR NLS RanBP3 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 157 units >NUCLEAR NLS Pho4p experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 157 units >NUCLEAR NLS DNAhelicaseQ1 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 157 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, 157 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, 157 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, 157 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, 157 units >NUCLEAR NLS GAL4 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 157 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, 157 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, 157 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, 157 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, 157 units >NUCLEAR NLS TR2 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 157 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, 157 units >NUCLEAR NLS polyomaVP1 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 157 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, 157 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, 157 units >NUCLEAR NLS Rex experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 157 units >NUCLEAR NLS SRY experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 157 units >NUCLEAR NLS SRY experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 157 units >NUCLEAR NLS SOX9 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 157 units >NUCLEAR NLS SOX9 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 157 units >NUCLEAR NLS NS5A experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 157 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, 157 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, 157 units >NUCLEAR NLS adenovE1a experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 157 units >NUCLEAR NLS ystDNApolalpha experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 157 units >NUCLEAR NLS hVDR experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 157 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, 157 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, 157 units >NUCLEAR NLS cFOS experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 157 units >NUCLEAR NLS cJUN experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 157 units >NUCLEAR NLS hDNApolalpha experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 157 units >NUCLEAR NLS hDNAtopoII experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 157 units >NUCLEAR NLS hDNAtopoII experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 157 units >NUCLEAR NLS hBLM experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 157 units >NUCLEAR NLS hARNT experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 157 units >NUCLEAR NLS influenzaNP experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 157 units >NUCLEAR NLS influenzaNP experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 157 units >NUCLEAR NLS p54 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 157 units >NUCLEAR NLS hProTalpha experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 157 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, 157 units >NUCLEAR NLS protHsc9 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 157 units >NUCLEAR NLS protHsci experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 157 units >NUCLEAR NLS protHsc3 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 157 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, 157 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, 157 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, 157 units >NUCLEAR NLS MyoD experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 157 units >NUCLEAR NLS MyoD experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 157 units >NUCLEAR NLS opaque2 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 157 units >NUCLEAR NLS CTP experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 157 units >NUCLEAR NLS HCV experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 157 units >NUCLEAR NLS HCV experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 157 units >NUCLEAR NLS p110RB1 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 157 units >NUCLEAR NLS experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 157 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, 157 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, 157 units >NUCLEAR NLS Nucloplasmin experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 157 units >NUCLEAR NLS Nucleolin experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 157 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, 157 units >NUCLEAR NLS Nab2 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 157 units >NUCLEAR NLS M9 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 157 units >NUCLEAR NLS lscMyc experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 157 units >NUCLEAR NLS humKprotein experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 157 units >NUCLEAR NLS FluA experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 157 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, 157 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, 157 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, 157 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, 157 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, 157 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, 157 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, 157 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, 157 units >NUCLEAR NLS p53 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 157 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, 157 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, 157 units >NUCLEAR NLS L29 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 157 units >NUCLEAR NLS L29 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 157 units >NUCLEAR NLS Max experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 157 units >NUCLEAR NLS L3 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 157 units >NUCLEAR NLS dyskerin experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 157 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, 157 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, 157 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: T38153.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: T38153 hypothetical protein SPAC22A12.13 - fission yeast 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: T38153.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: T38153 hypothetical protein SPAC22A12.13 - fission yeast 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= T38153 hypothetical protein SPAC22A12.13 - fission yeast (157 letters) Searching..................................done Results from profile search Score E Sequences producing significant alignments: (bits) Value DHHC Novel zinc finger domain with DHHC signature 21 1.00 INSL Insulinase like Metallo protease domain 20 1.9 KIN Protein kinase domain 19 3.8 CALC Calcineurin like Phosphoesterase domain 19 3.8 UBC Ubiquitin Conjugating enzyme domain 18 7.6 DNASE1 DNASE-1/Sphingomyelinase like domain 18 8.3 SNARE Alpha helical domains which are involved in vesicle fu... 18 9.6 PX PX domain 18 9.9 PAP Papain/bleomycin hydrolase like domain 18 10.0 >DHHC Novel zinc finger domain with DHHC signature Length = 217 Score = 21.3 bits (44), Expect = 1.00 Identities = 4/33 (12%), Positives = 4/33 (12%), Gaps = 3/33 (9%) Query: 75 FFEIHY---YLSRWWALAIPTWLFVLVIYIHVV 104 Sbjct: 69 ILVPLLPHHWVPAGYACMGAIFAGHLVVHLTAV 101 Score = 19.7 bits (40), Expect = 2.4 Identities = 5/17 (29%), Positives = 5/17 (29%) Query: 85 WWALAIPTWLFVLVIYI 101 Sbjct: 48 PHPLQIVAWLLYLFFAV 64 Score = 18.5 bits (37), Expect = 6.2 Identities = 3/31 (9%), Positives = 3/31 (9%) Query: 37 IMVKVPTYEYYGFVMYLVSMLGFGVYIVWAL 67 Sbjct: 67 FGILVPLLPHHWVPAGYACMGAIFAGHLVVH 97 >INSL Insulinase like Metallo protease domain Length = 433 Score = 20.3 bits (42), Expect = 1.9 Identities = 9/58 (15%), Positives = 9/58 (15%), Gaps = 1/58 (1%) Query: 27 IAEIDQQDWDIMVKVPTYEYYGFVMYLVSMLGFGVYIVWALTPAPVLKFFEIHYYLSR 84 Sbjct: 146 LRRGKDNPTTVLWEEFEKLVYKVSPYRFPIIGF-EETIRKFTREKLLKFYKSFYQPRN 202 Score = 18.7 bits (38), Expect = 5.0 Identities = 4/26 (15%), Positives = 4/26 (15%) Query: 3 VPPSPSLTTMFRTRSTTPDEEGTAIA 28 Sbjct: 237 IPTEPEQIGIRFKKLKDPRIEKAYWI 262 >KIN Protein kinase domain Length = 313 Score = 19.3 bits (39), Expect = 3.8 Identities = 9/59 (15%), Positives = 9/59 (15%) Query: 44 YEYYGFVMYLVSMLGFGVYIVWALTPAPVLKFFEIHYYLSRWWALAIPTWLFVLVIYIH 102 Sbjct: 91 ISIKDILKPNSKEQFEDVYIVSELMDTDLHQIITSPQPLSDDHCQYFVYQMLRGLKHIH 149 >CALC Calcineurin like Phosphoesterase domain Length = 274 Score = 19.0 bits (38), Expect = 3.8 Identities = 7/75 (9%), Positives = 7/75 (9%), Gaps = 9/75 (12%) Query: 45 EYYGFVMYLVSMLGFGVYIVWALTPAPVLKFFEIHYYLSRWW--------ALAIPTWLFV 96 Sbjct: 101 AEFLNQPPMNAAKHLLLGEHWQALLLDSQVYGVPHGQLSQHQLDLLKETLGKNPERYTLV 160 Query: 97 LVIYIHVVLNAYNTE 111 Sbjct: 161 -VLHHHLLPTNSAWL 174 >UBC Ubiquitin Conjugating enzyme domain Length = 144 Score = 18.2 bits (37), Expect = 7.6 Identities = 4/26 (15%), Positives = 4/26 (15%) Query: 31 DQQDWDIMVKVPTYEYYGFVMYLVSM 56 Sbjct: 26 DLTDLQVTIEGPEGTPYAGGLFRMKL 51 >DNASE1 DNASE-1/Sphingomyelinase like domain Length = 388 Score = 18.1 bits (36), Expect = 8.3 Identities = 7/34 (20%), Positives = 7/34 (20%) Query: 29 EIDQQDWDIMVKVPTYEYYGFVMYLVSMLGFGVY 62 Sbjct: 139 EILMYQPDVLCLQEVDHYFDTFQPILSRLGYQCT 172 >SNARE Alpha helical domains which are involved in vesicle fusion Length = 254 Score = 17.9 bits (36), Expect = 9.6 Identities = 8/40 (20%), Positives = 8/40 (20%), Gaps = 4/40 (10%) Query: 83 SRWWALAIPTWLF-VLVIYIHVVLNAYNTEVLTKPFSSLE 121 Sbjct: 179 SSAHQRLEPATLSGIVAFILSLLCGALN---LIRGFHAIE 215 >PX PX domain Length = 158 Score = 17.9 bits (36), Expect = 9.9 Identities = 8/96 (8%), Positives = 8/96 (8%), Gaps = 16/96 (16%) Query: 36 DIMVKVPTYEYYG----FVMYLVSMLGFGVYIVWALTPAPVLK----FFEIHYYLS-RWW 86 Sbjct: 6 IRHIALLGFEKRFIPSQHYVYMFLVKWQDLS------EKVVYRKFTEIYEFHKMLKEMFP 59 Query: 87 ALAIPTW-LFVLVIYIHVVLNAYNTEVLTKPFSSLE 121 Sbjct: 60 IEAGEIHTENRVIPHLPAPRWFDGQRAAESRQGTLT 95 >PAP Papain/bleomycin hydrolase like domain Length = 376 Score = 17.6 bits (35), Expect = 10.0 Identities = 1/15 (6%), Positives = 1/15 (6%) Query: 117 FSSLECIVDQYALVG 131 Sbjct: 156 MAAAGNIETLWRISF 170 Underlying Matrix: BLOSUM62 Number of sequences tested against query: 105 Number of sequences better than 10.0: 9 Number of calls to ALIGN: 12 Length of query: 157 Total length of test sequences: 20182 Effective length of test sequences: 17043.0 Effective search space size: 2173798.5 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= T38153 hypothetical protein SPAC22A12.13 - fission yeast (157 letters) Searching.................................................done Results from profile search Score E Sequences producing significant alignments: (bits) Value gi|730428 [2..438] P-loop containing nucleotide triphosphate... 25 0.83 gi|1431766 [1..557] N-terminal nucleophile aminohydrolases (... 22 7.4 >gi|730428 [2..438] P-loop containing nucleotide triphosphate hydrolases Length = 437 Score = 24.9 bits (54), Expect = 0.83 Identities = 15/51 (29%), Positives = 15/51 (29%), Gaps = 8/51 (15%) Query: 98 VIYIHVVLNAYNTEVLTKPFSS--------LECIVDQYALVGEEDGAAHGR 140 Sbjct: 259 IGYILGIAKAYCTRVGAGPFPTELYDGLEKQDPVGKHLGTVGHEFGATTGR 309 >gi|1431766 [1..557] N-terminal nucleophile aminohydrolases (Ntn hydrolases) Length = 557 Score = 21.9 bits (46), Expect = 7.4 Identities = 8/36 (22%), Positives = 8/36 (22%), Gaps = 2/36 (5%) Query: 35 WDIMVKVPTYEYYG--FVMYLVSMLGFGVYIVWALT 68 Sbjct: 33 YGIGLHGAGYDVTGNTPFAYPGLVFGHNGVISWGST 68 Underlying Matrix: BLOSUM62 Number of sequences tested against query: 1187 Number of sequences better than 10.0: 2 Number of calls to ALIGN: 2 Length of query: 157 Total length of test sequences: 256703 Effective length of test sequences: 214185.0 Effective search space size: 26084797.4 Initial X dropoff for ALIGN: 25.0 bits ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ calculation of internal repeats with prospero ***** PROSPERO v1.3 Tue Mar 5 16:43:36 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 T38153 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: T38153.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: T38153 hypothetical protein SPAC22A12.13 - fission yeast Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- TIGR00145 TIGR00145: conserved hypothetical protein T 2.7 4.4 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- TIGR00145 1/1 30 91 .. 268 331 .] 2.7 4.4 Alignments of top-scoring domains: TIGR00145: domain 1 of 1, from 30 to 91: score 2.7, E = 4.4 *->lgellnGwllapgllggqfPGiilpllpgyspnlywlllllplglll +++ + w++++ ++ ++ G +++l++++ +y++ +l p+ l T38153 30 IDQQD--WDIMVKVPTYEYYGFVMYLVSMLGFGVYIVWALTPAPVLK 74 vaealghrgltgklllk<-* + e ++++ +l+ + T38153 75 FFEIHYYLSRWWALAIP 91 // 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: T38153.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: T38153 hypothetical protein SPAC22A12.13 - fission yeast Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- TIGR00145 TIGR00145: conserved hypothetical protein T 2.7 6.1 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- TIGR00145 1/1 30 91 .. 268 331 .] 2.7 6.1 Alignments of top-scoring domains: TIGR00145: domain 1 of 1, from 30 to 91: score 2.7, E = 6.1 *->lgellnGwllapgllggqfPGiilpllpgyspnlywlllllplglll +++ + w++++ ++ ++ G +++l++++ +y++ +l p+ l T38153 30 IDQQD--WDIMVKVPTYEYYGFVMYLVSMLGFGVYIVWALTPAPVLK 74 vaealghrgltgklllk<-* + e ++++ +l+ + T38153 75 FFEIHYYLSRWWALAIP 91 // 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: T38153.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: T38153 hypothetical protein SPAC22A12.13 - fission yeast Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- OPR Octicosapeptide repeat -2.9 37 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- OPR 1/1 14 43 .. 1 30 [] -2.9 37 Alignments of top-scoring domains: OPR: domain 1 of 1, from 14 to 43: score -2.9, E = 37 *->tvtikYiDeDGDlVtivSdeDleeAlelar<-* +++ + De+G ++ ++ D++++++ ++ T38153 14 RTRSTTPDEEGTAIAEIDQQDWDIMVKVPT 43 // 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: T38153.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: T38153 hypothetical protein SPAC22A12.13 - fission yeast 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: T38153.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: T38153 hypothetical protein SPAC22A12.13 - fission yeast Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- COG1108 -0.6 88 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- COG1108 1/1 49 65 .. 276 292 .] -0.6 88 Alignments of top-scoring domains: COG1108: domain 1 of 1, from 49 to 65: score -0.6, E = 88 *->tllfllslllrkkygvl<-* ++ +l+s+l++++y v+ T38153 49 FVMYLVSMLGFGVYIVW 65 //