analysis of sequence from PIGL_SCHPO.fa ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ >PIGL_SCHPO MIWFWSTLLV TAIAVLSTAN ESSSGQEKLA VESILFVFAH PDDESMFFGP TIDYLGNQHS TRVHVLCLSN GNADGLGSVR EKELVVAASK YQIDKTNVHV VSDPQLQDGM QAKWDPTDVA KHISQIIERY NIKTLITFDN KGISGHPNHI ACYEGAMKIV KATPQVQVFV LESVNIFRKY ISYLDTIPTL VQSQAGRNDT IIIHADRKST QRIRDAMVRG HKSQMVWFRY GWIYLSKYMS NNVLKRAT ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ sec.str. with predator > PIGL_SCHPO . . . . . 1 MIWFWSTLLVTAIAVLSTANESSSGQEKLAVESILFVFAHPDDESMFFGP 50 ____HHHHHHHHHHHHH_________EEEHHHHHHEEE____________ . . . . . 51 TIDYLGNQHSTRVHVLCLSNGNADGLGSVREKELVVAASKYQIDKTNVHV 100 __________EEEEEEEE___________HHHHHHHHHHHHHH____EEE . . . . . 101 VSDPQLQDGMQAKWDPTDVAKHISQIIERYNIKTLITFDNKGISGHPNHI 150 E_________________HHHHHHHHHHHH___EEEE_____________ . . . . . 151 ACYEGAMKIVKATPQVQVFVLESVNIFRKYISYLDTIPTLVQSQAGRNDT 200 _HHHHHHH_______EEEEEEEEHHHHHHHHH______EEEE_______E . . . . 201 IIIHADRKSTQRIRDAMVRGHKSQMVWFRYGWIYLSKYMSNNVLKRAT 248 EEEE_____HHHHHHHHHH____EEEEEE_EEEE______________ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ method : 1 alpha-contents : 13.6 % beta-contents : 53.8 % coil-contents : 32.6 % class : beta method : 2 alpha-contents : 33.7 % beta-contents : 36.7 % coil-contents : 29.6 % class : mixed ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ GPI: learning from metazoa -9.82 -3.91 -5.01 -3.78 0.00 0.00 0.00 0.00 -3.28 -4.67 -1.26 -12.00 -12.00 0.00 -12.00 0.00 -67.72 -2.24 -3.31 -3.14 -5.38 0.00 0.00 -8.00 0.00 -0.09 -5.78 -1.26 -12.00 -12.00 0.00 -12.00 0.00 -65.20 ID: PIGL_SCHPO AC: xxx Len: 248 1:I 215 Sc: -65.20 Pv: 4.663556e-01 NO_GPI_SITE GPI: learning from protozoa -26.14 -12.35 -3.79 -0.53 -4.00 0.00 0.00 -0.17 -1.15 -4.67 -5.42 -12.00 -12.00 0.00 -12.00 0.00 -94.22 -38.98 -0.83 -1.17 -0.13 -4.00 0.00 0.00 0.00 -2.74 -4.37 -5.42 -12.00 -12.00 0.00 -12.00 0.00 -93.64 ID: PIGL_SCHPO AC: xxx Len: 248 1:I 221 Sc: -93.64 Pv: 7.619737e-01 NO_GPI_SITE ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ # SignalP euk predictions # name Cmax pos ? Ymax pos ? Smax pos ? Smean ? PIGL_SCHPO 0.589 26 Y 0.600 20 Y 0.992 6 Y 0.939 Y # SignalP gram- predictions # name Cmax pos ? Ymax pos ? Smax pos ? Smean ? PIGL_SCHPO 0.361 40 N 0.454 20 Y 0.997 9 Y 0.848 Y # SignalP gram+ predictions # name Cmax pos ? Ymax pos ? Smax pos ? Smean ? PIGL_SCHPO 0.516 152 Y 0.393 22 Y 0.999 10 Y 0.808 Y ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ low complexity regions: SEG 12 2.2 2.5 >PIGL_SCHPO 1-248 MIWFWSTLLVTAIAVLSTANESSSGQEKLA VESILFVFAHPDDESMFFGPTIDYLGNQHS TRVHVLCLSNGNADGLGSVREKELVVAASK YQIDKTNVHVVSDPQLQDGMQAKWDPTDVA KHISQIIERYNIKTLITFDNKGISGHPNHI ACYEGAMKIVKATPQVQVFVLESVNIFRKY ISYLDTIPTLVQSQAGRNDTIIIHADRKST QRIRDAMVRGHKSQMVWFRYGWIYLSKYMS NNVLKRAT low complexity regions: SEG 25 3.0 3.3 >PIGL_SCHPO 1-248 MIWFWSTLLVTAIAVLSTANESSSGQEKLA VESILFVFAHPDDESMFFGPTIDYLGNQHS TRVHVLCLSNGNADGLGSVREKELVVAASK YQIDKTNVHVVSDPQLQDGMQAKWDPTDVA KHISQIIERYNIKTLITFDNKGISGHPNHI ACYEGAMKIVKATPQVQVFVLESVNIFRKY ISYLDTIPTLVQSQAGRNDTIIIHADRKST QRIRDAMVRGHKSQMVWFRYGWIYLSKYMS NNVLKRAT low complexity regions: SEG 45 3.4 3.75 >PIGL_SCHPO 1-248 MIWFWSTLLVTAIAVLSTANESSSGQEKLA VESILFVFAHPDDESMFFGPTIDYLGNQHS TRVHVLCLSNGNADGLGSVREKELVVAASK YQIDKTNVHVVSDPQLQDGMQAKWDPTDVA KHISQIIERYNIKTLITFDNKGISGHPNHI ACYEGAMKIVKATPQVQVFVLESVNIFRKY ISYLDTIPTLVQSQAGRNDTIIIHADRKST QRIRDAMVRGHKSQMVWFRYGWIYLSKYMS NNVLKRAT 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 >PIGL_SCHPO MIWFWSTLLVTAIAVLSTANESSSGQEKLAVESILFVFAHPDDESMFFGPTIDYLGNQHS TRVHVLCLSNGNADGLGSVREKELVVAASKYQIDKTNVHVVSDPQLQDGMQAKWDPTDVA KHISQIIERYNIKTLITFDNKGISGHPNHIACYEGAMKIVKATPQVQVFVLESVNIFRKY ISYLDTIPTLVQSQAGRNDTIIIHADRKSTQRIRDAMVRGHKSQMVWFRYGWIYLSKYMS NNVLKRAT 1 - 248 MIWFWSTLLV TAIAVLSTAN ESSSGQEKLA VESILFVFAH PDDESMFFGP TIDYLGNQHS TRVHVLCLSN GNADGLGSVR EKELVVAASK YQIDKTNVHV VSDPQLQDGM QAKWDPTDVA KHISQIIERY NIKTLITFDN KGISGHPNHI ACYEGAMKIV KATPQVQVFV LESVNIFRKY ISYLDTIPTL VQSQAGRNDT IIIHADRKST QRIRDAMVRG HKSQMVWFRY GWIYLSKYMS NNVLKRAT low complexity regions: DUST >PIGL_SCHPO MIWFWSTLLVTAIAVLSTANESSSGQEKLAVESILFVFAHPDDESMFFGPTIDYLGNQHS TRVHVLCLSNGNADGLGSVREKELVVAASKYQIDKTNVHVVSDPQLQDGMQAKWDPTDVA KHISQIIERYNIKTLITFDNKGISGHPNHIACYEGAMKIVKATPQVQVFVLESVNIFRKY ISYLDTIPTLVQSQAGRNDTIIIHADRKSTQRIRDAMVRGHKSQMVWFRYGWIYLSKYMS NNVLKRAT ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ coiled coil prediction for PIGL_SCHPO sequence: 248 amino acids, 0 residue(s) in coiled coil state . | . | . | . | . | . 60 MIWFWSTLLV TAIAVLSTAN ESSSGQEKLA VESILFVFAH PDDESMFFGP TIDYLGNQHS ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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 TRVHVLCLSN GNADGLGSVR EKELVVAASK YQIDKTNVHV VSDPQLQDGM QAKWDPTDVA ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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 KHISQIIERY NIKTLITFDN KGISGHPNHI ACYEGAMKIV KATPQVQVFV LESVNIFRKY ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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 ISYLDTIPTL VQSQAGRNDT IIIHADRKST QRIRDAMVRG HKSQMVWFRY GWIYLSKYMS ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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 . NNVLKRAT ~~~~~~~~ -------- ~~~~~~~~ ~~~~~~~~ ~~~~~~~~ ~~~~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ prediction of transmembrane regions with toppred2 *********************************** *TOPPREDM with eukaryotic function* *********************************** PIGL_SCHPO.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: PIGL_SCHPO.fa.___inter___ (1 sequences) MIWFWSTLLVTAIAVLSTANESSSGQEKLAVESILFVFAHPDDESMFFGP TIDYLGNQHSTRVHVLCLSNGNADGLGSVREKELVVAASKYQIDKTNVHV VSDPQLQDGMQAKWDPTDVAKHISQIIERYNIKTLITFDNKGISGHPNHI ACYEGAMKIVKATPQVQVFVLESVNIFRKYISYLDTIPTLVQSQAGRNDT IIIHADRKSTQRIRDAMVRGHKSQMVWFRYGWIYLSKYMSNNVLKRAT (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 1 21 1.790 Certain ---------------------------------------------------------------------- Structure 1 Transmembrane segments included in this structure: Segment 1 Loop length 0 227 K+R profile 1.00 + CYT-EXT prof - 1.28 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 1.00 Tm probability: 1.00 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 2.00 (NEG-POS)/(NEG+POS): 0.0521 NEG: 0.0000 POS: 0.0000 -> Orientation: N-in CYT-EXT difference: -1.28 -> Orientation: N-in ---------------------------------------------------------------------- "PIGL_SCHPO" 248 1 21 #t 1.78958 ************************************ *TOPPREDM with prokaryotic function* ************************************ PIGL_SCHPO.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: PIGL_SCHPO.fa.___inter___ (1 sequences) MIWFWSTLLVTAIAVLSTANESSSGQEKLAVESILFVFAHPDDESMFFGP TIDYLGNQHSTRVHVLCLSNGNADGLGSVREKELVVAASKYQIDKTNVHV VSDPQLQDGMQAKWDPTDVAKHISQIIERYNIKTLITFDNKGISGHPNHI ACYEGAMKIVKATPQVQVFVLESVNIFRKYISYLDTIPTLVQSQAGRNDT IIIHADRKSTQRIRDAMVRGHKSQMVWFRYGWIYLSKYMSNNVLKRAT (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 1 21 1.790 Certain ---------------------------------------------------------------------- Structure 1 Transmembrane segments included in this structure: Segment 1 Loop length 0 227 K+R profile 0.00 + CYT-EXT prof - 1.28 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): 0.0521 NEG: 0.0000 POS: 0.0000 -> Orientation: N-in CYT-EXT difference: -1.28 -> Orientation: N-in ---------------------------------------------------------------------- "PIGL_SCHPO" 248 1 21 #t 1.78958 ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ SAPS. Version of April 11, 1996. Date run: Fri Mar 8 14:29:26 2002 File: /people/b_eisen/PIGL_SCHPO.fa.___saps___ ID PIGL_SCHPO DE - number of residues: 248; molecular weight: 28.0 kdal 1 MIWFWSTLLV TAIAVLSTAN ESSSGQEKLA VESILFVFAH PDDESMFFGP TIDYLGNQHS 61 TRVHVLCLSN GNADGLGSVR EKELVVAASK YQIDKTNVHV VSDPQLQDGM QAKWDPTDVA 121 KHISQIIERY NIKTLITFDN KGISGHPNHI ACYEGAMKIV KATPQVQVFV LESVNIFRKY 181 ISYLDTIPTL VQSQAGRNDT IIIHADRKST QRIRDAMVRG HKSQMVWFRY GWIYLSKYMS 241 NNVLKRAT -------------------------------------------------------------------------------- COMPOSITIONAL ANALYSIS (extremes relative to: swp23s) A : 17( 6.9%); C : 2( 0.8%); D : 14( 5.6%); E : 9( 3.6%); F : 9( 3.6%) G : 13( 5.2%); H : 9( 3.6%); I : 21( 8.5%); K : 15( 6.0%); L : 17( 6.9%) M : 7( 2.8%); N : 12( 4.8%); P : 7( 2.8%); Q : 13( 5.2%); R : 11( 4.4%) S : 21( 8.5%); T : 15( 6.0%); V : 22( 8.9%); W : 5( 2.0%); Y : 9( 3.6%) KR : 26 ( 10.5%); ED : 23 ( 9.3%); AGP : 37 ( 14.9%); KRED : 49 ( 19.8%); KR-ED : 3 ( 1.2%); FIKMNY : 73 ( 29.4%); LVIFM : 76 ( 30.6%); ST : 36 ( 14.5%). -------------------------------------------------------------------------------- CHARGE DISTRIBUTIONAL ANALYSIS 1 0000000000 0000000000 -00000-+00 0-00000000 0---000000 00-0000000 61 0+00000000 000-00000+ -+-000000+ 000-+00000 00-0000-00 00+0-00-00 121 +000000-+0 00+00000-0 +000000000 000-000+00 +000000000 0-00000++0 181 0000-00000 000000+0-0 00000-++00 0+0+-000+0 0+000000+0 000000+000 241 0000++00 A. CHARGE CLUSTERS. Positive charge clusters (cmin = 9/30 or 12/45 or 15/60): none Negative charge clusters (cmin = 9/30 or 11/45 or 14/60): none Mixed charge clusters (cmin = 14/30 or 19/45 or 24/60): none B. HIGH SCORING (UN)CHARGED SEGMENTS. There are no high scoring positive charge segments. There are no high scoring negative charge segments. There are no high scoring mixed charge segments. There are no high scoring uncharged segments. C. CHARGE RUNS AND PATTERNS. pattern (+)| (-)| (*)| (0)| (+0)| (-0)| (*0)|(+00)|(-00)|(*00)| (H.)|(H..)| lmin0 4 | 4 | 6 | 39 | 9 | 9 | 12 | 11 | 10 | 14 | 7 | 9 | lmin1 6 | 6 | 8 | 47 | 11 | 10 | 14 | 13 | 13 | 17 | 9 | 11 | lmin2 7 | 7 | 9 | 52 | 12 | 12 | 16 | 15 | 14 | 19 | 10 | 12 | (Significance level: 0.010000; Minimal displayed length: 6) There are no charge runs or patterns exceeding the given minimal lengths. Run count statistics: + runs >= 3: 0 - runs >= 3: 1, at 42; * runs >= 4: 1, at 80; 0 runs >= 26: 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: -3.387 M_0.01= 58.98; M_0.05= 47.62; M_0.30= 34.11 1) From 1 to 16: length= 16, score=38.00 1 MIWFWSTLLV TAIAVL L: 3(18.8%); A: 2(12.5%); V: 2(12.5%); T: 2(12.5%); I: 2(12.5%); W: 2(12.5%); 2. SPACINGS OF C. H2N-66-C-84-C-96-COOH 2*. SPACINGS OF C and H. (additional deluxe function for ALEX) H2N-39-H-18-H-4-H-2-C-31-H-22-H-23-H-2-H-2-C-51-H-16-H-27-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: 10 (Expected range: 2-- 25) 2. Histogram of spacings between consecutive amino acid multiplets: (1-5) 2 (6-10) 2 (11-20) 3 (>=21) 4 3. Clusters of amino acid multiplets (cmin = 8/30 or 11/45 or 13/60): none B. CHARGE ALPHABET. 1. Total number of charge multiplets: 4 (Expected range: 0-- 11) 3 +plets (f+: 10.5%), 1 -plets (f-: 9.3%) Total number of charge altplets: 6 (Critical number: 13) 2. Histogram of spacings between consecutive charge multiplets: (1-5) 1 (6-10) 0 (11-20) 0 (>=21) 4 -------------------------------------------------------------------------------- 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 There are no periodicities of the prescribed length. -------------------------------------------------------------------------------- SPACING ANALYSIS. There are no unusual spacings. ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ 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: PIGL_SCHPO.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: PIGL_SCHPO Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- TIR TIR domain -0.5 85 1 arrestin Arrestin (or S-antigen), N-terminal domain -2.4 95 1 DUF158 Uncharacterized LmbE-like protein, COG2120 -29.5 0.00032 1 ENTH ENTH domain -52.2 72 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- TIR 1/1 2 11 .. 141 150 .] -0.5 85 arrestin 1/1 157 169 .. 1 13 [. -2.4 95 ENTH 1/1 88 197 .. 1 131 [] -52.2 72 DUF158 1/1 24 248 .] 1 292 [] -29.5 0.00032 Alignments of top-scoring domains: TIR: domain 1 of 1, from 2 to 11: score -0.5, E = 85 *->ikfWkkalya<-* i+fW +l+ PIGL_SCHPO 2 IWFWSTLLVT 11 arrestin: domain 1 of 1, from 157 to 169: score -2.4, E = 95 *->lkavkmvvnvkVF<-* +k+vk + v VF PIGL_SCHPO 157 MKIVKATPQVQVF 169 ENTH: domain 1 of 1, from 88 to 197: score -52.2, E = 72 *->yseleiaVrkATnndpwgPkgkhldeIlelTyedeksfkeimstldk s+++i+ +++++ +++ +l + ++ + d+ ++ +s +++ PIGL_SCHPO 88 ASKYQID-----KTNVHVVSDPQLQDGMQAKW-DPTDVAKHISQIIE 128 RlledkgknWrvVyKaLillhyLlrnGservvqearlaTrnnyrireLed R + K+Li+++ G+++ + + + +++ + PIGL_SCHPO 129 RYNI----------KTLITFDNKGISGHPNHIACYE---GAMKIVKATPQ 165 frkFsvdssgkDqganiRkyakyLverleddgrl<-* +++ v +s + ++ i y + ++++ PIGL_SCHPO 166 VQV-FVLESVNIFRKYIS-YLDTIPTLVQSQAGR 197 DUF158: domain 1 of 1, from 24 to 248: score -29.5, E = 0.00032 *->ssenrLkdAkkVLavhAHPDDesigmGATiakftdqG.krVlvvtlT s + L +L+v+AHPDDes+ G Ti + q ++rV+v++l PIGL_SCHPO 24 SGQEKL-AVESILFVFAHPDDESMFFGPTIDYLGNQHsTRVHVLCLS 69 eGeegstlgsRWAqllaDsadeLaeiRreElaeAAriLGVkkhiqLglad G + d L+++R +El AA + + + PIGL_SCHPO 70 NG------NA----------DGLGSVREKELVVAASKYQI-DKTNVHVV- 101 rgldkGdlgtqlpDrgLaqsdLeevtkalVkviRelrPHvllVFdpnggy +ql D a+ d+ v k + ++i l +Fd g PIGL_SCHPO 102 -------SDPQLQDGMQAKWDPTDVAKHISQIIERYNIKTLITFDNKGIS 144 PYEgHPDHrrtHtVtaAaveaAgafagtpdfpgdpwtvpklYyvvlfLre gHP H+ +e A ++ ++ p+ f e PIGL_SCHPO 145 ---GHPNHIA-------CYEGAM------KI---VKATPQV---QVFVLE 172 kvsklsaefla.sfhRGPFEeWllkrdddidFfvsdDGiddliEakkqaR v+ + ++++ ++ P + + + d ++ i a++++ PIGL_SCHPO 173 SVNIFRKYISYlDTI--P--TLVQSQA-----GRND---TIIIHADRKS- 209 lr..klaAlfahatqsvsePllraiaellgereklykeEgfrlargsfp< ++ ++a + h q v+ ++ ++ + ++ PIGL_SCHPO 210 TQriRDAMVRGHKSQMVWFRYGWIYLSKYMSNN----------VLKRAT 248 -* PIGL_SCHPO - - // 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: PIGL_SCHPO.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: PIGL_SCHPO Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- DUF158 Uncharacterized LmbE-like protein, COG21 23.5 5.8e-06 1 TIR TIR domain -0.5 85 1 2-Hacid_DH_C D-isomer specific 2-hydroxyacid dehydrog -1.5 49 1 arrestin Arrestin (or S-antigen), N-terminal doma -2.4 95 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- TIR 1/1 2 11 .. 141 150 .] -0.5 85 DUF158 1/1 24 88 .. 1 81 [. 23.5 5.8e-06 2-Hacid_DH_C 1/1 135 146 .. 192 203 .] -1.5 49 arrestin 1/1 157 169 .. 1 13 [. -2.4 95 Alignments of top-scoring domains: TIR: domain 1 of 1, from 2 to 11: score -0.5, E = 85 *->ikfWkkalya<-* i+fW +l+ PIGL_SCHPO 2 IWFWSTLLVT 11 DUF158: domain 1 of 1, from 24 to 88: score 23.5, E = 5.8e-06 *->ssenrLkdAkkVLavhAHPDDesigmGATiakftdqG.krVlvvtlT s + L +L+v+AHPDDes+ G Ti + q ++rV+v++l PIGL_SCHPO 24 SGQEKL-AVESILFVFAHPDDESMFFGPTIDYLGNQHsTRVHVLCLS 69 eGeegstlgsRWAqllaDsadeLaeiRreElaeAA<-* G + d L+++R +El AA PIGL_SCHPO 70 NG------NA----------DGLGSVREKELVVAA 88 2-Hacid_DH_C: domain 1 of 1, from 135 to 146: score -1.5, E = 49 *->LlsmpNvilTPH<-* L++++N + +H PIGL_SCHPO 135 LITFDNKGISGH 146 arrestin: domain 1 of 1, from 157 to 169: score -2.4, E = 95 *->lkavkmvvnvkVF<-* +k+vk + v VF PIGL_SCHPO 157 MKIVKATPQVQVF 169 // 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: PIGL_SCHPO.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: PIGL_SCHPO 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: Fri Mar 8 14:31:20 2002 Sequence file: PIGL_SCHPO.fa ---------------------------------------- Sequence PIGL_SCHPO (248 residues): Matching pattern PS00001 ASN_GLYCOSYLATION: 20: NESS 198: NDTI Total matches: 2 Matching pattern PS00004 CAMP_PHOSPHO_SITE: 207: RKST 245: KRAT Total matches: 2 Matching pattern PS00005 PKC_PHOSPHO_SITE: 60: STR 78: SVR 210: TQR Total matches: 3 Matching pattern PS00006 CK2_PHOSPHO_SITE: 18: TANE 24: SGQE 78: SVRE 182: SYLD Total matches: 4 Matching pattern PS00008 MYRISTYL: 56: GNQHST 71: GNADGL Total matches: 2 Total no of hits in this sequence: 13 ======================================== 1314 pattern(s) searched in 1 sequence(s), 248 residues. Total no of hits in all sequences: 13. 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, 248 units >ER-GOLGI-traffic signal is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 248 units >INTRA-SIGNAL-M minimal SH3 binding is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 248 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, 248 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, 248 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, 248 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, 248 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, 248 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, 248 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, 248 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, 248 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, 248 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, 248 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, 248 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, 248 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, 248 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, 248 units >NUCLEAR NLS experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 248 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, 248 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, 248 units >NUCLEAR NLS HCDA experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 248 units >NUCLEAR NLS SV40 LrgT experimentally determined is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 248 units >NUCLEAR NLS H2B experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 248 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, 248 units >NUCLEAR NLS Amida experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 248 units >NUCLEAR NLS Amida experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 248 units >NUCLEAR NLS RanBP3 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 248 units >NUCLEAR NLS Pho4p experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 248 units >NUCLEAR NLS DNAhelicaseQ1 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 248 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, 248 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, 248 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, 248 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, 248 units >NUCLEAR NLS GAL4 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 248 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, 248 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, 248 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, 248 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, 248 units >NUCLEAR NLS TR2 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 248 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, 248 units >NUCLEAR NLS polyomaVP1 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 248 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, 248 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, 248 units >NUCLEAR NLS Rex experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 248 units >NUCLEAR NLS SRY experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 248 units >NUCLEAR NLS SRY experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 248 units >NUCLEAR NLS SOX9 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 248 units >NUCLEAR NLS SOX9 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 248 units >NUCLEAR NLS NS5A experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 248 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, 248 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, 248 units >NUCLEAR NLS adenovE1a experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 248 units >NUCLEAR NLS ystDNApolalpha experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 248 units >NUCLEAR NLS hVDR experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 248 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, 248 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, 248 units >NUCLEAR NLS cFOS experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 248 units >NUCLEAR NLS cJUN experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 248 units >NUCLEAR NLS hDNApolalpha experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 248 units >NUCLEAR NLS hDNAtopoII experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 248 units >NUCLEAR NLS hDNAtopoII experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 248 units >NUCLEAR NLS hBLM experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 248 units >NUCLEAR NLS hARNT experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 248 units >NUCLEAR NLS influenzaNP experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 248 units >NUCLEAR NLS influenzaNP experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 248 units >NUCLEAR NLS p54 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 248 units >NUCLEAR NLS hProTalpha experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 248 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, 248 units >NUCLEAR NLS protHsc9 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 248 units >NUCLEAR NLS protHsci experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 248 units >NUCLEAR NLS protHsc3 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 248 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, 248 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, 248 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, 248 units >NUCLEAR NLS MyoD experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 248 units >NUCLEAR NLS MyoD experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 248 units >NUCLEAR NLS opaque2 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 248 units >NUCLEAR NLS CTP experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 248 units >NUCLEAR NLS HCV experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 248 units >NUCLEAR NLS HCV experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 248 units >NUCLEAR NLS p110RB1 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 248 units >NUCLEAR NLS experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 248 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, 248 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, 248 units >NUCLEAR NLS Nucloplasmin experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 248 units >NUCLEAR NLS Nucleolin experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 248 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, 248 units >NUCLEAR NLS Nab2 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 248 units >NUCLEAR NLS M9 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 248 units >NUCLEAR NLS lscMyc experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 248 units >NUCLEAR NLS humKprotein experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 248 units >NUCLEAR NLS FluA experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 248 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, 248 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, 248 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, 248 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, 248 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, 248 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, 248 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, 248 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, 248 units >NUCLEAR NLS p53 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 248 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, 248 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, 248 units >NUCLEAR NLS L29 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 248 units >NUCLEAR NLS L29 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 248 units >NUCLEAR NLS Max experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 248 units >NUCLEAR NLS L3 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 248 units >NUCLEAR NLS dyskerin experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 248 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, 248 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, 248 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: PIGL_SCHPO.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: PIGL_SCHPO 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: PIGL_SCHPO.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: PIGL_SCHPO 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= PIGL_SCHPO (248 letters) Searching..................................done Results from profile search Score E Sequences producing significant alignments: (bits) Value DNASE1 DNASE-1/Sphingomyelinase like domain 24 0.22 SCP SCP/PR1 domain (Domain found in plant pathogenesis relat... 22 0.86 DAGKIN Diacyl glycerol kinase 20 2.9 ANK Ankyrin repeat 20 4.6 CYCLIN Cyclin/TFIIB domain 20 4.8 PDE cyclic NMP phosphodiesterase domain 19 5.3 MBL Metallo-betalactamase domain 19 6.1 RHOGEF RHO-type GTPase GDP exchange factor 19 7.7 CALC Calcineurin like Phosphoesterase domain 19 8.0 S1 S1 RNA binding domain 19 8.7 CATH Cathepsin like protease domain 19 9.1 >DNASE1 DNASE-1/Sphingomyelinase like domain Length = 388 Score = 24.0 bits (51), Expect = 0.22 Identities = 1/44 (2%), Positives = 1/44 (2%) Query: 59 HSTRVHVLCLSNGNADGLGSVREKELVVAASKYQIDKTNVHVVS 102 Sbjct: 198 LQDRFQLVNSAKIRLSARTLKTNQVAIAETLQCCETGRQLCFAV 241 >SCP SCP/PR1 domain (Domain found in plant pathogenesis related proteins and animal trypsin inhibitors) Length = 159 Score = 22.2 bits (47), Expect = 0.86 Identities = 7/20 (35%), Positives = 7/20 (35%) Query: 208 KSTQRIRDAMVRGHKSQMVW 227 Sbjct: 105 KKKFSGNNFLKTGHYTQMVW 124 >DAGKIN Diacyl glycerol kinase Length = 128 Score = 20.1 bits (42), Expect = 2.9 Identities = 8/38 (21%), Positives = 8/38 (21%), Gaps = 7/38 (18%) Query: 157 MKIVKATPQVQVFVLESVN-------IFRKYISYLDTI 187 Sbjct: 20 HTLCWLLNPRQVFDITSLKGPKFGLEMFRKVVTQLRIL 57 >ANK Ankyrin repeat Length = 323 Score = 19.5 bits (40), Expect = 4.6 Identities = 3/15 (20%), Positives = 3/15 (20%) Query: 147 PNHIACYEGAMKIVK 161 Sbjct: 233 ALILAVGHGHVAMVE 247 Score = 19.5 bits (40), Expect = 4.9 Identities = 5/23 (21%), Positives = 5/23 (21%), Gaps = 2/23 (8%) Query: 139 DNKGISGHPNHIACYEGAMKIVK 161 Sbjct: 95 TVAGCT--PLTFAAEAGHIGISA 115 Score = 19.1 bits (39), Expect = 6.5 Identities = 6/23 (26%), Positives = 6/23 (26%), Gaps = 2/23 (8%) Query: 139 DNKGISGHPNHIACYEGAMKIVK 161 Sbjct: 194 DKQGAT--ALLIAADQGQAGAVE 214 >CYCLIN Cyclin/TFIIB domain Length = 317 Score = 19.5 bits (40), Expect = 4.8 Identities = 5/31 (16%), Positives = 5/31 (16%) Query: 150 IACYEGAMKIVKATPQVQVFVLESVNIFRKY 180 Sbjct: 100 LTCAFLACKVDEFNVSSPQFVGNLRESPLGQ 130 >PDE cyclic NMP phosphodiesterase domain Length = 350 Score = 19.3 bits (39), Expect = 5.3 Identities = 12/57 (21%), Positives = 12/57 (21%), Gaps = 6/57 (10%) Query: 179 KYISYLDTIPTLVQ------SQAGRNDTIIIHADRKSTQRIRDAMVRGHKSQMVWFR 229 Sbjct: 90 QYLTHLDIFALLISCMCHDLNHPGFNNTFQVNAQTELSLEYNDISVLENHHAMLTFK 146 >MBL Metallo-betalactamase domain Length = 256 Score = 19.3 bits (39), Expect = 6.1 Identities = 6/78 (7%), Positives = 6/78 (7%), Gaps = 3/78 (3%) Query: 62 RVHVLCLSNGNADGLGSVREKELVVAASKYQIDKTNVHVVSDPQLQDGMQAKWDPTDVAK 121 Sbjct: 56 DITDIYVSHLHSDHVGGL---EYVGFSTMFDPNCGKPNLYLSQDIAADLWERSLAGGMEA 112 Query: 122 HISQIIERYNIKTLITFD 139 Sbjct: 113 IEGGMTEVDSYFQIHALG 130 >RHOGEF RHO-type GTPase GDP exchange factor Length = 176 Score = 18.7 bits (38), Expect = 7.7 Identities = 15/103 (14%), Positives = 15/103 (14%), Gaps = 13/103 (12%) Query: 82 KELVVAASKYQID-KTNVHVVSDPQLQDGMQAKWDPTDVAKHISQIIERYNIKTLITFDN 140 Sbjct: 3 NELIQTERVYVRELYTVLLGYRAEMDNPEMFDLM-PPLLRNKKDILF--GNMAEIYEF-- 57 Query: 141 KGISGHPNHIACYEGAMKIVKATPQVQVFVLESVNIFRKYISY 183 Sbjct: 58 -------HNDIFLSSLENCAHAPERVGPCFLERKDDFQMYAKY 93 >CALC Calcineurin like Phosphoesterase domain Length = 274 Score = 18.6 bits (37), Expect = 8.0 Identities = 6/64 (9%), Positives = 6/64 (9%), Gaps = 9/64 (14%) Query: 122 HISQIIERYNIKTLITFDNKGISGHPNHIACYEGAMKIVKATPQVQVFVLESVNIFRKYI 181 Sbjct: 204 HQEVNSEWNGYQVMAT------PATCIQFKPDCQYFSLDTLQPGWREIELHS---DGSIR 254 Query: 182 SYLD 185 Sbjct: 255 TEVK 258 >S1 S1 RNA binding domain Length = 305 Score = 18.7 bits (38), Expect = 8.7 Identities = 3/33 (9%), Positives = 3/33 (9%) Query: 97 NVHVVSDPQLQDGMQAKWDPTDVAKHISQIIER 129 Sbjct: 148 MHKDNMDALVGQVLKAHILEANQDNNKLVLTQR 180 >CATH Cathepsin like protease domain Length = 371 Score = 18.7 bits (38), Expect = 9.1 Identities = 14/52 (26%), Positives = 14/52 (26%), Gaps = 9/52 (17%) Query: 85 VVAASKYQIDKTNVHVVSDPQLQ-DGMQAKWD--------PTDVAKHISQII 127 Sbjct: 222 VTRKAYWQIHMEKVDVDNGLTVCKDGCEAIVDTGTSLITGPTDEIKQLQKAI 273 Underlying Matrix: BLOSUM62 Number of sequences tested against query: 105 Number of sequences better than 10.0: 11 Number of calls to ALIGN: 13 Length of query: 248 Total length of test sequences: 20182 Effective length of test sequences: 16637.0 Effective search space size: 3561275.3 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= PIGL_SCHPO (248 letters) Searching.................................................done Results from profile search Score E Sequences producing significant alignments: (bits) Value gi|2190590 [34..336] Periplasmic binding protein-like I 25 0.88 gi|113709 [8..375] Periplasmic binding protein-like I 25 1.5 gi|118558 [166..782] 7-bladed beta-propeller 25 1.8 gi|97186 [16..330] S-adenosyl-L-methionine-dependent methylt... 24 2.1 gi|2497537 [381..517] Pyruvate kinase, C-terminal domain 24 3.0 gi|1346693 [1..313] Phosphofructokinase 24 3.6 gi|127428 [1..429] S-adenosyl-L-methionine-dependent methylt... 23 5.4 gi|1351184 [55..290] ATP pyrophoshatases 23 6.2 gi|1929419 [192..338] Periplasmic binding protein-like I 23 7.2 gi|534844 [150..604] beta/alpha (TIM)-barrel 22 8.1 gi|2145626 [13..324] beta/alpha (TIM)-barrel 22 9.0 >gi|2190590 [34..336] Periplasmic binding protein-like I Length = 303 Score = 25.4 bits (55), Expect = 0.88 Identities = 11/127 (8%), Positives = 11/127 (8%), Gaps = 13/127 (10%) Query: 116 PTDVAKHISQIIERYNIKTLITFDNKGISGHPNHIACYEGAMKIVKATPQVQVFVLESVN 175 Sbjct: 119 NGQIGRATGDAMIKAGLKKAVTV-------TWKYAAGEEMVSGFKKSFTAGKGEVVKDIT 171 Query: 176 IFRKYISYLDTIPTLVQSQAGRNDTIIIHADRKSTQRIRDAMVRGHKSQMVWFRYGWIYL 235 Sbjct: 172 IAFPDVEFQSALAEIASLKP---DCVYAFF---SGGGALKFIKDYAAANLGIPLWGPGFL 225 Query: 236 SKYMSNN 242 Sbjct: 226 TDGVEAA 232 >gi|113709 [8..375] Periplasmic binding protein-like I Length = 368 Score = 24.7 bits (53), Expect = 1.5 Identities = 15/121 (12%), Positives = 15/121 (12%), Gaps = 12/121 (9%) Query: 116 PTDVAKHISQIIERYNIKTLITFDNKGISGHPNHIACYEGAMKIVKATPQVQVFVLESVN 175 Sbjct: 118 NQNSAPLAAYLIRHYGERVVFIGS--------DYIYPRESNHVMRHLYRQHGGTVL-EEI 168 Query: 176 IFRKYISYLDTIPTLVQSQAGRNDTIIIHADRKSTQRIRDAMVRGHKSQMVWFRYGWIYL 235 Sbjct: 169 YIPLYPSDDDLQRAVERIYQARADVVFSTV---VGTGTAELYRAIARRYGDGRRPPIASL 225 Query: 236 S 236 Sbjct: 226 T 226 >gi|118558 [166..782] 7-bladed beta-propeller Length = 617 Score = 24.5 bits (53), Expect = 1.8 Identities = 11/67 (16%), Positives = 11/67 (16%), Gaps = 5/67 (7%) Query: 91 YQIDKTNVHVVSDPQLQDGMQA-KWDPTDVAKHIS--QIIERYNIKTLITFDNKGISGHP 147 Sbjct: 339 FVLDRRNGQPIVPVTEKPVPQTVKRGPQTKGEFYSKTQPFSDLNLAPQDKLTDKDMWGAT 398 Query: 148 N--HIAC 152 Sbjct: 399 MLDQLMC 405 >gi|97186 [16..330] S-adenosyl-L-methionine-dependent methyltransferases Length = 315 Score = 24.1 bits (52), Expect = 2.1 Identities = 8/49 (16%), Positives = 8/49 (16%) Query: 176 IFRKYISYLDTIPTLVQSQAGRNDTIIIHADRKSTQRIRDAMVRGHKSQ 224 Sbjct: 185 LKQNIVSVEQAIGNLPSIESGKHSGLKWHYGRGHTEQQIEWMKHTPTGK 233 >gi|2497537 [381..517] Pyruvate kinase, C-terminal domain Length = 137 Score = 23.7 bits (51), Expect = 3.0 Identities = 8/55 (14%), Positives = 8/55 (14%), Gaps = 3/55 (5%) Query: 115 DPTD-VAKHISQIIERYNIKTLITFDNKGISGHPNHIACYEGAMKIVKATPQVQV 168 Sbjct: 11 DTVESIAMAAVSASLELNAGAIVVLTTSGKTAR--YLSKYRPVCPIVMVTRNPAA 63 >gi|1346693 [1..313] Phosphofructokinase Length = 313 Score = 23.7 bits (51), Expect = 3.6 Identities = 14/63 (22%), Positives = 14/63 (22%), Gaps = 3/63 (4%) Query: 39 AHPDDESMFFGPTIDYLGNQHSTRVHVLCLSNGNADGLGSVREKELVVAASKYQIDKTNV 98 Sbjct: 58 AVRAHYDRLFSFGGSPIG---NSRVKLTNVKDLVARGLVASGDDPLKVAADQLIADGVDV 114 Query: 99 HVV 101 Sbjct: 115 LHT 117 >gi|127428 [1..429] S-adenosyl-L-methionine-dependent methyltransferases Length = 429 Score = 23.0 bits (49), Expect = 5.4 Identities = 11/71 (15%), Positives = 11/71 (15%), Gaps = 9/71 (12%) Query: 107 QDGMQAKWDPTDVAKHISQIIERYNIKTLI-TFDNKGISG--HPNHIACYEGAMKIVKAT 163 Sbjct: 87 RDGMEYKCSN----CSHEHLITYEDYKKGVKCPKCEAVSKAKDERGTLFFE-TALLAEEK 141 Query: 164 PQVQVFVLESV 174 Sbjct: 142 -KPKFVILENV 151 >gi|1351184 [55..290] ATP pyrophoshatases Length = 236 Score = 22.9 bits (49), Expect = 6.2 Identities = 8/68 (11%), Positives = 8/68 (11%), Gaps = 4/68 (5%) Query: 76 LGSVREKELVVAASKYQIDKTNVHVVSDPQLQDGMQAKWDPTDVAKH--ISQIIERYNIK 133 Sbjct: 112 NGLEYYRNRCALTEDVPSGKYTPRNNFNWWKDIKMLD--FLADFGRHIRVQSMLARDSIS 169 Query: 134 TLITFDNK 141 Sbjct: 170 SRLQTKNG 177 >gi|1929419 [192..338] Periplasmic binding protein-like I Length = 147 Score = 22.6 bits (48), Expect = 7.2 Identities = 7/33 (21%), Positives = 7/33 (21%) Query: 112 AKWDPTDVAKHISQIIERYNIKTLITFDNKGIS 144 Sbjct: 26 SKCDPGQATKYLYELLYNDPIKIILMPGCSSVS 58 >gi|534844 [150..604] beta/alpha (TIM)-barrel Length = 455 Score = 22.3 bits (47), Expect = 8.1 Identities = 15/114 (13%), Positives = 15/114 (13%), Gaps = 13/114 (11%) Query: 28 KLAVESILFVFAHPDDESMFFGPTIDYLGNQHSTRVHVLCLSNGNADGLGSVREKELVVA 87 Sbjct: 260 TTLLKTQPALAWTLDELAAVKG-KCDFFGVDPYTYN--------TIKPLDNGTASCEANV 310 Query: 88 ASKYQIDKTNVHVVSDPQLQDGMQAKW----DPTDVAKHISQIIERYNIKTLIT 137 Sbjct: 311 TDTYWPTCVNVTVTEADNWSIGYRSQSYVYITPRQLRVSLNYIWQHWHVPIFIT 364 >gi|2145626 [13..324] beta/alpha (TIM)-barrel Length = 312 Score = 22.0 bits (46), Expect = 9.0 Identities = 11/39 (28%), Positives = 11/39 (28%), Gaps = 3/39 (7%) Query: 119 VAKHISQIIERYNIKTLITFDNKGI-SGHP--NHIACYE 154 Sbjct: 116 MSREIAELAIRFRDKGVVGFDIAGAEAGHPPTRHLDAFE 154 Underlying Matrix: BLOSUM62 Number of sequences tested against query: 1187 Number of sequences better than 10.0: 11 Number of calls to ALIGN: 11 Length of query: 248 Total length of test sequences: 256703 Effective length of test sequences: 208388.0 Effective search space size: 43265876.1 Initial X dropoff for ALIGN: 25.0 bits ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ calculation of internal repeats with prospero ***** PROSPERO v1.3 Fri Mar 8 14:31:56 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 PIGL_SCHPO 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: PIGL_SCHPO.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: PIGL_SCHPO 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: PIGL_SCHPO.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: PIGL_SCHPO 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: PIGL_SCHPO.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: PIGL_SCHPO 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: PIGL_SCHPO.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: PIGL_SCHPO Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- COG2120 -55.0 0.00055 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- COG2120 1/1 1 235 [. 1 317 [] -55.0 0.00055 Alignments of top-scoring domains: COG2120: domain 1 of 1, from 1 to 235: score -55.0, E = 0.00055 *->mfeinspleeaffkllreVlemtstsplaselrvLavfpHPDDEsiG m + s+l l e s+ + + + +L+vf+HPDDEs PIGL_SCHPO 1 MIWFWSTLLVTAIAVLSTANESSSGQEKLAVESILFVFAHPDDESMF 47 cGGTLakyaaaG.veVglvclTlGEmGenltqplldthetlgeiRreEla G T+ + + +++V+++cl + +++ lg +R++El+ PIGL_SCHPO 48 FGPTIDYLGNQHsTRVHVLCL------------SNGNADGLGSVREKELV 85 eAArvLGvekrillglgsrypDggLe....tepddqearvdlvqaqtalv AA++ ++k+ D +L ++ + d ++++ + q PIGL_SCHPO 86 VAASKYQIDKTNVHV----VSDPQLQdgmqAKWDPTDVAKHISQ------ 125 atdLravirelrPhvVltpdPwnGgdgHPDHrathelavaAvasagipkr +i++ + ++++t+d G gHP H+a++e a v ++++ PIGL_SCHPO 126 ------IIERYNIKTLITFDN-KGISGHPNHIACYEGAMKIVKATPQVQV 168 pndwgvsaavayytdlgasplqagsryqlnatldPdvllltsdelavtqk + ++ ++ + y + + P+++ PIGL_SCHPO 169 F---------------VLESVNIFRKYISYLDTIPTLV------------ 191 vvdisavaevKlaAiraHrtQfadtalferafplenerlelrveaaltwy ++Q++ +++ + ++ t++ PIGL_SCHPO 192 ------------------QSQAGRNDTIIIHADRKS-----------TQR 212 gleagvtyaegfrgeeslllailgl<-* + a v++ + + + ++ +l PIGL_SCHPO 213 IRDAMVRGHKSQMVWFR--YGWIYL 235 // 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: PIGL_SCHPO.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: PIGL_SCHPO Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- COG2120 7.0 0.39 1 COG0061 0.4 58 1 COG1005 -0.2 50 1 COG1992 -0.4 63 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- COG1005 1/1 8 20 .. 368 380 .] -0.2 50 COG2120 1/1 34 45 .. 34 45 .. 7.0 0.39 COG1992 1/1 115 130 .. 176 191 .] -0.4 63 COG0061 1/1 138 180 .. 1 47 [. 0.4 58 Alignments of top-scoring domains: COG1005: domain 1 of 1, from 8 to 20: score -0.2, E = 50 *->lvltAalvllviq<-* l++tA+ vl++++ PIGL_SCHPO 8 LLVTAIAVLSTAN 20 COG2120: domain 1 of 1, from 34 to 45: score 7.0, E = 0.39 *->vLavfpHPDDEs<-* +L+vf+HPDDEs PIGL_SCHPO 34 ILFVFAHPDDES 45 COG1992: domain 1 of 1, from 115 to 130: score -0.4, E = 63 *->nAveVvrklrlilrky<-* ++ +V++ + i+++y PIGL_SCHPO 115 DPTDVAKHISQIIERY 130 COG0061: domain 1 of 1, from 138 to 180: score 0.4, E = 58 *->vk.igIvgrpdreelalktaeelyewlkknfrgvtvevdeevaeele + + gI g+p++ +++ a+++++ + v+v+v e+v ++++ PIGL_SCHPO 138 FDnKGISGHPNHIA-CYEGAMKIVKATPQ----VQVFVLESVNIFRK 179 e<-* + PIGL_SCHPO 180 Y 180 //