analysis of sequence from tem13 ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ >sp|P04216|THY1_HUMAN THY-1 MEMBRANE GLYCOPROTEIN PRECURSOR (THY-1 ANTIGEN) (CDW90) (CD90 ANTIGEN) - Homo sapiens (Human). MNLAISIALLLTVLQVSRGQKVTSLTACLVDQSLRLDCRHENTSSSPIQY EFSLTRETKKHVLFGTVGVPEHTYRSRTNFTSKYHMKVLYLSAFTSKDEG TYTCALHHSGHSPPISSQNVTVLRDKLVKCEGISLLAQNTSWLLLLLLSL SLLQATDFMSL ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ sec.str. with predator > sp|P04216|THY1_HUMAN . . . . . 1 MNLAISIALLLTVLQVSRGQKVTSLTACLVDQSLRLDCRHENTSSSPIQY 50 ___HHHHHHHHHHHHH_____EEE__HHHHHHHHHHHHH_________HH . . . . . 51 EFSLTRETKKHVLFGTVGVPEHTYRSRTNFTSKYHMKVLYLSAFTSKDEG 100 HHHHHHHH___EEE__________________HHHHHHHHHEEE______ . . . . . 101 TYTCALHHSGHSPPISSQNVTVLRDKLVKCEGISLLAQNTSWLLLLLLSL 150 _EEEEEE_____________HHHHHHH______EEE____HHHHHHHHHH . 151 SLLQATDFMSL 161 HHHHHHH____ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ method : 1 alpha-contents : 24.9 % beta-contents : 53.1 % coil-contents : 22.1 % class : mixed method : 2 alpha-contents : 15.9 % beta-contents : 54.8 % coil-contents : 29.4 % class : mixed ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ GPI: learning from metazoa -5.17 -0.80 -0.02 -0.02 -4.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 -10.01 13.72 -0.80 -0.65 -0.06 0.00 0.00 0.00 -4.55 -0.14 0.00 0.00 0.00 0.00 0.00 0.00 0.00 7.51 ID: sp|P04216|THY1_HUMAN AC: xxx Len: 150 1:D 130 Sc: 7.51 Pv: 8.453277e-03 2:N 133 Sc: -10.01 Pv: 2.366370e-02 GPI: learning from protozoa -14.43 -0.72 0.00 0.00 -4.00 0.00 0.00 -2.48 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 -21.64 -9.81 -0.83 -0.01 0.00 -4.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 -14.65 ID: sp|P04216|THY1_HUMAN AC: xxx Len: 150 1:N 133 Sc: -14.65 Pv: 2.426271e-02 NO_GPI_SITE ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ # SignalP euk predictions # name Cmax pos ? Ymax pos ? Smax pos ? Smean ? sp|P04216|T 1.000 20 Y 0.852 20 Y 0.982 151 Y 0.874 Y # SignalP gram- predictions # name Cmax pos ? Ymax pos ? Smax pos ? Smean ? sp|P04216|T 0.399 156 N 0.469 156 Y 0.964 2 Y 0.319 N # SignalP gram+ predictions # name Cmax pos ? Ymax pos ? Smax pos ? Smean ? sp|P04216|T 0.517 156 Y 0.496 156 Y 0.971 151 Y 0.347 N ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ low complexity regions: SEG 12 2.2 2.5 >sp|P04216|THY1_HUMAN THY-1 MEMBRANE GLYCOPROTEIN PRECURSOR (THY-1 ANTIGEN) (CDW90) (CD90 ANTIGEN) - Homo sapiens (Human). 1-133 MNLAISIALLLTVLQVSRGQKVTSLTACLV DQSLRLDCRHENTSSSPIQYEFSLTRETKK HVLFGTVGVPEHTYRSRTNFTSKYHMKVLY LSAFTSKDEGTYTCALHHSGHSPPISSQNV TVLRDKLVKCEGI sllaqntswllllllslsll 134-153 154-161 QATDFMSL low complexity regions: SEG 25 3.0 3.3 >sp|P04216|THY1_HUMAN THY-1 MEMBRANE GLYCOPROTEIN PRECURSOR (THY-1 ANTIGEN) (CDW90) (CD90 ANTIGEN) - Homo sapiens (Human). 1-133 MNLAISIALLLTVLQVSRGQKVTSLTACLV DQSLRLDCRHENTSSSPIQYEFSLTRETKK HVLFGTVGVPEHTYRSRTNFTSKYHMKVLY LSAFTSKDEGTYTCALHHSGHSPPISSQNV TVLRDKLVKCEGI sllaqntswllllllslsll 134-153 154-161 QATDFMSL low complexity regions: SEG 45 3.4 3.75 >sp|P04216|THY1_HUMAN THY-1 MEMBRANE GLYCOPROTEIN PRECURSOR (THY-1 ANTIGEN) (CDW90) (CD90 ANTIGEN) - Homo sapiens (Human). 1-161 MNLAISIALLLTVLQVSRGQKVTSLTACLV DQSLRLDCRHENTSSSPIQYEFSLTRETKK HVLFGTVGVPEHTYRSRTNFTSKYHMKVLY LSAFTSKDEGTYTCALHHSGHSPPISSQNV TVLRDKLVKCEGISLLAQNTSWLLLLLLSL SLLQATDFMSL 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 >sp|P04216|THY1_HUMAN THY-1 MEMBRANE GLYCOPROTEIN PRECURSOR (THY-1 ANTIGEN) (CDW90) (CD90 ANTIGEN) - Homo sapiens (Human). MNLAISIALLLTVLQVSRGQKVTSLTACLVDQSLRLDCRHENTSSSPIQYEFSLTRETKK HVLFGTVGVPEHTYRSRTNFTSKYHMKVLYLSAFTSKDEGTYTCALHHSGHSPPISSQNV TVLRDKLVKCEGISLLAQNTSWllllllslslLQATDFMSL 1 - 142 MNLAISIALL LTVLQVSRGQ KVTSLTACLV DQSLRLDCRH ENTSSSPIQY EFSLTRETKK HVLFGTVGVP EHTYRSRTNF TSKYHMKVLY LSAFTSKDEG TYTCALHHSG HSPPISSQNV TVLRDKLVKC EGISLLAQNT SW 143 - 152 llllllsl sl 153 - 161 LQATDFMS L low complexity regions: DUST >sp|P04216|THY1_HUMAN THY-1 MEMBRANE GLYCOPROTEIN PRECURSOR (THY-1 ANTIGEN) (CDW90) (CD90 ANTIGEN) - Homo sapiens (Human). MNLAISIALLLTVLQVSRGQKVTSLTACLVDQSLRLDCRHENTSSSPIQYEFSLTRETKK HVLFGTVGVPEHTYRSRTNFTSKYHMKVLYLSAFTSKDEGTYTCALHHSGHSPPISSQNV TVLRDKLVKCEGISLLAQNTSWLLLLLLSLSLLQATDFMSL ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ coiled coil prediction for sp|P04216|THY1_HUMAN sequence: 150 amino acids, 0 residue(s) in coiled coil state . | . | . | . | . | . 60 MNLAISIALL LTVLQVSRGQ KVTSLTACLV DQSLRLDCRH ENTSSSPIQY EFSLTRETKK ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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 HVLFGTVGVP EHTYRSRTNF TSKYHMKVLY LSAFTSKDEG TYTCALHHSG HSPPISSQNV ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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 . | . | . | TVLRDKLVKC EGISLLAQNT SWLLLLLLSL ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ---------- ---------- ---------- ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ prediction of transmembrane regions with toppred2 *********************************** *TOPPREDM with eukaryotic function* *********************************** tem13.___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: tem13.___inter___ (1 sequences) MNLAISIALLLTVLQVSRGQKVTSLTACLVDQSLRLDCRHENTSSSPIQY EFSLTRETKKHVLFGTVGVPEHTYRSRTNFTSKYHMKVLYLSAFTSKDEG TYTCALHHSGHSPPISSQNVTVLRDKLVKCEGISLLAQNTSWLLLLLLSL SLLQATDFMSL (p)rokaryotic or (e)ukaryotic: e Charge-pair energy: 0 Length of full window (odd number!): 21 Length of core window (odd number!): 11 Number of residues to add to each end of helix: 1 Critical length: 60 Upper cutoff for candidates: 1 Lower cutoff for candidates: 0.6 Total of 2 structures are to be tested Candidate membrane-spanning segments: Helix Begin End Score Certainity 1 1 21 0.799 Putative 2 136 156 1.433 Certain ---------------------------------------------------------------------- Structure 1 Transmembrane segments included in this structure: Segment 1 2 Loop length 0 114 5 K+R profile 1.00 0.00 + CYT-EXT prof - - 0.55 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 1.00 Tm probability: 0.50 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): -2.00 (NEG-POS)/(NEG+POS): 1007125513474669412352.0000 NEG: 0.0000 POS: 0.0000 -> Orientation: N-out CYT-EXT difference: -0.55 -> Orientation: N-in ---------------------------------------------------------------------- Structure 2 Transmembrane segments included in this structure: Segment 2 Loop length 135 5 K+R profile + 0.00 CYT-EXT prof 0.57 - 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): -0.2000 NEG: 10.0000 POS: 15.0000 -> Orientation: N-in CYT-EXT difference: 0.57 -> Orientation: N-out ---------------------------------------------------------------------- "tem13" 161 1 21 #f 0.798958 136 156 #t 1.43333 ************************************ *TOPPREDM with prokaryotic function* ************************************ tem13.___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: tem13.___inter___ (1 sequences) MNLAISIALLLTVLQVSRGQKVTSLTACLVDQSLRLDCRHENTSSSPIQY EFSLTRETKKHVLFGTVGVPEHTYRSRTNFTSKYHMKVLYLSAFTSKDEG TYTCALHHSGHSPPISSQNVTVLRDKLVKCEGISLLAQNTSWLLLLLLSL SLLQATDFMSL (p)rokaryotic or (e)ukaryotic: p Charge-pair energy: 0 Length of full window (odd number!): 21 Length of core window (odd number!): 11 Number of residues to add to each end of helix: 1 Critical length: 60 Upper cutoff for candidates: 1 Lower cutoff for candidates: 0.6 Total of 2 structures are to be tested Candidate membrane-spanning segments: Helix Begin End Score Certainity 1 1 21 0.799 Putative 2 136 156 1.433 Certain ---------------------------------------------------------------------- Structure 1 Transmembrane segments included in this structure: Segment 1 2 Loop length 0 114 5 K+R profile 1.00 0.00 + CYT-EXT prof - - 0.55 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 1.00 Tm probability: 0.50 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): -2.00 (NEG-POS)/(NEG+POS): 1007125513474669412352.0000 NEG: 0.0000 POS: 0.0000 -> Orientation: N-out CYT-EXT difference: -0.55 -> Orientation: N-in ---------------------------------------------------------------------- Structure 2 Transmembrane segments included in this structure: Segment 2 Loop length 135 5 K+R profile + 0.00 CYT-EXT prof 0.57 - 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): -0.2000 NEG: 10.0000 POS: 15.0000 -> Orientation: N-in CYT-EXT difference: 0.57 -> Orientation: N-out ---------------------------------------------------------------------- "tem13" 161 1 21 #f 0.798958 136 156 #t 1.43333 ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ NOW EXECUTING: /bio_software/1D/stat/saps/saps-stroh/SAPS.SSPA/saps /people/maria/tem13.___saps___ SAPS. Version of April 11, 1996. Date run: Tue Oct 31 14:32:39 2000 File: /people/maria/tem13.___saps___ ID sp|P04216|THY1_HUMAN DE THY-1 MEMBRANE GLYCOPROTEIN PRECURSOR (THY-1 ANTIGEN) (CDW90) (CD90 ANTIGEN) - Homo sapiens (Human). number of residues: 161; molecular weight: 18.0 kdal 1 MNLAISIALL LTVLQVSRGQ KVTSLTACLV DQSLRLDCRH ENTSSSPIQY EFSLTRETKK 61 HVLFGTVGVP EHTYRSRTNF TSKYHMKVLY LSAFTSKDEG TYTCALHHSG HSPPISSQNV 121 TVLRDKLVKC EGISLLAQNT SWLLLLLLSL SLLQATDFMS L -------------------------------------------------------------------------------- COMPOSITIONAL ANALYSIS (extremes relative to: swp23s) A : 7( 4.3%); C : 4( 2.5%); D : 5( 3.1%); E : 6( 3.7%); F : 5( 3.1%) G : 6( 3.7%); H : 7( 4.3%); I : 5( 3.1%); K : 8( 5.0%); L : 28(17.4%) M : 3( 1.9%); N : 5( 3.1%); P : 4( 2.5%); Q : 7( 4.3%); R : 7( 4.3%) S : 21(13.0%); T : 16( 9.9%); V : 11( 6.8%); W : 1( 0.6%); Y : 5( 3.1%) KR : 15 ( 9.3%); ED : 11 ( 6.8%); AGP : 17 ( 10.6%); KRED : 26 ( 16.1%); KR-ED : 4 ( 2.5%); FIKMNY : 31 ( 19.3%); LVIFM : 52 ( 32.3%); ST : 37 ( 23.0%). -------------------------------------------------------------------------------- CHARGE DISTRIBUTIONAL ANALYSIS 1 0000000000 0000000+00 +000000000 -000+0-0+0 -000000000 -0000+-0++ 61 0000000000 -000+0+000 00+000+000 000000+--0 0000000000 0000000000 121 000+-+00+0 -000000000 0000000000 000000-000 0 A. CHARGE CLUSTERS. Positive charge clusters (cmin = 9/30 or 11/45 or 14/60): none Negative charge clusters (cmin = 7/30 or 9/45 or 11/60): none Mixed charge clusters (cmin = 12/30 or 17/45 or 21/60): 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 | 5 | 45 | 8 | 8 | 10 | 10 | 9 | 13 | 7 | 9 | lmin1 5 | 5 | 7 | 54 | 10 | 9 | 13 | 13 | 11 | 15 | 9 | 11 | lmin2 6 | 6 | 8 | 60 | 12 | 11 | 14 | 14 | 13 | 17 | 10 | 12 | (Significance level: 0.010000; Minimal displayed length: 6) There are no charge runs or patterns exceeding the given minimal lengths. Run count statistics: + runs >= 3: 0 - runs >= 3: 0 * runs >= 3: 2, at 97; 124; 0 runs >= 30: 0 -------------------------------------------------------------------------------- DISTRIBUTION OF OTHER AMINO ACID TYPES 1. HIGH SCORING SEGMENTS. There are no high scoring hydrophobic segments. There are no high scoring transmembrane segments. 2. SPACINGS OF C. H2N-27-C-9-C-65-C-25-C-31-COOH 2*. SPACINGS OF C and H. (additional deluxe function for ALEX) H2N-27-C-9-C-1-H-20-H-10-H-12-H-18-C-2-H-H-2-H-18-C-31-COOH -------------------------------------------------------------------------------- REPETITIVE STRUCTURES. A. SEPARATED, TANDEM, AND PERIODIC REPEATS: amino acid alphabet. Repeat core block length: 4 Aligned matching blocks: [ 80- 83] FTSK [ 94- 97] FTSK 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: 9 (Expected range: 1-- 22) 2. Histogram of spacings between consecutive amino acid multiplets: (1-5) 3 (6-10) 3 (11-20) 2 (>=21) 2 3. Clusters of amino acid multiplets (cmin = 11/30 or 14/45 or 16/60): none 4. Long amino acid multiplets (>= 5; Letter/Length/Position): L/6/143 B. CHARGE ALPHABET. 1. Total number of charge multiplets: 2 (Expected range: 0-- 7) 1 +plets (f+: 9.3%), 1 -plets (f-: 6.8%) Total number of charge altplets: 3 (Critica l number: 8) 2. Histogram of spacings between consecutive charge multiplets: (1-5) 0 (6-10) 0 (11-20) 0 (>=21) 3 -------------------------------------------------------------------------------- PERIODICITY ANALYSIS. A. AMINO ACID ALPHABET (core: 4; !-core: 5) Location Period Element Copies Core Errors 143- 148 1 L 6 6 ! 0 144- 153 2 L. 5 5 ! 0 B. CHARGE ALPHABET ({+= KR; -= ED; 0}; core: 5; !-core: 5) and HYDROPHOBICITY ALPHABET ({*= KRED; i= LVIF; 0}; core: 6; !-core: 8) Location Period Element Copies Core Errors 1- 14 2 i0 7 7 /0/2/ 143- 148 1 i 6 6 0 -------------------------------------------------------------------------------- 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: tem13 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: sp|P04216|THY1_HUMAN THY-1 MEMBRANE GLYCOPROTEIN PRECURSOR (THY-1 ANTIGEN) (CDW90) (CD90 ANTIGEN) - Homo sapiens (Human). Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- ig Immunoglobulin domain 26.8 9.5e-07 1 Ribosomal_S19 Ribosomal protein S19 6.8 1.4 1 phytochrome Phytochrome region -1.4 83 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- Ribosomal_S19 1/1 51 61 .. 71 81 .] 6.8 1.4 ig 1/1 31 106 .. 1 45 [] 26.8 9.5e-07 phytochrome 1/1 127 144 .. 30 47 .. -1.4 83 Alignments of top-scoring domains: Ribosomal_S19: domain 1 of 1, from 51 to 61: score 6.8, E = 1.4 *->EFapTRkfrgH<-* EF++TR +++H sp|P04216| 51 EFSLTRETKKH 61 ig: domain 1 of 1, from 31 to 106: score 26.8, E = 9.5e-07 *->GesvtLtCsvs..gfgpp.p.vtWlrngk.................. +s++L C+ +++++p +++++++r+ k++ ++ + ++++ +++ sp|P04216| 31 DQSLRLDCRHEntSSSPIqYeFSLTRETKkhvlfgtvgvpehtyrsr 77 .........lslti.svtpeDsgGtYtCvv<-* ++ +++ + +l ++ +t+ D+ GtYtC+ sp|P04216| 78 tnftskyhmKVLYLsAFTSKDE-GTYTCAL 106 phytochrome: domain 1 of 1, from 127 to 144: score -1.4, E = 83 *->LvkCDGAALyYkkkvwrl<-* LvkC+G L+ ++ w+l sp|P04216| 127 LVKCEGISLLAQNTSWLL 144 // 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: tem13 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: sp|P04216|THY1_HUMAN THY-1 MEMBRANE GLYCOPROTEIN PRECURSOR (THY-1 ANTIGEN) (CDW90) (CD90 ANTIGEN) - Homo sapiens (Human). Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- ig Immunoglobulin domain 26.8 9.5e-07 1 Ribosomal_S19 Ribosomal protein S19 6.8 1.4 1 DUF138 Domain of unknown function DUF138 0.2 73 1 phytochrome Phytochrome region -1.4 83 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- Ribosomal_S19 1/1 51 61 .. 71 81 .] 6.8 1.4 DUF138 1/1 74 99 .. 1 29 [. 0.2 73 ig 1/1 31 106 .. 1 45 [] 26.8 9.5e-07 phytochrome 1/1 127 144 .. 30 47 .. -1.4 83 Alignments of top-scoring domains: Ribosomal_S19: domain 1 of 1, from 51 to 61: score 6.8, E = 1.4 *->EFapTRkfrgH<-* EF++TR +++H sp|P04216| 51 EFSLTRETKKH 61 DUF138: domain 1 of 1, from 74 to 99: score 0.2, E = 73 *->wskklkski.erylyheevslLaAYvyedq<-* + s+++++++yh +v L+A+ ++d+ sp|P04216| 74 YR----SRTnFTSKYHMKVLYLSAFTSKDE 99 ig: domain 1 of 1, from 31 to 106: score 26.8, E = 9.5e-07 *->GesvtLtCsvs..gfgpp.p.vtWlrngk.................. +s++L C+ +++++p +++++++r+ k++ ++ + ++++ +++ sp|P04216| 31 DQSLRLDCRHEntSSSPIqYeFSLTRETKkhvlfgtvgvpehtyrsr 77 .........lslti.svtpeDsgGtYtCvv<-* ++ +++ + +l ++ +t+ D+ GtYtC+ sp|P04216| 78 tnftskyhmKVLYLsAFTSKDE-GTYTCAL 106 phytochrome: domain 1 of 1, from 127 to 144: score -1.4, E = 83 *->LvkCDGAALyYkkkvwrl<-* LvkC+G L+ ++ w+l sp|P04216| 127 LVKCEGISLLAQNTSWLL 144 // 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: tem13 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: sp|P04216|THY1_HUMAN THY-1 MEMBRANE GLYCOPROTEIN PRECURSOR (THY-1 ANTIGEN) (CDW90) (CD90 ANTIGEN) - Homo sapiens (Human). 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 Oct 31 14:34:32 2000 Sequence file: tem13 ---------------------------------------- Sequence sp|P04216|THY1_HUMAN (161 residues): Matching pattern PS00001 ASN_GLYCOSYLATION: 42: NTSS 79: NFTS 119: NVTV 139: NTSW Total matches: 4 Matching pattern PS00005 PKC_PHOSPHO_SITE: 33: SLR 58: TKK 73: TYR 81: TSK 95: TSK Total matches: 5 Matching pattern PS00006 CK2_PHOSPHO_SITE: 95: TSKD 96: SKDE Total matches: 2 Matching pattern PS00008 MYRISTYL: 19: GQKVTS 100: GTYTCA Total matches: 2 Total no of hits in this sequence: 13 ======================================== 1314 pattern(s) searched in 1 sequence(s), 161 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 ***** argv[1]=P argv[2]=-m /data/patterns/own/motif.fa argv[4]=-seq tem13 ***** 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, 161 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: tem13 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: sp|P04216|THY1_HUMAN THY-1 MEMBRANE GLYCOPROTEIN PRECURSOR (THY-1 ANTIGEN) (CDW90) (CD90 ANTIGEN) - Homo sapiens (Human). 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: tem13 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: sp|P04216|THY1_HUMAN THY-1 MEMBRANE GLYCOPROTEIN PRECURSOR (THY-1 ANTIGEN) (CDW90) (CD90 ANTIGEN) - Homo sapiens (Human). 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 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= sp|P04216|THY1_HUMAN THY-1 MEMBRANE GLYCOPROTEIN PRECURSOR (THY-1 ANTIGEN) (CDW90) (CD90 ANTIGEN) - Homo sapiens (Human). (161 letters) Searching..................................done Results from profile search Score E Sequences producing significant alignments: (bits) Value MATH The Meprin associated TRAF homology domain 22 0.55 CYCL cyclophilin like peptidyl prolyl isomerases 22 0.68 HISDAC Histone deacetylase domain 21 1.2 DHHC Novel zinc finger domain with DHHC signature 19 5.3 ACTIN Actin ATPase/ Cytoskeletal ATPase domain 19 5.4 PAP Papain/bleomycin hydrolase like domain 18 5.6 PBD Rho binding domain 19 5.8 INSL Insulinase like Metallo protease domain 18 7.2 UBHYD Ubiquitin C-terminal hydrolase domain 18 7.6 ARR Arrestin domain 18 8.6 UBC Ubiquitin Conjugating enzyme domain 18 9.0 SET Su(var)3-9, Enhancer of Zeste, trithorax domain (A chrom... 18 9.1 HOMEO Homeodomain (HTH DNa binding domain) 18 10.0 >MATH The Meprin associated TRAF homology domain Length = 209 Score = 21.8 bits (46), Expect = 0.55 Identities = 4/23 (17%), Positives = 9/23 (38%) Query: 33 SLRLDCRHENTSSSPIQYEFSLT 55 L L + S ++ +F + Sbjct: 83 YLSLYLLLVSCPKSEVRAKFKFS 105 >CYCL cyclophilin like peptidyl prolyl isomerases Length = 165 Score = 21.7 bits (46), Expect = 0.68 Identities = 13/30 (43%), Positives = 18/30 (59%), Gaps = 7/30 (23%) Query: 42 NTSSSPIQYEFSLTRETK----KHVLFGTV 67 NT+ S Q+ F T +T+ KHV+FG V Sbjct: 106 NTNGS--QF-FICTAKTEWLDGKHVVFGKV 132 >HISDAC Histone deacetylase domain Length = 433 Score = 20.6 bits (43), Expect = 1.2 Identities = 13/43 (30%), Positives = 18/43 (41%), Gaps = 12/43 (27%) Query: 83 KYHMKVLYL-----------SAFTSKDEGTYTCALHHSGHSPP 114 +YH +VLY+ AF + D TC+ H G P Sbjct: 175 RYHPRVLYIDIDVHHGDGVEEAFYTTDR-VMTCSFHKYGEFFP 216 Score = 18.7 bits (38), Expect = 4.6 Identities = 5/40 (12%), Positives = 14/40 (34%), Gaps = 6/40 (15%) Query: 64 FGTVGVPEHTYRSRTNFTSKYHMKVLYLSAFTSKDEGTYT 103 G + + + N+ + + ++ + G YT Sbjct: 281 LGCFNLSMEGHANCVNYVKSFGIPMMVVG------GGGYT 314 >DHHC Novel zinc finger domain with DHHC signature Length = 217 Score = 18.5 bits (37), Expect = 5.3 Identities = 7/24 (29%), Positives = 12/24 (49%) Query: 95 TSKDEGTYTCALHHSGHSPPISSQ 118 T+ ++ +T SG SP + Q Sbjct: 14 TAPEKSVWTAPAQPSGPSPELQGQ 37 >ACTIN Actin ATPase/ Cytoskeletal ATPase domain Length = 376 Score = 18.6 bits (38), Expect = 5.4 Identities = 9/34 (26%), Positives = 12/34 (34%), Gaps = 3/34 (8%) Query: 79 NFTSKYHMKVLYLSAFTSKDEGTYTCALHHSGHS 112 N + Y LS + S G T + SG Sbjct: 129 NVPAMYVAIQAVLSLYAS---GRTTGIVLDSGDG 159 >PAP Papain/bleomycin hydrolase like domain Length = 376 Score = 18.4 bits (37), Expect = 5.6 Identities = 3/22 (13%), Positives = 9/22 (40%) Query: 100 GTYTCALHHSGHSPPISSQNVT 121 G+ TC + + + ++ Sbjct: 348 GSNTCGITKFPLTARVQKPDMK 369 >PBD Rho binding domain Length = 61 Score = 18.6 bits (37), Expect = 5.8 Identities = 7/11 (63%), Positives = 8/11 (72%) Query: 76 SRTNFTSKYHM 86 S TNFT K H+ Sbjct: 3 SPTNFTHKVHV 13 >INSL Insulinase like Metallo protease domain Length = 433 Score = 18.3 bits (37), Expect = 7.2 Identities = 6/14 (42%), Positives = 8/14 (56%) Query: 91 LSAFTSKDEGTYTC 104 ++A TSKD Y Sbjct: 94 INAGTSKDYTYYHV 107 >UBHYD Ubiquitin C-terminal hydrolase domain Length = 884 Score = 18.0 bits (36), Expect = 7.6 Identities = 21/64 (32%), Positives = 33/64 (50%), Gaps = 12/64 (18%) Query: 83 KYHMKVLYLSAFTSKDEGTYTCALHHSGH-SPPISSQNVTVLRDKL-VKCEGISLLAQNT 140 K H +L+L + K T +L++ GH PIS + +RD L V C+ + Q+T Sbjct: 463 KDHDVMLFLKMYDPK-----TRSLNYCGHIYTPISCK----IRDLLPVMCDRAGFI-QDT 512 Query: 141 SWLL 144 S +L Sbjct: 513 SLIL 516 >ARR Arrestin domain Length = 454 Score = 17.9 bits (36), Expect = 8.6 Identities = 6/14 (42%), Positives = 8/14 (56%) Query: 44 SSSPIQYEFSLTRE 57 SS + E SL +E Sbjct: 224 SSGLLHMEVSLDKE 237 >UBC Ubiquitin Conjugating enzyme domain Length = 144 Score = 17.8 bits (36), Expect = 9.0 Identities = 4/28 (14%), Positives = 8/28 (28%), Gaps = 2/28 (7%) Query: 62 VLFGTVGVPEH--TYRSRTNFTSKYHMK 87 + G G P +R + + Sbjct: 33 TIEGPEGTPYAGGLFRMKLLLGKDFPAS 60 >SET Su(var)3-9, Enhancer of Zeste, trithorax domain (A chromatin associated domain) Length = 219 Score = 18.0 bits (36), Expect = 9.1 Identities = 4/46 (8%), Positives = 9/46 (18%), Gaps = 1/46 (2%) Query: 20 QKVTSLTACLV-DQSLRLDCRHENTSSSPIQYEFSLTRETKKHVLF 64 V L + RL + + + + Sbjct: 46 AAVKQRIQRLCYREEKRLAVSSLAKWLGQLHKQRLRAPKNPPVAIC 91 >HOMEO Homeodomain (HTH DNa binding domain) Length = 65 Score = 17.8 bits (36), Expect = 10.0 Identities = 2/9 (22%), Positives = 4/9 (44%) Query: 75 RSRTNFTSK 83 + R F+ Sbjct: 7 KRRVLFSQA 15 Underlying Matrix: BLOSUM62 Number of sequences tested against query: 105 Number of sequences better than 10.0: 13 Number of calls to ALIGN: 14 Length of query: 161 Total length of test sequences: 20182 Effective length of test sequences: 16536.0 Effective search space size: 2086753.0 Initial X dropoff for ALIGN: 25.0 bits Y. Wolf's SCOP PSSM IMPALA version 1.1 [20-December-1999] Reference: Alejandro A. Schaffer, Yuri I. Wolf, Chris P. Ponting, Eugene V. Koonin, L. Aravind, Stephen F. Altschul (1999), "IMPALA: Matching a Protein Sequence Against a Collection of "PSI-BLAST-Constructed Position-Specific Score Matrices", Bioinformatics 15:1000-1011. Query= sp|P04216|THY1_HUMAN THY-1 MEMBRANE GLYCOPROTEIN PRECURSOR (THY-1 ANTIGEN) (CDW90) (CD90 ANTIGEN) - Homo sapiens (Human). (161 letters) Searching.................................................done Results from profile search Score E Sequences producing significant alignments: (bits) Value gi|1515350 [4..198] Cyclophilin 23 2.5 gi|1070649 [50..283] 4-bladed beta-propeller 23 3.1 gi|1166598 [22..183] alpha/beta-Hydrolases 23 3.3 gi|1083654 [20..356] 6-bladed beta-propeller 22 5.5 gi|2088814 [406..557] Cyclophilin 22 6.2 gi|435746 [11..204] 4-helical cytokines 22 7.5 gi|2136468 [19..195] Lipocalins 21 8.6 gi|1552874 [10..205] NAD(P)-binding Rossmann-fold domains 22 9.2 gi|1223762 [9..227] Galactose-binding domain-like 21 9.7 gi|1780973 [457..589] Ribonuclease H-like motif 21 9.8 >gi|1515350 [4..198] Cyclophilin Length = 195 Score = 23.3 bits (50), Expect = 2.5 Identities = 11/30 (36%), Positives = 15/30 (49%), Gaps = 7/30 (23%) Query: 42 NTSSSPIQYEFSLTRETK----KHVLFGTV 67 NT++S Q+ F T KH +FG V Sbjct: 135 NTNNS--QF-FITTYAAPHLNGKHSIFGQV 161 >gi|1070649 [50..283] 4-bladed beta-propeller Length = 234 Score = 22.9 bits (49), Expect = 3.1 Identities = 17/72 (23%), Positives = 23/72 (31%), Gaps = 12/72 (16%) Query: 49 QYEFS-----LTRETKKHVLFGTVGVPEHTYRSR-TNFTSKYHMKV-----LYLSAFTSK 97 F+ + V + P +RS N T H L LSA S Sbjct: 158 FLRFNPVSGEVPPGYPLDVRDYFLSCPGRGHRSSHRNSTQHGHESTRCDPDLVLSAMVSD 217 Query: 98 DEG-TYTCALHH 108 + G TY + H Sbjct: 218 NHGATYVFSGSH 229 >gi|1166598 [22..183] alpha/beta-Hydrolases Length = 162 Score = 22.9 bits (49), Expect = 3.3 Identities = 7/76 (9%), Positives = 20/76 (26%), Gaps = 8/76 (10%) Query: 62 VLFGTVGVPEHTYRSRTNFTSKYHMKVL----YLSAFTSKDEGTYTCALHHSGHSPPISS 117 + + T+ +++ ++ F + T A H++ Sbjct: 67 YAWSGPRSGDETFVKMLKEHVFEQYRIVRDGDFVPDFPLRISQTLPAAHHNTFEIYYPK- 125 Query: 118 QNVTVLRDKLVKCEGI 133 + D C+ Sbjct: 126 ---HMTTDNYRICDQA 138 >gi|1083654 [20..356] 6-bladed beta-propeller Length = 337 Score = 22.2 bits (47), Expect = 5.5 Identities = 11/46 (23%), Positives = 15/46 (31%), Gaps = 4/46 (8%) Query: 55 TRETKKHVLFGTVGVPEHTYRSRTNFTSKYHMKVLYLSAFTSKDEG 100 ++TK LF R + + V L TS D G Sbjct: 73 DKQTKTLFLFFIA----VPGRVSEQHQLQTRVNVTRLCRVTSTDYG 114 >gi|2088814 [406..557] Cyclophilin Length = 152 Score = 22.1 bits (47), Expect = 6.2 Identities = 5/30 (16%), Positives = 9/30 (29%), Gaps = 7/30 (23%) Query: 42 NTSSSPIQYEFSLTRETK----KHVLFGTV 67 SS + + L ++ G V Sbjct: 93 TVFSS--LF-YVLLDKSGPSVVDGCPIGDV 119 >gi|435746 [11..204] 4-helical cytokines Length = 194 Score = 21.8 bits (46), Expect = 7.5 Identities = 7/22 (31%), Positives = 10/22 (44%) Query: 137 AQNTSWLLLLLLSLSLLQATDF 158 A LL L +SLL++ Sbjct: 60 ALTLQQEQLLSLIMSLLRSWTP 81 >gi|2136468 [19..195] Lipocalins Length = 177 Score = 21.5 bits (45), Expect = 8.6 Identities = 3/53 (5%), Positives = 14/53 (25%), Gaps = 3/53 (5%) Query: 73 TYRSRTNFTSKYHMKVLYLSAFTSKDE--GTYTCALHHSGHSPPISSQNVTVL 123 T + R + + + + + E + + + ++ Sbjct: 56 TAKGRVRLLNNWDVCA-DMVGTFTDTEDPAKFKMKYWGVASFLQKGNDDHWII 107 >gi|1552874 [10..205] NAD(P)-binding Rossmann-fold domains Length = 196 Score = 21.5 bits (44), Expect = 9.2 Identities = 5/73 (6%), Positives = 14/73 (18%) Query: 36 LDCRHENTSSSPIQYEFSLTRETKKHVLFGTVGVPEHTYRSRTNFTSKYHMKVLYLSAFT 95 L C ++ ++ + + S + V ++ Sbjct: 30 LACLPDDPRREDAAAAMKQAGARSVELIDFDALDTDSHPKMIEAAFSGGDVDVAIVAFGL 89 Query: 96 SKDEGTYTCALHH 108 D Sbjct: 90 LGDAEELWQNQRK 102 >gi|1223762 [9..227] Galactose-binding domain-like Length = 219 Score = 21.3 bits (44), Expect = 9.7 Identities = 18/64 (28%), Positives = 26/64 (40%), Gaps = 13/64 (20%) Query: 72 HTYRSRTNFTS--KYHMKVLYLSAFTSKDEGTYTCALHHSGHSPPISSQNVTVLRDKLVK 129 H YR TS K H L F+ D LHH +P + +Q V +++ Sbjct: 95 HYYRRPAFSTSDDKQH-----LGMFSEADYNPVGSYLHHFDLTPALRNQRV------IIR 143 Query: 130 CEGI 133 EG+ Sbjct: 144 FEGV 147 >gi|1780973 [457..589] Ribonuclease H-like motif Length = 133 Score = 21.4 bits (45), Expect = 9.8 Identities = 6/26 (23%), Positives = 10/26 (38%), Gaps = 3/26 (11%) Query: 108 HSGHSPPISSQNVTVLRDKLVKCEGI 133 H+ P++ N D LV + Sbjct: 111 HTNLPGPLTKANEQA--DLLVS-SAL 133 Underlying Matrix: BLOSUM62 Number of sequences tested against query: 1187 Number of sequences better than 10.0: 10 Number of calls to ALIGN: 10 Length of query: 161 Total length of test sequences: 256703 Effective length of test sequences: 207231.0 Effective search space size: 24736309.4 Initial X dropoff for ALIGN: 25.0 bits