analysis of sequence from NP_176323.1.fa ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ >NP_176323.1 hypothetical protein [Arabidopsis thaliana]. mlslnqevhg pktsevygfv gsisivvatv ifliwgyvpd kflesigiyy ypskywamam pmysmvtllv alvfyiglnf mstskptsln tlfddysred vnflplmkng edrpidpisd iditrindlm fdshlak ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ sec.str. with predator > NP_176323.1 . . . . . 1 MLSLNQEVHGPKTSEVYGFVGSISIVVATVIFLIWGYVPDKFLESIGIYY 50 ______________EEEEEE_EEEEEEHHHHHHHH_______________ . . . . . 51 YPSKYWAMAMPMYSMVTLLVALVFYIGLNFMSTSKPTSLNTLFDDYSRED 100 ____________HHHHHHHHHHHHHHHH______________________ . . . 101 VNFLPLMKNGEDRPIDPISDIDITRINDLMFDSHLAK 137 ____________________________HHHHHH___ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ Warning no amino acid in given sequence!!! method : 1 alpha-contents : 18.3 % beta-contents : 30.7 % coil-contents : 51.0 % class : mixed method : 2 alpha-contents : 28.3 % beta-contents : 34.3 % coil-contents : 37.4 % class : mixed ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ GPI: learning from metazoa -35.19 -1.88 -0.37 -0.04 -4.00 0.00 0.00 0.00 -0.34 -4.29 -1.83 -12.00 -12.00 0.00 0.00 0.00 -71.95 -19.20 -1.13 -0.65 -2.26 -4.00 0.00 0.00 0.00 -0.20 -5.02 -1.83 -12.00 -12.00 0.00 -12.00 0.00 -70.28 ID: NP_176323.1 AC: xxx Len: 137 1:I 109 Sc: -70.28 Pv: 5.719716e-01 NO_GPI_SITE GPI: learning from protozoa -12.23 -0.98 -0.71 -0.59 -4.00 0.00 0.00 0.00 -0.15 -5.72 -7.17 -12.00 -12.00 0.00 -12.00 0.00 -67.54 -13.52 -1.14 -0.86 -0.01 -4.00 0.00 0.00 -0.35 -0.42 -4.03 -7.17 -12.00 -12.00 0.00 -12.00 0.00 -67.49 ID: NP_176323.1 AC: xxx Len: 137 1:I 118 Sc: -67.49 Pv: 3.115970e-01 NO_GPI_SITE ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ # SignalP euk predictions # name Cmax pos ? Ymax pos ? Smax pos ? Smean ? NP_176323.1 0.478 85 Y 0.600 85 Y 0.980 68 Y 0.460 N # SignalP gram- predictions # name Cmax pos ? Ymax pos ? Smax pos ? Smean ? NP_176323.1 0.212 137 N 0.259 85 N 0.945 66 Y 0.352 N # SignalP gram+ predictions # name Cmax pos ? Ymax pos ? Smax pos ? Smean ? NP_176323.1 0.284 87 N 0.340 87 N 0.960 65 Y 0.427 N ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ low complexity regions: SEG 12 2.2 2.5 >NP_176323.1 hypothetical protein [Arabidopsis thaliana]. 1-111 MLSLNQEVHGPKTSEVYGFVGSISIVVATV IFLIWGYVPDKFLESIGIYYYPSKYWAMAM PMYSMVTLLVALVFYIGLNFMSTSKPTSLN TLFDDYSREDVNFLPLMKNGE drpidpisdiditri 112-126 127-137 NDLMFDSHLAK low complexity regions: SEG 25 3.0 3.3 >NP_176323.1 hypothetical protein [Arabidopsis thaliana]. 1-137 MLSLNQEVHGPKTSEVYGFVGSISIVVATV IFLIWGYVPDKFLESIGIYYYPSKYWAMAM PMYSMVTLLVALVFYIGLNFMSTSKPTSLN TLFDDYSREDVNFLPLMKNGEDRPIDPISD IDITRINDLMFDSHLAK low complexity regions: SEG 45 3.4 3.75 >NP_176323.1 hypothetical protein [Arabidopsis thaliana]. 1-137 MLSLNQEVHGPKTSEVYGFVGSISIVVATV IFLIWGYVPDKFLESIGIYYYPSKYWAMAM PMYSMVTLLVALVFYIGLNFMSTSKPTSLN TLFDDYSREDVNFLPLMKNGEDRPIDPISD IDITRINDLMFDSHLAK 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 >NP_176323.1 hypothetical protein [Arabidopsis thaliana]. MLSLNQEVHGPKTSEVYGFVGSISIVVATVIFLIWGYVPDKFLESIGIYYYPSKYWAMAM PMYSMVTLLVALVFYIGLNFMSTSKPTSLNTLFDDYSREDVNFLPLMKNGEDRPIDPISD IDITRINDLMFDSHLAK 1 - 137 MLSLNQEVHG PKTSEVYGFV GSISIVVATV IFLIWGYVPD KFLESIGIYY YPSKYWAMAM PMYSMVTLLV ALVFYIGLNF MSTSKPTSLN TLFDDYSRED VNFLPLMKNG EDRPIDPISD IDITRINDLM FDSHLAK low complexity regions: DUST >NP_176323.1 hypothetical protein [Arabidopsis thaliana]. mlslnqevhgpktsevygfvgsisivvatvifliwgyvpdkflesigiyyypskywamam pmysmvtllvalvfyiglnfmstskptslntlfddysredvnflplmkngedrpidpisd iditrindlmfdshlak ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ coiled coil prediction for NP_176323.1 sequence: 137 amino acids, 0 residue(s) in coiled coil state . | . | . | . | . | . 60 mlslnqevhg pktsevygfv gsisivvatv ifliwgyvpd kflesigiyy ypskywamam ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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 pmysmvtllv alvfyiglnf mstskptsln tlfddysred vnflplmkng edrpidpisd ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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 . | . iditrindlm fdshlak ~~~~~~~~~~ ~~~~~~~ ---------- ------- ~~~~~~~~~~ ~~~~~~~ ~~~~~~~~~~ ~~~~~~~ ~~~~~~~~~~ ~~~~~~~ ~~~~~~~~~~ ~~~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ prediction of transmembrane regions with toppred2 *********************************** *TOPPREDM with eukaryotic function* *********************************** NP_176323.1.fa.___inter___ is a single sequence Using hydrophobicity file: /bio_software/2D/toppredm/lib/Engelman-Steitz.scale Using cyt/ext file: /bio_software/2D/toppredm/lib/Cyt-Ext.prok Using sequence file: NP_176323.1.fa.___inter___ (1 sequences) MLSLNQEVHGPKTSEVYGFVGSISIVVATVIFLIWGYVPDKFLESIGIYY YPSKYWAMAMPMYSMVTLLVALVFYIGLNFMSTSKPTSLNTLFDDYSRED VNFLPLMKNGEDRPIDPISDIDITRINDLMFDSHLAK (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 18 38 2.228 Certain 2 58 78 2.121 Certain ---------------------------------------------------------------------- Structure 1 Transmembrane segments included in this structure: Segment 1 2 Loop length 17 19 59 K+R profile 2.00 6.00 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): 0.00 (NEG-POS)/(NEG+POS): 0.3333 NEG: 2.0000 POS: 1.0000 -> Orientation: undecided CYT-EXT difference: 0.00 -> Orientation: undecided ---------------------------------------------------------------------- "NP_176323" 137 18 38 #t 2.22812 58 78 #t 2.12083 ************************************ *TOPPREDM with prokaryotic function* ************************************ NP_176323.1.fa.___inter___ is a single sequence Using hydrophobicity file: /bio_software/2D/toppredm/lib/Engelman-Steitz.scale Using cyt/ext file: /bio_software/2D/toppredm/lib/Cyt-Ext.prok Using sequence file: NP_176323.1.fa.___inter___ (1 sequences) MLSLNQEVHGPKTSEVYGFVGSISIVVATVIFLIWGYVPDKFLESIGIYY YPSKYWAMAMPMYSMVTLLVALVFYIGLNFMSTSKPTSLNTLFDDYSRED VNFLPLMKNGEDRPIDPISDIDITRINDLMFDSHLAK (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 18 38 2.228 Certain 2 58 78 2.121 Certain ---------------------------------------------------------------------- Structure 1 Transmembrane segments included in this structure: Segment 1 2 Loop length 17 19 59 K+R profile 1.00 6.00 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): 0.00 (NEG-POS)/(NEG+POS): 0.3333 NEG: 2.0000 POS: 1.0000 -> Orientation: undecided CYT-EXT difference: 0.00 -> Orientation: undecided ---------------------------------------------------------------------- "NP_176323" 137 18 38 #t 2.22812 58 78 #t 2.12083 ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ SAPS. Version of April 11, 1996. Date run: Mon Dec 3 12:16:04 2001 File: /people/b_eisen/NP_176323.1.fa.___saps___ ID NP_176323.1 DE hypothetical protein [Arabidopsis thaliana]. number of residues: 137; molecular weight: 15.6 kdal 1 MLSLNQEVHG PKTSEVYGFV GSISIVVATV IFLIWGYVPD KFLESIGIYY YPSKYWAMAM 61 PMYSMVTLLV ALVFYIGLNF MSTSKPTSLN TLFDDYSRED VNFLPLMKNG EDRPIDPISD 121 IDITRINDLM FDSHLAK -------------------------------------------------------------------------------- COMPOSITIONAL ANALYSIS (extremes relative to: swp23s) A : 5( 3.6%); C : 0( 0.0%); D : 10( 7.3%); E : 5( 3.6%); F : 8( 5.8%) G : 7( 5.1%); H : 2( 1.5%); I : 12( 8.8%); K : 6( 4.4%); L : 14(10.2%) M : 8( 5.8%); N : 6( 4.4%); P : 8( 5.8%); Q : 1( 0.7%); R : 3( 2.2%) S : 13( 9.5%); T : 7( 5.1%); V : 11( 8.0%); W : 2( 1.5%); Y : 9( 6.6%) KR : 9 ( 6.6%); ED : 15 ( 10.9%); AGP : 20 ( 14.6%); KRED : 24 ( 17.5%); KR-ED : -6 ( -4.4%); FIKMNY : 49 ( 35.8%); LVIFM : 53 ( 38.7%); ST : 20 ( 14.6%). -------------------------------------------------------------------------------- CHARGE DISTRIBUTIONAL ANALYSIS 1 000000-000 0+00-00000 0000000000 000000000- +00-000000 000+000000 61 0000000000 0000000000 0000+00000 000--00+-- 0000000+00 --+00-000- 121 0-00+00-00 0-0000+ A. CHARGE CLUSTERS. Positive charge clusters (cmin = 7/30 or 9/45 or 11/60): none Negative charge clusters (cmin = 10/30 or 13/45 or 16/60): 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 | 4 | 5 | 40 | 7 | 9 | 10 | 9 | 10 | 13 | 5 | 7 | lmin1 5 | 6 | 7 | 49 | 9 | 11 | 13 | 11 | 13 | 15 | 7 | 8 | lmin2 6 | 7 | 8 | 54 | 10 | 12 | 14 | 12 | 14 | 17 | 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: 0 * runs >= 4: 0 0 runs >= 27: 1, at 55; -------------------------------------------------------------------------------- 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: -2.328 M_0.01= 74.99; M_0.05= 58.44; M_0.30= 38.74 1) From 16 to 38: length= 23, score=64.00 * 16 VYGFVGSISI VVATVIFLIW GYV G: 3(13.0%); V: 6(26.1%); I: 4(17.4%); 2) From 57 to 78: length= 22, score=49.00 57 AMAMPMYSMV TLLVALVFYI GL L: 4(18.2%); A: 3(13.6%); V: 3(13.6%); M: 4(18.2%); 2. SPACINGS OF C. H2N-137-COOH 2*. SPACINGS OF C and H. (additional deluxe function for ALEX) H2N-8-H-124-H-3-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: 4 (Expected range: 0-- 17) 2. Histogram of spacings between consecutive amino acid multiplets: (1-5) 0 (6-10) 0 (11-20) 1 (>=21) 4 3. Clusters of amino acid multiplets (cmin = 7/30 or 9/45 or 11/60): none B. CHARGE ALPHABET. 1. Total number of charge multiplets: 3 (Expected range: 0-- 7) 0 +plets (f+: 6.6%), 3 -plets (f-: 10.9%) Total number of charge altplets: 3 (Critical number: 8) 2. Histogram of spacings between consecutive charge multiplets: (1-5) 1 (6-10) 0 (11-20) 1 (>=21) 2 -------------------------------------------------------------------------------- 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 26- 49 4 i..0 6 6 /0/././2/ 58- 81 2 i0 11 8 /1/4/ -------------------------------------------------------------------------------- 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: NP_176323.1.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: NP_176323.1 hypothetical protein [Arabidopsis thaliana]. 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 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: NP_176323.1.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: NP_176323.1 hypothetical protein [Arabidopsis thaliana]. Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- SCFA_trans Short chain fatty acid transporter -0.5 42 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- SCFA_trans 1/1 68 81 .. 465 478 .] -0.5 42 Alignments of top-scoring domains: SCFA_trans: domain 1 of 1, from 68 to 81: score -0.5, E = 42 *->IfagiilviGLyll<-* +++++++ iGL ++ NP_176323. 68 LLVALVFYIGLNFM 81 // 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: NP_176323.1.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: NP_176323.1 hypothetical protein [Arabidopsis thaliana]. Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- KELCH-ma -10.4 80 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- KELCH-ma 1/1 30 76 .. 1 55 [] -10.4 80 Alignments of top-scoring domains: KELCH-ma: domain 1 of 1, from 30 to 76: score -10.4, E = 80 *->kiYvvGGfdgttrclpgegqrlksvEvYDpetnkWrpvpsMptpRsg +i+ + G+ + +l s+ +Y + ++ W + +M ++ + NP_176323. 30 VIFLIWGYVP--------DKFLESIGIYYYPSKYWAMAMPMYSMVTL 68 agvaving<-* + v+ NP_176323. 69 LVALVFYI 76 // ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ Start with Prosite --------------------------------------------------------- | ppsearch (c) 1994 EMBL Data Library | | based on MacPattern (c) 1990-1994 R. Fuchs | --------------------------------------------------------- PROSITE pattern search started: Mon Dec 3 12:18:05 2001 Sequence file: NP_176323.1.fa ---------------------------------------- Sequence NP_176323.1 (137 residues): Matching pattern PS00005 PKC_PHOSPHO_SITE: 83: TSK Total matches: 1 Matching pattern PS00006 CK2_PHOSPHO_SITE: 91: TLFD 97: SRED 119: SDID Total matches: 3 Total no of hits in this sequence: 4 ======================================== 1314 pattern(s) searched in 1 sequence(s), 137 residues. Total no of hits in all sequences: 4. 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, 0 units >ER-GOLGI-traffic signal is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >INTRA-SIGNAL-M minimal SH3 binding is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 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, 0 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, 0 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, 0 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, 0 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, 0 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, 0 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, 0 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, 0 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, 0 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, 0 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, 0 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, 0 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, 0 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, 0 units >NUCLEAR NLS experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 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, 0 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, 0 units >NUCLEAR NLS HCDA experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS SV40 LrgT experimentally determined is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS H2B experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 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, 0 units >NUCLEAR NLS Amida experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS Amida experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS RanBP3 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS Pho4p experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS DNAhelicaseQ1 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 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, 0 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, 0 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, 0 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, 0 units >NUCLEAR NLS GAL4 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 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, 0 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, 0 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, 0 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, 0 units >NUCLEAR NLS TR2 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 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, 0 units >NUCLEAR NLS polyomaVP1 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 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, 0 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, 0 units >NUCLEAR NLS Rex experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS SRY experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS SRY experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS SOX9 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS SOX9 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS NS5A experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 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, 0 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, 0 units >NUCLEAR NLS adenovE1a experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS ystDNApolalpha experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS hVDR experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 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, 0 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, 0 units >NUCLEAR NLS cFOS experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS cJUN experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS hDNApolalpha experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS hDNAtopoII experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS hDNAtopoII experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS hBLM experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS hARNT experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS influenzaNP experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS influenzaNP experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS p54 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS hProTalpha experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 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, 0 units >NUCLEAR NLS protHsc9 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS protHsci experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS protHsc3 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 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, 0 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, 0 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, 0 units >NUCLEAR NLS MyoD experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS MyoD experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS opaque2 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS CTP experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS HCV experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS HCV experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS p110RB1 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 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, 0 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, 0 units >NUCLEAR NLS Nucloplasmin experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS Nucleolin experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 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, 0 units >NUCLEAR NLS Nab2 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS M9 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS lscMyc experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS humKprotein experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS FluA experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 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, 0 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, 0 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, 0 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, 0 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, 0 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, 0 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, 0 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, 0 units >NUCLEAR NLS p53 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 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, 0 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, 0 units >NUCLEAR NLS L29 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS L29 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS Max experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS L3 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 units >NUCLEAR NLS dyskerin experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 0 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, 0 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, 0 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: NP_176323.1.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: NP_176323.1 hypothetical protein [Arabidopsis thaliana]. 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: NP_176323.1.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: NP_176323.1 hypothetical protein [Arabidopsis thaliana]. 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= NP_176323.1 hypothetical protein [Arabidopsis thaliana]. (137 letters) Searching..................................done Results from profile search Score E Sequences producing significant alignments: (bits) Value DHHC Novel zinc finger domain with DHHC signature 24 0.080 KELCH Kelch repeat- beta propeller like domain 21 1.1 LAMNT Lamin N-terminal domain 20 1.3 SNARE Alpha helical domains which are involved in vesicle fu... 19 2.6 KIN Protein kinase domain 19 2.7 FYVE Zinc Finger domain involved in PtdIns(3)P binding 19 3.7 PH Pleckstrin homology domain (lipid and protein interactio... 18 8.0 SWIB SWIB domain (A chromatin associated domain) 18 9.6 CBS cystathionine beta -synthase domain (A predicted ligand... 18 9.9 >DHHC Novel zinc finger domain with DHHC signature Length = 217 Score = 24.4 bits (52), Expect = 0.080 Identities = 7/64 (10%), Positives = 7/64 (10%), Gaps = 6/64 (9%) Query: 23 ISIVVATVIFLIWGYVPDKFLESIGIYYYPSKYWAMAMPMYSMVTLLVALVFYIGLNFMS 82 Sbjct: 51 LQIVAWLLYLFFAVIGFGILVPLLPHHWVPAGYACM------GAIFAGHLVVHLTAVSID 104 Query: 83 TSKP 86 Sbjct: 105 PADD 108 >KELCH Kelch repeat- beta propeller like domain Length = 319 Score = 20.7 bits (43), Expect = 1.1 Identities = 4/36 (11%), Positives = 4/36 (11%) Query: 21 GSISIVVATVIFLIWGYVPDKFLESIGIYYYPSKYW 56 Sbjct: 260 SCHAVASGNKLYVVGGYFGIQRCKTLDCYDPTLDVW 295 Score = 19.5 bits (40), Expect = 2.7 Identities = 8/60 (13%), Positives = 8/60 (13%), Gaps = 5/60 (8%) Query: 21 GSISIVVATVIFLIWGYVPDKFLESIGIYYYPSKYW----AMAMPMYSMVTLLVALVFYI 76 Sbjct: 214 YTAAAVLGNQIFIMGGDTEFS-ACSAYKFNSETYQWTKVGDVTAKRMSCHAVASGNKLYV 272 Score = 18.7 bits (38), Expect = 4.1 Identities = 6/39 (15%), Positives = 6/39 (15%), Gaps = 1/39 (2%) Query: 25 IVVATVIFLIWGYVPDKFLESIGIYYYPSKY-WAMAMPM 62 Sbjct: 66 CAIGCKVYITGGRGSENGVSKDVWVYDTLHEEWSKAAPM 104 >LAMNT Lamin N-terminal domain Length = 256 Score = 20.2 bits (42), Expect = 1.3 Identities = 6/34 (17%), Positives = 6/34 (17%), Gaps = 5/34 (14%) Query: 61 PMYSMVTLLVAL-----VFYIGLNFMSTSKPTSL 89 Sbjct: 111 LQHNEVNITIDLEQEFHVAYVWIQMANSPRPGSW 144 >SNARE Alpha helical domains which are involved in vesicle fusion Length = 254 Score = 19.4 bits (40), Expect = 2.6 Identities = 8/54 (14%), Positives = 8/54 (14%), Gaps = 3/54 (5%) Query: 55 YWAMAMPMYSMVTLLVALVFYIGLNFMSTSK---PTSLNTLFDDYSREDVNFLP 105 Sbjct: 181 AHQRLEPATLSGIVAFILSLLCGALNLIRGFHAIESLLQSDGEDFSYMIAFFLG 234 >KIN Protein kinase domain Length = 313 Score = 19.3 bits (39), Expect = 2.7 Identities = 5/39 (12%), Positives = 5/39 (12%) Query: 29 TVIFLIWGYVPDKFLESIGIYYYPSKYWAMAMPMYSMVT 67 Sbjct: 191 TEYVATRWYRAPEVILSWNKYTKAIDIWSVGCIFAELLG 229 >FYVE Zinc Finger domain involved in PtdIns(3)P binding Length = 99 Score = 18.9 bits (38), Expect = 3.7 Identities = 3/14 (21%), Positives = 3/14 (21%) Query: 102 NFLPLMKNGEDRPI 115 Sbjct: 74 NWTTYPPMGYETKI 87 >PH Pleckstrin homology domain (lipid and protein interaction domain) Length = 138 Score = 17.6 bits (35), Expect = 8.0 Identities = 6/70 (8%), Positives = 6/70 (8%) Query: 42 FLESIGIYYYPSKYWAMAMPMYSMVTLLVALVFYIGLNFMSTSKPTSLNTLFDDYSREDV 101 Sbjct: 37 ILTDNCLYYFEYTTDKEPRGIIPLENLSIREVDDPRKPNCFELYIPNNKGQLIKACKTEA 96 Query: 102 NFLPLMKNGE 111 Sbjct: 97 DGRVVEGNHM 106 >SWIB SWIB domain (A chromatin associated domain) Length = 81 Score = 17.5 bits (35), Expect = 9.6 Identities = 6/20 (30%), Positives = 6/20 (30%) Query: 19 FVGSISIVVATVIFLIWGYV 38 Sbjct: 45 IIGLKSGTSHDAIFSIYKYI 64 >CBS cystathionine beta -synthase domain (A predicted ligand binding domain) Length = 214 Score = 17.6 bits (35), Expect = 9.9 Identities = 5/48 (10%), Positives = 5/48 (10%), Gaps = 1/48 (2%) Query: 79 NFMSTSKPTSLNTLFDDYSREDVNFLPLMKNGEDRPIDPISDIDITRI 126 Sbjct: 74 EVITVYEDDEARNVVLKFVKYKVVSIPVL-TRDGRVIGMVRNCDVVKT 120 Underlying Matrix: BLOSUM62 Number of sequences tested against query: 105 Number of sequences better than 10.0: 9 Number of calls to ALIGN: 11 Length of query: 137 Total length of test sequences: 20182 Effective length of test sequences: 16941.0 Effective search space size: 1803056.3 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= NP_176323.1 hypothetical protein [Arabidopsis thaliana]. (137 letters) Searching.................................................done Results from profile search Score E Sequences producing significant alignments: (bits) Value gi|137043 [102..336] Uracil-DNA glycosylase 22 4.8 gi|2392177 [88..197] OB-fold 21 9.2 >gi|137043 [102..336] Uracil-DNA glycosylase Length = 235 Score = 22.1 bits (47), Expect = 4.8 Identities = 11/37 (29%), Positives = 11/37 (29%), Gaps = 3/37 (8%) Query: 77 GLNFMS---TSKPTSLNTLFDDYSREDVNFLPLMKNG 110 Sbjct: 71 GLAFSVKPPTPAPPSLKNIYKELKQEYPDFVEDNKVG 107 >gi|2392177 [88..197] OB-fold Length = 110 Score = 21.3 bits (44), Expect = 9.2 Identities = 9/29 (31%), Positives = 9/29 (31%), Gaps = 4/29 (13%) Query: 51 YPSKYWAMAMPMYSMVTLLVALVFYIGLN 79 Sbjct: 51 YDGKYWS----MYSRLRKMLYLIYVAGIS 75 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: 137 Total length of test sequences: 256703 Effective length of test sequences: 213024.0 Effective search space size: 21385973.3 Initial X dropoff for ALIGN: 25.0 bits ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ calculation of internal repeats with prospero ***** PROSPERO v1.3 Mon Dec 3 12:18:41 2001 ***** 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 NP_176323.1 using self-comparison ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ TIGRFAM hmmpfam - search a single seq against HMM database HMMER 2.1.1 (Dec 1998) Copyright (C) 1992-1998 Washington University School of Medicine HMMER is freely distributed under the GNU General Public License (GPL). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - HMM file: /data/patterns/tigrfam/tigrfam.hmm Sequence file: NP_176323.1.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: NP_176323.1 hypothetical protein [Arabidopsis thaliana]. 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: NP_176323.1.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: NP_176323.1 hypothetical protein [Arabidopsis thaliana]. 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: NP_176323.1.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: NP_176323.1 hypothetical protein [Arabidopsis thaliana]. 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: NP_176323.1.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: NP_176323.1 hypothetical protein [Arabidopsis thaliana]. 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: NP_176323.1.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: NP_176323.1 hypothetical protein [Arabidopsis thaliana]. Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- COG0370 4.2 1.9 1 COG2930 2.5 10 1 COG1099 -0.4 60 1 COG2968 -0.8 82 1 COG3104 -1.7 77 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- COG3104 1/1 15 35 .. 569 589 .. -1.7 77 COG0370 1/1 61 74 .. 765 777 .] 4.2 1.9 COG2930 1/1 60 85 .. 1 26 [. 2.5 10 COG2968 1/1 59 92 .. 1 34 [. -0.8 82 COG1099 1/1 129 135 .. 1 7 [. -0.4 60 Alignments of top-scoring domains: COG3104: domain 1 of 1, from 15 to 35: score -1.7, E = 77 *->rvFgqiglitlatgillllla<-* +v+g+ g i+++++ +++l++ NP_176323. 15 EVYGFVGSISIVVATVIFLIW 35 COG0370: domain 1 of 1, from 61 to 74: score 4.2, E = 1.9 *->PeySliwI.vlLLf<-* P+yS+++ v L+f NP_176323. 61 PMYSMVTLlVALVF 74 COG2930: domain 1 of 1, from 60 to 85: score 2.5, E = 10 *->mPRLPyktfLlaLallassafagaee<-* mP + t+L+aL ++ f + ++ NP_176323. 60 MPMYSMVTLLVALVFYIGLNFMSTSK 85 COG2968: domain 1 of 1, from 59 to 92: score -0.8, E = 82 *->vrtkivlrrktiaLvalvllaasvllspasanel<-* ++ ++ +++aLv ++l + + p+s+n+l NP_176323. 59 AMPMYSMVTLLVALVFYIGLNFMSTSKPTSLNTL 92 COG1099: domain 1 of 1, from 129 to 135: score -0.4, E = 60 *->mmiDsHl<-* +m+DsHl NP_176323. 129 LMFDSHL 135 //