analysis of sequence from NP_177574.1 ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ >NP_177574.1 putative dolichyl-phosphate mannosyltransferase polypeptide 2 [Arabidopsis thaliana]. MELADRAVGL LLSSISLSIF TYYTFWVIIL PFVDSDHFIH KYFLPQDYAI LVPVFAGIAL LSLISVFIGM VMLKSKKKKA ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ sec.str. with predator > NP_177574.1 . . . . . 1 MELADRAVGLLLSSISLSIFTYYTFWVIILPFVDSDHFIHKYFLPQDYAI 50 ___HHHHHHHHH_______EEEEEEEEEEEE_______EEEE_____EEE . . . 51 LVPVFAGIALLSLISVFIGMVMLKSKKKKA 80 EHHHHH_HHHHHHHHHHHHHHHHHH_____ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ method : 1 alpha-contents : 22.9 % beta-contents : 77.1 % coil-contents : 0.0 % class : mixed method : 2 alpha-contents : 0.0 % beta-contents : 100.0 % coil-contents : 0.0 % class : beta ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ GPI: learning from metazoa -27.14 -3.38 -0.60 -1.07 -4.00 0.00 -4.00 -3.12 -0.28 -1.33 -2.58 0.00 0.00 -32.00 0.00 0.00 -79.50 -22.85 -2.94 -1.10 -0.03 -4.00 -4.00 0.00 -0.64 0.00 -1.62 -2.58 0.00 0.00 -32.00 0.00 0.00 -71.76 ID: NP_177574.1 AC: xxx Len: 80 1:I 50 Sc: -71.76 Pv: 6.038111e-01 NO_GPI_SITE GPI: learning from protozoa -20.72 -3.18 -4.36 -4.79 -4.00 0.00 -8.00 -9.16 -0.41 -1.35 -9.33 0.00 -12.00 -32.00 0.00 0.00 -109.30 -27.83 -2.50 -0.58 0.00 -4.00 0.00 -28.00 0.00 -0.55 -7.52 -9.33 -12.00 0.00 0.00 -12.00 0.00 -104.30 ID: NP_177574.1 AC: xxx Len: 80 1:I 70 Sc: -104.30 Pv: 9.167527e-01 NO_GPI_SITE ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ # SignalP euk predictions # name Cmax pos ? Ymax pos ? Smax pos ? Smean ? NP_177574.1 1.000 36 Y 0.697 36 Y 0.919 61 Y 0.640 Y # SignalP gram- predictions # name Cmax pos ? Ymax pos ? Smax pos ? Smean ? NP_177574.1 0.182 57 N 0.250 22 N 0.922 57 Y 0.565 Y # SignalP gram+ predictions # name Cmax pos ? Ymax pos ? Smax pos ? Smean ? NP_177574.1 0.303 52 N 0.250 80 N 0.973 73 Y 0.506 N ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ low complexity regions: SEG 12 2.2 2.5 >NP_177574.1 putative dolichyl-phosphate mannosyltransferase polypeptide 2 [Arabidopsis thaliana]. 1-9 MELADRAVG lllssislsi 10-19 20-80 FTYYTFWVIILPFVDSDHFIHKYFLPQDYA ILVPVFAGIALLSLISVFIGMVMLKSKKKK A low complexity regions: SEG 25 3.0 3.3 >NP_177574.1 putative dolichyl-phosphate mannosyltransferase polypeptide 2 [Arabidopsis thaliana]. 1-80 MELADRAVGLLLSSISLSIFTYYTFWVIIL PFVDSDHFIHKYFLPQDYAILVPVFAGIAL LSLISVFIGMVMLKSKKKKA low complexity regions: SEG 45 3.4 3.75 >NP_177574.1 putative dolichyl-phosphate mannosyltransferase polypeptide 2 [Arabidopsis thaliana]. 1-80 MELADRAVGLLLSSISLSIFTYYTFWVIIL PFVDSDHFIHKYFLPQDYAILVPVFAGIAL LSLISVFIGMVMLKSKKKKA 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_177574.1 putative dolichyl-phosphate mannosyltransferase polypeptide 2 [Arabidopsis thaliana]. MELADRAVGLLLSSISLSIFTYYTFWVIILPFVDSDHFIHKYFLPQDYAILVPVFAGIAL LSLISVFIGMVMLKSKKKKA 1 - 80 MELADRAVGL LLSSISLSIF TYYTFWVIIL PFVDSDHFIH KYFLPQDYAI LVPVFAGIAL LSLISVFIGM VMLKSKKKKA low complexity regions: DUST >NP_177574.1 putative dolichyl-phosphate mannosyltransferase polypeptide 2 [Arabidopsis thaliana]. MELADRAVGLLLSSISLSIFTYYTFWVIILPFVDSDHFIHKYFLPQDYAILVPVFAGIAL LSLISVFIGMVMLKSKKKKA ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ coiled coil prediction for NP_177574.1 sequence: 80 amino acids, 0 residue(s) in coiled coil state . | . | . | . | . | . 60 MELADRAVGL LLSSISLSIF TYYTFWVIIL PFVDSDHFIH KYFLPQDYAI LVPVFAGIAL ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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 . | . | LSLISVFIGM VMLKSKKKKA ~~~~~~~~~~ ~~~~~~~~~~ ---------- ---------- ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ prediction of transmembrane regions with toppred2 *********************************** *TOPPREDM with eukaryotic function* *********************************** NP_177574.1.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_177574.1.fa.___inter___ (1 sequences) MELADRAVGLLLSSISLSIFTYYTFWVIILPFVDSDHFIHKYFLPQDYAI LVPVFAGIALLSLISVFIGMVMLKSKKKKA (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 13 33 1.981 Certain 2 53 73 2.336 Certain ---------------------------------------------------------------------- Structure 1 Transmembrane segments included in this structure: Segment 1 2 Loop length 12 19 7 K+R profile 2.00 5.00 1.00 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): 1.00 (NEG-POS)/(NEG+POS): 0.3333 NEG: 2.0000 POS: 1.0000 -> Orientation: N-in CYT-EXT difference: 0.00 -> Orientation: undecided ---------------------------------------------------------------------- "NP_177574" 80 13 33 #t 1.98125 53 73 #t 2.33646 ************************************ *TOPPREDM with prokaryotic function* ************************************ NP_177574.1.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_177574.1.fa.___inter___ (1 sequences) MELADRAVGLLLSSISLSIFTYYTFWVIILPFVDSDHFIHKYFLPQDYAI LVPVFAGIALLSLISVFIGMVMLKSKKKKA (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 13 33 1.981 Certain 2 53 73 2.336 Certain ---------------------------------------------------------------------- Structure 1 Transmembrane segments included in this structure: Segment 1 2 Loop length 12 19 7 K+R profile 2.00 5.00 1.00 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): 1.00 (NEG-POS)/(NEG+POS): 0.3333 NEG: 2.0000 POS: 1.0000 -> Orientation: N-in CYT-EXT difference: 0.00 -> Orientation: undecided ---------------------------------------------------------------------- "NP_177574" 80 13 33 #t 1.98125 53 73 #t 2.33646 ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ SAPS. Version of April 11, 1996. Date run: Thu Dec 6 14:58:35 2001 File: /people/b_eisen/NP_177574.1.fa.___saps___ ID NP_177574.1 DE putative dolichyl-phosphate mannosyltransferase polypeptide 2 [Arabidopsis thaliana]. number of residues: 80; molecular weight: 9.1 kdal 1 MELADRAVGL LLSSISLSIF TYYTFWVIIL PFVDSDHFIH KYFLPQDYAI LVPVFAGIAL 61 LSLISVFIGM VMLKSKKKKA -------------------------------------------------------------------------------- COMPOSITIONAL ANALYSIS (extremes relative to: swp23s) A : 6( 7.5%); C : 0( 0.0%); D : 4( 5.0%); E : 1( 1.2%); F : 7( 8.8%) G : 3( 3.8%); H : 2( 2.5%); I : 9(11.2%); K : 6( 7.5%); L : 12(15.0%) M : 3( 3.8%); N : 0( 0.0%); P : 3( 3.8%); Q : 1( 1.2%); R : 1( 1.2%) S : 8(10.0%); T : 2( 2.5%); V : 7( 8.8%); W : 1( 1.2%); Y : 4( 5.0%) KR : 7 ( 8.8%); ED : 5 ( 6.2%); AGP : 12 ( 15.0%); KRED : 12 ( 15.0%); KR-ED : 2 ( 2.5%); FIKMNY : 29 ( 36.2%); LVIFM : 38 ( 47.5%); ST : 10 ( 12.5%). -------------------------------------------------------------------------------- CHARGE DISTRIBUTIONAL ANALYSIS 1 0-00-+0000 0000000000 0000000000 000-0-0000 +00000-000 0000000000 61 0000000000 000+0++++0 A. CHARGE CLUSTERS. Positive charge clusters (cmin = 8/30 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 16/45 or 20/60): none B. HIGH SCORING (UN)CHARGED SEGMENTS. ______________________________________ High scoring positive charge segments: score= 2.00 frequency= 0.088 ( KR ) score= 0.00 frequency= 0.000 ( BZX ) score= -1.00 frequency= 0.850 ( LAGSVTIPNFQYHMCW ) score= -2.00 frequency= 0.063 ( ED ) Expected score/letter: -0.800 M_0.01= 7.71; M_0.05= 6.13 1) From 74 to 80: length= 7, score= 8.00 ** 74 KSKKKKA A: 1(14.3%); S: 1(14.3%); K: 5(71.4%); 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 | 3 | 5 | 44 | 8 | 7 | 9 | 9 | 8 | 11 | 6 | 7 | lmin1 5 | 4 | 6 | 53 | 9 | 9 | 11 | 11 | 10 | 14 | 7 | 9 | lmin2 6 | 5 | 7 | 59 | 11 | 10 | 13 | 13 | 12 | 16 | 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: 1, at 76; - runs >= 3: 0 * runs >= 3: 1, at 76; 0 runs >= 29: 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-80-COOH 2*. SPACINGS OF C and H. (additional deluxe function for ALEX) H2N-36-H-2-H-40-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: 6 (Expected range: 0-- 13) 2. Histogram of spacings between consecutive amino acid multiplets: (1-5) 3 (6-10) 2 (11-20) 1 (>=21) 1 3. Clusters of amino acid multiplets (cmin = 13/30 or 16/45 or 20/60): none B. CHARGE ALPHABET. 1. Total number of charge multiplets: 1 (Expected range: 0-- 4) 1 +plets (f+: 8.8%), 0 -plets (f-: 6.2%) Total number of charge altplets: 1 (Critical number: 5) 2. Histogram of spacings between consecutive charge multiplets: (1-5) 1 (6-10) 0 (11-20) 0 (>=21) 1 -------------------------------------------------------------------------------- PERIODICITY ANALYSIS. A. AMINO ACID ALPHABET (core: 4; !-core: 4) Location Period Element Copies Core Errors 76- 79 1 K 4 4 ! 0 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 52- 75 3 i.. 8 8 0 -------------------------------------------------------------------------------- SPACING ANALYSIS. Not evaluated (sequence length < 100 aa, too short). ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ 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_177574.1.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: NP_177574.1 putative dolichyl-phosphate mannosyltransferase polypeptide 2 [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_177574.1.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: NP_177574.1 putative dolichyl-phosphate mannosyltransferase polypeptide 2 [Arabidopsis thaliana]. Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- HAMP HAMP domain 2.1 50 1 Zip ZIP Zinc transporter 0.9 54 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- Zip 1/1 48 65 .. 161 178 .] 0.9 54 HAMP 1/1 54 78 .. 1 25 [. 2.1 50 Alignments of top-scoring domains: Zip: domain 1 of 1, from 48 to 65: score 0.9, E = 54 *->llkflalllGfalMllla<-* ++ ++ +++G+al++l++ NP_177574. 48 YAILVPVFAGIALLSLIS 65 HAMP: domain 1 of 1, from 54 to 78: score 2.1, E = 50 *->lvlvlllalllllllvlllarrllr<-* ++++++l+ l++++++ ++ ++ ++ NP_177574. 54 VFAGIALLSLISVFIGMVMLKSKKK 78 // 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_177574.1.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: NP_177574.1 putative dolichyl-phosphate mannosyltransferase polypeptide 2 [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 Prosite --------------------------------------------------------- | ppsearch (c) 1994 EMBL Data Library | | based on MacPattern (c) 1990-1994 R. Fuchs | --------------------------------------------------------- PROSITE pattern search started: Thu Dec 6 15:01:00 2001 Sequence file: NP_177574.1.fa ---------------------------------------- Sequence NP_177574.1 (80 residues): Matching pattern PS00005 PKC_PHOSPHO_SITE: 75: SKK Total matches: 1 Matching pattern PS00008 MYRISTYL: 9: GLLLSS Total matches: 1 Total no of hits in this sequence: 2 ======================================== 1314 pattern(s) searched in 1 sequence(s), 80 residues. Total no of hits in all sequences: 2. 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, 80 units >ER-GOLGI-traffic signal is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 80 units >INTRA-SIGNAL-M minimal SH3 binding is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 80 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, 80 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, 80 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, 80 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, 80 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, 80 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, 80 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, 80 units >TM-CYTOPLASMIC-M di-hydrophobic endocytosis motifs for internalized transmembrane proteins is the MOTIF name >NP_177574.1 putative dolichyl-phosphate mannosyltransferase polypeptide 2 [Arabidopsis thaliana]. ;LENGTH=80; DIRECT_SEQUENCE n 1 solutions m %_D 47-47 %_XXXL 48-51 %_V 52-52 f >STATISTICS Total : 1 solutions in 1 sequences, 80 units; out of 1 sequences, 80 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, 80 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, 80 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, 80 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, 80 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, 80 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, 80 units >NUCLEAR NLS experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 80 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, 80 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, 80 units >NUCLEAR NLS HCDA experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 80 units >NUCLEAR NLS SV40 LrgT experimentally determined is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 80 units >NUCLEAR NLS H2B experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 80 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, 80 units >NUCLEAR NLS Amida experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 80 units >NUCLEAR NLS Amida experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 80 units >NUCLEAR NLS RanBP3 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 80 units >NUCLEAR NLS Pho4p experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 80 units >NUCLEAR NLS DNAhelicaseQ1 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 80 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, 80 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, 80 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, 80 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, 80 units >NUCLEAR NLS GAL4 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 80 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, 80 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, 80 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, 80 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, 80 units >NUCLEAR NLS TR2 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 80 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, 80 units >NUCLEAR NLS polyomaVP1 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 80 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, 80 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, 80 units >NUCLEAR NLS Rex experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 80 units >NUCLEAR NLS SRY experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 80 units >NUCLEAR NLS SRY experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 80 units >NUCLEAR NLS SOX9 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 80 units >NUCLEAR NLS SOX9 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 80 units >NUCLEAR NLS NS5A experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 80 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, 80 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, 80 units >NUCLEAR NLS adenovE1a experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 80 units >NUCLEAR NLS ystDNApolalpha experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 80 units >NUCLEAR NLS hVDR experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 80 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, 80 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, 80 units >NUCLEAR NLS cFOS experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 80 units >NUCLEAR NLS cJUN experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 80 units >NUCLEAR NLS hDNApolalpha experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 80 units >NUCLEAR NLS hDNAtopoII experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 80 units >NUCLEAR NLS hDNAtopoII experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 80 units >NUCLEAR NLS hBLM experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 80 units >NUCLEAR NLS hARNT experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 80 units >NUCLEAR NLS influenzaNP experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 80 units >NUCLEAR NLS influenzaNP experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 80 units >NUCLEAR NLS p54 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 80 units >NUCLEAR NLS hProTalpha experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 80 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, 80 units >NUCLEAR NLS protHsc9 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 80 units >NUCLEAR NLS protHsci experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 80 units >NUCLEAR NLS protHsc3 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 80 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, 80 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, 80 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, 80 units >NUCLEAR NLS MyoD experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 80 units >NUCLEAR NLS MyoD experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 80 units >NUCLEAR NLS opaque2 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 80 units >NUCLEAR NLS CTP experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 80 units >NUCLEAR NLS HCV experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 80 units >NUCLEAR NLS HCV experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 80 units >NUCLEAR NLS p110RB1 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 80 units >NUCLEAR NLS experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 80 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, 80 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, 80 units >NUCLEAR NLS Nucloplasmin experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 80 units >NUCLEAR NLS Nucleolin experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 80 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, 80 units >NUCLEAR NLS Nab2 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 80 units >NUCLEAR NLS M9 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 80 units >NUCLEAR NLS lscMyc experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 80 units >NUCLEAR NLS humKprotein experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 80 units >NUCLEAR NLS FluA experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 80 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, 80 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, 80 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, 80 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, 80 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, 80 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, 80 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, 80 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, 80 units >NUCLEAR NLS p53 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 80 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, 80 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, 80 units >NUCLEAR NLS L29 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 80 units >NUCLEAR NLS L29 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 80 units >NUCLEAR NLS Max experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 80 units >NUCLEAR NLS L3 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 80 units >NUCLEAR NLS dyskerin experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 80 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, 80 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, 80 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_177574.1.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: NP_177574.1 putative dolichyl-phosphate mannosyltransferase polypeptide 2 [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_177574.1.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: NP_177574.1 putative dolichyl-phosphate mannosyltransferase polypeptide 2 [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_177574.1 putative dolichyl-phosphate mannosyltransferase polypeptide 2 [Arabidopsis thaliana]. (80 letters) Searching..................................done Results from profile search Score E Sequences producing significant alignments: (bits) Value DNASE1 DNASE-1/Sphingomyelinase like domain 20 1.1 DHHC Novel zinc finger domain with DHHC signature 20 1.1 HISDAC Histone deacetylase domain 18 2.5 PP2C PP2C type phosphatase domain 18 3.1 LON The LON serine protease domain 17 5.3 DSP Dual specificity protein phosphatase 17 6.9 UBA Ubiquitin pathway associated domain 17 7.7 INSL Insulinase like Metallo protease domain 17 7.9 CATH Cathepsin like protease domain 17 8.3 JAB JAB1 associated domain involved in proteolysis 17 8.8 SEC14D Sec14 related lipid binding domain 17 9.5 >DNASE1 DNASE-1/Sphingomyelinase like domain Length = 388 Score = 19.7 bits (40), Expect = 1.1 Identities = 4/29 (13%), Positives = 4/29 (13%) Query: 10 LLLSSISLSIFTYYTFWVIILPFVDSDHF 38 Sbjct: 344 RVNAALGLPTEEQIGPNRLPSFNYPSDHL 372 >DHHC Novel zinc finger domain with DHHC signature Length = 217 Score = 19.7 bits (40), Expect = 1.1 Identities = 13/53 (24%), Positives = 13/53 (24%), Gaps = 2/53 (3%) Query: 17 LSIFTYYTFWVIILPFVDSDHFIHKYFLPQDYAILVPVFAGIALLSLISVFIG 69 Sbjct: 54 VAWLLYLFFAVIGFGILVP--LLPHHWVPAGYACMGAIFAGHLVVHLTAVSID 104 >HISDAC Histone deacetylase domain Length = 433 Score = 18.3 bits (37), Expect = 2.5 Identities = 6/29 (20%), Positives = 6/29 (20%) Query: 4 ADRAVGLLLSSISLSIFTYYTFWVIILPF 32 Sbjct: 273 GDSLSGDRLGCFNLSMEGHANCVNYVKSF 301 >PP2C PP2C type phosphatase domain Length = 254 Score = 18.3 bits (37), Expect = 3.1 Identities = 2/38 (5%), Positives = 2/38 (5%), Gaps = 1/38 (2%) Query: 2 ELADRAVGLLLSSISLSIFTYYTFWVIILPFVDSDHFI 39 Sbjct: 158 AQAKVHPWRHVLFQCLGRQDLNFI-EVEALDAQPGDTF 194 >LON The LON serine protease domain Length = 132 Score = 17.4 bits (35), Expect = 5.3 Identities = 10/45 (22%), Positives = 10/45 (22%), Gaps = 4/45 (8%) Query: 32 FVDSDHFIHKYFLPQDYAILVPVFAGIAL-LSLISVFIGMVMLKS 75 Sbjct: 7 YEKRDIHVH---VPEGATPKDGPSAGIAMCTALVSCLTGNPVRAD 48 >DSP Dual specificity protein phosphatase Length = 185 Score = 16.8 bits (33), Expect = 6.9 Identities = 8/42 (19%), Positives = 8/42 (19%), Gaps = 4/42 (9%) Query: 38 FIHKYFLPQDYAILVPVFAGIALLSLISVFIGMVMLKSKKKK 79 Sbjct: 108 FIDQALAQKNGRVLVHCREGYSR----SPTLVIAYLMMRQKM 145 >UBA Ubiquitin pathway associated domain Length = 255 Score = 16.9 bits (33), Expect = 7.7 Identities = 7/13 (53%), Positives = 7/13 (53%) Query: 4 ADRAVGLLLSSIS 16 Sbjct: 49 PDRAVEYLLMGIP 61 >INSL Insulinase like Metallo protease domain Length = 433 Score = 16.7 bits (33), Expect = 7.9 Identities = 2/12 (16%), Positives = 2/12 (16%) Query: 41 KYFLPQDYAILV 52 Sbjct: 412 RYIKEDKYSEIL 423 >CATH Cathepsin like protease domain Length = 371 Score = 16.7 bits (33), Expect = 8.3 Identities = 5/32 (15%), Positives = 5/32 (15%), Gaps = 8/32 (25%) Query: 15 ISLSIFTYY--------TFWVIILPFVDSDHF 38 Sbjct: 182 MEKNLFSFYLNRDPKGATGGELLFGGVDPQYY 213 >JAB JAB1 associated domain involved in proteolysis Length = 136 Score = 16.7 bits (33), Expect = 8.8 Identities = 13/43 (30%), Positives = 13/43 (30%), Gaps = 2/43 (4%) Query: 6 RAVGLLLSSISLSIFTYYTFWVIILPFVDSDHFIHKYFLPQDY 48 Sbjct: 27 RVVGVLLGSWQKKVLDVSN--SFAVPFDEDDKDDSVWFLDHDY 67 >SEC14D Sec14 related lipid binding domain Length = 248 Score = 16.7 bits (33), Expect = 9.5 Identities = 4/13 (30%), Positives = 4/13 (30%) Query: 24 TFWVIILPFVDSD 36 Sbjct: 180 TTYNVVKPFLKSK 192 Underlying Matrix: BLOSUM62 Number of sequences tested against query: 105 Number of sequences better than 10.0: 11 Number of calls to ALIGN: 11 Length of query: 80 Total length of test sequences: 20182 Effective length of test sequences: 17146.0 Effective search space size: 874585.9 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_177574.1 putative dolichyl-phosphate mannosyltransferase polypeptide 2 [Arabidopsis thaliana]. (80 letters) Searching.................................................done Results from profile search Score E Sequences producing significant alignments: (bits) Value gi|135024 [2..113] Cell cycle regulatory proteins 24 0.52 gi|1001780 [277..448] beta-Lactamase/D-ala carboxypeptidase 20 6.5 >gi|135024 [2..113] Cell cycle regulatory proteins Length = 112 Score = 24.1 bits (51), Expect = 0.52 Identities = 8/35 (22%), Positives = 8/35 (22%), Gaps = 10/35 (28%) Query: 29 ILPFVDSDHFIHKYF----------LPQDYAILVP 53 Sbjct: 17 LEPFIDQIHYSPRYADDEYEYRHVMLPKAMLKAIP 51 >gi|1001780 [277..448] beta-Lactamase/D-ala carboxypeptidase Length = 172 Score = 20.4 bits (42), Expect = 6.5 Identities = 11/21 (52%), Positives = 11/21 (52%) Query: 45 PQDYAILVPVFAGIALLSLIS 65 Sbjct: 88 PQDLALLLVKLQGGELLSLKS 108 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: 80 Total length of test sequences: 256703 Effective length of test sequences: 215349.0 Effective search space size: 9700993.8 Initial X dropoff for ALIGN: 25.0 bits ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ calculation of internal repeats with prospero ***** PROSPERO v1.3 Thu Dec 6 15:02:27 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_177574.1 using self-comparison > 1 NP_177574.1 len 80 from 51 to 61 vs NP_177574.1 len 80 from 63 to 73 score 28 eval 8.413960e-02 identity 45.45% K 7.643278e-02 L 3.080130e-01 H 1.172183e+00 alpha 9.183338e-02 51 LVPVFAGIALL 61 NP_177574.1 |: || |: :| 63 LISVFIGMVML 73 NP_177574.1 ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ 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_177574.1.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: NP_177574.1 putative dolichyl-phosphate mannosyltransferase polypeptide 2 [Arabidopsis thaliana]. Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- TIGR00161 TIGR00161: conserved hypothetical protein T -0.4 42 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- TIGR00161 1/1 32 76 .. 1 46 [. -0.4 42 Alignments of top-scoring domains: TIGR00161: domain 1 of 1, from 32 to 76: score -0.4, E = 42 *->lvdletevctvdkvdvenpivlegfPGvGlvGsiagwlliedlklk< vd++ ++ ++ + + +i++ f G+ l+ i+ + + lk k NP_177574. 32 FVDSDHFI-HKYFLPQDYAILVPVFAGIALLSLISVFIGMVMLKSK 76 -* NP_177574. - - // 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_177574.1.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: NP_177574.1 putative dolichyl-phosphate mannosyltransferase polypeptide 2 [Arabidopsis thaliana]. Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- TIGR00688 rarD: rarD protein -0.2 50 1 TIGR00161 TIGR00161: conserved hypothetical protein T -0.4 41 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- TIGR00688 1/1 7 41 .. 1 36 [. -0.2 50 TIGR00161 1/1 32 76 .. 1 46 [. -0.4 41 Alignments of top-scoring domains: TIGR00688: domain 1 of 1, from 7 to 41: score -0.2, E = 50 *->fkGvlvsllalflwGyfplywkllkplpaldilghr<-* + G+l s+++l ++ y +++w ++ p d + h+ NP_177574. 7 AVGLLLSSISLSIFTY-YTFWVIILPFVDSDHFIHK 41 TIGR00161: domain 1 of 1, from 32 to 76: score -0.4, E = 41 *->lvdletevctvdkvdvenpivlegfPGvGlvGsiagwlliedlklk< vd++ ++ ++ + + +i++ f G+ l+ i+ + + lk k NP_177574. 32 FVDSDHFI-HKYFLPQDYAILVPVFAGIALLSLISVFIGMVMLKSK 76 -* NP_177574. - - // 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_177574.1.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: NP_177574.1 putative dolichyl-phosphate mannosyltransferase polypeptide 2 [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_177574.1.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: NP_177574.1 putative dolichyl-phosphate mannosyltransferase polypeptide 2 [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_177574.1.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: NP_177574.1 putative dolichyl-phosphate mannosyltransferase polypeptide 2 [Arabidopsis thaliana]. Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- COG2244 3.5 3.6 1 COG0239 1.1 62 1 COG1009 -1.2 69 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- COG0239 1/1 46 60 .. 1 15 [. 1.1 62 COG1009 1/1 19 77 .. 1 64 [. -1.2 69 COG2244 1/1 48 79 .. 191 222 .. 3.5 3.6 Alignments of top-scoring domains: COG0239: domain 1 of 1, from 46 to 60: score 1.1, E = 62 *->mmlksllavalGGAl<-* +++++l++v++G Al NP_177574. 46 QDYAILVPVFAGIAL 60 COG1009: domain 1 of 1, from 19 to 77: score -1.2, E = 69 *->mmmnlllliillPll...galvlllfggrsrlirktggllagvfsll + ++ ++i+lP+++++ ++ ++++ + +++l+ vf+ NP_177574. 19 IFTYYTFWVIILPFVdsdHFIHKYFLP-------QDYAILVPVFA-G 57 lvlsallsallillflgqgg<-* ++l++l+s+++++++l++ + NP_177574. 58 IALLSLISVFIGMVMLKSKK 77 COG2244: domain 1 of 1, from 48 to 79: score 3.5, E = 3.6 *->aAalaavigalvvgavlslligliklgrkflk<-* +A+l++v+++ ++++++s++ig+++l++k+ k NP_177574. 48 YAILVPVFAGIALLSLISVFIGMVMLKSKKKK 79 //