analysis of sequence from NP_014008.1.fa ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ >NP_014008.1 Gpi12p [Saccharomyces cerevisiae]. MKMLRRTKVN FSKLLYKITK LAIVLTILYI YFTPKIVSRN NASLQHIFPH KYGDYEINLV IAHPDDEVMF FSPIISQLNS YFPRTVPFNI ICLSKGNAEG LGETRVRELN ESAALLLHNE RAVSVQVMDF QDGMDEIWDI DSITSSLSQK IDIKNHNLNQ IIVTFDSYGV SNHINHKSCY AAVKKLVDDY AQPKTKRNEQ PPHVTALYLR SYKNNIVLKY NSFIWEILKI LYDLISPFRR IIQALPPNTA AEKDKLSLMN THAQYVLAFA TMLNAHESQV VWFRYGWWIF SRFVFVNEFD VYTY ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ sec.str. with predator > NP_014008.1 . . . . . 1 MKMLRRTKVNFSKLLYKITKLAIVLTILYIYFTPKIVSRNNASLQHIFPH 50 ______HHHHHHHHHHHHHHHHHHHHHHHHH___EEEEE___________ . . . . . 51 KYGDYEINLVIAHPDDEVMFFSPIISQLNSYFPRTVPFNIICLSKGNAEG 100 ________EEEE____EEEE__________________EEEEE_______ . . . . . 101 LGETRVRELNESAALLLHNERAVSVQVMDFQDGMDEIWDIDSITSSLSQK 150 __HHHHHHHHHHHHHHHHHHHEEEEEEEE______EEEE__________E . . . . . 151 IDIKNHNLNQIIVTFDSYGVSNHINHKSCYAAVKKLVDDYAQPKTKRNEQ 200 EE_______EEEEEE____________HHHHHHHHHHHHH__________ . . . . . 201 PPHVTALYLRSYKNNIVLKYNSFIWEILKILYDLISPFRRIIQALPPNTA 250 ___HHHHHHHH___EEEEEE__HHHHHHHHHHHH____HHHHH______H . . . . . 251 AEKDKLSLMNTHAQYVLAFATMLNAHESQVVWFRYGWWIFSRFVFVNEFD 300 HHHHHHHHHHHHHHHHHHHHHHHHH___EEEEEE__EEEEEEEEEEEE__ 301 VYTY 304 ____ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ method : 1 alpha-contents : 28.5 % beta-contents : 52.8 % coil-contents : 18.8 % class : mixed method : 2 alpha-contents : 21.3 % beta-contents : 43.5 % coil-contents : 35.2 % class : mixed ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ GPI: learning from metazoa -16.22 -2.30 -1.71 -2.96 0.00 0.00 0.00 0.00 -0.76 -6.80 -2.97 -12.00 -12.00 0.00 -12.00 0.00 -69.71 -11.97 -1.71 -2.25 -1.00 -4.00 0.00 0.00 0.00 -3.28 -5.84 -2.97 -12.00 -12.00 0.00 -12.00 0.00 -69.02 ID: NP_014008.1 AC: xxx Len: 304 1:I 278 Sc: -69.02 Pv: 5.449578e-01 NO_GPI_SITE GPI: learning from protozoa -41.30 -0.76 -1.08 -0.10 -4.00 0.00 0.00 0.00 -2.14 -5.24 -10.43 -12.00 -12.00 0.00 -12.00 0.00 -101.05 -36.65 -2.73 -1.21 -0.46 -4.00 0.00 0.00 0.00 -3.18 -5.43 -10.43 -12.00 -12.00 0.00 -12.00 0.00 -100.09 ID: NP_014008.1 AC: xxx Len: 304 1:I 277 Sc: -100.09 Pv: 8.647725e-01 NO_GPI_SITE ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ # SignalP euk predictions # name Cmax pos ? Ymax pos ? Smax pos ? Smean ? NP_014008.1 0.543 39 Y 0.570 39 Y 0.852 24 N 0.628 Y # SignalP gram- predictions # name Cmax pos ? Ymax pos ? Smax pos ? Smean ? NP_014008.1 0.398 276 N 0.259 39 N 0.939 6 Y 0.589 Y # SignalP gram+ predictions # name Cmax pos ? Ymax pos ? Smax pos ? Smean ? NP_014008.1 0.776 276 Y 0.417 251 Y 0.974 5 Y 0.259 N ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ low complexity regions: SEG 12 2.2 2.5 >NP_014008.1 Gpi12p [Saccharomyces cerevisiae]. 1-304 MKMLRRTKVNFSKLLYKITKLAIVLTILYI YFTPKIVSRNNASLQHIFPHKYGDYEINLV IAHPDDEVMFFSPIISQLNSYFPRTVPFNI ICLSKGNAEGLGETRVRELNESAALLLHNE RAVSVQVMDFQDGMDEIWDIDSITSSLSQK IDIKNHNLNQIIVTFDSYGVSNHINHKSCY AAVKKLVDDYAQPKTKRNEQPPHVTALYLR SYKNNIVLKYNSFIWEILKILYDLISPFRR IIQALPPNTAAEKDKLSLMNTHAQYVLAFA TMLNAHESQVVWFRYGWWIFSRFVFVNEFD VYTY low complexity regions: SEG 25 3.0 3.3 >NP_014008.1 Gpi12p [Saccharomyces cerevisiae]. 1-12 MKMLRRTKVNFS kllykitklaivltilyiyftpki 13-36 37-304 VSRNNASLQHIFPHKYGDYEINLVIAHPDD EVMFFSPIISQLNSYFPRTVPFNIICLSKG NAEGLGETRVRELNESAALLLHNERAVSVQ VMDFQDGMDEIWDIDSITSSLSQKIDIKNH NLNQIIVTFDSYGVSNHINHKSCYAAVKKL VDDYAQPKTKRNEQPPHVTALYLRSYKNNI VLKYNSFIWEILKILYDLISPFRRIIQALP PNTAAEKDKLSLMNTHAQYVLAFATMLNAH ESQVVWFRYGWWIFSRFVFVNEFDVYTY low complexity regions: SEG 45 3.4 3.75 >NP_014008.1 Gpi12p [Saccharomyces cerevisiae]. 1-304 MKMLRRTKVNFSKLLYKITKLAIVLTILYI YFTPKIVSRNNASLQHIFPHKYGDYEINLV IAHPDDEVMFFSPIISQLNSYFPRTVPFNI ICLSKGNAEGLGETRVRELNESAALLLHNE RAVSVQVMDFQDGMDEIWDIDSITSSLSQK IDIKNHNLNQIIVTFDSYGVSNHINHKSCY AAVKKLVDDYAQPKTKRNEQPPHVTALYLR SYKNNIVLKYNSFIWEILKILYDLISPFRR IIQALPPNTAAEKDKLSLMNTHAQYVLAFA TMLNAHESQVVWFRYGWWIFSRFVFVNEFD VYTY 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_014008.1 Gpi12p [Saccharomyces cerevisiae]. MKMLRRTKVNFSKLLYKITKLAIVLTILYIYFTPKIVSRNNASLQHIFPHKYGDYEINLV IAHPDDEVMFFSPIISQLNSYFPRTVPFNIICLSKGNAEGLGETRVRELNESAALLLHNE RAVSVQVMDFQDGMDEIWDIDSITSSLSQKIDIKNHNLNQIIVTFDSYGVSNHINHKSCY AAVKKLVDDYAQPKTKRNEQPPHVTALYLRSYKNNIVLKYNSFIWEILKILYDLISPFRR IIQALPPNTAAEKDKLSLMNTHAQYVLAFATMLNAHESQVVWFRYGWWIFSRFVFVNEFD VYTY 1 - 304 MKMLRRTKVN FSKLLYKITK LAIVLTILYI YFTPKIVSRN NASLQHIFPH KYGDYEINLV IAHPDDEVMF FSPIISQLNS YFPRTVPFNI ICLSKGNAEG LGETRVRELN ESAALLLHNE RAVSVQVMDF QDGMDEIWDI DSITSSLSQK IDIKNHNLNQ IIVTFDSYGV SNHINHKSCY AAVKKLVDDY AQPKTKRNEQ PPHVTALYLR SYKNNIVLKY NSFIWEILKI LYDLISPFRR IIQALPPNTA AEKDKLSLMN THAQYVLAFA TMLNAHESQV VWFRYGWWIF SRFVFVNEFD VYTY low complexity regions: DUST >NP_014008.1 Gpi12p [Saccharomyces cerevisiae]. MKMLRRTKVNFSKLLYKITKLAIVLTILYIYFTPKIVSRNNASLQHIFPHKYGDYEINLV IAHPDDEVMFFSPIISQLNSYFPRTVPFNIICLSKGNAEGLGETRVRELNESAALLLHNE RAVSVQVMDFQDGMDEIWDIDSITSSLSQKIDIKNHNLNQIIVTFDSYGVSNHINHKSCY AAVKKLVDDYAQPKTKRNEQPPHVTALYLRSYKNNIVLKYNSFIWEILKILYDLISPFRR IIQALPPNTAAEKDKLSLMNTHAQYVLAFATMLNAHESQVVWFRYGWWIFSRFVFVNEFD VYTY ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ coiled coil prediction for NP_014008.1 sequence: 304 amino acids, 0 residue(s) in coiled coil state . | . | . | . | . | . 60 MKMLRRTKVN FSKLLYKITK LAIVLTILYI YFTPKIVSRN NASLQHIFPH KYGDYEINLV ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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 IAHPDDEVMF FSPIISQLNS YFPRTVPFNI ICLSKGNAEG LGETRVRELN ESAALLLHNE ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border ---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~11111111 1111111111 * 21 MTK -w class ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif. ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~55555555 555555~~~~ * 14 M'95 -w local . | . | . | . | . | . 180 RAVSVQVMDF QDGMDEIWDI DSITSSLSQK IDIKNHNLNQ IIVTFDSYGV SNHINHKSCY ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border ---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar 111~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif. ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~2222 2222222222 ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local . | . | . | . | . | . 240 AAVKKLVDDY AQPKTKRNEQ PPHVTALYLR SYKNNIVLKY NSFIWEILKI LYDLISPFRR ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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 . | . | . | . | . | . 300 IIQALPPNTA AEKDKLSLMN THAQYVLAFA TMLNAHESQV VWFRYGWWIF SRFVFVNEFD ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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 VYTY ~~~~ ---- ~~~~ ~~~~ ~~~~ ~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ prediction of transmembrane regions with toppred2 *********************************** *TOPPREDM with eukaryotic function* *********************************** NP_014008.1.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_014008.1.fa.___inter___ (1 sequences) MKMLRRTKVNFSKLLYKITKLAIVLTILYIYFTPKIVSRNNASLQHIFPH KYGDYEINLVIAHPDDEVMFFSPIISQLNSYFPRTVPFNIICLSKGNAEG LGETRVRELNESAALLLHNERAVSVQVMDFQDGMDEIWDIDSITSSLSQK IDIKNHNLNQIIVTFDSYGVSNHINHKSCYAAVKKLVDDYAQPKTKRNEQ PPHVTALYLRSYKNNIVLKYNSFIWEILKILYDLISPFRRIIQALPPNTA AEKDKLSLMNTHAQYVLAFATMLNAHESQVVWFRYGWWIFSRFVFVNEFD VYTY (p)rokaryotic or (e)ukaryotic: e Charge-pair energy: 0 Length of full window (odd number!): 21 Length of core window (odd number!): 11 Number of residues to add to each end of helix: 1 Critical length: 60 Upper cutoff for candidates: 1 Lower cutoff for candidates: 0.6 Total of 2 structures are to be tested Candidate membrane-spanning segments: Helix Begin End Score Certainity 1 18 38 1.237 Certain 2 256 276 0.742 Putative ---------------------------------------------------------------------- Structure 1 Transmembrane segments included in this structure: Segment 1 2 Loop length 17 217 28 K+R profile 8.00 2.00 + CYT-EXT prof - - 0.76 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 10.00 Tm probability: 0.35 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 4.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 7.0000 -> Orientation: N-in CYT-EXT difference: -0.76 -> Orientation: N-in ---------------------------------------------------------------------- Structure 2 Transmembrane segments included in this structure: Segment 1 Loop length 17 266 K+R profile 8.00 + CYT-EXT prof - 1.09 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 8.00 Tm probability: 1.00 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 4.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 7.0000 -> Orientation: N-in CYT-EXT difference: -1.09 -> Orientation: N-in ---------------------------------------------------------------------- "NP_014008" 304 18 38 #t 1.2375 256 276 #f 0.741667 ************************************ *TOPPREDM with prokaryotic function* ************************************ NP_014008.1.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_014008.1.fa.___inter___ (1 sequences) MKMLRRTKVNFSKLLYKITKLAIVLTILYIYFTPKIVSRNNASLQHIFPH KYGDYEINLVIAHPDDEVMFFSPIISQLNSYFPRTVPFNIICLSKGNAEG LGETRVRELNESAALLLHNERAVSVQVMDFQDGMDEIWDIDSITSSLSQK IDIKNHNLNQIIVTFDSYGVSNHINHKSCYAAVKKLVDDYAQPKTKRNEQ PPHVTALYLRSYKNNIVLKYNSFIWEILKILYDLISPFRRIIQALPPNTA AEKDKLSLMNTHAQYVLAFATMLNAHESQVVWFRYGWWIFSRFVFVNEFD VYTY (p)rokaryotic or (e)ukaryotic: p Charge-pair energy: 0 Length of full window (odd number!): 21 Length of core window (odd number!): 11 Number of residues to add to each end of helix: 1 Critical length: 60 Upper cutoff for candidates: 1 Lower cutoff for candidates: 0.6 Total of 2 structures are to be tested Candidate membrane-spanning segments: Helix Begin End Score Certainity 1 18 38 1.237 Certain 2 256 276 0.742 Putative ---------------------------------------------------------------------- Structure 1 Transmembrane segments included in this structure: Segment 1 2 Loop length 17 217 28 K+R profile 7.00 2.00 + CYT-EXT prof - - 0.76 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 9.00 Tm probability: 0.35 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 4.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 7.0000 -> Orientation: N-in CYT-EXT difference: -0.76 -> Orientation: N-in ---------------------------------------------------------------------- Structure 2 Transmembrane segments included in this structure: Segment 1 Loop length 17 266 K+R profile 7.00 + CYT-EXT prof - 1.09 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 7.00 Tm probability: 1.00 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 4.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 7.0000 -> Orientation: N-in CYT-EXT difference: -1.09 -> Orientation: N-in ---------------------------------------------------------------------- "NP_014008" 304 18 38 #t 1.2375 256 276 #f 0.741667 ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ SAPS. Version of April 11, 1996. Date run: Fri Mar 8 14:48:10 2002 File: /people/b_eisen/NP_014008.1.fa.___saps___ ID NP_014008.1 DE Gpi12p [Saccharomyces cerevisiae]. number of residues: 304; molecular weight: 35.4 kdal 1 MKMLRRTKVN FSKLLYKITK LAIVLTILYI YFTPKIVSRN NASLQHIFPH KYGDYEINLV 61 IAHPDDEVMF FSPIISQLNS YFPRTVPFNI ICLSKGNAEG LGETRVRELN ESAALLLHNE 121 RAVSVQVMDF QDGMDEIWDI DSITSSLSQK IDIKNHNLNQ IIVTFDSYGV SNHINHKSCY 181 AAVKKLVDDY AQPKTKRNEQ PPHVTALYLR SYKNNIVLKY NSFIWEILKI LYDLISPFRR 241 IIQALPPNTA AEKDKLSLMN THAQYVLAFA TMLNAHESQV VWFRYGWWIF SRFVFVNEFD 301 VYTY -------------------------------------------------------------------------------- COMPOSITIONAL ANALYSIS (extremes relative to: swp23s) A : 18( 5.9%); C : 2( 0.7%); D : 15( 4.9%); E : 13( 4.3%); F : 17( 5.6%) G- : 7( 2.3%); H : 10( 3.3%); I : 28( 9.2%); K : 20( 6.6%); L : 29( 9.5%) M : 7( 2.3%); N : 22( 7.2%); P : 12( 3.9%); Q : 11( 3.6%); R : 13( 4.3%) S : 22( 7.2%); T : 14( 4.6%); V : 22( 7.2%); W : 5( 1.6%); Y : 17( 5.6%) KR : 33 ( 10.9%); ED : 28 ( 9.2%); AGP : 37 ( 12.2%); KRED : 61 ( 20.1%); KR-ED : 5 ( 1.6%); FIKMNY+ : 111 ( 36.5%); LVIFM : 103 ( 33.9%); ST : 36 ( 11.8%). -------------------------------------------------------------------------------- CHARGE DISTRIBUTIONAL ANALYSIS 1 0+00++0+00 00+000+00+ 0000000000 0000+000+0 0000000000 +00-0-0000 61 0000---000 0000000000 000+000000 0000+000-0 00-0+0+-00 -00000000- 121 +0000000-0 0-00--00-0 -00000000+ 0-0+000000 00000-0000 000000+000 181 000++00--0 000+0++0-0 000000000+ 00+00000+0 00000-00+0 00-00000++ 241 0000000000 0-+-+00000 0000000000 000000-000 000+000000 0+00000-0- 301 0000 A. CHARGE CLUSTERS. Positive charge clusters (cmin = 10/30 or 13/45 or 16/60): none Negative charge clusters (cmin = 9/30 or 11/45 or 14/60): none Mixed charge clusters (cmin = 14/30 or 19/45 or 24/60): none B. HIGH SCORING (UN)CHARGED SEGMENTS. There are no high scoring positive charge segments. There are no high scoring negative charge segments. There are no high scoring mixed charge segments. There are no high scoring uncharged segments. C. CHARGE RUNS AND PATTERNS. pattern (+)| (-)| (*)| (0)| (+0)| (-0)| (*0)|(+00)|(-00)|(*00)| (H.)|(H..)| lmin0 5 | 4 | 6 | 39 | 9 | 9 | 12 | 11 | 10 | 14 | 7 | 9 | lmin1 6 | 6 | 8 | 47 | 11 | 11 | 14 | 14 | 13 | 17 | 9 | 11 | lmin2 7 | 7 | 9 | 52 | 13 | 12 | 16 | 15 | 14 | 19 | 10 | 12 | (Significance level: 0.010000; Minimal displayed length: 6) There are no charge runs or patterns exceeding the given minimal lengths. Run count statistics: + runs >= 3: 0 - runs >= 3: 1, at 65; * runs >= 4: 1, at 252; 0 runs >= 26: 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-91-C-86-C-125-COOH 2*. SPACINGS OF C and H. (additional deluxe function for ALEX) H2N-45-H-3-H-12-H-28-C-25-H-37-H-16-H-2-H-2-C-23-H-58-H-13-H-28-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: 22 (Expected range: 5-- 30) 2. Histogram of spacings between consecutive amino acid multiplets: (1-5) 9 (6-10) 2 (11-20) 6 (>=21) 6 3. Clusters of amino acid multiplets (cmin = 12/30 or 16/45 or 19/60): none B. CHARGE ALPHABET. 1. Total number of charge multiplets: 7 (Expected range: 0-- 13) 4 +plets (f+: 10.9%), 3 -plets (f-: 9.2%) Total number of charge altplets: 3 (Critical number: 15) 2. Histogram of spacings between consecutive charge multiplets: (1-5) 2 (6-10) 1 (11-20) 0 (>=21) 5 -------------------------------------------------------------------------------- PERIODICITY ANALYSIS. A. AMINO ACID ALPHABET (core: 4; !-core: 5) Location Period Element Copies Core Errors 93- 124 8 L....A.. 4 4 /0/././././1/././ B. CHARGE ALPHABET ({+= KR; -= ED; 0}; core: 5; !-core: 6) and HYDROPHOBICITY ALPHABET ({*= KRED; i= LVIF; 0}; core: 6; !-core: 9) Location Period Element Copies Core Errors 15- 32 3 i0. 6 6 /0/2/./ 70- 93 4 i.00 6 6 /0/./2/1/ -------------------------------------------------------------------------------- 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_014008.1.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: NP_014008.1 Gpi12p [Saccharomyces cerevisiae]. Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- BRO BRO family, N-terminus -40.8 84 1 DUF158 Uncharacterized LmbE-like protein, COG2120 -95.2 8 1 DUF215 Domain of unknown function DUF215 -102.8 95 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- BRO 1/1 145 229 .. 1 121 [] -40.8 84 DUF215 1/1 19 232 .. 1 155 [] -102.8 95 DUF158 1/1 54 273 .. 1 292 [] -95.2 8 Alignments of top-scoring domains: BRO: domain 1 of 1, from 145 to 229: score -40.8, E = 84 *->MalvkigeFkfgeDtitlryvlneeqevyFvAKDIAeiLkYkntkdA +l++ ++ k+ ++ ++v+ + +y v + I ++k ++ A NP_014008. 145 SSLSQKIDIKNHN--LNQIIVTFD---SYGVSNHI----NHKSCYAA 182 IrkHVddkyKstyeelinrksdlasvsvykqgDPLYlqphTvlInksGvi ++k Vdd + +++ + ++ + + v NP_014008. 183 VKKLVDDYAQPKTKRN-EQ-----PPH---------------------VT 205 eLImkSklpyAkefqnwliEevlP<-* L ++S + +++ + n +i e l NP_014008. 206 ALYLRSYKNNIVLKYNSFIWEILK 229 DUF215: domain 1 of 1, from 19 to 232: score -102.8, E = 95 *->ilRLPsTGilTSWCAsqePNhyLkiifittyYfnYsaMifPFLlsll ++ ++++i+ +Yf+ + +++ +sl NP_014008. 19 -------------------TKLAIVLTILYIYFT-PKIVSRNNASL- 44 RLilIvfPqrHnKldkiiefleilelnvvkwykiNskilkiaiPfifIYP +fP+++ y iN +i + f++P NP_014008. 45 ---QHIFPHKYGD------------------YEINLVIAHPDDEVMFFSP 73 ifFTFFliPAvGyCRQLsg......PypFGSvfiyytgswfgis...... i+ +QL + +++ P++ ++ +g++ g+ +++ ++ NP_014008. 74 II------------SQLNSyfprtvPFN---IICLSKGNAEGLGetrvre 108 .................................................. +++ ++++ + + + +++ ++ + ++ +++ +++ + ++++ NP_014008. 109 lnesaalllhneravsvqvmdfqdgmdeiwdidsitsslsqkidiknhnl 158 .................................................. ++ + ++ + +++ ++++ ++ ++ ++++++++++++ + NP_014008. 159 nqiivtfdsygvsnhinhkscyaavkklvddyaqpktkrneqpphvtaly 208 ....rNsyfllfNtvfWLslclii<-* ++ +N++ l +N+++W +l ++ NP_014008. 209 lrsyKNNIVLKYNSFIWEILKILY 232 DUF158: domain 1 of 1, from 54 to 273: score -95.2, E = 8 *->ssenrLkdAkkVLavhAHPDDesigmGATiakftd...qGkrVlvvt + e L v AHPDDe++ i + + ++ + +++ NP_014008. 54 DYEINL--------VIAHPDDEVMFFSPIISQLNSyfpRTVPFNIIC 92 lTeGeegstlgsRWAqllaDsadeLaeiRreElaeAAriLGVkkh...iq l G ++ lg R El e+A +L ++ ++q NP_014008. 93 LSKG-NAEGLGE---------------TRVRELNESAALLLHNERavsVQ 126 LgladrgldkGdlgtqlpDrgLaqsdLeevtkalVkviRelrPH....vl q ++ ++d t +l + i + H+ +++ NP_014008. 127 VMDF-----------QDGMDEIWDID--SITSSLSQKIDIKN-HnlnqII 162 lVFdpnggyPYEgHPDHrrtHtVtaAaveaAgafagtpdfpgdpwtvpkl ++Fd +g+ H++ H+ Aav ++ d+ p+t NP_014008. 163 VTFDSYGVS------NHIN-HKSCYAAVKKLVD-----DY-AQPKTKRNE 199 YyvvlfLrekvsklsaeflasfhRGPFEeWllkrdddidFfvsdDGiddl + a+ l+s + + +lk + F + +l NP_014008. 200 ---------QPPHVTALYLRSYK----NNIVLKYN---SFIWEI--LKIL 231 iEakkqaRlrklaAlfahatqsvsePllraiaellgerekly.keEgfrl + + r Al + ++ +++ l + + ++l NP_014008. 232 YDLISPF-RRIIQALPPNTAAEK-------------DKLSLMnTHAQYVL 267 argsfp<-* a NP_014008. 268 AFATML 273 // 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_014008.1.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: NP_014008.1 Gpi12p [Saccharomyces cerevisiae]. Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- Papilloma_E5 Papillomavirus E5 1.7 45 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- Papilloma_E5 1/1 258 268 .. 64 74 .] 1.7 45 Alignments of top-scoring domains: Papilloma_E5: domain 1 of 1, from 258 to 268: score 1.7, E = 45 *->lIHlHAqyLlq<-* l ++HAqy l NP_014008. 258 LMNTHAQYVLA 268 // 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_014008.1.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: NP_014008.1 Gpi12p [Saccharomyces cerevisiae]. Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- [no hits above thresholds] Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- [no hits above thresholds] Alignments of top-scoring domains: [no hits above thresholds] // ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ Start with Prosite --------------------------------------------------------- | ppsearch (c) 1994 EMBL Data Library | | based on MacPattern (c) 1990-1994 R. Fuchs | --------------------------------------------------------- PROSITE pattern search started: Fri Mar 8 14:50:05 2002 Sequence file: NP_014008.1.fa ---------------------------------------- Sequence NP_014008.1 (304 residues): Matching pattern PS00001 ASN_GLYCOSYLATION: 10: NFSK 41: NASL 110: NESA Total matches: 3 Matching pattern PS00005 PKC_PHOSPHO_SITE: 33: TPK 148: SQK 195: TKR 211: SYK Total matches: 4 Matching pattern PS00006 CK2_PHOSPHO_SITE: 249: TAAE Total matches: 1 Matching pattern PS00008 MYRISTYL: 96: GNAEGL 100: GLGETR Total matches: 2 Total no of hits in this sequence: 10 ======================================== 1314 pattern(s) searched in 1 sequence(s), 304 residues. Total no of hits in all sequences: 10. 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, 304 units >ER-GOLGI-traffic signal is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 304 units >INTRA-SIGNAL-M minimal SH3 binding is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 304 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, 304 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, 304 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, 304 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, 304 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, 304 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, 304 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, 304 units >TM-CYTOPLASMIC-M di-hydrophobic endocytosis motifs for internalized transmembrane proteins is the MOTIF name >NP_014008.1 Gpi12p [Saccharomyces cerevisiae]. ;LENGTH=304; DIRECT_SEQUENCE n 1 solutions m %_E 111-111 %_XXXL 112-115 %_L 116-116 f >STATISTICS Total : 1 solutions in 1 sequences, 304 units; out of 1 sequences, 304 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, 304 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, 304 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, 304 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, 304 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, 304 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, 304 units >NUCLEAR NLS experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 304 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, 304 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, 304 units >NUCLEAR NLS HCDA experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 304 units >NUCLEAR NLS SV40 LrgT experimentally determined is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 304 units >NUCLEAR NLS H2B experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 304 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, 304 units >NUCLEAR NLS Amida experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 304 units >NUCLEAR NLS Amida experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 304 units >NUCLEAR NLS RanBP3 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 304 units >NUCLEAR NLS Pho4p experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 304 units >NUCLEAR NLS DNAhelicaseQ1 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 304 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, 304 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, 304 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, 304 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, 304 units >NUCLEAR NLS GAL4 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 304 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, 304 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, 304 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, 304 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, 304 units >NUCLEAR NLS TR2 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 304 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, 304 units >NUCLEAR NLS polyomaVP1 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 304 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, 304 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, 304 units >NUCLEAR NLS Rex experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 304 units >NUCLEAR NLS SRY experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 304 units >NUCLEAR NLS SRY experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 304 units >NUCLEAR NLS SOX9 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 304 units >NUCLEAR NLS SOX9 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 304 units >NUCLEAR NLS NS5A experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 304 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, 304 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, 304 units >NUCLEAR NLS adenovE1a experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 304 units >NUCLEAR NLS ystDNApolalpha experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 304 units >NUCLEAR NLS hVDR experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 304 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, 304 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, 304 units >NUCLEAR NLS cFOS experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 304 units >NUCLEAR NLS cJUN experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 304 units >NUCLEAR NLS hDNApolalpha experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 304 units >NUCLEAR NLS hDNAtopoII experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 304 units >NUCLEAR NLS hDNAtopoII experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 304 units >NUCLEAR NLS hBLM experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 304 units >NUCLEAR NLS hARNT experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 304 units >NUCLEAR NLS influenzaNP experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 304 units >NUCLEAR NLS influenzaNP experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 304 units >NUCLEAR NLS p54 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 304 units >NUCLEAR NLS hProTalpha experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 304 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, 304 units >NUCLEAR NLS protHsc9 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 304 units >NUCLEAR NLS protHsci experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 304 units >NUCLEAR NLS protHsc3 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 304 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, 304 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, 304 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, 304 units >NUCLEAR NLS MyoD experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 304 units >NUCLEAR NLS MyoD experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 304 units >NUCLEAR NLS opaque2 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 304 units >NUCLEAR NLS CTP experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 304 units >NUCLEAR NLS HCV experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 304 units >NUCLEAR NLS HCV experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 304 units >NUCLEAR NLS p110RB1 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 304 units >NUCLEAR NLS experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 304 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, 304 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, 304 units >NUCLEAR NLS Nucloplasmin experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 304 units >NUCLEAR NLS Nucleolin experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 304 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, 304 units >NUCLEAR NLS Nab2 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 304 units >NUCLEAR NLS M9 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 304 units >NUCLEAR NLS lscMyc experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 304 units >NUCLEAR NLS humKprotein experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 304 units >NUCLEAR NLS FluA experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 304 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, 304 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, 304 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, 304 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, 304 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, 304 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, 304 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, 304 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, 304 units >NUCLEAR NLS p53 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 304 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, 304 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, 304 units >NUCLEAR NLS L29 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 304 units >NUCLEAR NLS L29 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 304 units >NUCLEAR NLS Max experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 304 units >NUCLEAR NLS L3 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 304 units >NUCLEAR NLS dyskerin experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 304 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, 304 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, 304 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_014008.1.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: NP_014008.1 Gpi12p [Saccharomyces cerevisiae]. 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_014008.1.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: NP_014008.1 Gpi12p [Saccharomyces cerevisiae]. 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_014008.1 Gpi12p [Saccharomyces cerevisiae]. (304 letters) Searching..................................done Results from profile search Score E Sequences producing significant alignments: (bits) Value UBHYD Ubiquitin C-terminal hydrolase domain 21 2.7 HISDAC Histone deacetylase domain 21 3.0 RASGAP RAS-type GTPase GTP hydrolysis activating protein 20 3.7 CYCLIN Cyclin/TFIIB domain 20 5.4 PUM Pumilio repeat RNA binding domain 20 5.4 HOMEO Homeodomain (HTH DNa binding domain) 19 6.3 PCNA Proliferating Cell nuclear antigen like domain 19 7.5 SH3 Src Homology domain 3 19 9.9 >UBHYD Ubiquitin C-terminal hydrolase domain Length = 884 Score = 20.7 bits (43), Expect = 2.7 Identities = 4/56 (7%), Positives = 4/56 (7%) Query: 209 LRSYKNNIVLKYNSFIWEILKILYDLISPFRRIIQALPPNTAAEKDKLSLMNTHAQ 264 Sbjct: 20 LRKAVYMMPTEGDDSSKSVPLALQRVFYELQHSDKPVGTKKLTKSFGWETLDSFMQ 75 >HISDAC Histone deacetylase domain Length = 433 Score = 20.6 bits (43), Expect = 3.0 Identities = 7/21 (33%), Positives = 7/21 (33%), Gaps = 2/21 (9%) Query: 65 DDEVMFFSPIISQLNSYFPRT 85 Sbjct: 200 TDRVMTCS--FHKYGEFFPGT 218 >RASGAP RAS-type GTPase GTP hydrolysis activating protein Length = 292 Score = 20.1 bits (41), Expect = 3.7 Identities = 8/32 (25%), Positives = 8/32 (25%) Query: 43 SLQHIFPHKYGDYEINLVIAHPDDEVMFFSPI 74 Sbjct: 14 TADHVFPLATYDDLMNLLLESVDQRPITVSAV 45 >CYCLIN Cyclin/TFIIB domain Length = 317 Score = 19.5 bits (40), Expect = 5.4 Identities = 7/59 (11%), Positives = 7/59 (11%), Gaps = 4/59 (6%) Query: 217 VLKYNSFIWEILKILYDLISPF---RRIIQALPPNTAAEKDKLSLMNTHAQYVLAFATM 272 Sbjct: 137 ILEYELLLIQQLNFHLIVHNPYRPFEGFLIDLKTRYPI-LENPEILRKTADDFLNRIAL 194 >PUM Pumilio repeat RNA binding domain Length = 337 Score = 19.8 bits (41), Expect = 5.4 Identities = 4/31 (12%), Positives = 4/31 (12%) Query: 50 HKYGDYEINLVIAHPDDEVMFFSPIISQLNS 80 Sbjct: 211 DQFGNYIIQFLLDIKELDFYLLAELFNRLSN 241 >HOMEO Homeodomain (HTH DNa binding domain) Length = 65 Score = 19.4 bits (40), Expect = 6.3 Identities = 6/15 (40%), Positives = 6/15 (40%), Gaps = 1/15 (6%) Query: 270 ATMLNAHESQV-VWF 283 Sbjct: 39 ASMIHLTPTQVKIWF 53 >PCNA Proliferating Cell nuclear antigen like domain Length = 280 Score = 19.4 bits (40), Expect = 7.5 Identities = 8/36 (22%), Positives = 8/36 (22%) Query: 134 MDEIWDIDSITSSLSQKIDIKNHNLNQIIVTFDSYG 169 Sbjct: 139 PEETLDFDFCSTNVMNKIILQSEGLREAFSELDMTG 174 >SH3 Src Homology domain 3 Length = 90 Score = 19.0 bits (39), Expect = 9.9 Identities = 6/19 (31%), Positives = 6/19 (31%) Query: 190 YAQPKTKRNEQPPHVTALY 208 Sbjct: 67 FVQIIKPLPQPPPQCKALY 85 Underlying Matrix: BLOSUM62 Number of sequences tested against query: 105 Number of sequences better than 10.0: 8 Number of calls to ALIGN: 8 Length of query: 304 Total length of test sequences: 20182 Effective length of test sequences: 16637.0 Effective search space size: 4505045.9 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_014008.1 Gpi12p [Saccharomyces cerevisiae]. (304 letters) Searching.................................................done Results from profile search Score E Sequences producing significant alignments: (bits) Value gi|544020 [86..429] Nitrogenase iron-molybdenum protein, alp... 24 3.7 gi|1352256 [4..245] NAD(P)-binding Rossmann-fold domains 24 3.9 gi|84873 [335..1022] P-loop containing nucleotide triphospha... 23 5.4 gi|128242 [2..526] Nitrogenase iron-molybdenum protein, alph... 23 5.8 gi|1657653 [5..162] NAD(P)-binding Rossmann-fold domains 23 6.1 gi|2494016 [1..267] Single-stranded left-handed beta-helix 23 6.6 gi|485123 [360..500] alpha/beta-Hydrolases 23 8.9 gi|1465871 [5..212] NAD(P)-binding Rossmann-fold domains 23 9.1 >gi|544020 [86..429] Nitrogenase iron-molybdenum protein, alpha and beta chains Length = 344 Score = 23.7 bits (51), Expect = 3.7 Identities = 12/102 (11%), Positives = 12/102 (11%), Gaps = 18/102 (17%) Query: 139 DIDSITSSLSQKIDIKNHNLNQIIVTFDSYGVSNHINHKSCYAAVKKLVDDYAQPKTKRN 198 Sbjct: 18 DLQNFADRASIISDSN-------VIFADVDHYRVN-ELQAADRTLEQVVRYY----LDRS 65 Query: 199 EQPPHVTALYLRSYKNNIVLKYNSF------IWEILKILYDL 234 Sbjct: 66 HRQETLDQSVTDAPSANLIGIFTLGFHNQHDCRELRRLLRDL 107 >gi|1352256 [4..245] NAD(P)-binding Rossmann-fold domains Length = 242 Score = 23.8 bits (50), Expect = 3.9 Identities = 16/151 (10%), Positives = 16/151 (10%), Gaps = 8/151 (5%) Query: 128 MDFQDGMDEIWDIDSITSSLSQKIDIKNHNLNQIIVTFDSYGVSNHINHKSCYAAVKKLV 187 Sbjct: 98 TPFHIQAEVTMETNFFGTRDVCKELLPLIKPQGRVVNVSSMVSLRALKNCRLELQQKFRS 157 Query: 188 DDYAQPKTKRNEQPPHVTALYLRSYKNNIVLKYNSFIWEILKILYDLISPFRRIIQALPP 247 Sbjct: 158 ETITE-EELVGLMNKFVEDTKKGVHAEEGWPNSAYGVTKIGVTVLSRIL-------ARKL 209 Query: 248 NTAAEKDKLSLMNTHAQYVLAFATMLNAHES 278 Sbjct: 210 NEQRREDKILLNACCPGWVRTDMAGPKATKS 240 >gi|84873 [335..1022] P-loop containing nucleotide triphosphate hydrolases Length = 688 Score = 23.3 bits (50), Expect = 5.4 Identities = 7/29 (24%), Positives = 7/29 (24%) Query: 196 KRNEQPPHVTALYLRSYKNNIVLKYNSFI 224 Sbjct: 59 SRSENQPHIFSVADIAYQDMLHHKEPQHI 87 >gi|128242 [2..526] Nitrogenase iron-molybdenum protein, alpha and beta chains Length = 525 Score = 23.3 bits (50), Expect = 5.8 Identities = 15/100 (15%), Positives = 15/100 (15%), Gaps = 24/100 (24%) Query: 139 DIDSITSSLSQKIDIKNHNLNQIIVTFD--SYGVSNHINHKSCYAAVKKLVDDYAQPKTK 196 Sbjct: 152 DILAVAATASKEIGIP-------VHAFSCEGYKGVSQS---AGHHIANNTVMTDIIGKGN 201 Query: 197 RNEQPPHVTALYLRSYKNNIVLKYNSF--IWEILKILYDL 234 Sbjct: 202 KEQKKYSI----------NVLGEYNIGGDAWEMDRVLEKI 231 >gi|1657653 [5..162] NAD(P)-binding Rossmann-fold domains Length = 158 Score = 23.0 bits (48), Expect = 6.1 Identities = 6/34 (17%), Positives = 6/34 (17%) Query: 159 NQIIVTFDSYGVSNHINHKSCYAAVKKLVDDYAQ 192 Sbjct: 100 EGQVGKSDQIDTQTPMNPTTNYGISKKFAEQALQ 133 >gi|2494016 [1..267] Single-stranded left-handed beta-helix Length = 267 Score = 23.0 bits (49), Expect = 6.6 Identities = 6/32 (18%), Positives = 6/32 (18%) Query: 222 SFIWEILKILYDLISPFRRIIQALPPNTAAEK 253 Sbjct: 213 HAIRNAYKILYRNGKTLEEAREEIAQLAADNN 244 >gi|485123 [360..500] alpha/beta-Hydrolases Length = 141 Score = 22.5 bits (48), Expect = 8.9 Identities = 7/40 (17%), Positives = 7/40 (17%), Gaps = 2/40 (5%) Query: 130 FQDGMDEIWDIDSITSSLSQKIDIKNHNLNQIIVTFDSYG 169 Sbjct: 62 MLRSARYVFD-TLNKNKILNDLFISNPSY-QLVVCGHSLG 99 >gi|1465871 [5..212] NAD(P)-binding Rossmann-fold domains Length = 208 Score = 22.7 bits (47), Expect = 9.1 Identities = 4/44 (9%), Positives = 4/44 (9%) Query: 149 QKIDIKNHNLNQIIVTFDSYGVSNHINHKSCYAAVKKLVDDYAQ 192 Sbjct: 114 ASSVAVSFIGEPLDNVTEDDPLPDPKKYLDFYSASKAEAETYVL 157 Underlying Matrix: BLOSUM62 Number of sequences tested against query: 1187 Number of sequences better than 10.0: 8 Number of calls to ALIGN: 8 Length of query: 304 Total length of test sequences: 256703 Effective length of test sequences: 209547.0 Effective search space size: 55445046.3 Initial X dropoff for ALIGN: 25.0 bits ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ calculation of internal repeats with prospero ***** PROSPERO v1.3 Fri Mar 8 14:50:42 2002 ***** Copyright 2000, Richard Mott, Wellcome Trust Centre for Human Genetics, University of Oxford For help see http://www.well.ox.ac.uk/ariadne For usage use -help using gap penalty 11+1k using matrix BLOSUM62 printing all alignments with eval < 0.100000 using sequence1 NP_014008.1 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_014008.1.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: NP_014008.1 Gpi12p [Saccharomyces cerevisiae]. 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_014008.1.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: NP_014008.1 Gpi12p [Saccharomyces cerevisiae]. Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- TIGR00056 TIGR00056: conserved hypothetical protein T -0.8 67 1 TIGR00054 TIGR00054: membrane-associated zinc metallo -1.3 82 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- TIGR00056 1/1 70 80 .. 265 275 .] -0.8 67 TIGR00054 1/1 256 277 .. 1 22 [. -1.3 82 Alignments of top-scoring domains: TIGR00056: domain 1 of 1, from 70 to 80: score -0.8, E = 67 *->vLSaimFqLGi<-* ++S i++qL++ NP_014008. 70 FFSPIISQLNS 80 TIGR00054: domain 1 of 1, from 256 to 277: score -1.3, E = 82 *->msflwiLasFIiaLavLIfVHE<-* +s +++ a +++a+a+ HE NP_014008. 256 LSLMNTHAQYVLAFATMLNAHE 277 // 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_014008.1.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: NP_014008.1 Gpi12p [Saccharomyces cerevisiae]. 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_014008.1.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: NP_014008.1 Gpi12p [Saccharomyces cerevisiae]. Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- COG2120 -110.7 9.1 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- COG2120 1/1 29 296 .. 1 317 [] -110.7 9.1 Alignments of top-scoring domains: COG2120: domain 1 of 1, from 29 to 296: score -110.7, E = 9.1 *->mfeinspleeaffkllreVlemtstsplaselrvLavfpHPDDEsiG + + + l+ + ++ ++ +v +HPDDE+ NP_014008. 29 YIYFTPKIVSRNNASLQHIFPHKYG-----DYEINLVIAHPDDEVMF 70 cGGTLak...yaaaGveVglvclTlGEmGenltqplldthetlgeiRreE + + + ++y + v+ ++cl ++ ++e lge+R +E NP_014008. 71 FSPIISQlnsYFPRTVPFNIICL------------SKGNAEGLGETRVRE 108 laeAArvL.....GvekrillglgsrypDggLe...........tepddq l e+A++L ++++ v+ ++++ + g+ + + ++ +++ ++ + NP_014008. 109 LNESAALLlhnerAVSVQVMDF------QDGMDeiwdidsitssLSQKID 152 earvdlvqaqtalvatdLravirelrPhvVltpdPwnGgdgHPDHrathe ++ ++l+q ++t+d +G+ H H ++ NP_014008. 153 IKNHNLNQ--------------------IIVTFDS-YGVSNHINHKSCYA 181 lavaAvasagipkrpndwgvsaavayytdlgasplqagsryqlnatldPd +++ v+ +pk ++ + ++ t+l+++ + n+++ ++ NP_014008. 182 AVKKLVDDYAQPKTKRNE-QPP---HVTALYLRSYKNNIVLKYNSFIWEI 227 vllltsdelavtqkvvdisavaevKlaAiraHrtQfadtalferafplen ++ ++ + is+ + +A+ + ta ++ l n NP_014008. 228 LK------ILY----DLISPFRR-IIQALP------PNTAAEKDKLSLMN 260 erlelrveaaltwygleagvtyaegfrgeeslllailgl<-* + ++ +++ + l a ++ fr++ + +++ NP_014008. 261 THAQY---VLAFATMLNAHESQVVWFRYGWWIFSRFVFV 296 // 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_014008.1.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: NP_014008.1 Gpi12p [Saccharomyces cerevisiae]. Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- COG2020 2.1 23 1 COG3014 -1.7 64 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- COG3014 1/1 207 222 .. 496 511 .] -1.7 64 COG2020 1/1 256 288 .. 1 33 [. 2.1 23 Alignments of top-scoring domains: COG3014: domain 1 of 1, from 207 to 222: score -1.7, E = 64 *->LYvRsFKnGFvLsrLK<-* LY Rs+Kn vL NP_014008. 207 LYLRSYKNNIVLKYNS 222 COG2020: domain 1 of 1, from 256 to 288: score 2.1, E = 23 *->lsalavavshsvplvaggillrfnvrvvvlgll<-* ls + + +++++++++++++ v+ + +g++ NP_014008. 256 LSLMNTHAQYVLAFATMLNAHESQVVWFRYGWW 288 //