analysis of sequence from tem41 ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ >tem41FGENES-M 1.5 MKDPAARDDRIYVTNYYYGNSLVEFRNLENFKQGRWSNMYKLPYNWIGTGHVVYQGAFYY NRAFTKNIIKYDLRQRFVASWALLPDVVYEDTTPWKWRGHSDIDFAVDESGLWVIYPAVD DRDEAQPEVIVLSRLDPGDLSVHRETTWKTRLRRNSYGNCFLVCGILYAVDTYNQQEGQV AYAFDTHTGTDARPQLPFLNEHAYTTQIDYNPKERVLYAWDNGHQLTYTLHFVV ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ sec.str. with predator > tem41FGENES-M . . . . . 1 MKDPAARDDRIYVTNYYYGNSLVEFRNLENFKQGRWSNMYKLPYNWIGTG 50 _________EEEEE_______EEEE_________________________ . . . . . 51 HVVYQGAFYYNRAFTKNIIKYDLRQRFVASWALLPDVVYEDTTPWKWRGH 100 EEEEEE___________HHHHHHHHHHHHHH_____EEEE__________ . . . . . 101 SDIDFAVDESGLWVIYPAVDDRDEAQPEVIVLSRLDPGDLSVHRETTWKT 150 ___EEE_____EEEEEE__________EEEEEEE___________HHHHH . . . . . 151 RLRRNSYGNCFLVCGILYAVDTYNQQEGQVAYAFDTHTGTDARPQLPFLN 200 HHH______EEEEEEEEEEE_________EEEEEE______________H . . . 201 EHAYTTQIDYNPKERVLYAWDNGHQLTYTLHFVV 234 HHHHHH________EEEEE______EEEEEE___ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ method : 1 alpha-contents : 15.1 % beta-contents : 40.5 % coil-contents : 44.4 % class : mixed method : 2 alpha-contents : 21.9 % beta-contents : 33.0 % coil-contents : 45.1 % class : mixed ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ GPI: learning from metazoa -23.52 -0.70 -0.96 0.00 -4.00 0.00 0.00 -0.07 -0.30 -4.84 -3.38 -12.00 -12.00 -8.00 -12.00 0.00 -81.78 -15.63 -0.42 -0.04 0.00 -4.00 -4.00 -28.00 0.00 -0.14 -11.10 -3.38 -12.00 0.00 0.00 0.00 0.00 -78.71 ID: tem41FGENES-M AC: xxx Len: 180 1:I 170 Sc: -78.71 Pv: 7.526874e-01 NO_GPI_SITE GPI: learning from protozoa -27.59 -6.47 -1.92 -1.49 -4.00 0.00 0.00 -1.02 0.00 -4.14 -11.60 -12.00 -12.00 -8.00 -12.00 0.00 -102.23 -26.38 -6.19 -7.81 -3.11 -4.00 0.00 0.00 0.00 -0.04 -4.49 -11.60 0.00 -12.00 -8.00 -12.00 0.00 -95.61 ID: tem41FGENES-M AC: xxx Len: 180 1:I 154 Sc: -95.61 Pv: 7.959174e-01 NO_GPI_SITE ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ # SignalP euk predictions # name Cmax pos ? Ymax pos ? Smax pos ? Smean ? tem41FGENES 0.250 173 N 0.206 173 N 0.445 89 N 0.090 N # SignalP gram- predictions # name Cmax pos ? Ymax pos ? Smax pos ? Smean ? tem41FGENES 0.445 170 N 0.439 170 Y 0.858 75 N 0.157 N # SignalP gram+ predictions # name Cmax pos ? Ymax pos ? Smax pos ? Smean ? tem41FGENES 0.332 170 N 0.294 91 N 0.851 158 N 0.176 N ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ low complexity regions: SEG 12 2.2 2.5 >tem41FGENES-M 1.5 1-234 MKDPAARDDRIYVTNYYYGNSLVEFRNLEN FKQGRWSNMYKLPYNWIGTGHVVYQGAFYY NRAFTKNIIKYDLRQRFVASWALLPDVVYE DTTPWKWRGHSDIDFAVDESGLWVIYPAVD DRDEAQPEVIVLSRLDPGDLSVHRETTWKT RLRRNSYGNCFLVCGILYAVDTYNQQEGQV AYAFDTHTGTDARPQLPFLNEHAYTTQIDY NPKERVLYAWDNGHQLTYTLHFVV low complexity regions: SEG 25 3.0 3.3 >tem41FGENES-M 1.5 1-234 MKDPAARDDRIYVTNYYYGNSLVEFRNLEN FKQGRWSNMYKLPYNWIGTGHVVYQGAFYY NRAFTKNIIKYDLRQRFVASWALLPDVVYE DTTPWKWRGHSDIDFAVDESGLWVIYPAVD DRDEAQPEVIVLSRLDPGDLSVHRETTWKT RLRRNSYGNCFLVCGILYAVDTYNQQEGQV AYAFDTHTGTDARPQLPFLNEHAYTTQIDY NPKERVLYAWDNGHQLTYTLHFVV low complexity regions: SEG 45 3.4 3.75 >tem41FGENES-M 1.5 1-234 MKDPAARDDRIYVTNYYYGNSLVEFRNLEN FKQGRWSNMYKLPYNWIGTGHVVYQGAFYY NRAFTKNIIKYDLRQRFVASWALLPDVVYE DTTPWKWRGHSDIDFAVDESGLWVIYPAVD DRDEAQPEVIVLSRLDPGDLSVHRETTWKT RLRRNSYGNCFLVCGILYAVDTYNQQEGQV AYAFDTHTGTDARPQLPFLNEHAYTTQIDY NPKERVLYAWDNGHQLTYTLHFVV 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 >tem41FGENES-M 1.5 MKDPAARDDRIYVTNYYYGNSLVEFRNLENFKQGRWSNMYKLPYNWIGTGHVVYQGAFYY NRAFTKNIIKYDLRQRFVASWALLPDVVYEDTTPWKWRGHSDIDFAVDESGLWVIYPAVD DRDEAQPEVIVLSRLDPGDLSVHRETTWKTRLRRNSYGNCFLVCGILYAVDTYNQQEGQV AYAFDTHTGTDARPQLPFLNEHAYTTQIDYNPKERVLYAWDNGHQLTYTLHFVV 1 - 234 MKDPAARDDR IYVTNYYYGN SLVEFRNLEN FKQGRWSNMY KLPYNWIGTG HVVYQGAFYY NRAFTKNIIK YDLRQRFVAS WALLPDVVYE DTTPWKWRGH SDIDFAVDES GLWVIYPAVD DRDEAQPEVI VLSRLDPGDL SVHRETTWKT RLRRNSYGNC FLVCGILYAV DTYNQQEGQV AYAFDTHTGT DARPQLPFLN EHAYTTQIDY NPKERVLYAW DNGHQLTYTL HFVV low complexity regions: DUST >tem41FGENES-M 1.5 MKDPAARDDRIYVTNYYYGNSLVEFRNLENFKQGRWSNMYKLPYNWIGTGHVVYQGAFYY NRAFTKNIIKYDLRQRFVASWALLPDVVYEDTTPWKWRGHSDIDFAVDESGLWVIYPAVD DRDEAQPEVIVLSRLDPGDLSVHRETTWKTRLRRNSYGNCFLVCGILYAVDTYNQQEGQV AYAFDTHTGTDARPQLPFLNEHAYTTQIDYNPKERVLYAWDNGHQLTYTLHFVV ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ coiled coil prediction for tem41FGENES-M sequence: 180 amino acids, 0 residue(s) in coiled coil state . | . | . | . | . | . 60 MKDPAARDDR IYVTNYYYGN SLVEFRNLEN FKQGRWSNMY KLPYNWIGTG HVVYQGAFYY ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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 NRAFTKNIIK YDLRQRFVAS WALLPDVVYE DTTPWKWRGH SDIDFAVDES GLWVIYPAVD ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border ---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif. ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local . | . | . | . | . | . 180 DRDEAQPEVI VLSRLDPGDL SVHRETTWKT RLRRNSYGNC FLVCGILYAV DTYNQQEGQV ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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 ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ prediction of transmembrane regions with toppred2 *********************************** *TOPPREDM with eukaryotic function* *********************************** tem41.___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: tem41.___inter___ (1 sequences) MKDPAARDDRIYVTNYYYGNSLVEFRNLENFKQGRWSNMYKLPYNWIGTG HVVYQGAFYYNRAFTKNIIKYDLRQRFVASWALLPDVVYEDTTPWKWRGH SDIDFAVDESGLWVIYPAVDDRDEAQPEVIVLSRLDPGDLSVHRETTWKT RLRRNSYGNCFLVCGILYAVDTYNQQEGQVAYAFDTHTGTDARPQLPFLN EHAYTTQIDYNPKERVLYAWDNGHQLTYTLHFVV (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 1 155 175 0.695 Putative ---------------------------------------------------------------------- Structure 1 Transmembrane segments included in this structure: Segment 1 Loop length 154 59 K+R profile + 3.00 CYT-EXT prof 0.85 - For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: -3.00 Tm probability: 0.24 -> Orientation: N-out Charge-difference over N-terminal Tm (+-15 residues): 6.00 (NEG-POS)/(NEG+POS): 0.0000 NEG: 21.0000 POS: 21.0000 -> Orientation: N-in CYT-EXT difference: 0.85 -> Orientation: N-out ---------------------------------------------------------------------- Structure 2 Transmembrane segments included in this structure: Segment Loop length 234 K+R profile + CYT-EXT prof 0.87 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 0.00 Tm probability: 1.00 -> Orientation: undecided Charge-difference over N-terminal Tm (+-15 residues): 0.00 (NEG-POS)/(NEG+POS): 0.0943 NEG: 29.0000 POS: 24.0000 -> Orientation: undecided CYT-EXT difference: 0.87 -> Orientation: N-out ---------------------------------------------------------------------- "tem41" 234 155 175 #f 0.694792 ************************************ *TOPPREDM with prokaryotic function* ************************************ tem41.___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: tem41.___inter___ (1 sequences) MKDPAARDDRIYVTNYYYGNSLVEFRNLENFKQGRWSNMYKLPYNWIGTG HVVYQGAFYYNRAFTKNIIKYDLRQRFVASWALLPDVVYEDTTPWKWRGH SDIDFAVDESGLWVIYPAVDDRDEAQPEVIVLSRLDPGDLSVHRETTWKT RLRRNSYGNCFLVCGILYAVDTYNQQEGQVAYAFDTHTGTDARPQLPFLN EHAYTTQIDYNPKERVLYAWDNGHQLTYTLHFVV (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 1 155 175 0.695 Putative ---------------------------------------------------------------------- Structure 1 Transmembrane segments included in this structure: Segment 1 Loop length 154 59 K+R profile + 3.00 CYT-EXT prof 0.85 - For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: -3.00 Tm probability: 0.24 -> Orientation: N-out Charge-difference over N-terminal Tm (+-15 residues): 6.00 (NEG-POS)/(NEG+POS): 0.0000 NEG: 21.0000 POS: 21.0000 -> Orientation: N-in CYT-EXT difference: 0.85 -> Orientation: N-out ---------------------------------------------------------------------- Structure 2 Transmembrane segments included in this structure: Segment Loop length 234 K+R profile + CYT-EXT prof 0.87 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 0.00 Tm probability: 1.00 -> Orientation: undecided Charge-difference over N-terminal Tm (+-15 residues): 0.00 (NEG-POS)/(NEG+POS): 0.0943 NEG: 29.0000 POS: 24.0000 -> Orientation: undecided CYT-EXT difference: 0.87 -> Orientation: N-out ---------------------------------------------------------------------- "tem41" 234 155 175 #f 0.694792 ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ NOW EXECUTING: /bio_software/1D/stat/saps/saps-stroh/SAPS.SSPA/saps /people/maria/tem41.___saps___ SAPS. Version of April 11, 1996. Date run: Thu Nov 2 11:56:46 2000 File: /people/maria/tem41.___saps___ ID tem41FGENES-M DE 1.5 number of residues: 234; molecular weight: 27.6 kdal 1 MKDPAARDDR IYVTNYYYGN SLVEFRNLEN FKQGRWSNMY KLPYNWIGTG HVVYQGAFYY 61 NRAFTKNIIK YDLRQRFVAS WALLPDVVYE DTTPWKWRGH SDIDFAVDES GLWVIYPAVD 121 DRDEAQPEVI VLSRLDPGDL SVHRETTWKT RLRRNSYGNC FLVCGILYAV DTYNQQEGQV 181 AYAFDTHTGT DARPQLPFLN EHAYTTQIDY NPKERVLYAW DNGHQLTYTL HFVV -------------------------------------------------------------------------------- COMPOSITIONAL ANALYSIS (extremes relative to: swp23s) A : 15( 6.4%); C : 2( 0.9%); D+ : 19( 8.1%); E : 10( 4.3%); F : 10( 4.3%) G : 13( 5.6%); H : 7( 3.0%); I : 9( 3.8%); K : 8( 3.4%); L : 18( 7.7%) M : 2( 0.9%); N : 14( 6.0%); P : 10( 4.3%); Q : 10( 4.3%); R : 16( 6.8%) S- : 8( 3.4%); T : 16( 6.8%); V : 19( 8.1%); W+ : 8( 3.4%); Y++: 20( 8.5%) KR : 24 ( 10.3%); ED : 29 ( 12.4%); AGP : 38 ( 16.2%); KRED : 53 ( 22.6%); KR-ED : -5 ( -2.1%); FIKMNY : 63 ( 26.9%); LVIFM : 58 ( 24.8%); ST : 24 ( 10.3%). -------------------------------------------------------------------------------- CHARGE DISTRIBUTIONAL ANALYSIS 1 0+-000+--+ 0000000000 000-0+00-0 0+00+00000 +000000000 0000000000 61 0+000+000+ 0-0+0+0000 00000-000- -0000+0+00 0-0-000--0 000000000- 121 -+--000-00 000+0-00-0 000+-000+0 +0++000000 0000000000 -00000-000 181 0000-00000 -0+0000000 -0000000-0 00+-+00000 -000000000 0000 A. CHARGE CLUSTERS. Positive charge clusters (cmin = 9/30 or 12/45 or 15/60): none Negative charge clusters (cmin = 10/30 or 14/45 or 17/60): none Mixed charge clusters (cmin = 15/30 or 21/45 or 26/60): none B. HIGH SCORING (UN)CHARGED SEGMENTS. There are no high scoring positive charge segments. There are no high scoring negative charge segments. There are no high scoring mixed charge segments. There are no high scoring uncharged segments. C. CHARGE RUNS AND PATTERNS. pattern (+)| (-)| (*)| (0)| (+0)| (-0)| (*0)|(+00)|(-00)|(*00)| (H.)|(H..)| lmin0 4 | 5 | 7 | 33 | 9 | 9 | 12 | 10 | 11 | 14 | 7 | 8 | lmin1 6 | 6 | 8 | 40 | 11 | 11 | 15 | 13 | 13 | 17 | 8 | 10 | lmin2 7 | 7 | 10 | 45 | 12 | 13 | 16 | 14 | 15 | 19 | 9 | 12 | (Significance level: 0.010000; Minimal displayed length: 6) (*00) 18(1,0,0); at 25- 43: FRNLENFKQGRWSNMYKLP (1. quartile) 0+00-00+00+00000+00 Run count statistics: + runs >= 3: 0 - runs >= 3: 0 * runs >= 4: 2, at 7; 120; 0 runs >= 22: 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-159-C-3-C-70-COOH 2*. SPACINGS OF C and H. (additional deluxe function for ALEX) H2N-50-H-48-H-42-H-16-C-3-C-22-H-14-H-21-H-6-H-3-COOH -------------------------------------------------------------------------------- REPETITIVE STRUCTURES. A. SEPARATED, TANDEM, AND PERIODIC REPEATS: amino acid alphabet. Repeat core block length: 4 B. SEPARATED AND TANDEM REPEATS: 11-letter reduced alphabet. (i= LVIF; += KR; -= ED; s= AG; o= ST; n= NQ; a= YW; p= P; h= H; m= M; c= C) Repeat core block length: 8 -------------------------------------------------------------------------------- MULTIPLETS. A. AMINO ACID ALPHABET. 1. Total number of amino acid multiplets: 15 (Expected range: 2-- 24) 2. Histogram of spacings between consecutive amino acid multiplets: (1-5) 5 (6-10) 4 (11-20) 1 (>=21) 6 3. Clusters of amino acid multiplets (cmin = 11/30 or 14/45 or 17/60): none B. CHARGE ALPHABET. 1. Total number of charge multiplets: 6 (Expected range: 0-- 13) 1 +plets (f+: 10.3%), 5 -plets (f-: 12.4%) Total number of charge altplets: 6 (Critical number: 15) 2. Histogram of spacin gs between consecutive charge multiplets: (1-5) 1 (6-10) 1 (11-20) 2 (>=21) 3 -------------------------------------------------------------------------------- PERIODICITY ANALYSIS. A. AMINO ACID ALPHABET (core: 4; !-core: 5) Location Period Element Copies Core Errors There are no periodicities of the prescribed length. B. CHARGE ALPHABET ({+= KR; -= ED; 0}; core: 5; !-core: 6) and HYDROPHOBICITY ALPHABET ({*= KRED; i= LVIF; 0}; core: 6; !-core: 8) Location Period Element Copies Core Errors There are no periodicities of the prescribed length. -------------------------------------------------------------------------------- SPACING ANALYSIS. There are no unusual spacings. ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ Start with Pfam (from /data/patterns/pfam) hmmpfam - search a single seq against HMM database HMMER 2.1.1 (Dec 1998) Copyright (C) 1992-1998 Washington University School of Medicine HMMER is freely distributed under the GNU General Public License (GPL). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - HMM file: /data/patterns/pfam/Pfam Sequence file: tem41 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: tem41FGENES-M 1.5 Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- OLF Olfactomedin-like domain 195.8 6.7e-55 1 TonB_boxC TonB dependent receptor C-terminal region 0.9 73 1 E1_N E1 Protein, N terminal domain 0.4 47 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- E1_N 1/1 18 24 .. 155 161 .] 0.4 47 TonB_boxC 1/1 194 229 .. 1 36 [. 0.9 73 OLF 1/1 1 234 [] 1 293 [] 195.8 6.7e-55 Alignments of top-scoring domains: E1_N: domain 1 of 1, from 18 to 24: score 0.4, E = 47 *->yGntevE<-* yGn++vE tem41FGENE 18 YGNSLVE 24 TonB_boxC: domain 1 of 1, from 194 to 229: score 0.9, E = 73 *->nplsqiPrhtanlgldYdlpegpLegltlgggvryv<-* +l+++++h+++++ dY++ e L + g +++y+ tem41FGENE 194 PQLPFLNEHAYTTQIDYNPKERVLYAWDNGHQLTYT 229 OLF: domain 1 of 1, from 1 to 234: score 195.8, E = 6.7e-55 *->giLagVskPvllkesekiagksGaWmkDplpnstkTkkrvWvmDgva mkDp++ +r++v+ + tem41FGENE 1 -------------------------MKDPAARD----DRIYVTNYY- 17 DGrvlrvvrEYssmsdfldgknkikykLphLiKNKLNNTFalsGTGvVVY +++ ++ E f +g+ + ykLp+ + GTG VVY tem41FGENE 18 --YGN-SLVEFRNLENFKQGRWSNMYKLPY----------NWIGTGHVVY 54 nGsLYFnkfeSrsivRyeLeTgvvkkeellpeAgYndrfpYPDHTFEECN G+ Y+n + +++i++y+L+ + v +llp Y d+ p tem41FGENE 55 QGAFYYNRAFTKNIIKYDLRQRFVASWALLPDVVYEDTTPW--------- 95 ATDRHVWLawgghsDiDLaVDEnGLWvIYAT.....EqnaGkIVisKlnP w+ghsDiD+aVDE+GLWvIY ++++E+ + IV+s+l+P tem41FGENE 96 --------KWRGHSDIDFAVDESGLWVIYPAvddrdEAQPEVIVLSRLDP 137 asLev..entWnTeynKrsaanAFiICGvLYvvkSvYEDDDaeslgtkit L v++e tW T + s +n F +CG+LY v ++ ++ tem41FGENE 138 GDLSVhrETTWKTRLRRNSYGNCFLVCGILYAVDT------YNQQEGQVA 181 YaYdTntgkeklldipfeNkYqyismLdYNPlDrkLYawdNghllkYdvk Ya+dT tg++ + pf N y + +dYNP++r LYawdNgh+l+Y + tem41FGENE 182 YAFDTHTGTDARPQLPFLNEHAYTTQIDYNPKERVLYAWDNGHQLTYTLH 231 Lee<-* + tem41FGENE 232 FVV 234 // 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: tem41 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: tem41FGENES-M 1.5 Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- OLF Olfactomedin-like domain 221.7 1e-62 1 ALA_synthase Aminolevulinic acid synthase domain 1.7 74 1 TonB_boxC TonB dependent receptor C-terminal regio 0.9 73 1 E1_N E1 Protein, N terminal domain 0.4 47 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- E1_N 1/1 18 24 .. 155 161 .] 0.4 47 ALA_synthase 1/1 58 68 .. 1 11 [. 1.7 74 TonB_boxC 1/1 194 229 .. 1 36 [. 0.9 73 OLF 1/1 1 234 [] 26 293 .] 221.7 1e-62 Alignments of top-scoring domains: E1_N: domain 1 of 1, from 18 to 24: score 0.4, E = 47 *->yGntevE<-* yGn++vE tem41FGENE 18 YGNSLVE 24 ALA_synthase: domain 1 of 1, from 58 to 68: score 1.7, E = 74 *->FdYdafFnkel<-* F+Y+++F+k + tem41FGENE 58 FYYNRAFTKNI 68 TonB_boxC: domain 1 of 1, from 194 to 229: score 0.9, E = 73 *->nplsqiPrhtanlgldYdlpegpLegltlgggvryv<-* +l+++++h+++++ dY++ e L + g +++y+ tem41FGENE 194 PQLPFLNEHAYTTQIDYNPKERVLYAWDNGHQLTYT 229 OLF: domain 1 of 1, from 1 to 234: score 221.7, E = 1e-62 *->mkDplpnstkTkkrvWvmDgvaDGrvlrvvrEYssmsdfldgknkik mkDp++ +r++v+ + +++ ++ E f +g+ + tem41FGENE 1 MKDPAARD----DRIYVTNYY---YGN-SLVEFRNLENFKQGRWSNM 39 ykLphLiKNKLNNTFalsGTGvVVYnGsLYFnkfeSrsivRyeLeTgvvk ykLp+ + GTG VVY G+ Y+n + +++i++y+L+ + v tem41FGENE 40 YKLPY----------NWIGTGHVVYQGAFYYNRAFTKNIIKYDLRQRFVA 79 keellpeAgYndrfpYPDHTFEECNATDRHVWLawgghsDiDLaVDEnGL +llp Y d+ p w+ghsDiD+aVDE+GL tem41FGENE 80 SWALLPDVVYEDTTPW-----------------KWRGHSDIDFAVDESGL 112 WvIYAT.....EqnaGkIVisKlnPasLev..entWnTeynKrsaanAFi WvIY ++++E+ + IV+s+l+P L v++e tW T + s +n F tem41FGENE 113 WVIYPAvddrdEAQPEVIVLSRLDPGDLSVhrETTWKTRLRRNSYGNCFL 162 ICGvLYvvkSvYEDDDaeslgtkitYaYdTntgkeklldipfeNkYqyis +CG+LY v ++ ++ Ya+dT tg++ + pf N y + tem41FGENE 163 VCGILYAVDT------YNQQEGQVAYAFDTHTGTDARPQLPFLNEHAYTT 206 mLdYNPlDrkLYawdNghllkYdvkLee<-* +dYNP++r LYawdNgh+l+Y + + tem41FGENE 207 QIDYNPKERVLYAWDNGHQLTYTLHFVV 234 // 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: tem41 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: tem41FGENES-M 1.5 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 Nov 2 11:58:28 2000 Sequence file: tem41 ---------------------------------------- Sequence tem41FGENES-M (234 residues): Matching pattern PS00004 CAMP_PHOSPHO_SITE: 153: RRNS Total matches: 1 Matching pattern PS00005 PKC_PHOSPHO_SITE: 147: TWK Total matches: 1 Matching pattern PS00006 CK2_PHOSPHO_SITE: 21: SLVE 101: SDID 133: SRLD 188: TGTD 206: TQID Total matches: 5 Matching pattern PS00008 MYRISTYL: 165: GILYAV Total matches: 1 Total no of hits in this sequence: 8 ======================================== 1314 pattern(s) searched in 1 sequence(s), 234 residues. Total no of hits in all sequences: 8. Search time: 00:00 min ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ Start with Profile Search ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ Start with motif search against own library ***** bioMotif : Version V41a DB, 1999 Nov 11 ***** argv[1]=P argv[2]=-m /data/patterns/own/motif.fa argv[4]=-seq tem41 ***** 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, 234 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: tem41 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: tem41FGENES-M 1.5 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: tem41 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: tem41FGENES-M 1.5 Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- [no hits above thresholds] Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- [no hits above thresholds] Alignments of top-scoring domains: [no hits above thresholds] // ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ L. Aravind's signalling DB IMPALA version 1.1 [20-December-1999] Reference: Alejandro A. Schaffer, Yuri I. Wolf, Chris P. Ponting, Eugene V. Koonin, L. Aravind, Stephen F. Altschul (1999), "IMPALA: Matching a Protein Sequence Against a Collection of "PSI-BLAST-Constructed Position-Specific Score Matrices", Bioinformatics 15:1000-1011. Query= tem41FGENES-M 1.5 (234 letters) Searching..................................done Results from profile search Score E Sequences producing significant alignments: (bits) Value KELCH Kelch repeat- beta propeller like domain 31 0.001 HOG HOG- intein(HINT) like domain 19 6.4 MATH The Meprin associated TRAF homology domain 19 7.4 KH HnRNP K homology domain (A RNA binding domain) 19 8.2 SNARE Alpha helical domains which are involved in vesicle fu... 19 8.8 AP2 A plant specific DNA binding domain (Apetala 2 like) 19 9.5 >KELCH Kelch repeat- beta propeller like domain Length = 319 Score = 31.2 bits (70), Expect = 0.001 Identities = 10/65 (15%), Positives = 19/65 (28%), Gaps = 7/65 (10%) Query: 30 NFKQGRWSNMYKLPYNWIGTGHVVYQGAFY----YNRAFTKNIIKYDLRQRFVASWALLP 85 + + RW+ P W T V + + K++ W + Sbjct: 196 DQCENRWTVPATCPQPWRYTAAAVLGNQIFIMGGDTEFSACSAYKFNSETY---QWTKVG 252 Query: 86 DVVYE 90 DV + Sbjct: 253 DVTAK 257 Score = 24.2 bits (52), Expect = 0.19 Identities = 7/63 (11%), Positives = 13/63 (20%), Gaps = 9/63 (14%) Query: 30 NFKQGRWSNMYKLPYNWIGTGHVVYQGAFY------YNRAFTKNIIKYDLRQRFVASWAL 83 + K +P Y +K++ YD W+ Sbjct: 44 DQKAKEIIPKADIPSPRKEFSACAIGCKVYITGGRGSENGVSKDVWVYDTLHE---EWSK 100 Query: 84 LPD 86 Sbjct: 101 AAP 103 Score = 24.2 bits (52), Expect = 0.19 Identities = 11/49 (22%), Positives = 23/49 (46%) Query: 5 AARDDRIYVTNYYYGNSLVEFRNLENFKQGRWSNMYKLPYNWIGTGHVV 53 A +++YV Y+G + + + W+++ +PY+ I T V Sbjct: 264 VASGNKLYVVGGYFGIQRCKTLDCYDPTLDVWNSITTVPYSLIPTAFVS 312 Score = 23.4 bits (50), Expect = 0.32 Identities = 8/61 (13%), Positives = 19/61 (31%), Gaps = 9/61 (14%) Query: 8 DDRIYV-------TNYYYGNSLVEFRNLENF--KQGRWSNMYKLPYNWIGTGHVVYQGAF 58 +YV T + V + +E++ +W+ + L V + Sbjct: 117 KHCLYVVGGHTAATGCLPASPSVSLKQVEHYDPTINKWTMVAPLREGVSNAAVVSAKLKL 176 Query: 59 Y 59 + Sbjct: 177 F 177 Score = 19.9 bits (41), Expect = 3.2 Identities = 10/95 (10%), Positives = 25/95 (25%), Gaps = 9/95 (9%) Query: 97 WRGHSDIDFAVDESGLWVIYPAVDDRDEAQPEVIVLSRLDPGDLSVHRETTWKTRLRRNS 156 G S+ + L+ + ++ + D + T + Sbjct: 161 REGVSNAAVVSAKLKLFAFG----GTSVSHDKLPKVQCYDQCENRWTVPAT----CPQPW 212 Query: 157 YGNCFLVC-GILYAVDTYNQQEGQVAYAFDTHTGT 190 V ++ + + AY F++ T Sbjct: 213 RYTAAAVLGNQIFIMGGDTEFSACSAYKFNSETYQ 247 >HOG HOG- intein(HINT) like domain Length = 389 Score = 19.2 bits (39), Expect = 6.4 Identities = 6/21 (28%), Positives = 11/21 (51%), Gaps = 1/21 (4%) Query: 213 KERVLYAWD-NGHQLTYTLHF 232 + V +WD + H +LH+ Sbjct: 99 RLLVTESWDEDYHHGQESLHY 119 >MATH The Meprin associated TRAF homology domain Length = 209 Score = 19.0 bits (39), Expect = 7.4 Identities = 4/16 (25%), Positives = 5/16 (31%) Query: 25 FRNLENFKQGRWSNMY 40 L + G W N Sbjct: 183 ECRLADELGGLWENSR 198 >KH HnRNP K homology domain (A RNA binding domain) Length = 92 Score = 18.7 bits (38), Expect = 8.2 Identities = 5/36 (13%), Positives = 14/36 (38%) Query: 98 RGHSDIDFAVDESGLWVIYPAVDDRDEAQPEVIVLS 133 + I ++SG +I + Q + + ++ Sbjct: 44 KSGDTIRQLQEKSGCKMILVQDNQSVSDQSKPLRIT 79 >SNARE Alpha helical domains which are involved in vesicle fusion Length = 254 Score = 18.6 bits (38), Expect = 8.8 Identities = 6/63 (9%), Positives = 15/63 (23%), Gaps = 21/63 (33%) Query: 163 VCGILYAVDTYNQQEGQVAYAF-----------------DTHTGTDARPQLP-FLNEHAY 204 V ++ + Y +A++F +T + F+ Sbjct: 68 VSYMMLCTENYPN---VLAFSFLDELQKEFITTYNMMKTNTAVRPYCFIEFDNFIQRTKQ 124 Query: 205 TTQ 207 Sbjct: 125 RYN 127 >AP2 A plant specific DNA binding domain (Apetala 2 like) Length = 218 Score = 18.5 bits (37), Expect = 9.5 Identities = 9/46 (19%), Positives = 17/46 (36%), Gaps = 4/46 (8%) Query: 25 FRNLENFKQGRWSNMYKLP----YNWIGTGHVVYQGAFYYNRAFTK 66 +R + G+W + + P W+GT A ++ A Sbjct: 36 YRGVRKRNWGKWVSEIREPRKKSRIWLGTFPSPEMAARAHDVAALS 81 Underlying Matrix: BLOSUM62 Number of sequences tested against query: 105 Number of sequences better than 10.0: 6 Number of calls to ALIGN: 10 Length of query: 234 Total length of test sequences: 20182 Effective length of test sequences: 17043.0 Effective search space size: 3482620.3 Initial X dropoff for ALIGN: 25.0 bits Y. Wolf's SCOP PSSM IMPALA version 1.1 [20-December-1999] Reference: Alejandro A. Schaffer, Yuri I. Wolf, Chris P. Ponting, Eugene V. Koonin, L. Aravind, Stephen F. Altschul (1999), "IMPALA: Matching a Protein Sequence Against a Collection of "PSI-BLAST-Constructed Position-Specific Score Matrices", Bioinformatics 15:1000-1011. Query= tem41FGENES-M 1.5 (234 letters) Searching.................................................done Results from profile search Score E Sequences producing significant alignments: (bits) Value gi|1055187 [23..334] Phosphoglycerate mutase-like 25 0.94 gi|136000 [3..610] type I DNA topoisomerase 25 0.94 gi|730933 [142..476] Cysteine proteinases 24 2.0 gi|482303 [240..626] 7-bladed beta-propeller 24 2.8 gi|2408097 [1..121] DNA-binding 3-helical bundle 23 4.7 gi|1827898 [3..132] N-terminal domain of enolase & muconate-... 23 5.8 gi|2114264 [95..597] type I DNA topoisomerase 23 6.1 gi|407037 [59..572] Heme-dependent peroxidases 23 7.6 gi|1360139 [98..407] 7-bladed beta-propeller 22 9.5 gi|549660 [99..278] 7-bladed beta-propeller 22 9.8 >gi|1055187 [23..334] Phosphoglycerate mutase-like Length = 312 Score = 25.3 bits (55), Expect = 0.94 Identities = 5/47 (10%), Positives = 10/47 (20%), Gaps = 3/47 (6%) Query: 182 YAFDTHT--GTDARPQLPFLNEHAYT-TQIDYNPKERVLYAWDNGHQ 225 + NE AY + + V+ + Sbjct: 125 ENLPALILEKEAGLAVPSWFNEGAYKESLHVFYSALAVMSSVGEYKS 171 >gi|136000 [3..610] type I DNA topoisomerase Length = 608 Score = 25.3 bits (55), Expect = 0.94 Identities = 15/76 (19%), Positives = 29/76 (37%), Gaps = 14/76 (18%) Query: 71 YDL-RQRFVASWALLPDVVYEDTT------PWKWRGHSDIDFAVDESGLWVIYPAVDDRD 123 Y+L ++++ PD V+ K+ + + E+G W +RD Sbjct: 401 YNLIARQYLMQ--FCPDAVFRKCVIELDIAKGKFVAKARF---LAEAG-WRTLLGSKERD 454 Query: 124 EAQPEVIVLSRLDPGD 139 E + + L + GD Sbjct: 455 E-ENDGTPLPVVAKGD 469 >gi|730933 [142..476] Cysteine proteinases Length = 335 Score = 24.1 bits (52), Expect = 2.0 Identities = 13/51 (25%), Positives = 20/51 (38%), Gaps = 5/51 (9%) Query: 2 KDPAARDDRIYVTNYYYGNSLVEFRNLENFKQGRWSNMYK---LPYNWIGT 49 D A R+D YV ++++ + G WS Y P W G+ Sbjct: 64 TDVARRNDPKYVCR--VLSAMINGNDDNGVISGNWSGNYTGGVDPRTWNGS 112 >gi|482303 [240..626] 7-bladed beta-propeller Length = 387 Score = 23.8 bits (51), Expect = 2.8 Identities = 12/86 (13%), Positives = 23/86 (25%), Gaps = 14/86 (16%) Query: 8 DDRIYVTNYYYGNSLVEFRNLENFKQGRWSNMYKLPYN-WIGTGHVVYQGAFYY------ 60 + +I VT + + W + + + G + Sbjct: 86 NGQIVVTGGNDAKKTSLY----DSSSDSWIPGPDMQVARGYQSSATMSDGRVFTIGGSWS 141 Query: 61 NRAFTKNIIKYDLRQRFVASWALLPD 86 F KN Y + +W LP+ Sbjct: 142 GGVFEKNGEVYSPSSK---TWTSLPN 164 >gi|2408097 [1..121] DNA-binding 3-helical bundle Length = 121 Score = 23.0 bits (49), Expect = 4.7 Identities = 6/18 (33%), Positives = 10/18 (55%), Gaps = 1/18 (5%) Query: 18 YGNSLVEFRNLENFKQGR 35 YG EFR+ ++F+ Sbjct: 95 YGEGAWEFRH-DDFQLHH 111 >gi|1827898 [3..132] N-terminal domain of enolase & muconate-lactonizing enzyme Length = 130 Score = 22.9 bits (49), Expect = 5.8 Identities = 4/50 (8%), Positives = 6/50 (12%), Gaps = 5/50 (10%) Query: 59 YYNRAFTKNIIKYDLRQRFVASWALLPDVVYEDTTPWKWRGHSDIDFAVD 108 I+ L L +D Sbjct: 62 QLLDDMAAMIVNEPLAPV-SLEAMLA----KRFCLAGYTGLIRMAAAGID 106 >gi|2114264 [95..597] type I DNA topoisomerase Length = 503 Score = 22.9 bits (49), Expect = 6.1 Identities = 7/24 (29%), Positives = 11/24 (45%), Gaps = 3/24 (12%) Query: 71 YDL-RQRFVASWALLPDVVYEDTT 93 RQ F+A+ + D Y +T Sbjct: 300 KGELRQHFIAT--VSHDCKYLQST 321 >gi|407037 [59..572] Heme-dependent peroxidases Length = 514 Score = 22.5 bits (48), Expect = 7.6 Identities = 6/18 (33%), Positives = 9/18 (49%) Query: 18 YGNSLVEFRNLENFKQGR 35 YG +L L F+ G+ Sbjct: 162 YGETLDRQHKLRLFQDGK 179 >gi|1360139 [98..407] 7-bladed beta-propeller Length = 310 Score = 22.2 bits (47), Expect = 9.5 Identities = 10/90 (11%), Positives = 25/90 (27%), Gaps = 20/90 (22%) Query: 30 NFKQGRWSNMYKLPYNWIGT-------GHVVYQGAFYYNRAFTKNIIKYDLRQRFVASWA 82 + + + P+N G ++ G + + I ++ + +W Sbjct: 15 DPLANTLTPIPAPPFNIFCAGHSFLEDGRLLITGGHVDSHVGVPDAIIFNPKSG---AWD 71 Query: 83 LLPD----------VVYEDTTPWKWRGHSD 102 +PD + G +D Sbjct: 72 NVPDMNDKRWYPNNTTLANGDVLVLSGETD 101 >gi|549660 [99..278] 7-bladed beta-propeller Length = 180 Score = 22.0 bits (46), Expect = 9.8 Identities = 12/101 (11%), Positives = 30/101 (28%), Gaps = 3/101 (2%) Query: 92 TTPWKWRGHSD--IDFAVDESGLWVIYPAVDDRDEAQPEVIVLSRLDPGDLSVHRE-TTW 148 + + S A D SGL ++ + + + + ++ + Sbjct: 46 ISKPQVIIPSLVPNCIAYDPSGLVFALGNPENFEIGLYNLKKIQEGPFLIIKINDATFSQ 105 Query: 149 KTRLRRNSYGNCFLVCGILYAVDTYNQQEGQVAYAFDTHTG 189 +L ++ G LV + ++ GQ + Sbjct: 106 WNKLEFSNNGKYLLVGSSIGKHLIFDAFTGQQLFELIGTRA 146 Underlying Matrix: BLOSUM62 Number of sequences tested against query: 1187 Number of sequences better than 10.0: 10 Number of calls to ALIGN: 10 Length of query: 234 Total length of test sequences: 256703 Effective length of test sequences: 214185.0 Effective search space size: 42561074.2 Initial X dropoff for ALIGN: 25.0 bits