analysis of sequence from NP_492873.1.fa ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ >NP_492873.1 Y52B11C.1.p [Caenorhabditis elegans]. MLPLILLIVT LLLVLLLIFA VRSHPIPLLS QSRILLLIAH PDDETMFFSP TIRALLQAGH RVFVLCISNG NFDGLGKIRA RELSRAASKL GISASDVICL DYDEFADGDT WNRNALCQIV MRHVEVLAAD TVISFDSHGV SGHHNHARYR P ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ sec.str. with predator > NP_492873.1 . . . . . 1 MLPLILLIVTLLLVLLLIFAVRSHPIPLLSQSRILLLIAHPDDETMFFSP 50 ___HHHHHHHHHHHHHHHHHHH______HHHHHHHEEEE_____EEE_HH . . . . . 51 TIRALLQAGHRVFVLCISNGNFDGLGKIRARELSRAASKLGISASDVICL 100 HHHHHHHH___EEEEE________HHHHHHHHHHHHHHH_______EEEE . . . . . 101 DYDEFADGDTWNRNALCQIVMRHVEVLAADTVISFDSHGVSGHHNHARYR 150 E_____________HHHHHHHHHHHHH____EEE________________ 151 P 151 _ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ method : 1 alpha-contents : 44.6 % beta-contents : 42.1 % coil-contents : 13.3 % class : mixed method : 2 alpha-contents : 44.1 % beta-contents : 38.3 % coil-contents : 17.6 % class : mixed ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ GPI: learning from metazoa -9.35 -3.16 -2.98 -4.81 0.00 0.00 -8.00 0.00 0.00 -15.40 -4.91 -12.00 -12.00 -4.00 -12.00 0.00 -88.61 0.70 -0.28 -0.42 -1.69 0.00 0.00 -28.00 0.00 -1.24 -15.40 -4.91 -12.00 0.00 0.00 -12.00 0.00 -75.25 ID: NP_492873.1 AC: xxx Len: 151 1:I 141 Sc: -75.25 Pv: 6.797217e-01 NO_GPI_SITE GPI: learning from protozoa -21.20 -1.13 -1.56 0.00 -4.00 0.00 -4.00 0.00 0.00 -12.88 -15.77 -12.00 -12.00 -4.00 -12.00 0.00 -100.54 -9.91 -0.25 0.00 0.00 -4.00 0.00 -28.00 0.00 -0.43 -12.88 -15.77 -12.00 0.00 0.00 -12.00 0.00 -95.24 ID: NP_492873.1 AC: xxx Len: 151 1:I 141 Sc: -95.24 Pv: 7.896198e-01 NO_GPI_SITE ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ # SignalP euk predictions # name Cmax pos ? Ymax pos ? Smax pos ? Smean ? NP_492873.1 1.000 24 Y 0.827 24 Y 0.995 10 Y 0.973 Y # SignalP gram- predictions # name Cmax pos ? Ymax pos ? Smax pos ? Smean ? NP_492873.1 0.402 55 N 0.329 26 N 0.995 9 Y 0.842 Y # SignalP gram+ predictions # name Cmax pos ? Ymax pos ? Smax pos ? Smean ? NP_492873.1 0.418 81 N 0.319 129 N 0.991 13 Y 0.463 N ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ low complexity regions: SEG 12 2.2 2.5 >NP_492873.1 Y52B11C.1.p [Caenorhabditis elegans]. 1-1 M lplillivtlllvllli 2-18 19-151 FAVRSHPIPLLSQSRILLLIAHPDDETMFF SPTIRALLQAGHRVFVLCISNGNFDGLGKI RARELSRAASKLGISASDVICLDYDEFADG DTWNRNALCQIVMRHVEVLAADTVISFDSH GVSGHHNHARYRP low complexity regions: SEG 25 3.0 3.3 >NP_492873.1 Y52B11C.1.p [Caenorhabditis elegans]. 1-1 M lplillivtlllvlllifavrshpipllsq 2-38 srillli 39-151 AHPDDETMFFSPTIRALLQAGHRVFVLCIS NGNFDGLGKIRARELSRAASKLGISASDVI CLDYDEFADGDTWNRNALCQIVMRHVEVLA ADTVISFDSHGVSGHHNHARYRP low complexity regions: SEG 45 3.4 3.75 >NP_492873.1 Y52B11C.1.p [Caenorhabditis elegans]. 1-1 M lplillivtlllvlllifavrshpipllsq 2-38 srillli 39-151 AHPDDETMFFSPTIRALLQAGHRVFVLCIS NGNFDGLGKIRARELSRAASKLGISASDVI CLDYDEFADGDTWNRNALCQIVMRHVEVLA ADTVISFDSHGVSGHHNHARYRP 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_492873.1 Y52B11C.1.p [Caenorhabditis elegans]. mlplillivtlllvllliFAVRSHPIPLLSQSRILLLIAHPDDETMFFSPTIRALLQAGH RVFVLCISNGNFDGLGKIRARELSRAASKLGISASDVICLDYDEFADGDTWNRNALCQIV MRHVEVLAADTVISFDSHGVSGHHNHARYRP 1 - 18 mlplillivt lllvllli 19 - 151 FA VRSHPIPLLS QSRILLLIAH PDDETMFFSP TIRALLQAGH RVFVLCISNG NFDGLGKI RA RELSRAASKL GISASDVICL DYDEFADGDT WNRNALCQIV MRHVEVLAAD TVISFDSH GV SGHHNHARYR P low complexity regions: DUST >NP_492873.1 Y52B11C.1.p [Caenorhabditis elegans]. MLPLILLIVTLLLVLLLIFAVRSHPIPLLSQSRILLLIAHPDDETMFFSPTIRALLQAGH RVFVLCISNGNFDGLGKIRARELSRAASKLGISASDVICLDYDEFADGDTWNRNALCQIV MRHVEVLAADTVISFDSHGVSGHHNHARYRP ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ coiled coil prediction for NP_492873.1 sequence: 151 amino acids, 0 residue(s) in coiled coil state . | . | . | . | . | . 60 MLPLILLIVT LLLVLLLIFA VRSHPIPLLS QSRILLLIAH PDDETMFFSP TIRALLQAGH ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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 RVFVLCISNG NFDGLGKIRA RELSRAASKL GISASDVICL DYDEFADGDT WNRNALCQIV ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border ---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif. ~~~~~~~~~~ ~~~~~~2222 2222222222 ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local . | . | . | MRHVEVLAAD TVISFDSHGV SGHHNHARYR P ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~ ---------- ---------- ---------- - ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ prediction of transmembrane regions with toppred2 *********************************** *TOPPREDM with eukaryotic function* *********************************** NP_492873.1.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_492873.1.fa.___inter___ (1 sequences) MLPLILLIVTLLLVLLLIFAVRSHPIPLLSQSRILLLIAHPDDETMFFSP TIRALLQAGHRVFVLCISNGNFDGLGKIRARELSRAASKLGISASDVICL DYDEFADGDTWNRNALCQIVMRHVEVLAADTVISFDSHGVSGHHNHARYR P (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 1 21 2.635 Certain ---------------------------------------------------------------------- Structure 1 Transmembrane segments included in this structure: Segment 1 Loop length 0 130 K+R profile 1.00 + CYT-EXT prof - 0.10 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 1.00 Tm probability: 1.00 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): -2.00 (NEG-POS)/(NEG+POS): 5.0000 NEG: 0.0000 POS: 0.0000 -> Orientation: N-out CYT-EXT difference: -0.10 -> Orientation: N-in ---------------------------------------------------------------------- "NP_492873" 151 1 21 #t 2.63542 ************************************ *TOPPREDM with prokaryotic function* ************************************ NP_492873.1.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_492873.1.fa.___inter___ (1 sequences) MLPLILLIVTLLLVLLLIFAVRSHPIPLLSQSRILLLIAHPDDETMFFSP TIRALLQAGHRVFVLCISNGNFDGLGKIRARELSRAASKLGISASDVICL DYDEFADGDTWNRNALCQIVMRHVEVLAADTVISFDSHGVSGHHNHARYR P (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 1 21 2.635 Certain ---------------------------------------------------------------------- Structure 1 Transmembrane segments included in this structure: Segment 1 Loop length 0 130 K+R profile 0.00 + CYT-EXT prof - 0.10 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 0.00 Tm probability: 1.00 -> Orientation: undecided Charge-difference over N-terminal Tm (+-15 residues): -2.00 (NEG-POS)/(NEG+POS): 5.0000 NEG: 0.0000 POS: 0.0000 -> Orientation: N-out CYT-EXT difference: -0.10 -> Orientation: N-in ---------------------------------------------------------------------- "NP_492873" 151 1 21 #t 2.63542 ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ SAPS. Version of April 11, 1996. Date run: Fri Mar 8 14:38:23 2002 File: /people/b_eisen/NP_492873.1.fa.___saps___ ID NP_492873.1 DE Y52B11C.1.p [Caenorhabditis elegans]. number of residues: 151; molecular weight: 16.7 kdal 1 MLPLILLIVT LLLVLLLIFA VRSHPIPLLS QSRILLLIAH PDDETMFFSP TIRALLQAGH 61 RVFVLCISNG NFDGLGKIRA RELSRAASKL GISASDVICL DYDEFADGDT WNRNALCQIV 121 MRHVEVLAAD TVISFDSHGV SGHHNHARYR P -------------------------------------------------------------------------------- COMPOSITIONAL ANALYSIS (extremes relative to: swp23s) A : 13( 8.6%); C : 3( 2.0%); D : 10( 6.6%); E : 4( 2.6%); F : 7( 4.6%) G : 8( 5.3%); H : 8( 5.3%); I : 13( 8.6%); K : 2( 1.3%); L : 24(15.9%) M : 3( 2.0%); N : 5( 3.3%); P : 6( 4.0%); Q : 3( 2.0%); R : 11( 7.3%) S : 12( 7.9%); T : 5( 3.3%); V : 11( 7.3%); W : 1( 0.7%); Y : 2( 1.3%) KR : 13 ( 8.6%); ED : 14 ( 9.3%); AGP : 27 ( 17.9%); KRED : 27 ( 17.9%); KR-ED : -1 ( -0.7%); FIKMNY : 32 ( 21.2%); LVIFM : 58 ( 38.4%); ST : 17 ( 11.3%). -------------------------------------------------------------------------------- CHARGE DISTRIBUTIONAL ANALYSIS 1 0000000000 0000000000 0+00000000 00+0000000 0---000000 00+0000000 61 +000000000 00-000+0+0 +-00+000+0 00000-0000 -0--00-0-0 00+0000000 121 0+00-0000- 00000-0000 0000000+0+ 0 A. CHARGE CLUSTERS. Positive charge clusters (cmin = 8/30 or 11/45 or 13/60): none Negative charge clusters (cmin = 9/30 or 11/45 or 14/60): none Mixed charge clusters (cmin = 13/30 or 18/45 or 22/60): none B. HIGH SCORING (UN)CHARGED SEGMENTS. There are no high scoring positive charge segments. There are no high scoring negative charge segments. There are no high scoring mixed charge segments. There are no high scoring uncharged segments. C. CHARGE RUNS AND PATTERNS. pattern (+)| (-)| (*)| (0)| (+0)| (-0)| (*0)|(+00)|(-00)|(*00)| (H.)|(H..)| lmin0 4 | 4 | 5 | 40 | 8 | 8 | 11 | 10 | 10 | 13 | 7 | 9 | lmin1 5 | 5 | 7 | 49 | 10 | 10 | 13 | 12 | 12 | 16 | 9 | 11 | lmin2 6 | 6 | 8 | 54 | 11 | 11 | 14 | 13 | 14 | 17 | 10 | 13 | (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 42; * runs >= 4: 0 0 runs >= 27: 0 -------------------------------------------------------------------------------- DISTRIBUTION OF OTHER AMINO ACID TYPES 1. HIGH SCORING SEGMENTS. __________________________________ High scoring hydrophobic segments: 2.00 (LVIFM) 1.00 (AGYCW) 0.00 (BZX) -2.00 (PH) -4.00 (STNQ) -8.00 (KEDR) Expected score/letter: -1.331 M_0.01= 31.87; M_0.05= 25.23 1) From 1 to 21: length= 21, score=31.00 * 1 MLPLILLIVT LLLVLLLIFA V L: 10(47.6%); V: 3(14.3%); I: 3(14.3%); ____________________________________ High scoring transmembrane segments: 5.00 (LVIF) 2.00 (AGM) 0.00 (BZX) -1.00 (YCW) -2.00 (ST) -6.00 (P) -8.00 (H) -10.00 (NQ) -16.00 (KR) -17.00 (ED) Expected score/letter: -2.272 M_0.01= 83.84; M_0.05= 65.40; M_0.30= 43.46 1) From 1 to 21: length= 21, score=81.00 * 1 MLPLILLIVT LLLVLLLIFA V L: 10(47.6%); V: 3(14.3%); I: 3(14.3%); 2. SPACINGS OF C. H2N-65-C-32-C-17-C-34-COOH 2*. SPACINGS OF C and H. (additional deluxe function for ALEX) H2N-23-H-15-H-19-H-5-C-32-C-17-C-5-H-14-H-4-H-H-1-H-5-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: 11 (Expected range: 0-- 20) 2. Histogram of spacings between consecutive amino acid multiplets: (1-5) 4 (6-10) 4 (11-20) 2 (>=21) 2 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: 2 (Expected range: 0-- 7) 0 +plets (f+: 8.6%), 2 -plets (f-: 9.3%) Total number of charge altplets: 1 (Critical number: 9) 2. Histogram of spacings between consecutive charge multiplets: (1-5) 0 (6-10) 0 (11-20) 0 (>=21) 3 -------------------------------------------------------------------------------- PERIODICITY ANALYSIS. A. AMINO ACID ALPHABET (core: 4; !-core: 5) Location Period Element Copies Core Errors 11- 18 2 L. 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 1- 21 1 i 18 9 ! 3 19- 72 9 i.0000... 6 6 /0/./2/2/0/2/./././ -------------------------------------------------------------------------------- SPACING ANALYSIS. Location (Quartile) Spacing Rank P-value Interpretation 50- 151 (3.) P( 101)P 1 of 7 0.0075 large maximal spacing 104- 125 (4.) E( 21)E 5 of 5 0.0086 large minimal spacing ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ 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_492873.1.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: NP_492873.1 Y52B11C.1.p [Caenorhabditis elegans]. 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_492873.1.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: NP_492873.1 Y52B11C.1.p [Caenorhabditis elegans]. Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- DUF158 Uncharacterized LmbE-like protein, COG2 14.2 0.003 1 Chitin_bind_3 Chitin binding domain 1.0 16 1 IMPDH_C IMP dehydrogenase / GMP reductase C ter -0.7 75 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- Chitin_bind_3 1/1 8 24 .. 1 17 [. 1.0 16 IMPDH_C 1/1 54 71 .. 1 18 [. -0.7 75 DUF158 1/1 29 94 .. 1 88 [. 14.2 0.003 Alignments of top-scoring domains: Chitin_bind_3: domain 1 of 1, from 8 to 24: score 1.0, E = 16 *->llillfalallpaVrsH<-* ++ ll++l+l+ aVrsH NP_492873. 8 IVTLLLVLLLIFAVRSH 24 IMPDH_C: domain 1 of 1, from 54 to 71: score -0.7, E = 75 *->aLveAGvDVIvlDsadGf<-* aL +AG V vl ++G+ NP_492873. 54 ALLQAGHRVFVLCISNGN 71 DUF158: domain 1 of 1, from 29 to 94: score 14.2, E = 0.003 *->ssenrLkdAkkVLavhAHPDDesigmGATiakftdqGkrVlvvtlTe s+ r L AHPDDe + Ti + G+rV v++ NP_492873. 29 LSQSRI------LLLIAHPDDETMFFSPTIRALLQAGHRVFVLCISN 69 GeegstlgsRWAqllaDsadeLaeiRreElaeAAriLGVkk<-* G +g + iR El AA LG ++ NP_492873. 70 G---NFDGL-------------GKIRARELSRAASKLGISA 94 // 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_492873.1.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: NP_492873.1 Y52B11C.1.p [Caenorhabditis elegans]. 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 14:40:15 2002 Sequence file: NP_492873.1.fa ---------------------------------------- Sequence NP_492873.1 (151 residues): Matching pattern PS00005 PKC_PHOSPHO_SITE: 51: TIR Total matches: 1 Matching pattern PS00006 CK2_PHOSPHO_SITE: 93: SASD Total matches: 1 Matching pattern PS00008 MYRISTYL: 70: GNFDGL 91: GISASD Total matches: 2 Total no of hits in this sequence: 4 ======================================== 1314 pattern(s) searched in 1 sequence(s), 151 residues. Total no of hits in all sequences: 4. Search time: 00:00 min ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ Start with Profile Search ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ Start with motif search against own library ***** bioMotif : Version V41a DB, 1999 Nov 11 ***** SeqTyp=2 : PROTEIN search; >APC D-Box is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 151 units >ER-GOLGI-traffic signal is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 151 units >INTRA-SIGNAL-M minimal SH3 binding is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 151 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, 151 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, 151 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, 151 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, 151 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, 151 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, 151 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, 151 units >TM-CYTOPLASMIC-M di-hydrophobic endocytosis motifs for internalized transmembrane proteins is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 151 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, 151 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, 151 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, 151 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, 151 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, 151 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, 151 units >NUCLEAR NLS experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 151 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, 151 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, 151 units >NUCLEAR NLS HCDA experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 151 units >NUCLEAR NLS SV40 LrgT experimentally determined is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 151 units >NUCLEAR NLS H2B experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 151 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, 151 units >NUCLEAR NLS Amida experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 151 units >NUCLEAR NLS Amida experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 151 units >NUCLEAR NLS RanBP3 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 151 units >NUCLEAR NLS Pho4p experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 151 units >NUCLEAR NLS DNAhelicaseQ1 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 151 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, 151 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, 151 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, 151 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, 151 units >NUCLEAR NLS GAL4 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 151 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, 151 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, 151 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, 151 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, 151 units >NUCLEAR NLS TR2 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 151 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, 151 units >NUCLEAR NLS polyomaVP1 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 151 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, 151 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, 151 units >NUCLEAR NLS Rex experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 151 units >NUCLEAR NLS SRY experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 151 units >NUCLEAR NLS SRY experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 151 units >NUCLEAR NLS SOX9 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 151 units >NUCLEAR NLS SOX9 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 151 units >NUCLEAR NLS NS5A experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 151 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, 151 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, 151 units >NUCLEAR NLS adenovE1a experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 151 units >NUCLEAR NLS ystDNApolalpha experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 151 units >NUCLEAR NLS hVDR experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 151 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, 151 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, 151 units >NUCLEAR NLS cFOS experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 151 units >NUCLEAR NLS cJUN experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 151 units >NUCLEAR NLS hDNApolalpha experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 151 units >NUCLEAR NLS hDNAtopoII experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 151 units >NUCLEAR NLS hDNAtopoII experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 151 units >NUCLEAR NLS hBLM experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 151 units >NUCLEAR NLS hARNT experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 151 units >NUCLEAR NLS influenzaNP experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 151 units >NUCLEAR NLS influenzaNP experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 151 units >NUCLEAR NLS p54 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 151 units >NUCLEAR NLS hProTalpha experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 151 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, 151 units >NUCLEAR NLS protHsc9 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 151 units >NUCLEAR NLS protHsci experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 151 units >NUCLEAR NLS protHsc3 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 151 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, 151 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, 151 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, 151 units >NUCLEAR NLS MyoD experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 151 units >NUCLEAR NLS MyoD experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 151 units >NUCLEAR NLS opaque2 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 151 units >NUCLEAR NLS CTP experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 151 units >NUCLEAR NLS HCV experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 151 units >NUCLEAR NLS HCV experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 151 units >NUCLEAR NLS p110RB1 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 151 units >NUCLEAR NLS experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 151 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, 151 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, 151 units >NUCLEAR NLS Nucloplasmin experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 151 units >NUCLEAR NLS Nucleolin experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 151 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, 151 units >NUCLEAR NLS Nab2 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 151 units >NUCLEAR NLS M9 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 151 units >NUCLEAR NLS lscMyc experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 151 units >NUCLEAR NLS humKprotein experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 151 units >NUCLEAR NLS FluA experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 151 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, 151 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, 151 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, 151 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, 151 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, 151 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, 151 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, 151 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, 151 units >NUCLEAR NLS p53 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 151 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, 151 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, 151 units >NUCLEAR NLS L29 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 151 units >NUCLEAR NLS L29 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 151 units >NUCLEAR NLS Max experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 151 units >NUCLEAR NLS L3 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 151 units >NUCLEAR NLS dyskerin experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 151 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, 151 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, 151 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_492873.1.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: NP_492873.1 Y52B11C.1.p [Caenorhabditis elegans]. 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_492873.1.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: NP_492873.1 Y52B11C.1.p [Caenorhabditis elegans]. 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_492873.1 Y52B11C.1.p [Caenorhabditis elegans]. (151 letters) Searching..................................done Results from profile search Score E Sequences producing significant alignments: (bits) Value SNARE Alpha helical domains which are involved in vesicle fu... 24 0.14 RRM RNA recognition motif domain 23 0.31 BRCT BRCA C-terminal domain 21 1.3 CALMO Calmodulin like EF-hand domains 20 2.0 HOG HOG- intein(HINT) like domain 19 3.4 DHHC Novel zinc finger domain with DHHC signature 18 6.4 PBD Rho binding domain 18 7.0 SWIB SWIB domain (A chromatin associated domain) 18 7.6 CYCLIN Cyclin/TFIIB domain 18 9.3 >SNARE Alpha helical domains which are involved in vesicle fusion Length = 254 Score = 23.7 bits (51), Expect = 0.14 Identities = 13/59 (22%), Positives = 13/59 (22%), Gaps = 5/59 (8%) Query: 1 MLPLILLIVTLLLVLLLIFAVRSHPIPLLSQSRILLLIAHPDDETM--FFSPTIRALLQ 57 Sbjct: 186 EPATLSGIVAFILSLLCGALNLIRGFHAIESL---LQSDGEDFSYMIAFFLGTAACLYQ 241 >RRM RNA recognition motif domain Length = 110 Score = 22.6 bits (48), Expect = 0.31 Identities = 16/96 (16%), Positives = 16/96 (16%), Gaps = 18/96 (18%) Query: 59 GHRVFVLCISNGNFDGLGKIRARELSRAASKLGISASDVICLDYDEFADGDTWNRNALCQ 118 Sbjct: 20 ARSIYV-----GNVD--YGATAEELEAHFHGCGSVNRVTIL------CDKFSGHPKGFAY 66 Query: 119 IVMRHVEVLAADTVISFDSHGVSGHH---NHARYRP 151 Sbjct: 67 IEFSDKE--SVRTSLALDESLFRGRQIKVIPKRTNR 100 >BRCT BRCA C-terminal domain Length = 138 Score = 20.6 bits (43), Expect = 1.3 Identities = 7/40 (17%), Positives = 7/40 (17%), Gaps = 3/40 (7%) Query: 62 VFVLCISNGNFDGLGKIRARELSRAASKLGISASDVICLD 101 Sbjct: 11 VIVF---SGIVPMGEKLERTDIYRLCTQFGAVIVPDVTDD 47 >CALMO Calmodulin like EF-hand domains Length = 147 Score = 20.0 bits (41), Expect = 2.0 Identities = 10/48 (20%), Positives = 10/48 (20%), Gaps = 13/48 (27%) Query: 73 DGLGKIRARELSRAASKLGISASDVI-------------CLDYDEFAD 107 Sbjct: 96 NGDGLISAAELKHVLTSIGEKLTDAEVDDMLREVSDGSGEINIQQFAA 143 >HOG HOG- intein(HINT) like domain Length = 389 Score = 19.2 bits (39), Expect = 3.4 Identities = 5/36 (13%), Positives = 5/36 (13%) Query: 37 LIAHPDDETMFFSPTIRALLQAGHRVFVLCISNGNF 72 Sbjct: 248 LVSVWQPESQKLTFVFAHRIEEKNQVLVRDVETGEL 283 >DHHC Novel zinc finger domain with DHHC signature Length = 217 Score = 18.1 bits (36), Expect = 6.4 Identities = 10/32 (31%), Positives = 10/32 (31%) Query: 3 PLILLIVTLLLVLLLIFAVRSHPIPLLSQSRI 34 Sbjct: 48 PHPLQIVAWLLYLFFAVIGFGILVPLLPHHWV 79 >PBD Rho binding domain Length = 61 Score = 18.2 bits (36), Expect = 7.0 Identities = 6/11 (54%), Positives = 6/11 (54%) Query: 109 DTWNRNALCQI 119 Sbjct: 41 DDWNRNSKAVI 51 >SWIB SWIB domain (A chromatin associated domain) Length = 81 Score = 17.9 bits (36), Expect = 7.6 Identities = 7/28 (25%), Positives = 7/28 (25%), Gaps = 1/28 (3%) Query: 30 SQSRILLLIAH-PDDETMFFSPTIRALL 56 Sbjct: 19 VECTISILRKSSPEEPFMSYSPQLTAII 46 >CYCLIN Cyclin/TFIIB domain Length = 317 Score = 17.6 bits (35), Expect = 9.3 Identities = 7/35 (20%), Positives = 7/35 (20%) Query: 21 VRSHPIPLLSQSRILLLIAHPDDETMFFSPTIRAL 55 Sbjct: 174 ILENPEILRKTADDFLNRIALTDAYLLYTPSQIAL 208 Underlying Matrix: BLOSUM62 Number of sequences tested against query: 105 Number of sequences better than 10.0: 9 Number of calls to ALIGN: 9 Length of query: 151 Total length of test sequences: 20182 Effective length of test sequences: 16941.0 Effective search space size: 2043786.3 Initial X dropoff for ALIGN: 25.0 bits Y. Wolf's SCOP PSSM IMPALA version 1.1 [20-December-1999] Reference: Alejandro A. Schaffer, Yuri I. Wolf, Chris P. Ponting, Eugene V. Koonin, L. Aravind, Stephen F. Altschul (1999), "IMPALA: Matching a Protein Sequence Against a Collection of "PSI-BLAST-Constructed Position-Specific Score Matrices", Bioinformatics 15:1000-1011. Query= NP_492873.1 Y52B11C.1.p [Caenorhabditis elegans]. (151 letters) Searching.................................................done Results from profile search Score E Sequences producing significant alignments: (bits) Value gi|115902 [9..166] EF Hand-like 25 0.64 gi|1311386 [1..490] beta/alpha (TIM)-barrel 25 0.77 gi|2127787 [36..400] Periplasmic binding protein-like I 25 1.0 gi|477637 [13..271] NAD(P)-binding Rossmann-fold domains 24 1.2 gi|119785 [198..307] Catalytic domain of malonyl-CoA ACP tra... 24 1.4 gi|117484 [2..138] Double-stranded beta-helix 24 1.5 gi|2496719 [14..187] NAD(P)-binding Rossmann-fold domains 24 1.8 gi|1942967 [3..222] L-2-Haloacid dehalogenase 23 2.5 gi|1805705 [1..215] NAD(P)-binding Rossmann-fold domains 23 2.6 gi|1352256 [4..245] NAD(P)-binding Rossmann-fold domains 23 2.8 gi|625921 [2..242] NAD(P)-binding Rossmann-fold domains 23 2.9 gi|1657653 [5..162] NAD(P)-binding Rossmann-fold domains 23 3.1 gi|421277 [11..339] NAD(P)-binding Rossmann-fold domains 23 3.5 gi|1552874 [10..205] NAD(P)-binding Rossmann-fold domains 23 3.8 gi|2506153 [10..236] NAD(P)-binding Rossmann-fold domains 23 3.9 gi|1236183 [77..466] 6-bladed beta-propeller 22 4.3 gi|584960 [16..180] EF Hand-like 22 4.3 gi|2688351 [1..345] NAD(P)-binding Rossmann-fold domains 22 4.4 gi|2496573 [26..203] NAD(P)-binding Rossmann-fold domains 22 4.4 gi|2120533 [2..254] NAD(P)-binding Rossmann-fold domains 22 4.7 gi|2706599 [57..185] C-type lectin-like 22 6.3 gi|2493473 [2..191] EF Hand-like 22 6.6 gi|1684733 [3..247] NAD(P)-binding Rossmann-fold domains 22 6.7 gi|2145626 [13..324] beta/alpha (TIM)-barrel 22 6.8 gi|1723793 [7..233] NAD(P)-binding Rossmann-fold domains 22 7.0 gi|1297373 [446..704] beta/alpha (TIM)-barrel 22 7.1 gi|2618754 [18..216] NAD(P)-binding Rossmann-fold domains 21 7.7 gi|1465871 [5..212] NAD(P)-binding Rossmann-fold domains 22 8.4 gi|999515 [1..176] NAD(P)-binding Rossmann-fold domains 22 8.6 gi|1916731 [13..224] NAD(P)-binding Rossmann-fold domains 21 9.1 gi|1652715 [5..195] NAD(P)-binding Rossmann-fold domains 21 9.3 gi|2668623 [1020..1117] Actin depolymerizing proteins 21 9.7 gi|293973 [1..262] NAD(P)-binding Rossmann-fold domains 21 9.8 gi|1587000 [31..229] NAD(P)-binding Rossmann-fold domains 21 10.0 >gi|115902 [9..166] EF Hand-like Length = 158 Score = 25.1 bits (54), Expect = 0.64 Identities = 10/47 (21%), Positives = 10/47 (21%), Gaps = 12/47 (25%) Query: 73 DGLGKIRARELSRAASKLGISASDVI------------CLDYDEFAD 107 Sbjct: 107 NADGQINADEFAAWLTALGMSKAEAAEAFNQVDTNGNGELSLDELLT 153 >gi|1311386 [1..490] beta/alpha (TIM)-barrel Length = 490 Score = 25.0 bits (54), Expect = 0.77 Identities = 17/137 (12%), Positives = 17/137 (12%), Gaps = 28/137 (20%) Query: 40 HPDDETMFFSPTIRALLQAGHRVFVLCIS----------NGNFDGLGKIRARELSRAASK 89 Sbjct: 67 VAIDEYHRYKEDIGIMKDMNLDAYRFSISWPRVLPKGKLSGGVNREGINYYNNLINEVLA 126 Query: 90 LGISASDVICLDYDE----FADGDT-WNRNALCQIVMRHVEVLAA---DTVISFD----- 136 Sbjct: 127 NGMQP--YVTLFHWDVPQALEDEYRGFLGRNIVDDFRDYAELCFKEFGDRVKHWITLNEP 184 Query: 137 ---SHGVSGHHNHARYR 150 Sbjct: 185 WGVSMNAYAYGTFAPGR 201 >gi|2127787 [36..400] Periplasmic binding protein-like I Length = 365 Score = 24.6 bits (53), Expect = 1.0 Identities = 6/46 (13%), Positives = 6/46 (13%) Query: 28 LLSQSRILLLIAHPDDETMFFSPTIRALLQAGHRVFVLCISNGNFD 73 Sbjct: 197 IAGKGNDTGVIFIGYEEVATLLSQIDDNSPLLKHVWIGCDGTANSK 242 >gi|477637 [13..271] NAD(P)-binding Rossmann-fold domains Length = 259 Score = 24.2 bits (51), Expect = 1.2 Identities = 5/35 (14%), Positives = 5/35 (14%) Query: 49 SPTIRALLQAGHRVFVLCISNGNFDGLGKIRAREL 83 Sbjct: 12 ANLVTELLDRGYAVRSFDRAPSPLGDHAGLEVIEG 46 >gi|119785 [198..307] Catalytic domain of malonyl-CoA ACP transacylase Length = 110 Score = 24.1 bits (52), Expect = 1.4 Identities = 1/21 (4%), Positives = 1/21 (4%) Query: 44 ETMFFSPTIRALLQAGHRVFV 64 Sbjct: 56 NPVQWTKSVEYMAAQGVEHLY 76 >gi|117484 [2..138] Double-stranded beta-helix Length = 137 Score = 24.1 bits (52), Expect = 1.5 Identities = 10/49 (20%), Positives = 10/49 (20%) Query: 59 GHRVFVLCISNGNFDGLGKIRARELSRAASKLGISASDVICLDYDEFAD 107 Sbjct: 56 GKEMILSYLNQGDFIGELGLFEEGQERSAWVRAKTACEVAEISYKKFRQ 104 >gi|2496719 [14..187] NAD(P)-binding Rossmann-fold domains Length = 174 Score = 23.8 bits (50), Expect = 1.8 Identities = 6/49 (12%), Positives = 6/49 (12%) Query: 49 SPTIRALLQAGHRVFVLCISNGNFDGLGKIRARELSRAASKLGISASDV 97 Sbjct: 12 GRVAAALTTGLPDAGLLANGSFRVRALVPKGEDISELRKQGMEIATGDL 60 >gi|1942967 [3..222] L-2-Haloacid dehalogenase Length = 220 Score = 23.3 bits (49), Expect = 2.5 Identities = 17/153 (11%), Positives = 17/153 (11%), Gaps = 42/153 (27%) Query: 17 LIFAVRSHPIPLLSQSRILLLIAHPDDETMF-FSPTIRALLQAGHRVFVLC--------- 66 Sbjct: 66 LRFTCRHLGLDLDYRTRSTLCDYYLRLYPFSEVPDSLRELKRRGLKLYILSNGSPQSIDY 125 Query: 67 -------------ISNGNFDGLGKIRARELSRAASKLGISASDVICLDYDEFADGDTWN- 112 Sbjct: 126 VVSHYGLRDGFDHLLSVDPVQVYKPDNRVYELYEQYLGLDRSYILFV-------SSNYWD 178 Query: 113 ----RNALCQIVM-------RHVEVLAADTVIS 134 Sbjct: 179 YTGYRYFGFPTCWINRTGNVFEEMGQTPDWEVT 211 >gi|1805705 [1..215] NAD(P)-binding Rossmann-fold domains Length = 215 Score = 23.1 bits (48), Expect = 2.6 Identities = 4/101 (3%), Positives = 4/101 (3%), Gaps = 6/101 (5%) Query: 51 TIRALLQAGHRVFVLCISNGNFDGLGKIRARELSRAASKLGISASDVICLDYDEFADG-- 108 Sbjct: 19 LVQEFVKDKNIRHIIATARDVEKATDLKAISDPRVTALQLEVTCDKSMDTFVSKVEEIVG 78 Query: 109 ----DTWNRNALCQIVMRHVEVLAADTVISFDSHGVSGHHN 145 Sbjct: 79 SDGLNLLVNNAGNAVDYPCKAKPNRALFAEQLNVNTTSVVI 119 >gi|1352256 [4..245] NAD(P)-binding Rossmann-fold domains Length = 242 Score = 23.0 bits (48), Expect = 2.8 Identities = 7/69 (10%), Positives = 7/69 (10%), Gaps = 5/69 (7%) Query: 51 TIRALLQAGHRVFVLCISNGNFDGLGKIRARELSRAASKLGISASDVICLDYDEFADGDT 110 Sbjct: 18 ITRDLCRKFSGDVVLAARD---EERGQTAVQKLQAEGLSPRFHQLDI--DNPQSIRALRD 72 Query: 111 WNRNALCQI 119 Sbjct: 73 FLLKEYGGL 81 >gi|625921 [2..242] NAD(P)-binding Rossmann-fold domains Length = 241 Score = 23.1 bits (48), Expect = 2.9 Identities = 6/96 (6%), Positives = 6/96 (6%), Gaps = 10/96 (10%) Query: 51 TIRALLQAGHRVFVLCISNGNFDGLGKIRARELSRAASKLGISASDVICLDYDEFADGDT 110 Sbjct: 16 AVEALTRDGYTVVCHDATFADAAER----------QRFESENPGTVALAEQKPERLVDAT 65 Query: 111 WNRNALCQIVMRHVEVLAADTVISFDSHGVSGHHNH 146 Sbjct: 66 LQHGEAIDTIVSNDYIPRPMNRLPIEGTSEADIRQV 101 >gi|1657653 [5..162] NAD(P)-binding Rossmann-fold domains Length = 158 Score = 23.0 bits (48), Expect = 3.1 Identities = 9/73 (12%), Positives = 9/73 (12%), Gaps = 3/73 (4%) Query: 51 TIRALLQAGHRVFVLCISNGNFDGLGKIRARELSRAASKLGISASDVICLDYDEFADGDT 110 Sbjct: 14 LKDKLIEQGHQVDQINVRNQLWKSTSFKDYDVLIHTA---ALVHNNSPQARLTDYMQVNM 70 Query: 111 WNRNALCQIVMRH 123 Sbjct: 71 LLTKQLAQKAKAE 83 >gi|421277 [11..339] NAD(P)-binding Rossmann-fold domains Length = 329 Score = 22.7 bits (47), Expect = 3.5 Identities = 3/21 (14%), Positives = 3/21 (14%) Query: 49 SPTIRALLQAGHRVFVLCISN 69 Sbjct: 13 GWLSLWLQTMGATVKGYSLAP 33 >gi|1552874 [10..205] NAD(P)-binding Rossmann-fold domains Length = 196 Score = 22.7 bits (47), Expect = 3.8 Identities = 7/44 (15%), Positives = 7/44 (15%) Query: 51 TIRALLQAGHRVFVLCISNGNFDGLGKIRARELSRAASKLGISA 94 Sbjct: 16 ICERYLHNSAARIVLACLPDDPRREDAAAAMKQAGARSVELIDF 59 >gi|2506153 [10..236] NAD(P)-binding Rossmann-fold domains Length = 227 Score = 22.7 bits (47), Expect = 3.9 Identities = 2/23 (8%), Positives = 2/23 (8%) Query: 51 TIRALLQAGHRVFVLCISNGNFD 73 Sbjct: 13 LAWHFINQKQPVIVSYRTHYPAI 35 >gi|1236183 [77..466] 6-bladed beta-propeller Length = 390 Score = 22.4 bits (47), Expect = 4.3 Identities = 18/53 (33%), Positives = 18/53 (33%), Gaps = 8/53 (15%) Query: 66 CISNGNFDGLGKIRAREL-SRAASKLG------ISASDVICLDYDEFADGDTW 111 Sbjct: 261 CESNGD-KGLGGIKGGFVHQRMASKTGRWYSRTMSKTERMGMELYVRYDGDPW 312 >gi|584960 [16..180] EF Hand-like Length = 165 Score = 22.4 bits (47), Expect = 4.3 Identities = 13/47 (27%), Positives = 13/47 (27%), Gaps = 14/47 (29%) Query: 73 DGLGKIRARELSRAASKLGISASDVI--------------CLDYDEF 105 Sbjct: 113 DGSGSISLDEWKAYGRISGICSSDEDAEKTFKHCDLDNSGKLDVDEM 159 >gi|2688351 [1..345] NAD(P)-binding Rossmann-fold domains Length = 345 Score = 22.3 bits (46), Expect = 4.4 Identities = 13/77 (16%), Positives = 13/77 (16%), Gaps = 2/77 (2%) Query: 49 SPTIRALLQAGHRVFVLCISNGNFDGL-GKIRARELSRAASKLGISASDVICL-DYDEFA 106 Sbjct: 14 FHVAKKLVEKGHEVLGIDVLNDYYELKFKHERLEALGFCSKDVKTHKIIKSEKYNNLSFA 73 Query: 107 DGDTWNRNALCQIVMRH 123 Sbjct: 74 YLDILNKDKLLELFKDH 90 >gi|2496573 [26..203] NAD(P)-binding Rossmann-fold domains Length = 178 Score = 22.3 bits (46), Expect = 4.4 Identities = 3/25 (12%), Positives = 3/25 (12%) Query: 51 TIRALLQAGHRVFVLCISNGNFDGL 75 Sbjct: 14 LTARLAQNPLINRVIAVDAIAPSKD 38 >gi|2120533 [2..254] NAD(P)-binding Rossmann-fold domains Length = 253 Score = 22.3 bits (46), Expect = 4.7 Identities = 4/57 (7%), Positives = 4/57 (7%), Gaps = 5/57 (8%) Query: 51 TIRALLQAGHRVFVLCISNGNFDGLGKIRARELSRAASKLGISASDVICLDYDEFAD 107 Sbjct: 19 LCKKILQNKGIAILADINENH-----LSILKTELENEFKKELLSLRLDITSKESLNC 70 >gi|2706599 [57..185] C-type lectin-like Length = 129 Score = 21.7 bits (45), Expect = 6.3 Identities = 7/29 (24%), Positives = 7/29 (24%) Query: 95 SDVICLDYDEFADGDTWNRNALCQIVMRH 123 Sbjct: 80 NSGTAAVYNNFAEGYPNNVYGDCIHYMTT 108 >gi|2493473 [2..191] EF Hand-like Length = 190 Score = 22.0 bits (46), Expect = 6.6 Identities = 4/36 (11%), Positives = 4/36 (11%) Query: 73 DGLGKIRARELSRAASKLGISASDVICLDYDEFADG 108 Sbjct: 40 GENGTLSREDFQRIPELAINPLGDRIINAFFSEGED 75 Score = 21.6 bits (45), Expect = 6.7 Identities = 7/54 (12%), Positives = 7/54 (12%), Gaps = 19/54 (35%) Query: 73 DGLGKIRARELSRAASKLGISASDVI-------------------CLDYDEFAD 107 Sbjct: 124 DKDDKISRDELLQVLRMMVGVNISDEQLGSIADRTIQEADQDGDSAISFTEFVK 177 >gi|1684733 [3..247] NAD(P)-binding Rossmann-fold domains Length = 245 Score = 21.9 bits (45), Expect = 6.7 Identities = 17/95 (17%), Positives = 17/95 (17%), Gaps = 9/95 (9%) Query: 51 TIRALLQAGHRVFVLCISNGNFDGLGKIRARELSRAASKLGISASDVICLDY-----DEF 105 Sbjct: 21 LCAALLQRGARVLAMSRSIGGLEPL----LETHAEQLQWLSGDVTSADDLAQLARRAAQL 76 Query: 106 ADGDTWNRNALCQIVMRHVEVLAADTVISFDSHGV 140 Sbjct: 77 GPVHYLVPNAGIAELADGLDMAAFDRQWAVNGAGA 111 >gi|2145626 [13..324] beta/alpha (TIM)-barrel Length = 312 Score = 21.6 bits (45), Expect = 6.8 Identities = 29/106 (27%), Positives = 29/106 (27%), Gaps = 11/106 (10%) Query: 48 FSPTIRALL--QAGHRVFVLCISNGNFDGLGKIRARELSRAASKLGISASDVICLDYDEF 105 Sbjct: 29 FSHTVAVMQTPEALHRVAYECVEDLAADSVVYAEVRFAPELHIDEGLSFDEVLASVLAGF 88 Query: 106 ADGD---TWNRNAL---CQI-VMRHVEVL--AADTVISFDSHGVSG 142 Sbjct: 89 ADGERACAAEGNAITVRCLVTAMRHAAMSREIAELAIRFRDKGVVG 134 >gi|1723793 [7..233] NAD(P)-binding Rossmann-fold domains Length = 227 Score = 21.5 bits (44), Expect = 7.0 Identities = 1/23 (4%), Positives = 1/23 (4%) Query: 49 SPTIRALLQAGHRVFVLCISNGN 71 Sbjct: 12 LHLIQQFFDINPKPDIHIFDVRD 34 >gi|1297373 [446..704] beta/alpha (TIM)-barrel Length = 259 Score = 21.8 bits (46), Expect = 7.1 Identities = 7/35 (20%), Positives = 7/35 (20%) Query: 111 WNRNALCQIVMRHVEVLAADTVISFDSHGVSGHHN 145 Sbjct: 103 WDQNNKAKSLVAWIKRWEADGETKIDGIGSQMHVT 137 >gi|2618754 [18..216] NAD(P)-binding Rossmann-fold domains Length = 199 Score = 21.4 bits (44), Expect = 7.7 Identities = 7/44 (15%), Positives = 7/44 (15%) Query: 54 ALLQAGHRVFVLCISNGNFDGLGKIRARELSRAASKLGISASDV 97 Sbjct: 19 GLMKPGSVLLLVARSETLLQELKEELRGLTGTAQPAVRCVAVDL 62 >gi|1465871 [5..212] NAD(P)-binding Rossmann-fold domains Length = 208 Score = 21.5 bits (44), Expect = 8.4 Identities = 4/27 (14%), Positives = 4/27 (14%) Query: 49 SPTIRALLQAGHRVFVLCISNGNFDGL 75 Sbjct: 11 AHVISALQKIGCKERIIVVDPCPQEFK 37 >gi|999515 [1..176] NAD(P)-binding Rossmann-fold domains Length = 176 Score = 21.6 bits (45), Expect = 8.6 Identities = 11/22 (50%), Positives = 11/22 (50%) Query: 130 DTVISFDSHGVSGHHNHARYRP 151 Sbjct: 117 DKGILFVGSGVSGGEDGARYGP 138 >gi|1916731 [13..224] NAD(P)-binding Rossmann-fold domains Length = 212 Score = 21.2 bits (43), Expect = 9.1 Identities = 5/21 (23%), Positives = 5/21 (23%) Query: 51 TIRALLQAGHRVFVLCISNGN 71 Sbjct: 19 TGGRWAAAGMYVTIADIQPLE 39 >gi|1652715 [5..195] NAD(P)-binding Rossmann-fold domains Length = 191 Score = 21.5 bits (44), Expect = 9.3 Identities = 2/21 (9%), Positives = 2/21 (9%) Query: 51 TIRALLQAGHRVFVLCISNGN 71 Sbjct: 21 LVESFLEHGAAKVYAAVRKLE 41 >gi|2668623 [1020..1117] Actin depolymerizing proteins Length = 98 Score = 21.4 bits (45), Expect = 9.7 Identities = 12/47 (25%), Positives = 12/47 (25%), Gaps = 5/47 (10%) Query: 55 LLQAGHRVFVLCISNGNFDGLGKIRARELS---RAASKLGISASDVI 98 Sbjct: 32 LLLSPHHCFLWVGEFAN--VIEKAKASELASLIQTKRELGCRATYIQ 76 >gi|293973 [1..262] NAD(P)-binding Rossmann-fold domains Length = 262 Score = 21.2 bits (43), Expect = 9.8 Identities = 6/30 (20%), Positives = 6/30 (20%) Query: 49 SPTIRALLQAGHRVFVLCISNGNFDGLGKI 78 Sbjct: 14 SNIVKALNQRGITDIVAVDNLTKGEKFKNL 43 >gi|1587000 [31..229] NAD(P)-binding Rossmann-fold domains Length = 199 Score = 21.1 bits (43), Expect = 10.0 Identities = 5/18 (27%), Positives = 5/18 (27%) Query: 51 TIRALLQAGHRVFVLCIS 68 Sbjct: 16 FVQQLLLRGDTVEAGVRS 33 Underlying Matrix: BLOSUM62 Number of sequences tested against query: 1187 Number of sequences better than 10.0: 34 Number of calls to ALIGN: 35 Length of query: 151 Total length of test sequences: 256703 Effective length of test sequences: 213024.0 Effective search space size: 24432756.5 Initial X dropoff for ALIGN: 25.0 bits ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ calculation of internal repeats with prospero ***** PROSPERO v1.3 Fri Mar 8 14:40:50 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_492873.1 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_492873.1.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: NP_492873.1 Y52B11C.1.p [Caenorhabditis elegans]. 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_492873.1.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: NP_492873.1 Y52B11C.1.p [Caenorhabditis elegans]. Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- TIGR00083 ribF: riboflavin biosynthesis protein RibF -1.0 78 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- TIGR00083 1/1 64 75 .. 1 10 [. -1.0 78 Alignments of top-scoring domains: TIGR00083: domain 1 of 1, from 64 to 75: score -1.0, E = 78 *->sLaI..GyFDGl<-* +L I++G+FDGl NP_492873. 64 VLCIsnGNFDGL 75 // 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_492873.1.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: NP_492873.1 Y52B11C.1.p [Caenorhabditis elegans]. 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_492873.1.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: NP_492873.1 Y52B11C.1.p [Caenorhabditis elegans]. Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- COG3232 -60.1 78 1 COG2707 -84.5 84 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- COG2707 1/1 4 140 .. 1 151 [] -84.5 84 COG3232 1/1 45 151 .] 1 129 [] -60.1 78 Alignments of top-scoring domains: COG2707: domain 1 of 1, from 4 to 140: score -84.5, E = 84 *->lmfsqaaLfLviLlaLGliSnNqsitiSvlVLLiikqtgLsqKff.P l + ++L+Lv+Ll+ ++ S+ ++ +LL+i + ff+P NP_492873. 4 LILLIVTLLLVLLLIFAVRSHPIPLLSQSRILLLIAHPDDETMFFsP 50 liekkGlnlG..IiILTIGVLsPiaSGkiqlpplg.veaflswkmlvAia +i l G+++ +L I G + lg++ a + +++ ++ NP_492873. 51 TIRAL-LQAGhrVFVLCIS------NG--NFDGLGkIRARELSRAASKLG 91 vGvlVAwLAgrGVpLlgnqPhlvtgLviGTilgVAlfgGvPVGPLIaAGi + ++ V l + ++ l + + v V +++ NP_492873. 92 -------ISASDVICLDYDEFADGDTWNRNALCQIVMRHVEVLAADT--V 132 lyLlmgkv<-* +++ v NP_492873. 133 ISFDSHGV 140 COG3232: domain 1 of 1, from 45 to 151: score -60.1, E = 78 *->MPHLvlEYTdNldeEinvpeLLEklna..aLlASPGlF.piggIkSR ++ + ++ LL+ ++ +L S G F+++g I++R NP_492873. 45 ----TMFFSPTIR------ALLQAGHRvfVLCISNGNFdGLGKIRAR 81 avRLeeyrlgDesedsvAFvHlsLeilAGRdaEtkrelgeaLfEVLaahf + + lg + + +v +L d t aL+ + h+ NP_492873. 82 ELSRAASKLGIS-ASDV----ICLDYDEFADGDTWNR--NALCQIVMRHV 124 AevraeRglalSvEirEmdeasfaKrnNvherlrk<-* + a + +d + N h+r+r NP_492873. 125 EVLAAD-------TVISFDSHGVSGHHN-HARYRP 151 // 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_492873.1.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: NP_492873.1 Y52B11C.1.p [Caenorhabditis elegans]. Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- COG2120 30.1 8.2e-08 1 COG1994 2.9 6.2 1 COG1317 -0.2 59 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- COG1994 1/1 1 35 [. 185 221 .. 2.9 6.2 COG2120 1/1 27 94 .. 27 106 .. 30.1 8.2e-08 COG1317 1/1 115 144 .. 287 317 .] -0.2 59 Alignments of top-scoring domains: COG1994: domain 1 of 1, from 1 to 35: score 2.9, E = 6.2 *->llnlaLaiFnlipilpndglavlnllpippldgskal<-* +l+l+L i++l+ l+++ +++ +++pip l++s++l NP_492873. 1 MLPLILLIVTLL--LVLLLIFAVRSHPIPLLSQSRIL 35 COG2120: domain 1 of 1, from 27 to 94: score 30.1, E = 8.2e-08 *->plaselrvLavfpHPDDEsiGcGGTLakyaaaGveVglvclTlGEmG pl s r+L++ +HPDDE+ + T+ ++ +aG++V+++c NP_492873. 27 PLLSQSRILLLIAHPDDETMFFSPTIRALLQAGHRVFVLCI------ 67 enltqplldthetlgeiRreElaeAArvLGvek<-* + + + lg iR++El +AA++LG+++ NP_492873. 68 ------SNGNFDGLGKIRARELSRAASKLGISA 94 COG1317: domain 1 of 1, from 115 to 144: score -0.2, E = 59 *->klleilkesateekaSdiridlDasaldngq<-* +l+ i++++++ a d+ i+ D+ +++ NP_492873. 115 ALCQIVMRHVEVL-AADTVISFDSHGVSGHH 144 //