SAPS. Version of January 7, 1995. Date run: Sat Dec 15 08:56:51 2007 File: alignp1_in.txt ID SQ; SV 1; XXX; XXX; XXX; XXX; 357 BP. DE SEQUENCE 357 AA; 40007 MW; 721EAC06CEE4552FCRC64; number of residues: 357; molecular weight: 40.0 kdal 1 MSATALRIAP IASRTFQRRL GYLLAGVATG AAATVAYKAQ KNNNYYKYNN NNNNNSGFKA 61 GALAAAAGVV HLAHEEDKKT ADYQKVYNLI AERLRDDDEY DNYIGYGPVL VRLAWHSSGT 121 WDKNDNTGGS YGGTYRYKKE SQDPSNAGLE NAAKFLEPVK KQFPWISYGD LYTLGGVVGI 181 QELQGPKIPW RSGRTDLPED MTPDNGRLPD GDKDANYVRN FYKRLDFNDR EVVALLGAHA 241 LGKTHLKNSG FEGPWGAANN IFTNEFYLNL LNEDWKLEKN DAGNLQYNSP KGYMMLPTDY 301 ALIQDSNYLK IVKEYAADQD AFFRDFSKAF AALLERGIDF PKNQPVHIFK TLDEQGL -------------------------------------------------------------------------------- COMPOSITIONAL ANALYSIS (extremes relative to: swp23s) A++: 38(10.6%); C- : 0( 0.0%); D++: 27( 7.6%); E : 17( 4.8%); F : 15( 4.2%) G++: 31( 8.7%); H- : 6( 1.7%); I++: 12( 3.4%); K++: 26( 7.3%); L : 34( 9.5%) M- : 4( 1.1%); N++: 31( 8.7%); P++: 15( 4.2%); Q++: 12( 3.4%); R++: 16( 4.5%) S++: 14( 3.9%); T++: 15( 4.2%); V++: 15( 4.2%); W- : 6( 1.7%); Y++: 23( 6.4%) KR ++: 42 ( 11.8%); ED ++: 44 ( 12.3%); AGP ++: 84 ( 23.5%); KRED ++: 86 ( 24.1%); KR-ED --: -2 ( -0.6%); FIKMNY++: 111 ( 31.1%); LVIFM ++: 80 ( 22.4%); ST ++: 29 ( 8.1%). -------------------------------------------------------------------------------- CHARGE DISTRIBUTIONAL ANALYSIS 1 000000+000 000+000++0 0000000000 0000000+00 +00000+000 00000000+0 61 0000000000 0000---++0 0-00+00000 0-+0+----0 -000000000 0+00000000 121 0-+0-00000 00000+0++- 00-000000- 000+00-00+ +00000000- 0000000000 181 0-0000+000 +00+0-00-- 000-00+00- 0-+-0000+0 00++0-00-+ -000000000 241 00+000+000 0-00000000 0000-00000 00--0+0-+0 -000000000 +0000000-0 301 0000-0000+ 00+-000-0- 000+-00+00 0000-+00-0 0+0000000+ 00--000 A. CHARGE CLUSTERS. Positive charge clusters (cmin = 10/30 or 13/45 or 17/60): none Negative charge clusters (cmin = 10/30 or 14/45 or 17/60): none Mixed charge clusters (cmin = 16/30 or 22/45 or 27/60): 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)| lmin0 5 | 5 | 7 | 33 | 9 | 10 | 13 | 11 | 11 | 15 | lmin1 6 | 6 | 9 | 40 | 11 | 12 | 15 | 14 | 14 | 18 | lmin2 7 | 7 | 10 | 44 | 13 | 13 | 17 | 15 | 16 | 20 | There are no charge runs or patterns exceeding the given minimal lengths. Run count statistics: + runs >= 3: 0 - runs >= 3: 2, at 75; 96; * runs >= 5: 2, at 75; 95; 0 runs >= 22: 0 -------------------------------------------------------------------------------- DISTRIBUTION OF OTHER AMINO ACID TYPES 1. HIGH SCORING SEGMENTS. There are no high scoring hydrophobic segments. ____________________________________ High scoring transmembrane segments: 5.00 (LVIF) 2.00 (AGM) 0.00 (BZX) -1.00 (YCW) -2.00 (ST) -6.00 (P) -8.00 (H) -10.00 (NQ) -16.00 (KR) -17.00 (ED) Expected score/letter: -4.339 M_0.01= 49.59; M_0.05= 40.70; M_0.30= 30.12 1) From 20 to 36: length= 17, score=38.00 20 LGYLLAGVAT GAAATVA L: 3(17.6%); A: 6(35.3%); G: 3(17.6%); V: 2(11.8%); T: 2(11.8%); 2. SPACINGS OF C. H2N-357-COOH -------------------------------------------------------------------------------- REPETITIVE STRUCTURES. A. SEPARATED, TANDEM, AND PERIODIC REPEATS: amino acid alphabet. Repeat core block length: 4 Aligned matching blocks: [ 55- 58] NSGF [ 248- 251] NSGF 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: 29 (Expected range: 8-- 36) 2. Histogram of spacings between consecutive amino acid multiplets: (1-5) 13 (6-10) 7 (11-20) 5 (>=21) 5 3. Clusters of amino acid multiplets (cmin = 13/30 or 17/45 or 21/60): none 4. Long amino acid multiplets (>= 5; Letter/Length/Position): N/7/49 B. CHARGE ALPHABET. 1. Total number of charge multiplets: 10 (Expected range: 0-- 19) 5 +plets (f+: 11.8%), 5 -plets (f-: 12.3%) Total number of charge altplets: 11 (Critical number: 22) 2. Histogram of spacings between consecutive charge multiplets: (1-5) 2 (6-10) 0 (11-20) 2 (>=21) 7 -------------------------------------------------------------------------------- PERIODICITY ANALYSIS. A. AMINO ACID ALPHABET (core: 4; !-core: 5) Location Period Element Copies Core Errors 49- 55 1 N 7 7 ! 0 60- 67 2 A. 4 4 0 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. Location (Quartile) Spacing Rank P-value Interpretation 0- 75 (1.) -( 75)- 1 of 45 0.0006 large maximal spacing