CHARGE DISTRIBUTIONAL ANALYSIS
The distribution of charges in the protein sequence is evaluated in terms of clusters, high scoring segments, and runs and periodic patterns. Clus- ters indicate regions of typically 30 to 60 residues exhibiting a rela- tively high charge concentration. For high scoring charge segments, posi- tive scores are assigned to charge residues of the appropriate type and negative scores to all other residues. A significant cumulative positive score again indicates a region of high charge concentration. The cluster method and the scoring method will generally pick out the same segments (with the scoring method often delimiting the segment to a narrower range), conferring robustness to the results. Short segments of high charge concentration are displayed as runs (with errors). Periodic pat- terns focus on those with charges every second or third position, with possible relevance to amphipathic secondary structures; other periodic patterns are displayed in the general periodicity analysis section of the output.
1 00+00+0++0 0000000000 0000000000 0000-00+00 000+-00000 0-000000-0
61 0000000000 0+0000-000 +00-0-0-0- 0000-0++00 0000000000 00000-0000
121 0-0000+000 +0-00+000- 0000-00-00 0000-0000+ 000+000-00 000000000-
181 -00+000+00 0000+0-000 000+00-000 -00-000+00 00000-000- --0-00-00+
241 0+0-00-0+0 000+000++0 00000-0000 -+-00000-0 --00+0+00- 0000+0000+
301 000000+000 000000-000 +000000000 0-0000000+ -000-00000 -000000000
361 000-0--000 00000000+0 00000000-0 0000--0000 0000000++0 0+000+-0+0
421 000000++00 0000-00000 00000+0000 0000000000 00000000-- 00000-0000
481 0000000000 00000000-0 0000000000 0000000000 000++0-00- 00000000+0
541 -000000000 0-+-0---00 00000+000+ -0+0+00-+- 0+00000000 000--00-+0
601 00000+0000 000-000000 00000000+0 +000+0-000 00000+0-00 000000-000
661 000000000- -0-000+000 00000-+000 0-000-0+00 000000-000 0000000000
721 0+0000000+ 000-0+0000 000-0+0000 0+-0000000 00+0--0000 0000-00000
781 000000-000 00+0000000 000000000- 000-000000 00-0+-00+0 0000000000
841 000+-00000 00000000+- ++000000+0 00+000-00+ 00+0000000 00000--000
901 0000000000 00000+00-0 -000000000 0-000000+0 -0000000-0 0000000000
961 0000000000 -0-000-000 0-0000+000 0000000000 -000000000 0000000000
1021 00-0000000 --0+000000 00+0000000 0000000000 0000000-00 0000000000
1081 0000000000 00+0000000 0000000000 000-000000 0-00000000 0000000000
1141 0000000000 0000000000 -000000000 0000000000 00000+000+ 0000000000
1201 -+000+0000 -+0000000- 00000-0000 00000-0-00 0000000000 00-0000000
1261 -000000+
A. CHARGE CLUSTERS.
Positive, negative, and mixed charge clusters are distinguished. In each
case, cmin indicates the minimum number of charges required for a signifi-
cant charge cluster corresponding to the given window size; e.g., cmin =
9/30 or 12/45 or 15/60 means that significance requires at least 9 charges
in a segment of 30 (or fewer) residues, or 12 charges in a segment of
length 45, or 15 charges in a segment of length 60. In the case of posi-
tive and negative charge clusters, these counts refer to net charge, i.e.,
charges of the opposite sign within the window are counted as -1. The
sizes of the clusters are optimized for display to indicate the segment of
highest charge concentration, but a minimum size of 20 residues is
required. A mixed charge cluster that begins and ends within 15 residues
of the endpoints of a pure charge cluster is not displayed (since its sig-
nificance rests mostly on the charged residues comprising the displayed
pure charge cluster), unless the -v (verbose output) flag is set, in which
case both the pure and the mixed charge cluster are displayed. On the
other hand, pure charge clusters that are embedded in mixed charge clus-
ters are displayed separately (indicated by a * preceding the specifica-
tion of location).
For each cluster are given its location in the sequence (From, to),
the quartile of the location (1st, 2nd, 3rd, or 4th quarter of the
sequence), length, count, and t-value (standard deviations above the mean;
to accommodate the multiple tests performed, the t-value significance
threshold is set to 4.0 for sequences up to 750 residues, to 4.5 for
sequences of length 750-1500 residues, and to 5.0 for longer sequences);
also indicated are residues comprising at least 10% of the cluster.
Positive charge clusters (cmin = 8/30 or 11/45 or 13/60): none
Negative charge clusters (cmin = 10/30 or 13/45 or 16/60): none
Mixed charge clusters (cmin = 14/30 or 18/45 or 23/60):
1) From 552 to 582: ERDGEEEAAAQYGSKLNGREYKVKVLDKDGK
-+-0---0000000+000+-0+0+00-+-0+
quartile: 2; size: 31, +count: 7, -count: 8, 0count: 16; t-value: 4.70 *
G: 4 (12.9%); K: 5 (16.1%); E: 5 (16.1%);
B. HIGH SCORING (UN)CHARGED SEGMENTS.
For each scoring scheme (scores assigned to residues as displayed), SAPS displays segments of the sequence with aggregate score exceeding the par- ticular threshold values M_0.01 (1% significance level, segments labeled with **), M_0.05 (5% significance level, segments labeled *), or other- wise as indicated. A minimal segment length is set as shown. The expected score/letter should be sufficiently large negative, and the average infor- mation per letter should be sufficiently large positive in order for the scoring statistics to apply properly (the program prints out when the con- ditions are not met and skips evaluations).
______________________________________ High scoring positive charge segments:
score= 2.00 frequency= 0.072 ( KR ) score= 0.00 frequency= 0.000 ( BZX ) score= -1.00 frequency= 0.832 ( LAGSVTIPNFQYHMCW ) score= -2.00 frequency= 0.096 ( ED )
Expected score/letter: -0.881; Average information/letter: 1.973 Minimal length of displayed segments set to: 20
M_0.01= 9.33 (cv= 6.16, lambda= 1.15953, k= 0.39565, x= 3.17;
90% confidence interval for segment length: 8 +- 6)
M_0.05= 7.92 (x= 1.76)
- of segments (>=20 residues) exceeding M_0.05: none
______________________________________
High scoring negative charge segments:
score= 2.00 frequency= 0.096 ( ED ) score= 0.00 frequency= 0.000 ( BZX ) score= -1.00 frequency= 0.832 ( LAGSVTIPNFQYHMCW ) score= -2.00 frequency= 0.072 ( KR )
Expected score/letter: -0.783; Average information/letter: 1.431 Minimal length of displayed segments set to: 20
M_0.01= 10.95 (cv= 7.33, lambda= 0.97470, k= 0.34200, x= 3.62;
90% confidence interval for segment length: 11 +- 9)
M_0.05= 9.28 (x= 1.95)
- of segments (>=20 residues) exceeding M_0.05: none
___________________________________
High scoring mixed charge segments:
score= 1.00 frequency= 0.168 ( KEDR ) score= 0.00 frequency= 0.000 ( BZX ) score= -1.00 frequency= 0.832 ( LAGSVTIPNFQYHMCW )
Expected score/letter: -0.664; Average information/letter: 1.533 Minimal length of displayed segments set to: 20
M_0.01= 6.94 (cv= 4.47, lambda= 1.60000, k= 0.52997, x= 2.48;
90% confidence interval for segment length: 10 +- 7)
M_0.05= 5.93 (x= 1.46)
- of segments (>=20 residues) exceeding M_0.05: none
________________________________
High scoring uncharged segments:
score= 1.00 frequency= 0.832 ( LAGSVTIPNFQYHMCW ) score= 0.00 frequency= 0.000 ( BZX ) score= -8.00 frequency= 0.168 ( KEDR )
Expected score/letter: -0.512 Average information/letter: 0.065 < .10; too small !
C. CHARGE RUNS AND PATTERNS.
The table below shows the charge runs and patterns searched for (* stands
for + or -) and the required minimum number of matches to the pattern
allowing for at most 0 (lmin0), 1 (lmin1), or 2 (lmin2) mismatches or
insertions/deletions (1% significance level). Occurrences are arranged in
the order in which they appear in the sequence. For each run or pattern
are displayed its length (number of matches) and a triplet giving the
number of mismatches, insertions and deletions. 0-runs are further charac-
terized by their composition (residues comprising more than 10% of the
run).
Run count statistics are compiled for runs of lengths at least 2/3 of
the minimal significant length (lmin0); given are the number and locations
of such runs.
pattern (+)| (-)| (*)| (0)| (+0)| (-0)| (*0)|(+00)|(-00)|(*00)| (H.)|(H..)|
lmin0 4 | 5 | 6 | 54 | 9 | 10 | 13 | 11 | 13 | 16 | 5 | 5 |
lmin1 6 | 6 | 8 | 65 | 11 | 12 | 15 | 14 | 15 | 19 | 6 | 7 |
lmin2 7 | 8 | 9 | 73 | 13 | 14 | 17 | 16 | 17 | 21 | 7 | 8 |
(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: 2, at 230; 556; * runs >= 4: 1, at 859; 0 runs >= 36: 1, at 1123;
