PROSITE pattern based filter

Zinc - patterns

R-[RK]-H-H-C-R-x-C-G
C-x2-C-x(12,16)-H-x5-H
W-x-C-X(2,4)-C-x(3)-N-X(6)-C-x(2)-C
C-x(2)-C-x(4,8)-[RHDGSCV]-[YWFMVIL]-x-[CS]-x(2,5)-[CHEQ]- x-[DNSAGE]-[YFVLI]-x-[LIVF]-C-x(2)-C
C-x(2,4)-C-x(3)-[LIVMFYWC]-x(8)-H-x(3,5)-H
C-x-H-x-[LIVMFY]-C-x(2)-C-[LIVMYA]
C-x-[DN]-C-x(4,5)-[ST]-x(2)-W-[HR]-[RK]-x(3)-[GN]-x(3,4)- C-N-[AS]-C
C-[KR]-x-C-x(3)-I-x-K-x(3)-[RG]-x(16,18)-W-[FYH]-H-x(2)-C
C-[DES]-x-C-x(3)-I-x(3)-R-x(4)-P-x(4)-C-x(2)-C
C-x(2)-C-x(9)-[LIVMQSAR]-[QH]-[STQL]-[RA]-[SACR]-x-[DE]- [DET]-[PGSEA]-x(6)-C-x(2,5)-C-x(3)-[FW]
G-H-E-x(2)-G-x(5)-[GA]-x(2)-[IVSAC]
[GSD]-[DEQH]-x(2)-L-x(3)-[SA](2)-G-G-x-G-x(4)-Q-x(2)-[KR]
[LIVM](2)-[FYW]-x(10)-C-x(2)-C-G-x(2)-[FY]-K-L
[GA]-[IMFAT]-H-[LIVF]-H-x(2)-[GP]-[SDG]-x-[STAGDE]
G-[GN]-[SGA]-G-x-R-x-[SGA]-C-x(2)-[IV]
H-Y-x-[GT]-D-[LIVM]-[DNS]-x-P-x-H-[PA]-x-N
[PK]-x-[LIVMFY]-x-[LIVMFY]-x(4)-H-[STAG]-x-E-x-[LIVM]- [STAG]-x(6)-[LIVMFYTA]
H-[STAG]-x(3)-[LIVME]-x(2)-[LIVMFYW]-P-[FYW]
[GSTALIVN]-x(2)-H-E-[LIVMFYW]-{DEHRKP}-H-x-[LIVMFYWGSPQ]
G-x(8,9)-G-x-[STA]-H-[LIVMFY]-[LIVMC]-[DERN]-[HRKL]- [LMFAT]-x-[LFSTH]-x-[GSTAN]-[GST]
[CH]-[AGV]-E-x(2)-[LIVMFGAT]-[LIVM]-x(17,33)-P-C-x(2,8)-C- x(3)-[LIVM]

Iron - patterns

[STALIV]-[LIVF]-x-[DE]-x(6,7)-P-x(4)-[ALIV]-x-[GST]-x(2)- D-[TAIVM]-[LIVMF]-x(4)-E
[GSW]-x-[LIVTSACD]-[GH]-x(2)-[GSAE]-[GSHYQ]-x-[LIVTP]-[GAST]-[GAS]-x(3)-[LIVMT]-x-[HNS]-[GA]-x-[GTAC]
[STV]-G-C-x(3)-C-x(6)-[DE]-[LIVMF]-[GAT]-[LIVMF]
H-[EQ]-x(3)-H-x-[LM]-[NEQHRC]-[GSTA]-H-[LIVMSTAC](2)-x-E
[LIVMAC]-H-P-[LIVM]-x-[KRQ]-[LIVMF](2)-x-[AP]-H
[FW]-[SGNH]-x-[GD]-x-[RKHPT]-x-C-[LIVMFAP]-[GAD]
D-x-W-E-H-[STA]-[FY](2)
C-{C}-{C}-[GA]-{C}-C-[GAST]-{CPDEKRHFYW}-C
C-x(2)-[STAQ]-x-[STAMV]-C-[STA]-T-C-[HR]
C-x(2)-C-x(2)-C-x(3)-C-[PEG]
C-x(6,9)-[LIVM]-x(3)-G-[YW]-C-x(2)-[FYW]
C-[TK]-H-L-G-C-[LIVST]
C-P-C-H-x-[GSA]
E-x-[KR]-E-x(2)-E-[KR]-[LF]-[LIVMA]-x(2)-Q-N-x-R-x-G-R
D-x(2)-[LIVMF]-[STAC]-[DH]-F-[LI]-[EN]-x(2)-[FY]-L-x(6)- [LIVM]-[KN]

Copper - patterns

M-[LIVMF](3)-x(3)-K-[MY]-A-C-x(2)-C-I-[KR]-x-H-[KR]-x(3)- C-x-H-x(8)-[KR]-x-[KR]-G-R-P
[LIVM]-[LIVMA]-[LIVMF]-x(4)-[ST]-x(2)-N-Y-[DE]-[YN]
T-x-[GS]-x(2)-H-[LIVMF]-x(3)-E-[DE]-x-P
W-x-W-H-x-C-H-x-H-Y-H-S-M-[DE]
[YWG]-[LIVFYWTA](2)-[VGS]-H-[LNP]-x-V-x(44,47)-H-H
V-x-H-x(33,40)-C-x(3)-C-x(3)-H-x(2)-M
G-x-[FYW]-x-[LIVMFYW]-x-[CST]-x(8)-G-[LM]-x(3)-[LIVMFYW]
H-C-H-x(3)-H-x(3)-[AG]-[LM]
H-H-M-x(2)-F-x-C
H-x-F-x(4)-H-T-H-x(2)-G
[GA]-x(0,2)-[YSA]-x(0,1)-[VFY]-x-C-x(1,2)-[PG]-x(0,1)-H- x(2,4)-[MQ]


Redox motif internal aminoacids concervation based filter


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Redox motif patterns


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Cystein-rich regions based filter

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Expectation value

The statistical significance threshold for reporting matches against database sequences; the default value for PSIBlast in our program is 0.0001, meaning that 0.0001 matches are expected to be found merely by chance, according to the stochastic model of Karlin and Altschul (1990). If the statistical significance ascribed to a match is greater than the EXPECT threshold, the match will not be reported. Lower EXPECT thresholds are more stringent, leading to fewer chance matches being reported. Increasing the threshold shows less stringent matches.

Expectation value for multipass model

Two different Expectation value settings need to be specified in the PSI-BLAST program. The first of these sets the threshold for the initial BLAST search. In this example, the initial (BLAST) E value is set at 0.0001. The second Expectation value is the threshold value for inclusion in the position specific matrix used for PSI-BLAST iterations. In our example the PSI-BLAST E value is left at the default setting of 0.001. The E values specified in this example allow the user to see (and selectively, based on prior knowledge, include) all of the BLAST hits up to E=0.0001; but to automatically include only those hits exceeding a relatively rigorous E value threshold of 0.001.

Conservation profile CutOff limit

A database of known thioredoxin-fold proteins (more than 500 proteins) was constructed from the NCBI non-redundant database and was used to optimize the parameters of conservation profile searches. For subsequent genomic searches, these parameters were set as follows: expectation value, 0.0001; optimal number of iterations, 3; and conservation cutoff limit, 65% identity of cysteine, serine or threonine among homologs present in the NCBI non-redundant database. Only the following replacements were allowed: Cys to Ser, Ala, Gly and Thr; Ser to Cys, Ala, Gly, Thr; Thr to Cys, Ser, Ala, Gly; Proteins that did not satisfy these requirements were automatically removed from further analysis.