RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy4296
(103 letters)
>2rhk_C Cleavage and polyadenylation specificity factor subunit 4;
influenza A, nonstructural protein, viral protein: HOST
complex, Zn finger; 1.95A {Homo sapiens}
Length = 72
Score = 89.1 bits (221), Expect = 3e-25
Identities = 50/62 (80%), Positives = 57/62 (91%)
Query: 26 RHITGDRSVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSRFNACHNKECPFLHIDP 85
H++G+++VVCKHWLRGLCKKGDQCEFLHEYDMTKM ECYFYS+F C NKECPFLHIDP
Sbjct: 9 SHMSGEKTVVCKHWLRGLCKKGDQCEFLHEYDMTKMSECYFYSKFGECSNKECPFLHIDP 68
Query: 86 DS 87
+S
Sbjct: 69 ES 70
Score = 26.7 bits (59), Expect = 0.53
Identities = 7/37 (18%), Positives = 13/37 (35%)
Query: 25 LRHITGDRSVVCKHWLRGLCKKGDQCEFLHEYDMTKM 61
L + C + + +C FLH +K+
Sbjct: 36 LHEYDMTKMSECYFYSKFGECSNKECPFLHIDPESKI 72
>2d9n_A Cleavage and polyadenylation specificity factor, 30 kDa subunit;
CCCH zinc-finger, structural genomics, NPPSFA; NMR
{Homo sapiens}
Length = 77
Score = 84.9 bits (210), Expect = 1e-23
Identities = 50/58 (86%), Positives = 55/58 (94%)
Query: 30 GDRSVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSRFNACHNKECPFLHIDPDS 87
G+++VVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYS+F C NKECPFLHIDP+S
Sbjct: 7 GEKTVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSKFGECSNKECPFLHIDPES 64
Score = 38.3 bits (89), Expect = 2e-05
Identities = 8/46 (17%), Positives = 16/46 (34%), Gaps = 1/46 (2%)
Query: 24 PLRH-ITGDRSVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYS 68
H + C + + +C FLH +K+ +C +
Sbjct: 28 EFLHEYDMTKMPECYFYSKFGECSNKECPFLHIDPESKIKDCPWSG 73
>2cqe_A KIAA1064 protein; CCCH zinc-finger, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens} SCOP: g.66.1.1 g.66.1.1
Length = 98
Score = 54.3 bits (130), Expect = 2e-11
Identities = 11/54 (20%), Positives = 24/54 (44%), Gaps = 4/54 (7%)
Query: 32 RSVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSRFNACHNKECPFLHIDP 85
+ +CK ++ G C + + C ++H P +++ N + +C F H
Sbjct: 12 KRELCKFYITGFCARAENCPYMHGD----FPCKLYHTTGNCINGDDCMFSHDPL 61
Score = 31.2 bits (70), Expect = 0.016
Identities = 10/32 (31%), Positives = 12/32 (37%), Gaps = 1/32 (3%)
Query: 35 VCKH-WLRGLCKKGDQCEFLHEYDMTKMPECY 65
CK G C GD C F H+ + E
Sbjct: 38 PCKLYHTTGNCINGDDCMFSHDPLTEETRELL 69
>2rpp_A Muscleblind-like protein 2; zinc finger domain, C3H, alternative
splicing, cytoplasm, metal-binding, nucleus,
RNA-binding, zinc, zinc-finger; NMR {Homo sapiens}
Length = 89
Score = 40.6 bits (94), Expect = 5e-06
Identities = 16/70 (22%), Positives = 30/70 (42%), Gaps = 7/70 (10%)
Query: 22 PFPLRHITGDRSVVCKHWLRGLCKKGDQ-CEFLH-----EYDMTKMPECYFYSRFNACHN 75
P+R VC+ + RG C + D+ C+F H + + ++ C+ + C
Sbjct: 6 SGPVRDTKWLTLEVCRQFQRGTCSRSDEECKFAHPPKSCQVENGRVIACFDSLK-GRCSR 64
Query: 76 KECPFLHIDP 85
+ C +LH
Sbjct: 65 ENCKYLHPPT 74
>3d2q_A Muscleblind-like protein 1; tandem zinc finger domain,
alternative splicing, metal- binding, nucleus,
RNA-binding, zinc, zinc-finger, metal binding; 1.50A
{Homo sapiens} PDB: 3d2s_A
Length = 70
Score = 39.3 bits (91), Expect = 9e-06
Identities = 18/60 (30%), Positives = 27/60 (45%), Gaps = 9/60 (15%)
Query: 31 DRSVVCKHWLRGLCKKGD-QCEFLHEYDMT-------KMPECYFYSRFNACHNKECPFLH 82
DR VC+ + RG C +G+ C F H D T + C Y + C ++C + H
Sbjct: 4 DRLEVCREYQRGNCNRGENDCRFAHPADSTMIDTNDNTVTVCMDYIK-GRCSREKCKYFH 62
Score = 23.9 bits (51), Expect = 6.0
Identities = 6/28 (21%), Positives = 15/28 (53%), Gaps = 1/28 (3%)
Query: 27 HITGDRSVVCKHWLRGLCKKGDQCEFLH 54
+ VC +++G C + ++C++ H
Sbjct: 36 DTNDNTVTVCMDYIKGRCSR-EKCKYFH 62
>3d2n_A Muscleblind-like protein 1; tandem zinc finger domain,
alternative splicing, metal- binding, nucleus,
RNA-binding, zinc, zinc-finger, metal binding; 2.70A
{Homo sapiens}
Length = 83
Score = 38.9 bits (90), Expect = 2e-05
Identities = 15/57 (26%), Positives = 26/57 (45%), Gaps = 7/57 (12%)
Query: 35 VCKHWLRGLCKKGD-QCEFLHEYDMT-----KMPECYFYSRFNACHNKECPFLHIDP 85
VC+ + RG C + D +C+F H ++ C+ + C + C +LH P
Sbjct: 11 VCREFQRGTCSRPDTECKFAHPSKSCQVENGRVIACFDSLK-GRCSRENCKYLHPPP 66
Score = 24.7 bits (53), Expect = 3.4
Identities = 9/33 (27%), Positives = 16/33 (48%), Gaps = 1/33 (3%)
Query: 22 PFPLRHITGDRSVVCKHWLRGLCKKGDQCEFLH 54
P + R + C L+G C + + C++LH
Sbjct: 32 PSKSCQVENGRVIACFDSLKGRCSR-ENCKYLH 63
>2e5s_A Otthump00000018578; ZF-CCCHX2 domain, muscleblind-like 2, isoform
1, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 98
Score = 39.1 bits (90), Expect = 2e-05
Identities = 17/69 (24%), Positives = 29/69 (42%), Gaps = 9/69 (13%)
Query: 22 PFPLRHITGDRSVVCKHWLRGLCKKGD-QCEFLHEYDMT-------KMPECYFYSRFNAC 73
+ + D+ VC+ + RG C +G+ C F H D T + C Y + C
Sbjct: 9 TATQKLLRTDKLEVCREFQRGNCARGETDCRFAHPADSTMIDTSDNTVTVCMDYIK-GRC 67
Query: 74 HNKECPFLH 82
++C + H
Sbjct: 68 MREKCKYFH 76
>1m9o_A Tristetraproline; Cys3His type zinc finger, metal binding
protein; NMR {Mus musculus} SCOP: g.66.1.1 PDB: 1rgo_A
Length = 77
Score = 36.9 bits (85), Expect = 8e-05
Identities = 13/58 (22%), Positives = 22/58 (37%), Gaps = 11/58 (18%)
Query: 36 CKHWLR-GLCKKGDQCEFLH---------EYDMTKMPECYFYSRFNACHN-KECPFLH 82
C+ + G C+ G +C+F H + K C+ + C C F+H
Sbjct: 15 CRTYSESGRCRYGAKCQFAHGLGELRQANRHPKYKTELCHKFKLQGRCPYGSRCHFIH 72
>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A
{Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A
Length = 240
Score = 38.6 bits (89), Expect = 1e-04
Identities = 10/52 (19%), Positives = 19/52 (36%), Gaps = 5/52 (9%)
Query: 26 RHITGDRSVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSRFNACHNKE 77
R + C + +G+C G +CE+LH +P+ +
Sbjct: 63 RGDNDGQLFFCLFFAKGMCCLGPKCEYLHH-----IPDEEDIGKLALRTEVL 109
Score = 25.5 bits (55), Expect = 3.2
Identities = 8/35 (22%), Positives = 15/35 (42%)
Query: 64 CYFYSRFNACHNKECPFLHIDPDSMIEASVGMVHR 98
C F+++ C +C +LH PD + +
Sbjct: 73 CLFFAKGMCCLGPKCEYLHHIPDEEDIGKLALRTE 107
>3u9g_A Zinc finger CCCH-type antiviral protein 1; zinc finger protein;
1.80A {Rattus norvegicus}
Length = 229
Score = 33.6 bits (76), Expect = 0.005
Identities = 16/57 (28%), Positives = 24/57 (42%), Gaps = 6/57 (10%)
Query: 32 RSVVCKHWLRGLCKKGDQCEFLHEYDMTKMPE-CYFY---SRFNACHNKE-CPFLHI 83
++ H L GL ++ + L + D +PE C Y R C + C LHI
Sbjct: 122 FQILKNHELSGLNQE-ELACLLVQSDPFFLPEICKSYKGEGRKQTCGQPQPCERLHI 177
Score = 26.3 bits (57), Expect = 1.8
Identities = 13/52 (25%), Positives = 19/52 (36%), Gaps = 13/52 (25%)
Query: 35 VCKHW----LRGLCKKGDQCEFLHEYDMTKMPECYFYSRFNACHNKECPFLH 82
+CK + + C + CE LH C ++R N C C H
Sbjct: 153 ICKSYKGEGRKQTCGQPQPCERLH--------ICEHFTRGN-CSYLNCLRSH 195
>2d9m_A Zinc finger CCCH-type domain containing protein 7A; CCCH
zinc-finger, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 69
Score = 28.7 bits (64), Expect = 0.10
Identities = 7/20 (35%), Positives = 13/20 (65%)
Query: 35 VCKHWLRGLCKKGDQCEFLH 54
+C ++ G C +G+ C+F H
Sbjct: 22 ICDRYMNGTCPEGNSCKFAH 41
>2lhn_A Nuclear polyadenylated RNA-binding protein NAB2; nuclear protein;
NMR {Saccharomyces cerevisiae S288C}
Length = 80
Score = 28.0 bits (62), Expect = 0.20
Identities = 13/51 (25%), Positives = 18/51 (35%), Gaps = 10/51 (19%)
Query: 32 RSVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSRFNACHNKECPFLH 82
++C+ C + D C F H +C F C N C F H
Sbjct: 30 SHIMCREGAN--CTRID-CLFGH----PINEDCRF---GVNCKNIYCLFRH 70
Score = 23.7 bits (51), Expect = 9.5
Identities = 7/23 (30%), Positives = 11/23 (47%), Gaps = 3/23 (13%)
Query: 60 KMPECYFYSRFNACHNKECPFLH 82
+ +C F + C NK C + H
Sbjct: 8 SLEQCKFGTH---CTNKRCKYRH 27
>3pt1_A UPF0364 protein YMR027W; alpha/beta fold, carbohydrate phosphatase,
F6P binding, HYDR; HET: F6P; 1.77A {Saccharomyces
cerevisiae}
Length = 471
Score = 27.4 bits (60), Expect = 0.86
Identities = 16/69 (23%), Positives = 24/69 (34%), Gaps = 14/69 (20%)
Query: 24 PLRHITGD---RSVVCKHWLRGLCKKGD----QCEFLHEYDMTKMPECYFYSRFNACHNK 76
PLR T + + V + L K + E+L E Y Y R N +
Sbjct: 72 PLRPFTEEEIKIANVPLSFNEYLKKHPEVNWGAVEWLFS-------EVYLYRRVNVLFQR 124
Query: 77 ECPFLHIDP 85
+C + D
Sbjct: 125 QCEWAKFDI 133
>2p6p_A Glycosyl transferase; X-RAY-diffraction,urdamycina-biosynthesis;
1.88A {Streptomyces fradiae}
Length = 384
Score = 25.1 bits (55), Expect = 5.7
Identities = 6/30 (20%), Positives = 11/30 (36%)
Query: 12 PSFQAPGVLVPFPLRHITGDRSVVCKHWLR 41
PS + +RH+ R + W+
Sbjct: 176 PSLRPANAAPARMMRHVATSRQCPLEPWMY 205
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.328 0.143 0.495
Gapped
Lambda K H
0.267 0.0502 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,680,180
Number of extensions: 85021
Number of successful extensions: 223
Number of sequences better than 10.0: 1
Number of HSP's gapped: 210
Number of HSP's successfully gapped: 29
Length of query: 103
Length of database: 6,701,793
Length adjustment: 68
Effective length of query: 35
Effective length of database: 4,803,165
Effective search space: 168110775
Effective search space used: 168110775
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 51 (24.0 bits)