RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy16623
(93 letters)
>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA
complex; NMR {Rous sarcoma virus}
Length = 61
Score = 46.8 bits (111), Expect = 6e-09
Identities = 17/44 (38%), Positives = 23/44 (52%), Gaps = 4/44 (9%)
Query: 44 CYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFAREC 87
CY C GHYQ CP+K + ++ C CN GH A++C
Sbjct: 7 CYTCGSPGHYQAQCPKKRKSGNSRER----CQLCNGMGHNAKQC 46
Score = 29.1 bits (65), Expect = 0.050
Identities = 6/17 (35%), Positives = 10/17 (58%)
Query: 71 GIVCYKCNNYGHFAREC 87
+CY C + GH+ +C
Sbjct: 4 RGLCYTCGSPGHYQAQC 20
Score = 22.9 bits (49), Expect = 9.8
Identities = 7/30 (23%), Positives = 11/30 (36%)
Query: 37 SSTSTIQCYNCFDFGHYQYSCPQKSSADAR 66
S S +C C GH C ++ +
Sbjct: 26 SGNSRERCQLCNGMGHNAKQCRKRDGNQGQ 55
>1cl4_A Protein (GAG polyprotein); nucleocapsid protein, RNA binding
protein, retrovirus, viral protein; NMR {Mason-pfizer
monkey virus} SCOP: g.40.1.1 PDB: 1dsv_A
Length = 60
Score = 46.9 bits (111), Expect = 7e-09
Identities = 13/44 (29%), Positives = 22/44 (50%), Gaps = 1/44 (2%)
Query: 44 CYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFAREC 87
C+ C GH+ +C + + +A G+ C +C H+A EC
Sbjct: 4 CFKCGKKGHFAKNCHEHAHNNAEPKVPGL-CPRCKRGKHWANEC 46
Score = 23.4 bits (50), Expect = 7.1
Identities = 5/23 (21%), Positives = 7/23 (30%)
Query: 44 CYNCFDFGHYQYSCPQKSSADAR 66
C C H+ C K+
Sbjct: 33 CPRCKRGKHWANECKSKTDNQGN 55
>3ts2_A Protein LIN-28 homolog A; microrna biogenesis, protein-RNA complex,
PRE-element, CCHC knuckle; HET: GMP; 2.01A {Mus
musculus} PDB: 3trz_A* 3ts0_A*
Length = 148
Score = 41.5 bits (97), Expect = 4e-06
Identities = 12/63 (19%), Positives = 19/63 (30%), Gaps = 8/63 (12%)
Query: 30 FVLRVEMSSTSTIQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFARECAT 89
F + E +CYNC H+ C C+ C + H C
Sbjct: 86 FCIGSERRPKGGDRCYNCGGLDHHAKECKLPPQ--------PKKCHFCQSINHMVASCPL 137
Query: 90 ESP 92
++
Sbjct: 138 KAQ 140
Score = 30.4 bits (68), Expect = 0.041
Identities = 7/24 (29%), Positives = 9/24 (37%)
Query: 44 CYNCFDFGHYQYSCPQKSSADARG 67
C+ C H SCP K+
Sbjct: 122 CHFCQSINHMVASCPLKAQQGPSS 145
>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding,
exosome, RNA protein; NMR {Saccharomyces cerevisiae}
Length = 124
Score = 40.9 bits (95), Expect = 5e-06
Identities = 14/57 (24%), Positives = 19/57 (33%), Gaps = 11/57 (19%)
Query: 42 IQCYNCFDFGHYQYSCPQ-----------KSSADARGDKVGIVCYKCNNYGHFAREC 87
+QC C H + CP + + I CY C GHF +C
Sbjct: 65 VQCTLCKSKKHSKERCPSIWRAYILVDDNEKAKPKVLPFHTIYCYNCGGKGHFGDDC 121
Score = 38.6 bits (89), Expect = 4e-05
Identities = 15/56 (26%), Positives = 23/56 (41%), Gaps = 8/56 (14%)
Query: 40 STIQCYNCFDFGHYQYSCPQKSSA--------DARGDKVGIVCYKCNNYGHFAREC 87
+ +C NC GH + CP + +R I C KC+ GH+ +C
Sbjct: 3 AAPKCNNCSQRGHLKKDCPHIICSYCGATDDHYSRHCPKAIQCSKCDEVGHYRSQC 58
Score = 34.0 bits (77), Expect = 0.002
Identities = 14/48 (29%), Positives = 18/48 (37%), Gaps = 8/48 (16%)
Query: 40 STIQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFAREC 87
IQC C + GHY+ CP K + C C + H C
Sbjct: 41 KAIQCSKCDEVGHYRSQCPHKWKK--------VQCTLCKSKKHSKERC 80
Score = 28.2 bits (62), Expect = 0.21
Identities = 10/22 (45%), Positives = 12/22 (54%)
Query: 39 TSTIQCYNCFDFGHYQYSCPQK 60
TI CYNC GH+ C +K
Sbjct: 103 FHTIYCYNCGGKGHFGDDCKEK 124
>2cqf_A RNA-binding protein LIN-28; CCHC zinc-finger, structural
genomics, NPPSFA, national project on protein
structural and functional analyses; NMR {Homo sapiens}
Length = 63
Score = 37.6 bits (87), Expect = 3e-05
Identities = 12/51 (23%), Positives = 17/51 (33%), Gaps = 8/51 (15%)
Query: 37 SSTSTIQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFAREC 87
S +S +CYNC H+ C C+ C + H C
Sbjct: 3 SGSSGDRCYNCGGLDHHAKECKL--------PPQPKKCHFCQSISHMVASC 45
Score = 27.6 bits (61), Expect = 0.21
Identities = 7/24 (29%), Positives = 9/24 (37%)
Query: 44 CYNCFDFGHYQYSCPQKSSADARG 67
C+ C H SCP K+
Sbjct: 32 CHFCQSISHMVASCPLKAQQGPSA 55
>3nyb_B Protein AIR2; polya RNA polymerase, zinc knuckle protein, RNA
surveillance binds to TRF4P/AIR2P heterodimer; 2.70A
{Saccharomyces cerevisiae}
Length = 83
Score = 38.1 bits (88), Expect = 3e-05
Identities = 14/57 (24%), Positives = 19/57 (33%), Gaps = 11/57 (19%)
Query: 42 IQCYNCFDFGHYQYSCPQ-----------KSSADARGDKVGIVCYKCNNYGHFAREC 87
+QC C H + CP + + I CY C GHF +C
Sbjct: 6 VQCTLCKSKKHSKERCPSIWRAYILVDDNEKAKPKVLPFHTIYCYNCGGKGHFGDDC 62
Score = 29.6 bits (66), Expect = 0.051
Identities = 11/32 (34%), Positives = 17/32 (53%)
Query: 32 LRVEMSSTSTIQCYNCFDFGHYQYSCPQKSSA 63
+ ++ TI CYNC GH+ C +K S+
Sbjct: 37 AKPKVLPFHTIYCYNCGGKGHFGDDCKEKRSS 68
>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA,
transcription-RNA complex; NMR {Homo sapiens}
Length = 74
Score = 36.5 bits (84), Expect = 8e-05
Identities = 10/51 (19%), Positives = 16/51 (31%), Gaps = 8/51 (15%)
Query: 42 IQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFARECATESP 92
+CYNC H+ C C+ C + H C ++
Sbjct: 25 DRCYNCGGLDHHAKECKLPPQPKK--------CHFCQSISHMVASCPLKAQ 67
Score = 30.7 bits (69), Expect = 0.016
Identities = 8/22 (36%), Positives = 10/22 (45%)
Query: 66 RGDKVGIVCYKCNNYGHFAREC 87
+ G CY C H A+EC
Sbjct: 19 KRRSKGDRCYNCGGLDHHAKEC 40
Score = 26.1 bits (57), Expect = 0.83
Identities = 7/23 (30%), Positives = 9/23 (39%)
Query: 44 CYNCFDFGHYQYSCPQKSSADAR 66
C+ C H SCP K+
Sbjct: 49 CHFCQSISHMVASCPLKAQQGPS 71
>2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein,
retrovirus zinc finger-like domains; NMR {Equine
infectious anemia virus}
Length = 37
Score = 31.8 bits (72), Expect = 0.003
Identities = 15/47 (31%), Positives = 20/47 (42%), Gaps = 11/47 (23%)
Query: 43 QCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFARECAT 89
CYNC GH C VC+KC GHF+++C +
Sbjct: 2 TCYNCGKPGHLSSQCRA-----------PKVCFKCKQPGHFSKQCRS 37
>2ysa_A Retinoblastoma-binding protein 6; zinc finger, CCHC, structural
genomics, NPPSFA, national project on protein
structural and functional analyses; NMR {Homo sapiens}
Length = 55
Score = 29.4 bits (66), Expect = 0.031
Identities = 7/19 (36%), Positives = 11/19 (57%)
Query: 71 GIVCYKCNNYGHFARECAT 89
G C++C GH+ + C T
Sbjct: 7 GYTCFRCGKPGHYIKNCPT 25
Score = 25.2 bits (55), Expect = 1.1
Identities = 7/26 (26%), Positives = 10/26 (38%)
Query: 44 CYNCFDFGHYQYSCPQKSSADARGDK 69
C+ C GHY +CP +
Sbjct: 10 CFRCGKPGHYIKNCPTNGDKNFESGP 35
>2ec7_A GAG polyprotein (PR55GAG); nucleocapsid protein, HIV-2, RNA
recognition, zinc finger, viral protein; NMR {Human
immunodeficiency virus type 2} SCOP: g.40.1.1
Length = 49
Score = 28.0 bits (62), Expect = 0.12
Identities = 14/49 (28%), Positives = 20/49 (40%), Gaps = 13/49 (26%)
Query: 41 TIQCYNCFDFGHYQYSC--PQKSSADARGDKVGIVCYKCNNYGHFAREC 87
I+C+NC GH C P++ C+KC GH +C
Sbjct: 6 VIRCWNCGKEGHSARQCRAPRRQG-----------CWKCGKTGHVMAKC 43
Score = 23.0 bits (49), Expect = 9.6
Identities = 8/21 (38%), Positives = 11/21 (52%)
Query: 67 GDKVGIVCYKCNNYGHFAREC 87
+ I C+ C GH AR+C
Sbjct: 2 QQRKVIRCWNCGKEGHSARQC 22
>1dsq_A Nucleic acid binding protein P14; CCHC type zinc finger,
virus/viral protein; NMR {Mouse mammary tumor virus}
SCOP: g.40.1.1
Length = 26
Score = 26.9 bits (59), Expect = 0.19
Identities = 9/20 (45%), Positives = 11/20 (55%)
Query: 71 GIVCYKCNNYGHFARECATE 90
G VC+ C GH R+C E
Sbjct: 2 GPVCFSCGKTGHIKRDCKEE 21
>1a1t_A Nucleocapsid protein; stem-loop RNA, viral protein/RNA complex;
NMR {Human immunodeficiency virus 1} SCOP: g.40.1.1
PDB: 1mfs_A 1f6u_A* 1aaf_A 2l4l_A 2exf_A 2jzw_A*
1bj6_A* 1esk_A 1q3y_A 1q3z_A 2e1x_A 2iwj_A
Length = 55
Score = 27.3 bits (60), Expect = 0.20
Identities = 15/49 (30%), Positives = 23/49 (46%), Gaps = 13/49 (26%)
Query: 41 TIQCYNCFDFGHYQYSC--PQKSSADARGDKVGIVCYKCNNYGHFAREC 87
T++C+NC GH +C P+K C+KC GH ++C
Sbjct: 12 TVKCFNCGKEGHIAKNCRAPRKKG-----------CWKCGKEGHQMKDC 49
Score = 23.8 bits (51), Expect = 3.9
Identities = 7/22 (31%), Positives = 11/22 (50%)
Query: 66 RGDKVGIVCYKCNNYGHFAREC 87
R + + C+ C GH A+ C
Sbjct: 7 RNQRKTVKCFNCGKEGHIAKNC 28
>3gv2_A Ca, fusion protein consisting of capsid protein P24, linker and
carbon dioxide-concentrating...; hexameric retroviral
capsid; 7.00A {Human immunodeficiency virus type 1}
Length = 342
Score = 27.6 bits (61), Expect = 0.49
Identities = 3/47 (6%), Positives = 9/47 (19%), Gaps = 13/47 (27%)
Query: 41 TIQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFAREC 87
++ G+ + + AR +
Sbjct: 253 MVKAGRITIVGYIR-------AGSARF------TLNIRGDVQEVKTA 286
>1u6p_A GAG polyprotein; MLV, A-minor K-turn, stem loop, bulge, G-U
mismatch, G-A MIS U mismatch, A-C mismatch, zinc
finger, NC, viral protein-RN; HET: AP7; NMR {Moloney
murine leukemia virus} SCOP: g.40.1.1 PDB: 1wwd_A
1wwe_A 1wwf_A 1wwg_A
Length = 56
Score = 26.2 bits (57), Expect = 0.58
Identities = 8/24 (33%), Positives = 11/24 (45%)
Query: 43 QCYNCFDFGHYQYSCPQKSSADAR 66
QC C + GH+ CP+K
Sbjct: 25 QCAYCKEKGHWAKDCPKKPRGPRG 48
>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein,
metal binding protein; NMR {Synthetic}
Length = 39
Score = 25.6 bits (56), Expect = 0.67
Identities = 11/48 (22%), Positives = 18/48 (37%), Gaps = 13/48 (27%)
Query: 42 IQCYNCFDFGHYQYSC--PQKSSADARGDKVGIVCYKCNNYGHFAREC 87
+ C+NC GH C P++ C+ C + H +C
Sbjct: 1 LTCFNCGKPGHTARMCRQPRQEG-----------CWNCGSKEHRFAQC 37
>1q3o_A Shank1; PDZ, GKAP, peptide binding protein; 1.80A {Rattus
norvegicus} SCOP: b.36.1.1 PDB: 1q3p_A 3qjm_A 3qjn_A
3o5n_A*
Length = 109
Score = 25.9 bits (57), Expect = 1.5
Identities = 15/56 (26%), Positives = 24/56 (42%), Gaps = 2/56 (3%)
Query: 18 LLIIKQRNEGLLFVLRVEMSSTSTIQCYNCFDFGHYQYSCP--QKSSADARGDKVG 71
+L+ K+ +EG FVLR + T + F QY + A G ++G
Sbjct: 11 VLLQKKDSEGFGFVLRGAKAQTPIEEFTPTPAFPALQYLESVDEGGVAWRAGLRMG 66
>1a6b_B Momulv, zinc finger protein NCP10; nucleocapsid protein,
intercalation, nucleic acid, retrovirus, viral
protein/DNA complex; HET: DNA; NMR {Synthetic} SCOP:
g.40.1.1
Length = 40
Score = 24.4 bits (52), Expect = 2.1
Identities = 8/18 (44%), Positives = 11/18 (61%)
Query: 43 QCYNCFDFGHYQYSCPQK 60
QC C + GH+ CP+K
Sbjct: 12 QCAYCKEKGHWAKDCPKK 29
>1nc8_A Nucleocapsid protein; HIV-2, RNA recognition, zinc finger, viral
protein; NMR {Human immunodeficiency virus 2} SCOP:
g.40.1.1 PDB: 2di2_A
Length = 29
Score = 23.3 bits (50), Expect = 3.9
Identities = 8/21 (38%), Positives = 11/21 (52%)
Query: 67 GDKVGIVCYKCNNYGHFAREC 87
+ I C+ C GH AR+C
Sbjct: 2 QQRKVIRCWNCGKEGHSARQC 22
>1pie_A Galactokinase; galactose, galactosemia, transferase; HET: GLA;
2.10A {Lactococcus lactis} SCOP: d.14.1.5 d.58.26.7
Length = 419
Score = 23.9 bits (52), Expect = 9.1
Identities = 7/34 (20%), Positives = 17/34 (50%)
Query: 6 ENSLWNNYVLGILLIIKQRNEGLLFVLRVEMSST 39
+ LW+NYV G+++++K + + +
Sbjct: 116 DGELWSNYVKGMIVMLKGAGYEIDKGFELLIKGE 149
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
0.323 0.136 0.438
Gapped
Lambda K H
0.267 0.0554 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,326,105
Number of extensions: 60817
Number of successful extensions: 222
Number of sequences better than 10.0: 1
Number of HSP's gapped: 205
Number of HSP's successfully gapped: 44
Length of query: 93
Length of database: 6,701,793
Length adjustment: 60
Effective length of query: 33
Effective length of database: 5,026,533
Effective search space: 165875589
Effective search space used: 165875589
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 51 (23.8 bits)