RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy16600
(152 letters)
>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding,
exosome, RNA protein; NMR {Saccharomyces cerevisiae}
Length = 124
Score = 62.5 bits (151), Expect = 1e-13
Identities = 38/145 (26%), Positives = 49/145 (33%), Gaps = 27/145 (18%)
Query: 5 STIQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNY-GHFARECATESVTCYNCS 63
+ +C NC GH + CP +C C H++R C +++ C C
Sbjct: 3 AAPKCNNCSQRGHLKKDCPHI------------ICSYCGATDDHYSRHC-PKAIQCSKCD 49
Query: 64 GQGHVAKDCTVKSSII-CYNCNSSGHFARNCPNDSSKRCYACHQAGHMAKECPGQTAGKS 122
GH C K + C C S H CP S R Y AK
Sbjct: 50 EVGHYRSQCPHKWKKVQCTLCKSKKHSKERCP--SIWRAYILVDDNEKAKPKVLPFHTI- 106
Query: 123 PEPVVDMSLTCYVCGHQGHLSYDCK 147
CY CG +GH DCK
Sbjct: 107 ---------YCYNCGGKGHFGDDCK 122
Score = 48.6 bits (115), Expect = 3e-08
Identities = 26/98 (26%), Positives = 44/98 (44%), Gaps = 16/98 (16%)
Query: 56 SVTCYNCSGQGHVAKDCTVKSSIICYNCNSS-GHFARNCPNDSSKRCYACHQAGHMAKEC 114
+ C NCS +GH+ KDC IC C ++ H++R+CP + +C C + GH +C
Sbjct: 4 APKCNNCSQRGHLKKDCPHI---ICSYCGATDDHYSRHCPK--AIQCSKCDEVGHYRSQC 58
Query: 115 PGQTAGKSPEPVVDMSLTCYVCGHQGHLSYDCKLVQKS 152
P + C +C + H C + ++
Sbjct: 59 PHKWKKV----------QCTLCKSKKHSKERCPSIWRA 86
Score = 41.3 bits (96), Expect = 2e-05
Identities = 17/77 (22%), Positives = 28/77 (36%), Gaps = 15/77 (19%)
Query: 75 KSSIICYNCNSSGHFARNCPNDSSKRCYACHQAGHMAKECPGQTAGKSPEPVVDMSLTCY 134
+++ C NC+ GH ++CP+ C H ++ CP ++ C
Sbjct: 2 EAAPKCNNCSQRGHLKKDCPHIICSYC--GATDDHYSRHCP-------------KAIQCS 46
Query: 135 VCGHQGHLSYDCKLVQK 151
C GH C K
Sbjct: 47 KCDEVGHYRSQCPHKWK 63
Score = 34.8 bits (79), Expect = 0.003
Identities = 24/92 (26%), Positives = 31/92 (33%), Gaps = 29/92 (31%)
Query: 5 STIQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFAREC------------ 52
IQC C + GHY+ CP K + C C + H C
Sbjct: 41 KAIQCSKCDEVGHYRSQCPHKWKK--------VQCTLCKSKKHSKERCPSIWRAYILVDD 92
Query: 53 ---------ATESVTCYNCSGQGHVAKDCTVK 75
++ CYNC G+GH DC K
Sbjct: 93 NEKAKPKVLPFHTIYCYNCGGKGHFGDDCKEK 124
>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA
complex; NMR {Rous sarcoma virus}
Length = 61
Score = 49.5 bits (118), Expect = 3e-09
Identities = 18/56 (32%), Positives = 28/56 (50%), Gaps = 5/56 (8%)
Query: 75 KSSIICYNCNSSGHFARNCPN-----DSSKRCYACHQAGHMAKECPGQTAGKSPEP 125
++ +CY C S GH+ CP +S +RC C+ GH AK+C + + P
Sbjct: 2 RARGLCYTCGSPGHYQAQCPKKRKSGNSRERCQLCNGMGHNAKQCRKRDGNQGQRP 57
Score = 42.2 bits (99), Expect = 2e-06
Identities = 14/49 (28%), Positives = 16/49 (32%), Gaps = 5/49 (10%)
Query: 58 TCYNCSGQGHVAKDCT-----VKSSIICYNCNSSGHFARNCPNDSSKRC 101
CY C GH C S C CN GH A+ C +
Sbjct: 6 LCYTCGSPGHYQAQCPKKRKSGNSRERCQLCNGMGHNAKQCRKRDGNQG 54
Score = 40.2 bits (94), Expect = 8e-06
Identities = 12/51 (23%), Positives = 18/51 (35%), Gaps = 6/51 (11%)
Query: 97 SSKRCYACHQAGHMAKECPGQTAGKSPEPVVDMSLTCYVCGHQGHLSYDCK 147
+ CY C GH +CP + C +C GH + C+
Sbjct: 3 ARGLCYTCGSPGHYQAQCP------KKRKSGNSRERCQLCNGMGHNAKQCR 47
Score = 39.5 bits (92), Expect = 2e-05
Identities = 19/58 (32%), Positives = 26/58 (44%), Gaps = 4/58 (6%)
Query: 9 CYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFARECATESVTCYNCSGQG 66
CY C GHYQ CP+K + ++ C CN GH A++C G+G
Sbjct: 7 CYTCGSPGHYQAQCPKKRKSGNSRER----CQLCNGMGHNAKQCRKRDGNQGQRPGKG 60
Score = 38.7 bits (90), Expect = 3e-05
Identities = 14/44 (31%), Positives = 19/44 (43%), Gaps = 6/44 (13%)
Query: 36 GIVCYKCNNYGHFAREC------ATESVTCYNCSGQGHVAKDCT 73
+CY C + GH+ +C C C+G GH AK C
Sbjct: 4 RGLCYTCGSPGHYQAQCPKKRKSGNSRERCQLCNGMGHNAKQCR 47
>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 = 49.2 bits (117), Expect = 2e-08
Identities = 15/42 (35%), Positives = 21/42 (50%), Gaps = 1/42 (2%)
Query: 59 CYNCSGQGHVAKDCTVKSSI-ICYNCNSSGHFARNCPNDSSK 99
CYNC G H AK+C + C+ C S H +CP + +
Sbjct: 100 CYNCGGLDHHAKECKLPPQPKKCHFCQSINHMVASCPLKAQQ 141
Score = 46.2 bits (109), Expect = 3e-07
Identities = 14/40 (35%), Positives = 18/40 (45%), Gaps = 1/40 (2%)
Query: 80 CYNCNSSGHFARNCPNDS-SKRCYACHQAGHMAKECPGQT 118
CYNC H A+ C K+C+ C HM CP +
Sbjct: 100 CYNCGGLDHHAKECKLPPQPKKCHFCQSINHMVASCPLKA 139
Score = 38.5 bits (89), Expect = 2e-04
Identities = 14/51 (27%), Positives = 16/51 (31%), Gaps = 10/51 (19%)
Query: 96 DSSKRCYACHQAGHMAKECPGQTAGKSPEPVVDMSLTCYVCGHQGHLSYDC 146
RCY C H AKEC K C+ C H+ C
Sbjct: 95 KGGDRCYNCGGLDHHAKECKLPPQPKK----------CHFCQSINHMVASC 135
Score = 35.4 bits (81), Expect = 0.002
Identities = 10/45 (22%), Positives = 14/45 (31%), Gaps = 8/45 (17%)
Query: 8 QCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFAREC 52
+CYNC H+ C C+ C + H C
Sbjct: 99 RCYNCGGLDHHAKECKLPPQ--------PKKCHFCQSINHMVASC 135
Score = 28.1 bits (62), Expect = 0.97
Identities = 7/24 (29%), Positives = 9/24 (37%)
Query: 9 CYNCFDFGHYQYSCPQKSSADARG 32
C+ C H SCP K+
Sbjct: 122 CHFCQSINHMVASCPLKAQQGPSS 145
>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 = 45.7 bits (108), Expect = 8e-08
Identities = 15/47 (31%), Positives = 20/47 (42%), Gaps = 8/47 (17%)
Query: 80 CYNCNSSGHFARNCPNDSSKR--------CYACHQAGHMAKECPGQT 118
C+ C GHFA+NC + C C + H A EC +T
Sbjct: 4 CFKCGKKGHFAKNCHEHAHNNAEPKVPGLCPRCKRGKHWANECKSKT 50
Score = 39.9 bits (93), Expect = 1e-05
Identities = 13/46 (28%), Positives = 20/46 (43%), Gaps = 8/46 (17%)
Query: 58 TCYNCSGQGHVAKDC--------TVKSSIICYNCNSSGHFARNCPN 95
+C+ C +GH AK+C K +C C H+A C +
Sbjct: 3 SCFKCGKKGHFAKNCHEHAHNNAEPKVPGLCPRCKRGKHWANECKS 48
Score = 39.9 bits (93), Expect = 1e-05
Identities = 13/47 (27%), Positives = 18/47 (38%), Gaps = 3/47 (6%)
Query: 101 CYACHQAGHMAKECPGQTAGKSPEPVVDMSLTCYVCGHQGHLSYDCK 147
C+ C + GH AK C + V C C H + +CK
Sbjct: 4 CFKCGKKGHFAKNCHEHAHNNAEPKVPG---LCPRCKRGKHWANECK 47
Score = 38.4 bits (89), Expect = 4e-05
Identities = 13/44 (29%), Positives = 22/44 (50%), Gaps = 1/44 (2%)
Query: 9 CYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFAREC 52
C+ C GH+ +C + + +A G+ C +C H+A EC
Sbjct: 4 CFKCGKKGHFAKNCHEHAHNNAEPKVPGL-CPRCKRGKHWANEC 46
>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA
complex; NMR {Homo sapiens}
Length = 74
Score = 44.2 bits (104), Expect = 4e-07
Identities = 14/37 (37%), Positives = 17/37 (45%), Gaps = 1/37 (2%)
Query: 80 CYNCNSSGHFARNCPNDS-SKRCYACHQAGHMAKECP 115
CYNC H A+ C K+C+ C HM CP
Sbjct: 27 CYNCGGLDHHAKECKLPPQPKKCHFCQSISHMVASCP 63
Score = 41.9 bits (98), Expect = 3e-06
Identities = 15/47 (31%), Positives = 22/47 (46%), Gaps = 1/47 (2%)
Query: 55 ESVTCYNCSGQGHVAKDCTV-KSSIICYNCNSSGHFARNCPNDSSKR 100
+ CYNC G H AK+C + C+ C S H +CP + +
Sbjct: 23 KGDRCYNCGGLDHHAKECKLPPQPKKCHFCQSISHMVASCPLKAQQG 69
Score = 38.4 bits (89), Expect = 5e-05
Identities = 13/49 (26%), Positives = 19/49 (38%), Gaps = 2/49 (4%)
Query: 31 RGDKVGIVCYKCNNYGHFARECATE--SVTCYNCSGQGHVAKDCTVKSS 77
+ G CY C H A+EC C+ C H+ C +K+
Sbjct: 19 KRRSKGDRCYNCGGLDHHAKECKLPPQPKKCHFCQSISHMVASCPLKAQ 67
Score = 34.2 bits (78), Expect = 0.002
Identities = 14/47 (29%), Positives = 16/47 (34%), Gaps = 10/47 (21%)
Query: 100 RCYACHQAGHMAKECPGQTAGKSPEPVVDMSLTCYVCGHQGHLSYDC 146
RCY C H AKEC K C+ C H+ C
Sbjct: 26 RCYNCGGLDHHAKECKLPPQPK----------KCHFCQSISHMVASC 62
Score = 29.6 bits (66), Expect = 0.10
Identities = 10/46 (21%), Positives = 14/46 (30%), Gaps = 8/46 (17%)
Query: 7 IQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFAREC 52
+CYNC H+ C C+ C + H C
Sbjct: 25 DRCYNCGGLDHHAKECKLPPQPKK--------CHFCQSISHMVASC 62
>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 = 43.8 bits (103), Expect = 5e-07
Identities = 15/42 (35%), Positives = 18/42 (42%), Gaps = 1/42 (2%)
Query: 75 KSSIICYNCNSSGHFARNCPNDSS-KRCYACHQAGHMAKECP 115
S CYNC H A+ C K+C+ C HM CP
Sbjct: 5 SSGDRCYNCGGLDHHAKECKLPPQPKKCHFCQSISHMVASCP 46
Score = 40.7 bits (95), Expect = 6e-06
Identities = 15/49 (30%), Positives = 22/49 (44%), Gaps = 1/49 (2%)
Query: 53 ATESVTCYNCSGQGHVAKDCTV-KSSIICYNCNSSGHFARNCPNDSSKR 100
+ CYNC G H AK+C + C+ C S H +CP + +
Sbjct: 4 GSSGDRCYNCGGLDHHAKECKLPPQPKKCHFCQSISHMVASCPLKAQQG 52
Score = 35.7 bits (82), Expect = 4e-04
Identities = 13/44 (29%), Positives = 18/44 (40%), Gaps = 2/44 (4%)
Query: 36 GIVCYKCNNYGHFARECATESV--TCYNCSGQGHVAKDCTVKSS 77
G CY C H A+EC C+ C H+ C +K+
Sbjct: 7 GDRCYNCGGLDHHAKECKLPPQPKKCHFCQSISHMVASCPLKAQ 50
Score = 34.9 bits (80), Expect = 0.001
Identities = 15/52 (28%), Positives = 17/52 (32%), Gaps = 10/52 (19%)
Query: 95 NDSSKRCYACHQAGHMAKECPGQTAGKSPEPVVDMSLTCYVCGHQGHLSYDC 146
S RCY C H AKEC K C+ C H+ C
Sbjct: 4 GSSGDRCYNCGGLDHHAKECKLPPQPKK----------CHFCQSISHMVASC 45
Score = 30.3 bits (68), Expect = 0.048
Identities = 14/66 (21%), Positives = 22/66 (33%), Gaps = 8/66 (12%)
Query: 2 SSTSTIQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFARECATESVTCYN 61
S +S +CYNC H+ C C+ C + H C ++ +
Sbjct: 3 SGSSGDRCYNCGGLDHHAKECKL--------PPQPKKCHFCQSISHMVASCPLKAQQGPS 54
Query: 62 CSGQGH 67
G G
Sbjct: 55 AQGSGP 60
>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 = 40.3 bits (94), Expect = 8e-06
Identities = 17/46 (36%), Positives = 25/46 (54%)
Query: 75 KSSIICYNCNSSGHFARNCPNDSSKRCYACHQAGHMAKECPGQTAG 120
+ I C+NC GH AR C + C+ C + GH+ +CP + AG
Sbjct: 4 RKVIRCWNCGKEGHSARQCRAPRRQGCWKCGKTGHVMAKCPERQAG 49
Score = 33.0 bits (75), Expect = 0.003
Identities = 13/39 (33%), Positives = 19/39 (48%)
Query: 56 SVTCYNCSGQGHVAKDCTVKSSIICYNCNSSGHFARNCP 94
+ C+NC +GH A+ C C+ C +GH CP
Sbjct: 6 VIRCWNCGKEGHSARQCRAPRRQGCWKCGKTGHVMAKCP 44
Score = 30.7 bits (69), Expect = 0.022
Identities = 15/43 (34%), Positives = 19/43 (44%), Gaps = 1/43 (2%)
Query: 32 GDKVGIVCYKCNNYGHFAREC-ATESVTCYNCSGQGHVAKDCT 73
+ I C+ C GH AR+C A C+ C GHV C
Sbjct: 2 QQRKVIRCWNCGKEGHSARQCRAPRRQGCWKCGKTGHVMAKCP 44
>3nyb_B Protein AIR2; polya RNA polymerase, zinc knuckle protein, RNA
surveillance binds to TRF4P/AIR2P heterodimer; 2.70A
{Saccharomyces cerevisiae}
Length = 83
Score = 39.6 bits (92), Expect = 2e-05
Identities = 15/64 (23%), Positives = 20/64 (31%)
Query: 37 IVCYKCNNYGHFARECATESVTCYNCSGQGHVAKDCTVKSSIICYNCNSSGHFARNCPND 96
+ C C + H C + +I CYNC GHF +C
Sbjct: 6 VQCTLCKSKKHSKERCPSIWRAYILVDDNEKAKPKVLPFHTIYCYNCGGKGHFGDDCKEK 65
Query: 97 SSKR 100
S R
Sbjct: 66 RSSR 69
Score = 38.9 bits (90), Expect = 4e-05
Identities = 19/70 (27%), Positives = 25/70 (35%), Gaps = 12/70 (17%)
Query: 78 IICYNCNSSGHFARNCPNDSSKRCYACHQAGHMAKECPGQTAGKSPEPVVDMSLTCYVCG 137
+ C C S H CP S R Y P+ + ++ CY CG
Sbjct: 6 VQCTLCKSKKHSKERCP--SIWRAY----------ILVDDNEKAKPKVLPFHTIYCYNCG 53
Query: 138 HQGHLSYDCK 147
+GH DCK
Sbjct: 54 GKGHFGDDCK 63
Score = 38.1 bits (88), Expect = 1e-04
Identities = 18/71 (25%), Positives = 25/71 (35%), Gaps = 9/71 (12%)
Query: 7 IQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFARECATESVTCYNCSGQG 66
+QC C H + CP +N + ++ CYNC G+G
Sbjct: 6 VQCTLCKSKKHSKERCP---------SIWRAYILVDDNEKAKPKVLPFHTIYCYNCGGKG 56
Query: 67 HVAKDCTVKSS 77
H DC K S
Sbjct: 57 HFGDDCKEKRS 67
Score = 25.4 bits (55), Expect = 3.6
Identities = 11/24 (45%), Positives = 14/24 (58%)
Query: 5 STIQCYNCFDFGHYQYSCPQKSSA 28
TI CYNC GH+ C +K S+
Sbjct: 45 HTIYCYNCGGKGHFGDDCKEKRSS 68
>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 = 38.8 bits (90), Expect = 3e-05
Identities = 16/45 (35%), Positives = 25/45 (55%)
Query: 75 KSSIICYNCNSSGHFARNCPNDSSKRCYACHQAGHMAKECPGQTA 119
+ ++ C+NC GH A+NC K C+ C + GH K+C + A
Sbjct: 10 RKTVKCFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDCTERQA 54
Score = 33.0 bits (75), Expect = 0.004
Identities = 14/39 (35%), Positives = 23/39 (58%)
Query: 55 ESVTCYNCSGQGHVAKDCTVKSSIICYNCNSSGHFARNC 93
++V C+NC +GH+AK+C C+ C GH ++C
Sbjct: 11 KTVKCFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDC 49
Score = 32.7 bits (74), Expect = 0.005
Identities = 16/44 (36%), Positives = 22/44 (50%), Gaps = 1/44 (2%)
Query: 31 RGDKVGIVCYKCNNYGHFAREC-ATESVTCYNCSGQGHVAKDCT 73
R + + C+ C GH A+ C A C+ C +GH KDCT
Sbjct: 7 RNQRKTVKCFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDCT 50
Score = 23.8 bits (51), Expect = 9.3
Identities = 15/47 (31%), Positives = 23/47 (48%), Gaps = 11/47 (23%)
Query: 100 RCYACHQAGHMAKECPGQTAGKSPEPVVDMSLTCYVCGHQGHLSYDC 146
+C+ C + GH+AK C ++P C+ CG +GH DC
Sbjct: 14 KCFNCGKEGHIAKNC------RAPR-----KKGCWKCGKEGHQMKDC 49
>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein,
metal binding protein; NMR {Synthetic}
Length = 39
Score = 36.0 bits (83), Expect = 3e-04
Identities = 13/38 (34%), Positives = 18/38 (47%)
Query: 78 IICYNCNSSGHFARNCPNDSSKRCYACHQAGHMAKECP 115
+ C+NC GH AR C + C+ C H +CP
Sbjct: 1 LTCFNCGKPGHTARMCRQPRQEGCWNCGSKEHRFAQCP 38
Score = 33.3 bits (76), Expect = 0.002
Identities = 15/38 (39%), Positives = 19/38 (50%)
Query: 57 VTCYNCSGQGHVAKDCTVKSSIICYNCNSSGHFARNCP 94
+TC+NC GH A+ C C+NC S H CP
Sbjct: 1 LTCFNCGKPGHTARMCRQPRQEGCWNCGSKEHRFAQCP 38
Score = 29.1 bits (65), Expect = 0.072
Identities = 12/38 (31%), Positives = 16/38 (42%), Gaps = 1/38 (2%)
Query: 37 IVCYKCNNYGHFAREC-ATESVTCYNCSGQGHVAKDCT 73
+ C+ C GH AR C C+NC + H C
Sbjct: 1 LTCFNCGKPGHTARMCRQPRQEGCWNCGSKEHRFAQCP 38
>2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein,
retrovirus zinc finger-like domains; NMR {Equine
infectious anemia virus}
Length = 37
Score = 32.6 bits (74), Expect = 0.003
Identities = 15/35 (42%), Positives = 20/35 (57%), Gaps = 2/35 (5%)
Query: 80 CYNCNSSGHFARNCPNDSSKRCYACHQAGHMAKEC 114
CYNC GH + C + K C+ C Q GH +K+C
Sbjct: 3 CYNCGKPGHLSSQCR--APKVCFKCKQPGHFSKQC 35
Score = 32.2 bits (73), Expect = 0.005
Identities = 14/38 (36%), Positives = 23/38 (60%), Gaps = 2/38 (5%)
Query: 58 TCYNCSGQGHVAKDCTVKSSIICYNCNSSGHFARNCPN 95
TCYNC GH++ C ++ +C+ C GHF++ C +
Sbjct: 2 TCYNCGKPGHLSSQC--RAPKVCFKCKQPGHFSKQCRS 37
Score = 24.5 bits (53), Expect = 3.5
Identities = 12/49 (24%), Positives = 19/49 (38%), Gaps = 13/49 (26%)
Query: 99 KRCYACHQAGHMAKECPGQTAGKSPEPVVDMSLTCYVCGHQGHLSYDCK 147
+ CY C + GH++ +C C+ C GH S C+
Sbjct: 1 QTCYNCGKPGHLSSQCRAPKV-------------CFKCKQPGHFSKQCR 36
Score = 24.1 bits (52), Expect = 4.0
Identities = 15/47 (31%), Positives = 20/47 (42%), Gaps = 11/47 (23%)
Query: 8 QCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFARECAT 54
CYNC GH C VC+KC GHF+++C +
Sbjct: 2 TCYNCGKPGHLSSQCRA-----------PKVCFKCKQPGHFSKQCRS 37
>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 = 33.3 bits (76), Expect = 0.022
Identities = 5/74 (6%), Positives = 12/74 (16%), Gaps = 7/74 (9%)
Query: 46 GHFARECATESVTCYNCSGQGHVAKDCTVKSSIICYNCNSSGHFARNCPNDSSKRCYACH 105
+V G + + + G+ S++
Sbjct: 225 RPELMSAQ-SAVGSIETIGFPGILA--AADAMVKAGRITIVGYIRAG----SARFTLNIR 277
Query: 106 QAGHMAKECPGQTA 119
K
Sbjct: 278 GDVQEVKTAMAAGI 291
Score = 31.4 bits (71), Expect = 0.086
Identities = 5/43 (11%), Positives = 9/43 (20%), Gaps = 3/43 (6%)
Query: 31 RGDKVGIVCYKCNNYGHFARECATESVTCYNCSGQGHVAKDCT 73
+ + G+ A + N G K
Sbjct: 248 AAADAMVKAGRITIVGYIR---AGSARFTLNIRGDVQEVKTAM 287
Score = 30.3 bits (68), Expect = 0.20
Identities = 4/56 (7%), Positives = 11/56 (19%), Gaps = 13/56 (23%)
Query: 6 TIQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFARECATESVTCYN 61
++ G+ + + AR + + N
Sbjct: 253 MVKAGRITIVGYIR-------AGSARF------TLNIRGDVQEVKTAMAAGIDAIN 295
>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 = 28.7 bits (64), Expect = 0.14
Identities = 8/22 (36%), Positives = 12/22 (54%)
Query: 79 ICYNCNSSGHFARNCPNDSSKR 100
C+ C GH+ +NCP + K
Sbjct: 9 TCFRCGKPGHYIKNCPTNGDKN 30
Score = 26.4 bits (58), Expect = 0.91
Identities = 7/19 (36%), Positives = 11/19 (57%)
Query: 36 GIVCYKCNNYGHFARECAT 54
G C++C GH+ + C T
Sbjct: 7 GYTCFRCGKPGHYIKNCPT 25
Score = 25.2 bits (55), Expect = 2.6
Identities = 7/15 (46%), Positives = 9/15 (60%)
Query: 101 CYACHQAGHMAKECP 115
C+ C + GH K CP
Sbjct: 10 CFRCGKPGHYIKNCP 24
>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 = 1.3
Identities = 11/30 (36%), Positives = 16/30 (53%), Gaps = 1/30 (3%)
Query: 101 CYACHQAGHMAKECPGQTAG-KSPEPVVDM 129
C C + GH AK+CP + G + P P +
Sbjct: 26 CAYCKEKGHWAKDCPKKPRGPRGPRPQTSL 55
>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 = 25.3 bits (55), Expect = 1.4
Identities = 9/19 (47%), Positives = 11/19 (57%)
Query: 75 KSSIICYNCNSSGHFARNC 93
+ I C+NC GH AR C
Sbjct: 4 RKVIRCWNCGKEGHSARQC 22
Score = 24.5 bits (53), Expect = 2.9
Identities = 7/17 (41%), Positives = 11/17 (64%)
Query: 56 SVTCYNCSGQGHVAKDC 72
+ C+NC +GH A+ C
Sbjct: 6 VIRCWNCGKEGHSARQC 22
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 27.7 bits (61), Expect = 2.1
Identities = 8/53 (15%), Positives = 15/53 (28%), Gaps = 12/53 (22%)
Query: 23 PQKSSADARGDKVGIVCYK-CNNYGHFARECATESVTCYNCSGQ-----GHVA 69
P + +A + + V + G + YN Q G +
Sbjct: 1814 PGRVAASFSQEALQYVVERVGKRTGWLV------EIVNYNVENQQYVAAGDLR 1860
>1nlt_A Protein YDJ1, mitochondrial protein import protein MAS5;
beta-strands, chaperone, heat shock, mitochondrion;
2.70A {Saccharomyces cerevisiae} SCOP: b.4.1.1 b.4.1.1
g.54.1.1
Length = 248
Score = 26.8 bits (60), Expect = 3.0
Identities = 17/79 (21%), Positives = 23/79 (29%), Gaps = 26/79 (32%)
Query: 56 SVTCYNCSGQGHVAKDCTVKSSIICYNCNSSGH-------------FARNCPN------- 95
+ C C G+G K VK C +CN G F C
Sbjct: 38 QILCKECEGRG--GKKGAVKK---CTSCNGQGIKFVTRQMGPMIQRFQTECDVCHGTGDI 92
Query: 96 -DSSKRCYACHQAGHMAKE 113
D RC +C+ +
Sbjct: 93 IDPKDRCKSCNGKKVENER 111
>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 = 24.7 bits (53), Expect = 3.0
Identities = 10/34 (29%), Positives = 14/34 (41%)
Query: 90 ARNCPNDSSKRCYACHQAGHMAKECPGQTAGKSP 123
R +C C + GH AK+CP + G
Sbjct: 2 ERRRSQLDRDQCAYCKEKGHWAKDCPKKPRGPRG 35
>2rb7_A Peptidase, M20/M25/M40 family; YP_387682.1, CO-catalytic
metallopeptidase, peptidase family M20/M25/M40,
structural genomics; HET: MSE PGE PG4; 1.60A
{Desulfovibrio desulfuricans subsp}
Length = 364
Score = 26.4 bits (59), Expect = 3.7
Identities = 4/28 (14%), Positives = 10/28 (35%), Gaps = 5/28 (17%)
Query: 122 SPEPVVD-----MSLTCYVCGHQGHLSY 144
+P+ V+ + + G H +
Sbjct: 166 NPQQVITKEKGIIDIKLTCTGKAAHGAR 193
>2x6w_A Tail spike protein; viral protein, beta-helix, hydrolase; HET: RAM
GLC GLA NAG NDG; 1.35A {Enterobacteria phage HK620} PDB:
2vji_A 2vjj_A* 2x85_A* 2x6x_A* 2x6y_A*
Length = 600
Score = 26.4 bits (57), Expect = 5.7
Identities = 8/43 (18%), Positives = 13/43 (30%)
Query: 60 YNCSGQGHVAKDCTVKSSIICYNCNSSGHFARNCPNDSSKRCY 102
+N G + C + + NCP + CY
Sbjct: 205 WNGYGSNCYVRKCRFINLVNSSVNADHSTVYVNCPYSGVESCY 247
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
0.321 0.132 0.448
Gapped
Lambda K H
0.267 0.0548 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,196,759
Number of extensions: 118705
Number of successful extensions: 741
Number of sequences better than 10.0: 1
Number of HSP's gapped: 612
Number of HSP's successfully gapped: 235
Length of query: 152
Length of database: 6,701,793
Length adjustment: 85
Effective length of query: 67
Effective length of database: 4,328,508
Effective search space: 290010036
Effective search space used: 290010036
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 53 (24.6 bits)