BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 023488
(281 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2EC7|A Chain A, Solution Structure Of Human Immunodificiency Virus Type-2
Nucleocapsid Protein
Length = 49
Score = 38.1 bits (87), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 25/47 (53%), Gaps = 6/47 (12%)
Query: 131 CYNCGQAGHSLAQCPQPLQDGGTKFASCFICKEQGHLSKNCPQNAHG 177
C+NCG+ GHS QC P + G C+ C + GH+ CP+ G
Sbjct: 9 CWNCGKEGHSARQCRAPRRQG------CWKCGKTGHVMAKCPERQAG 49
>pdb|2IHX|A Chain A, Solution Structure Of The Rous Sarcoma Virus Nucleocapsid
Protein:upsi Rna Packaging Signal Complex
Length = 61
Score = 37.4 bits (85), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 18/42 (42%), Positives = 24/42 (57%), Gaps = 1/42 (2%)
Query: 130 LCYNCGQAGHSLAQCPQPLQDGGTKFASCFICKEQGHLSKNC 171
LCY CG GH AQCP+ + G ++ C +C GH +K C
Sbjct: 6 LCYTCGSPGHYQAQCPKKRKSGNSR-ERCQLCNGMGHNAKQC 46
Score = 28.5 bits (62), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 14/41 (34%), Positives = 17/41 (41%)
Query: 104 ICLVCRRRGHTLKNCPSKNDETESTKLCYNCGQAGHSLAQC 144
+C C GH CP K S + C C GH+ QC
Sbjct: 6 LCYTCGSPGHYQAQCPKKRKSGNSRERCQLCNGMGHNAKQC 46
>pdb|2BL6|A Chain A, Solution Structure Of The Zn Complex Of Eiav Ncp11(22-58)
Peptide, Including Two Cchc Zn-Binding Motifs
Length = 37
Score = 35.8 bits (81), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 19/43 (44%), Positives = 23/43 (53%), Gaps = 8/43 (18%)
Query: 129 KLCYNCGQAGHSLAQCPQPLQDGGTKFASCFICKEQGHLSKNC 171
+ CYNCG+ GH +QC P CF CK+ GH SK C
Sbjct: 1 QTCYNCGKPGHLSSQCRAP--------KVCFKCKQPGHFSKQC 35
>pdb|2LLI|A Chain A, Low Resolution Structure Of Rna-Binding Subunit Of The
Tramp Complex
Length = 124
Score = 33.5 bits (75), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 35/128 (27%), Positives = 43/128 (33%), Gaps = 41/128 (32%)
Query: 105 CLVCRRRGHTLKNCP-------SKNDETESTKL-----CYNCGQAGHSLAQCPQPLQDGG 152
C C +RGH K+CP D+ S C C + GH +QCP
Sbjct: 7 CNNCSQRGHLKKDCPHIICSYCGATDDHYSRHCPKAIQCSKCDEVGHYRSQCPHKW---- 62
Query: 153 TKFASCFICKEQGHLSKNCPQNA-------------------HGIYPKGGCCKICGGVTH 193
K C +CK + H + CP H IY C CGG H
Sbjct: 63 -KKVQCTLCKSKKHSKERCPSIWRAYILVDDNEKAKPKVLPFHTIY-----CYNCGGKGH 116
Query: 194 LARDCPNK 201
DC K
Sbjct: 117 FGDDCKEK 124
Score = 28.9 bits (63), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 32/75 (42%), Gaps = 18/75 (24%)
Query: 80 CFICKAKEHIAKHCPMKAEWEKNKICLVCRRRGHTLKNCPSKN------DETESTK---- 129
C C H CP K W+K + C +C+ + H+ + CPS D+ E K
Sbjct: 45 CSKCDEVGHYRSQCPHK--WKKVQ-CTLCKSKKHSKERCPSIWRAYILVDDNEKAKPKVL 101
Query: 130 -----LCYNCGQAGH 139
CYNCG GH
Sbjct: 102 PFHTIYCYNCGGKGH 116
Score = 27.7 bits (60), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 24/86 (27%), Positives = 29/86 (33%), Gaps = 16/86 (18%)
Query: 126 ESTKLCYNCGQAGHSLAQCPQPLQD--GGT---------KFASCFICKEQGHLSKNCPQN 174
E+ C NC Q GH CP + G T K C C E GH CP
Sbjct: 2 EAAPKCNNCSQRGHLKKDCPHIICSYCGATDDHYSRHCPKAIQCSKCDEVGHYRSQCPHK 61
Query: 175 AHGIYPKGGCCKICGGVTHLARDCPN 200
+ C +C H CP+
Sbjct: 62 WKKVQ-----CTLCKSKKHSKERCPS 82
>pdb|2L4L|A Chain A, Structural Insights Into The Ctar Dna Recognition By The
Hiv-1 Nucleocapsid Protein: Role Of Sugar Deoxyriboses
In The Binding Polarity Of Nc
Length = 45
Score = 33.5 bits (75), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 24/43 (55%), Gaps = 6/43 (13%)
Query: 131 CYNCGQAGHSLAQCPQPLQDGGTKFASCFICKEQGHLSKNCPQ 173
C+NCG+ GH+ C P + G C+ C ++GH K+C +
Sbjct: 5 CFNCGKEGHTARNCRAPRKKG------CWKCGKEGHQMKDCTE 41
Score = 31.6 bits (70), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 23/46 (50%), Gaps = 5/46 (10%)
Query: 101 KNKICLVCRRRGHTLKNCPSKNDETESTKLCYNCGQAGHSLAQCPQ 146
KN C C + GHT +NC + K C+ CG+ GH + C +
Sbjct: 1 KNVKCFNCGKEGHTARNCRA-----PRKKGCWKCGKEGHQMKDCTE 41
>pdb|2EXF|A Chain A, Solution Structure Of The Hiv-1 Nucleocapsid (Ncp7(12-55))
Complexed With The Dna (-) Primer Binding Site
pdb|2JZW|A Chain A, How The Hiv-1 Nucleocapsid Protein Binds And Destabilises
The (-)primer Binding Site During Reverse Transcription
Length = 44
Score = 33.1 bits (74), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 24/43 (55%), Gaps = 6/43 (13%)
Query: 131 CYNCGQAGHSLAQCPQPLQDGGTKFASCFICKEQGHLSKNCPQ 173
C+NCG+ GH+ C P + G C+ C ++GH K+C +
Sbjct: 4 CFNCGKEGHTARNCRAPRKKG------CWKCGKEGHQMKDCTE 40
Score = 30.0 bits (66), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 22/45 (48%), Gaps = 5/45 (11%)
Query: 102 NKICLVCRRRGHTLKNCPSKNDETESTKLCYNCGQAGHSLAQCPQ 146
N C C + GHT +NC + K C+ CG+ GH + C +
Sbjct: 1 NVKCFNCGKEGHTARNCRA-----PRKKGCWKCGKEGHQMKDCTE 40
>pdb|1BJ6|A Chain A, 1h Nmr Of (12-53) Ncp7D(ACGCC) COMPLEX, 10 STRUCTURES
pdb|1ESK|A Chain A, Solution Structure Of Ncp7 From Hiv-1
Length = 42
Score = 33.1 bits (74), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 24/43 (55%), Gaps = 6/43 (13%)
Query: 131 CYNCGQAGHSLAQCPQPLQDGGTKFASCFICKEQGHLSKNCPQ 173
C+NCG+ GH+ C P + G C+ C ++GH K+C +
Sbjct: 4 CFNCGKEGHTARNCRAPRKKG------CWKCGKEGHQMKDCTE 40
Score = 29.6 bits (65), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 21/42 (50%), Gaps = 5/42 (11%)
Query: 105 CLVCRRRGHTLKNCPSKNDETESTKLCYNCGQAGHSLAQCPQ 146
C C + GHT +NC + K C+ CG+ GH + C +
Sbjct: 4 CFNCGKEGHTARNCRA-----PRKKGCWKCGKEGHQMKDCTE 40
>pdb|1A1T|A Chain A, Structure Of The Hiv-1 Nucleocapsid Protein Bound To The
Sl3 Psi-Rna Recognition Element, Nmr, 25 Structures
pdb|1MFS|A Chain A, Dynamical Behavior Of The Hiv-1 Nucleocapsid Protein; Nmr,
30 Structures
Length = 55
Score = 32.7 bits (73), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 24/46 (52%), Gaps = 6/46 (13%)
Query: 128 TKLCYNCGQAGHSLAQCPQPLQDGGTKFASCFICKEQGHLSKNCPQ 173
T C+NCG+ GH C P + G C+ C ++GH K+C +
Sbjct: 12 TVKCFNCGKEGHIAKNCRAPRKKG------CWKCGKEGHQMKDCTE 51
Score = 29.3 bits (64), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 20/42 (47%), Gaps = 5/42 (11%)
Query: 105 CLVCRRRGHTLKNCPSKNDETESTKLCYNCGQAGHSLAQCPQ 146
C C + GH KNC + K C+ CG+ GH + C +
Sbjct: 15 CFNCGKEGHIAKNCRA-----PRKKGCWKCGKEGHQMKDCTE 51
Score = 28.9 bits (63), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 23/48 (47%), Gaps = 6/48 (12%)
Query: 154 KFASCFICKEQGHLSKNCPQNAHGIYPKGGCCKICGGVTHLARDCPNK 201
K CF C ++GH++KNC P+ C CG H +DC +
Sbjct: 11 KTVKCFNCGKEGHIAKNCR------APRKKGCWKCGKEGHQMKDCTER 52
Score = 27.7 bits (60), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 22/42 (52%), Gaps = 4/42 (9%)
Query: 80 CFICKAKEHIAKHCPMKAEWEKNKICLVCRRRGHTLKNCPSK 121
CF C + HIAK+C + K C C + GH +K+C +
Sbjct: 15 CFNCGKEGHIAKNCRA----PRKKGCWKCGKEGHQMKDCTER 52
>pdb|1F6U|A Chain A, Nmr Structure Of The Hiv-1 Nucleocapsid Protein Bound To
Stem-Loop Sl2 Of The Psi-Rna Packaging Signal.
Implications For Genome Recognition
Length = 56
Score = 32.7 bits (73), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 24/46 (52%), Gaps = 6/46 (13%)
Query: 128 TKLCYNCGQAGHSLAQCPQPLQDGGTKFASCFICKEQGHLSKNCPQ 173
T C+NCG+ GH C P + G C+ C ++GH K+C +
Sbjct: 12 TVKCFNCGKEGHIAKNCRAPRKKG------CWKCGKEGHQMKDCTE 51
Score = 29.3 bits (64), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 20/42 (47%), Gaps = 5/42 (11%)
Query: 105 CLVCRRRGHTLKNCPSKNDETESTKLCYNCGQAGHSLAQCPQ 146
C C + GH KNC + K C+ CG+ GH + C +
Sbjct: 15 CFNCGKEGHIAKNCRA-----PRKKGCWKCGKEGHQMKDCTE 51
Score = 28.9 bits (63), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 23/48 (47%), Gaps = 6/48 (12%)
Query: 154 KFASCFICKEQGHLSKNCPQNAHGIYPKGGCCKICGGVTHLARDCPNK 201
K CF C ++GH++KNC P+ C CG H +DC +
Sbjct: 11 KTVKCFNCGKEGHIAKNCR------APRKKGCWKCGKEGHQMKDCTER 52
Score = 27.7 bits (60), Expect = 8.0, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 22/42 (52%), Gaps = 4/42 (9%)
Query: 80 CFICKAKEHIAKHCPMKAEWEKNKICLVCRRRGHTLKNCPSK 121
CF C + HIAK+C + K C C + GH +K+C +
Sbjct: 15 CFNCGKEGHIAKNCRA----PRKKGCWKCGKEGHQMKDCTER 52
>pdb|2M3Z|A Chain A, Nmr Solution Structure Of Hiv-1 Nucleocapsid Protein In
Complex With An Inhibitor Displaying A 2 Inhibitors:1 Nc
Stoichiometry
Length = 55
Score = 32.7 bits (73), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 24/46 (52%), Gaps = 6/46 (13%)
Query: 128 TKLCYNCGQAGHSLAQCPQPLQDGGTKFASCFICKEQGHLSKNCPQ 173
T C+NCG+ GH C P + G C+ C ++GH K+C +
Sbjct: 12 TVKCFNCGKEGHIAKNCRAPRKKG------CWKCGKEGHQMKDCTE 51
Score = 29.3 bits (64), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 20/42 (47%), Gaps = 5/42 (11%)
Query: 105 CLVCRRRGHTLKNCPSKNDETESTKLCYNCGQAGHSLAQCPQ 146
C C + GH KNC + K C+ CG+ GH + C +
Sbjct: 15 CFNCGKEGHIAKNCRA-----PRKKGCWKCGKEGHQMKDCTE 51
Score = 28.5 bits (62), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 23/48 (47%), Gaps = 6/48 (12%)
Query: 154 KFASCFICKEQGHLSKNCPQNAHGIYPKGGCCKICGGVTHLARDCPNK 201
K CF C ++GH++KNC P+ C CG H +DC +
Sbjct: 11 KTVKCFNCGKEGHIAKNCR------APRKKGCWKCGKEGHQMKDCTER 52
Score = 27.3 bits (59), Expect = 8.6, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 22/42 (52%), Gaps = 4/42 (9%)
Query: 80 CFICKAKEHIAKHCPMKAEWEKNKICLVCRRRGHTLKNCPSK 121
CF C + HIAK+C + K C C + GH +K+C +
Sbjct: 15 CFNCGKEGHIAKNCRA----PRKKGCWKCGKEGHQMKDCTER 52
>pdb|2A51|A Chain A, Structure Of The (13-51) Domain Of The Nucleocapsid
Protein Ncp8 From Sivlhoest
Length = 39
Score = 32.3 bits (72), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 16/43 (37%), Positives = 23/43 (53%), Gaps = 6/43 (13%)
Query: 131 CYNCGQAGHSLAQCPQPLQDGGTKFASCFICKEQGHLSKNCPQ 173
C+NCG+ GH+ C QP Q+G C+ C + H CP+
Sbjct: 3 CFNCGKPGHTARMCRQPRQEG------CWNCGSKEHRFAQCPK 39
>pdb|1AAF|A Chain A, Nucleocapsid Zinc Fingers Detected In Retroviruses: Exafs
Studies On Intact Viruses And The Solution-State
Structure Of The Nucleocapsid Protein From Hiv-1
Length = 55
Score = 32.3 bits (72), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 23/43 (53%), Gaps = 6/43 (13%)
Query: 131 CYNCGQAGHSLAQCPQPLQDGGTKFASCFICKEQGHLSKNCPQ 173
C+NCG+ GH C P + G C+ C ++GH K+C +
Sbjct: 15 CFNCGKEGHIAKNCRAPRKRG------CWKCGKEGHQMKDCTE 51
Score = 29.3 bits (64), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 23/48 (47%), Gaps = 6/48 (12%)
Query: 154 KFASCFICKEQGHLSKNCPQNAHGIYPKGGCCKICGGVTHLARDCPNK 201
K CF C ++GH++KNC P+ C CG H +DC +
Sbjct: 11 KIIKCFNCGKEGHIAKNCR------APRKRGCWKCGKEGHQMKDCTER 52
Score = 28.1 bits (61), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 13/42 (30%), Positives = 20/42 (47%), Gaps = 5/42 (11%)
Query: 105 CLVCRRRGHTLKNCPSKNDETESTKLCYNCGQAGHSLAQCPQ 146
C C + GH KNC + + C+ CG+ GH + C +
Sbjct: 15 CFNCGKEGHIAKNCRA-----PRKRGCWKCGKEGHQMKDCTE 51
>pdb|1CL4|A Chain A, Nucleocapsid Protein From Mason-Pfizer Monkey Virus (Mpmv)
Length = 60
Score = 31.2 bits (69), Expect = 0.74, Method: Compositional matrix adjust.
Identities = 20/48 (41%), Positives = 27/48 (56%), Gaps = 2/48 (4%)
Query: 156 ASCFICKEQGHLSKNCPQNAH-GIYPK-GGCCKICGGVTHLARDCPNK 201
SCF C ++GH +KNC ++AH PK G C C H A +C +K
Sbjct: 2 GSCFKCGKKGHFAKNCHEHAHNNAEPKVPGLCPRCKRGKHWANECKSK 49
Score = 28.5 bits (62), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 20/51 (39%), Positives = 24/51 (47%), Gaps = 4/51 (7%)
Query: 77 GESCFICKAKEHIAKHCPM----KAEWEKNKICLVCRRRGHTLKNCPSKND 123
G SCF C K H AK+C AE + +C C+R H C SK D
Sbjct: 1 GGSCFKCGKKGHFAKNCHEHAHNNAEPKVPGLCPRCKRGKHWANECKSKTD 51
>pdb|3TS0|A Chain A, Mouse Lin28a In Complex With Let-7f-1 Microrna Pre-Element
pdb|3TS0|B Chain B, Mouse Lin28a In Complex With Let-7f-1 Microrna Pre-Element
Length = 146
Score = 29.3 bits (64), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 28/55 (50%), Gaps = 3/55 (5%)
Query: 75 KPGESCFICKAKEHIAKHCPMKAEWEKNKICLVCRRRGHTLKNCPSKNDETESTK 129
K G+ C+ C +H AK C + + +K C C+ H + +CP K + S++
Sbjct: 93 KGGDRCYNCGGLDHHAKECKLPPQPKK---CHFCQSINHMVASCPLKAQQGPSSQ 144
Score = 29.3 bits (64), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 19/45 (42%), Gaps = 5/45 (11%)
Query: 131 CYNCGQAGHSLAQCPQPLQDGGTKFASCFICKEQGHLSKNCPQNA 175
CYNCG H +C P Q C C+ H+ +CP A
Sbjct: 98 CYNCGGLDHHAKECKLPPQP-----KKCHFCQSINHMVASCPLKA 137
>pdb|1NC8|A Chain A, High-Resolution Solution Nmr Structure Of The Minimal
Active Domain Of The Human Immunodeficiency Virus Type-2
Nucleocapsid Protein, 15 Structures
Length = 29
Score = 29.3 bits (64), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 11/21 (52%), Positives = 14/21 (66%)
Query: 131 CYNCGQAGHSLAQCPQPLQDG 151
C+NCG+ GHS QC P + G
Sbjct: 9 CWNCGKEGHSARQCRAPRRQG 29
>pdb|3TRZ|A Chain A, Mouse Lin28a In Complex With Let-7d Microrna Pre-Element
pdb|3TRZ|B Chain B, Mouse Lin28a In Complex With Let-7d Microrna Pre-Element
pdb|3TRZ|C Chain C, Mouse Lin28a In Complex With Let-7d Microrna Pre-Element
pdb|3TRZ|D Chain D, Mouse Lin28a In Complex With Let-7d Microrna Pre-Element
pdb|3TRZ|E Chain E, Mouse Lin28a In Complex With Let-7d Microrna Pre-Element
pdb|3TRZ|F Chain F, Mouse Lin28a In Complex With Let-7d Microrna Pre-Element
pdb|3TS2|A Chain A, Mouse Lin28a In Complex With Let-7g Microrna Pre-Element
pdb|3TS2|B Chain B, Mouse Lin28a In Complex With Let-7g Microrna Pre-Element
Length = 148
Score = 29.3 bits (64), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 28/55 (50%), Gaps = 3/55 (5%)
Query: 75 KPGESCFICKAKEHIAKHCPMKAEWEKNKICLVCRRRGHTLKNCPSKNDETESTK 129
K G+ C+ C +H AK C + + +K C C+ H + +CP K + S++
Sbjct: 95 KGGDRCYNCGGLDHHAKECKLPPQPKK---CHFCQSINHMVASCPLKAQQGPSSQ 146
Score = 29.3 bits (64), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 19/45 (42%), Gaps = 5/45 (11%)
Query: 131 CYNCGQAGHSLAQCPQPLQDGGTKFASCFICKEQGHLSKNCPQNA 175
CYNCG H +C P Q C C+ H+ +CP A
Sbjct: 100 CYNCGGLDHHAKECKLPPQP-----KKCHFCQSINHMVASCPLKA 139
>pdb|1Q3Y|A Chain A, Nmr Structure Of The Cys28his Mutant (D Form) Of The
Nucleocapsid Protein Ncp7 Of Hiv-1.
pdb|1Q3Z|A Chain A, Nmr Structure Of The Cys28his Mutant (e Form) Of The
Nucleocapsid Protein Ncp7 Of Hiv-1
Length = 42
Score = 29.3 bits (64), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 23/43 (53%), Gaps = 6/43 (13%)
Query: 131 CYNCGQAGHSLAQCPQPLQDGGTKFASCFICKEQGHLSKNCPQ 173
C+NCG+ GH+ P + G C+ C ++GH K+C +
Sbjct: 4 CFNCGKEGHTARNHRAPRKKG------CWKCGKEGHQMKDCTE 40
Score = 28.1 bits (61), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 14/45 (31%), Positives = 21/45 (46%), Gaps = 5/45 (11%)
Query: 102 NKICLVCRRRGHTLKNCPSKNDETESTKLCYNCGQAGHSLAQCPQ 146
N C C + GHT ++N K C+ CG+ GH + C +
Sbjct: 1 NVKCFNCGKEGHT-----ARNHRAPRKKGCWKCGKEGHQMKDCTE 40
>pdb|1U6P|A Chain A, Nmr Structure Of The Mlv Encapsidation Signal Bound To The
Nucleocapsid Protein
pdb|1WWD|A Chain A, Nmr Structure Determined For Mlv Nc Complex With Rna
Sequence Aacagu
pdb|1WWE|A Chain A, Nmr Structure Determined For Mlv Nc Complex With Rna
Sequence Uuuugcu
pdb|1WWF|A Chain A, Nmr Structure Determined For Mlv Nc Complex With Rna
Sequence Ccuccgu
pdb|1WWG|A Chain A, Nmr Structure Determined For Mlv Nc Complex With Rna
Sequence Uaucug
Length = 56
Score = 29.3 bits (64), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 12/25 (48%), Positives = 17/25 (68%), Gaps = 2/25 (8%)
Query: 158 CFICKEQGHLSKNCPQNAHGIYPKG 182
C CKE+GH +K+CP+ G P+G
Sbjct: 26 CAYCKEKGHWAKDCPKKPRG--PRG 48
>pdb|2CQF|A Chain A, Solution Structure Of The Zinc-Finger Domain In Lin-28
Length = 63
Score = 28.9 bits (63), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 15/53 (28%), Positives = 26/53 (49%), Gaps = 3/53 (5%)
Query: 77 GESCFICKAKEHIAKHCPMKAEWEKNKICLVCRRRGHTLKNCPSKNDETESTK 129
G+ C+ C +H AK C + + +K C C+ H + +CP K + S +
Sbjct: 7 GDRCYNCGGLDHHAKECKLPPQPKK---CHFCQSISHMVASCPLKAQQGPSAQ 56
>pdb|1A6B|B Chain B, Nmr Structure Of The Complex Between The Zinc Finger
Protein Ncp10 Of Moloney Murine Leukemia Virus And A
Sequence Of The Psi-Packaging Domain Of Hiv-1, 20
Structures
Length = 40
Score = 28.9 bits (63), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 12/26 (46%), Positives = 17/26 (65%), Gaps = 2/26 (7%)
Query: 157 SCFICKEQGHLSKNCPQNAHGIYPKG 182
C CKE+GH +K+CP+ G P+G
Sbjct: 12 QCAYCKEKGHWAKDCPKKPRG--PRG 35
>pdb|2LI8|A Chain A, The Solution Structure Of The Lin28-Znf Domains Bound To
Aggagau Of Pre-Let-7 Mirna
Length = 74
Score = 28.5 bits (62), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 15/53 (28%), Positives = 26/53 (49%), Gaps = 3/53 (5%)
Query: 77 GESCFICKAKEHIAKHCPMKAEWEKNKICLVCRRRGHTLKNCPSKNDETESTK 129
G+ C+ C +H AK C + + +K C C+ H + +CP K + S +
Sbjct: 24 GDRCYNCGGLDHHAKECKLPPQPKK---CHFCQSISHMVASCPLKAQQGPSAQ 73
Score = 28.1 bits (61), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 19/45 (42%), Gaps = 5/45 (11%)
Query: 131 CYNCGQAGHSLAQCPQPLQDGGTKFASCFICKEQGHLSKNCPQNA 175
CYNCG H +C P Q C C+ H+ +CP A
Sbjct: 27 CYNCGGLDHHAKECKLPPQP-----KKCHFCQSISHMVASCPLKA 66
>pdb|2YSA|A Chain A, Solution Structure Of The Zinc Finger Cchc Domain From The
Human Retinoblastoma-Binding Protein 6 (Retinoblastoma-
Binding Q Protein 1, Rbq-1)
Length = 55
Score = 27.7 bits (60), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 11/24 (45%), Positives = 14/24 (58%)
Query: 152 GTKFASCFICKEQGHLSKNCPQNA 175
G+ +CF C + GH KNCP N
Sbjct: 4 GSSGYTCFRCGKPGHYIKNCPTNG 27
>pdb|3NYB|B Chain B, Structure And Function Of The Polymerase Core Of Tramp, A
Rna Surveillance Complex
Length = 83
Score = 27.3 bits (59), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 32/76 (42%), Gaps = 22/76 (28%)
Query: 97 AEWEKNKICLVCRRRGHTLKNCPSKN------DETESTK---------LCYNCGQAGHSL 141
W+K + C +C+ + H+ + CPS D+ E K CYNCG GH
Sbjct: 1 GSWKKVQ-CTLCKSKKHSKERCPSIWRAYILVDDNEKAKPKVLPFHTIYCYNCGGKGHFG 59
Query: 142 AQCPQ------PLQDG 151
C + P +DG
Sbjct: 60 DDCKEKRSSRVPNEDG 75
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.317 0.133 0.424
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,746,336
Number of Sequences: 62578
Number of extensions: 300261
Number of successful extensions: 647
Number of sequences better than 100.0: 30
Number of HSP's better than 100.0 without gapping: 19
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 506
Number of HSP's gapped (non-prelim): 101
length of query: 281
length of database: 14,973,337
effective HSP length: 98
effective length of query: 183
effective length of database: 8,840,693
effective search space: 1617846819
effective search space used: 1617846819
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)