RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy3970
(104 letters)
>1d9n_A Methyl-CPG-binding protein MBD1; PCM1, methylation, DNA binding
domain, gene regulation; NMR {Homo sapiens} SCOP:
d.10.1.3 PDB: 1ig4_A*
Length = 75
Score = 83.1 bits (205), Expect = 6e-23
Identities = 24/69 (34%), Positives = 37/69 (53%)
Query: 21 KKRYECPQLPPGWYREEVTRNKGLSVGKVDVFYYSPCGKKLRTRSEVLQVIRGNIPGVSF 80
+ +CP L PGW R EV R G + G+ D +Y SP G ++R++ E+ + + F
Sbjct: 3 EDWLDCPALGPGWKRREVFRKSGATCGRSDTYYQSPTGDRIRSKVELTRYLGPACDLTLF 62
Query: 81 DFRSGKLNS 89
DF+ G L
Sbjct: 63 DFKQGILCY 71
>2ky8_A Methyl-CPG-binding domain protein 2; DNA binding domain,
transcription-DNA complex; HET: DNA 5CM TED; NMR
{Gallus gallus}
Length = 72
Score = 83.0 bits (205), Expect = 8e-23
Identities = 32/67 (47%), Positives = 46/67 (68%)
Query: 21 KKRYECPQLPPGWYREEVTRNKGLSVGKVDVFYYSPCGKKLRTRSEVLQVIRGNIPGVSF 80
+ R +CP LPPGW +EEV R GLS GK DV+Y+SP GKK R++ ++ + + + F
Sbjct: 5 QGRTDCPALPPGWKKEEVIRKSGLSAGKSDVYYFSPSGKKFRSKPQLARYLGNAVDLSCF 64
Query: 81 DFRSGKL 87
DFR+GK+
Sbjct: 65 DFRTGKM 71
>3c2i_A Methyl-CPG-binding protein 2; water mediated recognition; HET:
DNA 5CM; 2.50A {Homo sapiens} PDB: 1qk9_A
Length = 97
Score = 69.4 bits (169), Expect = 3e-17
Identities = 24/82 (29%), Positives = 35/82 (42%), Gaps = 4/82 (4%)
Query: 20 TKKRYECPQLPPGWYREEVTRNKGLSVGKVDVFYYSPCGKKLRTRSEVLQVIRGN----I 75
Y+ P LP GW R+ R G S GK DV+ +P GK R++ E++ +
Sbjct: 15 RGPMYDDPTLPEGWTRKLKQRKSGRSAGKYDVYLINPQGKAFRSKVELIMYFEKVGDTSL 74
Query: 76 PGVSFDFRSGKLNSLQKHRNKQ 97
FDF S +H +
Sbjct: 75 DPNDFDFTVTGRGSPSRHHHHH 96
>1ub1_A MECP2, attachment region binding protein; chicken
methyl-CPG-binding protein 2 (cmecp2), MAR-binding
protein (ARBP), spectroscopy; NMR {Gallus gallus} SCOP:
d.10.1.3
Length = 133
Score = 68.0 bits (165), Expect = 3e-16
Identities = 23/81 (28%), Positives = 34/81 (41%), Gaps = 4/81 (4%)
Query: 21 KKRYECPQLPPGWYREEVTRNKGLSVGKVDVFYYSPCGKKLRTRSEVLQVIRGN----IP 76
Y+ P LP GW R+ R G S GK DV+ +P GK R++ E++ +
Sbjct: 30 GPMYDDPTLPEGWTRKLKQRKSGRSAGKYDVYLINPQGKAFRSKVELIAYFEKVGDTSLD 89
Query: 77 GVSFDFRSGKLNSLQKHRNKQ 97
FDF S + +
Sbjct: 90 PNDFDFTVTGRGSPSRREQRP 110
>1v7w_A Chitobiose phosphorylase; beta-sandwich, (alpha/alpha)6 barrel,
transferase; HET: NDG NAG; 1.60A {Vibrio proteolyticus}
SCOP: a.102.1.4 b.30.5.3 PDB: 1v7v_A* 1v7x_A*
Length = 807
Score = 26.2 bits (57), Expect = 2.2
Identities = 16/71 (22%), Positives = 27/71 (38%), Gaps = 5/71 (7%)
Query: 9 SLVSNLLKMLPTKKRYEC-PQLPPGWYREEVTRNKGLSVGKVDVFYYSPCGKKLRTRSEV 67
++ + +L + P +P W EVTR + + V +P +S
Sbjct: 718 AVTNYILGVQSGFTGLSVDPCIPSDWPGFEVTRQWRGATYHIQV--ENPDHVSKGVKSIT 775
Query: 68 L--QVIRGNIP 76
L I+G IP
Sbjct: 776 LNGAPIQGRIP 786
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 26.0 bits (56), Expect = 3.1
Identities = 21/94 (22%), Positives = 33/94 (35%), Gaps = 21/94 (22%)
Query: 18 LPTKKRYEC--PQLPPGWYREEVTR--NKGLSVGKVDVFYYSPCGKKLRT-----RSEVL 68
L + + E P + Y E+ R N K +V P KLR R
Sbjct: 94 LMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPY-LKLRQALLELRPAKN 152
Query: 69 QVIRGNIPGVSFDFRSGK----LNSLQKHRNKQR 98
+I G + G SGK L+ ++ + +
Sbjct: 153 VLIDG-VLG------SGKTWVALDVCLSYKVQCK 179
Score = 25.6 bits (55), Expect = 4.2
Identities = 10/97 (10%), Positives = 20/97 (20%), Gaps = 32/97 (32%)
Query: 1 MLANDSPLSLVSNLLKMLPTKKRYECPQLPPGWYREEVT---RNKGLSVGKVDVFYYSPC 57
+ + + + LL ++ V L + S
Sbjct: 380 VFPPSAHIP--TILLSLIWFDVIKSDV--------MVVVNKLHKYSLVEKQPKESTIS-- 427
Query: 58 GKKLRTRSEVLQVIRGNIPGVSFDFRSGKLNSLQKHR 94
IP + + + N HR
Sbjct: 428 -----------------IPSIYLELKVKLENEYALHR 447
>1qme_A Penicillin-binding protein 2X; peptidoglycan synthesis,
resistance, cell WALL, transmembrane; 2.4A
{Streptococcus pneumoniae} SCOP: d.11.1.1 d.11.1.1
d.175.1.1 e.3.1.1 PDB: 1qmf_A* 1pyy_A* 1rp5_A 1pmd_A
1k25_A 2zc3_B* 2z2l_B* 2z2m_B* 2zc4_B* 2zc3_A* 2z2l_A*
2z2m_A* 2zc4_A* 2zc3_C* 2z2l_C* 2z2m_C* 2zc4_C*
Length = 702
Score = 24.7 bits (54), Expect = 6.6
Identities = 6/29 (20%), Positives = 10/29 (34%)
Query: 47 GKVDVFYYSPCGKKLRTRSEVLQVIRGNI 75
G + KK+ + + RG I
Sbjct: 3 GTRFGTDLAKEAKKVHQTTRTVPAKRGTI 31
>3e90_B NS3 protease; trypsin-like serine protease, protease inhibitor,
catalytic histidine, induced FIT, ATP-binding, capsid
protein, helicase; HET: NKK; 2.45A {West nile virus}
Length = 198
Score = 24.2 bits (52), Expect = 9.4
Identities = 11/47 (23%), Positives = 16/47 (34%), Gaps = 5/47 (10%)
Query: 12 SNLLKMLPTKKRYECPQLPPGWYREEV-----TRNKGLSVGKVDVFY 53
+L P+ K Y+ G YR + G V VF+
Sbjct: 5 GGVLWDTPSPKEYKKGDTTTGVYRIMTRGLLGSYQAGAGVMVEGVFH 51
>2dc4_A PH1012 protein, 165AA long hypothetical protein; dimer, X-RAY
diffraction, structural genomics, NPPSFA; 1.65A
{Pyrococcus horikoshii}
Length = 165
Score = 24.1 bits (52), Expect = 9.8
Identities = 7/17 (41%), Positives = 10/17 (58%)
Query: 48 KVDVFYYSPCGKKLRTR 64
+ DV++ P K LR R
Sbjct: 31 QEDVYFELPSPKLLRVR 47
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
0.318 0.137 0.412
Gapped
Lambda K H
0.267 0.0571 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,502,210
Number of extensions: 75701
Number of successful extensions: 165
Number of sequences better than 10.0: 1
Number of HSP's gapped: 165
Number of HSP's successfully gapped: 10
Length of query: 104
Length of database: 6,701,793
Length adjustment: 69
Effective length of query: 35
Effective length of database: 4,775,244
Effective search space: 167133540
Effective search space used: 167133540
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (23.8 bits)