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= 002603
(902 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2GFU|A Chain A, Nmr Solution Structure Of The Pwwp Domain Of Mismatch
Repair Protein Hmsh6
Length = 134
Score = 45.4 bits (106), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 31/63 (49%), Gaps = 2/63 (3%)
Query: 161 EFCVGDFVWGKIKSYPWWPGQIYDSSDASDYALKVKPRDRLLVAYFD--GTFAWCHPSQL 218
+F GD VW K++ YPWWP +Y+ + + R+ V +FD T W L
Sbjct: 22 DFSPGDLVWAKMEGYPWWPSLVYNHPFDGTFIREKGKSVRVHVQFFDDSPTRGWVSKRLL 81
Query: 219 KPF 221
KP+
Sbjct: 82 KPY 84
>pdb|1KHC|A Chain A, Crystal Structure Of The Pwwp Domain Of Mammalian Dna
Methyltransferase Dnmt3b
Length = 147
Score = 45.1 bits (105), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 36/129 (27%), Positives = 57/129 (44%), Gaps = 16/129 (12%)
Query: 161 EFCVGDFVWGKIKSYPWWPGQIYDSSDASDYALKVKPRDRLLVAYFDGTFAWCHPSQLKP 220
EF +GD VWGKIK + WWP + S + P R + + DG F+ +L
Sbjct: 11 EFGIGDLVWGKIKGFSWWPAMVVSWKATSK--RQAMPGMRWVQWFGDGKFSEISADKLVA 68
Query: 221 ---FEKNFEDMSRQ---SSSKSFVNAVQNAVHEIGRLVELKMTCSCVPKESLDGLARPL- 273
F ++F + S K+ + ++ A G+ T S P ESL+ +P+
Sbjct: 69 LGLFSQHFNLATFNKLVSYRKAMYHTLEKARVRAGK------TFSSSPGESLEDQLKPML 122
Query: 274 -AANSGVRP 281
A+ G +P
Sbjct: 123 EWAHGGFKP 131
>pdb|3FLG|A Chain A, The Pwwp Domain Of Human Dna
(Cytosine-5-)-Methyltransferase 3 Beta
pdb|3QKJ|A Chain A, The Pwwp Domain Of Human Dna
(Cytosine-5-)-Methyltransferase 3 Beta In Complex With A
Bis-Tris Molecule
pdb|3QKJ|B Chain B, The Pwwp Domain Of Human Dna
(Cytosine-5-)-Methyltransferase 3 Beta In Complex With A
Bis-Tris Molecule
pdb|3QKJ|C Chain C, The Pwwp Domain Of Human Dna
(Cytosine-5-)-Methyltransferase 3 Beta In Complex With A
Bis-Tris Molecule
pdb|3QKJ|D Chain D, The Pwwp Domain Of Human Dna
(Cytosine-5-)-Methyltransferase 3 Beta In Complex With A
Bis-Tris Molecule
Length = 151
Score = 43.1 bits (100), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 18/38 (47%), Positives = 23/38 (60%), Gaps = 1/38 (2%)
Query: 145 SDSEKGEEDNSSDGNYEFCVGDFVWGKIKSYPWWPGQI 182
+DS G+ DG EF +GD VWGKIK + WWP +
Sbjct: 3 ADSGDGDSSEYQDGK-EFGIGDLVWGKIKGFSWWPAMV 39
>pdb|4FU6|A Chain A, Crystal Structure Of The Psip1 Pwwp Domain
Length = 153
Score = 42.7 bits (99), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 24/79 (30%), Positives = 39/79 (49%), Gaps = 7/79 (8%)
Query: 161 EFCVGDFVWGKIKSYPWWPGQIYDSSDASDYALKVKPRDRLLVAYFDGTF--AWCHPSQL 218
+F GD ++ K+K YP WP ++ + D + VKP L +F GT A+ P +
Sbjct: 22 DFKPGDLIFAKMKGYPHWPARVDEVPDGA-----VKPPTNKLPIFFFGTHETAFLGPKDI 76
Query: 219 KPFEKNFEDMSRQSSSKSF 237
P+ +N E + + K F
Sbjct: 77 FPYSENKEKYGKPNKRKGF 95
>pdb|3QBY|A Chain A, Crystal Structure Of The Pwwp Domain Of Human
Hepatoma-Derived Growth Factor 2
pdb|3QBY|B Chain B, Crystal Structure Of The Pwwp Domain Of Human
Hepatoma-Derived Growth Factor 2
pdb|3QBY|C Chain C, Crystal Structure Of The Pwwp Domain Of Human
Hepatoma-Derived Growth Factor 2
pdb|3QJ6|A Chain A, The Crystal Structure Of Pwwp Domain Of Human
Hepatoma-Derived Growth Factor 2 In Complex With
H3k79me3 Peptide
Length = 94
Score = 42.0 bits (97), Expect = 0.001, Method: Composition-based stats.
Identities = 29/92 (31%), Positives = 43/92 (46%), Gaps = 10/92 (10%)
Query: 160 YEFCVGDFVWGKIKSYPWWPGQIYDSSDASDYALKVKPRDRLLVAYFDGTF--AWCHPSQ 217
+ F GD V+ K+K YP WP +I D +D + VKP +F GT A+ P
Sbjct: 4 HAFKPGDLVFAKMKGYPHWPARIDDIADGA-----VKPPPNKYPIFFFGTHETAFLGPKD 58
Query: 218 LKPFEKNFEDMSRQSSSKSFVNA---VQNAVH 246
L P++K + + + K F +QN H
Sbjct: 59 LFPYDKCKDKYGKPNKRKGFNEGLWEIQNNPH 90
>pdb|3EAE|A Chain A, Pwwp Domain Of Human Hepatoma-Derived Growth Factor 2
(Hdgf2)
pdb|3EAE|B Chain B, Pwwp Domain Of Human Hepatoma-Derived Growth Factor 2
(Hdgf2)
Length = 93
Score = 42.0 bits (97), Expect = 0.002, Method: Composition-based stats.
Identities = 29/92 (31%), Positives = 43/92 (46%), Gaps = 10/92 (10%)
Query: 160 YEFCVGDFVWGKIKSYPWWPGQIYDSSDASDYALKVKPRDRLLVAYFDGTF--AWCHPSQ 217
+ F GD V+ K+K YP WP +I D +D + VKP +F GT A+ P
Sbjct: 3 HAFKPGDLVFAKMKGYPHWPARIDDIADGA-----VKPPPNKYPIFFFGTHETAFLGPKD 57
Query: 218 LKPFEKNFEDMSRQSSSKSFVNA---VQNAVH 246
L P++K + + + K F +QN H
Sbjct: 58 LFPYDKCKDKYGKPNKRKGFNEGLWEIQNNPH 89
>pdb|2M16|A Chain A, P75/ledgf Pwwp Domain
Length = 97
Score = 39.7 bits (91), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 24/79 (30%), Positives = 39/79 (49%), Gaps = 7/79 (8%)
Query: 161 EFCVGDFVWGKIKSYPWWPGQIYDSSDASDYALKVKPRDRLLVAYFDGTF--AWCHPSQL 218
+F GD ++ K+K YP WP ++ + D + VKP L +F GT A+ P +
Sbjct: 8 DFKPGDLIFAKMKGYPHWPARVDEVPDGA-----VKPPTNKLPIFFFGTHETAFLGPKDI 62
Query: 219 KPFEKNFEDMSRQSSSKSF 237
P+ +N E + + K F
Sbjct: 63 FPYSENKEKYGKPNKRKGF 81
>pdb|2B8A|A Chain A, High Resolution Structure Of The Hdgf Pwwp Domain
Length = 110
Score = 37.7 bits (86), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 25/79 (31%), Positives = 39/79 (49%), Gaps = 7/79 (8%)
Query: 161 EFCVGDFVWGKIKSYPWWPGQIYDSSDASDYALKVKPRDRLLVAYFDGTF--AWCHPSQL 218
E+ GD V+ K+K YP WP +I + +A+ VK +F GT A+ P L
Sbjct: 9 EYKCGDLVFAKMKGYPHWPARIDEMPEAA-----VKSTANKYQVFFFGTHETAFLGPKDL 63
Query: 219 KPFEKNFEDMSRQSSSKSF 237
P+E++ E + + K F
Sbjct: 64 FPYEESKEKFGKPNKRKGF 82
>pdb|1RI0|A Chain A, Nmr Structure Of The N-Terminal Hath Domain Of Human Hdgf
Length = 110
Score = 37.7 bits (86), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 25/79 (31%), Positives = 39/79 (49%), Gaps = 7/79 (8%)
Query: 161 EFCVGDFVWGKIKSYPWWPGQIYDSSDASDYALKVKPRDRLLVAYFDGTF--AWCHPSQL 218
E+ GD V+ K+K YP WP +I + +A+ VK +F GT A+ P L
Sbjct: 19 EYKCGDLVFAKMKGYPHWPARIDEMPEAA-----VKSTANKYQVFFFGTHETAFLGPKDL 73
Query: 219 KPFEKNFEDMSRQSSSKSF 237
P+E++ E + + K F
Sbjct: 74 FPYEESKEKFGKPNKRKGF 92
>pdb|2NLU|A Chain A, Domain-Swapped Dimer Of The Pwwp Module Of Human Hepatoma-
Derived Growth Factor
pdb|2NLU|B Chain B, Domain-Swapped Dimer Of The Pwwp Module Of Human Hepatoma-
Derived Growth Factor
Length = 100
Score = 37.7 bits (86), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 25/79 (31%), Positives = 39/79 (49%), Gaps = 7/79 (8%)
Query: 161 EFCVGDFVWGKIKSYPWWPGQIYDSSDASDYALKVKPRDRLLVAYFDGTF--AWCHPSQL 218
E+ GD V+ K+K YP WP +I + +A+ VK +F GT A+ P L
Sbjct: 9 EYKCGDLVFAKMKGYPHWPARIDEMPEAA-----VKSTANKYQVFFFGTHETAFLGPKDL 63
Query: 219 KPFEKNFEDMSRQSSSKSF 237
P+E++ E + + K F
Sbjct: 64 FPYEESKEKFGKPNKRKGF 82
>pdb|3LLR|A Chain A, Crystal Structure Of The Pwwp Domain Of Human Dna
(Cytosine-5-)- Methyltransferase 3 Alpha
pdb|3LLR|B Chain B, Crystal Structure Of The Pwwp Domain Of Human Dna
(Cytosine-5-)- Methyltransferase 3 Alpha
pdb|3LLR|C Chain C, Crystal Structure Of The Pwwp Domain Of Human Dna
(Cytosine-5-)- Methyltransferase 3 Alpha
pdb|3LLR|D Chain D, Crystal Structure Of The Pwwp Domain Of Human Dna
(Cytosine-5-)- Methyltransferase 3 Alpha
pdb|3LLR|E Chain E, Crystal Structure Of The Pwwp Domain Of Human Dna
(Cytosine-5-)- Methyltransferase 3 Alpha
Length = 154
Score = 36.2 bits (82), Expect = 0.092, Method: Compositional matrix adjust.
Identities = 11/21 (52%), Positives = 17/21 (80%)
Query: 162 FCVGDFVWGKIKSYPWWPGQI 182
F +G+ VWGK++ + WWPG+I
Sbjct: 17 FGIGELVWGKLRGFSWWPGRI 37
>pdb|1N27|A Chain A, Solution Structure Of The Pwwp Domain Of Mouse Hepatoma-
Derived Growth Factor, Related Protein 3
Length = 96
Score = 34.7 bits (78), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 25/86 (29%), Positives = 41/86 (47%), Gaps = 7/86 (8%)
Query: 154 NSSDGNYEFCVGDFVWGKIKSYPWWPGQIYDSSDASDYALKVKPRDRLLVAYFDGTF--A 211
SS + E+ GD V+ K+K YP WP +I + + + VKP +F GT A
Sbjct: 1 GSSGSSGEYKAGDLVFAKMKGYPHWPARIDELPEGA-----VKPPANKYPIFFFGTHETA 55
Query: 212 WCHPSQLKPFEKNFEDMSRQSSSKSF 237
+ P L P+++ + + + K F
Sbjct: 56 FLGPKDLFPYKEYKDKFGKSNKRKGF 81
>pdb|1W25|A Chain A, Response Regulator Pled In Complex With C-digmp
pdb|1W25|B Chain B, Response Regulator Pled In Complex With C-digmp
pdb|2V0N|A Chain A, Activated Response Regulator Pled In Complex With C-Digmp
And Gtp-Alpha-S
pdb|2V0N|B Chain B, Activated Response Regulator Pled In Complex With C-Digmp
And Gtp-Alpha-S
Length = 459
Score = 30.4 bits (67), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 36/75 (48%), Gaps = 1/75 (1%)
Query: 626 MTKAAGNLIGSKSPANLMCSDEVVRKKDAKNVGAEHEKSDSSNPEKMKPDQRTVVDTMKV 685
+ AA L G ++ +E ++ A +G EH S+PEK K VD + V
Sbjct: 141 IAGAAARLDGLGGRVLIVDDNERQAQRVAAELGVEHRPVIESDPEKAKISAGGPVDLVIV 200
Query: 686 KASAKDVISGIRSTA 700
A+AK+ G+R TA
Sbjct: 201 NAAAKN-FDGLRFTA 214
>pdb|2L89|A Chain A, Solution Structure Of Pdp1 Pwwp Domain Reveals Its Unique
Binding Sites For Methylated H4k20 And Dna
Length = 108
Score = 30.0 bits (66), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 31/70 (44%), Gaps = 6/70 (8%)
Query: 155 SSDGNYEFCVGDFVWGKIKSYPWWPGQIYDSSDASDYALKVKPRDRLL--VAYF-DGTFA 211
S+D F GD + K YPWWP + + D +L +L V +F D FA
Sbjct: 1 SADDRLNF--GDRILVKAPGYPWWPALLLRRKETKD-SLNTNSSFNVLYKVLFFPDFNFA 57
Query: 212 WCHPSQLKPF 221
W + +KP
Sbjct: 58 WVKRNSVKPL 67
>pdb|2DAQ|A Chain A, Solution Structure Of Second Pwwp Domain Of Whsc1l1
Protein
Length = 110
Score = 30.0 bits (66), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 26/95 (27%), Positives = 46/95 (48%), Gaps = 9/95 (9%)
Query: 168 VWGKIKSYPWWPGQIYD--SSDASDYALKVKPRDRLLVAYFDGTFAWCHPSQLKPF---E 222
VW K+ +Y WWP +I + S + LK D + + + W H ++ P+ +
Sbjct: 15 VWVKLGNYRWWPAEICNPRSVPLNIQGLKHDLGDFPVFFFGSHDYYWVHQGRVFPYVEGD 74
Query: 223 KNFEDMSRQSSSKSFVNAVQNAVHEIGRLVELKMT 257
K+F + + S +K+F A++ A R ELK +
Sbjct: 75 KSFAE-GQTSINKTFKKALEEAAK---RFQELKAS 105
>pdb|2WB4|A Chain A, Activated Diguanylate Cyclase Pled In Complex With
C-Di-Gmp
pdb|2WB4|B Chain B, Activated Diguanylate Cyclase Pled In Complex With
C-Di-Gmp
Length = 459
Score = 30.0 bits (66), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 36/75 (48%), Gaps = 1/75 (1%)
Query: 626 MTKAAGNLIGSKSPANLMCSDEVVRKKDAKNVGAEHEKSDSSNPEKMKPDQRTVVDTMKV 685
+ AA L G ++ +E ++ A +G EH S+PEK K VD + V
Sbjct: 142 IAGAAARLDGLGGRVLIVDDNERQAQRVAAELGVEHRPVIESDPEKAKISAGGPVDLVIV 201
Query: 686 KASAKDVISGIRSTA 700
A+AK+ G+R TA
Sbjct: 202 NAAAKN-FDGLRFTA 215
>pdb|3QED|A Chain A, The Structure And Function Of An Arabinan-Specific
Alpha-1,2- Arabinofuranosidase Identified From Screening
The Activities Of Bacterial Gh43 Glycoside Hydrolases
pdb|3QED|B Chain B, The Structure And Function Of An Arabinan-Specific
Alpha-1,2- Arabinofuranosidase Identified From Screening
The Activities Of Bacterial Gh43 Glycoside Hydrolases
pdb|3QED|C Chain C, The Structure And Function Of An Arabinan-Specific
Alpha-1,2- Arabinofuranosidase Identified From Screening
The Activities Of Bacterial Gh43 Glycoside Hydrolases
pdb|3QED|D Chain D, The Structure And Function Of An Arabinan-Specific
Alpha-1,2- Arabinofuranosidase Identified From Screening
The Activities Of Bacterial Gh43 Glycoside Hydrolases
Length = 314
Score = 30.0 bits (66), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 16/43 (37%), Positives = 23/43 (53%), Gaps = 3/43 (6%)
Query: 114 GREDGGDFNRREDVGSLNEKRENPDGEIREMSDSEKGEEDNSS 156
GR DGG + R S++E NPDG I+ + + +G N S
Sbjct: 266 GRPDGGQYRRSV---SIDELFYNPDGTIKRIVXTTEGVAPNKS 305
>pdb|3PMI|A Chain A, Pwwp Domain Of Human Mutated Melanoma-Associated Antigen 1
pdb|3PMI|B Chain B, Pwwp Domain Of Human Mutated Melanoma-Associated Antigen 1
pdb|3PMI|C Chain C, Pwwp Domain Of Human Mutated Melanoma-Associated Antigen 1
pdb|3PMI|D Chain D, Pwwp Domain Of Human Mutated Melanoma-Associated Antigen 1
Length = 134
Score = 29.6 bits (65), Expect = 8.7, Method: Compositional matrix adjust.
Identities = 11/21 (52%), Positives = 13/21 (61%)
Query: 162 FCVGDFVWGKIKSYPWWPGQI 182
F VG VW K K YP+WP +
Sbjct: 5 FEVGXLVWHKHKKYPFWPAVV 25
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
0.307 0.126 0.349
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 25,923,919
Number of Sequences: 62578
Number of extensions: 1095301
Number of successful extensions: 2130
Number of sequences better than 100.0: 30
Number of HSP's better than 100.0 without gapping: 18
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 2095
Number of HSP's gapped (non-prelim): 43
length of query: 902
length of database: 14,973,337
effective HSP length: 108
effective length of query: 794
effective length of database: 8,214,913
effective search space: 6522640922
effective search space used: 6522640922
T: 11
A: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.6 bits)
S2: 56 (26.2 bits)