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= psy13437
(80 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2DIQ|A Chain A, Solution Structure Of The Tudor Domain Of Tudor And Kh
Domain Containing Protein
Length = 110
Score = 58.2 bits (139), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 29/65 (44%), Positives = 39/65 (60%), Gaps = 1/65 (1%)
Query: 2 GGWFRAQILAVDVVNASCQVKFVDYGGYLTLETSALRQIRADFLSLPFQAIECGLANIVP 61
G W+RA++L + N + + FVD+G LR +R+DFLSLPFQAIEC LA I
Sbjct: 47 GSWYRARVLGT-LENGNLDLYFVDFGDNGDCPLKDLRALRSDFLSLPFQAIECSLARIAS 105
Query: 62 VGTDG 66
+ G
Sbjct: 106 GPSSG 110
>pdb|3FDR|A Chain A, Crystal Structure Of Tdrd2
Length = 94
Score = 53.9 bits (128), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 25/54 (46%), Positives = 34/54 (62%), Gaps = 1/54 (1%)
Query: 2 GGWFRAQILAVDVVNASCQVKFVDYGGYLTLETSALRQIRADFLSLPFQAIECG 55
G W+RA++L + N + + FVD+G LR +R+DFLSLPFQAIEC
Sbjct: 42 GSWYRARVLGT-LENGNLDLYFVDFGDNGDCPLKDLRALRSDFLSLPFQAIECS 94
>pdb|4B9X|A Chain A, Structure Of Extended Tudor Domain Td3 From Mouse Tdrd1
Length = 226
Score = 47.0 bits (110), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 23/60 (38%), Positives = 35/60 (58%), Gaps = 1/60 (1%)
Query: 2 GGWFRAQILAVDVVNASCQVKFVDYGGYLTLETSALRQIRADFLSLPFQAIECGLANIVP 61
G W+RA + + + + + +V FVDYG + T L+ I FL LPFQ ++C L +I P
Sbjct: 80 GNWYRALVKEI-LPSGNVKVHFVDYGNVEEVTTDQLQAILPQFLLLPFQGMQCWLVDIQP 138
>pdb|4B9W|A Chain A, Structure Of Extended Tudor Domain Td3 From Mouse Tdrd1 In
Complex With Mili Peptide Containing Dimethylarginine
45.
pdb|4B9W|B Chain B, Structure Of Extended Tudor Domain Td3 From Mouse Tdrd1 In
Complex With Mili Peptide Containing Dimethylarginine 45
Length = 201
Score = 47.0 bits (110), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 23/60 (38%), Positives = 35/60 (58%), Gaps = 1/60 (1%)
Query: 2 GGWFRAQILAVDVVNASCQVKFVDYGGYLTLETSALRQIRADFLSLPFQAIECGLANIVP 61
G W+RA + + + + + +V FVDYG + T L+ I FL LPFQ ++C L +I P
Sbjct: 80 GNWYRALVKEI-LPSGNVKVHFVDYGNVEEVTTDQLQAILPQFLLLPFQGMQCWLVDIQP 138
>pdb|2WAC|A Chain A, Extended Tudor Domain Of Drosophila Melanogaster Tudor-Sn
( P100)
pdb|2WAC|B Chain B, Extended Tudor Domain Of Drosophila Melanogaster Tudor-Sn
( P100)
Length = 218
Score = 35.4 bits (80), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 24/64 (37%), Positives = 34/64 (53%), Gaps = 3/64 (4%)
Query: 4 WFRAQILAVDVVNASCQVKFVDYGGYLTLETSALRQIRADFLSLPFQAIECGLANIVPVG 63
W+RA++ V NA+ V ++DYG TL T+ L + F S A E LA +V +
Sbjct: 68 WYRAKVERVQGSNAT--VLYIDYGNKETLPTNRLAALPPAFSSEKPYATEYALA-LVALP 124
Query: 64 TDGE 67
TD E
Sbjct: 125 TDNE 128
>pdb|3PNW|C Chain C, Crystal Structure Of The Tudor Domain Of Human Tdrd3 In
Complex With An Anti-tdrd3 Fab
pdb|3PNW|F Chain F, Crystal Structure Of The Tudor Domain Of Human Tdrd3 In
Complex With An Anti-tdrd3 Fab
pdb|3PNW|I Chain I, Crystal Structure Of The Tudor Domain Of Human Tdrd3 In
Complex With An Anti-tdrd3 Fab
pdb|3PNW|L Chain L, Crystal Structure Of The Tudor Domain Of Human Tdrd3 In
Complex With An Anti-tdrd3 Fab
pdb|3PNW|O Chain O, Crystal Structure Of The Tudor Domain Of Human Tdrd3 In
Complex With An Anti-tdrd3 Fab
pdb|3PNW|R Chain R, Crystal Structure Of The Tudor Domain Of Human Tdrd3 In
Complex With An Anti-tdrd3 Fab
pdb|3PNW|U Chain U, Crystal Structure Of The Tudor Domain Of Human Tdrd3 In
Complex With An Anti-tdrd3 Fab
pdb|3PNW|X Chain X, Crystal Structure Of The Tudor Domain Of Human Tdrd3 In
Complex With An Anti-tdrd3 Fab
Length = 77
Score = 29.3 bits (64), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 12/39 (30%), Positives = 23/39 (58%)
Query: 5 FRAQILAVDVVNASCQVKFVDYGGYLTLETSALRQIRAD 43
+RA++ A+ + VKF+DYG Y + S ++ I+ +
Sbjct: 35 YRAEVEALHSSGMTAVVKFIDYGNYEEVLLSNIKPIQTE 73
>pdb|3PMT|A Chain A, Crystal Structure Of The Tudor Domain Of Human Tudor
Domain-Containing Protein 3
Length = 59
Score = 28.9 bits (63), Expect = 0.72, Method: Compositional matrix adjust.
Identities = 12/39 (30%), Positives = 23/39 (58%)
Query: 5 FRAQILAVDVVNASCQVKFVDYGGYLTLETSALRQIRAD 43
+RA++ A+ + VKF+DYG Y + S ++ I+ +
Sbjct: 21 YRAEVEALHSSGMTAVVKFIDYGNYEEVLLSNIKPIQTE 59
>pdb|2LIV|A Chain A, Periplasmic Binding Protein Structure And Function.
Refined X-Ray Structures Of The
LeucineISOLEUCINEVALINE-Binding Protein And Its Complex
With Leucine
Length = 344
Score = 28.1 bits (61), Expect = 1.2, Method: Composition-based stats.
Identities = 21/56 (37%), Positives = 26/56 (46%), Gaps = 1/56 (1%)
Query: 21 VKFVDYGGYLTLETSALRQIRADFLSLPFQAIECGLANIVPVGTDGEYNIILIVER 76
+ FV YGGY LRQ RA L F E G+AN+ GE L+V +
Sbjct: 194 IDFVYYGGYHPEMGQILRQARAAGLKTQFMGPE-GVANVSLSNIAGESAEGLLVTK 248
>pdb|1Z15|A Chain A, Crystal Structure Analysis Of Periplasmic
Leu/ile/val-binding Protein In Superopen Form
pdb|1Z16|A Chain A, Crystal Structure Analysis Of Periplasmic
Leu/ile/val-binding Protein With Bound Leucine
pdb|1Z17|A Chain A, Crystal Structure Analysis Of Periplasmic
LeuILEVAL-Binding Protein With Bound Ligand Isoleucine
pdb|1Z18|A Chain A, Crystal Structure Analysis Of Periplasmic
LeuILEVAL-Binding Protein With Bound Valine
Length = 344
Score = 28.1 bits (61), Expect = 1.2, Method: Composition-based stats.
Identities = 21/56 (37%), Positives = 26/56 (46%), Gaps = 1/56 (1%)
Query: 21 VKFVDYGGYLTLETSALRQIRADFLSLPFQAIECGLANIVPVGTDGEYNIILIVER 76
+ FV YGGY LRQ RA L F E G+AN+ GE L+V +
Sbjct: 194 IDFVYYGGYHPEMGQILRQARAAGLKTQFMGPE-GVANVSLSNIAGESAEGLLVTK 248
>pdb|2LTO|A Chain A, Tdrd3 Complex
Length = 58
Score = 27.7 bits (60), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 12/36 (33%), Positives = 21/36 (58%)
Query: 5 FRAQILAVDVVNASCQVKFVDYGGYLTLETSALRQI 40
+RA++ A+ + VKF+DYG Y + S ++ I
Sbjct: 21 YRAEVEALHSSGMTAVVKFIDYGNYEEVLLSNIKPI 56
>pdb|3S6W|A Chain A, Crystal Structure Of Tudor Domain Of Human Tdrd3
Length = 54
Score = 27.7 bits (60), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 12/36 (33%), Positives = 21/36 (58%)
Query: 5 FRAQILAVDVVNASCQVKFVDYGGYLTLETSALRQI 40
+RA++ A+ + VKF+DYG Y + S ++ I
Sbjct: 19 YRAEVEALHSSGMTAVVKFIDYGNYEEVLLSNIKPI 54
>pdb|2D9T|A Chain A, Solution Structure Of The Tudor Domain Of Tudor Domain
Containing Protein 3 From Mouse
Length = 78
Score = 27.7 bits (60), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 11/39 (28%), Positives = 22/39 (56%)
Query: 5 FRAQILAVDVVNASCQVKFVDYGGYLTLETSALRQIRAD 43
+RA++ A+ + VKF DYG Y + S ++ ++ +
Sbjct: 27 YRAEVEALHSSGMTAVVKFTDYGNYEEVLLSNIKPVQTE 65
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
0.325 0.144 0.431
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,306,671
Number of Sequences: 62578
Number of extensions: 71213
Number of successful extensions: 284
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 274
Number of HSP's gapped (non-prelim): 14
length of query: 80
length of database: 14,973,337
effective HSP length: 49
effective length of query: 31
effective length of database: 11,907,015
effective search space: 369117465
effective search space used: 369117465
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 45 (21.9 bits)