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= psy4551
(321 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 = 66.6 bits (161), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 44/125 (35%), Positives = 60/125 (48%), Gaps = 32/125 (25%)
Query: 69 IELDQLVESMTDYYNQKANQETHRLTEVKPGQIVAALLHLDQKWYRAQVM-TVKPGQIVA 127
++LD+LV MT +Y ++ V G IVAA L + WYRA+V+ T++ G
Sbjct: 10 LQLDKLVNEMTQHYENSVPEDL----TVHVGDIVAAPLPTNGSWYRARVLGTLENGN--- 62
Query: 128 ALLHLDQKWYRAQVMTVSDSTPPTLELYFVDYGDSMDMPQPSVYQLNPTFLGLRFQAIEC 187
L+LYFVD+GD+ D P + L FL L FQAIEC
Sbjct: 63 ------------------------LDLYFVDFGDNGDCPLKDLRALRSDFLSLPFQAIEC 98
Query: 188 SLANV 192
SLA +
Sbjct: 99 SLARI 103
>pdb|3FDR|A Chain A, Crystal Structure Of Tdrd2
Length = 94
Score = 64.7 bits (156), Expect = 7e-11, Method: Compositional matrix adjust.
Identities = 43/123 (34%), Positives = 59/123 (47%), Gaps = 32/123 (26%)
Query: 67 RAIELDQLVESMTDYYNQKANQETHRLTEVKPGQIVAALLHLDQKWYRAQVM-TVKPGQI 125
R+++LD+LV MT +Y ++ V G IVAA L + WYRA+V+ T++ G
Sbjct: 3 RSLQLDKLVNEMTQHYENSVPEDL----TVHVGDIVAAPLPTNGSWYRARVLGTLENGN- 57
Query: 126 VAALLHLDQKWYRAQVMTVSDSTPPTLELYFVDYGDSMDMPQPSVYQLNPTFLGLRFQAI 185
L+LYFVD+GD+ D P + L FL L FQAI
Sbjct: 58 --------------------------LDLYFVDFGDNGDCPLKDLRALRSDFLSLPFQAI 91
Query: 186 ECS 188
ECS
Sbjct: 92 ECS 94
>pdb|4B9X|A Chain A, Structure Of Extended Tudor Domain Td3 From Mouse Tdrd1
Length = 226
Score = 60.5 bits (145), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 41/155 (26%), Positives = 71/155 (45%), Gaps = 31/155 (20%)
Query: 55 NPDRFWVQIMNDRAIE-LDQLVESMTDYYNQKANQETHRLTEVKPGQIVAALLHLDQKWY 113
+P F+ + D A+E LD L +S+ DY QK +
Sbjct: 28 SPGEFYCHFLKDDALEKLDDLNQSLADYCAQKPPNG-----------------------F 64
Query: 114 RAQVMTVKPGQIVAALLHLDQKWYRAQVMTVSDSTPPTLELYFVDYGDSMDMPQPSVYQL 173
+A++ G+ A D WYRA V + S ++++FVDYG+ ++ + +
Sbjct: 65 KAEI-----GRPCCAFFSGDGNWYRALVKEILPSG--NVKVHFVDYGNVEEVTTDQLQAI 117
Query: 174 NPTFLGLRFQAIECSLANVRPVGDVWSEEAISCFE 208
P FL L FQ ++C L +++P W++EA + F+
Sbjct: 118 LPQFLLLPFQGMQCWLVDIQPPNKHWTKEATARFQ 152
>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 = 59.7 bits (143), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 41/155 (26%), Positives = 71/155 (45%), Gaps = 31/155 (20%)
Query: 55 NPDRFWVQIMNDRAIE-LDQLVESMTDYYNQKANQETHRLTEVKPGQIVAALLHLDQKWY 113
+P F+ + D A+E LD L +S+ DY QK +
Sbjct: 28 SPGEFYCHFLKDDALEKLDDLNQSLADYCAQKPPNG-----------------------F 64
Query: 114 RAQVMTVKPGQIVAALLHLDQKWYRAQVMTVSDSTPPTLELYFVDYGDSMDMPQPSVYQL 173
+A++ G+ A D WYRA V + S ++++FVDYG+ ++ + +
Sbjct: 65 KAEI-----GRPCCAFFSGDGNWYRALVKEILPSG--NVKVHFVDYGNVEEVTTDQLQAI 117
Query: 174 NPTFLGLRFQAIECSLANVRPVGDVWSEEAISCFE 208
P FL L FQ ++C L +++P W++EA + F+
Sbjct: 118 LPQFLLLPFQGMQCWLVDIQPPNKHWTKEATARFQ 152
>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 = 54.3 bits (129), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 47/156 (30%), Positives = 72/156 (46%), Gaps = 21/156 (13%)
Query: 119 TVKPGQIVAALLHLDQKWYRAQVMTVSDSTPPTLELYFVDYGDSMDMPQPSVYQLNPTFL 178
T K G +VAA LD +WYRA+V V S L ++DYG+ +P + L P F
Sbjct: 51 TPKRGDLVAAQFTLDNQWYRAKVERVQGSNATVL---YIDYGNKETLPTNRLAALPPAFS 107
Query: 179 GLRFQAIECSLANVR-PVGDVWSEEAISCFED--LTHVAQWKVLLARVESYKETSTDLRS 235
+ A E +LA V P + EEA+ F + L H Q V L +
Sbjct: 108 SEKPYATEYALALVALPTDNEDKEEALRAFSEDVLNHKVQLNVELK------------VT 155
Query: 236 GSPLPCVSLFDTSGEQDVNISQELISRGFAVSSKSG 271
GSP +L D + + V+ ++L++ G ++ + G
Sbjct: 156 GSP-NLATLRDPTTK--VDFGKQLVAEGLVLAEQRG 188
>pdb|3BDL|A Chain A, Crystal Structure Of A Truncated Human Tudor-Sn
Length = 570
Score = 37.7 bits (86), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 28/46 (60%), Gaps = 2/46 (4%)
Query: 132 LDQKWYRAQVMTVSDSTPPTLELYFVDYGDSMDMPQPSVYQLNPTF 177
+D +WYRA+V V +P + ++++DYG+ +P + L+P F
Sbjct: 423 VDGEWYRARVEKVE--SPAKIHVFYIDYGNREVLPSTRLGTLSPAF 466
>pdb|3OMG|A Chain A, Structure Of Human Snd1 Extended Tudor Domain In Complex
With The Symmetrically Dimethylated Arginine Piwil1
Peptide R14me2s
pdb|3OMG|B Chain B, Structure Of Human Snd1 Extended Tudor Domain In Complex
With The Symmetrically Dimethylated Arginine Piwil1
Peptide R14me2s
pdb|3OMC|A Chain A, Structure Of Human Snd1 Extended Tudor Domain In Complex
With The Symmetrically Dimethylated Arginine Piwil1
Peptide R4me2s
pdb|3OMC|B Chain B, Structure Of Human Snd1 Extended Tudor Domain In Complex
With The Symmetrically Dimethylated Arginine Piwil1
Peptide R4me2s
Length = 261
Score = 37.4 bits (85), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 36/64 (56%), Gaps = 4/64 (6%)
Query: 132 LDQKWYRAQVMTVSDSTPPTLELYFVDYGDSMDMPQPSVYQLNPTFLG--LRFQAIECSL 189
+D +WYRA+V V +P + ++++DYG+ +P + L+P F L QA E +
Sbjct: 92 VDGEWYRARVEKVE--SPAKIHVFYIDYGNREVLPSTRLGTLSPAFSTRVLPAQATEYAF 149
Query: 190 ANVR 193
A ++
Sbjct: 150 AFIQ 153
>pdb|2O4X|A Chain A, Crystal Structure Of Human P100 Tudor Domain
Length = 217
Score = 37.0 bits (84), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 28/46 (60%), Gaps = 2/46 (4%)
Query: 132 LDQKWYRAQVMTVSDSTPPTLELYFVDYGDSMDMPQPSVYQLNPTF 177
+D +WYRA+V V +P + ++++DYG+ +P + L+P F
Sbjct: 63 VDGEWYRARVEKVE--SPAKIHVFYIDYGNREVLPSTRLGTLSPAF 106
>pdb|2HQX|A Chain A, Crystal Structure Of Human P100 Tudor Domain Conserved
Region
pdb|2HQX|B Chain B, Crystal Structure Of Human P100 Tudor Domain Conserved
Region
pdb|2HQE|A Chain A, Crystal Structure Of Human P100 Tudor Domain: Large
Fragment
pdb|2HQE|B Chain B, Crystal Structure Of Human P100 Tudor Domain: Large
Fragment
Length = 246
Score = 37.0 bits (84), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 36/64 (56%), Gaps = 4/64 (6%)
Query: 132 LDQKWYRAQVMTVSDSTPPTLELYFVDYGDSMDMPQPSVYQLNPTFLG--LRFQAIECSL 189
+D +WYRA+V V +P + ++++DYG+ +P + L+P F L QA E +
Sbjct: 77 VDGEWYRARVEKVE--SPAKIHVFYIDYGNREVLPSTRLGTLSPAFSTRVLPAQATEYAF 134
Query: 190 ANVR 193
A ++
Sbjct: 135 AFIQ 138
>pdb|2E6N|A Chain A, Solution Structure Of The Tudor Domain Of Staphylococcal
Nuclease Domain-Containing Protein 1
Length = 104
Score = 36.6 bits (83), Expect = 0.019, Method: Composition-based stats.
Identities = 15/46 (32%), Positives = 28/46 (60%), Gaps = 2/46 (4%)
Query: 132 LDQKWYRAQVMTVSDSTPPTLELYFVDYGDSMDMPQPSVYQLNPTF 177
+D +WYRA+V V +P + ++++DYG+ +P + L+P F
Sbjct: 45 VDGEWYRARVEKVE--SPAKIHVFYIDYGNREVLPSTRLGTLSPAF 88
>pdb|2O4X|B Chain B, Crystal Structure Of Human P100 Tudor Domain
Length = 91
Score = 36.2 bits (82), Expect = 0.024, Method: Composition-based stats.
Identities = 15/46 (32%), Positives = 28/46 (60%), Gaps = 2/46 (4%)
Query: 132 LDQKWYRAQVMTVSDSTPPTLELYFVDYGDSMDMPQPSVYQLNPTF 177
+D +WYRA+V V +P + ++++DYG+ +P + L+P F
Sbjct: 37 VDGEWYRARVEKVE--SPAKIHVFYIDYGNREVLPSTRLGTLSPAF 80
>pdb|3NTH|A Chain A, Crystal Structure Of Tudor And Aubergine [r13(Me2s)]
Complex
pdb|3NTI|A Chain A, Crystal Structure Of Tudor And Aubergine [r15(Me2s)]
Complex
Length = 172
Score = 31.2 bits (69), Expect = 0.91, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 25/43 (58%), Gaps = 2/43 (4%)
Query: 120 VKPGQIVAALLHLDQKWYRAQVMTVSDSTPPTLELYFVDYGDS 162
+K G + A D+ +YRAQ+ V D E++F+D+G++
Sbjct: 50 LKEGALCVAQFPEDEVFYRAQIRKVLDDG--KCEVHFIDFGNN 90
Score = 30.4 bits (67), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 34/65 (52%), Gaps = 6/65 (9%)
Query: 56 PDRFWVQIMNDRAIELDQLVESMTDYYNQKANQETHRLTEVKPGQIVAALLHLDQKWYRA 115
P F+VQ+ +D L+Q+ + + D A Q+ +++K G + A D+ +YRA
Sbjct: 16 PMSFYVQMESD-VPALEQMTDKLLD-----AEQDLPAFSDLKEGALCVAQFPEDEVFYRA 69
Query: 116 QVMTV 120
Q+ V
Sbjct: 70 QIRKV 74
>pdb|3NTK|A Chain A, Crystal Structure Of Tudor
pdb|3NTK|B Chain B, Crystal Structure Of Tudor
Length = 169
Score = 30.8 bits (68), Expect = 0.94, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 25/43 (58%), Gaps = 2/43 (4%)
Query: 120 VKPGQIVAALLHLDQKWYRAQVMTVSDSTPPTLELYFVDYGDS 162
+K G + A D+ +YRAQ+ V D E++F+D+G++
Sbjct: 48 LKEGALCVAQFPEDEVFYRAQIRKVLDDG--KCEVHFIDFGNN 88
Score = 30.4 bits (67), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 34/65 (52%), Gaps = 6/65 (9%)
Query: 56 PDRFWVQIMNDRAIELDQLVESMTDYYNQKANQETHRLTEVKPGQIVAALLHLDQKWYRA 115
P F+VQ+ +D L+Q+ + + D A Q+ +++K G + A D+ +YRA
Sbjct: 14 PMSFYVQMESD-VPALEQMTDKLLD-----AEQDLPAFSDLKEGALCVAQFPEDEVFYRA 67
Query: 116 QVMTV 120
Q+ V
Sbjct: 68 QIRKV 72
>pdb|2D9T|A Chain A, Solution Structure Of The Tudor Domain Of Tudor Domain
Containing Protein 3 From Mouse
Length = 78
Score = 29.6 bits (65), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 17/41 (41%), Positives = 23/41 (56%), Gaps = 1/41 (2%)
Query: 121 KPGQIVAALLHLDQKWYRAQVMTVSDSTPPTLELYFVDYGD 161
KPG AL D K+YRA+V + S+ T + F DYG+
Sbjct: 11 KPGDECFALYWEDNKFYRAEVEAL-HSSGMTAVVKFTDYGN 50
>pdb|2LTO|A Chain A, Tdrd3 Complex
Length = 58
Score = 29.3 bits (64), Expect = 2.7, Method: Composition-based stats.
Identities = 17/41 (41%), Positives = 24/41 (58%), Gaps = 1/41 (2%)
Query: 121 KPGQIVAALLHLDQKWYRAQVMTVSDSTPPTLELYFVDYGD 161
KPG AL D K+YRA+V + S+ T + F+DYG+
Sbjct: 5 KPGDECFALYWEDNKFYRAEVEALH-SSGMTAVVKFIDYGN 44
>pdb|3S6W|A Chain A, Crystal Structure Of Tudor Domain Of Human Tdrd3
Length = 54
Score = 29.3 bits (64), Expect = 2.8, Method: Composition-based stats.
Identities = 17/41 (41%), Positives = 24/41 (58%), Gaps = 1/41 (2%)
Query: 121 KPGQIVAALLHLDQKWYRAQVMTVSDSTPPTLELYFVDYGD 161
KPG AL D K+YRA+V + S+ T + F+DYG+
Sbjct: 3 KPGDECFALYWEDNKFYRAEVEALH-SSGMTAVVKFIDYGN 42
>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 = 3.8, Method: Composition-based stats.
Identities = 17/41 (41%), Positives = 24/41 (58%), Gaps = 1/41 (2%)
Query: 121 KPGQIVAALLHLDQKWYRAQVMTVSDSTPPTLELYFVDYGD 161
KPG AL D K+YRA+V + S+ T + F+DYG+
Sbjct: 5 KPGDECFALYWEDNKFYRAEVEALH-SSGMTAVVKFIDYGN 44
>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 = 28.5 bits (62), Expect = 5.8, Method: Composition-based stats.
Identities = 17/41 (41%), Positives = 24/41 (58%), Gaps = 1/41 (2%)
Query: 121 KPGQIVAALLHLDQKWYRAQVMTVSDSTPPTLELYFVDYGD 161
KPG AL D K+YRA+V + S+ T + F+DYG+
Sbjct: 19 KPGDECFALYWEDNKFYRAEVEALH-SSGMTAVVKFIDYGN 58
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
0.312 0.127 0.369
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,503,249
Number of Sequences: 62578
Number of extensions: 370091
Number of successful extensions: 750
Number of sequences better than 100.0: 25
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 18
Number of HSP's that attempted gapping in prelim test: 733
Number of HSP's gapped (non-prelim): 34
length of query: 321
length of database: 14,973,337
effective HSP length: 99
effective length of query: 222
effective length of database: 8,778,115
effective search space: 1948741530
effective search space used: 1948741530
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 51 (24.3 bits)