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= 003964
(783 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 35.8 bits (81), Expect = 0.084, Method: Compositional matrix adjust.
Identities = 14/34 (41%), Positives = 22/34 (64%)
Query: 195 RTLFVRNINSNVEDLELRSLFEQYGDIRTLYTAC 228
R L V I + V++++LR LFE+YG I ++ C
Sbjct: 43 RNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVC 76
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 33.9 bits (76), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 35/79 (44%), Gaps = 9/79 (11%)
Query: 195 RTLFVRNINSNVEDLELRSLFEQYGDIRTL-----YTACKHRGF----FYDVXXXXXXXX 245
R L+V + V+D L + F +GDI + Y KHRGF F
Sbjct: 13 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 72
Query: 246 XXNRSDINGKRIKLEPSRP 264
N S++ G+ I++ ++P
Sbjct: 73 NMNESELFGRTIRVNLAKP 91
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 33.5 bits (75), Expect = 0.53, Method: Compositional matrix adjust.
Identities = 26/88 (29%), Positives = 40/88 (45%), Gaps = 12/88 (13%)
Query: 184 AGEHPYGEHPSRTLFVRNINSNVEDLELRSLFEQYGDIRTLYTACK------HRGF-FYD 236
+G+ P + S+ L VRNI E+R LF +G+++T+ K HRGF F D
Sbjct: 6 SGQVPKKQTTSKIL-VRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVD 64
Query: 237 VXXXXXXXXXXN----RSDINGKRIKLE 260
N + + G+R+ LE
Sbjct: 65 FITKQDAKKAFNALCHSTHLYGRRLVLE 92
>pdb|2XS5|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Mvh Rna, Uguuc
pdb|2XS5|B Chain B, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Mvh Rna, Uguuc
pdb|2XS7|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Sycp3 Rna, Uuguuu
Length = 87
Score = 33.1 bits (74), Expect = 0.61, Method: Composition-based stats.
Identities = 22/84 (26%), Positives = 38/84 (45%), Gaps = 12/84 (14%)
Query: 188 PYGEHPSRTLFVRNINSNVEDLELRSLFEQYGDIRTLYTACKHRG---------FFYDVX 238
P G+ T+FV I+ +++ E+RS F +YG ++ + G F+ DV
Sbjct: 3 PEGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVD 62
Query: 239 XXXXXXXXXNRSDINGKRIKLEPS 262
N +GK++KL P+
Sbjct: 63 VQKIVESQIN---FHGKKLKLGPA 83
>pdb|2XS2|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Rna, Uuguucuu
Length = 102
Score = 32.7 bits (73), Expect = 0.90, Method: Compositional matrix adjust.
Identities = 22/84 (26%), Positives = 38/84 (45%), Gaps = 12/84 (14%)
Query: 188 PYGEHPSRTLFVRNINSNVEDLELRSLFEQYGDIRTLYTACKHRG---------FFYDVX 238
P G+ T+FV I+ +++ E+RS F +YG ++ + G F+ DV
Sbjct: 3 PEGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVD 62
Query: 239 XXXXXXXXXNRSDINGKRIKLEPS 262
N +GK++KL P+
Sbjct: 63 VQKIVESQIN---FHGKKLKLGPA 83
>pdb|3PGW|S Chain S, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|L Chain L, Crystal Structure Of Human U1 Snrnp
Length = 437
Score = 31.6 bits (70), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 13/37 (35%), Positives = 21/37 (56%)
Query: 195 RTLFVRNINSNVEDLELRSLFEQYGDIRTLYTACKHR 231
+TLFV +N + + +LR FE YG I+ ++ R
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKR 139
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 31.2 bits (69), Expect = 2.3, Method: Composition-based stats.
Identities = 17/72 (23%), Positives = 34/72 (47%), Gaps = 4/72 (5%)
Query: 196 TLFVRNINSNVEDLELRSLFEQYGDIRTLYTACKHRGFFYDVXXXXXXXXXXNRS----D 251
TL+V + + + +LR+ F Q+G+IRT+ + + F +S
Sbjct: 14 TLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQCAFIQFATRQAAEVAAEKSFNKLI 73
Query: 252 INGKRIKLEPSR 263
+NG+R+ ++ R
Sbjct: 74 VNGRRLNVKWGR 85
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 30.8 bits (68), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 14/46 (30%), Positives = 22/46 (47%)
Query: 190 GEHPSRTLFVRNINSNVEDLELRSLFEQYGDIRTLYTACKHRGFFY 235
G S +FV ++ + ELR F QYGD+ ++ R F +
Sbjct: 1 GSSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAF 46
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 30.8 bits (68), Expect = 3.3, Method: Composition-based stats.
Identities = 14/42 (33%), Positives = 25/42 (59%)
Query: 194 SRTLFVRNINSNVEDLELRSLFEQYGDIRTLYTACKHRGFFY 235
+RTL +N++ N+ + EL+ +FE +IR + K +G Y
Sbjct: 16 ARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAY 57
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 30.4 bits (67), Expect = 3.5, Method: Composition-based stats.
Identities = 20/76 (26%), Positives = 35/76 (46%), Gaps = 12/76 (15%)
Query: 196 TLFVRNINSNVEDLELRSLFEQYGDIRTLYTACKHRG---------FFYDVXXXXXXXXX 246
T+FV I+ +++ E+RS F +YG ++ + G F+ DV
Sbjct: 12 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVESQ 71
Query: 247 XNRSDINGKRIKLEPS 262
N +GK++KL P+
Sbjct: 72 IN---FHGKKLKLGPA 84
>pdb|1FJE|B Chain B, Solution Structure Of Nucleolin Rbd12 In Complex With Snre
Rna
pdb|1RKJ|A Chain A, Solution Structure Of The Complex Formed By The Two N-
Terminal Rna-Binding Domains Of Nucleolin And A Pre-Rrna
Target
Length = 175
Score = 30.4 bits (67), Expect = 3.7, Method: Composition-based stats.
Identities = 14/42 (33%), Positives = 25/42 (59%)
Query: 194 SRTLFVRNINSNVEDLELRSLFEQYGDIRTLYTACKHRGFFY 235
+RTL +N++ N+ + EL+ +FE +IR + K +G Y
Sbjct: 99 ARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAY 140
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 30.4 bits (67), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 32/69 (46%), Gaps = 3/69 (4%)
Query: 197 LFVRNINSNVEDLELRSLFEQYGDIRTLYTACKHRGFFY--DVXXXXXXXXXXNRSDING 254
LF+ N+ + E+RSLFEQYG + K+ GF + D + ++G
Sbjct: 11 LFIGNLPREATEQEIRSLFEQYGKVLEC-DIIKNYGFVHIEDKTAAEDAIRNLHHYKLHG 69
Query: 255 KRIKLEPSR 263
I +E S+
Sbjct: 70 VNINVEASK 78
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 30.4 bits (67), Expect = 3.8, Method: Composition-based stats.
Identities = 16/51 (31%), Positives = 25/51 (49%)
Query: 185 GEHPYGEHPSRTLFVRNINSNVEDLELRSLFEQYGDIRTLYTACKHRGFFY 235
G+ E +RTL +N+ V EL+ +FE +IR + K +G Y
Sbjct: 84 GKDSKKERDARTLLAKNLPYKVTQDELKEVFEDAAEIRLVSKDGKSKGIAY 134
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 30.4 bits (67), Expect = 3.9, Method: Composition-based stats.
Identities = 22/83 (26%), Positives = 35/83 (42%), Gaps = 9/83 (10%)
Query: 190 GEHPSRTLFVRNINSNVEDLELRSLFEQYGDIRTL-----YTACKHRGF----FYDVXXX 240
G R L+V + V+D L + F +GDI + Y KHRGF F
Sbjct: 1 GSTTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 60
Query: 241 XXXXXXXNRSDINGKRIKLEPSR 263
N S++ G+ I++ ++
Sbjct: 61 AAAIDNMNESELFGRTIRVNLAK 83
>pdb|1ZXX|A Chain A, The Crystal Structure Of Phosphofructokinase From
Lactobacillus Delbrueckii
Length = 319
Score = 29.6 bits (65), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 14/28 (50%), Positives = 16/28 (57%)
Query: 634 KYTSKMLLAAIDENHRGTYDFLYLPIDF 661
K TS +L DE+HRG YD L L D
Sbjct: 290 KVTSHDILDLFDESHRGDYDLLKLNADL 317
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 29.6 bits (65), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 12/39 (30%), Positives = 21/39 (53%)
Query: 655 LYLPIDFKNKCNVGYAFINMVSPSHIISFYEAFNGKKWE 693
L+ PID K G+AF+ + P H + Y +G+ ++
Sbjct: 38 LHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQ 76
>pdb|2JRA|A Chain A, A Novel Domain-Swapped Solution Nmr Structure Of Protein
Rpa2121 From Rhodopseudomonas Palustris. Northeast
Structural Genomics Target Rpt6
pdb|2JRA|B Chain B, A Novel Domain-Swapped Solution Nmr Structure Of Protein
Rpa2121 From Rhodopseudomonas Palustris. Northeast
Structural Genomics Target Rpt6
Length = 67
Score = 29.6 bits (65), Expect = 6.8, Method: Composition-based stats.
Identities = 15/50 (30%), Positives = 27/50 (54%)
Query: 579 LGTTSNEAFTERGRTRRVENCGSQVDSKKQYQLDLDKIISGEDTRTTLMI 628
LG +A + G R V G+Q+DS++ + +D + +I+ D R L +
Sbjct: 8 LGADPTQAASSPGGARAVSIVGNQIDSRELFTVDREIVIAHGDDRYRLRL 57
>pdb|3LPY|A Chain A, Crystal Structure Of The Rrm Domain Of Cyp33
pdb|3LPY|B Chain B, Crystal Structure Of The Rrm Domain Of Cyp33
Length = 79
Score = 29.6 bits (65), Expect = 7.0, Method: Composition-based stats.
Identities = 21/74 (28%), Positives = 32/74 (43%), Gaps = 9/74 (12%)
Query: 195 RTLFVRNINSNVEDLELRSLFEQYGDIRTL-----YTACKHRGF----FYDVXXXXXXXX 245
R L+V + V+D L + F +GDI + Y KHRGF F
Sbjct: 3 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 62
Query: 246 XXNRSDINGKRIKL 259
N S++ G+ I++
Sbjct: 63 NMNESELFGRTIRV 76
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 29.6 bits (65), Expect = 7.0, Method: Composition-based stats.
Identities = 21/74 (28%), Positives = 32/74 (43%), Gaps = 9/74 (12%)
Query: 195 RTLFVRNINSNVEDLELRSLFEQYGDIRTL-----YTACKHRGF----FYDVXXXXXXXX 245
R L+V + V+D L + F +GDI + Y KHRGF F
Sbjct: 64 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 123
Query: 246 XXNRSDINGKRIKL 259
N S++ G+ I++
Sbjct: 124 NMNESELFGRTIRV 137
>pdb|3MDF|A Chain A, Crystal Structure Of The Rrm Domain Of Cyclophilin 33
pdb|3MDF|B Chain B, Crystal Structure Of The Rrm Domain Of Cyclophilin 33
Length = 85
Score = 29.6 bits (65), Expect = 7.3, Method: Composition-based stats.
Identities = 21/78 (26%), Positives = 34/78 (43%), Gaps = 9/78 (11%)
Query: 195 RTLFVRNINSNVEDLELRSLFEQYGDIRTL-----YTACKHRGF----FYDVXXXXXXXX 245
R L+V + V+D L + F +GDI + Y KHRGF F
Sbjct: 8 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 67
Query: 246 XXNRSDINGKRIKLEPSR 263
N S++ G+ I++ ++
Sbjct: 68 NMNESELFGRTIRVNLAK 85
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 29.3 bits (64), Expect = 9.4, Method: Composition-based stats.
Identities = 16/48 (33%), Positives = 27/48 (56%), Gaps = 1/48 (2%)
Query: 184 AGEHPYGEHPSRTLFVRNINSNVEDLELRSLFEQYGDIRTLYTACKHR 231
+G +H + LF+ I N+++ +L+ LFE++G I L T K R
Sbjct: 3 SGSSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYEL-TVLKDR 49
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 0.132 0.391
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 24,985,511
Number of Sequences: 62578
Number of extensions: 1123187
Number of successful extensions: 3380
Number of sequences better than 100.0: 32
Number of HSP's better than 100.0 without gapping: 17
Number of HSP's successfully gapped in prelim test: 15
Number of HSP's that attempted gapping in prelim test: 3361
Number of HSP's gapped (non-prelim): 33
length of query: 783
length of database: 14,973,337
effective HSP length: 106
effective length of query: 677
effective length of database: 8,340,069
effective search space: 5646226713
effective search space used: 5646226713
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 55 (25.8 bits)