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= psy1775
(304 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1K1G|A Chain A, Structural Basis For Recognition Of The Intron Branch Site
Rna By Splicing Factor 1
Length = 131
Score = 143 bits (361), Expect = 1e-34, Method: Compositional matrix adjust.
Identities = 69/87 (79%), Positives = 81/87 (93%)
Query: 196 VNDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIIIRGKGSVKEGKVGRKDGQP 255
V+DKVMIPQDE+P+INFVGLLIGPRGNTLK++EK+ AKI+IRGKGSVKEGKVGRKDGQ
Sbjct: 7 VSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQM 66
Query: 256 LPGENEPLHAYVTAHNPENVKKAVDRL 282
LPGE+EPLHA VTA+ ENVKKAV+++
Sbjct: 67 LPGEDEPLHALVTANTMENVKKAVEQI 93
>pdb|2M09|A Chain A, Structure, Phosphorylation And U2af65 Binding Of The
Nterminal Domain Of Splicing Factor 1 During 3 Splice
Site Recognition
Length = 121
Score = 81.6 bits (200), Expect = 5e-16, Method: Compositional matrix adjust.
Identities = 40/66 (60%), Positives = 48/66 (72%)
Query: 140 SPSPEPIYSSDGKRMNTREYRTRKKLEEERHDLIQKMFKVNXXXXXXXXXXXXXXXVNDK 199
SPSPEPIY+S+GKR+NTRE+RTRKKLEEERH+LI +M +N V+DK
Sbjct: 56 SPSPEPIYNSEGKRLNTREFRTRKKLEEERHNLITEMVALNPDFKPPADYKPPATRVSDK 115
Query: 200 VMIPQD 205
VMIPQD
Sbjct: 116 VMIPQD 121
>pdb|2M0G|A Chain A, Structure, Phosphorylation And U2af65 Binding Of The
Nterminal Domain Of Splicing Factor 1 During 3 Splice
Site Recognition
Length = 145
Score = 79.7 bits (195), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 40/66 (60%), Positives = 47/66 (71%)
Query: 140 SPSPEPIYSSDGKRMNTREYRTRKKLEEERHDLIQKMFKVNXXXXXXXXXXXXXXXVNDK 199
SPSPEPIY+S+GKR+NTRE+RTRKKLEEERH+LI +M +N V DK
Sbjct: 80 SPSPEPIYNSEGKRLNTREFRTRKKLEEERHNLITEMVALNPDFKPPADYKPPATRVCDK 139
Query: 200 VMIPQD 205
VMIPQD
Sbjct: 140 VMIPQD 145
>pdb|2BL5|A Chain A, Solution Structure Of The Kh-Qua2 Region Of The Xenopus
Star-Gsg Quaking Protein
Length = 140
Score = 70.9 bits (172), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 38/98 (38%), Positives = 63/98 (64%), Gaps = 7/98 (7%)
Query: 196 VNDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIIIRGKGSVKEGKVGRKD-GQ 254
+ +K+ +P E+PD NFVG ++GPRG T K +E +TG KI++RGKGS+++ K ++ G+
Sbjct: 2 LQEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRGK 61
Query: 255 P-LPGENEPLHAYVTAHNPEN-----VKKAVDRLVCLV 286
P NE LH +T + +N +K+AV+ + L+
Sbjct: 62 PNWEHLNEDLHVLITVEDAQNRAELKLKRAVEEVKKLL 99
>pdb|4FXX|A Chain A, Structure Of Sf1 Coiled-coil Domain
pdb|4FXX|B Chain B, Structure Of Sf1 Coiled-coil Domain
pdb|4FXX|C Chain C, Structure Of Sf1 Coiled-coil Domain
pdb|4FXX|D Chain D, Structure Of Sf1 Coiled-coil Domain
Length = 112
Score = 69.3 bits (168), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 31/41 (75%), Positives = 38/41 (92%)
Query: 140 SPSPEPIYSSDGKRMNTREYRTRKKLEEERHDLIQKMFKVN 180
SPSPEPIY+S+GKR+NTRE+RTRKKLEEERH+LI +M +N
Sbjct: 60 SPSPEPIYNSEGKRLNTREFRTRKKLEEERHNLITEMVALN 100
>pdb|4FXW|B Chain B, Structure Of Phosphorylated Sf1 Complex With U2af65-uhm
Domain
pdb|4FXW|D Chain D, Structure Of Phosphorylated Sf1 Complex With U2af65-uhm
Domain
Length = 124
Score = 54.3 bits (129), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 24/35 (68%), Positives = 31/35 (88%)
Query: 146 IYSSDGKRMNTREYRTRKKLEEERHDLIQKMFKVN 180
IY+S+GKR+NTRE+RTRKKLEEERH+LI + +N
Sbjct: 78 IYNSEGKRLNTREFRTRKKLEEERHNLITEXVALN 112
>pdb|2YQR|A Chain A, Solution Structure Of The Kh Domain In Kiaa0907 Protein
Length = 119
Score = 36.2 bits (82), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 32/104 (30%), Positives = 52/104 (50%), Gaps = 13/104 (12%)
Query: 196 VNDKVMIPQDEH-PDINFVGLLIGPRGNTLKSMEKDTGAKIIIRGKGS-VKEGKVGRKDG 253
V DK+ + + P N + GP + L+ ++ +TGAK+ +RGKGS E GR+
Sbjct: 12 VQDKLFVGLEHAVPTFNVKEKVEGPGCSYLQHIQIETGAKVFLRGKGSGCIEPASGREA- 70
Query: 254 QPLPGENEPLHAYVTAHNPENV---KKAVDRLVCLVSARPRARF 294
EP++ Y++ PE + KK + L+ V A +RF
Sbjct: 71 ------FEPMYIYISHPKPEGLAAAKKLCENLLQTVHAE-YSRF 107
>pdb|2IHX|A Chain A, Solution Structure Of The Rous Sarcoma Virus
Nucleocapsid Protein:upsi Rna Packaging Signal Complex
Length = 61
Score = 33.1 bits (74), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 21/54 (38%), Positives = 25/54 (46%), Gaps = 7/54 (12%)
Query: 44 CTNCGASDHKSWLCPDKPNITNS-TLCSSCGGAGHIARDCREK------RPGMG 90
C CG+ H CP K NS C C G GH A+ CR++ RPG G
Sbjct: 7 CYTCGSPGHYQAQCPKKRKSGNSRERCQLCNGMGHNAKQCRKRDGNQGQRPGKG 60
>pdb|3NYB|B Chain B, Structure And Function Of The Polymerase Core Of Tramp,
A Rna Surveillance Complex
Length = 83
Score = 32.3 bits (72), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 26/60 (43%), Gaps = 16/60 (26%)
Query: 43 RCTNCGASDHKSWLCPD--------------KPNIT--NSTLCSSCGGAGHIARDCREKR 86
+CT C + H CP KP + ++ C +CGG GH DC+EKR
Sbjct: 7 QCTLCKSKKHSKERCPSIWRAYILVDDNEKAKPKVLPFHTIYCYNCGGKGHFGDDCKEKR 66
>pdb|1ZIN|A Chain A, Adenylate Kinase With Bound Ap5a
pdb|1ZIO|A Chain A, Phosphotransferase
pdb|1ZIP|A Chain A, Bacillus Stearothermophilus Adenylate Kinase
Length = 217
Score = 31.2 bits (69), Expect = 0.79, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 24/52 (46%), Gaps = 7/52 (13%)
Query: 25 WAFHPILKKGTLRENEGPR--CTNCGASDHKSWLCPDKPNITNSTLCSSCGG 74
+ H +++ L E R C NCGA+ H + P KP + C CGG
Sbjct: 109 YVIHIDVRQDVLMERLTGRRICRNCGATYHLIFHPPAKPGV-----CDKCGG 155
>pdb|1DTJ|A Chain A, Crystal Structure Of Nova-2 Kh3 K-Homology Rna-Binding
Domain
pdb|1DTJ|B Chain B, Crystal Structure Of Nova-2 Kh3 K-Homology Rna-Binding
Domain
pdb|1DTJ|C Chain C, Crystal Structure Of Nova-2 Kh3 K-Homology Rna-Binding
Domain
pdb|1DTJ|D Chain D, Crystal Structure Of Nova-2 Kh3 K-Homology Rna-Binding
Domain
Length = 76
Score = 30.4 bits (67), Expect = 1.2, Method: Composition-based stats.
Identities = 16/41 (39%), Positives = 22/41 (53%)
Query: 211 NFVGLLIGPRGNTLKSMEKDTGAKIIIRGKGSVKEGKVGRK 251
N VG ++G G TL ++ TGA+I I KG G R+
Sbjct: 12 NLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRR 52
>pdb|1E3H|A Chain A, Semet Derivative Of Streptomyces Antibioticus PnpaseGPSI
Enzyme
Length = 757
Score = 30.4 bits (67), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 27/47 (57%), Gaps = 6/47 (12%)
Query: 200 VMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIIIRGKGSVKEG 246
V IP D+ +G +IGP+ + +++DTGA+I I G++ G
Sbjct: 602 VKIPVDK------IGEVIGPKRQXINQIQEDTGAEITIEDDGTIYIG 642
>pdb|1EC6|A Chain A, Crystal Structure Of Nova-2 Kh3 K-Homology Rna-Binding
Domain Bound To 20-Mer Rna Hairpin
pdb|1EC6|B Chain B, Crystal Structure Of Nova-2 Kh3 K-Homology Rna-Binding
Domain Bound To 20-Mer Rna Hairpin
Length = 87
Score = 30.0 bits (66), Expect = 1.7, Method: Composition-based stats.
Identities = 16/41 (39%), Positives = 22/41 (53%)
Query: 211 NFVGLLIGPRGNTLKSMEKDTGAKIIIRGKGSVKEGKVGRK 251
N VG ++G G TL ++ TGA+I I KG G R+
Sbjct: 12 NLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRR 52
>pdb|1E3P|A Chain A, Tungstate Derivative Of Streptomyces Antibioticus Pnpase
Gpsi Enzyme
Length = 757
Score = 30.0 bits (66), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 12/37 (32%), Positives = 24/37 (64%)
Query: 210 INFVGLLIGPRGNTLKSMEKDTGAKIIIRGKGSVKEG 246
++ +G +IGP+ + +++DTGA+I I G++ G
Sbjct: 606 VDKIGEVIGPKRQMINQIQEDTGAEITIEDDGTIYIG 642
>pdb|4IPA|A Chain A, Structure Of A Thermophilic Arx1
pdb|4IPA|B Chain B, Structure Of A Thermophilic Arx1
pdb|4IPA|C Chain C, Structure Of A Thermophilic Arx1
pdb|4IPA|D Chain D, Structure Of A Thermophilic Arx1
Length = 423
Score = 29.6 bits (65), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 25/56 (44%), Gaps = 1/56 (1%)
Query: 114 LGEGPPPDKRQRDNDSYRKNNTSGSLSPSPEPIYSSDGKRMNTREYRTRKKLEEER 169
LG G QR R NNT P+ IYS K+ T + R +LE+ER
Sbjct: 259 LGSGKVKQFEQRATLHRRTNNTYALKRPTSRKIYSEVQKKFGTFPFSLR-QLEDER 313
>pdb|1DT4|A Chain A, Crystal Structure Of Nova-1 Kh3 K-Homology Rna-Binding
Domain
Length = 73
Score = 29.6 bits (65), Expect = 2.1, Method: Composition-based stats.
Identities = 16/41 (39%), Positives = 21/41 (51%)
Query: 211 NFVGLLIGPRGNTLKSMEKDTGAKIIIRGKGSVKEGKVGRK 251
N VG ++G G TL ++ TG +I I KG G RK
Sbjct: 12 NLVGAILGKGGKTLVEYQELTGCRIQISKKGEFLPGTRNRK 52
>pdb|1DSQ|A Chain A, Structure Of The Mmtv Nucleocapsid Protein (Zinc Finger
1)
Length = 21
Score = 28.9 bits (63), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 11/18 (61%), Positives = 14/18 (77%)
Query: 68 LCSSCGGAGHIARDCREK 85
+C SCG GHI RDC+E+
Sbjct: 4 VCFSCGKTGHIKRDCKEE 21
>pdb|2LLI|A Chain A, Low Resolution Structure Of Rna-Binding Subunit Of The
Tramp Complex
Length = 124
Score = 28.5 bits (62), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 25/59 (42%), Gaps = 16/59 (27%)
Query: 43 RCTNCGASDHKSWLCPD--------------KPNIT--NSTLCSSCGGAGHIARDCREK 85
+CT C + H CP KP + ++ C +CGG GH DC+EK
Sbjct: 66 QCTLCKSKKHSKERCPSIWRAYILVDDNEKAKPKVLPFHTIYCYNCGGKGHFGDDCKEK 124
>pdb|2DGR|A Chain A, Solution Structure Of The Second Kh Domain In Ring Finger
And Kh Domain Containing Protein 1
Length = 83
Score = 28.5 bits (62), Expect = 5.3, Method: Composition-based stats.
Identities = 20/77 (25%), Positives = 36/77 (46%), Gaps = 20/77 (25%)
Query: 213 VGLLIGPRGNTLKSMEKDTGAKIIIRGKGSVKEGKVGRKDGQPLPGENEPLHAYVTAHNP 272
VGL++GP+G T+K +++ T I+ G+ + EP+ A P
Sbjct: 21 VGLVVGPKGATIKRIQQRTHTYIVTPGR------------------DKEPVFAVTGM--P 60
Query: 273 ENVKKAVDRLVCLVSAR 289
ENV +A + + ++ R
Sbjct: 61 ENVDRAREEIEAHITLR 77
>pdb|2LI8|A Chain A, The Solution Structure Of The Lin28-Znf Domains Bound To
Aggagau Of Pre-Let-7 Mirna
Length = 74
Score = 28.1 bits (61), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 16/35 (45%)
Query: 37 RENEGPRCTNCGASDHKSWLCPDKPNITNSTLCSS 71
R ++G RC NCG DH + C P C S
Sbjct: 20 RRSKGDRCYNCGGLDHHAKECKLPPQPKKCHFCQS 54
>pdb|2OPV|A Chain A, Solution Nmr Structure Of The Second Domain Of Ksrp
Length = 85
Score = 28.1 bits (61), Expect = 7.0, Method: Composition-based stats.
Identities = 15/44 (34%), Positives = 25/44 (56%), Gaps = 6/44 (13%)
Query: 199 KVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIIIRGKGS 242
++MIP + GL+IG G T+K +++ G K+I+ GS
Sbjct: 17 EIMIPAGK------AGLVIGKGGETIKQLQERAGVKMILIQDGS 54
>pdb|2E3U|A Chain A, Crystal Structure Analysis Of Dim2p From Pyrococcus
Horikoshii Ot3
pdb|3AEV|B Chain B, Crystal Structure Of AEIF2ALPHA-Adim2p-Rrna Complex From
Pyrococcus Horikoshii Ot3
Length = 219
Score = 27.7 bits (60), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 15/39 (38%), Positives = 22/39 (56%), Gaps = 2/39 (5%)
Query: 201 MIPQDEHPDI--NFVGLLIGPRGNTLKSMEKDTGAKIII 237
Q+E+ I + + +LIG +G T K +EK T KI I
Sbjct: 31 FFKQEEYVKIPKDRIAVLIGKKGQTKKEIEKRTKTKITI 69
>pdb|1HVN|E Chain E, Zinc-And Sequence-Dependent Binding To Nucleic Acids By
The N-Terminal Zinc Finger Domain Of The Hiv-1
Nucleocapsid Protein: Nmr Structure Of The Complex With
The Psi-Site Analog, DACGCC
pdb|1HVO|E Chain E, Zinc-And Sequence-Dependent Binding To Nucleic Acids By
The N-Terminal Zinc Finger Domain Of The Hiv-1
Nucleocapsid Protein: Nmr Structure Of The Complex With
The Psi-Site Analog, DACGCC
pdb|2ZNF|A Chain A, High-Resolution Structure Of An Hiv Zinc Fingerlike
Domain Via A New Nmr-Based Distance Geometry Approach
Length = 18
Score = 27.7 bits (60), Expect = 8.8, Method: Composition-based stats.
Identities = 10/15 (66%), Positives = 12/15 (80%)
Query: 69 CSSCGGAGHIARDCR 83
C +CG GHIAR+CR
Sbjct: 3 CFNCGKEGHIARNCR 17
>pdb|1J4W|A Chain A, Complex Of The Kh3 And Kh4 Domains Of Fbp With A
Single_stranded 29mer Dna Oligonucleotide From The Fuse
Element Of The C-Myc Oncogene
Length = 174
Score = 27.7 bits (60), Expect = 9.3, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 21/33 (63%), Gaps = 6/33 (18%)
Query: 209 DINFV------GLLIGPRGNTLKSMEKDTGAKI 235
+ NF+ GL+IG G T+KS+ + +GA+I
Sbjct: 105 EFNFIVPTGKTGLIIGKGGETIKSISQQSGARI 137
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
0.315 0.136 0.417
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,020,186
Number of Sequences: 62578
Number of extensions: 436064
Number of successful extensions: 685
Number of sequences better than 100.0: 45
Number of HSP's better than 100.0 without gapping: 35
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 627
Number of HSP's gapped (non-prelim): 66
length of query: 304
length of database: 14,973,337
effective HSP length: 98
effective length of query: 206
effective length of database: 8,840,693
effective search space: 1821182758
effective search space used: 1821182758
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 51 (24.3 bits)