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= psy9171
(118 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2CQ1|A Chain A, Solution Structure Of Rna Binding Domain In Ptb-Like
Protein L
Length = 101
Score = 71.2 bits (173), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 31/45 (68%), Positives = 38/45 (84%)
Query: 24 KSDFKPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKNQ 68
K D PSRV+HIR +P EVTE E+I LG+PFG+VTN+L+LKGKNQ
Sbjct: 9 KMDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKNQ 53
>pdb|1SJQ|A Chain A, Nmr Structure Of Rrm1 From Human Polypyrimidine Tract
Binding Protein Isoform 1 (Ptb1)
Length = 105
Score = 65.9 bits (159), Expect = 5e-12, Method: Compositional matrix adjust.
Identities = 29/40 (72%), Positives = 36/40 (90%)
Query: 29 PSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKNQ 68
PSRVIHIR +P +VTE E+I LG+PFG+VTN+L+LKGKNQ
Sbjct: 15 PSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKNQ 54
>pdb|2AD9|A Chain A, Solution Structure Of Polypyrimidine Tract Binding
Protein Rbd1 Complexed With Cucucu Rna
Length = 119
Score = 65.9 bits (159), Expect = 5e-12, Method: Compositional matrix adjust.
Identities = 29/40 (72%), Positives = 36/40 (90%)
Query: 29 PSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKNQ 68
PSRVIHIR +P +VTE E+I LG+PFG+VTN+L+LKGKNQ
Sbjct: 30 PSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKNQ 69
>pdb|1X4F|A Chain A, Solution Structure Of The Second Rrm Domain In Matrin 3
Length = 112
Score = 34.7 bits (78), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 12/39 (30%), Positives = 28/39 (71%), Gaps = 1/39 (2%)
Query: 31 RVIHIRNIPNE-VTEAEIIHLGIPFGRVTNVLVLKGKNQ 68
RVIH+ N+P+ +++ ++ L P+G++ N ++++ K+Q
Sbjct: 26 RVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKSQ 64
>pdb|3TYT|A Chain A, Crystal Structure Of A Heterogeneous Nuclear
Ribonucleoprotein L (Hnrpl) From Mus Musculus At 1.60 A
Resolution
Length = 205
Score = 32.3 bits (72), Expect = 0.073, Method: Compositional matrix adjust.
Identities = 17/42 (40%), Positives = 22/42 (52%), Gaps = 2/42 (4%)
Query: 29 PSRVIHIRNIPNEVTEAEIIHLGIPFG--RVTNVLVLKGKNQ 68
PS V+H N P EVTE + G R T+V V GK++
Sbjct: 122 PSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSE 163
>pdb|3S01|A Chain A, Crystal Structure Of A Heterogeneous Nuclear
Ribonucleoprotein L (Hnrpl) From Mus Musculus At 2.15 A
Resolution
Length = 212
Score = 32.0 bits (71), Expect = 0.092, Method: Compositional matrix adjust.
Identities = 17/42 (40%), Positives = 22/42 (52%), Gaps = 2/42 (4%)
Query: 29 PSRVIHIRNIPNEVTEAEIIHLGIPFG--RVTNVLVLKGKNQ 68
PS V+H N P EVTE + G R T+V V GK++
Sbjct: 122 PSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSE 163
>pdb|3TO8|A Chain A, Crystal Structure Of The Two C-Terminal Rrm Domains Of
Heterogeneous Nuclear Ribonucleoprotein L (Hnrnp L)
Length = 218
Score = 30.8 bits (68), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 16/42 (38%), Positives = 22/42 (52%), Gaps = 2/42 (4%)
Query: 29 PSRVIHIRNIPNEVTEAEIIHLGIPFG--RVTNVLVLKGKNQ 68
PS V+H N P EVTE + G R ++V V GK++
Sbjct: 128 PSNVLHFFNAPLEVTEENFFEICDELGVKRPSSVKVFSGKSE 169
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 29.3 bits (64), Expect = 0.60, Method: Compositional matrix adjust.
Identities = 13/32 (40%), Positives = 21/32 (65%)
Query: 29 PSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNV 60
PSRV+++ +IP + TE +I+ L G V N+
Sbjct: 1 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINL 32
>pdb|2X1A|A Chain A, Structure Of Rna15 Rrm With Rna Bound (G)
pdb|2X1B|A Chain A, Structure Of Rna15 Rrm
Length = 97
Score = 29.3 bits (64), Expect = 0.61, Method: Compositional matrix adjust.
Identities = 13/32 (40%), Positives = 21/32 (65%)
Query: 29 PSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNV 60
PSRV+++ +IP + TE +I+ L G V N+
Sbjct: 2 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINL 33
>pdb|2KM8|B Chain B, Interdomain Rrm Packing Contributes To Rna Recognition
In The Rna15, Hrp1, Anchor Rna 3' Processing Ternary
Complex
Length = 84
Score = 28.9 bits (63), Expect = 0.75, Method: Compositional matrix adjust.
Identities = 13/32 (40%), Positives = 21/32 (65%)
Query: 29 PSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNV 60
PSRV+++ +IP + TE +I+ L G V N+
Sbjct: 3 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINL 34
>pdb|3R27|A Chain A, Crystal Structure Of The First Rrm Domain Of
Heterogeneous Nuclear Ribonucleoprotein L (Hnrnp L)
pdb|3R27|B Chain B, Crystal Structure Of The First Rrm Domain Of
Heterogeneous Nuclear Ribonucleoprotein L (Hnrnp L)
Length = 100
Score = 28.5 bits (62), Expect = 1.00, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 27/48 (56%), Gaps = 2/48 (4%)
Query: 21 DRQKSDFKPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKNQ 68
D K+ P V+HIR + + V EA+++ FG ++ V+V+ K Q
Sbjct: 14 DPHKTPASP--VVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKKRQ 59
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 28.1 bits (61), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 31/49 (63%), Gaps = 2/49 (4%)
Query: 16 VQAKLDRQKSDFKPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLK 64
VQA++ +Q+ P+ ++I N+P + E E+ ++ PFG+V + +L+
Sbjct: 13 VQAQMAKQQEQ-DPTN-LYISNLPLSMDEQELENMLKPFGQVISTRILR 59
>pdb|1WEX|A Chain A, Solution Structure Of Rrm Domain In Protein Bab28521
Length = 104
Score = 27.7 bits (60), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 12/39 (30%), Positives = 22/39 (56%)
Query: 30 SRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKNQ 68
S V+H+R + V EA+++ FG + V+++ K Q
Sbjct: 15 SPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQ 53
>pdb|2ADC|A Chain A, Solution Structure Of Polypyrimidine Tract Binding Protein
Rbd34 Complexed With Cucucu Rna
pdb|2EVZ|A Chain A, Structure Of Rna Binding Domains 3 And 4 Of Polypyrimidine
Tract Binding Protein
Length = 229
Score = 26.9 bits (58), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 9/21 (42%), Positives = 14/21 (66%)
Query: 27 FKPSRVIHIRNIPNEVTEAEI 47
F PS +H+ NIP V+E ++
Sbjct: 148 FPPSATLHLSNIPPSVSEEDL 168
>pdb|1QM9|A Chain A, Nmr, Representative Structure
Length = 198
Score = 26.9 bits (58), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 9/21 (42%), Positives = 14/21 (66%)
Query: 27 FKPSRVIHIRNIPNEVTEAEI 47
F PS +H+ NIP V+E ++
Sbjct: 117 FPPSATLHLSNIPPSVSEEDL 137
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 26.6 bits (57), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 10/40 (25%), Positives = 24/40 (60%), Gaps = 1/40 (2%)
Query: 29 PSR-VIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKN 67
PS+ +++ N+P +T ++ + +G+V V ++K K+
Sbjct: 14 PSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKD 53
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 26.2 bits (56), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 14/44 (31%), Positives = 25/44 (56%), Gaps = 1/44 (2%)
Query: 22 RQKSDFKPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKG 65
RQ+ + +R+ +R P +V E+E+ + PFG + V +L G
Sbjct: 24 RQEGELSNTRLF-VRPFPLDVQESELNEIFGPFGPMKEVKILNG 66
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
0.322 0.139 0.386
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,614,162
Number of Sequences: 62578
Number of extensions: 76321
Number of successful extensions: 158
Number of sequences better than 100.0: 20
Number of HSP's better than 100.0 without gapping: 15
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 140
Number of HSP's gapped (non-prelim): 23
length of query: 118
length of database: 14,973,337
effective HSP length: 81
effective length of query: 37
effective length of database: 9,904,519
effective search space: 366467203
effective search space used: 366467203
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 45 (21.9 bits)