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= 041714
(214 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2VOD|A Chain A, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Auauuuu
pdb|2VOD|B Chain B, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Auauuuu
pdb|2VON|A Chain A, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Auaauuu
pdb|2VON|B Chain B, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Auaauuu
pdb|2VOO|A Chain A, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Uuuuuuuu
pdb|2VOO|B Chain B, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Uuuuuuuu
pdb|2VOP|A Chain A, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Auuuu
Length = 193
Score = 72.0 bits (175), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 43/132 (32%), Positives = 77/132 (58%), Gaps = 8/132 (6%)
Query: 76 LKQRIIKQVEYYFSDENLPTDKYMMNLIRKNKEGFVPISVIASFRKLKRLTRNHAWIVAA 135
L+ +I Q+EYYF D NLP DK++ I+ + EG+VP+ ++ F +L RLT + IV A
Sbjct: 12 LEAKICHQIEYYFGDFNLPRDKFLKEQIKLD-EGWVPLEIMIKFNRLNRLTTDFNVIVEA 70
Query: 136 LRES--SLLVVSSNGKKVKRLNPLPVTEVRDP-----KLFTVLVENLPEDHSVENMQRIF 188
L +S L+ +S + K++R P+ EV D K +V ++ P D ++++++
Sbjct: 71 LSKSKAELMEISEDKTKIRRSPSKPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWL 130
Query: 189 AEAGKIKSICIR 200
+ G++ +I +R
Sbjct: 131 EDKGQVLNIQMR 142
>pdb|1ZH5|A Chain A, Structural Basis For Recognition Of Uuuoh 3'-Terminii Of
Nascent Rna Pol Iii Transcripts By La Autoantigen
pdb|1ZH5|B Chain B, Structural Basis For Recognition Of Uuuoh 3'-Terminii Of
Nascent Rna Pol Iii Transcripts By La Autoantigen
Length = 195
Score = 68.9 bits (167), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 43/132 (32%), Positives = 74/132 (56%), Gaps = 8/132 (6%)
Query: 76 LKQRIIKQVEYYFSDENLPTDKYMMNLIRKNKEGFVPISVIASFRKLKRLTRNHAWIVAA 135
L+ +I Q+EYYF D NLP DK++ I+ + EG+VP+ + F +L RLT + IV A
Sbjct: 14 LEAKICHQIEYYFGDFNLPRDKFLKEQIKLD-EGWVPLEIXIKFNRLNRLTTDFNVIVEA 72
Query: 136 LRES--SLLVVSSNGKKVKRLNPLPVTEVRDP-----KLFTVLVENLPEDHSVENMQRIF 188
L +S L +S + K++R P+ EV D K +V ++ P D ++++++
Sbjct: 73 LSKSKAELXEISEDKTKIRRSPSKPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWL 132
Query: 189 AEAGKIKSICIR 200
+ G++ +I R
Sbjct: 133 EDKGQVLNIQXR 144
>pdb|1YTY|A Chain A, Structural Basis For Recognition Of Uuuoh 3'-Terminii Of
Nascent Rna Pol Iii Transcripts By La Autoantigen
pdb|1YTY|B Chain B, Structural Basis For Recognition Of Uuuoh 3'-Terminii Of
Nascent Rna Pol Iii Transcripts By La Autoantigen
Length = 194
Score = 68.9 bits (167), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 43/132 (32%), Positives = 74/132 (56%), Gaps = 8/132 (6%)
Query: 76 LKQRIIKQVEYYFSDENLPTDKYMMNLIRKNKEGFVPISVIASFRKLKRLTRNHAWIVAA 135
L+ +I Q+EYYF D NLP DK++ I+ + EG+VP+ + F +L RLT + IV A
Sbjct: 13 LEAKICHQIEYYFGDFNLPRDKFLKEQIKLD-EGWVPLEIXIKFNRLNRLTTDFNVIVEA 71
Query: 136 LRES--SLLVVSSNGKKVKRLNPLPVTEVRDP-----KLFTVLVENLPEDHSVENMQRIF 188
L +S L +S + K++R P+ EV D K +V ++ P D ++++++
Sbjct: 72 LSKSKAELXEISEDKTKIRRSPSKPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWL 131
Query: 189 AEAGKIKSICIR 200
+ G++ +I R
Sbjct: 132 EDKGQVLNIQXR 143
>pdb|1S29|A Chain A, La Autoantigen N-Terminal Domain
Length = 92
Score = 67.8 bits (164), Expect = 4e-12, Method: Compositional matrix adjust.
Identities = 33/87 (37%), Positives = 56/87 (64%)
Query: 72 LTDDLKQRIIKQVEYYFSDENLPTDKYMMNLIRKNKEGFVPISVIASFRKLKRLTRNHAW 131
L+ + KQ++ KQVE+YFSD N+ D ++ +N EGFV + + +F+++ +T +
Sbjct: 6 LSSENKQKLQKQVEFYFSDVNVQRDIFLKGKXAENAEGFVSLETLLTFKRVNSVTTDVKE 65
Query: 132 IVAALRESSLLVVSSNGKKVKRLNPLP 158
+V A+R S LV+S +G V+R +PLP
Sbjct: 66 VVEAIRPSEKLVLSEDGLXVRRRDPLP 92
>pdb|1S7A|A Chain A, Nmr Structure Of The La Motif Of Human La Protein
Length = 103
Score = 64.3 bits (155), Expect = 4e-11, Method: Compositional matrix adjust.
Identities = 36/91 (39%), Positives = 56/91 (61%), Gaps = 3/91 (3%)
Query: 76 LKQRIIKQVEYYFSDENLPTDKYMMNLIRKNKEGFVPISVIASFRKLKRLTRNHAWIVAA 135
L+ +I Q+EYYF D NLP DK++ I+ + EG+VP+ ++ F +L RLT + IV A
Sbjct: 13 LEAKICHQIEYYFGDFNLPRDKFLKEQIKLD-EGWVPLEIMIKFNRLNRLTTDFNVIVEA 71
Query: 136 LRES--SLLVVSSNGKKVKRLNPLPVTEVRD 164
L +S L+ +S + K++R P+ EV D
Sbjct: 72 LSKSKAELMEISEDKTKIRRSPSKPLPEVTD 102
>pdb|2CQK|A Chain A, Solution Structure Of The La Domain Of C-Mpl Binding
Protein
Length = 101
Score = 59.3 bits (142), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 31/83 (37%), Positives = 54/83 (65%), Gaps = 2/83 (2%)
Query: 70 AVLTDDLKQRIIKQVEYYFSDENLPTDKYMMNLIRKNKEGFVPISVIASFRKLKRLTRNH 129
AV T+DLK+ + KQ+E+ FS ENL D Y+++ + + + F+PI +A+ ++K+LT +
Sbjct: 8 AVSTEDLKECLKKQLEFCFSRENLSKDLYLIS--QMDSDQFIPIWTVANMEEIKKLTTDP 65
Query: 130 AWIVAALRESSLLVVSSNGKKVK 152
I+ LR S ++ V G+KV+
Sbjct: 66 DLILEVLRSSPMVQVDEKGEKVR 88
>pdb|3HTX|A Chain A, Crystal Structure Of Small Rna Methyltransferase Hen1
pdb|3HTX|D Chain D, Crystal Structure Of Small Rna Methyltransferase Hen1
Length = 950
Score = 33.5 bits (75), Expect = 0.096, Method: Compositional matrix adjust.
Identities = 18/51 (35%), Positives = 31/51 (60%), Gaps = 6/51 (11%)
Query: 74 DDLKQRIIKQVEYYFSDENL----PTDKYMMNLIRKNKE--GFVPISVIAS 118
D+ + I+ +++Y FSDE L P ++ +R++ E G VP+SVIA+
Sbjct: 105 DEARDEIVGRIKYIFSDEFLSAEHPLGAHLRAALRRDGERCGSVPVSVIAT 155
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 27.7 bits (60), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 14/41 (34%), Positives = 22/41 (53%)
Query: 169 TVLVENLPEDHSVENMQRIFAEAGKIKSICIRDPNVVEESK 209
TV V NLP + ++ RIF++ GK+ + I +SK
Sbjct: 18 TVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSK 58
>pdb|2GHP|A Chain A, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|B Chain B, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|C Chain C, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|D Chain D, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|E Chain E, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|F Chain F, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|G Chain G, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|H Chain H, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
Length = 292
Score = 27.7 bits (60), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 13/40 (32%), Positives = 23/40 (57%)
Query: 162 VRDPKLFTVLVENLPEDHSVENMQRIFAEAGKIKSICIRD 201
R+ +L TVLV+NLP+ ++ + + F G I + + D
Sbjct: 36 TRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVAD 75
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
0.314 0.132 0.377
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,880,770
Number of Sequences: 62578
Number of extensions: 209606
Number of successful extensions: 398
Number of sequences better than 100.0: 20
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 381
Number of HSP's gapped (non-prelim): 21
length of query: 214
length of database: 14,973,337
effective HSP length: 95
effective length of query: 119
effective length of database: 9,028,427
effective search space: 1074382813
effective search space used: 1074382813
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: 49 (23.5 bits)