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= 046325
(442 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1S29|A Chain A, La Autoantigen N-Terminal Domain
Length = 92
Score = 57.0 bits (136), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 29/86 (33%), Positives = 52/86 (60%)
Query: 136 LTDDLRAKIIKQVEYQFSDMSLLANETLSKHVNKDPEGFVPLSVIGSMKKIKSLVGNNHL 195
L+ + + K+ KQVE+ FSD+++ + L ++ EGFV L + + K++ S+ +
Sbjct: 6 LSSENKQKLQKQVEFYFSDVNVQRDIFLKGKXAENAEGFVSLETLLTFKRVNSVTTDVKE 65
Query: 196 LAQALRSSSKLIVSNDGKKVRRKHPF 221
+ +A+R S KL++S DG VRR+ P
Sbjct: 66 VVEAIRPSEKLVLSEDGLXVRRRDPL 91
>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 = 52.4 bits (124), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 36/131 (27%), Positives = 73/131 (55%), Gaps = 8/131 (6%)
Query: 140 LRAKIIKQVEYQFSDMSLLANETLSKHVNKDPEGFVPLSVIGSMKKIKSLVGNNHLLAQA 199
L AKI Q+EY F D +L ++ L + + D EG+VPL ++ ++ L + +++ +A
Sbjct: 12 LEAKICHQIEYYFGDFNLPRDKFLKEQIKLD-EGWVPLEIMIKFNRLNRLTTDFNVIVEA 70
Query: 200 L-RSSSKLI-VSNDGKKVRR--KHPF---TDKEREELQSCTVVAENLPEDHSHQNLEKIF 252
L +S ++L+ +S D K+RR P TD+ + ++++ +V + P D + ++++
Sbjct: 71 LSKSKAELMEISEDKTKIRRSPSKPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWL 130
Query: 253 GVVGSVKTIRI 263
G V I++
Sbjct: 131 EDKGQVLNIQM 141
>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 = 49.7 bits (117), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 35/130 (26%), Positives = 67/130 (51%), Gaps = 8/130 (6%)
Query: 140 LRAKIIKQVEYQFSDMSLLANETLSKHVNKDPEGFVPLSVIGSMKKIKSLVGNNHLLAQA 199
L AKI Q+EY F D +L ++ L + + D EG+VPL + ++ L + +++ +A
Sbjct: 14 LEAKICHQIEYYFGDFNLPRDKFLKEQIKLD-EGWVPLEIXIKFNRLNRLTTDFNVIVEA 72
Query: 200 LRSSSKLI--VSNDGKKVRR--KHPF---TDKEREELQSCTVVAENLPEDHSHQNLEKIF 252
L S + +S D K+RR P TD+ + ++++ +V + P D + ++++
Sbjct: 73 LSKSKAELXEISEDKTKIRRSPSKPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWL 132
Query: 253 GVVGSVKTIR 262
G V I+
Sbjct: 133 EDKGQVLNIQ 142
>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 = 49.7 bits (117), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 35/130 (26%), Positives = 67/130 (51%), Gaps = 8/130 (6%)
Query: 140 LRAKIIKQVEYQFSDMSLLANETLSKHVNKDPEGFVPLSVIGSMKKIKSLVGNNHLLAQA 199
L AKI Q+EY F D +L ++ L + + D EG+VPL + ++ L + +++ +A
Sbjct: 13 LEAKICHQIEYYFGDFNLPRDKFLKEQIKLD-EGWVPLEIXIKFNRLNRLTTDFNVIVEA 71
Query: 200 LRSSSKLI--VSNDGKKVRR--KHPF---TDKEREELQSCTVVAENLPEDHSHQNLEKIF 252
L S + +S D K+RR P TD+ + ++++ +V + P D + ++++
Sbjct: 72 LSKSKAELXEISEDKTKIRRSPSKPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWL 131
Query: 253 GVVGSVKTIR 262
G V I+
Sbjct: 132 EDKGQVLNIQ 141
>pdb|2CQK|A Chain A, Solution Structure Of The La Domain Of C-Mpl Binding
Protein
Length = 101
Score = 49.3 bits (116), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 31/89 (34%), Positives = 49/89 (55%), Gaps = 10/89 (11%)
Query: 135 VLTDDLRAKIIKQVEYQFSDMSLLANETLSKHV----NKDPEGFVPLSVIGSMKKIKSLV 190
V T+DL+ + KQ+E+ FS E LSK + D + F+P+ + +M++IK L
Sbjct: 9 VSTEDLKECLKKQLEFCFS------RENLSKDLYLISQMDSDQFIPIWTVANMEEIKKLT 62
Query: 191 GNNHLLAQALRSSSKLIVSNDGKKVRRKH 219
+ L+ + LRSS + V G+KVR H
Sbjct: 63 TDPDLILEVLRSSPMVQVDEKGEKVRPSH 91
>pdb|1S7A|A Chain A, Nmr Structure Of The La Motif Of Human La Protein
Length = 103
Score = 47.8 bits (112), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 27/80 (33%), Positives = 49/80 (61%), Gaps = 3/80 (3%)
Query: 140 LRAKIIKQVEYQFSDMSLLANETLSKHVNKDPEGFVPLSVIGSMKKIKSLVGNNHLLAQA 199
L AKI Q+EY F D +L ++ L + + D EG+VPL ++ ++ L + +++ +A
Sbjct: 13 LEAKICHQIEYYFGDFNLPRDKFLKEQIKLD-EGWVPLEIMIKFNRLNRLTTDFNVIVEA 71
Query: 200 L-RSSSKLI-VSNDGKKVRR 217
L +S ++L+ +S D K+RR
Sbjct: 72 LSKSKAELMEISEDKTKIRR 91
>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex
With Rna
pdb|2KM8|C Chain C, Interdomain Rrm Packing Contributes To Rna Recognition In
The Rna15, Hrp1, Anchor Rna 3' Processing Ternary
Complex
Length = 167
Score = 32.7 bits (73), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 14/45 (31%), Positives = 22/45 (48%)
Query: 230 QSCTVVAENLPEDHSHQNLEKIFGVVGSVKTIRICHPPESNSSRA 274
+SC + L D + NL + FG G+V ++I P + SR
Sbjct: 2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRG 46
>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 = 31.6 bits (70), Expect = 0.89, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 32/56 (57%), Gaps = 6/56 (10%)
Query: 134 NVLTDDLRAKIIKQVEYQFSDMSLLANETLSKH----VNKDPE--GFVPLSVIGSM 183
++ D+ R +I+ +++Y FSD L A L H + +D E G VP+SVI ++
Sbjct: 101 DLTVDEARDEIVGRIKYIFSDEFLSAEHPLGAHLRAALRRDGERCGSVPVSVIATV 156
>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos
Rna
pdb|1G2E|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The Tumor
Necrosis Factor Alpha Rna
Length = 167
Score = 30.0 bits (66), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 17/82 (20%), Positives = 35/82 (42%), Gaps = 10/82 (12%)
Query: 234 VVAENLPEDHSHQNLEKIFGVVGSVKTIRICHPPESNSSRAKSDFFVSNKLHALVEYEST 293
++ LP++ + + +FG +G +++ ++ + S + V Y
Sbjct: 5 LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLG----------YGFVNYIDP 54
Query: 294 DIAEKAVEKLNDERNWRKGLRV 315
AEKA+ LN R K ++V
Sbjct: 55 KDAEKAINTLNGLRLQTKTIKV 76
>pdb|2CPZ|A Chain A, Solution Structure Of Rna Binding Domain 3 In Cug Triplet
Repeat Rna-Binding Protein 1
pdb|2RQ4|A Chain A, Refinement Of Rna Binding Domain 3 In Cug Triplet Repeat
Rna-Binding Protein 1
pdb|2RQC|A Chain A, Solution Structure Of Rna-Binding Domain 3 Of Cugbp1 In
Complex With Rna (Ug)3
Length = 115
Score = 29.3 bits (64), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 19/93 (20%), Positives = 45/93 (48%), Gaps = 10/93 (10%)
Query: 225 EREELQSCTVVAENLPEDHSHQNLEKIFGVVGSVKTIRICHPPESNSSRAKSDFFVSNKL 284
++E + + +LP++ Q+L ++F G+V + ++ ++N S K
Sbjct: 19 QKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLS----------KC 68
Query: 285 HALVEYESTDIAEKAVEKLNDERNWRKGLRVRV 317
V Y++ A+ A++ +N + K L+V++
Sbjct: 69 FGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQL 101
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 28.5 bits (62), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 25/108 (23%), Positives = 42/108 (38%), Gaps = 14/108 (12%)
Query: 198 QALRSSSKLIVSNDGKKVRRKHPFTDKEREELQSCTVVAENLPEDHSHQNLEKIFGVVGS 257
+A++ + + V N KV P E ++ + NLP + L+ IFG GS
Sbjct: 60 RAIKVLNGITVRNKRLKVSYARP----GGESIKDTNLYVTNLPRTITDDQLDTIFGKYGS 115
Query: 258 VKTIRICHPPESNSSRAKSDFFVSNKLHALVEYESTDIAEKAVEKLND 305
+ I + R A V Y + A++A+ LN+
Sbjct: 116 IVQKNILRDKLTGRPRGV----------AFVRYNKREEAQEAISALNN 153
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 28.5 bits (62), Expect = 8.3, Method: Compositional matrix adjust.
Identities = 21/88 (23%), Positives = 36/88 (40%), Gaps = 18/88 (20%)
Query: 228 ELQSCTVVAENLPEDHSHQNLEKIFGVVGSVKTIRICHPPESNSSRAKSDFFVSNKLHAL 287
EL + + P D L +IFG G +K ++I + A
Sbjct: 1 ELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILNG------------------FAF 42
Query: 288 VEYESTDIAEKAVEKLNDERNWRKGLRV 315
VE+E + A KA+E+++ + + L V
Sbjct: 43 VEFEEAESAAKAIEEVHGKSFANQPLEV 70
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 28.1 bits (61), Expect = 9.1, Method: Compositional matrix adjust.
Identities = 19/81 (23%), Positives = 34/81 (41%), Gaps = 18/81 (22%)
Query: 224 KEREELQSCTVVAENLPEDHSHQNLEKIFGVVGSVKTIRICHPPESNSSRAKSDFFVSNK 283
++ EL + + P D L +IFG G +K ++I +
Sbjct: 24 RQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILNG----------------- 66
Query: 284 LHALVEYESTDIAEKAVEKLN 304
A VE+E + A KA+E+++
Sbjct: 67 -FAFVEFEEAESAAKAIEEVH 86
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 28.1 bits (61), Expect = 9.4, Method: Composition-based stats.
Identities = 21/85 (24%), Positives = 37/85 (43%), Gaps = 15/85 (17%)
Query: 238 NLPEDHSHQNLEKIFGVVGSVKTIRICHPPES---------------NSSRAKSDFFVSN 282
NLP + + + IFG G ++ IR+ + PE+ N+ S F VSN
Sbjct: 15 NLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHLSGFNVSN 74
Query: 283 KLHALVEYESTDIAEKAVEKLNDER 307
+ ++ Y + +K K +E+
Sbjct: 75 RYLVVLYYNANRAFQKMDTKKKEEQ 99
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 0.130 0.372
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,029,169
Number of Sequences: 62578
Number of extensions: 344552
Number of successful extensions: 623
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 13
Number of HSP's that attempted gapping in prelim test: 614
Number of HSP's gapped (non-prelim): 17
length of query: 442
length of database: 14,973,337
effective HSP length: 102
effective length of query: 340
effective length of database: 8,590,381
effective search space: 2920729540
effective search space used: 2920729540
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: 53 (25.0 bits)