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= 043731
(498 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 = 69.3 bits (168), Expect = 5e-12, Method: Compositional matrix adjust.
Identities = 41/99 (41%), Positives = 56/99 (56%), Gaps = 12/99 (12%)
Query: 4 LDEETAQAVLRQVEFYFSDSNIPTDEFLRGKISESSDAMVSLALICSFKRMKEHLHLGNV 63
L E Q + +QVEFYFSD N+ D FL+GK +E+++ VSL + +FKR+ N
Sbjct: 6 LSSENKQKLQKQVEFYFSDVNVQRDIFLKGKXAENAEGFVSLETLLTFKRV-------NS 58
Query: 64 KSEDIPEDTLEAVAETLRKSSSLKLSEDGMKVGRSAELP 102
+ D+ E V E +R S L LSEDG+ V R LP
Sbjct: 59 VTTDVKE-----VVEAIRPSEKLVLSEDGLXVRRRDPLP 92
>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 = 55.1 bits (131), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 45/178 (25%), Positives = 85/178 (47%), Gaps = 24/178 (13%)
Query: 1 MASLDEETAQAVLRQVEFYFSDSNIPTDEFLRGKISESSDAMVSLALICSFKRMKEHLHL 60
MA+L+ + + Q+E+YF D N+P D+FL+ +I + + V L ++ F R+
Sbjct: 9 MAALEAK----ICHQIEYYFGDFNLPRDKFLKEQI-KLDEGWVPLEIMIKFNRLNRLTTD 63
Query: 61 GNVKSEDIPEDTLEAVAETLRKSSS--LKLSEDGMKVGRSAELPTAE---EMKEQLDVRT 115
NV + E L KS + +++SED K+ RS P E E K + R+
Sbjct: 64 FNV------------IVEALSKSKAELMEISEDKTKIRRSPSKPLPEVTDEYKNDVKNRS 111
Query: 116 IAATPLEYDVKREDVEAFFSQHVKVNSVRLPRHVADKRLFCGTALIEFSTEEDAEKVL 173
+ D +D++ + +V ++++ R + + F G+ + F + E A+K +
Sbjct: 112 VYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL--HKAFKGSIFVVFDSIESAKKFV 167
>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 = 50.8 bits (120), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 42/167 (25%), Positives = 76/167 (45%), Gaps = 20/167 (11%)
Query: 12 VLRQVEFYFSDSNIPTDEFLRGKISESSDAMVSLALICSFKRMKEHLHLGNVKSEDIPED 71
+ Q+E+YF D N+P D+FL+ +I + + V L + F R+ NV
Sbjct: 18 ICHQIEYYFGDFNLPRDKFLKEQI-KLDEGWVPLEIXIKFNRLNRLTTDFNV-------- 68
Query: 72 TLEAVAETLRKSSS--LKLSEDGMKVGRSAELPTAE---EMKEQLDVRTIAATPLEYDVK 126
+ E L KS + ++SED K+ RS P E E K + R++ D
Sbjct: 69 ----IVEALSKSKAELXEISEDKTKIRRSPSKPLPEVTDEYKNDVKNRSVYIKGFPTDAT 124
Query: 127 REDVEAFFSQHVKVNSVRLPRHVADKRLFCGTALIEFSTEEDAEKVL 173
+D++ + +V +++ R + + F G+ + F + E A+K +
Sbjct: 125 LDDIKEWLEDKGQVLNIQXRRTL--HKAFKGSIFVVFDSIESAKKFV 169
>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 = 50.8 bits (120), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 42/167 (25%), Positives = 76/167 (45%), Gaps = 20/167 (11%)
Query: 12 VLRQVEFYFSDSNIPTDEFLRGKISESSDAMVSLALICSFKRMKEHLHLGNVKSEDIPED 71
+ Q+E+YF D N+P D+FL+ +I + + V L + F R+ NV
Sbjct: 17 ICHQIEYYFGDFNLPRDKFLKEQI-KLDEGWVPLEIXIKFNRLNRLTTDFNV-------- 67
Query: 72 TLEAVAETLRKSSS--LKLSEDGMKVGRSAELPTAE---EMKEQLDVRTIAATPLEYDVK 126
+ E L KS + ++SED K+ RS P E E K + R++ D
Sbjct: 68 ----IVEALSKSKAELXEISEDKTKIRRSPSKPLPEVTDEYKNDVKNRSVYIKGFPTDAT 123
Query: 127 REDVEAFFSQHVKVNSVRLPRHVADKRLFCGTALIEFSTEEDAEKVL 173
+D++ + +V +++ R + + F G+ + F + E A+K +
Sbjct: 124 LDDIKEWLEDKGQVLNIQXRRTLH--KAFKGSIFVVFDSIESAKKFV 168
>pdb|1S7A|A Chain A, Nmr Structure Of The La Motif Of Human La Protein
Length = 103
Score = 44.3 bits (103), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 29/96 (30%), Positives = 47/96 (48%), Gaps = 15/96 (15%)
Query: 12 VLRQVEFYFSDSNIPTDEFLRGKISESSDAMVSLALICSFKRMKEHLHLGNVKSEDIPED 71
+ Q+E+YF D N+P D+FL+ +I + + V L ++ F R+ NV
Sbjct: 17 ICHQIEYYFGDFNLPRDKFLKEQI-KLDEGWVPLEIMIKFNRLNRLTTDFNV-------- 67
Query: 72 TLEAVAETLRKSSS--LKLSEDGMKVGRSAELPTAE 105
+ E L KS + +++SED K+ RS P E
Sbjct: 68 ----IVEALSKSKAELMEISEDKTKIRRSPSKPLPE 99
>pdb|1OWX|A Chain A, Solution Structure Of The C-Terminal Rrm Of Human La
(La225- 334)
Length = 121
Score = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 26/74 (35%), Positives = 34/74 (45%), Gaps = 2/74 (2%)
Query: 330 DVVMREDLKSVFHKFGTVKFIDFKIGAESGYIRFEEPEGXXXXXXXXXXXQEGGLSVKNF 389
D REDL +F G +K+IDF GA+ G I F+E G L ++N
Sbjct: 29 DQTCREDLHILFSNHGEIKWIDFVRGAKEGIILFKEK--AKEALGKAKDANNGNLQLRNK 86
Query: 390 IAVLEPVTGEAEKE 403
E + GE EKE
Sbjct: 87 EVTWEVLEGEVEKE 100
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 38.9 bits (89), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 39/119 (32%), Positives = 56/119 (47%), Gaps = 24/119 (20%)
Query: 77 AETLRKSSSLKLSEDGMKV-GRSAEL--PTAEEMKEQLDVRTIAATPLEYDVKREDVEAF 133
AE L K+ L G+KV G +L P ++ K++ D RT+ A L Y V +++++
Sbjct: 58 AEDLEKALELT----GLKVFGNEIKLEKPKGKDSKKERDARTLLAKNLPYKVTQDELKEV 113
Query: 134 FSQHVKVNSVRLPRHVADKRLFCGTALIEFSTEEDAEKVL--KQG---------LFYAG 181
F ++ R V+ G A IEF TE DAEK KQG L+Y G
Sbjct: 114 FEDAAEI------RLVSKDGKSKGIAYIEFKTEADAEKTFEEKQGTEIDGRSISLYYTG 166
>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 = 32.3 bits (72), Expect = 0.61, Method: Compositional matrix adjust.
Identities = 36/119 (30%), Positives = 55/119 (46%), Gaps = 24/119 (20%)
Query: 77 AETLRKSSSLKLSEDGMKV-GRSAEL--PTAEEMKEQLDVRTIAATPLEYDVKREDVEAF 133
AE L K+ L G+KV G +L P + K+ RT+ A L +++ ++++
Sbjct: 64 AEDLEKALELT----GLKVFGNEIKLEKPKGRDSKKVRAARTLLAKNLSFNITEDELKEV 119
Query: 134 FSQHVKVNSVRLPRHVADKRLFCGTALIEFSTEEDAEKVL--KQG---------LFYAG 181
F +++ R V+ G A IEF +E DAEK L KQG L+Y G
Sbjct: 120 FEDALEI------RLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTG 172
>pdb|2LMI|A Chain A, Nmr Structure Of The Protein Bc040485 From Homo Sapiens
Length = 107
Score = 32.3 bits (72), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 35/74 (47%), Gaps = 7/74 (9%)
Query: 112 DVRTIAATPLEYDVKREDVEAFFSQHVKV----NSVRLPRHVADKRLFCGTALIEFSTEE 167
DV I A L + EDV FFS ++ N + + KR G ALIE +E+
Sbjct: 10 DVFLIRAQGLPWSCTMEDVLNFFSD-CRIRNGENGIHFLLNRDGKRR--GDALIEMESEQ 66
Query: 168 DAEKVLKQGLFYAG 181
D +K L++ Y G
Sbjct: 67 DVQKALEKHRMYMG 80
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 30.8 bits (68), Expect = 1.6, Method: Composition-based stats.
Identities = 19/78 (24%), Positives = 37/78 (47%), Gaps = 6/78 (7%)
Query: 96 GRSAELPTAEEMKEQLDVRTIAATPLEYDVKREDVEAFFSQHVKVNSVRLPRHVADKRLF 155
G S ++P + + L VR I + + ++ FS ++ +VRLP+ +
Sbjct: 4 GSSGQVPKKQTTSKIL-VRNIP-----FQANQREIRELFSTFGELKTVRLPKKMTGTGAH 57
Query: 156 CGTALIEFSTEEDAEKVL 173
G ++F T++DA+K
Sbjct: 58 RGFGFVDFITKQDAKKAF 75
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 30.8 bits (68), Expect = 1.9, Method: Composition-based stats.
Identities = 16/55 (29%), Positives = 27/55 (49%)
Query: 121 LEYDVKREDVEAFFSQHVKVNSVRLPRHVADKRLFCGTALIEFSTEEDAEKVLKQ 175
L +V ++ + FS + K+ + +P L G A +EF ++AEK LK
Sbjct: 12 LTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKH 66
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 30.0 bits (66), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 38/80 (47%), Gaps = 17/80 (21%)
Query: 113 VRTIAATPLEYDVKREDVEAFFSQHVKVNSVRLPRHVADKRLFCGTALIEFSTEEDAEKV 172
RT+ A L +++ ++++ F +++ R V+ G A IEF +E DAEK
Sbjct: 16 ARTLLAKNLSFNITEDELKEVFEDALEI------RLVSQDGKSKGIAYIEFKSEADAEKN 69
Query: 173 L--KQG---------LFYAG 181
L KQG L+Y G
Sbjct: 70 LEEKQGAEIDGRSVSLYYTG 89
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 29.3 bits (64), Expect = 4.9, Method: Composition-based stats.
Identities = 20/57 (35%), Positives = 30/57 (52%), Gaps = 5/57 (8%)
Query: 109 EQLDVRTIAATPLEYDVKREDVEAFFSQHVKVNSVRLPRHVADK--RLFCGTALIEF 163
E+ D RT+ L ++ D+E FFS KV VR+ ++D+ R G A +EF
Sbjct: 21 EERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRI---ISDRNSRRSKGIAYVEF 74
>pdb|3UWT|A Chain A, Crystal Structure Of A Rna Binding Domain Of Poly-U
Binding Splicing Factor 60kda (Puf60) From Homo Sapiens
At 2.50 A Resolution
Length = 200
Score = 29.3 bits (64), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 20/79 (25%), Positives = 36/79 (45%), Gaps = 5/79 (6%)
Query: 74 EAVAETLRKSSSLKLSEDGMKVGRSAELPTAEEMKEQL-----DVRTIAATPLEYDVKRE 128
EA L + +S+ L +KVGR + + A+ + +QL I + D+ +
Sbjct: 65 EAAQLALEQXNSVXLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDD 124
Query: 129 DVEAFFSQHVKVNSVRLPR 147
D+++ F K+ S L R
Sbjct: 125 DIKSVFEAFGKIKSCTLAR 143
>pdb|3OHM|B Chain B, Crystal Structure Of Activated G Alpha Q Bound To Its
Effector Phospholipase C Beta 3
Length = 885
Score = 29.3 bits (64), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 28/60 (46%), Gaps = 6/60 (10%)
Query: 407 LLRGNQERHR------DVKGEEKHLEAENKAASEKMIQQEDAQIKPGKFEQHEKPGISSG 460
+L N++RHR D G ++ LE N A SE E + + G PG+S+G
Sbjct: 462 ILVKNKKRHRPSAGGPDSAGRKRPLEQSNSALSESSAATEPSSPQLGSPSSDSCPGLSNG 521
>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of
Fbp-Interacting Repressor (Fir)
pdb|2KXH|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fir In
The Complex With Fbp Nbox Peptide
Length = 199
Score = 28.9 bits (63), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 25/108 (23%), Positives = 45/108 (41%), Gaps = 20/108 (18%)
Query: 60 LGNVKSEDIPEDTL---------------EAVAETLRKSSSLKLSEDGMKVGRSAELPTA 104
G +KS D+ D++ EA L + +S+ L +KVGR + + A
Sbjct: 37 FGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQA 96
Query: 105 EEMKEQL-----DVRTIAATPLEYDVKREDVEAFFSQHVKVNSVRLPR 147
+ + +QL I + D+ +D+++ F K+ S L R
Sbjct: 97 QPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLAR 144
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 28.9 bits (63), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 15/63 (23%), Positives = 33/63 (52%), Gaps = 6/63 (9%)
Query: 124 DVKREDVEAFFSQHVKVNSVRLPRHVADKRLFCGTALIEFSTEEDAEKVLKQGLFYAGVE 183
D+ E+++ FF Q+ +V V +P+ F A + F+ ++ A+ + + L G+
Sbjct: 22 DMTAEELQQFFCQYGEVVDVFIPKP------FRAFAFVTFADDKVAQSLCGEDLIIKGIS 75
Query: 184 LHL 186
+H+
Sbjct: 76 VHI 78
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 28.9 bits (63), Expect = 7.4, Method: Composition-based stats.
Identities = 12/38 (31%), Positives = 23/38 (60%), Gaps = 3/38 (7%)
Query: 332 VMREDLKSVFHKFGTVKFIDFKI---GAESGYIRFEEP 366
+ +D++ VF+K+G ++ ID K G ++ FE+P
Sbjct: 34 IRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDP 71
>pdb|2QFJ|A Chain A, Crystal Structure Of First Two Rrm Domains Of Fir Bound To
Ssdna From A Portion Of Fuse
pdb|2QFJ|B Chain B, Crystal Structure Of First Two Rrm Domains Of Fir Bound To
Ssdna From A Portion Of Fuse
Length = 216
Score = 28.9 bits (63), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 26/108 (24%), Positives = 47/108 (43%), Gaps = 20/108 (18%)
Query: 60 LGNVKSEDIPEDTL---------------EAVAETLRKSSSLKLSEDGMKVGRSAELPTA 104
G +KS D+ D++ EA L + +S+ L +KVGR + + A
Sbjct: 52 FGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQA 111
Query: 105 EEMKEQL--DVRT---IAATPLEYDVKREDVEAFFSQHVKVNSVRLPR 147
+ + +QL + R I + D+ +D+++ F K+ S L R
Sbjct: 112 QPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLAR 159
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 28.5 bits (62), Expect = 9.5, Method: Composition-based stats.
Identities = 15/63 (23%), Positives = 32/63 (50%), Gaps = 6/63 (9%)
Query: 124 DVKREDVEAFFSQHVKVNSVRLPRHVADKRLFCGTALIEFSTEEDAEKVLKQGLFYAGVE 183
D+ +++ FFSQ+ V V +P+ F A + F+ ++ A+ + + L G+
Sbjct: 16 DMTEDELREFFSQYGDVMDVFIPKP------FRAFAFVTFADDQIAQSLCGEDLIIKGIS 69
Query: 184 LHL 186
+H+
Sbjct: 70 VHI 72
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
0.311 0.129 0.358
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,730,983
Number of Sequences: 62578
Number of extensions: 469983
Number of successful extensions: 833
Number of sequences better than 100.0: 25
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 17
Number of HSP's that attempted gapping in prelim test: 819
Number of HSP's gapped (non-prelim): 30
length of query: 498
length of database: 14,973,337
effective HSP length: 103
effective length of query: 395
effective length of database: 8,527,803
effective search space: 3368482185
effective search space used: 3368482185
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: 53 (25.0 bits)