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= psy5142
(410 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 = 157 bits (396), Expect = 1e-38, Method: Compositional matrix adjust.
Identities = 84/176 (47%), Positives = 119/176 (67%), Gaps = 9/176 (5%)
Query: 11 GNSGAEAEVSKLENQIIEQIEYYFSDINLARDKFLQGEIKKDDGWVELTTMLKFARLAKM 70
G++G +++ LE +I QIEYYF D NL RDKFL+ +IK D+GWV L M+KF RL ++
Sbjct: 1 GSNGDNEKMAALEAKICHQIEYYFGDFNLPRDKFLKEQIKLDEGWVPLEIMIKFNRLNRL 60
Query: 71 TTEAKVIVDALKKSTSKLIEVNEDGTKIRRNPEKELPTFDIDFVKDLIAQSLYVKYIPVD 130
TT+ VIV+AL KS ++L+E++ED TKIRR+P K LP ++ D+ +S+Y+K P D
Sbjct: 61 TTDFNVIVEALSKSKAELMEISEDKTKIRRSPSKPLPEVTDEYKNDVKNRSVYIKGFPTD 120
Query: 131 ATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKENAEKFL 186
ATLDDIK++ + ++ NI MR K FKGSIFV FD+ E+A+KF+
Sbjct: 121 ATLDDIKEWLEDKG----QVLNIQMRR-----TLHKAFKGSIFVVFDSIESAKKFV 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 = 149 bits (376), Expect = 3e-36, Method: Compositional matrix adjust.
Identities = 84/181 (46%), Positives = 115/181 (63%), Gaps = 12/181 (6%)
Query: 6 SSATNGNSGAEAEVSKLENQIIEQIEYYFSDINLARDKFLQGEIKKDDGWVELTTMLKFA 65
S A NG++ A LE +I QIEYYF D NL RDKFL+ +IK D+GWV L +KF
Sbjct: 1 SXAENGDNEKXA---ALEAKICHQIEYYFGDFNLPRDKFLKEQIKLDEGWVPLEIXIKFN 57
Query: 66 RLAKMTTEAKVIVDALKKSTSKLIEVNEDGTKIRRNPEKELPTFDIDFVKDLIAQSLYVK 125
RL ++TT+ VIV+AL KS ++L E++ED TKIRR+P K LP ++ D+ +S+Y+K
Sbjct: 58 RLNRLTTDFNVIVEALSKSKAELXEISEDKTKIRRSPSKPLPEVTDEYKNDVKNRSVYIK 117
Query: 126 YIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKENAEKF 185
P DATLDDIK++ + + N Q + K FKGSIFV FD+ E+A+KF
Sbjct: 118 GFPTDATLDDIKEWLEDKGQ---------VLNIQXRRTLHKAFKGSIFVVFDSIESAKKF 168
Query: 186 L 186
+
Sbjct: 169 V 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 = 147 bits (372), Expect = 7e-36, Method: Compositional matrix adjust.
Identities = 83/179 (46%), Positives = 114/179 (63%), Gaps = 12/179 (6%)
Query: 8 ATNGNSGAEAEVSKLENQIIEQIEYYFSDINLARDKFLQGEIKKDDGWVELTTMLKFARL 67
A NG++ A LE +I QIEYYF D NL RDKFL+ +IK D+GWV L +KF RL
Sbjct: 2 AENGDNEKXA---ALEAKICHQIEYYFGDFNLPRDKFLKEQIKLDEGWVPLEIXIKFNRL 58
Query: 68 AKMTTEAKVIVDALKKSTSKLIEVNEDGTKIRRNPEKELPTFDIDFVKDLIAQSLYVKYI 127
++TT+ VIV+AL KS ++L E++ED TKIRR+P K LP ++ D+ +S+Y+K
Sbjct: 59 NRLTTDFNVIVEALSKSKAELXEISEDKTKIRRSPSKPLPEVTDEYKNDVKNRSVYIKGF 118
Query: 128 PVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKENAEKFL 186
P DATLDDIK++ + + N Q + K FKGSIFV FD+ E+A+KF+
Sbjct: 119 PTDATLDDIKEWLEDKGQ---------VLNIQXRRTLHKAFKGSIFVVFDSIESAKKFV 168
>pdb|1S7A|A Chain A, Nmr Structure Of The La Motif Of Human La Protein
Length = 103
Score = 110 bits (274), Expect = 2e-24, Method: Compositional matrix adjust.
Identities = 52/97 (53%), Positives = 71/97 (73%)
Query: 11 GNSGAEAEVSKLENQIIEQIEYYFSDINLARDKFLQGEIKKDDGWVELTTMLKFARLAKM 70
+G +++ LE +I QIEYYF D NL RDKFL+ +IK D+GWV L M+KF RL ++
Sbjct: 2 AENGDNEKMAALEAKICHQIEYYFGDFNLPRDKFLKEQIKLDEGWVPLEIMIKFNRLNRL 61
Query: 71 TTEAKVIVDALKKSTSKLIEVNEDGTKIRRNPEKELP 107
TT+ VIV+AL KS ++L+E++ED TKIRR+P K LP
Sbjct: 62 TTDFNVIVEALSKSKAELMEISEDKTKIRRSPSKPLP 98
>pdb|1S29|A Chain A, La Autoantigen N-Terminal Domain
Length = 92
Score = 63.9 bits (154), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 32/73 (43%), Positives = 54/73 (73%), Gaps = 3/73 (4%)
Query: 29 QIEYYFSDINLARDKFLQGEIKKD-DGWVELTTMLKFARLAKMTTEAKVIVDALKKSTSK 87
Q+E+YFSD+N+ RD FL+G+ ++ +G+V L T+L F R+ +TT+ K +V+A++ S K
Sbjct: 17 QVEFYFSDVNVQRDIFLKGKXAENAEGFVSLETLLTFKRVNSVTTDVKEVVEAIRPS-EK 75
Query: 88 LIEVNEDGTKIRR 100
L+ ++EDG +RR
Sbjct: 76 LV-LSEDGLXVRR 87
>pdb|1S79|A Chain A, Solution Structure Of The Central Rrm Of Human La Protein
Length = 103
Score = 52.4 bits (124), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 31/71 (43%), Positives = 44/71 (61%), Gaps = 9/71 (12%)
Query: 116 DLIAQSLYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVT 175
D+ +S+Y+K P DATLDDIK++ + ++ NI MR K FKGSIFV
Sbjct: 8 DVKNRSVYIKGFPTDATLDDIKEWLEDKG----QVLNIQMRR-----TLHKAFKGSIFVV 58
Query: 176 FDNKENAEKFL 186
FD+ E+A+KF+
Sbjct: 59 FDSIESAKKFV 69
>pdb|2CQK|A Chain A, Solution Structure Of The La Domain Of C-Mpl Binding
Protein
Length = 101
Score = 41.6 bits (96), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 45/71 (63%), Gaps = 3/71 (4%)
Query: 29 QIEYYFSDINLARDKFLQGEIKKDDGWVELTTMLKFARLAKMTTEAKVIVDALKKSTSKL 88
Q+E+ FS NL++D +L ++ D ++ + T+ + K+TT+ +I++ L+ +S +
Sbjct: 21 QLEFCFSRENLSKDLYLISQMDSDQ-FIPIWTVANMEEIKKLTTDPDLILEVLR--SSPM 77
Query: 89 IEVNEDGTKIR 99
++V+E G K+R
Sbjct: 78 VQVDEKGEKVR 88
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 30.4 bits (67), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 22/42 (52%)
Query: 154 IMRNYQDKLANQKKFKGSIFVTFDNKENAEKFLNENKDKNLK 195
++ +Y+ K K+KG+ FVT N E AE +N L+
Sbjct: 42 LLSDYELKYCFVDKYKGTAFVTLLNGEQAEAAINAFHQSRLR 83
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 30.0 bits (66), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 22/42 (52%)
Query: 154 IMRNYQDKLANQKKFKGSIFVTFDNKENAEKFLNENKDKNLK 195
++ +Y+ K K+KG+ FVT N E AE +N L+
Sbjct: 42 LLSDYELKYCFVDKYKGTAFVTLLNGEQAEAAINAFHQSRLR 83
>pdb|3H2U|B Chain B, Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Complex With
Human Vinculin Tail Domain Vt
pdb|3H2U|D Chain D, Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Complex With
Human Vinculin Tail Domain Vt
Length = 283
Score = 30.0 bits (66), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 22/42 (52%)
Query: 154 IMRNYQDKLANQKKFKGSIFVTFDNKENAEKFLNENKDKNLK 195
++ +Y+ K K+KG+ FVT N E AE +N L+
Sbjct: 40 LLSDYELKYCFVDKYKGTAFVTLLNGEQAEAAINAFHQSRLR 81
>pdb|1CDO|A Chain A, Alcohol Dehydrogenase (E.C.1.1.1.1) (Ee Isozyme) Complexed
With Nicotinamide Adenine Dinucleotide (Nad), And Zinc
pdb|1CDO|B Chain B, Alcohol Dehydrogenase (E.C.1.1.1.1) (Ee Isozyme) Complexed
With Nicotinamide Adenine Dinucleotide (Nad), And Zinc
Length = 374
Score = 29.3 bits (64), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 15/54 (27%), Positives = 27/54 (50%)
Query: 161 KLANQKKFKGSIFVTFDNKENAEKFLNENKDKNLKFNENCEHKNAEKFLNENKD 214
+L + +KGS+F F K+ K + DK +K +E H+ + +N+ D
Sbjct: 307 QLIAGRTWKGSMFGGFKGKDGVPKMVKAYLDKKVKLDEFITHRMPLESVNDAID 360
>pdb|1WI6|A Chain A, Solution Structure Of The Rna Binding Domain From Mouse
Hypothetical Protein Bab23670
Length = 88
Score = 28.9 bits (63), Expect = 5.4, Method: Composition-based stats.
Identities = 15/45 (33%), Positives = 23/45 (51%)
Query: 154 IMRNYQDKLANQKKFKGSIFVTFDNKENAEKFLNENKDKNLKFNE 198
++ +Y+ K K+KG+ FVT N E AE +N L+ E
Sbjct: 25 LLSDYELKYCFVDKYKGTAFVTLLNGEQAEAAINTFHQSRLRERE 69
>pdb|3IYG|Z Chain Z, Ca Model Of Bovine TricCCT DERIVED FROM A 4.0 ANGSTROM
Cryo-Em Map
Length = 517
Score = 28.5 bits (62), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 19/59 (32%), Positives = 31/59 (52%), Gaps = 3/59 (5%)
Query: 261 NTEGSKQVVLELPTGALLKISDIKEPVSREDIREVLEKVQTDDQE---IVFIEFNVGEP 316
+ +G Q+ ++ ALL I + S D++E L KVQ + E +V ++ N GEP
Sbjct: 420 SVKGRAQLGVQAFADALLIIPKVLAQNSGFDLQETLVKVQAEHSESGQLVGVDLNTGEP 478
>pdb|1SEV|A Chain A, Mature And Translocatable Forms Of Glyoxysomal Malate
Dehydrogenase Have Different Activities And Stabilities
But Similar Crystal Structures
pdb|1SEV|B Chain B, Mature And Translocatable Forms Of Glyoxysomal Malate
Dehydrogenase Have Different Activities And Stabilities
But Similar Crystal Structures
Length = 362
Score = 28.1 bits (61), Expect = 9.9, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 37/77 (48%), Gaps = 2/77 (2%)
Query: 277 LLKISDIKEPVS--REDIREVLEKVQTDDQEIVFIEFNVGEPTAFVRYKKENNAEAVLKA 334
L +S +K P S +E+I + +++Q E+V + G T + Y A+A L+
Sbjct: 226 LPLLSQVKPPSSFTQEEISYLTDRIQNGGTEVVEAKAGAGSATLSMAYAAVKFADACLRG 285
Query: 335 LGSKEIVIKDVKVSIEV 351
L VI+ VS +V
Sbjct: 286 LRGDAGVIECAFVSSQV 302
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
0.310 0.130 0.349
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,803,395
Number of Sequences: 62578
Number of extensions: 510004
Number of successful extensions: 1383
Number of sequences better than 100.0: 52
Number of HSP's better than 100.0 without gapping: 16
Number of HSP's successfully gapped in prelim test: 36
Number of HSP's that attempted gapping in prelim test: 1356
Number of HSP's gapped (non-prelim): 56
length of query: 410
length of database: 14,973,337
effective HSP length: 101
effective length of query: 309
effective length of database: 8,652,959
effective search space: 2673764331
effective search space used: 2673764331
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 53 (25.0 bits)