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= psy14559
(405 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2JWN|A Chain A, Solution Nmr Structure Of The Protease-Resistent Domain Of
Xenopus Laevis Epabp2
pdb|2JWN|B Chain B, Solution Nmr Structure Of The Protease-Resistent Domain Of
Xenopus Laevis Epabp2
Length = 124
Score = 41.6 bits (96), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 25/90 (27%), Positives = 51/90 (56%), Gaps = 3/90 (3%)
Query: 151 PPLPITYDTKKIEEIRRTLVAINIEESVSPQELVDFFQKVGTVNYIR-FCTRENDTNK-Y 208
PP P++ + KK E +R++ N++ + Q+L F G++N I C + + K Y
Sbjct: 22 PPQPLSAEEKK-EIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGY 80
Query: 209 ALVEFSDQACVIPALKLNGTNLKGKTLQMF 238
A +EF+++ V A+ ++ T +G+T+++
Sbjct: 81 AYIEFAERNSVDAAVAMDETVFRGRTIKVL 110
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 38.5 bits (88), Expect = 0.006, Method: Composition-based stats.
Identities = 27/88 (30%), Positives = 42/88 (47%), Gaps = 3/88 (3%)
Query: 167 RTLVAINIEESVSPQELVDFFQKVGTVNYIRFC-TRENDTNK-YALVEFSDQACVIPALK 224
R++ NI + ++L D F +VG V R RE K Y E+ DQ + A++
Sbjct: 9 RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMR 68
Query: 225 -LNGTNLKGKTLQMFHSTQSIQKPEAKS 251
LNG G+ L++ ++ K E KS
Sbjct: 69 NLNGREFSGRALRVDNAASEKNKEELKS 96
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 38.1 bits (87), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 33/68 (48%), Gaps = 2/68 (2%)
Query: 167 RTLVAINIEESVSPQELVDFFQKVGTVNYIRFCTREND--TNKYALVEFSDQACVIPALK 224
RT+ + + + P++L DFF VG V +R + N + A VEF + V A+
Sbjct: 26 RTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG 85
Query: 225 LNGTNLKG 232
L G L G
Sbjct: 86 LTGQRLLG 93
>pdb|3B4D|A Chain A, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|A Chain A, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|B Chain B, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|C Chain C, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|D Chain D, Crystal Structure Of Human Pabpn1 Rrm
Length = 96
Score = 33.1 bits (74), Expect = 0.32, Method: Composition-based stats.
Identities = 20/78 (25%), Positives = 42/78 (53%), Gaps = 2/78 (2%)
Query: 162 IEEIRRTLVAINIEESVSPQELVDFFQKVGTVNYIR-FCTRENDTNK-YALVEFSDQACV 219
+E R++ N++ + +EL F G+VN + C + + K +A +EFSD+ V
Sbjct: 1 MEADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESV 60
Query: 220 IPALKLNGTNLKGKTLQM 237
+L L+ + +G+ +++
Sbjct: 61 RTSLALDESLFRGRQIKV 78
>pdb|3UCG|A Chain A, Crystal Structure Of A Rna Binding Domain Of Hypothetical
Polyadenylate-Binding Protein (Pabpn1) From Homo Sapiens
At 1.95 A Resolution
Length = 89
Score = 32.7 bits (73), Expect = 0.33, Method: Composition-based stats.
Identities = 19/73 (26%), Positives = 40/73 (54%), Gaps = 2/73 (2%)
Query: 167 RTLVAINIEESVSPQELVDFFQKVGTVNYIR-FCTRENDTNK-YALVEFSDQACVIPALK 224
R++ N++ + +EL F G+VN + C + + K +A +EFSD+ V +L
Sbjct: 7 RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLA 66
Query: 225 LNGTNLKGKTLQM 237
L+ + +G+ +++
Sbjct: 67 LDESLFRGRQIKV 79
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 31.2 bits (69), Expect = 0.97, Method: Composition-based stats.
Identities = 22/77 (28%), Positives = 34/77 (44%), Gaps = 2/77 (2%)
Query: 163 EEIRRTLVAINIEESVSPQELVDFFQKVGTVNYIRFCT-RENDTNKYALVEFSDQACVIP 221
EE RT+ N+E V + L + F + G + + C RE + V F V
Sbjct: 13 EEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSY 72
Query: 222 ALK-LNGTNLKGKTLQM 237
A+ LNG L G+ + +
Sbjct: 73 AIALLNGIRLYGRPINV 89
>pdb|1VYU|A Chain A, Beta3 Subunit Of Voltage-Gated Ca2+-Channel
pdb|1VYU|B Chain B, Beta3 Subunit Of Voltage-Gated Ca2+-Channel
Length = 351
Score = 30.0 bits (66), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 29/124 (23%), Positives = 50/124 (40%), Gaps = 31/124 (25%)
Query: 50 VSIPVQSRICYVKFFDEKC--------------VGISQHLTNTVFIDRALVVTPYNSGEI 95
V+ V++ + Y DE+C + I + +N +I R LV + I
Sbjct: 45 VAFAVRTNVSYCGVLDEECPVQGSGVNFEAKDFLHIKEKYSNDWWIGR-LVKEGGDIAFI 103
Query: 96 PDEQR--ALEIAAQQQGPNSGEPKLPAHVTN--------------QIEGVPPNQVISTHD 139
P QR ++ + +Q+ SG P + + N Q E VPP V+ +
Sbjct: 104 PSPQRLESIRLKQEQKARRSGNPSSLSDIGNRRSPPPSLAKQKQKQAEHVPPYDVVPSXR 163
Query: 140 PVLV 143
PV++
Sbjct: 164 PVVL 167
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding
Protein 14
Length = 90
Score = 29.6 bits (65), Expect = 3.0, Method: Composition-based stats.
Identities = 24/76 (31%), Positives = 37/76 (48%), Gaps = 9/76 (11%)
Query: 173 NIEESVSPQELVDFFQKVGTVNYIRFCTRENDTNK-YALVEFSDQACVIPAL-KLNGTNL 230
N+ + + QEL F++ G V E D K YA V +A A+ +LNG +
Sbjct: 16 NVSAACTSQELRSLFERRGRV-------IECDVVKDYAFVHMEKEADAKAAIAQLNGKEV 68
Query: 231 KGKTLQMFHSTQSIQK 246
KGK + + ST+ +K
Sbjct: 69 KGKRINVELSTKGQKK 84
>pdb|3OSE|A Chain A, Structure Of The Kinase Associated Domain 1 (Ka1) From
Mark1 Kinase
Length = 120
Score = 28.5 bits (62), Expect = 6.4, Method: Composition-based stats.
Identities = 21/70 (30%), Positives = 32/70 (45%), Gaps = 14/70 (20%)
Query: 162 IEEIRRTLVAINIEESVSPQELVDFFQKVGTVNYIRFCTRENDTNKYALVEFSDQACVIP 221
+ EIR+ L A N D+ QK ++ FC D + +LV++ + C +P
Sbjct: 43 MREIRKVLDANN----------CDYEQKE---RFLLFCV-HGDARQDSLVQWEMEVCKLP 88
Query: 222 ALKLNGTNLK 231
L LNG K
Sbjct: 89 RLSLNGVRFK 98
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
0.317 0.134 0.380
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,566,844
Number of Sequences: 62578
Number of extensions: 411490
Number of successful extensions: 1013
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 1009
Number of HSP's gapped (non-prelim): 12
length of query: 405
length of database: 14,973,337
effective HSP length: 101
effective length of query: 304
effective length of database: 8,652,959
effective search space: 2630499536
effective search space used: 2630499536
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)