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= 046567
(246 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3NYB|A Chain A, Structure And Function Of The Polymerase Core Of Tramp, A
Rna Surveillance Complex
Length = 323
Score = 99.4 bits (246), Expect = 2e-21, Method: Compositional matrix adjust.
Identities = 53/128 (41%), Positives = 80/128 (62%), Gaps = 5/128 (3%)
Query: 113 EIVDFCDFLSPTSDEREVRNTAVEAVFDVIKYIWPKCKPEVFGSFRTGLYLPTSDID-VV 171
EI DF ++SP+ +E E+RN + + + +K +WP VFGS+ T LYLP SDID VV
Sbjct: 24 EIKDFVAYISPSREEIEIRNQTISTIREAVKQLWPDADLHVFGSYSTDLYLPGSDIDCVV 83
Query: 172 IMESGIHNPATGLQALSRALLQRGIAKKIQVIAKARVPIVKFVEKKSG----VSFDIRHF 227
E G L +L+ L ++ +A +++V+AKARVPI+KFVE SG VSF+ +
Sbjct: 84 TSELGGKESRNNLYSLASHLKKKNLATEVEVVAKARVPIIKFVEPHSGIHIAVSFERTNG 143
Query: 228 MDICRVIR 235
++ ++IR
Sbjct: 144 IEAAKLIR 151
>pdb|4E7X|A Chain A, Structural Basis For The Activity Of A Cytoplasmic Rna
Terminal U- Transferase
pdb|4E7X|B Chain B, Structural Basis For The Activity Of A Cytoplasmic Rna
Terminal U- Transferase
pdb|4E7X|C Chain C, Structural Basis For The Activity Of A Cytoplasmic Rna
Terminal U- Transferase
pdb|4E7X|D Chain D, Structural Basis For The Activity Of A Cytoplasmic Rna
Terminal U- Transferase
pdb|4E80|A Chain A, Structural Basis For The Activity Of A Cytoplasmic Rna
Terminal U- Transferase
pdb|4E80|B Chain B, Structural Basis For The Activity Of A Cytoplasmic Rna
Terminal U- Transferase
pdb|4E80|C Chain C, Structural Basis For The Activity Of A Cytoplasmic Rna
Terminal U- Transferase
pdb|4E80|D Chain D, Structural Basis For The Activity Of A Cytoplasmic Rna
Terminal U- Transferase
pdb|4E8F|A Chain A, Structural Basis For The Activity Of A Cytoplasmic Rna
Terminal U- Transferase
pdb|4E8F|B Chain B, Structural Basis For The Activity Of A Cytoplasmic Rna
Terminal U- Transferase
Length = 405
Score = 47.8 bits (112), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 52/180 (28%), Positives = 79/180 (43%), Gaps = 21/180 (11%)
Query: 71 GVDDVEEVEPKTPPAKSAEPRMENRWFKGNSRFKSPMLQLHKEIVDFC----DFLSPTSD 126
GV VEE+E AE K S K P HKE FC + + +
Sbjct: 11 GVHTVEEIE--------AEIHKNLHISKSCSYQKVP--NSHKEFTKFCYEVYNEIKISDK 60
Query: 127 EREVRNTAVEAVFDVIKYIWPKCKPEVFGSFRTGLYLPTSDIDV-VIMESGIHNPATGLQ 185
E + + A++ + +K I P + FGS +GL L SD+D+ V+M+S + + LQ
Sbjct: 61 EFKEKRAALDTLRLCLKRISPDAELVAFGSLESGLALKNSDMDLCVLMDSRVQSDTIALQ 120
Query: 186 ALSRALLQRGIAKKIQVIAKARVPIVKFV-EKKSGVSFDIRHFMDICRVIRMVCHTWGLV 244
L+ G K + +AR+PI+K + K+G F DI R+ H L+
Sbjct: 121 -FYEELIAEGFEGKF--LQRARIPIIKLTSDTKNG--FGASFQCDIGFNNRLAIHNTLLL 175
>pdb|4FHX|A Chain A, Crystal Structures Of The Cid1 Poly (U) Polymerase Reveal
The Mechanism For Utp Selectivity - H336n Mutant Bound
To Mgatp
Length = 349
Score = 46.6 bits (109), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 40/140 (28%), Positives = 66/140 (47%), Gaps = 11/140 (7%)
Query: 111 HKEIVDFC----DFLSPTSDEREVRNTAVEAVFDVIKYIWPKCKPEVFGSFRTGLYLPTS 166
HKE FC + + + E + + A++ + +K I P + FGS +GL L S
Sbjct: 13 HKEFTKFCYEVYNEIKISDKEFKEKRAALDTLRLCLKRISPDAELVAFGSLESGLALKNS 72
Query: 167 DIDV-VIMESGIHNPATGLQALSRALLQRGIAKKIQVIAKARVPIVKFV-EKKSGVSFDI 224
D+D+ V+M+S + + LQ L+ G K + +AR+PI+K + K+G F
Sbjct: 73 DMDLCVLMDSRVQSDTIALQ-FYEELIAEGFEGKF--LQRARIPIIKLTSDTKNG--FGA 127
Query: 225 RHFMDICRVIRMVCHTWGLV 244
DI R+ H L+
Sbjct: 128 SFQCDIGFNNRLAIHNTLLL 147
>pdb|4FH3|A Chain A, Crystal Structures Of The Cid1 Poly (U) Polymerase Reveal
The Mechanism For Utp Selectivity
pdb|4FH5|A Chain A, Crystal Structures Of The Cid1 Poly (U) Polymerase Reveal
The Mechanism For Utp Selectivity - Mgutp Bound
pdb|4FHP|A Chain A, Crystal Structures Of The Cid1 Poly (U) Polymerase Reveal
The Mechanism For Utp Selectivity - Cautp Bound
pdb|4FHV|A Chain A, Crystal Structures Of The Cid1 Poly (U) Polymerase Reveal
The Mechanism For Utp Selectivity - Mgctp Bound
pdb|4FHW|A Chain A, Crystal Structures Of The Cid1 Poly (U) Polymerase Reveal
The Mechanism For Utp Selectivity - Mggtp Bound
pdb|4FHY|A Chain A, Crystal Structures Of The Cid1 Poly (U) Polymerase Reveal
The Mechanism For Utp Selectivity - Mg 3'-Datp Bound
Length = 349
Score = 46.6 bits (109), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 40/140 (28%), Positives = 66/140 (47%), Gaps = 11/140 (7%)
Query: 111 HKEIVDFC----DFLSPTSDEREVRNTAVEAVFDVIKYIWPKCKPEVFGSFRTGLYLPTS 166
HKE FC + + + E + + A++ + +K I P + FGS +GL L S
Sbjct: 13 HKEFTKFCYEVYNEIKISDKEFKEKRAALDTLRLCLKRISPDAELVAFGSLESGLALKNS 72
Query: 167 DIDV-VIMESGIHNPATGLQALSRALLQRGIAKKIQVIAKARVPIVKFV-EKKSGVSFDI 224
D+D+ V+M+S + + LQ L+ G K + +AR+PI+K + K+G F
Sbjct: 73 DMDLCVLMDSRVQSDTIALQ-FYEELIAEGFEGKF--LQRARIPIIKLTSDTKNG--FGA 127
Query: 225 RHFMDICRVIRMVCHTWGLV 244
DI R+ H L+
Sbjct: 128 SFQCDIGFNNRLAIHNTLLL 147
>pdb|4EP7|A Chain A, Functional Implications From The Cid1 Poly(U) Polymerase
Crystal Structure
pdb|4EP7|B Chain B, Functional Implications From The Cid1 Poly(U) Polymerase
Crystal Structure
Length = 340
Score = 46.6 bits (109), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 40/140 (28%), Positives = 66/140 (47%), Gaps = 11/140 (7%)
Query: 111 HKEIVDFC----DFLSPTSDEREVRNTAVEAVFDVIKYIWPKCKPEVFGSFRTGLYLPTS 166
HKE FC + + + E + + A++ + +K I P + FGS +GL L S
Sbjct: 4 HKEFTKFCYEVYNEIKISDKEFKEKRAALDTLRLCLKRISPDAELVAFGSLESGLALKNS 63
Query: 167 DIDV-VIMESGIHNPATGLQALSRALLQRGIAKKIQVIAKARVPIVKFV-EKKSGVSFDI 224
D+D+ V+M+S + + LQ L+ G K + +AR+PI+K + K+G F
Sbjct: 64 DMDLCVLMDSRVQSDTIALQ-FYEELIAEGFEGKF--LQRARIPIIKLTSDTKNG--FGA 118
Query: 225 RHFMDICRVIRMVCHTWGLV 244
DI R+ H L+
Sbjct: 119 SFQCDIGFNNRLAIHNTLLL 138
>pdb|2HHP|A Chain A, Structure Of Yeast Poly(A) Polymerase In A Closed
Conformation
Length = 530
Score = 33.9 bits (76), Expect = 0.088, Method: Compositional matrix adjust.
Identities = 22/71 (30%), Positives = 35/71 (49%), Gaps = 2/71 (2%)
Query: 154 FGSFRTGLYLPTSDIDVVIMESGIHNPATGLQALSRALLQRGIAKKIQVIAKARVPIVKF 213
+GS+R G++ P SDID +++ L +R +I + A VPI+K
Sbjct: 87 YGSYRLGVHGPGSDIDTLVVVPKHVTREDFFTVFDSLLRERKELDEIAPVPDAFVPIIKI 146
Query: 214 VEKKSGVSFDI 224
K SG+S D+
Sbjct: 147 --KFSGISIDL 155
>pdb|2O1P|A Chain A, Structure Of Yeast Poly(A) Polymerase In A Somewhat Closed
State
pdb|2O1P|B Chain B, Structure Of Yeast Poly(A) Polymerase In A Somewhat Closed
State
Length = 546
Score = 33.9 bits (76), Expect = 0.091, Method: Compositional matrix adjust.
Identities = 22/71 (30%), Positives = 35/71 (49%), Gaps = 2/71 (2%)
Query: 154 FGSFRTGLYLPTSDIDVVIMESGIHNPATGLQALSRALLQRGIAKKIQVIAKARVPIVKF 213
+GS+R G++ P SDID +++ L +R +I + A VPI+K
Sbjct: 87 YGSYRLGVHGPGSDIDTLVVVPKHVTREDFFTVFDSLLRERKELDEIAPVPDAFVPIIKI 146
Query: 214 VEKKSGVSFDI 224
K SG+S D+
Sbjct: 147 --KFSGISIDL 155
>pdb|1FA0|A Chain A, Structure Of Yeast Poly(A) Polymerase Bound To Manganate
And 3'-Datp
pdb|1FA0|B Chain B, Structure Of Yeast Poly(A) Polymerase Bound To Manganate
And 3'-Datp
pdb|3C66|A Chain A, Yeast Poly(A) Polymerase In Complex With Fip1 Residues
80-105
pdb|3C66|B Chain B, Yeast Poly(A) Polymerase In Complex With Fip1 Residues
80-105
Length = 537
Score = 33.9 bits (76), Expect = 0.091, Method: Compositional matrix adjust.
Identities = 22/71 (30%), Positives = 35/71 (49%), Gaps = 2/71 (2%)
Query: 154 FGSFRTGLYLPTSDIDVVIMESGIHNPATGLQALSRALLQRGIAKKIQVIAKARVPIVKF 213
+GS+R G++ P SDID +++ L +R +I + A VPI+K
Sbjct: 87 YGSYRLGVHGPGSDIDTLVVVPKHVTREDFFTVFDSLLRERKELDEIAPVPDAFVPIIKI 146
Query: 214 VEKKSGVSFDI 224
K SG+S D+
Sbjct: 147 --KFSGISIDL 155
>pdb|3HJ1|A Chain A, Minor Editosome-Associated Tutase 1 With Bound Utp
pdb|3HJ1|B Chain B, Minor Editosome-Associated Tutase 1 With Bound Utp
Length = 387
Score = 33.1 bits (74), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 25/99 (25%), Positives = 42/99 (42%), Gaps = 15/99 (15%)
Query: 138 VFDVIKYIWPKCKPEVFGSFRTGLYLPTSDIDVVIMESGIHNPATGLQALSRALLQRG-- 195
V D+ K E+FGS +G P SD D+ + N + LQ + R Q
Sbjct: 38 VLDIGMLAVNKAHVELFGSHVSGFCTPHSDADISLT---YRNFSPWLQGMERVDEQNNKR 94
Query: 196 ---IAKKIQVIA-------KARVPIVKFVEKKSGVSFDI 224
K+ + +AR+P+V+F + +G+ D+
Sbjct: 95 MTRFGKEASAMGMEDVRYIRARIPVVQFTDGVTGIHCDV 133
>pdb|2Q66|A Chain A, Structure Of Yeast Poly(A) Polymerase With Atp And
Oligo(A)
Length = 525
Score = 31.2 bits (69), Expect = 0.63, Method: Compositional matrix adjust.
Identities = 21/68 (30%), Positives = 33/68 (48%), Gaps = 2/68 (2%)
Query: 154 FGSFRTGLYLPTSDIDVVIMESGIHNPATGLQALSRALLQRGIAKKIQVIAKARVPIVKF 213
+GS+R G++ P SDID +++ L +R +I + A VPI+K
Sbjct: 83 YGSYRLGVHGPGSDIDTLVVVPKHVTREDFFTVFDSLLRERKELDEIAPVPDAFVPIIKI 142
Query: 214 VEKKSGVS 221
K SG+S
Sbjct: 143 --KFSGIS 148
>pdb|3HIY|A Chain A, Minor Editosome-Associated Tutase 1 With Bound Utp And Mg
pdb|3HIY|B Chain B, Minor Editosome-Associated Tutase 1 With Bound Utp And Mg
pdb|3HJ4|A Chain A, Minor Editosome-Associated Tutase 1
pdb|3HJ4|B Chain B, Minor Editosome-Associated Tutase 1
Length = 384
Score = 30.8 bits (68), Expect = 0.68, Method: Compositional matrix adjust.
Identities = 25/99 (25%), Positives = 40/99 (40%), Gaps = 15/99 (15%)
Query: 138 VFDVIKYIWPKCKPEVFGSFRTGLYLPTSDIDVVIMESGIHNPATGLQALSRALLQRG-- 195
V D+ K E+FGS +G P SD D+ + N + LQ R Q
Sbjct: 35 VLDIGXLAVNKAHVELFGSHVSGFCTPHSDADISLT---YRNFSPWLQGXERVDEQNNKR 91
Query: 196 ---IAKKIQVIA-------KARVPIVKFVEKKSGVSFDI 224
K+ +AR+P+V+F + +G+ D+
Sbjct: 92 XTRFGKEASAXGXEDVRYIRARIPVVQFTDGVTGIHCDV 130
>pdb|1T3I|A Chain A, Structure Of Slr0077SUFS, THE ESSENTIAL CYSTEINE
Desulfurase From Synechocystis Pcc 6803
pdb|1T3I|B Chain B, Structure Of Slr0077SUFS, THE ESSENTIAL CYSTEINE
Desulfurase From Synechocystis Pcc 6803
Length = 420
Score = 29.3 bits (64), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 16/63 (25%), Positives = 30/63 (47%)
Query: 165 TSDIDVVIMESGIHNPATGLQALSRALLQRGIAKKIQVIAKARVPIVKFVEKKSGVSFDI 224
T I++V G++N G + ++ + Q++A ++KFV+ SFD+
Sbjct: 100 TEAINLVAYSWGMNNLKAGDEIITTVMEHHSNLVPWQMVAAKTGAVLKFVQLDEQESFDL 159
Query: 225 RHF 227
HF
Sbjct: 160 EHF 162
>pdb|2QK2|A Chain A, Structural Basis Of Microtubule Plus End Tracking By
Xmap215 And Eb1
Length = 242
Score = 28.9 bits (63), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 36/130 (27%), Positives = 61/130 (46%), Gaps = 20/130 (15%)
Query: 111 HKEIVDFCDFLSPTSDE-----REVRNTAVEAVFDVIKYIW---PKCKPEVFGSFRTGLY 162
H +++D D LS + E + T + +V++ + PK + +G+ + L
Sbjct: 3 HXDLLDPVDILSKXPKDFYDKLEEKKWTLRKESLEVLEKLLTDHPKLENGEYGALVSALK 62
Query: 163 -LPTSDIDVVIMESGIHNPATGLQALSRALLQRGIAKKIQVIAKARVP--IVKFVEKKSG 219
+ T D +VV++ A + L ALL +G+AK+ A A VP + KF EKK
Sbjct: 63 KVITKDSNVVLV-------AXAGKCL--ALLAKGLAKRFSNYASACVPSLLEKFKEKKPN 113
Query: 220 VSFDIRHFMD 229
V +R +D
Sbjct: 114 VVTALREAID 123
>pdb|2RFF|A Chain A, Crystal Structure Of A Putative Nucleotidyltransferase
(Np_343093.1) From Sulfolobus Solfataricus At 1.40 A
Resolution
Length = 111
Score = 28.9 bits (63), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 13/26 (50%), Positives = 17/26 (65%)
Query: 153 VFGSFRTGLYLPTSDIDVVIMESGIH 178
+FGS G YL TSDID++ + GI
Sbjct: 38 IFGSRARGDYLDTSDIDILFVFKGIK 63
>pdb|3QG5|A Chain A, The Mre11:rad50 Complex Forms An Atp Dependent Molecular
Clamp In Dna Double-Strand Break Repair
pdb|3QG5|B Chain B, The Mre11:rad50 Complex Forms An Atp Dependent Molecular
Clamp In Dna Double-Strand Break Repair
Length = 365
Score = 27.7 bits (60), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 13/38 (34%), Positives = 20/38 (52%)
Query: 171 VIMESGIHNPATGLQALSRALLQRGIAKKIQVIAKARV 208
+I + GI PA GL RAL+ +A + +A R+
Sbjct: 267 IIKDWGIERPARGLSGGERALISISLAXSLAEVASGRL 304
>pdb|3THO|A Chain A, Crystal Structure Of Mre11:rad50 In Its AtpADP BOUND STATE
Length = 382
Score = 27.3 bits (59), Expect = 8.0, Method: Compositional matrix adjust.
Identities = 13/38 (34%), Positives = 20/38 (52%)
Query: 171 VIMESGIHNPATGLQALSRALLQRGIAKKIQVIAKARV 208
+I + GI PA GL RAL+ +A + +A R+
Sbjct: 284 IIKDWGIERPARGLSGGERALISISLAMSLAEVASGRL 321
>pdb|3QF7|A Chain A, The Mre11:rad50 Complex Forms An Atp Dependent Molecular
Clamp In Dna Double-Strand Break Repair
pdb|3QF7|B Chain B, The Mre11:rad50 Complex Forms An Atp Dependent Molecular
Clamp In Dna Double-Strand Break Repair
Length = 365
Score = 27.3 bits (59), Expect = 8.8, Method: Compositional matrix adjust.
Identities = 13/38 (34%), Positives = 20/38 (52%)
Query: 171 VIMESGIHNPATGLQALSRALLQRGIAKKIQVIAKARV 208
+I + GI PA GL RAL+ +A + +A R+
Sbjct: 267 IIKDWGIERPARGLSGGERALISISLAMSLAEVASGRL 304
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
0.319 0.136 0.409
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,371,678
Number of Sequences: 62578
Number of extensions: 293014
Number of successful extensions: 568
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 555
Number of HSP's gapped (non-prelim): 17
length of query: 246
length of database: 14,973,337
effective HSP length: 96
effective length of query: 150
effective length of database: 8,965,849
effective search space: 1344877350
effective search space used: 1344877350
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)