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= 020365
(327 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1Q79|A Chain A, Crystal Structure Of Mammalian Poly(A) Polymerase
Length = 514
Score = 132 bits (332), Expect = 3e-31, Method: Compositional matrix adjust.
Identities = 83/231 (35%), Positives = 115/231 (49%), Gaps = 11/231 (4%)
Query: 2 LVSRFFRVYTQWRWPNPVMMCPIEMGELGFSVWDPRKNPKDRSHRMPIITPAYHCMNSSY 61
LV +FF V+++W WPNPV++ E L VWDPR NP DR H MPIITPAY NS+Y
Sbjct: 268 LVHKFFLVFSKWEWPNPVLLKQPEECNLNLPVWDPRVNPSDRYHLMPIITPAYPQQNSTY 327
Query: 62 KVSLGTLQVMTEQFQCGNRICEVRAYFEIELGKAEWSALFEHYPFFEAYENYLQVDIVXX 121
VS+ T VM E+F+ G I + EI L KAEWS LFE FF+ Y++Y+ +
Sbjct: 328 NVSVSTRMVMVEEFKQGLAITD-----EILLSKAEWSKLFEAPNFFQKYKHYIVLLASAP 382
Query: 122 XXXXLLTWKGWVESRFRQLTLKIEQD---TNGLLQCHPYPNKYIDPSKPCPNSAFFWGLS 178
L W G VES+ R L +E++ T + +P +P K + + GL
Sbjct: 383 TEKQRLEWVGLVESKIRILVGSLEKNEFITLAHVNPQSFPAPKENPDKEEFRTMWVIGLV 442
Query: 179 RKEVGTSKECQ---QFDFQGTVKNFRRGIDNYRVRREGRDIYFSYVCRRHL 226
K+ S+ +D Q R N ++ I +V R+ L
Sbjct: 443 FKKTENSENLSVDLTYDIQSFTDTVYRQAINSKMFEVDMKIAAMHVKRKQL 493
>pdb|1Q78|A Chain A, Crystal Structure Of Poly(A) Polymerase In Complex With
3'- Datp And Magnesium Chloride
Length = 514
Score = 132 bits (331), Expect = 3e-31, Method: Compositional matrix adjust.
Identities = 83/231 (35%), Positives = 115/231 (49%), Gaps = 11/231 (4%)
Query: 2 LVSRFFRVYTQWRWPNPVMMCPIEMGELGFSVWDPRKNPKDRSHRMPIITPAYHCMNSSY 61
LV +FF V+++W WPNPV++ E L VWDPR NP DR H MPIITPAY NS+Y
Sbjct: 268 LVHKFFLVFSKWEWPNPVLLKQPEECNLNLPVWDPRVNPSDRYHLMPIITPAYPQQNSTY 327
Query: 62 KVSLGTLQVMTEQFQCGNRICEVRAYFEIELGKAEWSALFEHYPFFEAYENYLQVDIVXX 121
VS+ T VM E+F+ G I + EI L KAEWS LFE FF+ Y++Y+ +
Sbjct: 328 NVSVSTRMVMVEEFKQGLAITD-----EILLSKAEWSKLFEAPNFFQKYKHYIVLLASAP 382
Query: 122 XXXXLLTWKGWVESRFRQLTLKIEQD---TNGLLQCHPYPNKYIDPSKPCPNSAFFWGLS 178
L W G VES+ R L +E++ T + +P +P K + + GL
Sbjct: 383 TEKQRLEWVGLVESKIRILVGSLEKNEFITLAHVNPQSFPAPKENPDKEEFRTMWVIGLV 442
Query: 179 RKEVGTSKECQ---QFDFQGTVKNFRRGIDNYRVRREGRDIYFSYVCRRHL 226
K+ S+ +D Q R N ++ I +V R+ L
Sbjct: 443 FKKTENSENLSVDLTYDIQSFTDTVYRQAINSKMFEVDMKIAAMHVKRKQL 493
>pdb|1F5A|A Chain A, Crystal Structure Of Mammalian Poly(A) Polymerase
Length = 513
Score = 117 bits (292), Expect = 1e-26, Method: Compositional matrix adjust.
Identities = 81/231 (35%), Positives = 112/231 (48%), Gaps = 11/231 (4%)
Query: 2 LVSRFFRVYTQWRWPNPVMMCPIEMGELGFSVWDPRKNPKDRSHRMPIITPAYHCMNSSY 61
LV +FF V+++W WPNPV++ E L VWDPR NP DR H PIITPAY NS+Y
Sbjct: 268 LVHKFFLVFSKWEWPNPVLLKQPEECNLNLPVWDPRVNPSDRYHLXPIITPAYPQQNSTY 327
Query: 62 KVSLGTLQVMTEQFQCGNRICEVRAYFEIELGKAEWSALFEHYPFFEAYENYLQVDIVXX 121
VS+ T V E+F+ G I + EI L KAEWS LFE FF+ Y++Y+ +
Sbjct: 328 NVSVSTRXVXVEEFKQGLAITD-----EILLSKAEWSKLFEAPNFFQKYKHYIVLLASAP 382
Query: 122 XXXXLLTWKGWVESRFRQLTLKIEQD---TNGLLQCHPYPNKYIDPSKPCPNSAFFWGLS 178
L W G VES+ R L +E++ T + +P +P K + + GL
Sbjct: 383 TEKQRLEWVGLVESKIRILVGSLEKNEFITLAHVNPQSFPAPKENPDKEEFRTXWVIGLV 442
Query: 179 RKEVGTSKECQ---QFDFQGTVKNFRRGIDNYRVRREGRDIYFSYVCRRHL 226
K+ S+ +D Q R N + I +V R+ L
Sbjct: 443 FKKTENSENLSVDLTYDIQSFTDTVYRQAINSKXFEVDXKIAAXHVKRKQL 493
>pdb|2Q66|A Chain A, Structure Of Yeast Poly(A) Polymerase With Atp And
Oligo(A)
Length = 525
Score = 112 bits (280), Expect = 3e-25, Method: Compositional matrix adjust.
Identities = 62/171 (36%), Positives = 96/171 (56%), Gaps = 8/171 (4%)
Query: 1 MLVSRFFRVYTQWRWPNPVMMCPIEMGELGFSVWDPRKNPKDRSHRMPIITPAYHCMNSS 60
++++RFF + ++W WP PV++ PIE G L VW+P+ +DRSHRMP+ITPAY M ++
Sbjct: 250 VILNRFFIILSEWNWPQPVILKPIEDGPLQVRVWNPKIYAQDRSHRMPVITPAYPSMCAT 309
Query: 61 YKVSLGTLQVMTEQFQCGNRICEVRAYFEIELGKAEWSALFEHYPFFEAYENYLQVDI-V 119
+ ++ T +V+ ++F G +I +I K W+ LFE FF Y+ YL++
Sbjct: 310 HNITESTKKVILQEFVRGVQITN-----DIFSNKKSWANLFEKNDFFFRYKFYLEITAYT 364
Query: 120 XXXXXXLLTWKGWVESRFRQLTLKIEQDTNGLLQCHPYPNKYIDPSKPCPN 170
L W G VES+ R L +K+E G+ HP+ K + S CP
Sbjct: 365 RGSDEQHLKWSGLVESKVRLLVMKLEV-LAGIKIAHPF-TKPFESSYCCPT 413
>pdb|2HHP|A Chain A, Structure Of Yeast Poly(A) Polymerase In A Closed
Conformation
Length = 530
Score = 112 bits (280), Expect = 3e-25, Method: Compositional matrix adjust.
Identities = 62/171 (36%), Positives = 96/171 (56%), Gaps = 8/171 (4%)
Query: 1 MLVSRFFRVYTQWRWPNPVMMCPIEMGELGFSVWDPRKNPKDRSHRMPIITPAYHCMNSS 60
++++RFF + ++W WP PV++ PIE G L VW+P+ +DRSHRMP+ITPAY M ++
Sbjct: 254 VILNRFFIILSEWNWPQPVILKPIEDGPLQVRVWNPKIYAQDRSHRMPVITPAYPSMCAT 313
Query: 61 YKVSLGTLQVMTEQFQCGNRICEVRAYFEIELGKAEWSALFEHYPFFEAYENYLQVDI-V 119
+ ++ T +V+ ++F G +I +I K W+ LFE FF Y+ YL++
Sbjct: 314 HNITESTKKVILQEFVRGVQITN-----DIFSNKKSWANLFEKNDFFFRYKFYLEITAYT 368
Query: 120 XXXXXXLLTWKGWVESRFRQLTLKIEQDTNGLLQCHPYPNKYIDPSKPCPN 170
L W G VES+ R L +K+E G+ HP+ K + S CP
Sbjct: 369 RGSDEQHLKWSGLVESKVRLLVMKLEV-LAGIKIAHPF-TKPFESSYCCPT 417
>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 = 112 bits (280), Expect = 3e-25, Method: Compositional matrix adjust.
Identities = 62/171 (36%), Positives = 96/171 (56%), Gaps = 8/171 (4%)
Query: 1 MLVSRFFRVYTQWRWPNPVMMCPIEMGELGFSVWDPRKNPKDRSHRMPIITPAYHCMNSS 60
++++RFF + ++W WP PV++ PIE G L VW+P+ +DRSHRMP+ITPAY M ++
Sbjct: 254 VILNRFFIILSEWNWPQPVILKPIEDGPLQVRVWNPKIYAQDRSHRMPVITPAYPSMCAT 313
Query: 61 YKVSLGTLQVMTEQFQCGNRICEVRAYFEIELGKAEWSALFEHYPFFEAYENYLQVDI-V 119
+ ++ T +V+ ++F G +I +I K W+ LFE FF Y+ YL++
Sbjct: 314 HNITESTKKVILQEFVRGVQITN-----DIFSNKKSWANLFEKNDFFFRYKFYLEITAYT 368
Query: 120 XXXXXXLLTWKGWVESRFRQLTLKIEQDTNGLLQCHPYPNKYIDPSKPCPN 170
L W G VES+ R L +K+E G+ HP+ K + S CP
Sbjct: 369 RGSDEQHLKWSGLVESKVRLLVMKLEV-LAGIKIAHPF-TKPFESSYCCPT 417
>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 = 112 bits (280), Expect = 3e-25, Method: Compositional matrix adjust.
Identities = 62/171 (36%), Positives = 96/171 (56%), Gaps = 8/171 (4%)
Query: 1 MLVSRFFRVYTQWRWPNPVMMCPIEMGELGFSVWDPRKNPKDRSHRMPIITPAYHCMNSS 60
++++RFF + ++W WP PV++ PIE G L VW+P+ +DRSHRMP+ITPAY M ++
Sbjct: 254 VILNRFFIILSEWNWPQPVILKPIEDGPLQVRVWNPKIYAQDRSHRMPVITPAYPSMCAT 313
Query: 61 YKVSLGTLQVMTEQFQCGNRICEVRAYFEIELGKAEWSALFEHYPFFEAYENYLQVDI-V 119
+ ++ T +V+ ++F G +I +I K W+ LFE FF Y+ YL++
Sbjct: 314 HNITESTKKVILQEFVRGVQITN-----DIFSNKKSWANLFEKNDFFFRYKFYLEITAYT 368
Query: 120 XXXXXXLLTWKGWVESRFRQLTLKIEQDTNGLLQCHPYPNKYIDPSKPCPN 170
L W G VES+ R L +K+E G+ HP+ K + S CP
Sbjct: 369 RGSDEQHLKWSGLVESKVRLLVMKLEV-LAGIKIAHPF-TKPFESSYCCPT 417
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
0.320 0.136 0.439
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,578,343
Number of Sequences: 62578
Number of extensions: 439716
Number of successful extensions: 892
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 871
Number of HSP's gapped (non-prelim): 7
length of query: 327
length of database: 14,973,337
effective HSP length: 99
effective length of query: 228
effective length of database: 8,778,115
effective search space: 2001410220
effective search space used: 2001410220
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: 52 (24.6 bits)