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= 008889
(550 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 = 275 bits (704), Expect = 4e-74, Method: Compositional matrix adjust.
Identities = 146/305 (47%), Positives = 192/305 (62%), Gaps = 12/305 (3%)
Query: 6 NVDEQTVRSLNGCRVADQILKHVPNVEHFRMTLRCLKFWAKRRGVYSNVTGFLGGVNWAL 65
N+D + +RSLNGCRV D+IL VPN+++FR+TLR +K WAKR +YSN+ GFLGGV+WA+
Sbjct: 192 NLDIRXIRSLNGCRVTDEILHLVPNIDNFRLTLRAIKLWAKRHNIYSNILGFLGGVSWAM 251
Query: 66 LVARVCQLYPNAIPSMLVSRFFRVYTQWRWPNPVMLCPIEEDELGFSVWDPRKNPRDRSH 125
LVAR CQLYPNAI S LV +FF V+++W WPNPV+L EE L VWDPR NP DR H
Sbjct: 252 LVARTCQLYPNAIASTLVHKFFLVFSKWEWPNPVLLKQPEECNLNLPVWDPRVNPSDRYH 311
Query: 126 HMPIITPAYPCMNSSYNVSLSTLRVMTEQFQWGNRICEEIELNKAQWSALFEPYLFFEAY 185
MPIITPAYP NS+YNVS+ST VM E+F+ G I +EI L+KA+WS LFE FF+ Y
Sbjct: 312 LMPIITPAYPQQNSTYNVSVSTRMVMVEEFKQGLAITDEILLSKAEWSKLFEAPNFFQKY 371
Query: 186 KNYLQVDIVXXXXXXLLTWKGWVESRFRQLTLKIERDTNGLL-----QCHPYPNEYIDPS 240
K+Y+ + L W G VES+ R L +E++ L Q P P E +P
Sbjct: 372 KHYIVLLASAPTEKQRLEWVGLVESKIRILVGSLEKNEFITLAHVNPQSFPAPKE--NPD 429
Query: 241 KPCPNSAFFMGLRRKEGVTGKERQ---QFDIRGTVDN-FREEIGMYMFWKPGMDIYVSHV 296
K + + +GL K+ + +DI+ D +R+ I MF + M I HV
Sbjct: 430 KEEFRTMWVIGLVFKKTENSENLSVDLTYDIQSFTDTVYRQAINSKMF-EVDMKIAAMHV 488
Query: 297 RRRQL 301
+R+QL
Sbjct: 489 KRKQL 493
>pdb|1Q78|A Chain A, Crystal Structure Of Poly(A) Polymerase In Complex With
3'- Datp And Magnesium Chloride
Length = 514
Score = 275 bits (703), Expect = 4e-74, Method: Compositional matrix adjust.
Identities = 146/305 (47%), Positives = 192/305 (62%), Gaps = 12/305 (3%)
Query: 6 NVDEQTVRSLNGCRVADQILKHVPNVEHFRMTLRCLKFWAKRRGVYSNVTGFLGGVNWAL 65
N+D + +RSLNGCRV D+IL VPN+++FR+TLR +K WAKR +YSN+ GFLGGV+WA+
Sbjct: 192 NLDIRXIRSLNGCRVTDEILHLVPNIDNFRLTLRAIKLWAKRHNIYSNILGFLGGVSWAM 251
Query: 66 LVARVCQLYPNAIPSMLVSRFFRVYTQWRWPNPVMLCPIEEDELGFSVWDPRKNPRDRSH 125
LVAR CQLYPNAI S LV +FF V+++W WPNPV+L EE L VWDPR NP DR H
Sbjct: 252 LVARTCQLYPNAIASTLVHKFFLVFSKWEWPNPVLLKQPEECNLNLPVWDPRVNPSDRYH 311
Query: 126 HMPIITPAYPCMNSSYNVSLSTLRVMTEQFQWGNRICEEIELNKAQWSALFEPYLFFEAY 185
MPIITPAYP NS+YNVS+ST VM E+F+ G I +EI L+KA+WS LFE FF+ Y
Sbjct: 312 LMPIITPAYPQQNSTYNVSVSTRMVMVEEFKQGLAITDEILLSKAEWSKLFEAPNFFQKY 371
Query: 186 KNYLQVDIVXXXXXXLLTWKGWVESRFRQLTLKIERDTNGLL-----QCHPYPNEYIDPS 240
K+Y+ + L W G VES+ R L +E++ L Q P P E +P
Sbjct: 372 KHYIVLLASAPTEKQRLEWVGLVESKIRILVGSLEKNEFITLAHVNPQSFPAPKE--NPD 429
Query: 241 KPCPNSAFFMGLRRKEGVTGKERQ---QFDIRGTVDN-FREEIGMYMFWKPGMDIYVSHV 296
K + + +GL K+ + +DI+ D +R+ I MF + M I HV
Sbjct: 430 KEEFRTMWVIGLVFKKTENSENLSVDLTYDIQSFTDTVYRQAINSKMF-EVDMKIAAMHV 488
Query: 297 RRRQL 301
+R+QL
Sbjct: 489 KRKQL 493
>pdb|1F5A|A Chain A, Crystal Structure Of Mammalian Poly(A) Polymerase
Length = 513
Score = 253 bits (646), Expect = 2e-67, Method: Compositional matrix adjust.
Identities = 142/305 (46%), Positives = 187/305 (61%), Gaps = 12/305 (3%)
Query: 6 NVDEQTVRSLNGCRVADQILKHVPNVEHFRMTLRCLKFWAKRRGVYSNVTGFLGGVNWAL 65
N+D + +RSLNGCRV D+IL VPN+++FR+TLR +K WAKR +YSN+ GFLGGV+WA
Sbjct: 192 NLDIRCIRSLNGCRVTDEILHLVPNIDNFRLTLRAIKLWAKRHNIYSNILGFLGGVSWAX 251
Query: 66 LVARVCQLYPNAIPSMLVSRFFRVYTQWRWPNPVMLCPIEEDELGFSVWDPRKNPRDRSH 125
LVAR CQLYPNAI S LV +FF V+++W WPNPV+L EE L VWDPR NP DR H
Sbjct: 252 LVARTCQLYPNAIASTLVHKFFLVFSKWEWPNPVLLKQPEECNLNLPVWDPRVNPSDRYH 311
Query: 126 HMPIITPAYPCMNSSYNVSLSTLRVMTEQFQWGNRICEEIELNKAQWSALFEPYLFFEAY 185
PIITPAYP NS+YNVS+ST V E+F+ G I +EI L+KA+WS LFE FF+ Y
Sbjct: 312 LXPIITPAYPQQNSTYNVSVSTRXVXVEEFKQGLAITDEILLSKAEWSKLFEAPNFFQKY 371
Query: 186 KNYLQVDIVXXXXXXLLTWKGWVESRFRQLTLKIERDTNGLL-----QCHPYPNEYIDPS 240
K+Y+ + L W G VES+ R L +E++ L Q P P E +P
Sbjct: 372 KHYIVLLASAPTEKQRLEWVGLVESKIRILVGSLEKNEFITLAHVNPQSFPAPKE--NPD 429
Query: 241 KPCPNSAFFMGLRRKEGVTGKERQ---QFDIRGTVDN-FREEIGMYMFWKPGMDIYVSHV 296
K + + +GL K+ + +DI+ D +R+ I F + I HV
Sbjct: 430 KEEFRTXWVIGLVFKKTENSENLSVDLTYDIQSFTDTVYRQAINSKXF-EVDXKIAAXHV 488
Query: 297 RRRQL 301
+R+QL
Sbjct: 489 KRKQL 493
>pdb|2HHP|A Chain A, Structure Of Yeast Poly(A) Polymerase In A Closed
Conformation
Length = 530
Score = 231 bits (590), Expect = 6e-61, Method: Compositional matrix adjust.
Identities = 116/278 (41%), Positives = 172/278 (61%), Gaps = 3/278 (1%)
Query: 2 SVLNNVDEQTVRSLNGCRVADQILKHVPNVEHFRMTLRCLKFWAKRRGVYSNVTGFLGGV 61
++L N+DE+ +R+LNG RV D+IL+ VP FR+ LR +K WA+RR VY+N+ GF GGV
Sbjct: 175 NLLRNLDEKDLRALNGTRVTDEILELVPKPNVFRIALRAIKLWAQRRAVYANIFGFPGGV 234
Query: 62 NWALLVARVCQLYPNAIPSMLVSRFFRVYTQWRWPNPVMLCPIEEDELGFSVWDPRKNPR 121
WA+LVAR+CQLYPNA +++++RFF + ++W WP PV+L PIE+ L VW+P+ +
Sbjct: 235 AWAMLVARICQLYPNACSAVILNRFFIILSEWNWPQPVILKPIEDGPLQVRVWNPKIYAQ 294
Query: 122 DRSHHMPIITPAYPCMNSSYNVSLSTLRVMTEQFQWGNRICEEIELNKAQWSALFEPYLF 181
DRSH MP+ITPAYP M +++N++ ST +V+ ++F G +I +I NK W+ LFE F
Sbjct: 295 DRSHRMPVITPAYPSMCATHNITESTKKVILQEFVRGVQITNDIFSNKKSWANLFEKNDF 354
Query: 182 FEAYKNYLQVDIVXX-XXXXLLTWKGWVESRFRQLTLKIERDTNGLLQCHPYPNEYIDPS 240
F YK YL++ L W G VES+ R L +K+E G+ HP+ + + S
Sbjct: 355 FFRYKFYLEITAYTRGSDEQHLKWSGLVESKVRLLVMKLEV-LAGIKIAHPFTKPF-ESS 412
Query: 241 KPCPNSAFFMGLRRKEGVTGKERQQFDIRGTVDNFREE 278
CP + ++ K G E ++ D +EE
Sbjct: 413 YCCPTEDDYEMIQDKYGSHKTETALNALKLVTDENKEE 450
>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 = 231 bits (590), Expect = 6e-61, Method: Compositional matrix adjust.
Identities = 116/278 (41%), Positives = 172/278 (61%), Gaps = 3/278 (1%)
Query: 2 SVLNNVDEQTVRSLNGCRVADQILKHVPNVEHFRMTLRCLKFWAKRRGVYSNVTGFLGGV 61
++L N+DE+ +R+LNG RV D+IL+ VP FR+ LR +K WA+RR VY+N+ GF GGV
Sbjct: 175 NLLRNLDEKDLRALNGTRVTDEILELVPKPNVFRIALRAIKLWAQRRAVYANIFGFPGGV 234
Query: 62 NWALLVARVCQLYPNAIPSMLVSRFFRVYTQWRWPNPVMLCPIEEDELGFSVWDPRKNPR 121
WA+LVAR+CQLYPNA +++++RFF + ++W WP PV+L PIE+ L VW+P+ +
Sbjct: 235 AWAMLVARICQLYPNACSAVILNRFFIILSEWNWPQPVILKPIEDGPLQVRVWNPKIYAQ 294
Query: 122 DRSHHMPIITPAYPCMNSSYNVSLSTLRVMTEQFQWGNRICEEIELNKAQWSALFEPYLF 181
DRSH MP+ITPAYP M +++N++ ST +V+ ++F G +I +I NK W+ LFE F
Sbjct: 295 DRSHRMPVITPAYPSMCATHNITESTKKVILQEFVRGVQITNDIFSNKKSWANLFEKNDF 354
Query: 182 FEAYKNYLQVDIVXX-XXXXLLTWKGWVESRFRQLTLKIERDTNGLLQCHPYPNEYIDPS 240
F YK YL++ L W G VES+ R L +K+E G+ HP+ + + S
Sbjct: 355 FFRYKFYLEITAYTRGSDEQHLKWSGLVESKVRLLVMKLEV-LAGIKIAHPFTKPF-ESS 412
Query: 241 KPCPNSAFFMGLRRKEGVTGKERQQFDIRGTVDNFREE 278
CP + ++ K G E ++ D +EE
Sbjct: 413 YCCPTEDDYEMIQDKYGSHKTETALNALKLVTDENKEE 450
>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 = 231 bits (590), Expect = 7e-61, Method: Compositional matrix adjust.
Identities = 116/278 (41%), Positives = 172/278 (61%), Gaps = 3/278 (1%)
Query: 2 SVLNNVDEQTVRSLNGCRVADQILKHVPNVEHFRMTLRCLKFWAKRRGVYSNVTGFLGGV 61
++L N+DE+ +R+LNG RV D+IL+ VP FR+ LR +K WA+RR VY+N+ GF GGV
Sbjct: 175 NLLRNLDEKDLRALNGTRVTDEILELVPKPNVFRIALRAIKLWAQRRAVYANIFGFPGGV 234
Query: 62 NWALLVARVCQLYPNAIPSMLVSRFFRVYTQWRWPNPVMLCPIEEDELGFSVWDPRKNPR 121
WA+LVAR+CQLYPNA +++++RFF + ++W WP PV+L PIE+ L VW+P+ +
Sbjct: 235 AWAMLVARICQLYPNACSAVILNRFFIILSEWNWPQPVILKPIEDGPLQVRVWNPKIYAQ 294
Query: 122 DRSHHMPIITPAYPCMNSSYNVSLSTLRVMTEQFQWGNRICEEIELNKAQWSALFEPYLF 181
DRSH MP+ITPAYP M +++N++ ST +V+ ++F G +I +I NK W+ LFE F
Sbjct: 295 DRSHRMPVITPAYPSMCATHNITESTKKVILQEFVRGVQITNDIFSNKKSWANLFEKNDF 354
Query: 182 FEAYKNYLQVDIVXX-XXXXLLTWKGWVESRFRQLTLKIERDTNGLLQCHPYPNEYIDPS 240
F YK YL++ L W G VES+ R L +K+E G+ HP+ + + S
Sbjct: 355 FFRYKFYLEITAYTRGSDEQHLKWSGLVESKVRLLVMKLEV-LAGIKIAHPFTKPF-ESS 412
Query: 241 KPCPNSAFFMGLRRKEGVTGKERQQFDIRGTVDNFREE 278
CP + ++ K G E ++ D +EE
Sbjct: 413 YCCPTEDDYEMIQDKYGSHKTETALNALKLVTDENKEE 450
>pdb|2Q66|A Chain A, Structure Of Yeast Poly(A) Polymerase With Atp And
Oligo(A)
Length = 525
Score = 231 bits (589), Expect = 7e-61, Method: Compositional matrix adjust.
Identities = 116/278 (41%), Positives = 172/278 (61%), Gaps = 3/278 (1%)
Query: 2 SVLNNVDEQTVRSLNGCRVADQILKHVPNVEHFRMTLRCLKFWAKRRGVYSNVTGFLGGV 61
++L N+DE+ +R+LNG RV D+IL+ VP FR+ LR +K WA+RR VY+N+ GF GGV
Sbjct: 171 NLLRNLDEKDLRALNGTRVTDEILELVPKPNVFRIALRAIKLWAQRRAVYANIFGFPGGV 230
Query: 62 NWALLVARVCQLYPNAIPSMLVSRFFRVYTQWRWPNPVMLCPIEEDELGFSVWDPRKNPR 121
WA+LVAR+CQLYPNA +++++RFF + ++W WP PV+L PIE+ L VW+P+ +
Sbjct: 231 AWAMLVARICQLYPNACSAVILNRFFIILSEWNWPQPVILKPIEDGPLQVRVWNPKIYAQ 290
Query: 122 DRSHHMPIITPAYPCMNSSYNVSLSTLRVMTEQFQWGNRICEEIELNKAQWSALFEPYLF 181
DRSH MP+ITPAYP M +++N++ ST +V+ ++F G +I +I NK W+ LFE F
Sbjct: 291 DRSHRMPVITPAYPSMCATHNITESTKKVILQEFVRGVQITNDIFSNKKSWANLFEKNDF 350
Query: 182 FEAYKNYLQVDIVXX-XXXXLLTWKGWVESRFRQLTLKIERDTNGLLQCHPYPNEYIDPS 240
F YK YL++ L W G VES+ R L +K+E G+ HP+ + + S
Sbjct: 351 FFRYKFYLEITAYTRGSDEQHLKWSGLVESKVRLLVMKLEV-LAGIKIAHPFTKPF-ESS 408
Query: 241 KPCPNSAFFMGLRRKEGVTGKERQQFDIRGTVDNFREE 278
CP + ++ K G E ++ D +EE
Sbjct: 409 YCCPTEDDYEMIQDKYGSHKTETALNALKLVTDENKEE 446
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
0.318 0.133 0.412
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,913,374
Number of Sequences: 62578
Number of extensions: 703912
Number of successful extensions: 1403
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 1387
Number of HSP's gapped (non-prelim): 9
length of query: 550
length of database: 14,973,337
effective HSP length: 104
effective length of query: 446
effective length of database: 8,465,225
effective search space: 3775490350
effective search space used: 3775490350
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: 54 (25.4 bits)