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= 007342
(607 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 = 309 bits (791), Expect = 3e-84, Method: Compositional matrix adjust.
Identities = 166/356 (46%), Positives = 227/356 (63%), Gaps = 13/356 (3%)
Query: 7 EVTELHPVPDAHVPVMKFKFSGVSIDLLYARLSLWVIPEDLDISQDSILQNADEQTVRSL 66
EV +L V +A VPV+K F G+ ID+L+ARL+L IPEDLD+ DS+L+N D + +RSL
Sbjct: 142 EVKDLRAVEEAFVPVIKLXFDGIEIDILFARLALQTIPEDLDLRDDSLLKNLDIRXIRSL 201
Query: 67 NGCRVTDQILRLVPKIQNFRTTLRCMRFWAKRRGVYSNVAGFLGGINWALLVARICQLYP 126
NGCRVTD+IL LVP I NFR TLR ++ WAKR +YSN+ GFLGG++WA+LVAR CQLYP
Sbjct: 202 NGCRVTDEILHLVPNIDNFRLTLRAIKLWAKRHNIYSNILGFLGGVSWAMLVARTCQLYP 261
Query: 127 NAVPSMLVSRFFRVYTQWRWPNPVLLCAIEEGSLGLQVWDPRRNPKDKYHLMPIITPAYP 186
NA+ S LV +FF V+++W WPNPVLL EE +L L VWDPR NP D+YHLMPIITPAYP
Sbjct: 262 NAIASTLVHKFFLVFSKWEWPNPVLLKQPEECNLNLPVWDPRVNPSDRYHLMPIITPAYP 321
Query: 187 CMNSSYNVSTSTLRIMMDEFQRGHEICEAMEKNEADVDWDTLFEPFTFFEAYKNYLRIDI 246
NS+YNVS ST +M++EF++G I + + ++A +W LFE FF+ YK+Y+ +
Sbjct: 322 QQNSTYNVSVSTRMVMVEEFKQGLAITDEILLSKA--EWSKLFEAPNFFQKYKHYIVLLA 379
Query: 247 SAENADDLRNWKGWVESRLRQLTLKIERHTYNML-----QCHPHPGDFSDKSKPLYCSYF 301
SA W G VES++R L +E++ + L Q P P + DK + +
Sbjct: 380 SAPTEKQRLEWVGLVESKIRILVGSLEKNEFITLAHVNPQSFPAPKENPDKEE-FRTMWV 438
Query: 302 MGLQRKQGVPVGEGEQFDIRLTVKEFKQAVSMYTLR----KPGMQISVAHVTRRNL 353
+GL K+ E D+ ++ F V + + M+I+ HV R+ L
Sbjct: 439 IGLVFKK-TENSENLSVDLTYDIQSFTDTVYRQAINSKMFEVDMKIAAMHVKRKQL 493
>pdb|1Q78|A Chain A, Crystal Structure Of Poly(A) Polymerase In Complex With
3'- Datp And Magnesium Chloride
Length = 514
Score = 308 bits (788), Expect = 7e-84, Method: Compositional matrix adjust.
Identities = 166/356 (46%), Positives = 227/356 (63%), Gaps = 13/356 (3%)
Query: 7 EVTELHPVPDAHVPVMKFKFSGVSIDLLYARLSLWVIPEDLDISQDSILQNADEQTVRSL 66
EV +L V +A VPV+K F G+ ID+L+ARL+L IPEDLD+ DS+L+N D + +RSL
Sbjct: 142 EVKDLRAVEEAFVPVIKLCFDGIEIDILFARLALQTIPEDLDLRDDSLLKNLDIRXIRSL 201
Query: 67 NGCRVTDQILRLVPKIQNFRTTLRCMRFWAKRRGVYSNVAGFLGGINWALLVARICQLYP 126
NGCRVTD+IL LVP I NFR TLR ++ WAKR +YSN+ GFLGG++WA+LVAR CQLYP
Sbjct: 202 NGCRVTDEILHLVPNIDNFRLTLRAIKLWAKRHNIYSNILGFLGGVSWAMLVARTCQLYP 261
Query: 127 NAVPSMLVSRFFRVYTQWRWPNPVLLCAIEEGSLGLQVWDPRRNPKDKYHLMPIITPAYP 186
NA+ S LV +FF V+++W WPNPVLL EE +L L VWDPR NP D+YHLMPIITPAYP
Sbjct: 262 NAIASTLVHKFFLVFSKWEWPNPVLLKQPEECNLNLPVWDPRVNPSDRYHLMPIITPAYP 321
Query: 187 CMNSSYNVSTSTLRIMMDEFQRGHEICEAMEKNEADVDWDTLFEPFTFFEAYKNYLRIDI 246
NS+YNVS ST +M++EF++G I + + ++A +W LFE FF+ YK+Y+ +
Sbjct: 322 QQNSTYNVSVSTRMVMVEEFKQGLAITDEILLSKA--EWSKLFEAPNFFQKYKHYIVLLA 379
Query: 247 SAENADDLRNWKGWVESRLRQLTLKIERHTYNML-----QCHPHPGDFSDKSKPLYCSYF 301
SA W G VES++R L +E++ + L Q P P + DK + +
Sbjct: 380 SAPTEKQRLEWVGLVESKIRILVGSLEKNEFITLAHVNPQSFPAPKENPDKEE-FRTMWV 438
Query: 302 MGLQRKQGVPVGEGEQFDIRLTVKEFKQAVSMYTLR----KPGMQISVAHVTRRNL 353
+GL K+ E D+ ++ F V + + M+I+ HV R+ L
Sbjct: 439 IGLVFKK-TENSENLSVDLTYDIQSFTDTVYRQAINSKMFEVDMKIAAMHVKRKQL 493
>pdb|1F5A|A Chain A, Crystal Structure Of Mammalian Poly(A) Polymerase
Length = 513
Score = 290 bits (741), Expect = 2e-78, Method: Compositional matrix adjust.
Identities = 163/356 (45%), Positives = 222/356 (62%), Gaps = 13/356 (3%)
Query: 7 EVTELHPVPDAHVPVMKFKFSGVSIDLLYARLSLWVIPEDLDISQDSILQNADEQTVRSL 66
EV +L V +A VPV+K F G+ ID+L+ARL+L IPEDLD+ DS+L+N D + +RSL
Sbjct: 142 EVKDLRAVEEAFVPVIKLCFDGIEIDILFARLALQTIPEDLDLRDDSLLKNLDIRCIRSL 201
Query: 67 NGCRVTDQILRLVPKIQNFRTTLRCMRFWAKRRGVYSNVAGFLGGINWALLVARICQLYP 126
NGCRVTD+IL LVP I NFR TLR ++ WAKR +YSN+ GFLGG++WA LVAR CQLYP
Sbjct: 202 NGCRVTDEILHLVPNIDNFRLTLRAIKLWAKRHNIYSNILGFLGGVSWAXLVARTCQLYP 261
Query: 127 NAVPSMLVSRFFRVYTQWRWPNPVLLCAIEEGSLGLQVWDPRRNPKDKYHLMPIITPAYP 186
NA+ S LV +FF V+++W WPNPVLL EE +L L VWDPR NP D+YHL PIITPAYP
Sbjct: 262 NAIASTLVHKFFLVFSKWEWPNPVLLKQPEECNLNLPVWDPRVNPSDRYHLXPIITPAYP 321
Query: 187 CMNSSYNVSTSTLRIMMDEFQRGHEICEAMEKNEADVDWDTLFEPFTFFEAYKNYLRIDI 246
NS+YNVS ST + ++EF++G I + + ++A +W LFE FF+ YK+Y+ +
Sbjct: 322 QQNSTYNVSVSTRXVXVEEFKQGLAITDEILLSKA--EWSKLFEAPNFFQKYKHYIVLLA 379
Query: 247 SAENADDLRNWKGWVESRLRQLTLKIERHTYNML-----QCHPHPGDFSDKSKPLYCSYF 301
SA W G VES++R L +E++ + L Q P P + DK + +
Sbjct: 380 SAPTEKQRLEWVGLVESKIRILVGSLEKNEFITLAHVNPQSFPAPKENPDKEE-FRTXWV 438
Query: 302 MGLQRKQGVPVGEGEQFDIRLTVKEFKQAVSMYTLRKPGMQ----ISVAHVTRRNL 353
+GL K+ E D+ ++ F V + + I+ HV R+ L
Sbjct: 439 IGLVFKK-TENSENLSVDLTYDIQSFTDTVYRQAINSKXFEVDXKIAAXHVKRKQL 493
>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 = 277 bits (708), Expect = 2e-74, Method: Compositional matrix adjust.
Identities = 130/274 (47%), Positives = 188/274 (68%), Gaps = 3/274 (1%)
Query: 1 MLTEMPEVTELHPVPDAHVPVMKFKFSGVSIDLLYARLSLWVIPEDLDISQDSILQNADE 60
+L E E+ E+ PVPDA VP++K KFSG+SIDL+ ARL +P L +S ++L+N DE
Sbjct: 123 LLRERKELDEIAPVPDAFVPIIKIKFSGISIDLICARLDQPQVPLSLTLSDKNLLRNLDE 182
Query: 61 QTVRSLNGCRVTDQILRLVPKIQNFRTTLRCMRFWAKRRGVYSNVAGFLGGINWALLVAR 120
+ +R+LNG RVTD+IL LVPK FR LR ++ WA+RR VY+N+ GF GG+ WA+LVAR
Sbjct: 183 KDLRALNGTRVTDEILELVPKPNVFRIALRAIKLWAQRRAVYANIFGFPGGVAWAMLVAR 242
Query: 121 ICQLYPNAVPSMLVSRFFRVYTQWRWPNPVLLCAIEEGSLGLQVWDPRRNPKDKYHLMPI 180
ICQLYPNA +++++RFF + ++W WP PV+L IE+G L ++VW+P+ +D+ H MP+
Sbjct: 243 ICQLYPNACSAVILNRFFIILSEWNWPQPVILKPIEDGPLQVRVWNPKIYAQDRSHRMPV 302
Query: 181 ITPAYPCMNSSYNVSTSTLRIMMDEFQRGHEICEAMEKNEADVDWDTLFEPFTFFEAYKN 240
ITPAYP M +++N++ ST ++++ EF RG +I + N+ W LFE FF YK
Sbjct: 303 ITPAYPSMCATHNITESTKKVILQEFVRGVQITNDIFSNKK--SWANLFEKNDFFFRYKF 360
Query: 241 YLRIDISAENADDLR-NWKGWVESRLRQLTLKIE 273
YL I +D+ W G VES++R L +K+E
Sbjct: 361 YLEITAYTRGSDEQHLKWSGLVESKVRLLVMKLE 394
>pdb|2HHP|A Chain A, Structure Of Yeast Poly(A) Polymerase In A Closed
Conformation
Length = 530
Score = 276 bits (707), Expect = 2e-74, Method: Compositional matrix adjust.
Identities = 130/274 (47%), Positives = 188/274 (68%), Gaps = 3/274 (1%)
Query: 1 MLTEMPEVTELHPVPDAHVPVMKFKFSGVSIDLLYARLSLWVIPEDLDISQDSILQNADE 60
+L E E+ E+ PVPDA VP++K KFSG+SIDL+ ARL +P L +S ++L+N DE
Sbjct: 123 LLRERKELDEIAPVPDAFVPIIKIKFSGISIDLICARLDQPQVPLSLTLSDKNLLRNLDE 182
Query: 61 QTVRSLNGCRVTDQILRLVPKIQNFRTTLRCMRFWAKRRGVYSNVAGFLGGINWALLVAR 120
+ +R+LNG RVTD+IL LVPK FR LR ++ WA+RR VY+N+ GF GG+ WA+LVAR
Sbjct: 183 KDLRALNGTRVTDEILELVPKPNVFRIALRAIKLWAQRRAVYANIFGFPGGVAWAMLVAR 242
Query: 121 ICQLYPNAVPSMLVSRFFRVYTQWRWPNPVLLCAIEEGSLGLQVWDPRRNPKDKYHLMPI 180
ICQLYPNA +++++RFF + ++W WP PV+L IE+G L ++VW+P+ +D+ H MP+
Sbjct: 243 ICQLYPNACSAVILNRFFIILSEWNWPQPVILKPIEDGPLQVRVWNPKIYAQDRSHRMPV 302
Query: 181 ITPAYPCMNSSYNVSTSTLRIMMDEFQRGHEICEAMEKNEADVDWDTLFEPFTFFEAYKN 240
ITPAYP M +++N++ ST ++++ EF RG +I + N+ W LFE FF YK
Sbjct: 303 ITPAYPSMCATHNITESTKKVILQEFVRGVQITNDIFSNKK--SWANLFEKNDFFFRYKF 360
Query: 241 YLRIDISAENADDLR-NWKGWVESRLRQLTLKIE 273
YL I +D+ W G VES++R L +K+E
Sbjct: 361 YLEITAYTRGSDEQHLKWSGLVESKVRLLVMKLE 394
>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 = 276 bits (707), Expect = 2e-74, Method: Compositional matrix adjust.
Identities = 130/274 (47%), Positives = 188/274 (68%), Gaps = 3/274 (1%)
Query: 1 MLTEMPEVTELHPVPDAHVPVMKFKFSGVSIDLLYARLSLWVIPEDLDISQDSILQNADE 60
+L E E+ E+ PVPDA VP++K KFSG+SIDL+ ARL +P L +S ++L+N DE
Sbjct: 123 LLRERKELDEIAPVPDAFVPIIKIKFSGISIDLICARLDQPQVPLSLTLSDKNLLRNLDE 182
Query: 61 QTVRSLNGCRVTDQILRLVPKIQNFRTTLRCMRFWAKRRGVYSNVAGFLGGINWALLVAR 120
+ +R+LNG RVTD+IL LVPK FR LR ++ WA+RR VY+N+ GF GG+ WA+LVAR
Sbjct: 183 KDLRALNGTRVTDEILELVPKPNVFRIALRAIKLWAQRRAVYANIFGFPGGVAWAMLVAR 242
Query: 121 ICQLYPNAVPSMLVSRFFRVYTQWRWPNPVLLCAIEEGSLGLQVWDPRRNPKDKYHLMPI 180
ICQLYPNA +++++RFF + ++W WP PV+L IE+G L ++VW+P+ +D+ H MP+
Sbjct: 243 ICQLYPNACSAVILNRFFIILSEWNWPQPVILKPIEDGPLQVRVWNPKIYAQDRSHRMPV 302
Query: 181 ITPAYPCMNSSYNVSTSTLRIMMDEFQRGHEICEAMEKNEADVDWDTLFEPFTFFEAYKN 240
ITPAYP M +++N++ ST ++++ EF RG +I + N+ W LFE FF YK
Sbjct: 303 ITPAYPSMCATHNITESTKKVILQEFVRGVQITNDIFSNKK--SWANLFEKNDFFFRYKF 360
Query: 241 YLRIDISAENADDLR-NWKGWVESRLRQLTLKIE 273
YL I +D+ W G VES++R L +K+E
Sbjct: 361 YLEITAYTRGSDEQHLKWSGLVESKVRLLVMKLE 394
>pdb|2Q66|A Chain A, Structure Of Yeast Poly(A) Polymerase With Atp And
Oligo(A)
Length = 525
Score = 273 bits (699), Expect = 1e-73, Method: Compositional matrix adjust.
Identities = 129/274 (47%), Positives = 187/274 (68%), Gaps = 3/274 (1%)
Query: 1 MLTEMPEVTELHPVPDAHVPVMKFKFSGVSIDLLYARLSLWVIPEDLDISQDSILQNADE 60
+L E E+ E+ PVPDA VP++K KFSG+SI L+ ARL +P L +S ++L+N DE
Sbjct: 119 LLRERKELDEIAPVPDAFVPIIKIKFSGISIALICARLDQPQVPLSLTLSDKNLLRNLDE 178
Query: 61 QTVRSLNGCRVTDQILRLVPKIQNFRTTLRCMRFWAKRRGVYSNVAGFLGGINWALLVAR 120
+ +R+LNG RVTD+IL LVPK FR LR ++ WA+RR VY+N+ GF GG+ WA+LVAR
Sbjct: 179 KDLRALNGTRVTDEILELVPKPNVFRIALRAIKLWAQRRAVYANIFGFPGGVAWAMLVAR 238
Query: 121 ICQLYPNAVPSMLVSRFFRVYTQWRWPNPVLLCAIEEGSLGLQVWDPRRNPKDKYHLMPI 180
ICQLYPNA +++++RFF + ++W WP PV+L IE+G L ++VW+P+ +D+ H MP+
Sbjct: 239 ICQLYPNACSAVILNRFFIILSEWNWPQPVILKPIEDGPLQVRVWNPKIYAQDRSHRMPV 298
Query: 181 ITPAYPCMNSSYNVSTSTLRIMMDEFQRGHEICEAMEKNEADVDWDTLFEPFTFFEAYKN 240
ITPAYP M +++N++ ST ++++ EF RG +I + N+ W LFE FF YK
Sbjct: 299 ITPAYPSMCATHNITESTKKVILQEFVRGVQITNDIFSNKK--SWANLFEKNDFFFRYKF 356
Query: 241 YLRIDISAENADDLR-NWKGWVESRLRQLTLKIE 273
YL I +D+ W G VES++R L +K+E
Sbjct: 357 YLEITAYTRGSDEQHLKWSGLVESKVRLLVMKLE 390
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 0.133 0.405
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 17,093,392
Number of Sequences: 62578
Number of extensions: 689775
Number of successful extensions: 1288
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1270
Number of HSP's gapped (non-prelim): 10
length of query: 607
length of database: 14,973,337
effective HSP length: 104
effective length of query: 503
effective length of database: 8,465,225
effective search space: 4258008175
effective search space used: 4258008175
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: 54 (25.4 bits)