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= 006232
(655 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 = 343 bits (881), Expect = 1e-94, Method: Compositional matrix adjust.
Identities = 185/402 (46%), Positives = 249/402 (61%), Gaps = 14/402 (3%)
Query: 9 LIGLGYDKYSVHGPGADIDTLCVGPRHATREEDFFGELHQMLTEMPEVTELHPVPDAHVP 68
+ G + VH GADID LCV PRH R DFF + L EV +L V +A VP
Sbjct: 97 IFTFGSYRLGVHTKGADIDALCVAPRHVDRS-DFFTSFYDKLKLQEEVKDLRAVEEAFVP 155
Query: 69 VMKFKFSGVSIDLLYARLSLWVIPEDLDISQDSILQNADEQTVRSLNGCRVTDQILRLVP 128
V+K F G+ ID+L+ARL+L IPEDLD+ DS+L+N D + +RSLNGCRVTD+IL LVP
Sbjct: 156 VIKLXFDGIEIDILFARLALQTIPEDLDLRDDSLLKNLDIRXIRSLNGCRVTDEILHLVP 215
Query: 129 KIQNFRTTLRCMRFWAKRRGVYSNVAGFLGGINWALLVARICQLYPNAVPSMLVSRFFRV 188
I NFR TLR ++ WAKR +YSN+ GFLGG++WA+LVAR CQLYPNA+ S LV +FF V
Sbjct: 216 NIDNFRLTLRAIKLWAKRHNIYSNILGFLGGVSWAMLVARTCQLYPNAIASTLVHKFFLV 275
Query: 189 YTQWRWPNPVLLCAIEEGSLGLQVWDPRRNPKDKYHLMPIITPAYPCMNSSYNVSTSTLR 248
+++W WPNPVLL EE +L L VWDPR NP D+YHLMPIITPAYP NS+YNVS ST
Sbjct: 276 FSKWEWPNPVLLKQPEECNLNLPVWDPRVNPSDRYHLMPIITPAYPQQNSTYNVSVSTRM 335
Query: 249 IMMDEFQRGHEICEAMEKNEADVDWDTLFEPFTFFEAYKNYLRIDISAENADDLRNWKGW 308
+M++EF++G I + + ++A +W LFE FF+ YK+Y+ + SA W G
Sbjct: 336 VMVEEFKQGLAITDEILLSKA--EWSKLFEAPNFFQKYKHYIVLLASAPTEKQRLEWVGL 393
Query: 309 VESRLRQLTLKIERHTYNML-----QCHPHPGDFSDKSKPLYCSYFMGLQRKQGVPVGEG 363
VES++R L +E++ + L Q P P + DK + + +GL K+ E
Sbjct: 394 VESKIRILVGSLEKNEFITLAHVNPQSFPAPKENPDKEE-FRTMWVIGLVFKK-TENSEN 451
Query: 364 EQFDIRLTVKEFKQAVSMYTLR----KPGMQISVAHVTRRNL 401
D+ ++ F V + + M+I+ HV R+ L
Sbjct: 452 LSVDLTYDIQSFTDTVYRQAINSKMFEVDMKIAAMHVKRKQL 493
>pdb|1Q78|A Chain A, Crystal Structure Of Poly(A) Polymerase In Complex With
3'- Datp And Magnesium Chloride
Length = 514
Score = 342 bits (878), Expect = 3e-94, Method: Compositional matrix adjust.
Identities = 185/402 (46%), Positives = 249/402 (61%), Gaps = 14/402 (3%)
Query: 9 LIGLGYDKYSVHGPGADIDTLCVGPRHATREEDFFGELHQMLTEMPEVTELHPVPDAHVP 68
+ G + VH GADID LCV PRH R DFF + L EV +L V +A VP
Sbjct: 97 IFTFGSYRLGVHTKGADIDALCVAPRHVDRS-DFFTSFYDKLKLQEEVKDLRAVEEAFVP 155
Query: 69 VMKFKFSGVSIDLLYARLSLWVIPEDLDISQDSILQNADEQTVRSLNGCRVTDQILRLVP 128
V+K F G+ ID+L+ARL+L IPEDLD+ DS+L+N D + +RSLNGCRVTD+IL LVP
Sbjct: 156 VIKLCFDGIEIDILFARLALQTIPEDLDLRDDSLLKNLDIRXIRSLNGCRVTDEILHLVP 215
Query: 129 KIQNFRTTLRCMRFWAKRRGVYSNVAGFLGGINWALLVARICQLYPNAVPSMLVSRFFRV 188
I NFR TLR ++ WAKR +YSN+ GFLGG++WA+LVAR CQLYPNA+ S LV +FF V
Sbjct: 216 NIDNFRLTLRAIKLWAKRHNIYSNILGFLGGVSWAMLVARTCQLYPNAIASTLVHKFFLV 275
Query: 189 YTQWRWPNPVLLCAIEEGSLGLQVWDPRRNPKDKYHLMPIITPAYPCMNSSYNVSTSTLR 248
+++W WPNPVLL EE +L L VWDPR NP D+YHLMPIITPAYP NS+YNVS ST
Sbjct: 276 FSKWEWPNPVLLKQPEECNLNLPVWDPRVNPSDRYHLMPIITPAYPQQNSTYNVSVSTRM 335
Query: 249 IMMDEFQRGHEICEAMEKNEADVDWDTLFEPFTFFEAYKNYLRIDISAENADDLRNWKGW 308
+M++EF++G I + + ++A +W LFE FF+ YK+Y+ + SA W G
Sbjct: 336 VMVEEFKQGLAITDEILLSKA--EWSKLFEAPNFFQKYKHYIVLLASAPTEKQRLEWVGL 393
Query: 309 VESRLRQLTLKIERHTYNML-----QCHPHPGDFSDKSKPLYCSYFMGLQRKQGVPVGEG 363
VES++R L +E++ + L Q P P + DK + + +GL K+ E
Sbjct: 394 VESKIRILVGSLEKNEFITLAHVNPQSFPAPKENPDKEE-FRTMWVIGLVFKK-TENSEN 451
Query: 364 EQFDIRLTVKEFKQAVSMYTLR----KPGMQISVAHVTRRNL 401
D+ ++ F V + + M+I+ HV R+ L
Sbjct: 452 LSVDLTYDIQSFTDTVYRQAINSKMFEVDMKIAAMHVKRKQL 493
>pdb|1F5A|A Chain A, Crystal Structure Of Mammalian Poly(A) Polymerase
Length = 513
Score = 324 bits (831), Expect = 9e-89, Method: Compositional matrix adjust.
Identities = 182/402 (45%), Positives = 244/402 (60%), Gaps = 14/402 (3%)
Query: 9 LIGLGYDKYSVHGPGADIDTLCVGPRHATREEDFFGELHQMLTEMPEVTELHPVPDAHVP 68
+ G + VH GADID LCV PRH R DFF + L EV +L V +A VP
Sbjct: 97 IFTFGSYRLGVHTKGADIDALCVAPRHVDRS-DFFTSFYDKLKLQEEVKDLRAVEEAFVP 155
Query: 69 VMKFKFSGVSIDLLYARLSLWVIPEDLDISQDSILQNADEQTVRSLNGCRVTDQILRLVP 128
V+K F G+ ID+L+ARL+L IPEDLD+ DS+L+N D + +RSLNGCRVTD+IL LVP
Sbjct: 156 VIKLCFDGIEIDILFARLALQTIPEDLDLRDDSLLKNLDIRCIRSLNGCRVTDEILHLVP 215
Query: 129 KIQNFRTTLRCMRFWAKRRGVYSNVAGFLGGINWALLVARICQLYPNAVPSMLVSRFFRV 188
I NFR TLR ++ WAKR +YSN+ GFLGG++WA LVAR CQLYPNA+ S LV +FF V
Sbjct: 216 NIDNFRLTLRAIKLWAKRHNIYSNILGFLGGVSWAXLVARTCQLYPNAIASTLVHKFFLV 275
Query: 189 YTQWRWPNPVLLCAIEEGSLGLQVWDPRRNPKDKYHLMPIITPAYPCMNSSYNVSTSTLR 248
+++W WPNPVLL EE +L L VWDPR NP D+YHL PIITPAYP NS+YNVS ST
Sbjct: 276 FSKWEWPNPVLLKQPEECNLNLPVWDPRVNPSDRYHLXPIITPAYPQQNSTYNVSVSTRX 335
Query: 249 IMMDEFQRGHEICEAMEKNEADVDWDTLFEPFTFFEAYKNYLRIDISAENADDLRNWKGW 308
+ ++EF++G I + + ++A +W LFE FF+ YK+Y+ + SA W G
Sbjct: 336 VXVEEFKQGLAITDEILLSKA--EWSKLFEAPNFFQKYKHYIVLLASAPTEKQRLEWVGL 393
Query: 309 VESRLRQLTLKIERHTYNML-----QCHPHPGDFSDKSKPLYCSYFMGLQRKQGVPVGEG 363
VES++R L +E++ + L Q P P + DK + + +GL K+ E
Sbjct: 394 VESKIRILVGSLEKNEFITLAHVNPQSFPAPKENPDKEE-FRTXWVIGLVFKK-TENSEN 451
Query: 364 EQFDIRLTVKEFKQAVSMYTLRKPGMQ----ISVAHVTRRNL 401
D+ ++ F V + + I+ HV R+ L
Sbjct: 452 LSVDLTYDIQSFTDTVYRQAINSKXFEVDXKIAAXHVKRKQL 493
>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 = 315 bits (806), Expect = 6e-86, Method: Compositional matrix adjust.
Identities = 150/310 (48%), Positives = 211/310 (68%), Gaps = 4/310 (1%)
Query: 13 GYDKYSVHGPGADIDTLCVGPRHATREEDFFGELHQMLTEMPEVTELHPVPDAHVPVMKF 72
G + VHGPG+DIDTL V P+H TRE DFF +L E E+ E+ PVPDA VP++K
Sbjct: 88 GSYRLGVHGPGSDIDTLVVVPKHVTRE-DFFTVFDSLLRERKELDEIAPVPDAFVPIIKI 146
Query: 73 KFSGVSIDLLYARLSLWVIPEDLDISQDSILQNADEQTVRSLNGCRVTDQILRLVPKIQN 132
KFSG+SIDL+ ARL +P L +S ++L+N DE+ +R+LNG RVTD+IL LVPK
Sbjct: 147 KFSGISIDLICARLDQPQVPLSLTLSDKNLLRNLDEKDLRALNGTRVTDEILELVPKPNV 206
Query: 133 FRTTLRCMRFWAKRRGVYSNVAGFLGGINWALLVARICQLYPNAVPSMLVSRFFRVYTQW 192
FR LR ++ WA+RR VY+N+ GF GG+ WA+LVARICQLYPNA +++++RFF + ++W
Sbjct: 207 FRIALRAIKLWAQRRAVYANIFGFPGGVAWAMLVARICQLYPNACSAVILNRFFIILSEW 266
Query: 193 RWPNPVLLCAIEEGSLGLQVWDPRRNPKDKYHLMPIITPAYPCMNSSYNVSTSTLRIMMD 252
WP PV+L IE+G L ++VW+P+ +D+ H MP+ITPAYP M +++N++ ST ++++
Sbjct: 267 NWPQPVILKPIEDGPLQVRVWNPKIYAQDRSHRMPVITPAYPSMCATHNITESTKKVILQ 326
Query: 253 EFQRGHEICEAMEKNEADVDWDTLFEPFTFFEAYKNYLRIDISAENADDLR-NWKGWVES 311
EF RG +I + N+ W LFE FF YK YL I +D+ W G VES
Sbjct: 327 EFVRGVQITNDIFSNKK--SWANLFEKNDFFFRYKFYLEITAYTRGSDEQHLKWSGLVES 384
Query: 312 RLRQLTLKIE 321
++R L +K+E
Sbjct: 385 KVRLLVMKLE 394
>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 = 315 bits (806), Expect = 6e-86, Method: Compositional matrix adjust.
Identities = 150/310 (48%), Positives = 211/310 (68%), Gaps = 4/310 (1%)
Query: 13 GYDKYSVHGPGADIDTLCVGPRHATREEDFFGELHQMLTEMPEVTELHPVPDAHVPVMKF 72
G + VHGPG+DIDTL V P+H TRE DFF +L E E+ E+ PVPDA VP++K
Sbjct: 88 GSYRLGVHGPGSDIDTLVVVPKHVTRE-DFFTVFDSLLRERKELDEIAPVPDAFVPIIKI 146
Query: 73 KFSGVSIDLLYARLSLWVIPEDLDISQDSILQNADEQTVRSLNGCRVTDQILRLVPKIQN 132
KFSG+SIDL+ ARL +P L +S ++L+N DE+ +R+LNG RVTD+IL LVPK
Sbjct: 147 KFSGISIDLICARLDQPQVPLSLTLSDKNLLRNLDEKDLRALNGTRVTDEILELVPKPNV 206
Query: 133 FRTTLRCMRFWAKRRGVYSNVAGFLGGINWALLVARICQLYPNAVPSMLVSRFFRVYTQW 192
FR LR ++ WA+RR VY+N+ GF GG+ WA+LVARICQLYPNA +++++RFF + ++W
Sbjct: 207 FRIALRAIKLWAQRRAVYANIFGFPGGVAWAMLVARICQLYPNACSAVILNRFFIILSEW 266
Query: 193 RWPNPVLLCAIEEGSLGLQVWDPRRNPKDKYHLMPIITPAYPCMNSSYNVSTSTLRIMMD 252
WP PV+L IE+G L ++VW+P+ +D+ H MP+ITPAYP M +++N++ ST ++++
Sbjct: 267 NWPQPVILKPIEDGPLQVRVWNPKIYAQDRSHRMPVITPAYPSMCATHNITESTKKVILQ 326
Query: 253 EFQRGHEICEAMEKNEADVDWDTLFEPFTFFEAYKNYLRIDISAENADDLR-NWKGWVES 311
EF RG +I + N+ W LFE FF YK YL I +D+ W G VES
Sbjct: 327 EFVRGVQITNDIFSNKK--SWANLFEKNDFFFRYKFYLEITAYTRGSDEQHLKWSGLVES 384
Query: 312 RLRQLTLKIE 321
++R L +K+E
Sbjct: 385 KVRLLVMKLE 394
>pdb|2HHP|A Chain A, Structure Of Yeast Poly(A) Polymerase In A Closed
Conformation
Length = 530
Score = 315 bits (806), Expect = 7e-86, Method: Compositional matrix adjust.
Identities = 150/310 (48%), Positives = 211/310 (68%), Gaps = 4/310 (1%)
Query: 13 GYDKYSVHGPGADIDTLCVGPRHATREEDFFGELHQMLTEMPEVTELHPVPDAHVPVMKF 72
G + VHGPG+DIDTL V P+H TRE DFF +L E E+ E+ PVPDA VP++K
Sbjct: 88 GSYRLGVHGPGSDIDTLVVVPKHVTRE-DFFTVFDSLLRERKELDEIAPVPDAFVPIIKI 146
Query: 73 KFSGVSIDLLYARLSLWVIPEDLDISQDSILQNADEQTVRSLNGCRVTDQILRLVPKIQN 132
KFSG+SIDL+ ARL +P L +S ++L+N DE+ +R+LNG RVTD+IL LVPK
Sbjct: 147 KFSGISIDLICARLDQPQVPLSLTLSDKNLLRNLDEKDLRALNGTRVTDEILELVPKPNV 206
Query: 133 FRTTLRCMRFWAKRRGVYSNVAGFLGGINWALLVARICQLYPNAVPSMLVSRFFRVYTQW 192
FR LR ++ WA+RR VY+N+ GF GG+ WA+LVARICQLYPNA +++++RFF + ++W
Sbjct: 207 FRIALRAIKLWAQRRAVYANIFGFPGGVAWAMLVARICQLYPNACSAVILNRFFIILSEW 266
Query: 193 RWPNPVLLCAIEEGSLGLQVWDPRRNPKDKYHLMPIITPAYPCMNSSYNVSTSTLRIMMD 252
WP PV+L IE+G L ++VW+P+ +D+ H MP+ITPAYP M +++N++ ST ++++
Sbjct: 267 NWPQPVILKPIEDGPLQVRVWNPKIYAQDRSHRMPVITPAYPSMCATHNITESTKKVILQ 326
Query: 253 EFQRGHEICEAMEKNEADVDWDTLFEPFTFFEAYKNYLRIDISAENADDLR-NWKGWVES 311
EF RG +I + N+ W LFE FF YK YL I +D+ W G VES
Sbjct: 327 EFVRGVQITNDIFSNKK--SWANLFEKNDFFFRYKFYLEITAYTRGSDEQHLKWSGLVES 384
Query: 312 RLRQLTLKIE 321
++R L +K+E
Sbjct: 385 KVRLLVMKLE 394
>pdb|2Q66|A Chain A, Structure Of Yeast Poly(A) Polymerase With Atp And
Oligo(A)
Length = 525
Score = 311 bits (798), Expect = 6e-85, Method: Compositional matrix adjust.
Identities = 149/310 (48%), Positives = 210/310 (67%), Gaps = 4/310 (1%)
Query: 13 GYDKYSVHGPGADIDTLCVGPRHATREEDFFGELHQMLTEMPEVTELHPVPDAHVPVMKF 72
G + VHGPG+DIDTL V P+H TRE DFF +L E E+ E+ PVPDA VP++K
Sbjct: 84 GSYRLGVHGPGSDIDTLVVVPKHVTRE-DFFTVFDSLLRERKELDEIAPVPDAFVPIIKI 142
Query: 73 KFSGVSIDLLYARLSLWVIPEDLDISQDSILQNADEQTVRSLNGCRVTDQILRLVPKIQN 132
KFSG+SI L+ ARL +P L +S ++L+N DE+ +R+LNG RVTD+IL LVPK
Sbjct: 143 KFSGISIALICARLDQPQVPLSLTLSDKNLLRNLDEKDLRALNGTRVTDEILELVPKPNV 202
Query: 133 FRTTLRCMRFWAKRRGVYSNVAGFLGGINWALLVARICQLYPNAVPSMLVSRFFRVYTQW 192
FR LR ++ WA+RR VY+N+ GF GG+ WA+LVARICQLYPNA +++++RFF + ++W
Sbjct: 203 FRIALRAIKLWAQRRAVYANIFGFPGGVAWAMLVARICQLYPNACSAVILNRFFIILSEW 262
Query: 193 RWPNPVLLCAIEEGSLGLQVWDPRRNPKDKYHLMPIITPAYPCMNSSYNVSTSTLRIMMD 252
WP PV+L IE+G L ++VW+P+ +D+ H MP+ITPAYP M +++N++ ST ++++
Sbjct: 263 NWPQPVILKPIEDGPLQVRVWNPKIYAQDRSHRMPVITPAYPSMCATHNITESTKKVILQ 322
Query: 253 EFQRGHEICEAMEKNEADVDWDTLFEPFTFFEAYKNYLRIDISAENADDLR-NWKGWVES 311
EF RG +I + N+ W LFE FF YK YL I +D+ W G VES
Sbjct: 323 EFVRGVQITNDIFSNKK--SWANLFEKNDFFFRYKFYLEITAYTRGSDEQHLKWSGLVES 380
Query: 312 RLRQLTLKIE 321
++R L +K+E
Sbjct: 381 KVRLLVMKLE 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 0.135 0.411
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 18,912,689
Number of Sequences: 62578
Number of extensions: 776417
Number of successful extensions: 1427
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: 1402
Number of HSP's gapped (non-prelim): 10
length of query: 655
length of database: 14,973,337
effective HSP length: 105
effective length of query: 550
effective length of database: 8,402,647
effective search space: 4621455850
effective search space used: 4621455850
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: 55 (25.8 bits)